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Sample records for incremental reaction modeling

  1. Massive sulfide deposits and hydrothermal solutions: incremental reaction modeling of mineral precipitation and sulfur isotopic evolution

    SciTech Connect

    Janecky, D.R.

    1986-01-01

    Incremental reaction path modeling of chemical and sulfur isotopic reactions occurring in active hydrothermal vents on the seafloor, in combination with chemical and petrographic data from sulfide samples from the seafloor and massive sulfide ore deposits, allows a detailed examination of the processes involved. This paper presents theoretical models of reactions of two types: (1) adiabatic mixing between hydrothermal solution and seawater, and (2) reaction of hydrothermal solution with sulfide deposit materials. In addition, reaction of hydrothermal solution with sulfide deposit minerals and basalt in feeder zones is discussed.

  2. A Fast Incremental Gaussian Mixture Model

    PubMed Central

    Pinto, Rafael Coimbra; Engel, Paulo Martins

    2015-01-01

    This work builds upon previous efforts in online incremental learning, namely the Incremental Gaussian Mixture Network (IGMN). The IGMN is capable of learning from data streams in a single-pass by improving its model after analyzing each data point and discarding it thereafter. Nevertheless, it suffers from the scalability point-of-view, due to its asymptotic time complexity of O(NKD3) for N data points, K Gaussian components and D dimensions, rendering it inadequate for high-dimensional data. In this work, we manage to reduce this complexity to O(NKD2) by deriving formulas for working directly with precision matrices instead of covariance matrices. The final result is a much faster and scalable algorithm which can be applied to high dimensional tasks. This is confirmed by applying the modified algorithm to high-dimensional classification datasets. PMID:26444880

  3. Damage prediction in incremental forming by using Lemaitre damage model

    NASA Astrophysics Data System (ADS)

    Wu, Shenghua; Reis, Ana; Teixeira, Pedro; da Rocha, A. Barata; Lino, Jorge

    2012-09-01

    Incremental forming is an innovative flexible method used for manufacturing of the sheet metal products and brings a great insight for the small-batch-size or customized sheet products. Some experiments show that incremental sheet metal forming can undergo higher deformations than traditional sheet metal forming. The traditional method to evaluate formability like forming limit curve (FLD) etc can't give the right answer in incremental forming which is subjected to highly non-monotonic serrated strain paths. In this paper, the Lemaitre' damage model is presented and fully coupled with finite element simulation in commercial software ABAQUS to predict the failure in incremental forming. Results show that the prediction makes a great agreement with the relevant experiments.

  4. Incremental logistic regression for customizing automatic diagnostic models.

    PubMed

    Tortajada, Salvador; Robles, Montserrat; García-Gómez, Juan Miguel

    2015-01-01

    In the last decades, and following the new trends in medicine, statistical learning techniques have been used for developing automatic diagnostic models for aiding the clinical experts throughout the use of Clinical Decision Support Systems. The development of these models requires a large, representative amount of data, which is commonly obtained from one hospital or a group of hospitals after an expensive and time-consuming gathering, preprocess, and validation of cases. After the model development, it has to overcome an external validation that is often carried out in a different hospital or health center. The experience is that the models show underperformed expectations. Furthermore, patient data needs ethical approval and patient consent to send and store data. For these reasons, we introduce an incremental learning algorithm base on the Bayesian inference approach that may allow us to build an initial model with a smaller number of cases and update it incrementally when new data are collected or even perform a new calibration of a model from a different center by using a reduced number of cases. The performance of our algorithm is demonstrated by employing different benchmark datasets and a real brain tumor dataset; and we compare its performance to a previous incremental algorithm and a non-incremental Bayesian model, showing that the algorithm is independent of the data model, iterative, and has a good convergence.

  5. Incremental principal component pursuit for video background modeling

    DOEpatents

    Rodriquez-Valderrama, Paul A.; Wohlberg, Brendt

    2017-03-14

    An incremental Principal Component Pursuit (PCP) algorithm for video background modeling that is able to process one frame at a time while adapting to changes in background, with a computational complexity that allows for real-time processing, having a low memory footprint and is robust to translational and rotational jitter.

  6. An Enhanced Visualization Process Model for Incremental Visualization.

    PubMed

    Schulz, Hans-Jorg; Angelini, Marco; Santucci, Giuseppe; Schumann, Heidrun

    2016-07-01

    With today's technical possibilities, a stable visualization scenario can no longer be assumed as a matter of course, as underlying data and targeted display setup are much more in flux than in traditional scenarios. Incremental visualization approaches are a means to address this challenge, as they permit the user to interact with, steer, and change the visualization at intermediate time points and not just after it has been completed. In this paper, we put forward a model for incremental visualizations that is based on the established Data State Reference Model, but extends it in ways to also represent partitioned data and visualization operators to facilitate intermediate visualization updates. In combination, partitioned data and operators can be used independently and in combination to strike tailored compromises between output quality, shown data quantity, and responsiveness-i.e., frame rates. We showcase the new expressive power of this model by discussing the opportunities and challenges of incremental visualization in general and its usage in a real world scenario in particular.

  7. Data Stream Prediction Using Incremental Hidden Markov Models

    NASA Astrophysics Data System (ADS)

    Wakabayashi, Kei; Miura, Takao

    In this paper, we propose a new technique for time-series prediction. Here we assume that time-series data occur depending on event which is unobserved directly, and we estimate future data as output from the most likely event which will happen at the time. In this investigation we model time-series based on event sequence by using Hidden Markov Model(HMM), and extract time-series patterns as trained HMM parameters. However, we can’t apply HMM approach to data stream prediction in a straightforward manner. This is because Baum-Welch algorithm, which is traditional unsupervised HMM training algorithm, requires many stored historical data and scan it many times. Here we apply incremental Baum-Welch algorithm which is an on-line HMM training method, and estimate HMM parameters dynamically to adapt new time-series patterns. And we show some experimental results to see the validity of our method.

  8. Incremental and unifying modelling formalism for biological interaction networks

    PubMed Central

    Yartseva, Anastasia; Klaudel, Hanna; Devillers, Raymond; Képès, François

    2007-01-01

    Background An appropriate choice of the modeling formalism from the broad range of existing ones may be crucial for efficiently describing and analyzing biological systems. Results We propose a new unifying and incremental formalism for the representation and modeling of biological interaction networks. This formalism allows automated translations into other formalisms, thus enabling a thorough study of the dynamic properties of a biological system. As a first illustration, we propose a translation into the R. Thomas' multivalued logical formalism which provides a possible semantics; a methodology for constructing such models is presented on a classical benchmark: the λ phage genetic switch. We also show how to extract from our model a classical ODE description of the dynamics of a system. Conclusion This approach provides an additional level of description between the biological and mathematical ones. It yields, on the one hand, a knowledge expression in a form which is intuitive for biologists and, on the other hand, its representation in a formal and structured way. PMID:17996051

  9. A comparative study of velocity increment generation between the rigid body and flexible models of MMET

    SciTech Connect

    Ismail, Norilmi Amilia

    2016-02-01

    The motorized momentum exchange tether (MMET) is capable of generating useful velocity increments through spin–orbit coupling. This study presents a comparative study of the velocity increments between the rigid body and flexible models of MMET. The equations of motions of both models in the time domain are transformed into a function of true anomaly. The equations of motion are integrated, and the responses in terms of the velocity increment of the rigid body and flexible models are compared and analysed. Results show that the initial conditions, eccentricity, and flexibility of the tether have significant effects on the velocity increments of the tether.

  10. An incremental-iterative method for modeling damage evolution in voxel-based microstructure models

    NASA Astrophysics Data System (ADS)

    Zhu, Qi-Zhi; Yvonnet, Julien

    2015-02-01

    Numerical methods motivated by rapid advances in image processing techniques have been intensively developed during recent years and increasingly applied to simulate heterogeneous materials with complex microstructure. The present work aims at elaborating an incremental-iterative numerical method for voxel-based modeling of damage evolution in quasi-brittle microstructures. The iterative scheme based on the Lippmann-Schwinger equation in the real space domain (Yvonnet, in Int J Numer Methods Eng 92:178-205, 2012) is first cast into an incremental form so as to implement nonlinear material models efficiently. In the proposed scheme, local strain increments at material grid points are computed iteratively by a mapping operation through a transformation array, while local stresses are determined using a constitutive model that accounts for material degradation by damage. For validation, benchmark studies and numerical simulations using microtomographic data of concrete are performed. For each test, numerical predictions by the incremental-iterative scheme and the finite element method, respectively, are presented and compared for both global responses and local damage distributions. It is emphasized that the proposed incremental-iterative formulation can be straightforwardly applied in the framework of other Lippmann-Schwinger equation-based schemes, like the fast Fourier transform method.

  11. Application of a shear-modified GTN model to incremental sheet forming

    NASA Astrophysics Data System (ADS)

    Smith, Jacob; Malhotra, Rajiv; Liu, W. K.; Cao, Jian

    2013-12-01

    This paper investigates the effects of using a shear-modified Gurson-Tvergaard-Needleman model, which is based on the mechanics of voids, for simulating material behavior in the incremental forming process. The problem chosen for analysis is a simplified version of the NUMISHEET 2014 incremental forming benchmark test. The implications of the shear-modification of the model specifically for incremental sheet forming processes are confirmed using finite element analysis. It is shown that including the shear term has a significant effect on fracture timing in incremental forming, which is not well reflected in the observed tensile test simulations for calibration. The numerical implementation and the need for comprehensive calibration of the model are briefly discussed.

  12. Modeling of surface reactions

    SciTech Connect

    Ray, T.R.

    1993-01-01

    Mathematical models are used to elucidate properties of the monomer-monomer and monomer-dimer type chemical reactions on a two-dimensional surface. The authors use mean-field and lattice gas models, detailing similarities and differences due to correlations in the lattice gas model. The monomer-monomer, or AB surface reaction model, with no diffusion, is investigated for various reaction rates k. Study of the exact rate equations reveals that poisoning always occurs if the adsorption rates of the reactants are unequal. If the adsorption rates of the reactants are equal, simulations show slow poisoning, associated with clustering of reactants. This behavior is also shown for the two-dimensional voter model. The authors analyze precisely the slow poisoning kinetics by an analytic treatment for the AB reaction with infinitesimal reaction rate, and by direct comparison with the voter model. They extend the results to incorporate the effects of place-exchange diffusion, and they compare the AB reaction with infinitesimal reaction rate and no diffusion to the voter model with diffusion at rate 1/2. They also consider the relationship of the voter model to the monomer-dimer model, and investigate the latter model for small reaction rates. The monomer-dimer, or AB[sub 2] surface reaction model is also investigated. Specifically, they consider the ZGB-model for CO-oxidation, and in generalizations of this model which include adspecies diffusion. A theory of nucleation to describe properties of non-equilibrium first-order transitions, specifically the evolution between [open quote]reactive[close quote] steady states and trivial adsorbing states, is derived. The behavior of the [open quote]epidemic[close quote] survival probability, P[sub s], for a non-poisoned patch surrounded by a poisoned background is determined below the poisoning transition.

  13. Quality and Growth Implications of Incremental Costing Models for Distance Education Units

    ERIC Educational Resources Information Center

    Crawford, C. B.; Gould, Lawrence V.; King, Dennis; Parker, Carl

    2010-01-01

    The purpose of this article is to explore quality and growth implications emergent from various incremental costing models applied to distance education units. Prior research relative to costing models and three competing costing models useful in the current distance education environment are discussed. Specifically, the simple costing model, unit…

  14. Integrating Incremental Learning and Episodic Memory Models of the Hippocampal Region

    ERIC Educational Resources Information Center

    Meeter, M.; Myers, C. E.; Gluck, M. A.

    2005-01-01

    By integrating previous computational models of corticohippocampal function, the authors develop and test a unified theory of the neural substrates of familiarity, recollection, and classical conditioning. This approach integrates models from 2 traditions of hippocampal modeling, those of episodic memory and incremental learning, by drawing on an…

  15. Interpreting incremental value of markers added to risk prediction models.

    PubMed

    Pencina, Michael J; D'Agostino, Ralph B; Pencina, Karol M; Janssens, A Cecile J W; Greenland, Philip

    2012-09-15

    The discrimination of a risk prediction model measures that model's ability to distinguish between subjects with and without events. The area under the receiver operating characteristic curve (AUC) is a popular measure of discrimination. However, the AUC has recently been criticized for its insensitivity in model comparisons in which the baseline model has performed well. Thus, 2 other measures have been proposed to capture improvement in discrimination for nested models: the integrated discrimination improvement and the continuous net reclassification improvement. In the present study, the authors use mathematical relations and numerical simulations to quantify the improvement in discrimination offered by candidate markers of different strengths as measured by their effect sizes. They demonstrate that the increase in the AUC depends on the strength of the baseline model, which is true to a lesser degree for the integrated discrimination improvement. On the other hand, the continuous net reclassification improvement depends only on the effect size of the candidate variable and its correlation with other predictors. These measures are illustrated using the Framingham model for incident atrial fibrillation. The authors conclude that the increase in the AUC, integrated discrimination improvement, and net reclassification improvement offer complementary information and thus recommend reporting all 3 alongside measures characterizing the performance of the final model.

  16. The Incremental Launching Method for Educational Virtual Model

    NASA Astrophysics Data System (ADS)

    Martins, Octávio; Sampaio, A. Z.

    This paper describes the application of virtual reality technology to the development of an educational model related to the construction of a bridge. The model allow the visualization of the physical progression of the work following a planned construction sequence, the observation of details of the form of every component of the works and carry the study of the type and method of operation of the equipment applied in the construction. The model admit interaction and then some degree of collaboration between students and teachers in the analyses of aspects concerning geometric forms, working methodology or other technical issues observed using the application. The model presents distinct advantage as educational aids in first-degree courses in Civil Engineering.

  17. Recognizing and Incrementally Evolving Texture Concepts in Dynamic Environments: A Model Generalization Approach

    DTIC Science & Technology

    1991-11-01

    learning. While the initial acquisition of texture models is driven by a teacher, the evolution of these models is performed over a sequence of images...learning processes to improve its models. This paper presents both an outline of the iterative evolution methodology and the investigation of an incremental...model generalization approach as a part of the evolution of texture models. Experiments were run in a partially-supervised mode rather than a fully

  18. The balanced scorecard: an incremental approach model to health care management.

    PubMed

    Pineno, Charles J

    2002-01-01

    The balanced scorecard represents a technique used in strategic management to translate an organization's mission and strategy into a comprehensive set of performance measures that provide the framework for implementation of strategic management. This article develops an incremental approach for decision making by formulating a specific balanced scorecard model with an index of nonfinancial as well as financial measures. The incremental approach to costs, including profit contribution analysis and probabilities, allows decisionmakers to assess, for example, how their desire to meet different health care needs will cause changes in service design. This incremental approach to the balanced scorecard may prove to be useful in evaluating the existence of causality relationships between different objective and subjective measures to be included within the balanced scorecard.

  19. Situation model updating in young and older adults: Global versus incremental mechanisms.

    PubMed

    Bailey, Heather R; Zacks, Jeffrey M

    2015-06-01

    Readers construct mental models of situations described by text. Activity in narrative text is dynamic, so readers must frequently update their situation models when dimensions of the situation change. Updating can be incremental, such that a change leads to updating just the dimension that changed, or global, such that the entire model is updated. Here, we asked whether older and young adults make differential use of incremental and global updating. Participants read narratives containing changes in characters and spatial location and responded to recognition probes throughout the texts. Responses were slower when probes followed a change, suggesting that situation models were updated at changes. When either dimension changed, responses to probes for both dimensions were slowed; this provides evidence for global updating. Moreover, older adults showed stronger evidence of global updating than did young adults. One possibility is that older adults perform more global updating to offset reduced ability to manipulate information in working memory.

  20. Situation Model Updating in Young and Older Adults: Global versus Incremental Mechanisms

    PubMed Central

    Bailey, Heather R.; Zacks, Jeffrey M.

    2015-01-01

    Readers construct mental models of situations described by text. Activity in narrative text is dynamic, so readers must frequently update their situation models when dimensions of the situation change. Updating can be incremental, such that a change leads to updating just the dimension that changed, or global, such that the entire model is updated. Here, we asked whether older and young adults make differential use of incremental and global updating. Participants read narratives containing changes in characters and spatial location and responded to recognition probes throughout the texts. Responses were slower when probes followed a change, suggesting that situation models were updated at changes. When either dimension changed, responses to probes for both dimensions were slowed; this provides evidence for global updating. Moreover, older adults showed stronger evidence of global updating than did young adults. One possibility is that older adults perform more global updating to offset reduced ability to manipulate information in working memory. PMID:25938248

  1. Sensitivity to gaze-contingent contrast increments in naturalistic movies: An exploratory report and model comparison

    PubMed Central

    Wallis, Thomas S. A.; Dorr, Michael; Bex, Peter J.

    2015-01-01

    Sensitivity to luminance contrast is a prerequisite for all but the simplest visual systems. To examine contrast increment detection performance in a way that approximates the natural environmental input of the human visual system, we presented contrast increments gaze-contingently within naturalistic video freely viewed by observers. A band-limited contrast increment was applied to a local region of the video relative to the observer's current gaze point, and the observer made a forced-choice response to the location of the target (≈25,000 trials across five observers). We present exploratory analyses showing that performance improved as a function of the magnitude of the increment and depended on the direction of eye movements relative to the target location, the timing of eye movements relative to target presentation, and the spatiotemporal image structure at the target location. Contrast discrimination performance can be modeled by assuming that the underlying contrast response is an accelerating nonlinearity (arising from a nonlinear transducer or gain control). We implemented one such model and examined the posterior over model parameters, estimated using Markov-chain Monte Carlo methods. The parameters were poorly constrained by our data; parameters constrained using strong priors taken from previous research showed poor cross-validated prediction performance. Atheoretical logistic regression models were better constrained and provided similar prediction performance to the nonlinear transducer model. Finally, we explored the properties of an extended logistic regression that incorporates both eye movement and image content features. Models of contrast transduction may be better constrained by incorporating data from both artificial and natural contrast perception settings. PMID:26057546

  2. Incremental N-mode SVD for large-scale multilinear generative models.

    PubMed

    Lee, Minsik; Choi, Chong-Ho

    2014-10-01

    Tensor decomposition is frequently used in image processing and machine learning for its ability to express higher order characteristics of data. Among tensor decomposition methods, N-mode singular value decomposition (SVD) is widely used owing to its simplicity. However, the data dimension often becomes too large to perform N-mode SVD directly due to memory limitation. An incremental method to N-mode SVD can be used to resolve this issue, but existing approaches only provide a result, which is just enough to solve discriminative problems, not the full factorization result. In this paper, we present a complete derivation of the incremental N-mode SVD, which can be applied to generative models, accompanied by a technique that can reduce the computational cost by reordering calculations. The proposed incremental N-mode SVD can also be used effectively to update the current result of N-mode SVD when new training data is received. The proposed method provides a very good approximation of N -mode SVD for the experimental data, and requires much less computation in updating a multilinear model.

  3. A Model Based Approach to Increase the Part Accuracy in Robot Based Incremental Sheet Metal Forming

    SciTech Connect

    Meier, Horst; Laurischkat, Roman; Zhu Junhong

    2011-01-17

    One main influence on the dimensional accuracy in robot based incremental sheet metal forming results from the compliance of the involved robot structures. Compared to conventional machine tools the low stiffness of the robot's kinematic results in a significant deviation of the planned tool path and therefore in a shape of insufficient quality. To predict and compensate these deviations offline, a model based approach, consisting of a finite element approach, to simulate the sheet forming, and a multi body system, modeling the compliant robot structure, has been developed. This paper describes the implementation and experimental verification of the multi body system model and its included compensation method.

  4. Incremental Refinement of FAÇADE Models with Attribute Grammar from 3d Point Clouds

    NASA Astrophysics Data System (ADS)

    Dehbi, Y.; Staat, C.; Mandtler, L.; Pl¨umer, L.

    2016-06-01

    Data acquisition using unmanned aerial vehicles (UAVs) has gotten more and more attention over the last years. Especially in the field of building reconstruction the incremental interpretation of such data is a demanding task. In this context formal grammars play an important role for the top-down identification and reconstruction of building objects. Up to now, the available approaches expect offline data in order to parse an a-priori known grammar. For mapping on demand an on the fly reconstruction based on UAV data is required. An incremental interpretation of the data stream is inevitable. This paper presents an incremental parser of grammar rules for an automatic 3D building reconstruction. The parser enables a model refinement based on new observations with respect to a weighted attribute context-free grammar (WACFG). The falsification or rejection of hypotheses is supported as well. The parser can deal with and adapt available parse trees acquired from previous interpretations or predictions. Parse trees derived so far are updated in an iterative way using transformation rules. A diagnostic step searches for mismatches between current and new nodes. Prior knowledge on façades is incorporated. It is given by probability densities as well as architectural patterns. Since we cannot always assume normal distributions, the derivation of location and shape parameters of building objects is based on a kernel density estimation (KDE). While the level of detail is continuously improved, the geometrical, semantic and topological consistency is ensured.

  5. Developing Risk Prediction Models for Kidney Injury and Assessing Incremental Value for Novel Biomarkers

    PubMed Central

    Kerr, Kathleen F.; Meisner, Allison; Thiessen-Philbrook, Heather; Coca, Steven G.

    2014-01-01

    The field of nephrology is actively involved in developing biomarkers and improving models for predicting patients’ risks of AKI and CKD and their outcomes. However, some important aspects of evaluating biomarkers and risk models are not widely appreciated, and statistical methods are still evolving. This review describes some of the most important statistical concepts for this area of research and identifies common pitfalls. Particular attention is paid to metrics proposed within the last 5 years for quantifying the incremental predictive value of a new biomarker. PMID:24855282

  6. Incremental checking of Master Data Management model based on contextual graphs

    NASA Astrophysics Data System (ADS)

    Lamolle, Myriam; Menet, Ludovic; Le Duc, Chan

    2015-10-01

    The validation of models is a crucial step in distributed heterogeneous systems. In this paper, an incremental validation method is proposed in the scope of a Model Driven Engineering (MDE) approach, which is used to develop a Master Data Management (MDM) field represented by XML Schema models. The MDE approach presented in this paper is based on the definition of an abstraction layer using UML class diagrams. The validation method aims to minimise the model errors and to optimisethe process of model checking. Therefore, the notion of validation contexts is introduced allowing the verification of data model views. Description logics specify constraints that the models have to check. An experimentation of the approach is presented through an application developed in ArgoUML IDE.

  7. Is incremental hemodialysis ready to return on the scene? From empiricism to kinetic modelling.

    PubMed

    Basile, Carlo; Casino, Francesco Gaetano; Kalantar-Zadeh, Kamyar

    2017-03-23

    Most people who make the transition to maintenance dialysis therapy are treated with a fixed dose thrice-weekly hemodialysis regimen without considering their residual kidney function (RKF). The RKF provides effective and naturally continuous clearance of both small and middle molecules, plays a major role in metabolic homeostasis, nutritional status, and cardiovascular health, and aids in fluid management. The RKF is associated with better patient survival and greater health-related quality of life, although these effects may be confounded by patient comorbidities. Preservation of the RKF requires a careful approach, including regular monitoring, avoidance of nephrotoxins, gentle control of blood pressure to avoid intradialytic hypotension, and an individualized dialysis prescription including the consideration of incremental hemodialysis. There is currently no standardized method for applying incremental hemodialysis in practice. Infrequent (once- to twice-weekly) hemodialysis regimens are often used arbitrarily, without knowing which patients would benefit the most from them or how to escalate the dialysis dose as RKF declines over time. The recently heightened interest in incremental hemodialysis has been hindered by the current limitations of the urea kinetic models (UKM) which tend to overestimate the dialysis dose required in the presence of substantial RKF. This is due to an erroneous extrapolation of the equivalence between renal urea clearance (Kru) and dialyser urea clearance (Kd), correctly assumed by the UKM, to the clinical domain. In this context, each ml/min of Kd clears the urea from the blood just as 1 ml/min of Kru does. By no means should such kinetic equivalence imply that 1 ml/min of Kd is clinically equivalent to 1 ml/min of urea clearance provided by the native kidneys. A recent paper by Casino and Basile suggested a variable target model (VTM) as opposed to the fixed model, because the VTM gives more clinical weight to the RKF and allows

  8. Evaluation of an Incremental Ventilation Energy Model for Estimating Impacts of Air Sealing and Mechanical Ventilation

    SciTech Connect

    Logue, Jennifer M.; Turner, Willliam JN; Walker, Iain S.; Singer, Brett C.

    2012-07-01

    Changing the rate of airflow through a home affects the annual thermal conditioning energy. Large-scale changes to airflow rates of the housing stock can significantly alter the energy consumption of the residential energy sector. However, the complexity of existing residential energy models hampers the ability to estimate the impact of policy changes on a state or nationwide level. The Incremental Ventilation Energy (IVE) model developed in this study was designed to combine the output of simple airflow models and a limited set of home characteristics to estimate the associated change in energy demand of homes. The IVE model was designed specifically to enable modelers to use existing databases of home characteristics to determine the impact of policy on ventilation at a population scale. In this report, we describe the IVE model and demonstrate that its estimates of energy change are comparable to the estimates of a wellvalidated, complex residential energy model when applied to homes with limited parameterization. Homes with extensive parameterization would be more accurately characterized by complex residential energy models. The demonstration included a range of home types, climates, and ventilation systems that cover a large fraction of the residential housing sector.

  9. Stochastic Modeling Of Biochemical Reactions

    DTIC Science & Technology

    2006-11-01

    chemical reactions. Often for these reactions, the dynamics of the first M-order statistical moments of the species populations do not form a closed...results a stochastic model for gene expression is investigated. We show that in gene expression mechanisms , in which a protein inhibits its own...chemical reactions [7, 8, 4, 9, 10]. Since one is often interested in only the first and second order statistical moments for the number of molecules of

  10. Impulse processing: A dynamical systems model of incremental eye movements in the visual world paradigm

    PubMed Central

    Kukona, Anuenue; Tabor, Whitney

    2011-01-01

    The visual world paradigm presents listeners with a challenging problem: they must integrate two disparate signals, the spoken language and the visual context, in support of action (e.g., complex movements of the eyes across a scene). We present Impulse Processing, a dynamical systems approach to incremental eye movements in the visual world that suggests a framework for integrating language, vision, and action generally. Our approach assumes that impulses driven by the language and the visual context impinge minutely on a dynamical landscape of attractors corresponding to the potential eye-movement behaviors of the system. We test three unique predictions of our approach in an empirical study in the visual world paradigm, and describe an implementation in an artificial neural network. We discuss the Impulse Processing framework in relation to other models of the visual world paradigm. PMID:21609355

  11. Assessment of synthetic winds through spectral modelling, rainflow count analysis and statistics of increments

    NASA Astrophysics Data System (ADS)

    Beyer, Hans Georg; Chougule, Abhijit

    2016-04-01

    While wind energy industry growing rapidly and siting of wind turbines onshore as well as offshore is increasing, many wind engineering model tools have been developed for the assessment of loads on wind turbines due to varying wind speeds. In order to have proper wind turbine design and performance analysis, it is important to have an accurate representation of the incoming wind field. To ease the analysis, tools for the generation of synthetic wind fields have been developed, e.g the widely used TurbSim procedure. We analyse respective synthetic data sets on one hand in view of the similarity of the spectral characteristics of measured and synthetic sets. In addition, second order characteristics with direct relevance to load assessment as given by the statistics of increments and rainflow count results are inspected.

  12. Impulse processing: a dynamical systems model of incremental eye movements in the visual world paradigm.

    PubMed

    Kukona, Anuenue; Tabor, Whitney

    2011-08-01

    The Visual World Paradigm (VWP) presents listeners with a challenging problem: They must integrate two disparate signals, the spoken language and the visual context, in support of action (e.g., complex movements of the eyes across a scene). We present Impulse Processing, a dynamical systems approach to incremental eye movements in the visual world that suggests a framework for integrating language, vision, and action generally. Our approach assumes that impulses driven by the language and the visual context impinge minutely on a dynamical landscape of attractors corresponding to the potential eye-movement behaviors of the system. We test three unique predictions of our approach in an empirical study in the VWP, and describe an implementation in an artificial neural network. We discuss the Impulse Processing framework in relation to other models of the VWP.

  13. Modeling the incremental cost and water conversion functions for hydro-thermal coordination studies

    SciTech Connect

    El-Hawary, M.E.; Mbamalu, G.A.N. )

    1991-01-01

    The solution of an optimization problem using variational means relies on Lagrange multiplier functions, called the adjoint variables to augment the physical constraints to the cost function. The multipliers usually have en economic interpretation, and in the optimal economic operation of an electric power system, one set of multipliers signifies the incremental cost of power delivered at a bus, and the other set relates to the water worth at a given reservoir. The solution of the optimization problem involves iterative techniques to obtain the optimal strategy in terms of power generations and water releases, as well as the adjoint variables. Good initial estimates are of paramount importance to a successful implementation of any iteration scheme specially those that are Newton based. There is an observed pattern of dependence of the adjoint variables and the system state as described by power demands and water availability. Finding such relationships is useful for generation planning activities as well as in providing initial guesses in the numerical solution of the problem. This paper proposes statistical models for predicting the incremental cost function {lambda} and the water conversion factor {nu} usually encountered in the hydro-thermal power system optimization problem. The method treats the active power demand and the volume of water available as the independent variables. The Least squares and the iteratively reweighted Least squares procedures are used to estimate model parameters. The approach treats the power system as a variable head hydro-thermal system, Kron's loss formula is used to characterize the system performance and losses. Results for an example using a 4 plant network are presented in order to demonstrate the applicability of this approach.

  14. Reduction of chemical reaction models

    NASA Technical Reports Server (NTRS)

    Frenklach, Michael

    1991-01-01

    An attempt is made to reconcile the different terminologies pertaining to reduction of chemical reaction models. The approaches considered include global modeling, response modeling, detailed reduction, chemical lumping, and statistical lumping. The advantages and drawbacks of each of these methods are pointed out.

  15. An incrementally non-linear model for clays with directional stiffness and a small strain emphasis

    NASA Astrophysics Data System (ADS)

    Tu, Xuxin

    In response to construction activities and loads from permanent structures, soil generally is subjected to a variety of loading modes varying both in time and location. It also has been increasingly appreciated that the strains around well-designed foundations, excavations and tunnels are mostly small, with soil responses at this strain level generally being non-linear and anisotropic. To make accurate prediction of the performance of a geo-system, it is highly desirable to understand soil behavior at small strains along multiple loading directions, and accordingly to incorporate these responses in an appropriate constitutive model implemented in a finite element analysis. This dissertation presents a model based on a series of stress probe tests with small strain measurements performed on compressible Chicago glacial clays. The proposed model is formulated in an original constitutive framework, in which the tangent stiffness matrix is constructed in accordance with the mechanical nature of frictional materials and the tangent moduli therein are described explicitly. The stiffness description includes evolution relations with regard to length of stress path, and directionality relations in terms of stress path direction. The former relations provide distinctive definitions for small-strain and large-strain behaviors, and distinguish soil responses in shearing and compression. The latter relations make this model incrementally non-linear and thus capable of modeling inelastic behavior. A new algorithm based on a classical substepping scheme is developed to numerically integrate this model. A consistent tangent matrix is derived for the proposed model with the upgraded substepping scheme. The code is written in FORTRAN and implemented in FEM via UMAT of ABAQUS. The model is exercised in a variety of applications ranging from oedometer, triaxial and biaxial test simulations to a C-class prediction for a well-instrumented excavation. The computed results indicate that

  16. The evolution of sensitive periods in a model of incremental development

    PubMed Central

    Panchanathan, Karthik; Frankenhuis, Willem E.

    2016-01-01

    Sensitive periods, in which experience shapes phenotypic development to a larger extent than other periods, are widespread in nature. Despite a recent focus on neural–physiological explanation, few formal models have examined the evolutionary selection pressures that result in developmental mechanisms that produce sensitive periods. Here, we present such a model. We model development as a specialization process during which individuals incrementally adapt to local environmental conditions, while receiving a constant stream of cost-free, imperfect cues to the environmental state. We compute optimal developmental programmes across a range of ecological conditions and use these programmes to simulate developmental trajectories and obtain distributions of mature phenotypes. We highlight four main results. First, matching the empirical record, sensitive periods often result from experience or from a combination of age and experience, but rarely from age alone. Second, individual differences in sensitive periods emerge as a result of stochasticity in cues: individuals who obtain more consistent cue sets lose their plasticity at faster rates. Third, in some cases, experience shapes phenotypes only at a later life stage (lagged effects). Fourth, individuals might perseverate along developmental trajectories despite accumulating evidence suggesting the alternate trajectory is more likely to match the ecology. PMID:26817766

  17. Propulsive Reaction Control System Model

    NASA Technical Reports Server (NTRS)

    Brugarolas, Paul; Phan, Linh H.; Serricchio, Frederick; San Martin, Alejandro M.

    2011-01-01

    This software models a propulsive reaction control system (RCS) for guidance, navigation, and control simulation purposes. The model includes the drive electronics, the electromechanical valve dynamics, the combustion dynamics, and thrust. This innovation follows the Mars Science Laboratory entry reaction control system design, and has been created to meet the Mars Science Laboratory (MSL) entry, descent, and landing simulation needs. It has been built to be plug-and-play on multiple MSL testbeds [analysis, Monte Carlo, flight software development, hardware-in-the-loop, and ATLO (assembly, test and launch operations) testbeds]. This RCS model is a C language program. It contains two main functions: the RCS electronics model function that models the RCS FPGA (field-programmable-gate-array) processing and commanding of the RCS valve, and the RCS dynamic model function that models the valve and combustion dynamics. In addition, this software provides support functions to initialize the model states, set parameters, access model telemetry, and access calculated thruster forces.

  18. The Crucial Role of Error Correlation for Uncertainty Modeling of CFD-Based Aerodynamics Increments

    NASA Technical Reports Server (NTRS)

    Hemsch, Michael J.; Walker, Eric L.

    2011-01-01

    The Ares I ascent aerodynamics database for Design Cycle 3 (DAC-3) was built from wind-tunnel test results and CFD solutions. The wind tunnel results were used to build the baseline response surfaces for wind-tunnel Reynolds numbers at power-off conditions. The CFD solutions were used to build increments to account for Reynolds number effects. We calculate the validation errors for the primary CFD code results at wind tunnel Reynolds number power-off conditions and would like to be able to use those errors to predict the validation errors for the CFD increments. However, the validation errors are large compared to the increments. We suggest a way forward that is consistent with common practice in wind tunnel testing which is to assume that systematic errors in the measurement process and/or the environment will subtract out when increments are calculated, thus making increments more reliable with smaller uncertainty than absolute values of the aerodynamic coefficients. A similar practice has arisen for the use of CFD to generate aerodynamic database increments. The basis of this practice is the assumption of strong correlation of the systematic errors inherent in each of the results used to generate an increment. The assumption of strong correlation is the inferential link between the observed validation uncertainties at wind-tunnel Reynolds numbers and the uncertainties to be predicted for flight. In this paper, we suggest a way to estimate the correlation coefficient and demonstrate the approach using code-to-code differences that were obtained for quality control purposes during the Ares I CFD campaign. Finally, since we can expect the increments to be relatively small compared to the baseline response surface and to be typically of the order of the baseline uncertainty, we find that it is necessary to be able to show that the correlation coefficients are close to unity to avoid overinflating the overall database uncertainty with the addition of the increments.

  19. Dynamical model of surrogate reactions

    SciTech Connect

    Aritomo, Y.; Chiba, S.; Nishio, K.

    2011-08-15

    A new dynamical model is developed to describe the whole process of surrogate reactions: Transfer of several nucleons at an initial stage, thermal equilibration of residues leading to washing out of shell effects, and decay of populated compound nuclei are treated in a unified framework. Multidimensional Langevin equations are employed to describe time evolution of collective coordinates with a time-dependent potential energy surface corresponding to different stages of surrogate reactions. The new model is capable of calculating spin distributions of the compound nuclei, one of the most important quantities in the surrogate technique. Furthermore, various observables of surrogate reactions can be calculated, for example, energy and angular distribution of ejectile and mass distributions of fission fragments. These features are important to assess validity of the proposed model itself, to understand mechanisms of the surrogate reactions, and to determine unknown parameters of the model. It is found that spin distributions of compound nuclei produced in {sup 18}O+{sup 238}U{yields}{sup 16}O+{sup 240}*U and {sup 18}O+{sup 236}U{yields}{sup 16}O+{sup 238}*U reactions are equivalent and much less than 10({h_bar}/2{pi}) and therefore satisfy conditions proposed by Chiba and Iwamoto [Phys. Rev. C 81, 044604 (2010)] if they are used as a pair in the surrogate ratio method.

  20. Detection of bird nests during mechanical weeding by incremental background modeling and visual saliency.

    PubMed

    Steen, Kim Arild; Therkildsen, Ole Roland; Green, Ole; Karstoft, Henrik

    2015-03-02

    Mechanical weeding is an important tool in organic farming. However, the use of mechanical weeding in conventional agriculture is increasing, due to public demands to lower the use of pesticides and an increased number of pesticide-resistant weeds. Ground nesting birds are highly susceptible to farming operations, like mechanical weeding, which may destroy the nests and reduce the survival of chicks and incubating females. This problem has limited focus within agricultural engineering. However, when the number of machines increases, destruction of nests will have an impact on various species. It is therefore necessary to explore and develop new technology in order to avoid these negative ethical consequences. This paper presents a vision-based approach to automated ground nest detection. The algorithm is based on the fusion of visual saliency, which mimics human attention, and incremental background modeling, which enables foreground detection with moving cameras. The algorithm achieves a good detection rate, as it detects 28 of 30 nests at an average distance of 3.8 m, with a true positive rate of 0.75.

  1. Incremental Change or Initial Differences? Testing Two Models of Marital Deterioration

    PubMed Central

    Lavner, Justin A.; Bradbury, Thomas N.; Karney, Benjamin R.

    2012-01-01

    Most couples begin marriage intent on maintaining a fulfilling relationship, but some newlyweds soon struggle while others continue to experience high levels of satisfaction. Do these diverse outcomes result from an incremental process that unfolds over time, as prevailing models suggest, or are they a manifestation of initial differences that are largely evident at the start of the marriage? Using eight waves of data collected over the first 4 years of marriage (N = 502 spouses, or 251 newlywed marriages), we tested these competing perspectives first by identifying three qualitatively distinct relationship satisfaction trajectory groups and then by determining the extent to which spouses in these groups were differentiated on the basis of (a) initial scores and (b) 4-year changes in a set of established predictor variables, including relationship problems, aggression, attributions, stress, and self-esteem. The majority of spouses exhibited high, stable satisfaction over the first four years of marriage, whereas declining satisfaction was isolating among couples with relatively low initial satisfaction. Across all predictor variables, initial values afforded stronger discrimination of outcome groups than did rates of change in these variables. Thus, readily-measured initial differences are potent antecedents of relationship deterioration, and studies are now needed to clarify the specific ways in which initial indices of risk come to influence changes in spouses’ judgments of relationship satisfaction. PMID:22709260

  2. Modelling reaction kinetics inside cells

    PubMed Central

    Grima, Ramon; Schnell, Santiago

    2009-01-01

    In the past decade, advances in molecular biology such as the development of non-invasive single molecule imaging techniques have given us a window into the intricate biochemical activities that occur inside cells. In this article we review four distinct theoretical and simulation frameworks: (1) non-spatial and deterministic, (2) spatial and deterministic, (3) non-spatial and stochastic and (4) spatial and stochastic. Each framework can be suited to modelling and interpreting intracellular reaction kinetics. By estimating the fundamental length scales, one can roughly determine which models are best suited for the particular reaction pathway under study. We discuss differences in prediction between the four modelling methodologies. In particular we show that taking into account noise and space does not simply add quantitative predictive accuracy but may also lead to qualitatively different physiological predictions, unaccounted for by classical deterministic models. PMID:18793122

  3. Incremental expansions for the ground-state energy of the two-dimensional Hubbard model

    SciTech Connect

    Malek, J.; Flach, S.; Kladko, K.

    1999-02-01

    A generalization of Faddeev{close_quote}s approach of the three-body problem to the many-body problem leads to the method of increments. This method was recently applied to account for the ground-state properties of Hubbard-Peierls chains [J. Malek, K. Kladko, and S. Flach, JETP Lett. {bold 67}, 1052 (1998)]. Here we generalize this approach to two-dimensional square lattices and explicitly treat the incremental expansion up to third order. Comparing our numerical results with various other approaches (Monte Carlo, cumulant approaches) we show that incremental expansions are very efficient because good accuracy with these approaches is achieved treating lattice segments composed of eight sites only. {copyright} {ital 1999} {ital The American Physical Society}

  4. Optimizing the Teaching-Learning Process Through a Linear Programming Model--Stage Increment Model.

    ERIC Educational Resources Information Center

    Belgard, Maria R.; Min, Leo Yoon-Gee

    An operations research method to optimize the teaching-learning process is introduced in this paper. In particular, a linear programing model is proposed which, unlike dynamic or control theory models, allows the computer to react to the responses of a learner in seconds or less. To satisfy the assumptions of linearity, the seemingly complicated…

  5. New Scaling Model for Variables and Increments with Heavy-Tailed Distributions

    NASA Astrophysics Data System (ADS)

    Riva, Monica; Guadagnini, Alberto; Neuman, Shlomo P.

    2015-04-01

    Many earth, environmental, ecological, biological, physical, social, financial and other variables, Y , exhibit (i) asymmetry in sample frequency distributions, as well as (ii) symmetry in distributions of their spatial and/or temporal increments, ΔY , at diverse separation distances (or lags), with sharp peaks and heavy tails which appear to decay asymptotically (often toward exponential tails of the Gaussian distribution) as lag increases. No model known to us captures all of these behaviors in a unique and consistent manner. We propose a new model that does so upon treating Y (x) as a random function of a coordinate x in the Euclidean (spatial) domain or time, forming a stationary random field (or process) with constant ensemble mean (expectation) . We express the zero-mean random fluctuation Y '(x) = Y (x) - in sub-Gaussian form. In the classical sub-Gaussian form, Y '(x) = UG(x), where G(x) is a zero-mean stationary Gaussian random field (or process) and the subordinator U is an independent non-negative random variable (Samorodnitsky and Taqqu, 2014). We generalize this by writing Y '(x) = U(x)G(x) in which U(x) is iid. This enables us to analyze, and synthetically generate, heavy-tailed non-Gaussian distributions of both Y and ΔY in both probability space (across an infinite ensemble of random realizations) and real space (in a single realization). We derive analytical expressions for probability distribution functions (pdf s) of Y and ΔY as well as their lead statistical moments. We show that when U is lognormal Y follows the well-known normal-lognormal distribution (NLN, of which the Gaussian distribution is a particular case) with constant parameters. The NLN pdf has been successfully used to interpret financial (Clark, 1973) and environmental (Guadagnini et al., 2014) data. However, ΔY is not NLN and forcing the latter on the former gives a false and widely accepted impression that (a) parameters of the ΔY pdf vary with lag and (b) the pdfs

  6. Modeling the complex bromate-iodine reaction.

    PubMed

    Machado, Priscilla B; Faria, Roberto B

    2009-05-07

    In this article, it is shown that the FLEK model (ref 5 ) is able to model the experimental results of the bromate-iodine clock reaction. Five different complex chemical systems, the bromate-iodide clock and oscillating reactions, the bromite-iodide clock and oscillating reactions, and now the bromate-iodine clock reaction are adequately accounted for by the FLEK model.

  7. Linking impulse response functions to reaction time: Rod and cone reaction time data and a computational model

    PubMed Central

    Cao, Dingcai; Zele, Andrew J.; Pokorny, Joel

    2007-01-01

    Reaction times for incremental and decremental stimuli were measured at five suprathreshold contrasts for six retinal illuminance levels where rods alone (0.002–0.2 Trolands), rods and cones (2–20 Trolands) or cones alone (200 Trolands) mediated detection. A 4-primary photostimulator allowed independent control of rod or cone excitations. This is the first report of reaction times to isolated rod or cone stimuli at mesopic light levels under the same adaptation conditions. The main findings are: 1) For rods, responses to decrements were faster than increments, but cone reaction times were closely similar. 2) At light levels where both systems were functional, rod reaction times were ~20 ms longer. The data were fitted with a computational model that incorporates rod and cone impulse response functions and a stimulus-dependent neural sensory component that triggers a motor response. Rod and cone impulse response functions were derived from published psychophysical two-pulse threshold data and temporal modulation transfer functions. The model fits were accomplished with a limited number of free parameters: two global parameters to estimate the irreducible minimum reaction time for each receptor type, and one local parameter for each reaction time versus contrast function. This is the first model to provide a neural basis for the variation in reaction time with retinal illuminance, stimulus contrast, stimulus polarity, and receptor class modulated. PMID:17346763

  8. Modeling Reading Development: Cumulative, Incremental Learning in a Computational Model of Word Naming

    ERIC Educational Resources Information Center

    Monaghan, Padraic; Ellis, Andrew W.

    2010-01-01

    Natural reading development gradually builds up to the adult vocabulary over a period of years. This has an effect on lexical processing: early-acquired words are processed more quickly and more accurately than later-acquired words. We present a connectionist model of reading, learning to map orthography onto phonology to simulate this natural…

  9. Incremental haemodialysis.

    PubMed

    Wong, Jonathan; Vilar, Enric; Davenport, Andrew; Farrington, Ken

    2015-10-01

    Thrice-weekly haemodialysis schedules have become the standard default haemodialysis prescription worldwide. Whereas the measurement of residual renal function is accepted practice for peritoneal dialysis patients and the importance of residual renal function in determining technique success is well established, few centres routinely assess residual renal function in haemodialysis patients. Although intradialytic hypotension and episodes of acute kidney injury may predispose to an earlier loss of residual renal function, a significant proportion of haemodialysis patients maintain some residual function long after dialysis initiation. As such, an incremental approach to the initiation of dialysis with careful monitoring of residual renal function may potentially provide some haemodialysis patients with an improved quality of life and greater preservation of residual renal function whilst fewer dialysis sessions may reduce health care costs. Prospective trials are required to determine the optimum approach to the initiation of haemodialysis for the oliguric patient. Once residual renal function has been lost, then dialysis prescriptions should be re-examined to consider the use of longer or more frequent treatment sessions and switching from low-flux to high-flux dialysis or haemodiafiltration to offset retention of middle sized molecules and protein-bound azotaemic solutes.

  10. Modeling the Radar Return of Powerlines Using an Incremental Length Diffraction Coefficient Approach

    NASA Astrophysics Data System (ADS)

    Macdonald, Douglas

    DIRSIG consistently underestimated the scattered return, especially away from specular observation angles. This underestimation was particularly pronounced for the dihedral targets which have a low acceptance angle in elevation, probably caused by the lack of a physical optics capability in DIRSIG. Powerlines were not apparent in the simulated data. For modeling powerlines outside of DIRSIG using a standalone approach, an Incremental Length Diffraction Coefficient (ILDC) method was used. Traditionally, this method is used to model the scattered radiation from the edge of a wedge, for example the edges on the wings of a stealth aircraft. The Physical Theory of Diffraction provides the 2D diffraction coefficient and the ILDC method performs an integral along the edge to extend this solution to three dimensions. This research takes the ILDC approach but instead of using the wedge diffraction coefficient, the exact far-field diffraction coefficient for scattering from a finite length cylinder is used. Wavenumber-diameter products are limited to less than or about 10. For typical powerline diameters, this translates to X-band frequencies and lower. The advantage of this method is it allows exact 2D solutions to be extended to powerline geometries where sag is present and it is shown to be more accurate than a pure physical optics approach for frequencies lower than millimeter wave. The Radar Cross Sections produced by this method were accurate to within the experimental uncertainty of measured RF anechoic chamber data for both X and C-band frequencies across an 80 degree arc for 5 different target types and diameters. For the X-band data, the mean error was 6.0% for data with 9.5% measurement uncertainty. For the C-band data, the mean error was 11.8% for data with 14.3% measurement uncertainty. The best results were obtained for X-band data in the HH polarization channel within a 20 degree arc about normal incidence. For this configuration, a mean error of 3.0% for data with

  11. Menu modeling with MyPyramid food patterns: incremental dietary changes lead to dramatic improvements in diet quality of menus.

    PubMed

    Hornick, Betsy A; Krester, Alison J; Nicklas, Theresa A

    2008-12-01

    The MyPyramid food guidance system provides recommended food intake patterns for members of each sex at various age and activity levels. These food intake patterns are based on recommendations of the Dietary Guidelines for Americans 2005. Actual consumption patterns of American adults compared to MyPyramid recommendations indicate that substantial changes are needed to meet the goals of MyPyramid. One method for encouraging dietary change, known as the small steps approach, involves small, gradual changes to meet a desired endpoint. Menu modeling was used to evaluate the effects of gradual dietary changes on diet quality. Seven days of baseline menus were developed to model the intake of adult women aged 31 to 50 years. Incremental changes were made to each baseline menu to create a series of three transitional menus and a final target menu. Target menus met MyPyramid energy and nutrient intake goals. Diet quality was measured for each baseline, transitional, and target menu using the Healthy Eating Index-2005. The average Healthy Eating Index-2005 score for baseline menus compared to target menus increased by more than 50 points with incremental increases observed for each transitional menu. This analysis demonstrates that small, practical changes in food choices that bring consumers closer to meeting MyPyramid recommendations result in gradual and dramatic improvements in diet quality. Food and nutrition professionals can use menu modeling to provide concrete examples and specific guidance for making progressive changes in food selections to meet current dietary recommendations.

  12. Incremental Particle Swarm Optimization

    NASA Astrophysics Data System (ADS)

    Xu, Xiaohua; Pan, Zhoujin; Xi, Yanqiu; Chen, Ling

    By simulating the population size of the human evolution, a PSO algorithm with increment of particle size (IPPSO) was proposed. Without changing the PSO operations, IPPSO can obtain better solutions with less time cost by modifying the structure of traditional PSO. Experimental results show that IPPSO using logistic model is more efficient and requires less computation time than using linear function in solving more complex program problems.

  13. Ductile Fracture Prediction in Rotational Incremental Forming for Magnesium Alloy Sheets Using Combined Kinematic/Isotropic Hardening Model

    NASA Astrophysics Data System (ADS)

    Nguyen, Duc-Toan; Park, Jin-Gee; Kim, Young-Suk

    2010-08-01

    To predict the ductile fracture of a magnesium alloy sheet when using rotational incremental forming, a combined kinematic and isotropic hardening law is implemented and evaluated from the histories of the ductile fracture value ( I) using a finite element analysis. Here, the criterion for a ductile fracture, as developed by Oyane ( J. Mech. Work. Technol., 1980, vol. 4, pp. 65-81), is applied via a user material based on a finite element analysis. To simulate the effect of the large amount of heat generation at elements in the contact area due to the friction energy of the rotational tool-specimen interface on the equivalent stress-strain evolution in incremental forming, the Johnson-Cook (JC) model was applied and the results compared with equivalent stress-strain curves obtained from tensile tests at elevated temperatures. The finite element (FE) simulation results for a ductile fracture were compared with the experimental results for a (80 mm × 80 mm × 25 mm) square shape with a 45 and 60 deg wall angle, respectively, and a (80 mm × 80 mm × 20 mm) square shape with a 70 deg wall angle. The trends of the FE simulation results agreed quite well with the experimental results. Finally, the effects of the process parameters, i.e., the tool down-step and tool radius, on the ductile fracture value and FLC at fracture (FLCF) were also investigated using the FE simulation results.

  14. Incremental Benefits of Screening Colonoscopy over Sigmoidoscopy in Average-risk Populations: a model-driven analysis

    PubMed Central

    Jeon, Jihyoun; Meza, Rafael; Hazelton, William D.; Renehan, Andrew G.; Luebeck, E. Georg

    2015-01-01

    Purpose Screening colonoscopy and flexible sigmoidoscopy (FSG) reduce the risk of colorectal cancer (CRC), but the magnitude and duration of protection, particularly against right-sided cancer, remain uncertain. We computed the incremental benefit of colonoscopy over FSG using a validated mathematical model, which reflects colorectal neoplasia growth characteristics while allowing uncertainty in endoscopic detection and removal of adenomas. Methods We calibrated models of CRC incidence within a multistage clonal expansion framework to data from: (i) San Francisco-Oakland SEER registry (reference population); and (ii) FSG long-term follow up data from 50,757 individuals after a negative FSG in the Kaiser Permanente system. We compared the residual CRC risks after FSG with full-length colonoscopy. Results Our model mirrors trial data with 10-year CRC risk reductions after FSG screening at age 50 years of approximately one third; the optimal age for a ‘once-only’ FSG exam was between ages 50 to 60 years; and the greater benefit was for men compared with women. There were considerable incremental gains in reduction of CRC risk by colonoscopy compared with FSG with the greatest benefit for screening colonoscopy at age 50 years. These results held up against lowering the right-sided adenoma detection sensitivity by 30%, as well as reducing the curative efficacy of polypectomy throughout the colon. Conclusions Mathematical modeling of CRC screening, which takes account of important aspects of tumor biology, demonstrates superior risk reductions by colonoscopy over FSG. Our predictions provide further rationale for recommending screening colonoscopy in average-risk populations before the age of 60. PMID:25783458

  15. Model parameter estimation approach based on incremental analysis for lithium-ion batteries without using open circuit voltage

    NASA Astrophysics Data System (ADS)

    Wu, Hongjie; Yuan, Shifei; Zhang, Xi; Yin, Chengliang; Ma, Xuerui

    2015-08-01

    To improve the suitability of lithium-ion battery model under varying scenarios, such as fluctuating temperature and SoC variation, dynamic model with parameters updated realtime should be developed. In this paper, an incremental analysis-based auto regressive exogenous (I-ARX) modeling method is proposed to eliminate the modeling error caused by the OCV effect and improve the accuracy of parameter estimation. Then, its numerical stability, modeling error, and parametric sensitivity are analyzed at different sampling rates (0.02, 0.1, 0.5 and 1 s). To identify the model parameters recursively, a bias-correction recursive least squares (CRLS) algorithm is applied. Finally, the pseudo random binary sequence (PRBS) and urban dynamic driving sequences (UDDSs) profiles are performed to verify the realtime performance and robustness of the newly proposed model and algorithm. Different sampling rates (1 Hz and 10 Hz) and multiple temperature points (5, 25, and 45 °C) are covered in our experiments. The experimental and simulation results indicate that the proposed I-ARX model can present high accuracy and suitability for parameter identification without using open circuit voltage.

  16. TRW’s Ada Process Model for Incremental Development of Large Software Systems

    DTIC Science & Technology

    1990-01-01

    TRW’s Ada Process Model has proven to be key to the Command Center Processing and Display System-Replacement (CCPDS-R) project’s success to data in...developing over 3000,000 lines of Ada source code executing in a distributed VAX VMS environment. The Ada Process Model is, in simplest terms, a...software progress metrics. This paper provides an overview of the techniques and benefits of the Ada Process Model and describes some of the experience and

  17. A Self-Organizing Incremental Spatiotemporal Associative Memory Networks Model for Problems with Hidden State

    PubMed Central

    2016-01-01

    Identifying the hidden state is important for solving problems with hidden state. We prove any deterministic partially observable Markov decision processes (POMDP) can be represented by a minimal, looping hidden state transition model and propose a heuristic state transition model constructing algorithm. A new spatiotemporal associative memory network (STAMN) is proposed to realize the minimal, looping hidden state transition model. STAMN utilizes the neuroactivity decay to realize the short-term memory, connection weights between different nodes to represent long-term memory, presynaptic potentials, and synchronized activation mechanism to complete identifying and recalling simultaneously. Finally, we give the empirical illustrations of the STAMN and compare the performance of the STAMN model with that of other methods. PMID:27891146

  18. Serpentinization reaction pathways: implications for modeling approach

    SciTech Connect

    Janecky, D.R.

    1986-01-01

    Experimental seawater-peridotite reaction pathways to form serpentinites at 300/sup 0/C, 500 bars, can be accurately modeled using the EQ3/6 codes in conjunction with thermodynamic and kinetic data from the literature and unpublished compilations. These models provide both confirmation of experimental interpretations and more detailed insight into hydrothermal reaction processes within the oceanic crust. The accuracy of these models depends on careful evaluation of the aqueous speciation model, use of mineral compositions that closely reproduce compositions in the experiments, and definition of realistic reactive components in terms of composition, thermodynamic data, and reaction rates.

  19. A Networks Approach to Modeling Enzymatic Reactions.

    PubMed

    Imhof, P

    2016-01-01

    Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is beneficial to obtain a comprehensive picture of possible reaction paths and competing mechanisms. By combining individually generated intermediate states and chemical transition steps a network of such pathways can be constructed. Transition networks are a discretized representation of a potential energy landscape consisting of a multitude of reaction pathways connecting the end states of the reaction. The graph structure of the network allows an easy identification of the energetically most favorable pathways as well as a number of alternative routes.

  20. Mixed Integer Programming Model and Incremental Optimization for Delivery and Storage Planning Using Truck Terminals

    NASA Astrophysics Data System (ADS)

    Sakakibara, Kazutoshi; Tian, Yajie; Nishikawa, Ikuko

    We discuss the planning of transportation by trucks over a multi-day period. Each truck collects loads from suppliers and delivers them to assembly plants or a truck terminal. By exploiting the truck terminal as a temporal storage, we aim to increase the load ratio of each truck and to minimize the lead time for transportation. In this paper, we show a mixed integer programming model which represents each product explicitly, and discuss the decomposition of the problem into a problem of delivery and storage, and a problem of vehicle routing. Based on this model, we propose a relax-and-fix type heuristic in which decision variables are fixed one by one by mathematical programming techniques such as branch-and-bound methods.

  1. Incremental Model-Based Clustering for Large Datasets With Small Clusters

    DTIC Science & Technology

    2003-12-10

    Paulia Flower Image Data These data describe an RGB (3-band) image of a St. Paulia flower shown in Figure 4. There are 46,656 pixels after background...removal. The small yellow flower centers are particularly eyecatching. Figure 4: RGB Image of a St. Paulia flower . There are 46,656 data pixels after...background removal. Note the small yellow flower centers. Results for the model-based clustering strategies on the flower image of Figure 4 are summarized

  2. Two-Dimensional, Two-Phase Modeling of Multi-Increment Bagged Artillery Charges

    DTIC Science & Technology

    1983-02-01

    the solid-phase is assumed to depend on the local average pressure according to an empirical relationship. The model also accounts for...solid propellant. Time- Dependence of Specific Heats With c used to signify a specific heat at either constant volume or constant pressure , we have...flamespreading in respect to the structure of the longitudinal pressure field throughout the entire interior ballistic cycle. Previously, TDNOVA was

  3. Modeling Incremental Initial Active Duty Continuation Probabilities in the Selected Marine Corps Reserve

    DTIC Science & Technology

    2014-03-01

    Military Manpower, last modified November 21, 2003, 2, http://biotech.law.lsu.edu/ blaw /dodd/corres/pdf2/d11451p.pdf. 26 Figure 5. AFQT Score...http://biotech.law.lsu.edu/ blaw /dodd/corres/pdf2/d11451p.pdf. Erhardt, Bruce J. Jr. “Development of a Markov Model for Forecasting Continuation...Technical Information Center Ft. Belvoir, Virginia 2. Dudley Knox Library Naval Postgraduate School Monterey, California

  4. Modeling of turbulent chemical reaction

    NASA Technical Reports Server (NTRS)

    Chen, J.-Y.

    1995-01-01

    Viewgraphs are presented on modeling turbulent reacting flows, regimes of turbulent combustion, regimes of premixed and regimes of non-premixed turbulent combustion, chemical closure models, flamelet model, conditional moment closure (CMC), NO(x) emissions from turbulent H2 jet flames, probability density function (PDF), departures from chemical equilibrium, mixing models for PDF methods, comparison of predicted and measured H2O mass fractions in turbulent nonpremixed jet flames, experimental evidence of preferential diffusion in turbulent jet flames, and computation of turbulent reacting flows.

  5. Calibrating reaction rates for the CREST model

    NASA Astrophysics Data System (ADS)

    Handley, Caroline A.; Christie, Michael A.

    2017-01-01

    The CREST reactive-burn model uses entropy-dependent reaction rates that, until now, have been manually tuned to fit shock-initiation and detonation data in hydrocode simulations. This paper describes the initial development of an automatic method for calibrating CREST reaction-rate coefficients, using particle swarm optimisation. The automatic method is applied to EDC32, to help develop the first CREST model for this conventional high explosive.

  6. Animal models of idiosyncratic drug reactions.

    PubMed

    Ng, Winnie; Lobach, Alexandra R M; Zhu, Xu; Chen, Xin; Liu, Feng; Metushi, Imir G; Sharma, Amy; Li, Jinze; Cai, Ping; Ip, Julia; Novalen, Maria; Popovic, Marija; Zhang, Xiaochu; Tanino, Tadatoshi; Nakagawa, Tetsuya; Li, Yan; Uetrecht, Jack

    2012-01-01

    If we could predict and prevent idiosyncratic drug reactions (IDRs) it would have a profound effect on drug development and therapy. Given our present lack of mechanistic understanding, this goal remains elusive. Hypothesis testing requires valid animal models with characteristics similar to the idiosyncratic reactions that occur in patients. Although it has not been conclusively demonstrated, it appears that almost all IDRs are immune-mediated, and a dominant characteristic is a delay between starting the drug and the onset of the adverse reaction. In contrast, most animal models are acute and therefore involve a different mechanism than idiosyncratic reactions. There are, however, a few animal models such as the nevirapine-induced skin rash in rats that have characteristics very similar to the idiosyncratic reaction that occurs in humans and presumably have a very similar mechanism. These models have allowed testing hypotheses that would be impossible to test in any other way. In addition there are models in which there is a delayed onset of mild hepatic injury that resolves despite continued treatment similar to the "adaptation" reactions that are more common than severe idiosyncratic hepatotoxicity in humans. This probably represents the development of immune tolerance. However, most attempts to develop animal models by stimulating the immune system have been failures. A specific combination of MHC and T cell receptor may be required, but it is likely more complex. Animal studies that determine the requirements for an immune response would provide vital clues about risk factors for IDRs in patients.

  7. Quasiglobal reaction model for ethylene combustion

    NASA Technical Reports Server (NTRS)

    Singh, D. J.; Jachimowski, Casimir J.

    1994-01-01

    The objective of this study is to develop a reduced mechanism for ethylene oxidation. The authors are interested in a model with a minimum number of species and reactions that still models the chemistry with reasonable accuracy for the expected combustor conditions. The model will be validated by comparing the results to those calculated with a detailed kinetic model that has been validated against the experimental data.

  8. Cortical and trabecular bone adaptation to incremental load magnitudes using the mouse tibial axial compression loading model.

    PubMed

    Weatherholt, Alyssa M; Fuchs, Robyn K; Warden, Stuart J

    2013-01-01

    The mouse tibial axial compression loading model has recently been described to allow simultaneous exploration of cortical and trabecular bone adaptation within the same loaded element. However, the model frequently induces cortical woven bone formation and has produced inconsistent results with regards to trabecular bone adaptation. The aim of this study was to investigate bone adaptation to incremental load magnitudes using the mouse tibial axial compression loading model, with the ultimate goal of revealing a load that simultaneously induced lamellar cortical and trabecular bone adaptation. Adult (16 weeks old) female C57BL/6 mice were randomly divided into three load magnitude groups (5, 7 and 9N), and had their right tibia axially loaded using a continuous 2-Hz haversine waveform for 360 cycles/day, 3 days/week for 4 consecutive weeks. In vivo peripheral quantitative computed tomography was used to longitudinally assess midshaft tibia cortical bone adaptation, while ex vivo micro-computed tomography and histomorphometry were used to assess both midshaft tibia cortical and proximal tibia trabecular bone adaptation. A dose response to loading magnitude was observed within cortical bone, with increasing load magnitude inducing increasing levels of lamellar cortical bone adaptation within the upper two thirds of the tibial diaphysis. Greatest cortical bone adaptation was observed at the midshaft where there was a 42% increase in estimated mechanical properties (polar moment of inertia) in the highest (9N) load group. A dose response to load magnitude was not clearly evident within trabecular bone, with only the highest load (9N) being able to induce measureable adaptation (31% increase in trabecular bone volume fraction at the proximal tibia). The ultimate finding was that a load of 9N (engendering a tensile strain of 1833 με on medial surface of the midshaft tibia) was able to simultaneously induce measurable lamellar cortical and trabecular bone adaptation

  9. Turbulent group reaction model of spray dryer

    SciTech Connect

    Ma, H.K.; Huang, H.S.; Chiu, H.H.

