Science.gov

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. 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. PMID:25417079

  4. 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.

  5. Functional data analysis on ground reaction force of military load carriage increment

    NASA Astrophysics Data System (ADS)

    Din, Wan Rozita Wan; Rambely, Azmin Sham

    2014-06-01

    Analysis of ground reaction force on military load carriage is done through functional data analysis (FDA) statistical technique. The main objective of the research is to investigate the effect of 10% load increment and to find the maximum suitable load for the Malaysian military. Ten military soldiers age 31 ± 6.2 years, weigh 71.6 ± 10.4 kg and height of 166.3 ± 5.9 cm carrying different military load range from 0% body weight (BW) up to 40% BW participated in an experiment to gather the GRF and kinematic data using Vicon Motion Analysis System, Kirstler force plates and thirty nine body markers. The analysis is conducted in sagittal, medial lateral and anterior posterior planes. The results show that 10% BW load increment has an effect when heel strike and toe-off for all the three planes analyzed with P-value less than 0.001 at 0.05 significant levels. FDA proves to be one of the best statistical techniques in analyzing the functional data. It has the ability to handle filtering, smoothing and curve aligning according to curve features and points of interest.

  6. A K-12 Faculty Salary-Growth Model That Provides Equitable Strategic Increments.

    ERIC Educational Resources Information Center

    Koehler, W. F.

    1996-01-01

    A salary-growth model for teacher compensation is proposed that provides equitable strategic increments, that is, equitable increments as rewards for contributing to the rectification of educational shortcomings. Traditional teacher-pay plans have been flawed in the lack of salary differentials for training and experience. (SLD)

  7. 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.

  8. 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…

  9. 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.

  10. 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…

  11. Incremental forms of Schapery's model: convergence and inversion to simulate strain controlled ramps

    NASA Astrophysics Data System (ADS)

    Varna, Janis; Pupure, Liva; Joffe, Roberts

    2016-04-01

    Schapery's nonlinear viscoelastic model is written in incremental form, and three different approximations of nonlinearity functions in the time increment are systematically analysed with respect to the convergence rate. It is shown that secant slope is the best approximation of the time shift factor, leading to significantly higher convergence rate. This incremental form of the viscoelastic model, Zapas' model for viscoplasticity, supplemented with terms accounting for damage effect is used to predict inelastic behaviour of material in stress controlled tests. Then the incremental formulation is inverted to simulate stress development in ramps where strain is the input parameter. A comparison with tests shows good ability of the model in inverted form to predict stress-strain response as long as the applied strain is increasing. However, in strain controlled ramps with unloading, the inverted model shows unrealistic hysteresis loops. This is believed to be a proof of the theoretically known incompatibility of the stress and strain controlled formulations for nonlinear materials. It also shows limitations of material models identified in stress controlled tests for use in strain controlled tests.

  12. Nested incremental modeling in the development of computational theories: the CDP+ model of reading aloud.

    PubMed

    Perry, Conrad; Ziegler, Johannes C; Zorzi, Marco

    2007-04-01

    At least 3 different types of computational model have been shown to account for various facets of both normal and impaired single word reading: (a) the connectionist triangle model, (b) the dual-route cascaded model, and (c) the connectionist dual process model. Major strengths and weaknesses of these models are identified. In the spirit of nested incremental modeling, a new connectionist dual process model (the CDP+ model) is presented. This model builds on the strengths of 2 of the previous models while eliminating their weaknesses. Contrary to the dual-route cascaded model, CDP+ is able to learn and produce graded consistency effects. Contrary to the triangle and the connectionist dual process models, CDP+ accounts for serial effects and has more accurate nonword reading performance. CDP+ also beats all previous models by an order of magnitude when predicting individual item-level variance on large databases. Thus, the authors show that building on existing theories by combining the best features of previous models--a nested modeling strategy that is commonly used in other areas of science but often neglected in psychology--results in better and more powerful computational models. PMID:17500628

  13. 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.

  14. A prediction model for Atlantic named storm frequency using a year-by-year increment approach

    NASA Astrophysics Data System (ADS)

    Fan, K.

    2010-12-01

    This paper presents a year-by-year incremental approach to forecasting the Atlantic named storm frequency (ATSF) for the hurricane season (June 1- November 30). The year-by-year increase or decrease in the ATSF is first forecasted to yield a net ATSF prediction. Six key predictors for the year-by-year increment in the number of Atlantic named tropical storms have been identified that are available before May 1. The forecast model for the year-by-year increment of the ATSF is first established using a multi-linear regression method based on data taken from the years of 1965-1999, and the forecast model of the ATSF is then derived. The prediction model for the ATSF shows good prediction skill. Compared to the climatological average mean absolute error (MAE) of 4.1, the percentage improvement in the MAE is 29 % for the hindcast period of 2004-2009 and 46 % for the cross-validation test from 1985-2009 (26 yrs). This work demonstrates that the year-by-year incremental approach has the potential to improve operational forecasting skill for the ATSF.

  15. 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.

  16. 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

  17. 77 FR 20648 - Certain Digital Models, Digital Data, and Treatment Plans for Use in Making Incremental Dental...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-05

    ... COMMISSION Certain Digital Models, Digital Data, and Treatment Plans for Use in Making Incremental Dental Positioning Adjustment Appliances, the Appliances Made Therefrom, and Methods of Making the Same; Institution... of certain digital models, digital data, and treatment plans for use in making incremental...

  18. 40 CFR Table 1 to Subpart Dddd of... - Model Rule-Increments of Progress and Compliance Schedules

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 7 2014-07-01 2014-07-01 false Model Rule-Increments of Progress and Compliance Schedules 1 Table 1 to Subpart DDDD of Part 60 Protection of Environment ENVIRONMENTAL PROTECTION.... DDDD, Table 1 Table 1 to Subpart DDDD of Part 60—Model Rule—Increments of Progress and...

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. Modeling smog chamber measurements of incremental reactivities of volatile organic compounds

    NASA Astrophysics Data System (ADS)

    Chang, T. Y.; Nance, B. I.; Kelly, N. A.

    A series of experiments performed at the GM chamber facility provided useful data for the evaluation of two current chemical mechanisms used in airshed models (SAPRC97 and SAPRC93 mechanisms) and a test of their predictions of maximum incremental reactivities which describe the change in ozone caused by adding a small amount of a compound to a polluted urban mixture under high-NO x conditions. In general, the SAPRC97 detailed mechanism performed well in simulating the volatile organic compound (VOC) reactivity experiments for most test species; however, it had a tendency to underpredict incremental reactivities. For base-case runs containing a nine-component urban-surrogate mixture under high-NO x conditions, where maximum concentrations of either O 3 or the smog produced (SP=the initial NO oxidized plus the ozone produced) were not attained during a 12-h irradiation, the SAPRC97 performed well while the SAPRC93 underestimated SP or O 3 significantly. Under low-NO x conditions where SP or O 3 maximums were attained, the SAPRC97 as well as the SAPRC93 underpredicted SP or O 3 for runs containing the urban-surrogate mixture. Simulations of incremental reactivity experiments and special chamber runs showed that the SAPRC97 mechanism performed poorly for n-octane and some aromatic isomers such as ethylbenzene and p-xylene, while it performed well for other aromatic isomers such as toluene, m-xylene and 1,3,5-trimethylbenzene. Although, additional chamber data for aromatic isomers is needed to further clarify the parameterized chemical mechanisms for aromatic isomers, the newer SAPRC97 mechanism appears to be much improved over the older SAPRC93 mechanism for simulating aromatic chemistry.

  4. Relaxed incremental variational approach for the modeling of damage-induced stress hysteresis in arterial walls.

    PubMed

    Schmidt, Thomas; Balzani, Daniel

    2016-05-01

    In this paper, a three-dimensional relaxed incremental variational damage model is proposed, which enables the description of complex softening hysteresis as observed in supra-physiologically loaded arterial tissues, and which thereby avoids a loss of convexity of the underlying formulation. The proposed model extends the relaxed formulation of Balzani and Ortiz [2012. Relaxed incremental variational formulation for damage at large strains with application to fiber-reinforced materials and materials with truss-like microstructures. Int. J. Numer. Methods Eng. 92, 551-570], such that the typical stress-hysteresis observed in arterial tissues under cyclic loading can be described. This is mainly achieved by constructing a modified one-dimensional model accounting for cyclic loading in the individual fiber direction and numerically homogenizing the response taking into account a fiber orientation distribution function. A new solution strategy for the identification of the convexified stress potential is proposed based on an evolutionary algorithm which leads to an improved robustness compared to solely Newton-based optimization schemes. In order to enable an efficient adjustment of the new model to experimentally observed softening hysteresis, an adjustment scheme using a surrogate model is proposed. Therewith, the relaxed formulation is adjusted to experimental data in the supra-physiological domain of the media and adventitia of a human carotid artery. The performance of the model is then demonstrated in a finite element example of an overstretched artery. Although here three-dimensional thick-walled atherosclerotic arteries are considered, it is emphasized that the formulation can also directly be applied to thin-walled simulations of arteries using shell elements or other fiber-reinforced biomembranes.

  5. An incremental DPMM-based method for trajectory clustering, modeling, and retrieval.

    PubMed

    Hu, Weiming; Li, Xi; Tian, Guodong; Maybank, Stephen; Zhang, Zhongfei

    2013-05-01

    Trajectory analysis is the basis for many applications, such as indexing of motion events in videos, activity recognition, and surveillance. In this paper, the Dirichlet process mixture model (DPMM) is applied to trajectory clustering, modeling, and retrieval. We propose an incremental version of a DPMM-based clustering algorithm and apply it to cluster trajectories. An appropriate number of trajectory clusters is determined automatically. When trajectories belonging to new clusters arrive, the new clusters can be identified online and added to the model without any retraining using the previous data. A time-sensitive Dirichlet process mixture model (tDPMM) is applied to each trajectory cluster for learning the trajectory pattern which represents the time-series characteristics of the trajectories in the cluster. Then, a parameterized index is constructed for each cluster. A novel likelihood estimation algorithm for the tDPMM is proposed, and a trajectory-based video retrieval model is developed. The tDPMM-based probabilistic matching method and the DPMM-based model growing method are combined to make the retrieval model scalable and adaptable. Experimental comparisons with state-of-the-art algorithms demonstrate the effectiveness of our algorithm. PMID:23520251

  6. 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

  7. 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.

  8. Estimation of Forest Biomass Increment Using Tree-ring data and Hydro-Ecological Modeling in a Rugged Forested Landscape

    NASA Astrophysics Data System (ADS)

    Lee, B.; Kang, S.; Kim, E.; Kim, Y.

    2006-12-01

    Terrestrial carbon sequestration by forest biomass is an important component of global carbon cycle, which is closely related to the greenhouse effect and climate system. Many researchers have studied on how to estimate forest biomass accurately and they utilized various methods including ecological modeling, remote sensing, and field measurements. However, it is still highly uncertain to estimate the forest biomass accurately and predict the future change. In particular, where water limitation is likely expected, carbon and water relations should be considered importantly in predicting vegetation primary production. The main objective of this study is to estimate biomass increments in the Gwangneung Experimental Forest (GEF) and to compare them with the simulation results of RHESSys, a GIS-based hydro-ecological model designed to simulate water and nutrient fluxes. We measured biomass and to estimate biomass increments using tree-ring data from 1991 to 2004, and they were calculated by using the single tree biomass equation. Average biomass increment during the study period was 271.38 g C m-2yr-1. RHESSys simulations need to a certain number of years to allow carbon and nitrogen stores to stabilize (spin up), which provides initial condition of the model simulation from 1991 to 2004. The data of Leaf Area Index (LAI) and daily stream discharge were used for model calibration. In addition, the results of biomass increment measurement from 1991 to 1997 in GEF were used for model parameterization, and those from 1998 to 2004 were used for validation. Our preliminary simulation results indicated that the simulation results of RHESSys model on the biomass increment was reasonably accurate, but in order to improve the prediction accuracy of this model, we concluded that various efforts on model verification and field data collection are required. *Keyword: Biomass increment, Hydro-Ecological Model. *Acknowledgement : This work was supported by the 2nd phase Brain Korea

  9. The Variance Reaction Time Model

    ERIC Educational Resources Information Center

    Sikstrom, Sverker

    2004-01-01

    The variance reaction time model (VRTM) is proposed to account for various recognition data on reaction time, the mirror effect, receiver-operating-characteristic (ROC) curves, etc. The model is based on simple and plausible assumptions within a neural network: VRTM is a two layer neural network where one layer represents items and one layer…

  10. Degradation reliability modeling based on an independent increment process with quadratic variance

    NASA Astrophysics Data System (ADS)

    Wang, Zhihua; Zhang, Yongbo; Wu, Qiong; Fu, Huimin; Liu, Chengrui; Krishnaswamy, Sridhar

    2016-03-01

    Degradation testing is an important technique for assessing life time information of complex systems and highly reliable products. Motivated by fatigue crack growth (FCG) data and our previous study, this paper develops a novel degradation modeling approach, in which degradation is represented by an independent increment process with linear mean and general quadratic variance functions of test time or transformed test time if necessary. Based on the constructed degradation model, closed-form expressions of failure time distribution (FTD) and its percentiles can be straightforwardly derived and calculated. A one-stage method is developed to estimate model parameters and FTD. Simulation studies are conducted to validate the proposed approach, and the results illustrate that the approach can provide reasonable estimates even for small sample size situations. Finally, the method is verified by the FCG data set given as the motivating example, and the results show that it can be considered as an effective degradation modeling approach compared with the multivariate normal model and graphic approach.

  11. 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.

  12. 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.

  13. Detection of Bird Nests during Mechanical Weeding by Incremental Background Modeling and Visual Saliency

    PubMed Central

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

    2015-01-01

    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. PMID:25738766

  14. 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.

  15. 78 FR 46610 - Certain Digital Models, Digital Data, and Treatment Plans for Use in Making Incremental Dental...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-01

    ... (``Align''), on March 1, 2012, as corrected on March 22, 2012. 77 FR 20648 (April 5, 2012). The complaint... Presidential Memorandum of July 21, 2005, 70 FR 43251 (July 26, 2005). During this period, the subject articles... COMMISSION Certain Digital Models, Digital Data, and Treatment Plans for Use in Making Incremental...

  16. 78 FR 29157 - Certain Digital Models, Digital Data, and Treatment Plans for Use, in Making Incremental Dental...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-17

    ... From the Federal Register Online via the Government Publishing Office INTERNATIONAL TRADE COMMISSION Certain Digital Models, Digital Data, and Treatment Plans for Use, in Making Incremental Dental Positioning Adjustment Appliances Made Therefrom, and Methods of Making the Same Investigation No. 337-...

  17. 78 FR 46611 - Certain Digital Models, Digital Data, and Treatment Plans for Use in Making Incremental Dental...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-01

    ... (``Align''), on March 1, 2012, as corrected on March 22, 2012. 77 FR 20648 (April 5, 2012). The complaint... Presidential Memorandum of July 21, 2005, 70 FR 43251 (July 26, 2005). During this period, the subject articles... COMMISSION Certain Digital Models, Digital Data, and Treatment Plans for Use in Making Incremental...

  18. 40 CFR Table 1 to Subpart Dddd of... - Model Rule-Increments of Progress and Compliance Schedules

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 6 2010-07-01 2010-07-01 false Model Rule-Increments of Progress and Compliance Schedules 1 Table 1 to Subpart DDDD of Part 60 Protection of Environment ENVIRONMENTAL PROTECTION... Construction On or Before November 30, 1999 Pt. 60, Subpt. DDDD, Table 1 Table 1 to Subpart DDDD of Part...

  19. 40 CFR Table 1 to Subpart Dddd of... - Model Rule-Increments of Progress and Compliance Schedules

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Compliance Schedules 1 Table 1 to Subpart DDDD of Part 60 Protection of Environment ENVIRONMENTAL PROTECTION.... DDDD, Table 1 Table 1 to Subpart DDDD of Part 60—Model Rule—Increments of Progress and Compliance...: At 76 FR 15484, Mar. 21, 2011, table 1 to subpart DDDD of part 60 was revised, effective May 20,...

  20. 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.

  1. 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}

  2. Reaction models in nuclear astrophysics

    NASA Astrophysics Data System (ADS)

    Descouvemont, Pierre

    2016-05-01

    We present different reaction models commonly used in nuclear astrophysics, in particular for the nucleosynthesis of light elements. Pioneering works were performed within the potential model, where the internal structure of the colliding nuclei is completely ignored. Significant advances in microscopic cluster models provided the first microscopic description of the 3He(α,&gamma)7 Be reaction more than thirty years ago. In this approach, the calculations are based on an effective nucleon-nucleon interaction, but the cluster approximation should be made to simplify the calculations. Nowadays, modern microscopic calculations are able to go beyond the cluster approximation, and aim at finding exact solutions of the Schrödinger equation with realistic nucleon-nucleon interactions. We discuss recent examples on the d+d reactions at low energies.

  3. 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

  4. 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

  5. Substitution patterns in aromatic rings by increment analysis. Model development and application to natural organic matter.

    PubMed

    Perdue, E M; Hertkorn, N; Kettrup, A

    2007-02-01

    The aromatic region of two-dimensional heteronuclear 1H, 13C NMR spectra of natural organic matter and related materials (e.g., 1H and 13C chemical shifts ranging from approximately 5 to 10 and 80 to 140 ppm, respectively) is highly complex and difficult to interpret using conventional approaches. In principle, this region of the NMR spectrum should be amenable to detailed analysis, because the effects of many common substituents on the chemical shifts of aromatic carbon and hydrogen are well documented. This paper describes the development of a model for prediction of substitution patterns in aromatic rings by increment analysis (SPARIA). In the forward mode, SPARIA is used to predict the chemical shifts of 1H and 13C on aromatic moieties containing every possible combination of eight common substituents that are likely to be representative of substituents on aromatic moieties in natural organic matter. The accuracy of SPARIA in the forward mode is evaluated for 29 aromatic compounds (100 peaks) by comparison of predicted chemical shifts for 1H and 13C with experimental values and with predictions of commercially available software for prediction of NMR spectra. The most important development in this paper is the inverse mode that is built into SPARIA. Given chemical shifts for 1H and 13C (such as may be obtained from a two-dimensional, heteronuclear NMR spectrum), the inverse mode of SPARIA calculates all possible combinations of the eight selected substituents that yield chemical shifts within a specified window of chemical shift for both 1H and 13C. Both the distribution of possible substitution patterns and simple descriptive statistics of the distribution are thus obtained. The inverse mode of SPARIA has been tested on the 29 aromatic compounds (100 peaks) that were used to evaluate its forward mode, and the dependence of the inverse process on the size of the chemical shift window has been evaluated. Finally, the inverse mode of SPARIA has been applied to

  6. Tool Path Design of Incremental Open-Die Disk Forging Using Physical Modeling

    NASA Astrophysics Data System (ADS)

    Lee, Sung-Uk; Yang, Dong-Yol

    A small-batch product of large-sized parts is usually manufactured using incremental open-die forging. In order to control the overall change in the shape of a part, it is essential to be able to predict the shape changes that occur during each step. This paper addresses shape changes of a material according to the forging path. Rapid prediction of metal flows for continuing incremental deformation using theoretical methods is difficult. Accordingly, instead of a theoretical approach, an experiment that tests the tendency of the metal flow for development of forming processes is required. For the sake of convenience, simulative experiments are carried out using plasticine at room temperature. In present study, the tool movement is dominant parameters to with respect to changing the shape of the workpiece.

  7. 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…

  8. Spatial model of autocatalytic reactions

    NASA Astrophysics Data System (ADS)

    de Anna, Pietro; di Patti, Francesca; Fanelli, Duccio; McKane, Alan J.; Dauxois, Thierry

    2010-05-01

    Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles—membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive protocells, and they could have provided the ideal environment for prebiotic reactions to occur. In this paper, we investigate the stochastic dynamics of a set of autocatalytic reactions, within a spatially bounded domain, so as to mimic a primordial cell. The discreteness of the constituents of the autocatalytic reactions gives rise to large sustained oscillations even when the number of constituents is quite large. These oscillations are spatiotemporal in nature, unlike those found in previous studies, which consisted only of temporal oscillations. We speculate that these oscillations may have a role in seeding membrane instabilities which lead to vesicle division. In this way synchronization could be achieved between protocell growth and the reproduction rate of the constituents (the protogenetic material) in simple protocells.

  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 enzyme kinetic reaction.

    PubMed

    Atangana, Abdon

    2015-09-01

    The Enzymatic control reactions model was presented within the scope of fractional calculus. In order to accommodate the usual initial conditions, the fractional derivative used is in Caputo sense. The methodologies of the three analytical methods were used to derive approximate solution of the fractional nonlinear system of differential equations. Two methods use integral operator and the other one uses just an integral. Numerical results obtained exhibit biological behavior of real world problem.

  11. Tracking and recognition face in videos with incremental local sparse representation model

    NASA Astrophysics Data System (ADS)

    Wang, Chao; Wang, Yunhong; Zhang, Zhaoxiang

    2013-10-01

    This paper addresses the problem of tracking and recognizing faces via incremental local sparse representation. First a robust face tracking algorithm is proposed via employing local sparse appearance and covariance pooling method. In the following face recognition stage, with the employment of a novel template update strategy, which combines incremental subspace learning, our recognition algorithm adapts the template to appearance changes and reduces the influence of occlusion and illumination variation. This leads to a robust video-based face tracking and recognition with desirable performance. In the experiments, we test the quality of face recognition in real-world noisy videos on YouTube database, which includes 47 celebrities. Our proposed method produces a high face recognition rate at 95% of all videos. The proposed face tracking and recognition algorithms are also tested on a set of noisy videos under heavy occlusion and illumination variation. The tracking results on challenging benchmark videos demonstrate that the proposed tracking algorithm performs favorably against several state-of-the-art methods. In the case of the challenging dataset in which faces undergo occlusion and illumination variation, and tracking and recognition experiments under significant pose variation on the University of California, San Diego (Honda/UCSD) database, our proposed method also consistently demonstrates a high recognition rate.

  12. Incremental learning of Bayesian sensorimotor models: from low-level behaviours to large-scale structure of the environment

    NASA Astrophysics Data System (ADS)

    Diard, Julien; Gilet, Estelle; Simonin, Éva; Bessière, Pierre

    2010-12-01

    This paper concerns the incremental learning of hierarchies of representations of space in artificial or natural cognitive systems. We propose a mathematical formalism for defining space representations (Bayesian Maps) and modelling their interaction in hierarchies of representations (sensorimotor interaction operator). We illustrate our formalism with a robotic experiment. Starting from a model based on the proximity to obstacles, we learn a new one related to the direction of the light source. It provides new behaviours, like phototaxis and photophobia. We then combine these two maps so as to identify parts of the environment where the way the two modalities interact is recognisable. This classification is a basis for learning a higher level of abstraction map that describes the large-scale structure of the environment. In the final model, the perception-action cycle is modelled by a hierarchy of sensorimotor models of increasing time and space scales, which provide navigation strategies of increasing complexities.

  13. The dark side of incremental learning: A model of cumulative semantic interference during lexical access in speech production

    PubMed Central

    Oppenheim, Gary M.; Dell, Gary S.; Schwartz, Myrna F.

    2010-01-01

    Naming a picture of a dog primes the subsequent naming of a picture of a dog (repetition priming) and interferes with the subsequent naming of a picture of a cat (semantic interference). Behavioral studies suggest that these effects derive from persistent changes in the way that words are activated and selected for production, and some have claimed that the findings are only understandable by positing a competitive mechanism for lexical selection. We present a simple model of lexical retrieval in speech production that applies error-driven learning to its lexical activation network. This model naturally produces repetition priming and semantic interference effects. It predicts the major findings from several published experiments, demonstrating that these effects may arise from incremental learning. Furthermore, analysis of the model suggests that competition during lexical selection is not necessary for semantic interference if the learning process is itself competitive. PMID:19854436

  14. Modeling the complex bromate-iodine reaction.

    PubMed

    Machado, Priscilla B; Faria, Roberto B

    2009-05-01

    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. PMID:19361181

  15. Incremental Testing of the Community Multiscale Air Quality (CMAQ) Modeling System Version 4.7

    EPA Science Inventory

    This paper describes the scientific and structural updates to the latest release of the Community Multiscale Air Quality (CMAQ) modeling system version 4.7 (v4.7) and points the reader to additional resources for further details. The model updates were evaluated relative to obse...

  16. Graphical assessment of incremental value of novel markers in prediction models: From statistical to decision analytical perspectives.

    PubMed

    Steyerberg, Ewout W; Vedder, Moniek M; Leening, Maarten J G; Postmus, Douwe; D'Agostino, Ralph B; Van Calster, Ben; Pencina, Michael J

    2015-07-01

    New markers may improve prediction of diagnostic and prognostic outcomes. We aimed to review options for graphical display and summary measures to assess the predictive value of markers over standard, readily available predictors. We illustrated various approaches using previously published data on 3264 participants from the Framingham Heart Study, where 183 developed coronary heart disease (10-year risk 5.6%). We considered performance measures for the incremental value of adding HDL cholesterol to a prediction model. An initial assessment may consider statistical significance (HR = 0.65, 95% confidence interval 0.53 to 0.80; likelihood ratio p < 0.001), and distributions of predicted risks (densities or box plots) with various summary measures. A range of decision thresholds is considered in predictiveness and receiver operating characteristic curves, where the area under the curve (AUC) increased from 0.762 to 0.774 by adding HDL. We can furthermore focus on reclassification of participants with and without an event in a reclassification graph, with the continuous net reclassification improvement (NRI) as a summary measure. When we focus on one particular decision threshold, the changes in sensitivity and specificity are central. We propose a net reclassification risk graph, which allows us to focus on the number of reclassified persons and their event rates. Summary measures include the binary AUC, the two-category NRI, and decision analytic variants such as the net benefit (NB). Various graphs and summary measures can be used to assess the incremental predictive value of a marker. Important insights for impact on decision making are provided by a simple graph for the net reclassification risk. PMID:25042996

  17. Numerical Modeling of Detachment Folding: a 2D Approach with Application to Incremental Coseismic Fold Growth in Taiwan

    NASA Astrophysics Data System (ADS)

    Strayer, Luther; Suppe, John; Graveleau, Fabien

    2010-05-01

    -Chi-like earthquakes with 8 m slip terminating in the fold and about 45 non-Chi-Chi events with 8 m slip passing through the fold. In order to understand the incremental, but not necessarily dynamical, development of the Tungshih and other similar anticlines we are developing 2D numerical models similar to this structure using both idealized initial states (flat layers, level ground surface, etc.) and deformed states derived from the natural prototype (seismic profiles, surface data, etc.). We are taking this two-pronged approach because while our main goal is to re-create the last 12 m increment of growth on the Cholan structure, having knowledge of the nature and extent of the strains (damage to the rockmass) required to get to this initial pre-Chi-Chi state will likely be important with regard to setting up the 'natural' example model. In other words-knowing where the rockmass is weakened or anisotropic due to prior deformation will aid in defining the character and distribution of material properties in our incremental model. We are using both continuum and discrete modeling methods and are examining the feasibility of developing a coupled continuous/discrete model in which deeper the levels of the structure is modeled as a continuum and the near surface is simulated using a bonded particle-based method. The particle nature of the discrete formulation lends itself particularly well to addressing the inherently discontinuous nature of shallow-level deformation. Both techniques rely on finite-difference formulations, which we believe have significant advantages over traditional finite-element modeling approaches. Results expected from this modeling work include, among others: 1) better understanding of the mechanical controls of the evolution of detachment folds in general; 2) knowledge of the slip-transfer mechanisms at core of the Tungshih anticline and mechanical conditions that allow us to re-create the surface deformation documented at Cholan; 3) an understanding of the

  18. Small-Sample Robust Estimators of Noncentrality-Based and Incremental Model Fit

    ERIC Educational Resources Information Center

    Herzog, Walter; Boomsma, Anne

    2009-01-01

    Traditional estimators of fit measures based on the noncentral chi-square distribution (root mean square error of approximation [RMSEA], Steiger's [gamma], etc.) tend to overreject acceptable models when the sample size is small. To handle this problem, it is proposed to employ Bartlett's (1950), Yuan's (2005), or Swain's (1975) correction of the…

  19. Estimating marginal and incremental effects on health outcomes using flexible link and variance function models.

    PubMed

    Basu, Anirban; Rathouz, Paul J

    2005-01-01

    We propose an extension to the estimating equations in generalized linear models to estimate parameters in the link function and variance structure simultaneously with regression coefficients. Rather than focusing on the regression coefficients, the purpose of these models is inference about the mean of the outcome as a function of a set of covariates, and various functionals of the mean function used to measure the effects of the covariates. A commonly used functional in econometrics, referred to as the marginal effect, is the partial derivative of the mean function with respect to any covariate, averaged over the empirical distribution of covariates in the model. We define an analogous parameter for discrete covariates. The proposed estimation method not only helps to identify an appropriate link function and to suggest an underlying distribution for a specific application but also serves as a robust estimator when no specific distribution for the outcome measure can be identified. Using Monte Carlo simulations, we show that the resulting parameter estimators are consistent. The method is illustrated with an analysis of inpatient expenditure data from a study of hospitalists.

