Sample records for approach chemical models

  1. Modeling drug- and chemical- induced hepatotoxicity with systems biology approaches

    Directory of Open Access Journals (Sweden)

    Sudin eBhattacharya


    Full Text Available We provide an overview of computational systems biology approaches as applied to the study of chemical- and drug-induced toxicity. The concept of ‘toxicity pathways’ is described in the context of the 2007 US National Academies of Science report, Toxicity testing in the 21st Century: A Vision and A Strategy. Pathway mapping and modeling based on network biology concepts are a key component of the vision laid out in this report for a more biologically-based analysis of dose-response behavior and the safety of chemicals and drugs. We focus on toxicity of the liver (hepatotoxicity – a complex phenotypic response with contributions from a number of different cell types and biological processes. We describe three case studies of complementary multi-scale computational modeling approaches to understand perturbation of toxicity pathways in the human liver as a result of exposure to environmental contaminants and specific drugs. One approach involves development of a spatial, multicellular virtual tissue model of the liver lobule that combines molecular circuits in individual hepatocytes with cell-cell interactions and blood-mediated transport of toxicants through hepatic sinusoids, to enable quantitative, mechanistic prediction of hepatic dose-response for activation of the AhR toxicity pathway. Simultaneously, methods are being developing to extract quantitative maps of intracellular signaling and transcriptional regulatory networks perturbed by environmental contaminants, using a combination of gene expression and genome-wide protein-DNA interaction data. A predictive physiological model (DILIsymTM to understand drug-induced liver injury (DILI, the most common adverse event leading to termination of clinical development programs and regulatory actions on drugs, is also described. The model initially focuses on reactive metabolite-induced DILI in response to administration of acetaminophen, and spans multiple biological scales.

  2. Modeling Warfare in Social Animals: A "Chemical" Approach (United States)

    Santarlasci, Alisa; Martelloni, Gianluca; Frizzi, Filippo; Santini, Giacomo; Bagnoli, Franco


    We present here a general method for modelling the dynamics of battles among social animals. The proposed method exploits the procedures widely used to model chemical reactions, but still uncommon in behavioural studies. We applied this methodology to the interpretation of experimental observations of battles between two species of ants (Lasius neglectus and Lasius paralienus), but this scheme may have a wider applicability and can be extended to other species as well. We performed two types of experiment labelled as interaction and mortality. The interaction experiments are designed to obtain information on the combat dynamics and lasted one hour. The mortality ones provide information on the casualty rates of the two species and lasted five hours. We modelled the interactions among ants using a chemical model which considers the single ant individuals and fighting groups analogously to atoms and molecules. The mean-field behaviour of the model is described by a set of non-linear differential equations. We also performed stochastic simulations of the corresponding agent-based model by means of the Gillespie event-driven integration scheme. By fitting the stochastic trajectories with the deterministic model, we obtained the probability distribution of the reaction parameters. The main result that we obtained is a dominance phase diagram, that gives the average trajectory of a generic battle, for an arbitrary number of opponents. This phase diagram was validated with some extra experiments. With respect to other war models (e.g., Lanchester's ones), our chemical model considers all phases of the battle and not only casualties. This allows a more detailed description of the battle (with a larger number of parameters), allowing the development of more sophisticated models (e.g., spatial ones), with the goal of distinguishing collective effects from the strategic ones. PMID:25369269

  3. Strongly Interacting Matter at Finite Chemical Potential: Hybrid Model Approach (United States)

    Srivastava, P. K.; Singh, C. P.


    Search for a proper and realistic equation of state (EOS) for strongly interacting matter used in the study of the QCD phase diagram still appears as a challenging problem. Recently, we constructed a hybrid model description for the quark-gluon plasma (QGP) as well as hadron gas (HG) phases where we used an excluded volume model for HG and a thermodynamically consistent quasiparticle model for the QGP phase. The hybrid model suitably describes the recent lattice results of various thermodynamical as well as transport properties of the QCD matter at zero baryon chemical potential (μB). In this paper, we extend our investigations further in obtaining the properties of QCD matter at finite value of μB and compare our results with the most recent results of lattice QCD calculation.

  4. Comparison of modeling approaches to prioritize chemicals based on estimates of exposure and exposure potential (United States)

    Mitchell, Jade; Arnot, Jon A.; Jolliet, Olivier; Georgopoulos, Panos G.; Isukapalli, Sastry; Dasgupta, Surajit; Pandian, Muhilan; Wambaugh, John; Egeghy, Peter; Cohen Hubal, Elaine A.; Vallero, Daniel A.


    While only limited data are available to characterize the potential toxicity of over 8 million commercially available chemical substances, there is even less information available on the exposure and use-scenarios that are required to link potential toxicity to human and ecological health outcomes. Recent improvements and advances such as high throughput data gathering, high performance computational capabilities, and predictive chemical inherency methodology make this an opportune time to develop an exposure-based prioritization approach that can systematically utilize and link the asymmetrical bodies of knowledge for hazard and exposure. In response to the US EPA’s need to develop novel approaches and tools for rapidly prioritizing chemicals, a “Challenge” was issued to several exposure model developers to aid the understanding of current systems in a broader sense and to assist the US EPA’s effort to develop an approach comparable to other international efforts. A common set of chemicals were prioritized under each current approach. The results are presented herein along with a comparative analysis of the rankings of the chemicals based on metrics of exposure potential or actual exposure estimates. The analysis illustrates the similarities and differences across the domains of information incorporated in each modeling approach. The overall findings indicate a need to reconcile exposures from diffuse, indirect sources (far-field) with exposures from directly, applied chemicals in consumer products or resulting from the presence of a chemical in a microenvironment like a home or vehicle. Additionally, the exposure scenario, including the mode of entry into the environment (i.e. through air, water or sediment) appears to be an important determinant of the level of agreement between modeling approaches. PMID:23707726

  5. Modeling the binding affinity of structurally diverse industrial chemicals to carbon using the artificial intelligence approaches. (United States)

    Gupta, Shikha; Basant, Nikita; Rai, Premanjali; Singh, Kunwar P


    Binding affinity of chemical to carbon is an important characteristic as it finds vast industrial applications. Experimental determination of the adsorption capacity of diverse chemicals onto carbon is both time and resource intensive, and development of computational approaches has widely been advocated. In this study, artificial intelligence (AI)-based ten different qualitative and quantitative structure-property relationship (QSPR) models (MLPN, RBFN, PNN/GRNN, CCN, SVM, GEP, GMDH, SDT, DTF, DTB) were established for the prediction of the adsorption capacity of structurally diverse chemicals to activated carbon following the OECD guidelines. Structural diversity of the chemicals and nonlinear dependence in the data were evaluated using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. The generalization and prediction abilities of the constructed models were established through rigorous internal and external validation procedures performed employing a wide series of statistical checks. In complete dataset, the qualitative models rendered classification accuracies between 97.04 and 99.93%, while the quantitative models yielded correlation (R(2)) values of 0.877-0.977 between the measured and the predicted endpoint values. The quantitative prediction accuracies for the higher molecular weight (MW) compounds (class 4) were relatively better than those for the low MW compounds. Both in the qualitative and quantitative models, the Polarizability was the most influential descriptor. Structural alerts responsible for the extreme adsorption behavior of the compounds were identified. Higher number of carbon and presence of higher halogens in a molecule rendered higher binding affinity. Proposed QSPR models performed well and outperformed the previous reports. A relatively better performance of the ensemble learning models (DTF, DTB) may be attributed to the strengths of the bagging and boosting algorithms which enhance the predictive accuracies. The

  6. Modeling of Scale-Dependent Bacterial Growth by Chemical Kinetics Approach

    Directory of Open Access Journals (Sweden)

    Haydee Martínez


    Full Text Available We applied the so-called chemical kinetics approach to complex bacterial growth patterns that were dependent on the liquid-surface-area-to-volume ratio (SA/V of the bacterial cultures. The kinetic modeling was based on current experimental knowledge in terms of autocatalytic bacterial growth, its inhibition by the metabolite CO2, and the relief of inhibition through the physical escape of the inhibitor. The model quantitatively reproduces kinetic data of SA/V-dependent bacterial growth and can discriminate between differences in the growth dynamics of enteropathogenic E. coli, E. coli  JM83, and Salmonella typhimurium on one hand and Vibrio cholerae on the other hand. Furthermore, the data fitting procedures allowed predictions about the velocities of the involved key processes and the potential behavior in an open-flow bacterial chemostat, revealing an oscillatory approach to the stationary states.

  7. New Approaches for Collaborative Sharing of Chemical Model Data and Analysis Tools

    Energy Technology Data Exchange (ETDEWEB)

    Schuchardt, K; Oluwole, O; Pitz, W; Rahn, L A; Green, Jr., W H; Leahy, D; Pancerella, C; Sj?berg, M; Dec, J


    The urgent need for high-efficiency, low-emission energy utilization technologies for transportation, power generation, and manufacturing processes presents difficult challenges to the combustion research community. The required predictive understanding requires systematic knowledge across the full range of physical scales involved in combustion processes--from the properties and interactions of individual molecules to the dynamics and products of turbulent multi-phase reacting flows. Innovative experimental techniques and computational approaches are revolutionizing the rate at which chemical science research can produce the new information necessary to advance our combustion knowledge. But the increased volume and complexity of this information often makes it even more difficult to derive the systems-level knowledge we need. Combustion researchers have responded by forming interdisciplinary communities intent on sharing information and coordinating research priorities. Such efforts face many barriers, however, including lack of data accessibility and interoperability, missing metadata and pedigree information, efficient approaches for sharing data and analysis tools, and the challenges of working together across geography, disciplines, and a very diverse spectrum of applications and funding. This challenge is especially difficult for those developing, sharing and/or using detailed chemical models of combustion to treat the oxidation of practical fuels. This is a very complex problem, and the development of new chemistry models requires a series of steps that involve acquiring and keeping track of a large amount of data and its pedigree. Also, this data is developed using a diverse range of codes and experiments spanning ab initio chemistry codes, laboratory kinetics and flame experiments, all the way to reacting flow simulations on massively parallel computers. Each of these processes typically requires different data formats, and often the data and/or analysis

  8. An approach to modeling coupled thermal-hydraulic-chemical processes in geothermal systems (United States)

    Palguta, Jennifer; Williams, Colin F.; Ingebritsen, Steven E.; Hickman, Stephen H.; Sonnenthal, Eric


    Interactions between hydrothermal fluids and rock alter mineralogy, leading to the formation of secondary minerals and potentially significant physical and chemical property changes. Reactive transport simulations are essential for evaluating the coupled processes controlling the geochemical, thermal and hydrological evolution of geothermal systems. The objective of this preliminary investigation is to successfully replicate observations from a series of hydrothermal laboratory experiments [Morrow et al., 2001] using the code TOUGHREACT. The laboratory experiments carried out by Morrow et al. [2001] measure permeability reduction in fractured and intact Westerly granite due to high-temperature fluid flow through core samples. Initial permeability and temperature values used in our simulations reflect these experimental conditions and range from 6.13 × 10−20 to 1.5 × 10−17 m2 and 150 to 300 °C, respectively. The primary mineralogy of the model rock is plagioclase (40 vol.%), K-feldspar (20 vol.%), quartz (30 vol.%), and biotite (10 vol.%). The simulations are constrained by the requirement that permeability, relative mineral abundances, and fluid chemistry agree with experimental observations. In the models, the granite core samples are represented as one-dimensional reaction domains. We find that the mineral abundances, solute concentrations, and permeability evolutions predicted by the models are consistent with those observed in the experiments carried out by Morrow et al. [2001] only if the mineral reactive surface areas decrease with increasing clay mineral abundance. This modeling approach suggests the importance of explicitly incorporating changing mineral surface areas into reactive transport models.

  9. Predicting dissolved oxygen concentration using kernel regression modeling approaches with nonlinear hydro-chemical data. (United States)

    Singh, Kunwar P; Gupta, Shikha; Rai, Premanjali


    Kernel function-based regression models were constructed and applied to a nonlinear hydro-chemical dataset pertaining to surface water for predicting the dissolved oxygen levels. Initial features were selected using nonlinear approach. Nonlinearity in the data was tested using BDS statistics, which revealed the data with nonlinear structure. Kernel ridge regression, kernel principal component regression, kernel partial least squares regression, and support vector regression models were developed using the Gaussian kernel function and their generalization and predictive abilities were compared in terms of several statistical parameters. Model parameters were optimized using the cross-validation procedure. The proposed kernel regression methods successfully captured the nonlinear features of the original data by transforming it to a high dimensional feature space using the kernel function. Performance of all the kernel-based modeling methods used here were comparable both in terms of predictive and generalization abilities. Values of the performance criteria parameters suggested for the adequacy of the constructed models to fit the nonlinear data and their good predictive capabilities.

  10. Beyond the pseudo-time-dependent approach: chemical models of dense core precursors

    CERN Document Server

    Hassel, G E; Bergin, E A


    Context: Chemical models of dense cloud cores often utilize the so-called pseudo-time-dependent approximation, in which the physical conditions are held fixed and uniform as the chemistry occurs. In this approximation, the initial abundances chosen, which are totally atomic in nature except for molecular hydrogen, are artificial. A more detailed approach to the chemistry of dense cold cores should include the physical evolution during their early stages of formation. Aims: Our major goal is to investigate the initial synthesis of molecular ices and gas-phase molecules as cold molecular gas begins to form behind a shock in the diffuse interstellar medium. The abundances calculated as the conditions evolve can then be utilized as reasonable initial conditions for a theory of the chemistry of dense cores. Methods: Hydrodynamic shock-wave simulations of the early stages of cold core formation are used to determine the time-dependent physical conditions for a gas-grain chemical network. We follow the cold post-sho...

  11. Predicting carcinogenicity of diverse chemicals using probabilistic neural network modeling approaches

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Kunwar P., E-mail: [Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research, New Delhi (India); Environmental Chemistry Division, CSIR-Indian Institute of Toxicology Research, Post Box 80, Mahatma Gandhi Marg, Lucknow 226 001 (India); Gupta, Shikha; Rai, Premanjali [Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research, New Delhi (India); Environmental Chemistry Division, CSIR-Indian Institute of Toxicology Research, Post Box 80, Mahatma Gandhi Marg, Lucknow 226 001 (India)


    Robust global models capable of discriminating positive and non-positive carcinogens; and predicting carcinogenic potency of chemicals in rodents were developed. The dataset of 834 structurally diverse chemicals extracted from Carcinogenic Potency Database (CPDB) was used which contained 466 positive and 368 non-positive carcinogens. Twelve non-quantum mechanical molecular descriptors were derived. Structural diversity of the chemicals and nonlinearity in the data were evaluated using Tanimoto similarity index and Brock–Dechert–Scheinkman statistics. Probabilistic neural network (PNN) and generalized regression neural network (GRNN) models were constructed for classification and function optimization problems using the carcinogenicity end point in rat. Validation of the models was performed using the internal and external procedures employing a wide series of statistical checks. PNN constructed using five descriptors rendered classification accuracy of 92.09% in complete rat data. The PNN model rendered classification accuracies of 91.77%, 80.70% and 92.08% in mouse, hamster and pesticide data, respectively. The GRNN constructed with nine descriptors yielded correlation coefficient of 0.896 between the measured and predicted carcinogenic potency with mean squared error (MSE) of 0.44 in complete rat data. The rat carcinogenicity model (GRNN) applied to the mouse and hamster data yielded correlation coefficient and MSE of 0.758, 0.71 and 0.760, 0.46, respectively. The results suggest for wide applicability of the inter-species models in predicting carcinogenic potency of chemicals. Both the PNN and GRNN (inter-species) models constructed here can be useful tools in predicting the carcinogenicity of new chemicals for regulatory purposes. - Graphical abstract: Figure (a) shows classification accuracies (positive and non-positive carcinogens) in rat, mouse, hamster, and pesticide data yielded by optimal PNN model. Figure (b) shows generalization and predictive

  12. A model for planning the chemical integrated system under uncertainty by the grey programming approach

    DEFF Research Database (Denmark)

    Ren, Jingzheng; Tan, Shiyu; Dong, Lichun


    A model to optimize the planning of the chemical integrated system comprised by multi-devices and multi-products has been proposed in this paper. With the objective to make more profits, the traditional model for optimizing production planning has been proposed. The price of chemicals, the market...... demand, and the production capacity have been considered as mutative variables, then an improved model in which some parameters are not constant has been developed and a new method to solve the grey linear programming has been proposed. In the grey programming model, the value of credibility can...

  13. In silico prediction of toxicity of non-congeneric industrial chemicals using ensemble learning based modeling approaches

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Kunwar P., E-mail:; Gupta, Shikha


    Ensemble learning approach based decision treeboost (DTB) and decision tree forest (DTF) models are introduced in order to establish quantitative structure–toxicity relationship (QSTR) for the prediction of toxicity of 1450 diverse chemicals. Eight non-quantum mechanical molecular descriptors were derived. Structural diversity of the chemicals was evaluated using Tanimoto similarity index. Stochastic gradient boosting and bagging algorithms supplemented DTB and DTF models were constructed for classification and function optimization problems using the toxicity end-point in T. pyriformis. Special attention was drawn to prediction ability and robustness of the models, investigated both in external and 10-fold cross validation processes. In complete data, optimal DTB and DTF models rendered accuracies of 98.90%, 98.83% in two-category and 98.14%, 98.14% in four-category toxicity classifications. Both the models further yielded classification accuracies of 100% in external toxicity data of T. pyriformis. The constructed regression models (DTB and DTF) using five descriptors yielded correlation coefficients (R{sup 2}) of 0.945, 0.944 between the measured and predicted toxicities with mean squared errors (MSEs) of 0.059, and 0.064 in complete T. pyriformis data. The T. pyriformis regression models (DTB and DTF) applied to the external toxicity data sets yielded R{sup 2} and MSE values of 0.637, 0.655; 0.534, 0.507 (marine bacteria) and 0.741, 0.691; 0.155, 0.173 (algae). The results suggest for wide applicability of the inter-species models in predicting toxicity of new chemicals for regulatory purposes. These approaches provide useful strategy and robust tools in the screening of ecotoxicological risk or environmental hazard potential of chemicals. - Graphical abstract: Importance of input variables in DTB and DTF classification models for (a) two-category, and (b) four-category toxicity intervals in T. pyriformis data. Generalization and predictive abilities of the

  14. Predicting aquatic toxicities of chemical pesticides in multiple test species using nonlinear QSTR modeling approaches. (United States)

    Basant, Nikita; Gupta, Shikha; Singh, Kunwar P


    In this study, we established nonlinear quantitative-structure toxicity relationship (QSTR) models for predicting the toxicities of chemical pesticides in multiple aquatic test species following the OECD (Organization for Economic Cooperation and Development) guidelines. The decision tree forest (DTF) and decision tree boost (DTB) based QSTR models were constructed using a pesticides toxicity dataset in Selenastrum capricornutum and a set of six descriptors. Other six toxicity data sets were used for external validation of the constructed QSTRs. Global QSTR models were also constructed using the combined dataset of all the seven species. The diversity in chemical structures and nonlinearity in the data were evaluated. Model validation was performed deriving several statistical coefficients for the test data and the prediction and generalization abilities of the QSTRs were evaluated. Both the QSTR models identified WPSA1 (weighted charged partial positive surface area) as the most influential descriptor. The DTF and DTB QSTRs performed relatively better than the single decision tree (SDT) and support vector machines (SVM) models used as a benchmark here and yielded R(2) of 0.886 and 0.964 between the measured and predicted toxicity values in the complete dataset (S. capricornutum). The QSTR models applied to six other aquatic species toxicity data yielded R(2) of >0.92 (DTF) and >0.97 (DTB), respectively. The prediction accuracies of the global models were comparable with those of the S. capricornutum models. The results suggest for the appropriateness of the developed QSTR models to reliably predict the aquatic toxicity of chemicals and can be used for regulatory purpose.

  15. An investigation of sulfate production in clouds using a flow-through chemical reactor model approach (United States)

    Hong, M. S.; Carmichael, G. R.


    A flow-through chemical reactor model is developed to describe the mass transfer and chemical processes that atmospheric gases undergo in clouds. The model includes the simultaneous absorption of SO2, NH3, O3, NO(x), HNO3, CO2 and H2O2, the accompanying dissociation and oxidation reactions in cloud water, considers electrical neutrality, and includes qualitative parameterization of cloud microphysics. The model is used to assess the importance of the oxidation reactions H2O2-S(IV), O3-S(IV), and S(IV)-Mn(2+) catalysis, and the effects of cloud parameters such as drop size, rain intensity, liquid water content, and updraft velocity. Both precipitating and nonprecipitating clouds are studied. Model results predict sulfate production rates varying from 3 percent/hr to 230 percent/hr. The actual rate is highly dependent on the chemical composition of the uptake air and the physical conditions of the cloud. Model results also show that both the H2O2 and the O3 oxidation reactions can be significant.

  16. A generalised chemical precipitation modelling approach in wastewater treatment applied to calcite

    DEFF Research Database (Denmark)

    Mbamba, Christian Kazadi; Batstone, Damien J.; Flores Alsina, Xavier


    , the present study aims to identify a broadly applicable precipitation modelling approach. The study uses two experimental platforms applied to calcite precipitating from synthetic aqueous solutions to identify and validate the model approach. Firstly, dynamic pH titration tests are performed to define...... of the mineral particulate state (Xcryst) and, for calcite, have a 2nd order dependency (exponent n ¼ 2.05 ± 0.29) on thermodynamic supersaturation (s). Parameter analysis indicated that the model was more tolerant to a fast kinetic coefficient (kcryst) and so, in general, it is recommended that a large kcryst...

  17. Modeling the reactivities of hydroxyl radical and ozone towards atmospheric organic chemicals using quantitative structure-reactivity relationship approaches. (United States)

    Gupta, Shikha; Basant, Nikita; Mohan, Dinesh; Singh, Kunwar P


    The persistence and the removal of organic chemicals from the atmosphere are largely determined by their reactions with the OH radical and O3. Experimental determinations of the kinetic rate constants of OH and O3 with a large number of chemicals are tedious and resource intensive and development of computational approaches has widely been advocated. Recently, ensemble machine learning (EML) methods have emerged as unbiased tools to establish relationship between independent and dependent variables having a nonlinear dependence. In this study, EML-based, temperature-dependent quantitative structure-reactivity relationship (QSRR) models have been developed for predicting the kinetic rate constants for OH (kOH) and O3 (kO3) reactions with diverse chemicals. Structural diversity of chemicals was evaluated using a Tanimoto similarity index. The generalization and prediction abilities of the constructed models were established through rigorous internal and external validation performed employing statistical checks. In test data, the EML QSRR models yielded correlation (R (2)) of ≥0.91 between the measured and the predicted reactivities. The applicability domains of the constructed models were determined using methods based on descriptors range, Euclidean distance, leverage, and standardization approaches. The prediction accuracies for the higher reactivity compounds were relatively better than those of the low reactivity compounds. Proposed EML QSRR models performed well and outperformed the previous reports. The proposed QSRR models can make predictions of rate constants at different temperatures. The proposed models can be useful tools in predicting the reactivities of chemicals towards OH radical and O3 in the atmosphere.

  18. A chemical energy approach of avascular tumor growth: multiscale modeling and qualitative results. (United States)

    Ampatzoglou, Pantelis; Dassios, George; Hadjinicolaou, Maria; Kourea, Helen P; Vrahatis, Michael N


    In the present manuscript we propose a lattice free multiscale model for avascular tumor growth that takes into account the biochemical environment, mitosis, necrosis, cellular signaling and cellular mechanics. This model extends analogous approaches by assuming a function that incorporates the biochemical energy level of the tumor cells and a mechanism that simulates the behavior of cancer stem cells. Numerical simulations of the model are used to investigate the morphology of the tumor at the avascular phase. The obtained results show similar characteristics with those observed in clinical data in the case of the Ductal Carcinoma In Situ (DCIS) of the breast.

  19. A hybrid moment equation approach to gas-grain chemical modeling

    CERN Document Server

    Du, Fujun


    [Context] The stochasticity of grain chemistry requires special care in modeling. Previously methods based on the modified rate equation, the master equation, the moment equation, and Monte Carlo simulations have been used. [Aims] We attempt to develop a systematic and efficient way to model the gas-grain chemistry with a large reaction network as accurately as possible. [Methods] We present a hybrid moment equation approach which is a general and automatic method where the generating function is used to generate the moment equations. For large reaction networks, the moment equation is cut off at the second order, and a switch scheme is used when the average population of certain species reaches 1. For small networks, the third order moments can also be utilized to achieve a higher accuracy. [Results] For physical conditions in which the surface reactions are important, our method provides a major improvement over the rate equation approach, when benchmarked against the rigorous Monte Carlo results. For eithe...

  20. Reduction of chemical reaction models (United States)

    Frenklach, Michael


    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.

  1. A discussion of regulatory requirements and air dispersion modeling approaches applicable to U.S. chemical demilitarization facilities. (United States)

    Higgins, B W; Robbins, L B; Litynski, J


    Owners of hazardous waste treatment, storage, and disposal facilities, and certain major air pollution sources, must conduct several separate ambient air dispersion modeling analyses before beginning construction of new facilities or modifying existing facilities. These analyses are critical components of the environmental permitting and facility certification processes and must be completed to the satisfaction of federal, state, and local regulatory authorities. The U.S. Army has conducted air dispersion modeling for its proposed chemical agent disposal facilities to fulfill the following environmental regulatory and risk management requirements: (1) Resource Conservation and Recovery Act human health and ecological risk assessment analysis for the hazardous waste treatment and storage permit applications, (2) Quantitative Risk Assessment to support the site-specific risk management programs, and (3) Prevention of Significant Deterioration ambient air impact analysis for the air permit applications. The purpose of these air dispersion modeling studies is to show that the potential impacts on human health and the environment, due to operation of the chemical agent disposal facilities, are acceptable. This paper describes and compares the types of air dispersion models, modeling input data requirements, modeling algorithms, and approaches used to satisfy the three environmental regulatory and risk management requirements listed above. Although this paper discusses only one industry (i.e., chemical demilitarization), the information it contains could help those in other industries who need to communicate to the public the purpose and objectives of each modeling analysis. It may also be useful in integrating the results of each analysis into an overarching summary of compliance and potential risks.