    1987-01-01

    A turbulent group reaction model consisting of several sub-models was developed for the prediction of SO/sub 2/ removal efficiency in spray dryers. Mathematical models are developed on the basis of Eulerian-type turbulent Navier-Stokes equations for both gas and condensed phases with interphase transport considerations. The group reaction number, G, is defined as the ratio of the SO/sub 2/ absorption rate to a reference convective mass flux. This number represents the fraction of SO/sub 2/ absorbed into the lime slurry. The model is incorporated into a computer code which permits the investigation of spray dryer design concepts and operating conditions. Hence, it provides a theoretical basis for spray dryer performance optimization and scale-up. This investigation can be a practical guide to achieve high SO/sub 2/ removal efficiency in a spray dryer.

  10. Relative effects of increment and pedestal duration on the detection of intensity increments a

    PubMed Central

    Valente, Daniel L.; Patra, Harisadhan; Jesteadt, Walt

    2011-01-01

    The detection of a brief increment in the intensity of a longer duration pedestal is commonly used as a measure of intensity-resolution. Increment detection is known to improve with increasing duration of the increment and also with increasing duration of the pedestal, but the relative effects of these two parameters have not been explored in the same study. In several past studies of the effects of increment duration, pedestal duration was increased as increment duration increased. In the present study, increment and pedestal duration were independently manipulated. Increment-detection thresholds were determined for four subjects with normal-hearing using a 500- or 4000-Hz pedestal presented at 60 dB sound pressure level (SPL). Increment durations were 10, 20, 40, 80, 160, and 320 ms. Pedestal durations were 20, 40, 80, 160, and 320 ms. Each increment duration was combined with all pedestals of equal or greater duration. Multiple-regression analyses indicate that increment detection under these conditions is determined primarily by pedestal duration. Follow-up experiments ruled out effects of off-frequency listening or overshoot. The results suggest that effects of increment duration have been confounded by effects of pedestal duration in studies that co-varied increment and pedestal duration. Implications for models of temporal integration are discussed. PMID:21476665

  11. CT findings for intracerebral hemorrhage have little incremental impact on post-stroke mortality prediction model performance

    PubMed Central

    Zahuranec, Darin B.; Sánchez, Brisa N.; Brown, Devin L.; Wing, Jeffrey J.; Smith, Melinda A.; Garcia, Nelda M.; Meurer, William J.; Morgenstern, Lewis B.; Lisabeth, Lynda D.

    2012-01-01

    Background Stroke outcome studies often combine cases of intracerebral hemorrhage (ICH) and ischemic stroke (IS). These studies of mixed stroke typically ignore computed tomography (CT) findings for ICH cases, though the impact of omitting these traditional predictors of ICH mortality is unknown. We investigated the incremental impact of ICH CT findings on mortality prediction model performance. Methods Cases of ICH and IS (2000–2003) were identified from the Brain Attack Surveillance in Corpus Christi (BASIC) project. Base models predicting 30-day mortality included demographics, stroke type, and clinical findings (National Institutes of Health Stroke Scale (NIHSS) +/− Glasgow coma scale (GCS)). The impact of adding CT data (volume, intraventricular hemorrhage, infratentorial location) was assessed with the area under the curve (AUC), unweighted sum of squared residuals (Ŝ), and integrated discrimination improvement (IDI). The model assessment was performed first for the mixed case of IS and ICH, and then repeated for ICH cases alone to determine whether any lack of improvement in model performance with CT data for mixed stroke type was due to IS cases naturally forming a larger proportion of the total sample than ICH. Results A total of 1,256 cases were included (86% IS, 14% ICH). Thirty-day mortality was 16% overall (11% for IS; 43% for ICH). When both clinical scales (NIHSS and GCS) were included, none of the model performance measures showed improvement with the addition of CT findings whether considering IS and ICH together (ΔAUC: 0.002, 95% CI −0.01, 0.02; ΔŜ: −3.0, 95% CI −9.1, 2.6; IDI: 0.017, 95% CI −0.004, 0.05) or considering ICH cases alone (ΔAUC: 0.02, 95% CI −0.02, 0.08; Δ Ŝ: −2.0, 95% CI −9.7, 3.4); IDI 0.065, 95% CI −0.03, 0.21). If NIHSS was the only clinical scale included, there was still no improvement in AUC or Ŝ when CT findings were added for the sample with IS/ICH combined (ΔAUC: 0.005, 95%CI −0.01, 0.02;

  12. Theory and modeling of stereoselective organic reactions.

    PubMed

    Houk, K N; Paddon-Row, M N; Rondan, N G; Wu, Y D; Brown, F K; Spellmeyer, D C; Metz, J T; Li, Y; Loncharich, R J

    1986-03-07

    Theoretical investigations of the transition structures of additions and cycloadditions reveal details about the geometries of bond-forming processes that are not directly accessible by experiment. The conformational analysis of transition states has been developed from theoretical generalizations about the preferred angle of attack by reagents on multiple bonds and predictions of conformations with respect to partially formed bonds. Qualitative rules for the prediction of the stereochemistries of organic reactions have been devised, and semi-empirical computational models have also been developed to predict the stereoselectivities of reactions of large organic molecules, such as nucleophilic additions to carbonyls, electrophilic hydroborations and cycloadditions, and intramolecular radical additions and cycloadditions.

  13. Reaction Wheel Disturbance Model Extraction Software - RWDMES

    NASA Technical Reports Server (NTRS)

    Blaurock, Carl

    2009-01-01

    The RWDMES is a tool for modeling the disturbances imparted on spacecraft by spinning reaction wheels. Reaction wheels are usually the largest disturbance source on a precision pointing spacecraft, and can be the dominating source of pointing error. Accurate knowledge of the disturbance environment is critical to accurate prediction of the pointing performance. In the past, it has been difficult to extract an accurate wheel disturbance model since the forcing mechanisms are difficult to model physically, and the forcing amplitudes are filtered by the dynamics of the reaction wheel. RWDMES captures the wheel-induced disturbances using a hybrid physical/empirical model that is extracted directly from measured forcing data. The empirical models capture the tonal forces that occur at harmonics of the spin rate, and the broadband forces that arise from random effects. The empirical forcing functions are filtered by a physical model of the wheel structure that includes spin-rate-dependent moments (gyroscopic terms). The resulting hybrid model creates a highly accurate prediction of wheel-induced forces. It accounts for variation in disturbance frequency, as well as the shifts in structural amplification by the whirl modes, as the spin rate changes. This software provides a point-and-click environment for producing accurate models with minimal user effort. Where conventional approaches may take weeks to produce a model of variable quality, RWDMES can create a demonstrably high accuracy model in two hours. The software consists of a graphical user interface (GUI) that enables the user to specify all analysis parameters, to evaluate analysis results and to iteratively refine the model. Underlying algorithms automatically extract disturbance harmonics, initialize and tune harmonic models, and initialize and tune broadband noise models. The component steps are described in the RWDMES user s guide and include: converting time domain data to waterfall PSDs (power spectral

  14. Thermal models, stable isotopes and cooling ages from the incrementally constructed Tuolumne batholith, Sierra Nevada: why large chambers did exist

    NASA Astrophysics Data System (ADS)

    Paterson, S. R.; Okaya, D. A.; Memeti, V.; Mundil, R.; Lackey, J.; Clemens-Knott, D.

    2009-12-01

    Our studies of the zoned, 1100 km2, 95-85 Ma Tuolumne batholith are in part designed to evaluate the thermal evolution of normally zoned, large magma bodies formed by the amalgamation of a few to many magma pulses. We use finite difference models with full spatial heterogeneity of rock properties, fine-scale internal grid spacing allowing for rock geometries at scales between sub-m to km’s, small internal time steps for runs over durations of days to millions of years and latent heat of fusion. Our initial stable isotopic studies, including δ18O variation in zircon (6-6.5‰), titanite (4.5-5.2‰), quartz (9-10‰), and whole rock (7-9 ‰) (Lackey et al. 2008, J. Pet.) and of the dD of biotites (-65 to -75‰) reveal isotopic exchange during magmatic cooling but the absence of a pervasive hydrothermal circulation system. We thus excluded advective cooling from our models. A range of incremental chamber construction scenarios are modeled including (1) repeated intrusions of rectangular or elliptical geometry (sills, dikes, or blobs); (2) a sequence of intrusions emplaced at specified but arbitrary times or according to a time rate with pulse shapes fixed or set to randomly vary within a range of dimensions and aspect ratios; (3) sheeted dike complexes in which the thermal model expands according to an extension rate to accommodate the emplacement of new dikes with width and time between dikes coupled to growth rate; (4) nested diapiric pulses; and (5) nested, irregularly shaped bodies based on maps or cross-sections that are digitally rendered into rock types, assigned thermal properties and intruded at specified times as new magma pulses. This wide range of batholith construction scenarios naturally results in a wide range of length and timescales of magma chambers. However, many likely scenarios for the TB, based on flux rates constrained by mapping and geochronology indicate that (1) the lobes of the Tuolumne batholith will crystallize in 100

  15. Increments toward what?

    PubMed

    Weil, A

    2001-01-01

    Incremental proposals to expand health insurance coverage, such as expansions of the State Children's Health Insurance Program (SCHIP) or creation of new tax credits, should be examined for the values that underlie them and for how they structure future options for additional incremental coverage expansions. This paper examines five design issues in incremental reform: who determines coverage options for the newly insured; what risk pool do they enter; what is the government's contribution toward their coverage; what barriers are created by efforts to encourage efficiency; and how are issues of federalism handled? Tax credits are a departure from past approaches, while an SCHIP expansion is a continuation of current policy directions.

  16. Global Microscopic Models for Nuclear Reaction Calculations

    SciTech Connect

    Goriely, S.

    2005-05-24

    Important effort has been devoted in the last decades to measuring reaction cross sections. Despite such effort, many nuclear applications still require the use of theoretical predictions to estimate experimentally unknown cross sections. Most of the nuclear ingredients in the calculations of reaction cross sections need to be extrapolated in an energy and/or mass domain out of reach of laboratory simulations. In addition, some applications often involve a large number of unstable nuclei, so that only global approaches can be used. For these reasons, when the nuclear ingredients to the reaction models cannot be determined from experimental data, it is highly recommended to consider preferentially microscopic or semi-microscopic global predictions based on sound and reliable nuclear models which, in turn, can compete with more phenomenological highly-parameterized models in the reproduction of experimental data. The latest developments made in deriving such microscopic models for practical applications are reviewed. It mainly concerns nuclear structure properties (masses, deformations, radii, etc.), level densities at the equilibrium deformation, {gamma}-ray strength, as well as fission barriers and level densities at the fission saddle points.

  17. Data assimilation in a coupled physical-biogeochemical model of the California Current System using an incremental lognormal 4-dimensional variational approach: Part 1-Model formulation and biological data assimilation twin experiments

    NASA Astrophysics Data System (ADS)

    Song, Hajoon; Edwards, Christopher A.; Moore, Andrew M.; Fiechter, Jerome

    2016-10-01

    A quadratic formulation for an incremental lognormal 4-dimensional variational assimilation method (incremental L4DVar) is introduced for assimilation of biogeochemical observations into a 3-dimensional ocean circulation model. L4DVar assumes that errors in the model state are lognormally rather than Gaussian distributed, and implicitly ensures that state estimates are positive definite, making this approach attractive for biogeochemical variables. The method is made practical for a realistic implementation having a large state vector through linear assumptions that render the cost function quadratic and allow application of existing minimization techniques. A simple nutrient-phytoplankton-zooplankton-detritus (NPZD) model is coupled to the Regional Ocean Modeling System (ROMS) and configured for the California Current System. Quadratic incremental L4DVar is evaluated in a twin model framework in which biological fields only are in error and compared to G4DVar which assumes Gaussian distributed errors. Five-day assimilation cycles are used and statistics from four years of model integration analyzed. The quadratic incremental L4DVar results in smaller root-mean-squared errors and better statistical agreement with reference states than G4DVar while maintaining a positive state vector. The additional computational cost and implementation effort are trivial compared to the G4DVar system, making quadratic incremental L4DVar a practical and beneficial option for realistic biogeochemical state estimation in the ocean.

  18. Incremental Contingency Planning

    NASA Technical Reports Server (NTRS)

    Dearden, Richard; Meuleau, Nicolas; Ramakrishnan, Sailesh; Smith, David E.; Washington, Rich

    2003-01-01

    There has been considerable work in AI on planning under uncertainty. However, this work generally assumes an extremely simple model of action that does not consider continuous time and resources. These assumptions are not reasonable for a Mars rover, which must cope with uncertainty about the duration of tasks, the energy required, the data storage necessary, and its current position and orientation. In this paper, we outline an approach to generating contingency plans when the sources of uncertainty involve continuous quantities such as time and resources. The approach involves first constructing a "seed" plan, and then incrementally adding contingent branches to this plan in order to improve utility. The challenge is to figure out the best places to insert contingency branches. This requires an estimate of how much utility could be gained by building a contingent branch at any given place in the seed plan. Computing this utility exactly is intractable, but we outline an approximation method that back propagates utility distributions through a graph structure similar to that of a plan graph.

  19. Reaction-contingency based bipartite Boolean modelling

    PubMed Central

    2013-01-01

    Background Intracellular signalling systems are highly complex, rendering mathematical modelling of large signalling networks infeasible or impractical. Boolean modelling provides one feasible approach to whole-network modelling, but at the cost of dequantification and decontextualisation of activation. That is, these models cannot distinguish between different downstream roles played by the same component activated in different contexts. Results Here, we address this with a bipartite Boolean modelling approach. Briefly, we use a state oriented approach with separate update rules based on reactions and contingencies. This approach retains contextual activation information and distinguishes distinct signals passing through a single component. Furthermore, we integrate this approach in the rxncon framework to support automatic model generation and iterative model definition and validation. We benchmark this method with the previously mapped MAP kinase network in yeast, showing that minor adjustments suffice to produce a functional network description. Conclusions Taken together, we (i) present a bipartite Boolean modelling approach that retains contextual activation information, (ii) provide software support for automatic model generation, visualisation and simulation, and (iii) demonstrate its use for iterative model generation and validation. PMID:23835289

  20. No-Core Shell Model and Reactions

    SciTech Connect

    Navratil, P; Ormand, W E; Caurier, E; Bertulani, C

    2005-04-29

    There has been a significant progress in ab initio approaches to the structure of light nuclei. Starting from realistic two- and three-nucleon interactions the ab initio no-core shell model (NCSM) can predict low-lying levels in p-shell nuclei. It is a challenging task to extend ab initio methods to describe nuclear reactions. In this contribution, we present a brief overview of the NCSM with examples of recent applications as well as the first steps taken toward nuclear reaction applications. In particular, we discuss cross section calculations of p+{sup 6}Li and {sup 6}He+p scattering as well as a calculation of the astrophysically important {sup 7}Be(p, {gamma}){sup 8}B S-factor.

  1. Theory and modeling of stereoselective organic reactions

    SciTech Connect

    Houk, K.N.; Paddon-Row, M.N.; Rondan, N.G.; Wu, Y.D.; Brown, F.K.; Spellmeyer, D.C.; Metz, J.T.; Li, Y.; Loncharich, R.J.

    1986-03-07

    Theoretical investigations of the transition structures of additions and cycloadditions reveal details about the geometrics of bond-forming processes that are not directly accessible by experiment. The conformational analysis of transition states has been developed from theoretical generalizations about the preferred angle of attack by reagents on multiple bonds and predictions of conformations with respect to partially formed bonds. Qualitative rules for the prediction of the stereochemistries of organic reactions have been devised, and semi-empirical computational models have also been developed to predict the stereoselectivities of reactions of large organic molecules, such as nucleophilic additions to carbonyls, electrophilic hydroborations and cycloadditions, and intramolecular radical additions and cycloadditions. 52 references, 7 figures.

  2. No-Core Shell Model and Reactions

    SciTech Connect

    Navratil, Petr; Ormand, W. Erich; Caurier, Etienne; Bertulani, Carlos

    2005-10-14

    There has been a significant progress in ab initio approaches to the structure of light nuclei. Starting from realistic two- and three-nucleon interactions the ab initio no-core shell model (NCSM) can predict low-lying levels in p-shell nuclei. It is a challenging task to extend ab initio methods to describe nuclear reactions. In this contribution, we present a brief overview of the NCSM with examples of recent applications as well as the first steps taken toward nuclear reaction applications. In particular, we discuss cross section calculations of p+6Li and 6He+p scattering as well as a calculation of the astrophysically important 7Be(p,{gamma})8B S-factor.

  3. Photochemical reactions of various model protocell systems

    NASA Technical Reports Server (NTRS)

    Folsome, C. E.

    1986-01-01

    Models for the emergence of cellular life on the primitive Earth, and for physical environments of that era have been studied that embody these assumptions: (1) pregenetic cellular forms were phase-bounded systems primarily photosynthetic in nature, and (2) the early Earth environment was anoxic (lacking appreciable amounts of free hydrogen). It was found that organic structures can also be formed under anoxic conditions (N2, CO3=, H2O) by protracted longwavelength UV radiation. Apparently these structures form initially as organic layers upon CaCO3 crystalloids. The question remains as to whether the UV photosynthetic ability of such phase bounded structures is a curiosity, or a general property of phase bounded systems which is of direct interest to the emergence of cellular life. The question of the requirement and sailient features of a phase boundary for UV photosynthetic abilities was addressed by searching for similar general physical properties which might be manifest in a variety of other simple protocell-like structures. Since it has been shown that laboratory protocell models can effect the UV photosynthesis of low molecular weight compounds, this reaction is being used as an assay to survey other types of structures for similar UV photosynthetic reactions. Various kinds of structures surveyed are: (1) proteinoids; (2) liposomes; (3) reconstituted cell membrane spheroids; (4) coacervates; and (5) model protocells formed under anoxic conditions.

  4. Leveraging modeling approaches: reaction networks and rules.

    PubMed

    Blinov, Michael L; Moraru, Ion I

    2012-01-01

    We have witnessed an explosive growth in research involving mathematical models and computer simulations of intracellular molecular interactions, ranging from metabolic pathways to signaling and gene regulatory networks. Many software tools have been developed to aid in the study of such biological systems, some of which have a wealth of features for model building and visualization, and powerful capabilities for simulation and data analysis. Novel high-resolution and/or high-throughput experimental techniques have led to an abundance of qualitative and quantitative data related to the spatiotemporal distribution of molecules and complexes, their interactions kinetics, and functional modifications. Based on this information, computational biology researchers are attempting to build larger and more detailed models. However, this has proved to be a major challenge. Traditionally, modeling tools require the explicit specification of all molecular species and interactions in a model, which can quickly become a major limitation in the case of complex networks - the number of ways biomolecules can combine to form multimolecular complexes can be combinatorially large. Recently, a new breed of software tools has been created to address the problems faced when building models marked by combinatorial complexity. These have a different approach for model specification, using reaction rules and species patterns. Here we compare the traditional modeling approach with the new rule-based methods. We make a case for combining the capabilities of conventional simulation software with the unique features and flexibility of a rule-based approach in a single software platform for building models of molecular interaction networks.

  5. Airborne observed and receptor-oriented modelled urban increments of anthropogenic CO2, CO and NOX concentrations in the megacity of London in summer 2012

    NASA Astrophysics Data System (ADS)

    Font Font, Anna Maria; Morguí, Josep Anton; Lee, James; McQuaid, Jim B.; Barratt, Benjamin

    2014-05-01

    A better characterization of the emissions and the dynamics of anthropogenic CO2 in large-urban centres are needed to implement more effective mitigation measures to combat climate change. This study aims to establish a representative emissions ratio of anthropogenic CO2 (CO2ff) in the megacity of London using CO and NOX as tracers. Observations of CO2, CO and NOX mixing ratios obtained onboard the NERC-ARSF aircraft undertaken on 12 July 2012 over the city of London were used. Airborne observations were taken at ~380 m along four transects crossing London, two in the morning (10:30 to 12:30 GMT) and two in the afternoon (15:30-16:30 GMT). The ratio of the amounts of CO and CO2 in excess of natural abundances (denoted as ΔCO and ΔCO2, respectively) from the airborne observations was used to determine the fraction of CO2 derived from burning fossil fuels (CO2ff). Total observations of CO and CO2 were compared to NOX observations and background concentrations were determined as the intercept when NOX mixing ratios equalled zero derived from standardised major axis linear regression. Excess concentrations were calculated by subtracting total amounts minus the background. ΔCO showed good correlation with ΔCO2 in the morning transects (R=0.95) but not in the afternoon (R=-0.50). The mean (±1σ) CO/CO2ff was derived from linear regression using the morning measurements and valued 5.0±0.4 ppb ppm-1. Lagrangian Particle Dispersion (LPD) simulations in backward mode were undertaken to model urban increments of anthropogenic CO2 and CO and to calculate the emissions ratio from the emissions inventory EDGAR v4.2. The LPD model FLEXPART was run with the meteorological data from the European Centre for Medium-Range Weather Forecasts (spatial resolution of 0.2 x 0.2 degrees; 91 vertical levels) and multiplied with the EDGAR emissions inventory (spatial resolution 0.1 x 0.1 degrees) to obtain an increment at each receptor point along the transects. Annual and temporal

  6. Development and Validation of Reaction Wheel Disturbance Models: Empirical Model

    NASA Astrophysics Data System (ADS)

    Masterson, R. A.; Miller, D. W.; Grogan, R. L.

    2002-01-01

    Accurate disturbance models are necessary to predict the effects of vibrations on the performance of precision space-based telescopes, such as the Space Interferometry Mission (SIM). There are many possible disturbance sources on such spacecraft, but mechanical jitter from the reaction wheel assembly (RWA) is anticipated to be the largest. A method has been developed and implemented in the form of a MATLAB toolbox to extract parameters for an empirical disturbance model from RWA micro-vibration data. The disturbance model is based on one that was used to predict the vibration behaviour of the Hubble Space Telescope (HST) wheels and assumes that RWA disturbances consist of discrete harmonics of the wheel speed with amplitudes proportional to the wheel speed squared. The MATLAB toolbox allows the extension of this empirical disturbance model for application to any reaction wheel given steady state vibration data. The toolbox functions are useful for analyzing RWA vibration data, and the model provides a good estimate of the disturbances over most wheel speeds. However, it is shown that the disturbances are under-predicted by a model of this form over some wheel speed ranges. The poor correlation is due to the fact that the empirical model does not account for disturbance amplifications caused by interactions between the harmonics and the structural modes of the wheel. Experimental data from an ITHACO Space Systems E-type reaction wheel are used to illustrate the model development and validation process.

  7. Model Experiment of Thermal Runaway Reactions Using the Aluminum-Hydrochloric Acid Reaction

    ERIC Educational Resources Information Center

    Kitabayashi, Suguru; Nakano, Masayoshi; Nishikawa, Kazuyuki; Koga, Nobuyoshi

    2016-01-01

    A laboratory exercise for the education of students about thermal runaway reactions based on the reaction between aluminum and hydrochloric acid as a model reaction is proposed. In the introductory part of the exercise, the induction period and subsequent thermal runaway behavior are evaluated via a simple observation of hydrogen gas evolution and…

  8. Building process knowledge using inline spectroscopy, reaction calorimetry and reaction modeling--the integrated approach.

    PubMed

    Tummala, Srinivas; Shabaker, John W; Leung, Simon S W

    2005-11-01

    For over two decades, reaction engineering tools and techniques such as reaction calorimetry, inline spectroscopy and, to a more limited extent, reaction modeling, have been employed within the pharmaceutical industry to ensure safe and robust scale-up of organic reactions. Although each of these techniques has had a significant impact on the landscape of process development, an effective integrated approach is now being realized that combines calorimetry and spectroscopy with predictive modeling tools. This paper reviews some recent advances in the use of these reaction engineering tools in process development within the pharmaceutical industry and discusses their potential impact on the effective application of the integrated approach.

  9. Testing the Relations Between Impulsivity-Related Traits, Suicidality, and Nonsuicidal Self-Injury: A Test of the Incremental Validity of the UPPS Model

    PubMed Central

    Lynam, Donald R.; Miller, Joshua D.; Miller, Drew J.; Bornovalova, Marina A.; Lejuez, C. W.

    2011-01-01

    Borderline personality disorder (BPD) has received significant attention as a predictor of suicidal behavior (SB) and nonsuicidal self-injury (NSSI). Despite significant promise, trait impulsivity has received less attention. Understanding the relations between impulsivity and SB and NSSI is confounded, unfortunately, by the heterogeneous nature of impulsivity. This study examined the relations among 4 personality pathways to impulsive behavior studied via the UPPS model of impulsivity and SB and NSSI in a residential sample of drug abusers (N = 76). In this study, we tested whether these 4 impulsivity-related traits (i.e., Negative Urgency, Sensation Seeking, Lack of Premeditation, and Lack of Perseverance) provide incremental validity in the statistical prediction of SB and NSSI above and beyond BPD; they do. We also tested whether BPD symptoms provide incremental validity in the prediction of SB and NSSI above and beyond these impulsivity-related traits; they do not. In addition to the main effects of Lack of Premeditation and Negative Urgency, we found evidence of a robust interaction between these 2 personality traits. The current results argue strongly for the consideration of these 2 impulsivity-related domains—alone and in interaction—when attempting to understand and predict SB and NSSI. PMID:21833346

  10. Testing the relations between impulsivity-related traits, suicidality, and nonsuicidal self-injury: a test of the incremental validity of the UPPS model.

    PubMed

    Lynam, Donald R; Miller, Joshua D; Miller, Drew J; Bornovalova, Marina A; Lejuez, C W

    2011-04-01

    Borderline personality disorder (BPD) has received significant attention as a predictor of suicidal behavior (SB) and nonsuicidal self-injury (NSSI). Despite significant promise, trait impulsivity has received less attention. Understanding the relations between impulsivity and SB and NSSI is confounded, unfortunately, by the heterogeneous nature of impulsivity. This study examined the relations among 4 personality pathways to impulsive behavior studied via the UPPS model of impulsivity and SB and NSSI in a residential sample of drug abusers (N = 76). In this study, we tested whether these 4 impulsivity-related traits (i.e., Negative Urgency, Sensation Seeking, Lack of Premeditation, and Lack of Perseverance) provide incremental validity in the statistical prediction of SB and NSSI above and beyond BPD; they do. We also tested whether BPD symptoms provide incremental validity in the prediction of SB and NSSI above and beyond these impulsivity-related traits; they do not. In addition to the main effects of Lack of Premeditation and Negative Urgency, we found evidence of a robust interaction between these 2 personality traits. The current results argue strongly for the consideration of these 2 impulsivity-related domains--alone and in interaction--when attempting to understand and predict SB and NSSI.

  11. Model for reaction kinetics in pyrolysis of wood

    SciTech Connect

    Ahuja, P.; Singh, P.C.; Upadhyay, S.N.; Kumar, S.

    1996-12-31

    A reaction model for the pyrolysis of small and large particles of wood Is developed. The chemical reactions that take place when biomass is pyrolyzed are the devolatilization reactions (primary) and due to the vapour-solid interactions (secondary). In the case of small particles, when the volatiles are immediately removed by the purge gas, only primary reactions occur and the reaction model is described by weight loss and char forming reactions. The of heterogeneous secondary reactions occur in the case of large particles due to the interaction between the volatiles and the hot nascent primary char. A chain reaction mechanism of secondary char formation is proposed. The model takes both the volatiles retention time and cracking and repolymerization reactions of the vapours with the decomposing solid as well as autocatalysis into consideration. 7 refs., 3 figs., 2 tabs.

  12. Incremental full configuration interaction

    NASA Astrophysics Data System (ADS)

    Zimmerman, Paul M.

    2017-03-01

    The incremental expansion provides a polynomial scaling method for computing electronic correlation energies. This article details a new algorithm and implementation for the incremental expansion of full configuration interaction (FCI), called iFCI. By dividing the problem into n-body interaction terms, accurate correlation energies can be recovered at low n in a highly parallel computation. Additionally, relatively low-cost approximations are possible in iFCI by solving for each incremental energy to within a specified threshold. Herein, systematic tests show that FCI-quality energies can be asymptotically reached for cases where dynamic correlation is dominant as well as where static correlation is vital. To further reduce computational costs and allow iFCI to reach larger systems, a select-CI approach (heat-bath CI) requiring two parameters is incorporated. Finally, iFCI provides the first estimate of FCI energies for hexatriene with a polarized double zeta basis set, which has 32 electrons correlated in 118 orbitals, corresponding to a FCI dimension of over 1038.

  13. A Generalized Kinetic Model for Heterogeneous Gas-Solid Reactions

    SciTech Connect

    Xu, Zhijie; Sun, Xin; Khaleel, Mohammad A.

    2012-08-15

    We present a generalized kinetic model for gas-solid heterogeneous reactions taking place at the interface between two phases. The model studies the reaction kinetics by taking into account the reactions at the interface, as well as the transport process within the product layer. The standard unreacted shrinking core model relies on the assumption of quasi-static diffusion that results in a steady-state concentration profile of gas reactant in the product layer. By relaxing this assumption and resolving the entire problem, general solutions can be obtained for reaction kinetics, including the reaction front velocity and the conversion (volume fraction of reacted solid). The unreacted shrinking core model is shown to be accurate and in agreement with the generalized model for slow reaction (or fast diffusion), low concentration of gas reactant, and small solid size. Otherwise, a generalized kinetic model should be used.

  14. A simple reaction-rate model for turbulent diffusion flames

    NASA Technical Reports Server (NTRS)

    Bangert, L. H.

    1975-01-01

    A simple reaction rate model is proposed for turbulent diffusion flames in which the reaction rate is proportional to the turbulence mixing rate. The reaction rate is also dependent on the mean mass fraction and the mean square fluctuation of mass fraction of each reactant. Calculations are compared with experimental data and are generally successful in predicting the measured quantities.

  15. Freezing increment in keratophakia.

    PubMed

    Swinger, C A; Wisnicki, H J

    In homoplastic keratomileusis, keratophakia, and epikeratophakia, the corneal tissue that provides the final refractive lenticule undergoes a conformational change when frozen. Because corneal tissue is composed primarily of water, an assumed value of 9.08% (approximate volumic percentage expansion of water when frozen) is frequently used for the increase in thickness, or freezing increment, rather than measuring it directly. We evaluated 32 cases of clinical keratophakia and found the increase in thickness to average 37 +/- 21%. In this series of 32 cases, the percentage of patients with a greater than 4 D residual refractive error was 16%. If an assumed freezing increment of 9.08% had been used, the percentage would have been 28%, with two-thirds of these 28% manifesting a marked undercorrection. Because of a lack of studies documenting the behavior of corneal tissue following cryoprotection and freezing, it is suggested that measurements be taken during homoplastic surgery to minimize the potential for significant inaccuracy in obtaining the desired optic result.

  16. Polymerization as a Model Chain Reaction

    ERIC Educational Resources Information Center

    Morton, Maurice

    1973-01-01

    Describes the features of the free radical, anionic, and cationic mechanisms of chain addition polymerization. Indicates that the nature of chain reactions can be best taught through the study of macromolecules. (CC)

  17. Modelling Chemical Reasoning to Predict and Invent Reactions.

    PubMed

    Segler, Marwin H S; Waller, Mark P

    2016-11-11

    The ability to reason beyond established knowledge allows organic chemists to solve synthetic problems and invent novel transformations. Herein, we propose a model that mimics chemical reasoning, and formalises reaction prediction as finding missing links in a knowledge graph. We have constructed a knowledge graph containing 14.4 million molecules and 8.2 million binary reactions, which represents the bulk of all chemical reactions ever published in the scientific literature. Our model outperforms a rule-based expert system in the reaction prediction task for 180 000 randomly selected binary reactions. The data-driven model generalises even beyond known reaction types, and is thus capable of effectively (re-)discovering novel transformations (even including transition metal-catalysed reactions). Our model enables computers to infer hypotheses about reactivity and reactions by only considering the intrinsic local structure of the graph and because each single reaction prediction is typically achieved in a sub-second time frame, the model can be used as a high-throughput generator of reaction hypotheses for reaction discovery.

  18. Detailed reduction of reaction mechanisms for flame modeling

    NASA Technical Reports Server (NTRS)

    Wang, Hai; Frenklach, Michael

    1991-01-01

    A method for reduction of detailed chemical reaction mechanisms, introduced earlier for ignition system, was extended to laminar premixed flames. The reduction is based on testing the reaction and reaction-enthalpy rates of the 'full' reaction mechanism using a zero-dimensional model with the flame temperature profile as a constraint. The technique is demonstrated with numerical tests performed on the mechanism of methane combustion.

  19. Evaluation of incremental reactivity and its uncertainty in Southern California.

    PubMed

    Martien, Philip T; Harley, Robert A; Milford, Jana B; Russell, Armistead G

    2003-04-15

    The incremental reactivity (IR) and relative incremental reactivity (RIR) of carbon monoxide and 30 individual volatile organic compounds (VOC) were estimated for the South Coast Air Basin using two photochemical air quality models: a 3-D, grid-based model and a vertically resolved trajectory model. Both models include an extended version of the SAPRC99 chemical mechanism. For the 3-D modeling, the decoupled direct method (DDM-3D) was used to assess reactivities. The trajectory model was applied to estimate uncertainties in reactivities due to uncertainties in chemical rate parameters, deposition parameters, and emission rates using Monte Carlo analysis with Latin hypercube sampling. For most VOC, RIRs were found to be consistent in rankings with those produced by Carter using a box model. However, 3-D simulations show that coastal regions, upwind of most of the emissions, have comparatively low IR but higher RIR than predicted by box models for C4-C5 alkenes and carbonyls that initiate the production of HOx radicals. Biogenic VOC emissions were found to have a lower RIR than predicted by box model estimates, because emissions of these VOC were mostly downwind of the areas of primary ozone production. Uncertainties in RIR of individual VOC were found to be dominated by uncertainties in the rate parameters of their primary oxidation reactions. The coefficient of variation (COV) of most RIR values ranged from 20% to 30%, whereas the COV of absolute incremental reactivity ranged from about 30% to 40%. In general, uncertainty and variability both decreased when relative rather than absolute reactivity metrics were used.

  20. Reaction chain modeling of denitrification reactions during a push-pull test.

    PubMed

    Boisson, A; de Anna, P; Bour, O; Le Borgne, T; Labasque, T; Aquilina, L

    2013-05-01

    Field quantitative estimation of reaction kinetics is required to enhance our understanding of biogeochemical reactions in aquifers. We extended the analytical solution developed by Haggerty et al. (1998) to model an entire 1st order reaction chain and estimate the kinetic parameters for each reaction step of the denitrification process. We then assessed the ability of this reaction chain to model biogeochemical reactions by comparing it with experimental results from a push-pull test in a fractured crystalline aquifer (Ploemeur, French Brittany). Nitrates were used as the reactive tracer, since denitrification involves the sequential reduction of nitrates to nitrogen gas through a chain reaction (NO3(-)→NO2(-)→NO→N2O→N2) under anaerobic conditions. The kinetics of nitrate consumption and by-product formation (NO2(-), N2O) during autotrophic denitrification were quantified by using a reactive tracer (NO3(-)) and a non-reactive tracer (Br(-)). The formation of reaction by-products (NO2(-), N2O, N2) has not been previously considered using a reaction chain approach. Comparison of Br(-) and NO3(-) breakthrough curves showed that 10% of the injected NO3(-) molar mass was transformed during the 12 h experiment (2% into NO2(-), 1% into N2O and the rest into N2 and NO). Similar results, but with slower kinetics, were obtained from laboratory experiments in reactors. The good agreement between the model and the field data shows that the complete denitrification process can be efficiently modeled as a sequence of first order reactions. The 1st order kinetics coefficients obtained through modeling were as follows: k1=0.023 h(-1), k2=0.59 h(-1), k3=16 h(-1), and k4=5.5 h(-1). A next step will be to assess the variability of field reactivity using the methodology developed for modeling push-pull tracer tests.

  1. Robust incremental condition estimation

    SciTech Connect

    Bischof, C.H.; Tang, P.T.P.

    1991-03-29

    This paper presents an improved version of incremental condition estimation, a technique for tracking the extremal singular values of a triangular matrix as it is being constructed one column at a time. We present a new motivation for this estimation technique using orthogonal projections. The paper focuses on an implementation of this estimation scheme in an accurate and consistent fashion. In particular, we address the subtle numerical issues arising in the computation of the eigensystem of a symmetric rank-one perturbed diagonal 2 {times} 2 matrix. Experimental results show that the resulting scheme does a good job in estimating the extremal singular values of triangular matrices, independent of matrix size and matrix condition number, and that it performs qualitatively in the same fashion as some of the commonly used nonincremental condition estimation schemes.

  2. Quantal release, incremental detection, and long-period Ca2+ oscillations in a model based on regulatory Ca2+-binding sites along the permeation pathway.

    PubMed Central

    Dupont, G; Swillens, S

    1996-01-01

    Quantal release, incremental detection, and oscillations are three types of Ca2+ responses that can be obtained in different conditions, after stimulation of the intracellular Ca2+ stores by submaximum concentrations of inositol 1,4,5-triphosphate (InsP3). All three phenomena are thought to occur through the regulatory properties of the InsP3 receptor/Ca2+ channel. In the present study, we perform further analysis of the model (Swillens et al., 1994, Proc. Natl. Acad. Sci. USA. 91:10074-10078) previously proposed for transient InsP3-induced Ca2+ release, based on the bell-shaped dependence of the InsP3 receptor activity on the Ca2+ level and on the existence of an intermediate Ca2+ domain located around the mouth of the channel. We show that Ca2+ oscillations also arise in the latter model. Conditions for the occurrence of the various behaviors are investigated. Numerical simulations also show that the existence of an intermediate Ca2+ domain can markedly increase the period of oscillations. Periods on the order of 1 min can indeed be accounted for by the model when one assigns realistic values to the kinetic constants of the InsP3 receptor, which, in the absence of a domain, lead to oscillations with periods of a few seconds. Finally, theoretical support in favor of a positive cooperativity in the regulation of the InsP3 receptor by Ca2+ is presented. Images FIGURE 7 PMID:8889149

  3. Modeling the isotope effect in Walden inversion reactions

    NASA Astrophysics Data System (ADS)

    Schechter, Israel

    1991-05-01

    A simple model to explain the isotope effect in the Walden exchange reaction is suggested. It is developed in the spirit of the line-of-centers models, and considers a hard-sphere collision that transfers energy from the relative translation to the desired vibrational mode, as well as geometrical properties and steric requirements. This model reproduces the recently measured cross sections for the reactions of hydrogen with isotopic silanes and older measurements of the substitution reactions of tritium atoms with isotopic methanes. Unlike previously given explanations, this model explains the effect of the attacking atom as well as of the other participating atoms. The model provides also qualitative explanation of the measured relative yields and thresholds of CH 3T and CH 2TF from the reaction T + CH 3F. Predictions for isotope effects and cross sections of some unmeasured reactions are given.

  4. Isolating the roles of different forcing agents in global stratospheric temperature changes using model integrations with incrementally added single forcings

    NASA Astrophysics Data System (ADS)

    Aquila, V.; Swartz, W. H.; Waugh, D. W.; Colarco, P. R.; Pawson, S.; Polvani, L. M.; Stolarski, R. S.

    2016-07-01

    Satellite instruments show a cooling of global stratospheric temperatures over the whole data record (1979-2014). This cooling is not linear and includes two descending steps in the early 1980s and mid-1990s. The 1979-1995 period is characterized by increasing concentrations of ozone-depleting substances (ODSs) and by the two major volcanic eruptions of El Chichón (1982) and Mount Pinatubo (1991). The 1995-present period is characterized by decreasing ODS concentrations and by the absence of major volcanic eruptions. Greenhouse gas (GHG) concentrations increase over the whole time period. In order to isolate the roles of different forcing agents in the global stratospheric temperature changes, we performed a set of simulations using the NASA Goddard Earth Observing System Chemistry-Climate Model with prescribed sea surface temperatures. We find that in our model simulations the cooling of the stratosphere from 1979 to present is mostly driven by changes in GHG concentrations in the middle and upper stratosphere and by GHG and ODS changes in the lower stratosphere. While the cooling trend caused by increasing GHGs is roughly constant over the satellite era, changing ODS concentrations cause a significant stratospheric cooling only up to the mid-1990s, when they start to decrease because of the implementation of the Montreal Protocol. Sporadic volcanic events and the solar cycle have a distinct signature in the time series of stratospheric temperature anomalies but do not play a statistically significant role in the long-term trends from 1979 to 2014. Several factors combine to produce the step-like behavior in the stratospheric temperatures: in the lower stratosphere, the flattening starting in the mid-1990s is due to the decrease in ozone-depleting substances; Mount Pinatubo and the solar cycle cause the abrupt steps through the aerosol-associated warming and the volcanically induced ozone depletion. In the middle and upper stratosphere, changes in solar

  5. Improved bleeding scores using Gelfoam(®) Powder with incremental concentrations of bovine thrombin in a swine liver lesion model.

    PubMed

    Morse, Dennis C; Silva, Elif; Bartrom, Jolee; Young, Kelli; Bass, Eric J; Potter, David; Bieber, Trevor

    2016-10-01

    Topical hemostatic agents are used intra-operatively to prevent uncontrolled bleeding. Gelfoam(®) Powder contains a hemostatic agent prepared from purified pork skin gelatin, the efficacy of which is increased when combined with thrombin. However, the effect of increasing concentrations of thrombin on resultant hemostasis is not known. This study sought to evaluate the ability of various concentrations of thrombin in combination with Gelfoam Powder to control bleeding using a swine liver lesion model. Ten pigs underwent a midline laparotomy. Circular lesions were created in the left medial, right medial, and left lateral lobes; six lesions per lobe. Gelfoam Powder was hydrated with Thrombin-JMI(®) diluted to 250, 375, and 770 IU/mL. Each concentration was applied to two lesion sites per lobe. Bleeding scores were measured at 3, 6, 9, and 12 min using a 6-point system; comparison of bleeding scores was performed using ANOVA with the post hoc Tukey test. The bleeding scores with thrombin concentrations at 770 IU/mL were significantly lower than at 250 and 375 IU/mL at all four time points. The percentage of biopsies with a clinically acceptable bleeding score rose from 37.9, 46.6, and 71.2 % at 3 min to 55.2, 69.0, and 88.1 % at 12 min in the 250, 375, and 770 IU/mL thrombin groups, respectively. The study showed that the hemostatic response to thrombin was dose-related: using higher concentrations of thrombin with Gelfoam Powder yielded improved hemostasis, as determined by lower bleeding scores.

  6. Effect of reactions in small eddies on biomass gasification with eddy dissipation concept - Sub-grid scale reaction model.

    PubMed

    Chen, Juhui; Yin, Weijie; Wang, Shuai; Meng, Cheng; Li, Jiuru; Qin, Bai; Yu, Guangbin

    2016-07-01

    Large-eddy simulation (LES) approach is used for gas turbulence, and eddy dissipation concept (EDC)-sub-grid scale (SGS) reaction model is employed for reactions in small eddies. The simulated gas molar fractions are in better agreement with experimental data with EDC-SGS reaction model. The effect of reactions in small eddies on biomass gasification is emphatically analyzed with EDC-SGS reaction model. The distributions of the SGS reaction rates which represent the reactions in small eddies with particles concentration and temperature are analyzed. The distributions of SGS reaction rates have the similar trend with those of total reactions rates and the values account for about 15% of the total reactions rates. The heterogeneous reaction rates with EDC-SGS reaction model are also improved during the biomass gasification process in bubbling fluidized bed.

  7. Modelling couplings between reaction, fluid flow and deformation: Kinetics

    NASA Astrophysics Data System (ADS)

    Malvoisin, Benjamin; Podladchikov, Yury Y.; Connolly, James A. D.

    2016-04-01

    Mineral assemblages out of equilibrium are commonly found in metamorphic rocks testifying of the critical role of kinetics for metamorphic reactions. As experimentally determined reaction rates in fluid-saturated systems generally indicate complete reaction in less than several years, i.e. several orders of magnitude faster than field-based estimates, metamorphic reaction kinetics are generally thought to be controlled by transport rather than by processes at the mineral surface. However, some geological processes like earthquakes or slow-slip events have shorter characteristic timescales, and transport processes can be intimately related to mineral surface processes. Therefore, it is important to take into account the kinetics of mineral surface processes for modelling fluid/rock interactions. Here, a model coupling reaction, fluid flow and deformation was improved by introducing a delay in the achievement of equilibrium. The classical formalism for dissolution/precipitation reactions was used to consider the influence of the distance from equilibrium and of temperature on the reaction rate, and a dependence on porosity was introduced to model evolution of reacting surface area during reaction. The fitting of experimental data for three reactions typically occurring in metamorphic systems (serpentine dehydration, muscovite dehydration and calcite decarbonation) indicates a systematic faster kinetics close from equilibrium on the dehydration side than on the hydration side. This effect is amplified through the porosity term in the reaction rate since porosity is formed during dehydration. Numerical modelling indicates that this difference in reaction rate close from equilibrium plays a key role in microtextures formation. The developed model can be used in a wide variety of geological systems where couplings between reaction, deformation and fluid flow have to be considered.

  8. Modeling Second-Order Chemical Reactions using Cellular Automata

    NASA Astrophysics Data System (ADS)

    Hunter, N. E.; Barton, C. C.; Seybold, P. G.; Rizki, M. M.

    2012-12-01

    Cellular automata (CA) are discrete, agent-based, dynamic, iterated, mathematical computational models used to describe complex physical, biological, and chemical systems. Unlike the more computationally demanding molecular dynamics and Monte Carlo approaches, which use "force fields" to model molecular interactions, CA models employ a set of local rules. The traditional approach for modeling chemical reactions is to solve a set of simultaneous differential rate equations to give deterministic outcomes. CA models yield statistical outcomes for a finite number of ingredients. The deterministic solutions appear as limiting cases for conditions such as a large number of ingredients or a finite number of ingredients and many trials. Here we present a 2-dimensional, probabilistic CA model of a second-order gas phase reaction A + B → C, using a MATLAB basis. Beginning with a random distribution of ingredients A and B, formation of C emerges as the system evolves. The reaction rate can be varied based on the probability of favorable collisions of the reagents A and B. The model permits visualization of the conversion of reagents to products, and allows one to plot concentration vs. time for A, B and C. We test hypothetical reaction conditions such as: limiting reagents, the effects of reaction probabilities, and reagent concentrations on the reaction kinetics. The deterministic solutions of the reactions emerge as statistical averages in the limit of the large number of cells in the array. Modeling results for dynamic processes in the atmosphere will be presented.

  9. Directed Incremental Symbolic Execution

    NASA Technical Reports Server (NTRS)

    Person, Suzette; Yang, Guowei; Rungta, Neha; Khurshid, Sarfraz

    2011-01-01

    The last few years have seen a resurgence of interest in the use of symbolic execution -- a program analysis technique developed more than three decades ago to analyze program execution paths. Scaling symbolic execution and other path-sensitive analysis techniques to large systems remains challenging despite recent algorithmic and technological advances. An alternative to solving the problem of scalability is to reduce the scope of the analysis. One approach that is widely studied in the context of regression analysis is to analyze the differences between two related program versions. While such an approach is intuitive in theory, finding efficient and precise ways to identify program differences, and characterize their effects on how the program executes has proved challenging in practice. In this paper, we present Directed Incremental Symbolic Execution (DiSE), a novel technique for detecting and characterizing the effects of program changes. The novelty of DiSE is to combine the efficiencies of static analysis techniques to compute program difference information with the precision of symbolic execution to explore program execution paths and generate path conditions affected by the differences. DiSE is a complementary technique to other reduction or bounding techniques developed to improve symbolic execution. Furthermore, DiSE does not require analysis results to be carried forward as the software evolves -- only the source code for two related program versions is required. A case-study of our implementation of DiSE illustrates its effectiveness at detecting and characterizing the effects of program changes.

  10. Chemical reactions simulated by ground-water-quality models

    USGS Publications Warehouse

    Grove, David B.; Stollenwerk, Kenneth G.

    1987-01-01

    Recent literature concerning the modeling of chemical reactions during transport in ground water is examined with emphasis on sorption reactions. The theory of transport and reactions in porous media has been well documented. Numerous equations have been developed from this theory, to provide both continuous and sequential or multistep models, with the water phase considered for both mobile and immobile phases. Chemical reactions can be either equilibrium or non-equilibrium, and can be quantified in linear or non-linear mathematical forms. Non-equilibrium reactions can be separated into kinetic and diffusional rate-limiting mechanisms. Solutions to the equations are available by either analytical expressions or numerical techniques. Saturated and unsaturated batch, column, and field studies are discussed with one-dimensional, laboratory-column experiments predominating. A summary table is presented that references the various kinds of models studied and their applications in predicting chemical concentrations in ground waters.

  11. Abundances in Astrophysical Environments: Reaction Network Simulations with Reaction Rates from Many-nucleon Modeling

    NASA Astrophysics Data System (ADS)

    Amason, Charlee; Dreyfuss, Alison; Launey, Kristina; Draayer, Jerry

    2017-01-01

    We use the ab initio (first-principle) symmetry-adapted no-core shell model (SA-NCSM) to calculate reaction rates of significance to type I X-ray burst nucleosynthesis. We consider the 18O(p,γ)19F reaction, which may influence the production of fluorine, as well as the 16O(α,γ)20Ne reaction, which is key to understanding the production of heavier elements in the universe. Results are compared to those obtained in the no-core sympletic shell model (NCSpM) with a schematic interaction. We discuss how these reaction rates affect the relevant elemental abundances. We thank the NSF for supporting this work through the REU Site in Physics & Astronomy (NSF grant #1560212) at Louisiana State University. This work was also supported by the U.S. NSF (OCI-0904874, ACI -1516338) and the U.S. DOE (DE-SC0005248).

  12. Incremental Parsing with Adjoining Operation

    NASA Astrophysics Data System (ADS)

    Kato, Yoshihide; Matsubara, Shigeki

    This paper describes an incremental parser based on an adjoining operation. By using the operation, we can avoid the problem of infinite local ambiguity. This paper further proposes a restricted version of the adjoining operation, which preserves lexical dependencies of partial parse trees. Our experimental results showed that the restriction enhances the accuracy of the incremental parsing.

  13. Comparison of DSMC reaction models with QCT reaction rates for nitrogen

    NASA Astrophysics Data System (ADS)

    Wysong, Ingrid J.; Gimelshein, Sergey F.

    2016-11-01

    Four empirical models of chemical reactions extensively used in the direct simulation Monte Carlo method in the past are analyzed via comparison of temperature and vibrational level dependent equilibrium and non-equilibrium reaction rates with available classical trajectory and direct molecular simulations for nitrogen dissociation. The considered models are total collision energy, quantum kinetic, vibration-dissociation favoring, and weak vibrational bias. The weak vibrational bias model was found to provide good agreement with benchmark vibrationally-specific dissociation rates, while significant differences were observed for the others.

  14. Heavy Ion Reaction Modeling for Hadrontherapy Applications

    SciTech Connect

    Cerutti, F.; Ferrari, A.; Enghardt, W.; Gadioli, E.; Mairani, A.; Parodi, K.; Sommerer, F.

    2007-10-26

    A comprehensive and reliable description of nucleus-nucleus interactions represents a crucial need in different interdisciplinary fields. In particular, hadrontherapy monitoring by means of in-beam positron emission tomography (PET) requires, in addition to measuring, the capability of calculating the activity of {beta}{sup +}-decaying nuclei produced in the irradiated tissue. For this purpose, in view of treatment monitoring at the Heidelberg Ion Therapy (HIT) facility, the transport and interaction Monte Carlo code FLUKA is a promising candidate. It is provided with the description of heavy ion reactions at intermediate and low energies by two specific event generators. In-beam PET experiments performed at GSI for a few beam-target combinations have been simulated and first comparisons between the measured and calculated {beta}{sup +}-activity are available.

  15. Reading and a Diffusion Model Analysis of Reaction Time

    PubMed Central

    Naples, Adam; Katz, Leonard; Grigorenko, Elena L.

    2012-01-01

    Processing speed is associated with reading performance. However, the literature is not clear either on the definition of processing speed or on why and how it contributes to reading performance. In this study we demonstrated that processing speed, as measured by reaction time, is not a unitary construct. Using the diffusion model of two-choice reaction time, we assessed processing speed in a series of same-different reaction time tasks for letter and number strings. We demonstrated that the association between reaction time and reading performance is driven by processing speed for reading-related information, but not motor or sensory encoding speed. PMID:22612543

  16. EMPIRE: A Reaction Model Code for Nuclear Astrophysics

    NASA Astrophysics Data System (ADS)

    Palumbo, A.; Herman, M.; Capote, R.

    2014-06-01

    The correct modeling of abundances requires knowledge of nuclear cross sections for a variety of neutron, charged particle and γ induced reactions. These involve targets far from stability and are therefore difficult (or currently impossible) to measure. Nuclear reaction theory provides the only way to estimate values of such cross sections. In this paper we present application of the EMPIRE reaction code to nuclear astrophysics. Recent measurements are compared to the calculated cross sections showing consistent agreement for n-, p- and α-induced reactions of strophysical relevance.

  17. Formal modeling of a system of chemical reactions under uncertainty.

    PubMed

    Ghosh, Krishnendu; Schlipf, John

    2014-10-01

    We describe a novel formalism representing a system of chemical reactions, with imprecise rates of reactions and concentrations of chemicals, and describe a model reduction method, pruning, based on the chemical properties. We present two algorithms, midpoint approximation and interval approximation, for construction of efficient model abstractions with uncertainty in data. We evaluate computational feasibility by posing queries in computation tree logic (CTL) on a prototype of extracellular-signal-regulated kinase (ERK) pathway.

  18. Turing patterns in a reaction-diffusion model with the Degn-Harrison reaction scheme

    NASA Astrophysics Data System (ADS)

    Li, Shanbing; Wu, Jianhua; Dong, Yaying

    2015-09-01

    In this paper, we consider a reaction-diffusion model with Degn-Harrison reaction scheme. Some fundamental analytic properties of nonconstant positive solutions are first investigated. We next study the stability of constant steady-state solution to both ODE and PDE models. Our result also indicates that if either the size of the reactor or the effective diffusion rate is large enough, then the system does not admit nonconstant positive solutions. Finally, we establish the global structure of steady-state bifurcations from simple eigenvalues by bifurcation theory and the local structure of the steady-state bifurcations from double eigenvalues by the techniques of space decomposition and implicit function theorem.

  19. Modified version of the combined model of photonucleon reactions

    SciTech Connect

    Ishkhanov, B. S.; Orlin, V. N.

    2015-07-15

    A refined version of the combined photonucleon-reaction model is described. This version makes it possible to take into account the effect of structural features of the doorway dipole state on photonucleon reactions in the energy range of E{sub γ} ≤ 30 MeV. In relation to the previous version of the model, the treatment of isospin effects at the preequilibrium and evaporation reaction stages is refined; in addition, the description of the semidirect effect caused by nucleon emission from the doorway dipole state is improved. The model in question is used to study photonucleon reactions on the isotopes {sup 35-56}Ca and {sup 102-134}Sn in the energy range indicated above.

  20. NUCLEAR REACTION MODELING FOR RIA ISOL TARGET DESIGN

    SciTech Connect

    S. MASHNIK; ET AL

    2001-03-01

    Los Alamos scientists are collaborating with researchers at Argonne and Oak Ridge on the development of improved nuclear reaction physics for modeling radionuclide production in ISOL targets. This is being done in the context of the MCNPX simulation code, which is a merger of MCNP and the LAHET intranuclear cascade code, and simulates both nuclear reaction cross sections and radiation transport in the target. The CINDER code is also used to calculate the time-dependent nuclear decays for estimating induced radioactivities. They give an overview of the reaction physics improvements they are addressing, including intranuclear cascade (INC) physics, where recent high-quality inverse-kinematics residue data from GSI have led to INC spallation and fission model improvements; and preequilibrium reactions important in modeling (p,xn) and (p,xnyp) cross sections for the production of nuclides far from stability.

  1. Regimes of chemical reaction waves initiated by nonuniform initial conditions for detailed chemical reaction models.

    PubMed

    Liberman, M A; Kiverin, A D; Ivanov, M F

    2012-05-01

    Regimes of chemical reaction wave propagation initiated by initial temperature nonuniformity in gaseous mixtures, whose chemistry is governed by chain-branching kinetics, are studied using a multispecies transport model and a detailed chemical model. Possible regimes of reaction wave propagation are identified for stoichiometric hydrogen-oxygen and hydrogen-air mixtures in a wide range of initial pressures and temperature levels, depending on the initial non-uniformity steepness. The limits of the regimes of reaction wave propagation depend upon the values of the spontaneous wave speed and the characteristic velocities of the problem. It is shown that one-step kinetics cannot reproduce either quantitative neither qualitative features of the ignition process in real gaseous mixtures because the difference between the induction time and the time when the exothermic reaction begins significantly affects the ignition, evolution, and coupling of the spontaneous reaction wave and the pressure wave, especially at lower temperatures. We show that all the regimes initiated by the temperature gradient occur for much shallower temperature gradients than predicted by a one-step model. The difference is very large for lower initial pressures and for slowly reacting mixtures. In this way the paper provides an answer to questions, important in practice, about the ignition energy, its distribution, and the scale of the initial nonuniformity required for ignition in one or another regime of combustion wave propagation.

  2. Regimes of chemical reaction waves initiated by nonuniform initial conditions for detailed chemical reaction models

    NASA Astrophysics Data System (ADS)

    Liberman, M. A.; Kiverin, A. D.; Ivanov, M. F.

    2012-05-01

    Regimes of chemical reaction wave propagation initiated by initial temperature nonuniformity in gaseous mixtures, whose chemistry is governed by chain-branching kinetics, are studied using a multispecies transport model and a detailed chemical model. Possible regimes of reaction wave propagation are identified for stoichiometric hydrogen-oxygen and hydrogen-air mixtures in a wide range of initial pressures and temperature levels, depending on the initial non-uniformity steepness. The limits of the regimes of reaction wave propagation depend upon the values of the spontaneous wave speed and the characteristic velocities of the problem. It is shown that one-step kinetics cannot reproduce either quantitative neither qualitative features of the ignition process in real gaseous mixtures because the difference between the induction time and the time when the exothermic reaction begins significantly affects the ignition, evolution, and coupling of the spontaneous reaction wave and the pressure wave, especially at lower temperatures. We show that all the regimes initiated by the temperature gradient occur for much shallower temperature gradients than predicted by a one-step model. The difference is very large for lower initial pressures and for slowly reacting mixtures. In this way the paper provides an answer to questions, important in practice, about the ignition energy, its distribution, and the scale of the initial nonuniformity required for ignition in one or another regime of combustion wave propagation.

  3. Biogeochemical Transport and Reaction Model (BeTR) v1

    SciTech Connect

    TANG, JINYUN

    2016-04-18

    The Biogeochemical Transport and Reaction Model (BeTR) is a F90 code that enables reactive transport modeling in land modules of earth system models (e.g. CESM, ACME). The code adopts the Objective-Oriented-Design, and allows users to plug in their own biogeochemical (BGC) formulations/codes, and compare them to other existing BGC codes in those ESMs. The code takes information of soil physics variables, such as variables, such as temperature, moisture, soil density profile; water flow, etc., from a land model to track the movement of different chemicals in presence of biogeochemical reactions.

  4. Strong plasma screening in thermonuclear reactions: Electron drop model

    NASA Astrophysics Data System (ADS)

    Kravchuk, P. A.; Yakovlev, D. G.

    2014-01-01

    We analyze enhancement of thermonuclear fusion reactions due to strong plasma screening in dense matter using a simple electron drop model. In the model we assume fusion in a potential that is screened by an effective electron cloud around colliding nuclei (extended Salpeter ion-sphere model). We calculate the mean-field screened Coulomb potentials for atomic nuclei with equal and nonequal charges, appropriate astrophysical S factors, and enhancement factors of reaction rates. As a byproduct, we study the analytic behavior of the screening potential at small separations between the reactants. In this model, astrophysical S factors depend not only on nuclear physics but on plasma screening as well. The enhancement factors are in good agreement with calculations by other methods. This allows us to formulate a combined, pure analytic model of strong plasma screening in thermonuclear reactions. The results can be useful for simulating nuclear burning in white dwarfs and neutron stars.

  5. Assessing the Incremental Value of KABC-II Luria Model Scores in Predicting Achievement: What Do They Tell Us beyond the MPI?

    ERIC Educational Resources Information Center

    McGill, Ryan J.; Spurgin, Angelia R.

    2016-01-01

    The current study examined the incremental validity of the Luria interpretive scheme for the Kaufman Assessment Battery for Children-Second Edition (KABC-II) for predicting scores on the Kaufman Test of Educational Achievement-Second Edition (KTEA-II). All participants were children and adolescents (N = 2,025) drawn from the nationally…

  6. Knockout reactions on p-shell nuclei for tests of structure and reaction models

    NASA Astrophysics Data System (ADS)

    Kuchera, A. N.; Bazin, D.; Babo, M.; Baumann, T.; Bowry, M.; Bradt, J.; Brown, J.; Deyoung, P. A.; Elman, B.; Finck, J. E.; Gade, A.; Grinyer, G. F.; Jones, M. D.; Lunderberg, E.; Redpath, T.; Rogers, W. F.; Stiefel, K.; Thoennessen, M.; Weisshaar, D.; Whitmore, K.

    2015-10-01

    A series of knockout reactions on p-shell nuclei were studied to extract exclusive cross sections and to investigate the neutron knockout mechanism. The measured cross sections provide stringent tests of shell model and ab initio calculations while measurements of neutron+residual coincidences test the accuracy and validity of reaction models used to predict cross sections. Six different beams ranging from A = 7 to 12 were produced at the NSCL totaling measurements of nine different reaction settings. The reaction settings were determined by the magnetic field of the Sweeper magnet which bends the residues into charged particle detectors. The reaction target was surrounded by the high efficiency CsI array, CAESAR, to tag gamma rays for cross section measurements of low-lying excited states. Additionally, knocked out neutrons were detected with MoNA-LISA in coincidence with the charged residuals. Preliminary results will be discussed. This work is partially supported by the National Science Foundation under Grant No. PHY11-02511 and the Department of Energy National Nuclear Security Administration under Award No. DE-NA0000979.

  7. A Lattice Boltzmann Model for Oscillating Reaction-Diffusion

    NASA Astrophysics Data System (ADS)

    Rodríguez-Romo, Suemi; Ibañez-Orozco, Oscar; Sosa-Herrera, Antonio

    2016-07-01

    A computational algorithm based on the lattice Boltzmann method (LBM) is proposed to model reaction-diffusion systems. In this paper, we focus on how nonlinear chemical oscillators like Belousov-Zhabotinsky (BZ) and the chlorite-iodide-malonic acid (CIMA) reactions can be modeled by LBM and provide with new insight into the nature and applications of oscillating reactions. We use Gaussian pulse initial concentrations of sulfuric acid in different places of a bidimensional reactor and nondiffusive boundary walls. We clearly show how these systems evolve to a chaotic attractor and produce specific pattern images that are portrayed in the reactions trajectory to the corresponding chaotic attractor and can be used in robotic control.

  8. Uncertainty quantification for quantum chemical models of complex reaction networks.

    PubMed

    Proppe, Jonny; Husch, Tamara; Simm, Gregor N; Reiher, Markus

    2016-12-22

    For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided. On the other hand, a highly resolved time evolution may not be necessary to still determine quantitative fluxes in a reaction network if one is interested in specific time scales. In this paper, we present discrete-time kinetic simulations in discrete state space taking free energy uncertainties into account. The method builds upon thermo-chemical data obtained from electronic structure calculations in a condensed-phase model. Our kinetic approach supports the analysis of general reaction networks spanning multiple time scales, which is here demonstrated for the example of the formose reaction. An important application of our approach is the detection of regions in a reaction network which require further investigation, given the uncertainties introduced by both approximate electronic structure methods and kinetic models. Such cases can then be studied in greater detail with more sophisticated first-principles calculations and kinetic simulations.