  20. Connectionist and diffusion models of reaction time.

    PubMed

    Ratcliff, R; Van Zandt, T; McKoon, G

    1999-04-01

    Two connectionist frameworks, GRAIN (J. L. McClelland, 1993) and brain-state-in-a-box (J. A. Anderson, 1991), and R. Ratcliff's (1978) diffusion model were evaluated using data from a signal detection task. Dependent variables included response probabilities, reaction times for correct and error responses, and shapes of reaction-time distributions. The diffusion model accounted for all aspects of the data, including error reaction times that had previously been a problem for all response-time models. The connectionist models accounted for many aspects of the data adequately, but each failed to a greater or lesser degree in important ways except for one model that was similar to the diffusion model. The findings advance the development of the diffusion model and show that the long tradition of reaction-time research and theory is a fertile domain for development and testing of connectionist assumptions about how decisions are generated over time.

  1. Chemical-reaction model for Mexican wave

    NASA Astrophysics Data System (ADS)

    Nagatani, Takashi

    2003-05-01

    We present a chemical-reaction model to describe the Mexican wave ( La Ola) in football stadia. The spectator's action is described in terms of chemical reactions. The model is governed by three reaction rates k 1, k 2, and k3. We study the nonlinear waves on one- and two-dimensional lattices. The Mexican wave is formulated as a clockwise forwardly propagating wave. Waves are growing or disappear, depending on the values of reaction rates. In the specific case of k1= k2= k3=1, the nonlinear-wave equation produces a propagating pulse like soliton.

  2. 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.

  3. 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.

  4. 40 CFR Table 1 to Subpart Mmmm of... - Model Rule-Increments of Progress and Compliance Schedules for Existing Sewage Sludge...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Compliance Schedules for Existing Sewage Sludge Incineration Units 1 Table 1 to Subpart MMMM of Part 60... Incineration Units Pt. 60, Subpt. MMMM, Table 1 Table 1 to Subpart MMMM of Part 60—Model Rule—Increments of Progress and Compliance Schedules for Existing Sewage Sludge Incineration Units Comply with...

  5. 40 CFR Table 1 to Subpart Mmmm of... - Model Rule-Increments of Progress and Compliance Schedules for Existing Sewage Sludge...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Compliance Schedules for Existing Sewage Sludge Incineration Units 1 Table 1 to Subpart MMMM of Part 60... Incineration Units Pt. 60, Subpt. MMMM, Table 1 Table 1 to Subpart MMMM of Part 60—Model Rule—Increments of Progress and Compliance Schedules for Existing Sewage Sludge Incineration Units Comply with...

  6. 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.

  7. Source Apportionment of the Anthropogenic Increment to Ozone, Formaldehyde, and Nitrogen Dioxide by the Path-Integral Method in a 3D Model.

    PubMed

    Dunker, Alan M; Koo, Bonyoung; Yarwood, Greg

    2015-06-01

    The anthropogenic increment of a species is the difference in concentration between a base-case simulation with all emissions included and a background simulation without the anthropogenic emissions. The Path-Integral Method (PIM) is a new technique that can determine the contributions of individual anthropogenic sources to this increment. The PIM was applied to a simulation of O3 formation in July 2030 in the U.S., using the Comprehensive Air Quality Model with Extensions and assuming advanced controls on light-duty vehicles (LDVs) and other sources. The PIM determines the source contributions by integrating first-order sensitivity coefficients over a range of emissions, a path, from the background case to the base case. There are many potential paths, with each representing a specific emission-control strategy leading to zero anthropogenic emissions, i.e., controlling all sources together versus controlling some source(s) preferentially are different paths. Three paths were considered, and the O3, formaldehyde, and NO2 anthropogenic increments were apportioned to five source categories. At rural and urban sites in the eastern U.S. and for all three paths, point sources typically have the largest contribution to the O3 and NO2 anthropogenic increments, and either LDVs or area sources, the smallest. Results for formaldehyde are more complex. PMID:25938820

  8. Mathematical model to predict drivers' reaction speeds.

    PubMed

    Long, Benjamin L; Gillespie, A Isabella; Tanaka, Martin L

    2012-02-01

    Mental distractions and physical impairments can increase the risk of accidents by affecting a driver's ability to control the vehicle. In this article, we developed a linear mathematical model that can be used to quantitatively predict drivers' performance over a variety of possible driving conditions. Predictions were not limited only to conditions tested, but also included linear combinations of these tests conditions. Two groups of 12 participants were evaluated using a custom drivers' reaction speed testing device to evaluate the effect of cell phone talking, texting, and a fixed knee brace on the components of drivers' reaction speed. Cognitive reaction time was found to increase by 24% for cell phone talking and 74% for texting. The fixed knee brace increased musculoskeletal reaction time by 24%. These experimental data were used to develop a mathematical model to predict reaction speed for an untested condition, talking on a cell phone with a fixed knee brace. The model was verified by comparing the predicted reaction speed to measured experimental values from an independent test. The model predicted full braking time within 3% of the measured value. Although only a few influential conditions were evaluated, we present a general approach that can be expanded to include other types of distractions, impairments, and environmental conditions. PMID:22431214

  9. Mathematical model to predict drivers' reaction speeds.

    PubMed

    Long, Benjamin L; Gillespie, A Isabella; Tanaka, Martin L

    2012-02-01

    Mental distractions and physical impairments can increase the risk of accidents by affecting a driver's ability to control the vehicle. In this article, we developed a linear mathematical model that can be used to quantitatively predict drivers' performance over a variety of possible driving conditions. Predictions were not limited only to conditions tested, but also included linear combinations of these tests conditions. Two groups of 12 participants were evaluated using a custom drivers' reaction speed testing device to evaluate the effect of cell phone talking, texting, and a fixed knee brace on the components of drivers' reaction speed. Cognitive reaction time was found to increase by 24% for cell phone talking and 74% for texting. The fixed knee brace increased musculoskeletal reaction time by 24%. These experimental data were used to develop a mathematical model to predict reaction speed for an untested condition, talking on a cell phone with a fixed knee brace. The model was verified by comparing the predicted reaction speed to measured experimental values from an independent test. The model predicted full braking time within 3% of the measured value. Although only a few influential conditions were evaluated, we present a general approach that can be expanded to include other types of distractions, impairments, and environmental conditions.

  10. 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

  11. 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.

  12. Theory and Modeling of Asymmetric Catalytic Reactions.

    PubMed

    Lam, Yu-Hong; Grayson, Matthew N; Holland, Mareike C; Simon, Adam; Houk, K N

    2016-04-19

    Modern density functional theory and powerful contemporary computers have made it possible to explore complex reactions of value in organic synthesis. We describe recent explorations of mechanisms and origins of stereoselectivities with density functional theory calculations. The specific functionals and basis sets that are routinely used in computational studies of stereoselectivities of organic and organometallic reactions in our group are described, followed by our recent studies that uncovered the origins of stereocontrol in reactions catalyzed by (1) vicinal diamines, including cinchona alkaloid-derived primary amines, (2) vicinal amidophosphines, and (3) organo-transition-metal complexes. Two common cyclic models account for the stereoselectivity of aldol reactions of metal enolates (Zimmerman-Traxler) or those catalyzed by the organocatalyst proline (Houk-List). Three other models were derived from computational studies described in this Account. Cinchona alkaloid-derived primary amines and other vicinal diamines are venerable asymmetric organocatalysts. For α-fluorinations and a variety of aldol reactions, vicinal diamines form enamines at one terminal amine and activate electrophilically with NH(+) or NF(+) at the other. We found that the stereocontrolling transition states are cyclic and that their conformational preferences are responsible for the observed stereoselectivity. In fluorinations, the chair seven-membered cyclic transition states is highly favored, just as the Zimmerman-Traxler chair six-membered aldol transition state controls stereoselectivity. In aldol reactions with vicinal diamine catalysts, the crown transition states are favored, both in the prototype and in an experimental example, shown in the graphic. We found that low-energy conformations of cyclic transition states occur and control stereoselectivities in these reactions. Another class of bifunctional organocatalysts, the vicinal amidophosphines, catalyzes the (3 + 2) annulation

  13. Post-combustion reactions and modeling

    NASA Astrophysics Data System (ADS)

    Story, Scott R.

    Owing to the presence of carbon, oxygen and hydrogen in many iron and steelmaking processes, vast quantities of combustible gases rich in CO along with Hsb2 are often created. To take advantage this potential chemical energy, extra amounts of oxygen may be supplied to the process in order to combust these species, through a practice known as post combustion. Effective post combustion is important in many steelmaking processes. Post combustion is strongly affected by fluid flow. However, in the presence of carbon and iron at high temperatures reactions known as "de-postcombustion" occur where carbon or Fe is oxidised. These reactions depend on kinetics and fluid flow. To address the lack of information at high temperature, the kinetics of carbon oxidation by COsb2 and Hsb2O has been studied at temperatures between 1300sp° C and 1500sp° C. At 1500sp° C, the graphite-Hsb2O reaction was found to occur at a similar rate to the graphite-COsb2 reaction. The overriding importance of internal pore structure was demonstrated in the results, particularly as it develops in the reacted layer during the course of the reaction. Such changes are believed to be responsible for the continuous rate increase observed in non-porous glassy carbon and the consistently higher rates measured in graphite than in coke at high temperatures. The results of this work have also been used to clarify the role of the gas-carbon reaction in the kinetics of FeO reduction in bath smelting slags by solid carbon. Under high stirring conditions in the slag it has been found that the gas-carbon reaction may play a significant role, particularly when coke is the carbonaceous material. The second component of this study was directed toward understanding the effect of fluid flow on post combustion in the electric arc furnace (EAF). In particular the objective was to determine if computational fluid dynamics (CFD) can be a useful tool for optimising post combustion. The post combustion degree (PCD) was

  14. 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.

  15. 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.

  16. Modelling enzyme reaction mechanisms, specificity and catalysis.

    PubMed

    Mulholland, Adrian J

    2005-10-15

    Modern modelling methods can now give uniquely detailed understanding of enzyme-catalyzed reactions, including the analysis of mechanisms and the identification of determinants of specificity and catalytic efficiency. A new field of computational enzymology has emerged that has the potential to contribute significantly to structure-based design and to develop predictive models of drug metabolism and, for example, of the effects of genetic polymorphisms. This review outlines important techniques in this area, including quantum-chemical model studies and combined quantum-mechanics and molecular-mechanics (QM/MM) methods. Some recent applications to enzymes of pharmacological interest are also covered, showing the types of problems that can be tackled and the insight they can give.

  17. Thermodynamic performance for a chemical reactions model

    NASA Astrophysics Data System (ADS)

    Gonzalez-Narvaez, R. E.; Sánchez-Salas, N.; Chimal-Eguía, J. C.

    2015-01-01

    This paper presents the analysis efficiency of a chemical reaction model of four states, such that their activated states can occur at any point (fixed but arbitrary) of the transition from one state to another. This mechanism operates under a single heat reservoir temperature, unlike the internal combustion engines where there are two thermal sources. Different efficiencies are compared to this model, which operate at different optimum engine regimes. Thus, some analytical methods are used to give an approximate expression, facilitating the comparison between them. Finally, the result is compared with that obtained by other authors considered a general model of an isothermal molecular machine. Taking into account the above, the results seems to follow a similar behaviour for all the optimized engines, which resemble that observed in the case of heat engine efficiencies.

  18. 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

  19. Modeling stochasticity in biochemical reaction networks

    NASA Astrophysics Data System (ADS)

    Constantino, P. H.; Vlysidis, M.; Smadbeck, P.; Kaznessis, Y. N.

    2016-03-01

    Small biomolecular systems are inherently stochastic. Indeed, fluctuations of molecular species are substantial in living organisms and may result in significant variation in cellular phenotypes. The chemical master equation (CME) is the most detailed mathematical model that can describe stochastic behaviors. However, because of its complexity the CME has been solved for only few, very small reaction networks. As a result, the contribution of CME-based approaches to biology has been very limited. In this review we discuss the approach of solving CME by a set of differential equations of probability moments, called moment equations. We present different approaches to produce and to solve these equations, emphasizing the use of factorial moments and the zero information entropy closure scheme. We also provide information on the stability analysis of stochastic systems. Finally, we speculate on the utility of CME-based modeling formalisms, especially in the context of synthetic biology efforts.

  20. 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.

  1. Circumnutation modeled by reaction-diffusion equations

    SciTech Connect

    Lubkin, S.R.

    1992-01-01

    In studies of biological oscillators, plants are only rarely examined. The authors study a common sub-diurnal oscillation of plants, called circumnutation. Based on experimental evidence that the oscillations consist of a turgor wave traveling around a growing plant part, circumnutation is modeled by a nonlinear reaction-diffusion system with cylindrical geometry. Because of its simplicity, and because biological oscillations are so common, an oscillatory [lambda]-[omega] reaction-diffusion system is chosen for the model. The authors study behavior of traveling waves in [lambda]-[omega] systems. The authors show the existence of Hopf bifurcations and the stability of the limit cycles born at the Hopf bifurcation for some parameter values. Using a Lindstedt-type perturbation scheme, the authors construct periodic solutions of the [lambda]-[omega] system near a Hopf bifurcation and show that the periodic solutions superimposed on the original traveling wave have the effect of altering its overall frequency and amplitude. Circumnutating plants generally display a strong directional preference to their oscillations, which is species-dependent. Circumnutation is modeled by a [lambda]-[omega] system on an annulus of variable width, which does not possess reflection symmetry about any axis. The annulus represents a region of high potassium concentration in the cross-section of the stem. The asymmetry of the annulus represents the anatomical asymmetry of the plant. Traveling waves are constructed on this variable-width annulus by a perturbation scheme, and perturbing the width of the annulus alters the amplitude and frequency of traveling waves on the domain by a small (order [epsilon][sup 2]) amount. The speed, frequency, and stability are unaffected by the direction of travel of the wave on the annulus. This indicates that the [lambda]-[omega] system on a variable-width domain cannot account for directional preferences of traveling waves in biological systems.

  2. 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…

  3. 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.

  4. 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.

  5. 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. PMID:12731843

  6. 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.

  7. 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.

  8. 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

  9. 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)

  10. 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. PMID:27334382

  11. Kinetics of the monomer-monomer surface reaction model

    SciTech Connect

    Evans, J.W.; Ray, T.R. )

    1993-02-01

    The two-dimensional monomer-monomer ([ital AB]) surface reaction model without diffusion is considered for infinitesimal, finite, and infinite reaction rates [ital k]. For equal reactant adsorption rates, in all cases, simulations reveal the same form of slow poisoning, associated with clustering of reactants. This behavior is also the same as that found in simulations of the two-dimensional [ital voter] [ital model] studied in interacting-particle systems theory. The voter model can also be obtained from the dimer-dimer or monomer-dimer surface reaction models with infinitesimal reaction rate. We provide a detailed elucidation of the slow poisoning kinetics via an analytic treatment for the [ital k]=0[sup +] [ital AB] reaction and the voter models. This analysis is extended to incorporate the effects of place-exchange diffusion which slows, but does not prevent poisoning. We also show that the [ital k]=0[sup +] [ital AB] reaction with no diffusion is equivalent to the voter model with diffusion at rate 1/2. Identical behavior of the monomer-monomer reaction and the voter model is also found in an epidemic'' analysis, where one considers the evolution of a surface poisoned by one species, except for a small patch. Finally, we apply our findings to elucidate the behavior of the monomer-dimer surface reaction model for small reaction rates.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  14. Kinetic modeling of reactions in heated monosaccharide-casein systems.

    PubMed

    Brands, Carline M J; van Boekel, Martinus A J S

    2002-11-01

    In the present study, a kinetic model of the Maillard reaction occurring in heated monosaccharide-casein systems was proposed. Its parameters, the reaction rate constants, were estimated via multiresponse modeling. The determinant criterion was used as the statistical fit criterion instead of the familiar least squares to avoid statistical problems. The kinetic model was extensively tested by varying the reaction conditions. Different sugars (glucose, fructose, galactose, and tagatose) were studied regarding their effect on the reaction kinetics. This study has shown the power of multiresponse modeling for the unraveling of complicated reaction routes as occur in the Maillard reaction. The iterative process of proposing a model, confronting it with experiments, and criticizing the model was passed through four times to arrive at a model that was largely consistent with all results obtained. A striking difference was found between aldose and ketose sugars as suggested by the modeling results: not the ketoses themselves but only their reaction products were found to be reactive in the Maillard reaction.

  15. Complex wave patterns in an effective reaction-diffusion model for chemical reactions in microemulsions.

    PubMed

    Alonso, Sergio; John, Karin; Bär, Markus

    2011-03-01

    An effective medium theory is employed to derive a simple qualitative model of a pattern forming chemical reaction in a microemulsion. This spatially heterogeneous system is composed of water nanodroplets randomly distributed in oil. While some steps of the reaction are performed only inside the droplets, the transport through the extended medium occurs by diffusion of intermediate chemical reactants as well as by collisions of the droplets. We start to model the system with heterogeneous reaction-diffusion equations and then derive an equivalent effective spatially homogeneous reaction-diffusion model by using earlier results on homogenization in heterogeneous reaction-diffusion systems [S.Alonso, M.Bär, and R.Kapral, J. Chem. Phys. 134, 214102 (2009)]. We study the linear stability of the spatially homogeneous state in the resulting effective model and obtain a phase diagram of pattern formation, that is qualitatively similar to earlier experimental results for the Belousov-Zhabotinsky reaction in an aerosol OT (AOT)-water-in-oil microemulsion [V.K.Vanag and I.R.Epstein, Phys. Rev. Lett. 87, 228301 (2001)]. Moreover, we reproduce many patterns that have been observed in experiments with the Belousov-Zhabotinsky reaction in an AOT oil-in-water microemulsion by direct numerical simulations.

  16. 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.

  17. 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. PMID:27010338

  18. 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.

  19. Development of reaction models for ground-water systems

    USGS Publications Warehouse

    Plummer, L.N.; Parkhurst, D.L.; Thorstenson, D.C.

    1983-01-01

    Methods are described for developing geochemical reaction models from the observed chemical compositions of ground water along a hydrologic flow path. The roles of thermodynamic speciation programs, mass balance calculations, and reaction-path simulations in developing and testing reaction models are contrasted. Electron transfer is included in the mass balance equations to properly account for redox reactions in ground water. The mass balance calculations determine net mass transfer models which must be checked against the thermodynamic calculations of speciation and reaction-path programs. Although reaction-path simulations of ground-water chemistry are thermodynamically valid, they must be checked against the net mass transfer defined by the mass balance calculations. An example is given testing multiple reaction hypotheses along a flow path in the Floridan aquifer where several reaction models are eliminated. Use of carbon and sulfur isotopic data with mass balance calculations indicates a net reaction of incongruent dissolution of dolomite (dolomite dissolution with calcite precipitation) driven irreversibly by gypsum dissolution, accompanied by minor sulfate reduction, ferric hydroxide dissolution, and pyrite precipitation in central Florida. Along the flow path, the aquifer appears to be open to CO2 initially, and open to organic carbon at more distant points down gradient. ?? 1983.

  20. Supramolecular structures modeling photosynthetic reaction center function

    SciTech Connect

    Wasielewski, M.R.; Gaines, G.L. III; Gosztola, D.; Niemczyk, M.P.; Svec, W.A.

    1992-08-20

    Work in our laboratory has focused on the influence of solvent motion on the rates and energetics of photochemical charge separation in glassy solids. The efficiencies of many nonadiabatic electron transfer reactions involving photochemical electron donors with relatively low excited state energies, such as porphyrins and chlorophylls, are poor in the solid state. Recent work has shown that placing a porphyrin-acceptor system in a glassy solid at low temperature significantly raises the energy of ks ion-pair state. This destabilization can be as much as 0.8 eV relative to the ion pair state energy in a polar liquid. This contrasts sharply with photosynthetic reaction centers, which maintain medium-independent electron transfer rates with relatively small free energies of charge separation. Using this information we have set out to design photochemical systems that produce long-lived radical ion pairs in glassy solids with high quantum efficiency. These systems maintain their efficiency when placed in other glassy matrices, such as polymers. An important consequence of this effort is the design of molecules that minimize the electronic interaction between the oxidized donor and reduced acceptor. This minimization can be attained by careful design of the spacer groups linking the donor and acceptor and by using more than a single electron transfer step to increase the distance between the separated charges as is done in natural photosynthesis.

  1. 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.

  2. Reaction rate modeling of PBXN-110

    NASA Astrophysics Data System (ADS)

    Miller, P. J.; Sutherland, G. T.

    1996-05-01

    The reactive rate model for Navy explosive PBXN-110 has been determined. The rate parameters for the Lee-Tarver model were evaluated by comparing the results of DYNA2D hydrocode simulations to the embedded gauge data of gas-gun tests in which the shock loading is mostly one-dimensional. The model parameters were refined such that the failure diameter of the explosive could be reproduced in the calculations. The model was used to simulate a series of Navy sensitivity tests. These are reported here and include detonation curvature, detonation velocity dependency on charge diameter, Modified Gap, and Underwater Sensitivity tests.

  3. 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.

  4. Reading and a diffusion model analysis of reaction time.

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    Weber, Arthur L.

    2007-04-01

    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 of 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.

  6. 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

  7. 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…

  8. Parallel incremental compilation. Doctoral thesis

    SciTech Connect

    Gafter, N.M.

    1990-06-01

    The time it takes to compile a large program has been a bottleneck in the software development process. When an interactive programming environment with an incremental compiler is used, compilation speed becomes even more important, but existing incremental compilers are very slow for some types of program changes. We describe a set of techniques that enable incremental compilation to exploit fine-grained concurrency in a shared-memory multi-processor and achieve asymptotic improvement over sequential algorithms. Because parallel non-incremental compilation is a special case of parallel incremental compilation, the design of a parallel compiler is a corollary of our result. Instead of running the individual phases concurrently, our design specifies compiler phases that are mutually sequential. However, each phase is designed to exploit fine-grained parallelism. By allowing each phase to present its output as a complete structure rather than as a stream of data, we can apply techniques such as parallel prefix and parallel divide-and-conquer, and we can construct applicative data structures to achieve sublinear execution time. Parallel algorithms for each phase of a compiler are presented to demonstrate that a complete incremental compiler can achieve execution time that is asymptotically less than sequential algorithms.

  9. Spallation reactions: A successful interplay between modeling and applications

    NASA Astrophysics Data System (ADS)

    David, J.-C.

    2015-06-01

    The spallation reactions are a type of nuclear reaction which occur in space by interaction of the cosmic rays with interstellar bodies. The first spallation reactions induced with an accelerator took place in 1947 at the Berkeley cyclotron (University of California) with 200MeV deuterons and 400MeV alpha beams. They highlighted the multiple emission of neutrons and charged particles and the production of a large number of residual nuclei far different from the target nuclei. In the same year, R. Serber described the reaction in two steps: a first and fast one with high-energy particle emission leading to an excited remnant nucleus, and a second one, much slower, the de-excitation of the remnant. In 2010 IAEA organized a workshop to present the results of the most widely used spallation codes within a benchmark of spallation models. If one of the goals was to understand the deficiencies, if any, in each code, one remarkable outcome points out the overall high-quality level of some models and so the great improvements achieved since Serber. Particle transport codes can then rely on such spallation models to treat the reactions between a light particle and an atomic nucleus with energies spanning from few tens of MeV up to some GeV. An overview of the spallation reactions modeling is presented in order to point out the incomparable contribution of models based on basic physics to numerous applications where such reactions occur. Validations or benchmarks, which are necessary steps in the improvement process, are also addressed, as well as the potential future domains of development. Spallation reactions modeling is a representative case of continuous studies aiming at understanding a reaction mechanism and which end up in a powerful tool.

  10. Surface tension increment due to solute addition

    NASA Astrophysics Data System (ADS)

    Hsin, Wei Lun; Sheng, Yu-Jane; Lin, Shi-Yow; Tsao, Heng-Kwong

    2004-03-01

    Addition of solute into solvent may lead to an increase in surface tension, such as salt in water and water in alcohol, due to solute depletion at the interface. The repulsion of the solute from the interface may originate from electrostatic forces or solute-solvent attraction. On the basis of the square-well model for the interface-solute interaction, we derive the surface tension increment Δγ by both canonical and grand-canonical routes (Gibbs adsorption isotherm) for a spherical droplet. The surface tension is increased linearly with the bulk concentration of the solute cb and the interaction range λ. The theoretical results are consistent with those obtained by experiments and Monte Carlo simulations up to a few molarity. For weak repulsion, the increment is internal energy driven. When the repulsion is large enough, the surface tension increment is entropy driven and approaches the asymptotic limit, Δγ≃cbkBTλ, due to the nearly complete depletion of the solute at the interface. Our result may shed some light on the surface tension increment for electrolyte solutions with concentration above 0.2M.

  11. The future of computational modelling in reaction engineering.

    PubMed

    Kraft, Markus; Mosbach, Sebastian

    2010-08-13

    In this paper, we outline the future of modelling in reaction engineering. Specifically, we use the example of particulate emission formation in internal combustion engines to demonstrate what modelling can achieve at present, and to illustrate the ultimately inevitable steps that need to be taken in order to create a new generation of engineering models. PMID:20603373

  12. 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.

  13. 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.

  14. 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.

  15. Biomass torrefaction: modeling of reaction thermochemistry.

    PubMed

    Bates, Richard B; Ghoniem, Ahmed F

    2013-04-01

    Based on the evolution of volatile and solid products predicted by a previous model for willow torrefaction (Bates and Ghoniem, 2012) a thermochemical model has been developed to describe their thermal, chemical, and physical properties as well as the rates of heat release. The first stage of torrefaction, associated with hemicellulose decomposition, is exothermic releasing between 40 and 280 kJ/kginitial. The second stage is associated with the decomposition of the remaining lignocellulosic components, completes over a longer period, and is predicted to be either endothermic or exothermic depending on the temperature and assumed solid properties. Cumulative heat release increases with the degree of torrefaction quantified by the mass loss. The rate of mass loss and rate of heat release increase with higher temperatures. The higher heating value of volatiles produced during torrefaction was estimated to be between 4.4 and 16 MJ/kg increasing with the level of mass loss.

  16. 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.

  17. Gene dosage imbalances: action, reaction, and models.

    PubMed

    Veitia, Reiner A; Potier, Marie Claude

    2015-06-01

    Single-gene deletions, duplications, and misregulation, as well as aneuploidy, can lead to stoichiometric imbalances within macromolecular complexes and cellular networks, causing their malfunction. Such alterations can be responsible for inherited or somatic genetic disorders including Mendelian diseases, aneuploid syndromes, and cancer. We review the effects of gene dosage alterations at the transcriptomic and proteomic levels, and the various responses of the cell to counteract their effects. Furthermore, we explore several biochemical models and ideas that can provide the rationale for treatments modulating the effects of gene dosage imbalances.

  18. 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.

  19. 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.

  20. Modeling Corrosion Reactions of Steel in a Dilute Carbonate Solution

    NASA Astrophysics Data System (ADS)

    Eliyan, Faysal Fayez; Alfantazi, Akram

    2016-02-01

    This research models the corrosion reactions of a high-strength steel in an aerated, dilute, carbonate solution during a single-cycle voltammetry. Based on a previous study (Eliyan et al. in J Mater Eng Perform 24(6):1-8, 2015) and a literature survey, the corrosion reactions of the cathodic reduction, anodic dissolution, and passivation, as well as the interfacial interactions and the chemistry of the corrosion products are illustrated in schematics. The paper provides a visual guide on the corrosion reactions for steel in carbonate solutions based on the available mechanistic details that were reported and are still being investigated in literature.