  2. Modeling short-term variability of semivolatile organic chemicals in air at a local scale: an integrated modeling approach. (United States)

    Morselli, Melissa; Ghirardello, Davide; Semplice, Matteo; Di Guardo, Antonio


    Monitoring campaigns from different locations have recently shown how air concentrations of persistent semivolatile contaminants such as polychlorinated biphenyls (PCBs) often exhibit short-term (less than 24 h) variations. The observed patterns have been ascribed to different factors, such as temperature-mediated air-surface exchange and variability of planetary boundary layer (PBL) height and dynamics. Here, we present a new modeling approach developed in order to investigate the short-term variability in air concentrations of organic pollutants at a local scale. A new dynamic multimedia box model is supplied by a meteorological preprocessor (AERMET) with hourly values of air compartment height and wind speed. The resulting model is tested against an existing dataset of PCB air concentrations measured in Zurich, Switzerland. Results show the importance of such modeling approach in elucidating the short- and long-term behavior of semivolatile contaminants in the air/soil system.

  3. Sequential application of ligand and structure based modeling approaches to index chemicals for their hH4R antagonism.

    Directory of Open Access Journals (Sweden)

    Matteo Pappalardo

    Full Text Available The human histamine H4 receptor (hH4R, a member of the G-protein coupled receptors (GPCR family, is an increasingly attractive drug target. It plays a key role in many cell pathways and many hH4R ligands are studied for the treatment of several inflammatory, allergic and autoimmune disorders, as well as for analgesic activity. Due to the challenging difficulties in the experimental elucidation of hH4R structure, virtual screening campaigns are normally run on homology based models. However, a wealth of information about the chemical properties of GPCR ligands has also accumulated over the last few years and an appropriate combination of these ligand-based knowledge with structure-based molecular modeling studies emerges as a promising strategy for computer-assisted drug design. Here, two chemoinformatics techniques, the Intelligent Learning Engine (ILE and Iterative Stochastic Elimination (ISE approach, were used to index chemicals for their hH4R bioactivity. An application of the prediction model on external test set composed of more than 160 hH4R antagonists picked from the chEMBL database gave enrichment factor of 16.4. A virtual high throughput screening on ZINC database was carried out, picking ∼ 4000 chemicals highly indexed as H4R antagonists' candidates. Next, a series of 3D models of hH4R were generated by molecular modeling and molecular dynamics simulations performed in fully atomistic lipid membranes. The efficacy of the hH4R 3D models in discrimination between actives and non-actives were checked and the 3D model with the best performance was chosen for further docking studies performed on the focused library. The output of these docking studies was a consensus library of 11 highly active scored drug candidates. Our findings suggest that a sequential combination of ligand-based chemoinformatics approaches with structure-based ones has the potential to improve the success rate in discovering new biologically active GPCR drugs and

  4. Hybrid Approach for Modeling Chemical Kinetics and Turbulence Effects on Combustion-Instability Project (United States)

    National Aeronautics and Space Administration — Combustion instabilities pose a significant technical risk in the development of liquid and solid rocket motors. Much of the effort in modeling combustion...

  5. A Novel Approach for Modeling Chemical Reaction in Generalized Fluid System Simulation Program (United States)

    Sozen, Mehmet; Majumdar, Alok


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

  6. Nitrate source apportionment using a combined dual isotope, chemical and bacterial property, and Bayesian model approach in river systems (United States)

    Xia, Yongqiu; Li, Yuefei; Zhang, Xinyu; Yan, Xiaoyuan


    Nitrate (NO3-) pollution is a serious problem worldwide, particularly in countries with intensive agricultural and population activities. Previous studies have used δ15N-NO3- and δ18O-NO3- to determine the NO3- sources in rivers. However, this approach is subject to substantial uncertainties and limitations because of the numerous NO3- sources, the wide isotopic ranges, and the existing isotopic fractionations. In this study, we outline a combined procedure for improving the determination of NO3- sources in a paddy agriculture-urban gradient watershed in eastern China. First, the main sources of NO3- in the Qinhuai River were examined by the dual-isotope biplot approach, in which we narrowed the isotope ranges using site-specific isotopic results. Next, the bacterial groups and chemical properties of the river water were analyzed to verify these sources. Finally, we introduced a Bayesian model to apportion the spatiotemporal variations of the NO3- sources. Denitrification was first incorporated into the Bayesian model because denitrification plays an important role in the nitrogen pathway. The results showed that fertilizer contributed large amounts of NO3- to the surface water in traditional agricultural regions, whereas manure effluents were the dominant NO3- source in intensified agricultural regions, especially during the wet seasons. Sewage effluents were important in all three land uses and exhibited great differences between the dry season and the wet season. This combined analysis quantitatively delineates the proportion of NO3- sources from paddy agriculture to urban river water for both dry and wet seasons and incorporates isotopic fractionation and uncertainties in the source compositions.

  7. Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: a comprehensive quantum chemical approach. (United States)

    Yurenko, Yevgen P; Novotný, Jan; Sklenář, Vladimir; Marek, Radek


    The study aimed to cast light on the structure and internal energetics of guanine- and xanthine-based model DNA quadruplexes and the physico-chemical nature of the non-covalent interactions involved. Several independent approaches were used for this purpose: DFT-D3 calculations, Quantum Theory of Atoms in Molecules, Natural Bond Orbital Analysis, Energy Decomposition Analysis, Compliance Constant Theory, and Non-Covalent Interaction Analysis. The results point to an excellent degree of structural and energetic compatibility between the two types of model quadruplexes. This fact stems from both the structural features (close values of van der Waals volumes, pore radii, geometrical parameters of the H-bonds) and the energetic characteristics (comparable values of the energies of formation). It was established that hydrogen bonding makes the greatest (∼50%) contribution to the internal stability of the DNA quadruplexes, whereas the aromatic base stacking and ion coordination terms are commensurable and account for the rest. Energy decomposition analysis performed for guanine (Gua) and xanthine (Xan) quartets B4 and higher-order structures consisting of two or three stacked quartets indicates that whereas Gua structures benefit from a high degree of H-bond cooperativity, Xan models are characterized by a more favorable and cooperative π-π stacking. The results of electron density topological analysis show that Na(+)/K(+) ion coordination deeply affects the network of non-covalent interactions in Gua models due to the change in the twist angle between the stacked tetrads. For Xan models, ion coordination makes tetrads in stacks more planar without changing the twist angle. Therefore, the presence of the ion seems to be essential for the formation of planar stacks in Xan-based DNA quadruplexes. Detailed study of the nature of ion-base coordination suggests that this interaction has a partially covalent character and cannot be considered as purely electrostatic

  8. Sequential identification of model parameters by derivative double two-dimensional correlation spectroscopy and calibration-free approach for chemical reaction systems. (United States)

    Spegazzini, Nicolas; Siesler, Heinz W; Ozaki, Yukihiro


    A sequential identification approach by two-dimensional (2D) correlation analysis for the identification of a chemical reaction model, activation, and thermodynamic parameters is presented in this paper. The identification task is decomposed into a sequence of subproblems. The first step is the construction of a reaction model with the suggested information by model-free 2D correlation analysis using a novel technique called derivative double 2D correlation spectroscopy (DD2DCOS), which enables one to analyze intensities with nonlinear behavior and overlapped bands. The second step is a model-based 2D correlation analysis where the activation and thermodynamic parameters are estimated by an indirect implicit calibration or a calibration-free approach. In this way, a minimization process for the spectral information by sample-sample 2D correlation spectroscopy and kinetic hard modeling (using ordinary differential equations) of the chemical reaction model is carried out. The sequential identification by 2D correlation analysis is illustrated with reference to the isomeric structure of diphenylurethane synthesized from phenylisocyanate and phenol. The reaction was investigated by FT-IR spectroscopy. The activation and thermodynamic parameters of the isomeric structures of diphenylurethane linked through a hydrogen bonding equilibrium were studied by means of an integration of model-free and model-based 2D correlation analysis called a sequential identification approach. The study determined the enthalpy (ΔH = 15.25 kJ/mol) and entropy (TΔS = 13.20 kJ/mol) of C═O···H hydrogen bonding of diphenylurethane through direct calculation from the differences in the kinetic parameters (δΔ(‡)H, -TδΔ(‡)S) at equilibrium in the chemical reaction system.

  9. Chemical kinetics and combustion modeling

    Energy Technology Data Exchange (ETDEWEB)

    Miller, J.A. [Sandia National Laboratories, Livermore, CA (United States)


    The goal of this program is to gain qualitative insight into how pollutants are formed in combustion systems and to develop quantitative mathematical models to predict their formation rates. The approach is an integrated one, combining low-pressure flame experiments, chemical kinetics modeling, theory, and kinetics experiments to gain as clear a picture as possible of the process in question. These efforts are focused on problems involved with the nitrogen chemistry of combustion systems and on the formation of soot and PAH in flames.

  10. Chemical kinetics modeling

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, C.K.; Pitz, W.J. [Lawrence Livermore National Laboratory, CA (United States)


    This project emphasizes numerical modeling of chemical kinetics of combustion, including applications in both practical combustion systems and in controlled laboratory experiments. Elementary reaction rate parameters are combined into mechanisms which then describe the overall reaction of the fuels being studied. Detailed sensitivity analyses are used to identify those reaction rates and product species distributions to which the results are most sensitive and therefore warrant the greatest attention from other experimental and theoretical research programs. Experimental data from a variety of environments are combined together to validate the reaction mechanisms, including results from laminar flames, shock tubes, flow systems, detonations, and even internal combustion engines.

  11. Development of a quantitative approach using surface-enhanced Raman chemical imaging: first step for the determination of an impurity in a pharmaceutical model. (United States)

    De Bleye, C; Sacré, P-Y; Dumont, E; Netchacovitch, L; Chavez, P-F; Piel, G; Lebrun, P; Hubert, Ph; Ziemons, E


    This publication reports, for the first time, the development of a quantitative approach using surface-enhanced Raman chemical imaging (SER-CI). A pharmaceutical model presented as tablets based on paracetamol, which is the most sold drug around the world, was used to develop this approach. 4-Aminophenol is the main impurity of paracetamol and is actively researched in pharmaceutical formulations because of its toxicity. As its concentration is generally very low (<0.1%, w/w), conventional Raman chemical imaging cannot be used. In this context, a SER-CI method was developed to quantify 4-aminophenol assessing a limit of quantification below its limit of specification of 1000 ppm. Citrate-reduced silver nanoparticles were used as SERS substrate and these nanoparticles were functionalized using 1-butanethiol. Different ways to cover the tablets surface by butanethiol-functionalized silver nanoparticles were tested and a homogeneity study of the silver nanoparticles covering was realized. This homogeneity study was performed in order to choose the best way to cover the surface of tablets by silver colloid. Afterwards, the optimization of the SER-CI approach was necessary and different spectral intensity normalizations were tested. Finally, a quantitative approach using SER-CI was developed enabling to quantify 4-aminophenol from 0.025% to 0.2% in paracetamol tablets. This quantitative approach was tested on two different series of tablets using different batches of silver nanoparticles.

  12. A chemical approach to understanding oxide surfaces (United States)

    Enterkin, James A.; Becerra-Toledo, Andres E.; Poeppelmeier, Kenneth R.; Marks, Laurence D.


    Chemical bonding has often been ignored in favor of physics based energetic considerations in attempts to understand the structure, stability, and reactivity of oxide surfaces. Herein, we analyze the chemical bonding in published structures of the SrTiO3, MgO, and NiO surfaces using bond valence sum (BVS) analysis. These simple chemical bonding theories compare favorably with far more complex quantum mechanical calculations in assessing surface structure stability. Further, the coordination and bonding of surface structures explains the observed stability in a readily comprehensible manner. Finally, we demonstrate how simple chemical bonding models accurately predict the adsorption of foreign species onto surfaces, and how such models can be used to predict changes in surface structures.

  13. Chemical Approaches to Nuclear Receptors in Metabolism (United States)

    Margolis, Ronald N.; Moore, David D.; Willson, Timothy M.; Guy, R. Kip


    The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) sponsored a workshop, “Chemical Approaches to Nuclear Receptors and Metabolism,” in April 2009 to explore how chemical and molecular biology and physiology can be exploited to further our understanding of nuclear receptor structure, function, and role in disease. Signaling cascades involving nuclear receptors are more complex and interrelated than once thought. Nuclear receptors continue to be attractive targets for drug discovery. The overall goal of this workshop was to identify gaps in our understanding of the complexity of ligand activities and begin to address them by (i) increasing the collaboration of investigators from different disciplines, (ii) developing a better understanding of chemical modulation of nuclear receptor action, and (iii) identifying opportunities and roadblocks in the path of translating basic research to discovery of new therapeutics. PMID:19654413

  14. Engineering electrical properties of graphene: chemical approaches (United States)

    Kim, Yong-Jin; Kim, Yuna; Novoselov, Konstantin; Hong, Byung Hee


    To ensure the high performance of graphene-based devices, it is necessary to engineer the electrical properties of graphene with enhanced conductivity, controlled work function, opened or closed bandgaps, etc. This can be performed by various non-covalent chemical approaches, including molecular adsorption, substrate-induced doping, polymerization on graphene, deposition of metallic thin films or nanoparticles, etc. In addition, covalent approaches such as the substitution of carbon atoms with boron or nitrogen and the functionalization with hydrogen or fluorine are useful to tune the bandgaps more efficiently, with better uniformity and stability. In this review, representative examples of chemically engineered graphene and its device applications will be reviewed, and remaining challenges will be discussed.

  15. Modeling of turbulent chemical reaction (United States)

    Chen, J.-Y.


    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.

  16. A decision analytic approach to exposure-based chemical prioritization.

    Directory of Open Access Journals (Sweden)

    Jade Mitchell

    Full Text Available The manufacture of novel synthetic chemicals has increased in volume and variety, but often the environmental and health risks are not fully understood in terms of toxicity and, in particular, exposure. While efforts to assess risks have generally been effective when sufficient data are available, the hazard and exposure data necessary to assess risks adequately are unavailable for the vast majority of chemicals in commerce. The US Environmental Protection Agency has initiated the ExpoCast Program to develop tools for rapid chemical evaluation based on potential for exposure. In this context, a model is presented in which chemicals are evaluated based on inherent chemical properties and behaviorally-based usage characteristics over the chemical's life cycle. These criteria are assessed and integrated within a decision analytic framework, facilitating rapid assessment and prioritization for future targeted testing and systems modeling. A case study outlines the prioritization process using 51 chemicals. The results show a preliminary relative ranking of chemicals based on exposure potential. The strength of this approach is the ability to integrate relevant statistical and mechanistic data with expert judgment, allowing for an initial tier assessment that can further inform targeted testing and risk management strategies.

  17. Chemical approaches to studying stem cell biology

    Institute of Scientific and Technical Information of China (English)

    Wenlin Li; Kai Jiang; Wanguo Wei; Yan Shi; Sheng Ding


    Stem cells,including both pluripotent stem cells and multipotent somatic stem cells,hold great potential for interrogating the mechanisms of tissue development,homeostasis and pathology,and for treating numerous devastating diseases.Establishment of in vitro platforms to faithfully maintain and precisely manipulate stem cell fates is essential to understand the basic mechanisms of stem cell biology,and to translate stem cells into regenerative medicine.Chemical approaches have recently provided a number of small molecules that can be used to control cell selfrenewal,lineage differentiation,reprogramming and regeneration.These chemical modulators have been proven to be versatile tools for probing stem cell biology and manipulating cell fates toward desired outcomes.Ultimately,this strategy is promising to be a new frontier for drug development aimed at endogenous stem cell modulation.

  18. Approaches to measuring entanglement in chemical magnetometers. (United States)

    Tiersch, M; Guerreschi, G G; Clausen, J; Briegel, H J


    Chemical magnetometers are radical pair systems such as solutions of pyrene and N,N-dimethylaniline (Py-DMA) that show magnetic field effects in their spin dynamics and their fluorescence. We investigate the existence and decay of quantum entanglement in free geminate Py-DMA radical pairs and discuss how entanglement can be assessed in these systems. We provide an entanglement witness and propose possible observables for experimentally estimating entanglement in radical pair systems with isotropic hyperfine couplings. As an application, we analyze how the field dependence of the entanglement lifetime in Py-DMA could in principle be used for magnetometry and illustrate the propagation of measurement errors in this approach.

  19. Radiative transfer modeling of surface chemical deposits (United States)

    Reichardt, Thomas A.; Kulp, Thomas J.


    Remote detection of a surface-bound chemical relies on the recognition of a pattern, or "signature," that is distinct from the background. Such signatures are a function of a chemical's fundamental optical properties, but also depend upon its specific morphology. Importantly, the same chemical can exhibit vastly different signatures depending on the size of particles composing the deposit. We present a parameterized model to account for such morphological effects on surface-deposited chemical signatures. This model leverages computational tools developed within the planetary and atmospheric science communities, beginning with T-matrix and ray-tracing approaches for evaluating the scattering and extinction properties of individual particles based on their size and shape, and the complex refractive index of the material itself. These individual-particle properties then serve as input to the Ambartsumian invariant imbedding solution for the reflectance of a particulate surface composed of these particles. The inputs to the model include parameters associated with a functionalized form of the particle size distribution (PSD) as well as parameters associated with the particle packing density and surface roughness. The model is numerically inverted via Sandia's Dakota package, optimizing agreement between modeled and measured reflectance spectra, which we demonstrate on data acquired on five size-selected silica powders over the 4-16 μm wavelength range. Agreements between modeled and measured reflectance spectra are assessed, while the optimized PSDs resulting from the spectral fitting are then compared to PSD data acquired from independent particle size measurements.

  20. Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions (United States)

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


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

  1. Quantum chemical approach to estimating the thermodynamics of metabolic reactions. (United States)

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


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

  2. Chemical Modeling of Nesquehonite Solubility in Li + Na + K + NH4 + Mg + CI + H2O System with a Speclatlon-based Approach

    Institute of Scientific and Technical Information of China (English)

    王道广; 李志宝


    A chemical model,based on Pitzer activity coefficient model,is developed with a speciation approach to describe the solubility and chemistry of nesquehonite in concentrated chloride solutions.The chemical equilibrium constants for nesquehonite and aqueous species,i.e.0 3 MgCO,3 MgHCO,and MgOH +,are precisely calculated as a function of temperature according to the Van't Hoff equation by use of standard Gibbs free energy,standard formation enthalpy and heat capacity.The most recent solubility data are regressed to obtain new Pitzer parameters with good agreement.The predictive ability of the new model is improved significantly in comparison with previous models.The behavior of speciation chemistry for nesquehonite in various chloride media is explained through this modeling work on the basis of the 2 3 Mg /CO bearing species distribution,activity coefficient and pH changes.

  3. Material Modelling - Composite Approach

    DEFF Research Database (Denmark)

    Nielsen, Lauge Fuglsang


    , and internal stresses caused by drying shrinkage with experimental results reported in the literature on the mechanical behavior of mature concretes. It is then concluded that the model presented applied in general with respect to age at loading.From a stress analysis point of view the most important finding......This report is part of a research project on "Control of Early Age Cracking" - which, in turn, is part of the major research programme, "High Performance Concrete - The Contractor's Technology (HETEK)", coordinated by the Danish Road Directorate, Copenhagen, Denmark, 1997.A composite......-rheological model of concrete is presented by which consistent predictions of creep, relaxation, and internal stresses can be made from known concrete composition, age at loading, and climatic conditions. No other existing "creep prediction method" offers these possibilities in one approach.The model...

  4. Protein engineering approaches to chemical biotechnology. (United States)

    Chen, Zhen; Zeng, An-Ping


    Protein engineering for the improvement of properties of biocatalysts and for the generation of novel metabolic pathways plays more and more important roles in chemical biotechnology aiming at the production of chemicals from biomass. Although widely used in single-enzyme catalysis process, protein engineering is only being increasingly explored in recent years to achieve more complex in vitro and in vivo biocatalytic processes. This review focuses on major contributions of protein engineering to chemical biotechnology in the field of multi-enzymatic cascade catalysis and metabolic engineering. Especially, we discuss and highlight recent strategies for combining pathway design and protein engineering for the production of novel products.

  5. Approaches to Chemical and Biochemical Information and Signal Processing (United States)

    Privman, Vladimir


    We outline models and approaches for error control required to prevent buildup of noise when ``gates'' and other ``network elements'' based on (bio)chemical reaction processes are utilized to realize stable, scalable networks for information and signal processing. We also survey challenges and possible future research. [4pt] [1] Control of Noise in Chemical and Biochemical Information Processing, V. Privman, Israel J. Chem. 51, 118-131 (2010).[0pt] [2] Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic, V. Privman, J. Halamek, M. A. Arugula, D. Melnikov, V. Bocharova and E. Katz, J. Phys. Chem. B 114, 14103-14109 (2010).[0pt] [3] Towards Biosensing Strategies Based on Biochemical Logic Systems, E. Katz, V. Privman and J. Wang, in: Proc. Conf. ICQNM 2010 (IEEE Comp. Soc. Conf. Publ. Serv., Los Alamitos, California, 2010), pages 1-9.

  6. Modelling the influence of inulin as a fat substitute in comminuted meat products on their physico-chemical characteristics and eating quality using a mixture design approach. (United States)

    Keenan, Derek F; Resconi, Virginia C; Kerry, Joseph P; Hamill, Ruth M


    The effects of fat substitution using two commercial inulin products on the physico-chemical properties and eating quality of a comminuted meat product (breakfast sausage) were modelled using a specialised response surface experiment specially developed for mixtures. 17 treatments were assigned representing a different substitution level for fat with inulin. Sausages were formulated to contain pork shoulder, back fat/inulin, water, rusk and seasoning (44.3, 18.7, 27.5, 7 and 2.5% w/w). Composition, sensory, instrumental texture and colour characteristics were assessed. Fructan analysis showed that inulin was unaffected by heat or processing treatments. Models showed increasing inulin inclusions decreased cook loss (pinulin concentration, with panellists also scoring products containing inulin as less tender (pinulin to deliver a prebiotic health effect.

  7. Chemical modeling of exoplanet atmospheres

    CERN Document Server

    Venot, Olivia


    The past twenty years have revealed the diversity of planets that exist in the Universe. It turned out that most of exoplanets are different from the planets of our Solar System and thus, everything about them needs to be explored. Thanks to current observational technologies, we are able to determine some information about the atmospheric composition, the thermal structure and the dynamics of these exoplanets, but many questions remain still unanswered. To improve our knowledge about exoplanetary systems, more accurate observations are needed and that is why the Exoplanet Characterisation Observatory (EChO) is an essential space mission. Thanks to its large spectral coverage and high spectral resolution, EChO will provide exoplanetary spectra with an unprecedented accuracy, allowing to improve our understanding of exoplanets. In this work, we review what has been done to date concerning the chemical modeling of exoplanet atmospheres and what are the main characteristics of warm exoplanet atmospheres, which a...

  8. Chemical and instrumental approaches to cheese analysis. (United States)

    Subramanian, Anand; Rodriguez-Saona, Luis


    Overcoming the complexity of cheese matrix to reliably analyze cheese composition, flavor, and ripening changes has been a challenge. Several sample isolation or fractionation methods, chemical and enzymatic assays, and instrumental methods have been developed over the decades. While some of the methods are well established standard methods, some still need to be researched and improved. This chapter reviews the chemical and instrumental methods available to determine cheese composition and monitor biochemical events (e.g., glycolysis, lipolysis, and proteolysis) during cheese ripening that lead to the formation of cheese flavor. Chemical and enzymatic methods available for analysis of cheese composition (fat, protein, lactose, salt, nitrogen content, moisture, etc.) are presented. Electrophoretic, chromatographic, and spectroscopic techniques are also reviewed in the light of their application to monitor cheese ripening and flavor compounds. Novel instrumental methods based on Fourier-transform infrared spectroscopy that are currently being researched and applied to cheese analysis are introduced.

  9. Chemical reaction network approaches to Biochemical Systems Theory. (United States)

    Arceo, Carlene Perpetua P; Jose, Editha C; Marin-Sanguino, Alberto; Mendoza, Eduardo R


    This paper provides a framework to represent a Biochemical Systems Theory (BST) model (in either GMA or S-system form) as a chemical reaction network with power law kinetics. Using this representation, some basic properties and the application of recent results of Chemical Reaction Network Theory regarding steady states of such systems are shown. In particular, Injectivity Theory, including network concordance [36] and the Jacobian Determinant Criterion [43], a "Lifting Theorem" for steady states [26] and the comprehensive results of Müller and Regensburger [31] on complex balanced equilibria are discussed. A partial extension of a recent Emulation Theorem of Cardelli for mass action systems [3] is derived for a subclass of power law kinetic systems. However, it is also shown that the GMA and S-system models of human purine metabolism [10] do not display the reactant-determined kinetics assumed by Müller and Regensburger and hence only a subset of BST models can be handled with their approach. Moreover, since the reaction networks underlying many BST models are not weakly reversible, results for non-complex balanced equilibria are also needed.

  10. Cellular biosensing: chemical and genetic approaches. (United States)

    Haruyama, Tetsuya


    Biosensors have been developed to determine the concentration of specific compounds in situ. They are already widely employed as a practical technology in the clinical and healthcare fields. Recently, another concept of biosensing has been receiving attention: biosensing for the evaluation of molecular potency. The development of this novel concept has been supported by the development of related technologies, as such as molecular design, molecular biology (genetic engineering) and cellular/tissular engineering. This review is addresses this new concept of biosensing and its application to the evaluation of the potency of chemicals in biological systems, in the field of cellular/tissular engineering. Cellular biosensing may provide information on both pharmaceutical and chemical safety, and on drug efficacy in vitro as a screening tool.

  11. Review of existing terrestrial bioaccumulation models and terrestrial bioaccumulation modeling needs for organic chemicals (United States)

    Protocols for terrestrial bioaccumulation assessments are far less-developed than for aquatic systems. This manuscript reviews modeling approaches that can be used to assess the terrestrial bioaccumulation potential of commercial organic chemicals. Models exist for plant, inver...