  9. A practical guide to modelling enzyme-catalysed reactions

    PubMed Central

    Lonsdale, Richard; Harvey, Jeremy N.; Mulholland, Adrian J.

    2012-01-01

    Molecular modelling and simulation methods are increasingly at the forefront of elucidating mechanisms of enzyme-catalysed reactions, and shedding light on the determinants of specificity and efficiency of catalysis. These methods have the potential to assist in drug discovery and the design of novel protein catalysts. This Tutorial Review highlights some of the most widely used modelling methods and some successful applications. Modelling protocols commonly applied in studying enzyme-catalysed reactions are outlined here, and some practical implications are considered, with cytochrome P450 enzymes used as a specific example. PMID:22278388

  10. Computerized reduction of elementary reaction sets for CFD combustion modeling

    NASA Technical Reports Server (NTRS)

    Wikstrom, Carl V.

    1992-01-01

    Modeling of chemistry in Computational Fluid Dynamics can be the most time-consuming aspect of many applications. If the entire set of elementary reactions is to be solved, a set of stiff ordinary differential equations must be integrated. Some of the reactions take place at very high rates, requiring short time steps, while others take place more slowly and make little progress in the short time step integration.

  11. Simple Reaction Time and Statistical Facilitation: A Parallel Grains Model

    ERIC Educational Resources Information Center

    Miller, Jeff; Ulrich, Rolf

    2003-01-01

    A race-like model is developed to account for various phenomena arising in simple reaction time (RT) tasks. Within the model, each stimulus is represented by a number of grains of information or activation processed in parallel. The stimulus is detected when a criterion number of activated grains reaches a decision center. Using the concept of…

  12. An Investigation of Model Catalyzed Hydrocarbon Formation Reactions

    SciTech Connect

    Tysoe, W. T.

    2001-05-02

    Work was focused on two areas aimed at understanding the chemistry of realistic catalytic systems: (1) The synthesis and characterization of model supported olefin metathesis catalysts. (2) Understanding the role of the carbonaceous layer present on Pd(111) single crystal model catalysts during reaction.

  13. A mathematical model for foreign body reactions in 2D

    PubMed Central

    Su, Jianzhong; Gonzales, Humberto Perez; Todorov, Michail; Kojouharov, Hristo; Tang, Liping

    2010-01-01

    The foreign body reactions are commonly referred to the network of immune and inflammatory reactions of human or animals to foreign objects placed in tissues. They are basic biological processes, and are also highly relevant to bioengineering applications in implants, as fibrotic tissue formations surrounding medical implants have been found to substantially reduce the effectiveness of devices. Despite of intensive research on determining the mechanisms governing such complex responses, few mechanistic mathematical models have been developed to study such foreign body reactions. This study focuses on a kinetics-based predictive tool in order to analyze outcomes of multiple interactive complex reactions of various cells/proteins and biochemical processes and to understand transient behavior during the entire period (up to several months). A computational model in two spatial dimensions is constructed to investigate the time dynamics as well as spatial variation of foreign body reaction kinetics. The simulation results have been consistent with experimental data and the model can facilitate quantitative insights for study of foreign body reaction process in general. PMID:21532988

  14. Implementing Kernel Methods Incrementally by Incremental Nonlinear Projection Trick.

    PubMed

    Kwak, Nojun

    2016-05-20

    Recently, the nonlinear projection trick (NPT) was introduced enabling direct computation of coordinates of samples in a reproducing kernel Hilbert space. With NPT, any machine learning algorithm can be extended to a kernel version without relying on the so called kernel trick. However, NPT is inherently difficult to be implemented incrementally because an ever increasing kernel matrix should be treated as additional training samples are introduced. In this paper, an incremental version of the NPT (INPT) is proposed based on the observation that the centerization step in NPT is unnecessary. Because the proposed INPT does not change the coordinates of the old data, the coordinates obtained by INPT can directly be used in any incremental methods to implement a kernel version of the incremental methods. The effectiveness of the INPT is shown by applying it to implement incremental versions of kernel methods such as, kernel singular value decomposition, kernel principal component analysis, and kernel discriminant analysis which are utilized for problems of kernel matrix reconstruction, letter classification, and face image retrieval, respectively.

  15. Development and Calibration of Reaction Models for Multilayered Nanocomposites

    NASA Astrophysics Data System (ADS)

    Vohra, Manav

    This dissertation focuses on the development and calibration of reaction models for multilayered nanocomposites. The nanocomposites comprise sputter deposited alternating layers of distinct metallic elements. Specifically, we focus on the equimolar Ni-Al and Zr-Al multilayered systems. Computational models are developed to capture the transient reaction phenomena as well as understand the dependence of reaction properties on the microstructure, composition and geometry of the multilayers. Together with the available experimental data, simulations are used to calibrate the models and enhance the accuracy of their predictions. Recent modeling efforts for the Ni-Al system have investigated the nature of self-propagating reactions in the multilayers. Model fidelity was enhanced by incorporating melting effects due to aluminum [Besnoin et al. (2002)]. Salloum and Knio formulated a reduced model to mitigate computational costs associated with multi-dimensional reaction simulations [Salloum and Knio (2010a)]. However, exist- ing formulations relied on a single Arrhenius correlation for diffusivity, estimated for the self-propagating reactions, and cannot be used to quantify mixing rates at lower temperatures within reasonable accuracy [Fritz (2011)]. We thus develop a thermal model for a multilayer stack comprising a reactive Ni-Al bilayer (nanocalorimeter) and exploit temperature evolution measurements to calibrate the diffusion parameters associated with solid state mixing (≈720 K - 860 K) in the bilayer. The equimolar Zr-Al multilayered system when reacted aerobically is shown to exhibit slow aerobic oxidation of zirconium (in the intermetallic), sustained for about 2-10 seconds after completion of the formation reaction. In a collaborative effort, we aim to exploit the sustained heat release for bio-agent defeat application. A simplified computational model is developed to capture the extended reaction regime characterized by oxidation of Zr-Al multilayers

  16. Chemical and mathematical modeling of asphaltene reaction pathways

    SciTech Connect

    Salvage, P.E.

    1986-01-01

    Precipitated asphaltene was subjected to pyrolysis and hydropyrolysis, both neat and in solvents, and catalytic hydroprocessing. A solvent extraction procedure defined gas, maltene, asphaltene, and coke product fractions. The apparent first order rate constant for asphaltene conversion at 400/sup 0/C was relatively insensitive to the particular reaction scheme. The yield of gases likewise showed little variation and was always less than 10%. On the other hand, the maltene and coke yields were about 20% and 60%, respectively, from neat pyrolysis, and about 60% and less than 5%, respectively, from catalytic reactions. The temporal variations of the product fractions allowed discernment of asphaltene reaction pathways. The primary reaction of asphaltene was to residual asphaltene, maltenes, and gases. The residual asphaltene reacted thermally to coke and catalytically to maltenes at the expense of coke. Secondary degradation of these primary products led to lighter compounds. Reaction mechanism for pyrolysis of asphaltene model compounds and alkylaromstics were determined. The model compound kinetics results were combined with a stochastic description of asphaltene structure in a mathematical model of asphaltene pyrolysis. Individual molecular product were assigned to either the gas, maltene, asphaltene, or coke product fractions, and summation of the weights of each constituted the model's predictions. The temporal variation of the product fractions from simulated asphaltene pyrolysis compared favorably with experimental results.

  17. First principles based mean field model for oxygen reduction reaction.

    PubMed

    Jinnouchi, Ryosuke; Kodama, Kensaku; Hatanaka, Tatsuya; Morimoto, Yu

    2011-12-21

    A first principles-based mean field model was developed for the oxygen reduction reaction (ORR) taking account of the coverage- and material-dependent reversible potentials of the elementary steps. This model was applied to the simulation of single crystal surfaces of Pt, Pt alloy and Pt core-shell catalysts under Ar and O(2) atmospheres. The results are consistent with those shown by past experimental and theoretical studies on surface coverages under Ar atmosphere, the shape of the current-voltage curve for the ORR on Pt(111) and the material-dependence of the ORR activity. This model suggests that the oxygen associative pathway including HO(2)(ads) formation is the main pathway on Pt(111), and that the rate determining step (RDS) is the removal step of O(ads) on Pt(111). This RDS is accelerated on several highly active Pt alloys and core-shell surfaces, and this acceleration decreases the reaction intermediate O(ads). The increase in the partial pressure of O(2)(g) increases the surface coverage with O(ads) and OH(ads), and this coverage increase reduces the apparent reaction order with respect to the partial pressure to less than unity. This model shows details on how the reaction pathway, RDS, surface coverages, Tafel slope, reaction order and material-dependent activity are interrelated.

  18. Stability Analysis of a Model for Foreign Body Fibrotic Reactions

    PubMed Central

    Ibraguimov, A.; Owens, L.; Su, J.; Tang, L.

    2012-01-01

    Implanted medical devices often trigger immunological and inflammatory reactions from surrounding tissues. The foreign body-mediated tissue responses may result in varying degrees of fibrotic tissue formation. There is an intensive research interest in the area of wound healing modeling, and quantitative methods are proposed to systematically study the behavior of this complex system of multiple cells, proteins, and enzymes. This paper introduces a kinetics-based model for analyzing reactions of various cells/proteins and biochemical processes as well as their transient behavior during the implant healing in 2-dimensional space. In particular, we provide a detailed modeling study of different roles of macrophages (MΦ) and their effects on fibrotic reactions. The main mathematical result indicates that the stability of the inflamed steady state depends primarily on the reaction dynamics of the system. However, if the said equilibrium is unstable by its reaction-only system, the spatial diffusion and chemotactic effects can help to stabilize when the model is dominated by classical and regulatory macrophages over the inflammatory macrophages. The mathematical proof and counter examples are given for these conclusions. PMID:23193430

  19. The fundamental diagram of pedestrian model with slow reaction

    NASA Astrophysics Data System (ADS)

    Fang, Jun; Qin, Zheng; Hu, Hao; Xu, Zhaohui; Li, Huan

    2012-12-01

    The slow-to-start models are a classical cellular automata model in simulating vehicle traffic. However, to our knowledge, the slow-to-start effect has not been considered in modeling pedestrian dynamics. We verify the similar behavior between pedestrian and vehicle, and propose an new lattice gas (LG) model called the slow reaction (SR) model to describe the pedestrian’s delayed reaction in single-file movement. We simulate and reproduce Seyfried’s field experiments at the Research Centre Jülich, and use its empirical data to validate our SR model. We compare the SR model with the standard LG model. We tested different probabilities of slow reaction ps in the SR model and found the simulation data of ps=0.3 fit the empirical data best. The RMS error of the mean velocity of the SR model is smaller than that of the standard LG model. In the range of ps=0.1-0.3, our fundamental diagram between velocity and density by simulation coincides with field experiments. The distribution of individual velocity in the fundamental diagram in the SR model agrees with the empirical data better than that of the standard LG model. In addition, we observe stop-and-go waves and phase separation in pedestrian flow by simulation. We reproduced the phenomena of uneven distribution of interspaces by the SR model while the standard LG model did not. The SR model can reproduce the evolution of spatio-temporal structures of pedestrian flow with higher fidelity to Seyfried’s experiments than the standard LG model.

  20. Implementation of a vibrationally linked chemical reaction model for DSMC

    NASA Technical Reports Server (NTRS)

    Carlson, A. B.; Bird, Graeme A.

    1994-01-01

    A new procedure closely linking dissociation and exchange reactions in air to the vibrational levels of the diatomic molecules has been implemented in both one- and two-dimensional versions of Direct Simulation Monte Carlo (DSMC) programs. The previous modeling of chemical reactions with DSMC was based on the continuum reaction rates for the various possible reactions. The new method is more closely related to the actual physics of dissociation and is more appropriate to the particle nature of DSMC. Two cases are presented: the relaxation to equilibrium of undissociated air initially at 10,000 K, and the axisymmetric calculation of shuttle forebody heating during reentry at 92.35 km and 7500 m/s. Although reaction rates are not used in determining the dissociations or exchange reactions, the new method produces rates which agree astonishingly well with the published rates derived from experiment. The results for gas properties and surface properties also agree well with the results produced by earlier DSMC models, equilibrium air calculations, and experiment.

  1. Parallel Incremental Compilation

    DTIC Science & Technology

    1990-06-01

    Seshadri et al., 1988] are taking a more wholistic approach to concurrency in compilation. In their model, the program is divided up along natural...symbol table references. Deleted and inserted references are put on the symbol’s reference list. Special care must be taken to maintain the invariants of...design as well. The primary design principle is the top-down division of the translation task into a number of much simpler mutually sequential

  2. Computerized reduction of elementary reaction sets for combustion modeling

    NASA Technical Reports Server (NTRS)

    Wikstrom, Carl V.

    1991-01-01

    If the entire set of elementary reactions is to be solved in the modeling of chemistry in computational fluid dynamics, a set of stiff ordinary differential equations must be integrated. Some of the reactions take place at very high rates, requiring short time steps, while others take place more slowly and make little progress in the short time step integration. The goal is to develop a procedure to automatically obtain sets of finite rate equations, consistent with a partial equilibrium assumptions, from an elementary set appropriate to local conditions. The possibility of computerized reaction reduction was demonstrated. However, the ability to use the reduced reaction set depends on the ability of the CFD approach in incorporate partial equilibrium calculations into the computer code. Therefore, the results should be tested on a code with partial equilibrium capability.

  3. A chain reaction approach to modelling gene pathways

    PubMed Central

    Cheng, Gary C.; Chen, Dung-Tsa; Chen, James J.; Soong, Seng-jaw; Lamartiniere, Coral; Barnes, Stephen

    2012-01-01

    Background Of great interest in cancer prevention is how nutrient components affect gene pathways associated with the physiological events of puberty. Nutrient-gene interactions may cause changes in breast or prostate cells and, therefore, may result in cancer risk later in life. Analysis of gene pathways can lead to insights about nutrient-gene interactions and the development of more effective prevention approaches to reduce cancer risk. To date, researchers have relied heavily upon experimental assays (such as microarray analysis, etc.) to identify genes and their associated pathways that are affected by nutrient and diets. However, the vast number of genes and combinations of gene pathways, coupled with the expense of the experimental analyses, has delayed the progress of gene-pathway research. The development of an analytical approach based on available test data could greatly benefit the evaluation of gene pathways, and thus advance the study of nutrient-gene interactions in cancer prevention. In the present study, we have proposed a chain reaction model to simulate gene pathways, in which the gene expression changes through the pathway are represented by the species undergoing a set of chemical reactions. We have also developed a numerical tool to solve for the species changes due to the chain reactions over time. Through this approach we can examine the impact of nutrient-containing diets on the gene pathway; moreover, transformation of genes over time with a nutrient treatment can be observed numerically, which is very difficult to achieve experimentally. We apply this approach to microarray analysis data from an experiment which involved the effects of three polyphenols (nutrient treatments), epigallo-catechin-3-O-gallate (EGCG), genistein, and resveratrol, in a study of nutrient-gene interaction in the estrogen synthesis pathway during puberty. Results In this preliminary study, the estrogen synthesis pathway was simulated by a chain reaction model. By

  4. A chain reaction approach to modelling gene pathways.

    PubMed

    Cheng, Gary C; Chen, Dung-Tsa; Chen, James J; Soong, Seng-Jaw; Lamartiniere, Coral; Barnes, Stephen

    2012-08-01

    BACKGROUND: Of great interest in cancer prevention is how nutrient components affect gene pathways associated with the physiological events of puberty. Nutrient-gene interactions may cause changes in breast or prostate cells and, therefore, may result in cancer risk later in life. Analysis of gene pathways can lead to insights about nutrient-gene interactions and the development of more effective prevention approaches to reduce cancer risk. To date, researchers have relied heavily upon experimental assays (such as microarray analysis, etc.) to identify genes and their associated pathways that are affected by nutrient and diets. However, the vast number of genes and combinations of gene pathways, coupled with the expense of the experimental analyses, has delayed the progress of gene-pathway research. The development of an analytical approach based on available test data could greatly benefit the evaluation of gene pathways, and thus advance the study of nutrient-gene interactions in cancer prevention. In the present study, we have proposed a chain reaction model to simulate gene pathways, in which the gene expression changes through the pathway are represented by the species undergoing a set of chemical reactions. We have also developed a numerical tool to solve for the species changes due to the chain reactions over time. Through this approach we can examine the impact of nutrient-containing diets on the gene pathway; moreover, transformation of genes over time with a nutrient treatment can be observed numerically, which is very difficult to achieve experimentally. We apply this approach to microarray analysis data from an experiment which involved the effects of three polyphenols (nutrient treatments), epigallo-catechin-3-O-gallate (EGCG), genistein, and resveratrol, in a study of nutrient-gene interaction in the estrogen synthesis pathway during puberty. RESULTS: In this preliminary study, the estrogen synthesis pathway was simulated by a chain reaction model. By

  5. Modeling human behaviors and reactions under dangerous environment.

    PubMed

    Kang, J; Wright, D K; Qin, S F; Zhao, Y

    2005-01-01

    This paper describes the framework of a real-time simulation system to model human behavior and reactions in dangerous environments. The system utilizes the latest 3D computer animation techniques, combined with artificial intelligence, robotics and psychology, to model human behavior, reactions and decision making under expected/unexpected dangers in real-time in virtual environments. The development of the system includes: classification on the conscious/subconscious behaviors and reactions of different people; capturing different motion postures by the Eagle Digital System; establishing 3D character animation models; establishing 3D models for the scene; planning the scenario and the contents; and programming within Virtools Dev. Programming within Virtools Dev is subdivided into modeling dangerous events, modeling character's perceptions, modeling character's decision making, modeling character's movements, modeling character's interaction with environment and setting up the virtual cameras. The real-time simulation of human reactions in hazardous environments is invaluable in military defense, fire escape, rescue operation planning, traffic safety studies, and safety planning in chemical factories, the design of buildings, airplanes, ships and trains. Currently, human motion modeling can be realized through established technology, whereas to integrate perception and intelligence into virtual human's motion is still a huge undertaking. The challenges here are the synchronization of motion and intelligence, the accurate modeling of human's vision, smell, touch and hearing, the diversity and effects of emotion and personality in decision making. There are three types of software platforms which could be employed to realize the motion and intelligence within one system, and their advantages and disadvantages are discussed.

  6. Mathematical properties of models of the reaction-diffusion type

    NASA Astrophysics Data System (ADS)

    Beccaria, M.; Soliani, G.

    Nonlinear systems of the reaction-diffusion (RD) type, including Gierer-Meinhardt models of autocatalysis, are studied using Lie algebras coming from their prolongation structure. Depending on the form of the functions of the fields characterizing the reactions among them, we consider both quadratic and cubic RD equations. On the basis of the prolongation algebra associated with a given RD model, we distinguish the model as a completely linearizable or a partially linearizable system. In this classification a crucial role is played by the relative sign of the diffusion coefficients, which strongly influence the properties of the system. In correspondence to the above situations, different algebraic characterizations, together with exact and approximate solutions, are found. Interesting examples are the quadratic RD model, which admits an exact solution in terms of the elliptic Weierstrass function, and the cubic Gierer-Meinhardt model, whose prolongation algebra leads to the similitude group in the plane.

  7. A model for reaction rates in turbulent reacting flows

    NASA Technical Reports Server (NTRS)

    Chinitz, W.; Evans, J. S.

    1984-01-01

    To account for the turbulent temperature and species-concentration fluctuations, a model is presented on the effects of chemical reaction rates in computer analyses of turbulent reacting flows. The model results in two parameters which multiply the terms in the reaction-rate equations. For these two parameters, graphs are presented as functions of the mean values and intensity of the turbulent fluctuations of the temperature and species concentrations. These graphs will facilitate incorporation of the model into existing computer programs which describe turbulent reacting flows. When the model was used in a two-dimensional parabolic-flow computer code to predict the behavior of an experimental, supersonic hydrogen jet burning in air, some improvement in agreement with the experimental data was obtained in the far field in the region near the jet centerline. Recommendations are included for further improvement of the model and for additional comparisons with experimental data.

  8. Increment detection of bandlimited noises in the chinchilla.

    PubMed

    Shofner, W P; Yost, W A; Sheft, S

    1993-03-01

    A positive reinforcement, adaptive tracking procedure was used to study the intensity discrimination abilities of six chinchillas to noise signals. Increment detection thresholds were obtained using a two-down, one-up tracking rule. The effect of overall noise masker level and the effect of noise bandwidth on increment detection thresholds were studied. The continuous noise masker and the signal increment had equal bandwidths. Increment detection thresholds are independent of overall level for wideband noise; the asymptotic DL for wideband noise is 1.334 dB. In addition, increment detection thresholds decrease as the bandwidth of the noise increases. The observed slope of the bandwidth function for the chinchilla is independent of overall level and is around -2.8 dB/decade. The slope of the bandwidth function obtained for the chinchilla is similar to values reported for human subjects under similar conditions, but is less than the slope predicted by the ideal energy detector model.

  9. Including Rebinding Reactions in Well-Mixed Models of Distributive Biochemical Reactions.

    PubMed

    Lawley, Sean D; Keener, James P

    2016-11-15

    The behavior of biochemical reactions requiring repeated enzymatic substrate modification depends critically on whether the enzymes act processively or distributively. Whereas processive enzymes bind only once to a substrate before carrying out a sequence of modifications, distributive enzymes release the substrate after each modification and thus require repeated bindings. Recent experimental and computational studies have revealed that distributive enzymes can act processively due to rapid rebindings (so-called quasi-processivity). In this study, we derive an analytical estimate of the probability of rapid rebinding and show that well-mixed ordinary differential equation models can use this probability to quantitatively replicate the behavior of spatial models. Importantly, rebinding requires that connections be added to the well-mixed reaction network; merely modifying rate constants is insufficient. We then use these well-mixed models to suggest experiments to 1) detect quasi-processivity and 2) test the theory. Finally, we show that rapid rebindings drastically alter the reaction's Michaelis-Menten rate equations.

  10. Modeling the Reaction of Fe Atoms with CCl4

    SciTech Connect

    Camaioni, Donald M.; Ginovska, Bojana; Dupuis, Michel

    2009-01-05

    The reaction of zero-valent iron with carbon tetrachloride (CCl4) in gas phase was studied using density functional theory. Temperature programmed desorption experiments over a range of Fe and CCl4 coverages on a FeO(111) surface, demonstrate a rich surface chemistry with several reaction products (C2Cl4, C2Cl6, OCCl2, CO, FeCl2, FeCl3) observed. The reactivity of Fe and CCl4 was studied under three stoichiometries, one Fe with one CCl4, one Fe with two CCl4 molecules and two Fe with one CCl4, modeling the environment of the experimental work. The electronic structure calculations give insight into the reactions leading to the experimentally observed products and suggest that novel Fe-C-Cl containing species are important intermediates in these reactions. The intermediate complexes are formed in highly exothermic reactions, in agreement with the experimentally observed reactivity with the surface at low temperature (30 K). This initial survey of the reactivity of Fe with CCl4 identifies some potential reaction pathways that are important in the effort to use Fe nano-particles to differentiate harmful pathways that lead to the formation of contaminants like chloroform (CHCl3) from harmless pathways that lead to products such as formate (HCO2-) or carbon oxides in water and soil. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  11. Calibration of Complex Subsurface Reaction Models Using a Surrogate-Model Approach

    EPA Science Inventory

    Application of model assessment techniques to complex subsurface reaction models involves numerous difficulties, including non-trivial model selection, parameter non-uniqueness, and excessive computational burden. To overcome these difficulties, this study introduces SAMM (Simult...

  12. A Multiple Reaction Modelling Framework for Microbial Electrochemical Technologies

    PubMed Central

    Oyetunde, Tolutola; Sarma, Priyangshu M.; Ahmad, Farrukh; Rodríguez, Jorge

    2017-01-01

    A mathematical model for the theoretical evaluation of microbial electrochemical technologies (METs) is presented that incorporates a detailed physico-chemical framework, includes multiple reactions (both at the electrodes and in the bulk phase) and involves a variety of microbial functional groups. The model is applied to two theoretical case studies: (i) A microbial electrolysis cell (MEC) for continuous anodic volatile fatty acids (VFA) oxidation and cathodic VFA reduction to alcohols, for which the theoretical system response to changes in applied voltage and VFA feed ratio (anode-to-cathode) as well as membrane type are investigated. This case involves multiple parallel electrode reactions in both anode and cathode compartments; (ii) A microbial fuel cell (MFC) for cathodic perchlorate reduction, in which the theoretical impact of feed flow rates and concentrations on the overall system performance are investigated. This case involves multiple electrode reactions in series in the cathode compartment. The model structure captures interactions between important system variables based on first principles and provides a platform for the dynamic description of METs involving electrode reactions both in parallel and in series and in both MFC and MEC configurations. Such a theoretical modelling approach, largely based on first principles, appears promising in the development and testing of MET control and optimization strategies. PMID:28054959

  13. A Multiple Reaction Modelling Framework for Microbial Electrochemical Technologies.

    PubMed

    Oyetunde, Tolutola; Sarma, Priyangshu M; Ahmad, Farrukh; Rodríguez, Jorge

    2017-01-04

    A mathematical model for the theoretical evaluation of microbial electrochemical technologies (METs) is presented that incorporates a detailed physico-chemical framework, includes multiple reactions (both at the electrodes and in the bulk phase) and involves a variety of microbial functional groups. The model is applied to two theoretical case studies: (i) A microbial electrolysis cell (MEC) for continuous anodic volatile fatty acids (VFA) oxidation and cathodic VFA reduction to alcohols, for which the theoretical system response to changes in applied voltage and VFA feed ratio (anode-to-cathode) as well as membrane type are investigated. This case involves multiple parallel electrode reactions in both anode and cathode compartments; (ii) A microbial fuel cell (MFC) for cathodic perchlorate reduction, in which the theoretical impact of feed flow rates and concentrations on the overall system performance are investigated. This case involves multiple electrode reactions in series in the cathode compartment. The model structure captures interactions between important system variables based on first principles and provides a platform for the dynamic description of METs involving electrode reactions both in parallel and in series and in both MFC and MEC configurations. Such a theoretical modelling approach, largely based on first principles, appears promising in the development and testing of MET control and optimization strategies.

  14. Examining the role of finite reaction times in swarming models

    NASA Astrophysics Data System (ADS)

    Copenhagen, Katherine; Quint, David; Gopinathan, Ajay

    2015-03-01

    Modeling collective behavior in biological and artificial systems has had much success in recent years at predicting and mimicing real systems by utilizing techniques borrowed from modelling many particle systems interacting with physical forces. However unlike inert particles interacting with instantaneous forces, living organisms have finite reaction times, and behaviors that vary from individual to individual. What constraints do these physiological effects place on the interactions between individuals in order to sustain a robust ordered state? We use a self-propelled agent based model in continuous space based on previous models by Vicsek and Couzin including alignment and separation maintaining interactions to examine the behavior of a single cohesive group of organisms. We found that for very short reaction times the system is able to form an ordered state even in the presence of heterogeneities. However for larger more physiological reaction times organisms need a buffer zone with no cohesive interactions in order to maintain an ordered state. Finally swarms with finite reaction times and behavioral heterogeneities are able to dynamically sort out individuals with impaired function and sustain order.

  15. Transactional Model of Coping, Appraisals, and Emotional Reactions to Stress.

    ERIC Educational Resources Information Center

    Brack, Greg; McCarthy, Christopher J.

    A study investigated the relationship of transactional models of stress management and appraisal-emotion relationships to emotions produced by taking a new job. The participants, 231 graduate students, completed measures of cognitive appraisals, stress coping resources, and emotional reactions at the time of taking a new job and some time later.…

  16. Modeling shock-driven reaction in low density PMDI foam

    NASA Astrophysics Data System (ADS)

    Brundage, Aaron; Alexander, C. Scott; Reinhart, William; Peterson, David

    Shock experiments on low density polyurethane foams reveal evidence of reaction at low impact pressures. However, these reaction thresholds are not evident over the low pressures reported for historical Hugoniot data of highly distended polyurethane at densities below 0.1 g/cc. To fill this gap, impact data given in a companion paper for polymethylene diisocyanate (PMDI) foam with a density of 0.087 g/cc were acquired for model validation. An equation of state (EOS) was developed to predict the shock response of these highly distended materials over the full range of impact conditions representing compaction of the inert material, low-pressure decomposition, and compression of the reaction products. A tabular SESAME EOS of the reaction products was generated using the JCZS database in the TIGER equilibrium code. In particular, the Arrhenius Burn EOS, a two-state model which transitions from an unreacted to a reacted state using single step Arrhenius kinetics, as implemented in the shock physics code CTH, was modified to include a statistical distribution of states. Hence, a single EOS is presented that predicts the onset to reaction due to shock loading in PMDI-based polyurethane foams. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's NNSA under Contract DE-AC04-94AL85000.

  17. Kinetic modelling of GlmU reactions - prioritization of reaction for therapeutic application.

    PubMed

    Singh, Vivek K; Das, Kaveri; Seshadri, Kothandaraman

    2012-01-01

    Mycobacterium tuberculosis(Mtu), a successful pathogen, has developed resistance against the existing anti-tubercular drugs necessitating discovery of drugs with novel action. Enzymes involved in peptidoglycan biosynthesis are attractive targets for antibacterial drug discovery. The bifunctional enzyme mycobacterial GlmU (Glucosamine 1-phosphate N-acetyltransferase/ N-acetylglucosamine-1-phosphate uridyltransferase) has been a target enzyme for drug discovery. Its C- and N- terminal domains catalyze acetyltransferase (rxn-1) and uridyltransferase (rxn-2) activities respectively and the final product is involved in peptidoglycan synthesis. However, the bifunctional nature of GlmU poses difficulty in deciding which function to be intervened for therapeutic advantage. Genetic analysis showed this as an essential gene but it is still unclear whether any one or both of the activities are critical for cell survival. Often enzymatic activity with suitable high-throughput assay is chosen for random screening, which may not be the appropriate biological function inhibited for maximal effect. Prediction of rate-limiting function by dynamic network analysis of reactions could be an option to identify the appropriate function. With a view to provide insights into biochemical assays with appropriate activity for inhibitor screening, kinetic modelling studies on GlmU were undertaken. Kinetic model of Mtu GlmU-catalyzed reactions was built based on the available kinetic data on Mtu and deduction from Escherichia coli data. Several model variants were constructed including coupled/decoupled, varying metabolite concentrations and presence/absence of product inhibitions. This study demonstrates that in coupled model at low metabolite concentrations, inhibition of either of the GlmU reactions cause significant decrement in the overall GlmU rate. However at higher metabolite concentrations, rxn-2 showed higher decrement. Moreover, with available intracellular concentration of the

  18. Complex reaction noise in a molecular quasispecies model

    NASA Astrophysics Data System (ADS)

    Hochberg, David; Zorzano, María-Paz; Morán, Federico

    2006-05-01

    We have derived exact Langevin equations for a model of quasispecies dynamics. The inherent multiplicative reaction noise is complex and its statistical properties are specified completely. The numerical simulation of the complex Langevin equations is carried out using the Cholesky decomposition for the noise covariance matrix. This internal noise, which is due to diffusion-limited reactions, produces unavoidable spatio-temporal density fluctuations about the mean field value. In two dimensions, this noise strictly vanishes only in the perfectly mixed limit, a situation difficult to attain in practice.

  19. Spatiotemporal patterns in a reaction-diffusion model with the Degn-Harrison reaction scheme

    NASA Astrophysics Data System (ADS)

    Peng, Rui; Yi, Feng-qi; Zhao, Xiao-qiang

    Spatial and temporal patterns generated in ecological and chemical systems have become a central object of research in recent decades. In this work, we are concerned with a reaction-diffusion model with the Degn-Harrison reaction scheme, which accounts for the qualitative feature of the respiratory process in a Klebsiella aerogenes bacterial culture. We study the global stability of the constant steady state, existence and nonexistence of nonconstant steady states as well as the Hopf and steady state bifurcations. In particular, our results show the existence of Turing patterns and inhomogeneous periodic oscillatory patterns while the system parameters are all spatially homogeneous. These results also exhibit the critical role of the system parameters in leading to the formation of spatiotemporal patterns.

  20. Benchmark 3 - Incremental sheet forming

    NASA Astrophysics Data System (ADS)

    Elford, Michael; Saha, Pradip; Seong, Daeyong; Haque, MD Ziaul; Yoon, Jeong Whan

    2013-12-01

    Benchmark-3 is designed to predict strains, punch load and deformed profile after spring-back during single tool incremental sheet forming. AA 7075-O material has been selected. A corn shape is formed to 45 mm depth with an angle of 45°. Problem description, material properties, and simulation reports with experimental data are summarized.

  1. Classic and contemporary approaches to modeling biochemical reactions

    PubMed Central

    Chen, William W.; Niepel, Mario; Sorger, Peter K.

    2010-01-01

    Recent interest in modeling biochemical networks raises questions about the relationship between often complex mathematical models and familiar arithmetic concepts from classical enzymology, and also about connections between modeling and experimental data. This review addresses both topics by familiarizing readers with key concepts (and terminology) in the construction, validation, and application of deterministic biochemical models, with particular emphasis on a simple enzyme-catalyzed reaction. Networks of coupled ordinary differential equations (ODEs) are the natural language for describing enzyme kinetics in a mass action approximation. We illustrate this point by showing how the familiar Briggs-Haldane formulation of Michaelis-Menten kinetics derives from the outer (or quasi-steady-state) solution of a dynamical system of ODEs describing a simple reaction under special conditions. We discuss how parameters in the Michaelis-Menten approximation and in the underlying ODE network can be estimated from experimental data, with a special emphasis on the origins of uncertainty. Finally, we extrapolate from a simple reaction to complex models of multiprotein biochemical networks. The concepts described in this review, hitherto of interest primarily to practitioners, are likely to become important for a much broader community of cellular and molecular biologists attempting to understand the promise and challenges of “systems biology” as applied to biochemical mechanisms. PMID:20810646

  2. Modelling biochemical reaction systems by stochastic differential equations with reflection.

    PubMed

    Niu, Yuanling; Burrage, Kevin; Chen, Luonan

    2016-05-07

    In this paper, we gave a new framework for modelling and simulating biochemical reaction systems by stochastic differential equations with reflection not in a heuristic way but in a mathematical way. The model is computationally efficient compared with the discrete-state Markov chain approach, and it ensures that both analytic and numerical solutions remain in a biologically plausible region. Specifically, our model mathematically ensures that species numbers lie in the domain D, which is a physical constraint for biochemical reactions, in contrast to the previous models. The domain D is actually obtained according to the structure of the corresponding chemical Langevin equations, i.e., the boundary is inherent in the biochemical reaction system. A variant of projection method was employed to solve the reflected stochastic differential equation model, and it includes three simple steps, i.e., Euler-Maruyama method was applied to the equations first, and then check whether or not the point lies within the domain D, and if not perform an orthogonal projection. It is found that the projection onto the closure D¯ is the solution to a convex quadratic programming problem. Thus, existing methods for the convex quadratic programming problem can be employed for the orthogonal projection map. Numerical tests on several important problems in biological systems confirmed the efficiency and accuracy of this approach.

  3. EMPIRE: Nuclear Reaction Model Code System for Data Evaluation

    NASA Astrophysics Data System (ADS)

    Herman, M.; Capote, R.; Carlson, B. V.; Obložinský, P.; Sin, M.; Trkov, A.; Wienke, H.; Zerkin, V.

    2007-12-01

    EMPIRE is a modular system of nuclear reaction codes, comprising various nuclear models, and designed for calculations over a broad range of energies and incident particles. A projectile can be a neutron, proton, any ion (including heavy-ions) or a photon. The energy range extends from the beginning of the unresolved resonance region for neutron-induced reactions (∽ keV) and goes up to several hundred MeV for heavy-ion induced reactions. The code accounts for the major nuclear reaction mechanisms, including direct, pre-equilibrium and compound nucleus ones. Direct reactions are described by a generalized optical model (ECIS03) or by the simplified coupled-channels approach (CCFUS). The pre-equilibrium mechanism can be treated by a deformation dependent multi-step direct (ORION + TRISTAN) model, by a NVWY multi-step compound one or by either a pre-equilibrium exciton model with cluster emission (PCROSS) or by another with full angular momentum coupling (DEGAS). Finally, the compound nucleus decay is described by the full featured Hauser-Feshbach model with γ-cascade and width-fluctuations. Advanced treatment of the fission channel takes into account transmission through a multiple-humped fission barrier with absorption in the wells. The fission probability is derived in the WKB approximation within the optical model of fission. Several options for nuclear level densities include the EMPIRE-specific approach, which accounts for the effects of the dynamic deformation of a fast rotating nucleus, the classical Gilbert-Cameron approach and pre-calculated tables obtained with a microscopic model based on HFB single-particle level schemes with collective enhancement. A comprehensive library of input parameters covers nuclear masses, optical model parameters, ground state deformations, discrete levels and decay schemes, level densities, fission barriers, moments of inertia and γ-ray strength functions. The results can be converted into ENDF-6 formatted files using the

  4. A model for reaction-assisted polymer dissolution in LIGA.

    SciTech Connect

    Larson, Richard S.

    2004-05-01

    A new chemically-oriented mathematical model for the development step of the LIGA process is presented. The key assumption is that the developer can react with the polymeric resist material in order to increase the solubility of the latter, thereby partially overcoming the need to reduce the polymer size. The ease with which this reaction takes place is assumed to be determined by the number of side chain scissions that occur during the x-ray exposure phase of the process. The dynamics of the dissolution process are simulated by solving the reaction-diffusion equations for this three-component, two-phase system, the three species being the unreacted and reacted polymers and the solvent. The mass fluxes are described by the multicomponent diffusion (Stefan-Maxwell) equations, and the chemical potentials are assumed to be given by the Flory-Huggins theory. Sample calculations are used to determine the dependence of the dissolution rate on key system parameters such as the reaction rate constant, polymer size, solid-phase diffusivity, and Flory-Huggins interaction parameters. A simple photochemistry model is used to relate the reaction rate constant and the polymer size to the absorbed x-ray dose. The resulting formula for the dissolution rate as a function of dose and temperature is ?t to an extensive experimental data base in order to evaluate a set of unknown global parameters. The results suggest that reaction-assisted dissolution is very important at low doses and low temperatures, the solubility of the unreacted polymer being too small for it to be dissolved at an appreciable rate. However, at high doses or at higher temperatures, the solubility is such that the reaction is no longer needed, and dissolution can take place via the conventional route. These results provide an explanation for the observed dependences of both the dissolution rate and its activation energy on the absorbed dose.

  5. Reaction-diffusion processes and metapopulation models on duplex networks

    NASA Astrophysics Data System (ADS)

    Xuan, Qi; Du, Fang; Yu, Li; Chen, Guanrong

    2013-03-01

    Reaction-diffusion processes, used to model various spatially distributed dynamics such as epidemics, have been studied mostly on regular lattices or complex networks with simplex links that are identical and invariant in transferring different kinds of particles. However, in many self-organized systems, different particles may have their own private channels to keep their purities. Such division of links often significantly influences the underlying reaction-diffusion dynamics and thus needs to be carefully investigated. This article studies a special reaction-diffusion process, named susceptible-infected-susceptible (SIS) dynamics, given by the reaction steps β→α and α+β→2β, on duplex networks where links are classified into two groups: α and β links used to transfer α and β particles, which, along with the corresponding nodes, consist of an α subnetwork and a β subnetwork, respectively. It is found that the critical point of particle density to sustain reaction activity is independent of the network topology if there is no correlation between the degree sequences of the two subnetworks, and this critical value is suppressed or extended if the two degree sequences are positively or negatively correlated, respectively. Based on the obtained results, it is predicted that epidemic spreading may be promoted on positive correlated traffic networks but may be suppressed on networks with modules composed of different types of diffusion links.

  6. Light radioactive nuclei capture reactions with phenomenological potential models

    SciTech Connect

    Guimaraes, V.; Bertulani, C. A.

    2010-05-21

    Light radioactive nuclei play an important role in many astrophysical environments. Due to very low cross sections of some neutron and proton capture reactions by these radioactive nuclei at energies of astrophysical interest, direct laboratory measurements are very difficult. For radioactive nuclei such as {sup 8}Li and {sup 8}B, the direct measurement of neutron capture reactions is impossible. Indirect methods have been applied to overcome these difficulties. In this work we will report on the results and discussion of phenomenological potential models used to determine some proton and neutron capture reactions. As a test we show the results for the {sup 16}O(p,gamma){sup 17}F{sub gs}(5/2{sup +}) and {sup 16}O(p,gamma){sup 17}F{sub ex}(1/2{sup +}) capture reactions. We also computed the nucleosynthesis cross sections for the {sup 7}Li(n,gamma){sup 8}Li{sub gs}, {sup 8}Li(n,gamma){sup 9}Li{sub gs} and {sup 8}B(p,gamma){sup 9}C{sub gs} capture reactions.

  7. A model study of sequential enzyme reactions and electrostatic channeling.

    PubMed

    Eun, Changsun; Kekenes-Huskey, Peter M; Metzger, Vincent T; McCammon, J Andrew

    2014-03-14

    We study models of two sequential enzyme-catalyzed reactions as a basic functional building block for coupled biochemical networks. We investigate the influence of enzyme distributions and long-range molecular interactions on reaction kinetics, which have been exploited in biological systems to maximize metabolic efficiency and signaling effects. Specifically, we examine how the maximal rate of product generation in a series of sequential reactions is dependent on the enzyme distribution and the electrostatic composition of its participant enzymes and substrates. We find that close proximity between enzymes does not guarantee optimal reaction rates, as the benefit of decreasing enzyme separation is countered by the volume excluded by adjacent enzymes. We further quantify the extent to which the electrostatic potential increases the efficiency of transferring substrate between enzymes, which supports the existence of electrostatic channeling in nature. Here, a major finding is that the role of attractive electrostatic interactions in confining intermediate substrates in the vicinity of the enzymes can contribute more to net reactive throughput than the directional properties of the electrostatic fields. These findings shed light on the interplay of long-range interactions and enzyme distributions in coupled enzyme-catalyzed reactions, and their influence on signaling in biological systems.

  8. Modeling reaction fronts of separated condensed phase reactants

    NASA Astrophysics Data System (ADS)

    Koundinyan, Sushilkumar; Stewart, D. Scott; Matalon, Moshe

    2017-01-01

    We present a Gibbs free energy approach to modeling reaction fronts in condensed phase reactive materials. The current interest is in chemical reactions of condensed phase reactants that are initially separated. In energetic materials such reactions are observed to occur extremely fast and at relatively sharp fronts. The condensed phase combustion process differs in several aspects from classical gaseous combustion due to the disparity between the characteristic thermal conductivity length and the mass diffusion lengths and a volume, temperature, stress, mass fraction equation of state that principally depends only on the component reference volumes and the current mixture composition. To retain a simple planar configuration, we consider the two reactants, in solid phase, are in motion towards each other characterized by counter-flow geometry. We apply the model to a simplified Titanium-Boron system and present the analysis of reaction zone length for various strain rates. The numerical results are validated with asymptotic approximations at the Burke-Schumann (complete combustion) limit.

  9. Modeling reaction fronts of separated condensed phase reactants

    NASA Astrophysics Data System (ADS)

    Koundinyan, Sushilkumar; Matalon, Moshe; Stewart, D. Scott; Bdzil, John

    2015-06-01

    We present a Gibbs free energy approach to modeling reaction fronts in condensed phase reactive materials. The current interest is in chemical reactions of condensed phase reactants that are initially separated. In energetic materials such reactions are observed to occur extremely fast and at relatively sharp fronts. The solid-to-solid combustion process differs in several aspects from classical gaseous combustion due to the disparity between the characteristic thermal conductivity length and the mass diffusion lengths and a volume, temperature, stress, mass fraction equation of state that principally depends only on the component reference volumes and the current mixture composition. To retain a simple planar configuration, we consider the two reactants, in solid phase, are in motion towards each other characterized by counter-flow geometry. We apply the model to a simplified Titanium-Boron system and present the analysis of reaction zone length for various strain rates. The numerical results are validated with asymptotic approximations at the Burke-Schumann limit. Supported by HDTRA1-10-1-0020 (DTRA), AF Sub MO C00039417-1 (AFOSR/TRE).

  10. Towards many-body based nuclear reaction modelling

    NASA Astrophysics Data System (ADS)

    Hilaire, Stéphane; Goriely, Stéphane

    2016-06-01

    The increasing need for cross sections far from the valley of stability poses a challenge for nuclear reaction models. So far, predictions of cross sections have relied on more or less phenomenological approaches, depending on parameters adjusted to available experimental data or deduced from systematic expressions. While such predictions are expected to be reliable for nuclei not too far from the experimentally known regions, it is clearly preferable to use more fundamental approaches, based on sound physical principles, when dealing with very exotic nuclei. Thanks to the high computer power available today, all the ingredients required to model a nuclear reaction can now be (and have been) microscopically (or semi-microscopically) determined starting from the information provided by a nucleon-nucleon effective interaction. This concerns nuclear masses, optical model potential, nuclear level densities, photon strength functions, as well as fission barriers. All these nuclear model ingredients, traditionally given by phenomenological expressions, now have a microscopic counterpart implemented in the TALYS nuclear reaction code. We are thus now able to perform fully microscopic cross section calculations. The quality of these ingredients and the impact of using them instead of the usually adopted phenomenological parameters will be discussed. Perspectives for the coming years will be drawn on the improvements one can expect.

  11. Incremental learning for automated knowledge capture.

    SciTech Connect

    Benz, Zachary O.; Basilico, Justin Derrick; Davis, Warren Leon,; Dixon, Kevin R.; Jones, Brian S.; Martin, Nathaniel; Wendt, Jeremy Daniel

    2013-12-01

    People responding to high-consequence national-security situations need tools to help them make the right decision quickly. The dynamic, time-critical, and ever-changing nature of these situations, especially those involving an adversary, require models of decision support that can dynamically react as a situation unfolds and changes. Automated knowledge capture is a key part of creating individualized models of decision making in many situations because it has been demonstrated as a very robust way to populate computational models of cognition. However, existing automated knowledge capture techniques only populate a knowledge model with data prior to its use, after which the knowledge model is static and unchanging. In contrast, humans, including our national-security adversaries, continually learn, adapt, and create new knowledge as they make decisions and witness their effect. This artificial dichotomy between creation and use exists because the majority of automated knowledge capture techniques are based on traditional batch machine-learning and statistical algorithms. These algorithms are primarily designed to optimize the accuracy of their predictions and only secondarily, if at all, concerned with issues such as speed, memory use, or ability to be incrementally updated. Thus, when new data arrives, batch algorithms used for automated knowledge capture currently require significant recomputation, frequently from scratch, which makes them ill suited for use in dynamic, timecritical, high-consequence decision making environments. In this work we seek to explore and expand upon the capabilities of dynamic, incremental models that can adapt to an ever-changing feature space.

  12. Boundary effects in a surface reaction model for CO oxidation

    NASA Astrophysics Data System (ADS)

    Brosilow, Benjamin J.; Gulari, Erdogan; Ziff, Robert M.

    1993-01-01

    The surface reaction model of Ziff, Gulari, and Barshad (ZGB) is investigated on finite systems with ``hard'' oxygen boundary conditions. The rate of production of CO2 is calculated as a function of y and system size. When the rate of CO adsorption y is above the first-order transition value y2, the reactive region is found to extend into the system a distance ξ which scales as (y-y2)-0.40 when y→y2.

  13. Diffusion-controlled reactions modeling in Geant4-DNA

    SciTech Connect

    Karamitros, M.; Luan, S.; Bernal, M.A.; Allison, J.; Baldacchino, G.; Davidkova, M.; Francis, Z.; Friedland, W.; Ivantchenko, V.; Ivantchenko, A.; Mantero, A.; Nieminem, P.; Santin, G.; Tran, H.N.; Stepan, V.; Incerti, S.

    2014-10-01

    Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k–d tree data structure for quickly locating, for a given molecule, its closest reactants. The

  14. Diffusion-controlled reactions modeling in Geant4-DNA

    NASA Astrophysics Data System (ADS)

    Karamitros, M.; Luan, S.; Bernal, M. A.; Allison, J.; Baldacchino, G.; Davidkova, M.; Francis, Z.; Friedland, W.; Ivantchenko, V.; Ivantchenko, A.; Mantero, A.; Nieminem, P.; Santin, G.; Tran, H. N.; Stepan, V.; Incerti, S.

    2014-10-01

    Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k-d tree data structure for quickly locating, for a given molecule, its closest reactants. The

  15. Incremental Bayesian Category Learning From Natural Language.

    PubMed

    Frermann, Lea; Lapata, Mirella

    2016-08-01

    Models of category learning have been extensively studied in cognitive science and primarily tested on perceptual abstractions or artificial stimuli. In this paper, we focus on categories acquired from natural language stimuli, that is, words (e.g., chair is a member of the furniture category). We present a Bayesian model that, unlike previous work, learns both categories and their features in a single process. We model category induction as two interrelated subproblems: (a) the acquisition of features that discriminate among categories, and (b) the grouping of concepts into categories based on those features. Our model learns categories incrementally using particle filters, a sequential Monte Carlo method commonly used for approximate probabilistic inference that sequentially integrates newly observed data and can be viewed as a plausible mechanism for human learning. Experimental results show that our incremental learner obtains meaningful categories which yield a closer fit to behavioral data compared to related models while at the same time acquiring features which characterize the learned categories. (An earlier version of this work was published in Frermann and Lapata .).

  16. Modeling Reaction Control System Effects on Mars Odyssey

    NASA Technical Reports Server (NTRS)

    Hanna, Jill L.; Chavis, Zachary Q.; Wilmoth, Richard G.; Bushnell, Dennis M. (Technical Monitor)

    2002-01-01

    During the Mars 2001 Odyssey aerobraking mission, NASA Langley Research Center performed 6 degree of freedom (6-DOF) simulations to determine rotational motion of the spacecraft. The main objective of this study was to assess the reaction control system models and their effects on the atmospheric flight of Odyssey. Based on these models, a comparison was made between data derived from flight measurements to simulated rotational motion of the spacecraft during aerobraking at Mars. The differences between the simulation and flight derived Odyssey data were then used to adjust the aerodynamic parameters to achieve a better correlation.

  17. The power induced effects module: A FORTRAN code which estimates lift increments due to power induced effects for V/STOL flight

    NASA Technical Reports Server (NTRS)

    Sandlin, Doral R.; Howard, Kipp E.

    1991-01-01

    A user friendly FORTRAN code that can be used for preliminary design of V/STOL aircraft is described. The program estimates lift increments, due to power induced effects, encountered by aircraft in V/STOL flight. These lift increments are calculated using empirical relations developed from wind tunnel tests and are due to suckdown, fountain, ground vortex, jet wake, and the reaction control system. The code can be used as a preliminary design tool along with NASA Ames' Aircraft Synthesis design code or as a stand-alone program for V/STOL aircraft designers. The Power Induced Effects (PIE) module was validated using experimental data and data computed from lift increment routines. Results are presented for many flat plate models along with the McDonnell Aircraft Company's MFVT (mixed flow vectored thrust) V/STOL preliminary design and a 15 percent scale model of the YAV-8B Harrier V/STOL aircraft. Trends and magnitudes of lift increments versus aircraft height above the ground were predicted well by the PIE module. The code also provided good predictions of the magnitudes of lift increments versus aircraft forward velocity. More experimental results are needed to determine how well the code predicts lift increments as they vary with jet deflection angle and angle of attack. The FORTRAN code is provided in the appendix.

  18. A Discrete Model to Study Reaction-Diffusion-Mechanics Systems

    PubMed Central

    Weise, Louis D.; Nash, Martyn P.; Panfilov, Alexander V.

    2011-01-01

    This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects. PMID:21804911

  19. A discrete model to study reaction-diffusion-mechanics systems.

    PubMed

    Weise, Louis D; Nash, Martyn P; Panfilov, Alexander V

    2011-01-01

    This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.

  20. Trichloramine Removal with Activated Carbon Is Governed by Two Reductive Reactions: A Theoretical Approach with Diffusion-Reaction Models.

    PubMed

    Matsushita, Taku; Matsui, Yoshihiko; Ikekame, Shohei; Sakuma, Miki; Shirasaki, Nobutaka

    2017-04-06

    Mechanisms underlying trichloramine removal with activated carbon treatment were proven by batch experiments and theoretical analysis with diffusion-reaction models. The observed values of trichloramine and free chlorine were explained only by the model in which (1) both trichloramine and free chlorine were involved as reactants, (2) the removals of reactants were affected both by the intraparticle diffusion and by the reaction with activated carbon, and (3) trichloramine decomposition was governed by two distinct reductive reactions. One reductive reaction was expressed as a first-order reaction: the reductive reaction of trichloramine with the basal plane of PAC, which consists of graphene sheets. The other reaction was expressed as a second-order reaction: the reductive reaction of trichloramine with active functional groups located on the edge of the basal plane. Free chlorine competitively reacted with both the basal plane and the active functional groups. The fact that the model prediction succeeded even in experiments with different activated carbon doses, with different initial trichloramine concentrations, and with different sizes of activated carbon particles clearly proved that the mechanisms described in the model were reasonable for explaining trichloramine removal with activated carbon treatment.

  1. Transalkylation reactions in fossil fuels and related model compounds

    SciTech Connect

    Farcasiu, M.; Forbus, T.R.; LaPierre, R.B.

    1983-02-01

    The alkyl substituents of high molecular weight polycyclic aromatic constituents of petroleum residues are transferable to exogenous monocyclic aromatics (benzene, toluene, o-xylene, etc.) by acid catalyzed (CF/sub 3/SO/sub 3/H) Friedel Crafts transalkylation. Analysis (GC-MS) of the volatile alkylated monocyclic aromatic products provides a method for the determination of the alkyl group content/structure of the starting fossil fuel mixture. Both model systems, using alkylated naphthalenes, phenanthrenes, pyrenes and dibenzothiophenes and demineralized shale oil or petroleum resid were studied. The model studies (alkyl chain length 2-10 carbons) revealed the following reaction pathways to predominate: (1) transalkylation rates/equilibria are independent of chain length; (2) n-alkyl groups are transfered without rearrangement or fragmentation; (3) reaction rate depends upon the aromatic moiety; (4) formation of dixylylmethanes via benzyl carbenium ions is significant (12 to 25% of product; and (5) significant minor products at longer reaction times are alkyl tetralins, tetralins, napthalenes and alkylated acceptors having a chain length reduced by (-CH/sub 2/-)/sub 4/.

  2. Coupled Disturbance Modelling And Validation Of A Reaction Wheel Model

    NASA Astrophysics Data System (ADS)

    Zhang, Zhe; Aglietti, Gugliemo S.

    2012-07-01

    Microvibrations of a RWA are usually studied in either hard-mounted or coupled conditions, although coupled wheel-structure disturbances are more representative than the hard-mounted disturbances. The coupled analysis method of the wheel-structure is not as well developed as the hard-mounted one. A coupled disturbance analysis method is proposed in this paper. One of the most important factors in coupled disturbance analysis - the accelerance or dynamic mass of the wheel is measured and results are validated with an equivalent FE model. The wheel hard-mounted disturbances are also measured from a vibration measurement platform particularly designed for this study. Wheel structural modes are solved from its analytical disturbance model and validated with the test results. The wheel-speed dependent accelerance analysis method is proposed.

  3. Modelling charge transfer reactions with the frozen density embedding formalism

    SciTech Connect

    Pavanello, Michele; Neugebauer, Johannes

    2011-12-21

    The frozen density embedding (FDE) subsystem formulation of density-functional theory is a useful tool for studying charge transfer reactions. In this work charge-localized, diabatic states are generated directly with FDE and used to calculate electronic couplings of hole transfer reactions in two {pi}-stacked nucleobase dimers of B-DNA: 5{sup '}-GG-3{sup '} and 5{sup '}-GT-3{sup '}. The calculations rely on two assumptions: the two-state model, and a small differential overlap between donor and acceptor subsystem densities. The resulting electronic couplings agree well with benchmark values for those exchange-correlation functionals that contain a high percentage of exact exchange. Instead, when semilocal GGA functionals are used the electronic couplings are grossly overestimated.

  4. Homogeneous models for mechanisms of surface reactions: Propylene ammoxidation

    SciTech Connect

    Chan, D.M.T.; Nugent, W.A.; Fultz, W.C.; Rose, D.C.; Tulip, T.H.

    1987-04-01

    The proposed active sites on the catalyst surface in heterogeneous propylene ammoxidation have been successfully modelled by structurally characterized pinacolato W(VI) tert-butylimido complexes. These compounds exist as an equilibrating mixture of amine-bis(imido) and imido-bis(amido) complexes, the position of this equilibrium is dependent on the electronic nature of the glycolate ligand. Both of the C-N bond-forming reactions proposed in recent studies by Grasselli et al. (1) have been reproduced using discrete Group VI d{sup 0} organoimido complexes under mild conditions suitable for detailed mechanistic studies. These reactions are: (1) oxidative trapping of radicals at molybdenum imido sites, and (2) migration of the allyl group from oxygen to an imido nitrogen atom.

  5. Chemical reaction fouling model for single-phase heat transfer

    SciTech Connect

    Panchal, C.B.; Watkinson, A.P.

    1993-08-01

    A fouling model was developed on the premise that the chemical reaction for generation of precursor can take place in the bulk fluid, in the thermalboundary layer, or at the fluid/wall interface, depending upon the interactive effects of flu id dynamics, heat and mass transfer, and the controlling chemical reaction. The analysis was used to examine the experimental data for fouling deposition of polyperoxides produced by autoxidation of indene in kerosene. The effects of fluid and wall temperatures for two flow geometries were analyzed. The results showed that the relative effects of physical parameters on the fouling rate would differ for the three fouling mechanisms; therefore, it is important to identify the controlling mechanism in applying the closed-flow-loop data to industrial conditions.

  6. Modelling charge transfer reactions with the frozen density embedding formalism.

    PubMed

    Pavanello, Michele; Neugebauer, Johannes

    2011-12-21

    The frozen density embedding (FDE) subsystem formulation of density-functional theory is a useful tool for studying charge transfer reactions. In this work charge-localized, diabatic states are generated directly with FDE and used to calculate electronic couplings of hole transfer reactions in two π-stacked nucleobase dimers of B-DNA: 5'-GG-3' and 5'-GT-3'. The calculations rely on two assumptions: the two-state model, and a small differential overlap between donor and acceptor subsystem densities. The resulting electronic couplings agree well with benchmark values for those exchange-correlation functionals that contain a high percentage of exact exchange. Instead, when semilocal GGA functionals are used the electronic couplings are grossly overestimated.

  7. A reaction-diffusion model of cytosolic hydrogen peroxide.

    PubMed

    Lim, Joseph B; Langford, Troy F; Huang, Beijing K; Deen, William M; Sikes, Hadley D

    2016-01-01

    As a signaling molecule in mammalian cells, hydrogen peroxide (H2O2) determines the thiol/disulfide oxidation state of several key proteins in the cytosol. Localization is a key concept in redox signaling; the concentrations of signaling molecules within the cell are expected to vary in time and in space in manner that is essential for function. However, as a simplification, all theoretical studies of intracellular hydrogen peroxide and many experimental studies to date have treated the cytosol as a well-mixed compartment. In this work, we incorporate our previously reported reduced kinetic model of the network of reactions that metabolize hydrogen peroxide in the cytosol into a model that explicitly treats diffusion along with reaction. We modeled a bolus addition experiment, solved the model analytically, and used the resulting equations to quantify the spatiotemporal variations in intracellular H2O2 that result from this kind of perturbation to the extracellular H2O2 concentration. We predict that micromolar bolus additions of H2O2 to suspensions of HeLa cells (0.8 × 10(9)cells/l) result in increases in the intracellular concentration that are localized near the membrane. These findings challenge the assumption that intracellular concentrations of H2O2 are increased uniformly throughout the cell during bolus addition experiments and provide a theoretical basis for differing phenotypic responses of cells to intracellular versus extracellular perturbations to H2O2 levels.

  8. A reaction-based paradigm to model reactive chemical transport in groundwater with general kinetic and equilibrium reactions.

    PubMed

    Zhang, Fan; Yeh, Gour-Tsyh; Parker, Jack C; Brooks, Scott C; Pace, Molly N; Kim, Young-Jin; Jardine, Philip M; Watson, David B

    2007-06-16

    This paper presents a reaction-based water quality transport model in subsurface flow systems. Transport of chemical species with a variety of chemical and physical processes is mathematically described by M partial differential equations (PDEs). Decomposition via Gauss-Jordan column reduction of the reaction network transforms M species reactive transport equations into two sets of equations: a set of thermodynamic equilibrium equations representing N(E) equilibrium reactions and a set of reactive transport equations of M-N(E) kinetic-variables involving no equilibrium reactions (a kinetic-variable is a linear combination of species). The elimination of equilibrium reactions from reactive transport equations allows robust and efficient numerical integration. The model solves the PDEs of kinetic-variables rather than individual chemical species, which reduces the number of reactive transport equations and simplifies the reaction terms in the equations. A variety of numerical methods are investigated for solving the coupled transport and reaction equations. Simulation comparisons with exact solutions were performed to verify numerical accuracy and assess the effectiveness of various numerical strategies to deal with different application circumstances. Two validation examples involving simulations of uranium transport in soil columns are presented to evaluate the ability of the model to simulate reactive transport with complex reaction networks involving both kinetic and equilibrium reactions.

  9. 18 CFR 154.309 - Incremental expansions.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Incremental expansions... Changes § 154.309 Incremental expansions. (a) For every expansion for which incremental rates are charged... costs and revenues associated with the expansion, until the Commission authorizes the costs of...

  10. 18 CFR 154.309 - Incremental expansions.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Incremental expansions... Changes § 154.309 Incremental expansions. (a) For every expansion for which incremental rates are charged... costs and revenues associated with the expansion, until the Commission authorizes the costs of...

  11. 18 CFR 154.309 - Incremental expansions.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Incremental expansions... Changes § 154.309 Incremental expansions. (a) For every expansion for which incremental rates are charged... costs and revenues associated with the expansion, until the Commission authorizes the costs of...

  12. 18 CFR 154.309 - Incremental expansions.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Incremental expansions... Changes § 154.309 Incremental expansions. (a) For every expansion for which incremental rates are charged... costs and revenues associated with the expansion, until the Commission authorizes the costs of...

  13. 18 CFR 154.309 - Incremental expansions.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Incremental expansions... Changes § 154.309 Incremental expansions. (a) For every expansion for which incremental rates are charged... costs and revenues associated with the expansion, until the Commission authorizes the costs of...

  14. 14 CFR 1260.53 - Incremental funding.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 5 2013-01-01 2013-01-01 false Incremental funding. 1260.53 Section 1260... AGREEMENTS General Special Conditions § 1260.53 Incremental funding. Incremental Funding October 2000 (a... this award. NASA contemplates making additional allotments of funds during performance of this...

  15. 14 CFR 1260.53 - Incremental funding.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 5 2011-01-01 2010-01-01 true Incremental funding. 1260.53 Section 1260.53... Special Conditions § 1260.53 Incremental funding. Incremental Funding October 2000 (a) Only $___ of the amount indicated on the face of this award is available for payment and allotted to this award....

  16. 14 CFR 1274.918 - Incremental funding.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 5 2013-01-01 2013-01-01 false Incremental funding. 1274.918 Section 1274... COMMERCIAL FIRMS Other Provisions and Special Conditions § 1274.918 Incremental funding. Incremental Funding... amount indicated on the cover page of this agreement is available for payment. NASA may supplement...

  17. 14 CFR 1274.918 - Incremental funding.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Incremental funding. 1274.918 Section 1274... COMMERCIAL FIRMS Other Provisions and Special Conditions § 1274.918 Incremental funding. Incremental Funding... amount indicated on the cover page of this agreement is available for payment. NASA may supplement...

  18. 14 CFR 1274.918 - Incremental funding.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 5 2011-01-01 2010-01-01 true Incremental funding. 1274.918 Section 1274... COMMERCIAL FIRMS Other Provisions and Special Conditions § 1274.918 Incremental funding. Incremental Funding... amount indicated on the cover page of this agreement is available for payment. NASA may supplement...