  1. 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

  2. Evaluation of maillard reaction variables and their effect on heterocyclic amine formation in chemical model systems.

    PubMed

    Dennis, Cara; Karim, Faris; Smith, J Scott

    2015-02-01

    Heterocyclic amines (HCAs), highly mutagenic and potentially carcinogenic by-products, form during Maillard browning reactions, specifically in muscle-rich foods. Chemical model systems allow examination of in vitro formation of HCAs while eliminating complex matrices of meat. Limited research has evaluated the effects of Maillard reaction parameters on HCA formation. Therefore, 4 essential Maillard variables (precursors molar concentrations, water amount, sugar type, and sugar amounts) were evaluated to optimize a model system for the study of 4 HCAs: 2-amino-3-methylimidazo-[4,5-f]quinoline, 2-amino-3-methylimidazo[4,5-f]quinoxaline, 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline, and 2-amino-3,4,8-trimethyl-imidazo[4,5-f]quinoxaline. Model systems were dissolved in diethylene glycol, heated at 175 °C for 40 min, and separated using reversed-phase liquid chromatography. To define the model system, precursor amounts (threonine and creatinine) were adjusted in molar increments (0.2/0.2, 0.4/0.4, 0.6/0.6, and 0.8/0.8 mmol) and water amounts by percentage (0%, 5%, 10%, and 15%). Sugars (lactose, glucose, galactose, and fructose) were evaluated in several molar amounts proportional to threonine and creatinine (quarter, half, equi, and double). The precursor levels and amounts of sugar were significantly different (P < 0.05) in regards to total HCA formation, with 0.6/0.6/1.2 mmol producing higher levels. Water concentration and sugar type also had a significant effect (P < 0.05), with 5% water and lactose producing higher total HCA amounts. A model system containing threonine (0.6 mmol), creatinine (0.6 mmol), and glucose (1.2 mmol), with 15% water was determined to be the optimal model system with glucose and 15% water being a better representation of meat systems. PMID:25597341

  3. Evaluation of maillard reaction variables and their effect on heterocyclic amine formation in chemical model systems.

    PubMed

    Dennis, Cara; Karim, Faris; Smith, J Scott

    2015-02-01

    Heterocyclic amines (HCAs), highly mutagenic and potentially carcinogenic by-products, form during Maillard browning reactions, specifically in muscle-rich foods. Chemical model systems allow examination of in vitro formation of HCAs while eliminating complex matrices of meat. Limited research has evaluated the effects of Maillard reaction parameters on HCA formation. Therefore, 4 essential Maillard variables (precursors molar concentrations, water amount, sugar type, and sugar amounts) were evaluated to optimize a model system for the study of 4 HCAs: 2-amino-3-methylimidazo-[4,5-f]quinoline, 2-amino-3-methylimidazo[4,5-f]quinoxaline, 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline, and 2-amino-3,4,8-trimethyl-imidazo[4,5-f]quinoxaline. Model systems were dissolved in diethylene glycol, heated at 175 °C for 40 min, and separated using reversed-phase liquid chromatography. To define the model system, precursor amounts (threonine and creatinine) were adjusted in molar increments (0.2/0.2, 0.4/0.4, 0.6/0.6, and 0.8/0.8 mmol) and water amounts by percentage (0%, 5%, 10%, and 15%). Sugars (lactose, glucose, galactose, and fructose) were evaluated in several molar amounts proportional to threonine and creatinine (quarter, half, equi, and double). The precursor levels and amounts of sugar were significantly different (P < 0.05) in regards to total HCA formation, with 0.6/0.6/1.2 mmol producing higher levels. Water concentration and sugar type also had a significant effect (P < 0.05), with 5% water and lactose producing higher total HCA amounts. A model system containing threonine (0.6 mmol), creatinine (0.6 mmol), and glucose (1.2 mmol), with 15% water was determined to be the optimal model system with glucose and 15% water being a better representation of meat systems.

  4. 40 CFR 60.2595 - What if I do not meet an increment of progress?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... or Before November 30, 1999 Model Rule-Increments of Progress § 60.2595 What if I do not meet an... Administrator postmarked within 10 business days after the date for that increment of progress in table 1...

  5. Polymerase chain reaction in natural convection systems: A convection-diffusion-reaction model

    NASA Astrophysics Data System (ADS)

    Yariv, E.; Ben-Dov, G.; Dorfman, K. D.

    2005-09-01

    We present a rational scheme for modeling natural convection-driven polymerase chain reaction (PCR), where many copies of a DNA template are made by cycling between hot and cold regions via a circulatory, buoyancy-driven flow. This process is described here in the framework of multiple-species formulation, using evolution equations which govern the concentrations of the various DNA species in the carrying solution. In the intermediate asymptotic limit, where a stationary amplification rate is achieved, these equations provide an eigenvalue problem for computing the exponential amplification rate of double-stranded DNA. The scheme is demonstrated using a simplified model of a Rayleigh-Bénard cell. In contrast to what may have been anticipated, diffusion tends to enhance the growth rate. The present model, intended to be used as a template for more device-specific analyses, provides a starting point for understanding the effects of the competing mechanisms (reaction, convection and diffusion) upon the amplification efficiency.

  6. Molecular modeling of the reaction pathway and hydride transfer reactions of HMG-CoA reductase.

    PubMed

    Haines, Brandon E; Steussy, C Nicklaus; Stauffacher, Cynthia V; Wiest, Olaf

    2012-10-01

    HMG-CoA reductase catalyzes the four-electron reduction of HMG-CoA to mevalonate and is an enzyme of considerable biomedical relevance because of the impact of its statin inhibitors on public health. Although the reaction has been studied extensively using X-ray crystallography, there are surprisingly no computational studies that test the mechanistic hypotheses suggested for this complex reaction. Theozyme and quantum mechanical (QM)/molecular mechanical (MM) calculations up to the B3LYP/6-31g(d,p)//B3LYP/6-311++g(2d,2p) level of theory were employed to generate an atomistic description of the enzymatic reaction process and its energy profile. The models generated here predict that the catalytically important Glu83 is protonated prior to hydride transfer and that it acts as the general acid or base in the reaction. With Glu83 protonated, the activation energies calculated for the sequential hydride transfer reactions, 21.8 and 19.3 kcal/mol, are in qualitative agreement with the experimentally determined rate constant for the entire reaction (1 s(-1) to 1 min(-1)). When Glu83 is not protonated, the first hydride transfer reaction is predicted to be disfavored by >20 kcal/mol, and the activation energy is predicted to be higher by >10 kcal/mol. While not involved in the reaction as an acid or base, Lys267 is critical for stabilization of the transition state in forming an oxyanion hole with the protonated Glu83. Molecular dynamics simulations and MM/Poisson-Boltzmann surface area free energy calculations predict that the enzyme active site stabilizes the hemithioacetal intermediate better than the aldehyde intermediate. This suggests a mechanism in which cofactor exchange occurs before the breakdown of the hemithioacetal. Slowing the conversion to aldehyde would provide the enzyme with a mechanism to protect it from solvent and explain why the free aldehyde is not observed experimentally. Our results support the hypothesis that the pK(a) of an active site acidic

  7. Three Dimensional Thermal Abuse Reaction Model for Lithium Ion Batteries

    2006-06-29

    Three dimensional computer models for simulating thermal runaway of lithium ion battery was developed. The three-dimensional model captures the shapes and dimensions of cell components and the spatial distributions of materials and temperatures, so we could consider the geometrical features, which are critical especially in large cells. An array of possible exothermic reactions, such as solid-electrolyte-interface (SEI) layer decomposition, negative active/electrolyte reaction, and positive active/electrolyte reaction, were considered and formulated to fit experimental data frommore » accelerating rate calorimetry and differential scanning calorimetry. User subroutine code was written to implement NREL developed approach and to utilize a commercially available solver. The model is proposed to use for simulation a variety of lithium-ion battery safety events including thermal heating and short circuit.« less

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1994-04-01

    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.

  10. Concerted reactions of polynuclear metalloenzymes and their functional chemical models

    NASA Astrophysics Data System (ADS)

    Dzhabiev, T. S.; Shilov, A. E.

    2011-03-01

    The mechanisms of the many-electron oxidation of water by a chemical model of the manganese oxidase cofactor in photosynthesis photosystem II (manganese(IV) clusters) and nitrogen reduction in chemical models of nitrogenase cofactor (vanadium(II) and molybdenum(III) clusters) were considered. The hypothesis was suggested according to which polynuclear enzyme cofactors and their functional chemical models performed two important functions, catalyzed noncomplementary processes and effected many-substrate concerted reactions with decreased activation energies.

  11. 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.

  12. CSIRO's multiphase reaction models and their industrial applications

    NASA Astrophysics Data System (ADS)

    Zhang, L.; Jahanshahi, S.; Sun, S.; Chen, C.; Bourke, B.; Wright, S.; Somerville, M.

    2002-11-01

    The status and ongoing work on a multiphase reaction model developed at the Commonwealth Scientific & Industrial Research Organization are outlined in this article. The package enables metallurgists to simulate reactions in pyrometallurgical processes with respect to equilibrium between various phases and to calculate slag viscosity at elevated temperatures. The models have been validated against measurements on physico-chemical properties of melts and solid phases produced in industrial processes. A number of examples of the application of the package to ferrous and non-ferrous smelting and refining processes are presented.

  13. 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

  14. Three-reaction model for the anaerobic digestion of microalgae.

    PubMed

    Mairet, Francis; Bernard, Olivier; Cameron, Elliot; Ras, Monique; Lardon, Laurent; Steyer, Jean-Philippe; Chachuat, Benoît

    2012-02-01

    Coupling an anaerobic digester to a microalgal culture has received increasing attention as an alternative process for combined bioenergy production and depollution. In this article, a dynamic model for anaerobic digestion of microalgae is developed with the aim of improving the management of such a coupled system. This model describes the dynamics of inorganic nitrogen and volatile fatty acids since both can lead to inhibition and therefore process instability. Three reactions are considered: Two hydrolysis-acidogenesis steps in parallel for sugars/lipids and for proteins, followed by a methanogenesis step. The proposed model accurately reproduces experimental data for anaerobic digestion of the freshwater microalgae Chlorella vulgaris with an organic loading rate of 1 gCOD L(-1) d(-1). In particular, the three-reaction pathway allows to adequately represent the observed decoupling between biogas production and nitrogen release. The reduced complexity of this model makes it suitable for developing advanced, model-based control and monitoring strategies.

  15. 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.

  16. Advanced modeling of reaction cross sections for light nuclei

    SciTech Connect

    Resler, D.A.

    1991-01-01

    The shell model/R-matrix technique of calculating nuclear reaction cross sections for light projectiles incident on light nuclei is discussed, particularly in the application of the technique to thermonuclear reactions. Details are presented on the computational methods for the shell model which display how easily the calculations can be performed. Results of the shell model/R-matrix technique are discussed as are some of the problems encountered in picking an appropriate nucleon-nucleon interaction for the large model spaces which must be used for current problems. The status of our work on developing an effective nucleon-nucleon interaction for use in large-basis shell model calculations is presented. This new interaction is based on a combination of global constraints and microscopic nuclear data. 23 refs., 6 figs., 2 tabs.

  17. Modelling population growth with delayed nonlocal reaction in 2-dimensions.

    PubMed

    Liang, Dong; Wu, Jianhong; Zhang, Fan

    2005-01-01

    In this paper, we consider the population growth of a single species living in a two-dimensional spatial domain. New reaction-difusion equation models with delayed nonlocal reaction are developed in two-dimensional bounded domains combining diferent boundary conditions. The important feature of the models is the reflection of the joint efect of the difusion dynamics and the nonlocal maturation delayed efect. We consider and ana- lyze numerical solutions of the mature population dynamics with some wellknown birth functions. In particular, we observe and study the occurrences of asymptotically stable steady state solutions and periodic waves for the two-dimensional problems with nonlocal delayed reaction. We also investigate numerically the efects of various parameters on the period, the peak and the shape of the periodic wave as well as the shape of the asymptotically stable steady state solution.

  18. A Generic Microdisturbanace Transmissibility Model For Reaction Wheels

    NASA Astrophysics Data System (ADS)

    Penate Castro, Jose; Seiler, Rene

    2012-07-01

    The increasing demand for space missions with high- precision pointing requirements for their payload instruments is underlining the importance of studying the impact of micro-level disturbances on the overall performance of spacecraft. For example, a satellite with an optical telescope taking high-resolution images might be very sensitive to perturbations, generated by moving equipment and amplified by the structure of the equipment itself as well as that of the host spacecraft that is accommodating both, the sources of mechanical disturbances and sensitive payload instruments. One of the major sources of mechanical disturbances inside a satellite may be found with reaction wheels. For investigation of their disturbance generation and propagation characteristics, a finite element model with parametric geometry definition has been developed. The model covers the main structural features of typical reaction wheel assemblies and can be used for a transmissibility representation of the equipment. With the parametric geometry definition approach, a wide range of different reaction wheel types and sizes can be analysed, without the need for (re-)defining an individual reaction wheel configuration from scratch. The reaction wheel model can be combined with a finite element model of the spacecraft structure and the payload for an end-to-end modelling and simulation of the microdisturbance generation and propagation. The finite element model has been generated in Patran® Command Language (PCL), which provides a powerful and time-efficient way to change parameters in the model, for creating a new or modifying an existing geometry, without requiring comprehensive manual interactions in the modelling pre-processor. As part of the overall modelling approach, a tailored structural model of the mechanical ball bearings has been implemented, which is one of the more complex problems to deal with, among others, due to the anisotropic stiffness and damping characteristics

  19. 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...

  20. 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.

  1. Modeling charge transfer in the photosynthetic reaction center

    NASA Astrophysics Data System (ADS)

    Pudlak, Michal; Pinčak, Richard

    2003-12-01

    In this work, we present a model to elucidate the unidirectionality of the primary charge-separation process in the bacterial reaction centers. We have used a model of three sites/molecules with electron transfer beginning at site 1 with an option to proceed to site 2 or site 3. We used a stochastic model with arbitrary correlation functions. We get the quantum yields of electron escape via the sites 2,3 in two limiting cases that correspond to a spectral density of underdamped and overdamped Brownian oscillator. In the fast modulation limit of an overdamped regime we get the effect, which was named “fear of death,” in which for strong enough sink parameters the electron has a tendency to avoid the place with greater sink. The presented model was used to provide a plausible explanation of the temperature dependence of the quantum yields of the Rhodobacter sphaeroides photosynthetic reaction center in the high-temperature regime.

  2. Cohabitation reaction-diffusion model for virus focal infections

    NASA Astrophysics Data System (ADS)

    Amor, Daniel R.; Fort, Joaquim

    2014-12-01

    The propagation of virus infection fronts has been typically modeled using a set of classical (noncohabitation) reaction-diffusion equations for interacting species. However, for some single-species systems it has been recently shown that noncohabitation reaction-diffusion equations may lead to unrealistic descriptions. We argue that previous virus infection models also have this limitation, because they assume that a virion can simultaneously reproduce inside a cell and diffuse away from it. For this reason, we build a several-species cohabitation model that does not have this limitation. Furthermore, we perform a sensitivity analysis for the most relevant parameters of the model, and we compare the predicted infection speed with observed data for two different strains of the T7 virus.

  3. 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.

  4. 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

  5. Reaction-diffusion processes and metapopulation models in heterogeneous networks

    NASA Astrophysics Data System (ADS)

    Colizza, Vittoria; Pastor-Satorras, Romualdo; Vespignani, Alessandro

    2007-04-01

    Dynamical reaction-diffusion processes and metapopulation models are standard modelling approaches for a wide array of phenomena in which local quantities-such as density, potentials and particles-diffuse and interact according to the physical laws. Here, we study the behaviour of the basic reaction-diffusion process (given by the reaction steps B-->A and B+A-->2B) defined on networks with heterogeneous topology and no limit on the nodes' occupation number. We investigate the effect of network topology on the basic properties of the system's phase diagram and find that the network heterogeneity sustains the reaction activity even in the limit of a vanishing density of particles, eventually suppressing the critical point in density-driven phase transitions, whereas phase transition and critical points independent of the particle density are not altered by topological fluctuations. This work lays out a theoretical and computational microscopic framework for the study of a wide range of realistic metapopulation and agent-based models that include the complex features of real-world networks.

  6. 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.

  7. Simple model for lambda-doublet propensities in bimolecular reactions

    NASA Technical Reports Server (NTRS)

    Bronikowski, Michael J.; Zare, Richard N.

    1990-01-01

    A simple geometric model is presented to account for lambda-doublet propensities in bimolecular reactions A + BC - AB + C. It applies to reactions in which AB is formed in a pi state, and in which the unpaired molecular orbital responsible for lambda-doubling arises from breaking the B-C bond. The lambda-doublet population ratio is predicted to be 2:1 provided that: (1) the motion of A in the transition state determines the plane of rotation of AB; (2) the unpaired pi orbital lying initially along the B-C bond may be resolved into a projection onto the AB plane of rotation and a projection perpendicular to this plane; (3) there is no preferred geometry for dissociation of ABC. The 2:1 lambda-doublet ratio is the 'unconstrained dynamics prior' lambda-doublet distribution for such reactions.

  8. Fluid dynamic modeling of nano-thermite reactions

    SciTech Connect

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

    2014-03-14

    This paper presents a direct numerical method based on gas dynamic equations to predict pressure evolution during the discharge of nanoenergetic materials. The direct numerical method provides for modeling reflections of the shock waves from the reactor walls that generates pressure-time fluctuations. The results of gas pressure prediction are consistent with the experimental evidence and estimates based on the self-similar solution. Artificial viscosity provides sufficient smoothing of shock wave discontinuity for the numerical procedure. The direct numerical method is more computationally demanding and flexible than self-similar solution, in particular it allows study of a shock wave in its early stage of reaction and allows the investigation of “slower” reactions, which may produce weaker shock waves. Moreover, numerical results indicate that peak pressure is not very sensitive to initial density and reaction time, providing that all the material reacts well before the shock wave arrives at the end of the reactor.

  9. 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

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

    PubMed

    Niu, Yuanling; Burrage, Kevin; Chen, Luonan

    2016-05-01

    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.

  11. Predictability and reduced order modeling in stochastic reaction networks.

    SciTech Connect

    Najm, Habib N.; Debusschere, Bert J.; Sargsyan, Khachik

    2008-10-01

    Many systems involving chemical reactions between small numbers of molecules exhibit inherent stochastic variability. Such stochastic reaction networks are at the heart of processes such as gene transcription, cell signaling or surface catalytic reactions, which are critical to bioenergy, biomedical, and electrical storage applications. The underlying molecular reactions are commonly modeled with chemical master equations (CMEs), representing jump Markov processes, or stochastic differential equations (SDEs), rather than ordinary differential equations (ODEs). As such reaction networks are often inferred from noisy experimental data, it is not uncommon to encounter large parametric uncertainties in these systems. Further, a wide range of time scales introduces the need for reduced order representations. Despite the availability of mature tools for uncertainty/sensitivity analysis and reduced order modeling in deterministic systems, there is a lack of robust algorithms for such analyses in stochastic systems. In this talk, we present advances in algorithms for predictability and reduced order representations for stochastic reaction networks and apply them to bistable systems of biochemical interest. To study the predictability of a stochastic reaction network in the presence of both parametric uncertainty and intrinsic variability, an algorithm was developed to represent the system state with a spectral polynomial chaos (PC) expansion in the stochastic space representing parametric uncertainty and intrinsic variability. Rather than relying on a non-intrusive collocation-based Galerkin projection [1], this PC expansion is obtained using Bayesian inference, which is ideally suited to handle noisy systems through its probabilistic formulation. To accommodate state variables with multimodal distributions, an adaptive multiresolution representation is used [2]. As the PC expansion directly relates the state variables to the uncertain parameters, the formulation lends

  12. 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

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    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.

  15. 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.

  16. 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.

  17. 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.

  18. Mathematical modeling of precipitation and dissolution reactions in microbiological systems.

    PubMed

    Rittmann, Bruce E; Banaszak, James E; VanBriesen, Jeanne M; Reed, Donald T

    2002-01-01

    We expand the biogeochemical model CCBATCH to include a precipitation/dissolution sub-model that contains kinetic and equilibrium options. This advancement extends CCBATCH's usefulness to situations in which microbial reactions cause or are affected by formation or dissolution of a solid phase. The kinetic option employs a rate expression that explicitly includes the intrinsic kinetics for reaction or mass-transport control, the difference from thermodynamic equilibrium, and the aqueous concentration of the rate-limiting metal or ligand. The equilibrium feature can be used alone, and it also serves as check that the kinetic rate never is too fast and "overshoots" equilibrium. The features of the expanded CCBATCH are illustrated by an example in which the precipitation of Fe(OH)3(s) allows the biodegradation of citric acid, even though complexes are strong and not bioavailable. Precipitation releases citrate ligand, and biodegradation of the citrate increases the pH.

  19. 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.

  20. A model reduction method for biochemical reaction networks

    PubMed Central

    2014-01-01

    Background In this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill kinetics. The method proceeds by a stepwise reduction in the number of complexes, defined as the left and right-hand sides of the reactions in the network. It is based on the Kron reduction of the weighted Laplacian matrix, which describes the graph structure of the complexes and reactions in the network. It does not rely on prior knowledge of the dynamic behaviour of the network and hence can be automated, as we demonstrate. The reduced network has fewer complexes, reactions, variables and parameters as compared to the original network, and yet the behaviour of a preselected set of significant metabolites in the reduced network resembles that of the original network. Moreover the reduced network largely retains the structure and kinetics of the original model. Results We apply our method to a yeast glycolysis model and a rat liver fatty acid beta-oxidation model. When the number of state variables in the yeast model is reduced from 12 to 7, the difference between metabolite concentrations in the reduced and the full model, averaged over time and species, is only 8%. Likewise, when the number of state variables in the rat-liver beta-oxidation model is reduced from 42 to 29, the difference between the reduced model and the full model is 7.5%. Conclusions The method has improved our understanding of the dynamics of the two networks. We found that, contrary to the general disposition, the first few metabolites which were deleted from the network during our stepwise reduction approach, are not those with the shortest convergence times. It shows that our reduction approach performs differently from other approaches that are based on time-scale separation. The method can be used to facilitate fitting of the parameters or to embed a detailed model of

  1. 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

  2. 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

  3. 14 CFR 1260.53 - 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. 1260.53 Section 1260.53 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION GRANTS AND COOPERATIVE AGREEMENTS General Special Conditions § 1260.53 Incremental funding. Incremental Funding October 2000...

  4. 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 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION GRANTS AND COOPERATIVE AGREEMENTS General Special Conditions § 1260.53 Incremental funding. Incremental Funding October 2000 (a) Only $___ of...

  5. 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... Agreement, as required, until it is fully funded. Any work beyond the funding limit will be at the...

  6. 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... Agreement, as required, until it is fully funded. Any work beyond the funding limit will be at the...

  7. 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... Agreement, as required, until it is fully funded. Any work beyond the funding limit will be at the...

  8. 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... Agreement, as required, until it is fully funded. Any work beyond the funding limit will be at the...

  9. 14 CFR 1260.53 - 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. 1260.53 Section 1260.53 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION GRANTS AND COOPERATIVE AGREEMENTS General Special Conditions § 1260.53 Incremental funding. Incremental Funding October 2000...

  10. 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 1260.53 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION GRANTS AND COOPERATIVE AGREEMENTS General Special Conditions § 1260.53 Incremental funding. Incremental Funding October 2000...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. Reaction-diffusion models of within-feather pigmentation patterning.

    PubMed

    Prum, Richard O; Williamson, Scott

    2002-04-22

    Feathers are complex, branched keratin structures that exhibit a diversity of pigmentation patterns. Feather pigments are transferred into developing feather keratinocytes from pigment cells that migrate into the tubular feather germ from the dermis. Within-feather pigment patterns are determined by differential pigmentation of keratinocytes within independent barb ridges during feather development. Little is known about the molecular mechanisms that determine which keratinocytes receive pigment. We apply reaction-diffusion models to the growth of within-feather pigment patterns based on a realistic model of feather growth. These models accurately simulate the growth of a diversity of the within-feather pigmentation patterns found in real feathers, including a central patch, a 'hollow' central patch, concentric central patches, bars, chevrons, a central circular spot, rows of paired spots, and arrays of offset dots. The models can also simulate the complex transitions between distinct pigmentation patterns among feathers observed in real avian plumages, including transitions from bars to chevrons, bars to paired dots, and bars to arrays of dots. The congruence between the developmental dynamics of the simulated and observed feather patterns indicates that the reaction-diffusion models provide a realistic and accurate description of the determination of pigment pattern within avian feather follicles. The models support the hypothesis that within-feather pigmentation patterning is determined by antagonistic interactions among molecular expression gradients within the tubular follicle and feather germ.

  17. Turing instability in reaction-diffusion models on complex networks

    NASA Astrophysics Data System (ADS)

    Ide, Yusuke; Izuhara, Hirofumi; Machida, Takuya

    2016-09-01

    In this paper, the Turing instability in reaction-diffusion models defined on complex networks is studied. Here, we focus on three types of models which generate complex networks, i.e. the Erdős-Rényi, the Watts-Strogatz, and the threshold network models. From analysis of the Laplacian matrices of graphs generated by these models, we numerically reveal that stable and unstable regions of a homogeneous steady state on the parameter space of two diffusion coefficients completely differ, depending on the network architecture. In addition, we theoretically discuss the stable and unstable regions in the cases of regular enhanced ring lattices which include regular circles, and networks generated by the threshold network model when the number of vertices is large enough.

  18. Heterogeneous reactions in a stratospheric box model: A sensitivity study

    NASA Astrophysics Data System (ADS)

    Danilin, Michael Y.; McConnell, John C.

    1994-12-01

    Recent laboratory data concerning the reactions of HCl and HOx on/in sulfuric acid aerosol (Hanson et al., 1994), N2O5 and ClONO2 hydrolysis on the frozen aerosol (Hanson and Ravishankara, 1993a) and the temperature dependence of the HNO3 absorption cross section (Burkholder et al., 1993) indicate that a reevaluation of the role of heterogeneous reactions in the chemical balance of the stratosphere is required. A chemical module prepared for a three-dimensional (3-D) global chemistry transport model (CTM) and a general circulation model (GCM) has been used to carry out a sensitivity study of the effects of heterogeneous reactions on/in the sulfate aerosol and on the polar stratospheric cloud (PSC) particles. We present here results for the latitudes 60°S, 70°S and 75°S at the 50-mbar level. Our findings indicate that (1) the new values of the HNO3 cross sections result in lower mixing ratios for NOx and make ozone more vulnerable to catalytic destruction by ClOx; (2) the effect of the heterogeneous reactions OH + HNO3(a) → H2O + NO3 and HO2 +HO2(a) → H2O2 + O2 are small in comparison with the same gas phase reactions and play a negligible role for the ozone balance; (3) the HCl reactions in the sulfuric acid aerosol at 60°S and 70°S increase the chlorine activation up to 0.53 parts per billion by volume (ppbv) and 0.72 ppbv, respectively, for liquid aerosol and up to 0.87 ppbv for frozen aerosol at 70°S for volcanic conditions and this results in considerable ozone depletion at these latitudes; (4) studying the ozone "hole" phenomenon, we have considered the different initial ratios of ClONO2/HCl, of N2O5, galactic cosmic rays (GCRs), and longer lifetimes for the PSC. We have speculated an existence of the reaction N2O5 + HCl(a) → ClNO2 + HNO3.

  19. Universal Model for Exoergic Bimolecular Reactions and Inelastic Processes

    NASA Astrophysics Data System (ADS)

    Gao, Bo

    2010-12-01

    From a rigorous multichannel quantum-defect formulation of bimolecular processes, we derive a fully quantal and analytic model for the total rate of exoergic bimolecular reactions or inelastic processes that is applicable over a wide range of temperatures including the ultracold regime. The theory establishes a connection between the ultracold chemistry and the regular chemistry by showing that the same theory that gives the quantum threshold behavior agrees with the classical Gorin model at higher temperatures. In between, it predicts that the rates for identical bosonic molecules and distinguishable molecules would first decrease with temperature outside of the Wigner threshold region, before rising after a minimum is reached.

  20. Mathematical Identification of Critical Reactions in the Interlocked Feedback Model

    PubMed Central

    Kurata, Hiroyuki; Tanaka, Takayuki; Ohnishi, Fumitaka

    2007-01-01

    Dynamic simulations are necessary for understanding the mechanism of how biochemical networks generate robust properties to environmental stresses or genetic changes. Sensitivity analysis allows the linking of robustness to network structure. However, it yields only local properties regarding a particular choice of plausible parameter values, because it is hard to know the exact parameter values in vivo. Global and firm results are needed that do not depend on particular parameter values. We propose mathematical analysis for robustness (MAR) that consists of the novel evolutionary search that explores all possible solution vectors of kinetic parameters satisfying the target dynamics and robustness analysis. New criteria, parameter spectrum width and the variability of solution vectors for parameters, are introduced to determine whether the search is exhaustive. In robustness analysis, in addition to single parameter sensitivity analysis, robustness to multiple parameter perturbation is defined. Combining the sensitivity analysis and the robustness analysis to multiple parameter perturbation enables identifying critical reactions. Use of MAR clearly identified the critical reactions responsible for determining the circadian cycle in the Drosophila interlocked circadian clock model. In highly robust models, while the parameter vectors are greatly varied, the critical reactions with a high sensitivity are uniquely determined. Interestingly, not only the per-tim loop but also the dclk-cyc loop strongly affect the period of PER, although the dclk-cyc loop hardly changes its amplitude and it is not potentially influential. In conclusion, MAR is a powerful method to explore wide parameter space without human-biases and to link a robust property to network architectures without knowing the exact parameter values. MAR identifies the reactions critically responsible for determining the period and amplitude in the interlocked feedback model and suggests that the circadian

  1. 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

  2. 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

  3. 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.