  12. Chemical Leasing business models and corporate social responsibility. (United States)

    Moser, Frank; Jakl, Thomas; Joas, Reihard; Dondi, Francesco


    Chemical Leasing is a service-oriented business model that shifts the focus from increasing sales volume of chemicals towards a value-added approach. Recent pilot projects have shown the economic benefits of introducing Chemical Leasing business models in a broad range of sectors. A decade after its introduction, the promotion of Chemical Leasing is still predominantly done by the public sector and international organizations. We show in this paper that awareness-raising activities to disseminate information on this innovative business model mainly focus on the economic benefits. We argue that selling Chemical Leasing business models solely on the grounds of economic and ecological considerations falls short of branding it as a corporate social responsibility initiative, which, for this paper, is defined as a stakeholder-oriented concept that extends beyond the organization's boundaries and is driven by an ethical understanding of the organization's responsibility for the impact of its business activities. For the analysis of Chemical Leasing business models, we introduce two case studies from the water purification and metal degreasing fields, focusing on employees and local communities as two specific stakeholder groups of the company introducing Chemical Leasing. The paper seeks to demonstrate that Chemical Leasing business models can be branded as a corporate social responsibility initiative by outlining the vast potential of Chemical Leasing to improve occupational health and safety and to strengthen the ability of companies to protect the environment from the adverse effects of the chemicals they apply.

  13. Rapidity-dependent chemical potentials in a statistical approach (United States)

    Broniowski, Wojciech; Biedroń, Bartłomiej


    We present a single-freeze-out model with thermal and geometric parameters dependent on the position within the fireball and use it to describe the rapidity distribution and transverse-momentum spectra of pions, kaons, protons and antiprotons measured at RHIC at \\sqrt{s_NN}=200\\,\\, GeV by BRAHMS. THERMINATOR is used to perform the necessary simulation, which includes all resonance decays. The result of the fit to the data is the expected growth of the baryon and strange chemical potentials with the spatial rapidity αpar. The value of the baryon chemical potential at αpar ~ 3 is about 200 MeV, i.e. it lies in the range of the highest SPS energies. The chosen geometry of the fireball has a decreasing transverse size as the magnitude of αpar is increased, which also corresponds to decreasing transverse flow. The strange chemical potential obtained from the fit to the K+/K- ratio is such that the local strangeness density in the fireball is compatible with zero. The resulting rapidity distribution of net protons are described qualitatively within the statistical approach. As a result of our study, the knowledge of the 'topography' of the fireball is acquired, allowing for other analyses and predictions. Research supported by the Polish Ministry of Education and Science, grants N202 034 32/0918 and 2 P03B 02828.

  14. Mathematical Modeling of Chemical Stoichiometry (United States)

    Croteau, Joshua; Fox, William P.; Varazo, Kristofoland


    In beginning chemistry classes, students are taught a variety of techniques for balancing chemical equations. The most common method is inspection. This paper addresses using a system of linear mathematical equations to solve for the stoichiometric coefficients. Many linear algebra books carry the standard balancing of chemical equations as an…

  15. Chemical reactor modeling multiphase reactive flows

    CERN Document Server

    Jakobsen, Hugo A


    Chemical Reactor Modeling closes the gap between Chemical Reaction Engineering and Fluid Mechanics.  The second edition consists of two volumes: Volume 1: Fundamentals. Volume 2: Chemical Engineering Applications In volume 1 most of the fundamental theory is presented. A few numerical model simulation application examples are given to elucidate the link between theory and applications. In volume 2 the chemical reactor equipment to be modeled are described. Several engineering models are introduced and discussed. A survey of the frequently used numerical methods, algorithms and schemes is provided. A few practical engineering applications of the modeling tools are presented and discussed. The working principles of several experimental techniques employed in order to get data for model validation are outlined. The monograph is based on lectures regularly taught in the fourth and fifth years graduate courses in transport phenomena and chemical reactor modeling, and in a post graduate course in modern reactor m...

  16. Modeling Microscopic Chemical Sensors in Capillaries

    CERN Document Server

    Hogg, Tad


    Nanotechnology-based microscopic robots could provide accurate in vivo measurement of chemicals in the bloodstream for detailed biological research and as an aid to medical treatment. Quantitative performance estimates of such devices require models of how chemicals in the blood diffuse to the devices. This paper models microscopic robots and red blood cells (erythrocytes) in capillaries using realistic distorted cell shapes. The models evaluate two sensing scenarios: robots moving with the cells past a chemical source on the vessel wall, and robots attached to the wall for longer-term chemical monitoring. Using axial symmetric geometry with realistic flow speeds and diffusion coefficients, we compare detection performance with a simpler model that does not include the cells. The average chemical absorption is quantitatively similar in both models, indicating the simpler model is an adequate design guide to sensor performance in capillaries. However, determining the variation in forces and absorption as cells...

  17. Approaching Chemical Accuracy with Quantum Monte Carlo

    CERN Document Server

    Petruzielo, F R; Umrigar, C J


    A quantum Monte Carlo study of the atomization energies for the G2 set of molecules is presented. Basis size dependence of diffusion Monte Carlo atomization energies is studied with a single determinant Slater-Jastrow trial wavefunction formed from Hartree-Fock orbitals. With the largest basis set, the mean absolute deviation from experimental atomization energies for the G2 set is 3.0 kcal/mol. Optimizing the orbitals within variational Monte Carlo improves the agreement between diffusion Monte Carlo and experiment, reducing the mean absolute deviation to 2.1 kcal/mol. Moving beyond a single determinant Slater-Jastrow trial wavefunction, diffusion Monte Carlo with a small complete active space Slater-Jastrow trial wavefunction results in near chemical accuracy. In this case, the mean absolute deviation from experimental atomization energies is 1.2 kcal/mol. It is shown from calculations on systems containing phosphorus that the accuracy can be further improved by employing a larger active space.

  18. Predicting allergic contact dermatitis: a hierarchical structure activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors (United States)

    Basak, Subhash C.; Mills, Denise; Hawkins, Douglas M.


    A hierarchical classification study was carried out based on a set of 70 chemicals—35 which produce allergic contact dermatitis (ACD) and 35 which do not. This approach was implemented using a regular ridge regression computer code, followed by conversion of regression output to binary data values. The hierarchical descriptor classes used in the modeling include topostructural (TS), topochemical (TC), and quantum chemical (QC), all of which are based solely on chemical structure. The concordance, sensitivity, and specificity are reported. The model based on the TC descriptors was found to be the best, while the TS model was extremely poor.

  19. Coulombic Models in Chemical Bonding. (United States)

    Sacks, Lawrence J.


    Compares the coulumbic point charge model for hydrogen chloride with the valence bond model. It is not possible to assign either a nonpolar or ionic canonical form of the valence bond model, while the covalent-ionic bond distribution does conform to the point charge model. (JM)

  20. Chemical equilibrium modeling of detonation

    Energy Technology Data Exchange (ETDEWEB)

    Fried, Laurence E. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bastea, Sorin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)


    Energetic materials are unique for having a strong exothermic reactivity, which has made them desirable for both military and commercial applications. Energetic materials are commonly divided into high explosives, propellants, and pyrotechnics. We will focus on high explosive (HE) materials here, although there is a great deal of commonality between the classes of energetic materials. Furthermore the history of HE materials is long, their condensed-phase chemical properties are poorly understood.

  1. Integrating exposure into chemical alternatives assessment using a qualitative approach

    DEFF Research Database (Denmark)

    Greggs, Bill; Arnold, Scott; Burns, Thomas J.;


    could trigger a higher-tiered, more quantitative exposure assessment on the alternatives being considered. This talk will demonstrate an approach for including chemical- and product-related exposure information in a qualitative AA comparison. Starting from existing hazard AAs, a series of four chemical...... Sustainable Chemical Alternatives Technical Committee, which consists of scientists from academia, industry, government, and NGOs, has developed a qualitative comparative exposure approach. Conducting such a comparison can screen for alternatives that are expected to have a higher exposure potential, which......-product application scenarios were examined to test the concept, to understand the effort required, and to determine the value of exposure data in AA decision-making. The group has developed a classification approach for ingredient and product parameters to support comparisons between alternatives as well...

  2. A kinetic model for chemical neurotransmission (United States)

    Ramirez-Santiago, Guillermo; Martinez-Valencia, Alejandro; Fernandez de Miguel, Francisco

    Recent experimental observations in presynaptic terminals at the neuromuscular junction indicate that there are stereotyped patterns of cooperativeness in the fusion of adjacent vesicles. That is, a vesicle in hemifusion process appears on the side of a fused vesicle and which is followed by another vesicle in a priming state while the next one is in a docking state. In this talk we present a kinetic model for this morphological pattern in which each vesicle state previous to the exocytosis is represented by a kinetic state. This chain states kinetic model can be analyzed by means of a Master equation whose solution is simulated with the stochastic Gillespie algorithm. With this approach we have reproduced the responses to the basal release in the absence of stimulation evoked by the electrical activity and the phenomena of facilitation and depression of neuromuscular synapses. This model offers new perspectives to understand the underlying phenomena in chemical neurotransmission based on molecular interactions that result in the cooperativity between vesicles during neurotransmitter release. DGAPA Grants IN118410 and IN200914 and Conacyt Grant 130031.

  3. Error estimation and adaptive chemical transport modeling

    Directory of Open Access Journals (Sweden)

    Malte Braack


    Full Text Available We present a numerical method to use several chemical transport models of increasing accuracy and complexity in an adaptive way. In largest parts of the domain, a simplified chemical model may be used, whereas in certain regions a more complex model is needed for accuracy reasons. A mathematically derived error estimator measures the modeling error and provides information where to use more accurate models. The error is measured in terms of output functionals. Therefore, one has to consider adjoint problems which carry sensitivity information. This concept is demonstrated by means of ozone formation and pollution emission.

  4. New Source Model for Chemical Explosions

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaoning [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)


    With sophisticated inversion scheme, we recover characteristics of SPE explosions such as corner frequency fc and moment M0, which are used to develop a new source model for chemical explosions.

  5. Chemical genetics approaches for selective intervention in epigenetics. (United States)

    Runcie, Andrew C; Chan, Kwok-Ho; Zengerle, Michael; Ciulli, Alessio


    Chemical genetics is the use of biologically active small molecules (chemical probes) to investigate the functions of gene products, through the modulation of protein activity. Recent years have seen significant progress in the application of chemical genetics to study epigenetics, following the development of new chemical probes, a growing appreciation of the role of epigenetics in disease and a recognition of the need and utility of high-quality, cell-active chemical probes. In this review, we single out the bromodomain reader domains as a prime example of both the success, and challenges facing chemical genetics. The difficulty in generating single-target selectivity has long been a thorn in the side of chemical genetics, however, recent developments in advanced forms of chemical genetics promise to bypass this, and other, limitations. The 'bump-and-hole' approach has now been used to probe - for the first time - the BET bromodomain subfamily with single-target selectivity and may be applicable to other epigenetic domains. Meanwhile, PROTAC compounds have been shown to be significantly more efficacious than standard domain inhibitors, and have the potential to enhance target selectivity.

  6. Computer-Aided Multiscale Modelling for Chemical Process Engineering

    DEFF Research Database (Denmark)

    Morales Rodriguez, Ricardo; Gani, Rafiqul


    T) for model translation, analysis and solution. The integration of ModDev, MoT and ICAS or any other external software or process simulator (using COM-Objects) permits the generation of different models and/or process configurations for purposes of simulation, design and analysis. Consequently, it is possible......Chemical processes are generally modeled through monoscale approaches, which, while not adequate, satisfy a useful role in product-process design. In this case, use of a multi-dimensional and multi-scale model-based approach has importance in product-process development. A computer-aided framework...... for model generation, analysis, solution and implementation is necessary for the development and application of the desired model-based approach for product-centric process design/analysis. This goal is achieved through the combination of a system for model development (ModDev), and a modelling tool (Mo...

  7. Chemical Kinetic Modeling of Advanced Transportation Fuels

    Energy Technology Data Exchange (ETDEWEB)

    PItz, W J; Westbrook, C K; Herbinet, O


    Development of detailed chemical kinetic models for advanced petroleum-based and nonpetroleum based fuels is a difficult challenge because of the hundreds to thousands of different components in these fuels and because some of these fuels contain components that have not been considered in the past. It is important to develop detailed chemical kinetic models for these fuels since the models can be put into engine simulation codes used for optimizing engine design for maximum efficiency and minimal pollutant emissions. For example, these chemistry-enabled engine codes can be used to optimize combustion chamber shape and fuel injection timing. They also allow insight into how the composition of advanced petroleum-based and non-petroleum based fuels affect engine performance characteristics. Additionally, chemical kinetic models can be used separately to interpret important in-cylinder experimental data and gain insight into advanced engine combustion processes such as HCCI and lean burn engines. The objectives are: (1) Develop detailed chemical kinetic reaction models for components of advanced petroleum-based and non-petroleum based fuels. These fuels models include components from vegetable-oil-derived biodiesel, oil-sand derived fuel, alcohol fuels and other advanced bio-based and alternative fuels. (2) Develop detailed chemical kinetic reaction models for mixtures of non-petroleum and petroleum-based components to represent real fuels and lead to efficient reduced combustion models needed for engine modeling codes. (3) Characterize the role of fuel composition on efficiency and pollutant emissions from practical automotive engines.

  8. Reduced Chemical Kinetic Model for Titan Entries

    Directory of Open Access Journals (Sweden)

    Romain Savajano


    Full Text Available A reduced chemical kinetic model for Titan's atmosphere has been developed. This new model with 18 species and 28 reactions includes the mainfeatures of a more complete scheme, respecting the radiative fluxes. It has been verified against three key elements: a sensitivity analysis, the equilibrium chemical composition using shock tube simulations in CHEMKIN, and the results of computational fluid dynamics (CFDs simulations.

  9. Modelling Chemical Reasoning to Predict Reactions


    Segler, Marwin H. S.; Waller, Mark P.


    The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as finding missing links in a knowledge graph. We have constructed a knowledge graph containing 14.4 million molecules and 8.2 million binary reactions, which represents the bulk of all chemical reactions ever published in the scientific literature. Our model outpe...

  10. Integrating exposure into chemical alternatives assessment using a qualitative approach

    DEFF Research Database (Denmark)

    Greggs, Bill; Arnold, Scott; Burns, T. E.


    Most alternatives assessments (AA) published to date are largely hazard-based rankings, and as such may not represent a fully informed consideration of the advantages and disadvantages of possible alternatives. With an assessment goal of identifying an alternative chemical that is more sustainable...... Sustainable Chemical Alternatives Technical Committee, which consists of scientists from academia, industry, government, and NGOs, has developed a qualitative comparative exposure approach. Conducting such a comparison can screen for alternatives that are expected to have a higher human or environmental...... exposure potential, which could trigger a higher-tiered, more quantitative exposure assessment on the alternatives being considered, minimizing the likelihood of regrettable substitution. This talk will demonstrate an approach for including chemical- and product-related exposure information...

  11. Human exposure assessment: Approaches for chemicals (REACH) and biocides (BPD)

    NARCIS (Netherlands)

    Hemmen, J.J. van; Gerritsen-Ebben, R.


    The approaches that are indicated in the various guidance documents for the assessment of human exposure for chemicals and biocides are summarised. This reflects the TNsG (Technical notes for Guidance) version 2: human exposure assessment for biocidal products (1) under the BPD (Biocidal Products Di

  12. Design of tailor-made chemical blend using a decomposition-based computer-aided approach

    DEFF Research Database (Denmark)

    Yunus, Nor Alafiza; Gernaey, Krist; Manan, Z.A.;


    Computer aided techniques form an efficient approach to solve chemical product design problems such as the design of blended liquid products (chemical blending). In chemical blending, one tries to find the best candidate, which satisfies the product targets defined in terms of desired product...... the desired product attributes. Alternatively, rigorous modeling could also be used in this final step. In other words, the candidates are quickly generated and screened until a small number is left for final selection and evaluation by experiments and/or rigorous modeling. This paper presents a design...... methodology for blended liquid products that identifies a set of feasible chemical blends. The blend design problem is formulated as a Mixed Integer Nonlinear Programming (MINLP) model where the objective is to find the optimal blended gasoline or diesel product subject to types of chemicals...

  13. A chemical-biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives. (United States)

    Grimm, Fabian A; Iwata, Yasuhiro; Sirenko, Oksana; Chappell, Grace A; Wright, Fred A; Reif, David M; Braisted, John; Gerhold, David L; Yeakley, Joanne M; Shepard, Peter; Seligmann, Bruce; Roy, Tim; Boogaard, Peter J; Ketelslegers, Hans B; Rohde, Arlean M; Rusyn, Ivan


    Comparative assessment of potential human health impacts is a critical step in evaluating both chemical alternatives and existing products on the market. Most alternatives assessments are conducted on a chemical-by-chemical basis and it is seldom acknowledged that humans are exposed to complex products, not individual substances. Indeed, substances of Unknown or Variable composition, Complex reaction products, and Biological materials (UVCBs) are ubiquitous in commerce yet they present a major challenge for registration and health assessments. Here, we present a comprehensive experimental and computational approach to categorize UVCBs according to global similarities in their bioactivity using a suite of in vitro models. We used petroleum substances, an important group of UVCBs which are grouped for regulatory approval and read-across primarily on physico-chemical properties and the manufacturing process, and only partially based on toxicity data, as a case study. We exposed induced pluripotent stem cell-derived cardiomyocytes and hepatocytes to DMSO-soluble extracts of 21 petroleum substances from five product groups. Concentration-response data from high-content imaging in cardiomyocytes and hepatocytes, as well as targeted high-throughput transcriptomic analysis of the hepatocytes, revealed distinct groups of petroleum substances. Data integration showed that bioactivity profiling affords clustering of petroleum substances in a manner similar to the manufacturing process-based categories. Moreover, we observed a high degree of correlation between bioactivity profiles and physico-chemical properties, as well as improved groupings when chemical and biological data were combined. Altogether, we demonstrate how novel in vitro screening approaches can be effectively utilized in combination with physico-chemical characteristics to group complex substances and enable read-across. This approach allows for rapid and scientifically-informed evaluation of health impacts of

  14. A systems engineering approach to manage the complexity in sustainable chemical product-process design

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    This paper provides a perspective on model-data based solution approaches for chemical product-process design, which consists of finding the identity of the candidate chemical product, designing the process that can sustainably manufacture it and verifying the performance of the product during...... application. The chemical product tree is potentially very large and a wide range of options exist for selecting the product to make, the raw material to use as well as the processing route to employ. It is shown that systematic computer-aided methods and tools integrated within a model-data based design...

  15. Gradient Bundle Analysis: A Full Topological Approach to Chemical Bonding

    CERN Document Server

    Morgenstern, Amanda


    The "chemical bond" is a central concept in molecular sciences, but there is no consensus as to what a bond actually is. Therefore, a variety of bonding models have been developed, each defining the structure of molecules in a different manner with the goal of explaining and predicting chemical properties. This thesis describes the initial development of gradient bundle analysis (GBA), a chemical bonding model that creates a high resolution picture of chemical interactions within the charge density framework. GBA is based on concepts from the quantum theory of atoms in molecules (QTAIM), but uses a more complete picture of the topology and geometry of the electron charge density to understand and predict bonding interactions. Gradient bundles are defined as volumes bounded by zero-flux surfaces (ZFSs) in the gradient of the charge density with well-defined energies. The structure of gradient bundles provides an avenue for detecting the locations of valence electrons, which correspond to reactive regions in a ...

  16. Modeling chlorine dioxide bleaching of chemical pulp


    Tarvo, Ville


    This doctoral thesis deals with the phenomenon-based modeling of pulp bleaching. Previous bleaching models typically utilize one or two empirical correlations to predict the kinetics in kappa number development. Empirical correlations are simple to develop, but their parameters are often tied to the validation system. A major benefit of physico-chemical phenomenon models is that they are valid regardless of the reaction environment. Furthermore, modeling the bleaching processes at molecular l...

  17. Chemical Kinetic Models for Advanced Engine Combustion

    Energy Technology Data Exchange (ETDEWEB)

    Pitz, William J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Mehl, Marco [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Westbrook, Charles K. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)


    The objectives for this project are as follows: Develop detailed chemical kinetic models for fuel components used in surrogate fuels for compression ignition (CI), homogeneous charge compression ignition (HCCI) and reactivity-controlled compression-ignition (RCCI) engines; and Combine component models into surrogate fuel models to represent real transportation fuels. Use them to model low-temperature combustion strategies in HCCI, RCCI, and CI engines that lead to low emissions and high efficiency.

  18. Mathematical modeling a chemical engineer's perspective

    CERN Document Server

    Rutherford, Aris


    Mathematical modeling is the art and craft of building a system of equations that is both sufficiently complex to do justice to physical reality and sufficiently simple to give real insight into the situation. Mathematical Modeling: A Chemical Engineer's Perspective provides an elementary introduction to the craft by one of the century's most distinguished practitioners.Though the book is written from a chemical engineering viewpoint, the principles and pitfalls are common to all mathematical modeling of physical systems. Seventeen of the author's frequently cited papers are reprinted to illus

  19. A computational approach to chemical etiologies of diabetes

    DEFF Research Database (Denmark)

    Audouze, Karine Marie Laure; Brunak, Søren; Grandjean, Philippe


    Computational meta-analysis can link environmental chemicals to genes and proteins involved in human diseases, thereby elucidating possible etiologies and pathogeneses of non-communicable diseases. We used an integrated computational systems biology approach to examine possible pathogenetic...... linkages in type 2 diabetes (T2D) through genome-wide associations, disease similarities, and published empirical evidence. Ten environmental chemicals were found to be potentially linked to T2D, the highest scores were observed for arsenic, 2,3,7,8-tetrachlorodibenzo-p-dioxin, hexachlorobenzene...

  20. A Comprehensive Approach for Pectin Chemical and Functional Characterization

    DEFF Research Database (Denmark)

    de Sousa, António Felipe Gomes Teixeira

    In this work, a comprehensive approach for the chemical and functional analysis of pectin was used in order to relate the different extraction conditions used to the polymer structure and the final functional (mainly gelling) properties. A wide range of methods were utilized including chemical...... and chromatographic characterization methods (HPAEC and HPSEC), rheological measurements of elasticity, and biological epitopes detection using carbohydrate microarrays. The end product of this study is expected to contribute to the knowledge of pectin polymeric conformation and structure-function properties as well...

  1. Chemical Evolution models of Local Group galaxies

    CERN Document Server

    Tosi, M P


    Status quo and perspectives of standard chemical evolution models of Local Group galaxies are summarized, discussing what we have learnt from them, what we know we have not learnt yet, and what I think we will learn in the near future. It is described how Galactic chemical evolution models have helped showing that: i) stringent constraints on primordial nucleosynthesis can be derived from the observed Galactic abundances of the light elements, ii) the Milky Way has been accreting external gas from early epochs to the present time, iii) the vast majority of Galactic halo stars have formed quite rapidly at early epochs. Chemical evolution models for the closest dwarf galaxies, although still uncertain so far, are expected to become extremely reliable in the nearest future, thanks to the quality of new generation photometric and spectroscopic data which are currently being acquired.

  2. Engineered Barrier System: Physical and Chemical Environment Model

    Energy Technology Data Exchange (ETDEWEB)

    D. M. Jolley; R. Jarek; P. Mariner


    The conceptual and predictive models documented in this Engineered Barrier System: Physical and Chemical Environment Model report describe the evolution of the physical and chemical conditions within the waste emplacement drifts of the repository. The modeling approaches and model output data will be used in the total system performance assessment (TSPA-LA) to assess the performance of the engineered barrier system and the waste form. These models evaluate the range of potential water compositions within the emplacement drifts, resulting from the interaction of introduced materials and minerals in dust with water seeping into the drifts and with aqueous solutions forming by deliquescence of dust (as influenced by atmospheric conditions), and from thermal-hydrological-chemical (THC) processes in the drift. These models also consider the uncertainty and variability in water chemistry inside the drift and the compositions of introduced materials within the drift. This report develops and documents a set of process- and abstraction-level models that constitute the engineered barrier system: physical and chemical environment model. Where possible, these models use information directly from other process model reports as input, which promotes integration among process models used for total system performance assessment. Specific tasks and activities of modeling the physical and chemical environment are included in the technical work plan ''Technical Work Plan for: In-Drift Geochemistry Modeling'' (BSC 2004 [DIRS 166519]). As described in the technical work plan, the development of this report is coordinated with the development of other engineered barrier system analysis model reports.

  3. Heat transfer modeling an inductive approach

    CERN Document Server

    Sidebotham, George


    This innovative text emphasizes a "less-is-more" approach to modeling complicated systems such as heat transfer by treating them first as "1-node lumped models" that yield simple closed-form solutions. The author develops numerical techniques for students to obtain more detail, but also trains them to use the techniques only when simpler approaches fail. Covering all essential methods offered in traditional texts, but with a different order, Professor Sidebotham stresses inductive thinking and problem solving as well as a constructive understanding of modern, computer-based practice. Readers learn to develop their own code in the context of the material, rather than just how to use packaged software, offering a deeper, intrinsic grasp behind models of heat transfer. Developed from over twenty-five years of lecture notes to teach students of mechanical and chemical engineering at The Cooper Union for the Advancement of Science and Art, the book is ideal for students and practitioners across engineering discipl...

  4. Chemical-reaction model for Mexican wave (United States)

    Nagatani, Takashi


    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.

  5. The TSCA interagency testing committee`s approaches to screening and scoring chemicals and chemical groups: 1977-1983

    Energy Technology Data Exchange (ETDEWEB)

    Walker, J.D. [Environmental Protection Agency, Washington, DC (United States)


    This paper describes the TSCA interagency testing committee`s (ITC) approaches to screening and scoring chemicals and chemical groups between 1977 and 1983. During this time the ITC conducted five scoring exercises to select chemicals and chemical groups for detailed review and to determine which of these chemicals and chemical groups should be added to the TSCA Section 4(e) Priority Testing List. 29 refs., 1 fig., 2 tabs.

  6. Chemical Kinetic Modeling of 2-Methylhexane Combustion

    KAUST Repository

    Mohamed, Samah Y.


    Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important for investigating the combustion behavior of diesel, gasoline, and aviation fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracy in certain portions of the models. This study focuses on updating thermodynamic data and kinetic model for a gasoline surrogate fuel, 2-methylhexane, with recently published group values and rate rules. These update provides a better agreement with rapid compression machine measurements of ignition delay time, while also strengthening the fundamental basis of the model.