  19. 14 CFR 1274.918 - Incremental funding.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 5 2012-01-01 2012-01-01 false Incremental funding. 1274.918 Section 1274... COMMERCIAL FIRMS Other Provisions and Special Conditions § 1274.918 Incremental funding. Incremental Funding... amount indicated on the cover page of this agreement is available for payment. NASA may supplement...

  20. Modeling the Reactions of Energetic Materials in the Condensed Phase

    SciTech Connect

    Fried, L E; Manaa, M R; Lewis, J P

    2003-12-03

    High explosive (HE) materials are unique for having a strong exothermic reactivity, which has made them desirable for both military and commercial applications. Although the history of HE materials is long, condensed-phase properties are poorly understood. Understanding the condensed-phase properties of HE materials is important for determining stability and performance. Information regarding HE material properties (for example, the physical, chemical, and mechanical behaviors of the constituents in plastic-bonded explosive, or PBX, formulations) is necessary in efficiently building the next generation of explosives as the quest for more powerful energetic materials (in terms of energy per volume) moves forward. In addition, understanding the reaction mechanisms has important ramifications in disposing of such materials safely and cheaply, as there exist vast stockpiles of HE materials with corresponding contamination of earth and groundwater at these sites, as well as a military testing sites The ability to model chemical reaction processes in condensed phase energetic materials is rapidly progressing. Chemical equilibrium modeling is a mature technique with some limitations. Progress in this area continues, but is hampered by a lack of knowledge of condensed phase reaction mechanisms and rates. Atomistic modeling is much more computationally intensive, and is currently limited to very short time scales. Nonetheless, this methodology promises to yield the first reliable insights into the condensed phase processes responsible for high explosive detonation. Further work is necessary to extend the timescales involved in atomistic simulations. Recent work in implementing thermostat methods appropriate to shocks may promise to overcome some of these difficulties. Most current work on energetic material reactivity assumes that electronically adiabatic processes dominate. The role of excited states is becoming clearer, however. These states are not accessible in perfect

  1. Systematic development of reduced reaction mechanisms for dynamic modeling

    NASA Technical Reports Server (NTRS)

    Frenklach, M.; Kailasanath, K.; Oran, E. S.

    1986-01-01

    A method for systematically developing a reduced chemical reaction mechanism for dynamic modeling of chemically reactive flows is presented. The method is based on the postulate that if a reduced reaction mechanism faithfully describes the time evolution of both thermal and chain reaction processes characteristic of a more complete mechanism, then the reduced mechanism will describe the chemical processes in a chemically reacting flow with approximately the same degree of accuracy. Here this postulate is tested by producing a series of mechanisms of reduced accuracy, which are derived from a full detailed mechanism for methane-oxygen combustion. These mechanisms were then tested in a series of reactive flow calculations in which a large-amplitude sinusoidal perturbation is applied to a system that is initially quiescent and whose temperature is high enough to start ignition processes. Comparison of the results for systems with and without convective flow show that this approach produces reduced mechanisms that are useful for calculations of explosions and detonations. Extensions and applicability to flames are discussed.

  2. Reaction-diffusion-branching models of stock price fluctuations

    NASA Astrophysics Data System (ADS)

    Tang, Lei-Han; Tian, Guang-Shan

    Several models of stock trading (Bak et al., Physica A 246 (1997) 430.) are analyzed in analogy with one-dimensional, two-species reaction-diffusion-branching processes. Using heuristic and scaling arguments, we show that the short-time market price variation is subdiffusive with a Hurst exponent H=1/4. Biased diffusion towards the market price and blind-eyed copying lead to crossovers to the empirically observed random-walk behavior ( H=1/2) at long times. The calculated crossover forms and diffusion constants are shown to agree well with simulation data.

  3. ZGB surface reaction model with high diffusion rates

    NASA Astrophysics Data System (ADS)

    Evans, J. W.

    1993-02-01

    The diffusionless ZGB (monomer-dimer) surface reaction model exhibits a discontinuous transition to a monomer-poisoned state when the fraction of monomer adsorption attempts exceeds 0.525. It has been claimed that this transition shifts to 2/3 with introduction of rapid diffusion of the monomer species, or of both species. We show this is not the case, 2/3 representing the spinodal rather than the transition point. For equal diffusion rates of both species, we find that the transition only shifts to 0.5951±0.0002.

  4. ZGB surface reaction model with high diffusion rates

    SciTech Connect

    Evans, J.W. )

    1993-02-01

    The diffusionless ZGB (monomer--dimer) surface reaction model exhibits a discontinuous transition to a monomer-poisoned state when the fraction of monomer adsorption attempts exceeds 0.525. It has been claimed that this transition shifts to 2/3 with introduction of rapid diffusion of the monomer species, or of both species. We show this is not the case, 2/3 representing the spinodal rather than the transition point. For equal diffusion rates of both species, we find that the transition only shifts to 0.5951[plus minus]0.0002.

  5. Compressive tracking with incremental multivariate Gaussian distribution

    NASA Astrophysics Data System (ADS)

    Li, Dongdong; Wen, Gongjian; Zhu, Gao; Zeng, Qiaoling

    2016-09-01

    Various approaches have been proposed for robust visual tracking, among which compressive tracking (CT) yields promising performance. In CT, Haar-like features are efficiently extracted with a very sparse measurement matrix and modeled as an online updated naïve Bayes classifier to account for target appearance change. The naïve Bayes classifier ignores overlap between Haar-like features and assumes that Haar-like features are independently distributed, which leads to drift in complex scenario. To address this problem, we present an extended CT algorithm, which assumes that all Haar-like features are correlated with each other and have multivariate Gaussian distribution. The mean vector and covariance matrix of multivariate normal distribution are incrementally updated with constant computational complexity to adapt to target appearance change. Each frame is associated with a temporal weight to expend less modeling power on old observation. Based on temporal weight, an update scheme with changing but convergent learning rate is derived with strict mathematic proof. Compared with CT, our extended algorithm achieves a richer representation of target appearance. The incremental multivariate Gaussian distribution is integrated into the particle filter framework to achieve better tracking performance. Extensive experiments on the CVPR2013 tracking benchmark demonstrate that our proposed tracker achieves superior performance both qualitatively and quantitatively over several state-of-the-art trackers.

  6. Triple-{alpha} reaction rate constrained by stellar evolution models

    SciTech Connect

    Suda, Takuma; Hirschi, Raphael; Fujimoto, Masayuki Y.

    2012-11-12

    We investigate the quantitative constraint on the triple-{alpha} reaction rate based on stellar evolution theory, motivated by the recent significant revision of the rate proposed by nuclear physics calculations. Targeted stellar models were computed in order to investigate the impact of that rate in the mass range of 0.8{<=}M/M{sub Circled-Dot-Operator }{<=}25 and in the metallicity range between Z= 0 and Z= 0.02. The revised rate has a significant impact on the evolution of low-and intermediate-mass stars, while its influence on the evolution of massive stars (M > 10M{sub Circled-Dot-Operator }) is minimal. We find that employing the revised rate suppresses helium shell flashes on AGB phase for stars in the initial mass range 0.8{<=}M/M{sub Circled-Dot-Operator }{<=}6, which is contradictory to what is observed. The absence of helium shell flashes is due to the weak temperature dependence of the revised triple-{alpha} reaction cross section at the temperature involved. In our models, it is suggested that the temperature dependence of the cross section should have at least {nu} > 10 at T = 1-1.2 Multiplication-Sign 10{sup 8}K where the cross section is proportional to T{sup {nu}}. We also derive the helium ignition curve to estimate the maximum cross section to retain the low-mass first red giants. The semi-analytically derived ignition curves suggest that the reaction rate should be less than {approx} 10{sup -29} cm{sup 6} s{sup -1} mole{sup -2} at Almost-Equal-To 10{sup 7.8} K, which corresponds to about three orders of magnitude larger than that of the NACRE compilation.

  7. MARLEY: Model of Argon Reaction Low Energy Yields

    NASA Astrophysics Data System (ADS)

    Gardiner, Steven; Bilton, Kyle; Grant, Christopher; Pantic, Emilija; Svoboda, Robert

    2015-10-01

    Core-collapse supernovae are sources of tremendous numbers of neutrinos with energies of up to about 50 MeV. In recent years, there has been growing interest in building detectors that are sensitive to supernova neutrinos. Such detectors can provide information about the initial stages of stellar collapse, early warning signals for light emission from supernovae, and opportunities to study neutrino oscillation physics over astronomical distances. In an effort to enable supernova neutrino detection in next-generation experiments like DUNE, the CAPTAIN collaboration plans to make the first direct measurement of cross sections for neutrino interactions on argon in the supernova energy regime. To help predict neutrino event signatures in the CAPTAIN liquid argon time projection chamber (LArTPC), we have developed a first-of-its-kind Monte Carlo event generator called MARLEY (Model of Argon Reaction Low Energy Yields). This generator attempts to model the complicated nuclear structure dependence of low-energy neutrino-nucleus reactions in sufficient detail for use in LArTPC simulations. In this talk we present some preliminary results calculated using MARLEY and discuss how the current version of the generator may be improved and expanded.

  8. Analytical model for heterogeneous reactions in mixed porous media

    SciTech Connect

    Hatfield, K.; Burris, D.R.; Wolfe, N.L.

    1996-08-01

    The funnel/gate system is a developing technology for passive ground-water plume management and treatment. This technology uses sheet pilings as a funnel to force polluted ground water through a highly permeable zone of reactive porous media (the gate) where contaminants are degraded by biotic or abiotic heterogeneous reactions. This paper presents a new analytical nonequilibrium model for solute transport in saturated, nonhomogeneous or mixed porous media that could assist efforts to design funnel/gate systems and predict their performance. The model incorporates convective/dispersion transport, dissolved constituent decay, surface-mediated degradation, and time-dependent mass transfer between phases. Simulation studies of equilibrium and nonequilibrium transport conditions reveal manifestations of rate-limited degradation when mass-transfer times are longer than system hydraulic residence times, or when surface-mediated reaction rates are faster than solute mass-transfer processes (i.e., sorption, film diffusion, or intraparticle diffusion). For example, steady-state contaminant concentrations will be higher under a nonequilibrium transport scenario than would otherwise be expected when assuming equilibrium conditions. Thus, a funnel/gate system may fail to achieve desired ground-water treatment if the possibility of mass-transfer-limited degradation is not considered.

  9. Geochemical controls on shale groundwaters: Results of reaction path modeling

    SciTech Connect

    Von Damm, K.L.; VandenBrook, A.J.

    1989-03-01

    The EQ3NR/EQ6 geochemical modeling code was used to simulate the reaction of several shale mineralogies with different groundwater compositions in order to elucidate changes that may occur in both the groundwater compositions, and rock mineralogies and compositions under conditions which may be encountered in a high-level radioactive waste repository. Shales with primarily illitic or smectitic compositions were the focus of this study. The reactions were run at the ambient temperatures of the groundwaters and to temperatures as high as 250/degree/C, the approximate temperature maximum expected in a repository. All modeling assumed that equilibrium was achieved and treated the rock and water assemblage as a closed system. Graphite was used as a proxy mineral for organic matter in the shales. The results show that the presence of even a very small amount of reducing mineral has a large influence on the redox state of the groundwaters, and that either pyrite or graphite provides essentially the same results, with slight differences in dissolved C, Fe and S concentrations. The thermodynamic data base is inadequate at the present time to fully evaluate the speciation of dissolved carbon, due to the paucity of thermodynamic data for organic compounds. In the illitic cases the groundwaters resulting from interaction at elevated temperatures are acid, while the smectitic cases remain alkaline, although the final equilibrium mineral assemblages are quite similar. 10 refs., 8 figs., 15 tabs.

  10. In silico strain optimization by adding reactions to metabolic models.

    PubMed

    Correia, Sara; Rocha, Miguel

    2012-07-24

    Nowadays, the concerns about the environment and the needs to increase the productivity at low costs, demand for the search of new ways to produce compounds with industrial interest. Based on the increasing knowledge of biological processes, through genome sequencing projects, and high-throughput experimental techniques as well as the available computational tools, the use of microorganisms has been considered as an approach to produce desirable compounds. However, this usually requires to manipulate these organisms by genetic engineering and/ or changing the enviromental conditions to make the production of these compounds possible. In many cases, it is necessary to enrich the genetic material of those microbes with hereologous pathways from other species and consequently adding the potential to produce novel compounds. This paper introduces a new plug-in for the OptFlux Metabolic Engineering platform, aimed at finding suitable sets of reactions to add to the genomes of selected microbes (wild type strain), as well as finding complementary sets of deletions, so that the mutant becomes able to overproduce compounds with industrial interest, while preserving their viability. The necessity of adding reactions to the metabolic model arises from existing gaps in the original model or motivated by the productions of new compounds by the organism. The optimization methods used are metaheuristics such as Evolutionary Algorithms and Simulated Annealing. The usefulness of this plug-in is demonstrated by a case study, regarding the production of vanillin by the bacterium E. coli.

  11. A Transport Model for Nuclear Reactions Induced by Radioactive Beams

    SciTech Connect

    Li Baoan; Chen Liewen; Das, Champak B.; Das Gupta, Subal; Gale, Charles; Ko, C.M.; Yong, G.-C.; Zuo Wei

    2005-10-14

    Major ingredients of an isospin and momentum dependent transport model for nuclear reactions induced by radioactive beams are outlined. Within the IBUU04 version of this model we study several experimental probes of the equation of state of neutron-rich matter, especially the density dependence of the nuclear symmetry energy. Comparing with the recent experimental data from NSCL/MSU on isospin diffusion, we found a nuclear symmetry energy of Esym({rho}) {approx_equal} 31.6({rho}/{rho}0)1.05 at subnormal densities. Predictions on several observables sensitive to the density dependence of the symmetry energy at supranormal densities accessible at GSI and the planned Rare Isotope Accelerator (RIA) are also made.

  12. Mass transfer model for two-layer TBP oxidation reactions

    SciTech Connect

    Laurinat, J.E.

    1994-09-28

    To prove that two-layer, TBP-nitric acid mixtures can be safely stored in the canyon evaporators, it must be demonstrated that a runaway reaction between TBP and nitric acid will not occur. Previous bench-scale experiments showed that, at typical evaporator temperatures, this reaction is endothermic and therefore cannot run away, due to the loss of heat from evaporation of water in the organic layer. However, the reaction would be exothermic and could run away if the small amount of water in the organic layer evaporates before the nitric acid in this layer is consumed by the reaction. Provided that there is enough water in the aqueous layer, this would occur if the organic layer is sufficiently thick so that the rate of loss of water by evaporation exceeds the rate of replenishment due to mixing with the aqueous layer. This report presents measurements of mass transfer rates for the mixing of water and butanol in two-layer, TBP-aqueous mixtures, where the top layer is primarily TBP and the bottom layer is comprised of water or aqueous salt solution. Mass transfer coefficients are derived for use in the modeling of two-layer TBP-nitric acid oxidation experiments. Three cases were investigated: (1) transfer of water into the TBP layer with sparging of both the aqueous and TBP layers, (2) transfer of water into the TBP layer with sparging of just the TBP layer, and (3) transfer of butanol into the aqueous layer with sparging of both layers. The TBP layer was comprised of 99% pure TBP (spiked with butanol for the butanol transfer experiments), and the aqueous layer was comprised of either water or an aluminum nitrate solution. The liquid layers were air sparged to simulate the mixing due to the evolution of gases generated by oxidation reactions. A plastic tube and a glass frit sparger were used to provide different size bubbles. Rates of mass transfer were measured using infrared spectrophotometers provided by SRTC/Analytical Development.

  13. Ions interacting with planar aromatic molecules: Modeling electron transfer reactions

    SciTech Connect

    Forsberg, B. O.; Alexander, J. D.; Chen, T.; Pettersson, A. T.; Gatchell, M.; Cederquist, H.; Zettergren, H.

    2013-02-07

    We present theoretical absolute charge exchange cross sections for multiply charged cations interacting with the Polycyclic Aromatic Hydrocarbon (PAH) molecules pyrene C{sub 14}H{sub 10}, coronene C{sub 24}H{sub 12}, or circumcoronene C{sub 54}H{sub 18}. These planar, nearly circular, PAHs are modelled as conducting, infinitely thin, and perfectly circular discs, which are randomly oriented with respect to straight line ion trajectories. We present the analytical solution for the potential energy surface experienced by an electron in the field of such a charged disc and a point-charge at an arbitrary position. The location and height of the corresponding potential energy barrier from this simple model are in close agreement with those from much more computationally demanding Density Functional Theory (DFT) calculations in a number of test cases. The model results compare favourably with available experimental data on single- and multiple electron transfer reactions and we demonstrate that it is important to include the orientation dependent polarizabilities of the molecules (model discs) in particular for the larger PAHs. PAH ionization energy sequences from DFT are tabulated and used as model inputs. Absolute cross sections for the ionization of PAH molecules, and PAH ionization energies such as the ones presented here may be useful when considering the roles of PAHs and their ions in, e.g., interstellar chemistry, stellar atmospheres, and in related photoabsorption and photoemission spectroscopies.

  14. Property Differencing for Incremental Checking

    NASA Technical Reports Server (NTRS)

    Yang, Guowei; Khurshid, Sarfraz; Person, Suzette; Rungta, Neha

    2014-01-01

    This paper introduces iProperty, a novel approach that facilitates incremental checking of programs based on a property di erencing technique. Speci cally, iProperty aims to reduce the cost of checking properties as they are initially developed and as they co-evolve with the program. The key novelty of iProperty is to compute the di erences between the new and old versions of expected properties to reduce the number and size of the properties that need to be checked during the initial development of the properties. Furthermore, property di erencing is used in synergy with program behavior di erencing techniques to optimize common regression scenarios, such as detecting regression errors or checking feature additions for conformance to new expected properties. Experimental results in the context of symbolic execution of Java programs annotated with properties written as assertions show the e ectiveness of iProperty in utilizing change information to enable more ecient checking.

  15. A Reaction-Diffusion Model of Cholinergic Retinal Waves

    PubMed Central

    Lansdell, Benjamin; Ford, Kevin; Kutz, J. Nathan

    2014-01-01

    Prior to receiving visual stimuli, spontaneous, correlated activity in the retina, called retinal waves, drives activity-dependent developmental programs. Early-stage waves mediated by acetylcholine (ACh) manifest as slow, spreading bursts of action potentials. They are believed to be initiated by the spontaneous firing of Starburst Amacrine Cells (SACs), whose dense, recurrent connectivity then propagates this activity laterally. Their inter-wave interval and shifting wave boundaries are the result of the slow after-hyperpolarization of the SACs creating an evolving mosaic of recruitable and refractory cells, which can and cannot participate in waves, respectively. Recent evidence suggests that cholinergic waves may be modulated by the extracellular concentration of ACh. Here, we construct a simplified, biophysically consistent, reaction-diffusion model of cholinergic retinal waves capable of recapitulating wave dynamics observed in mice retina recordings. The dense, recurrent connectivity of SACs is modeled through local, excitatory coupling occurring via the volume release and diffusion of ACh. In addition to simulation, we are thus able to use non-linear wave theory to connect wave features to underlying physiological parameters, making the model useful in determining appropriate pharmacological manipulations to experimentally produce waves of a prescribed spatiotemporal character. The model is used to determine how ACh mediated connectivity may modulate wave activity, and how parameters such as the spontaneous activation rate and sAHP refractory period contribute to critical wave size variability. PMID:25474327

  16. Reaction Diffusion Modeling of Calcium Dynamics with Realistic ER Geometry

    PubMed Central

    Means, Shawn; Smith, Alexander J.; Shepherd, Jason; Shadid, John; Fowler, John; Wojcikiewicz, Richard J. H.; Mazel, Tomas; Smith, Gregory D.; Wilson, Bridget S.

    2006-01-01

    We describe a finite-element model of mast cell calcium dynamics that incorporates the endoplasmic reticulum's complex geometry. The model is built upon a three-dimensional reconstruction of the endoplasmic reticulum (ER) from an electron tomographic tilt series. Tetrahedral meshes provide volumetric representations of the ER lumen, ER membrane, cytoplasm, and plasma membrane. The reaction-diffusion model simultaneously tracks changes in cytoplasmic and ER intraluminal calcium concentrations and includes luminal and cytoplasmic protein buffers. Transport fluxes via PMCA, SERCA, ER leakage, and Type II IP3 receptors are also represented. Unique features of the model include stochastic behavior of IP3 receptor calcium channels and comparisons of channel open times when diffusely distributed or aggregated in clusters on the ER surface. Simulations show that IP3R channels in close proximity modulate activity of their neighbors through local Ca2+ feedback effects. Cytoplasmic calcium levels rise higher, and ER luminal calcium concentrations drop lower, after IP3-mediated release from receptors in the diffuse configuration. Simulation results also suggest that the buffering capacity of the ER, and not restricted diffusion, is the predominant factor influencing average luminal calcium concentrations. PMID:16617072

  17. An Equilibrium-Based Model of Gas Reaction and Detonation

    SciTech Connect

    Trowbridge, L.D.

    2000-04-01

    During gaseous diffusion plant operations, conditions leading to the formation of flammable gas mixtures may occasionally arise. Currently, these could consist of the evaporative coolant CFC-114 and fluorinating agents such as F2 and ClF3. Replacement of CFC-114 with a non-ozone-depleting substitute is planned. Consequently, in the future, the substitute coolant must also be considered as a potential fuel in flammable gas mixtures. Two questions of practical interest arise: (1) can a particular mixture sustain and propagate a flame if ignited, and (2) what is the maximum pressure that can be generated by the burning (and possibly exploding) gas mixture, should it ignite? Experimental data on these systems, particularly for the newer coolant candidates, are limited. To assist in answering these questions, a mathematical model was developed to serve as a tool for predicting the potential detonation pressures and for estimating the composition limits of flammability for these systems based on empirical correlations between gas mixture thermodynamics and flammability for known systems. The present model uses the thermodynamic equilibrium to determine the reaction endpoint of a reactive gas mixture and uses detonation theory to estimate an upper bound to the pressure that could be generated upon ignition. The model described and documented in this report is an extended version of related models developed in 1992 and 1999.

  18. A multi-pathway model for photosynthetic reaction center

    NASA Astrophysics Data System (ADS)

    Qin, M.; Shen, H. Z.; Yi, X. X.

    2016-03-01

    Charge separation occurs in a pair of tightly coupled chlorophylls at the heart of photosynthetic reaction centers of both plants and bacteria. Recently it has been shown that quantum coherence can, in principle, enhance the efficiency of a solar cell, working like a quantum heat engine. Here, we propose a biological quantum heat engine (BQHE) motivated by Photosystem II reaction center (PSII RC) to describe the charge separation. Our model mainly considers two charge-separation pathways which is more than that typically considered in the published literature. We explore how these cross-couplings increase the current and power of the charge separation and discuss the effects of multiple pathways in terms of current and power. The robustness of the BQHE against the charge recombination in natural PSII RC and dephasing induced by environments is also explored, and extension from two pathways to multiple pathways is made. These results suggest that noise-induced quantum coherence helps to suppress the influence of acceptor-to-donor charge recombination, and besides, nature-mimicking architectures with engineered multiple pathways for charge separations might be better for artificial solar energy devices considering the influence of environments.

  19. MOMDIS: a Glauber model computer code for knockout reactions

    NASA Astrophysics Data System (ADS)

    Bertulani, C. A.; Gade, A.

    2006-09-01

    A computer program is described to calculate momentum distributions in stripping and diffraction dissociation reactions. A Glauber model is used with the scattering wavefunctions calculated in the eikonal approximation. The program is appropriate for knockout reactions at intermediate energy collisions ( 30 MeV⩽E/nucleon⩽2000 MeV). It is particularly useful for reactions involving unstable nuclear beams, or exotic nuclei (e.g., neutron-rich nuclei), and studies of single-particle occupancy probabilities (spectroscopic factors) and other related physical observables. Such studies are an essential part of the scientific program of radioactive beam facilities, as in for instance the proposed RIA (Rare Isotope Accelerator) facility in the US. Program summaryTitle of program: MOMDIS (MOMentum DIStributions) Catalogue identifier:ADXZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXZ_v1_0 Computers: The code has been created on an IBM-PC, but also runs on UNIX or LINUX machines Operating systems: WINDOWS or UNIX Program language used: Fortran-77 Memory required to execute with typical data: 16 Mbytes of RAM memory and 2 MB of hard disk space No. of lines in distributed program, including test data, etc.: 6255 No. of bytes in distributed program, including test data, etc.: 63 568 Distribution format: tar.gz Nature of physical problem: The program calculates bound wavefunctions, eikonal S-matrices, total cross-sections and momentum distributions of interest in nuclear knockout reactions at intermediate energies. Method of solution: Solves the radial Schrödinger equation for bound states. A Numerov integration is used outwardly and inwardly and a matching at the nuclear surface is done to obtain the energy and the bound state wavefunction with good accuracy. The S-matrices are obtained using eikonal wavefunctions and the "t- ρρ" method to obtain the eikonal phase-shifts. The momentum distributions are obtained by means of a Gaussian expansion of

  20. Modelling the Maillard reaction during the cooking of a model cheese.

    PubMed

    Bertrand, Emmanuel; Meyer, Xuân-Mi; Machado-Maturana, Elizabeth; Berdagué, Jean-Louis; Kondjoyan, Alain

    2015-10-01

    During processing and storage of industrial processed cheese, odorous compounds are formed. Some of them are potentially unwanted for the flavour of the product. To reduce the appearance of these compounds, a methodological approach was employed. It consists of: (i) the identification of the key compounds or precursors responsible for the off-flavour observed, (ii) the monitoring of these markers during the heat treatments applied to the cheese medium, (iii) the establishment of an observable reaction scheme adapted from a literature survey to the compounds identified in the heated cheese medium (iv) the multi-responses stoichiokinetic modelling of these reaction markers. Systematic two-dimensional gas chromatography time-of-flight mass spectrometry was used for the semi-quantitation of trace compounds. Precursors were quantitated by high-performance liquid chromatography. The experimental data obtained were fitted to the model with 14 elementary linked reactions forming a multi-response observable reaction scheme.

  1. A reaction-diffusion model for long bones growth.

    PubMed

    Garzón-Alvarado, D A; García-Aznar, J M; Doblaré, M

    2009-10-01

    Bone development is characterized by differentiation and growth of chondrocytes from the proliferation zone to the hypertrophying one. These two cellular processes are controlled by a complex signalling regulatory loop between different biochemical signals, whose production depends on the current cell density, constituting a coupled cell-chemical system. In this work, a mathematical model of the process of early bone growth is presented, extending and generalizing other earlier approaches on the same topic. A reaction-diffusion regulatory loop between two chemical factors: parathyroid hormone-related peptide (PTHrP) and Indian hedgehog (Ihh) is hypothesized, where PTHrP is activated by Ihh and inhibits Ihh production. Chondrocytes proliferation and hypertrophy are described by means of population equations being both regulated by the PTHrP and Ihh concentrations. In the initial stage of bone growth, these two cellular proceses are considered to be directionally dependent, modelling the well known column cell formation, characteristic of endochondral ossification. This coupled set of equations is solved within a finite element framework, getting an estimation of the chondrocytes spatial distribution, growth of the diaphysis and formation of the epiphysis of a long bone. The results obtained are qualitatively similar to the actual physiological ones and quantitatively close to some available experimental data. Finally, this extended approach allows finding important relations between the model parameters to get stability of the physiological process and getting additional insight on the spatial and directional distribution of cells and paracrine factors.

  2. Estimating marginal and incremental effects in the analysis of medical expenditure panel data using marginalized two-part random-effects generalized Gamma models: Evidence from China healthcare cost data.

    PubMed

    Zhang, Bo; Liu, Wei; Hu, Yingyao

    2017-01-01

    Conditional two-part random-effects models have been proposed for the analysis of healthcare cost panel data that contain both zero costs from the non-users of healthcare facilities and positive costs from the users. These models have been extended to accommodate more flexible data structures when using the generalized Gamma distribution to model the positive healthcare expenditures. However, a major drawback with the extended model, which is inherited from the conditional models, is that it is fairly difficult to make direct marginal inference with respect to overall healthcare costs that includes both zeros and non-zeros, or even on positive healthcare costs. In this article, we first propose two types of marginalized two-part random-effects generalized Gamma models (m2RGGMs): Type I m2RGGMs for the inference on positive healthcare costs and Type II m2RGGMs for the inference on overall healthcare costs. Then, the concepts of marginal effect and incremental effect of a covariate on overall and positive healthcare costs are introduced, and estimation of these effects is carefully discussed. Especially, we derive the variance estimates of these effects by following the delta methods and Taylor series approximations for the purpose of making marginal inference. Parameter estimates of Type I and Type II m2RGGMs are obtained through maximum likelihood estimation. An empirical analysis of longitudinal healthcare costs collected in the China Health and Nutrition Survey is conducted using the proposed methodologies.

  3. Chemical Reaction and Flow Modeling in Fullerene and Nanotube Production

    NASA Technical Reports Server (NTRS)

    Scott, Carl D.; Farhat, Samir; Greendyke, Robert B.

    2004-01-01

    The development of processes to produce fullerenes and carbon nanotubes has largely been empirical. Fullerenes were first discovered in the soot produced by laser ablation of graphite [1]and then in the soot of electric arc evaporated carbon. Techniques and conditions for producing larger and larger quantities of fullerenes depended mainly on trial and error empirical variations of these processes, with attempts to scale them up by using larger electrodes and targets and higher power. Various concepts of how fullerenes and carbon nanotubes were formed were put forth, but very little was done based on chemical kinetics of the reactions. This was mainly due to the complex mixture of species and complex nature of conditions in the reactors. Temperatures in the reactors varied from several thousand degrees Kelvin down to near room temperature. There are hundreds of species possible, ranging from atomic carbon to large clusters of carbonaceous soot, and metallic catalyst atoms to metal clusters, to complexes of metals and carbon. Most of the chemical kinetics of the reactions and the thermodynamic properties of clusters and complexes have only been approximated. In addition, flow conditions in the reactors are transient or unsteady, and three dimensional, with steep spatial gradients of temperature and species concentrations. All these factors make computational simulations of reactors very complex and challenging. This article addresses the development of the chemical reaction involved in fullerene production and extends this to production of carbon nanotubes by the laser ablation/oven process and by the electric arc evaporation process. In addition, the high-pressure carbon monoxide (HiPco) process is discussed. The article is in several parts. The first one addresses the thermochemical aspects of modeling; and considers the development of chemical rate equations, estimates of reaction rates, and thermodynamic properties where they are available. The second part

  4. Model reactions and natural occurrence of furans from hypersaline environments

    NASA Astrophysics Data System (ADS)

    Krause, T.; Tubbesing, C.; Benzing, K.; Schöler, H. F.

    2014-05-01

    Volatile organic compounds like furan and its derivatives are important for atmospheric properties and reactions. In this work the known abiotic formation of furan from catechol under Fenton-like conditions with Fe3+ sulfate was revised by the use of a bispidine Fe2+ complex as a model compound for iron with well-known characteristics. While total yields were comparable to those with the Fe3+ salt, the bispidine Fe2+ complex is a better catalyst as the turnover numbers of the active iron species were higher. Additionally, the role of iron and pH is discussed in relation to furan formation from model compounds and in natural sediment and water samples collected from the Dead Sea and several salt lakes in Western Australia. Various alkylated furans and even traces of halogenated furans (3-chlorofuran and 3-bromofuran) were found in some Australian samples. 3-chlorofuran was found in three sediments and four water samples, whereas 3-bromofuran was detected in three water samples. Further, the emission of furans is compared to the abundance of several possible precursors such as isoprene and aromatic hydrocarbons as well as to the related thiophenes. It is deduced that the emissions of volatile organic compounds such as furans contribute to the formation of ultra-fine particles in the vicinity of salt lakes and are important for the local climate.

  5. Chemical Model Systems for Cellular Nitros(yl)ation Reactions

    PubMed Central

    Daiber, Andreas; Schildknecht, Stefan; Müller, Johanna; Bachschmid, Markus M.; Ullrich, Volker

    2014-01-01

    S-nitros(yl)ation belongs to the redox-based posttranslational modifications of proteins but the underlying chemistry is controversial. In contrast to current concepts involving the autoxidation of nitric oxide (•NO, nitrogen monoxide), we and others have proposed the formation of peroxynitrite (oxoperoxonitrate(1-)) as an essential intermediate. This requires low cellular fluxes of •NO and superoxide (•O2−), for which model systems have been introduced. We here propose two new systems for nitros(yl)ation that avoid the shortcomings of previous models. Based on the thermal decomposition of 3-morpholinosydnonimine, equal fluxes of •NO and •O2− were generated and modulated by the addition of •NO donors or Cu,Zn-superoxide dismutase. As reactants for S-nitros(yl)ation, NADP+-dependent isocitrate dehydrogenase and glutathione were employed, for which optimal S-nitros(yl)ation was observed at nanomolar fluxes of •NO and •O2− at a ratio of about 3:1. The previously used reactants phenol and diaminonaphthalene, (C- and N-nitrosation) demonstrated potential participation of multiple pathways for nitros(yl)ation. According to our data, neither peroxynitrite nor autoxidation of •NO was as efficient as the 3•NO/1•O2− system in mediating S-nitros(yl)ation. In theory this could lead to an elusive nitrosonium (nitrosyl cation)-like species in the first step and to N2O3 in the subsequent reaction. Which of these two species or whether both together will participate in biological S-nitros(yl)ation remains to be elucidated. Finally, we developed several hypothetical scenarios to which the described U flux model could apply, providing conditions that allow either direct electrophilic substitution at a thiolate or S-nitros(yl)ation via transnitrosation from S-nitrosoglutathione. PMID:19477267

  6. Reaction time in ankle movements: a diffusion model analysis

    PubMed Central

    Michmizos, Konstantinos P.; Krebs, Hermano Igo

    2015-01-01

    Reaction time (RT) is one of the most commonly used measures of neurological function and dysfunction. Despite the extensive studies on it, no study has ever examined the RT in the ankle. Twenty-two subjects were recruited to perform simple, 2- and 4-choice RT tasks by visually guiding a cursor inside a rectangular target with their ankle. RT did not change with spatial accuracy constraints imposed by different target widths in the direction of the movement. RT increased as a linear function of potential target stimuli, as would be predicted by Hick–Hyman law. Although the slopes of the regressions were similar, the intercept in dorsal–plantar (DP) direction was significantly smaller than the intercept in inversion–eversion (IE) direction. To explain this difference, we used a hierarchical Bayesian estimation of the Ratcliff's (Psychol Rev 85:59, 1978) diffusion model parameters and divided processing time into cognitive components. The model gave a good account of RTs, their distribution and accuracy values, and hence provided a testimony that the non-decision processing time (overlap of posterior distributions between DP and IE < 0.045), the boundary separation (overlap of the posterior distributions < 0.1) and the evidence accumulation rate (overlap of the posterior distributions < 0.01) components of the RT accounted for the intercept difference between DP and IE. The model also proposed that there was no systematic change in non-decision processing time or drift rate when spatial accuracy constraints were altered. The results were in agreement with the memory drum hypothesis and could be further justified neurophysiologically by the larger innervation of the muscles controlling DP movements. This study might contribute to assessing deficits in sensorimotor control of the ankle and enlighten a possible target for correction in the framework of our on-going effort to develop robotic therapeutic interventions to the ankle of children with cerebral palsy

  7. A comprehensive model to determine the effects of temperature and species fluctuations on reaction rates in turbulent reaction flows

    NASA Technical Reports Server (NTRS)

    Magnotti, F.; Diskin, G.; Matulaitis, J.; Chinitz, W.

    1984-01-01

    The use of silane (SiH4) as an effective ignitor and flame stabilizing pilot fuel is well documented. A reliable chemical kinetic mechanism for prediction of its behavior at the conditions encountered in the combustor of a SCRAMJET engine was calculated. The effects of hydrogen addition on hydrocarbon ignition and flame stabilization as a means for reduction of lengthy ignition delays and reaction times were studied. The ranges of applicability of chemical kinetic models of hydrogen-air combustors were also investigated. The CHARNAL computer code was applied to the turbulent reaction rate modeling.

  8. Comprehensive model to determine the effects of temperature and species fluctuations on reaction rates in turbulent reaction flows

    SciTech Connect

    Magnotti, F.; Diskin, G.; Matulaitis, J.; Chinitz, W.

    1984-01-01

    The use of silane (SiH4) as an effective ignitor and flame stabilizing pilot fuel is well documented. A reliable chemical kinetic mechanism for prediction of its behavior at the conditions encountered in the combustor of a SCRAMJET engine was calculated. The effects of hydrogen addition on hydrocarbon ignition and flame stabilization as a means for reduction of lengthy ignition delays and reaction times were studied. The ranges of applicability of chemical kinetic models of hydrogen-air combustors were also investigated. The CHARNAL computer code was applied to the turbulent reaction rate modeling.

  9. Webpage Segments Classification with Incremental Knowledge Acquisition

    NASA Astrophysics Data System (ADS)

    Guo, Wei; Kim, Yang Sok; Kang, Byeong Ho

    This paper suggests an incremental information extraction method for social network analysis of web publications. For this purpose, we employed an incremental knowledge acquisition method, called MCRDR (Multiple Classification Ripple-Down Rules), to classify web page segments. Our experimental results show that our MCRDR-based web page segments classification system successfully supports easy acquisition and maintenance of information extraction rules.

  10. 12 CFR 3.208 - Incremental risk.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... association's measure of potential losses due to incremental risk over a one-year time horizon at a one-tail... incremental risk over a one-year time horizon and at a one-tail, 99.9 percent confidence level, either under..., or rolls over, its trading positions at the beginning of each liquidity horizon over the...

  11. A simple diffusion-reaction model for resid hydroprocessing catalysts

    SciTech Connect

    Adkins, B.D.; Limmer, K.R. )

    1990-08-01

    It is commonly accepted that the intraparticle diffusion characteristics of resid hydroprocessing catalysts can play an important role in determining their performance. It is also commonly accepted that diffusion characteristics are determined by properties of the catalyst which are at least partially reflected in measurements such as surface area and pore size. One approach to experimentally determine the appropriate region on the diffusion-reaction curve is to vary V{sub P}/S{sub P} for a fixed pore structure. One example (among many) of this approach is the paper of Gosselink and Stork in which the authors modeled the fixed-bed HDS performance of Shell 444 catalyst on heavy gasoil in crushed (particle diameter 0.2 mm) and uncrushed (1.5 mm) form. The method has the advantage of minimizing unaccountable differences in pore structures, but is susceptible to major variations in external mass and heat transfer. An alternative is to vary the pore structure widely while exploring only commercially meaningful variations in V{sub P}/S{sub P}. This is the approach used in the study.

  12. Human Systems Integration Model Analyses in Support of the Joint Service Transportable Decontamination System - Small-Scale Increment I Acquisition Program

    DTIC Science & Technology

    2011-02-01

    4.3.2 Heat Stress Model Technical Bulletin ( TB ) MED 507 (12) describes maximal exposure limits for wet bulb globe temperatures without impairing mental...preventive measures to reduce heat stress factors, as described in TB MED 507 (12), ARL-MR-346 (8), or FM 3-11.5 (5), is required to preclude serious...and Heat Casualty Management; TB MED 507; Headquarters, Washington, DC, 2003. 34 13. U.S. Department of the Army. Health Hazard Assessment Report

  13. Simulations of diffusion-reaction equations with implications to turbulent combustion modeling

    NASA Technical Reports Server (NTRS)

    Girimaji, Sharath S.

    1993-01-01

    An enhanced diffusion-reaction reaction system (DRS) is proposed as a statistical model for the evolution of multiple scalars undergoing mixing and reaction in an isotropic turbulence field. The DRS model is close enough to the scalar equations in a reacting flow that other statistical models of turbulent mixing that decouple the velocity field from scalar mixing and reaction (e.g. mapping closure model, assumed-pdf models) cannot distinguish the model equations from the original equations. Numerical simulations of DRS are performed for three scalars evolving from non-premixed initial conditions. A simple one-step reversible reaction is considered. The data from the simulations are used (1) to study the effect of chemical conversion on the evolution of scalar statistics, and (2) to evaluate other models (mapping-closure model, assumed multivariate beta-pdf model).

  14. Data assimilation in a coupled physical-biogeochemical model of the California current system using an incremental lognormal 4-dimensional variational approach: Part 3-Assimilation in a realistic context using satellite and in situ observations

    NASA Astrophysics Data System (ADS)

    Song, Hajoon; Edwards, Christopher A.; Moore, Andrew M.; Fiechter, Jerome

    2016-10-01

    A fully coupled physical and biogeochemical ocean data assimilation system is tested in a realistic configuration of the California Current System using the Regional Ocean Modeling System. In situ measurements for sea surface temperature and salinity as well as satellite observations for temperature, sea level and chlorophyll are used for the year 2000. Initial conditions of the combined physical and biogeochemical state are adjusted at the start of each 3-day assimilation cycle. Data assimilation results in substantial reduction of root-mean-square error (RMSE) over unconstrained model output. RMSE for physical variables is slightly lower when assimilating only physical variables than when assimilating both physical variables and surface chlorophyll. Surface chlorophyll RMSE is lowest when assimilating both physical variables and surface chlorophyll. Estimates of subsurface, nitrate and chlorophyll show modest improvements over the unconstrained model run relative to independent, unassimilated in situ data. Assimilation adjustments to the biogeochemical initial conditions are investigated within different regions of the California Current System. The incremental, lognormal 4-dimensional data assimilation method tested here represents a viable approach to coupled physical biogeochemical state estimation at practical computational cost.

  15. Ares I Reaction Control System Propellant Feedline Decontamination Modeling

    NASA Technical Reports Server (NTRS)

    Pasch, James J.

    2010-01-01

    The objective of the work presented here is to quantify the effects of purge gas temperature, pressure, and mass flow rate on Hydrazine (Hz) decontamination rates of the Ares I Roll Control System and Reaction Control System. A survey of experts in this field revealed the absence of any decontamination rate prediction models. Three basic decontamination methods were identified for analysis and modeling. These include low pressure eduction, high flow rate purge, and pulse purge. For each method, an approach to predict the Hz mass transfer rate, as a function of system pressure, temperature, and purge gas mass flow rate, is developed based on the applicable physics. The models show that low pressure eduction is two orders of magnitude more effective than the high velocity purge, which in turn is two orders of magnitude more effective than the pure diffusion component of pulse purging of deadheads. Eduction subjects the system to low pressure conditions that promote the extraction of Hz vapors. At 120 F, Hz is saturated at approximately 1 psia. At lower pressures and 120 F, Hz will boil, which is an extremely efficient means to remove liquid Hz. The Hz boiling rate is predicted by equating the rate at which energy is added to the saturated liquid Hz through heaters at the tube outer wall with the energy removed from the liquid through evaporation. Boil-off fluxes were predicted by iterating through the range of local pressures with limits set by the minimum allowed pressure of 0.2 psia and maximum allowed wall temperature of 120 F established by the heaters, which gives a saturation pressure of approximately 1.0 psia. Figure 1 shows the resulting boil-off fluxes as a function of local eduction pressure. As depicted in figure 1, the flux is a strong inverse function of eduction pressure, and that minimizing the eduction pressure maximizes the boil-off flux. Also, higher outer wall temperatures lead to higher boil-off fluxes and allow for boil-off over a greater range

  16. Modeling Scalable Pattern Generation in DNA Reaction Networks

    PubMed Central

    Allen, Peter B.; Chen, Xi; Simpson, Zack B.; Ellington, Andrew D.

    2013-01-01

    We have developed a theoretical framework for developing patterns in multiple dimensions using controllable diffusion and designed reactions implemented in DNA. This includes so-called strand displacement reactions in which one single-stranded DNA hybridizes to a hemi-duplex DNA and displaces another single-stranded DNA, reversibly or irreversibly. These reactions can be designed to proceed with designed rate and molecular specificity. By also controlling diffusion by partial complementarity to a stationary, cross-linked DNA, we can generate predictable patterns. We demonstrate this with several simulations showing deterministic, predictable shapes in space. PMID:25506295

  17. Transport Properties of a Kinetic Model for Chemical Reactions without Barriers

    SciTech Connect

    Alves, Giselle M.; Kremer, Gilberto M.; Soares, Ana Jacinta

    2011-05-20

    A kinetic model of the Boltzmann equation for chemical reactions without energy barrier is considered here with the aim of evaluating the reaction rate and characterizing the transport coefficient of shear viscosity for the reactive system. The Chapman-Enskog solution of the Boltzmann equation is used to compute the chemical reaction effects, in a flow regime for which the reaction process is close to the final equilibrium state. Some numerical results are provided illustrating that the considered chemical reaction without energy barrier can induce an appreciable influence on the reaction rate and on the transport coefficient of shear viscosity.

  18. Modeling Adsorption and Reactions of Organic Molecules at Metal Surfaces

    PubMed Central

    2014-01-01

    Conspectus The understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid inorganic/organic systems (HIOS) are relevant for many applications in catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. Obviously, the predictive modeling and understanding of the structure and stability of such hybrid systems is an essential prerequisite for tuning their electronic properties and functions. At present, density-functional theory (DFT) is the most promising approach to study the structure, stability, and electronic properties of complex systems, because it can be applied to both molecules and solids comprising thousands of atoms. However, state-of-the-art approximations to DFT do not provide a consistent and reliable description for HIOS, which is largely due to two issues: (i) the self-interaction of the electrons with themselves arising from the Hartree term of the total energy that is not fully compensated in approximate exchange-correlation functionals, and (ii) the lack of long-range part of the ubiquitous van der Waals (vdW) interactions. The self-interaction errors sometimes lead to incorrect description of charge transfer and electronic level alignment in HIOS, although for molecules adsorbed on metals these effects will often cancel out in total energy differences. Regarding vdW interactions, several promising vdW-inclusive DFT-based methods have been recently demonstrated to yield remarkable accuracy for intermolecular interactions in the gas phase. However, the majority of these approaches neglect the nonlocal collective electron response in the vdW energy tail, an effect that is particularly strong in condensed phases and at interfaces between different materials. Here we show that the recently developed DFT+vdWsurf method that accurately accounts for the collective electronic

  19. Modeling adsorption and reactions of organic molecules at metal surfaces.

    PubMed

    Liu, Wei; Tkatchenko, Alexandre; Scheffler, Matthias

    2014-11-18

    CONSPECTUS: The understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid inorganic/organic systems (HIOS) are relevant for many applications in catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. Obviously, the predictive modeling and understanding of the structure and stability of such hybrid systems is an essential prerequisite for tuning their electronic properties and functions. At present, density-functional theory (DFT) is the most promising approach to study the structure, stability, and electronic properties of complex systems, because it can be applied to both molecules and solids comprising thousands of atoms. However, state-of-the-art approximations to DFT do not provide a consistent and reliable description for HIOS, which is largely due to two issues: (i) the self-interaction of the electrons with themselves arising from the Hartree term of the total energy that is not fully compensated in approximate exchange-correlation functionals, and (ii) the lack of long-range part of the ubiquitous van der Waals (vdW) interactions. The self-interaction errors sometimes lead to incorrect description of charge transfer and electronic level alignment in HIOS, although for molecules adsorbed on metals these effects will often cancel out in total energy differences. Regarding vdW interactions, several promising vdW-inclusive DFT-based methods have been recently demonstrated to yield remarkable accuracy for intermolecular interactions in the gas phase. However, the majority of these approaches neglect the nonlocal collective electron response in the vdW energy tail, an effect that is particularly strong in condensed phases and at interfaces between different materials. Here we show that the recently developed DFT+vdW(surf) method that accurately accounts for the collective electronic

  20. Processes of incremental message planning during conversation.

    PubMed

    Brown-Schmidt, Sarah; Konopka, Agnieszka E

    2015-06-01

    Speaking begins with the formulation of an intended preverbal message and linguistic encoding of this information. The transition from thought to speech occurs incrementally, with cascading planning at subsequent levels of production. In this article, we aim to specify the mechanisms that support incremental message preparation. We contrast two hypotheses about the mechanisms responsible for incorporating message-level information into a linguistic plan. According to the Initial Preparation view, messages can be encoded as fluent utterances if all information is ready before speaking begins. By contrast, on the Continuous Incrementality view, messages can be continually prepared and updated throughout the production process, allowing for fluent production even if new information is added to the message while speaking is underway. Testing these hypotheses, eye-tracked speakers in two experiments produced unscripted, conjoined noun phrases with modifiers. Both experiments showed that new message elements can be incrementally incorporated into the utterance even after articulation begins, consistent with a Continuous Incrementality view of message planning, in which messages percolate to linguistic encoding immediately as that information becomes available in the mind of the speaker. We conclude by discussing the functional role of incremental message planning in conversational speech and the situations in which this continuous incremental planning would be most likely to be observed.

  1. Empirical valence bond model of an SN2 reaction in polar and nonpolar solvents

    NASA Astrophysics Data System (ADS)

    Benjamin, Ilan

    2008-08-01

    A new model for the substitution nucleophilic reaction (SN2) in solution is described using the empirical valence bond (EVB) method. The model includes a generalization to three dimensions of a collinear gas phase EVB model developed by Mathis et al. [J. Mol. Liq. 61, 81 (1994)] and a parametrization of solute-solvent interactions of four different solvents (water, ethanol, chloroform, and carbon tetrachloride). The model is used to compute (in these four solvents) reaction free energy profiles, reaction and solvent dynamics, a two-dimensional reaction/solvent free energy map, as well as a number of other properties that in the past have mostly been estimated.

  2. A general paradigm to model reaction-based biogeochemical processes in batch systems

    NASA Astrophysics Data System (ADS)

    Fang, Yilin; Yeh, Gour-Tsyh; Burgos, William D.

    2003-04-01

    This paper presents the development and illustration of a numerical model of reaction-based geochemical and biochemical processes with mixed equilibrium and kinetic reactions. The objective is to provide a general paradigm for modeling reactive chemicals in batch systems, with expectations that it is applicable to reactive chemical transport problems. The unique aspects of the paradigm are to simultaneously (1) facilitate the segregation (isolation) of linearly independent kinetic reactions and thus enable the formulation and parameterization of individual rates one reaction by one reaction when linearly dependent kinetic reactions are absent, (2) enable the inclusion of virtually any type of equilibrium expressions and kinetic rates users want to specify, (3) reduce problem stiffness by eliminating all fast reactions from the set of ordinary differential equations governing the evolution of kinetic variables, (4) perform systematic operations to remove redundant fast reactions and irrelevant kinetic reactions, (5) systematically define chemical components and explicitly enforce mass conservation, (6) accomplish automation in decoupling fast reactions from slow reactions, and (7) increase the robustness of numerical integration of the governing equations with species switching schemes. None of the existing models to our knowledge has included these scopes simultaneously. This model (BIOGEOCHEM) is a general computer code to simulate biogeochemical processes in batch systems from a reaction-based mechanistic standpoint, and is designed to be easily coupled with transport models. To make the model applicable to a wide range of problems, programmed reaction types include aqueous complexation, adsorption-desorption, ion-exchange, oxidation-reduction, precipitation-dissolution, acid-base reactions, and microbial mediated reactions. In addition, user-specified reaction types can be programmed into the model. Any reaction can be treated as fast/equilibrium or slow

  3. Chemical reaction networks as a model to describe UVC- and radiolytically-induced reactions of simple compounds.

    PubMed

    Dondi, Daniele; Merli, Daniele; Albini, Angelo; Zeffiro, Alberto; Serpone, Nick

    2012-05-01

    When a chemical system is submitted to high energy sources (UV, ionizing radiation, plasma sparks, etc.), as is expected to be the case of prebiotic chemistry studies, a plethora of reactive intermediates could form. If oxygen is present in excess, carbon dioxide and water are the major products. More interesting is the case of reducing conditions where synthetic pathways are also possible. This article examines the theoretical modeling of such systems with random-generated chemical networks. Four types of random-generated chemical networks were considered that originated from a combination of two connection topologies (viz., Poisson and scale-free) with reversible and irreversible chemical reactions. The results were analyzed taking into account the number of the most abundant products required for reaching 50% of the total number of moles of compounds at equilibrium, as this may be related to an actual problem of complex mixture analysis. The model accounts for multi-component reaction systems with no a priori knowledge of reacting species and the intermediates involved if system components are sufficiently interconnected. The approach taken is relevant to an earlier study on reactions that may have occurred in prebiotic systems where only a few compounds were detected. A validation of the model was attained on the basis of results of UVC and radiolytic reactions of prebiotic mixtures of low molecular weight compounds likely present on the primeval Earth.

  4. Incremental Discriminant Analysis in Tensor Space

    PubMed Central

    Chang, Liu; Weidong, Zhao; Tao, Yan; Qiang, Pu; Xiaodan, Du

    2015-01-01

    To study incremental machine learning in tensor space, this paper proposes incremental tensor discriminant analysis. The algorithm employs tensor representation to carry on discriminant analysis and combine incremental learning to alleviate the computational cost. This paper proves that the algorithm can be unified into the graph framework theoretically and analyzes the time and space complexity in detail. The experiments on facial image detection have shown that the algorithm not only achieves sound performance compared with other algorithms, but also reduces the computational issues apparently. PMID:26339229

  5. A variable reaction rate model for chlorine decay in drinking water due to the reaction with dissolved organic matter.

    PubMed

    Hua, Pei; Vasyukova, Ekaterina; Uhl, Wolfgang

    2015-05-15

    A second order kinetic model for simulating chlorine decay in bulk water due to the reaction with dissolved organic matter (DOM) was developed. It takes into account the decreasing reactivity of dissolved organic matter using a variable reaction rate coefficient (VRRC) which decreases with an increasing conversion. The concentration of reducing species is surrogated by the maximum chlorine demand. Temperature dependency, respectively, is described by the Arrhenius-relationship. The accuracy and adequacy of the proposed model to describe chlorine decay in bulk water were evaluated and shown for very different waters and different conditions such as water mixing or rechlorination by applying statistical tests. It is thus very well suited for application in water quality modeling for distribution systems.

  6. Comparison of the Incremental Validity of the Old and New MCAT.

    ERIC Educational Resources Information Center

    Wolf, Fredric M.; And Others

    The predictive and incremental validity of both the Old and New Medical College Admission Test (MCAT) was examined and compared with a sample of over 300 medical students. Results of zero order and incremental validity coefficients, as well as prediction models resulting from all possible subsets regression analyses using Mallow's Cp criterion,…

  7. Reaction cross sections for two direct simulation Monte Carlo models: Accuracy and sensitivity analysis

    NASA Astrophysics Data System (ADS)

    Wysong, Ingrid; Gimelshein, Sergey; Gimelshein, Natalia; McKeon, William; Esposito, Fabrizio

    2012-04-01

    The quantum kinetic chemical reaction model proposed by Bird for the direct simulation Monte Carlo method is based on collision kinetics with no assumed Arrhenius-related parameters. It demonstrates an excellent agreement with the best estimates for thermal reaction rates coefficients and with two-temperature nonequilibrium rate coefficients for high-temperature air reactions. This paper investigates this model further, concentrating on the non-thermal reaction cross sections as a function of collision energy, and compares its predictions with those of the earlier total collision energy model, also by Bird, as well as with available quasi-classical trajectory cross section predictions (this paper also publishes for the first time a table of these computed reaction cross sections). A rarefied hypersonic flow over a cylinder is used to examine the sensitivity of the number of exchange reactions to the differences in the two models under a strongly nonequilibrium velocity distribution.

  8. Separate and combined effects of gabapentin and [INCREMENT]9-tetrahydrocannabinol in humans discriminating [INCREMENT]9-tetrahydrocannabinol.

    PubMed

    Lile, Joshua A; Wesley, Michael J; Kelly, Thomas H; Hays, Lon R

    2016-04-01

    The aim of the present study was to examine a potential mechanism of action of gabapentin to manage cannabis-use disorders by determining the interoceptive effects of gabapentin in cannabis users discriminating [INCREMENT]-tetrahydrocannabinol ([INCREMENT]-THC) using a pharmacologically selective drug-discrimination procedure. Eight cannabis users learned to discriminate 30 mg oral [INCREMENT]-THC from placebo and then received gabapentin (600 and 1200 mg), [INCREMENT]-THC (5, 15, and 30 mg), and placebo alone and in combination. Self-report, task performance, and physiological measures were also collected. [INCREMENT]-THC served as a discriminative stimulus, produced positive subjective effects, elevated heart rate, and impaired psychomotor performance. Both doses of gabapentin substituted for the [INCREMENT]-THC discriminative stimulus and engendered subjective and performance-impairing effects that overlapped with those of [INCREMENT]-THC when administered alone. When administered concurrently, gabapentin shifted the discriminative-stimulus effects of [INCREMENT]-THC leftward/upward, and combinations of [INCREMENT]-THC and gabapentin generally produced larger effects on cannabinoid-sensitive outcomes relative to [INCREMENT]-THC alone. These results suggest that one mechanism by which gabapentin might facilitate cannabis abstinence is by producing effects that overlap with those of cannabinoids.

  9. Mathematical model of reaction rate oscillations on a chain of nm-sized catalyst particles

    NASA Astrophysics Data System (ADS)

    Peskov, N. V.; Slinko, M. M.; Jaeger, N. I.

    2003-05-01

    The model of reaction rate oscillations over the surface of nanoparticles embedded into zeolite matrix is numerically investigated. The reaction rate oscillations on each particle are described by a lumped model. The reactions on separate particles interact via the gas diffusion through the pores, which is modeled in the frame of the Maxwell-Stefan approach. The reaction reveals a complex dynamical behavior if a nonhomogeneous distribution of reagent concentrations exists along the chain of particles with a sufficiently large gradient near the ends of the chain.

  10. MELTING OF GLASS BATCH: MODEL FOR MULTIPLE OVERLAPPING GAS-EVOLVING REACTIONS

    SciTech Connect

    Pokorny, Richard; Pierce, David A.; Hrma, Pavel R.

    2012-08-10

    In this study, we present a model for the kinetics of multiple overlapping reactions. Mathematical representation of the kinetics of gas-evolving reactions is crucial for the modeling of the feed-to-glass conversion in a waste-glass melter. The model simulates multiple gas-evolving reactions that occur during heating of a high-alumina high-level waste melter feed. To obtain satisfactory kinetic parameters, we employed Kissinger's method combined with least-squares analysis. The power-law kinetics with variable reaction order sufficed for obtaining excellent agreement with measured thermogravimetric analysis data.

  11. MELTING OF GLASS BATCH - MODEL FOR MULTIPLE OVERLAPPING GAS-EVOLVING REACTIONS

    SciTech Connect

    KRUGER AA; PIERCE DA; POKORNY R; HRMA PR

    2012-02-07

    In this study, we present a model for the kinetics of multiple overlapping reactions. Mathematical representation of the kinetics of gas-evolving reactions is crucial for the modeling of the feed-to-glass conversion in a waste-glass melter. The model simulates multiple gas-evolving reactions that occur during heating of a high-alumina high-level waste melter feed. To obtain satisfactory kinetic parameters, we employed Kissinger's method combined with least-squares analysis. The power-law kinetics with variable reaction order sufficed for obtaining excellent agreement with measured thermogravimetric analysis data.

  12. External Device to Incrementally Skid the Habitat (E-DISH)

    NASA Technical Reports Server (NTRS)

    Brazell, J. W.; Introne, Steve; Bedell, Lisa; Credle, Ben; Holp, Graham; Ly, Siao; Tait, Terry

    1994-01-01

    A Mars habitat transport system was designed as part of the NASA Mars exploration program. The transport system, the External Device to Incrementally Skid the Habitat (E - DISH), will be used to transport Mars habitats from their landing sites to the colony base and will be detached after unloading. The system requirements for Mars were calculated and scaled for model purposes. Specific model materials are commonly found and recommendations for materials for the Mars design are included.

  13. Modeled Neutron Induced Nuclear Reaction Cross Sections for Radiochemistry in the region of Iriduim and Gold

    SciTech Connect

    Hoffman, R D; Dietrich, F S; Kelley, K; Escher, J; Bauer, R; Mustafa, M

    2008-02-26

    We have developed a set of modeled nuclear reaction cross sections for use in radiochemical diagnostics. Systematics for the input parameters required by the Hauser-Feshbach statistical model were developed and used to calculate neutron induced nuclear reaction cross sections for targets ranging from osmium (Z = 76) to gold (Z = 79). Of particular interest are the cross sections on Ir and Au including reactions on isomeric targets.

  14. Large Deviations for Processes with Independent Increments.

    DTIC Science & Technology

    1984-10-01

    generating function of the increments exists and thus the sample paths of such stochastic processes lie in the space of functions of bounded variation . The...BV[O,1], the space of functions of bounded variation and the topology is that of weak*-convergence. Varadhan (1966) studied the LDP for similar...increments and no Gaussian component which are considered as elements of BV[0,1], the space of functions of bounded variation . The final section

  15. A Joint Modeling Approach for Reaction Time and Accuracy in Psycholinguistic Experiments

    ERIC Educational Resources Information Center

    Loeys, T.; Rosseel, Y.; Baten, K.

    2011-01-01

    In the psycholinguistic literature, reaction times and accuracy can be analyzed separately using mixed (logistic) effects models with crossed random effects for item and subject. Given the potential correlation between these two outcomes, a joint model for the reaction time and accuracy may provide further insight. In this paper, a Bayesian…

  16. Folding model description of reactions with exotic nuclei

    SciTech Connect

    Ibraheem, Awad A.; Hassanain, M. A.; Mokhtar, S. R.; Zaki, M. A.; Mahmoud, Zakaria M. M.; Farid, M. El-Azab

    2012-08-15

    Microscopic folding calculations based upon the effective M3Y nucleon-nucleon interaction and the nuclearmatter densities of the interacting nuclei have been carried out to explain recently measured experimental data of the {sup 6}He+{sup 120}Sn elastic scattering cross section at four different laboratory energies near the Coulomb barrier. The extracted reaction cross sections are also considered.

  17. Geometrical Models of the Phase Space Structures Governing Reaction Dynamics

    DTIC Science & Technology

    2009-08-01

    s.wiggins@bristol.ac.uk Abstract Hamiltonian dynamical systems possessing equilibria of saddle × centre × · · · × centre stability type display...definition of the phase space structures in the normal form coordinates . . . . . . . . 6 2.3 The foliation of the reaction region by Lagrangian ...McGehee representation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 3.4 Implications for Nonlinear Hamiltonian Vector Fields

  18. A Comparative Study of Failure with Incremental Forming

    NASA Astrophysics Data System (ADS)

    Wu, S. H.; Song, N. N.; Pires, F. M. Andrade

    2016-08-01

    Incremental forming (ISF) is an innovative flexible sheet metal forming process which can be used to manufacture complex shapes from various materials. Due to its flexibility, it has attracted more and more attention over recent decades. Localized deformation and shear through the thickness are essential characteristics of ISF. These lead to specific failure modes and formability of ISF that are different from the conventional stamping process. In this contribution, three continuum damage models (Lemaitre, Gurson, extended GTN models) are formulated and fully coupled with the finite element simulation in a commercial software ABAQUS to predict failure in incremental forming. A comparative investigation of these three damage models has been carried out to analyze both the deformation behavior and failure mechanisms.

  19. Model Adherend Surface Effects on Epoxy Cure Reactions

    DTIC Science & Technology

    1990-11-01

    of X-ray photoelectro spectroscopy and reflection absorption infrarcd spectroscopy. They concluded that the catalytic action of the acidic hydroxyl...that an acidic carbon surface (produced by oxidation) resulted in selective amine adsorption and the catalytic acceleration of its reaction with the...subject of this report. EXPERIMENTAL The epoxy resins used in this study consisted of Epon 826, a diglycidyl ether of bisphenol A ( DGEBA ) resin (Shell

  20. A C library for retrieving specific reactions from the BioModels database

    PubMed Central

    Neal, M. L.; Galdzicki, M.; Gallimore, J. T.; Sauro, H. M.