  4. Prediction of adverse drug reactions using decision tree modeling.

    PubMed

    Hammann, F; Gutmann, H; Vogt, N; Helma, C; Drewe, J

    2010-07-01

    Drug safety is of great importance to public health. The detrimental effects of drugs not only limit their application but also cause suffering in individual patients and evoke distrust of pharmacotherapy. For the purpose of identifying drugs that could be suspected of causing adverse reactions, we present a structure-activity relationship analysis of adverse drug reactions (ADRs) in the central nervous system (CNS), liver, and kidney, and also of allergic reactions, for a broad variety of drugs (n = 507) from the Swiss drug registry. Using decision tree induction, a machine learning method, we determined the chemical, physical, and structural properties of compounds that predispose them to causing ADRs. The models had high predictive accuracies (78.9-90.2%) for allergic, renal, CNS, and hepatic ADRs. We show the feasibility of predicting complex end-organ effects using simple models that involve no expensive computations and that can be used (i) in the selection of the compound during the drug discovery stage, (ii) to understand how drugs interact with the target organ systems, and (iii) for generating alerts in postmarketing drug surveillance and pharmacovigilance.

  5. 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/.

  6. Reactions of Lignin Model Compounds in Ionic Liquids

    SciTech Connect

    Holladay, John E.; Binder, Joseph B.; Gray, Michel J.; White, James F.; Zhang, Z. Conrad

    2009-09-15

    Lignin, a readily available form of biomass, awaits novel chemistry for converting it to valuable aromatic chemicals. Recent work has demonstrated that ionic liquids are excellent solvents for processing woody biomass and lignin. Seeking to exploit ionic liquids as media for depolymerization of lignin, we investigated reactions of lignin model compounds in these solvents. Using Brønsted acid catalysts in 1-ethyl-3-methylimidazolium triflate at moderate temperatures, we obtained up to 11.6% yield of the dealkylation product guaiacol from the model compound eugenol and cleaved phenethyl phenyl ether, a model for lignin ethers. Despite these successes, acid catalysis failed in dealkylation of the unsaturated model compound 4-ethylguaiacol and did not produce monomeric products from organosolv lignin, demonstrating that further work is required to understand the complex chemistry of lignin depolymerization.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Modelling Violent Reaction Following Low Speed Impact on Confined Explosives

    NASA Astrophysics Data System (ADS)

    Curtis, John; Jones, Andrew; Hughes, Christopher; Reaugh, John

    2011-06-01

    To ensure the safe storage and deployment of explosives it is important to understand the mechanisms that give rise to ignition and reaction growth in low speed impacts. The LLNL High Explosive Response to Mechanical Stimulus (HERMES) material model, integrated in LS-DYNA, has been developed to model the progress of the reaction after such an impact. The low speed impact characteristics of an HMX based formulation have been determined in the AWE Steven Test. Axisymmetric simulations have been performed to determine the characteristics of the model. The sensitivity study included looking at the influence of friction, material strength and confinement. By comparing the experimental and calculated results, the key parameters which determine the response in this configuration have been determined. The model qualitatively predicts the point of ignition within the vehicle. Future refinements are discussed. JER's activity was performed under the auspices of the US DOE by LLNL under Contract DE-AC52-07NA27344, and partially funded by the Joint US DoD/DOE Munitions Technology Development Program.

  12. 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.

  13. 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.

  14. Reaction times to weak test lights. [psychophysics biological model

    NASA Technical Reports Server (NTRS)

    Wandell, B. A.; Ahumada, P.; Welsh, D.

    1984-01-01

    Maloney and Wandell (1984) describe a model of the response of a single visual channel to weak test lights. The initial channel response is a linearly filtered version of the stimulus. The filter output is randomly sampled over time. Each time a sample occurs there is some probability increasing with the magnitude of the sampled response - that a discrete detection event is generated. Maloney and Wandell derive the statistics of the detection events. In this paper a test is conducted of the hypothesis that the reaction time responses to the presence of a weak test light are initiated at the first detection event. This makes it possible to extend the application of the model to lights that are slightly above threshold, but still within the linear operating range of the visual system. A parameter-free prediction of the model proposed by Maloney and Wandell for lights detected by this statistic is tested. The data are in agreement with the prediction.

  15. 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

  16. Deuterium cluster model for low energy nuclear reactions (LENR)

    NASA Astrophysics Data System (ADS)

    Miley, George; Hora, Heinrich

    2007-11-01

    For studying the possible reactions of high density deuterons on the background of a degenerate electron gas, a summary of experimental observations resulted in the possibility of reactions in pm distance and more than ksec duration similar to the K-shell electron capture [1]. The essential reason was the screening of the deuterons by a factor of 14 based on the observations. Using the bosonic properties for a cluster formation of the deuterons and a model of compound nuclear reactions [2], the measured distribution of the resulting nuclei may be explained as known from the Maruhn-Greiner theory for fission. The local maximum of the distribution at the main minimum indicates the excited states of the compound nuclei during their intermediary state. This measured local maximum may be an independent proof for the deuteron clusters at LENR. [1] H. Hora, G.H. Miley et al. Physics Letters A175, 138 (1993) [2] H. Hora and G.H. Miley, APS March Meeting 2007, Program p. 116

  17. 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.

  18. Parametric Pattern Selection in a Reaction-Diffusion Model

    PubMed Central

    Stich, Michael; Ghoshal, Gourab; Pérez-Mercader, Juan

    2013-01-01

    We compare spot patterns generated by Turing mechanisms with those generated by replication cascades, in a model one-dimensional reaction-diffusion system. We determine the stability region of spot solutions in parameter space as a function of a natural control parameter (feed-rate) where degenerate patterns with different numbers of spots coexist for a fixed feed-rate. While it is possible to generate identical patterns via both mechanisms, we show that replication cascades lead to a wider choice of pattern profiles that can be selected through a tuning of the feed-rate, exploiting hysteresis and directionality effects of the different pattern pathways. PMID:24204813

  19. Reaction-diffusion modelling of bacterial colony patterns

    NASA Astrophysics Data System (ADS)

    Mimura, Masayasu; Sakaguchi, Hideo; Matsushita, Mitsugu

    2000-07-01

    It is well known from experiments that bacterial species Bacillus subtilis exhibit various colony patterns. These are essentially classified into five types in the morphological diagram, depending on the substrate softness and nutrient concentration. (A) diffusion-limited aggregation-like; (B) Eden-like; (C) concentric ring-like; (D) disk-like; and (E) dense branching morphology-like. There arises the naive question of whether the diversity of colony patterns observed in experiments is caused by different effects or governed by the same underlying principles. Our research has led us to propose reaction-diffusion models to describe the morphological diversity of colony patterns except for Eden-like ones.

  20. 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.

  1. Triple-α reaction rate constrained by stellar evolution models

    NASA Astrophysics Data System (ADS)

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

    2012-11-01

    We investigate the quantitative constraint on the triple-α 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/Msolar<=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 > 10Msolar) 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/Msolar<=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-α 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 ν > 10 at T = 1-1.2×108K where the cross section is proportional to Tν. 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 ~ 10-29 cm6 s-1 mole-2 at ~ 107.8 K, which corresponds to about three orders of magnitude larger than that of the NACRE compilation.

  2. 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.

  3. 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.

  4. MODELING OF SYNGAS REACTIONS AND HYDROGEN GENERATION OVER SULFIDES

    SciTech Connect

    Kamil Klier; Jeffery A. Spirko; Michael L. Neiman

    2004-10-01

    The objective of the research is to analyze pathways of reactions of hydrogen with oxides of carbon over sulfides, and to predict which characteristics of the sulfide catalyst (nature of metal, defect structure) give rise to the lowest barriers toward oxygenated hydrocarbon product. Reversal of these pathways entails the generation of hydrogen, which is also proposed for study. During this study, adsorption reactions of H atoms and H{sub 2} molecules with MoS{sub 2}, both in molecular and solid form, have been modeled using high-level density functional theory. The relative stabilities of pure MoS{sub 2} edges were calculated and small clusters exhibiting properties of the edges were modeled. The results were finalized and published in the journal ''Surface Science''. Hydrogen adsorption energies on both the edges and the clusters were calculated, and the thermodynamics of hydrogen adsorption on both systems were evaluated. The adsorption locations and vibrational frequencies were also determined. These additional results were published in a second paper in ''Surface Science''. Most recently, the bonding and effect of alkali and transition metal ions was investigated on the MoS{sub 2} clusters. Potassium atoms bind to the clusters and increase the binding of hydrogen to the clusters while reducing the activation barriers for hydrogen adsorption. Silver attaches to the Mo7S14 cluster and donates its odd electron to the nearby Mo atoms and should have a similar effect to hydrogen as potassium does.

  5. 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.

  6. 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.

  7. A reaction-diffusion model of human brain development.

    PubMed

    Lefèvre, Julien; Mangin, Jean-François

    2010-04-01

    Cortical folding exhibits both reproducibility and variability in the geometry and topology of its patterns. These two properties are obviously the result of the brain development that goes through local cellular and molecular interactions which have important consequences on the global shape of the cortex. Hypotheses to explain the convoluted aspect of the brain are still intensively debated and do not focus necessarily on the variability of folds. Here we propose a phenomenological model based on reaction-diffusion mechanisms involving Turing morphogens that are responsible for the differential growth of two types of areas, sulci (bottom of folds) and gyri (top of folds). We use a finite element approach of our model that is able to compute the evolution of morphogens on any kind of surface and to deform it through an iterative process. Our model mimics the progressive folding of the cortical surface along foetal development. Moreover it reveals patterns of reproducibility when we look at several realizations of the model from a noisy initial condition. However this reproducibility must be tempered by the fact that a same fold engendered by the model can have different topological properties, in one or several parts. These two results on the reproducibility and variability of the model echo the sulcal roots theory that postulates the existence of anatomical entities around which the folding organizes itself. These sulcal roots would correspond to initial conditions in our model. Last but not least, the parameters of our model are able to produce different kinds of patterns that can be linked to developmental pathologies such as polymicrogyria and lissencephaly. The main significance of our model is that it proposes a first approach to the issue of reproducibility and variability of the cortical folding. PMID:20421989

  8. 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

    ... Commenced Construction On or Before November 30, 1999 Model Rule-Increments of Progress § 60.2590 When must... increments of progress must be postmarked no later than 10 business days after the compliance date for...

  9. 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.

  10. Improved VSM for Incremental Text Classification

    NASA Astrophysics Data System (ADS)

    Yang, Zhen; Lei, Jianjun; Wang, Jian; Zhang, Xing; Guo, Jim

    2008-11-01

    As a simple classification method VSM has been widely applied in text information processing field. There are some problems for traditional VSM to select a refined vector model representation, which can make a good tradeoff between complexity and performance, especially for incremental text mining. To solve these problems, in this paper, several improvements, such as VSM based on improved TF, TFIDF and BM25, are discussed. And then maximum mutual information feature selection is introduced to achieve a low dimension VSM with less complexity, and at the same time keep an acceptable precision. The experimental results of spam filtering and short messages classification shows that the algorithm can achieve higher precision than existing algorithms under same conditions.

  11. 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.

  12. 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

  13. 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

  14. Antioxidative properties of Iberis amara extracts in biochemical model reactions.

    PubMed

    Schempp, Harald; Toth, Angela; Weiser, Dieter; Elstner, Erich F

    2003-01-01

    Gastro-intestinal disorders such as the non-ulcer dyspepsia and irritable bowel syndrome expatiate on/with inflammatory processes of the gastro-intestinal mucosa. Iberogast is used in treatment of such disorders. Iberis amara L. extract (IAE) is one of nine components of the drug. There is increasing evidence that mediators of inflammation processes in the stomach and intestine include reactive oxygen species (ROS), arising from several enzymic reactions characteristic for inflammatory events. In this study it was shown that Iberis amara extract (STW 6) has the potential for scavenging ROS, dependent on the individual test system. Biochemical model reactions relevant for the formation of ROS in vivo at inflammatory sites were used. Inhibition of the formation of ROS could be shown to be excellent in test systems known to preferentially produce reactive species (myeloperoxidase-generated HOCl, peroxynitrite) with high affinities to sulfur-containing compounds, e.g. mustard oil glycosides such as glucoiberin. Furthermore ROS, generated during xanthine oxidase (XOD)-catalysed oxidation of xanthine into uric acid, were also efficiently decreased by IAE. However, an inhibition of XOD could be excluded, but chelation of metal ions (Fe, Cu) decreasing their redox-cycling activities seems to play a role. A major activity of IAE proved to represent inhibition of lipid peroxidation processes, shown as delay of the lag phase of the Cu(II)-induced LDL oxidation as well as protection of alpha-linolenic acid from peroxidation by singlet oxygen.

  15. A multi-pathway model for photosynthetic reaction center.

    PubMed

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

    2016-03-28

    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. PMID:27036480

  16. 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.

  17. Prediction of Path Deviation in Robot Based Incremental Sheet Metal Forming by Means of a New Solid-Shell Finite Element Technology and a Finite Elastoplastic Model with Combined Hardening

    NASA Astrophysics Data System (ADS)

    Kiliclar, Yalin; Laurischkat, Roman; Vladimirov, Ivaylo N.; Reese, Stefanie

    2011-08-01

    The presented project deals with a robot based incremental sheet metal forming process, which is called roboforming and has been developed at the Chair of Production Systems. It is characterized by flexible shaping using a freely programmable path-synchronous movement of two industrial robots. The final shape is produced by the incremental infeed of the forming tool in depth direction and its movement along the part contour in lateral direction. However, the resulting geometries formed in roboforming deviate several millimeters from the reference geometry. This results from the compliance of the involved machine structures and the springback effects of the workpiece. The project aims to predict these deviations caused by resiliences and to carry out a compensative path planning based on this prediction. Therefore a planning tool is implemented which compensates the robots's compliance and the springback effects of the sheet metal. The forming process is simulated by means of a finite element analysis using a material model developed at the Institute of Applied Mechanics (IFAM). It is based on the multiplicative split of the deformation gradient in the context of hyperelasticity and combines nonlinear kinematic and isotropic hardening. Low-order finite elements used to simulate thin sheet structures, such as used for the experiments, have the major problem of locking, a nonphysical stiffening effect. For an efficient finite element analysis a special solid-shell finite element formulation based on reduced integration with hourglass stabilization has been developed. To circumvent different locking effects, the enhanced assumed strain (EAS) and the assumed natural strain (ANS) concepts are included in this formulation. Having such powerful tools available we obtain more accurate geometries.

  18. Photodynamic therapy: computer modeling of diffusion and reaction phenomena

    NASA Astrophysics Data System (ADS)

    Hampton, James A.; Mahama, Patricia A.; Fournier, Ronald L.; Henning, Jeffery P.

    1996-04-01

    We have developed a transient, one-dimensional mathematical model for the reaction and diffusion phenomena that occurs during photodynamic therapy (PDT). This model is referred to as the PDTmodem program. The model is solved by the Crank-Nicholson finite difference technique and can be used to predict the fates of important molecular species within the intercapillary tissue undergoing PDT. The following factors govern molecular oxygen consumption and singlet oxygen generation within a tumor: (1) photosensitizer concentration; (2) fluence rate; and (3) intercapillary spacing. In an effort to maximize direct tumor cell killing, the model allows educated decisions to be made to insure the uniform generation and exposure of singlet oxygen to tumor cells across the intercapillary space. Based on predictions made by the model, we have determined that the singlet oxygen concentration profile within the intercapillary space is controlled by the product of the drug concentration, and light fluence rate. The model predicts that at high levels of this product, within seconds singlet oxygen generation is limited to a small core of cells immediately surrounding the capillary. The remainder of the tumor tissue in the intercapillary space is anoxic and protected from the generation and toxic effects of singlet oxygen. However, at lower values of this product, the PDT-induced anoxic regions are not observed. An important finding is that an optimal value of this product can be defined that maintains the singlet oxygen concentration throughout the intercapillary space at a near constant level. Direct tumor cell killing is therefore postulated to depend on the singlet oxygen exposure, defined as the product of the uniform singlet oxygen concentration and the time of exposure, and not on the total light dose.

  19. 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.

  20. Spatially resolved flamelet statistics for reaction rate modeling

    SciTech Connect

    Chew, T.C.; Bray, K.N.C.; Britter, R.E. . Dept. of Engineering)

    1990-04-01

    Using two-dimensional laser sheet tomography of Bunsen flames, important spatial statistics relating to premixed turbulent combustion modeling are measured. The integral length scale of flame wrinkling, evaluated along contours of reaction progress variable ({bar {ital c}}), is found to be almost constant for all values of {bar {ital c}}. Its magnitude is measured to be very close to the integral length scale in the unreacted turbulent flow. The flamelet crossing angle distribution in the plane of visualization is found to vary along a {bar {ital c}} contour reflecting the nonhomogeneity in the flame, but the overall distributions for different {bar {ital c}} values are approximately the same. The overall mean cosine value is found to be very close to 0.5. Other parameters of interest, including {bar {ital c}} contours, flamelet crossing lengths, and crossing frequencies, are also examined.

  1. a Model Study of Complex Behavior in the Belousov - Reaction.

    NASA Astrophysics Data System (ADS)

    Lindberg, David Mark

    1988-12-01

    We have studied the complex oscillatory behavior in a model of the Belousov-Zhabotinskii (BZ) reaction in a continuously-fed stirred tank reactor (CSTR). The model consisted of a set of nonlinear ordinary differential equations derived from a reduced mechanism of the chemical system. These equations were integrated numerically on a computer, which yielded the concentrations of the constituent chemicals as functions of time. In addition, solutions were tracked as functions of a single parameter, the stability of the solutions was determined, and bifurcations of the solutions were located and studied. The intent of this study was to use this BZ model to explore further a region of complex oscillatory behavior found in experimental investigations, the most thorough of which revealed an alternating periodic-chaotic (P-C) sequence of states. A P-C sequence was discovered in the model which showed the same qualitative features as the experimental sequence. In order to better understand the P-C sequence, a detailed study was conducted in the vicinity of the P-C sequence, with two experimentally accessible parameters as control variables. This study mapped out the bifurcation sets, and included examination of the dynamics of the stable periodic, unstable periodic, and chaotic oscillatory motion. Observations made from the model results revealed a rough symmetry which suggests a new way of looking at the P-C sequence. Other nonlinear phenomena uncovered in the model were boundary and interior crises, several codimension-two bifurcations, and similarities in the shapes of areas of stability for periodic orbits in two-parameter space. Each earlier model study of this complex region involved only a limited one-parameter scan and had limited success in producing agreement with experiments. In contrast, for those regions of complex behavior that have been studied experimentally, the observations agree qualitatively with our model results. Several new predictions of the model

  2. Physics Based Reaction Burn Model Prediction of Reaction Initiation and Growth in RDX for Thin and Thick Impactor

    NASA Astrophysics Data System (ADS)

    Dwivedi, Sunil; Horie, Yasuyuki

    2011-06-01

    PBRB model for reactive composites simulates the reaction initiation and growth leading to detonation with built-in models for multiple individual as well as coupled phenomena: pre-existing statistical pore distribution, energy dissipation during shock loading and hot spot formations, surface temperature increase of the planar pore surfaces, surface reaction by sublimation, gas phase reaction, gas phase temperature rise and reverse heat flow to the pore surface aiding the surface reaction, solid phase heat conduction, etc. 1D idealized hot spot cell (1DHSC) version of the 3D PBRB model has been converted to a vectorized EOS form for the first time. Results validating the model with the pop plot of RDX in agreement with data through simulation of an assumed plate impact experiment will be presented. In addition, the effect of the surface sublimation model parameters on the rate of reaction, detonation shock pressure, and von-Neumann's peak for thin and thick inert impactor will be presented. We acknowledge Dr. Betsy Rice (ARL), Dr. Suhithi Peiris (DTRA) and Dr. John Brennan (ARL) for their support and discussion. This work is supported by Eglin AFB contract FA8651-08-0108/027 and in part by DTRA contract HDTRA-1-10-1-0035.

  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. A new receptor model-incremental lifetime cancer risk method to quantify the carcinogenic risks associated with sources of particle-bound polycyclic aromatic hydrocarbons from Chengdu in China.

    PubMed

    Liu, Gui-Rong; Peng, Xing; Wang, Rong-Kang; Tian, Ying-Ze; Shi, Guo-Liang; Wu, Jian-Hui; Zhang, Pu; Zhou, Lai-Dong; Feng, Yin-Chang

    2015-01-01

    PM10 and PM2.5 samples were simultaneously collected during a one-year monitoring period in Chengdu. The concentrations of 16 particle-bound polycyclic aromatic hydrocarbons (Σ16PAHs) were measured. Σ16PAHs concentrations varied from 16.85 to 160.24 ng m(-3) and 14.93 to 111.04ngm(-3) for PM10 and PM2.5, respectively. Three receptor models (principal component analysis (PCA), positive matrix factorization (PMF), and Multilinear Engine 2 (ME2)) were applied to investigate the sources and contributions of PAHs. The results obtained from the three receptor models were compared. Diesel emissions, gasoline emissions, and coal and wood combustion were the primary sources. Source apportionment results indicated that these models were able to track the ΣPAHs. For the first time, the cancer risks for each identified source were quantitatively calculated for ingestion and dermal contact routes by combining the incremental lifetime cancer risk (ILCR) values with the estimated source contributions. The results showed that gasoline emissions posed the highest cancer risk, even though it contributed less to Σ16PAHs. The results and method from this work can provide useful information for quantifying the toxicity of source categories and studying human health in the future. PMID:25464284

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    Volatile organic compounds like furan and its derivatives are important for atmospheric properties and reactions. In this paper the known abiotic formation of furan from catechol under Fenton-like conditions with Fe3+ sulphate 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 turnover numbers of the active iron species increased. Additionally, the role of iron and pH will be discussed during 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 these samples. Furthermore, 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 assumed 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 therefore important for the local climate.

  6. 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.

  7. Learned Helplessness: A Model to Understand and Overcome a Child's Extreme Reaction to Failure.

    ERIC Educational Resources Information Center

    Balk, David

    1983-01-01

    The author reviews literature on childrens' reactions to perceived failure and offers "learned helplessness" as a model to explain why a child who makes a mistake gives up. Suggestions for preventing these reactions are given. (Author/JMK)

  8. Modeling reaction noise with a desired accuracy by using the X level approach reaction noise estimator (XARNES) method.

    PubMed

    Konkoli, Zoran

    2012-07-21

    A novel computational method for modeling reaction noise characteristics has been suggested. The method can be classified as a moment closure method. The approach is based on the concept of correlation forms which are used for describing spatially extended many body problems where particle numbers change in space and time. In here, it was shown how the formalism of spatially extended correlation forms can be adapted to study well mixed reaction systems. Stochastic fluctuations in particle numbers are described by selectively capturing correlation effects up to the desired order, ξ. The method is referred to as the ξ-level Approximation Reaction Noise Estimator method (XARNES). For example, the ξ=1 description is equivalent to the mean field theory (first-order effects), the ξ=2 case corresponds to the previously developed PARNES method (pair effects), etc. The main idea is that inclusion of higher order correlation effects should lead to better (more accurate) results. Several models were used to test the method, two versions of a simple complex formation model, the Michaelis-Menten model of enzymatic kinetics, the smallest bistable reaction network, a gene expression network with negative feedback, and a random large network. It was explicitly demonstrated that increase in ξ indeed improves accuracy in all cases investigated. The approach has been implemented as automatic software using the Mathematica programming language. The user only needs to input reaction rates, stoichiometry coefficients, and the desired level of computation ξ.

  9. 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

  10. Tables of Nuclear Cross Sections and Reaction Rates: AN Addendum to the Paper ``ASTROPHYSICAL Reaction Rates from Statistical Model Calculations'' ()

    NASA Astrophysics Data System (ADS)

    Rauscher, Thomas; Thielemann, Friedrich-Karl

    2001-09-01

    In a previous publication (ATOMIC DATAAND NUCLEAR DATA TABLES75, 1 (2000)), we gave seven-parameter analytical fits to theoretical reaction rates derived from nuclear cross sections calculated in the statistical model (Hauser-Feshbach formalism) for targets with 10<=Z<=83 (Ne to Bi) and for a mass range reaching the neutron and proton driplines. Reactions considered were (n,γ), (n,p), (n,α), (p,γ), (p,α), (α,γ), and their inverse reactions. Here, we present the theoretical nuclear cross sections and astrophysical reaction rates from which those rate fits were derived, and we provide these data as on-line electronic files. Corresponding to the fitted rates, two complete data sets are provided, one of which includes a phenomenological treatment of shell quenching for neutron-rich nuclei.

  11. 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.

  12. 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.

  13. 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

  14. Glauber model for {alpha}-nucleus total reaction cross section

    SciTech Connect

    Chauhan, Deeksha; Khan, Z. A.

    2009-11-15

    The Coulomb-modified Glauber model is employed to calculate the total reaction cross section ({sigma}{sub R}) for {alpha} particles from {sup 9}Be, {sup 12}C, {sup 16}O, {sup 28}Si, {sup 40}Ca, {sup 58,60}Ni, {sup 112,116,120,124}Sn, and {sup 208}Pb at 117.2, 163.9, and 192.4 MeV and from the lighter nuclei also at 69.6 MeV. Our main focus in this work is to assess the suitability of semiphenomenological parametrization of the NN amplitude (SPNN), used recently [Deeksha Chauhan and Z. A. Khan, Eur. Phys. J. A 41, 179 (2009)], in the analysis of {sigma}{sub R} at the energies under consideration. Using the realistic form factors for the colliding nuclei, it is found that the SPNN works reasonably well and we have quite a satisfactory account of the {sigma}{sub R} data in all the cases. Moreover, our analysis suggests that the SPNN could be taken as fairly stable to describe simultaneously the elastic angular distribution and the {sigma}{sub R} for a wide range of target nuclei in the relatively low-energy region.

  15. 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).

  16. 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.

  17. 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. PMID:26313650

  18. 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

  19. 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

  20. 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,…

  1. Chemical reaction model for oil and gas generation from type 1 and type 2 kerogen

    SciTech Connect

    Braun, R.L.; Burnham, A.K.

    1993-06-01

    A global model for the generation of oil and gas from petroleum source rocks is presented. The model consists of 13 chemical species and 10 reactions, including an alternate-pathway mechanism for kerogen pyrolysis. Reaction rate parameters and stoichiometry coefficients determined from a variety of pyrolysis data are given for both type I and type II kerogen. Use of the chemical reaction model is illustrated for typical geologic conditions.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. Modelling of reaction cross sections and prompt neutron emission

    NASA Astrophysics Data System (ADS)

    Hambsch, F.-J.; Tudora, A.; Oberstedt, S.

    2010-10-01

    Accurate nuclear data concerning reaction cross sections and the emission of prompt fission neutrons (i.e. multiplicity and spectra) as well as other fission fragment data are of great importance for reactor physics design, especially for the new Generation IV nuclear energy systems. During the past years for several actinides (238U(n, f) and 237Np(n, f)) both the reaction cross sections and prompt neutron multiplicities and spectra have been calculated within the frame of the EFNUDAT project.

  7. Understanding the incremental value of novel diagnostic tests for tuberculosis.

    PubMed

    Arinaminpathy, Nimalan; Dowdy, David

    2015-12-01

    Tuberculosis is a major source of global mortality caused by infection, partly because of a tremendous ongoing burden of undiagnosed disease. Improved diagnostic technology may play an increasingly crucial part in global efforts to end tuberculosis, but the ability of diagnostic tests to curb tuberculosis transmission is dependent on multiple factors, including the time taken by a patient to seek health care, the patient's symptoms, and the patterns of transmission before diagnosis. Novel diagnostic assays for tuberculosis have conventionally been evaluated on the basis of characteristics such as sensitivity and specificity, using assumptions that probably overestimate the impact of diagnostic tests on transmission. We argue for a shift in focus to the evaluation of such tests' incremental value, defining outcomes that reflect each test's purpose (for example, transmissions averted) and comparing systems with the test against those without, in terms of those outcomes. Incremental value can also be measured in units of outcome per incremental unit of resource (for example, money or human capacity). Using a novel, simplified model of tuberculosis transmission that addresses some of the limitations of earlier tuberculosis diagnostic models, we demonstrate that the incremental value of any novel test depends not just on its accuracy, but also on elements such as patient behaviour, tuberculosis natural history and health systems. By integrating these factors into a single unified framework, we advance an approach to the evaluation of new diagnostic tests for tuberculosis that considers the incremental value at the population level and demonstrates how additional data could inform more-effective implementation of tuberculosis diagnostic tests under various conditions.

  8. The JigCell model builder: a spreadsheet interface for creating biochemical reaction network models.

    PubMed

    Vass, Marc T; Shaffer, Clifford A; Ramakrishnan, Naren; Watson, Layne T; Tyson, John J

    2006-01-01

    Converting a biochemical reaction network to a set of kinetic rate equations is tedious and error prone. We describe known interface paradigms for inputing models of intracellular regulatory networks: graphical layout (diagrams), wizards, scripting languages, and direct entry of chemical equations. We present the JigCell Model Builder, which allows users to define models as a set of reaction equations using a spreadsheet (an example of direct entry of equations) and outputs model definitions in the Systems Biology Markup Language, Level 2. We present the results of two usability studies. The spreadsheet paradigm demonstrated its effectiveness in reducing the number of errors made by modelers when compared to hand conversion of a wiring diagram to differential equations. A comparison of representatives of the four interface paradigms for a simple model of the cell cycle was conducted which measured time, mouse clicks, and keystrokes to enter the model, and the number of screens needed to view the contents of the model. All four paradigms had similar data entry times. The spreadsheet and scripting language approaches require significantly fewer screens to view the models than do the wizard or graphical layout approaches.