  7. Aesthetics of Chemical Products: Materials, Molecules, and Molecular Models

    Directory of Open Access Journals (Sweden)

    Joachim Schummer


    Full Text Available By comparing chemistry to art, chemists have recently made claims to the aesthetic value, even beauty, of some of their products. This paper takes these claims seriously and turns them into a systematic investigation of the aesthetics of chemical products. I distinguish three types of chemical products - materials, molecules, and molecular models - and use a wide variety of aesthetic theories suitable for an investigation of the corresponding sorts of objects. These include aesthetics of materials, idealistic aesthetics from Plato to Kant and Schopenhauer, psychological approaches of Ernst Gombrich and Rudolf Arnheim, and semiotic aesthetics of Nelson Goodman and Umberto Eco. Although the investigation does not support recent claims, I point out where aesthetics does and can play an import role in chemistry. Particularly, Eco's approach helps us understand that and how aesthetic experience can be a driving force in chemical research.

  8. Multi-scale modeling for sustainable chemical production

    DEFF Research Database (Denmark)

    Zhuang, Kai; Bakshi, Bhavik R.; Herrgard, Markus


    With recent advances in metabolic engineering, it is now technically possible to produce a wide portfolio of existing petrochemical products from biomass feedstock. In recent years, a number of modeling approaches have been developed to support the engineering and decision-making processes......, chemical industry, economy, and ecosystem. In addition, we propose a multi-scale approach for integrating the existing models into a cohesive framework. The major benefit of this proposed framework is that the design and decision-making at each scale can be informed, guided, and constrained by simulations...

  9. Probabilistic Approach to Risk Analysis of Chemical Spills at Sea

    Institute of Scientific and Technical Information of China (English)

    Magda Bogalecka; Krzysztof Kolowrocki


    Risk analysis of chemical spills at sea and their consequences for sea environment are discussed. Mutual interactions between the process of the sea accident initiating events, the process of the sea environment threats, and the process of the sea environment degradation are investigated. To describe these three particular processes, the separate semi-Markov models are built. Furthermore, these models are jointed into one general model of these processes interactions.Moreover, some comments on the method for statistical identification of the considered models are proposed.

  10. Chemical Evolution Model of M33 (United States)

    Robles-Valdez, F.; Carigi, L.


    We present a chemical evolution model (CEM) of M33 and we find that M33, which is smaller than both M31 and MW, shows a lower gas infall rate, SFR efficiency, and IMF M_{up}. Therefore the CEMs for large spiral galaxies (Carigi et al. 2005; Meneses-Goytia et al. 2011) can be scaled to a smaller galaxy.

  11. Modelling Chemical Reasoning to Predict Reactions

    CERN Document Server

    Segler, Marwin H S


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

  12. Modeling heterogeneous chemical processes on aerosol surface

    Institute of Scientific and Technical Information of China (English)

    Junjun Deng; Tijian Wang; Li Liu; Fei Jiang


    To explore the possible impact of heterogeneous chemical processes on atmospheric trace components,a coupled box model including gas-phase chemical processes,aerosol thermodynamic equilibrium processes,and heterogeneous chemical processes on the surface of dust,black carbon(BC)and sea salt is set up to simulate the effects of heterogeneous chemistry on the aerosol surface,and analyze the primary factors affecting the heterogeneous processes.Results indicate that heterogeneous chemical processes on the aerosol surface in the atmosphere will affect the concentrations of trace gases such as H2O2,HO2,O3,NO2,NO3,HNO3 and SO2,and aerosols such as SO42-,NO3-and NH4+.Sensitivity tests suggest that the magnitude of the impact of heterogeneous processes strongly depends on aerosol concentration and the surface uptake coefficients used in the box model.However,the impact of temperature on heterogeneous chemical processes is considerably less.The"renoxification"of HNO3 will affect the components of the troposphere such as nitrogen oxide and ozone.

  13. Tailor-made Design of Chemical Blends using Decomposition-based Computer-aided Approach

    DEFF Research Database (Denmark)

    Yunus, Nor Alafiza; Manan, Zainuddin Abd.; Gernaey, Krist;

    of desired properties of the product as design constraints. The blend design problem is solved using a decomposition approach, which eliminates infeasible and/or redundant candidates gradually. The decomposition method reduces the search space in a systematic way. This general blend design problem......Computer aided technique is an efficient approach to solve chemical product design problems such as design of blended liquid products (chemical blending). In chemical blending, one tries to find the best candidate, which satisfies the product targets defined in terms of desired product attributes...... the desired product attributes. Alternatively, rigorous modelling could also be used in this final step. In other words, the candidates are quickly generated and screened until a small number is left for final selection and evaluation by experiment and/or rigorous modelling. This paper presents a design...

  14. Computational approaches to the chemical conversion of carbon dioxide

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Daojian; Negreiros, Fabio R.; Apra, Edoardo; Fortunelli, Alessandro


    The conversion of CO2 into fuels and chemicals is viewed as an attractive route for controlling the atmospheric concentration of this greenhouse gas and recycling it, but its industrial application is limited by the low selectivity and activity of the current catalysts. Theoretical modeling, in particular density-functional theory (DFT) simulations, provides a powerful and effective tool to discover chemical reaction mechanisms and design new catalysts for the chemical conversion of CO2, overcoming the repetitious and time/labor consuming trial-and-error experimental processes. In this article we give a comprehensive survey of recent advances on mechanism determination by DFT calculations for the catalytic hydrogenation of CO2 into CO, CH4, CH3OH, and HCOOH, and CO2 methanation, as well as the photo- and electrochemical reduction of CO2. DFT-guided design procedures of new catalytic systems are also reviewed, and challenges and perspectives in this field are outlined.

  15. Multiple Model Approaches to Modelling and Control,

    DEFF Research Database (Denmark)

    on the ease with which prior knowledge can be incorporated. It is interesting to note that researchers in Control Theory, Neural Networks,Statistics, Artificial Intelligence and Fuzzy Logic have more or less independently developed very similar modelling methods, calling them Local ModelNetworks, Operating...... of introduction of existing knowledge, as well as the ease of model interpretation. This book attempts to outlinemuch of the common ground between the various approaches, encouraging the transfer of ideas.Recent progress in algorithms and analysis is presented, with constructive algorithms for automated model...

  16. Model Construct Based Enterprise Model Architecture and Its Modeling Approach

    Institute of Scientific and Technical Information of China (English)


    In order to support enterprise integration, a kind of model construct based enterprise model architecture and its modeling approach are studied in this paper. First, the structural makeup and internal relationships of enterprise model architecture are discussed. Then, the concept of reusable model construct (MC) which belongs to the control view and can help to derive other views is proposed. The modeling approach based on model construct consists of three steps, reference model architecture synthesis, enterprise model customization, system design and implementation. According to MC based modeling approach a case study with the background of one-kind-product machinery manufacturing enterprises is illustrated. It is shown that proposal model construct based enterprise model architecture and modeling approach are practical and efficient.

  17. Modeling in transport phenomena a conceptual approach

    CERN Document Server

    Tosun, Ismail


    Modeling in Transport Phenomena, Second Edition presents and clearly explains with example problems the basic concepts and their applications to fluid flow, heat transfer, mass transfer, chemical reaction engineering and thermodynamics. A balanced approach is presented between analysis and synthesis, students will understand how to use the solution in engineering analysis. Systematic derivations of the equations and the physical significance of each term are given in detail, for students to easily understand and follow up the material. There is a strong incentive in science and engineering to

  18. Models and Modelling Tools for Chemical Product and Process Design

    DEFF Research Database (Denmark)

    Gani, Rafiqul


    The design, development and reliability of a chemical product and the process to manufacture it, need to be consistent with the end-use characteristics of the desired product. One of the common ways to match the desired product-process characteristics is through trial and error based experiments......-based framework is that in the design, development and/or manufacturing of a chemical product-process, the knowledge of the applied phenomena together with the product-process design details can be provided with diverse degrees of abstractions and details. This would allow the experimental resources......, are the needed models for such a framework available? Or, are modelling tools that can help to develop the needed models available? Can such a model-based framework provide the needed model-based work-flows matching the requirements of the specific chemical product-process design problems? What types of models...

  19. Evaluation of Artificial Intelligence Based Models for Chemical Biodegradability Prediction

    Directory of Open Access Journals (Sweden)

    Aleksandar Sabljic


    Full Text Available This study presents a review of biodegradability modeling efforts including a detailed assessment of two models developed using an artificial intelligence based methodology. Validation results for these models using an independent, quality reviewed database, demonstrate that the models perform well when compared to another commonly used biodegradability model, against the same data. The ability of models induced by an artificial intelligence methodology to accommodate complex interactions in detailed systems, and the demonstrated reliability of the approach evaluated by this study, indicate that the methodology may have application in broadening the scope of biodegradability models. Given adequate data for biodegradability of chemicals under environmental conditions, this may allow for the development of future models that include such things as surface interface impacts on biodegradability for example.

  20. Multidimensional chemical modelling, II. Irradiated outflow walls

    CERN Document Server

    Bruderer, Simon; Doty, Steven D; van Dishoeck, Ewine F; Bourke, Tyler L


    Observations of the high-mass star forming region AFGL 2591 reveal a large abundance of CO+, a molecule known to be enhanced by far UV (FUV) and X-ray irradiation. In chemical models assuming a spherically symmetric envelope, the volume of gas irradiated by protostellar FUV radiation is very small due to the high extinction by dust. The abundance of CO+ is thus underpredicted by orders of magnitude. In a more realistic model, FUV photons can escape through an outflow region and irradiate gas at the border to the envelope. Thus, we introduce the first 2D axi-symmetric chemical model of the envelope of a high-mass star forming region to explain the CO+ observations as a prototypical FUV tracer. The model assumes an axi-symmetric power-law density structure with a cavity due to the outflow. The local FUV flux is calculated by a Monte Carlo radiative transfer code taking scattering on dust into account. A grid of precalculated chemical abundances, introduced in the first part of this series of papers, is used to ...

  1. A grand model for chemical product design

    DEFF Research Database (Denmark)

    Fung, Ka Y.; Ng, Ka M.; Zhang, Lei;


    Chemical engineering has been expanding its focus from primarily business-to-business products (B2B) to business-to-consumer (B2C) products. The production of B2B products generally emphasizes on process design and optimization, whereas the production of B2C products focuses on product quality......, ingredients and structure. Market and competitive analysis, government policies and regulations have to be explicitly considered in product design. All these considerations are accounted for in the Grand Product Design Model, which consists of a process model, a property model, a quality model, a cost model...... product composition changes with market conditions. Another is a hand lotion that illustrates how product quality affects the profit.(C) 2016 Elsevier Ltd. All rights reserved....

  2. Hydraulic Modeling of Lock Approaches (United States)


    cation was that the guidewall design changed from a solid wall to one on pilings in which water was allowed to flow through and/or under the wall ...develops innovative solutions in civil and military engineering, geospatial sciences, water resources, and environmental sciences for the Army, the...magnitudes and directions at lock approaches for open river conditions. The meshes were developed using the Surface- water Modeling System. The two

  3. Marine derived polysaccharides for biomedical applications: chemical modification approaches. (United States)

    d'Ayala, Giovanna Gomez; Malinconico, Mario; Laurienzo, Paola


    Polysaccharide-based biomaterials are an emerging class in several biomedical fields such as tissue regeneration, particularly for cartilage, drug delivery devices and gelentrapment systems for the immobilization of cells. Important properties of the polysaccharides include controllable biological activity, biodegradability, and their ability to form hydrogels. Most of the polysaccharides used derive from natural sources; particularly, alginate and chitin, two polysaccharides which have an extensive history of use in medicine, pharmacy and basic sciences, and can be easily extracted from marine plants (algae kelp) and crab shells, respectively. The recent rediscovery of poly-saccharidebased materials is also attributable to new synthetic routes for their chemical modification, with the aim of promoting new biological activities and/or to modify the final properties of the biomaterials for specific purposes. These synthetic strategies also involve the combination of polysaccharides with other polymers. A review of the more recent research in the field of chemical modification of alginate, chitin and its derivative chitosan is presented. Moreover, we report as case studies the results of our recent work concerning various different approaches and applications of polysaccharide-based biomaterials, such as the realization of novel composites based on calcium sulphate blended with alginate and with a chemically modified chitosan, the synthesis of novel alginate-poly(ethylene glycol) copolymers and the development of a family of materials based on alginate and acrylic polymers of potential interest as drug delivery systems.

  4. Marine Derived Polysaccharides for Biomedical Applications: Chemical Modification Approaches

    Directory of Open Access Journals (Sweden)

    Paola Laurienzo


    Full Text Available Polysaccharide-based biomaterials are an emerging class in several biomedical fields such as tissue regeneration, particularly for cartilage, drug delivery devices and gelentrapment systems for the immobilization of cells. Important properties of the polysaccharides include controllable biological activity, biodegradability, and their ability to form hydrogels. Most of the polysaccharides used derive from natural sources; particularly, alginate and chitin, two polysaccharides which have an extensive history of use in medicine, pharmacy and basic sciences, and can be easily extracted from marine plants (algae kelp and crab shells, respectively. The recent rediscovery of poly-saccharidebased materials is also attributable to new synthetic routes for their chemical modification, with the aim of promoting new biological activities and/or to modify the final properties of the biomaterials for specific purposes. These synthetic strategies also involve the combination of polysaccharides with other polymers. A review of the more recent research in the field of chemical modification of alginate, chitin and its derivative chitosan is presented. Moreover, we report as case studies the results of our recent work concerning various different approaches and applications of polysaccharide-based biomaterials, such as the realization of novel composites based on calcium sulphate blended with alginate and with a chemically modified chitosan, the synthesis of novel alginate-poly(ethylene glycol copolymers and the development of a family of materials based on alginate and acrylic polymers of potential interest as drug delivery systems.


    Directory of Open Access Journals (Sweden)

    Mariko Funasaki


    Full Text Available The market for natural cosmetics featuring ingredients derived from Amazon natural resources is growing worldwide. However, there is neither enough scientific basis nor quality control of these ingredients. This paper is an account of the chemical constituents and their biological activities of fourteen Amazonian species used in cosmetic industry, including açaí (Euterpe oleracea, andiroba (Carapa guianensis, bacuri (Platonia insignis, Brazil nut (Bertholletia excelsa, buriti (Mauritia vinifera or M. flexuosa, cumaru (Dipteryx odorata, cupuaçu (Theobroma grandiflorum, guarana (Paullinia cupana, mulateiro (Calycophyllum spruceanum, murumuru (Astrocaryum murumuru, patawa (Oenocarpus bataua or Jessenia bataua, pracaxi (Pentaclethra macroloba, rosewood (Aniba rosaeodora, and ucuuba (Virola sebifera. Based on the reviewed articles, we selected chemical markers for the quality control purpose and evaluated analytical methods. Even though chromatographic and spectroscopic methods are major analytical techniques in the studies of these species, molecular approaches will also be important as used in food and medicine traceability. Only a little phytochemical study is available about most of the Amazonian species and some species such as açaí and andiroba have many reports on chemical constituents, but studies on biological activities of isolated compounds and sampling with geographical variation are limited.

  6. Predictive Modeling of Chemical Hazard by Integrating Numerical Descriptors of Chemical Structures and Short-term Toxicity Assay Data (United States)

    Rusyn, Ivan; Sedykh, Alexander; Guyton, Kathryn Z.; Tropsha, Alexander


    Quantitative structure-activity relationship (QSAR) models are widely used for in silico prediction of in vivo toxicity of drug candidates or environmental chemicals, adding value to candidate selection in drug development or in a search for less hazardous and more sustainable alternatives for chemicals in commerce. The development of traditional QSAR models is enabled by numerical descriptors representing the inherent chemical properties that can be easily defined for any number of molecules; however, traditional QSAR models often have limited predictive power due to the lack of data and complexity of in vivo endpoints. Although it has been indeed difficult to obtain experimentally derived toxicity data on a large number of chemicals in the past, the results of quantitative in vitro screening of thousands of environmental chemicals in hundreds of experimental systems are now available and continue to accumulate. In addition, publicly accessible toxicogenomics data collected on hundreds of chemicals provide another dimension of molecular information that is potentially useful for predictive toxicity modeling. These new characteristics of molecular bioactivity arising from short-term biological assays, i.e., in vitro screening and/or in vivo toxicogenomics data can now be exploited in combination with chemical structural information to generate hybrid QSAR–like quantitative models to predict human toxicity and carcinogenicity. Using several case studies, we illustrate the benefits of a hybrid modeling approach, namely improvements in the accuracy of models, enhanced interpretation of the most predictive features, and expanded applicability domain for wider chemical space coverage. PMID:22387746

  7. Bayesian inference of chemical kinetic models from proposed reactions

    KAUST Repository

    Galagali, Nikhil


    © 2014 Elsevier Ltd. Bayesian inference provides a natural framework for combining experimental data with prior knowledge to develop chemical kinetic models and quantify the associated uncertainties, not only in parameter values but also in model structure. Most existing applications of Bayesian model selection methods to chemical kinetics have been limited to comparisons among a small set of models, however. The significant computational cost of evaluating posterior model probabilities renders traditional Bayesian methods infeasible when the model space becomes large. We present a new framework for tractable Bayesian model inference and uncertainty quantification using a large number of systematically generated model hypotheses. The approach involves imposing point-mass mixture priors over rate constants and exploring the resulting posterior distribution using an adaptive Markov chain Monte Carlo method. The posterior samples are used to identify plausible models, to quantify rate constant uncertainties, and to extract key diagnostic information about model structure-such as the reactions and operating pathways most strongly supported by the data. We provide numerical demonstrations of the proposed framework by inferring kinetic models for catalytic steam and dry reforming of methane using available experimental data.

  8. Thermal, chemical, and mechanical cookoff modeling

    Energy Technology Data Exchange (ETDEWEB)

    Hobbs, M.L.; Baer, M.R.; Gross, R.J.


    A Thermally Reactive, Elastic-plastic eXplosive code, TREX, has been developed to analyze coupled thermal, chemical and mechanical effects associated with cookoff simulation of confined or unconfined energetic materials. In confined systems, pressure buildup precedes thermal runaway, and unconfined energetic material expands to relieve high stress. The model was developed based on nucleation, decomposition chemistry, and elastic/plastic mechanical behavior of a material with a distribution of internal defects represented as clusters of spherical inclusions. A local force balance, with mass continuity constraints, forms the basis of the model requiring input of temperature and reacted gas fraction. This constitutive material model has been incorporated into a quasistatic mechanics code SANTOS as a material module which predicts stress history associated with a given strain history. The thermal-chemical solver XCHEM has been coupled to SANTOS to provide temperature and reacted gas fraction. Predicted spatial history variables include temperature, chemical species, solid/gas pressure, solid/gas density, local yield stress, and gas volume fraction. One-Dimensional Time to explosion (ODTX) experiments for TATB and PBX 9404 (HMX and NC) are simulated using global multistep kinetic mechanisms and the reactive elastic-plastic constitutive model. Pressure explosions, rather than thermal runaway, result in modeling slow cookoff experiments of confined conventional energetic materials such as TATB. For PBX 9404, pressure explosions also occur at fast cookoff conditions because of low temperature reactions of nitrocellulose resulting in substantial pressurization. A demonstrative calculation is also presented for reactive heat flow in a hollow, propellant-filled, stainless steel cylinder, representing a rocket motor. This example simulation show

  9. Molecule-based approach for computing chemical-reaction rates in upper atmosphere hypersonic flows.

    Energy Technology Data Exchange (ETDEWEB)

    Gallis, Michail A.; Bond, Ryan Bomar; Torczynski, John Robert


    This report summarizes the work completed during FY2009 for the LDRD project 09-1332 'Molecule-Based Approach for Computing Chemical-Reaction Rates in Upper-Atmosphere Hypersonic Flows'. The goal of this project was to apply a recently proposed approach for the Direct Simulation Monte Carlo (DSMC) method to calculate chemical-reaction rates for high-temperature atmospheric species. The new DSMC model reproduces measured equilibrium reaction rates without using any macroscopic reaction-rate information. Since it uses only molecular properties, the new model is inherently able to predict reaction rates for arbitrary nonequilibrium conditions. DSMC non-equilibrium reaction rates are compared to Park's phenomenological non-equilibrium reaction-rate model, the predominant model for hypersonic-flow-field calculations. For near-equilibrium conditions, Park's model is in good agreement with the DSMC-calculated reaction rates. For far-from-equilibrium conditions, corresponding to a typical shock layer, the difference between the two models can exceed 10 orders of magnitude. The DSMC predictions are also found to be in very good agreement with measured and calculated non-equilibrium reaction rates. Extensions of the model to reactions typically found in combustion flows and ionizing reactions are also found to be in very good agreement with available measurements, offering strong evidence that this is a viable and reliable technique to predict chemical reaction rates.

  10. Approaches to Modeling of Recrystallization

    Directory of Open Access Journals (Sweden)

    Håkan Hallberg


    Full Text Available Control of the material microstructure in terms of the grain size is a key component in tailoring material properties of metals and alloys and in creating functionally graded materials. To exert this control, reliable and efficient modeling and simulation of the recrystallization process whereby the grain size evolves is vital. The present contribution is a review paper, summarizing the current status of various approaches to modeling grain refinement due to recrystallization. The underlying mechanisms of recrystallization are briefly recollected and different simulation methods are discussed. Analytical and empirical models, continuum mechanical models and discrete methods as well as phase field, vertex and level set models of recrystallization will be considered. Such numerical methods have been reviewed previously, but with the present focus on recrystallization modeling and with a rapidly increasing amount of related publications, an updated review is called for. Advantages and disadvantages of the different methods are discussed in terms of applicability, underlying assumptions, physical relevance, implementation issues and computational efficiency.

  11. Modeling turbulence structure. Chemical kinetics interaction in turbulent reactive flows

    Energy Technology Data Exchange (ETDEWEB)

    Magnussen, B.F. [The Norwegian Univ. of Science and Technology, Trondheim (Norway)


    The challenge of the mathematical modelling is to transfer basic physical knowledge into a mathematical formulation such that this knowledge can be utilized in computational simulation of practical problems. The combustion phenomena can be subdivided into a large set of interconnected phenomena like flow, turbulence, thermodynamics, chemical kinetics, radiation, extinction, ignition etc. Combustion in one application differs from combustion in another area by the relative importance of the various phenomena. The difference in fuel, geometry and operational conditions often causes the differences. The computer offers the opportunity to treat the individual phenomena and their interactions by models with wide operational domains. The relative magnitude of the various phenomena therefore becomes the consequence of operational conditions and geometry and need not to be specified on the basis of experience for the given problem. In mathematical modelling of turbulent combustion, one of the big challenges is how to treat the interaction between the chemical reactions and the fluid flow i.e. the turbulence. Different scientists adhere to different concepts like the laminar flamelet approach, the pdf approach of the Eddy Dissipation Concept. Each of these approaches offers different opportunities and problems. All these models are based on a sound physical basis, however none of these have general validity in taking into consideration all detail of the physical chemical interaction. The merits of the models can only be judged by their ability to reproduce physical reality and consequences of operational and geometric conditions in a combustion system. The presentation demonstrates and discusses the development of a coherent combustion technology for energy conversion and safety based on the Eddy Dissipation Concept by Magnussen. (author) 30 refs.

  12. A quantum informational approach for dissecting chemical reactions

    CERN Document Server

    Duperrouzel, Corinne; Boguslawski, Katharina; Barcza, Gergerly; Legeza, Örs; Ayers, Paul W


    We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected which allows us to monitor the interplay of back-bonding and $\\pi$-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.

  13. Chemical Abstracts Service approach to management of large data bases. (United States)

    Huffenberger, M A; Wigington, R L


    When information handling is "the business," as it is at Chemical Abstract Service (CAS), the total organization must be involved in information management. Since 1967, when, as a result of long-range planning efforts, CAS adopted a "data-base approach" to management of both the processing system and the distribution of information files, CAS has been grappling with the problems of managing large collections of information in computer-based systems. This paper describes what has been done at CAS in the management of large files and what we see as necessary, as a result of our experience, to improve and complete the information management system that is the foundation of our production processes.

  14. Bioactives from fruit processing wastes: Green approaches to valuable chemicals. (United States)

    Banerjee, Jhumur; Singh, Ramkrishna; Vijayaraghavan, R; MacFarlane, Douglas; Patti, Antonio F; Arora, Amit


    Fruit processing industries contribute more than 0.5billion tonnes of waste worldwide. The global availability of this feedstock and its untapped potential has encouraged researchers to perform detailed studies on value-addition potential of fruit processing waste (FPW). Compared to general food or other biomass derived waste, FPW are found to be selective and concentrated in nature. The peels, pomace and seed fractions of FPW could potentially be a good feedstock for recovery of bioactive compounds such as pectin, lipids, flavonoids, dietary fibres etc. A novel bio-refinery approach would aim to produce a wider range of valuable chemicals from FPW. The wastes from majority of the extraction processes may further be used as renewable sources for production of biofuels. The literature on value addition to fruit derived waste is diverse. This paper presents a review of fruit waste derived bioactives. The financial challenges encountered in existing methods are also discussed.

  15. Chemically amplified resist modeling in OPC (United States)

    Zheng, Xin; Huang, Jason; Kuo, Fred; Kazarian, Aram; Chin, Fook; Fan, Yongfa


    The mechanism of chemically amplified resist plays a critical role in the modeling of the latent image. To achieve a practical model which can fit into the time frame of OPC, some simplifications and assumptions have to be made. We introduced regression kernels that take into account best exposure focus difference between isotropic pitch, dense, and line end features for the evaluation of image intensity. It compares the image intensity (signal) over small changes above and/or below the regressed "nominal" image position, which in principle corresponds to evaluating the intensity signal at various depths of a fixed resist profile thus can also be regressed for optimization during model development. Our calibration has shown that the model brought a great improvement in prediction for difficult structures such as dense features at or near the optical resolution limit and 2-dimensional features, which are the limiter of the overall model fitting accuracy for 45nm node and below. By replacing other existing techniques, total number of output kernels used for OPC operation is actually reduced with improvement of model accuracy. This model is proven to be a very effective yet accurate addition to the current OPC technology.

  16. ACE-Asia Chemical Transport Modeling Overview (United States)

    UNO, I.; Chin, M.; Collins, W.; Ginoux, P.; Rasch, P.; Carmichael, G. R.; Yienger, J. J.