    2014-01-01

    Summary: We describe libSBMLReactionFinder, a C library for retrieving specific biochemical reactions from the curated systems biology markup language models contained in the BioModels database. The library leverages semantic annotations in the database to associate reactions with human-readable descriptions, making the reactions retrievable through simple string searches. Our goal is to provide a useful tool for quantitative modelers who seek to accelerate modeling efforts through the reuse of previously published representations of specific chemical reactions. Availability and implementation: The library is open-source and dual licensed under the Mozilla Public License Version 2.0 and GNU General Public License Version 2.0. Project source code, downloads and documentation are available at http://code.google.com/p/lib-sbml-reaction-finder. Contact: mneal@uw.edu PMID:24078714

  1. Comparison of DSMC Reaction Models with QCT Reaction Rates for Nitrogen

    DTIC Science & Technology

    2016-07-17

    5e. TASK NUMBER 5f. WORK UNIT NUMBER Q1MK 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NO. Air ...ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM(S) Air Force Research Laboratory (AFMC) AFRL/RQR 11. SPONSOR/MONITOR’S REPORT 5 Pollux Drive NUMBER...simplified microscopic models and connect them to macroscopic counterparts • This work is first step: use recent high quality QCT calculations for

  2. SurfKin: an ab initio kinetic code for modeling surface reactions.

    PubMed

    Le, Thong Nguyen-Minh; Liu, Bin; Huynh, Lam K

    2014-10-05

    In this article, we describe a C/C++ program called SurfKin (Surface Kinetics) to construct microkinetic mechanisms for modeling gas-surface reactions. Thermodynamic properties of reaction species are estimated based on density functional theory calculations and statistical mechanics. Rate constants for elementary steps (including adsorption, desorption, and chemical reactions on surfaces) are calculated using the classical collision theory and transition state theory. Methane decomposition and water-gas shift reaction on Ni(111) surface were chosen as test cases to validate the code implementations. The good agreement with literature data suggests this is a powerful tool to facilitate the analysis of complex reactions on surfaces, and thus it helps to effectively construct detailed microkinetic mechanisms for such surface reactions. SurfKin also opens a possibility for designing nanoscale model catalysts.

  3. Generalized Holstein model for spin-dependent electron-transfer reactions

    NASA Astrophysics Data System (ADS)

    Yang, Li-Ping; Ai, Qing; Sun, C. P.

    2012-03-01

    Some chemical reactions are described by electron transfer (ET) processes. The underlying mechanism could be modeled as a polaron motion in the molecular crystal—the Holstein model. By taking spin degrees of freedom into consideration, we generalize the Holstein model (molecular crystal model) to microscopically describe an ET chemical reaction. In our model, the electron spins in the radical pair simultaneously interact with a magnetic field and their nuclear-spin environments. By virtue of the perturbation approach, we obtain the chemical reaction rates for different initial states. It is discovered that the chemical reaction rate of the triplet state demonstrates its dependence on the direction of the magnetic field while the counterpart of the singlet state does not. This difference is attributed to the explicit dependence of the triplet state on the direction when the axis is rotated. Our model may provide a possible candidate for the microscopic origin of the avian compass.

  4. Reactions of Trimethylaluminium: Modelling the Chemical Degradation of Synthetic Lubricants.

    PubMed

    Slaughter, Jonathan; Peel, Andrew J; Wheatley, Andrew E H

    2017-01-01

    In investigating and seeking to mimic the reactivity of trimethylaluminium (TMA) with synthetic, ester-based lubricating oils, the reaction of methyl propionate 1 was explored with 1, 2 and 3 equivalents of the organoaluminium reagent. Spectroscopic analysis points to the formation of the adduct 1(TMA) accompanied only by the low level 1:1 production of Me2 AlOCEtMe2 2 and Me2 AlOMe 3 when an equimolar amount of TMA is applied. The deployment of excess TMA favours reaction to give 2 and 3 over 1(TMA) adduct formation and spectroscopy reveals that in hydrocarbon solution substitution product 2 traps unreacted TMA to yield 2(TMA). The (1) H NMR spectroscopic observation of two Al-Me signals not attributable to free TMA and in the ratio 1:4 suggests the formation of a previously only postulated, symmetrical metallacycle in Me4 Al2 (μ(2) -Me)(μ(2) -OCEtMe2 ). In the presence of 3, 2(TMA) undergoes thermally induced exchange to yield Me4 Al2 (μ(2) -OMe)(μ(2) -OCEtMe2 ) 4 and TMA. The reaction of methyl phenylacetate 5 with TMA allows isolation of the crystalline product Me2 AlOCBnMe2 (TMA) 6(TMA), which allows the first observation of the Me4 Al2 (μ(2) -Me)(μ(2) -OR) motif in the solid state. Distances of 2.133(3) Å (Al-Mebridging ) and 1.951 Å (mean Al-Meterminal ) are recorded. The abstraction of TMA from 6(TMA) by the introduction of Et2 O has yielded 6, which exists as a dimer.

  5. Observers for Systems with Nonlinearities Satisfying an Incremental Quadratic Inequality

    NASA Technical Reports Server (NTRS)

    Acikmese, Ahmet Behcet; Corless, Martin

    2004-01-01

    We consider the problem of state estimation for nonlinear time-varying systems whose nonlinearities satisfy an incremental quadratic inequality. These observer results unifies earlier results in the literature; and extend it to some additional classes of nonlinearities. Observers are presented which guarantee that the state estimation error exponentially converges to zero. Observer design involves solving linear matrix inequalities for the observer gain matrices. Results are illustrated by application to a simple model of an underwater.

  6. Effects of spatial and temporal noise on a cubic-autocatalytic reaction-diffusion model

    NASA Astrophysics Data System (ADS)

    Gagnon, Jean-Sébastien; Hochberg, David; Pérez-Mercader, Juan

    2017-03-01

    We characterize the influence that external noise, with both spatial and temporal correlations, has on the scale dependence of the reaction parameters of a cubic autocatalytic reaction diffusion (CARD) system. Interpreting the CARD model as a primitive reaction scheme for a living system, the results indicate that power-law correlations in environmental fluctuations can either decrease or increase the rates of nutrient decay and the rate of autocatalysis (replication) on small spatial and temporal scales.

  7. Reaction Cross Sections for Two DSMC Models: Accuracy and Sensitivity Analysis

    DTIC Science & Technology

    2011-11-15

    trajectory (QCT) cross sections for N2+N dissociation and for N2+O endothermic exchange pro- vide a good test case. A DSMC simulation of a simple... endothermic reactions considered here, we have made the common simplifying assumption that Ea is equal to the heat of reaction. However, since some reactions...especially exothermic ones) have a non- negligible energy barrier, the QK model (like all others) in these cases would have to use an adjustable input

  8. Development and evaluation of a high-resolution reanalysis of the East Australian Current region using the Regional Ocean Modelling System (ROMS 3.4) and Incremental Strong-Constraint 4-Dimensional Variational (IS4D-Var) data assimilation

    NASA Astrophysics Data System (ADS)

    Kerry, Colette; Powell, Brian; Roughan, Moninya; Oke, Peter

    2016-10-01

    As with other Western Boundary Currents globally, the East Australian Current (EAC) is highly variable making it a challenge to model and predict. For the EAC region, we combine a high-resolution state-of-the-art numerical ocean model with a variety of traditional and newly available observations using an advanced variational data assimilation scheme. The numerical model is configured using the Regional Ocean Modelling System (ROMS 3.4) and takes boundary forcing from the BlueLink ReANalysis (BRAN3). For the data assimilation, we use an Incremental Strong-Constraint 4-Dimensional Variational (IS4D-Var) scheme, which uses the model dynamics to perturb the initial conditions, atmospheric forcing, and boundary conditions, such that the modelled ocean state better fits and is in balance with the observations. This paper describes the data assimilative model configuration that achieves a significant reduction of the difference between the modelled solution and the observations to give a dynamically consistent "best estimate" of the ocean state over a 2-year period. The reanalysis is shown to represent both assimilated and non-assimilated observations well. It achieves mean spatially averaged root mean squared (rms) residuals with the observations of 7.6 cm for sea surface height (SSH) and 0.4 °C for sea surface temperature (SST) over the assimilation period. The time-mean rms residual for subsurface temperature measured by Argo floats is a maximum of 0.9 °C between water depths of 100 and 300 m and smaller throughout the rest of the water column. Velocities at several offshore and continental shelf moorings are well represented in the reanalysis with complex correlations between 0.8 and 1 for all observations in the upper 500 m. Surface radial velocities from a high-frequency radar array are assimilated and the reanalysis provides surface velocity estimates with complex correlations with observed velocities of 0.8-1 across the radar footprint. A comparison with

  9. PhreeqcRM: A reaction module for transport simulators based on the geochemical model PHREEQC

    NASA Astrophysics Data System (ADS)

    Parkhurst, David L.; Wissmeier, Laurin

    2015-09-01

    PhreeqcRM is a geochemical reaction module designed specifically to perform equilibrium and kinetic reaction calculations for reactive transport simulators that use an operator-splitting approach. The basic function of the reaction module is to take component concentrations from the model cells of the transport simulator, run geochemical reactions, and return updated component concentrations to the transport simulator. If multicomponent diffusion is modeled (e.g., Nernst-Planck equation), then aqueous species concentrations can be used instead of component concentrations. The reaction capabilities are a complete implementation of the reaction capabilities of PHREEQC. In each cell, the reaction module maintains the composition of all of the reactants, which may include minerals, exchangers, surface complexers, gas phases, solid solutions, and user-defined kinetic reactants. PhreeqcRM assigns initial and boundary conditions for model cells based on standard PHREEQC input definitions (files or strings) of chemical compositions of solutions and reactants. Additional PhreeqcRM capabilities include methods to eliminate reaction calculations for inactive parts of a model domain, transfer concentrations and other model properties, and retrieve selected results. The module demonstrates good scalability for parallel processing by using multiprocessing with MPI (message passing interface) on distributed memory systems, and limited scalability using multithreading with OpenMP on shared memory systems. PhreeqcRM is written in C++, but interfaces allow methods to be called from C or Fortran. By using the PhreeqcRM reaction module, an existing multicomponent transport simulator can be extended to simulate a wide range of geochemical reactions. Results of the implementation of PhreeqcRM as the reaction engine for transport simulators PHAST and FEFLOW are shown by using an analytical solution and the reactive transport benchmark of MoMaS.

  10. Design and Performance Analysis of Incremental Networked Predictive Control Systems.

    PubMed

    Pang, Zhong-Hua; Liu, Guo-Ping; Zhou, Donghua

    2016-06-01

    This paper is concerned with the design and performance analysis of networked control systems with network-induced delay, packet disorder, and packet dropout. Based on the incremental form of the plant input-output model and an incremental error feedback control strategy, an incremental networked predictive control (INPC) scheme is proposed to actively compensate for the round-trip time delay resulting from the above communication constraints. The output tracking performance and closed-loop stability of the resulting INPC system are considered for two cases: 1) plant-model match case and 2) plant-model mismatch case. For the former case, the INPC system can achieve the same output tracking performance and closed-loop stability as those of the corresponding local control system. For the latter case, a sufficient condition for the stability of the closed-loop INPC system is derived using the switched system theory. Furthermore, for both cases, the INPC system can achieve a zero steady-state output tracking error for step commands. Finally, both numerical simulations and practical experiments on an Internet-based servo motor system illustrate the effectiveness of the proposed method.

  11. A model for lignin alteration - Part I: A kinetic reaction-network model

    USGS Publications Warehouse

    Payne, D.F.; Ortoleva, P.J.

    2001-01-01

    A new quantitative model is presented which simulates the maturation of lignin-derived sedimentary organic matter under geologic conditions. In this model, compositionally specific reactants evolve to specific intermediate and mobile products through balanced, nth order processes, by way of a network of sequential and parallel reactions. The chemical kinetic approach is based primarily on published observed structural transformations of naturally matured, lignin-derived, sedimentary organic matter. Assuming that Upper Cretaceous Williams Fork coal in the Piceance Basin is primarily lignin-derived, the model is calibrated for the Multi-Well Experiment(MWX) Site in this basin. This kind of approach may be applied to other selectively preserved chemical components of sedimentary organic matter. ?? 2001 Elsevier Science Ltd. All rights reserved.

  12. Modeling reaction and transport of multiple species in water distribution systems.

    PubMed

    Shang, Feng; Uber, James G; Rossman, Lewis A

    2008-02-01

    A general framework for modeling the reaction and transport of multiple, interacting chemical species in drinking water distribution systems is developed. It accommodates reactions between constituents in both the bulk flow (through pipes and storage tanks) and those attached to pipe walls. The framework has been implemented as an extension to the well-known EPANET programmer's toolkit (a library of functions that simulates hydraulic behavior and water quality transport in pipe networks). The implementation allows modelers to define the particular species of interest and their chemical equilibrium and reaction rate equations in a natural fashion using standard functional notation. It also employs several different numerical methods, including a stiff differential equation solver, to solve the reaction/equilibrium system throughout the pipe network using the standard EPANET transport algorithm. The flexibility and power of the framework is demonstrated with two examples that model water quality dynamics governed by different reaction/equilibrium systems.

  13. Computational study of a model system of enzyme-mediated [4+2] cycloaddition reaction.

    PubMed

    Gordeev, Evgeniy G; Ananikov, Valentine P

    2015-01-01

    A possible mechanistic pathway related to an enzyme-catalyzed [4+2] cycloaddition reaction was studied by theoretical calculations at density functional (B3LYP, O3LYP, M062X) and semiempirical levels (PM6-DH2, PM6) performed on a model system. The calculations were carried out for the key [4+2] cycloaddition step considering enzyme-catalyzed biosynthesis of Spinosyn A in a model reaction, where a reliable example of a biological Diels-Alder reaction was reported experimentally. In the present study it was demonstrated that the [4+2] cycloaddition reaction may benefit from moving along the energetically balanced reaction coordinate, which enabled the catalytic rate enhancement of the [4+2] cycloaddition pathway involving a single transition state. Modeling of such a system with coordination of three amino acids indicated a reliable decrease of activation energy by ~18.0 kcal/mol as compared to a non-catalytic transformation.

  14. The spatiotemporal master equation: Approximation of reaction-diffusion dynamics via Markov state modeling

    NASA Astrophysics Data System (ADS)

    Winkelmann, Stefanie; Schütte, Christof

    2016-12-01

    Accurate modeling and numerical simulation of reaction kinetics is a topic of steady interest. We consider the spatiotemporal chemical master equation (ST-CME) as a model for stochastic reaction-diffusion systems that exhibit properties of metastability. The space of motion is decomposed into metastable compartments, and diffusive motion is approximated by jumps between these compartments. Treating these jumps as first-order reactions, simulation of the resulting stochastic system is possible by the Gillespie method. We present the theory of Markov state models as a theoretical foundation of this intuitive approach. By means of Markov state modeling, both the number and shape of compartments and the transition rates between them can be determined. We consider the ST-CME for two reaction-diffusion systems and compare it to more detailed models. Moreover, a rigorous formal justification of the ST-CME by Galerkin projection methods is presented.

  15. Modeling Reaction Time and Accuracy of Multiple-Alternative Decisions

    PubMed Central

    Leite, Fábio P.; Ratcliff, Roger

    2009-01-01

    Several sequential sampling models using racing diffusion processes for multiple-alternative decisions were evaluated using data from two perceptual discrimination experiments. The structures of the models differed on a number of dimensions, including whether there was lateral inhibition between accumulators, whether there was decay in evidence, whether evidence could be negative, and whether there was variability in starting points. Data were collected from a letter discrimination task in which stimulus difficulty and probability of the response alternatives were varied along with number of response alternatives. Model fitting results ruled out a large number of model classes in favor of a smaller number of specific models, most of which showed a moderate to high degree of mimicking. The best-fitting models had zero to moderate values of decay, no inhibition, and assumed that the addition of alternatives either affected the subprocesses contributing to the nondecisional time, the degree of caution, or the quality of evidence extracted from stimuli. PMID:20045893

  16. Importance of cytochromes in cyclization reactions: quantum chemical study on a model reaction of proguanil to cycloguanil.

    PubMed

    Arfeen, Minhajul; Patel, Dhilon S; Abbat, Sheenu; Taxak, Nikhil; Bharatam, Prasad V

    2014-10-30

    Proguanil, an anti-malarial prodrug, undergoes cytochrome P450 catalyzed biotransformation to the pharmacologically active triazine metabolite (cycloguanil), which inhibits plasmodial dihydrofolate reductase. This cyclization is catalyzed by CYP2C19 and many anti-malarial lead compounds are being designed and synthesized to exploit this pathway. Quantum chemical calculations were performed using the model species (Cpd I for active species of cytochrome and N4-isopropyl-N6-methylbiguanide for proguanil) to elucidate the mechanism of the cyclization pathway. The overall reaction involves the loss of a water molecule, and is exothermic by approximately 55 kcal/mol, and involves a barrier of approximately 17 kcal/mol. The plausible reaction pathway involves the initial H-radical abstraction from the isopropyl group by Cpd I, followed by two alternative paths- (i) oxygen rebound to provide hydroxyl derivative and (ii) loss of additional H-radical to yield 1,3,5-triazatriene, which undergoes cyclization. This study helped in understanding the role of the active species of cytochromes in this important cyclization reaction.

  17. Calibration of model constants in a biological reaction model for sewage treatment plants.

    PubMed

    Amano, Ken; Kageyama, Kohji; Watanabe, Shoji; Takemoto, Takeshi

    2002-02-01

    Various biological reaction models have been proposed which estimate concentrations of soluble and insoluble components in effluent of sewage treatment plants. These models should be effective to develop a better operation system and plant design, but their formulas consist of nonlinear equations, and there are many model constants, which are not easy to calibrate. A technique has been proposed to decide the model constants by precise experiments, but it is not practical for design engineers or process operators to perform these experiments regularly. Other approaches which calibrate the model constants by mathematical techniques should be used. In this paper, the optimal regulator method of modern control theory is applied as a mathematical technique to calibrate the model constants. This method is applied in a small sewage treatment testing facility. Calibration of the model constants is examined to decrease the deviations between calculated and measured concentrations. Results show that calculated values of component concentrations approach measured values and the method is useful for actual plants.

  18. Consistent post-reaction vibrational energy redistribution in DSMC simulations using TCE model

    NASA Astrophysics Data System (ADS)

    Borges Sebastião, Israel; Alexeenko, Alina

    2016-10-01

    The direct simulation Monte Carlo (DSMC) method has been widely applied to study shockwaves, hypersonic reentry flows, and other nonequilibrium flow phenomena. Although there is currently active research on high-fidelity models based on ab initio data, the total collision energy (TCE) and Larsen-Borgnakke (LB) models remain the most often used chemistry and relaxation models in DSMC simulations, respectively. The conventional implementation of the discrete LB model, however, may not satisfy detailed balance when recombination and exchange reactions play an important role in the flow energy balance. This issue can become even more critical in reacting mixtures involving polyatomic molecules, such as in combustion. In this work, this important shortcoming is addressed and an empirical approach to consistently specify the post-reaction vibrational states close to thermochemical equilibrium conditions is proposed within the TCE framework. Following Bird's quantum-kinetic (QK) methodology for populating post-reaction states, the new TCE-based approach involves two main steps. The state-specific TCE reaction probabilities for a forward reaction are first pre-computed from equilibrium 0-D simulations. These probabilities are then employed to populate the post-reaction vibrational states of the corresponding reverse reaction. The new approach is illustrated by application to exchange and recombination reactions relevant to H2-O2 combustion processes.

  19. Reactions to Discrimination, Stigmatization, Ostracism, and Other Forms of Interpersonal Rejection: A Multimotive Model

    ERIC Educational Resources Information Center

    Richman, Laura Smart; Leary, Mark R.

    2009-01-01

    This article describes a new model that provides a framework for understanding people's reactions to threats to social acceptance and belonging as they occur in the context of diverse phenomena such as rejection, discrimination, ostracism, betrayal, and stigmatization. People's immediate reactions are quite similar across different forms of…

  20. Stochastic modeling of biochemical systems with multistep reactions using state-dependent time delay

    PubMed Central

    Wu, Qianqian; Tian, Tianhai

    2016-01-01

    To deal with the growing scale of molecular systems, sophisticated modelling techniques have been designed in recent years to reduce the complexity of mathematical models. Among them, a widely used approach is delayed reaction for simplifying multistep reactions. However, recent research results suggest that a delayed reaction with constant time delay is unable to describe multistep reactions accurately. To address this issue, we propose a novel approach using state-dependent time delay to approximate multistep reactions. We first use stochastic simulations to calculate time delay arising from multistep reactions exactly. Then we design algorithms to calculate time delay based on system dynamics precisely. To demonstrate the power of proposed method, two processes of mRNA degradation are used to investigate the function of time delay in determining system dynamics. In addition, a multistep pathway of metabolic synthesis is used to explore the potential of the proposed method to simplify multistep reactions with nonlinear reaction rates. Simulation results suggest that the state-dependent time delay is a promising and accurate approach to reduce model complexity and decrease the number of unknown parameters in the models. PMID:27553753

  1. A mesoscopic reaction rate model for shock initiation of multi-component PBX explosives.

    PubMed

    Liu, Y R; Duan, Z P; Zhang, Z Y; Ou, Z C; Huang, F L

    2016-11-05

    The primary goal of this research is to develop a three-term mesoscopic reaction rate model that consists of a hot-spot ignition, a low-pressure slow burning and a high-pressure fast reaction terms for shock initiation of multi-component Plastic Bonded Explosives (PBX). Thereinto, based on the DZK hot-spot model for a single-component PBX explosive, the hot-spot ignition term as well as its reaction rate is obtained through a "mixing rule" of the explosive components; new expressions for both the low-pressure slow burning term and the high-pressure fast reaction term are also obtained by establishing the relationships between the reaction rate of the multi-component PBX explosive and that of its explosive components, based on the low-pressure slow burning term and the high-pressure fast reaction term of a mesoscopic reaction rate model. Furthermore, for verification, the new reaction rate model is incorporated into the DYNA2D code to simulate numerically the shock initiation process of the PBXC03 and the PBXC10 multi-component PBX explosives, and the numerical results of the pressure histories at different Lagrange locations in explosive are found to be in good agreements with previous experimental data.

  2. Modeling Proton- and Light Ion-Induced Reactions at Low Energies in the MARS15 Code

    SciTech Connect

    Rakhno, I. L.; Mokhov, N. V.; Gudima, K. K.

    2015-04-25

    An implementation of both ALICE code and TENDL evaluated nuclear data library in order to describe nuclear reactions induced by low-energy projectiles in the Monte Carlo code MARS15 is presented. Comparisons between results of modeling and experimental data on reaction cross sections and secondary particle distributions are shown.

  3. Incremental SSVEP analysis for BCI implementation.

    PubMed

    Torres Müller, Sandra Mara; Freire Bastos-Filho, Teodiano; Sarcinelli-Filho, Mário

    2010-01-01

    This work presents an incremental analysis of EEG records containing Steady-State Visual Evoked Potential (SSVEP). This analysis consists of two steps: feature extraction, performed using a statistic test, and classification, performed by a decision tree. The result is a system with high classification rate (a test with six volunteers resulted in an average classification rate of 91.2%), high Information Transfer Rate (ITR) (a test with the same six volunteers resulted in an average value of 100.2 bits/min) and processing time, for each incremental analysis, of approximately 120 ms. These are very good features for an efficient Brain-Computer Interface (BCI) implementation.

  4. Optimization of Maillard Reaction in Model System of Glucosamine and Cysteine Using Response Surface Methodology

    PubMed Central

    Arachchi, Shanika Jeewantha Thewarapperuma; Kim, Ye-Joo; Kim, Dae-Wook; Oh, Sang-Chul; Lee, Yang-Bong

    2017-01-01

    Sulfur-containing amino acids play important roles in good flavor generation in Maillard reaction of non-enzymatic browning, so aqueous model systems of glucosamine and cysteine were studied to investigate the effects of reaction temperature, initial pH, reaction time, and concentration ratio of glucosamine and cysteine. Response surface methodology was applied to optimize the independent reaction parameters of cysteine and glucosamine in Maillard reaction. Box-Behnken factorial design was used with 30 runs of 16 factorial levels, 8 axial levels and 6 central levels. The degree of Maillard reaction was determined by reading absorption at 425 nm in a spectrophotometer and Hunter’s L, a, and b values. ΔE was consequently set as the fifth response factor. In the statistical analyses, determination coefficients (R2) for their absorbance, Hunter’s L, a, b values, and ΔE were 0.94, 0.79, 0.73, 0.96, and 0.79, respectively, showing that the absorbance and Hunter’s b value were good dependent variables for this model system. The optimum processing parameters were determined to yield glucosamine-cysteine Maillard reaction product with higher absorbance and higher colour change. The optimum estimated absorbance was achieved at the condition of initial pH 8.0, 111°C reaction temperature, 2.47 h reaction time, and 1.30 concentration ratio. The optimum condition for colour change measured by Hunter’s b value was 2.41 h reaction time, 114°C reaction temperature, initial pH 8.3, and 1.26 concentration ratio. These results can provide the basic information for Maillard reaction of aqueous model system between glucosamine and cysteine.

  5. Modeling the formation and reactions of benzene metabolites.

    PubMed

    Golding, Bernard T; Barnes, Martine L; Bleasdale, Christine; Henderson, Alistair P; Jiang, Dong; Li, Xin; Mutlu, Esra; Petty, Hannah J; Sadeghi, Majid M

    2010-03-19

    One or more of the muconaldehyde isomers is a putative product of benzene metabolism. As muconaldehydes are highly reactive dienals and potentially mutagenic they might be relevant to the carcinogenicity of benzene. Muconaldehydes may be derived through the action of a cytochrome P450 mono-oxygenase on benzene oxide-oxepin, which are established metabolites of benzene. Oxidation of benzene oxide-oxepin either by the one-electron oxidant cerium(IV) ammonium nitrate (CAN) or by iron(III) tris(1,10-phenanthroline) hexafluorophosphate in acetone at -78 degrees C or acetonitrile at -40 degrees C gave (E,Z)-muconaldehyde, which was a single diastereoisomer according to analysis by (1)H NMR spectroscopy. Reaction of toluene-1,2-oxide/2-methyloxepin with CAN gave (2E,4Z)-6-oxo-hepta-2,4-dienal. Similarly, the action of CAN on 1,6-dimethylbenzene oxide-2,7-dimethyloxepin gave (3Z,5E)-octa-3,5-diene-2,7-dione. In vivo, benzene oxide-oxepin could suffer one-electron oxidation by cytochrome P450 mono-oxygenase giving (E,Z)-muconaldehyde. The observations presented may be relevant to the toxicology of benzene oxide-oxepin and other arene oxide-oxepins as we have previously shown that (E,Z)-muconaldehyde, analogously to (Z,Z)-muconaldehyde, affords pyrrole adducts with the exocyclic amino groups of the DNA bases adenine and guanine. Independent of their possible toxicological significance, the experiments described provide preparatively useful routes to (E,Z)-muconaldehyde and its congeners. Methods are also described for the trapping and analysis of reactive benzene metabolites, e.g. using the Diels-Alder reaction with the dienophile 4-phenyl-1,2,4-triazoline-3,5-dione to trap arene oxides and with the diene 1,3-diphenylisobenzofuran to trap enals.

  6. The Sugar Model: Autocatalytic Activity of the Triose-Ammonia Reaction

    NASA Technical Reports Server (NTRS)

    Weber, Arthur L.

    2006-01-01

    Reaction of triose sugars with ammonia under anaerobic conditions yielded autocatalytic products. The autocatalytic behavior of the products was examined by measuring the effect of the crude triose-ammonia reaction product on the kinetics of a second identical triose-ammonia reaction. The reaction product showed autocatalytic activity by increasing both the rate of disappearance of triose and the rate formation of pyruvaldehyde, the product of triose dehydration. This synthetic process is considered a reasonable model of origin-of-life chemistry because it uses plausible prebiotic substrates, and resembles modern biosynthesis by employing the energized carbon groups of sugars to drive the synthesis of autocatalytic molecules.

  7. Piecewise linear and Boolean models of chemical reaction networks

    PubMed Central

    Veliz-Cuba, Alan; Kumar, Ajit; Josić, Krešimir

    2014-01-01

    Models of biochemical networks are frequently complex and high-dimensional. Reduction methods that preserve important dynamical properties are therefore essential for their study. Interactions in biochemical networks are frequently modeled using Hill functions (xn/(Jn + xn)). Reduced ODEs and Boolean approximations of such model networks have been studied extensively when the exponent n is large. However, while the case of small constant J appears in practice, it is not well understood. We provide a mathematical analysis of this limit, and show that a reduction to a set of piecewise linear ODEs and Boolean networks can be mathematically justified. The piecewise linear systems have closed form solutions that closely track those of the fully nonlinear model. The simpler, Boolean network can be used to study the qualitative behavior of the original system. We justify the reduction using geometric singular perturbation theory and compact convergence, and illustrate the results in network models of a toggle switch and an oscillator. PMID:25412739

  8. Increment Threshold Functions in Retinopathy of Prematurity

    PubMed Central

    Hansen, Ronald M.; Moskowitz, Anne; Bush, Jennifer N.; Fulton, Anne B.

    2016-01-01

    Purpose To assess scotopic background adaptation in subjects with a history of preterm birth and retinopathy of prematurity (ROP). Retinopathy of prematurity is known to have long-term effects on rod photoreceptor and rod mediated postreceptor retinal function. Methods Rod-mediated thresholds for detection of 3° diameter, 50 ms stimuli presented 20° from fixation were measured using a spatial forced choice method in 36 subjects (aged 9–17 years) with a history of preterm birth and 11 age similar term-born subjects. Thresholds were measured first in the dark-adapted condition and then in the presence of 6 steady background lights (−2.8 to +2.0 log scot td). A model of the increment threshold function was fit to each subject's thresholds to estimate the dark-adapted threshold (TDA) and the Eigengrau (A0, the background that elevates threshold 0.3 log unit above TDA). Results In subjects with a history of severe ROP, both TDA and A0 were significantly elevated relative to those in former preterms who never had ROP and term-born control subjects. Subjects who had mild ROP had normal TDA but elevated A0. Neither TDA nor A0 differed significantly between former preterms who never had ROP and term-born controls. Conclusions The results suggest that in severe ROP, threshold is affected at a preadaptation site, possibly the rod outer segment. In mild ROP, changes in the Eigengrau may reflect increased intrinsic noise in the photoreceptor or postreceptor circuitry or both. PMID:27145476

  9. 48 CFR 3452.232-71 - Incremental funding.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 7 2012-10-01 2012-10-01 false Incremental funding. 3452....232-71 Incremental funding. As prescribed in 3432.705-2, insert the following provision in solicitations if a cost-reimbursement contract using incremental funding is contemplated: Incremental...

  10. 48 CFR 3452.232-71 - Incremental funding.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 7 2011-10-01 2011-10-01 false Incremental funding. 3452....232-71 Incremental funding. As prescribed in 3432.705-2, insert the following provision in solicitations if a cost-reimbursement contract using incremental funding is contemplated: Incremental...

  11. 48 CFR 3452.232-71 - Incremental funding.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 7 2013-10-01 2012-10-01 true Incremental funding. 3452....232-71 Incremental funding. As prescribed in 3432.705-2, insert the following provision in solicitations if a cost-reimbursement contract using incremental funding is contemplated: Incremental...

  12. 48 CFR 3452.232-71 - Incremental funding.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 7 2014-10-01 2014-10-01 false Incremental funding. 3452....232-71 Incremental funding. As prescribed in 3432.705-2, insert the following provision in solicitations if a cost-reimbursement contract using incremental funding is contemplated: Incremental...

  13. Modeling and simulation of pressure waves generated by nano-thermite reactions

    NASA Astrophysics Data System (ADS)

    Martirosyan, Karen S.; Zyskin, Maxim; Jenkins, Charles M.; (Yuki) Horie, Yasuyuki

    2012-11-01

    This paper reports the modeling of pressure waves from the explosive reaction of nano-thermites consisting of mixtures of nanosized aluminum and oxidizer granules. Such nanostructured thermites have higher energy density (up to 26 kJ/cm3) and can generate a transient pressure pulse four times larger than that from trinitrotoluene (TNT) based on volume equivalence. A plausible explanation for the high pressure generation is that the reaction times are much shorter than the time for a shock wave to propagate away from the reagents region so that all the reaction energy is dumped into the gaseous products almost instantaneously and thereby a strong shock wave is generated. The goal of the modeling is to characterize the gas dynamic behavior for thermite reactions in a cylindrical reaction chamber and to model the experimentally measured pressure histories. To simplify the details of the initial stage of the explosive reaction, it is assumed that the reaction generates a one dimensional shock wave into an air-filled cylinder and propagates down the tube in a self-similar mode. Experimental data for Al/Bi2O3 mixtures were used to validate the model with attention focused on the ratio of specific heats and the drag coefficient. Model predictions are in good agreement with the measured pressure histories.

  14. Comparison of kinetic and equilibrium reaction models insimulating the behavior of porous media

    SciTech Connect

    Kowalsky, Michael B.; Moridis, George J.

    2006-11-29

    In this study we compare the use of kinetic and equilibriumreaction models in the simulation of gas (methane) hydrate behavior inporous media. Our objective is to evaluate through numerical simulationthe importance of employing kinetic versus equilibrium reaction modelsfor predicting the response of hydrate-bearing systems to externalstimuli, such as changes in pressure and temperature. Specifically, we(1) analyze and compare the responses simulated using both reactionmodels for natural gas production from hydrates in various settings andfor the case of depressurization in a hydrate-bearing core duringextraction; and (2) examine the sensitivity to factors such as initialhydrate saturation, hydrate reaction surface area, and numericaldiscretization. We find that for large-scale systems undergoing thermalstimulation and depressurization, the calculated responses for bothreaction models are remarkably similar, though some differences areobserved at early times. However, for modeling short-term processes, suchas the rapid recovery of a hydrate-bearing core, kinetic limitations canbe important, and neglecting them may lead to significantunder-prediction of recoverable hydrate. Assuming validity of the mostaccurate kinetic reaction model that is currently available, the use ofthe equilibrium reaction model often appears to be justified andpreferred for simulating the behavior of gas hydrates, given that thecomputational demands for the kinetic reaction model far exceed those forthe equilibrium reaction model.

  15. A hydrodynamics-reaction kinetics coupled model for evaluating bioreactors derived from CFD simulation.

    PubMed

    Wang, Xu; Ding, Jie; Guo, Wan-Qian; Ren, Nan-Qi

    2010-12-01

    Investigating how a bioreactor functions is a necessary precursor for successful reactor design and operation. Traditional methods used to investigate flow-field cannot meet this challenge accurately and economically. Hydrodynamics model can solve this problem, but to understand a bioreactor in sufficient depth, it is often insufficient. In this paper, a coupled hydrodynamics-reaction kinetics model was formulated from computational fluid dynamics (CFD) code to simulate a gas-liquid-solid three-phase biotreatment system for the first time. The hydrodynamics model is used to formulate prediction of the flow field and the reaction kinetics model then portrays the reaction conversion process. The coupled model is verified and used to simulate the behavior of an expanded granular sludge bed (EGSB) reactor for biohydrogen production. The flow patterns were visualized and analyzed. The coupled model also demonstrates a qualitative relationship between hydrodynamics and biohydrogen production. The advantages and limitations of applying this coupled model are discussed.

  16. A "Reaction Kinetics" Model for the Growth of Curriculum Projects.

    ERIC Educational Resources Information Center

    Tebbutt, Maurice J.; Atherton, Michael A.

    1979-01-01

    Presents a model for researchers to test the mechanisms which have been claimed to operate in curriculum diffusion. The method is different from generalizations based on observations or answers to questionnaires. (Author/KC)

  17. Statistical Model Calculations for (n,γ) Reactions

    NASA Astrophysics Data System (ADS)

    Beard, Mary; Uberseder, Ethan; Wiescher, Michael

    2015-05-01

    Hauser-Feshbach (HF) cross sections are of enormous importance for a wide range of applications, from waste transmutation and nuclear technologies, to medical applications, and nuclear astrophysics. It is a well-observed result that different nuclear input models sensitively affect HF cross section calculations. Less well known however are the effects on calculations originating from model-specific implementation details (such as level density parameter, matching energy, back-shift and giant dipole parameters), as well as effects from non-model aspects, such as experimental data truncation and transmission function energy binning. To investigate the effects or these various aspects, Maxwellian-averaged neutron capture cross sections have been calculated for approximately 340 nuclei. The relative effects of these model details will be discussed.

  18. Model creation of moving redox reaction boundary in agarose gel electrophoresis by traditional potassium permanganate method.

    PubMed

    Xie, Hai-Yang; Liu, Qian; Li, Jia-Hao; Fan, Liu-Yin; Cao, Cheng-Xi

    2013-02-21

    A novel moving redox reaction boundary (MRRB) model was developed for studying electrophoretic behaviors of analytes involving redox reaction on the principle of moving reaction boundary (MRB). Traditional potassium permanganate method was used to create the boundary model in agarose gel electrophoresis because of the rapid reaction rate associated with MnO(4)(-) ions and Fe(2+) ions. MRB velocity equation was proposed to describe the general functional relationship between velocity of moving redox reaction boundary (V(MRRB)) and concentration of reactant, and can be extrapolated to similar MRB techniques. Parameters affecting the redox reaction boundary were investigated in detail. Under the selected conditions, good linear relationship between boundary movement distance and time were obtained. The potential application of MRRB in electromigration redox reaction titration was performed in two different concentration levels. The precision of the V(MRRB) was studied and the relative standard deviations were below 8.1%, illustrating the good repeatability achieved in this experiment. The proposed MRRB model enriches the MRB theory and also provides a feasible realization of manual control of redox reaction process in electrophoretic analysis.

  19. Dynamic order reduction of thin-film deposition kinetics models: A reaction factorization approach

    SciTech Connect

    Adomaitis, Raymond A.

    2016-01-15

    A set of numerical tools for the analysis and dynamic dimension reduction of chemical vapor and atomic layer deposition (ALD) surface reaction models is developed in this work. The approach is based on a two-step process where in the first, the chemical species surface balance dynamic equations are factored to effectively decouple the (nonlinear) reaction rates, a process that eliminates redundant dynamic modes and that identifies conserved quantities. If successful, the second phase is implemented to factor out redundant dynamic modes when species relatively minor in concentration are omitted; if unsuccessful, the technique points to potential model structural problems. An alumina ALD process is used for an example consisting of 19 reactions and 23 surface and gas-phase species. Using the approach developed, the model is reduced by nineteen modes to a four-dimensional dynamic system without any knowledge of the reaction rate values. Results are interpreted in the context of potential model validation studies.

  20. Chaos in the Showalter-Noyes-Bar-Eli model of the Belousov-Zhabotinskii reaction

    NASA Astrophysics Data System (ADS)

    Lindberg, David; Turner, Jack S.; Barkley, Dwight

    1990-03-01

    The observation of robust, large-scale chaos in the Showalter-Noyes-Bar-Eli model of the Belousov-Zhabotinskii reaction is reported. The chaos observed is comparable to that found in CSTR experiments at low flow rates.

  1. The Coherent Flame Model for Turbulent Chemical Reactions

    DTIC Science & Technology

    1977-01-01

    the strained laminar diffusion flame may be determined by analysis, numerical computation, and by experiment without significant change to the model...numerical integration of the resulting differential equations. The model predicts the flame length and superficial comparison with experiments suggest a...of Hawthorne, et al.,(3 Hottel,(4 Karlovitz, et al.(5 Wohl,(6 and others. That brief period provided some provacative experiments through (7) (8

  2. Value-Driven Incremental Development (Poster)

    DTIC Science & Technology

    2014-10-27

    rework during development. Multi-dimensional Analysis What is the design implication of a release decision? Architecting for Incremental Assurance...measures are needed to make good release decisions? Selected FY14 Results • Improved rework analysis by making architectural dependency information...studies and surveys with organizations revealed architectural rework occurs in such context and can be managed by better quantification of technical

  3. Input-Based Incremental Vocabulary Instruction

    ERIC Educational Resources Information Center

    Barcroft, Joe

    2012-01-01

    This fascinating presentation of current research undoes numerous myths about how we most effectively learn new words in a second language. In clear, reader-friendly text, the author details the successful approach of IBI vocabulary instruction, which emphasizes the presentation of target vocabulary as input early on and the incremental (gradual)…

  4. Withholding Increments. Focus on School Law Series.

    ERIC Educational Resources Information Center

    Weger, Christine D.; Galante, Susan

    Local boards of education in New Jersey are authorized by law to withhold increments of staff members in certain circumstances. The purpose of this publication is to provide an analysis and summary of decisions involving a board's exercise of this authority, and it is intended to serve as a guide and a reference tool to be used in determining when…

  5. Existing School Buildings: Incremental Seismic Retrofit Opportunities.

    ERIC Educational Resources Information Center

    Federal Emergency Management Agency, Washington, DC.

    The intent of this document is to provide technical guidance to school district facility managers for linking specific incremental seismic retrofit opportunities to specific maintenance and capital improvement projects. The linkages are based on logical affinities, such as technical fit, location of the work within the building, cost saving…

  6. Incremental social learning in particle swarms.

    PubMed

    de Oca, Marco A Montes; Stutzle, Thomas; Van den Enden, Ken; Dorigo, Marco

    2011-04-01

    Incremental social learning (ISL) was proposed as a way to improve the scalability of systems composed of multiple learning agents. In this paper, we show that ISL can be very useful to improve the performance of population-based optimization algorithms. Our study focuses on two particle swarm optimization (PSO) algorithms: a) the incremental particle swarm optimizer (IPSO), which is a PSO algorithm with a growing population size in which the initial position of new particles is biased toward the best-so-far solution, and b) the incremental particle swarm optimizer with local search (IPSOLS), in which solutions are further improved through a local search procedure. We first derive analytically the probability density function induced by the proposed initialization rule applied to new particles. Then, we compare the performance of IPSO and IPSOLS on a set of benchmark functions with that of other PSO algorithms (with and without local search) and a random restart local search algorithm. Finally, we measure the benefits of using incremental social learning on PSO algorithms by running IPSO and IPSOLS on problems with different fitness distance correlations.

  7. Evidence for a transition state model compound of in-plane vinylic SN2 reaction.

    PubMed

    Yamaguchi, Torahiko; Yamamoto, Yohsuke; Fujiwara, Yoshihisa; Tanimoto, Yoshifumi

    2005-06-23

    [reaction: see text] To isolate a transition state model compound of an in-plane vinylic S(N)2 reaction, vinyl bromide 6 bearing a newly synthesized tridentate ligand derived from 1,8-dimethoxythioxanthen-9-one (5) was prepared as a precursor. Although irradiation of 6 gave demethylated benzofuran 12, a transient broad peak which indicates formation of the desired transition state model compound was observed in the laser flash photolytic study.

  8. Attitude Model of a Reaction Wheel/Fixed Thruster Based Satellite Using Telemetry Data

    DTIC Science & Technology

    2005-03-01

    thruster on/off indicators and reaction wheel rotor speeds, is investigated. Experimental tests using telemetry data received from the Air Force...Institute of Technology’s (AFIT) Simulated Satellite, SimSat, is used in verifying a Matlab model which outputs SimSat’s orientation from SimSat’s reaction ... wheel and thruster telemetry data. Software modeling results showed that it is possible to determine a satellite’s attitude from only the attitude

  9. Dynamical Coupled-Channel Model of Meson Production Reactions in the Nucleon Resonance Region

    SciTech Connect

    T.-S. H. Lee; A. Matsuyama; T. Sato

    2006-11-15

    A dynamical coupled-channel model is presented for investigating the nucleon resonances (N*) in the meson production reactions induced by pions and photons. Our objective is to extract the N* parameters and to investigate the meson production reaction mechanisms for mapping out the quark-gluon substructure of N* from the data. The model is based on an energy-independent Hamiltonian which is derived from a set of Lagrangians by using a unitary transformation method.

  10. Marginal increment analysis: a new statistical approach of testing for temporal periodicity in fish age verification.

    PubMed

    Okamura, H; Punt, A E; Semba, Y; Ichinokawa, M

    2013-04-01

    This paper proposes a new and flexible statistical method for marginal increment analysis that directly accounts for periodicity in circular data using a circular-linear regression model with random effects. The method is applied to vertebral marginal increment data for Alaska skate Bathyraja parmifera. The best fit model selected using the AIC indicates that growth bands are formed annually. Simulation, where the underlying characteristics of the data are known, shows that the method performs satisfactorily when uncertainty is not extremely high.

  11. A simple recipe for modeling reaction-rate in flows with turbulent-combustion

    NASA Technical Reports Server (NTRS)

    Girimaji, Sharath S.

    1991-01-01

    A computationally viable scheme to account for chemical reaction in turbulent flows is presented. The multivariate beta-pdf model for multiple scalar mixing forms the basis of this scheme. Using the model scalar joint pdf and a general form of the instantaneous reaction-rate, the unclosed chemical reaction terms are expressed as simple functions of scalar means and the turbulent scalar energy. The calculation procedure requires that the mean scalar equations and only one other transport equation - for the turbulent scalar energy - be solved.

  12. Reaction mechanism of WGS and PROX reactions catalyzed by Pt/oxide catalysts revealed by an FeO(111)/Pt(111) inverse model catalyst.

    PubMed

    Xu, Lingshun; Wu, Zongfang; Jin, Yuekang; Ma, Yunsheng; Huang, Weixin

    2013-08-07

    We have employed XPS and TDS to study the adsorption and surface reactions of H2O, CO and HCOOH on an FeO(111)/Pt(111) inverse model catalyst. The FeO(111)-Pt(111) interface of the FeO(111)/Pt(111) inverse model catalyst exposes coordination-unsaturated Fe(II) cations (Fe(II)CUS) and the Fe(II)CUS cations are capable of modifying the reactivity of neighbouring Pt sites. Water facilely dissociates on the Fe(II)CUS cations at the FeO(111)-Pt(111) interface to form hydroxyls that react to form both water and H2 upon heating. Hydroxyls on the Fe(II)CUS cations can react with CO(a) on the neighbouring Pt(111) sites to produce CO2 at low temperatures. Hydroxyls act as the co-catalyst in the CO oxidation by hydroxyls to CO2 (PROX reaction), while they act as one of the reactants in the CO oxidation by hydroxyls to CO2 and H2 (WGS reaction), and the recombinative reaction of hydroxyls to produce H2 is the rate-limiting step in the WGS reaction. A comparison of reaction behaviors between the interfacial CO(a) + OH reaction and the formate decomposition reaction suggest that formate is the likely surface intermediate of the CO(a) + OH reaction. These results provide some solid experimental evidence for the associative reaction mechanism of WGS and PROX reactions catalyzed by Pt/oxide catalysts.

  13. MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

    PubMed Central

    2012-01-01

    Background Increasingly, metabolite and reaction information is organized in the form of genome-scale metabolic reconstructions that describe the reaction stoichiometry, directionality, and gene to protein to reaction associations. A key bottleneck in the pace of reconstruction of new, high-quality metabolic models is the inability to directly make use of metabolite/reaction information from biological databases or other models due to incompatibilities in content representation (i.e., metabolites with multiple names across databases and models), stoichiometric errors such as elemental or charge imbalances, and incomplete atomistic detail (e.g., use of generic R-group or non-explicit specification of stereo-specificity). Description MetRxn is a knowledgebase that includes standardized metabolite and reaction descriptions by integrating information from BRENDA, KEGG, MetaCyc, Reactome.org and 44 metabolic models into a single unified data set. All metabolite entries have matched synonyms, resolved protonation states, and are linked to unique structures. All reaction entries are elementally and charge balanced. This is accomplished through the use of a workflow of lexicographic, phonetic, and structural comparison algorithms. MetRxn allows for the download of standardized versions of existing genome-scale metabolic models and the use of metabolic information for the rapid reconstruction of new ones. Conclusions The standardization in description allows for the direct comparison of the metabolite and reaction content between metabolic models and databases and the exhaustive prospecting of pathways for biotechnological production. This ever-growing dataset currently consists of over 76,000 metabolites participating in more than 72,000 reactions (including unresolved entries). MetRxn is hosted on a web-based platform that uses relational database models (MySQL). PMID:22233419

  14. On incremental non-linearity in granular media: phenomenological and multi-scale views

    NASA Astrophysics Data System (ADS)

    Darve, Félix; Nicot, François

    2005-12-01

    On the basis of fundamental constitutive laws such as elasticity, perfect plasticity, and pure viscosity, many elasto-viscoplastic constitutive relations have been developed since the 1970s through phenomenological approaches. In addition, a few more recent micro-mechanical models based on multi-scale approaches are now able to describe the main macroscopic features of the mechanical behaviour of granular media. The purpose of this paper is to compare a phenomenological constitutive relation and a micro-mechanical model with respect to a basic issue regularly raised about granular assemblies: the incrementally non-linear character of their behaviour. It is shown that both phenomenological and micro-mechanical models exhibit an incremental non-linearity. In addition, the multi-scale approach reveals that the macroscopic incremental non-linearity could stem from the change in the regime of local contacts between particles (from plastic regime to elastic regime) in terms of the incremental macroscopic loading direction. Copyright

  15. New Direction in Hydrogeochemical Transport Modeling: Incorporating Multiple Kinetic and Equilibrium Reaction Pathways

    SciTech Connect

    Steefel, C.I.

    2000-02-02

    At least two distinct kinds of hydrogeochemical models have evolved historically for use in analyzing contaminant transport, but each has important limitations. One kind, focusing on organic contaminants, treats biodegradation reactions as parts of relatively simple kinetic reaction networks with no or limited coupling to aqueous and surface complexation and mineral dissolution/precipitation reactions. A second kind, evolving out of the speciation and reaction path codes, is capable of handling a comprehensive suite of multicomponent complexation (aqueous and surface) and mineral precipitation and dissolution reactions, but has not been able to treat reaction networks characterized by partial redox disequilibrium and multiple kinetic pathways. More recently, various investigators have begun to consider biodegradation reactions in the context of comprehensive equilibrium and kinetic reaction networks (e.g. Hunter et al. 1998, Mayer 1999). Here we explore two examples of multiple equilibrium and kinetic reaction pathways using the reactive transport code GIMRT98 (Steefel, in prep.): (1) a computational example involving the generation of acid mine drainage due to oxidation of pyrite, and (2) a computational/field example where the rates of chlorinated VOC degradation are linked to the rates of major redox processes occurring in organic-rich wetland sediments overlying a contaminated aerobic aquifer.

  16. Activation energy for a model ferrous-ferric half reaction from transition path sampling.

    PubMed

    Drechsel-Grau, Christof; Sprik, Michiel

    2012-01-21

    Activation parameters for the model oxidation half reaction of the classical aqueous ferrous ion are compared for different molecular simulation techniques. In particular, activation free energies are obtained from umbrella integration and Marcus theory based thermodynamic integration, which rely on the diabatic gap as the reaction coordinate. The latter method also assumes linear response, and both methods obtain the activation entropy and the activation energy from the temperature dependence of the activation free energy. In contrast, transition path sampling does not require knowledge of the reaction coordinate and directly yields the activation energy [C. Dellago and P. G. Bolhuis, Mol. Simul. 30, 795 (2004)]. Benchmark activation energies from transition path sampling agree within statistical uncertainty with activation energies obtained from standard techniques requiring knowledge of the reaction coordinate. In addition, it is found that the activation energy for this model system is significantly smaller than the activation free energy for the Marcus model, approximately half the value, implying an equally large entropy contribution.

  17. Modeling the coupling of reaction kinetics and hydrodynamics in a collapsing cavity

    SciTech Connect

    Mishra, Sudib; Deymier, Pierre; Muralidharan, Krishna; Frantziskonis, G.; Pannala, Sreekanth; Simunovic, Srdjan

    2010-01-01

    We introduce a model of cavitation based on the multiphase Lattice Boltzmann method (LBM) that allows for coupling between the hydrodynamics of a collapsing cavity and supported solute chemical species. We demonstrate that this model can also be coupled to deterministic or stochastic chemical reactions. In a two-species model of chemical reactions (with a major and a minor specie), the major difference observed between the deterministic and stochastic reactions takes the form of random fluctuations in concentration of the minor species. We demonstrate that advection associated with the hydrodynamics of a collapsing cavity leads to highly inhomogeneous concentration of solutes. In turn these inhomogeneities in concentration may lead to significant increase in concentration-dependent reaction rates and can result in a local enhancement in the production of minor species.

  18. Reaction-diffusion model for the growth of avascular tumor

    NASA Astrophysics Data System (ADS)

    Ferreira, S. C.; Martins, M. L.; Vilela, M. J.

    2002-02-01

    A nutrient-limited model for avascular cancer growth including cell proliferation, motility, and death is presented. The model qualitatively reproduces commonly observed morphologies for primary tumors, and the simulated patterns are characterized by its gyration radius, total number of cancer cells, and number of cells on tumor periphery. These very distinct morphological patterns follow Gompertz growth curves, but exhibit different scaling laws for their surfaces. Also, the simulated tumors incorporate a spatial structure composed of a central necrotic core, an inner rim of quiescent cells and a narrow outer shell of proliferating cells in agreement with biological data. Finally, our results indicate that the competition for nutrients among normal and cancer cells may be a determining factor in generating papillary tumor morphology.

  19. Nicotiana tabacum as model for ozone - plant surface reactions

    NASA Astrophysics Data System (ADS)

    Jud, Werner; Fischer, Lukas; Wohlfahrt, Georg; Tissier, Alain; Canaval, Eva; Hansel, Armin

    2015-04-01

    Elevated tropospheric ozone concentrations are considered a toxic threat to plants, responsible for global crop losses with associated economic costs of several billion dollars per year. The ensuing injuries have been related to the uptake of ozone through the stomatal pores and oxidative effects damaging the internal leaf tissue. A striking question of current research is the environment and plant specific partitioning of ozone loss between gas phase, stomatal or plant surface sink terms. Here we show results from ozone fumigation experiments using various Nicotiana Tabacum varieties, whose surfaces are covered with different amounts of unsaturated diterpenoids exuded by their glandular trichomes. Exposure to elevated ozone levels (50 to 150 ppbv) for 5 to 15 hours in an exceptionally clean cuvette system did neither result in a reduction of photosynthesis nor caused any visible leaf damage. Both these ozone induced stress effects have been observed previously in ozone fumigation experiments with the ozone sensitive tobacco line Bel-W3. In our case ozone fumigation was accompanied by a continuous release of oxygenated volatile organic compounds, which could be clearly associated to their condensed phase precursors for the first time. Gas phase reactions of ozone were avoided by choosing a high enough gas exchange rate of the plant cuvette system. In the case of the Ambalema variety, that is known to exude only the diterpenoid cis-abienol, ozone fumigation experiments yield the volatiles formaldehyde and methyl vinyl ketone (MVK). The latter could be unequivocally separated from isomeric methacrolein (MACR) by the aid of a Selective Reagent Ion Time-of-Flight Mass Spectrometer (SRI-ToF-MS), which was switched every six minutes from H3O+ to NO+ primary ion mode and vice versa. Consistent with the picture of an ozone protection mechanism caused by reactive diterpenoids at the leaf surface are the results from dark-light experiments. The ozone loss obtained from the

  20. Mathematical model for describing reactions of residual chlorine with organic matter in reclaimed wastewater.

    PubMed

    Funamizu, N; Iwamoto, T; Takakuwa, T

    2004-01-01

    Among several applications of urban wastewater reuse, use of reclaimed wastewater to sustain stream flows has become attractive in the urban area. Since these rivers are used for recreational purposes and for restoring aquatic eco-system, the adequate control of residual chlorine is essential. Mathematical model for describing reactions between residual chlorine and organic matter in reclaimed wastewater has been developed. The model considers the effect of molecular weight distribution of organic matter on the reaction rate. Lab-scale experiments were performed to estimate reaction rates constants and to examine their temperature dependency. The experiments showed that 1) the smaller organic matter gave the larger reaction rate; 2) temperature effect on reaction rate was described by the Arrhenius formula; 3) decline of free chlorine had more temperature dependency than combined chlorine. The comparison of computed results with data from lab-scale experiments confirmed the validity of the model. We used the one-dimensional dispersion model with proposed reaction model and examined the seasonal variation of residual chlorine profile along the river sustained by reclaimed wastewater in Sapporo. Simulation showed that seasonal variation of nitrification performance in secondary treatment as well as change in temperature caused seasonal variation in residual chlorine profile along the river.

  1. The Quantum-Kinetic Chemical Reaction Model for Navier-Stokes Codes

    NASA Astrophysics Data System (ADS)

    Gallis, Michael A.; Wagnild, Ross M.; Torczynski, John R.

    2013-11-01

    The Quantum-Kinetic chemical reaction model of Bird is formulated as a non-equilibrium chemical reaction model for Navier-Stokes codes. The model is based solely on thermophysical, molecular-level information and is capable of reproducing measured equilibrium reaction rates without using any experimentally measured reaction-rate information. The model recognizes the principal role of vibrational energy in overcoming the reaction energy threshold. The effect of rotational non-equilibrium is introduced as a perturbation to the effect of vibrational non-equilibrium. Since the model uses only molecular-level properties, it is inherently able to predict reaction rates for arbitrary non-equilibrium conditions. This ability is demonstrated in the context of both Navier-Stokes and DSMC codes. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  2. Geographic Variations in Incremental Costs of Heart Disease Among Medicare Beneficiaries, by Type of Service, 2012

    PubMed Central

    Ritchey, Matthew; Hockenberry, Jason; Casper, Michele

    2016-01-01

    Using 2012 data on fee-for-service Medicare claims, we documented regional and county variation in incremental standardized costs of heart disease (ie, comparing costs between beneficiaries with heart disease and beneficiaries without heart disease) by type of service (eg, inpatient, outpatient, post-acute care). Absolute incremental total costs varied by region. Although the largest absolute incremental total costs of heart disease were concentrated in southern and Appalachian counties, geographic patterns of costs varied by type of service. These data can be used to inform development of policies and payment models that address the observed geographic disparities. PMID:28033089

  3. An approach for modeling surface reaction kinetics in chemical vapor deposition processes

    SciTech Connect

    Wang, Y.F.; Pollard, R.

    1995-05-01

    A methodology is presented for determining the rate constants of elementary surface reactions that can take place in chemical vapor deposition (CVD) processes. The calculations consider well-defined surfaces that can have one or more dangling bonds at a given site and adsorbates that can take up one or more different bonding configurations. Rate constants for each reaction are obtained independently of any process data using statistical mechanics, transition state theory, and bond dissociation energies. Specifically, the reactions are divided in transition state structures and determine preexponential factors, and the requirement of thermodynamic consistency is used to estimate activation energies. The level of sophistication of the calculations is suitable for treating the large number of plausible steps that could take place in a practical CVD system. Incorporation of the calculated rate constants into a reactor model that includes the effects of fluid flow, transport phenomena, and reactions in the gas and at the growing surface enables dominant reaction pathways and rate-limiting steps to be identified. Moreover, the dependence of growth rate and species compositions on operating conditions can be predicted without fitting any parameters. The utility of the approach is illustrated by modeling low pressure deposition of tungsten from tungsten hexafluoride and silane. This model treats 35 reactions in the gas and 213 reactions at the growing surface. Results are compared with available experimental data and sensitivity studies are used to assess the limitations of the approach.

  4. Chaos and fractals in dynamical models of transport and reaction.

    PubMed

    Gaspard, P; Claus, I

    2002-03-15

    This paper contains a discussion of dynamical randomness among the different methods of simulation of a fluid and its characterization by the concept of Kolmogorov-Sinai entropy per unit time. Moreover, a renormalization-group method is presented in order to construct the hydrodynamic and reactive modes of relaxation in chaotic models. The renormalization-group construction allows us to obtain the dispersion relation of these modes, i.e. their damping rate versus the wavenumber. Besides, these modes are characterized by a fractal dimension given in terms of a diffusion coefficient and a Lyapunov exponent.

  5. Optical model methods of predicting nuclide production from spallation reactions.

    PubMed

    Ramsey, C R; Townsend, L W; Tripathi, R K; Cucinotta, F A

    1998-02-01

    Quantum mechanical optical model methods for calculating isotope production cross sections from the spallation of heavy nuclei by high-energy protons are developed from a modified abrasion-ablation collision formalism. The abrasion step is treated quantum-mechanically as a knockout process which leaves the residual prefragment nucleus in an excited state. In ablation the prefragment deexcites to produce the final fragment. The excitation energies of the prefragments are estimated from a combination of liquid drop and frictional-spectator interaction considerations. Estimates of elemental and isotopic production cross sections are in good agreement with recently published cross section measurements.

  6. MODEL STUDIES OF MODE-SPECIFICITY IN UNIMOLECULAR REACTION DYNAMICS

    SciTech Connect

    Waite, Boyd A.; Miller, William H.

    1980-06-01

    Essentially exact quantum mechanical calculations are carried out to determine the energies and lifetimes of the quasi-bound states for a system of two (non~linearly) coupled oscillators (one of which is harmonic, the other being able to dissociate). For weak coupling the system displays mode-specificity, i.e., the unimolecular rate constants are not a monotonic function of the total energy, but increased coupling and frequency degeneracy tends to destroy mode-specificity. A somewhat surprising result is that for a given coupling the degree of modespecificity is roughly independent of the energy, in marked contrast to the fact that there is an energetic threshold for the onset of "stochastic trajectories" of the corresponding classical system; i.e., there seems to be no relation between statistical/mode-specific behavior of the unimolecular rate constants and stochastic/regular classical trajectories. In order to be able to treat more physically relevant models--i.e., those with more than two degrees of freedom--a semiclassical model is constructed and seen to be able to reproduce the accurate quantum mechanical rates reasonably well.

  7. Geometrical measurement of cardiac wavelength in reaction-diffusion models

    NASA Astrophysics Data System (ADS)

    Dupraz, Marie; Jacquemet, Vincent

    2014-09-01

    The dynamics of reentrant arrhythmias often consists in multiple wavelets propagating throughout an excitable medium. An arrhythmia can be sustained only if these reentrant waves have a sufficiently short wavelength defined as the distance traveled by the excitation wave during its refractory period. In a uniform medium, wavelength may be estimated as the product of propagation velocity and refractory period (electrophysiological wavelength). In order to accurately measure wavelength in more general substrates relevant to atrial arrhythmias (heterogeneous and anisotropic), we developed a mathematical framework to define geometrical wavelength at each time instant based on the length of streamlines following the propagation velocity field within refractory regions. Two computational methods were implemented: a Lagrangian approach in which a set of streamlines were integrated, and an Eulerian approach in which wavelength was the solution of a partial differential equation. These methods were compared in 1D/2D tissues and in a model of the left atrium. An advantage of geometrical definition of wavelength is that the wavelength of a wavelet can be tracked over time with high temporal resolution and smaller temporal variability in an anisotropic and heterogeneous medium. The results showed that the average electrophysiological wavelength was consistent with geometrical measurements of wavelength. Wavelets were however often shorter than the electrophysiological wavelength due to interactions with boundaries and other wavelets. These tools may help to assess more accurately the relation between substrate properties and wavelet dynamics in computer models.

  8. Modeling subsurface contaminant reactions and transport at the watershed scale

    SciTech Connect

    Gwo, J.P.; Jardine, P.M.; D`Azevedo, E.F.; Wilson, G.V.

    1997-12-01

    The objectives of this research are: (1) to numerically examine the multiscale effects of physical and chemical mass transfer processes on watershed scale, variably saturated subsurface contaminant transport, and (2) to conduct numerical simulations on watershed scale reactive solute transport and evaluate their implications to uncertainty characterization and cost benefit analysis. Concurrent physical and chemical nonequilibrium caused by inter aggregate gradients of pressure head and solute concentration and intra-aggregate geochemical and microbiological processes, respectively, may arise at various scales and flowpaths. To this date, experimental investigations of these complex processes at watershed scale remain a challenge and numerical studies are often needed for guidance of water resources management and decision making. This research integrates the knowledge bases developed during previous experimental and numerical investigations at a proposed waste disposal site at the Oak Ridge National Laboratory to study the concurrent effects of physical and chemical nonequilibrium. Comparison of numerical results with field data indicates that: (1) multiregion, preferential flow and solute transport exist under partially saturated condition and can be confirmed theoretically, and that (2) mass transfer between pore regions is an important process influencing contaminant movement in the subsurface. Simulations of watershed scale, multi species reactive solute transport suggest that dominance of geochemistry and hydrodynamics may occur simultaneously at different locales and influence the movement of one species relative to another. Execution times on the simulations of the reactive solute transport model also indicate that the model is ready to assist the selection of important parameters for site characterization.