  9. Chemical modeling of irreversible reactions in nuclear waste-water-rock systems

    SciTech Connect

    Wolery, T.J.

    1981-02-01

    Chemical models of aqueous geochemical systems are usually built on the concept of thermodynamic equilibrium. Though many elementary reactions in a geochemical system may be close to equilibrium, others may not be. Chemical models of aqueous fluids should take into account that many aqueous redox reactions are among the latter. The behavior of redox reactions may critically affect migration of certain radionuclides, especially the actinides. In addition, the progress of reaction in geochemical systems requires thermodynamic driving forces associated with elementary reactions not at equilibrium, which are termed irreversible reactions. Both static chemical models of fluids and dynamic models of reacting systems have been applied to a wide spectrum of problems in water-rock interactions. Potential applications in nuclear waste disposal range from problems in geochemical aspects of site evaluation to those of waste-water-rock interactions. However, much further work in the laboratory and the field will be required to develop and verify such applications of chemical modeling.

  10. 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.

  11. International Space Station Increment Operations Services

    NASA Astrophysics Data System (ADS)

    Michaelis, Horst; Sielaff, Christian

    2002-01-01

    The Industrial Operator (IO) has defined End-to-End services to perform efficiently all required operations tasks for the Manned Space Program (MSP) as agreed during the Ministerial Council in Edinburgh in November 2001. Those services are the result of a detailed task analysis based on the operations processes as derived from the Space Station Program Implementation Plans (SPIP) and defined in the Operations Processes Documents (OPD). These services are related to ISS Increment Operations and ATV Mission Operations. Each of these End-to-End services is typically characterised by the following properties: It has a clearly defined starting point, where all requirements on the end-product are fixed and associated performance metrics of the customer are well defined. It has a clearly defined ending point, when the product or service is delivered to the customer and accepted by him, according to the performance metrics defined at the start point. The implementation of the process might be restricted by external boundary conditions and constraints mutually agreed with the customer. As far as those are respected the IO has the free choice to select methods and means of implementation. The ISS Increment Operations Service (IOS) activities required for the MSP Exploitation program cover the complete increment specific cycle starting with the support to strategic planning and ending with the post increment evaluation. These activities are divided into sub-services including the following tasks: - ISS Planning Support covering the support to strategic and tactical planning up to the generation - Development &Payload Integration Support - ISS Increment Preparation - ISS Increment Execution These processes are tight together by the Increment Integration Management, which provides the planning and scheduling of all activities as well as the technical management of the overall process . The paper describes the entire End-to-End ISS Increment Operations service and the

  12. 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.

  13. Generalized Pseudo-Reaction Zone Model for Non-Ideal Explosives

    NASA Astrophysics Data System (ADS)

    Wescott, Bradley

    2007-06-01

    The pseudo-reaction zone model was proposed to improve engineering scale simulations when using Detonation Shock Dynamics with high explosives that have a slow reaction component. In this work an extension of the pseudo-reaction zone model is developed for non-ideal explosives that propagate well below their steady-planar Chapman-Jouguet velocity. A programmed burn method utilizing Detonation Shock Dynamics and a detonation velocity dependent pseudo-reaction rate has been developed for non-ideal explosives and applied to the explosive mixture of ammonium nitrate and fuel oil (ANFO). The pseudo-reaction rate is calibrated to the experimentally obtained normal detonation velocity---shock curvature relation. The generalized pseudo-reaction zone model proposed here predicts the cylinder expansion to within 1% by accounting for the slow reaction in ANFO.

  14. Choice (CRT) and simple reaction times (SRT) compared in laboratory technicians: Factors influencing reaction times and a predictive model

    SciTech Connect

    Miller, J.A.; Cohen, G.S.; Warshaw, R.; Thornton, J.C.; Kilburn, K.H.

    1989-01-01

    Choice reaction time (CRT) and simple reaction time (SRT) tests were administered to 151 female histology laboratory technicians to determine if occupational exposure to organic solvents and formaldehyde delayed either or both. The relationships between CRT and SRT latencies were evaluated using different testers, sequences of administration, and microcomputers. Formaldehyde exposure, cigarette smoking history, ethnicity, and alveolar CO levels did not significantly influence CRT and SRT. However, slightly different protocols did significantly affect SRT. A linear model demonstrated that logSRT (LSRT) and LogCRT (LCRT) were longer with increasing age, promising further clinical applications. It is concluded that both CRT and SRT measure some overlapping and some different neurologic pathways. Reaction times in large ''normal'' populations are needed to compare with groups exposed to potential neurotoxins.

  15. 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.

  16. 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.

  17. 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.

  18. Atmospheric response to Saharan dust deduced from ECMWF reanalysis increments

    NASA Astrophysics Data System (ADS)

    Kishcha, P.; Alpert, P.; Barkan, J.; Kirchner, I.; Machenhauer, B.

    2003-04-01

    This study focuses on the atmospheric temperature response to dust deduced from a new source of data - the European Reanalysis (ERA) increments. These increments are the systematic errors of global climate models, generated in reanalysis procedure. The model errors result not only from the lack of desert dust but also from a complex combination of many kinds of model errors. Over the Sahara desert the dust radiative effect is believed to be a predominant model defect which should significantly affect the increments. This dust effect was examined by considering correlation between the increments and remotely-sensed dust. Comparisons were made between April temporal variations of the ERA analysis increments and the variations of the Total Ozone Mapping Spectrometer aerosol index (AI) between 1979 and 1993. The distinctive structure was identified in the distribution of correlation composed of three nested areas with high positive correlation (> 0.5), low correlation, and high negative correlation (<-0.5). The innermost positive correlation area (PCA) is a large area near the center of the Sahara desert. For some local maxima inside this area the correlation even exceeds 0.8. The outermost negative correlation area (NCA) is not uniform. It consists of some areas over the eastern and western parts of North Africa with a relatively small amount of dust. Inside those areas both positive and negative high correlations exist at pressure levels ranging from 850 to 700 hPa, with the peak values near 775 hPa. Dust-forced heating (cooling) inside the PCA (NCA) is accompanied by changes in the static stability of the atmosphere above the dust layer. The reanalysis data of the European Center for Medium Range Weather Forecast(ECMWF) suggests that the PCA (NCA) corresponds mainly to anticyclonic (cyclonic) flow, negative (positive) vorticity, and downward (upward) airflow. These facts indicate an interaction between dust-forced heating /cooling and atmospheric circulation. The

  19. 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.

  20. Reaction-subdiffusion front propagation in a comblike model of spiny dendrites.

    PubMed

    Iomin, A; Méndez, V

    2013-07-01

    Fractional reaction-diffusion equations are derived by exploiting the geometrical similarities between a comb structure and a spiny dendrite. In the framework of the obtained equations, two scenarios of reaction transport in spiny dendrites are explored, where both a linear reaction in spines and nonlinear Fisher-Kolmogorov-Petrovskii-Piskunov reactions along dendrites are considered. In the framework of fractional subdiffusive comb model, we develop a Hamilton-Jacobi approach to estimate the overall velocity of the reaction front propagation. One of the main effects observed is the failure of the front propagation for both scenarios due to either the reaction inside the spines or the interaction of the reaction with the spines. In the first case the spines are the source of reactions, while in the latter case, the spines are a source of a damping mechanism. PMID:23944491

  1. Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models.

    PubMed

    Zhu, Rui; Ribeiro, Andre S; Salahub, Dennis; Kauffman, Stuart A

    2007-06-21

    Current advances in molecular biology enable us to access the rapidly increasing body of genetic information. It is still challenging to model gene systems at the molecular level. Here, we propose two types of reaction kinetic models for constructing genetic networks. Time delays involved in transcription and translation are explicitly considered to explore the effects of delays, which may be significant in genetic networks featured with feedback loops. One type of model is based on delayed effective reactions, each reaction modeling a biochemical process like transcription without involving intermediate reactions. The other is based on delayed virtual reactions, each reaction being converted from a mathematical function to model a biochemical function like gene inhibition. The latter stochastic models are derived from the corresponding mean-field models. The former ones are composed of single gene expression modules. We thus design a model of gene expression. This model is verified by our simulations using a delayed stochastic simulation algorithm, which accurately reproduces the stochastic kinetics in a recent experimental study. Various simplified versions of the model are given and evaluated. We then use the two methods to study the genetic toggle switch and the repressilator. We define the "on" and "off" states of genes and extract a binary code from the stochastic time series. The binary code can be described by the corresponding Boolean network models in certain conditions. We discuss these conditions, suggesting a method to connect Boolean models, mean-field models, and stochastic chemical models. PMID:17350653

  2. 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…

  3. 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.

  4. 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.

  5. 40 CFR 60.5100 - When must I submit the notifications of achievement of increments of progress?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Emission Guidelines and Compliance Times for Existing Sewage Sludge Incineration Units Model Rule... progress? Notifications for achieving increments of progress must be postmarked no later than 10...

  6. Modelling non-homogeneous stochastic reaction-diffusion systems: the case study of gemcitabine-treated non-small cell lung cancer growth

    PubMed Central

    2012-01-01

    diffusive transport in non-homogeneous media. The diffusion coefficient is explicitly expressed as a function depending on the local conditions of the medium, such as the concentration of molecular species, the viscosity of the medium and the temperature. We incorporated this generalized law in a reaction-based stochastic simulation framework implementing an efficient version of Gillespie algorithm for modeling the dynamics of the interactions between tumor cell, nutrients and gemcitabine in a spatial domain expressing a nutrient and drug concentration gradient. Results Using the mathematical framework of model we simulated the spatial growth of a 2D spheroidal tumor model in response to a treatment with gemcitabine and a dynamic gradient of oxygen and glucose. The parameters of the model have been taken from recet literature and also inferred from real tumor shrinkage curves measured in patients suffering from non-small cell lung cancer. The simulations qualitatively reproduce the time evolution of the morphologies of these tumors as well as the morphological patterns follow the growth curves observed in patients. Conclusions s This model is able to reproduce the observed increment/decrement of tumor size in response to the pharmacological treatment with gemcitabine. The formal specification of the model in Redi can be easily extended in an incremental way to include other relevant biophysical processes, such as local extracellular matrix remodelling, active cell migration and traction, and reshaping of host tissue vasculature, in order to be even more relevant to support the experimental investigation of cancer. PMID:23095709

  7. Stochastic modelling of biochemical systems of multi-step reactions using a simplified two-variable model

    PubMed Central

    2013-01-01

    Background A fundamental issue in systems biology is how to design simplified mathematical models for describing the dynamics of complex biochemical reaction systems. Among them, a key question is how to use simplified reactions to describe the chemical events of multi-step reactions that are ubiquitous in biochemistry and biophysics. To address this issue, a widely used approach in literature is to use one-step reaction to represent the multi-step chemical events. In recent years, a number of modelling methods have been designed to improve the accuracy of the one-step reaction method, including the use of reactions with time delay. However, our recent research results suggested that there are still deviations between the dynamics of delayed reactions and that of the multi-step reactions. Therefore, more sophisticated modelling methods are needed to accurately describe the complex biological systems in an efficient way. Results This work designs a two-variable model to simplify chemical events of multi-step reactions. In addition to the total molecule number of a species, we first introduce a new concept regarding the location of molecules in the multi-step reactions, which is the second variable to represent the system dynamics. Then we propose a simulation algorithm to compute the probability for the firing of the last step reaction in the multi-step events. This probability function is evaluated using a deterministic model of ordinary differential equations and a stochastic model in the framework of the stochastic simulation algorithm. The efficiency of the proposed two-variable model is demonstrated by the realization of mRNA degradation process based on the experimentally measured data. Conclusions Numerical results suggest that the proposed new two-variable model produces predictions that match the multi-step chemical reactions very well. The successful realization of the mRNA degradation dynamics indicates that the proposed method is a promising approach to

  8. 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...

  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, 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...

  11. 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...

  12. Cold-cap reactions in vitrification of nuclear waste glass: experiments and modeling

    SciTech Connect

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

    2013-05-01

    Cold-cap reactions are multiple overlapping reactions that occur in the waste-glass melter during the vitrification process when the melter feed is being converted to molten glass. In this study, we used differential scanning calorimetry (DSC) to investigate cold-cap reactions in a high-alumina high-level waste melter feed. To separate the reaction heat from both sensible heat and experimental instability, we employed the run/rerun method, which enabled us to define the degree of conversion based on the reaction heat and to estimate the heat capacity of the reacting feed. Assuming that the reactions are nearly independent and can be approximated by the nth order kinetics, we obtained the kinetic parameters using the Kissinger method combined with least squares analysis. The resulting mathematical simulation of the cold-cap reactions provides a key element for the development of an advanced cold-cap model.

  13. Incremental Support Vector Machine Framework for Visual Sensor Networks

    NASA Astrophysics Data System (ADS)

    Awad, Mariette; Jiang, Xianhua; Motai, Yuichi

    2006-12-01

    Motivated by the emerging requirements of surveillance networks, we present in this paper an incremental multiclassification support vector machine (SVM) technique as a new framework for action classification based on real-time multivideo collected by homogeneous sites. The technique is based on an adaptation of least square SVM (LS-SVM) formulation but extends beyond the static image-based learning of current SVM methodologies. In applying the technique, an initial supervised offline learning phase is followed by a visual behavior data acquisition and an online learning phase during which the cluster head performs an ensemble of model aggregations based on the sensor nodes inputs. The cluster head then selectively switches on designated sensor nodes for future incremental learning. Combining sensor data offers an improvement over single camera sensing especially when the latter has an occluded view of the target object. The optimization involved alleviates the burdens of power consumption and communication bandwidth requirements. The resulting misclassification error rate, the iterative error reduction rate of the proposed incremental learning, and the decision fusion technique prove its validity when applied to visual sensor networks. Furthermore, the enabled online learning allows an adaptive domain knowledge insertion and offers the advantage of reducing both the model training time and the information storage requirements of the overall system which makes it even more attractive for distributed sensor networks communication.

  14. 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)…

  15. 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. PMID:20875976

  16. Modeling the coupling between flow and transport developed by chemical reactions and density differences using TOUGHREACT.

    SciTech Connect

    Kim, Jeongkon; Scwartz, Franklin W.; Shi, Jianyou; Xu, Tianfu

    2003-04-01

    A complex pattern of coupling between fluid flow and mass transport develops when heterogeneous reactions occur. For instance, dissolution and precipitation reactions can change the physical properties of a medium, such as permeability and pore geometry. These changes influence fluid flow, which in turn impact the composition of dissolved constituents and solid-phase, and the rate and direction of advective transport. Two-dimensional modeling studies using TOUGHREACT were conducted to investigate the coupling between flow and transport developed as a consequence of difference in density, dissolution/precipitation, and medium heterogeneity. The model includes equilibrium reactions for aqueous species, kinetic reactions between the solid phases and aqueous constituents, and full coupling of porosity and permeability changes resulting from precipitation and dissolution reactions in porous media. Generally, the evolutions in the concentrations of the aqueous phase are intimately related to the reaction-front dynamics. Plugging of the medium contributed to significant transients in patterns of flow and mass transport.

  17. The modeling of chemical reactions and thermochemical nonequilibrium in particle simulation computations

    NASA Astrophysics Data System (ADS)

    Gallis, Michael A.; Harvey, John K.

    1998-06-01

    The treatment of chemical reactions and nonequilibrium energy exchange in Direct Simulation Monte Carlo calculations is examined. Details of a Maximum Entropy chemical reaction model are presented that is based on the classical scheme devised by Levine and Bernstein. Data are given for all of the significant reactions that occur in hypersonic reentry flight into the atmospheres of the Earth, Mars, and Venus. The method is an extension of that described and used previously by the authors (Gallis and Harvey [J. Fluid Mech. 312, 149 (1996); AIAA J. 34(7), 1378 (1996)]) and now includes carbon dioxide/nitrogen and ionic reactions. The model allows an appropriate dependence of each reaction on its controlling energy mode and avoids inappropriate use of equilibrium distributions to determine the reaction probabilities and post-collision energy reallocation. Sample flow solutions are given and comparisons are made with results obtained using continuum solvers.

  18. Generalized Pseudo-Reaction Zone Model for Non-Ideal Explosives

    NASA Astrophysics Data System (ADS)

    Wescott, B. L.

    2007-12-01

    The pseudo-reaction zone model was proposed to improve engineering scale simulations with high explosives that have a slow reaction component. In this work an extension of the pseudo-reaction zone model is developed for non-ideal explosives that propagate well below the steady-planar Chapman-Jouguet velocity. A programmed burn method utilizing Detonation Shock Dynamics (DSD) and a detonation velocity dependent pseudo-reaction rate has been developed for non-ideal explosives and applied to the explosive mixture of ammonium nitrate and fuel oil (ANFO). The pseudo-reaction rate is calibrated to the experimentally obtained normal detonation velocity—shock curvature relation. Cylinder test simulations predict the proper expansion to within 1% even though significant reaction occurs as the cylinder expands.

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

    PubMed

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

    2014-10-01

    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.

  20. 40 CFR 60.1605 - What if I do not meet an increment of progress?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Times for Small Municipal Waste Combustion Units Constructed on or Before August 30, 1999 Model Rule... increment of progress, you must submit a notification to the Administrator postmarked within 10...

  1. 40 CFR 60.5105 - What if I do not meet an increment of progress?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Times for Existing Sewage Sludge Incineration Units Model Rule-Increments of Progress § 60.5105 What if... submit a notification to the Administrator postmarked within 10 business days after the date for...

  2. 40 CFR 60.2835 - What if I do not meet an increment of progress?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... or Before November 30, 1999 Model Rule-Air Curtain Incinerators § 60.2835 What if I do not meet an... Administrator postmarked within 10 business days after the date for that increment of progress in table 1...

  3. Efficient Calculation of Accurate Reaction Energies-Assessment of Different Models in Electronic Structure Theory.

    PubMed

    Friedrich, Joachim

    2015-08-11

    In this work we analyze the accuracy and the efficiency of different schemes to obtain the complete basis set limit for CCSD(T). It is found that composite schemes using an MP2 increment to reach the basis set limit provide high accuracy combined with high efficiency. In these composite schemes the MP2-F12/cc-pVTZ-F12 method is suitable to compute the MP2 contribution at the basis set limit. We propose to use the def2-TZVP or the TZVPP basis sets at the coupled cluster level in combination with the cc-pVTZ-F12 basis set at the MP2 level to compute reaction energies close to the basis set limit, if high accuracy methods like CCSD(T)(F12*) or 56-extrapolations are no longer feasible due to the computational effort. The standard deviation of CCSD(T)+ΔMP2/cc-pVTZ-F12/def2-TZVP and CCSD(T)+ΔMP2/cc-pVTZ-F12/TZVPP is found to be only 0.93 and 0.65 kJ/mol for a test set of 51 closed shell reactions. Furthermore, we provide a comprehensive list of different computational strategies to obtain CCSD(T) reaction energies with an efficiency and accuracy measure. Finally we analyze how different choices of the exponent in the correlation factor (γ) change the results when using explicitly correlated methods. The statistical results in this study are based on a set of 51 reaction energies in the range of 0.7 to 631.5 kJ/mol.

  4. 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.

  5. 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.

  6. Dynamic Modeling of LD Converter Steelmaking: Reaction Modeling Using Gibbs' Free Energy Minimization

    NASA Astrophysics Data System (ADS)

    Sarkar, Rahul; Gupta, Pramod; Basu, Somnath; Ballal, Nidambur Bharath

    2015-04-01

    Slag-metal emulsion plays an important role in the oxidation kinetics of metalloids in oxygen steelmaking. The importance of droplet generation rate, droplet size, and its residence time in the slag-metal emulsion on the overall reaction kinetics has become evident in recent times. Residence times of the droplets are strongly dependent on the decarburization rate, the CO bubbles giving a buoyant force to the droplets. The present work aims at developing a mathematical model for predicting the composition evolutions of the slag and the metal phases as the blow proceeds in an LD converter. The process dynamics are modeled by dividing the LD convertor into three separate continuous stirred tank reactors. Oxidation reactions are assumed to be primarily taking place at the interface between the slag and the metal phases in the emulsion. Among the different mass transfer and reaction steps controlling the kinetics, the mass transfer of FeO in the slag phase and that of the metalloids within the metal droplet are assumed to be rate-controlling. For a Fe-C-X (X = Mn, Si etc.) droplet, simultaneous removal of elements have been modeled by Gibbs' free energy minimization at the slag-metal interface. Effects of droplet size, mass transfer coefficient, and initial carbon content on the mean residence time of metal droplets in the slag-metal emulsion have also been identified. Mixing in the metal phase is simulated in terms of metal exchange rate and the reactor weight ratio between the upper and the lower parts of the bath.

  7. 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.

  8. 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.

  9. 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

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

    PubMed

    Wu, Qianqian; Tian, Tianhai

    2016-08-24

    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.

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

    PubMed

    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

  12. 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

    2016-11-01

    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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. The sugar model: autocatalytic activity of the triose-ammonia reaction.

    PubMed

    Weber, Arthur L

    2007-04-01

    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 of 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. PMID:17225954

  18. (Process Models of Counselor Judgment: Proposal and Reactions.)

    ERIC Educational Resources Information Center

    Strohmer, Douglas C.; And Others

    1982-01-01

    Studied competing process models of counselors' clinical judgment for their capacity to account for variance in prognostic judgments and further tested for parsimony. Patton discusses problems of logic and data analysis in the model's formulation. Provides Stromer's response to the critique. (RC)

  19. Piecewise linear and Boolean models of chemical reaction networks.

    PubMed

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

    2014-12-01

    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 ([Formula: see text]). Reduced ODEs and Boolean approximations of such model networks have been studied extensively when the exponent [Formula: see text] is large. However, while the case of small constant [Formula: see text] 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.

  20. 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.

  1. Hydrocarbon ignition: Automatic generation of reaction mechanisms and applications to modeling of engine knock

    SciTech Connect

    Chevalier, C.; Warnatz, J. . Inst. fuer Technische Verbrennung); Pitz, W.J.; Westbrook, C.K. )

    1992-02-01

    A computational technique is described which automatically develops detailed chemical kinetic reaction mechanisms for large aliphatic hydrocarbon fuel molecules. This formulation uses the LISP language to apply general rules which identify the chemical species produced, the reactions between these species, and the elementary reaction rates for each reaction step. Reaction mechanisms for cetane (n-hexadecane) and most alkane fuels C{sub 7} and smaller are developed using this automatic technique, and detailed sensitivity analyses for n-heptane and cetane are described. These reaction mechanisms are then applied to calculation of knock tendencies in internal combustion engines. The model is used to study the influence of fuel molecule size and structure on knock tendency, to examine knocking properties of fuel mixtures, and to determine the mechanisms by which pro-knock and anti-knock additives change knock properties.

  2. 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.

  3. 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.

  4. Porphyrin-quinone compounds as synthetic models of the reaction centre in photosynthesis

    NASA Astrophysics Data System (ADS)

    Borovkov, V. V.; Evstigneeva, Rima P.; Strekova, L. N.; Filippovich, E. I.

    1989-06-01

    Data on the synthesis, steric structure, and photochemical properties of porphyrin-quinone compounds as synthetic models of the reaction centre in photosynthesis are examined and described systematically. The bibliography includes 113 references.

  5. Specific mass increment and nonequilibrium crystal growth

    NASA Astrophysics Data System (ADS)

    Martyushev, Leonid M.; Terentiev, Pavel S.

    2013-09-01

    Unsteady nonequilibrium crystallization of ammonium chloride from an aqueous solution resulting in the formation of irregular, so-called seaweed, structures is experimentally investigated. It is shown that specific increment of mass for the coexisting structures (or parts thereof) is the same and changes with time (t) according to the power law a/t-b, where the factor a=1.87±0.09 and the factor b is determined by the system relaxation time. The normalization of the power law to the total time of structure growth allows obtaining a universal law that describes the specific mass increment with time for both seaweed and dendrite structures (including the non-coexisting ones).

  6. A comparison of total reaction cross section models used in particle and heavy ion transport codes

    NASA Astrophysics Data System (ADS)

    Sihver, Lembit; Lantz, M.; Takechi, M.; Kohama, A.; Ferrari, A.; Cerutti, F.; Sato, T.

    To be able to calculate the nucleon-nucleus and nucleus-nucleus total reaction cross sections with precision is very important for studies of basic nuclear properties, e.g. nuclear structure. This is also of importance for particle and heavy ion transport calculations because, in all particle and heavy ion transport codes, the probability function that a projectile particle will collide within a certain distance x in the matter depends on the total reaction cross sections. Furthermore, the total reaction cross sections will also scale the calculated partial fragmentation cross sections. It is therefore crucial that accurate total reaction cross section models are used in the transport calculations. In this paper, different models for calculating nucleon-nucleus and nucleus-nucleus total reaction cross sections are compared and discussed.

  7. 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.

  8. Achieving incremental semantic interpretation through contextual representation.

    PubMed

    Sedivy, J C; Tanenhaus, M K; Chambers, C G; Carlson, G N

    1999-06-22

    While much work has been done investigating the role of context in the incremental processing of syntactic indeterminacies, relatively little is known about online semantic interpretation. The experiments in this article made use of the eye-tracking paradigm with spoken language and visual contexts in order to examine how, and when listeners make use of contextually-defined contrast in interpreting simple prenominal adjectives. Experiment 1 focused on intersective adjectives. Experiment 1A provided further evidence that intersective adjectives are processed incrementally. Experiment 1B compared response times to follow instructions such as 'Pick up the blue comb' under conditions where there were two blue objects (e.g. a blue pen and a blue comb), but only one of these objects had a contrasting member in the display. Responses were faster to objects with a contrasting member, establishing that the listeners initially assume a contrastive interpretation for intersective adjectives. Experiments 2 and 3 focused on vague scalar adjectives examining the time course with which listeners establish contrast for scalar adjectives such as tall using information provided by the head noun (e.g. glass) and information provided by the visual context. Use of head-based information was examined by manipulating the typicality of the target object (e.g. whether it was a good or poor example of a tall glass. Use of context-dependent contrast was examined by either having only a single glass in the display (the no contrast condition) or a contrasting object (e.g. a smaller glass). The pattern of results indicated that listeners interpreted the scalar adjective incrementally taking into account context-specific contrast prior to encountering the head. Moreover, the presence of a contrasting object, sharply reduced, and in some conditions completely eliminated, typicality effects. The results suggest a language processing system in which semantic interpretation, as well as syntactic

  9. Energy System Contributions During Incremental Exercise Test

    PubMed Central

    Bertuzzi, Rômulo; Nascimento, Eduardo M.F.; Urso, Rodrigo P.; Damasceno, Mayara; Lima-Silva, Adriano E.

    2013-01-01

    The main purpose of this study was to determine the relative contributions of the aerobic and glycolytic systems during an incremental exercise test (IET). Ten male recreational long-distance runners performed an IET consisting of three-minute incremental stages on a treadmill. The fractions of the contributions of the aerobic and glycolytic systems were calculated for each stage based on the oxygen uptake and the oxygen energy equivalents derived by blood lactate accumulation, respectively. Total metabolic demand (WTOTAL) was considered as the sum of these two energy systems. The aerobic (WAER) and glycolytic (WGLYCOL) system contributions were expressed as a percentage of the WTOTAL. The results indicated that WAER (86-95%) was significantly higher than WGLYCOL (5-14%) throughout the IET (p < 0.05). In addition, there was no evidence of the sudden increase in WGLYCOL that has been previously reported to support to the “anaerobic threshold” concept. These data suggest that the aerobic metabolism is predominant throughout the IET and that energy system contributions undergo a slow transition from low to high intensity. Key Points The aerobic metabolism contribution is the predominant throughout the maximal incremental test. The speed corresponding to the aerobic threshold can be considered the point in which aerobic metabolism reaches its maximal contribution. Glycolytic metabolism did not contribute largely to the energy expenditure at intensities above the anaerobic threshold. PMID:24149151

  10. 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.

  11. Reaction-diffusion processes and epidemic metapopulation models in complex networks

    NASA Astrophysics Data System (ADS)

    Vespignani, A.

    2008-08-01

    The correct description of reaction-diffusion phenomena requires a detailed knowledge of the contact networks defining the interactions between individuals and groups of individuals. For this reason, the study of reaction-diffusion processes has been recently widened with opportune models and methods dealing with the heterogeneity and large scale fluctuations observed in many real world networks. Here we present a brief overview of some recent results on reaction-diffusion processes in complex networks which provide useful insights into the dynamic behavior of epidemic metapopulation models.

  12. Ubiquity of, and geostatistics for, nonstationary increment random fields

    NASA Astrophysics Data System (ADS)

    O'Malley, Daniel; Cushman, John H.

    2013-07-01

    Nonstationary random fields such as fractional Brownian motion and fractional Lévy motion have been studied extensively in the hydrology literature. On the other hand, random fields that have nonstationary increments have seen little study. A mathematical argument is presented that demonstrates processes with stationary increments are the exception and processes with nonstationary increments are far more abundant. The abundance of nonstationary increment processes has important implications, e.g., in kriging where a translation-invariant variogram implicitly assumes stationarity of the increments. An approach to kriging for processes with nonstationary increments is presented and accompanied by some numerical results.