    ACE-Asia (Asia Pacific Regional Aerosol Characterization Experiment) was designed to increase our understanding of how atmospheric aerosol particles affect the Earth?s climate system. The intensive observation period was carried out during March to May, 2001, and more than 100 researchers from several countries (United States, Japan, Korea, China, and many other Asian countries) participated using aircraft, a research vessel, surface stations and numerical models. Aerosol transport forecast activities played an important role during the ACE-Asia intensive observation period. Three independent modeling groups operated chemical transport models in forecast mode and participated in flight planning activities at the operations center. These models were: MATCH (Model of Atmospheric Transport and Chemistry; Rasch and Collins); GOCART (Georgia Tech/Goddard Global Ozone Chemistry Aerosol Radiation and Transport model; Chin and Ginour) and CFORS (Research Institute for Applied Mechanics, Kyushu University + University of Iowa - Chemical weather FORecast System; Uno, Carmichael and Yienger). The MATCH model used in ACE-Asia was a transport model applied for the Asia region, driven by NCEP forecast meteorology. A unique feature of this model was that it assimilated satellite derived optical depths into its forecast algorithm. The GOCART model provided global aerosol forecast using forecast meteorological fields provided by the Goddard Earth Observing System Data Assimilation System (GEOS DAS). The CFORS model provided regional forecasts using a limited area transport model coupled with Regional Meteorological Modeling System (RAMS), initialized by NCEP and JMA forecasts. All models produced 3-d aerosol forecast products consisting of aerosol mass distributions and optical depths for sulfate, black carbon, organic carbon, sea salt, and dust. In the field these model products were made available to all participating scientists via the Web, and were also presented during the

  17. An Inverse Analysis Approach to the Characterization of Chemical Transport in Paints (United States)

    Willis, Matthew P.; Stevenson, Shawn M.; Pearl, Thomas P.; Mantooth, Brent A.


    The ability to directly characterize chemical transport and interactions that occur within a material (i.e., subsurface dynamics) is a vital component in understanding contaminant mass transport and the ability to decontaminate materials. If a material is contaminated, over time, the transport of highly toxic chemicals (such as chemical warfare agent species) out of the material can result in vapor exposure or transfer to the skin, which can result in percutaneous exposure to personnel who interact with the material. Due to the high toxicity of chemical warfare agents, the release of trace chemical quantities is of significant concern. Mapping subsurface concentration distribution and transport characteristics of absorbed agents enables exposure hazards to be assessed in untested conditions. Furthermore, these tools can be used to characterize subsurface reaction dynamics to ultimately design improved decontaminants or decontamination procedures. To achieve this goal, an inverse analysis mass transport modeling approach was developed that utilizes time-resolved mass spectroscopy measurements of vapor emission from contaminated paint coatings as the input parameter for calculation of subsurface concentration profiles. Details are provided on sample preparation, including contaminant and material handling, the application of mass spectrometry for the measurement of emitted contaminant vapor, and the implementation of inverse analysis using a physics-based diffusion model to determine transport properties of live chemical warfare agents including distilled mustard (HD) and the nerve agent VX. PMID:25226346

  18. A chemical genetics approach for specific differentiation of stem cells to somatic cells: a new promising therapeutical approach. (United States)

    Sachinidis, Agapios; Sotiriadou, Isaia; Seelig, Bianca; Berkessel, Albrecht; Hescheler, Jürgen


    Cell replacement therapy of severe degenerative diseases such as diabetes, myocardial infarction and Parkinson's disease through transplantation of somatic cells generated from embryonic stem (ES) cells is currently receiving considerable attention for the therapeutic applications. ES cells harvested from the inner cell mass (ICM) of the early embryo, can proliferate indefinitely in vitro while retaining the ability to differentiate into all somatic cells thereby providing an unlimited renewable source of somatic cells. In this context, identifying soluble factors, in particular chemically synthesized small molecules, and signal cascades involved in specific differentiation processes toward a defined tissue specific cell type are crucial for optimizing the generation of somatic cells in vitro for therapeutic approaches. However, experimental models are required allowing rapid and "easy-to-handle" parallel screening of chemical libraries to achieve this goal. Recently, the forward chemical genetic screening strategy has been postulated to screen small molecules in cellular systems for a specific desired phenotypic effect. The current review is focused on the progress of ES cell research in the context of the chemical genetics to identify small molecules promoting specific differentiation of ES cells to desired cell phenotype. Chemical genetics in the context of the cell ES-based cell replacement therapy remains a challenge for the near future for several scientific fields including chemistry, molecular biology, medicinal physics and robotic technologies.

  19. Modeling reservoir density underflow and interflow from a chemical spill (United States)

    Gu, R.; McCutcheon, S.C.; Wang, P.-F.


    An integral simulation model has been developed for understanding and simulating the process of a density current and the transport of spilled chemicals in a stratified reservoir. The model is capable of describing flow behavior and mixing mechanisms in different flow regimes (plunging flow, underflow, and interflow). It computes flow rate, velocity, flow thickness, mixing parameterized by entrainment and dilution, depths of plunging, separation and intrusion, and time of travel. The model was applied to the Shasta Reservoir in northern California during the July 1991 Sacramento River chemical spill. The simulations were used to assist in the emergency response, confirm remediation measures, and guide data collection. Spill data that were available after the emergency response are used to conduct a postaudit of the model results. Predicted flow parameters are presented and compared with observed interflow intrusion depth, travel time, and measured concentrations of spilled chemicals. In the reservoir, temperature difference between incoming river flow and ambient lake water played a dominant role during the processes of flow plunging, separation, and intrusion. With the integral approach, the gross flow behavior can be adequately described and information useful in the analysis of contaminated flow in a reservoir after a spill is provided.

  20. Chemically induced mouse models of intestinal inflammation. (United States)

    Wirtz, Stefan; Neufert, Clemens; Weigmann, Benno; Neurath, Markus F


    Animal models of intestinal inflammation are indispensable for our understanding of the pathogenesis of Crohn disease and ulcerative colitis, the two major forms of inflammatory bowel disease in humans. Here, we provide protocols for establishing murine 2,4,6-trinitro benzene sulfonic acid (TNBS)-, oxazolone- and both acute and chronic dextran sodium sulfate (DSS) colitis, the most widely used chemically induced models of intestinal inflammation. In the former two models, colitis is induced by intrarectal administration of the covalently reactive reagents TNBS/oxazolone, which are believed to induce a T-cell-mediated response against hapten-modified autologous proteins/luminal antigens. In the DSS model, mice are subjected several days to drinking water supplemented with DSS, which seems to be directly toxic to colonic epithelial cells of the basal crypts. The procedures for the hapten models of colitis and acute DSS colitis can be accomplished in about 2 weeks but the protocol for chronic DSS colitis takes about 2 months.

  1. Combinatorial QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis. (United States)

    Zhu, Hao; Tropsha, Alexander; Fourches, Denis; Varnek, Alexandre; Papa, Ester; Gramatica, Paola; Oberg, Tomas; Dao, Phuong; Cherkasov, Artem; Tetko, Igor V


    Selecting most rigorous quantitative structure-activity relationship (QSAR) approaches is of great importance in the development of robust and predictive models of chemical toxicity. To address this issue in a systematic way, we have formed an international virtual collaboratory consisting of six independent groups with shared interests in computational chemical toxicology. We have compiled an aqueous toxicity data set containing 983 unique compounds tested in the same laboratory over a decade against Tetrahymena pyriformis. A modeling set including 644 compounds was selected randomly from the original set and distributed to all groups that used their own QSAR tools for model development. The remaining 339 compounds in the original set (external set I) as well as 110 additional compounds (external set II) published recently by the same laboratory (after this computational study was already in progress) were used as two independent validation sets to assess the external predictive power of individual models. In total, our virtual collaboratory has developed 15 different types of QSAR models of aquatic toxicity for the training set. The internal prediction accuracy for the modeling set ranged from 0.76 to 0.93 as measured by the leave-one-out cross-validation correlation coefficient ( Q abs2). The prediction accuracy for the external validation sets I and II ranged from 0.71 to 0.85 (linear regression coefficient R absI2) and from 0.38 to 0.83 (linear regression coefficient R absII2), respectively. The use of an applicability domain threshold implemented in most models generally improved the external prediction accuracy but at the same time led to a decrease in chemical space coverage. Finally, several consensus models were developed by averaging the predicted aquatic toxicity for every compound using all 15 models, with or without taking into account their respective applicability domains. We find that consensus models afford higher prediction accuracy for the

  2. Chemical potential dependence of particle ratios within a unified thermal approach (United States)

    Bashir, I.; Nanda, H.; Uddin, S.


    A unified statistical thermal freeze-out model (USTFM) is used to study the chemical potential dependence of identified particle ratios at mid-rapidity in heavy-ion collisions. We successfully reproduce the experimental data ranging from SPS energies to LHC energies, suggesting the statistical nature of the particle production in these collisions and hence the validity of our approach. The behavior of the freeze-out temperature is studied with respect to chemical potential. The freeze-out temperature is found to be universal at the RHIC and LHC and is close to the QCD predicted phase transition temperature, suggesting that the chemical freeze-out occurs soon after the hadronization takes place.

  3. Chemical domain of QSAR models from atom-centered fragments. (United States)

    Kühne, Ralph; Ebert, Ralf-Uwe; Schüürmann, Gerrit


    A methodology to characterize the chemical domain of qualitative and quantitative structure-activity relationship (QSAR) models based on the atom-centered fragment (ACF) approach is introduced. ACFs decompose the molecule into structural pieces, with each non-hydrogen atom of the molecule acting as an ACF center. ACFs vary with respect to their size in terms of the path length covered in each bonding direction starting from a given central atom and how comprehensively the neighbor atoms (including hydrogen) are described in terms of element type and bonding environment. In addition to these different levels of ACF definitions, the ACF match mode as degree of strictness of the ACF comparison between a test compound and a given ACF pool (such as from a training set) has to be specified. Analyses of the prediction statistics of three QSAR models with their training sets as well as with external test sets and associated subsets demonstrate a clear relationship between the prediction performance and the levels of ACF definition and match mode. The findings suggest that second-order ACFs combined with a borderline match mode may serve as a generic and at the same time a mechanistically sound tool to define and evaluate the chemical domain of QSAR models. Moreover, four standard categories of the ACF-based membership to a given chemical domain (outside, borderline outside, borderline inside, inside) are introduced that provide more specific information about the expected QSAR prediction performance. As such, the ACF-based characterization of the chemical domain appears to be particularly useful for QSAR applications in the context of REACH and other regulatory schemes addressing the safety evaluation of chemical compounds.

  4. The Multiplexed Chemical Kinetic Photoionization Mass Spectrometer: A New Approach To Isomer-resolved Chemical Kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Osborne, David L.; Zou, Peng; Johnsen, Howard; Hayden, Carl C.; Taatjes, Craig A.; Knyazev, Vadim D.; North, Simon W.; Peterka, Darcy S.; Ahmed, Musahid; Leone, Stephen R.


    We have developed a multiplexed time- and photon-energy?resolved photoionizationmass spectrometer for the study of the kinetics and isomeric product branching of gasphase, neutral chemical reactions. The instrument utilizes a side-sampled flow tubereactor, continuously tunable synchrotron radiation for photoionization, a multi-massdouble-focusing mass spectrometer with 100percent duty cycle, and a time- and positionsensitive detector for single ion counting. This approach enables multiplexed, universal detection of molecules with high sensitivity and selectivity. In addition to measurement of rate coefficients as a function of temperature and pressure, different structural isomers can be distinguished based on their photoionization efficiency curves, providing a more detailed probe of reaction mechanisms. The multiplexed 3-dimensional data structure (intensity as a function of molecular mass, reaction time, and photoionization energy) provides insights that might not be available in serial acquisition, as well as additional constraints on data interpretation.

  5. Modelling stratospheric chemistry in a global three-dimensional chemical transport model

    Energy Technology Data Exchange (ETDEWEB)

    Rummukainen, M. [Finnish Meteorological Inst., Sodankylae (Finland). Sodankylae Observatory


    Numerical modelling of atmospheric chemistry aims to increase the understanding of the characteristics, the behavior and the evolution of atmospheric composition. These topics are of utmost importance in the study of climate change. The multitude of gases and particulates making up the atmosphere and the complicated interactions between them affect radiation transfer, atmospheric dynamics, and the impacts of anthropogenic and natural emissions. Chemical processes are fundamental factors in global warming, ozone depletion and atmospheric pollution problems in general. Much of the prevailing work on modelling stratospheric chemistry has so far been done with 1- and 2-dimensional models. Carrying an extensive chemistry parameterisation in a model with high spatial and temporal resolution is computationally heavy. Today, computers are becoming powerful enough to allow going over to 3-dimensional models. In order to concentrate on the chemistry, many Chemical Transport Models (CTM) are still run off-line, i.e. with precalculated and archived meteorology and radiation. In chemistry simulations, the archived values drive the model forward in time, without interacting with the chemical evolution. This is an approach that has been adopted in stratospheric chemistry modelling studies at the Finnish Meteorological Institute. In collaboration with the University of Oslo, a development project was initiated in 1993 to prepare a stratospheric chemistry parameterisation, fit for global 3-dimensional modelling. This article presents the parameterisation approach. Selected results are shown from basic photochemical simulations

  6. The Impact of Modeling Assumptions in Galactic Chemical Evolution Models

    CERN Document Server

    Côté, Benoit; Ritter, Christian; Herwig, Falk; Venn, Kim A


    We use the OMEGA galactic chemical evolution code to investigate how the assumptions used for the treatment of galactic inflows and outflows impact numerical predictions. The goal is to determine how our capacity to reproduce the chemical evolution trends of a galaxy is affected by the choice of implementation used to include those physical processes. In pursuit of this goal, we experiment with three different prescriptions for galactic inflows and outflows and use OMEGA within a Markov Chain Monte Carlo code to recover the set of input parameters that best reproduces the chemical evolution of nine elements in the dwarf spheroidal galaxy Sculptor. Despite their different degrees of intended physical realism, we found that all three prescriptions can reproduce in an almost identical way the stellar abundance trends observed in Sculptor. While the three models have the same capacity to fit the data, the best values recovered for the parameters controlling the number of Type Ia supernovae and the strength of gal...


    A wide variety of artificial intelligence (AI) and structure-activity relationship (SAR approaches have been applied to tackling the general problem of predicting rodent chemical carcinogenicity. Given the diversity of chemical structures and mechanisms relative to this endpoin...

  8. A Conceptual Framework for Predicting the Toxicity of Reactive Chemicals: Modeling Soft Electrophilicity (United States)

    Although the literature is replete with QSAR models developed for many toxic effects caused by reversible chemical interactions, the development of QSARs for the toxic effects of reactive chemicals lacks a consistent approach. While limitations exit, an appropriate starting-point...

  9. Chemical Mechanism Solvers in Air Quality Models

    Directory of Open Access Journals (Sweden)

    John C. Linford


    Full Text Available The solution of chemical kinetics is one of the most computationally intensivetasks in atmospheric chemical transport simulations. Due to the stiff nature of the system,implicit time stepping algorithms which repeatedly solve linear systems of equations arenecessary. This paper reviews the issues and challenges associated with the construction ofefficient chemical solvers, discusses several families of algorithms, presents strategies forincreasing computational efficiency, and gives insight into implementing chemical solverson accelerated computer architectures.

  10. A mesoscale chemical transport model (MEDIUM) nested in a global chemical transport model (MEDIANTE)

    Energy Technology Data Exchange (ETDEWEB)

    Claveau, J.; Ramaroson, R. [Office National d`Etudes et de Recherches Aerospatiales (ONERA), 92 - Chatillon (France)


    The lower stratosphere and upper troposphere (UT-LS) are frequently subject to mesoscale or local scale exchange of air masses occurring along discontinuities. This exchange (e.g. downward) can constitute one of the most important source of ozone from the stratosphere down to the middle troposphere where strong mixing dilutes the air mass and competing the non-linear chemistry. The distribution of the chemical species in the troposphere and the lower stratosphere depends upon various source emissions, e.g. from polluted boundary layer or from aircraft emissions. Global models, as well as chemical transport models describe the climatological state of the atmosphere and are not able to describe correctly the stratosphere and troposphere exchange. Mesoscale models go further in the description of smaller scales and can reasonably include a rather detailed chemistry. They can be used to assess the budget of NO{sub x} from aircraft emissions in a mesoscale domain. (author) 4 refs.

  11. Chemical leasing business models: a contribution to the effective risk management of chemical substances. (United States)

    Ohl, Cornelia; Moser, Frank


    Chemicals indisputably contribute greatly to the well-being of modern societies. Apart from such benefits, however, chemicals often pose serious threats to human health and the environment when improperly handled. Therefore, the European Commission has proposed a regulatory framework for the Registration, Evaluation and Authorization of Chemicals (REACH) that requires companies using chemicals to gather pertinent information on the properties of these substances. In this article, we argue that the crucial aspect of this information management may be the honesty and accuracy of the transfer of relevant knowledge from the producer of a chemical to its user. This may be particularly true if the application of potentially hazardous chemicals is not part of the user's core competency. Against this background, we maintain that the traditional sales concept provides no incentives for transferring this knowledge. The reason is that increased user knowledge of a chemical's properties may raise the efficiency of its application. That is, excessive and unnecessary usage will be eliminated. This, in turn, would lower the amount of chemicals sold and in competitive markets directly decrease profits of the producer. Through the introduction of chemical leasing business models, we attempt to present a strategy to overcome the incentive structure of classical sales models, which is counterproductive for the transfer of knowledge. By introducing two models (a Model A that differs least and a Model B that differs most from traditional sales concepts), we demonstrate that chemical leasing business models are capable of accomplishing the goal of Registration, Evaluation and Authorization of Chemicals: to effectively manage the risk of chemicals by reducing the total quantity of chemicals used, either by a transfer of applicable knowledge from the lessor to the lessee (Model A) or by efficient application of the chemical by the lessor him/herself (Model B).

  12. Integration Strategies for Efficient Multizone Chemical Kinetics Models

    Energy Technology Data Exchange (ETDEWEB)

    McNenly, M J; Havstad, M A; Aceves, S M; Pitz, W J


    Three integration strategies are developed and tested for the stiff, ordinary differential equation (ODE) integrators used to solve the fully coupled multizone chemical kinetics model. Two of the strategies tested are found to provide more than an order of magnitude of improvement over the original, basic level of usage for the stiff ODE solver. One of the faster strategies uses a decoupled, or segregated, multizone model to generate an approximate Jacobian. This approach yields a 35-fold reduction in the computational cost for a 20 zone model. Using the same approximate Jacobian as a preconditioner for an iterative Krylov-type linear system solver, the second improved strategy achieves a 75-fold reduction in the computational cost for a 20 zone model. The faster strategies achieve their cost savings with no significant loss of accuracy. The pressure, temperature and major species mass fractions agree with the solution from the original integration approach to within six significant digits; and the radical mass fractions agree with the original solution to within four significant digits. The faster strategies effectively change the cost scaling of the multizone model from cubic to quadratic, with respect to the number of zones. As a consequence of the improved scaling, the 40 zone model offers more than a 250-fold cost savings over the basic calculation.

  13. The Impact of Modeling Assumptions in Galactic Chemical Evolution Models (United States)

    Côté, Benoit; O’Shea, Brian W.; Ritter, Christian; Herwig, Falk; Venn, Kim A.


    We use the OMEGA galactic chemical evolution code to investigate how the assumptions used for the treatment of galactic inflows and outflows impact numerical predictions. The goal is to determine how our capacity to reproduce the chemical evolution trends of a galaxy is affected by the choice of implementation used to include those physical processes. In pursuit of this goal, we experiment with three different prescriptions for galactic inflows and outflows and use OMEGA within a Markov Chain Monte Carlo code to recover the set of input parameters that best reproduces the chemical evolution of nine elements in the dwarf spheroidal galaxy Sculptor. This provides a consistent framework for comparing the best-fit solutions generated by our different models. Despite their different degrees of intended physical realism, we found that all three prescriptions can reproduce in an almost identical way the stellar abundance trends observed in Sculptor. This result supports the similar conclusions originally claimed by Romano & Starkenburg for Sculptor. While the three models have the same capacity to fit the data, the best values recovered for the parameters controlling the number of SNe Ia and the strength of galactic outflows, are substantially different and in fact mutually exclusive from one model to another. For the purpose of understanding how a galaxy evolves, we conclude that only reproducing the evolution of a limited number of elements is insufficient and can lead to misleading conclusions. More elements or additional constraints such as the Galaxy’s star-formation efficiency and the gas fraction are needed in order to break the degeneracy between the different modeling assumptions. Our results show that the successes and failures of chemical evolution models are predominantly driven by the input stellar yields, rather than by the complexity of the Galaxy model itself. Simple models such as OMEGA are therefore sufficient to test and validate stellar yields. OMEGA

  14. In situ models, physico-chemical aspects. (United States)

    ten Cate, J M


    In situ (intra-oral) caries models are used for two purposes. First, they provide information about oral physiological processes. Such information helps to detail our knowledge of the oral ecosystem and to verify conclusions from in vitro experiments. Second, in situ models are utilized to test preventive agents in the phase between laboratory testing and clinical trials. Most investigations involving enamel inserts have been aimed at testing new dentifrices. The experimental designs of such studies usually do not allow one to draw conclusions on physico-chemical processes, e.g., because of single point measurements. Studies of model parameters (lesion type, lesion severity, and de/remineralization in time) constitute only a minority of the research reports. The most striking observation obtained with in situ models has been the significant differences in de/remineralization observed among individuals and, more importantly, within one individual during different time periods and between different sites in the same mouth (for review, see ten Cate et al., 1992). Regardless of this, some general findings can be inferred: During in situ demineralization, up to 62 vol% microns/day may be removed from enamel. For dentin specimens, this value may be as high as 89 vol% microns/day. For remineralization, during fluoride dentifrice treatment, a median deposition rate of 0.7%/day (for lesions with integrated mineral loss values between 2000 and 4000 vol% microns) is found. The rate of deposition seems to be correlated with the extent of the pre-formed lesion. This suggests that the number of sites (crystallite surface) available for calcium phosphate precipitation is an important parameter.(ABSTRACT TRUNCATED AT 250 WORDS)

  15. Chemical Kinetic Modeling of Biofuel Combustion (United States)

    Sarathy, Subram Maniam

    Bioalcohols, such as bioethanol and biobutanol, are suitable replacements for gasoline, while biodiesel can replace petroleum diesel. Improving biofuel engine performance requires understanding its fundamental combustion properties and the pathways of combustion. This study's contribution is experimentally validated chemical kinetic combustion mechanisms for biobutanol and biodiesel. Fundamental combustion data and chemical kinetic mechanisms are presented and discussed to improve our understanding of biofuel combustion. The net environmental impact of biobutanol (i.e., n-butanol) has not been studied extensively, so this study first assesses the sustainability of n-butanol derived from corn. The results indicate that technical advances in fuel production are required before commercializing biobutanol. The primary contribution of this research is new experimental data and a novel chemical kinetic mechanism for n-butanol combustion. The results indicate that under the given experimental conditions, n-butanol is consumed primarily via abstraction of hydrogen atoms to produce fuel radical molecules, which subsequently decompose to smaller hydrocarbon and oxygenated species. The hydroxyl moiety in n-butanol results in the direct production of the oxygenated species such as butanal, acetaldehyde, and formaldehyde. The formation of these compounds sequesters carbon from forming soot precursors, but they may introduce other adverse environmental and health effects. Biodiesel is a mixture of long chain fatty acid methyl esters derived from fats and oils. This research study presents high quality experimental data for one large fatty acid methyl ester, methyl decanoate, and models its combustion using an improved skeletal mechanism. The results indicate that methyl decanoate is consumed via abstraction of hydrogen atoms to produce fuel radicals, which ultimately lead to the production of alkenes. The ester moiety in methyl decanoate leads to the formation of low molecular

  16. Modeling Complex Chemical Systems: Problems and Solutions (United States)

    van Dijk, Jan


    Non-equilibrium plasmas in complex gas mixtures are at the heart of numerous contemporary technologies. They typically contain dozens to hundreds of species, involved in hundreds to thousands of reactions. Chemists and physicists have always been interested in what are now called chemical reduction techniques (CRT's). The idea of such CRT's is that they reduce the number of species that need to be considered explicitly without compromising the validity of the model. This is usually achieved on the basis of an analysis of the reaction time scales of the system under study, which identifies species that are in partial equilibrium after a given time span. The first such CRT that has been widely used in plasma physics was developed in the 1960's and resulted in the concept of effective ionization and recombination rates. It was later generalized to systems in which multiple levels are effected by transport. In recent years there has been a renewed interest in tools for chemical reduction and reaction pathway analysis. An example of the latter is the PumpKin tool. Another trend is that techniques that have previously been developed in other fields of science are adapted as to be able to handle the plasma state of matter. Examples are the Intrinsic Low Dimension Manifold (ILDM) method and its derivatives, which originate from combustion engineering, and the general-purpose Principle Component Analysis (PCA) technique. In this contribution we will provide an overview of the most common reduction techniques, then critically assess the pros and cons of the methods that have gained most popularity in recent years. Examples will be provided for plasmas in argon and carbon dioxide.

  17. Predicting acute aquatic toxicity of structurally diverse chemicals in fish using artificial intelligence approaches. (United States)

    Singh, Kunwar P; Gupta, Shikha; Rai, Premanjali


    The research aims to develop global modeling tools capable of categorizing structurally diverse chemicals in various toxicity classes according to the EEC and European Community directives, and to predict their acute toxicity in fathead minnow using set of selected molecular descriptors. Accordingly, artificial intelligence approach based classification and regression models, such as probabilistic neural networks (PNN), generalized regression neural networks (GRNN), multilayer perceptron neural network (MLPN), radial basis function neural network (RBFN), support vector machines (SVM), gene expression programming (GEP), and decision tree (DT) were constructed using the experimental toxicity data. Diversity and non-linearity in the chemicals' data were tested using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. Predictive and generalization abilities of various models constructed here were compared using several statistical parameters. PNN and GRNN models performed relatively better than MLPN, RBFN, SVM, GEP, and DT. Both in two and four category classifications, PNN yielded a considerably high accuracy of classification in training (95.85 percent and 90.07 percent) and validation data (91.30 percent and 86.96 percent), respectively. GRNN rendered a high correlation between the measured and model predicted -log LC50 values both for the training (0.929) and validation (0.910) data and low prediction errors (RMSE) of 0.52 and 0.49 for two sets. Efficiency of the selected PNN and GRNN models in predicting acute toxicity of new chemicals was adequately validated using external datasets of different fish species (fathead minnow, bluegill, trout, and guppy). The PNN and GRNN models showed good predictive and generalization abilities and can be used as tools for predicting toxicities of structurally diverse chemical compounds.