  9. Generalized kinetic model of catalyzed hydroliquefaction of coal incorporating tetralin dehydrogenation reaction

    SciTech Connect

    Ghosh, A.K.; Prasad, G.N.; Sridhar, T.

    1987-09-01

    A three-component kinetic model previously reported for uncatalyzed liquefaction has been used to simulate hydroliquefaction of Victorian brown coal with three different types of catalysts: iron-tin; iron; and haematite. The presence of catalyst is found to enhance hydrogenation of coal as well as the equilibrium hydrogenation-dehydrogenation reactions involving donor solvent. The thermal dissolution and autohydrogenation reaction rates are independent of catalyst used. Iron-tin-based catalyst has been found to be most effective for the hydrogenation reaction step. The simulation shows that the reactions producing hydrogen from tetralin are much slower than the coal-hydrogen reactions; hence, efforts aimed at efficient abstraction of hydrogen from the hydrogen donors may be beneficial.

  10. Neutron-induced reactions on AlF3 studied using the optical model

    NASA Astrophysics Data System (ADS)

    Ma, Chun-Wang; Lv, Cui-Juan; Zhang, Guo-Qiang; Wang, Hong-Wei; Zuo, Jia-Xu

    2015-08-01

    Neutron-induced reactions on 27Al and 19F nuclei are investigated using the optical model implemented in the TALYS 1.4 toolkit. Incident neutron energies in a wide range from 0.1 keV to 30 MeV are calculated. The cross sections for the main channels (n, np), (n, p), (n, α), (n, 2n), and (n, γ) and the total reaction cross section (n, tot) of the reactions are obtained. When the default parameters in TALYS 1.4 are adopted, the calculated results agree with the measured results. Based on the calculated results for the n + 27Al and n + 19F reactions, the results of the n + 27Al19F reactions are predicted. These results are useful both for the design of thorium-based molten salt reactors and for neutron activation analysis techniques.

  11. Mathematical modeling of an exothermic leaching reaction system: pressure oxidation of wide size arsenopyrite participates

    NASA Astrophysics Data System (ADS)

    Papangelakis, V. G.; Berk, D.; Demopoulos, G. P.

    1990-10-01

    In the design of processes involving exothermic reactions, as is the case of several sulfide leaching systems, it is desirable to utilize the energy liberated by the reaction to drive the reactor toward autogenous operation. For optimal reactor design, models which couple leaching kinetics and heat effects are needed. In this paper, the principles of modeling exothermic leaching reactions are outlined. The system investigated is the high-temperature (160 °C to 200 °C) pressure (O2) oxidation of arsenopyrite (FeAsS). The reaction system is characterized by three consecutive reactions: (1) heterogeneous dissolution of arsenopyrite particles, (2) homogeneous oxidation of iron(II) to iron(III), and (3) precipitation of scorodite (FeAsO4-2H2O). The overall kinetics is controlled by the arsenopyrite surface reaction. There was good agreement between laboratory-scale batch tests and model predictions. The model was expanded to simulate the performance of large-scale batch and single-stage continuous stirred tank reactor (CSTR) for the same rate-limiting regime. Emphasis is given to the identification of steady-state temperatures for autogenous processing. The effects of operating variables, such as feed temperature, slurry density, and retention time, on reactor operation and yield of leaching products are discussed.

  12. Reaction-based reactive transport modeling of Fe(III)

    SciTech Connect

    Kemner, K.M.; Kelly, S.D.; Burgos, Bill; Roden, Eric

    2006-06-01

    This research project (started Fall 2004) was funded by a grant to Argonne National Laboratory, The Pennsylvania State University, and The University of Alabama in the Integrative Studies Element of the NABIR Program (DE-FG04-ER63914/63915/63196). Dr. Eric Roden, formerly at The University of Alabama, is now at the University of Wisconsin, Madison. Our project focuses on the development of a mechanistic understanding and quantitative models of coupled Fe(III)/U(VI) reduction in FRC Area 2 sediments. This work builds on our previous studies of microbial Fe(III) and U(VI) reduction, and is directly aligned with the Scheibe et al. NABIR FRC Field Project at Area 2.

  13. Thermodynamic forward modeling of retrogressive hydration reactions induced by geofluid infiltration

    NASA Astrophysics Data System (ADS)

    Kuwatani, Tatsu; Toriumi, Mitsuhiro

    2017-01-01

    We have developed a new methodology for forward analysis of retrogressive hydration (rehydration) reactions by an improved thermodynamic forward modeling technique based on a differential thermodynamic approach (Gibbs' method). Based on natural observations and theoretical considerations, the progress of a rehydration reaction is modeled by incorporating a change in the effective bulk composition on account of the breakdown of the non-equilibrated phase and the amount of water infiltration into the system. Forward analyses of rehydration reactions under greenschist-facies conditions show that (1) the reaction progress of rehydration is proportional to the external water supply, and (2) the mineral compositions of equilibrated minerals are mainly controlled by P- T conditions and are similar to those in the global equilibrium model. Calculated results are in accordance with natural observations of rehydration reactions in greenschist-facies rocks, which supports the validity of the proposed model. The proposed model can be used as a basic forward model for various inversion analyses and numerical simulations and thus to understand the distribution and behavior of geofluids.[Figure not available: see fulltext.

  14. Modeling of atmospheric OH reaction rates using newly developed variable distance weighted zero order connectivity index

    NASA Astrophysics Data System (ADS)

    Markelj, Jernej; Pompe, Matevž

    2016-04-01

    A new variable distance weighted zero order connectivity index was used for development of structure-activity relationship for modeling reactivity of OH radical with alkanes and non-conjugated alkenes in the atmosphere. The proposed model is based on the assumptions that the total reaction rate can be obtained by summing all partial reaction rates and that all reaction sites are interrelated by influencing each other. The results suggest that these assumptions are justified. The model was compared with the EPA implemented model in the studied application domain and showed superior prediction capabilities. Further, optimized values of the weights that were used in our model permit some insight into mechanisms that govern the reaction OH + alkane/alkene. The most important conclusion is that the branching degree of the forming radical seems to play a major role in site specific reaction rates. Relative qualitative structural interpretation is possible, e.g. allylic site is suggested to be much more reactive than even tertiary sp3 carbon. Novel modeling software MACI, which was developed in our lab and is now available for research purposes, was used for calculations. Various variable topological indices that are again starting to be recognized because of their great potentials in simplicity, fast calculations, very good correlations and structural information, were implemented in the program.

  15. Numerical modeling of particle generation from ozone reactions with human-worn clothing in indoor environments

    NASA Astrophysics Data System (ADS)

    Rai, Aakash C.; Lin, Chao-Hsin; Chen, Qingyan

    2015-02-01

    Ozone-terpene reactions are important sources of indoor ultrafine particles (UFPs), a potential health hazard for human beings. Humans themselves act as possible sites for ozone-initiated particle generation through reactions with squalene (a terpene) that is present in their skin, hair, and clothing. This investigation developed a numerical model to probe particle generation from ozone reactions with clothing worn by humans. The model was based on particle generation measured in an environmental chamber as well as physical formulations of particle nucleation, condensational growth, and deposition. In five out of the six test cases, the model was able to predict particle size distributions reasonably well. The failure in the remaining case demonstrated the fundamental limitations of nucleation models. The model that was developed was used to predict particle generation under various building and airliner cabin conditions. These predictions indicate that ozone reactions with human-worn clothing could be an important source of UFPs in densely occupied classrooms and airliner cabins. Those reactions could account for about 40% of the total UFPs measured on a Boeing 737-700 flight. The model predictions at this stage are indicative and should be improved further.

  16. A model reaction assesses contribution of H-tunneling and coupled motions to enzyme catalysis.

    PubMed

    Liu, Qi; Zhao, Yu; Hammann, Blake; Eilers, James; Lu, Yun; Kohen, Amnon

    2012-08-17

    To assess the contribution of physical features to enzyme catalysis, the enzymatic reaction has to be compared to a relevant uncatalyzed reaction. While such comparisons have been conducted for some hydrolytic and radical reactions, it is most challenging for biological hydride transfer and redox reactions in general. Here, the same experimental tools used to study the H-tunneling and coupled motions for enzymatic hydride transfer between two carbons were used in the study of an uncatalyzed model reaction. The enzymatic oxidations of benzyl alcohol and its substituted analogues mediated by alcohol dehydrogenases were compared to the oxidations by 9-phenylxanthylium cation (PhXn(+)). The PhXn(+) serves as an NAD(+) model, while the solvent, acetonitrile, models the protein environment. Experimental comparisons included linear free energy relations with Hammett reaction constant (ρ) of zero versus -2.7; temperature-independent versus temperature-dependent primary KIEs; deflated secondary KIEs with deuteride transfer (i.e., primary-secondary coupled motion) versus no coupling between secondary KIEs and H- or D-transfer; and large versus small secondary KIEs for the enzymatic versus uncatalyzed alcohol oxidation. Some of the differences may come from differences in the order of microscopic steps between the catalyzed versus uncatalyzed reactions. However, several of these comparative experiments indicate that in contrast to the uncatalyzed reaction the transition state of the enzymatic reaction is better reorganized for H-tunneling and its H-donor is better rehybridized prior to the C-H→C transfer. These findings suggest an important role for these physical features in enzyme catalysis.

  17. A new model of reaction-driven cracking: fluid volume consumption and tensile failure during serpentinization

    NASA Astrophysics Data System (ADS)

    Eichenbaum-Pikser, J. M.; Spiegelman, M. W.; Kelemen, P. B.; Wilson, C. R.

    2013-12-01

    Reactive fluid flow plays an important role in a wide range of geodynamic processes, such as melt migration, formation of hydrous minerals on fault surfaces, and chemical weathering. These processes are governed by the complex coupling between fluid transport, reaction, and solid deformation. Reaction-driven cracking is a potentially critical feedback mechanism, by which volume change associated with chemical reaction drives fracture in the surrounding rock. It has been proposed to play a role in both serpentinization and carbonation of peridotite, motivating consideration of its application to mineral carbon sequestration. Previous studies of reactive cracking have focused on the increase in solid volume, and as such, have considered failure in compression. However, if the consumption of fluid is considered in the overall volume budget, the reaction can be net volume reducing, potentially leading to failure in tension. To explore these problems, we have formulated and solved a 2-D model of coupled porous flow, reaction kinetics, and elastic deformation using the finite element model assembler TerraFERMA (Wilson et al, G3 2013 submitted). The model is applied to the serpentinization of peridotite, which can be reasonably approximated as the transfer of a single reactive component (H2O) between fluid and solid phases, making it a simple test case to explore the process. The behavior of the system is controlled by the competition between the rate of volume consumption by the reaction, and the rate of volume replacement by fluid transport, as characterized by a nondimensional parameter χ, which depends on permeability, reaction rate, and the bulk modulus of the solid. Large values of χ correspond to fast fluid transport relative to reaction rate, resulting in a low stress, volume replacing regime. At smaller values of χ, fluid transport cannot keep up with the reaction, resulting in pore fluid under-pressure and tensile solid stresses. For the range of χ relevant

  18. Modeling photoexcited reactions of simple molecules in solution

    NASA Astrophysics Data System (ADS)

    Zhang, Jing

    Photoexcited iodine in rare gas systems offer a paradigm for understanding excited state condensed phase chemistry. Solvent induced nonadiabaticity plays an important role in the dynamics of these systems and modifies electronic structure by introducing off-diagonal coupling elements to our electronic Hamiltonian matrix. A semi-empirical electronic structure method, diatomics-in-molecules (DIM), together with its extension designed for ionic systems, diatomics-in-ionic-systems (DIIS), is applied to dynamical studies of photoexcited iodine in Ar and Xe rare gas systems. Mixed quantum-classical molecular dynamics implemented using a surface hopping algorithm is employed in a trajectory study which successfully describes the nonadiabatic nature of these systems. First we looked into the photoexcited I2 in its manifold of covalent states in solid Ar, focusing on the cage-bound but otherwise dissociative potential curves. Cage motions disturb the electronic structure and influence the coupling between electronic states to a large extent due to the large-scale intramolecular motion associated with stretching of the I2 bond resulting from double-photon excitation. Dynamical simulation with a surface hopping algorithm describes the cage-bound state photoexcitation dynamics which has only been simulated by other groups using classical methods that do not allow for nonadiabatic electronic transitions. A characteristic recursion time of the cage-bound state motion is found though our simulation which matches the experimental results, and our simulated pump-probe signals successfully reproduce the experimental spectrum. Finally we apply our potential model and surface hopping dynamical calculation method to the charge transfer complex Xe+2I- in xenon clusters. The states of this system are accessed at much higher energy than the covalent states. Charge transfer occurs between atoms and requires a significantly more complex potential energy model for which we use an extension

  19. Reactions to discrimination, stigmatization, ostracism, and other forms of interpersonal rejection: a multimotive model.

    PubMed

    Smart Richman, Laura; Leary, Mark R

    2009-04-01

    This article describes a new model that provides a framework for understanding people's reactions to threats to social acceptance and belonging as they occur in the context of diverse phenomena such as rejection, discrimination, ostracism, betrayal, and stigmatization. People's immediate reactions are quite similar across different forms of rejection in terms of negative affect and lowered self-esteem. However, following these immediate responses, people's reactions are influenced by construals of the rejection experience that predict 3 distinct motives for prosocial, antisocial, and socially avoidant behavioral responses. The authors describe the relational, contextual, and dispositional factors that affect which motives determine people's reactions to a rejection experience and the ways in which these 3 motives may work at cross-purposes. The multimotive model accounts for the myriad ways in which responses to rejection unfold over time and offers a basis for the next generation of research on interpersonal rejection.

  20. Monte Carlo analysis of uncertainty propagation in a stratospheric model. 2: Uncertainties due to reaction rates

    NASA Technical Reports Server (NTRS)

    Stolarski, R. S.; Butler, D. M.; Rundel, R. D.

    1977-01-01

    A concise stratospheric model was used in a Monte-Carlo analysis of the propagation of reaction rate uncertainties through the calculation of an ozone perturbation due to the addition of chlorine. Two thousand Monte-Carlo cases were run with 55 reaction rates being varied. Excellent convergence was obtained in the output distributions because the model is sensitive to the uncertainties in only about 10 reactions. For a 1 ppby chlorine perturbation added to a 1.5 ppby chlorine background, the resultant 1 sigma uncertainty on the ozone perturbation is a factor of 1.69 on the high side and 1.80 on the low side. The corresponding 2 sigma factors are 2.86 and 3.23. Results are also given for the uncertainties, due to reaction rates, in the ambient concentrations of stratospheric species.

  1. Dynamic Analysis of a Reaction-Diffusion Rumor Propagation Model

    NASA Astrophysics Data System (ADS)

    Zhao, Hongyong; Zhu, Linhe

    2016-06-01

    The rapid development of the Internet, especially the emergence of the social networks, leads rumor propagation into a new media era. Rumor propagation in social networks has brought new challenges to network security and social stability. This paper, based on partial differential equations (PDEs), proposes a new SIS rumor propagation model by considering the effect of the communication between the different rumor infected users on rumor propagation. The stabilities of a nonrumor equilibrium point and a rumor-spreading equilibrium point are discussed by linearization technique and the upper and lower solutions method, and the existence of a traveling wave solution is established by the cross-iteration scheme accompanied by the technique of upper and lower solutions and Schauder’s fixed point theorem. Furthermore, we add the time delay to rumor propagation and deduce the conditions of Hopf bifurcation and stability switches for the rumor-spreading equilibrium point by taking the time delay as the bifurcation parameter. Finally, numerical simulations are performed to illustrate the theoretical results.

  2. The mineralogic evolution of the Martian surface through time: Implications from chemical reaction path modeling studies

    NASA Technical Reports Server (NTRS)

    Plumlee, G. S.; Ridley, W. I.; Debraal, J. D.; Reed, M. H.

    1993-01-01

    Chemical reaction path calculations were used to model the minerals that might have formed at or near the Martian surface as a result of volcano or meteorite impact driven hydrothermal systems; weathering at the Martian surface during an early warm, wet climate; and near-zero or sub-zero C brine-regolith reactions in the current cold climate. Although the chemical reaction path calculations carried out do not define the exact mineralogical evolution of the Martian surface over time, they do place valuable geochemical constraints on the types of minerals that formed from an aqueous phase under various surficial and geochemically complex conditions.

  3. Flash Vacuum Pyrolysis of Lignin Model Compounds: Reaction Pathways of Aromatic Methoxy Groups

    SciTech Connect

    Britt, P.F.; Buchanan, A.C., III; Martineau, D.R.

    1999-03-21

    Currently, there is interest in utilizing lignin, a major constituent of biomass, as a renewable source of chemicals and fuels. High yields of liquid products can be obtained from the flash or fast pyrolysis of biomass, but the reaction pathways that lead to product formation are not understood. To provide insight into the primary reaction pathways under process relevant conditions, we are investigating the flash vacuum pyrolysis (FVP) of lignin model compounds at 500 C. This presentation will focus on the FVP of {beta}-ether linkages containing aromatic methoxy groups and the reaction pathways of methoxy-substituted phenoxy radicals.

  4. Catalytic conversion reactions in nanoporous systems with concentration-dependent selectivity: Statistical mechanical modeling

    DOE PAGES

    Garcia, Andres; Wang, Jing; Windus, Theresa L.; ...

    2016-05-20

    Statistical mechanical modeling is developed to describe a catalytic conversion reaction A → Bc or Bt with concentration-dependent selectivity of the products, Bc or Bt, where reaction occurs inside catalytic particles traversed by narrow linear nanopores. The associated restricted diffusive transport, which in the extreme case is described by single-file diffusion, naturally induces strong concentration gradients. Hence, by comparing kinetic Monte Carlo simulation results with analytic treatments, selectivity is shown to be impacted by strong spatial correlations induced by restricted diffusivity in the presence of reaction and also by a subtle clustering of reactants, A.

  5. Disproportionation of rosin on an industrial Pd/C catalyst: reaction pathway and kinetic model discrimination.

    PubMed

    Souto, Juan Carlos; Yustos, Pedro; Ladero, Miguel; Garcia-Ochoa, Felix

    2011-02-01

    In this work, a phenomenological study of the isomerisation and disproportionation of rosin acids using an industrial 5% Pd on charcoal catalyst from 200 to 240°C is carried out. Medium composition is determined by elemental microanalysis, GC-MS and GC-FID. Dehydrogenated and hydrogenated acid species molar amounts in the final product show that dehydrogenation is the main reaction. Moreover, both hydrogen and non-hydrogen concentration considering kinetic models are fitted to experimental data using a multivariable non-linear technique. Statistical discrimination among the proposed kinetic models lead to the conclusion hydrogen considering models fit much better to experimental results. The final kinetic model involves first-order isomerisation reactions of neoabietic and palustric acids to abietic acid, first-order dehydrogenation and hydrogenation of this latter acid, and hydrogenation of pimaric acids. Hydrogenation reactions are partial first-order regarding the acid and hydrogen.

  6. Modelling and simulating reaction-diffusion systems using coloured Petri nets.

    PubMed

    Liu, Fei; Blätke, Mary-Ann; Heiner, Monika; Yang, Ming

    2014-10-01

    Reaction-diffusion systems often play an important role in systems biology when developmental processes are involved. Traditional methods of modelling and simulating such systems require substantial prior knowledge of mathematics and/or simulation algorithms. Such skills may impose a challenge for biologists, when they are not equally well-trained in mathematics and computer science. Coloured Petri nets as a high-level and graphical language offer an attractive alternative, which is easily approachable. In this paper, we investigate a coloured Petri net framework integrating deterministic, stochastic and hybrid modelling formalisms and corresponding simulation algorithms for the modelling and simulation of reaction-diffusion processes that may be closely coupled with signalling pathways, metabolic reactions and/or gene expression. Such systems often manifest multiscaleness in time, space and/or concentration. We introduce our approach by means of some basic diffusion scenarios, and test it against an established case study, the Brusselator model.

  7. Reaction cross sections of intermediate energy {alpha} particles within a relativistic optical model

    SciTech Connect

    Ait-Tahar, S.; Nedjadi, Y.

    1995-07-01

    The suggestion made recently by H. Abele {ital et} {ital al}. that relativistic effects in the interaction of alpha particles with various nuclei at intermediate energies may remove the existing discrepancy between the theoretical predictions and the experimental data for the reaction cross section is investigated. We use a relativistic model based on the Kemmer-Duffin-Petiau equation and find that relativistic effects do not lead to a reduction in the reaction cross section within the present approach. Alternative explanations are discussed.

  8. Stabilization of helices in glycine and alanine dipeptides in a reaction field model of solvent

    SciTech Connect

    Shang, H.S. Lawrence Berkeley Lab., CA ); Head-Gordon, T. )

    1994-02-23

    We present molecular orbital calculations of the full conformational space of blocked glycine and alanine dipeptide in the presence of a reaction field representation of water. Secondary structures of right- and left-handed helices are found, in contrast to recent gas-phase results, indicating that the origin of helical stabilization in dipeptides is strictly due to environment. Limitations of the reaction field model and the various implications of stabilization due to environment are discussed. 43 refs., 2 figs., 3 tabs.

  9. Mimicry of the radical pair and triplet states in photosynthetic reaction centers with a synthetic model

    SciTech Connect

    Wasielewski, M.R.; Greenfield, S.R.; Svec, W.A.

    1997-08-01

    Results are presented on a photosynthetic model system that closely mimics the spin dynamics of triplet state formation found in photosynthetic reaction centers. This research will make it possible to design new models to probe the mechanism of the primary events of photosynthesis.

  10. Strontium Adsorption and Desorption Reactions in Model Drinking Water Distribution Systems

    DTIC Science & Technology

    2014-02-04

    RESPONSIBLE PERSON 19b. TELEPHONE NUMBER (Include area code) 11-04-2014 Journal Article Strontium adsorption and desorption reactions in model... strontium (Sr2+) adsorption to and desorption from iron corrosion products were examined in two model drinking water distribution systems (DWDS...used to control Sr2; desorption. calcium carbonate; drinking water distribution system; α-FeOOH; iron; strontium ; XANES Unclassified

  11. Gas Phase Model of Surface Reactions for N{2} Afterglows

    NASA Astrophysics Data System (ADS)

    Marković, V. Lj.; Petrović, Z. Lj.; Pejović, M. M.

    1996-07-01

    The adequacy of the homogeneous gas phase model as a representation of the surface losses of diffusing active particles in gas phase is studied. As an example the recent data obtained for the surface recombination coefficients are reanalyzed. The data were obtained by the application of the breakdown delay times which consists of the measurements of the breakdown delay times t_d as a function of the afterglow period tau. It was found that for the conditions of our experiment, the diffusion should not be neglected as the final results are significantly different when obtained by approximate gas phase representation and by exact numerical solution to the diffusion equation. While application of the gas phase effective coefficients to represent surface losses gives an error in the value of the recombination coefficient, it reproduces correctly other characteristics such as order of the process which can be obtained from simple fits to the experimental data. Dans cet article, nous étudions la validité du modèle approximatif représentant les pertes superficielles des particules actives qui diffusent de la phase gazeuse comme pertes dans la phase homogène du gaz. Les données actuelles du coefficient de recombination en surface sont utilisées par cette vérification . Les données experimentales sont obtenues en utilisant la technique qui consiste en la mesure du temps de retard du début de la décharge en fonction de la période de relaxation. Nous avons trouvé que, pour nos conditions expérimentales, la diffusion ne peut être négligée. Aussi, les résultats finals sont considérablement différents quand ils sont obtenus en utilisant le modèle approximatif par comparaison aves les résultats obtenus par la solution numérique exacte de l'équation de la diffusion. L'application des coefficients effectifs dans la phase gaseuse pour la présentation des pertes superficielles donne, pour les coefficients de la recombinaison, des valeurs qui diffèrent en

  12. Space-time quantitative source apportionment of soil heavy metal concentration increments.

    PubMed

    Yang, Yong; Christakos, George; Guo, Mingwu; Xiao, Lu; Huang, Wei

    2017-04-01

    Assessing the space-time trends and detecting the sources of heavy metal accumulation in soils have important consequences in the prevention and treatment of soil heavy metal pollution. In this study, we collected soil samples in the eastern part of the Qingshan district, Wuhan city, Hubei Province, China, during the period 2010-2014. The Cd, Cu, Pb and Zn concentrations in soils exhibited a significant accumulation during 2010-2014. The spatiotemporal Kriging technique, based on a quantitative characterization of soil heavy metal concentration variations in terms of non-separable variogram models, was employed to estimate the spatiotemporal soil heavy metal distribution in the study region. Our findings showed that the Cd, Cu, and Zn concentrations have an obvious incremental tendency from the southwestern to the central part of the study region. However, the Pb concentrations exhibited an obvious tendency from the northern part to the central part of the region. Then, spatial overlay analysis was used to obtain absolute and relative concentration increments of adjacent 1- or 5-year periods during 2010-2014. The spatial distribution of soil heavy metal concentration increments showed that the larger increments occurred in the center of the study region. Lastly, the principal component analysis combined with the multiple linear regression method were employed to quantify the source apportionment of the soil heavy metal concentration increments in the region. Our results led to the conclusion that the sources of soil heavy metal concentration increments should be ascribed to industry, agriculture and traffic. In particular, 82.5% of soil heavy metal concentration increment during 2010-2014 was ascribed to industrial/agricultural activities sources. Using STK and SOA to obtain the spatial distribution of heavy metal concentration increments in soils. Using PCA-MLR to quantify the source apportionment of soil heavy metal concentration increments.

  13. Models for identification of erroneous atom-to-atom mapping of reactions performed by automated algorithms.

    PubMed

    Muller, Christophe; Marcou, Gilles; Horvath, Dragos; Aires-de-Sousa, João; Varnek, Alexandre

    2012-12-21

    Machine learning (SVM and JRip rule learner) methods have been used in conjunction with the Condensed Graph of Reaction (CGR) approach to identify errors in the atom-to-atom mapping of chemical reactions produced by an automated mapping tool by ChemAxon. The modeling has been performed on the three first enzymatic classes of metabolic reactions from the KEGG database. Each reaction has been converted into a CGR representing a pseudomolecule with conventional (single, double, aromatic, etc.) bonds and dynamic bonds characterizing chemical transformations. The ChemAxon tool was used to automatically detect the matching atom pairs in reagents and products. These automated mappings were analyzed by the human expert and classified as "correct" or "wrong". ISIDA fragment descriptors generated for CGRs for both correct and wrong mappings were used as attributes in machine learning. The learned models have been validated in n-fold cross-validation on the training set followed by a challenge to detect correct and wrong mappings within an external test set of reactions, never used for learning. Results show that both SVM and JRip models detect most of the wrongly mapped reactions. We believe that this approach could be used to identify erroneous atom-to-atom mapping performed by any automated algorithm.

  14. Golden rule kinetics of transfer reactions in condensed phase: The microscopic model of electron transfer reactions in disordered solid matrices

    NASA Astrophysics Data System (ADS)

    Basilevsky, M. V.; Odinokov, A. V.; Titov, S. V.; Mitina, E. A.

    2013-12-01

    The algorithm for a theoretical calculation of transfer reaction rates for light quantum particles (i.e., the electron and H-atom transfers) in non-polar solid matrices is formulated and justified. The mechanism postulated involves a local mode (an either intra- or inter-molecular one) serving as a mediator which accomplishes the energy exchange between the reacting high-frequency quantum mode and the phonon modes belonging to the environment. This approach uses as a background the Fermi golden rule beyond the usually applied spin-boson approximation. The dynamical treatment rests on the one-dimensional version of the standard quantum relaxation equation for the reduced density matrix, which describes the frequency fluctuation spectrum for the local mode under consideration. The temperature dependence of a reaction rate is controlled by the dimensionless parameter ξ0 = ℏω0/kBT where ω0 is the frequency of the local mode and T is the temperature. The realization of the computational scheme is different for the high/intermediate (ξ0 < 1 - 3) and for low (ξ0 ≫ 1) temperature ranges. For the first (quasi-classical) kinetic regime, the Redfield approximation to the solution of the relaxation equation proved to be sufficient and efficient in practical applications. The study of the essentially quantum-mechanical low-temperature kinetic regime in its asymptotic limit requires the implementation of the exact relaxation equation. The coherent mechanism providing a non-vanishing reaction rate has been revealed when T → 0. An accurate computational methodology for the cross-over kinetic regime needs a further elaboration. The original model of the hopping mechanism for electronic conduction in photosensitive organic materials is considered, based on the above techniques. The electron transfer (ET) in active centers of such systems proceeds via local intra- and intermolecular modes. The active modes, as a rule, operate beyond the kinetic regimes, which are usually

  15. Golden rule kinetics of transfer reactions in condensed phase: the microscopic model of electron transfer reactions in disordered solid matrices.

    PubMed

    Basilevsky, M V; Odinokov, A V; Titov, S V; Mitina, E A

    2013-12-21

    The algorithm for a theoretical calculation of transfer reaction rates for light quantum particles (i.e., the electron and H-atom transfers) in non-polar solid matrices is formulated and justified. The mechanism postulated involves a local mode (an either intra- or inter-molecular one) serving as a mediator which accomplishes the energy exchange between the reacting high-frequency quantum mode and the phonon modes belonging to the environment. This approach uses as a background the Fermi golden rule beyond the usually applied spin-boson approximation. The dynamical treatment rests on the one-dimensional version of the standard quantum relaxation equation for the reduced density matrix, which describes the frequency fluctuation spectrum for the local mode under consideration. The temperature dependence of a reaction rate is controlled by the dimensionless parameter ξ0 = ℏω0/k(B)T where ω0 is the frequency of the local mode and T is the temperature. The realization of the computational scheme is different for the high/intermediate (ξ0 < 1 - 3) and for low (ξ0 ≫ 1) temperature ranges. For the first (quasi-classical) kinetic regime, the Redfield approximation to the solution of the relaxation equation proved to be sufficient and efficient in practical applications. The study of the essentially quantum-mechanical low-temperature kinetic regime in its asymptotic limit requires the implementation of the exact relaxation equation. The coherent mechanism providing a non-vanishing reaction rate has been revealed when T → 0. An accurate computational methodology for the cross-over kinetic regime needs a further elaboration. The original model of the hopping mechanism for electronic conduction in photosensitive organic materials is considered, based on the above techniques. The electron transfer (ET) in active centers of such systems proceeds via local intra- and intermolecular modes. The active modes, as a rule, operate beyond the kinetic regimes, which are usually

  16. A Film Depositional Model of Permeability for Mineral Reactions in Unsaturated Media.

    SciTech Connect

    Freedman, Vicky L.; Saripalli, Prasad; Bacon, Diana H.; Meyer, Philip D.

    2004-11-15

    A new modeling approach based on the biofilm models of Taylor et al. (1990, Water Resources Research, 26, 2153-2159) has been developed for modeling changes in porosity and permeability in saturated porous media and implemented in an inorganic reactive transport code. Application of the film depositional models to mineral precipitation and dissolution reactions requires that calculations of mineral films be dynamically changing as a function of time dependent reaction processes. Since calculations of film thicknesses do not consider mineral density, results show that the film porosity model does not adequately describe volumetric changes in the porous medium. These effects can be included in permeability calculations by coupling the film permeability models (Mualem and Childs and Collis-George) to a volumetric model that incorporates both mineral density and reactive surface area. Model simulations demonstrate that an important difference between the biofilm and mineral film models is in the translation of changes in mineral radii to changes in pore space. Including the effect of tortuosity on pore radii changes improves the performance of the Mualem permeability model for both precipitation and dissolution. Results from simulation of simultaneous dissolution and secondary mineral precipitation provides reasonable estimates of porosity and permeability. Moreover, a comparison of experimental and simulated data show that the model yields qualitatively reasonable results for permeability changes due to solid-aqueous phase reactions.

  17. Nuclear cycler: An incremental approach to the deflection of asteroids

    NASA Astrophysics Data System (ADS)

    Vasile, Massimiliano; Thiry, Nicolas

    2016-04-01

    This paper introduces a novel deflection approach based on nuclear explosions: the nuclear cycler. The idea is to combine the effectiveness of nuclear explosions with the controllability and redundancy offered by slow push methods within an incremental deflection strategy. The paper will present an extended model for single nuclear stand-off explosions in the proximity of elongated ellipsoidal asteroids, and a family of natural formation orbits that allows the spacecraft to deploy multiple bombs while being shielded by the asteroid during the detonation.

  18. Intervertebral reaction force prediction using an enhanced assembly of OpenSim models.

    PubMed

    Senteler, Marco; Weisse, Bernhard; Rothenfluh, Dominique A; Snedeker, Jess G

    2016-01-01

    OpenSim offers a valuable approach to investigating otherwise difficult to assess yet important biomechanical parameters such as joint reaction forces. Although the range of available models in the public repository is continually increasing, there currently exists no OpenSim model for the computation of intervertebral joint reactions during flexion and lifting tasks. The current work combines and improves elements of existing models to develop an enhanced model of the upper body and lumbar spine. Models of the upper body with extremities, neck and head were combined with an improved version of a lumbar spine from the model repository. Translational motion was enabled for each lumbar vertebrae with six controllable degrees of freedom. Motion segment stiffness was implemented at lumbar levels and mass properties were assigned throughout the model. Moreover, body coordinate frames of the spine were modified to allow straightforward variation of sagittal alignment and to simplify interpretation of results. Evaluation of model predictions for level L1-L2, L3-L4 and L4-L5 in various postures of forward flexion and moderate lifting (8 kg) revealed an agreement within 10% to experimental studies and model-based computational analyses. However, in an extended posture or during lifting of heavier loads (20 kg), computed joint reactions differed substantially from reported in vivo measures using instrumented implants. We conclude that agreement between the model and available experimental data was good in view of limitations of both the model and the validation datasets. The presented model is useful in that it permits computation of realistic lumbar spine joint reaction forces during flexion and moderate lifting tasks. The model and corresponding documentation are now available in the online OpenSim repository.

  19. Extended kinetic model of real-time polymerase chain reaction process

    NASA Astrophysics Data System (ADS)

    Fedorov, A. A.; Sochivko, D. G.; Varlamov, D. A.; Kurochkin, V. E.

    2016-11-01

    Real-time polymerase chain reaction (real-time PCR) is the main molecular genetic method used for qualitative and quantitative analysis of specific nucleic acid sequences in many areas of biomedical research. Theoretical study of pCr models allows to estimate the influence of various reaction components and parameters, and to determine the unknown parameter values by approximating the experimental real-time PCR curves. An extended kinetic model of real-time PCR is presented. The model takes into account the enzyme activity based on Michaelis-Menten kinetics, the hybridization of complementary DNA fragments, the presence of a fluorescent probe used for detection of the reaction products, and the temperature dependence of primers and probe hybridization.

  20. Mode specificity and product energy disposal in unimolecular reactions: insights from the sudden vector projection model.

    PubMed

    Li, Jun; Guo, Hua

    2014-04-03

    A simple model is proposed to predict mode specificity and product energy disposal in unimolecular dissociation reactions. This so-called Sudden Vector Projection (SVP) model quantifies the coupling of a reactant or product mode with the reaction coordinate at the transition state by projecting the corresponding normal mode vector onto the imaginary frequency mode at the saddle point. Due to the sudden assumption, SVP predictions for mode specificity are expected to be valid only when the reactant molecule has weak intermodal coupling. On the other hand, the sudden limit is generally satisfied for its predictions of product energy disposal in unimolecular reactions with a tight barrier. The SVP model is applied to several prototypical systems and the agreement with available experimental and theoretical results is satisfactory.

  1. Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures.

    PubMed

    Sankar, Punnaivanam; Aghila, Gnanasekaran

    2007-01-01

    The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.

  2. 40 CFR 60.2590 - When must I submit the notifications of achievement of increments of progress?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... achievement of increments of progress? 60.2590 Section 60.2590 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) STANDARDS OF PERFORMANCE FOR NEW STATIONARY SOURCES... Commenced Construction On or Before November 30, 1999 Model Rule-Increments of Progress § 60.2590 When...

  3. 40 CFR 60.2590 - When must I submit the notifications of achievement of increments of progress?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... achievement of increments of progress? 60.2590 Section 60.2590 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) STANDARDS OF PERFORMANCE FOR NEW STATIONARY SOURCES... Commenced Construction On or Before November 30, 1999 Model Rule-Increments of Progress § 60.2590 When...

  4. Nanolithographic Fabrication and Heterogeneous Reaction Studies ofTwo-Dimensional Platinum Model Catalyst Systems

    SciTech Connect

    Contreras, Anthony Marshall

    2006-05-20

    In order to better understand the fundamental components that govern catalytic activity, two-dimensional model platinum nanocatalyst arrays have been designed and fabricated. These catalysts arrays are meant to model the interplay of the metal and support important to industrial heterogeneous catalytic reactions. Photolithography and sub-lithographic techniques such as electron beam lithography, size reduction lithography and nanoimprint lithography have been employed to create these platinum nanoarrays. Both in-situ and ex-situ surface science techniques and catalytic reaction measurements were used to correlate the structural parameters of the system to catalytic activity.

  5. Reversible Reshaping of Supported Metal Nanoislands Under Reaction Conditions in a Minimalistic Lattice Model

    NASA Astrophysics Data System (ADS)

    Korobov, A.

    2016-05-01

    The shape of (nano)islands is among significant factors of the catalytic activity of supported catalysts. A lattice model of the reshaping under reaction conditions is suggested and studied by means of kinetic Monte Carlo simulations. It is rooted in experimental findings and is simplified as far as possible to still demonstrate reversible compact—ramified shape transitions. This simple model with complex behavior demonstrates several reshaping regimes and is considered as a possible sub-network of more realistic networks of heterogeneous catalytic reactions.

  6. Using synthetic model systems to understand charge separation and spin dynamics in photosynthetic reaction centers.

    SciTech Connect

    Wasielewski, M. R.

    1998-08-27

    Our current work in modeling reaction center dynamics has resulted in the observation of each major spin-dependent photochemical pathway that is observed in reaction centers. The development of new, simpler model systems has permitted us to probe deeply into the mechanistic issues that drive these dynamics. Based on these results we have returned to biomimetic chlorophyll-based electron donors to mimic these dynamics. Future studies will focus on the details of electronic structure and energetic of both the donor-acceptor molecules and their surrounding environment that dictate the mechanistic pathways and result in efficient photosynthetic charge separation.

  7. Influence of diffusive porosity architecture on kinetically-controlled reactions in mobile-immobile models

    NASA Astrophysics Data System (ADS)

    Babey, T.; Ginn, T. R.; De Dreuzy, J. R.

    2014-12-01

    Solute transport in porous media may be structured at various scales by geological features, from connectivity patterns of pores to fracture networks. This structure impacts solute repartition and consequently reactivity. Here we study numerically the influence of the organization of porous volumes within diffusive porosity zones on different reactions. We couple a mobile-immobile transport model where an advective zone exchanges with diffusive zones of variable structure to the geochemical modeling software PHREEQC. We focus on two kinetically-controlled reactions, a linear sorption and a nonlinear dissolution of a mineral. We show that in both cases the structure of the immobile zones has an important impact on the overall reaction rates. Through the Multi-Rate Mass Transfer (MRMT) framework, we show that this impact is very well captured by residence times-based models for the kinetic linear sorption, as it is mathematically equivalent to a modification of the initial diffusive structure; Consequently, the overall reaction rate could be easily extrapolated from a conservative tracer experiment. The MRMT models however struggle to reproduce the non-linearity and the threshold effects associated with the kinetic dissolution. A slower reaction, by allowing more time for diffusion to smooth out the concentration gradients, tends to increase their relevance. Figure: Left: Representation of a mobile-immobile model with a complex immobile architecture. The mobile zone is indicated by an arrow. Right: Total remaining mass of mineral in mobile-immobile models and in their equivalent MRMT models during a flush by a highly under-saturated solution. The models only differ by the organization of their immobile porous volumes.

  8. 14 CFR § 1274.918 - Incremental funding.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 14 Aeronautics and Space 5 2014-01-01 2014-01-01 false Incremental funding. § 1274.918 Section Â... WITH COMMERCIAL FIRMS Other Provisions and Special Conditions § 1274.918 Incremental funding. Incremental Funding July 2002 (a) Of the award amount indicated on the cover page of this Agreement, only...

  9. VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions

    NASA Astrophysics Data System (ADS)

    Kuechler, Erich R.; Giese, Timothy J.; York, Darrin M.

    2016-04-01

    To better represent the solvation effects observed along reaction pathways, and of ionic species in general, a charge-dependent variable-radii smooth conductor-like screening model (VR-SCOSMO) is developed. This model is implemented and parameterized with a third order density-functional tight binding quantum model, DFTB3/3OB-OPhyd, a quantum method which was developed for organic and biological compounds, utilizing a specific parameterization for phosphate hydrolysis reactions. Unlike most other applications with the DFTB3/3OB model, an auxiliary set of atomic multipoles is constructed from the underlying DFTB3 density matrix which is used to interact the solute with the solvent response surface. The resulting method is variational, produces smooth energies, and has analytic gradients. As a baseline, a conventional SCOSMO model with fixed radii is also parameterized. The SCOSMO and VR-SCOSMO models shown have comparable accuracy in reproducing neutral-molecule absolute solvation free energies; however, the VR-SCOSMO model is shown to reduce the mean unsigned errors (MUEs) of ionic compounds by half (about 2-3 kcal/mol). The VR-SCOSMO model presents similar accuracy as a charge-dependent Poisson-Boltzmann model introduced by Hou et al. [J. Chem. Theory Comput. 6, 2303 (2010)]. VR-SCOSMO is then used to examine the hydrolysis of trimethylphosphate and seven other phosphoryl transesterification reactions with different leaving groups. Two-dimensional energy landscapes are constructed for these reactions and calculated barriers are compared to those obtained from ab initio polarizable continuum calculations and experiment. Results of the VR-SCOSMO model are in good agreement in both cases, capturing the rate-limiting reaction barrier and the nature of the transition state.

  10. VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.

    PubMed

    Kuechler, Erich R; Giese, Timothy J; York, Darrin M

    2016-04-28

    To better represent the solvation effects observed along reaction pathways, and of ionic species in general, a charge-dependent variable-radii smooth conductor-like screening model (VR-SCOSMO) is developed. This model is implemented and parameterized with a third order density-functional tight binding quantum model, DFTB3/3OB-OPhyd, a quantum method which was developed for organic and biological compounds, utilizing a specific parameterization for phosphate hydrolysis reactions. Unlike most other applications with the DFTB3/3OB model, an auxiliary set of atomic multipoles is constructed from the underlying DFTB3 density matrix which is used to interact the solute with the solvent response surface. The resulting method is variational, produces smooth energies, and has analytic gradients. As a baseline, a conventional SCOSMO model with fixed radii is also parameterized. The SCOSMO and VR-SCOSMO models shown have comparable accuracy in reproducing neutral-molecule absolute solvation free energies; however, the VR-SCOSMO model is shown to reduce the mean unsigned errors (MUEs) of ionic compounds by half (about 2-3 kcal/mol). The VR-SCOSMO model presents similar accuracy as a charge-dependent Poisson-Boltzmann model introduced by Hou et al. [J. Chem. Theory Comput. 6, 2303 (2010)]. VR-SCOSMO is then used to examine the hydrolysis of trimethylphosphate and seven other phosphoryl transesterification reactions with different leaving groups. Two-dimensional energy landscapes are constructed for these reactions and calculated barriers are compared to those obtained from ab initio polarizable continuum calculations and experiment. Results of the VR-SCOSMO model are in good agreement in both cases, capturing the rate-limiting reaction barrier and the nature of the transition state.

  11. Computational Study of a Model System of Enzyme-Mediated [4+2] Cycloaddition Reaction

    PubMed Central

    2015-01-01

    A possible mechanistic pathway related to an enzyme-catalyzed [4+2] cycloaddition reac-tion was studied by theoretical calculations at density functional (B3LYP, O3LYP, M062X) and semiempirical levels (PM6-DH2, PM6) performed on a model system. The calculations were carried out for the key [4+2] cycloaddition step considering enzyme-catalyzed biosynthesis of Spinosyn A in a model reaction, where a reliable example of a biological Diels-Alder reaction was reported experimentally. In the present study it was demonstrated that the [4+2] cycloaddition reaction may benefit from moving along the energetically balanced reaction coordinate, which enabled the catalytic rate enhancement of the [4+2] cycloaddition pathway involving a single transition state. Modeling of such a system with coordination of three amino acids indicated a reliable decrease of activation energy by ~18.0 kcal/mol as compared to a non-catalytic transformation. PMID:25853669

  12. Supercritical water oxidation of quinazoline: Reaction kinetics and modeling.

    PubMed

    Gong, Yanmeng; Guo, Yang; Wang, Shuzhong; Song, Wenhan; Xu, Donghai

    2017-03-01

    This paper presents a first quantitative kinetic model for supercritical water oxidation (SCWO) of quinazoline that describes the formation and interconversion of intermediates and final products at 673-873 K. The set of 11 reaction pathways for phenol, pyrimidine, naphthalene, NH3, etc, involved in the simplified reaction network proved sufficient for fitting the experimental results satisfactorily. We validated the model prediction ability on CO2 yields at initial quinazoline loading not used in the parameter estimation. Reaction rate analysis and sensitivity analysis indicate that nearly all reactions reach their thermodynamic equilibrium within 300 s. The pyrimidine yielding from quinazoline is the dominant ring-opening pathway and provides a significant contribution to CO2 formation. Low sensitivity of NH3 decomposition rate to concentration confirms its refractory nature in SCWO. Nitrogen content in liquid products decreases whereas that in gaseous phase increases as reaction time prolonged. The nitrogen predicted by the model in gaseous phase combined with the experimental nitrogen in liquid products gives an accurate nitrogen balance of conversion process.

  13. Reaction mechanism of monoethanolamine with CO₂ in aqueous solution from molecular modeling.

    PubMed

    Xie, Hong-Bin; Zhou, Yanzi; Zhang, Yingkai; Johnson, J Karl

    2010-11-04

    We present a theoretical study of the reaction mechanism of monoethanolamine (MEA) with CO₂ in an aqueous solution. We have used molecular orbital reaction pathway calculations to compute reaction free energy landscapes for the reaction steps involved in the formation of carbamic acids and carbamates. We have used the conductor-like polarizable continuum model to calculate reactant, product, and transition state geometries and vibrational frequencies within density functional theory (DFT). We have also computed single point energies for all stationary structures using a coupled cluster approach with singles, doubles, and perturbational triple excitations using the DFT geometries. Our calculations indicate that a two-step reaction mechanism that proceeds via a zwitterion intermediate to form carbamate is the most favorable reaction channel. The first step, leading to formation of the zwitterion, is found to be rate-determining, and the activation free energies are 12.0 (10.2) and 11.3 (9.6) kcal/mol using Pauling (Bondi) radii within the CPCM model at the CCSD(T)/6-311++G(d,p) and CCSD(T)/6-311++G(2df,2p) levels of theory, respectively, using geometries and vibrational frequencies obtained at the B3LYP/6-311++G(d,p) level of theory. These results are in reasonable agreement with the experimental value of about 12 kcal/mol. The second step is an acid-base reaction between a zwitterion and MEA. We have developed a microkinetic model to estimate the effective reaction order at intermediate concentrations. Our model predicts an equilibrium concentration for the zwitterion on the order of 10⁻¹¹ mol/L, which explains why the existence of the zwitterion intermediate has never been detected experimentally. The effective reaction order from our model is close to unity, also in agreement with experiments. Complementary ab initio QM/MM molecular dynamics simulations with umbrella sampling have been carried out to determine the free energy profiles of zwitterion formation

  14. Reactions of aqueous chlorine and chlorine dioxide with model food compounds.

    PubMed Central

    Fukayama, M Y; Tan, H; Wheeler, W B; Wei, C I

    1986-01-01

    Chlorine and chlorine dioxide (ClO2), common disinfecting and bleaching chemicals used in the food industry, are potent oxidizing and chlorinating agents. Unfortunately, little is known about the nature of the reactions of chlorine with organic food constituents. This presentation reviews published information concerning the reactions of chlorine gas (Cl2[g]), aqueous chlorine, and ClO2 with model food compounds, the fate of chlorine during the chlorination of specific food products, and the potential toxicity of the reaction products. Fatty acids and their methyl esters react with chlorine with the degree of incorporation corresponding to their degree of unsaturation. Aqueous chlorine oxidizes and chlorinates lipids and amino acids much more readily than ClO2. Several amino acids are highly susceptible to oxidation and chlorination by chlorine compounds. Reactions of chlorine and ClO2 with several food products, including flour and shrimp, have also been characterized. In one model system, 99% of Cl2(g) either reacted with components of flour or was consumed by oxidation/chlorination reactions. The lipids extracted from the chlorinated flour contained significant amounts of chlorine. Exposure of shrimp to hypochlorous acid (HOCl) solution resulted in significant incorporation of chlorine into the edible portion. Although significant quantities of chlorine can be incorporated into specific model compounds and food products, the health risks associated with exposure to chlorinated organic products are unknown. Preliminary studies using the Ames Salmonella/microsome mutagenicity assay indicate that the reaction products from mixtures of aqueous chlorine and various lipids or tryptophan are nonmutagenic. Nevertheless, additional studies are warranted, so that the toxicological significance of these reaction products can be understood more fully. PMID:3545804

  15. Modelling of silicon oxynitridation by nitrous oxide using the reaction rate approach

    SciTech Connect

    Dominique Krzeminski, Christophe

    2013-12-14

    Large technological progress in oxynitridation processing leads to the introduction of silicon oxynitride as ultra-thin gate oxide. On the theoretical side, few studies have been dedicated to the process modelling of oxynitridation. Such an objective is a considerable challenge regarding the various atomistic mechanisms occurring during this fabrication step. In this article, some progress performed to adapt the reaction rate approach for the modelling of oxynitride growth by a nitrous ambient are reported. The Ellis and Buhrman's approach is used for the gas phase decomposition modelling. Taking into account the mass balance of the species at the interface between the oxynitride and silicon, a minimal kinetic model describing the oxide growth has been calibrated and implemented. The influence of nitrogen on the reaction rate has been introduced in an empirical way. The oxidation kinetics predicted with this minimal model compares well with several experiments.

  16. Noise-and delay-induced phase transitions of the dimer-monomer surface reaction model

    NASA Astrophysics Data System (ADS)

    Zeng, Chunhua; Wang, Hua

    2012-06-01

    The effects of noise and time-delayed feedback in the dimer-monomer (DM) surface reaction model are investigated. Applying small delay approximation, we construct a stochastic delayed differential equation and its Fokker-Planck equation to describe the state evolution of the DM reaction model. We show that the noise can only induce first-order irreversible phase transition (IPT) characteristic of the DM model, however the combination of the noise and time-delayed feedback can simultaneously induce first- and second-order IPT characteristics of the DM model. Therefore, it is shown that the well-known first- and second-order IPT characteristics of the DM model may be viewed as noise-and delay-induced phase transitions.

  17. Modeling of the peritectic reaction and macro-segregation in casting of low carbon steel

    NASA Astrophysics Data System (ADS)

    El-Bealy, M.; Fredriksson, H.

    1996-12-01

    Macro-microscopic models have been developed to describe the macrosegregation behavior associated with the peritectic reaction of low carbon steel. The macrosegregation model has been established on the basis of previously published work and experimental data. A microscopic model of a three-phase reaction L+ δ→ γ has been modeled by using Fredriksson’s approach. Four horizontal and unidirectional solidified experimental groups simulating continuous casting have been performed with a low carbon steel containing 0.13 wt pct carbon. The extent of macrosegregation of carbon was determined by wet chemical analysis of millings. It is confirmed, by comparing calculated results with experimental results, that this model successfully predicts the occurrence of macrosegregation. The results indicate that a peritectic reaction which is associated with a high cooling rate generates high thermal contraction and a high tensile strain rate at the peritectic temperature. Therefore, the macrosegregation, particularly at the ingot surface, is very sensitive to the cooling rate, where extremely high positive segregation was observed in the case of a high cooling rate. However, in the case of slow cooling rate, negative segregation was noted. The mechanism of macrosegregation with peritectic reaction is discussed in detail.

  18. Catalytic ignition model in a monolithic reactor with in-depth reaction

    NASA Technical Reports Server (NTRS)

    Tien, Ta-Ching; Tien, James S.

    1990-01-01

    Two transient models have been developed to study the catalytic ignition in a monolithic catalytic reactor. The special feature in these models is the inclusion of thermal and species structures in the porous catalytic layer. There are many time scales involved in the catalytic ignition problem, and these two models are developed with different time scales. In the full transient model, the equations are non-dimensionalized by the shortest time scale (mass diffusion across the catalytic layer). It is therefore accurate but is computationally costly. In the energy-integral model, only the slowest process (solid heat-up) is taken as nonsteady. It is approximate but computationally efficient. In the computations performed, the catalyst is platinum and the reactants are rich mixtures of hydrogen and oxygen. One-step global chemical reaction rates are used for both gas-phase homogeneous reaction and catalytic heterogeneous reaction. The computed results reveal the transient ignition processes in detail, including the structure variation with time in the reactive catalytic layer. An ignition map using reactor length and catalyst loading is constructed. The comparison of computed results between the two transient models verifies the applicability of the energy-integral model when the time is greater than the second largest time scale of the system. It also suggests that a proper combined use of the two models can catch all the transient phenomena while minimizing the computational cost.

  19. Development and application of a numerical model of kinetic and equilibrium microbiological and geochemical reactions (BIOKEMOD)

    NASA Astrophysics Data System (ADS)

    Salvage, Karen M.; Yeh, Gour-Tsyh

    1998-08-01

    This paper presents the conceptual and mathematical development of the numerical model titled BIOKEMOD, and verification simulations performed using the model. BIOKEMOD is a general computer model for simulation of geochemical and microbiological reactions in batch aqueous solutions. BIOKEMOD may be coupled with hydrologic transport codes for simulation of chemically and biologically reactive transport. The chemical systems simulated may include any mixture of kinetic and equilibrium reactions. The pH, pe, and ionic strength may be specified or simulated. Chemical processes included are aqueous complexation, adsorption, ion-exchange and precipitation/dissolution. Microbiological reactions address growth of biomass and degradation of chemicals by microbial metabolism of substrates, nutrients, and electron acceptors. Inhibition or facilitation of growth due to the presence of specific chemicals and a lag period for microbial acclimation to new substrates may be simulated if significant in the system of interest. Chemical reactions controlled by equilibrium are solved using the law of mass action relating the thermodynamic equilibrium constant to the activities of the products and reactants. Kinetic chemical reactions are solved using reaction rate equations based on collision theory. Microbiologically mediated reactions for substrate removal and biomass growth are assumed to follow Monod kinetics modified for the potentially limiting effects of substrate, nutrient, and electron acceptor availability. BIOKEMOD solves the ordinary differential and algebraic equations of mixed geochemical and biogeochemical reactions using the Newton-Raphson method with full matrix pivoting. Simulations may be either steady state or transient. Input to the program includes the stoichiometry and parameters describing the relevant chemical and microbiological reactions, initial conditions, and sources/sinks for each chemical species. Output includes the chemical and biomass concentrations

  20. Multiresponse kinetic modelling of Maillard reaction and caramelisation in a heated glucose/wheat flour system.

    PubMed

    Kocadağlı, Tolgahan; Gökmen, Vural

    2016-11-15

    The study describes the kinetics of the formation and degradation of α-dicarbonyl compounds in glucose/wheat flour system heated under low moisture conditions. Changes in the concentrations of glucose, fructose, individual free amino acids, lysine and arginine residues, glucosone, 1-deoxyglucosone, 3-deoxyglucosone, 3,4-dideoxyglucosone, 5-hydroxymethyl-2-furfural, glyoxal, methylglyoxal and diacetyl concentrations were determined to form a multiresponse kinetic model for isomerisation and degradation reactions of glucose. Degradation of Amadori product mainly produced 1-deoxyglucosone. Formation of 3-deoxyglucosone proceeded directly from glucose and also Amadori product degradation. Glyoxal formation was predominant from glucosone while methylglyoxal and diacetyl originated from 1-deoxyglucosone. Formation of 5-hydroxymethyl-2-furfural from fructose was found to be a key step. Multi-response kinetic modelling of Maillard reaction and caramelisation simultaneously indicated quantitatively predominant parallel and consecutive pathways and rate limiting steps by estimating the reaction rate constants.

  1. A New Sheet Metal Forming System Based on Incremental Punching

    NASA Astrophysics Data System (ADS)

    Luo, Yuanxin

    conducted by the mean of computer simulation in consideration of applying a large impulsive force. This study validates the machine stability and accuracy. One of the keys to successful application of sheet metal forming is to be able to predict the deformation and the strain/stress of the part incurred during the forming process. Because of the complexity of the ISMF process, it is not possible to derive an analytical method. The alternative is to use Finite Element Analysis (FEA). However, based on our experience, it takes about one week to solve a simple case. A mechanics model is therefore developed. It consists of two steps. The first step is to computer the final shape: the initial geometric surface is obtained using the punch positions; then using the minimum energy principle, the virtual forces drive the nodes of geometric surface to their lowest energy positions, which gives the final shape of the forming part. The second step is to predict the strain and stress distributions. This is done using the inverse Finite Element Modeling (FEM). An in-house computer software is developed using MATLABRTM. In order to verify the new mechanics model, numerical and experimental studies are conducted using the new incremental punching system. The final shape and thickness distributions of parts are compared to verify the mechanics model. It is found that the model prediction fits the experiment result well. Forming parameters are also investigated. To evaluate the capability of the presented ISMF process, the formability is studied by the means of theory and experiment. A modified M-K model is proposed for predicting the forming limit of the formed part which is undergoing a very complicated strain path. The maximum forming angle is also investigated by experiments.

  2. Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling

    PubMed Central

    Matsuura, Tomoaki; Tanimura, Naoki; Hosoda, Kazufumi; Yomo, Tetsuya; Shimizu, Yoshihiro

    2017-01-01

    To elucidate the dynamic features of a biologically relevant large-scale reaction network, we constructed a computational model of minimal protein synthesis consisting of 241 components and 968 reactions that synthesize the Met-Gly-Gly (MGG) peptide based on an Escherichia coli-based reconstituted in vitro protein synthesis system. We performed a simulation using parameters collected primarily from the literature and found that the rate of MGG peptide synthesis becomes nearly constant in minutes, thus achieving a steady state similar to experimental observations. In addition, concentration changes to 70% of the components, including intermediates, reached a plateau in a few minutes. However, the concentration change of each component exhibits several temporal plateaus, or a quasi-stationary state (QSS), before reaching the final plateau. To understand these complex dynamics, we focused on whether the components reached a QSS, mapped the arrangement of components in a QSS in the entire reaction network structure, and investigated time-dependent changes. We found that components in a QSS form clusters that grow over time but not in a linear fashion, and that this process involves the collapse and regrowth of clusters before the formation of a final large single cluster. These observations might commonly occur in other large-scale biological reaction networks. This developed analysis might be useful for understanding large-scale biological reactions by visualizing complex dynamics, thereby extracting the characteristics of the reaction network, including phase transitions. PMID:28167777

  3. Modeling of Sheath Ion-Molecule Reactions in Plasma Enhanced Chemical Vapor Deposition of Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Hash, David B.; Govindan, T. R.; Meyyappan, M.

    2004-01-01

    In many plasma simulations, ion-molecule reactions are modeled using ion energy independent reaction rate coefficients that are taken from low temperature selected-ion flow tube experiments. Only exothermic or nearly thermoneutral reactions are considered. This is appropriate for plasma applications such as high-density plasma sources in which sheaths are collisionless and ion temperatures 111 the bulk p!asma do not deviate significantly from the gas temperature. However, for applications at high pressure and large sheath voltages, this assumption does not hold as the sheaths are collisional and ions gain significant energy in the sheaths from Joule heating. Ion temperatures and thus reaction rates vary significantly across the discharge, and endothermic reactions become important in the sheaths. One such application is plasma enhanced chemical vapor deposition of carbon nanotubes in which dc discharges are struck at pressures between 1-20 Torr with applied voltages in the range of 500-700 V. The present work investigates The importance of the inclusion of ion energy dependent ion-molecule reaction rates and the role of collision induced dissociation in generating radicals from the feedstock used in carbon nanotube growth.

  4. Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling.

    PubMed

    Matsuura, Tomoaki; Tanimura, Naoki; Hosoda, Kazufumi; Yomo, Tetsuya; Shimizu, Yoshihiro

    2017-02-21

    To elucidate the dynamic features of a biologically relevant large-scale reaction network, we constructed a computational model of minimal protein synthesis consisting of 241 components and 968 reactions that synthesize the Met-Gly-Gly (MGG) peptide based on an Escherichia coli-based reconstituted in vitro protein synthesis system. We performed a simulation using parameters collected primarily from the literature and found that the rate of MGG peptide synthesis becomes nearly constant in minutes, thus achieving a steady state similar to experimental observations. In addition, concentration changes to 70% of the components, including intermediates, reached a plateau in a few minutes. However, the concentration change of each component exhibits several temporal plateaus, or a quasi-stationary state (QSS), before reaching the final plateau. To understand these complex dynamics, we focused on whether the components reached a QSS, mapped the arrangement of components in a QSS in the entire reaction network structure, and investigated time-dependent changes. We found that components in a QSS form clusters that grow over time but not in a linear fashion, and that this process involves the collapse and regrowth of clusters before the formation of a final large single cluster. These observations might commonly occur in other large-scale biological reaction networks. This developed analysis might be useful for understanding large-scale biological reactions by visualizing complex dynamics, thereby extracting the characteristics of the reaction network, including phase transitions.

  5. Matching of experimental and statistical-model thermonuclear reaction rates at high temperatures

    NASA Astrophysics Data System (ADS)

    Newton, J. R.; Longland, R.; Iliadis, C.

    2008-08-01

    We address the problem of extrapolating experimental thermonuclear reaction rates toward high stellar temperatures (T>1 GK) by using statistical model (Hauser-Feshbach) results. Reliable reaction rates at such temperatures are required for studies of advanced stellar burning stages, supernovae, and x-ray bursts. Generally accepted methods are based on the concept of a Gamow peak. We follow recent ideas that emphasized the fundamental shortcomings of the Gamow peak concept for narrow resonances at high stellar temperatures. Our new method defines the effective thermonuclear energy range (ETER) by using the 8th, 50th, and 92nd percentiles of the cumulative distribution of fractional resonant reaction rate contributions. This definition is unambiguous and has a straightforward probability interpretation. The ETER is used to define a temperature at which Hauser-Feshbach rates can be matched to experimental rates. This matching temperature is usually much higher compared to previous estimates that employed the Gamow peak concept. We suggest that an increased matching temperature provides more reliable extrapolated reaction rates since Hauser-Feshbach results are more trustwhorthy the higher the temperature. Our ideas are applied to 21 (p,γ), (p,α), and (α,γ) reactions on A=20-40 target nuclei. For many of the cases studied here, our extrapolated reaction rates at high temperatures differ significantly from those obtained using the Gamow peak concept.

  6. Approach for Estimating Exposures and Incremental Health ...

    EPA Pesticide Factsheets

    Approach for Estimating Exposures and Incremental Health Effects from Lead During Renovation, Repair, and Painting Activities in Public and Commercial Buildings” (Technical Approach Document). Also available for public review and comment are two supplementary documents: the detailed appendices for the Technical Approach Document and a supplementary report entitled “Developing a Concentration-Response Function for Pb Exposure and Cardiovascular Disease-Related Mortality.” Together, these documents describes an analysis for estimating exposures and incremental health effects created by renovations of public and commercial buildings (P&CBs). This analysis could be used to identify and evaluate hazards from renovation, repair, and painting activities in P&CBs. A general overview of how this analysis can be used to inform EPA’s hazard finding is described in the Framework document that was previously made available for public comment (79 FR 31072; FRL9910-44). The analysis can be used in any proposed rulemaking to estimate the reduction in deleterious health effects that would result from any proposed regulatory requirements to mitigate exposure from P&CB renovation activities. The Technical Approach Document describes in detail how the analyses under this approach have been performed and presents the results – expected changes in blood lead levels and health effects due to lead exposure from renovation activities.