  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. A reexamination of the abrasion-ablation model for the description of the nuclear fragmentation reaction

    NASA Astrophysics Data System (ADS)

    Gaimard, J.-J.; Schmidt, K.-H.

    1991-09-01

    The nuclear fragmentation reaction is studied as an important production mechanism for secondary beams. The geometrical abrasion model and a macroscopic evaporation model which describe the two steps of the reaction are reexamined. Several improvements and modifications of these models are discussed and a new model description incorporating these elements is proposed. In particular, the excitation energy and the angular-momentum distribution of the prefragments, the formulation of evaporation as a diffusion process and the role of microscopic structure in the production cross section are considered. The new model description preserves the simplicity and the transparency of the original models. The prediction of the new model are compared to those of the original models and to experimental cross sections. While the original models showed several systematic discrepancies in comparison to measured cross sections, the new model is able to reproduce the whole body of experimental data with satisfactory agreement.

  15. Genome-scale Metabolic Reaction Modeling: a New Approach to Geomicrobial Kinetics

    NASA Astrophysics Data System (ADS)

    McKernan, S. E.; Shapiro, B.; Jin, Q.

    2014-12-01

    Geomicrobial rates, rates of microbial metabolism in natural environments, are a key parameter of theoretical and practical problems in geobiology and biogeochemistry. Both laboratory- and field-based approaches have been applied to study rates of geomicrobial processes. Laboratory-based approaches analyze geomicrobial kinetics by incubating environmental samples under controlled laboratory conditions. Field methods quantify geomicrobial rates by observing the progress of geomicrobial processes. To take advantage of recent development in biogeochemical modeling and genome-scale metabolic modeling, we suggest that geomicrobial rates can also be predicted by simulating metabolic reaction networks of microbes. To predict geomicrobial rates, we developed a genome-scale metabolic model that describes enzyme reaction networks of microbial metabolism, and simulated the network model by accounting for the kinetics and thermodynamics of enzyme reactions. The model is simulated numerically to solve cellular enzyme abundance and hence metabolic rates under the constraints of cellular physiology. The new modeling approach differs from flux balance analysis of system biology in that it accounts for the thermodynamics and kinetics of enzymatic reactions. It builds on subcellular metabolic reaction networks, and hence also differs from classical biogeochemical reaction modeling. We applied the new approach to Methanosarcina acetivorans, an anaerobic, marine methanogen capable of disproportionating acetate to carbon dioxide and methane. The input of the new model includes (1) enzyme reaction network of acetoclastic methanogenesis, and (2) representative geochemical conditions of freshwater sedimentary environments. The output of the simulation includes the proteomics, metabolomics, and energy and matter fluxes of M. acetivorans. Our simulation results demonstrate the predictive power of the new modeling approach. Specifically, the results illustrate how methanogenesis rates vary

  16. 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.

  17. 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.

  18. 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.

  19. Modeling compressive reaction and estimating model uncertainty in shock loaded porous samples of Hexanitrostilbene (HNS)

    NASA Astrophysics Data System (ADS)

    Brundage, Aaron; Gump, Jared

    2011-06-01

    Neat pressings of HNS powders have been used in many explosive applications for over 50 years. However, characterization of its crystalline properties has lagged that of other explosives, and the solid stress has been inferred from impact experiments or estimated from mercury porosimetry. This lack of knowledge of the precise crystalline isotherm can contribute to large model uncertainty in the reacted response of pellets to shock impact. At high impact stresses, deflagration-to-detonation transition (DDT) processes initiated by compressive reaction have been interpreted from velocity interferometry at the surface of distended HNS-FP pellets. In particular, the Baer-Nunziato multiphase model in CTH, Sandia's Eulerian, finite volume shock propagation code, was used to predict compressive waves in pellets having approximately a 60% theoretical maximum density (TMD). These calculations were repeated with newly acquired isothermal compression measurements of fine-particle HNS using diamond anvil cells to compress the sample and powder x-ray diffraction to obtain the sample volume at each pressure point. Hence, estimating the model uncertainty provides a simple method for conveying the impact of future model improvements based upon new experimental data.

  20. Modeling compressive reaction and estimating model uncertainty in shock loaded porous samples of hexanitrostilbene (HNS)

    NASA Astrophysics Data System (ADS)

    Brundage, Aaron L.; Gump, Jared C.

    2012-03-01

    Neat pressings of HNS powders have been used in many explosive applications for over 50 years. However, characterization of its crystalline properties has lagged that of other explosives, and the solid stress has been inferred from impact experiments or estimated from mercury porosimetry. This lack of knowledge of the precise crystalline isotherm can contribute to large model uncertainty in the reacted response of pellets to shock impact. At high impact stresses, deflagration-to-detonation transition (DDT) processes initiated by compressive reaction have been interpreted from velocity interferometry at the surface of distended HNS-FP pellets. In particular, the Baer-Nunziato multiphase model in CTH, Sandia's Eulerian, finite volume shock propagation code, was used to predict compressive waves in pellets having approximately a 60% theoretical maximum density (TMD). These calculations were repeated with newly acquired isothermal compression measurements of fineparticle HNS using diamond anvil cells to compress the sample and powder x-ray diffraction to obtain the sample volume at each pressure point. Hence, estimating the model uncertainty provides a simple method for conveying the impact of future model improvements based upon new experimental data.

  1. Bulk reaction modeling of ducts with and without mean flow

    NASA Astrophysics Data System (ADS)

    Kakoty, S. K.; Roy, V. K.

    2002-07-01

    A general formulation for analysis of sound field in a uniform flow duct lined with bulk-reacting sound-absorbing material is presented here. Presented theoretical model predicts the rate of attenuation for symmetric as well as asymmetric modes in rectangular duct lined with loosely bound (bulk-reacting) sound-absorbing material, which allows acoustic propagation through the lining. The nature of attenuation in rectangular ducts lined on two and four sides with and without mean flow is discussed. Computed results are compared with published theoretical and experimental results. The presented model can be used as guidelines for the acoustic design of silencers, air-conditioning ducts, industrial fans, and other similar applications. copyright 2002 Acoustical Society of America.

  2. 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

  3. Dependence of X-Ray Burst Models on Nuclear Reaction Rates

    NASA Astrophysics Data System (ADS)

    Cyburt, R. H.; Amthor, A. M.; Heger, A.; Johnson, E.; Keek, L.; Meisel, Z.; Schatz, H.; Smith, K.

    2016-10-01

    X-ray bursts are thermonuclear flashes on the surface of accreting neutron stars, and reliable burst models are needed to interpret observations in terms of properties of the neutron star and the binary system. We investigate the dependence of X-ray burst models on uncertainties in (p, γ), (α, γ), and (α, p) nuclear reaction rates using fully self-consistent burst models that account for the feedbacks between changes in nuclear energy generation and changes in astrophysical conditions. A two-step approach first identified sensitive nuclear reaction rates in a single-zone model with ignition conditions chosen to match calculations with a state-of-the-art 1D multi-zone model based on the Kepler stellar evolution code. All relevant reaction rates on neutron-deficient isotopes up to mass 106 were individually varied by a factor of 100 up and down. Calculations of the 84 changes in reaction rate with the highest impact were then repeated in the 1D multi-zone model. We find a number of uncertain reaction rates that affect predictions of light curves and burst ashes significantly. The results provide insights into the nuclear processes that shape observables from X-ray bursts, and guidance for future nuclear physics work to reduce nuclear uncertainties in X-ray burst models.

  4. Toward a reaction rate model of condensed-phase RDX decomposition under high temperatures

    NASA Astrophysics Data System (ADS)

    Schweigert, Igor

    2015-06-01

    Shock ignition of energetic molecular solids is driven by microstructural heterogeneities, at which even moderate stresses can result in sufficiently high temperatures to initiate material decomposition and chemical energy release. Mesoscale modeling of these ``hot spots'' requires a reaction rate model that describes the energy release with a sub-microsecond resolution and under a wide range of temperatures. No such model is available even for well-studied energetic materials such as RDX. In this presentation, I will describe an ongoing effort to develop a reaction rate model of condensed-phase RDX decomposition under high temperatures using first-principles molecular dynamics, transition-state theory, and reaction network analysis. This work was supported by the Naval Research Laboratory, by the Office of Naval Research, and by the DoD High Performance Computing Modernization Program Software Application Institute for Multiscale Reactive Modeling of Insensitive Munitions.

  5. Toward a reaction rate model of condensed-phase RDX decomposition under high temperatures

    NASA Astrophysics Data System (ADS)

    Schweigert, Igor

    2014-03-01

    Shock ignition of energetic molecular solids is driven by microstructural heterogeneities, at which even moderate stresses can result in sufficiently high temperatures to initiate material decomposition and the release of the chemical energy. Mesoscale modeling of these ``hot spots'' requires a chemical reaction rate model that describes the energy release with a sub-microsecond resolution and under a wide range of temperatures. No such model is available even for well-studied energetic materials such as RDX. In this presentation, I will describe an ongoing effort to develop a reaction rate model of condensed-phase RDX decomposition under high temperatures using first-principles molecular dynamics, transition-state theory, and reaction network analysis. This work was supported by the Naval Research Laboratory, by the Office of Naval Research, and by the DOD High Performance Computing Modernization Program Software Application Institute for Multiscale Reactive Modeling of Insensitive Munitions.

  6. Exercise activates compensatory thermoregulatory reaction in rats: a modeling study.

    PubMed

    Yoo, Yeonjoo; LaPradd, Michelle; Kline, Hannah; Zaretskaia, Maria V; Behrouzvaziri, Abolhassan; Rusyniak, Daniel E; Molkov, Yaroslav I; Zaretsky, Dmitry V

    2015-12-15

    The importance of exercise is increasingly emphasized for maintaining health. However, exercise itself can pose threats to health such as the development of exertional heat shock in warm environments. Therefore, it is important to understand how the thermoregulation system adjusts during exercise and how alterations of this can contribute to heat stroke. To explore this we measured the core body temperature of rats (Tc) running for 15 min on a treadmill at various speeds in two ambient temperatures (Ta = 25°C and 32°C). We assimilated the experimental data into a mathematical model that describes temperature changes in two compartments of the body, representing the muscles and the core. In our model the core body generates heat to maintain normal body temperature, and dissipates it into the environment. The muscles produce additional heat during exercise. According to the estimation of model parameters, at Ta = 25°C, the heat generation in the core was progressively reduced with the increase of the treadmill speed to compensate for a progressive increase in heat production by the muscles. This compensation was ineffective at Ta = 32°C, which resulted in an increased rate of heat accumulation with increasing speed, as opposed to the Ta = 25°C case. Interestingly, placing an animal on a treadmill increased heat production in the muscles even when the treadmill speed was zero. Quantitatively, this "ready-to-run" phenomenon accounted for over half of the heat generation in the muscles observed at maximal treadmill speed. We speculate that this anticipatory response utilizes stress-related circuitry.

  7. 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.

  8. 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.

  9. A GPU Reaction Diffusion Soil-Microbial Model

    NASA Astrophysics Data System (ADS)

    Falconer, Ruth; Houston, Alasdair; Schmidt, Sonja; Otten, Wilfred

    2014-05-01

    Parallelised algorithms are frequent in bioinformatics as a consequence of the close link to informatics - however in the field of soil science and ecology they are less prevalent. A current challenge in soil ecology is to link habitat structure to microbial dynamics. Soil science is therefore entering the 'big data' paradigm as a consequence of integrating data pertinent to the physical soil environment obtained via imaging and theoretical models describing growth and development of microbial dynamics permitting accurate analyses of spatio-temporal properties of different soil microenvironments. The microenvironment is often captured by 3D imaging (CT tomography) which yields large datasets and when used in computational studies the physical sizes of the samples that are amenable to computation are less than 1 cm3. Today's commodity graphics cards are programmable and possess a data parallel architecture that in many cases is capable of out-performing the CPU in terms of computational rates. The programmable aspect is achieved via a low-level parallel programming language (CUDA, OpenCL and DirectX). We ported a Soil-Microbial Model onto the GPU using the DirectX Compute API. We noted a significant computational speed up as well as an increase in the physical size that can be simulated. Some of the drawbacks of such an approach were concerned with numerical precision and the steep learning curve associated with GPGPU technologies.

  10. 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.

  11. 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.

  12. Collecting, preparing, crossdating, and measuring tree increment cores

    USGS Publications Warehouse

    Phipps, R.L.

    1985-01-01

    Techniques for collecting and handling increment tree cores are described. Procedures include those for cleaning and caring for increment borers, extracting the sample from a tree, core surfacing, crossdating, and measuring. (USGS)

  13. 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.

  14. Reactions of coal model compounds in tetralin using microwave energy: Effects of catalysts

    SciTech Connect

    Eray, E.; Yagmur, E.; Simsek, E.H.; Alibeyli, R.; Togrul, T.

    2006-10-01

    Reaction mechanisms of model compounds of coal in tetralin by microwave energy were investigated. Diphenylmethane (DFM), phenyl-methyl ether (anisole), and phenyl-methyl ketone (acetophenon) were chosen as model compounds. Experiments were carried out for 10 minutes of microwave energy and different catalysts were used (pyratol, zeolite, BaCl{sub 2}, AlNiMo) to find out the distribution of reaction products of the model compounds. GC and GC/MS are used to analyze the reaction products. The main reaction products from DFM and tetralin under microwave radiation with catalysts were ethyl benzene, naphthalene, 2-methyl naphthalene, 3,4-dihydronaphthaleneone, 1-1'-ethyldene 1-benzene, and 1-methyl 4-phenyl methyl benzene. The main reaction products from anisole and tetralin under microwave radiation were ethyl benzene, phenol, methyl phenol, decahydronaphthalene, and tetrahydronaphthalenol. The main reaction products from acetophenon and tetralin under microwave radiation with catalysts were ethyl benzene, methoxy benzene, decahydronaphthalene, naphthalene, tetrahydronaphthalenol, 3,4-dihydronaphthalenone and 2-butene-1-one-1,3 diphenyl. The estimated mechanism of the model compounds with tetralin is compared with the results taken from GC/MS analysis. It is obtained that the results suggested theoretically were similar with the GC/MS results.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. A measurement model for general noise reaction in response to aircraft noise.

    PubMed

    Kroesen, Maarten; Schreckenberg, Dirk

    2011-01-01

    In this paper a measurement model for general noise reaction (GNR) in response to aircraft noise is developed to assess the performance of aircraft noise annoyance and a direct measure of general reaction as indicators of this concept. For this purpose GNR is conceptualized as a superordinate latent construct underlying particular manifestations. This conceptualization is empirically tested through estimation of a second-order factor model. Data from a community survey at Frankfurt Airport are used for this purpose (N=2206). The data fit the hypothesized factor structure well and support the conceptualization of GNR as a superordinate construct. It is concluded that noise annoyance and a direct measure of general reaction to noise capture a large part of the negative feelings and emotions in response to aircraft noise but are unable to capture all relevant variance. The paper concludes with recommendations for the valid measurement of community reaction and several directions for further research.

  1. Multicomponent transport with coupled geochemical and microbiological reactions: model description and example simulations

    NASA Astrophysics Data System (ADS)

    Tebes-Stevens, Caroline; J. Valocchi, Albert; VanBriesen, Jeanne M.; Rittmann, Bruce E.

    1998-08-01

    A reactive transport code (FEREACT) has been developed to examine the coupled effects of two-dimensional steady-state groundwater flow, equilibrium aqueous speciation reactions, and kinetically-controlled interphase reactions. The model uses an iterative two-step (SIA-1) solution algorithm to incorporate the effects of the geochemical and microbial reaction processes in the governing equation for solute transport in the subsurface. This SIA-1 method improves upon the convergence behavior of the traditional sequential iterative approach (SIA) through the inclusion of an additional first-order term from the Taylor Series expansion of the kinetic reaction rate expressions. The ability of FEREACT to simulate coupled reactive processes was demonstrated by modeling the transport of a radionuclide (cobalt, 60Co 2+) and an organic ligand (ethylenediaminetetraacetate, EDTA 4-) through a column packed with an iron oxide-coated sand. The reaction processes considered in this analysis included equilibrium aqueous speciation reactions and three types of kinetic reactions: adsorption, surface dissolution, and biodegradation.

  2. 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.

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

    DOE PAGES

    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.

  4. Combined activation strain model and energy decomposition analysis methods: a new way to understand pericyclic reactions.

    PubMed

    Fernández, Israel

    2014-05-01

    The recently introduced activation strain model (ASM) has allowed us to gain more insight into the intimacies of different fundamental processes in chemistry. In combination with the energy decomposition analysis (EDA) method, we have nowadays a very useful tool to quantitatively understand the physical factors that govern the activation barriers of reactions within organic and organometallic chemistry. In this Perspective article, we present selected illustrative examples of the application of this method to pericyclic reactions (Diels-Alder and double group transfer reactions) to show that this methodology nicely complements other more traditional, widely used theoretical methods.

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

    PubMed

    García, Andrés; Wang, Jing; Windus, Theresa L; Sadow, Aaron D; Evans, James W

    2016-05-01

    Statistical mechanical modeling is developed to describe a catalytic conversion reaction A→B^{c} or B^{t} with concentration-dependent selectivity of the products, B^{c} or B^{t}, 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. Furthermore, 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.

  6. 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.

  7. Standing wave patterns in CO oxidation reaction on Pt(110) surface: Experiments and modeling

    SciTech Connect

    Oertzen, A. von; Rotermund, H.H.; Mikhailov, A.S.; Ertl, G.

    2000-04-13

    Standing waves are a special type of spatio-temporal pattern observed in the CO oxidation reaction on Pt(110). The authors present new experimental data that indicate the important role played by the formation of subsurface oxygen. The formation of these patterns is correlated with reflective collisions of traveling waves that have previously been found in the same reaction. They also show that global coupling through the gas phase and external forcing are essential for stabilizing and synchronizing the standing wave patterns. The principal properties of the observed patterns are reproduced by numerical simulations based on an extended reaction-diffusion model.

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

    NASA Astrophysics Data System (ADS)

    García, Andrés; Wang, Jing; Windus, Theresa L.; Sadow, Aaron D.; Evans, James W.

    2016-05-01

    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. Furthermore, 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 .

  9. 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. PMID:25150626

  10. 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...

  11. 48 CFR 3452.232-71 - Incremental funding.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 7 2010-10-01 2010-10-01 false Incremental funding. 3452... 3452.232-71 Incremental funding. As prescribed in 3452.771, insert the following provision in solicitations: Incremental Funding (AUG 1987) (a) Sufficient funds are not presently available to cover...

  12. 14 CFR § 1260.53 - 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. § 1260.53 Section § 1260.53 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION GRANTS AND COOPERATIVE AGREEMENTS General Special Conditions § 1260.53 Incremental funding. Incremental Funding October 2000...

  13. Stability and bifurcation in a reaction-diffusion model with nonlocal delay effect

    NASA Astrophysics Data System (ADS)

    Guo, Shangjiang

    2015-08-01

    In this paper, the existence, stability, and multiplicity of spatially nonhomogeneous steady-state solution and periodic solutions for a reaction-diffusion model with nonlocal delay effect and Dirichlet boundary condition are investigated by using Lyapunov-Schmidt reduction. Moreover, we illustrate our general results by applications to models with a single delay and one-dimensional spatial domain.

  14. General model of a cascade of reactions with time delays: Global stability analysis

    NASA Astrophysics Data System (ADS)

    Bodnar, Marek

    2015-07-01

    The problem considered in this paper consists of a cascade of reactions with discrete as well as distributed delays, which arose in the context of Hes1 gene expression. For the abstract general model sufficient conditions for global stability are presented. Then the abstract result is applied to the Hes1 model.

  15. 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.

  16. Finite element modeling of contaminant transport in soils including the effect of chemical reactions.

    PubMed

    Javadi, A A; Al-Najjar, M M

    2007-05-17

    The movement of chemicals through soils to the groundwater is a major cause of degradation of water resources. In many cases, serious human and stock health implications are associated with this form of pollution. Recent studies have shown that the current models and methods are not able to adequately describe the leaching of nutrients through soils, often underestimating the risk of groundwater contamination by surface-applied chemicals, and overestimating the concentration of resident solutes. Furthermore, the effect of chemical reactions on the fate and transport of contaminants is not included in many of the existing numerical models for contaminant transport. In this paper a numerical model is presented for simulation of the flow of water and air and contaminant transport through unsaturated soils with the main focus being on the effects of chemical reactions. The governing equations of miscible contaminant transport including advection, dispersion-diffusion and adsorption effects together with the effect of chemical reactions are presented. The mathematical framework and the numerical implementation of the model are described in detail. The model is validated by application to a number of test cases from the literature and is then applied to the simulation of a physical model test involving transport of contaminants in a block of soil with particular reference to the effects of chemical reactions. Comparison of the results of the numerical model with the experimental results shows that the model is capable of predicting the effects of chemical reactions with very high accuracy. The importance of consideration of the effects of chemical reactions is highlighted.

  17. 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

  18. 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.

  19. Examining a social reaction model in the prediction of adolescent alcohol use.

    PubMed

    Litt, Dana M; Lewis, Melissa A

    2016-09-01

    The prototype willingness model (PWM; Gerrard et al., 2008) is a modified dual-processing model designed to improve the predictive value of existing health risk behavior by suggesting that there are two pathways to health risk behaviors: a reasoned path that is mediated by behavioral intention and a social reaction path that is mediated by behavioral willingness. Although there is evidence supporting the social reaction path to risk behavior among adolescents, most of this work has focused on specific components of the pathway such as prototypes or willingness rather than looking at the entire social reaction pathway as a whole. As such, the primary goal of the present study was to determine whether the social reaction pathway has acceptable fit for a sample of adolescents using a longitudinal design. Results from 835 adolescents support the social reaction pathway of the PWM model when applied to adolescent alcohol use. Specifically, prototypes, perceived vulnerability, and norms predicted willingness to drink, which in turn predicted drinking behavior (drinks per week and peak number of drinks) over a period of 12months. As such, these findings suggest that the social reaction pathway of the PWM is applicable to adolescent drinkers, meaning that adolescent drinking behavior is based on a less planned and socially based decision process. PMID:27155242

  20. 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.

  1. Model for anodic film growth on aluminum with coupled bulk transport and interfacial reactions.

    PubMed

    DeWitt, Stephen; Thornton, Katsuyo

    2014-05-13

    Films grown through the anodic oxidation of metal substrates are promising for applications ranging from solar cells to medical devices, but the underlying mechanisms of anodic growth are not fully understood. To provide a better understanding of these mechanisms, we present a new 1D model for the anodization of aluminum. In this model, a thin space charge region at the oxide/electrolyte interface couples the bulk ionic transport and the interfacial reactions. Charge builds up in this region, which alters the surface overpotential until the reaction and bulk fluxes are equal. The model reactions at the oxide/electrolyte interface are derived from the Våland-Heusler model, with modifications to allow for deviations from stoichiometry at the interface and the saturation of adsorption sites. The rate equations and equilibrium concentrations of adsorbed species at the oxide/electrolyte interface are obtained from the reactions using Butler-Volmer kinetics, whereas transport-limited reaction kinetics are utilized at the metal/oxide interface. The ionic transport through the bulk oxide is modeled using a newly proposed cooperative transport process, the counter-site defect mechanism. The model equations are evolved numerically. The model is parametrized and validated using experimental data in the literature for the rate of ejection of aluminum species into the electrolyte, embedded charge at the oxide/electrolyte interface, and the barrier thickness and growth rate of porous films. The parametrized model predicts that the embedded charge at the oxide/electrolyte interface decreases monotonically for increasing electrolyte pH at constant current density. The parametrized model also predicts that the embedded charge during potentiostatic anodization is at its steady-state value; the embedded charge at any given time is equal to the embedded charge during galvanostatic anodization at the same current. In addition to simulations of anodized barrier films, this model can be

  2. 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

  3. 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

  4. Steady deflagration of HMX with simple kinetics: A gas phase chain reaction model

    SciTech Connect

    Ward, M.J.; Brewster, M.Q.; Son, S.F.

    1998-08-01

    A new approach is presented for modeling steady combustion of energetic solids, in particular HMX. A simplified, global, gas phase chain reaction kinetic mechanism is employed. Specifically, a zero-order, high activation energy thermal decomposition initiation reaction in the condensed phase followed by a second-order, low activation energy chain reaction in the gas phase is assumed. A closed-form solution is obtained, which is based on the activation energy asymptotics analysis of Lengelle in the condensed phase and the assumption of zero activation energy in the gas phase. Comparisons between the model and a variety of experimental observations over a wide range of pressures and initial temperatures are presented and demonstrate the validity of the approach. The model provides excellent agreement with burning rate data (including sensitivity to pressure and initial temperature) and temperature profile data (in particular the gas phase). This suggests that in the realm of simplified, approximate kinetics modeling of energetic solids, the low gas phase activation energy limit is a more appropriate model than the classical high activation energy limit or heuristic flame sheet models. The model also indicates that the condensed phase reaction zone plays an important role in determining the deflagration rate of HMX, underscoring the need for better understanding of the chemistry in this zone.

  5. 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.

  6. Advanced Solution Methods for Microkinetic Models of Catalytic Reactions: A Methanol Synthesis Case Study

    SciTech Connect

    Rubert-Nason, Patricia; Mavrikakis, Manos; Maravelias, Christos T.; Grabow, Lars C.; Biegler, Lorenz T.

    2014-04-01

    Microkinetic models, combined with experimentally measured reaction rates and orders, play a key role in elucidating detailed reaction mechanisms in heterogeneous catalysis and have typically been solved as systems of ordinary differential equations. In this work, we demonstrate a new approach to fitting those models to experimental data. For the specific example treated here, by reformulating a typical microkinetic model for a continuous stirred tank reactor to a system of nonlinear equations, we achieved a 1000-fold increase in solution speed. The reduced computational cost allows a more systematic search of the parameter space, leading to better fits to the available experimental data. We applied this approach to the problem of methanol synthesis by CO/CO2 hydrogenation over a supported-Cu catalyst, an important catalytic reaction with a large industrial interest and potential for large-scale CO2 chemical fixation.

  7. Reaction-diffusion models of growing plant tips: bifurcations on hemispheres.

    PubMed

    Nagata, Wayne; Harrison, Lionel G; Wehner, Stephan

    2003-07-01

    We study two chemical models for pattern formation in growing plant tips. For hemisphere radius and parameter values together optimal for spherical surface harmonic patterns of index l = 3, the Brusselator model gives an 84% probability of dichotomous branching pattern and 16% of annular pattern, while the hyperchirality model gives 88% probability of dichotomous branching and 12% of annular pattern. The models are two-morphogen reaction-diffusion systems on the surface of a hemispherical shell, with Dirichlet boundary conditions. Bifurcation analysis shows that both models give possible mechanisms for dichotomous branching of the growing tips. Symmetries of the models are used in the analysis. PMID:12875335

  8. Nuclear Reactions X-Sections By Evaporation Model, Gamma-Cascades

    2000-06-27

    Calculation of energy-averaged cross sections for nuclear reactions with emission of particles and gamma rays and fission. The models employed are the evaporation model with inclusion of pre-equilibrium decay and gamma ray cascade model. Angular momentum and parity conservation are accounted for. Major improvement to the 1976 STAPRE program (NEA 0461) relates to level density approach, implemwnted in subroutine ZSTDE. Generalized superfluid model is incorporated, Boltzman-gas modelling of intrinsic state density and semi-empirical modelling ofmore » a few quasiparticle effects in total level density in equilibrium and saddle deformations of actinide nuclei.« less

  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. Modeling of Turing Structures in the Chlorite-Iodide-Malonic Acid-Starch Reaction System

    NASA Astrophysics Data System (ADS)

    Lengyel, Istivan; Epstein, Irving R.

    1991-02-01

    Recent experiments on the chlorite-iodide-malonic acid-starch reaction in a gel reactor give the first evidence of the existence of the symmetry breaking, reaction-diffusion structures predicted by Turing in 1952. A five-variable model that describes the temporal behavior of the system is reduced to a two-variable model, and its spatial behavior is analyzed. Structures have been found with wavelengths that are in good agreement with those observed experimentally. The gel plays a key role by binding key iodine species, thereby creating the necessary difference in the effective diffusion coefficients of the activator and inhibitor species, iodide and chlorite ions, respectively.

  11. 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.

  12. Application of a Sequential Reaction Model to PANS and Aldehyde Measurements in Two Urban Areas

    SciTech Connect

    Roberts, James M.; Stroud, C.; Jobson, B Tom T.; Trainer, Michael; Hereid, D.; Williams, E. J.; Fehsenfeld, Fred C.; Brune, W. H.; Martinez, M.; Harder, H.

    2001-12-15

    Measurements of peroxycarboxylic nitric anhydrides (= PAN, PPN, MPAN) and aldehydes (acetaldehyde, propanal, and methacrolein) were made at Nashville, Tennessee, in 1999 and Houston, Texas, in 2000. The data were interpreted with a sequential reaction model that included reaction of aldehydes with hydroxl radical and formation or loss of PANs mediated by peroxyacyl radicals. The comparison of the measured ratios with those predicted by the model showed disagreement for PAN/acetaldehyde and PPN/propanal in Nashville but agreement in Houston. These features are consistent with the relative importance of isoprene to PAN formation at each site.