  18. Uncertainty quantification for quantum chemical models of complex reaction networks. (United States)

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


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

  19. Continuous Molecular Fields Approach Applied to Structure-Activity Modeling

    CERN Document Server

    Baskin, Igor I


    The Method of Continuous Molecular Fields is a universal approach to predict various properties of chemical compounds, in which molecules are represented by means of continuous fields (such as electrostatic, steric, electron density functions, etc). The essence of the proposed approach consists in performing statistical analysis of functional molecular data by means of joint application of kernel machine learning methods and special kernels which compare molecules by computing overlap integrals of their molecular fields. This approach is an alternative to traditional methods of building 3D structure-activity and structure-property models based on the use of fixed sets of molecular descriptors. The methodology of the approach is described in this chapter, followed by its application to building regression 3D-QSAR models and conducting virtual screening based on one-class classification models. The main directions of the further development of this approach are outlined at the end of the chapter.

  20. The Competence of Modelling in Learning Chemical Change: A Study with Secondary School Students (United States)

    Oliva, José Mª; del Mar Aragón, María; Cuesta, Josefa


    The competence of modelling as part of learning about chemical change is analysed in a sample of 35 secondary students, ages 14-15 years, during their study of a curricular unit on this topic. The teaching approach followed is model based, with frequent use of analogies and mechanical models (fruits and bowls, Lego pieces, balls of plasticine,…

  1. Validation of Modeling Flow Approaching Navigation Locks (United States)


    instrumentation, direction vernier . ........................................................................ 8  Figure 11. Plan A lock approach, upstream approach...13-9 8 Figure 9. Tools and instrumentation, bracket attached to rail. Figure 10. Tools and instrumentation, direction vernier . Numerical model

  2. A review of models for near-field exposure pathways of chemicals in consumer products

    DEFF Research Database (Denmark)

    Huang, Lei; Ernstoff, Alexi; Fantke, Peter;


    Exposure to chemicals in consumer products has been gaining increasing attention, with multiple studies showing that near-field exposures from products is high compared to far-field exposures. Regarding the numerous chemical-product combinations, there is a need for an overarching review of models...... able to quantify the multiple transfers of chemicals from products used near-field to humans. The present review therefore aims at an in-depth overview of modeling approaches for near-field chemical release and human exposure pathways associated with consumer products. It focuses on lower...... in a “human receptor compartment”. We first focus on models of physical mass transfers from the product to ‘near-field’ compartments. For transfers of chemicals from article interior, adequate modeling of in-article diffusion and of partitioning between article surface and air/skin/food is key. Modeling...

  3. GREENSCOPE: A Method for Modeling Chemical Process ... (United States)

    Current work within the U.S. Environmental Protection Agency’s National Risk Management Research Laboratory is focused on the development of a method for modeling chemical process sustainability. The GREENSCOPE methodology, defined for the four bases of Environment, Economics, Efficiency, and Energy, can evaluate processes with over a hundred different indicators. These indicators provide a means for realizing the principles of green chemistry and green engineering in the context of sustainability. Development of the methodology has centered around three focal points. One is a taxonomy of impacts that describe the indicators and provide absolute scales for their evaluation. The setting of best and worst limits for the indicators allows the user to know the status of the process under study in relation to understood values. Thus, existing or imagined processes can be evaluated according to their relative indicator scores, and process modifications can strive towards realizable targets. A second area of focus is in advancing definitions of data needs for the many indicators of the taxonomy. Each of the indicators has specific data that is necessary for their calculation. Values needed and data sources have been identified. These needs can be mapped according to the information source (e.g., input stream, output stream, external data, etc.) for each of the bases. The user can visualize data-indicator relationships on the way to choosing selected ones for evalua

  4. Multidimensional thermal-chemical cookoff modeling

    Energy Technology Data Exchange (ETDEWEB)

    Baer, M.R.; Gross, R.J.; Gartling, D.K.; Hobbs, M.L.


    Multidimensional thermal/chemical modeling is an essential step in the development of a predictive capability for cookoff of energetic materials in systems subjected to abnormal thermal environments. COYOTE II is a state-of-the-art two- and three-dimensional finite element code for the solution of heat conduction problems including surface-to-surface thermal radiation heat transfer and decomposition chemistry. Multistep finite rate chemistry is incorporated into COYOTE II using an operator-splitting methodology; rate equations are solved element-by-element with a modified matrix-free stiff solver, CHEMEQ. COYOTE II is purposely designed with a user-oriented input structure compatible with the database, the pre-processing mesh generation, and the post-processing tools for data visualization shared with other engineering analysis codes available at Sandia National Laboratories. As demonstrated in a companion paper, decomposition during cookoff in a confined or semi-confined system leads to significant mechanical behavior. Although mechanical effect are not presently considered in COYOTE II, the formalism for including mechanics in multidimensions is under development.

  5. A new modified-rate approach for gas-grain chemical simulations

    CERN Document Server

    Garrod, R T


    Understanding grain-surface processes is crucial to interpreting the chemistry of the ISM. However, accurate surface chemistry models are computationally expensive and are difficult to integrate with gas-phase simulations. A new modified-rate method for solving grain-surface chemical systems is presented. Its purpose is accurately to model highly complex systems that can otherwise only be treated using the sometimes inadequate rate-equation approach. In contrast to previous rate-modification techniques, the functional form of the surface production rates was modified, and not simply the rate coefficient. This form is appropriate to the extreme "small-grain" limit, and can be verified using an analytical master-equation approach. Various further modifications were made to this basic form, to account for competition between processes, to improve estimates of surface occupation probabilities, and to allow a switch-over to the normal rate equations where these are applicable. The new method was tested against sys...

  6. The chemical transport model Oslo CTM3

    Directory of Open Access Journals (Sweden)

    O. A. Søvde


    Full Text Available We present here the global chemical transport model Oslo CTM3, an update of the Oslo CTM2. The update comprises a faster transport scheme, an improved wet scavenging scheme for large scale rain, updated photolysis rates and a new lightning parameterization. Oslo CTM3 is better parallelized and allows for stable, large time steps for advection, enabling more complex or high resolution simulations. Thorough comparisons between the Oslo CTM3, Oslo CTM2 and measurements are performed, and in general the Oslo CTM3 is found to reproduce measurements well. Inclusion of tropospheric sulfur chemistry and nitrate aerosols in CTM3 is shown to be important to reproduce tropospheric O3, OH and the CH4 lifetime well. Using the same meteorology to drive the two models, shows that some features related to transport are better resolved by the CTM3, such as polar cap transport, while features like transport close to the vortex edge are resolved better in the Oslo CTM2 due to its required shorter transport time step. The longer transport time steps in CTM3 result in larger errors e.g. near the jets, and when necessary, this can be remedied by using a shorter time step. An additional, more accurate and time consuming, treatment of polar cap transport is presented, however, both perform acceptably. A new treatment of the horizontal distribution of lightning is presented and found to compare well with measurements. Vertical distributions of lighting are updated, and tested against the old vertical distribution. The new profiles are found to produce more NOx in the tropical middle troposphere, and less at the surface and at high altitudes.

  7. Modeling release of chemicals from multilayer materials into food

    Directory of Open Access Journals (Sweden)

    Huang Xiu-Ling


    Full Text Available The migration of chemicals from materials into food is predictable by various mathematical models. In this article, a general mathematical model is developed to quantify the release of chemicals through multilayer packaging films based on Fick's diffusion. The model is solved numerically to elucidate the effects of different diffusivity values of different layers, distribution of chemical between two adjacent layers and between material and food, mass transfer at the interface of material and food on the migration process.

  8. Modeling Electric Double-Layers Including Chemical Reaction Effects

    DEFF Research Database (Denmark)

    Paz-Garcia, Juan Manuel; Johannesson, Björn; Ottosen, Lisbeth M.


    A physicochemical and numerical model for the transient formation of an electric double-layer between an electrolyte and a chemically-active flat surface is presented, based on a finite elements integration of the nonlinear Nernst-Planck-Poisson model including chemical reactions. The model works...

  9. A review of operational, regional-scale, chemical weather forecasting models in Europe

    Directory of Open Access Journals (Sweden)

    J. Kukkonen


    Full Text Available Numerical models that combine weather forecasting and atmospheric chemistry are here referred to as chemical weather forecasting models. Eighteen operational chemical weather forecasting models on regional and continental scales in Europe are described and compared in this article. Topics discussed in this article include how weather forecasting and atmospheric chemistry models are integrated into chemical weather forecasting systems, how physical processes are incorporated into the models through parameterization schemes, how the model architecture affects the predicted variables, and how air chemistry and aerosol processes are formulated. In addition, we discuss sensitivity analysis and evaluation of the models, user operational requirements, such as model availability and documentation, and output availability and dissemination. In this manner, this article allows for the evaluation of the relative strengths and weaknesses of the various modelling systems and modelling approaches. Finally, this article highlights the most prominent gaps of knowledge for chemical weather forecasting models and suggests potential priorities for future research directions, for the following selected focus areas: emission inventories, the integration of numerical weather prediction and atmospheric chemical transport models, boundary conditions and nesting of models, data assimilation of the various chemical species, improved understanding and parameterization of physical processes, better evaluation of models against data and the construction of model ensembles.

  10. Model Mapping Approach Based on Ontology Semantics

    Directory of Open Access Journals (Sweden)

    Jinkui Hou


    Full Text Available The mapping relations between different models are the foundation for model transformation in model-driven software development. On the basis of ontology semantics, model mappings between different levels are classified by using structural semantics of modeling languages. The general definition process for mapping relations is explored, and the principles of structure mapping are proposed subsequently. The approach is further illustrated by the mapping relations from class model of object oriented modeling language to the C programming codes. The application research shows that the approach provides a theoretical guidance for the realization of model mapping, and thus can make an effective support to model-driven software development

  11. An optimization approach to kinetic model reduction for combustion chemistry

    CERN Document Server

    Lebiedz, Dirk


    Model reduction methods are relevant when the computation time of a full convection-diffusion-reaction simulation based on detailed chemical reaction mechanisms is too large. In this article, we review a model reduction approach based on optimization of trajectories and show its applicability to realistic combustion models. As most model reduction methods, it identifies points on a slow invariant manifold based on time scale separation in the dynamics of the reaction system. The numerical approximation of points on the manifold is achieved by solving a semi-infinite optimization problem, where the dynamics enter the problem as constraints. The proof of existence of a solution for an arbitrarily chosen dimension of the reduced model (slow manifold) is extended to the case of realistic combustion models including thermochemistry by considering the properties of proper maps. The model reduction approach is finally applied to three models based on realistic reaction mechanisms: 1. ozone decomposition as a small t...

  12. Reduced Models in Chemical Kinetics via Nonlinear Data-Mining

    Directory of Open Access Journals (Sweden)

    Eliodoro Chiavazzo


    Full Text Available The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result, reactive flow solvers with detailed chemistry often become intractable even for large clusters of CPUs, especially when dealing with direct numerical simulation (DNS of turbulent combustion problems. This has motivated the development of several techniques for reducing the complexity of such kinetics models, where, eventually, only a few variables are considered in the development of the simplified model. Unfortunately, no generally applicable a priori recipe for selecting suitable parameterizations of the reduced model is available, and the choice of slow variables often relies upon intuition and experience. We present an automated approach to this task, consisting of three main steps. First, the low dimensional manifold of slow motions is (approximately sampled by brief simulations of the detailed model, starting from a rich enough ensemble of admissible initial conditions. Second, a global parametrization of the manifold is obtained through the Diffusion Map (DMAP approach, which has recently emerged as a powerful tool in data analysis/machine learning. Finally, a simplified model is constructed and solved on the fly in terms of the above reduced (slow variables. Clearly, closing this latter model requires nontrivial interpolation calculations, enabling restriction (mapping from the full ambient space to the reduced one and lifting (mapping from the reduced space to the ambient one. This is a key step in our approach, and a variety of interpolation schemes are reported and compared. The scope of the proposed procedure is presented and discussed by means of an illustrative combustion example.

  13. Towards an improved modeling of chemical weathering in the SoilGen soil evolution model (United States)

    Opolot, Emmanuel; Finke, Peter


    As the need for soil information particularly in the fields of agriculture, land evaluation, hydrology, biogeochemistry and climate change keeps increasing, models for soil evolution are increasingly becoming valuable tools to provide such soil information. Although still limited, such models are progressively being developed. The SoilGen model is one of such models with capabilities to provide soil information such as soil texture, pH, base saturation, organic carbon, CEC, etc over multi-millennia time scale. SoilGen is a mechanistic water flow driven pedogenetic model describing soil forming processes such as carbon cycling, clay migration, decalcification, bioturbation, physical weathering and chemical weathering. The model has been calibrated and confronted with field measurements in a number of case studies, giving plausible results. Discrepancies between measured and simulated soil properties as concluded from case studies have been mainly attributed to (i) the simple chemical weathering system (ii) poor estimates of initial data inputs such as bulk density and element fluxes, and (iii) incorrect values of variables that describe boundary conditions such as precipitation and potential evapotranspiration. This study focuses on extending the chemical weathering system, such that it can deal with a more heterogeneous composition of primary minerals and includes more elements such as Fe and Si. We propose and discuss here an extended description of chemical weathering in the model that is based on more primary minerals, taking into account the role of the specific area of these minerals, and the effect of physical weathering on these specific areas over time. In the initial stage, the proposed chemical weathering mechanism is also implemented in PHREEQC (a widely applied geochemical code with capabilities to simulate equilibrium reactions involving water and minerals, surface complexes and ion exchangers, etc.) to facilitate comparison with the model results

  14. A density functional theory-based chemical potential equalisation approach to molecular polarizability

    Indian Academy of Sciences (India)

    Amita Wadehra; Swapan K Ghosh


    The electron density changes in molecular systems in the presence of external electric fields are modeled for simplicity in terms of the induced charges and dipole moments at the individual atomic sites. A chemical potential equalisation scheme is proposed for the calculation of these quantities and hence the dipole polarizability within the framework of density functional theory based linear response theory. The resulting polarizability is expressed in terms of the contributions from individual atoms in the molecule. A few illustrative numerical calculations are shown to predict the molecular polarizabilities in good agreement with available results. The usefulness of the approach to the calculation of intermolecular interaction needed for computer simulation is highlighted.

  15. Review of existing terrestrial bioaccumulation models and terrestrial bioaccumulation modeling needs for organic chemicals. (United States)

    Gobas, Frank A P C; Burkhard, Lawrence P; Doucette, William J; Sappington, Keith G; Verbruggen, Eric M J; Hope, Bruce K; Bonnell, Mark A; Arnot, Jon A; Tarazona, Jose V


    Protocols for terrestrial bioaccumulation assessments are far less-developed than for aquatic systems. This article reviews modeling approaches that can be used to assess the terrestrial bioaccumulation potential of commercial organic chemicals. Models exist for plant, invertebrate, mammal, and avian species and for entire terrestrial food webs, including some that consider spatial factors. Limitations and gaps in terrestrial bioaccumulation modeling include the lack of QSARs for biotransformation and dietary assimilation efficiencies for terrestrial species; the lack of models and QSARs for important terrestrial species such as insects, amphibians and reptiles; the lack of standardized testing protocols for plants with limited development of plant models; and the limited chemical domain of existing bioaccumulation models and QSARs (e.g., primarily applicable to nonionic organic chemicals). There is an urgent need for high-quality field data sets for validating models and assessing their performance. There is a need to improve coordination among laboratory, field, and modeling efforts on bioaccumulative substances in order to improve the state of the science for challenging substances.

  16. A chemical model of meteoric ablation

    Directory of Open Access Journals (Sweden)

    T. Vondrak


    Full Text Available Most of the extraterrestrial dust entering the Earth's atmosphere ablates to produce metal vapours, which have significant effects on the aeronomy of the upper mesosphere and lower thermosphere. A new Chemical Ablation Model (CAMOD is described which treats the physics and chemistry of ablation, by including the following processes: sputtering by inelastic collisions with air molecules before the meteoroid melts; evaporation of atoms and oxides from the molten particle; diffusion-controlled migration of the volatile constituents (Na and K through the molten particle; and impact ionization of the ablated fragments by hyperthermal collisions with air molecules. Evaporation is based on thermodynamic equilibrium in the molten meteoroid (treated as a melt of metal oxides, and between the particle and surrounding vapour phase. The loss rate of each element is then determined assuming Langmuir evaporation. CAMOD successfully predicts the meteor head echo appearance heights, observed from incoherent scatter radars, over a wide range of meteoroid velocities. The model also confirms that differential ablation explains common-volume lidar observations of K, Ca and Ca+ in fresh meteor trails. CAMOD is then used to calculate the injection rates into the atmosphere of a variety of elements as a function of altitude, integrated over the meteoroid mass and velocity distributions. The most abundant elements (Fe, Mg and Si have peak injection rates around 85 km, with Na and K about 8 km higher. The more refractory element Ca ablates around 82 km with a Na:Ca ratio of 4:1, which does therefore not explain the depletion of atomic Ca to Na, by more than 2 orders of magnitude, in the upper mesosphere. Diffusion of the most volatile elements (Na and K does not appear to be rate-limiting except in the fastest meteoroids. Non-thermal sputtering causes ~35% mass loss from the fastest (~60–70 km s−1 and smallest (10−17–10

  17. A chemical model of meteoric ablation

    Directory of Open Access Journals (Sweden)

    T. Vondrak


    Full Text Available Most of the extraterrestrial dust entering the Earth's atmosphere ablates to produce metal vapours, which have significant effects on the aeronomy of the upper mesosphere and lower thermosphere. A new Chemical Ablation Model (CAMOD is described which treats the physics and chemistry of ablation, by including the following processes: sputtering by inelastic collisions with air molecules before the meteoroid melts; evaporation of atoms and oxides from the molten particle; diffusion-controlled migration of the volatile constituents (Na and K through the molten particle; and impact ionization of the ablated fragments by hyperthermal collisions with air molecules. Evaporation is based on thermodynamic equilibrium in the molten meteoroid (treated as a melt of metal oxides, and between the particle and surrounding vapour phase. The loss rate of each element is then determined assuming Langmuir evaporation. CAMOD successfully predicts the meteor head echo appearance heights, observed from incoherent scatter radars, over a wide range of meteoroid velocities. The model also confirms that differential ablation explains common-volume lidar observations of K, Ca and Ca+ in fresh meteor trails. CAMOD is then used to calculate the injection rates into the atmosphere of a variety of elements as a function of altitude, integrated over the meteoroid mass and velocity distributions. The most abundant elements (Fe, Mg and Si have peak injection rates around 85 km, with Na and K about 8 km higher. The more refractory element Ca ablates around 82 km with a Na:Ca ratio of 4:1, which does therefore not explain the depletion of atomic Ca to Na, by more than 2 orders of magnitude, in the upper mesosphere. Diffusion of the most volatile elements (Na and K does not appear to be rate-limiting except in the fastest meteoroids. Non-thermal sputtering causes ~35% mass loss from the fastest (~60–70 km s−1 and smallest (10−17–10

  18. Identification of previously unrecognized antiestrogenic chemicals using a novel virtual screening approach. (United States)

    Wang, Ching Y; Ai, Ni; Arora, Sonia; Erenrich, Eric; Nagarajan, Karthigeyan; Zauhar, Randy; Young, Douglas; Welsh, William J


    The physiological roles of estrogen in sexual differentiation and development, female and male reproductive processes, and bone health are complex and diverse. Numerous natural and synthetic chemical compounds, commonly known as endocrine disrupting chemicals (EDCs), have been shown to alter the physiological effects of estrogen in humans and wildlife. As such, these EDCs may cause unanticipated and even undesirable effects. Large-scale in vitro and in vivo screening of chemicals to assess their estrogenic activity would demand a prodigious investment of time, labor, and money and would require animal testing on an unprecedented scale. Approaches in silico are increasingly recognized as playing a vital role in screening and prioritizing chemicals to extend limited resources available for experimental testing. Here, we evaluated a multistep procedure that is suitable for in silico (virtual) screening of large chemical databases to identify compounds exhibiting estrogenic activity. This procedure incorporates Shape Signatures, a novel computational tool that rapidly compares molecules on the basis of similarity in shape, polarity, and other bio-relevant properties. Using 4-hydroxy tamoxifen (4-OH TAM) and diethylstilbestrol (DES) as input queries, we employed this scheme to search a sample database of approximately 200,000 commercially available organic chemicals for matches (hits). Of the eight compounds identified computationally as potentially (anti)estrogenic, biological evaluation confirmed two as heretofore unknown estrogen antagonists. Subsequent radioligand binding assays confirmed that two of these three compounds exhibit antiestrogenic activities comparable to 4-OH TAM. Molecular modeling studies of these ligands docked inside the binding pocket of estrogen receptor alpha (ERalpha) elucidated key ligand-receptor interactions that corroborate these experimental findings. The present study demonstrates the utility of our computational scheme for this and

  19. Fate modelling of chemical compounds with incomplete data sets

    DEFF Research Database (Denmark)

    Birkved, Morten; Heijungs, Reinout


    Impact assessment of chemical compounds in Life Cycle Impact Assessment (LCIA) and Environmental Risk Assessment (ERA) requires a vast amount of data on the properties of the chemical compounds being assessed. These data are used in multi-media fate and exposure models, to calculate risk levels...... in an approximate way. The idea is that not all data needed in a multi-media fate and exposure model are completely independent and equally important, but that there are physical-chemical and biological relationships between sets of chemical properties. A statistical model is constructed to underpin this assumption...

  20. Model based feature fusion approach

    NARCIS (Netherlands)

    Schwering, P.B.W.


    In recent years different sensor data fusion approaches have been analyzed and evaluated in the field of mine detection. In various studies comparisons have been made between different techniques. Although claims can be made for advantages for using certain techniques, until now there has been no si

  1. Geometrical approach to fluid models

    NARCIS (Netherlands)

    Kuvshinov, B. N.; Schep, T. J.


    Differential geometry based upon the Cartan calculus of differential forms is applied to investigate invariant properties of equations that describe the motion of continuous media. The main feature of this approach is that physical quantities are treated as geometrical objects. The geometrical notio

  2. Development of regionalized multimedia chemical fate models for China


    Zhu, Ying; Jones, Kevin; Sweetman, Andrew; Price, Oliver; Tao, Shu


    To balance the economic development with environmental safety and human health, China has released chemicals management legislation for which chemical prioritization and risk assessment are key issues. To support these ambitions two versions of an environmental fate and behaviour model SESAMe (Sino Evaluative Simplebox-MAMI models), have been developed with different resolutions and structures in this thesis. SESAMe is applied to hypothetical chemicals to investigate the influence of environm...

  3. Formal modeling of a system of chemical reactions under uncertainty. (United States)

    Ghosh, Krishnendu; Schlipf, John


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

  4. Global energy modeling - A biophysical approach

    Energy Technology Data Exchange (ETDEWEB)

    Dale, Michael


    This paper contrasts the standard economic approach to energy modelling with energy models using a biophysical approach. Neither of these approaches includes changing energy-returns-on-investment (EROI) due to declining resource quality or the capital intensive nature of renewable energy sources. Both of these factors will become increasingly important in the future. An extension to the biophysical approach is outlined which encompasses a dynamic EROI function that explicitly incorporates technological learning. The model is used to explore several scenarios of long-term future energy supply especially concerning the global transition to renewable energy sources in the quest for a sustainable energy system.

  5. Modelling the chemical evolution in galaxies with KROME

    CERN Document Server

    Bovino, Stefano; Capelo, Pedro R; Schleicher, Dominik R G; Banerjee, R


    In this paper we present and test chemical models for three-dimensional hydrodynamical simulations of galaxy evolution. The microphysics is modelled by employing the public chemistry package KROME and the chemical networks have been tested to work in a wide range of densities and temperatures. We describe a simple H/He network following the formation of H2, and a more sophisticated network which includes metals. Photochemistry, thermal processes, and different prescriptions for the H2 catalysis on dust are presented and tested within a simple one-zone framework. We explore the effect of changing some of the key parameters such as metallicity, radiation and non-equilibrium versus equilibrium metal cooling approximations on the transition between the different gas phases. We find that employing an accurate treatment of the dust-related processes induces a faster HI-H2 transition. In addition, we show when the equilibrium assumption for metal cooling holds, and how a non-equilibrium approach affects the thermal ...

  6. High-throughput exposure modeling to support prioritization of chemicals in personal care products

    DEFF Research Database (Denmark)

    Csiszar, Susan A.; Ernstoff, Alexi; Fantke, Peter;


    We demonstrate the application of a high-throughput modeling framework to estimate exposure to chemicals used in personal care products (PCPs). As a basis for estimating exposure, we use the product intake fraction (PiF), defined as the mass of chemical taken by an individual or population per mass...... intakes were associated with body lotion. Bioactive doses derived from high-throughput in vitro toxicity data were combined with the estimated PiFs to demonstrate an approach to estimate bioactive equivalent chemical content and to screen chemicals for risk....

  7. A probabilistic model for secondary structure prediction from protein chemical shifts. (United States)

    Mechelke, Martin; Habeck, Michael


    Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first- and second-order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence-based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts.

  8. The chronic diseases modelling approach

    NARCIS (Netherlands)

    Hoogenveen RT; Hollander AEM de; Genugten MLL van; CCM


    A mathematical model structure is described that can be used to simulate the changes of the Dutch public health state over time. The model is based on the concept of demographic and epidemiologic processes (events) and is mathematically based on the lifetable method. The population is divided over s

  9. Voltammetry as a Model for Teaching Chemical Instrumentation. (United States)

    Gunasingham, H.; Ang, K. P.


    Voltammetry is used as a model for teaching chemical instrumentation to chemistry undergraduates at the National University of Singapore. Lists six criteria used to select a successful teaching model and shows how voltammetry satisfies each criterion. (JN)

  10. Overview of chemical modeling of nuclear waste glass dissolution

    Energy Technology Data Exchange (ETDEWEB)

    Bourcier, W.L.


    Glass dissolution takes place through metal leaching and hydration of the glass surface accompanied by development of alternation layers of varying crystallinity. The reaction which controls the long-term glass dissolution rate appears to be surface layer dissolution. This reaction is reversible because the buildup of dissolved species in solution slows the dissolution rate due to a decreased dissolution affinity. Glass dissolution rates are therefore highly dependent on silica concentrations in solution because silica is the major component of the alteration layer. Chemical modeling of glass dissolution using reaction path computer codes has successfully been applied to short term experimental tests and used to predict long-term repository performance. Current problems and limitations of the models include a poorly defined long-term glass dissolution mechanism, the use of model parameters determined from the same experiments that the model is used to predict, and the lack of sufficient validation of key assumptions in the modeling approach. Work is in progress that addresses these issues. 41 refs., 7 figs., 2 tabs.