  7. Incremental Scheduling Engines: Cost Savings through Automation

    NASA Technical Reports Server (NTRS)

    Jaap, John; Phillips, Shaun

    2005-01-01

    As humankind embarks on longer space missions farther from home, the requirements and environments for scheduling the activities performed on these missions are changing. As we begin to prepare for these missions it is appropriate to evaluate the merits and applicability of the different types of scheduling engines. Scheduling engines temporally arrange tasks onto a timeline so that all constraints and ob.jectives are met and resources are not over-booked. Scheduling engines used to schedule space missions fall into three general categories: batch, mixed-initiative, and incremental. This paper, presents an assessment of the engine types, a discussion of the impact of human exploration of the moon and Mars on planning and scheduling, and the applicability of the different types of scheduling engines. This paper will pursue the hypothesis that incremental scheduling engines may have a place in the new environment; they have the potential to reduce cost, to improve the satisfaction of those who execute or benefit from a particular timeline (the customers), and to allow astronauts to plan their own tasks and those of their companion robots.

  8. Molecular simulations of RNA 2'-O-transesterification reaction models in solution.

    PubMed

    Radak, Brian K; Harris, Michael E; York, Darrin M

    2013-01-10

    We employ quantum mechanical/molecular mechanical umbrella sampling simulations to probe the free energy surfaces of a series of increasingly complex reaction models of RNA 2'-O-transesterification in aqueous solution under alkaline conditions. Such models are valuable for understanding the uncatalyzed processes underlying catalytic cleavage of the phosphodiester backbone of RNA, a reaction of fundamental importance in biology. The chemically reactive atoms are modeled by the AM1/d-PhoT quantum model for phosphoryl transfer, whereas the aqueous solvation environment is modeled with a molecular mechanics force field. Several simulation protocols were compared that used different ionic conditions and force field models. The results provide insight into how variation of the structural environment of the nucleophile and leaving group affects the free energy profile for the transesterification reaction. Results for a simple RNA backbone model are compared with recent experiments by Harris et al. on the specific base-catalyzed cleavage of a UpG dinucleotide. The calculated and measured free energies of activation match extremely well (ΔF(‡) = 19.9-20.8 vs 19.9 kcal/mol). Solvation is seen to play a crucial role and is characterized by a network of hydrogen bonds that envelopes the pentacoordinate dianionic phosphorane transition state and provides preferential stabilization relative to the reactant state.

  9. Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems.

    PubMed

    Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka; Nakano, Tadashi; Ishii, Kojiro

    2016-02-01

    Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism level in the conventional dynamic models would be because integrating multiple hierarchical levels makes the models unnecessarily complex unless supporting experimental data are present. Now that large amounts of molecular and ecological data are increasingly accessible in microbial experimental ecosystems, it is worthwhile to tackle the questions of their complex hierarchical dynamics. Here, we propose an approach that combines microbial experimental ecosystems and a hierarchical dynamic model named population-reaction model. We present a simple microbial experimental ecosystem as an example and show how the system can be analyzed by a population-reaction model. We also show that population-reaction models can be applied to various ecological concepts, such as predator-prey interactions, climate change, evolution, and stability of diversity. Our approach will reveal a path to the general understanding of various ecosystems and organisms.

  10. Mineral-fluid interaction in the lungs: insights from reaction-path modeling.

    PubMed

    Wood, Scott A; Taunton, Anne E; Normand, Charles; Gunter, Mickey E

    2006-11-01

    Thermodynamic modeling, in conjunction with available kinetic information, has been employed to investigate the fate of chrysotile and tremolite in the human lung. In particular, we focus on mineral-fluid reactions using techniques borrowed from geochemistry, including calculation of saturation indices, activity-ratio phase diagrams, and reaction-path modeling. Saturation index calculations show that fresh lung fluid is undersaturated with respect to both tremolite and chrysotile and these minerals should dissolve, in accordance with conclusions from previous work described in the literature. Modeling of reaction paths in both closed and open systems confirms previous suggestions that chrysotile dissolves faster than tremolite in lung fluid, which offers an explanation for the apparent increase in tremolite/chrysotile ratios in lungs of miners and millers over time. However, examination of activity-ratio phase diagrams and reaction-path model calculations raises the possibility not only that minerals dissolve congruently in lung fluid, but that secondary minerals such as talc or various Ca-Mg carbonates might potentially form in lung fluid as asbestiform minerals dissolve.

  11. Molecular Modeling as a Self-Taught Component of a Conventional Undergraduate Chemical Reaction Engineering Course

    ERIC Educational Resources Information Center

    Rothe, Erhard W.; Zygmunt, William E.

    2016-01-01

    We inserted a self-taught molecular modeling project into an otherwise conventional undergraduate chemical-reaction-engineering course. Our objectives were that students should (a) learn with minimal instructor intervention, (b) gain an appreciation for the relationship between molecular structure and, first, macroscopic state functions in…

  12. Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations

    SciTech Connect

    Pierce, Eric M.; Frugier, Pierre; Criscenti, Louise J.; Kwon, Kideok D.; Kerisit, Sebastien N.

    2014-07-12

    Describing the reactions that occur at the glass-water interface and control the development of the altered layer constitutes one of the main scientific challenges impeding existing models from providing accurate radionuclide release estimates. Radionuclide release estimates are a critical component of the safety basis for geologic repositories. The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products) represents a complex region, both physically and chemically, sandwiched between two distinct boundaries pristine glass surface at the inner most interface and aqueous solution at the outer most interface. Computational models, spanning different length and time-scales, are currently being developed to improve our understanding of this complex and dynamic process with the goal of accurately describing the pore-scale changes that occur as the system evolves. These modeling approaches include geochemical simulations [i.e., classical reaction path simulations and glass reactivity in allowance for alteration layer (GRAAL) simulations], Monte Carlo simulations, and Molecular Dynamics methods. Finally, in this manuscript, we discuss the advances and limitations of each modeling approach placed in the context of the glass-water reaction and how collectively these approaches provide insights into the mechanisms that control the formation and evolution of altered layers.

  13. Relating Derived Relations as a Model of Analogical Reasoning: Reaction Times and Event-Related Potentials

    ERIC Educational Resources Information Center

    Barnes-Holmes, Dermot; Regan, Donal; Barnes-Holmes, Yvonne; Commins, Sean; Walsh, Derek; Stewart, Ian; Smeets, Paul M.; Whelan, Robert; Dymond, Simon

    2005-01-01

    The current study aimed to test a Relational Frame Theory (RFT) model of analogical reasoning based on the relating of derived same and derived difference relations. Experiment 1 recorded reaction time measures of similar-similar (e.g., "apple is to orange as dog is to cat") versus different-different (e.g., "he is to his brother as…

  14. Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations

    DOE PAGES

    Pierce, Eric M.; Frugier, Pierre; Criscenti, Louise J.; ...

    2014-07-12

    Describing the reactions that occur at the glass-water interface and control the development of the altered layer constitutes one of the main scientific challenges impeding existing models from providing accurate radionuclide release estimates. Radionuclide release estimates are a critical component of the safety basis for geologic repositories. The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products) represents a complex region, both physically and chemically, sandwiched between two distinct boundaries pristine glass surface at the inner most interface and aqueous solution at the outer most interface. Computational models, spanning different length and time-scales, are currently being developed tomore » improve our understanding of this complex and dynamic process with the goal of accurately describing the pore-scale changes that occur as the system evolves. These modeling approaches include geochemical simulations [i.e., classical reaction path simulations and glass reactivity in allowance for alteration layer (GRAAL) simulations], Monte Carlo simulations, and Molecular Dynamics methods. Finally, in this manuscript, we discuss the advances and limitations of each modeling approach placed in the context of the glass-water reaction and how collectively these approaches provide insights into the mechanisms that control the formation and evolution of altered layers.« less

  15. Surface reaction network of CO oxidation on CeO2/Au(110) inverse model catalysts.

    PubMed

    Ding, Liangbing; Xiong, Feng; Jin, Yuekang; Wang, Zhengming; Sun, Guanghui; Huang, Weixin

    2016-11-30

    CeO2/Au(110) inverse model catalysts were prepared and their activity toward the adsorption and co-adsorption of O2, CO, CO2 and water was studied by means of X-ray photoelectron spectroscopy, low energy electron diffraction, thermal desorption spectra and temperature-programmed reaction spectra. The Au surface of CeO2/Au(110) inverse model catalysts molecularly adsorbs CO, CO2 and water, and the polycrystalline CeO2 surface of CeO2/Au(110) inverse model catalysts molecularly adsorbs O2, and molecularly and reactively adsorbs CO, CO2 and water. By controllably preparing co-adsorbed surface species on CeO2/Au(110) inverse model catalysts, we successfully identified various surface reaction pathways of CO oxidation to produce CO2 with different barriers both on the CeO2 surface and at the Au-CeO2 interface, including CO oxidation by various oxygen species, and water/hydroxyl group-involved CO oxidation. These results establish a surface reaction network of CO oxidation catalyzed by Au/CeO2 catalysts, greatly advancing the fundamental understandings of catalytic CO oxidation reactions.

  16. Reaction dynamics of {sup 34-38}Mg projectile with carbon target using Glauber model

    SciTech Connect

    Shama, Mahesh K.; Panda, R. N.; Sharma, Manoj K.; Patra, S. K.

    2015-08-28

    We have studied nuclear reaction cross-sections for {sup 34-38}Mg isotopes as projectile with {sup 12}C target at projectile energy 240AMeV using Glauber model with the conjunction of densities from relativistic mean filed formalism. We found good agreement with the available experimental data. The halo status of {sup 37}Mg is also investigated.

  17. On the Methods for Constructing Meson-Baryon Reaction Models within Relativistic Quantum Field Theory

    SciTech Connect

    B. Julia-Diaz, H. Kamano, T.-S. H. Lee, A. Matsuyama, T. Sato, N. Suzuki

    2009-04-01

    Within the relativistic quantum field theory, we analyze the differences between the $\\pi N$ reaction models constructed from using (1) three-dimensional reductions of Bethe-Salpeter Equation, (2) method of unitary transformation, and (3) time-ordered perturbation theory. Their relations with the approach based on the dispersion relations of S-matrix theory are dicusssed.

  18. A reduced model for the ICF Gamma-Ray reaction history diagnostic

    NASA Astrophysics Data System (ADS)

    Schmitt, M. J.; Wilson, D. C.; Hoffman, N. M.; Langenbrunner, J. R.; Herrmann, H. W.; Kim, Y. H.; Young, C. S.; Evans, S. C.; Cerjan, C. J.; Stoeffl, Wolfgang; Munro, D. H.; Dauffy, L. S.; Miller, K. M.; Horsfield, C. J.; Rubery, M. S.

    2010-08-01

    An analytic model for the gamma reaction history (GRH) diagnostic to be fielded on the National Ignition Facility is described. The application of the GRH diagnostic for the measurement of capsule rho-R during burn using 4.4 MeV carbon gamma rays is demonstrated by simulation.

  19. Representing effects of aqueous phase reactions in shallow cumuli in global models

    NASA Astrophysics Data System (ADS)

    Nie, Ji; Kuang, Zhiming; Jacob, Daniel J.; Guo, Jiahua

    2016-05-01

    Aqueous phase reactions are important, sometimes dominant (e.g., for SO2), pathways for the oxidation of air pollutants at the local and/or global scale. In many current chemical transport models (CTMs), the transport and aqueous reactions of chemical species are treated as split processes, and the subgrid-scale heterogeneity between cloudy and environmental air is not considered. Here using large eddy simulation (LES) with idealized aqueous reactions mimicking the oxidation of surface-originated SO2 by H2O2 in shallow cumuli, we show that the eddy diffusivity mass flux (EDMF) approach with a bulk plume can represent those processes quite well when entrainment/detrainment rates and eddy diffusivity are diagnosed using a conservative thermodynamic variable such as total water content. The reason is that a typical aqueous reaction such as SO2 aqueous oxidation is relatively slow compared to the in-cloud residence time of air parcels in shallow cumuli. As a result, the surface-originated SO2 is well correlated with and behaves like conservative thermodynamic variables that also have sources at the surface. Experiments with various reaction rate constants and relative abundances of SO2 and H2O2 indicate that when the reaction timescale approaches the in-cloud residence time of air parcels, the errors of the bulk plume approach start to increase. Treating chemical tracer transport and aqueous reaction as split processes leads to significant errors, especially when the reaction is fast compared to the in-cloud residence time. Overall, the EDMF approach shows large improvement over the CTM-like treatments in matching the LES results.

  20. Towards a Unified Model of Neutrino-Nucleus Reactions for Neutrino Oscillation Experiments.

    PubMed

    Nakamura, Satoshi; Kamano, Hiroyuki; Hayato, Yoshinari; Hirai, Masanori; Horiuchi, Wataru; Kumano, Shunzo; Murata, Tomoya; Saito, Koichi; Sakuda, Makoto; Sato, Toru; Suzuki, Yasuyuki

    2017-02-06

    A precise description of neutrino-nucleus reactions will play a key role in addressing fundamental questions such as the leptonic CP violation and the neutrino mass hierarchy through analyzing data from next-generation neutrino oscillation experiments. The neutrino energy relevant to the neutrino-nucleus reactions spans a broad range and, accordingly, the dominant reaction mechanism varies across the energy region from quasi-elastic scattering through nucleon resonance excitations to deep inelastic scattering. This corresponds to transitions of the effective degree of freedom for theoretical description from nucleons through meson-baryon to quarks. The main purpose of this review is to report our recent efforts towards a unified description of the neutrino-nucleus reactions over the wide energy range; recent overall progress in the field is also sketched. Starting with an overview of the current status of neutrino-nucleus scattering experiments, we formulate the cross section to be commonly used for the reactions over all the energy regions. A description of the neutrino-nucleon reactions follows and, in particular, a dynamical coupled-channels model for meson productions in and beyond the Δ(1232) region is discussed in detail. We then discuss the neutrino-nucleus reactions, putting emphasis on our theoretical approaches. We start the discussion with electroweak processes in few-nucleon systems studied with the correlated Gaussian method. Then we describe quasi-elastic scattering with nuclear spectral functions, and meson productions with a Δ-hole model. Nuclear modifications of the parton distribution functions determined through a global analysis are also discussed. Finally, we discuss issues to be addressed for future developments.

  1. Kinetic modeling of the reaction of HCl and solid lime at low temperatures

    SciTech Connect

    Fonseca, A.M.; Orfao, J.J.; Salcedo, R.L.

    1998-12-01

    Calcium hydroxide is a commonly used sorbent in the dry-scrubbing of hydrogen chloride from flue gases. In this study the kinetic parameters for the reaction between gaseous HCl and solid Ca(OH){sub 2} have been obtained at low temperatures in a fixed-bed laboratory reactor. The influence of the operating temperature (323--400 K), HCl concentration (150--1000 ppm), and humidity (0--11% M) was studied. The experimental results show that in the first few seconds a very fast chemical reaction occurs, with a reaction rate constant per unit surface area of solid larger than 10{sup {minus}3} ms{sup {minus}1}. This reaction was found to be first order relative to HCl concentration and its mechanism is apparently independent of the presence of moisture. However, the relative humidity of the gas has a major impact on the progress of the reaction: when no moisture is present the reaction stops after a short period of time (2--3 min), with very low maximum solid reactant conversions (<5%). For the experiments with humidified gas an almost complete conversion of Ca(OH){sub 2} was obtained after about 40 min of reaction time. For this case the grain model with product layer diffusion limitations is in very good agreement with the experimental results. The diffusion coefficient in the product layer obtained through this model varied from 10{sup {minus}13} to 10{sup {minus}11} m{sup 2}/s and the activation energy for this parameter was estimated at {approx}19 kJ/mol for the range of temperatures studied. A simple linear relationship describes well the effect of relative humidity of the gas on the diffusion coefficient in the solid product layer. In the presence of humidity, the very high conversions of the solid reactant show a good potential applicability to continuous dry-scrubbing at HCl at low temperatures.

  2. Estimating Reaction Rate Coefficients Within a Travel-Time Modeling Framework

    SciTech Connect

    Gong, R; Lu, C; Luo, Jian; Wu, Wei-min; Cheng, H.; Criddle, Craig; Kitanidis, Peter K.; Gu, Baohua; Watson, David B; Jardine, Philip M; Brooks, Scott C

    2011-03-01

    A generalized, efficient, and practical approach based on the travel-time modeling framework is developed to estimate in situ reaction rate coefficients for groundwater remediation in heterogeneous aquifers. The required information for this approach can be obtained by conducting tracer tests with injection of a mixture of conservative and reactive tracers and measurements of both breakthrough curves (BTCs). The conservative BTC is used to infer the travel-time distribution from the injection point to the observation point. For advection-dominant reactive transport with well-mixed reactive species and a constant travel-time distribution, the reactive BTC is obtained by integrating the solutions to advective-reactive transport over the entire travel-time distribution, and then is used in optimization to determine the in situ reaction rate coefficients. By directly working on the conservative and reactive BTCs, this approach avoids costly aquifer characterization and improves the estimation for transport in heterogeneous aquifers which may not be sufficiently described by traditional mechanistic transport models with constant transport parameters. Simplified schemes are proposed for reactive transport with zero-, first-, nth-order, and Michaelis-Menten reactions. The proposed approach is validated by a reactive transport case in a two-dimensional synthetic heterogeneous aquifer and a field-scale bioremediation experiment conducted at Oak Ridge, Tennessee. The field application indicates that ethanol degradation for U(VI)-bioremediation is better approximated by zero-order reaction kinetics than first-order reaction kinetics.

  3. Estimating reaction rate coefficients within a travel-time modeling framework.

    PubMed

    Gong, R; Lu, C; Wu, W-M; Cheng, H; Gu, B; Watson, D; Jardine, P M; Brooks, S C; Criddle, C S; Kitanidis, P K; Luo, J

    2011-01-01

    A generalized, efficient, and practical approach based on the travel-time modeling framework is developed to estimate in situ reaction rate coefficients for groundwater remediation in heterogeneous aquifers. The required information for this approach can be obtained by conducting tracer tests with injection of a mixture of conservative and reactive tracers and measurements of both breakthrough curves (BTCs). The conservative BTC is used to infer the travel-time distribution from the injection point to the observation point. For advection-dominant reactive transport with well-mixed reactive species and a constant travel-time distribution, the reactive BTC is obtained by integrating the solutions to advective-reactive transport over the entire travel-time distribution, and then is used in optimization to determine the in situ reaction rate coefficients. By directly working on the conservative and reactive BTCs, this approach avoids costly aquifer characterization and improves the estimation for transport in heterogeneous aquifers which may not be sufficiently described by traditional mechanistic transport models with constant transport parameters. Simplified schemes are proposed for reactive transport with zero-, first-, nth-order, and Michaelis-Menten reactions. The proposed approach is validated by a reactive transport case in a two-dimensional synthetic heterogeneous aquifer and a field-scale bioremediation experiment conducted at Oak Ridge, Tennessee. The field application indicates that ethanol degradation for U(VI)-bioremediation is better approximated by zero-order reaction kinetics than first-order reaction kinetics.

  4. Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions

    PubMed Central

    Jorgensen, Wiliiam L.

    2014-01-01

    A recent review (Acc. Chem. Res. 2010, 43:142–151) examined our use and development of a combined quantum and molecular mechanical (QM/MM) technique for modelling organic and enzymatic reactions. Advances included the PDDG/PM3 semiempirical QM (SQM) method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo simulations, and a polynomial quadrature method for rapidly treating proton-transfer reactions. The current article serves as a follow up on our progress. Highlights include new reactions, alternative SQM methods, a polarizable OPLS force field, and novel solvent environments, e.g., “on water” and room temperature ionic liquids. The methodology is strikingly accurate across a wide range of condensed-phase and antibody-catalyzed reactions including substitution, decarboxylation, elimination, isomerization, and pericyclic classes. Comparisons are made to systems treated with continuum-based solvents and ab initio or density functional theory (DFT) methods. Overall, the QM/MM methodology provides detailed characterization of reaction paths, proper configurational sampling, several advantages over implicit solvent models, and a reasonable computational cost. PMID:25431625

  5. Reaction pathways for the deoxygenation of vegetable oils and related model compounds.

    PubMed

    Gosselink, Robert W; Hollak, Stefan A W; Chang, Shu-Wei; van Haveren, Jacco; de Jong, Krijn P; Bitter, Johannes H; van Es, Daan S

    2013-09-01

    Vegetable oil-based feeds are regarded as an alternative source for the production of fuels and chemicals. Paraffins and olefins can be produced from these feeds through catalytic deoxygenation. The fundamentals of this process are mostly studied by using model compounds such as fatty acids, fatty acid esters, and specific triglycerides because of their structural similarity to vegetable oils. In this Review we discuss the impact of feedstock, reaction conditions, and nature of the catalyst on the reaction pathways of the deoxygenation of vegetable oils and its derivatives. As such, we conclude on the suitability of model compounds for this reaction. It is shown that the type of catalyst has a significant effect on the deoxygenation pathway, that is, group 10 metal catalysts are active in decarbonylation/decarboxylation whereas metal sulfide catalysts are more selective to hydrodeoxygenation. Deoxygenation studies performed under H2 showed similar pathways for fatty acids, fatty acid esters, triglycerides, and vegetable oils, as mostly deoxygenation occurs indirectly via the formation of fatty acids. Deoxygenation in the absence of H2 results in significant differences in reaction pathways and selectivities depending on the feedstock. Additionally, using unsaturated feedstocks under inert gas results in a high selectivity to undesired reactions such as cracking and the formation of heavies. Therefore, addition of H2 is proposed to be essential for the catalytic deoxygenation of vegetable oil feeds.

  6. Reactions of aqueous chlorine and chlorine dioxide with model food compounds

    SciTech Connect

    Fukayama, M.Y.; Tan, H.; Wheeler, W.B.; Wei, C.

    1986-11-01

    This presentation reviews published information concerning the reactions of chlorine gas (CL/sub 2/(g)), aqueous chlorine, and ClO/sub 2/ with model food compounds, the fate of chlorine during the chlorination of specific food products, and the potential toxicity of the reaction products. Fatty acids and their methyl esters react with chlorine with the degree of incorporation corresponding to their degree of unsaturation. Aqueous chlorine oxidizes and chlorinates lipids and amino acids much more readily than ClO/sub 2/. Several amino acids are highly susceptible to oxidation and chlorination by chlorine compounds. Reactions of chlorine and ClO/sub 2/ with several food products, including flour and shrimp, have also been characterized. Although significant quantities of chlorine can be incorporated into specific model compounds and food products, the health risks associated with exposure to chlorinated organic products are unknown. Preliminary studies using the Ames Salmonella/microsome mutagenicity assay indicate that the reaction products from mixtures of aqueous chlorine and various lipids or tryptophan are nonmutagenic. Nevertheless, additional studies are warranted, so that the toxicological significance of these reaction products can be understood more fully.

  7. Modeling of hydrogen evolution reaction on the surface of GaInP2

    NASA Astrophysics Data System (ADS)

    Choi, Woon Ih; Wood, Brandon; Schwegler, Eric; Ogitsu, Tadashi

    2012-02-01

    GaInP2 is promising candidate material for hydrogen production using sunlight. It reduces solvated proton into hydrogen molecule using light-induced excited electrons in the photoelectrochemical cell. However, it is challenging to model hydrogen evolution reaction (HER) using first-principles molecular dynamics. Instead, we use Anderson-Newns model and generalized solvent coordinate in Marcus-Hush theory to describe adiabatic free energy surface of HER. Model parameters are fitted from the DFT calculations. We model Volmer-Heyrovsky reaction path on the surfaces of CuPt phase of GaInP2. We also discuss effects of surface oxide and catalyst atoms that exist on top of bare surfaces in experimental circumstances.

  8. Impacts of frequency increment errors on frequency diverse array beampattern

    NASA Astrophysics Data System (ADS)

    Gao, Kuandong; Chen, Hui; Shao, Huaizong; Cai, Jingye; Wang, Wen-Qin

    2015-12-01

    Different from conventional phased array, which provides only angle-dependent beampattern, frequency diverse array (FDA) employs a small frequency increment across the antenna elements and thus results in a range angle-dependent beampattern. However, due to imperfect electronic devices, it is difficult to ensure accurate frequency increments, and consequently, the array performance will be degraded by unavoidable frequency increment errors. In this paper, we investigate the impacts of frequency increment errors on FDA beampattern. We derive the beampattern errors caused by deterministic frequency increment errors. For stochastic frequency increment errors, the corresponding upper and lower bounds of FDA beampattern error are derived. They are verified by numerical results. Furthermore, the statistical characteristics of FDA beampattern with random frequency increment errors, which obey Gaussian distribution and uniform distribution, are also investigated.

  9. A New Method for Incremental Testing of Finite State Machines

    NASA Technical Reports Server (NTRS)

    Pedrosa, Lehilton Lelis Chaves; Moura, Arnaldo Vieira

    2010-01-01

    The automatic generation of test cases is an important issue for conformance testing of several critical systems. We present a new method for the derivation of test suites when the specification is modeled as a combined Finite State Machine (FSM). A combined FSM is obtained conjoining previously tested submachines with newly added states. This new concept is used to describe a fault model suitable for incremental testing of new systems, or for retesting modified implementations. For this fault model, only the newly added or modified states need to be tested, thereby considerably reducing the size of the test suites. The new method is a generalization of the well-known W-method and the G-method, but is scalable, and so it can be used to test FSMs with an arbitrarily large number of states.

  10. Exploration of POD-Galerkin Techniques for Developing Reduced Order Models of Reaction-Advection Equations

    DTIC Science & Technology

    2014-04-01

    downstream boundary (when needed) is obtained by extrapolation, taking into account the hyperbolic character of the equation . By separating the...for Developing Reduced Order Models of Reaction-Advection Equations 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT...advection scalar equation is used as a representative equation to investigate the overall approach. Both linear and nonlinear model equations are

  11. A parametric duration model of the reaction times of drivers distracted by mobile phone conversations.

    PubMed

    Haque, Md Mazharul; Washington, Simon

    2014-01-01

    The use of mobile phones while driving is more prevalent among young drivers-a less experienced cohort with elevated crash risk. The objective of this study was to examine and better understand the reaction times of young drivers to a traffic event originating in their peripheral vision whilst engaged in a mobile phone conversation. The CARRS-Q advanced driving simulator was used to test a sample of young drivers on various simulated driving tasks, including an event that originated within the driver's peripheral vision, whereby a pedestrian enters a zebra crossing from a sidewalk. Thirty-two licensed drivers drove the simulator in three phone conditions: baseline (no phone conversation), hands-free and handheld. In addition to driving the simulator each participant completed questionnaires related to driver demographics, driving history, usage of mobile phones while driving, and general mobile phone usage history. The participants were 21-26 years old and split evenly by gender. Drivers' reaction times to a pedestrian in the zebra crossing were modelled using a parametric accelerated failure time (AFT) duration model with a Weibull distribution. Also tested where two different model specifications to account for the structured heterogeneity arising from the repeated measures experimental design. The Weibull AFT model with gamma heterogeneity was found to be the best fitting model and identified four significant variables influencing the reaction times, including phone condition, driver's age, license type (provisional license holder or not), and self-reported frequency of usage of handheld phones while driving. The reaction times of drivers were more than 40% longer in the distracted condition compared to baseline (not distracted). Moreover, the impairment of reaction times due to mobile phone conversations was almost double for provisional compared to open license holders. A reduction in the ability to detect traffic events in the periphery whilst distracted

  12. A thermochemical model for shock-induced reactions (heat detonations) in solids

    NASA Astrophysics Data System (ADS)

    Boslough, Mark B.

    1990-02-01

    Recent advances in studies of shock-induced chemistry in reactive solids have led to the recognition of a new class of energetic materials which are unique in their response to shock waves. Experimental work has shown that chemical energy can be released on a time scale shorter than shock-transit times in laboratory samples. However, for many compositions, the reaction products remain in the condensed state upon release from high pressure, and no sudden expansion takes place. Nevertheless, if such a reaction is sufficiently rapid, it can be modeled as a type of detonation, termed ``heat detonation'' in the present paper. It is shown that unlike an explosive detonation, an unsupported heat detonation will decay to zero unless certain conditions are met. An example of such a reaction is Fe2 O3 +2Al+shock→Al2 O3 +2Fe (the standard thermite reaction). A shock-wave equation of state is determined from a mixture theory for reacted and unreacted porous thermite. The calculated shock temperatures are compared to experimentally measured shock temperatures, demonstrating that a shock-induced reaction takes place. Interpretation of the measured temperature history in the context of the thermochemical model implies that the principal rate-controlling kinetic mechanism is dynamic mixing at the shock front. Despite the similarity in thermochemical modeling of heat detonations to explosive detonations, the two processes are qualitatively very different in reaction mechanism as well as in the form the energy takes upon release, with explosives producing mostly work and heat detonations producing mostly heat.

  13. Development and testing of a compartmentalized reaction network model for redox zones in contaminated aquifers

    USGS Publications Warehouse

    Abrams, R.H.; Loague, K.; Kent, D.B.

    1998-01-01

    The work reported here is the first part of a larger effort focused on efficient numerical simulation of redox zone development in contaminated aquifers. The sequential use of various electron acceptors, which is governed by the energy yield of each reaction, gives rise to redox zones. The large difference in energy yields between the various redox reactions leads to systems of equations that are extremely ill-conditioned. These equations are very difficult to solve, especially in the context of coupled fluid flow, solute transport, and geochemical simulations. We have developed a general, rational method to solve such systems where we focus on the dominant reactions, compartmentalizing them in a manner that is analogous to the redox zones that are often observed in the field. The compartmentalized approach allows us to easily solve a complex geochemical system as a function of time and energy yield, laying the foundation for our ongoing work in which we couple the reaction network, for the development of redox zones, to a model of subsurface fluid flow and solute transport. Our method (1) solves the numerical system without evoking a redox parameter, (2) improves the numerical stability of redox systems by choosing which compartment and thus which reaction network to use based upon the concentration ratios of key constituents, (3) simulates the development of redox zones as a function of time without the use of inhibition factors or switching functions, and (4) can reduce the number of transport equations that need to be solved in space and time. We show through the use of various model performance evaluation statistics that the appropriate compartment choice under different geochemical conditions leads to numerical solutions without significant error. The compartmentalized approach described here facilitates the next phase of this effort where we couple the redox zone reaction network to models of fluid flow and solute transport.

  14. Modeling of the interplay between single-file diffusion and conversion reaction in mesoporous systems

    SciTech Connect

    Wang, Jing

    2013-01-11

    We analyze the spatiotemporal behavior of species concentrations in a diffusion-mediated conversion reaction which occurs at catalytic sites within linear pores of nanometer diameter. A strict single-file (no passing) constraint occurs in the diffusion within such narrow pores. Both transient and steady-state behavior is precisely characterized by kinetic Monte Carlo simulations of a spatially discrete lattice–gas model for this reaction–diffusion process considering various distributions of catalytic sites. Exact hierarchical master equations can also be developed for this model. Their analysis, after application of mean-field type truncation approximations, produces discrete reaction–diffusion type equations (mf-RDE). For slowly varying concentrations, we further develop coarse-grained continuum hydrodynamic reaction–diffusion equations (h-RDE) incorporating a precise treatment of single-file diffusion (SFD) in this multispecies system. Noting the shortcomings of mf-RDE and h-RDE, we then develop a generalized hydrodynamic (GH) formulation of appropriate gh-RDE which incorporates an unconventional description of chemical diffusion in mixed-component quasi-single-file systems based on a refined picture of tracer diffusion for finite-length pores. The gh-RDE elucidate the non-exponential decay of the steady-state reactant concentration into the pore and the non-mean-field scaling of the reactant penetration depth. Then an extended model of a catalytic conversion reaction within a functionalized nanoporous material is developed to assess the effect of varying the reaction product – pore interior interaction from attractive to repulsive. The analysis is performed utilizing the generalized hydrodynamic formulation of the reaction-diffusion equations which can reliably capture the complex interplay between reaction and restricted transport for both irreversible and reversible reactions.

  15. A Luenberger observer for reaction-diffusion models with front position data

    NASA Astrophysics Data System (ADS)

    Collin, Annabelle; Chapelle, Dominique; Moireau, Philippe

    2015-11-01

    We propose a Luenberger observer for reaction-diffusion models with propagating front features, and for data associated with the location of the front over time. Such models are considered in various application fields, such as electrophysiology, wild-land fire propagation and tumor growth modeling. Drawing our inspiration from image processing methods, we start by proposing an observer for the eikonal-curvature equation that can be derived from the reaction-diffusion model by an asymptotic expansion. We then carry over this observer to the underlying reaction-diffusion equation by an ;inverse asymptotic analysis;, and we show that the associated correction in the dynamics has a stabilizing effect for the linearized estimation error. We also discuss the extension to joint state-parameter estimation by using the earlier-proposed ROUKF strategy. We then illustrate and assess our proposed observer method with test problems pertaining to electrophysiology modeling, including with a realistic model of cardiac atria. Our numerical trials show that state estimation is directly very effective with the proposed Luenberger observer, while specific strategies are needed to accurately perform parameter estimation - as is usual with Kalman filtering used in a nonlinear setting - and we demonstrate two such successful strategies.

  16. Scaffolding Students' Online Critiquing of Expert- and Peer-generated Molecular Models of Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Chang, Hsin-Yi; Chang, Hsiang-Chi

    2013-08-01

    In this study, we developed online critiquing activities using an open-source computer learning environment. We investigated how well the activities scaffolded students to critique molecular models of chemical reactions made by scientists, peers, and a fictitious peer, and whether the activities enhanced the students' understanding of science models and chemical reactions. The activities were implemented in an eighth-grade class with 28 students in a public junior high school in southern Taiwan. The study employed mixed research methods. Data collected included pre- and post-instructional assessments, post-instructional interviews, and students' electronic written responses and oral discussions during the critiquing activities. The results indicated that these activities guided the students to produce overall quality critiques. Also, the students developed a more sophisticated understanding of chemical reactions and scientific models as a result of the intervention. Design considerations for effective model critiquing activities are discussed based on observational results, including the use of peer-generated artefacts for critiquing to promote motivation and collaboration, coupled with critiques of scientific models to enhance students' epistemological understanding of model purpose and communication.

  17. Particle-scale CO2 adsorption kinetics modeling considering three reaction mechanisms

    SciTech Connect

    Suh, Dong-Myung; Sun, Xin

    2013-09-01

    In the presence of water (H2O), dry and wet adsorptions of carbon dioxide (CO2) and physical adsorption of H2O happen concurrently in a sorbent particle. The three reactions depend on each other and have a complicated, but important, effect on CO2 capturing via a solid sorbent. In this study, transport phenomena in the sorbent were modeled, including the tree reactions, and a numerical solving procedure for the model also was explained. The reaction variable distribution in the sorbent and their average values were calculated, and simulation results were compared with experimental data to validate the proposed model. Some differences, caused by thermodynamic parameters, were observed between them. However, the developed model reasonably simulated the adsorption behaviors of a sorbent. The weight gained by each adsorbed species, CO2 and H2O, is difficult to determine experimentally. It is known that more CO2 can be captured in the presence of water. Still, it is not yet known quantitatively how much more CO2 the sorbent can capture, nor is it known how much dry and wet adsorptions separately account for CO2 capture. This study addresses those questions by modeling CO2 adsorption in a particle and simulating the adsorption process using the model. As adsorption temperature changed into several values, the adsorbed amount of each species was calculated. The captured CO2 in the sorbent particle was compared quantitatively between dry and wet conditions. As the adsorption temperature decreased, wet adsorption increased. However, dry adsorption was reduced.

  18. Synthesis of superheavy elements: Uncertainty analysis to improve the predictive power of reaction models

    NASA Astrophysics Data System (ADS)

    Lü, Hongliang; Boilley, David; Abe, Yasuhisa; Shen, Caiwan

    2016-09-01

    Background: Synthesis of superheavy elements is performed by heavy-ion fusion-evaporation reactions. However, fusion is known to be hindered with respect to what can be observed with lighter ions. Thus some delicate ambiguities remain on the fusion mechanism that eventually lead to severe discrepancies in the calculated formation probabilities coming from different fusion models. Purpose: In the present work, we propose a general framework based upon uncertainty analysis in the hope of constraining fusion models. Method: To quantify uncertainty associated with the formation probability, we propose to propagate uncertainties in data and parameters using the Monte Carlo method in combination with a cascade code called kewpie2, with the aim of determining the associated uncertainty, namely the 95 % confidence interval. We also investigate the impact of different models or options, which cannot be modeled by continuous probability distributions, on the final results. An illustrative example is presented in detail and then a systematic study is carried out for a selected set of cold-fusion reactions. Results: It is rigorously shown that, at the 95 % confidence level, the total uncertainty of the empirical formation probability appears comparable to the discrepancy between calculated values. Conclusions: The results obtained from the present study provide direct evidence for predictive limitations of the existing fusion-evaporation models. It is thus necessary to find other ways to assess such models for the purpose of establishing a more reliable reaction theory, which is expected to guide future experiments on the production of superheavy elements.

  19. Incremental Sampling Methodology (ISM). Part 1, Section 4: Statistical Design. Aspects of Incremental Sampling

    DTIC Science & Technology

    2012-03-26

    1 Statistical Aspects of Incremental Sampling Kelly Black Neptune and Company, Inc. kblack@neptuneinc.org EMDQ – La Jolla, CA March 26, 2012 Report...NAME(S) AND ADDRESS(ES) Neptune and Company, Inc,1435 Garrison St Ste 110,Denver,CO,80215 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING

  20. Spatial modeling of dimerization reaction dynamics in the plasma membrane: Monte Carlo vs. continuum differential equations.

    PubMed

    Mayawala, Kapil; Vlachos, Dionisios G; Edwards, Jeremy S

    2006-06-01

    Bimolecular reactions in the plasma membrane, such as receptor dimerization, are a key signaling step for many signaling systems. For receptors to dimerize, they must first diffuse until a collision happens, upon which a dimerization reaction may occur. Therefore, study of the dynamics of cell signaling on the membrane may require the use of a spatial modeling framework. Despite the availability of spatial simulation methods, e.g., stochastic spatial Monte Carlo (MC) simulation and partial differential equation (PDE) based approaches, many biological models invoke well-mixed assumptions without completely evaluating the importance of spatial organization. Whether one is to utilize a spatial or non-spatial simulation framework is therefore an important decision. In order to evaluate the importance of spatial effects a priori, i.e., without performing simulations, we have assessed the applicability of a dimensionless number, known as second Damköhler number (Da), defined here as the ratio of time scales of collision and reaction, for 2-dimensional bimolecular reactions. Our study shows that dimerization reactions in the plasma membrane with Da approximately >0.1 (tested in the receptor density range of 10(2)-10(5)/microm(2)) require spatial modeling. We also evaluated the effective reaction rate constants of MC and simple deterministic PDEs. Our simulations show that the effective reaction rate constant decreases with time due to time dependent changes in the spatial distribution of receptors. As a result, the effective reaction rate constant of simple PDEs can differ from that of MC by up to two orders of magnitude. Furthermore, we show that the fluctuations in the number of copies of signaling proteins (noise) may also depend on the diffusion properties of the system. Finally, we used the spatial MC model to explore the effect of plasma membrane heterogeneities, such as receptor localization and reduced diffusivity, on the dimerization rate. Interestingly, our

  1. Accuracy of Reaction Cross Section for Exotic Nuclei in Glauber Model Based on MCMC Diagnostics

    NASA Astrophysics Data System (ADS)

    Rueter, Keiti; Novikov, Ivan

    2017-01-01

    Parameters of a nuclear density distribution for an exotic nuclei with halo or skin structures can be determined from the experimentally measured reaction cross-section. In the presented work, to extract parameters such as nuclear size information for a halo and core, we compare experimental data on reaction cross-sections with values obtained using expressions of the Glauber Model. These calculations are performed using a Markov Chain Monte Carlo algorithm. We discuss the accuracy of the Monte Carlo approach and its dependence on k*, the power law turnover point in the discreet power spectrum of the random number sequence and on the lag-1 autocorrelation time of the random number sequence.

  2. Giant dipole resonance in proton capture reactions using an extended quantum molecular dynamics model

    NASA Astrophysics Data System (ADS)

    Wang, K.; Ma, Y. G.; Zhang, G. Q.; Cao, X. G.; He, W. B.; Shen, W. Q.

    2017-01-01

    Proton capture reaction is an important process concerning the astrophysical origin of the elements. In present work, we focus on giant dipole resonance (GDR) in proton capture reactions, such as 11B(p ,γ )12C , 27Al(p ,γ )28Si , 39K(p ,γ )40Ca , and 67Co(p ,γ )68Ni in a framework of an extended quantum molecular dynamics model. The systematic properties of GDR parameters including the peak energy, the strength, and full width at half maximum (FWHM) have been studied. The dependence of FWHM on temperature has also been discussed. Some comparisons with experimental data have been presented.

  3. Comparison between phenomenological and ab-initio reaction and relaxation models in DSMC

    NASA Astrophysics Data System (ADS)

    Sebastião, Israel B.; Kulakhmetov, Marat; Alexeenko, Alina

    2016-11-01

    New state-specific vibrational-translational energy exchange and dissociation models, based on ab-initio data, are implemented in direct simulation Monte Carlo (DSMC) method and compared to the established Larsen-Borgnakke (LB) and total collision energy (TCE) phenomenological models. For consistency, both the LB and TCE models are calibrated with QCT-calculated O2+O data. The model comparison test cases include 0-D thermochemical relaxation under adiabatic conditions and 1-D normal shockwave calculations. The results show that both the ME-QCT-VT and LB models can reproduce vibrational relaxation accurately but the TCE model is unable to reproduce nonequilibrium rates even when it is calibrated to accurate equilibrium rates. The new reaction model does capture QCT-calculated nonequilibrium rates. For all investigated cases, we discuss the prediction differences based on the new model features.

  4. Activation energy for a model ferrous-ferric half reaction from transition path sampling

    NASA Astrophysics Data System (ADS)

    Drechsel-Grau, Christof; Sprik, Michiel

    2012-01-01

    Activation parameters for the model oxidation half reaction of the classical aqueous ferrous ion are compared for different molecular simulation techniques. In particular, activation free energies are obtained from umbrella integration and Marcus theory based thermodynamic integration, which rely on the diabatic gap as the reaction coordinate. The latter method also assumes linear response, and both methods obtain the activation entropy and the activation energy from the temperature dependence of the activation free energy. In contrast, transition path sampling does not require knowledge of the reaction coordinate and directly yields the activation energy [C. Dellago and P. G. Bolhuis, Mol. Simul. 30, 795 (2004), 10.1080/08927020412331294869]. Benchmark activation energies from transition path sampling agree within statistical uncertainty with activation energies obtained from standard techniques requiring knowledge of the reaction coordinate. In addition, it is found that the activation energy for this model system is significantly smaller than the activation free energy for the Marcus model, approximately half the value, implying an equally large entropy contribution.

  5. Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations

    SciTech Connect

    Pierce, Eric M.; Frugier, Pierre; Criscenti, Louise J.; Kwon, K. D.; Kerisit, Sebastien N.

    2014-07-12

    The altered layer (i.e., amorphous hydrated surface layer and crystalline reaction products)represents a complex region, both physically and chemically, sandwiched between two distinct boundaries - pristine glass surface at the inner most interface and aqueous solution at the outer most. The physico-chemical processes that control the development of this region have a significant impact on the long-term glass-water reaction. Computational models, spanning different length and time-scales, are currently being developed to improve our understanding of this complex and dynamic process with the goal of accurately describing the pore-scale changes that occur as the system evolves. These modeling approaches include Geochemical Reaction Path simulations, Glass Reactivity in Allowance for Alteration Layer simulations, Monte Carlo simulations, and Molecular Dynamics methods. Discussed in this manuscript are the advances and limitations of each modeling approach placed in the context of the glass water reaction and how collectively these approaches provide insights into the mechanisms that control the formation and evolution of altered layers; thus providing the fundamental data needed to develop pore-scale equations that enable more accurate predictions of nuclear waste glass corrosion in a geologic repository.

  6. SOA formation from partitioning and heterogeneous reactions: model study in the presence of inorganic species.

    PubMed

    Jang, Myoseon; Czoschke, Nadine M; Northcross, Amanda L; Cao, Gang; Shaof, David

    2006-05-01

    A predictive model for secondary organic aerosol (SOA) formation by both partitioning and heterogeneous reactions was developed for SOA created from ozonolysis of alpha-pinene in the presence of preexisting inorganic seed aerosols. SOA was created in a 2 m3 polytetrafluoroethylene film indoor chamber under darkness. Extensive sets of SOA experiments were conducted varying humidity, inorganic seed compositions comprising of ammonium sulfate and sulfuric acid, and amounts of inorganic seed mass. SOA mass was decoupled into partitioning (OM(P)) and heterogeneous aerosol production (OM(H)). The reaction rate constant for OM(H) production was subdivided into three categories (fast, medium, and slow) to consider different reactivity of organic products for the particle phase heterogeneous reactions. The influence of particle acidity on reaction rates was treated in a previous semiempirical model. Model OM(H) was developed with medium and strong acidic seed aerosols, and then extrapolated to OM(H) in weak acidic conditions, which are more relevant to atmospheric aerosols. To demonstrate the effects of preexisting glyoxal derivatives (e.g., glyoxal hydrate and dimer) on OM(H), SOA was created with a seed mixture comprising of aqueous glyoxal and inorganic species. Our results show that heterogeneous SOA formation was also influenced by preexisting reactive glyoxal derivatives.

  7. A particle-mesh algorithm for advection-reaction-diffusion equations with applications to plankton modeling

    NASA Astrophysics Data System (ADS)

    Paparella, F.; Oliveri, F.

    2009-04-01

    The interplay of advection, reaction and diffusion terms in ADR equations is a rather difficult one to be modeled numerically. The kind of spurious oscillations that is usually harmless for non-reacting scalars is often amplified without bounds by reaction terms. Furthermore, in most biogeochimical applications, such as mesoscale or global-scale plankton modeling, the diffusive fluxes may be smaller than the numerical ones. Inspired by the particle-mesh methods used by cosmologists, we propose to discretize on a grid only the diffusive term of the equation, and solve the advection-reaction terms as ordinary differential equations along the characteristic lines. Diffusion happens by letting the concentration field carried by each particle to relax towards the diffusive field known on the grid, without redistributing the particles. This method, in the limit of vanishing diffusivity and for a fixed mesh size, recovers the advection-reaction solution with no numerical diffusion. We show some example numerical solutions of the ADR equations stemming from a simple predator-prey model.

  8. A hot-atom reaction kinetic model for H abstraction from solid surfaces

    NASA Astrophysics Data System (ADS)

    Kammler, Th.; Kolovos-Vellianitis, D.; Küppers, J.

    2000-07-01

    Measurements of the abstraction reaction kinetics in the interaction of gaseous H atoms with D adsorbed on metal and semiconductor surfaces, H(g)+D(ad)/S→ products, have shown that the kinetics of the HD products are at variance with the expectations drawn from the operation of Eley-Rideal mechanisms. Furthermore, in addition to HD product molecules, D 2 products were observed which are not expected in an Eley-Rideal scenario. Products and kinetics of abstraction reactions on Ni(100), Pt(111), and Cu(111) surfaces were recently explained by a random-walk model based solely on the operation of hot-atom mechanistic steps. Based on the same reaction scenario, the present work provides numerical solutions of the appropriate kinetic equations in the limit of the steady-state approximation for hot-atom species. It is shown that the HD and D 2 product kinetics derived from global kinetic rate constants are the same as those obtained from local probabilities in the random walk model. The rate constants of the hot-atom kinetics provide a background for the interpretation of measured data, which was missing up to now. Assuming that reconstruction affects the competition between hot-atom sticking and hot-atom reaction, the application of the present model at D abstraction from Cu(100) surfaces reproduces the essential characteristics of the experimentally determined kinetics.

  9. Phase transitions in a holographic s + p model with back-reaction

    NASA Astrophysics Data System (ADS)

    Nie, Zhang-Yu; Cai, Rong-Gen; Gao, Xin; Li, Li; Zeng, Hui

    2015-11-01

    In a previous paper (Nie et al. in JHEP 1311:087, arXiv:1309.2204 [hep-th], 2013), we presented a holographic s + p superconductor model with a scalar triplet charged under an SU(2) gauge field in the bulk. We also study the competition and coexistence of the s-wave and p-wave orders in the probe limit. In this work we continue to study the model by considering the full back-reaction. The model shows a rich phase structure and various condensate behaviors such as the "n-type" and "u-type" ones, which are also known as reentrant phase transitions in condensed matter physics. The phase transitions to the p-wave phase or s + p coexisting phase become first order in strong back-reaction cases. In these first order phase transitions, the free energy curve always forms a swallow tail shape, in which the unstable s + p solution can also play an important role. The phase diagrams of this model are given in terms of the dimension of the scalar order and the temperature in the cases of eight different values of the back-reaction parameter, which show that the region for the s + p coexisting phase is enlarged with a small or medium back-reaction parameter but is reduced in the strong back-reaction cases.

  10. Dynamic modeling of biochemical reactions with application to signal transduction: principles and tools using Mathematica.

    PubMed

    Tóth, János; Rospars, Jean-Pierre

    2005-01-01

    Modeling of biochemical phenomena is based on formal reaction kinetics. This requires the translation of the original reaction systems into sets of differential equations expressing the effects of the various reaction steps. The temporal behavior of the system is obtained by solving the differential equations. We present the main concepts on which the formal approach of these two problems is based and we show how the amount of work needed to treat them can be significantly reduced by using a mathematical program package (Mathematica). Symbolic and numerical calculations can be performed with the programs presented and graphic presentations of the behavior of the system be obtained. The basic ideas are illustrated with three examples taken from the area of signal transduction and ion signaling.

  11. An under-met and over-met expectations model of employee reactions to merit raises.

    PubMed

    Schaubroeck, John; Shaw, Jason D; Duffy, Michelle K; Mitra, Atul

    2008-03-01

    The authors developed a model of how raise expectations influence the relationship between merit pay raises and employee reactions and tested it using a sample of hospital employees. Pay-for-performance (PFP) perceptions were consistently related to personal reactions (e.g., pay raise happiness, pay-level satisfaction, and turnover intentions). Merit pay raises were strongly related to reactions only among employees with high raise expectations and high PFP perceptions. The interactive effects of under-met/over-met expectations and PFP perceptions were mediated by the extent to which participants saw the raise as generous and they were happy with the raises they received. The authors discuss the implications of these findings for expectation-fulfillment theories, merit pay research, and the administration of incentives.

  12. Reactions of chlorine with selected aromatic models of aquatic humic material

    SciTech Connect

    Norwood, D.L.; Johnson, J.D.; Christman, R.F.; Hass, J.R.; Bobenrieth, M.J.

    1980-02-01

    A series of compounds designed to model the monomeric components of aquatic humic material was reacted with aqueous chlorine at pH 7. Chloroform production and chlorine demand were measured for each compound over varied time periods. All compounds studied produced measurable amounts of chloroform with resorcinol derivatives showing the greatest yields. In addition, the chlorination reactions of resorcinol and 3-methoxy-4-hydroxycinnamic acid were studied in depth with gas chromatography/mass spectrometry (GC/MS). The resorcinol reaction was found to proceed through several chlorinated intermediates, of which the most abundant was 3,5,5-trichlorocyclopent-3-ene-1,2-dione, to chloroform and chlorinated acids. Chlorination of the cinnamic acid derivative produced chlorinated substitution products and chlorophenols, which broke down upon further reaction to chloroacetic acids.

  13. Kinetic study of model reactions in the gas phase at the early stage of coke formation

    SciTech Connect

    Nohara, D.; Sakai, T. )

    1992-01-01

    This paper reports that the most probable gas-phase reactions at the early stage of coke formation were elucidated by kinetic study on the model reactions adopted for formation of cyclic compounds and growth of ring. It was revealed that the formation and growth of ring proceeded mainly through cycloaddition of butadiene or allyl radicals to unsaturated hydrocarbons at relatively low temperatures ({approximately}600{degrees}C), i.e., through a Diels-Alder type reaction. On the other hand, such growth of ring as formation of biphenyl accompanying dehydrogenation from benzene can proceed only at the higher temperatures. It was also revealed that in the growth of the ring, cycloaddition of butadiene favors a cyclic olefin molecule that possesses a nonconjugated double bond and a nearly planar structure.

  14. Nuclear reaction cross sections of exotic nuclei in the Glauber model for relativistic mean field densities

    SciTech Connect

    Patra, S. K.; Panda, R. N.; Arumugam, P.; Gupta, Raj K.

    2009-12-15

    We have calculated the total nuclear reaction cross sections of exotic nuclei in the framework of the Glauber model, using as inputs the standard relativistic mean field (RMF) densities and the densities obtained from the more recently developed effective-field-theory-motivated RMF (the E-RMF). Both light and heavy nuclei are taken as the representative targets, and the light neutron-rich nuclei as projectiles. We found the total nuclear reaction cross section to increase as a function of the mass number, for both the target and projectile nuclei. The differential nuclear elastic scattering cross sections are evaluated for some selected systems at various incident energies. We found a large dependence of the differential elastic scattering cross section on incident energy. Finally, we have applied the same formalism to calculate both the total nuclear reaction cross section and the differential nuclear elastic scattering cross section for the recently discussed superheavy nucleus with atomic number Z=122.

  15. Low Velocity Impact Experiments plus Modeling of the Resulting Reaction Violence in LX-10 Charges

    NASA Astrophysics Data System (ADS)

    Chidester, Steven; Garcia, Frank; Vandersall, Kevin; Tarver, Craig

    2011-06-01

    A new gas gun facility and improved instrumentation were used to study the mechanisms of low velocity impact ignition and growth of violent reaction. Cylindrical charges of the HMX based explosive LX-10 (95% HMX, 5% Viton binder) encased by lexan were impacted by 6.35 mm diameter hardened steel projectiles at velocities ranging from 47 to 500 m/s. Fast Phantom v12 cameras were employed to capture the times of first ignition. The degrees of resulting reaction violence were determined using Photonic Doppler Velocimetry (PDV) probes to measure the free surface velocity histories of attached aluminum foils. Analytical and hydrodynamic reactive flow models were used to estimate the relative violence of these LX-10 reactions compared to the intentional detonation of an equivalent LX-10 charge. This work was performed under the auspices of the U. S. Department of Energy by the Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.

  16. Effect of motion frequency spectrum on subjective comfort response. [modeling passenger reactions to commercial aircraft flights

    NASA Technical Reports Server (NTRS)

    Jacobson, I. D.; Schoultz, M. B.; Blake, J. C.

    1973-01-01

    In order to model passenger reaction to present and future aircraft environments, it is necessary to obtain data in several ways. First, of course, is the gathering of environmental and passenger reaction data on commercial aircraft flights. In addition, detailed analyses of particular aspects of human reaction to the environment are best studied in a controllable experimental situation. Thus the use of simulators, both flight and ground based, is suggested. It is shown that there is a reasonably high probability that the low frequency end of the spectrum will not be necessary for simulation purposes. That is, the fidelity of any simulation which omits the very low frequency content will not yield results which differ significantly from the real environment. In addition, there does not appear to be significant differences between the responses obtained in the airborne simulator environment versus those obtained on commercial flights.

  17. Catalytic conversion reactions in nanoporous systems with concentration-dependent selectivity: Statistical mechanical modeling

    SciTech Connect

    Garcia, Andres; Wang, Jing; Windus, Theresa L.; Sadow, Aaron D.; Evans, James W.

    2016-05-20

    Statistical mechanical modeling is developed to describe a catalytic conversion reaction A → Bc or Bt with concentration-dependent selectivity of the products, Bc or Bt, where reaction occurs inside catalytic particles traversed by narrow linear nanopores. The associated restricted diffusive transport, which in the extreme case is described by single-file diffusion, naturally induces strong concentration gradients. Hence, by comparing kinetic Monte Carlo simulation results with analytic treatments, selectivity is shown to be impacted by strong spatial correlations induced by restricted diffusivity in the presence of reaction and also by a subtle clustering of reactants, A.

  18. Implicit solvation model for density-functional study of nanocrystal surfaces and reaction pathways

    NASA Astrophysics Data System (ADS)

    Mathew, Kiran; Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Arias, T. A.; Hennig, Richard G.

    2014-02-01

    Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent effects. In this work, we implement an implicit solvation model that has a firm theoretical foundation into the widely used density-functional code Vienna ab initio Software Package. The implicit solvation model follows the framework of joint density functional theory. We describe the framework, our algorithm and implementation, and benchmarks for small molecular systems. We apply the solvation model to study the surface energies of different facets of semiconducting and metallic nanocrystals and the SN2 reaction pathway. We find that solvation reduces the surface energies of the nanocrystals, especially for the semiconducting ones and increases the energy barrier of the SN2 reaction.

  19. Abrasion-ablation model for neutron production in heavy ion reactions

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Wilson, John W.; Townsend, Lawrence W.

    1995-01-01

    In heavy ion reactions, neutron production at forward angles is observed to occur with a Gaussian shape that is centered near the beam energy and extends to energies well above that of the beam. This paper presents an abrasion-ablation model for making quantitative predictions of the neutron spectrum. To describe neutrons produced from the abrasion step of the reaction where the projectile and target overlap, the authors use the Glauber model and include effects of final-state interactions. They then use the prefragment mass distribution from abrasion with a statistical evaporation model to estimate the neutron spectrum resulting from ablation. Measurements of neutron production from Ne and Nb beams are compared with calculations, and good agreement is found.

  20. Modeling Bimolecular Reactions and Transport in Porous Media Via Particle Tracking

    SciTech Connect

    Dong Ding; David Benson; Amir Paster; Diogo Bolster

    2012-01-01

    We use a particle-tracking method to simulate several one-dimensional bimolecular reactive transport experiments. In this numerical method, the reactants are represented by particles: advection and dispersion dominate the flow, and molecular diffusion dictates, in large part, the reactions. The particle/particle reactions are determined by a combination of two probabilities dictated by the physics of transport and energetics of reaction. The first is that reactant particles occupy the same volume over a short time interval. The second is the conditional probability that two collocated particles favorably transform into a reaction. The first probability is a direct physical representation of the degree of mixing in an advancing displacement front, and as such lacks empirical parameters except for the user-defined number of particles. This number can be determined analytically from concentration autocovariance, if this type of data is available. The simulations compare favorably to two physical experiments. In one, the concentration of product, 1,2-naphthoquinoe-4-aminobenzene (NQAB) from reaction between 1,2-naphthoquinone-4-sulfonic acid (NQS) and aniline (AN), was measured at the outflow of a column filled with glass beads at different times. In the other, the concentration distribution of reactants (CuSO_4 and EDTA^{4-}) and products (CuEDTA^{4-}) were quantified by snapshots of transmitted light through a column packed with cryloite sand. The thermodynamic rate coefficient in the latter experiment was 10^7 times greater than the former experiment, making it essentially instantaneous. When compared to the solution of the advection-dispersion-reaction equation (ADRE) with the well-mixed reaction coefficient, the experiments and the particle-tracking simulations showed on the order of 20% to 40% less overall product, which is attributed to poor mixing. The poor mixing also leads to higher product concentrations on the edges of the mixing zones, which the particle

  1. A robust methodology for kinetic model parameter estimation for biocatalytic reactions.

    PubMed

    Al-Haque, Naweed; Santacoloma, Paloma A; Neto, Watson; Tufvesson, Pär; Gani, Rafiqul; Woodley, John M

    2012-01-01

    Effective estimation of parameters in biocatalytic reaction kinetic expressions are very important when building process models to enable evaluation of process technology options and alternative biocatalysts. The kinetic models used to describe enzyme-catalyzed reactions generally include several parameters, which are strongly correlated with each other. State-of-the-art methodologies such as nonlinear regression (using progress curves) or graphical analysis (using initial rate data, for example, the Lineweaver-Burke plot, Hanes plot or Dixon plot) often incorporate errors in the estimates and rarely lead to globally optimized parameter values. In this article, a robust methodology to estimate parameters for biocatalytic reaction kinetic expressions is proposed. The methodology determines the parameters in a systematic manner by exploiting the best features of several of the current approaches. The parameter estimation problem is decomposed into five hierarchical steps, where the solution of each of the steps becomes the input for the subsequent step to achieve the final model with the corresponding regressed parameters. The model is further used for validating its performance and determining the correlation of the parameters. The final model with the fitted parameters is able to describe both initial rate and dynamic experiments. Application of the methodology is illustrated with a case study using the ω-transaminase catalyzed synthesis of 1-phenylethylamine from acetophenone and 2-propylamine.

  2. Transport-reaction model for defect and carrier behavior within displacement cascades in gallium arsenide

    SciTech Connect

    Wampler, William R.; Myers, Samuel M.

    2014-02-01

    A model is presented for recombination of charge carriers at displacement damage in gallium arsenide, which includes clustering of the defects in atomic displacement cascades produced by neutron or ion irradiation. The carrier recombination model is based on an atomistic description of capture and emission of carriers by the defects with time evolution resulting from the migration and reaction of the defects. The physics and equations on which the model is based are presented, along with details of the numerical methods used for their solution. The model uses a continuum description of diffusion, field-drift and reaction of carriers and defects within a representative spherically symmetric cluster. The initial radial defect profiles within the cluster were chosen through pair-correlation-function analysis of the spatial distribution of defects obtained from the binary-collision code MARLOWE, using recoil energies for fission neutrons. Charging of the defects can produce high electric fields within the cluster which may influence transport and reaction of carriers and defects, and which may enhance carrier recombination through band-to-trap tunneling. Properties of the defects are discussed and values for their parameters are given, many of which were obtained from density functional theory. The model provides a basis for predicting the transient response of III-V heterojunction bipolar transistors to pulsed neutron irradiation.

  3. Comparison of kinetic and equilibrium reaction models insimulating gas hydrate behavior in porous media

    SciTech Connect

    Kowalsky, Michael B.; Moridis, George J.

    2006-11-29

    In this study we compare the use of kinetic and equilibriumreaction models in the simulation of gas (methane) hydrate behavior inporous media. Our objective is to evaluate through numerical simulationthe importance of employing kinetic versus equilibrium reaction modelsfor predicting the response of hydrate-bearing systems to externalstimuli, such as changes in pressure and temperature. Specifically, we(1) analyze and compare the responses simulated using both reactionmodels for natural gas production from hydrates in various settings andfor the case of depressurization in a hydrate-bearing core duringextraction; and (2) examine the sensitivity to factors such as initialhydrate saturation, hydrate reaction surface area, and numericaldiscretization. We find that for large-scale systems undergoing thermalstimulation and depressurization, the calculated responses for bothreaction models are remarkably similar, though some differences areobserved at early times. However, for modeling short-term processes, suchas the rapid recovery of a hydrate-bearing core, kinetic limitations canbe important, and neglecting them may lead to significantunder-prediction of recoverable hydrate. The use of the equilibriumreaction model often appears to be justified and preferred for simulatingthe behavior of gas hydrates, given that the computational demands forthe kinetic reaction model far exceed those for the equilibrium reactionmodel.

  4. BACKUP -- Recovering from incremental tape backups

    NASA Astrophysics Data System (ADS)

    Allan, P. M.

    The importance of making regular backups of your disks in well known, but it can be very frustrating to have a head crash and then discover that you cannot recover from your backups because the manuals do not tell you what to do. The DEC documentation covers most possibilities, but not the case where a removable pack is copied to a new pack, the new pack is then used as the current pack, and incremental backups to tape are then made. This situation is a fairly common one when you have two or more removable disk drives. This note covers backup and recovery in general terms, and details exactly what to do in the above mentioned case.