  13. 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.

  14. 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.

  15. 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.

  16. Gradual wavelet reconstruction of the velocity increments for turbulent wakes

    NASA Astrophysics Data System (ADS)

    Keylock, C. J.; Stresing, R.; Peinke, J.

    2015-02-01

    This work explores the properties of the velocity increment distributions for wakes of contrasting local Reynolds number and nature of generation (a cylinder wake and a multiscale-forced case, respectively). It makes use of a technique called gradual wavelet reconstruction (GWR) to generate constrained randomizations of the original data, the nature of which is a function of a parameter, ϑ. This controls the proportion of the energy between the Markov-Einstein length (˜ 0.8 Taylor scales) and integral scale that is fixed in place in the synthetic data. The properties of the increments for these synthetic data are then compared to the original data as a function of ϑ. We write a Fokker-Planck equation for the evolution of the velocity increments as a function of spatial scale, r, and, in line with previous work, expand the drift and diffusion terms in terms up to fourth order in the increments and find no terms are relevant beyond the quadratic terms. Only the linear contribution to the expansion of the drift coefficient is non-zero and it exhibits a consistent scaling with ϑ for different flows above a low threshold. For the diffusion coefficient, we find a local Reynolds number independence in the relation between the constant term and ϑ for the multiscale-forced wakes. This term characterizes small scale structure and can be contrasted with the results for the Kolmogorov capacity of the zero-crossings of the velocity signals, which measures structure over all scales and clearly distinguishes between the types of forcing. Using GWR shows that results for the linear and quadratic terms in the expansion of the diffusion coefficient are significant, providing a new means for identifying intermittency and anomalous scaling in turbulence datasets. All our data showed a similar scaling behavior for these parameters irrespective of forcing type or Reynolds number, indicating a degree of universality to the anomalous scaling of turbulence. Hence, these terms are a

  17. Quantitative models of hydrothermal fluid-mineral reaction: The Ischia case

    NASA Astrophysics Data System (ADS)

    Di Napoli, Rossella; Federico, Cinzia; Aiuppa, Alessandro; D'Antonio, Massimo; Valenza, Mariano

    2013-03-01

    The intricate pathways of fluid-mineral reactions occurring underneath active hydrothermal systems are explored in this study by applying reaction path modelling to the Ischia case study. Ischia Island, in Southern Italy, hosts a well-developed and structurally complex hydrothermal system which, because of its heterogeneity in chemical and physical properties, is an ideal test sites for evaluating potentialities/limitations of quantitative geochemical models of hydrothermal reactions. We used the EQ3/6 software package, version 7.2b, to model reaction of infiltrating waters (mixtures of meteoric water and seawater in variable proportions) with Ischia's reservoir rocks (the Mount Epomeo Green Tuff units; MEGT). The mineral assemblage and composition of such MEGT units were initially characterised by ad hoc designed optical microscopy and electron microprobe analysis, showing that phenocrysts (dominantly alkali-feldspars and plagioclase) are set in a pervasively altered (with abundant clay minerals and zeolites) groundmass. Reaction of infiltrating waters with MEGT minerals was simulated over a range of realistic (for Ischia) temperatures (95-260 °C) and CO2 fugacities (10-0.2 to 100.5) bar. During the model runs, a set of secondary minerals (selected based on independent information from alteration minerals' studies) was allowed to precipitate from model solutions, when saturation was achieved. The compositional evolution of model solutions obtained in the 95-260 °C runs were finally compared with compositions of Ischia's thermal groundwaters, demonstrating an overall agreement. Our simulations, in particular, well reproduce the Mg-depleting maturation path of hydrothermal solutions, and have end-of-run model solutions whose Na-K-Mg compositions well reflect attainment of full-equilibrium conditions at run temperature. High-temperature (180-260 °C) model runs are those best matching the Na-K-Mg compositions of Ischia's most chemically mature water samples

  18. 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.

  19. 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.

  20. Development of a physics-based degradation model for lithium ion polymer batteries considering side reactions

    NASA Astrophysics Data System (ADS)

    Fu, Rujian; Choe, Song-Yul; Agubra, Victor; Fergus, Jeffrey

    2015-03-01

    Experimental investigations conducted on a large format lithium ion polymer battery (LiPB) have revealed that side reactions taking place at anode are the major factor for degradation of the battery performance and lead to capacity and power fade. Side reactions consume ions and solvents from the electrolyte and produce deposits that increase the thickness of the solid electrolyte interphase (SEI) layer and form a new layer between composite anode and separator. These phenomena are described using physical principles based on the Tafel and Nernst equations that are integrated into the developed electrochemical-thermal model. The key parameters for the side reactions used in the model are experimentally determined from self-discharging behavior of the battery. The integrated model is then validated against experimental data obtained from different operating conditions. Analysis has revealed that the capacity fade is predominantly caused by loss of ions and active materials. The results also show that the rate of side reactions and degradations are more severe at charging process under high SOC and high C-rate due to low overpotential of the side reactions.

  1. Can Drosophila melanogaster represent a model system for the detection of reproductive adverse drug reactions?

    PubMed

    Avanesian, Agnesa; Semnani, Sahar; Jafari, Mahtab

    2009-08-01

    Once a molecule is identified as a potential drug, the detection of adverse drug reactions is one of the key components of its development and the FDA approval process. We propose using Drosophila melanogaster to screen for reproductive adverse drug reactions in the early stages of drug development. Compared with other non-mammalian models, D. melanogaster has many similarities to the mammalian reproductive system, including putative sex hormones and conserved proteins involved in genitourinary development. Furthermore, the D. melanogaster model would present significant advantages in time efficiency and cost-effectiveness compared with mammalian models. We present data on methotrexate (MTX) reproductive adverse events in multiple animal models, including fruit flies, as proof-of-concept for the use of the D. melanogaster model. PMID:19482095

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Health care reform? An American obsession with prescriptive incrementalism.

    PubMed

    Broyles, R W; Falcone, D J

    1996-01-01

    A rounded evaluation of the national health insurance proposals that now seem to be taken seriously by political elites requires conceptual organization. This article adopts a typology that describes each major proposal as a social, mixed or a private insurance scheme depending on the source(s) of funding, method of compensating hospitals and physicians, the unit of payment, and mechanism for financing capital. Not surprisingly, the analysis suggests that the social insurance model, closely resembling the Canadian system, is more likely to control inflation and redress distributional inequities than are other approaches. Why, then, has this approach not been adopted? The answer may be found in the widespread acceptance of disjointed incrementalism as a valid description of the policy process which yields an ideological orientation that can be termed "prescriptive incrementalism." This orientation is closely related to a belief in an "American exceptionalism," a belief that is not warranted by a cross-sectional examination of the political culture infusing issues about the proper role of government in health care financing and delivery. Unfortunately for advocates, the truly exceptional factor restricting the United States' ability to effect national health reform is a quite delberately obstruction-oriented political structure.

  7. Evaluation of the dimensional accuracy in single point incremental forming

    NASA Astrophysics Data System (ADS)

    Araújo, R.; Silva, M. B.; Montanari, L.; Teixeira, P.; Reis, A.; Martins, P. A. F.

    2013-12-01

    Incremental Sheet Forming (ISF) is a forming process widely used to obtain small batches or prototypes. By improving forming strategies, the process can be used in a wide range of applications. However, this technology still presents some drawbacks. The dimensional accuracy between the 3D CAD model and the final product is one of the key challenges for this technique. The springback phenomenon during the incremental forming process is an important reason for the lack of accuracy. In order to study the mechanism of this phenomenon, the geometry of the sheet metal was measured in two different stages of the conventional production chain. First, the geometry of the sheet metal part was acquired after the forming stage, without be released from the blank holder. Then, the final geometry was achieved after the cutting process from the original sheet. A 3D scanning system was used to measure and inspect the springback phenomenon of each step. A reverse method is proposed to design the new tool path for compensation of the springback.

  8. Thermal modelling of battery configuration and self-discharge reactions in vanadium redox flow battery

    NASA Astrophysics Data System (ADS)

    Tang, Ao; Bao, Jie; Skyllas-Kazacos, Maria

    2012-10-01

    During the operation of vanadium redox flow battery, the vanadium ions diffuse across the membrane as a result of concentration gradients between the two half-cells in the stack, leading to self-discharge reactions in both half-cells that will release heat to the electrolyte and subsequently increase the electrolyte temperature. In order to avoid possible thermal precipitation in the electrolyte solution and prevent possible overheating of the cell components, the electrolyte temperature needs to be known. In this study, the effect of the self-discharge reactions was incorporated into a thermal model based on energy and mass balances, developed for the purpose of electrolyte temperature control. Simulations results have shown that the proposed model can be used to investigate the thermal effect of the self-discharge reactions on both continuous charge-discharge cycling and during standby periods, and can help optimize battery designs and fabrication for different applications.

  9. 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. PMID:27283710

  10. Modeling pore collapse and chemical reactions in shock-loaded HMX crystals

    NASA Astrophysics Data System (ADS)

    Austin, R. A.; Barton, N. R.; Howard, W. M.; Fried, L. E.

    2014-05-01

    The localization of deformation in shock-loaded crystals of high explosive material leads to the formation of hot spots, which, if hot enough, initiate chemical reactions. The collapse of microscopic pores contained within a crystal is one such process that localizes energy and generates hot spots. Given the difficulty of resolving the details of pore collapse in shock compression experiments, it is useful to study the problem using direct numerical simulation. In this work, we focus on simulating the shock-induced closure of a single pore in crystalline β-HMX using a multiphysics finite element code. To address coupled thermal-mechanical-chemical responses, the model incorporates a crystal-mechanics-based description of thermoelasto-viscoplasticity, the crystal melting behavior, and transformation kinetics for a single-step decomposition reaction. The model is applied to stress wave amplitudes of up to 11 GPa to study the details of pore collapse, energy localization, and the early stages of reaction initiation.

  11. 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.

  12. Experimental and theoretical data on ion-molecule-reactions relevant for plasma modelling

    SciTech Connect

    Hansel, A.; Praxmarer, C.; Lindinger, W.

    1995-12-31

    Despite the fact that the rate coefficients of hundreds of ion-molecule-reactions have been published in the literature, much more data are required for the purpose of plasma modelling. Many ion molecule reactions have rate coefficients, k, as large as the collisional limiting value, k{sub c}, i.e. the rate coefficients k{sub c} at which ion-neutral collision complexes are formed are close to the actual rate coefficients observed. In the case of the interaction of an ion with a non polar molecule, k{sub c}, is determined by the Langevin limiting value k{sub L} being typically 10{sup -9} cm{sup 3} s{sup -1}. However, when ions react with polar molecules k{sub c} is predicted by the average dipole orientation (ADO) theory. These classical theories yield accurate rate coefficients at thermal and elevated temperatures for practically all proton transfer as well as for many charge transfer and hydrogen abstraction reactions. The agreement between experimental and calculated values is usually better than {plus_minus}20% and in the case of proton transfer reactions the agreement seems to be even better as recent investigations have shown. Even the interaction of the permanent ion dipole with non polar and polar neutrals can be taken into account to predict reaction rate coefficients as has been shown very recently in reactions of the highly polar ion ArH{sub 3}{sup +} with various neutrals.

  13. Mesoscale Simulations of Reaction Initiation and Growth in HE Composites using PBRB model

    NASA Astrophysics Data System (ADS)

    Dwivedi, Sunil; Brennan, John; Horie, Yasuyuki

    2013-06-01

    Two-dimensional (2D) finite element based mesoscale simulation results are presented to predict reaction initiation and growth in high energy (HE) composites using the physics based reactive urn (PBRB) model. The HE composites are modeled as an ensemble of grains with statistically-distributed second phase particles. Their shock response is modeled with elastic-inelastic deformation coupled with the PBRB equation-of-state model. The inter-grain response is described by the contact-cohesive model that allows grain boundary failure and creation of free surface with friction characteristics during compressive shock loading. The heat generation due to the non-linear elastic, inelastic, cohesive, and friction energy dissipation into pre-assumed statistically-distributed hot spots, surface sublimation, and gas phase reaction are described as coupled mechanisms by the PBRB model yielding the mean stress as a function of the reaction at any given time. The simulations predict the time and run to detonation with reasonable agreement with data. The relative merits of 1D hot spot idealization, embodied in the PBRB model, for generic mesoscale simulations will be discussed. This work is supported in part by the DTRA Grant HDTRA1-12-1-0004 and ARL Grant W911NF-12-2-0053.

  14. 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. PMID:26747638

  15. A reduced model for the ICF gamma-ray reaction history diagnostic

    SciTech Connect

    Schmitt, Mark J; Wilson, Douglas C; Hoffman, Nelson M; Langenbrunner, Jamie R; Hermann, 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

    2009-01-01

    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.

  16. 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 chalk is to…

  17. On the dynamics of a forced reaction-diffusion model for biological pattern formation.

    PubMed Central

    Tsonis, A A; Elsner, J B; Tsonis, P A

    1989-01-01

    Ideas from the theory of dynamical systems are applied in biological pattern formation. By considering a simple reaction-diffusion model subjected to an external excitation, we find that the system can give rise to a great variety of periodic, quasiperiodic, and chaotic evolutions. PMID:2740333

  18. Modeling Interfacial Glass-Water Reactions: Recent Advances and Current Limitations

    DOE PAGES

    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 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

  19. 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…

  20. Modeling Mechanism and Growth Reactions for New Nanofabrication Processes by Atomic Layer Deposition.

    PubMed

    Elliott, Simon D; Dey, Gangotri; Maimaiti, Yasheng; Ablat, Hayrensa; Filatova, Ekaterina A; Fomengia, Glen N

    2016-07-01

    Recent progress in the simulation of the chemistry of atomic layer deposition (ALD) is presented for technologically important materials such as alumina, silica, and copper metal. Self-limiting chemisorption of precursors onto substrates is studied using density functional theory so as to determine reaction pathways and aid process development. The main challenges for the future of ALD modeling are outlined.

  1. 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.

  2. 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.

  3. Application of the random pore model to the carbonation cyclic reaction

    SciTech Connect

    Grasa, G.; Murillo, R.; Alonso, M.; Abanades, J.C.

    2009-05-15

    Calcium oxide has been proved to be a suitable sorbent for high temperature CO{sub 2} capture processes based on the cyclic carbonation-calcination reaction. It is important to have reaction rate models that are able to describe the behavior of CaO particles with respect to the carbonation reaction. Fresh calcined lime is known to be a reactive solid toward carbonation, but the average sorbent particle in a CaO-based CO{sub 2} capture system experiences many carbonation-calcination cycles and the reactivity changes with the number of cycles. This study applies the random pore model (RPM) to estimate the intrinsic rate parameters for the carbonation reaction and develops a simple model to calculate particle conversion with time as a function of the number of cycles, partial pressure of CO{sub 2}, and temperature. This version of the RPM model integrates knowledge obtained in earlier works on intrinsic carbonation rates, critical product layer thickness, and pore structure evolution in highly cycled particles.

  4. 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.

  5. Educators' Year Long Reactions to the Implementation of a Response to Intervention (RTI) Model

    ERIC Educational Resources Information Center

    Sanger, Dixie; Friedli, Corey; Brunken, Cindy; Snow, Pamela; Ritzman, Mitzi

    2012-01-01

    Mixed methods were used to explore the reactions of educators before and after implementing the Response to Intervention (RTI) model in secondary settings during a school year. Eighteen participants from six middle schools and four high schools collaborated on interdisciplinary teams that involved classroom teachers, speech-language pathologists…

  6. 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.

  7. 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

  8. 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.

  9. Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions.

    PubMed

    Acevedo, Orlando; Jorgensen, Wiliiam L

    2014-09-01

    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

  10. 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.

  11. 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.

  12. 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.

  13. Controlling reactivity of nanoporous catalyst materials by tuning reaction product-pore interior interactions: Statistical mechanical modeling

    SciTech Connect

    Wang, Jing; Ackerman, David M.; Lin, Victor S.-Y.; Pruski, Marek; Evans, James W.

    2013-04-02

    Statistical mechanical modeling is performed of a catalytic conversion reaction within a functionalized nanoporous material to assess the effect of varying the reaction product-pore interior interaction from attractive to repulsive. A strong enhancement in reactivity is observed not just due to the shift in reaction equilibrium towards completion but also due to enhanced transport within the pore resulting from reduced loading. The latter effect is strongest for highly restricted transport (single-file diffusion), and applies even for irreversible reactions. The analysis is performed utilizing a generalized hydrodynamic formulation of the reaction-diffusion equations which can reliably capture the complex interplay between reaction and restricted transport.

  14. A Geochemical Reaction Model for Titration of Contaminated Soil and Groundwater at the Oak Ridge Reservation

    NASA Astrophysics Data System (ADS)

    Zhang, F.; Parker, J. C.; Gu, B.; Luo, W.; Brooks, S. C.; Spalding, B. P.; Jardine, P. M.; Watson, D. B.

    2007-12-01

    This study investigates geochemical reactions during titration of contaminated soil and groundwater at the Oak Ridge Reservation in eastern Tennessee. The soils and groundwater exhibits low pH and high concentrations of aluminum, calcium, magnesium, manganese, various trace metals such as nickel and cobalt, and radionuclides such as uranium and technetium. The mobility of many of the contaminant species diminishes with increasing pH. However, base additions to increase pH are strongly buffered by various precipitation/dissolution and adsorption/desorption reactions. The ability to predict acid-base behavior and associated geochemical effects is thus critical to evaluate remediation performance of pH manipulation strategies. This study was undertaken to develop a practical but generally applicable geochemical model to predict aqueous and solid-phase speciation during soil and groundwater titration. To model titration in the presence of aquifer solids, an approach proposed by Spalding and Spalding (2001) was utilized, which treats aquifer solids as a polyprotic acid. Previous studies have shown that Fe and Al-oxyhydroxides strongly sorb dissolved Ni, U and Tc species. In this study, since the total Fe concentration is much smaller than that of Al, only ion exchange reactions associated with Al hydroxides are considered. An equilibrium reaction model that includes aqueous complexation, precipitation, ion exchange, and soil buffering reactions was developed and implemented in the code HydroGeoChem 5.0 (HGC5). Comparison of model results with experimental titration curves for contaminated groundwater alone and for soil- water systems indicated close agreement. This study is expected to facilitate field-scale modeling of geochemical processes under conditions with highly variable pH to develop practical methods to control contaminant mobility at geochemically complex sites.

  15. 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

  16. 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.

  17. 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.

  18. Comparison of fast cascade plus statistical models for heavy ion induced multifragmentation reactions

    NASA Astrophysics Data System (ADS)

    Mustafa, M. G.; Blann, M.; Peilert, G.; Botvina, A.

    1994-05-01

    We consider the reaction 36Ar+197Au at incident 36Ar energies of 35, 50, 80, and 110A MeV, comparing calculations of precompound decay using the Boltzmann master equation (BME) and quantum molecular dynamics (QMD) models. We then estimate quasiequilibrated nuclei and excitations using the BME, and use these values as input into statistical multifragmentation models. For the latter we compare sequential binary decay as an extension of the Weisskopf-Ewing evaporation model, and a simultaneous multifragmentation for an expanded low density gas. The exclusive multiplicities predicted by these models are compared with experimental results.

  19. 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.

  20. 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.

  1. 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.

  2. 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…

  3. Validation of daily increments in otoliths of northern squawfish larvae

    USGS Publications Warehouse

    Wertheimer, R.H.; Barfoot, C.A.

    1998-01-01

    Otoliths from laboratory-reared northern squawfish, Ptychocheilus oregonensis, larvae were examined to determine the periodicity of increment deposition. Increment deposition began in both sagittae and lapilli after hatching. Reader counts indicated that increment formation was daily in sagittae of 1-29-day-old larvae. However, increment counts from lapilli were significantly less than the known ages of northern squawfish larvae, possibly because some increments were not detectable. Otolith readability and age agreement among readers were greatest for young (<11 days) northern squawfish larvae. This was primarily because a transitional zone of low-contrast material began forming in otoliths of 8-11-day-old larvae and persisted until approximately 20 days after hatching. Formation of the transition zone appeared to coincide with the onset of exogenous feeding and continued through yolk sac absorption. Our results indicate that aging wild-caught northern squawfish larvae using daily otolith increment counts is possible.

  4. Gamma emission in precompound reactions: 1, Statistical model and collective gamma decay

    SciTech Connect

    Hoering, A. Washington Univ., Seattle, WA . Inst. for Nuclear Theory); Weidenmueller, H.A. )

    1992-01-01

    We extend the theory of particle-induced precompound reactions by including gamma decay. We use the Brink-Axel hypothesis and consider the gamma emission of giant dipole resonances built on the ground state and on the excited states of the composite system. The latter are modeled as multiparticle multi-hole excitations. In this way, we combine the statistical ansatz and the chaining hypothesis typical for precompound reaction theories, with the collective aspects of gamma decay. Formulas for average S-matrix and average cross section are derived in this framework.

  5. Gamma emission in precompound reactions: 1, Statistical model and collective gamma decay

    SciTech Connect

    Hoering, A. |; Weidenmueller, H.A.

    1992-09-01

    We extend the theory of particle-induced precompound reactions by including gamma decay. We use the Brink-Axel hypothesis and consider the gamma emission of giant dipole resonances built on the ground state and on the excited states of the composite system. The latter are modeled as multiparticle multi-hole excitations. In this way, we combine the statistical ansatz and the chaining hypothesis typical for precompound reaction theories, with the collective aspects of gamma decay. Formulas for average S-matrix and average cross section are derived in this framework.

  6. Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations.

    PubMed

    Teraguchi, Shunsuke; Kumagai, Yutaro; Vandenbon, Alexis; Akira, Shizuo; Standley, Daron M

    2011-12-01

    We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic process, while reducing each biochemical quantity to a binary value at the level of individual cells. The system can be analytically represented by a finite set of ordinary linear differential equations, which provides a continuous time course prediction of each molecular state. Here we introduce our formalism and demonstrate it with several examples.

  7. 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.

  8. 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.

  9. Modeling pore collapse and chemical reactions in shock-loaded HMX crystals

    NASA Astrophysics Data System (ADS)

    Austin, Ryan; Barton, Nathan; Howard, William; Fried, Laurence

    2013-06-01

    The collapse of micron-sized pores in crystalline high explosives is the primary route to initiating thermal decomposition reactions under shock wave loading. Given the difficulty of resolving such processes in experiments, it is useful to study pore collapse using numerical simulation. A significant challenge that is encountered in such calculations is accounting for anisotropic mechanical responses and the effects of highly exothermic chemical reactions. In this work, we focus on simulating the shock-wave-induced collapse of a single pore in crystalline HMX using a multiphysics finite element code (ALE3D). The constitutive model set includes a crystal-mechanics-based model of thermoelasto-viscoplasticity and a single-step decomposition reaction with empirically determined kinetics. The model is exercised for shock stresses up to ~10 GPa to study the localization of energy about the collapsing pore and the early stages of reaction initiation. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 (LLNL-ABS-618941).

  10. Layered decomposition for the model order reduction of timescale separated biochemical reaction networks.

    PubMed

    Prescott, Thomas P; Papachristodoulou, Antonis

    2014-09-01

    Biochemical reaction networks tend to exhibit behaviour on more than one timescale and they are inevitably modelled by stiff systems of ordinary differential equations. Singular perturbation is a well-established method for approximating stiff systems at a given timescale. Standard applications of singular perturbation partition the state variable into fast and slow modules and assume a quasi-steady state behaviour in the fast module. In biochemical reaction networks, many reactants may take part in both fast and slow reactions; it is not necessarily the case that the reactants themselves are fast or slow. Transformations of the state space are often required in order to create fast and slow modules, which thus no longer model the original species concentrations. This paper introduces a layered decomposition, which is a natural choice when reaction speeds are separated in scale. The new framework ensures that model reduction can be carried out without seeking state space transformations, and that the effect of the fast dynamics on the slow timescale can be described directly in terms of the original species.

  11. 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.

  12. 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.

  13. 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. PMID:26512030

  14. 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.

  15. 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.

  16. 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.

  17. 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. PMID:18361641

  18. Ignition and Growth Modeling of Detonation Reaction Zone Experiments on Single Crystals of PETN and HMX

    NASA Astrophysics Data System (ADS)

    White, Bradley; Tarver, Craig

    2015-06-01

    Fedorov et al. reported nanosecond time resolved interface particle velocity records for detonation reaction zone profiles of single crystals of PETN and HMX with adjoining LiF windows. Von Neumann spike and Chapman-Jouguet pressures were measured, and reaction zone lengths and times wereinferred. The single crystal detonation velocities and von Neumann spike pressures are higher than those measured for heterogeneous PETN and HMX-based explosives pressed to 98-99% theoretical maximum density. Due to the absence of voids, the single crystal detonation reaction zone lengths and times for both PETN and HMX were longer than those for their heterogeneous explosives. Ignition and Growth modeling results are compared to the single crystal PETN and HMX measurements and to previous experimental results for pressed PETN and HMX charges. 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.

  19. 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.

  20. 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.

  1. Modeling spallation reactions in tungsten and uranium targets with the Geant4 toolkit

    NASA Astrophysics Data System (ADS)

    Malyshkin, Yury; Pshenichnov, Igor; Mishustin, Igor; Greiner, Walter

    2012-02-01

    We study primary and secondary reactions induced by 600 MeV proton beams in monolithic cylindrical targets made of natural tungsten and uranium by using Monte Carlo simulations with the Geant4 toolkit [1-3]. Bertini intranuclear cascade model, Binary cascade model and IntraNuclear Cascade Liège (INCL) with ABLA model [4] were used as calculational options to describe nuclear reactions. Fission cross sections, neutron multiplicity and mass distributions of fragments for 238U fission induced by 25.6 and 62.9 MeV protons are calculated and compared to recent experimental data [5]. Time distributions of neutron leakage from the targets and heat depositions are calculated. This project is supported by Siemens Corporate Technology.

  2. Generalized phenomenological model for the effect of electromigration on interfacial reaction

    NASA Astrophysics Data System (ADS)

    Hsu, Chia-Ming; Wong, David Shan-Hill; Chen, Sinn-Wen

    2007-07-01

    Intermetallic compound (IMC) formation is important for the reliability of microelectronic devices. In this work, a generalized phenomenological model was developed to explain the effects of electromigration on IMC growth by considering reaction and diffusion of two species. When both reaction and mass transfer are important, the model predicts cathode enhancement and anode thinning if the electromigration effect on the dominant diffusion species is more pronounced. Cathode suppression and anode enhancement occur when the electromigration effect on the minor diffusion species is more pronounced. Simultaneous cathode and anode suppressions happen when there are two diffusion species and the diffusion and electromigration fluxes are comparable. Simultaneous cathode and anode enhancements occur when mass transfer is the limiting step and diffusion flux is negligible compared to electromigration. This model was found to be consistent with experiment data on IMC growth in the literature given the limited amount of information on effective charge of various species.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. An analytical model of hydrogen evolution and oxidation reactions on electrodes partially covered with a catalyst.

    PubMed

    Kemppainen, Erno; Halme, Janne; Lund, Peter D

    2016-05-11

    Our previous theoretical study on the performance limits of the platinum (Pt) nanoparticle catalyst for the hydrogen evolution reaction (HER) had shown that the mass transport losses at a partially catalyst-covered planar electrode are independent of the catalyst loading. This suggests that the two-dimensional (2D) numerical model used could be simplified to a one-dimensional (1D) model to provide an easier but equally accurate description of the operation of these HER electrodes. In this article, we derive an analytical 1D model and show that it indeed gives results that are practically identical to the 2D numerical simulations. We discuss the general principles of the model and how it can be used to extend the applicability of existing electrochemical models of planar electrodes to low catalyst loadings suitable for operating photoelectrochemical devices under unconcentrated sunlight. Since the mass transport losses of the HER are often very sensitive to the H2 concentration, we also discuss the limiting current density of the hydrogen oxidation reaction (HOR) and how it is not necessarily independent of the reaction kinetics. The results give insight into the interplay of kinetic and mass-transport limitations at HER/HOR electrodes with implications for the design of kinetic experiments and the optimization of catalyst loadings in the photoelectrochemical cells.

  8. 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

  9. Recoupling pulse sequences with constant phase increments

    NASA Astrophysics Data System (ADS)

    Khaneja, Navin; Kumar, Ashutosh

    2016-10-01

    The paper studies a family of recoupling pulse sequences in magic angle spinning (MAS) solid state NMR, that are characterized by constant phase increments at regular intervals. These pulse sequences can be employed for both homonuclear and heteronuclear recoupling experiments and are robust to dispersion in chemical shifts and rf-inhomogeneity. The homonuclear pulse sequence consists of a building block (2 π) ϕp , where ϕp =p (n - 1) π/n, where n is number of blocks in a rotor period and p = 0, 1, 2, … . The pulse sequence repeats itself every rotor period when n is odd and every two rotor period when n is even. The heteronuclear recoupling pulse sequence consists of a building block (2 π) ϕ1p and (2 π) ϕ2p on channel I and S, where ϕ1p = p (2 n - 3) π/2 n, ϕ2p = p (2 n - 1) π/2 n and n is number of blocks in a rotor period. The recoupling pulse sequences mix the z magnetization. Experimental quantification of this method is shown for 13Cα -13CO , homonuclear recoupling in a sample of Glycine and 15N -13Cα , heteronuclear recoupling in Alanine. Application of this method is demonstrated on a sample of tripeptide N-formyl-[U-13C ,15N ]- Met-Leu-Phe-OH (MLF).