  11. Hazard identification of chemicals: A more efficient approach

    NARCIS (Netherlands)

    Feron, V.J.; Woutersen, R.A.; Vliet, P.W. van


    The OECD (organisation for economic co-operation and development) guidelines for hazard identification of chemicals have proved their worth in practice and are of great significance for designing adequate and relevant toxicity studies. However, assessment procedures are too time-consuming and too ex

  12. Learning Actions Models: Qualitative Approach

    DEFF Research Database (Denmark)

    Bolander, Thomas; Gierasimczuk, Nina


    identifiability (conclusively inferring the appropriate action model in finite time) and identifiability in the limit (inconclusive convergence to the right action model). We show that deterministic actions are finitely identifiable, while non-deterministic actions require more learning power......—they are identifiable in the limit.We then move on to a particular learning method, which proceeds via restriction of a space of events within a learning-specific action model. This way of learning closely resembles the well-known update method from dynamic epistemic logic. We introduce several different learning...

  13. Modeling Chemical Reactors I: Quiescent Reactors

    CERN Document Server

    Michoski, C E; Schmitz, P G


    We introduce a fully generalized quiescent chemical reactor system in arbitrary space $\\vdim =1,2$ or 3, with $n\\in\\mathbb{N}$ chemical constituents $\\alpha_{i}$, where the character of the numerical solution is strongly determined by the relative scaling between the local reactivity of species $\\alpha_{i}$ and the local functional diffusivity $\\mathscr{D}_{ij}(\\alpha)$ of the reaction mixture. We develop an operator time-splitting predictor multi-corrector RK--LDG scheme, and utilize $hp$-adaptivity relying only on the entropy $\\mathscr{S}_{\\mathfrak{R}}$ of the reactive system $\\mathfrak{R}$. This condition preserves these bounded nonlinear entropy functionals as a necessarily enforced stability condition on the coupled system. We apply this scheme to a number of application problems in chemical kinetics; including a difficult classical problem arising in nonequilibrium thermodynamics known as the Belousov-Zhabotinskii reaction where we utilize a concentration-dependent diffusivity tensor $\\mathscr{D}_{ij}(...

  14. A Unified Approach to Modeling and Programming

    DEFF Research Database (Denmark)

    Madsen, Ole Lehrmann; Møller-Pedersen, Birger


    of this paper is to go back to the future and get inspiration from SIMULA and propose a unied approach. In addition to reintroducing the contributions of SIMULA and the Scandinavian approach to object-oriented programming, we do this by discussing a number of issues in modeling and programming and argue3 why we......SIMULA was a language for modeling and programming and provided a unied approach to modeling and programming in contrast to methodologies based on structured analysis and design. The current development seems to be going in the direction of separation of modeling and programming. The goal...

  15. Electrochemical approaches for chemical and biological analysis on Mars (United States)

    Kounaves, Samuel P.


    Obtaining in situ chemical data from planetary bodies such as Mars or Europa can present significant challenges. The one analytical technique that has many of the requisite characteristics to meet such a challenge is electroanalysis. Described here are three electroanalytical devices designed for in situ geochemical and biological analysis on Mars. The Mars Environmental Compatibility Assessment (MECA) was built and flight qualified for the now cancelled NASA Mars 2001 Lander. Part of MECA consisted of four "cells" containing arrays of electrochemical based sensors for measuring the ionic species in soil samples. A next-generation MECA, the Robotic Chemical Analysis Laboratory (RCAL), uses a carousel-type system to allow for greater customization of analytical procedures. A second instrument, proposed as part of the 2007 CryoScout mission, consists of a flow-through inorganic chemical analyzer (MICA). CryoScout is a torpedo-like device designed for subsurface investigation of the stratigraphic climate record embedded in Mars' north polar cap. As the CryoScout melts its way through the ice cap, MICA will collect and analyze the meltwater for a variety of inorganics and chemical parameters. By analyzing the chemistry locked in the layers of dust, salt, and ice, geologists will be able to determine the recent history of climate, water, and atmosphere on Mars and link it to the past. Finally, electroanalysis shows its abilities in the detection of possible microorganism on Mars or elsewhere in the solar system. To identify an unknown microorganism, one that may not even use Earth-type biochemistry, requires a detection scheme which makes minimal assumptions and looks for the most general features. Recent work has demonstrated that the use of an array of electrochemical sensors which monitors the changes in a solution via electrical conductivity, pH, and ion selective electrodes, can be used to detect minute chemical perturbations caused by the growth of bacteria and

  16. Modelling Human Exposure to Chemicals in Food

    NARCIS (Netherlands)

    Slob W


    Exposure to foodborne chemicals is often estimated using the average consumption pattern in the human population. To protect the human population instead of the average individual, however, interindividual variability in consumption behaviour must be taken into account. This report shows how food

  17. Comparison of approaches for parameter estimation on stochastic models: Generic least squares versus specialized approaches. (United States)

    Zimmer, Christoph; Sahle, Sven


    Parameter estimation for models with intrinsic stochasticity poses specific challenges that do not exist for deterministic models. Therefore, specialized numerical methods for parameter estimation in stochastic models have been developed. Here, we study whether dedicated algorithms for stochastic models are indeed superior to the naive approach of applying the readily available least squares algorithm designed for deterministic models. We compare the performance of the recently developed multiple shooting for stochastic systems (MSS) method designed for parameter estimation in stochastic models, a stochastic differential equations based Bayesian approach and a chemical master equation based techniques with the least squares approach for parameter estimation in models of ordinary differential equations (ODE). As test data, 1000 realizations of the stochastic models are simulated. For each realization an estimation is performed with each method, resulting in 1000 estimates for each approach. These are compared with respect to their deviation to the true parameter and, for the genetic toggle switch, also their ability to reproduce the symmetry of the switching behavior. Results are shown for different set of parameter values of a genetic toggle switch leading to symmetric and asymmetric switching behavior as well as an immigration-death and a susceptible-infected-recovered model. This comparison shows that it is important to choose a parameter estimation technique that can treat intrinsic stochasticity and that the specific choice of this algorithm shows only minor performance differences.

  18. Chemical Approaches to Studying Labile Amino Acid Phosphorylation. (United States)

    Marmelstein, Alan M; Moreno, Javier; Fiedler, Dorothea


    Phosphorylation of serine, threonine, and tyrosine residues is the archetypal posttranslational modification of proteins. While phosphorylation of these residues has become standard textbook knowledge, phosphorylation of other amino acid side chains is underappreciated and minimally characterized by comparison. This disparity is rooted in the relative instability of these chemically distinct amino acid side chain moieties, namely phosphoramidates, acyl phosphates, thiophosphates, and phosphoanhydrides. In the case of the O-phosphorylated amino acids, synthetic constructs were critical to assessing their stability and developing tools for their study. As the chemical biology community has become more aware of these alternative phosphorylation sites, methodology has been developed for the synthesis of well-characterized standards and close mimics of these phosphorylated amino acids as well. In this article, we review the synthetic chemistry that is a prerequisite to progress in this field.

  19. Chemical named entities recognition: a review on approaches and applications


    Eltyeb, Safaa; Salim, Naomie


    The rapid increase in the flow rate of published digital information in all disciplines has resulted in a pressing need for techniques that can simplify the use of this information. The chemistry literature is very rich with information about chemical entities. Extracting molecules and their related properties and activities from the scientific literature to “text mine” these extracted data and determine contextual relationships helps research scientists, particularly those in drug developmen...

  20. Three-Tier Approach to Chemical Spill Response (United States)


    D. Chandler, Lt.Col., USAF, BSC USAF Medical Center/ SGB , Wright-Patterson AFB, Ohio 45433-5300 Major chemical spills create special problems in protec...lower levels. The SPEGL is set at a level to protect this tion of both public and worker health. The current standard of sensitive subpopulation...large, predicted, toxic hazard car- including sensitive subpopulatio-,s. The Occupational Safety ridors creating evacuation problems and additional

  1. Studies of Trace Gas Chemical Cycles Using Observations, Inverse Methods and Global Chemical Transport Models (United States)

    Prinn, Ronald G.


    For interpreting observational data, and in particular for use in inverse methods, accurate and realistic chemical transport models are essential. Toward this end we have, in recent years, helped develop and utilize a number of three-dimensional models including the Model for Atmospheric Transport and Chemistry (MATCH).

  2. Matrix Model Approach to Cosmology

    CERN Document Server

    Chaney, A; Stern, A


    We perform a systematic search for rotationally invariant cosmological solutions to matrix models, or more specifically the bosonic sector of Lorentzian IKKT-type matrix models, in dimensions $d$ less than ten, specifically $d=3$ and $d=5$. After taking a continuum (or commutative) limit they yield $d-1$ dimensional space-time surfaces, with an attached Poisson structure, which can be associated with closed, open or static cosmologies. For $d=3$, we obtain recursion relations from which it is possible to generate rotationally invariant matrix solutions which yield open universes in the continuum limit. Specific examples of matrix solutions have also been found which are associated with closed and static two-dimensional space-times in the continuum limit. The solutions provide for a matrix resolution of cosmological singularities. The commutative limit reveals other desirable features, such as a solution describing a smooth transition from an initial inflation to a noninflationary era. Many of the $d=3$ soluti...

  3. Szekeres models: a covariant approach

    CERN Document Server

    Apostolopoulos, Pantelis S


    We exploit the 1+1+2 formalism to covariantly describe the inhomogeneous and anisotropic Szekeres models. It is shown that an \\emph{average scale length} can be defined \\emph{covariantly} which satisfies a 2d equation of motion driven from the \\emph{effective gravitational mass} (EGM) contained in the dust cloud. The contributions to the EGM are encoded to the energy density of the dust fluid and the free gravitational field $E_{ab}$. In addition the notions of the Apparent and Absolute Apparent Horizons are briefly discussed and we give an alternative gauge-invariant form to define them in terms of the kinematical variables of the spacelike congruences. We argue that the proposed program can be used in order to express the Sachs optical equations in a covariant form and analyze the confrontation of a spatially inhomogeneous irrotational overdense fluid model with the observational data.

  4. Learning Actions Models: Qualitative Approach

    DEFF Research Database (Denmark)

    Bolander, Thomas; Gierasimczuk, Nina


    —they are identifiable in the limit.We then move on to a particular learning method, which proceeds via restriction of a space of events within a learning-specific action model. This way of learning closely resembles the well-known update method from dynamic epistemic logic. We introduce several different learning...... methods suited for finite identifiability of particular types of deterministic actions....

  5. Modeling software behavior a craftsman's approach

    CERN Document Server

    Jorgensen, Paul C


    A common problem with most texts on requirements specifications is that they emphasize structural models to the near exclusion of behavioral models-focusing on what the software is, rather than what it does. If they do cover behavioral models, the coverage is brief and usually focused on a single model. Modeling Software Behavior: A Craftsman's Approach provides detailed treatment of various models of software behavior that support early analysis, comprehension, and model-based testing. Based on the popular and continually evolving course on requirements specification models taught by the auth

  6. Harmonization of risk management approaches: radiation and chemical exposures

    Energy Technology Data Exchange (ETDEWEB)

    Srinivasan, P. [Bhabha Atomic Research Centre, Radiation Safety Systems Div., Mumbai (India)


    Assessment of occupational and public risk from the environmental pollutants like chemicals, radiation, etc demands that the effects be considered not only from each individual pollutant, but from the combination of all the pollutants. An integrated risk assessment system needs to be in place to have an overall risk perspective for the benefit of policy makers and decision takers to try to achieve risk reduction in totality. The basis for risk-based radiation dose limits is derived from epidemiological studies, which provide a rich source of data largely unavailable to chemical risk assessors. In addition, use of the principle of optimization as expressed in the ALARA concept has resulted in a safety culture, which is much more than just complying with stipulated limits. The conservative hypothesis of no-threshold dose-effect relation (ICRP) is universally assumed. The end-points and the severity of different classes of pollutants and even different pollutants in a same class vary over a wide range. Hence, it is difficult to arrive at a quantitative value for the net detriment that weighs the various types of end-points and various classes of pollutants. Once the risk due to other pollutants is quantified by some acceptable methodology, it can be expressed in terms of the Risk Equivalent Radiation Dose (R.E.R.D.) for easy comparison with options involving radiation exposure. This paper is an effort to use to quantify and present the risk due to exposure to chemicals and radiation in a common scale for the purpose of easy comparison to facilitate decision taking. (authors)

  7. Current approaches to gene regulatory network modelling

    Directory of Open Access Journals (Sweden)

    Brazma Alvis


    Full Text Available Abstract Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology models, network control logic models, and dynamic models. Here we will describe some examples for each of these categories. We will study the topology of gene regulatory networks in yeast in more detail, comparing a direct network derived from transcription factor binding data and an indirect network derived from genome-wide expression data in mutants. Regarding the network dynamics we briefly describe discrete and continuous approaches to network modelling, then describe a hybrid model called Finite State Linear Model and demonstrate that some simple network dynamics can be simulated in this model.

  8. New trajectory-driven aerosol and chemical process model Chemical and Aerosol Lagrangian Model (CALM

    Directory of Open Access Journals (Sweden)

    P. Tunved


    Full Text Available A new Chemical and Aerosol Lagrangian Model (CALM has been developed and tested. The model incorporates all central aerosol dynamical processes, from nucleation, condensation, coagulation and deposition to cloud formation and in-cloud processing. The model is tested and evaluated against observations performed at the SMEAR II station located at Hyytiälä (61° 51' N, 24° 17' E over a time period of two years, 2000–2001. The model shows good agreement with measurements throughout most of the year, but fails in reproducing the aerosol properties during the winter season, resulting in poor agreement between model and measurements especially during December–January. Nevertheless, through the rest of the year both trends and magnitude of modal concentrations show good agreement with observation, as do the monthly average size distribution properties. The model is also shown to capture individual nucleation events to a certain degree. This indicates that nucleation largely is controlled by the availability of nucleating material (as prescribed by the [H2SO4], availability of condensing material (in this model 15% of primary reactions of monoterpenes (MT are assumed to produce low volatile species and the properties of the size distribution (more specifically, the condensation sink. This is further demonstrated by the fact that the model captures the annual trend in nuclei mode concentration. The model is also used, alongside sensitivity tests, to examine which processes dominate the aerosol size distribution physical properties. It is shown, in agreement with previous studies, that nucleation governs the number concentration during transport from clean areas. It is also shown that primary number emissions almost exclusively govern the CN concentration when air from Central Europe is advected north over Scandinavia. We also show that biogenic emissions have a large influence on the amount of potential CCN observed

  9. Challenges in structural approaches to cell modeling. (United States)

    Im, Wonpil; Liang, Jie; Olson, Arthur; Zhou, Huan-Xiang; Vajda, Sandor; Vakser, Ilya A


    Computational modeling is essential for structural characterization of biomolecular mechanisms across the broad spectrum of scales. Adequate understanding of biomolecular mechanisms inherently involves our ability to model them. Structural modeling of individual biomolecules and their interactions has been rapidly progressing. However, in terms of the broader picture, the focus is shifting toward larger systems, up to the level of a cell. Such modeling involves a more dynamic and realistic representation of the interactomes in vivo, in a crowded cellular environment, as well as membranes and membrane proteins, and other cellular components. Structural modeling of a cell complements computational approaches to cellular mechanisms based on differential equations, graph models, and other techniques to model biological networks, imaging data, etc. Structural modeling along with other computational and experimental approaches will provide a fundamental understanding of life at the molecular level and lead to important applications to biology and medicine. A cross section of diverse approaches presented in this review illustrates the developing shift from the structural modeling of individual molecules to that of cell biology. Studies in several related areas are covered: biological networks; automated construction of three-dimensional cell models using experimental data; modeling of protein complexes; prediction of non-specific and transient protein interactions; thermodynamic and kinetic effects of crowding; cellular membrane modeling; and modeling of chromosomes. The review presents an expert opinion on the current state-of-the-art in these various aspects of structural modeling in cellular biology, and the prospects of future developments in this emerging field.

  10. Chemically induced intestinal damage models in zebrafish larvae. (United States)

    Oehlers, Stefan H; Flores, Maria Vega; Hall, Christopher J; Okuda, Kazuhide S; Sison, John Oliver; Crosier, Kathryn E; Crosier, Philip S


    Several intestinal damage models have been developed using zebrafish, with the aim of recapitulating aspects of human inflammatory bowel disease (IBD). These experimentally induced inflammation models have utilized immersion exposure to an array of colitogenic agents (including live bacteria, bacterial products, and chemicals) to induce varying severity of inflammation. This technical report describes methods used to generate two chemically induced intestinal damage models using either dextran sodium sulfate (DSS) or trinitrobenzene sulfonic acid (TNBS). Methods to monitor intestinal damage and inflammatory processes, and chemical-genetic methods to manipulate the host response to injury are also described.

  11. Frontiers and Approaches to Chemical Synthesis of Oligodeoxyribonucleotides



    The advantages and disadvantages of existing approaches to the synthesis of oligodeoxyribonucleotides (ODN) are discussed focusing on large-scale methods. The liquid phase and solid supported synthesis and the synthesis on soluble polymers are discussed. Different problems concerning the methods and implementation of the ODN synthesis are outlined depending on goals of using target oligomers.

  12. Distributed simulation a model driven engineering approach

    CERN Document Server

    Topçu, Okan; Oğuztüzün, Halit; Yilmaz, Levent


    Backed by substantive case studies, the novel approach to software engineering for distributed simulation outlined in this text demonstrates the potent synergies between model-driven techniques, simulation, intelligent agents, and computer systems development.

  13. Random matrix model approach to chiral symmetry

    CERN Document Server

    Verbaarschot, J J M


    We review the application of random matrix theory (RMT) to chiral symmetry in QCD. Starting from the general philosophy of RMT we introduce a chiral random matrix model with the global symmetries of QCD. Exact results are obtained for universal properties of the Dirac spectrum: i) finite volume corrections to valence quark mass dependence of the chiral condensate, and ii) microscopic fluctuations of Dirac spectra. Comparisons with lattice QCD simulations are made. Most notably, the variance of the number of levels in an interval containing $n$ levels on average is suppressed by a factor $(\\log n)/\\pi^2 n$. An extension of the random matrix model model to nonzero temperatures and chemical potential provides us with a schematic model of the chiral phase transition. In particular, this elucidates the nature of the quenched approximation at nonzero chemical potential.

  14. Upper Secondary Teachers' Knowledge for Teaching Chemical Bonding Models (United States)

    Bergqvist, Anna; Drechsler, Michal; Chang Rundgren, Shu-Nu


    Researchers have shown a growing interest in science teachers' professional knowledge in recent decades. The article focuses on how chemistry teachers impart chemical bonding, one of the most important topics covered in upper secondary school chemistry courses. Chemical bonding is primarily taught using models, which are key for understanding…

  15. THEORETICAL CHEMICAL ENGINEERING - Modeling and Simulation by Christo Boyadjiev

    Directory of Open Access Journals (Sweden)

    Simeon Oka


    Full Text Available Book Title: THEORETICAL CHEMICAL ENGINEERING - Modeling and Simulation Author(s: Christo Boyadjiev Institute of Chemical Engineering, Bulgarian Academy of Science, Sofia Publisher: Springer, 2010 ISBN: 978-3-642-10777-1 Review by: Prof. Simeon Oka, Ph. D., Scientific advisor - retired

  16. Evaluating uncertainties in an integrated approach for chemical risk assessment under REACH: more certain decisions?


    Vermeire, T.G.


    This thesis concentrates on uncertainty and variability in the risk assessment methodology for industrial chemicals as applied within the current regulatory framework for industrial chemicals in Europe, REACH (Registration, Evaluation, Authorisation and Restriction of Chemicals). The methodological approaches discussed address the risk assessment for both humans and the environment. The aim of this thesis is to investigate in what way the scientific process of risk assessment can improve deci...

  17. Toxicokinetic models and related tools in environmental risk assessment of chemicals. (United States)

    Grech, Audrey; Brochot, Céline; Dorne, Jean-Lou; Quignot, Nadia; Bois, Frédéric Y; Beaudouin, Rémy


    Environmental risk assessment of chemicals for the protection of ecosystems integrity is a key regulatory and scientific research field which is undergoing constant development in modelling approaches and harmonisation with human risk assessment. This review focuses on state-of-the-art toxicokinetic tools and models that have been applied to terrestrial and aquatic species relevant to environmental risk assessment of chemicals. Both empirical and mechanistic toxicokinetic models are discussed using the results of extensive literature searches together with tools and software for their calibration and an overview of applications in environmental risk assessment. These include simple tools such as one-compartment models, multi-compartment models to physiologically-based toxicokinetic (PBTK) models, mostly available for aquatic species such as fish species and a number of chemical classes including plant protection products, metals, persistent organic pollutants, nanoparticles. Data gaps and further research needs are highlighted.

  18. Chronic anal fissure: new approaches to chemical sphincterotomy

    Directory of Open Access Journals (Sweden)

    Mohammad hassan Emami


    Full Text Available

    • An anal fissure is a split in the mucosa extending from the anal verge towards the dentate line. It currently affects 10% of patients attending proctology clinics. Recent studies have highlighted the role of increased internal anal sphincter pressure and decreased anodermal blood flow in the pathogenesis of chronic anal fissures. Acute fissures usually heal with conservative management. Fissures lasting greater than two months with features of chronicity, are unlikely to heal with conservative management. Lateral internal sphincterotomy has been the treatment of choice for chronic anal fissures. Because of the disability associated with surgery for healing anal fissure and the risk of incontinence, medical alternatives for surgery have been sought. Among different chemical agents, Glyceryl trinitrate (GTN has been shown to be the first line treatment for chronic anal fissure but the transient sphincteric relaxation effect of pharmacologic agents such as GTN, makes them less effective than surgery. Although we have different forms of GTN products, they do not show a long acting effect on relaxing and enhancing the perfusion of anal sphincter, because they are soon metabolized. Most difficulties with current usage of drugs are due to poor compliance of patients. It can be taken into consideration that new formulation and novel combination of GTN with other treatments, in slow releasing forms may lead to acceptable strategies in the management of chronic anal fissure. As authors’ experience in this field, other clinical trials on the drug combination and slow releasing formulations are warranted to generate new data on the subject.
    • Key word: chronic anal fissure, review, chemical sphincterotomy 

  19. Development and Analysis of Group Contribution Plus Models for Property Prediction of Organic Chemical Systems

    DEFF Research Database (Denmark)

    Mustaffa, Azizul Azri

    Prediction of properties is important in chemical process-product design. Reliable property models are needed for increasingly complex and wider range of chemicals. Group-contribution methods provide useful tool but there is a need to validate them and improve their accuracy when complex chemicals...... are present in the mixtures. In accordance with that, a combined group-contribution and atom connectivity approach that is able to extend the application range of property models has been developed for mixture properties. This so-called Group-ContributionPlus (GCPlus) approach is a hybrid model which combines...... group contribution and molecular descriptor theories (such as connectivity indices – CI). Connectivity indices are formalisms defined via graph theoretical concepts intended to describe the topological characteristics of molecular structures. The main idea is the use of connectivity indices to describe...

  20. Cell reprogramming: a new chemical approach to stem cell biology and tissue regeneration. (United States)

    Anastasia, L; Piccoli, M; Garatti, A; Conforti, E; Scaringi, R; Bergante, S; Castelvecchio, S; Venerando, B; Menicanti, L; Tettamanti, G


    Generation of pluripotent stem cells (iPSCs) from adult fibroblasts starts a "new era" in stem cell biology, as it overcomes several key issues associated with previous approaches, including the ethical concerns associated with human embryonic stem cells. However, as the genetic approach for cell reprogramming has already shown potential safety issues, a chemical approach may be a safer and easier alternative. Moreover, a chemical approach could be advantageous not only for the de-differentiation phase, but also for inducing reprogrammed cells into the desired cell type with higher efficiency than current methodologies. Finally, a chemical approach may be envisioned to activate resident adult stem cells to proliferate and regenerate damaged tissues in situ, without the need for exogenous cell injections.

  1. New Chemical Kinetics Approach for DSMC Applications to Nonequilibrium Flows Project (United States)

    National Aeronautics and Space Administration — A new chemical kinetics model and database will be developed for aerothermodynamic analyses on entry vehicles. Unique features of this model include (1) the ability...

  2. Potts Flux Tube Model at Nonzero Chemical Potential

    CERN Document Server

    Condella, J; Condella, Jac; Tar, Carleton De


    We model the deconfinement phase transition in quantum chromodynamics at nonzero baryon number density and large quark mass by extending the flux tube model (three-state, three-dimensional Potts model) to nonzero chemical potential. In a direct numerical simulation we confirm mean-field-theory predictions that the deconfinement transition does not occur in a baryon-rich environment.


    Directory of Open Access Journals (Sweden)

    R. G. SILVA


    Full Text Available A new algorithm for model predictive control is presented. The algorithm utilizes a simultaneous solution and optimization strategy to solve the model's differential equations. The equations are discretized by equidistant collocation, and along with the algebraic model equations are included as constraints in a nonlinear programming (NLP problem. This algorithm is compared with the algorithm that uses orthogonal collocation on finite elements. The equidistant collocation algorithm results in simpler equations, providing a decrease in computation time for the control moves. Simulation results are presented and show a satisfactory performance of this algorithm.

  4. Constructing and visualizing chemical reaction networks from pi-calculus models


    M. John; H.-J. Schulz; H. Schumann; A. M. Uhrmacher; Andrea Unger


    International audience; The pi-calculus, in particular its stochastic version the stochastic pi-calculus, is a common modeling formalism to concisely describe the chemical reactions occurring in biochemical systems. However, it remains largely unexplored how to transform a biochemical model expressed in the stochastic pi-calculus back into a set of meaningful reactions. To this end, we present a two step approach of first translating model states to reaction sets and then visualizing sequence...

  5. Dual-transduction-mode sensing approach for chemical detection

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Liang (Frank); Swensen, James S.