  5. First-principles modeling of catalysts: novel algorithms and reaction mechanisms

    NASA Astrophysics Data System (ADS)

    Richard, Bryan Goldsmith

    A molecular level understanding of a reaction mechanism and the computation of rates requires knowledge of the stable structures and the corresponding transition states that connect them. Temperature, pressure, and environment effects must be included to bridge the 'materials gap' so one can reasonably compare ab initio (first-principles, i.e., having no empirical parameters) predictions with experimental measurements. In this thesis, a few critical problems pertaining to ab initio modeling of catalytic systems are addressed; namely, 1) the issue of building representative models of isolated metal atoms grafted on amorphous supports, 2) modeling inorganic catalytic reactions in non-ideal solutions where the solvent participates in the reaction mechanism, and 3) bridging the materials gap using ab initio thermodynamics to predict the stability of supported nanoparticles under experimental reaction conditions. In Chapter I, a background on first-principles modeling of heterogeneous and homogenous catalysts is provided. Subsequently, to address the problem of modeling catalysis by isolated metal atoms on amorphous supports, we present in Chapter II a sequential-quadratic programming algorithm that systematically predicts the structure and reactivity of isolated active sites on insulating amorphous supports. Modeling solution phase reactions is also a considerable challenge for first-principles modeling, yet when done correctly it can yield critical kinetic and mechanistic insight that can guide experimental investigations. In Chapter III, we examine the formation of peroxorhenium complexes by activation of H2O2, which is key in selective oxidation reactions catalyzed by CH3ReO3 (methyltrioxorhenium, MTO). New experiments and density functional theory (DFT) calculations were conducted to better understand the activation of H2O2 by MTO and to provide a strong experimental foundation for benchmarking computational studies involving MTO and its derivatives. It was found

  6. Radiative capture reaction for 17Ne formation within a full three-body model

    NASA Astrophysics Data System (ADS)

    Casal, J.; Garrido, E.; de Diego, R.; Arias, J. M.; Rodríguez-Gallardo, M.

    2016-11-01

    Background: The breakout from the hot Carbon-Nitrogen-Oxigen (CNO) cycles can trigger the rp-process in type I x-ray bursts. In this environment, a competition between 15O(α ,γ )19Ne and the two-proton capture reaction 15O(2 p ,γ )17Ne is expected. Purpose: Determine the three-body radiative capture reaction rate for 17Ne formation including sequential and direct, resonant and nonresonant contributions on an equal footing. Method: Two different discretization methods have been applied to generate 17Ne states in a full three-body model: the analytical transformed harmonic oscillator method and the hyperspherical adiabatic expansion method. The binary p -15O interaction has been adjusted to reproduce the known spectrum of the unbound 16F nucleus. The dominant E 1 contributions to the 15O(2 p ,γ )17Ne reaction rate have been calculated from the inverse photodissociation process. Results: Three-body calculations provide a reliable description of 17Ne states. The agreement with the available experimental data on 17Ne is discussed. It is shown that the 15O(2 p ,γ )17Ne reaction rates computed within the two methods agree in a broad range of temperatures. The present calculations are compared with a previous theoretical estimation of the reaction rate. Conclusions: It is found that the full three-body model provides a reaction rate several orders of magnitude larger than the only previous estimation. The implications for the rp-process in type I x-ray bursts should be investigated.

  7. Statistical model analysis of α -induced reaction cross sections of 64Zn at low energies

    NASA Astrophysics Data System (ADS)

    Mohr, P.; Gyürky, Gy.; Fülöp, Zs.

    2017-01-01

    Background: α -nucleus potentials play an essential role in the calculation of α -induced reaction cross sections at low energies in the statistical model. Uncertainties of these calculations are related to ambiguities in the adjustment of the potential parameters to experimental elastic scattering angular distributions (typically at higher energies) and to the energy dependence of the effective α -nucleus potentials. Purpose: The present work studies cross sections of α -induced reactions for 64Zn at low energies and their dependence on the chosen input parameters of the statistical model calculations. The new experimental data from the recent Atomki experiments allow for a χ2-based estimate of the uncertainties of calculated cross sections at very low energies. Method: Recently measured data for the (α ,γ ), (α ,n ), and (α ,p ) reactions on 64Zn are compared to calculations in the statistical model. A survey of the parameter space of the widely used computer code talys is given, and the properties of the obtained χ2 landscape are discussed. Results: The best fit to the experimental data at low energies shows χ2/F ≈7.7 per data point, which corresponds to an average deviation of about 30% between the best fit and the experimental data. Several combinations of the various ingredients of the statistical model are able to reach a reasonably small χ2/F , not exceeding the best-fit result by more than a factor of 2. Conclusions: The present experimental data for 64Zn in combination with the statistical model calculations allow us to constrain the astrophysical reaction rate within about a factor of 2. However, the significant excess of χ2/F of the best fit from unity demands further improvement of the statistical model calculations and, in particular, the α -nucleus potential.

  8. Tissue Reaction and Biocompatibility of Implanted Mineral Trioxide Aggregate with Silver Nanoparticles in a Rat Model

    PubMed Central

    Zand, Vahid; Lotfi, Mehrdad; Aghbali, Amirala; Mesgariabbasi, Mehran; Janani, Maryam; Mokhtari, Hadi; Tehranchi, Pardis; Pakdel, Seyyed Mahdi Vahid

    2016-01-01

    Introduction: Biocompatibility and antimicrobial activity of endodontic materials are of utmost importance. Considering the extensive applications of mineral trioxide aggregate (MTA) in dentistry and antimicrobial properties of silver nanoparticles, this study aimed to evaluate the subcutaneous inflammatory reaction of rat connective tissues to white MTA with and without nanosilver (NS) particles. Methods and Materials: Polyethylene tubes (1.1×8 mm) containing experimental materials (MTA and MTA+NS and empty control tubes) were implanted in subcutaneous tissues of seventy-five male rats. Animals were divided into five groups (n=15) according to the time of evaluation: group 1; after 7 days, group 2; after 15 days, group 3; after 30 days, group 4; after 60 days and group 5; after 90 days. The inflammatory reaction was graded and data was analyzed using the Kruskal-Wallis and Mann-Whitney U tests. Statistical significance was defined at 0.05. Results: Comparison of cumulative inflammatory reaction at all intervals revealed that the mean grade of inflammatory reaction to MTA, MTA+NS and control samples were 3, 2 and 2, respectively. According to the Mann-Whitney analysis there were no significant differences between MTA+NS and MTA (P=0.42). Conclusion: Incorporation of 1% nanosilver to MTA does not affect the inflammatory reaction of subcutaneous tissue in rat models. PMID:26843871

  9. Kinetic reaction modeling framework for identifying and quantifying reductant reactivity in heterogeneous aquifer sediments.

    PubMed

    Descourvieres, Carlos; Prommer, Henning; Oldham, Carolyn; Greskowiak, Janek; Hartog, Niels

    2010-09-01

    Water-sediment interactions triggered by the injection of oxidized aqueous solutions into anoxic groundwater systems usually modify both the aquifer matrix and control the final aqueous composition. The identification and quantification of these reactions in complex heterogeneous systems remains a challenge for the analysis and prediction of water quality changes. Driven by the proposed injection of large quantities of oxic water into a deep anoxic heterogeneous pyritic aquifer; this study was undertaken to quantify the reactivity of aquifer sediments with respect to oxidant consumption and to characterize the variability of the reaction rates across different lithological units. A total of 53 samples were incubated for periods of 14, 37, and 50 days, during which the gas-phase was continuously monitored and the aqueous composition analyzed. A geochemical modeling framework was developed that incorporated a mixed set of equilibrium and kinetic reactions and supported the interpretation and quantification of the geochemical controls. The good agreement between simulated and experimental results of O2 consumption, CO2 production, pH, major ions, and trace metals suggests that the framework was able to successfully quantify reaction rates of competing redox and buffering reactions for the different lithological aquifer material.

  10. Evolution of natural gas composition: Predictive multi-phase reaction-transport modeling

    SciTech Connect

    Ortoleva, P.J.; Chang, K.A.; Maxwell, J.M.

    1995-12-31

    A computational modeling approach is used to investigate reaction and transport processes affecting natural gas composition over geological time. Three basic stages are integrated -- gas generation from organic solids or liquids, interactions during source rock expulsion to the reservoir and reactions within the reservoir. Multi-phase dynamics is handled by solving the fully coupled problem of phase-to-phase transfer, intra-phase organic and inorganic reactions and redox and other reactions between fluid phase molecules and minerals. Effects of capillarity and relative permeability are accounted for. Correlations will be determined between gas composition, temperature history, the mineralogy of rocks with which the gas was in contact and the composition of source organic phases. Questions of H{sub 2}S scavenging by oxidizing minerals and the production or removal of CO{sub 2} are focused upon. Our three spatial dimensional, reaction-transport simulation approach has great promise for testing general concepts and as a practical tool for the exploration and production of natural gas.

  11. Incremental Transductive Learning Approaches to Schistosomiasis Vector Classification

    NASA Astrophysics Data System (ADS)

    Fusco, Terence; Bi, Yaxin; Wang, Haiying; Browne, Fiona

    2016-08-01

    The key issues pertaining to collection of epidemic disease data for our analysis purposes are that it is a labour intensive, time consuming and expensive process resulting in availability of sparse sample data which we use to develop prediction models. To address this sparse data issue, we present the novel Incremental Transductive methods to circumvent the data collection process by applying previously acquired data to provide consistent, confidence-based labelling alternatives to field survey research. We investigated various reasoning approaches for semi-supervised machine learning including Bayesian models for labelling data. The results show that using the proposed methods, we can label instances of data with a class of vector density at a high level of confidence. By applying the Liberal and Strict Training Approaches, we provide a labelling and classification alternative to standalone algorithms. The methods in this paper are components in the process of reducing the proliferation of the Schistosomiasis disease and its effects.

  12. Dynamically adjustable foot-ground contact model to estimate ground reaction force during walking and running.

    PubMed

    Jung, Yihwan; Jung, Moonki; Ryu, Jiseon; Yoon, Sukhoon; Park, Sang-Kyoon; Koo, Seungbum

    2016-03-01

    Human dynamic models have been used to estimate joint kinetics during various activities. Kinetics estimation is in demand in sports and clinical applications where data on external forces, such as the ground reaction force (GRF), are not available. The purpose of this study was to estimate the GRF during gait by utilizing distance- and velocity-dependent force models between the foot and ground in an inverse-dynamics-based optimization. Ten males were tested as they walked at four different speeds on a force plate-embedded treadmill system. The full-GRF model whose foot-ground reaction elements were dynamically adjusted according to vertical displacement and anterior-posterior speed between the foot and ground was implemented in a full-body skeletal model. The model estimated the vertical and shear forces of the GRF from body kinematics. The shear-GRF model with dynamically adjustable shear reaction elements according to the input vertical force was also implemented in the foot of a full-body skeletal model. Shear forces of the GRF were estimated from body kinematics, vertical GRF, and center of pressure. The estimated full GRF had the lowest root mean square (RMS) errors at the slow walking speed (1.0m/s) with 4.2, 1.3, and 5.7% BW for anterior-posterior, medial-lateral, and vertical forces, respectively. The estimated shear forces were not significantly different between the full-GRF and shear-GRF models, but the RMS errors of the estimated knee joint kinetics were significantly lower for the shear-GRF model. Providing COP and vertical GRF with sensors, such as an insole-type pressure mat, can help estimate shear forces of the GRF and increase accuracy for estimation of joint kinetics.

  13. A more robust model of the biodiesel reaction, allowing identification of process conditions for significantly enhanced rate and water tolerance.

    PubMed

    Eze, Valentine C; Phan, Anh N; Harvey, Adam P

    2014-03-01

    A more robust kinetic model of base-catalysed transesterification than the conventional reaction scheme has been developed. All the relevant reactions in the base-catalysed transesterification of rapeseed oil (RSO) to fatty acid methyl ester (FAME) were investigated experimentally, and validated numerically in a model implemented using MATLAB. It was found that including the saponification of RSO and FAME side reactions and hydroxide-methoxide equilibrium data explained various effects that are not captured by simpler conventional models. Both the experiment and modelling showed that the "biodiesel reaction" can reach the desired level of conversion (>95%) in less than 2min. Given the right set of conditions, the transesterification can reach over 95% conversion, before the saponification losses become significant. This means that the reaction must be performed in a reactor exhibiting good mixing and good control of residence time, and the reaction mixture must be quenched rapidly as it leaves the reactor.

  14. STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python.

    PubMed

    Wils, Stefan; De Schutter, Erik

    2009-01-01

    We describe how the use of the Python language improved the user interface of the program STEPS. STEPS is a simulation platform for modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional boundary conditions. Setting up such models is a complicated process that consists of many phases. Initial versions of STEPS relied on a static input format that did not cleanly separate these phases, limiting modelers in how they could control the simulation and becoming increasingly complex as new features and new simulation algorithms were added. We solved all of these problems by tightly integrating STEPS with Python, using SWIG to expose our existing simulation code.

  15. A Semi-Empirical Two Step Carbon Corrosion Reaction Model in PEM Fuel Cells

    SciTech Connect

    Young, Alan; Colbow, Vesna; Harvey, David; Rogers, Erin; Wessel, Silvia

    2013-01-01

    The cathode CL of a polymer electrolyte membrane fuel cell (PEMFC) was exposed to high potentials, 1.0 to 1.4 V versus a reversible hydrogen electrode (RHE), that are typically encountered during start up/shut down operation. While both platinum dissolution and carbon corrosion occurred, the carbon corrosion effects were isolated and modeled. The presented model separates the carbon corrosion process into two reaction steps; (1) oxidation of the carbon surface to carbon-oxygen groups, and (2) further corrosion of the oxidized surface to carbon dioxide/monoxide. To oxidize and corrode the cathode catalyst carbon support, the CL was subjected to an accelerated stress test cycled the potential from 0.6 VRHE to an upper potential limit (UPL) ranging from 0.9 to 1.4 VRHE at varying dwell times. The reaction rate constants and specific capacitances of carbon and platinum were fitted by evaluating the double layer capacitance (Cdl) trends. Carbon surface oxidation increased the Cdl due to increased specific capacitance for carbon surfaces with carbon-oxygen groups, while the second corrosion reaction decreased the Cdl due to loss of the overall carbon surface area. The first oxidation step differed between carbon types, while both reaction rate constants were found to have a dependency on UPL, temperature, and gas relative humidity.

  16. Low velocity impact experiments on the explosive LX-10 with modeling of reaction violence

    NASA Astrophysics Data System (ADS)

    Chidester, Steven; Garcia, Frank; Vandersall, Kevin S.; Tarver, Craig M.; Ferranti, Louis

    2012-03-01

    A new gas gun capability designed for the velocity range of ~20-400 m/s was used to study the mechanisms of low-velocity impact ignition and reaction violence of explosive targets in safety studies. Hemispherical charges of the HMX-based explosive LX-10 (95% HMX, 5% Viton binder) assembled in a polycarbonate target ring were impacted by a 6.35 mm diameter hardened steel rod protruding from a projectile at velocities ranging from 36 to 374 m/s. Digital high-speed (Phantom v12) cameras were utilized to capture the times of first ignition and a Photonic Doppler Velocimetry (PDV) probe placed at the rear of the target was used to measure the free surface velocity histories of an aluminum foil on the LX-10 surface to quantify the resulting reaction violence. The Ignition and Growth reactive flow model for LX-10 was used to compare the relative violence of these reactions to the intentional detonation of an equivalent LX-10 charge. It was found that comparing the model results to that of the experiment using this impactor geometry within the tested velocity range, the reaction violence increased with velocity from 45-374 m/s and only a small fraction of material appears to react during the impact.

  17. Upscaling of reaction rates in reactive transport using pore-scale reactive transport model

    NASA Astrophysics Data System (ADS)

    Yoon, H.; Dewers, T. A.; Arnold, B. W.; Major, J. R.; Eichhubl, P.; Srinivasan, S.

    2013-12-01

    Dissolved CO2 during geological CO2 storage may react with minerals in fractured rocks, confined aquifers, or faults, resulting in mineral precipitation and dissolution. The overall rate of reaction can be affected by coupled processes among hydrodynamics, transport, and reactions at the (sub) pore-scale. In this research pore-scale modeling of coupled fluid flow, reactive transport, and heterogeneous reaction at the mineral surface is applied to account for permeability alterations caused by precipitation-induced pore-blocking. This work is motivated by the observed CO2 seeps from a natural analog to geologic CO2 sequestration at Crystal Geyser, Utah. A key observation is the lateral migration of CO2 seep sites at a scale of ~ 100 meters over time. A pore-scale model provides fundamental mechanistic explanations of how calcite precipitation alters flow paths by pore plugging under different geochemical compositions and pore configurations. In addition, response function of reaction rates will be constructed from pore-scale simulations which account for a range of reaction regimes characterized by the Damkohler and Peclet numbers. Newly developed response functions will be used in a continuum scale model that may account for large-scale phenomena mimicking lateral migration of surface CO2 seeps. Comparison of field observations and simulations results will provide mechanistic explanations of the lateral migration and enhance our understanding of subsurface processes associated with the CO2 injection. This work is supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security

  18. Career Decision-Making Profiles vs. Styles: Convergent and Incremental Validity

    ERIC Educational Resources Information Center

    Gati, Itamar; Gadassi, Reuma; Mashiah-Cohen, Rona

    2012-01-01

    The present research investigated the convergent and incremental validity of the multidimensional model and questionnaire--the Career Decision-Making Profiles ("CDMP," Gati, Landman, Davidovitch, Peretz-Asulin, & Gadassi, 2010)--by comparing it to two prevalent decision-making style models. Study 1 compared the "CDMP" to the Vocational Decision…

  19. Comparison of Retention Rates Using Traditional, Drill Sandwich, and Incremental Rehearsal Flash Card Methods.

    ERIC Educational Resources Information Center

    MacQuarrie, Lara L.; Tucker, James A.; Burns, Matthew K.; Hartman, Brian

    2002-01-01

    Research has demonstrated increased retention from drill, but the data regarding drill format are inconsistent. Two commonly used models, Drill Sandwich (DS) and Incremental Rehearsal (IR), were compared to each other and to a traditional flashcard method. The IR model consistently led to significantly more words retained than the traditional or…

  20. Microsolvated transition state models for improved insight into chemical properties and reaction mechanisms.

    PubMed

    Sunoj, Raghavan B; Anand, Megha

    2012-10-05

    Over the years, several methods have been developed to effectively represent the chemical behavior of solutes in solvents. The environmental effects arising due to solvation can generally be achieved either through inclusion of discrete solvent molecules or by inscribing into a cavity in a homogeneous and continuum dielectric medium. In both these approaches of computational origin, the perturbations on the solute induced by the surrounding solvent are at the focus of the problem. While the rigor and method of inclusion of solvent effects vary, such solvation models have found widespread applications, as evident from modern chemical literature. A hybrid method, commonly referred to as cluster-continuum model (CCM), brings together the key advantages of discrete and continuum models. In this perspective, we intend to highlight the latent potential of CCM toward obtaining accurate estimates on a number of properties as well as reactions of contemporary significance. The objective has generally been achieved by choosing illustrative examples from the literature, besides expending efforts to bring out the complementary advantages of CCM as compared to continuum or discrete solvation models. The majority of examples emanate from the prevalent applications of CCM to organic reactions, although a handful of interesting organometallic reactions have also been discussed. In addition, increasingly accurate computations of properties like pK(a) and solvation of ions obtained using the CCM protocol are also presented.

  1. Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data

    PubMed Central

    Sriyudthsak, Kansuporn; Shiraishi, Fumihide; Hirai, Masami Yokota

    2016-01-01

    The high-throughput acquisition of metabolome data is greatly anticipated for the complete understanding of cellular metabolism in living organisms. A variety of analytical technologies have been developed to acquire large-scale metabolic profiles under different biological or environmental conditions. Time series data are useful for predicting the most likely metabolic pathways because they provide important information regarding the accumulation of metabolites, which implies causal relationships in the metabolic reaction network. Considerable effort has been undertaken to utilize these data for constructing a mathematical model merging system properties and quantitatively characterizing a whole metabolic system in toto. However, there are technical difficulties between benchmarking the provision and utilization of data. Although, hundreds of metabolites can be measured, which provide information on the metabolic reaction system, simultaneous measurement of thousands of metabolites is still challenging. In addition, it is nontrivial to logically predict the dynamic behaviors of unmeasurable metabolite concentrations without sufficient information on the metabolic reaction network. Yet, consolidating the advantages of advancements in both metabolomics and mathematical modeling remain to be accomplished. This review outlines the conceptual basis of and recent advances in technologies in both the research fields. It also highlights the potential for constructing a large-scale mathematical model by estimating model parameters from time series metabolome data in order to comprehensively understand metabolism at the systems level. PMID:27200361

  2. Identification of hydroxycinnamic acid-maillard reaction products in low-moisture baking model systems.

    PubMed

    Jiang, Deshou; Chiaro, Christopher; Maddali, Pranav; Prabhu, K Sandeep; Peterson, Devin G

    2009-11-11

    The chemistry and fate of hydroxycinnamic acids (ferulic, p-coumeric, caffeic, sinapic, and cinnamic acid) in a glucose/glycine simulated baking model (10% moisture at 200 degrees C for 15 min) were investigated. Liquid chromatography-mass spectrometry analysis of glucose/glycine and glucose/glycine/hydroxycinnamic acid model systems confirmed the phenolics reacted with Maillard intermediates; two main reaction product adducts were reported. On the basis of isotopomeric analysis, LC-MS, and NMR spectroscopy, structures of two ferulic acid-Maillard reaction products were identified as 6-(4-hydroxy-3-methoxyphenyl)-5-(hydroxymethyl)-8-oxabicyclo[3.2.1]oct-3-en-2-one (adduct I) and 2-(6-(furan-2-yl)-7-(4-hydroxy-3-methoxyphenyl)-1-methyl-3-oxo-2,5-diazabicyclo[2.2.2]oct-5-en-2-yl)acetic acid (adduct II). In addition, a pyrazinone-type Maillard product, 2-(5-(furan-2-yl)-6-methyl-2-oxopyrazin-1(2H)-yl) acetic acid (IIa), was identified as an intermediate for reaction product adduct II, whereas 3-deoxy-2-hexosulose was identified as an intermediate of adduct I. Both adducts I and II were suggested to be generated by pericyclic reaction mechanisms. Quantitative gas chromatography (GC) analysis and liquid chromatography (LC) also indicated that the addition of ferulic acid to a glucose/glycine model significantly reduced the generation of select Maillard-type aroma compounds, such as furfurals, methylpyrazines, 2-acetylfuran, 2-acetylpyridine, 2-acetylpyrrole, and cyclotene as well as inhibited color development in these Maillard models. In addition, adducts I and II suppressed the bacterial lipopolysaccharide (LPS)-mediated expression of two prototypical pro-inflammatory genes, inducible nitric oxide synthase (iNOS) and cyclooxygenase (COX)-2, in an in vitro murine macrophage model; ferulic acid reported negligible activity.

  3. A fractional model of a dynamical Brusselator reaction-diffusion system arising in triple collision and enzymatic reactions

    NASA Astrophysics Data System (ADS)

    Singh, Jagdev; Rashidi, M. M.; Kumar, Devendra; Swroop, Ram

    2016-12-01

    In this paper, we study a dynamical Brusselator reaction-diffusion system arising in triple collision and enzymatic reactions with time fractional Caputo derivative. The present article involves a more generalized effective approach, proposed for the Brusselator system say q-homotopy analysis transform method (q-HATM), providing the family of series solutions with nonlocal generalized effects. The convergence of the q-HATM series solution is adjusted and controlled by auxiliary parameter ℏ and asymptotic parameter n. The numerical results are demonstrated graphically. The outcomes of the study show that the q-HATM is computationally very effective and accurate to analyze nonlinear fractional differential equations.

  4. Reaction norm model with unknown environmental covariate to analyze heterosis by environment interaction.

    PubMed

    Su, G; Madsen, P; Lund, M S

    2009-05-01

    Crossbreeding is currently increasing in dairy cattle production. Several studies have shown an environment-dependent heterosis [i.e., an interaction between heterosis and environment (H x E)]. An H x E interaction is usually estimated from a few discrete environment levels. The present study proposes a reaction norm model to describe H x E interaction, which can deal with a large number of environment levels using few parameters. In the proposed model, total heterosis consists of an environment-independent part, which is described as a function of heterozygosity, and an environment-dependent part, which is described as a function of heterozygosity and environmental value (e.g., herd-year effect). A Bayesian approach is developed to estimate the environmental covariates, the regression coefficients of the reaction norm, and other parameters of the model simultaneously in both linear and nonlinear reaction norms. In the nonlinear reaction norm model, the H x E is approximated using linear splines. The approach was tested using simulated data, which were generated using an animal model with a reaction norm for heterosis. The simulation study includes 4 scenarios (the combinations of moderate vs. low heritability and moderate vs. low herd-year variation) of H x E interaction in a nonlinear form. In all scenarios, the proposed model predicted total heterosis very well. The correlation between true heterosis and predicted heterosis was 0.98 in the scenarios with low herd-year variation and 0.99 in the scenarios with moderate herd-year variation. This suggests that the proposed model and method could be a good approach to analyze H x E interactions and predict breeding values in situations in which heterosis changes gradually and continuously over an environmental gradient. On the other hand, it was found that a model ignoring H x E interaction did not significantly harm the prediction of breeding value under the simulated scenarios in which the variance for environment

  5. New paradigm for simplified combustion modeling of energetic solids: Branched chain gas reaction

    SciTech Connect

    Brewster, M.Q.; Ward, M.J.; Son, S.F.

    1997-09-01

    Two combustion models with simple but rational chemistry are compared: the classical high gas activation energy (E{sub g}/RT {much_gt} 1) Denison-Baum-Williams (DBW) model, and a new low gas activation energy (E{sub g}/RT {much_lt} 1) model recently proposed by Ward, Son, and Brewster (WSB). Both models make the same simplifying assumptions of constant properties, Lewis number unity, single-step, second order gas phase reaction, and single-step, zero order, high activation energy condensed phase decomposition. The only difference is in the gas reaction activation energy E{sub g} which is asymptotically large for DBW and vanishingly small for WSB. For realistic parameters the DBW model predicts a nearly constant temperature sensitivity {sigma}{sub p} and a pressure exponent n approaching 1. The WSB model predicts generally observed values of n = 0.7 to 0.9 and {sigma}{sub p}(T{sub o},P) with the generally observed variations with temperature (increasing) and pressure (decreasing). The WSB temperature profile also matches measured profiles better. Comparisons with experimental data are made using HMX as an illustrative example (for which WSB predictions for {sigma}{sub p}(T{sub o},P) are currently more accurate than even complex chemistry models). WSB has also shown good agreement with NC/NG double base propellant and HNF, suggesting that at the simplest level of combustion modeling, a vanishingly small gas activation energy is more realistic than an asymptotically large one. The authors conclude from this that the important (regression rate determining) gas reaction zone near the surface has more the character of chain branching than thermal decomposition.

  6. Numerical simulation of pseudoelastic shape memory alloys using the large time increment method

    NASA Astrophysics Data System (ADS)

    Gu, Xiaojun; Zhang, Weihong; Zaki, Wael; Moumni, Ziad

    2017-04-01

    The paper presents a numerical implementation of the large time increment (LATIN) method for the simulation of shape memory alloys (SMAs) in the pseudoelastic range. The method was initially proposed as an alternative to the conventional incremental approach for the integration of nonlinear constitutive models. It is adapted here for the simulation of pseudoelastic SMA behavior using the Zaki–Moumni model and is shown to be especially useful in situations where the phase transformation process presents little or lack of hardening. In these situations, a slight stress variation in a load increment can result in large variations of strain and local state variables, which may lead to difficulties in numerical convergence. In contrast to the conventional incremental method, the LATIN method solve the global equilibrium and local consistency conditions sequentially for the entire loading path. The achieved solution must satisfy the conditions of static and kinematic admissibility and consistency simultaneously after several iterations. 3D numerical implementation is accomplished using an implicit algorithm and is then used for finite element simulation using the software Abaqus. Computational tests demonstrate the ability of this approach to simulate SMAs presenting flat phase transformation plateaus and subjected to complex loading cases, such as the quasi-static behavior of a stent structure. Some numerical results are contrasted to those obtained using step-by-step incremental integration.

  7. Temperature Humidity and Sea Level Pressure Increments Induced by 1DVAR Analysis of GPS Refractivity

    NASA Technical Reports Server (NTRS)

    Poli, Paul; Joiner, Joanna; Kursinski, Emil Robert; Einaudi, Franco (Technical Monitor)

    2001-01-01

    The Global Positioning System (GPS) transmitted signals are affected by the atmosphere. Using the radio occultation technique, where a receiver is placed on a low-Earth-orbiting platform. it is possible to perform soundings. by measuring the bending angles of the rays. The information can be converted into atmospheric refractivity. We have developed a one dimensional variational (1DVAR) analysis that uses GPS/MET 1995 refractivity and 6-hour FVDAS (Finite Volume Data Assimilation System) forecasts as background information to constrain the retrievals. The analysis increments are defined as 1DVAR minus background temperature, humidity and sea level pressure. Before assimilating the 1DVAR profiles into the FVDAS. the increments need to be understood. First, some bias could be induced in the retrievals when confronted with actual biased data: second. bias in the back-round could create undesired bias in the retrievals. Anv bias in the analyses will ultimately change the climatology of the model the retrievals will be assimilated into. We relate the increments to the reduction of the difference between observed minus computed refractivity profiles. We also point out the difference in the mean increments using backgrounds which have assimilated either NESDIS TIROS Operational Vertical Sounder (TOVS) operational retrievals or Data Assimilation Office (DAO) TOVS interactive retrievals. The climatology of the model in terms of refractivity is significantly different and this impacts the GPS 1DVAR increments. This testifies that changing the basic load of assimilated data has an influence on the impact the GPS data may have in a DAS.

  8. Modelling the sulfide-oxygen reaction and associated pH gradients in porewaters

    NASA Astrophysics Data System (ADS)

    Boudreau, Bernard P.

    1991-01-01

    A diagenetic model is presented that describes the effects of the steady-state reaction between oxygen and sulfide on pH distributions in porewaters. The model includes consumption of O 2 and sulfide and the production of H + by this oxidation reaction, fast association-dissociation reactions in the dissolved carbonate and sulfide systems, and separate diffusive transport of each of these solute species. Two mathematical forms for the oxidation kinetics are examined. The first is a nonlinear product of the oxygen and total sulfide concentrations, and the second is a spatially dependent sink in the form of a Gaussian function. This model is applied to the data obtained by JøRGENSEN and REVSBECH (1983) in a Beggiatoa mat. Approximate numerical solution of the model with nonlinear kinetics shows that the oxygen and total sulfide profiles can be fit simultaneously with an oxidation rate constant of the order of 10 15 M -1 a -1. The best simulation to the associated pH profile is obtained by assuming a ΣCO 2 concentration of about 1.8 mM. This predicted profile agrees with the general shape and magnitude of the observed pH change; however, the calculated pH minimum is sharper than that seen in the data. Adoption of Gaussian kinetics leads to an analytical solution of the model, from which it is relatively easy to generate species profiles. With Gaussian kinetics, the model also predicts pH profiles similar to those observed except for the acuity of the minimum. The results of both kinetic models show that porewaters become rapidly undersaturated with respect to calcite. The best fit to the observed pH profile is obtained by reacting the oxygen and sulfide along a distinct interface in the sediments, while releasing the H + byproduct of this reaction over a zone of nonzero thickness. This finding could be attributed to the biological nature of the oxidation reaction in which Beggiatoa attempt to consume reactants at a discrete depth to optimize the energy yield, but

  9. Solvent free energy curves for electron transfer reactions: A nonlinear solvent response model

    NASA Astrophysics Data System (ADS)

    Ichiye, Toshiko

    1996-05-01

    Marcus theory for electron transfer assumes a linear response of the solvent so that both the reactant and product free energy curves are parabolic functions of the solvent polarization, each with the same solvent force constant k characterizing the curvature. Simulation data by other workers indicate that the assumption of parabolic free energy curves is good for the Fe2+-Fe3+ self-exchange reaction but that the k of the reactant and product free energy curves are different for the reaction D0+A0→D1-+A1+. However, the fluctuations sampled in these simulations were not large enough to reach the activation barrier region, which was thus treated either by umbrella sampling or by parabolic extrapolation. Here, we present free energy curves calculated from a simple model of ionic solvation developed in an earlier paper by Hyun, Babu, and Ichiye, which we refer to here as the HBI model. The HBI model describes the nonlinearity of the solvent response due to the orientation of polar solvent molecules. Since it is a continuum model, it may be considered the first-order nonlinear correction to the linear response Born model. Moreover, in the limit of zero charge or infinite radius, the Born model and the Marcus relations are recovered. Here, the full free energy curves are calculated using analytic expressions from the HBI model. The HBI reactant and product curves have different k for D0+A0→D1-+A1+ as in the simulations, but examining the full curves shows they are nonparabolic due to the nonlinear response of the solvent. On the other hand, the HBI curves are close to parabolic for the Fe2+-Fe3+ reaction, also in agreement with simulations, while those for another self-exchange reaction D0-A1+ show greater deviations from parabolic behavior than the Fe2+-Fe3+ reaction. This indicates that transitions from neutral to charged species will have the largest deviations. Thus, the second moment of the polarization is shown to be a measure of the deviation from Marcus

  10. Oxygen consumption rates in subseafloor basaltic crust derived from a reaction transport model.

    PubMed

    Orcutt, Beth N; Wheat, C Geoffrey; Rouxel, Olivier; Hulme, Samuel; Edwards, Katrina J; Bach, Wolfgang

    2013-01-01

    Oceanic crust is the largest potential habitat for life on Earth and may contain a significant fraction of Earth's total microbial biomass; yet, empirical analysis of reaction rates in basaltic crust is lacking. Here we report the first assessment of oxygen consumption in young (~8 Ma) and cool (<25 °C) basaltic crust, which we calculate from modelling dissolved oxygen and strontium pore water gradients in basal sediments collected during Integrated Ocean Drilling Program Expedition 336 to 'North Pond' on the western flank of the Mid-Atlantic Ridge. Dissolved oxygen is completely consumed within the upper to middle section of the sediment column, with an increase in concentration towards the sediment-basement interface, indicating an upward supply from oxic fluids circulating within the crust. A parametric reaction transport model of oxygen behaviour in upper basement suggests oxygen consumption rates of 1 nmol  cm(-3)ROCK d(-1) or less in young and cool basaltic crust.

  11. Analyzing critical propagation in a reaction-diffusion-advection model using unstable slow waves.

    PubMed

    Kneer, Frederike; Obermayer, Klaus; Dahlem, Markus A

    2015-02-01

    The effect of advection on the propagation and in particular on the critical minimal speed of traveling waves in a reaction-diffusion model is studied. Previous theoretical studies estimated this effect on the velocity of stable fast waves and predicted the existence of a critical advection strength below which propagating waves are not supported anymore. In this paper, an analytical expression for the advection-velocity relation of the unstable slow wave is derived. In addition, the critical advection strength is calculated taking into account the unstable slow wave solution. We also analyze a two-variable reaction-diffusion-advection model numerically in a wide parameter range. Due to the new control parameter (advection) we can find stable wave propagation in the otherwise non-excitable parameter regime, if the advection strength exceeds a critical value. Comparing theoretical predictions to numerical results, we find that they are in good agreement. Theory provides an explanation for the observed behaviour.

  12. Reaction of nitric oxide with heme proteins and model compounds of hemoglobin

    SciTech Connect

    Sharma, V.S.; Traylor, T.G.; Gardiner, R.; Mizukami, H.

    1987-06-30

    Rates for the reaction of nitric oxide with several ferric heme proteins and model compounds have been measured. The NO combination rates are markedly affected by the presence or absence of distal histidine. Elephant myoglobin in which the E7 distal histidine has been replaced by glutamine reacts with NO 500-1000 times faster than do the native hemoglobins or myoglobins. By contrast, there is not difference in the CO combination rate constants of sperm whale and elephant myoglobins. Studies on ferric model compounds for the R and T states of hemoglobin indicate that their NO combination rate constants are similar to those observed for the combination of CO with the corresponding ferro derivatives. The last observation suggests that the presence of an axial water molecule at the ligand binding site of ferric hemoglobin A prevents it from exhibiting significant cooperativity in its reactions with NO.

  13. Kinetic modeling of propane aromatization reaction over HZSM-5 and GaHZSM-5

    SciTech Connect

    Lukyanov, D.B.; Gnep, N.S.; Guisnet, M.R. . Catalyse en Chimie Organique)

    1995-02-01

    A detailed kinetic model for a propane aromatization reaction over HZSM-5 and GaHZSM-5 is developed. Kinetic modeling results show that propane transformation over HZSM-5 occurs via protolytic cracking and hydrogen transfer routes. The contributions of both routes in propane conversion are established. Rate constants of propane transformation steps are found to be at least 1,000 times lower than the rate constants of diene formation steps, which, in turn, are the slowest among the acid-catalyzed olefin aromatization steps. Gallium introduced into ZSM-5 catalyst is active in dehydrogenation of propane into propene, of olefins into dienes, and of naphthenes into aromatics. At the same time, gallium species catalyze propane transformation into methane and ethene hydrogenation into ethane. Both latter reactions appear to be the main reasons for the limit to aromatics selectivity over GaHZSM-5 catalysts.

  14. Probing Complex Free-Radical Reaction Pathways of Fuel Model Compounds

    SciTech Connect

    Buchanan III, A C; Kidder, Michelle; Beste, Ariana; Britt, Phillip F

    2012-01-01

    Fossil (e.g. coal) and renewable (e.g. woody biomass) organic energy resources have received considerable attention as possible sources of liquid transportation fuels and commodity chemicals. Knowledge of the reactivity of these complex materials has been advanced through fundamental studies of organic compounds that model constituent substructures. In particular, an improved understanding of thermochemical reaction pathways involving free-radical intermediates has arisen from detailed experimental kinetic studies and, more recently, advanced computational investigations. In this presentation, we will discuss our recent investigations of the fundamental pyrolysis pathways of model compounds that represent key substructures in the lignin component of woody biomass with a focus on molecules representative of the dominant beta-O-4 aryl ether linkages. Additional mechanistic insights gleaned from DFT calculations on the kinetics of key elementary reaction steps will also be presented, as well as a few thoughts on the significant contributions of Jim Franz to this area of free radical chemistry.

  15. Model of defect reactions and the influence of clustering in pulse-neutron-irradiated Si

    SciTech Connect

    Myers, S. M.; Cooper, P. J.; Wampler, W. R.

    2008-08-15

    Transient reactions among irradiation defects, dopants, impurities, and carriers in pulse-neutron-irradiated Si were modeled taking into account the clustering of the primal defects in recoil cascades. Continuum equations describing the diffusion, field drift, and reactions of relevant species were numerically solved for a submicrometer spherical volume, within which the starting radial distributions of defects could be varied in accord with the degree of clustering. The radial profiles corresponding to neutron irradiation were chosen through pair-correlation-function analysis of vacancy and interstitial distributions obtained from the binary-collision code MARLOWE, using a spectrum of primary recoil energies computed for a fast-burst fission reactor. Model predictions of transient behavior were compared with a variety of experimental results from irradiated bulk Si, solar cells, and bipolar-junction transistors. The influence of defect clustering during neutron bombardment was further distinguished through contrast with electron irradiation, where the primal point defects are more uniformly dispersed.

  16. Kinetic phase transitions in a contaminated monomer-dimer reaction model

    NASA Astrophysics Data System (ADS)

    Bustos, V.; Uñac, R. O.; Zgrablich, G.

    2000-12-01

    The irreversible kinetics of a monomer-dimer reaction on a catalyst surface [the Ziff-Gulari-Barshad (ZGB) model] in the presence of a contaminant species is studied by means of Monte Carlo simulation. The only processes allowed to the contaminant are adsorption and desorption; it is otherwise inert. The reaction window, delimited by a second order irreversible phase transition at low monomer concentration (lower bound transition) and by a first order one at high monomer concentration (upper bound transition) in the ZGB model is found to shrink with increasing contaminant concentration in a way that depends on its adsorption-desorption kinetics. Through epidemic analysis, it is also found that the upper bound transition changes from first to second order and that the lower bound transition can also be affected depending on the contaminant adsorption-desorption kinetics. The results may provide alternative explanations for experimental observations.

  17. Mass transfer model for two-layer TBP oxidation reactions: Revision 1

    SciTech Connect

    Laurinat, J.E.

    1994-11-04

    To prove that two-layer, TBP-nitric acid mixtures can be safely stored in the Canyon evaporators, it must be demonstrated that a runaway reaction between TBP and nitric acid will not occur. Previous bench-scale experiments showed that, at typical evaporator temperatures, this reaction is endothermic and therefore cannot run away, due to the loss of heat from evaporation of water in the organic layer. However, the reaction would be exothermic and could run away if the small amount of water in the organic layer evaporates before the nitric acid in this layer is consumed by the reaction. Provided that there is enough water in the aqueous layer, this would occur if the organic layer is sufficiently thick so that the rate of loss of water by evaporation exceeds the rate of replenishment due to mixing with the aqueous layer. Bubbles containing reaction products enhance the rate of transfer of water from the aqueous layer to the organic layer. These bubbles are generated by the oxidation of TBP and its reaction products in the organic layer and by the oxidation of butanol in the aqueous layer. Butanol is formed by the hydrolysis of TBP in the organic layer. For aqueous-layer bubbling to occur, butanol must transfer into the aqueous layer. Consequently, the rate of oxidation and bubble generation in the aqueous layer strongly depends on the rate of transfer of butanol from the organic to the aqueous layer. This report presents measurements of mass transfer rates for the mixing of water and butanol in two-layer, TBP-aqueous mixtures, where the top layer is primarily TBP and the bottom layer is comprised of water or aqueous salt solution. Mass transfer coefficients are derived for use in the modeling of two-layer TBP-nitric acid oxidation experiments.

  18. Incremental Cost-Effectiveness Analysis of Gestational Diabetes Mellitus Screening Strategies in Singapore.

    PubMed

    Chen, Pin Yu; Finkelstein, Eric A; Ng, Mor Jack; Yap, Fabian; Yeo, George S H; Rajadurai, Victor Samuel; Chong, Yap Seng; Gluckman, Peter D; Saw, Seang Mei; Kwek, Kenneth Y C; Tan, Kok Hian

    2016-01-01

    The objective of this study was to conduct an incremental cost-effectiveness analysis from the payer's perspective in Singapore of 3 gestational diabetes mellitus screening strategies: universal, targeted, or no screening. A decision tree model assessed the primary outcome: incremental cost per quality-adjusted life year (QALY) gained. Probabilities, costs, and utilities were derived from the literature, the Growing Up in Singapore Towards healthy Outcomes (GUSTO) birth cohort study, and the KK Women's and Children's Hospital's database. Relative to targeted screening using risk factors, universal screening generates an incremental cost-effectiveness ratio (ICER) of $USD10,630/QALY gained. Sensitivity analyses show that disease prevalence rates and intervention effectiveness of glycemic management have the biggest impacts on the ICERs. Based on the model and best available data, universal screening is a cost-effective approach for reducing the complications of gestational diabetes mellitus in Singapore as compared with the targeted screening approach or no screening.

  19. Modeling expected solute concentration in randomly heterogeneous flow systems with multicomponent reactions.

    PubMed

    Malmström, Maria E; Destouni, Georgia; Martinet, Philippe

    2004-05-01

    Many environmental problems require assessment of extensive reaction systems within natural subsurface flow systems exhibiting large physical and biogeochemical heterogeneity. We present an approach to couple stochastic advective-reactive modeling of physical solute transport (LaSAR) with the geochemical model PHREEQC for modeling solute concentrations in systems with variable flow velocity and multicomponent reactions. PHREEQC allows for general and flexible quantification of a multitude of linear and nonlinear geochemical processes, while LaSAR efficiently handles field-scale solute spreading in stochastic heterogeneous flow fields. The combined LaSAR-PHREEQC approach requires very modest computational efforts, thereby allowing a large number of reactive transport problems to be readily assessed and facilitating handling of quantifiable uncertainty in environmental model applications. Computational efficiency and explicit handling of field-scale dispersion without introduction of excessive fluid mixing that may impair model results are general advantages of the LaSAR compared with alternative solute transport modeling approaches. The LaSAR-PHREEQC approach is restricted to steady or unidirectional flow fields, and our specific application examples are limited to homogeneous reaction systems without local or transverse dispersion-diffusion, although these are not general methodological limitations. As a comprehensive application example, we simulate the spreading of acid mine drainage in a groundwater focusing on Zn2+ and including relevant, major-component geochemistry. Model results show that Zn2+ may be substantially attenuated by both sorption and precipitation, with flow heterogeneity greatly affecting expected solute concentrations downstream of the mine waste deposit in both cases.

  20. A coupled mechanical and chemical damage model for concrete affected by alkali–silica reaction

    SciTech Connect

    Pignatelli, Rossella; Comi, Claudia; Monteiro, Paulo J.M.

    2013-11-15

    To model the complex degradation phenomena occurring in concrete affected by alkali–silica reaction (ASR), we formulate a poro-mechanical model with two isotropic internal variables: the chemical and the mechanical damage. The chemical damage, related to the evolution of the reaction, is caused by the pressure generated by the expanding ASR gel on the solid concrete skeleton. The mechanical damage describes the strength and stiffness degradation induced by the external loads. As suggested by experimental results, degradation due to ASR is considered to be localized around reactive sites. The effect of the degree of saturation and of the temperature on the reaction development is also modeled. The chemical damage evolution is calibrated using the value of the gel pressure estimated by applying the electrical diffuse double-layer theory to experimental values of the surface charge density in ASR gel specimens reported in the literature. The chemo-damage model is first validated by simulating expansion tests on reactive specimens and beams; the coupled chemo-mechanical damage model is then employed to simulate compression and flexure tests results also taken from the literature. -- Highlights: •Concrete degradation due to ASR in variable environmental conditions is modeled. •Two isotropic internal variables – chemical and mechanical damage – are introduced. •The value of the swelling pressure is estimated by the diffuse double layer theory. •A simplified scheme is proposed to relate macro- and microscopic properties. •The chemo-mechanical damage model is validated by simulating tests in literature.

  1. Reaction-transport-mechanical (RTM) simulator Sym.CS: Putting together water-rock interaction, multi-phase and heat flow, composite petrophysics model, and fracture mechanics

    NASA Astrophysics Data System (ADS)

    Paolini, C.; Park, A. J.; Mellors, R. J.; Castillo, J.

    2009-12-01

    A typical CO2 sequestration scenario involves the use of multiple simulators for addressing multiphase fluid and heat flow, water-rock interaction and mass-transfer, rock mechanics, and other chemical and physical processes. The benefit of such workflow is that each model can be constrained rigorously; however, the drawback is final modeling results may achieve only a limited extent of the theoretically possible capabilities of each model. Furthermore, such an approach in modeling carbon sequestration cannot capture the nonlinearity of the various chemical and physical processes. Hence, the models can only provide guidelines for carbon sequestration processes with large margins of error. As an alternative, a simulator is being constructed by a multi-disciplinary team with the aim of implementing a large array of fundamental phenomenologies, including, but not limited to: water-rock interaction using elemental mass-balance and explicit mass-transfer and reaction coupling methods; multi-phase and heat flow, including super-critical CO2 and oil; fracture mechanics with anisotropic permeabilities; rheological rock mechanics based on incremental stress theory; and a composite petrophysics model capable of describing changing rock composition and properties. The modules representing the processes will be solved using a layered iteration method, with the goal of capturing the nonlinear feedback among all of the processes. The simulator will be constructed using proven optimization and modular, object-oriented, and service-oriented programming methods. Finally, a novel AJAX (asynchronous JavaScript and XML) user interface is being tested to host the simulator that will allow usage through an Internet browser. Currently, the water-rock interaction, composite petrophysics, and multi-phase fluid and heat flow modules are available for integration. Results of the water-rock interaction and petrophysics coupling has been used to model interaction between a CO2-charged water and

  2. Conditions for the critical phenomena in a dynamic model of an electrocatalytic reaction

    NASA Astrophysics Data System (ADS)

    Firstova, Natalia; Shchepakina, Elena

    2017-02-01

    In the paper, a detailed study of the critical phenomena mechanism in a model of an electrocatalytic reaction is carried out. The use of the geometric theory of integral manifolds allows us to show the relationship between the critical regime and the stability loss delay of the slow integral manifold of the corresponding differential system. The asymptotic formula for the critical value of the control parameter is obtained.

  3. New model to determine the central nervous system reaction to peripheral trauma

    SciTech Connect

    Sjoelund, B.H.W.; Wallstedt, L.

    1988-01-01

    Monitoring the activity of the central nervous system with the /sup 14/C-2-deoxyglucose method of Sokoloff was utilized to explore the possibility to develop a model for the study of central nervous system reaction to peripheral trauma. Preliminary evidence indicates that the activation caused by tactile stimuli to one hindlimb nerve is that expected from earlier physiologic studies. However, an increase of stimulation intensity to recruit nociceptive (pain) fibers seems to abolish the changes, indicating that inhibitory systems have been activated.

  4. Complex mixed-mode oscillatory patterns in a periodically forced excitable Belousov-Zhabotinsky reaction model.

    PubMed

    Español, Malena I; Rotstein, Horacio G

    2015-06-01

    The Oregonator is the simplest chemically plausible model for the Belousov-Zhabotinsky reaction. We investigate the response of the Oregonator to sinusoidal inputs with amplitudes and frequencies within plausible ranges. We focus on a regime where the unforced Oregonator is excitable (with no sustained oscillations). We use numerical simulations and dynamical systems tools to both characterize the response patterns and explain the underlying dynamic mechanisms.

  5. Physics-Based Multi-Scale Modeling of Shear Initiated Reactions in Energetic and Reactive Materials

    DTIC Science & Technology

    2010-04-01

    Physics-based Multi-scale Modeling of Shear Initiated Reactions in Energetic and Reactive Materials by John K. Brennan, Müge Fermen -Coker...Energetic and Reactive Materials John K. Brennan and Müge Fermen -Coker Weapons and Materials Research Directorate, ARL and Linhbao Tran Shock...Materials 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) John K. Brennan, Müge Fermen -Coker, and Linhbao Tran 5d

  6. Atmospheric Reaction Systems as Null-Models to Identify Structural Traces of Evolution in Metabolism

    PubMed Central

    Holme, Petter; Huss, Mikael; Lee, Sang Hoon

    2011-01-01

    The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species). For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection. PMID:21573072

  7. Incremental Reactivity Effects on Secondary Organic Aerosol Formation in Urban Atmospheres with and without Biogenic Influence

    NASA Astrophysics Data System (ADS)

    Kacarab, Mary; Li, Lijie; Carter, William P. L.; Cocker, David R., III

    2016-04-01

    Two different surrogate mixtures of anthropogenic and biogenic volatile organic compounds (VOCs) were developed to study secondary organic aerosol (SOA) formation at atmospheric reactivities similar to urban regions with varying biogenic influence levels. Environmental chamber simulations were designed to enable the study of the incremental aerosol formation from select anthropogenic (m-Xylene, 1,2,4-Trimethylbenzene, and 1-Methylnaphthalene) and biogenic (α-pinene) precursors under the chemical reactivity set by the two different surrogate mixtures. The surrogate reactive organic gas (ROG) mixtures were based on that used to develop the maximum incremental reactivity (MIR) factors for evaluation of O3 forming potential. Multiple incremental aerosol formation experiments were performed in the University of California Riverside (UCR) College of Engineering Center for Environmental Research and Technology (CE-CERT) dual 90m3 environmental chambers. Incremental aerosol yields were determined for each of the VOCs studied and compared to yields found from single precursor studies. Aerosol physical properties of density, volatility, and hygroscopicity were monitored throughout experiments. Bulk elemental chemical composition from high-resolution time of flight aerosol mass spectrometer (HR-ToF-AMS) data will also be presented. Incremental yields and SOA chemical and physical characteristics will be compared with data from previous single VOC studies conducted for these aerosol precursors following traditional VOC/NOx chamber experiments. Evaluation of the incremental effects of VOCs on SOA formation and properties are paramount in evaluating how to best extrapolate environmental chamber observations to the ambient atmosphere and provides useful insights into current SOA formation models. Further, the comparison of incremental SOA from VOCs in varying surrogate urban atmospheres (with and without strong biogenic influence) allows for a unique perspective on the impacts

  8. Micro-vibration model and parameter estimation method of a reaction wheel assembly

    NASA Astrophysics Data System (ADS)

    Kim, Dae-Kwan

    2014-09-01

    Reaction wheel assemblies (RWAs) are a source of disturbance in satellites, and they are regarded as the largest jitter contributor in optical payloads. In order to ensure a stringent jitter requirement, the wheel disturbance effects on spacecraft should be predicted precisely prior to launch through analytical or experimental approaches. For this purpose, the wheel disturbance should be identified and modeled accurately. In the present study, a micro-vibration model of the RWA is introduced through coupling an analytical wheel model and an empirical disturbance model; furthermore, a parameter estimation process of the coupled model from the micro-vibration disturbance data is proposed. In order to verify the modeling and estimation techniques, a micro-vibration model of a numerical RWA is established and its estimation error is validated. Then, the micro-vibration model is extended to consider an axial disturbance and a measurement offset effect. Finally, the micro-vibration model is applied to a commercial RWA and the model parameters are extracted from the disturbance test data of the RWA using the parameter estimation process. The analytical and experimental results demonstrate that the proposed micro-vibration model and parameter estimation process are effective in the dynamic disturbance modeling of RWAs.

  9. Reaction norm model to describe environmental sensitivity across first lactation in dairy cattle under tropical conditions.

    PubMed

    Bignardi, Annaiza Braga; El Faro, Lenira; Pereira, Rodrigo Junqueira; Ayres, Denise Rocha; Machado, Paulo Fernando; de Albuquerque, Lucia Galvão; Santana, Mário Luiz

    2015-10-01

    Reaction norm models have been widely used to study genotype by environment interaction (G × E) in animal breeding. The objective of this study was to describe environmental sensitivity across first lactation in Brazilian Holstein cows using a reaction norm approach. A total of 50,168 individual monthly test day (TD) milk yields (10 test days) from 7476 complete first lactations of Holstein cattle were analyzed. The statistical models for all traits (10 TDs and for 305-day milk yield) included the fixed effects of contemporary group, age of cow (linear and quadratic effects), and days in milk (linear effect), except for 305-day milk yield. A hierarchical reaction norm model (HRNM) based on the unknown covariate was used. The present study showed the presence of G × E in milk yield across first lactation of Holstein cows. The variation in the heritability estimates implies differences in the response to selection depending on the environment where the animals of this population are evaluated. In the average environment, the heritabilities for all traits were rather similar, in range from 0.02 to 0.63. The scaling effect of G × E predominated throughout most of lactation. Particularly during the first 2 months of lactation, G × E caused reranking of breeding values. It is therefore important to include the environmental sensitivity of animals according to the phase of lactation in the genetic evaluations of Holstein cattle in tropical environments.

  10. Formic Acid Decomposition on Au catalysts: DFT, Microkinetic Modeling, and Reaction Kinetics Experiments

    SciTech Connect

    Singh, Suyash; Li, Sha; Carrasquillo-Flores, Ronald; Alba-Rubio, Ana C.; Dumesic, James A.; Mavrikakis, Manos

    2014-04-01

    A combined theoretical and experimental approach is presented that uses a comprehensive mean-field microkinetic model, reaction kinetics experiments, and scanning transmission electron microscopy imaging to unravel the reaction mechanism and provide insights into the nature of active sites for formic acid (HCOOH) decomposition on Au/SiC catalysts. All input parameters for the microkinetic model are derived from periodic, self-consistent, generalized gradient approximation (GGA-PW91) density functional theory calculations on the Au(111), Au(100), and Au(211) surfaces and are subsequently adjusted to describe the experimental HCOOH decomposition rate and selectivity data. It is shown that the HCOOH decomposition follows the formate (HCOO) mediated path, with 100% selectivity toward the dehydrogenation products (CO21H2) under all reaction conditions. An analysis of the kinetic parameters suggests that an Au surface in which the coordination number of surface Au atoms is 4 may provide a better model for the active site of HCOOH decomposition on these specific supported Au catalysts.

  11. Reaction times in visual search can be explained by a simple model of neural synchronization.

    PubMed

    Kazanovich, Yakov; Borisyuk, Roman

    2017-03-01

    We present an oscillatory neural network model that can account for reaction times in visual search experiments. The model consists of a central oscillator that represents the central executive of the attention system and a number of peripheral oscillators that represent objects in the display. The oscillators are described as generalized Kuramoto type oscillators with adapted parameters. An object is considered as being included in the focus of attention if the oscillator associated with this object is in-phase with the central oscillator. The probability for an object to be included in the focus of attention is determined by its saliency that is described in formal terms as the strength of the connection from the peripheral oscillator to the central oscillator. By computer simulations it is shown that the model can reproduce reaction times in visual search tasks of various complexities. The dependence of the reaction time on the number of items in the display is represented by linear functions of different steepness which is in agreement with biological evidence.

  12. A Kinetic Ladle Furnace Process Simulation Model: Effective Equilibrium Reaction Zone Model Using FactSage Macro Processing

    NASA Astrophysics Data System (ADS)

    Van Ende, Marie-Aline; Jung, In-Ho

    2017-02-01

    The ladle furnace (LF) is widely used in the secondary steelmaking process in particular for the de-sulfurization, alloying, and reheating of liquid steel prior to the casting process. The Effective Equilibrium Reaction Zone model using the FactSage macro processing code was applied to develop a kinetic LF process model. The slag/metal interactions, flux additions to slag, various metallic additions to steel, and arcing in the LF process were taken into account to describe the variations of chemistry and temperature of steel and slag. The LF operation data for several steel grades from different plants were accurately described using the present kinetic model.

  13. Evolution of Autocatalytic Sets in Computational Models of Chemical Reaction Networks.

    PubMed

    Hordijk, Wim

    2016-06-01

    Several computational models of chemical reaction networks have been presented in the literature in the past, showing the appearance and (potential) evolution of autocatalytic sets. However, the notion of autocatalytic sets has been defined differently in different modeling contexts, each one having some shortcoming or limitation. Here, we review four such models and definitions, and then formally describe and analyze them in the context of a mathematical framework for studying autocatalytic sets known as RAF theory. The main results are that: (1) RAF theory can capture the various previous definitions of autocatalytic sets and is therefore more complete and general, (2) the formal framework can be used to efficiently detect and analyze autocatalytic sets in all of these different computational models, (3) autocatalytic (RAF) sets are indeed likely to appear and evolve in such models, and (4) this could have important implications for a possible metabolism-first scenario for the origin of life.

  14. Surface-subsurface model for a dimer-dimer catalytic reaction: a Monte Carlo simulation study

    NASA Astrophysics Data System (ADS)

    Khan, K. M.; Albano, E. V.

    2002-02-01

    The surface-subsurface model for a dimer-dimer reaction of the type A2 + 2B2→2AB2 has been studied through Monte Carlo simulation via a model based on the lattice gas non-thermal Langmuir-Hinshelwood mechanism, which involves the precursor motion of the B2 molecule. The motion of precursors is considered on the surface as well as in the subsurface. The most interesting feature of this model is that it yields a steady reactive window, which is separated by continuous and discontinuous irreversible phase transitions. The phase diagram is qualitatively similar to the well known Ziff, Gulari and Barshad (ZGB) model. The width of the window depends upon the mobility of precursors. The continuous transition disappears when the mobility of the surface precursors is extended to the third-nearest neighbourhood. The dependence of production rate on partial pressure of B2 dimer is predicted by simple mathematical equations in our model.

  15. Estimating biofilm reaction kinetics using hybrid mechanistic-neural network rate function model.

    PubMed

    Kumar, B Shiva; Venkateswarlu, Ch

    2012-01-01

    This work describes an alternative method for estimation of reaction rate of a biofilm process without using a model equation. A first principles model of the biofilm process is integrated with artificial neural networks to derive a hybrid mechanistic-neural network rate function model (HMNNRFM), and this combined model structure is used to estimate the complex kinetics of the biofilm process as a consequence of the validation of its steady state solution. The performance of the proposed methodology is studied with the aid of the experimental data of an anaerobic fixed bed biofilm reactor. The statistical significance of the method is also analyzed by means of the coefficient of determination (R2) and model efficiency (ME). The results demonstrate the effectiveness of HMNNRFM for estimating the complex kinetics of the biofilm process involved in the treatment of industry wastewater.

  16. Concrete modelling for expertise of structures affected by alkali aggregate reaction

    SciTech Connect

    Grimal, E.; Sellier, A.; Multon, S.; Le Pape, Y.; Bourdarot, E.

    2010-04-15

    Alkali aggregate reaction (AAR) affects numerous civil engineering structures and causes irreversible expansion and cracking. In order to control the safety level and the maintenance cost of its hydraulic dams, Electricite de France (EDF) must reach better comprehension and better prediction of the expansion phenomena. For this purpose, EDF has developed a numerical model based on the finite element method in order to assess the mechanical behaviour of damaged structures. The model takes the following phenomena into account: concrete creep, the stress induced by the formation of AAR gel and the mechanical damage. A rheological model was developed to assess the coupling between the different phenomena (creep, AAR and anisotropic damage). Experimental results were used to test the model. The results show the capability of the model to predict the experimental behaviour of beams subjected to AAR. In order to obtain such prediction, it is necessary to take all the phenomena occurring in the concrete into consideration.

  17. Evolution of Autocatalytic Sets in Computational Models of Chemical Reaction Networks

    NASA Astrophysics Data System (ADS)

    Hordijk, Wim

    2016-06-01

    Several computational models of chemical reaction networks have been presented in the literature in the past, showing the appearance and (potential) evolution of autocatalytic sets. However, the notion of autocatalytic sets has been defined differently in different modeling contexts, each one having some shortcoming or limitation. Here, we review four such models and definitions, and then formally describe and analyze them in the context of a mathematical framework for studying autocatalytic sets known as RAF theory. The main results are that: (1) RAF theory can capture the various previous definitions of autocatalytic sets and is therefore more complete and general, (2) the formal framework can be used to efficiently detect and analyze autocatalytic sets in all of these different computational models, (3) autocatalytic (RAF) sets are indeed likely to appear and evolve in such models, and (4) this could have important implications for a possible metabolism-first scenario for the origin of life.

  18. Comparison of Kinetic and Equilibrium Reaction Models inSimulating the Behavior of Gas Hydrates in Porous Media

    SciTech Connect

    Kowalsky, Michael B.; Moridis, George J.

    2006-05-12

    In this study we compare the use of kinetic and equilibrium reaction models in the simulation of gas (methane) hydrates in porous media. Our objective is to evaluate through numerical simulation the importance of employing kinetic versus equilibrium reaction models for predicting the response of hydrate-bearing systems to external stimuli, such as changes in pressure and temperature. Specifically, we (1) analyze and compare the responses simulated using both reaction models for production in various geological settings and for the case of depressurization in a core during extraction; and (2) examine the sensitivity to factors such as initial hydrate saturation, hydrate reaction surface area, and numerical discretization. We find that for systems undergoing thermal stimulation and depressurization, the calculated responses for both reaction models are remarkably similar, though some differences are observed at early times. Given these observations, and since the computational demands for the kinetic reaction model far exceed those for the equilibrium reaction model, the use of the equilibrium reaction model often appears to be justified and preferred for simulating the behavior of gas hydrates.

  19. The Flawed Four-Level Evaluation Model [and] Invited Reaction: Reaction to Holton Article [and] Final Word: Response to Reaction to Holton Article.

    ERIC Educational Resources Information Center

    Holton, Elwood F., III; Kirkpatrick, Donald L.

    1996-01-01

    Holton critiques Kirkpatrick's four-level evaluation model and presents a new model that accounts for primary intervening variables. Kirkpatrick argues that the criticism fails to account for his model's practical utility. Holton elaborates on the distinction between a model and a taxonomy. (SK)

  20. Testing biological activity of model Maillard reaction products: studies on gastric smooth muscle tissues.

    PubMed

    Argirova, Mariana D; Stefanova, Iliyana D; Krustev, Athanas D; Turiiski, Valentin I

    2010-03-01

    Water-soluble Maillard reaction products obtained from five different model systems were investigated for their effects upon the mechanical activity of rat gastric smooth muscle. Most of the total Maillard reaction products applied at concentration of 1.5 mg/ml evoked contractions; among them the product obtained from arginine and glucose (Arg-Glc) produced the most powerful contractions. The product obtained from glycine and ascorbic acid (Gly-AsA) was the only one that brought about relaxation response. The high molecular weight fractions (>3,500 Da) isolated from the reaction systems Arg-Glc and Gly-AsA demonstrated effects similar in type and amplitude to those evoked by non-fractioned reaction products. The results obtained suggest that moieties of molecules acting upon the muscle tonus originate mainly from lysine and arginine residues; that these structures are available in both low and high molecular pools in similar concentrations, and most likely these fragments act upon membrane-located cellular structures involved in calcium transport.