  10. Recoupling pulse sequences with constant phase increments.

    PubMed

    Khaneja, Navin; Kumar, Ashutosh

    2016-10-01

    The paper studies a family of recoupling pulse sequences in magic angle spinning (MAS) solid state NMR, that are characterized by constant phase increments at regular intervals. These pulse sequences can be employed for both homonuclear and heteronuclear recoupling experiments and are robust to dispersion in chemical shifts and rf-inhomogeneity. The homonuclear pulse sequence consists of a building block [Formula: see text] , where ϕ(p)=p(n-1)πn, where n is number of blocks in a rotor period and p=0,1,2,…. The pulse sequence repeats itself every rotor period when n is odd and every two rotor period when n is even. The heteronuclear recoupling pulse sequence consists of a building block [Formula: see text] and [Formula: see text] on channel I and S, where ϕ1(p)=p(2n-3)π2n,ϕ2(p)=p(2n-1)π2n and n is number of blocks in a rotor period. The recoupling pulse sequences mix the z magnetization. Experimental quantification of this method is shown for (13)Cα-(13)CO, homonuclear recoupling in a sample of Glycine and (15)N-(13)Cα, heteronuclear recoupling in Alanine. Application of this method is demonstrated on a sample of tripeptide N-formyl-[U-(13)C,(15)N]- Met-Leu-Phe-OH (MLF). PMID:27569693

  11. Incremental fusion of partial biometric information

    NASA Astrophysics Data System (ADS)

    Abboud, Ali J.; Jassim, Sabah A.

    2012-06-01

    Existing face recognition schemes are mostly based on extracting biometric feature vectors either from whole face images, or from a fixed facial region (e.g., eyes, nose, and mouth). Extreme variation in quality conditions between biometric enrolment and verification stages badly affects the performance of face recognition systems. Such problems have partly motivated several investigations into the use of partial facial features for face recognition. Nevertheless, partial face recognition is potentially useful in several applications, for instance, it used in forensics for detectives to identify individuals after some accidents such as fire or explosion. In this paper, we propose a scheme to fuse the biometric information of partial face images incrementally based on their recognition accuracy (or discriminative power) ranks. Such fusion scheme uses the optimal ratio of full/partial face images in each different quality condition. We found that such scheme is also useful for full face images to enhance authentication accuracy significantly. Nevertheless, it reduces the required storage requirements and processing time of the biometric system. Our experiments show that the required ratio of full/partial facial images to achieve optimal performance varies from (5%) to (80%) according to the quality conditions whereas the authentication accuracy improves significantly for low quality biometric samples.

  12. Evolution of cooperation driven by incremental learning

    NASA Astrophysics Data System (ADS)

    Li, Pei; Duan, Haibin

    2015-02-01

    It has been shown that the details of microscopic rules in structured populations can have a crucial impact on the ultimate outcome in evolutionary games. So alternative formulations of strategies and their revision processes exploring how strategies are actually adopted and spread within the interaction network need to be studied. In the present work, we formulate the strategy update rule as an incremental learning process, wherein knowledge is refreshed according to one's own experience learned from the past (self-learning) and that gained from social interaction (social-learning). More precisely, we propose a continuous version of strategy update rules, by introducing the willingness to cooperate W, to better capture the flexibility of decision making behavior. Importantly, the newly gained knowledge including self-learning and social learning is weighted by the parameter ω, establishing a strategy update rule involving innovative element. Moreover, we quantify the macroscopic features of the emerging patterns to inspect the underlying mechanisms of the evolutionary process using six cluster characteristics. In order to further support our results, we examine the time evolution course for these characteristics. Our results might provide insights for understanding cooperative behaviors and have several important implications for understanding how individuals adjust their strategies under real-life conditions.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. An Incremental Map Building Approach via Static Stixel Integration

    NASA Astrophysics Data System (ADS)

    Muffert, M.; Anzt, S.; Franke, U.

    2013-10-01

    This paper presents a stereo-vision based incremental mapping approach for urban regions. As input, we use the 3D representation called multi-layered Stixel World which is computed from dense disparity images. More and more, researchers of Driver Assistance Systems rely on efficient and compact 3D representations like the Stixel World. The developed mapping approach takes into account the motion state of obstacles, as well as free space information obtained from the Stixel World. The presented work is based on the well known occupancy grid mapping technique and is formulated with evidential theory. A detailed sensor model is described which is used to determine the information whether a grid cell is occupied, free or has an unknown state. The map update is solved in a time recursive manner by using the Dempster`s Rule of Combination. 3D results of complex inner city regions are shown and are compared with Google Earth images.

  18. 40 CFR 60.2830 - When must I submit the notifications of achievement of increments of progress?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Commenced Construction On or Before November 30, 1999 Model Rule-Air Curtain Incinerators § 60.2830 When... increments of progress must be postmarked no later than 10 business days after the compliance date for...

  19. 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. PMID:26979885

  20. 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.

  1. 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. PMID:24508659

  2. Unified semiclassical perturbation and infinite order sudden approximation, with application to the reaction path Hamiltonian model

    NASA Astrophysics Data System (ADS)

    Miller, William H.; Shi, Shenghua

    1981-09-01

    It is shown how two popular approximate dynamical models—the semiclassical perturbation (SCP) approximation and the infinite order sudden (IOS) approximation—can be combined in a consistent way that includes the correct features of both. Application of this unified SCP-IOS approximation to the reaction path Hamiltonian model of Miller, Handy, and Adam [J. Chem. Phys. 72, 99 (1980)] leads to extremely simple, explicit formulas for the reactive S matrix, product state distrubutions, etc., which can be readily applied to polyatomic systems. Initial numerical tests on a simple model problem indicate that the model is of useful accuracy.

  3. Modeling of On-Cell Reforming Reaction for Planar SOFC Stacks

    SciTech Connect

    Yang, Choongmo; Lim, Hyung-Tae; Hwang, Soon Cheol; Kim, Dohyung; Lai, Canhai; Koeppel, Brian J.; Recknagle, Kurtis P.; Khaleel, Mohammad A.

    2011-05-30

    Planar Solid Oxide Fuel Cell (SOFC) stack is known to suffer thermal problem from high stack temperature during operation to generate high current. On-Cell Reforming (OCR) phenomenon is often used to reduce stack temperature by an endothermic reaction of steam-methane reforming process. RIST conducted single-cell experiment to validate modeling tool to simulate OCR performance including temperature measurement. 2D modeling is used to check reforming rate during OCR using temperature measurement data, and 3D modeling is used to check overall thermal performance including furnace boundary conditions.

  4. 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. PMID:19623245

  5. [Distribution model of aluminum species in drinking water basing on the reaction kinetics].

    PubMed

    Wang, Wen-dong; Yang, Hong-wei; Wang, Xiao-chang; Jiang, Jing; Zhu, Wan-peng; Jiang, Zhan-peng

    2010-04-01

    The effects of excess aluminum on water distribution system and human health were mainly attributable to the presences of some aluminum species in drinking water. A prediction model for the concentrations of aluminum species was developed using three-layer front feedback artificial neural network method. Results showed that the reaction rates of both inorganic monomeric aluminum and soluble aluminum varied with reaction time and water quality parameters, such as water temperature, pH, total aluminum, fluoride, phosphate and silicate. Their reaction orders were both three. The reaction kinetic parameters of inorganic monomeric aluminum and soluble aluminum could be predicted effectively applying artificial neural network; the correlation coefficients of k and 1/C0(2) between calculated value and predicted value were both greater than 0.999. Aluminum species prediction results in the drinking water of City M showed that when the concentration of total aluminum was less than 0.05 mg x L(-1), the relative prediction error was large for inorganic monomeric aluminum. When the concentration of total aluminum was above 0.05 mg x L(-1), the model could predict inorganic monomeric aluminum and soluble aluminum concentrations effectively, with relative prediction errors of +/- 15% and +/- 10% respectively.

  6. 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.

  7. The activation strain model and molecular orbital theory: understanding and designing chemical reactions.

    PubMed

    Fernández, Israel; Bickelhaupt, F Matthias

    2014-07-21

    In this Tutorial Review, we make the point that a true understanding of trends in reactivity (as opposed to measuring or simply computing them) requires a causal reactivity model. To this end, we present and discuss the Activation Strain Model (ASM). The ASM establishes the desired causal relationship between reaction barriers, on one hand, and the properties of reactants and characteristics of reaction mechanisms, on the other hand. In the ASM, the potential energy surface ΔE(ζ) along the reaction coordinate ζ is decomposed into the strain ΔEstrain(ζ) of the reactants that become increasingly deformed as the reaction proceeds, plus the interaction ΔEint(ζ) between these deformed reactants, i.e., ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). The ASM can be used in conjunction with any quantum chemical program. An analysis of the method and its application to problems in organic and organometallic chemistry illustrate the power of the ASM as a unifying concept and a tool for rational design of reactants and catalysts.

  8. Beyond frontier molecular orbital theory: a systematic electron transfer model (ETM) for polar bimolecular organic reactions.

    PubMed

    Cahill, Katharine J; Johnson, Richard P

    2013-03-01

    Polar bimolecular reactions often begin as charge-transfer complexes and may proceed with a high degree of electron transfer character. Frontier molecular orbital (FMO) theory is predicated in part on this concept. We have developed an electron transfer model (ETM) in which we systematically transfer one electron between reactants and then use density functional methods to model the resultant radical or radical ion intermediates. Sites of higher reactivity are revealed by a composite spin density map (SDM) of odd electron character on the electron density surface, assuming that a new two-electron bond would occur preferentially at these sites. ETM correctly predicts regio- and stereoselectivity for a broad array of reactions, including Diels-Alder, dipolar and ketene cycloadditions, Birch reduction, many types of nucleophilic additions, and electrophilic addition to aromatic rings and polyenes. Conformational analysis of radical ions is often necessary to predict reaction stereochemistry. The electronic and geometric changes due to one-electron oxidation or reduction parallel the reaction coordinate for electrophilic or nucleophilic addition, respectively. The effect is more dramatic for one-electron reduction.

  9. Modeling the BZ reaction in gels with chemo-responsive crosslinks

    NASA Astrophysics Data System (ADS)

    Yashin, Victor V.; Kuksenok, Olga; Balazs, Anna C.

    2010-03-01

    We model chemo-responsive polymer gels, which expand and contract periodically in response to the ongoing oscillatory Belousov-Zhabotinsky (BZ) reaction. This behavior is due to a ruthenium catalyst, which is grafted to the polymers and affects the polymer-solvent interactions as it undergoes the redox oscillations in the course of the reaction. We consider a permanently crosslinked polymer gel that encompasses Ru(terpy)2 catalytic units having both the terpyridine ligands chemically bonded to the network. It is known that oxidation of the Ru metal-ion from Ru(II) to Ru(III) results in the dissociation of the Ru(terpy)2 complexes since the Ru(III) ions form only mono-complexes with terpyridine. Hence, the grafted Ru(terpy)2 units would effectively create crosslinks that break and re-form in the response to the BZ reaction. We modified the Oregonator model for the BZ reaction and took into account that the re-formation of Ru(terpy)2 complexes is frustrated by the gel network. The time-dependent elastic contribution of the Ru(terpy)2 crosslinks was described by the BKZ-type constitutive equation. We report on the results of simulations in 1D. We show, in particular, that compression of the sample leads to stiffening of the gel due to an increase in the crosslink density.

  10. 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

  11. Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data.

    PubMed

    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.

  12. Field theory for a reaction-diffusion model of quasispecies dynamics.

    PubMed

    Pastor-Satorras, R; Solé, R V

    2001-11-01

    RNA viruses are known to replicate with extremely high mutation rates. These rates are actually close to the so-called error threshold. This threshold is in fact a critical point beyond which genetic information is lost through a second-order phase transition, which has been dubbed as the "error catastrophe." Here we explore this phenomenon using a field theory approximation to the spatially extended Swetina-Schuster quasispecies model [J. Swetina and P. Schuster, Biophys. Chem. 16, 329 (1982)], a single-sharp-peak landscape. In analogy with standard absorbing-state phase transitions, we develop a reaction-diffusion model whose discrete rules mimic the Swetina-Schuster model. The field theory representation of the reaction-diffusion system is constructed. The proposed field theory belongs to the same universality class as a conserved reaction-diffusion model previously proposed [F. van Wijland et al., Physica A 251, 179 (1998)]. From the field theory, we obtain the full set of exponents that characterize the critical behavior at the error threshold. Our results present the error catastrophe from a different point of view and suggest that spatial degrees of freedom can modify several mean-field predictions previously considered, leading to the definition of characteristic exponents that could be experimentally measurable. PMID:11735970

  13. 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.

  14. Static and dynamical critical behavior of the monomer-monomer reaction model with desorption

    NASA Astrophysics Data System (ADS)

    da Costa, E. C.; Rusch, Flávio Roberto

    2016-06-01

    We studied in this work the monomer-monomer reaction model on a linear chain. The model is described by the following reaction: A + B → AB, where A and B are two monomers that arrive at the surface with probabilities yA and yB, respectively, and we have considered desorption of the monomer B with probability α. The model is studied in the adsorption controlled limit where the reaction rate is infinitely larger than the adsorption rate. We employ site and pair mean-field approximations as well as static and dynamical Monte Carlo simulations. We show that the model exhibits a continuous phase transition between an active steady state and an A-absorbing state, when the parameter yA is varied through a critical value, which depends on the value of α. Monte Carlo simulations and finite-size scaling analysis near the critical point are used to determine the static critical exponents β and ν⊥ and the dynamical critical exponents ν∥ and z. The results found for the monomer-monomer reaction model with B desorption, in the linear chain, are different from those found by E. V. Albano (Albano, 1992) and are in accordance with the values obtained by Jun Zhuo and Sidney Redner (Zhuo and Redner, 1993), and endorse the conjecture of Grassberger, which states that any system undergoing a continuous phase transition from an active steady state to a single absorbing state, exhibits the same critical behavior of the directed percolation universality class.

  15. 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

  16. [Kinetics modeling and reaction mechanism of ferrate(VI) oxidation of triclosan].

    PubMed

    Yang, Bin; Ying, Guang-Guo; Zhao, Jian-Liang

    2011-09-01

    Triclosan (TCS) is a broad-spectrum antibacterial agent widely used in many personal care products. We investigated oxidation of TCS by aqueous ferrate Fe(VI) to determine reaction kinetics, interpreted the reaction mechanism by a linear free-energy relationship, and evaluated the degradation efficiency. Second-order reaction kinetics was used to model Fe (VI) oxidation of TCS, with the apparent second-order rate constant (k(app)) being 531.9 L x (mol x s)(-1) at pH 8.5 and (24 +/- 1) degrees C. The half life (t1/2) is 25.8 s for an Fe( VI) concentration of 10 mg x L(-1). The rate constants of the reaction decrease with increasing pH values. These pH-dependent variations in k(app) could be distributed by considering species-specific reactions between Fe(VI) species and acid-base species of an ionizable TCS. Species-specific second-order reaction rate constants, k, were determined for reaction of HFeO4(-) with each of TCS's acid-base species. The value of k determined for neutral TCS was (4.1 +/- 3.5) x 10(2) L x (mol x s)(-1), while that measured for anionic TCS was (1.8 +/- 0.1) x 10(4) L x (mol x s)(-1). The reaction between HFeO4(-) and the dissociated TCS controls the overall reaction. A linear free-energy relationship illustrated the electrophilic oxidation mechanism. Fe (VI) reacts initially with TCS by electrophilic attack at the latter's phenol moiety. At a n[Fe(VI)]: n(TCS) > 7: 1, complete removal of TCS was achieved. And lower concentration of the humic acid could enhance the k(app) of Fe( VI) with TCS. In conclusion, Fe(VI) oxidation technology appears to be a promising tool for applications of WWTPs effluents and other decontamination processes.

  17. Code System to Calculate Nuclear Reaction Cross Sections by Evaporation Model.

    2000-11-27

    Version: 00 Both STAPRE and STAPREF are included in this package. STAPRE calculates energy-averaged cross sections for nuclear reactions with emission of particles and gamma rays and fission. The models employed are the evaporation model with inclusion of pre-equilibrium decay and a gamma-ray cascade model. Angular momentum and parity conservation are accounted for. Major improvement in the 1976 STAPRE program relates to level density approach, implemented in subroutine ZSTDE. Generalized superfluid model is incorporated, boltzman-gasmore » modeling of intrinsic state density and semi-empirical modeling of a few-quasiparticle effects in total level density at equilibrium and saddle deformations of actinide nuclei. In addition to the activation cross sections, particle and gamma-ray production spectra are calculated. Isomeric state populations and production cross sections for gamma rays from low excited levels are obtained, too. For fission a single or a double humped barrier may be chosen.« less

  18. Cell Length Independent PBRB Model for Simulations of HE Reaction Initiation, Growth, and Detonation

    NASA Astrophysics Data System (ADS)

    Dwivedi, Sunil

    2015-06-01

    It has been our focus to use the Physics Based Reaction Burn (PBRB) model to simulate reaction initiation, growth, and detonation of HE composites at the mesoscale. The idealization of hot spots as planar surfaces reduces the 3D model to a 1D hot spot cell (1DHSC) model. The idealization also renders the model dependent on the 1DHSC length and mesh size. New developments are presented making the PBRB model 1DHSC length independent. First, the accurate prediction of the gas-solid interface temperature and thermal gradient are essential, achieved through a finite difference scheme with 500-2000 thermal grid points. Second, keeping the burn mass constant while varying the 1DHSC length is essential, achieved by varying the hot spot specific surface area. 1D and 2D simulation results are presented for shock response of RDX at 1 km/s and 2 km/s impact velocities. The 5, 10, and 50 micro meters 1DHSC lengths yield near identical run-to-detonation, time-to-detonation, and detonation velocity in agreement with experimental data. It is concluded that the new developments make the PBRB model well suited as a generic EOS model for HE composites. - Dr. John Brennan, ARL is acknowledged for his interactions and support. This work is supported in part by ARL Grant W911NF-12-2-0053 and DTRA Grant HDTRA1-12-1-0004.

  19. 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

  20. 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.

  1. Periodic travelling waves in cyclic populations: field studies and reaction-diffusion models.

    PubMed

    Sherratt, Jonathan A; Smith, Matthew J

    2008-05-01

    Periodic travelling waves have been reported in a number of recent spatio-temporal field studies of populations undergoing multi-year cycles. Mathematical modelling has a major role to play in understanding these results and informing future empirical studies. We review the relevant field data and summarize the statistical methods used to detect periodic waves. We then discuss the mathematical theory of periodic travelling waves in oscillatory reaction-diffusion equations. We describe the notion of a wave family, and various ecologically relevant scenarios in which periodic travelling waves occur. We also discuss wave stability, including recent computational developments. Although we focus on oscillatory reaction-diffusion equations, a brief discussion of other types of model in which periodic travelling waves have been demonstrated is also included. We end by proposing 10 research challenges in this area, five mathematical and five empirical.

  2. 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.

  3. Studying Nuclear Level Densities of 238U in the Nuclear Reactions within the Macroscopic Nuclear Models

    NASA Astrophysics Data System (ADS)

    Razavi, Rohallah; Rahmatinejad, Azam; Kakavand, Tayeb; Taheri, Fariba; Aghajani, Maghsood; Khooy, Asghar

    2016-02-01

    In this work the nuclear level density parameters of 238U have been extracted in the back-shifted Fermi gas model (BSFGM), as well as the constant temperature model (CTM), through fitting with the recent experimental data on nuclear level densities measured by the Oslo group. The excitation functions for 238U(p,2nα)233Pa, and 238U(p,4n)235Np reactions and the fragment yields for the fragments of the 238U(p,f) reaction have been calculated using obtained level density parameters. The results are compared to their corresponding experimental values. It was found that the extracted excitation functions and the fragment yields in the CTM coincide well with the experimental values in the low-energy region. This finding is according to the claim made by the Oslo group that the extracted level densities of 238U show a constant temperature behaviour.

  4. The dynamics of single enzyme reactions: A reconsideration of Kramers' model for colored noise processes

    NASA Astrophysics Data System (ADS)

    Chaudhury, Srabanti; Chatterjee, Debarati; Cherayil, Binny J.

    2008-08-01

    The utility of an approximate heuristic version of Kramers' theory of reaction rates that was earlier used [Chaudhury and Cherayil, J. Chem. Phys. 125, 024904 (2006)] to successfully describe the nonexponential waiting time distributions of the enzyme β-galactosidase is reassessed. The original model, based on the Smoluchowski equation, is reformulated in terms of the phase space variables of the reaction coordinate, without neglecting inertial contributions. A new derivation of the Fokker-Planck equation (FPE) that describes the dynamics of this coordinate is presented. This derivation, based on functional methods, provides a more direct alternative to the existing distribution function approach used by Hanggi and Mojtabai [Phys. Rev. A 26, 1168 (1982)]. The time-dependent coefficients in the FPE, when incorporated into the exact expression for the transmission coefficient obtained from a reactive-flux formalism [Kohen and Tannor, J. Chem. Phys. 103, 6013 (1995)], are found to yield virtually the same results as the earlier heuristic model.

  5. 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.

  6. NN-->NNπ reaction near threshold in a covariant one-boson-exchange model

    NASA Astrophysics Data System (ADS)

    Shyam, R.; Mosel, U.

    1998-04-01

    We calculate the cross sections for the p(p,nπ+)p and p(p,pπ0)p reactions for proton beam energies near threshold in a covariant one-boson-exchange model, which incorporates the exchange of π, ρ, σ and ω mesons, treats both nucleon and delta isobar as intermediate states. The final state interaction effects are included within the Watson's theory. Within this model the ω and σ meson exchange terms contribute significantly at these energies, which, along with other meson exchanges, make it possible to reproduce the available experimental data for the total as well as differential cross sections for both the reactions. The cross sections at beam energies <=300 MeV are found to be almost free from the contributions of the Δ isobar excitation.

  7. 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.

  8. 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. PMID:15180064

  9. Stable Squares and Other Oscillatory Turing Patterns in a Reaction-Diffusion Model

    NASA Astrophysics Data System (ADS)

    Yang, Lingfa; Zhabotinsky, Anatol M.; Epstein, Irving R.

    2004-05-01

    We study the Brusselator reaction-diffusion model under conditions where the Hopf mode is supercritical and the Turing band is subcritical. Oscillating Turing patterns arise in the system when bulk oscillations lose their stability to spatial perturbations. Spatially uniform external periodic forcing can generate oscillating Turing patterns when both the Turing and Hopf modes are subcritical in the autonomous system. Most of the symmetric patterns show period doubling in both space and time. Patterns observed include squares, rhombi, stripes, and hexagons.

  10. 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.

  11. Incremental Seismic Rehabilitation of School Buildings (K-12).

    ERIC Educational Resources Information Center

    Krimgold, Frederick; Hattis, David; Green, Melvyn

    Asserting that the strategy of incremental seismic rehabilitation makes it possible for schools to get started now on improving earthquake safety, this manual provides school administrators with the information necessary to assess the seismic vulnerability of their buildings and to implement a program of incremental seismic rehabilitation for…

  12. Atmospheric reaction systems as null-models to identify structural traces of evolution in metabolism.

    PubMed

    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.

  13. Incremental impact of adding boys to current human papillomavirus vaccination programs: role of herd immunity.

    PubMed

    Brisson, Marc; van de Velde, Nicolas; Franco, Eduardo L; Drolet, Mélanie; Boily, Marie-Claude

    2011-08-01

    Our aim was to examine the potential incremental impact of vaccinating boys against human papillomavirus (HPV) on vaccine-type infection in females and males, using an individual-based HPV transmission-dynamic model. Under base assumptions (vaccine efficacy = 99%, duration of protection = 20 years, coverage = 70%), vaccinating 12-year-old boys, in addition to girls, resulted in an incremental reduction in HPV-16/18 (HPV-6/11) incidence over 70 years of 16% (3%) in females and 23% (4%) in males. The benefit of vaccinating boys decreased with improved vaccination coverage in girls. Given the important predicted herd immunity impact of vaccinating girls under moderate to high vaccine coverage, the potential incremental gains of vaccinating boys are limited.

  14. Incremental Validity of the Trait Emotional Intelligence Questionnaire-Short Form (TEIQue-SF).

    PubMed

    Siegling, A B; Vesely, Ashley K; Petrides, K V; Saklofske, Donald H

    2015-01-01

    This study examined the incremental validity of the adult short form of the Trait Emotional Intelligence Questionnaire (TEIQue-SF) in predicting 7 construct-relevant criteria beyond the variance explained by the Five-factor model and coping strategies. Additionally, the relative contributions of the questionnaire's 4 subscales were assessed. Two samples of Canadian university students completed the TEIQue-SF, along with measures of the Big Five, coping strategies (Sample 1 only), and emotion-laden criteria. The TEIQue-SF showed consistent incremental effects beyond the Big Five or the Big Five and coping strategies, predicting all 7 criteria examined across the 2 samples. Furthermore, 2 of the 4 TEIQue-SF subscales accounted for the measure's incremental validity. Although the findings provide good support for the validity and utility of the TEIQue-SF, directions for further research are emphasized.

  15. 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.

  16. Mass action realizations of reaction kinetic system models on various time scales

    NASA Astrophysics Data System (ADS)

    Hangos, K. M.; Szederkényi, G.

    2011-01-01

    Complex chemical reaction networks often exhibit different dynamic behaviour on different time scales. A combined approach is proposed in this work for determining physically meaningful mass action realizations of complex chemical reaction networks that describe its dynamic behaviour on different time scales. This is achieved by appropriately reducing the detailed overall mass action kinetic scheme using quasi steady state assumptions fit to the particular time scale, and then searching for an optimal realization using mixed integer linear programing. Furthermore, the relationship between the properties (reversibility, deficiency, stability) of the obtained realizations of the same system on different time scales are also investigated and related to the same properties of the detailed overall model. It is shown that the reduced models obtained by quasi steady state assumptions may show exotic nonlinear behaviour, such as oscillations, when the original detailed is globally asymptotically stable. The proposed methods are illustrated by using a simple Michaelis-Menten type reaction kinetic example. The simplified versions of the well known Brusselator model have also been investigated and presented as a case study.

  17. 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. PMID:26143280

  18. 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.

  19. Ventilation behavior during upper-body incremental exercise.

    PubMed

    Pires, Flávio O; Hammond, John; Lima-Silva, Adriano E; Bertuzzi, Rômulo C M; Kiss, Maria Augusta P D M

    2011-01-01

    This study tested the ventilation (VE) behavior during upper-body incremental exercise by mathematical models that calculate 1 or 2 thresholds and compared the thresholds identified by mathematical models with V-slope, ventilatory equivalent for oxygen uptake (VE/V(O2)), and ventilatory equivalent for carbon dioxide uptake (VE/V(CO2)). Fourteen rock climbers underwent an upper-body incremental test on a cycle ergometer with increases of approximately 20 W · min(-1) until exhaustion at a cranking frequency of approximately 90 rpm. The VE data were smoothed to 10-second averages for VE time plotting. The bisegmental and the 3-segmental linear regression models were calculated from 1 or 2 intercepts that best shared the VE curve in 2 or 3 linear segments. The ventilatory threshold(s) was determined mathematically by the intercept(s) obtained by bisegmental and 3-segmental models, by V-slope model, or visually by VE/V(O2) and VE/V(CO2). There was no difference between bisegmental (mean square error [MSE] = 35.3 ± 32.7 l · min(-1)) and 3-segmental (MSE = 44.9 ± 47.8 l · min(-1)) models in fitted data. There was no difference between ventilatory threshold identified by the bisegmental (28.2 ± 6.8 ml · kg(-1) · min(-1)) and second ventilatory threshold identified by the 3-segmental (30.0 ± 5.1 ml · kg(-1) · min(-1)), VE/V(O2) (28.8 ± 5.5 ml · kg(-1) · min(-1)), or V-slope (28.5 ± 5.6 ml · kg(-1) . min(-1)). However, the first ventilatory threshold identified by 3-segmental (23.1 ± 4.9 ml · kg(-1) · min(-1)) or by VE/V(O)2 (24.9 ± 4.4 ml · kg(-1) · min(-1)) was different from these 4. The VE behavior during upper-body exercise tends to show only 1 ventilatory threshold. These findings have practical implications because this point is frequently used for aerobic training prescription in healthy subjects, athletes, and in elderly or diseased populations. The ventilatory threshold identified by VE curve should be used for aerobic training prescription in

  20. 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

    2016-05-01

    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.