    Smart devices such as electronic nose have been developed for application in many fields like national security, defense, environmental regulation, health care, pipeline monitoring and food analysis. Despite a large array of individual sensors, these devices still lack the ability to identify a target at a very low concentration out of a mixture of odors, limited by a single type of transduction as the sensing response to distinguish one odor from another. Here, we propose a new sensor architecture empowering each individual sensor with multi-dimensional transduction signals. The resolving power of our proposed electronic nose is thereby multiplied by a set of different and independent variables which synergistically will provide a unique combined fingerprint for each analyte. We demonstrate this concept using a Light Emitting Organic Field-Effect Transistor (LEOFET). Sensing response has been observed on both electrical and optical output signals from a green LEOFET upon exposure to an explosive taggant, with optical signal exhibiting much higher sensitivity. This new sensor architecture opens a field of devices for smart detection of chemical and biological targets.

  6. Chemically Defined Medium and Caenorhabditis elegans: A Powerful Approach (United States)

    Szewczyk, N. J.; Kozak, E.; Conley, C. A.


    C. elegans has been established as a powerful genetic system. Growth in a chemically defined medium (C. elegans Maintenance Medium (CeMM)) now allows standardization and systematic manipulation of the nutrients that animals receive. Liquid cultivation allows automated culturing and experimentation and should be of me in large-scale growth and screening of animals. Here we present our initial results from developing culture systems with CeMM. We find that CeMM is versatile and culturing is simple. CeMM can be used in a solid or liquid state, it can be stored unused for at least a year, unattended actively growing cultures may be maintained longer than with standard techniques, and standard C. elegans protocols work well with animals grown in defined medium. We also find that there are caveats of using defined medium. Animals in defined medium grow more slowly than on standard medium, appear to display adaptation to the defined medium, and display altered growth rates as they change defined medium composition. As was suggested with the introduction of C. elegans as a potential genetic system, use of defined medium with C. elegans should prove a powerful tool.

  7. Tactical approach to maneuvering within the chemical contamination labyrinth

    Energy Technology Data Exchange (ETDEWEB)

    Joseph, T.W. [Department of Energy, Oak Ridge, TN (United States)


    The Department of Energy (DOE) recognized the need and accepts the responsibility for understanding the reality and mitigating the consequence of the complex chemical contamination legacy it inherited as well as controlling, reducing, and eliminating extant emissions and effluents. The key to maneuvering through this complicated and multifaceted labyrinth of concerns, from which a meaningful, high quality, and cost-effective restoration/mitigation machine is then set in motions, is the ability to perform accurate, factual, and explicit health and environmental/ecological risk assessments. Likewise, the common denominator for carrying out this essential task is to have access to comprehensive and reliable data of known quality with which to perform those analyses. DOE is committed to identifying the data universe; to technically scrutinize and ensure the quality of that data; to develop efficient and cost-effective means to maximize the handling, utilization, and sharing of that universe; and to undertake those assessments. DOE views this as an effort that can only be accomplished through a merging of the technical excellence that exists within federal and state agencies, academia, and industry. The task at hand is so large that only by integrating that intelligence base can we hope to accomplish the goals of establishing meaningful standards, developing functional and effective solutions, and providing quality guidance at a national scale.

  8. Numerical aspects of modelling of coupled chemical reactions and fluid flow in sedimentary basins

    Energy Technology Data Exchange (ETDEWEB)

    Holstad, Astrid


    Simulation of coupled chemical reactions and fluid flow in porous sedimentary basins, through long time periods, is a numerical challenge. In most models available today the equations representing such a physical problem are solved as PDEs (Partial Differential Equation) where efficient time-stepping with controlled error is very difficult. The DAE (Differential Algebraic Equation) system approach is used where robust adaptive time-stepping algorithms are available in solvers. In this report mathematical and numerical models are derived for coupled chemical reactions and fluid flow. The models have several interesting properties which are discussed. The performance of code is tested. 20 refs., 6 figs., 2 tabs.

  9. Center for Integrated Nanotechnologies (CINT) Chemical Release Modeling Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Stirrup, Timothy Scott [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)


    This evaluation documents the methodology and results of chemical release modeling for operations at Building 518, Center for Integrated Nanotechnologies (CINT) Core Facility. This evaluation is intended to supplement an update to the CINT [Standalone] Hazards Analysis (SHA). This evaluation also updates the original [Design] Hazards Analysis (DHA) completed in 2003 during the design and construction of the facility; since the original DHA, additional toxic materials have been evaluated and modeled to confirm the continued low hazard classification of the CINT facility and operations. This evaluation addresses the potential catastrophic release of the current inventory of toxic chemicals at Building 518 based on a standard query in the Chemical Information System (CIS).

  10. Towards consensus in chemical characterization modeling for LCA:

    DEFF Research Database (Denmark)

    Rosenbaum, Ralf; Hauschild, Michael Zwicky; Bachmann, Till;


    A comprehensive LCIA characterization model comparison is being undertaken in the UNEP/SETAC Life Cycle Initiative, focusing on toxicity impacts and directly involving the developers of all models included. The main objective is to identify where differences come from, what indispensable model...... components are and if there can be a consensus model built from them, leading towards recommended practice in chemical characterization for LCIA. The models were selected in an open process inviting all models identified to be capable of characterizing a chemical in terms of environmental fate, human...... exposure, human toxicity and ecotoxicity. The invitation was accepted by the developers of CalTOX, IMPACT 2002, USES-LCA, EDIP, WATSON, and EcoSense. A consistent chemical test set comprising 66 organic (generic, amphiphilic and dissociating) and inorganic (metals, salts) compounds was selected...

  11. Chemical Kinetic Models for HCCI and Diesel Combustion

    Energy Technology Data Exchange (ETDEWEB)

    Pitz, W J; Westbrook, C K; Mehl, M; Sarathy, S M


    Predictive engine simulation models are needed to make rapid progress towards DOE's goals of increasing combustion engine efficiency and reducing pollutant emissions. These engine simulation models require chemical kinetic submodels to allow the prediction of the effect of fuel composition on engine performance and emissions. Chemical kinetic models for conventional and next-generation transportation fuels need to be developed so that engine simulation tools can predict fuel effects. The objectives are to: (1) Develop detailed chemical kinetic models for fuel components used in surrogate fuels for diesel and HCCI engines; (2) Develop surrogate fuel models to represent real fuels and model low temperature combustion strategies in HCCI and diesel engines that lead to low emissions and high efficiency; and (3) Characterize the role of fuel composition on low temperature combustion modes of advanced combustion engines.

  12. A Set Theoretical Approach to Maturity Models

    DEFF Research Database (Denmark)

    Lasrado, Lester; Vatrapu, Ravi; Andersen, Kim Normann


    Maturity Model research in IS has been criticized for the lack of theoretical grounding, methodological rigor, empirical validations, and ignorance of multiple and non-linear paths to maturity. To address these criticisms, this paper proposes a novel set-theoretical approach to maturity models ch...

  13. Thermodynamically consistent model calibration in chemical kinetics

    Directory of Open Access Journals (Sweden)

    Goutsias John


    Full Text Available Abstract Background The dynamics of biochemical reaction systems are constrained by the fundamental laws of thermodynamics, which impose well-defined relationships among the reaction rate constants characterizing these systems. Constructing biochemical reaction systems from experimental observations often leads to parameter values that do not satisfy the necessary thermodynamic constraints. This can result in models that are not physically realizable and may lead to inaccurate, or even erroneous, descriptions of cellular function. Results We introduce a thermodynamically consistent model calibration (TCMC method that can be effectively used to provide thermodynamically feasible values for the parameters of an open biochemical reaction system. The proposed method formulates the model calibration problem as a constrained optimization problem that takes thermodynamic constraints (and, if desired, additional non-thermodynamic constraints into account. By calculating thermodynamically feasible values for the kinetic parameters of a well-known model of the EGF/ERK signaling cascade, we demonstrate the qualitative and quantitative significance of imposing thermodynamic constraints on these parameters and the effectiveness of our method for accomplishing this important task. MATLAB software, using the Systems Biology Toolbox 2.1, can be accessed from lab/software.html. An SBML file containing the thermodynamically feasible EGF/ERK signaling cascade model can be found in the BioModels database. Conclusions TCMC is a simple and flexible method for obtaining physically plausible values for the kinetic parameters of open biochemical reaction systems. It can be effectively used to recalculate a thermodynamically consistent set of parameter values for existing thermodynamically infeasible biochemical reaction models of cellular function as well as to estimate thermodynamically feasible values for the parameters of new

  14. Chemical reaction rates and non-equilibrium pressure of reacting gas mixtures in the state-to-state approach

    Energy Technology Data Exchange (ETDEWEB)

    Kustova, Elena V., E-mail: [Department of Mathematics and Mechanics, Saint Petersburg State University, 198504 Universitetskiy pr. 28, Saint Petersburg (Russian Federation); Kremer, Gilberto M., E-mail: [Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-980 Curitiba (Brazil)


    Highlights: • State-to-state approach for coupled vibrational relaxation and chemical reactions. • Self-consistent model for rates of non-equilibrium reactions and energy transitions. • In viscous flows mass action law is violated. • Cross coupling between reaction rates and non-equilibrium pressure in viscous flow. • Results allow implementing the state-to-state approach for viscous flow simulations. - Abstract: Viscous gas flows with vibrational relaxation and chemical reactions in the state-to-state approach are analyzed. A modified Chapman–Enskog method is used for the determination of chemical reaction and vibrational transition rates and non-equilibrium pressure. Constitutive equations depend on the thermodynamic forces: velocity divergence and chemical reaction/transition affinity. As an application, N{sub 2} flow with vibrational relaxation across a shock wave is investigated. Two distinct processes occur behind the shock: for small values of the distance the affinity is large and vibrational relaxation is in its initial stage; for large distances the affinity is small and the chemical reaction is in its final stage. The affinity contributes more to the transition rate than the velocity divergence and the effect of these two contributions are more important for small distances from the shock front. For the non-equilibrium pressure, the term associated with the bulk viscosity increases by a small amount the hydrostatic pressure.

  15. Particle production and chemical freezeout from the hybrid UrQMD approach at NICA energies

    CERN Document Server

    Tawfik, Abdel Nasser; Shalaby, Asmaa G; Hanafy, Mahmoud; Sorin, Alexander; Rogachevsky, Oleg; Scheinast, Werner


    The energy dependence of various particle ratios is calculated within the Ultra-Relativistic Quantum Molecular Dynamics approach and compared with the hadron resonance gas (HRG) model and measurements from various experiments, including RHIC-BES, SPS and AGS. It is found that the UrQMD particle ratios agree well with the experimental results at the RHIC-BES energies. Thus, we have utilized UrQMD in simulating particle ratios at other beam energies down to 3 GeV, which will be accessed at NICA and FAIR future facilities. We observe that the particle ratios for crossover and first-order phase transition, implemented in the hybrid UrQMD v3.4, are nearly indistinguishable, especially at low energies (at large baryon chemical potentials or high density).

  16. Particle production and chemical freezeout from the hybrid UrQMD approach at NICA energies

    Energy Technology Data Exchange (ETDEWEB)

    Nasser Tawfik, Abdel [Modern University for Technology and Information (MTI), Egyptian Center for Theoretical Physics (ECTP), Cairo (Egypt); World Laboratory for Cosmology and Particle Physics (WLCAPP), Cairo (Egypt); Abou-Salem, Loutfy I. [Benha University, Physics Department, Faculty of Science, Benha (Egypt); Shalaby, Asmaa G.; Hanafy, Mahmoud [World Laboratory for Cosmology and Particle Physics (WLCAPP), Cairo (Egypt); Benha University, Physics Department, Faculty of Science, Benha (Egypt); Sorin, Alexander [Joint Institute for Nuclear Research, Bogoliubov Laboratory of Theoretical Physics, Dubna, Moscow region (Russian Federation); Joint Institute for Nuclear Research, Veksler and Baldin Laboratory of High Energy Physics, Dubna, Moscow region (Russian Federation); National Research Nuclear University (MEPhI), Moscow (Russian Federation); Dubna International University, Dubna (Russian Federation); Rogachevsky, Oleg; Scheinast, Werner [Joint Institute for Nuclear Research, Veksler and Baldin Laboratory of High Energy Physics, Dubna, Moscow region (Russian Federation)


    The energy dependence of various particle ratios is calculated within the Ultra-relativistic Quantum Molecular Dynamics approach and compared with the hadron resonance gas (HRG) model and measurements from various experiments, including RHIC-BES, SPS and AGS. It is found that the UrQMD particle ratios agree well with the experimental results at the RHIC-BES energies. Thus, we have utilized UrQMD in simulating particle ratios at other beam energies down to 3GeV, which will be accessed at NICA and FAIR future facilities. We observe that the particle ratios for crossover and first-order phase transition, implemented in the hybrid UrQMD v3.4, are nearly indistinguishable, especially at low energies (at large baryon chemical potentials or high density). (orig.)

  17. Modeling diffuse pollution with a distributed approach. (United States)

    León, L F; Soulis, E D; Kouwen, N; Farquhar, G J


    The transferability of parameters for non-point source pollution models to other watersheds, especially those in remote areas without enough data for calibration, is a major problem in diffuse pollution modeling. A water quality component was developed for WATFLOOD (a flood forecast hydrological model) to deal with sediment and nutrient transport. The model uses a distributed group response unit approach for water quantity and quality modeling. Runoff, sediment yield and soluble nutrient concentrations are calculated separately for each land cover class, weighted by area and then routed downstream. The distributed approach for the water quality model for diffuse pollution in agricultural watersheds is described in this paper. Integrating the model with data extracted using GIS technology (Geographical Information Systems) for a local watershed, the model is calibrated for the hydrologic response and validated for the water quality component. With the connection to GIS and the group response unit approach used in this paper, model portability increases substantially, which will improve non-point source modeling at the watershed scale level.

  18. Gray box modeling of MSW degradation: Revealing its dominant (bio)chemical mechanism

    NARCIS (Netherlands)

    Van Turnhout, A.G.; Heimovaara, T.J.; Kleerebezem, R.


    In this paper we present an approach to describe organic degradation within immobile water regions of Municipal Solid Waste (MSW) landfills which is best described by the term “gray box” model. We use a simplified set of dominant (bio)chemical and physical reactions and realistic environmental condi


    Directory of Open Access Journals (Sweden)

    Ahmed T. Shawky


    Full Text Available Decision models which adopt rough set theory have been used effectively in many real world applications.However, rough decision models suffer the high computational complexity when dealing with datasets ofhuge size. In this research we propose a new rough decision model that allows making decisions based onmodularity mechanism. According to the proposed approach, large-size datasets can be divided intoarbitrary moderate-size datasets, then a group of rough decision models can be built as separate decisionmodules. The overall model decision is computed as the consensus decision of all decision modulesthrough some aggregation technique. This approach provides a flexible and a quick way for extractingdecision rules of large size information tables using rough decision models.

  20. Modular Approach with Rough Decision Models

    Directory of Open Access Journals (Sweden)

    Ahmed T. Shawky


    Full Text Available Decision models which adopt rough set theory have been used effectively in many real world applications.However, rough decision models suffer the high computational complexity when dealing with datasets ofhuge size. In this research we propose a new rough decision model that allows making decisions based onmodularity mechanism. According to the proposed approach, large-size datasets can be divided intoarbitrary moderate-size datasets, then a group of rough decision models can be built as separate decisionmodules. The overall model decision is computed as the consensus decision of all decision modulesthrough some aggregation technique. This approach provides a flexible and a quick way for extractingdecision rules of large size information tables using rough decision models.

  1. Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches (United States)

    Rosenow, Phil; Tonner, Ralf


    The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001).

  2. An Alternative Educational Approach for an Inorganic Chemistry Laboratory Course in Industrial and Chemical Engineering (United States)

    Garces, Andres; Sanchez-Barba, Luis Fernando


    We describe an alternative educational approach for an inorganic chemistry laboratory module named "Experimentation in Chemistry", which is included in Industrial Engineering and Chemical Engineering courses. The main aims of the new approach were to reduce the high levels of failure and dropout on the module and to make the content match the…

  3. Implementation and evaluation of an array of chemical solvers in a global chemical transport model

    Directory of Open Access Journals (Sweden)

    M. Lee


    Full Text Available This paper discusses the implementation and performance of an array of gas-phase chemistry solvers for the state-of-the-science GEOS-Chem global chemical transport model. The implementation is based on the Kinetic PreProcessor (KPP. Two perl parsers automatically generate the needed interfaces between GEOS-Chem and KPP, and allow access to the chemical simulation code without any additional programming effort. This work illustrates the potential of KPP to positively impact global chemical transport modeling by providing additional functionality as follows. (1 The user can select a highly efficient numerical integration method from an array of solvers available in the KPP library. (2 KPP offers extreme flexibility for studies that involve changing the chemical mechanism (e.g., a set of additional reactions is automatically translated into efficient code and incorporated into a modified global model. (3 This work provides immediate access to tangent linear, continuous adjoint, and discrete adjoint chemical models, with applications to sensitivity analysis and data assimilation.

  4. Stormwater infiltration trenches: a conceptual modelling approach. (United States)

    Freni, Gabriele; Mannina, Giorgio; Viviani, Gaspare


    In recent years, limitations linked to traditional urban drainage schemes have been pointed out and new approaches are developing introducing more natural methods for retaining and/or disposing of stormwater. These mitigation measures are generally called Best Management Practices or Sustainable Urban Drainage System and they include practices such as infiltration and storage tanks in order to reduce the peak flow and retain part of the polluting components. The introduction of such practices in urban drainage systems entails an upgrade of existing modelling frameworks in order to evaluate their efficiency in mitigating the impact of urban drainage systems on receiving water bodies. While storage tank modelling approaches are quite well documented in literature, some gaps are still present about infiltration facilities mainly dependent on the complexity of the involved physical processes. In this study, a simplified conceptual modelling approach for the simulation of the infiltration trenches is presented. The model enables to assess the performance of infiltration trenches. The main goal is to develop a model that can be employed for the assessment of the mitigation efficiency of infiltration trenches in an integrated urban drainage context. Particular care was given to the simulation of infiltration structures considering the performance reduction due to clogging phenomena. The proposed model has been compared with other simplified modelling approaches and with a physically based model adopted as benchmark. The model performed better compared to other approaches considering both unclogged facilities and the effect of clogging. On the basis of a long-term simulation of six years of rain data, the performance and the effectiveness of an infiltration trench measure are assessed. The study confirmed the important role played by the clogging phenomenon on such infiltration structures.

  5. Extension of association models to complex chemicals

    DEFF Research Database (Denmark)

    Avlund, Ane Søgaard

    Summary of “Extension of association models to complex chemicals”. Ph.D. thesis by Ane Søgaard Avlund The subject of this thesis is application of SAFT type equations of state (EoS). Accurate and predictive thermodynamic models are important in many industries including the petroleum industry....... The SAFT EoS was developed 20 years ago, and a large number of papers on the subject has been published since, but many issues still remain unsolved. These issues are both theoretical and practical. The SAFT theory does not account for intramolecular association, it can only treat flexible chains, and does...... not account for steric self-hindrance for tree-like structures. An important practical problem is how to obtain optimal and consistent parameters. Moreover, multifunctional associating molecules represent a special challenge. In this work two equations of state using the SAFT theory for association are used...

  6. Building Water Models, A Different Approach

    CERN Document Server

    Izadi, Saeed; Onufriev, Alexey V


    Simplified, classical models of water are an integral part of atomistic molecular simulations, especially in biology and chemistry where hydration effects are critical. Yet, despite several decades of effort, these models are still far from perfect. Presented here is an alternative approach to constructing point charge water models - currently, the most commonly used type. In contrast to the conventional approach, we do not impose any geometry constraints on the model other than symmetry. Instead, we optimize the distribution of point charges to best describe the "electrostatics" of the water molecule, which is key to many unusual properties of liquid water. The search for the optimal charge distribution is performed in 2D parameter space of key lowest multipole moments of the model, to find best fit to a small set of bulk water properties at room temperature. A virtually exhaustive search is enabled via analytical equations that relate the charge distribution to the multipole moments. The resulting "optimal"...

  7. Bayesian molecular design with a chemical language model. (United States)

    Ikebata, Hisaki; Hongo, Kenta; Isomura, Tetsu; Maezono, Ryo; Yoshida, Ryo


    The aim of computational molecular design is the identification of promising hypothetical molecules with a predefined set of desired properties. We address the issue of accelerating the material discovery with state-of-the-art machine learning techniques. The method involves two different types of prediction; the forward and backward predictions. The objective of the forward prediction is to create a set of machine learning models on various properties of a given molecule. Inverting the trained forward models through Bayes' law, we derive a posterior distribution for the backward prediction, which is conditioned by a desired property requirement. Exploring high-probability regions of the posterior with a sequential Monte Carlo technique, molecules that exhibit the desired properties can computationally be created. One major difficulty in the computational creation of molecules is the exclusion of the occurrence of chemically unfavorable structures. To circumvent this issue, we derive a chemical language model that acquires commonly occurring patterns of chemical fragments through natural language processing of ASCII strings of existing compounds, which follow the SMILES chemical language notation. In the backward prediction, the trained language model is used to refine chemical strings such that the properties of the resulting structures fall within the desired property region while chemically unfavorable structures are successfully removed. The present method is demonstrated through the design of small organic molecules with the property requirements on HOMO-LUMO gap and internal energy. The R package iqspr is available at the CRAN repository.

  8. Evaluation of the applicability of the Benchmark approach to existing toxicological data. Framework: Chemical compounds in the working place


    Appel MJ; Bouman HGM; Pieters MN; Slob W; Adviescentrum voor chemische arbeidsomstandigheden (ACCA) TNO; CSR


    Five chemicals used in workplace, for which a risk assessment had already been carried out, were selected and the relevant critical studies re-analyzed by the Benchmark approach. The endpoints involved included continuous, and ordinal data. Dose-response modeling could be reasonablyapplied to the dose-response data encountered, and Critical Effect Doses (CEDs) could be derived for almost all of the endpoints considered. The resulting benchmark dose for the study as a whole was close to the NO...

  9. Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

    KAUST Repository

    Klingbeil, Guido


    We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimize data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximizes parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie [14]. In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction system\\'s size. © 2006 IEEE.

  10. Cleaner combustion developing detailed chemical kinetic models

    CERN Document Server

    Battin-Leclerc, Frédérique; Blurock, Edward


    This overview compiles the on-going research in Europe to enlarge and deepen the understanding of the reaction mechanisms and pathways associated with the combustion of an increased range of fuels. Focus is given to the formation of a large number of hazardous minor pollutants and the inability of current combustion models to predict the  formation of minor products such as alkenes, dienes, aromatics, aldehydes and soot nano-particles which have a deleterious impact on both the environment and on human health. Cleaner Combustion describes, at a fundamental level, the reactive chemistry of min

  11. Visual Basic and Excel in Chemical Modeling (United States)

    Kaess, Michael; Easter, Jesse; Cohn, Kim


    A series of modules were prepared to model some topics in molecular mechanics and computational chemistry. In order to make modules that would be useful in personal, academic or professional situations and to make them easy to use on both IBM and Macintosh compatible computers as well as require little or no computational, advanced mathematical or programming skills we settled on Microsoft Excel as the program of choice. The release of Excel 5.0 incorporates Visual Basic. This allows the use of custom commands, menus, dialog boxes, buttons and custom on-line help.

  12. A Coupled Chemical and Mass Transport Model for Concrete Durability

    DEFF Research Database (Denmark)

    Jensen, Mads Mønster; Johannesson, Björn; Geiker, Mette Rica


    curves which is established from a set of mathematical criteria. The chemical degradation is modelled with the geochemical code iphreeqc, which provides a general tool for evaluating different paste compositions. The governing system of equations is solved by the finite element method with a Newton......-Raphson iteration scheme arising from the non-linearity. The overall model is a transient problem, solved using a single parameter formulation. The sorption hysteresis and chemical equilibrium is included as source or sink terms. The advantages with this formulation is that each node in the discrete system has......In this paper a general continuum theory is used to evaluate the service life of cement based materials, in terms of mass transport processes and chemical degradation of the solid matrix. The model established is a reactive mass transport model, based on an extended version of the Poisson...

  13. Chemical proteomics approaches for identifying the cellular targets of natural products. (United States)

    Wright, M H; Sieber, S A


    Covering: 2010 up to 2016Deconvoluting the mode of action of natural products and drugs remains one of the biggest challenges in chemistry and biology today. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to understand protein function. In the context of natural products, chemical proteomics can be used to identify the protein binding partners or targets of small molecules in live cells. Here, we highlight recent examples of chemical probes based on natural products and their application for target identification. The review focuses on probes that can be covalently linked to their target proteins (either via intrinsic chemical reactivity or via the introduction of photocrosslinkers), and can be applied "in situ" - in living systems rather than cell lysates. We also focus here on strategies that employ a click reaction, the copper-catalysed azide-alkyne cycloaddition reaction (CuAAC), to allow minimal functionalisation of natural product scaffolds with an alkyne or azide tag. We also discuss 'competitive mode' approaches that screen for natural products that compete with a well-characterised chemical probe for binding to a particular set of protein targets. Fuelled by advances in mass spectrometry instrumentation and bioinformatics, many modern strategies are now embracing quantitative proteomics to help define the true interacting partners of probes, and we highlight the opportunities this rapidly evolving technology provides in chemical proteomics. Finally, some of the limitations and challenges of chemical proteomics approaches are discussed.

  14. Two-Compartment Pharmacokinetic Models for Chemical Engineers (United States)

    Kanneganti, Kumud; Simon, Laurent


    The transport of potassium permanganate between two continuous-stirred vessels was investigated to help chemical and biomedical engineering students understand two-compartment pharmacokinetic models. Concepts of modeling, mass balance, parameter estimation and Laplace transform were applied to the two-unit process. A good agreement was achieved…

  15. Prioritising chemicals used in personal care products in China for environmental risk assessment: application of the RAIDAR model. (United States)

    Gouin, Todd; van Egmond, Roger; Price, Oliver R; Hodges, Juliet E N


    China represents a significant market for the sale of personal care products (PCPs). Given the continuous emission of hundreds of chemicals used in PCPs to waste water and the aquatic environment after regular use, methods for prioritising the environmental risk assessment for China are needed. In an effort to assess the prioritisation of chemicals used in PCPs in China, we have identified the chemical ingredients used in 2500 PCPs released to the Chinese market in 2009, and estimated the annual emission of these chemicals. The physical-chemical property data for these substances have been estimated and used as model inputs in the RAIDAR model. In general, the RAIDAR model provides an overall assessment of the multimedia fate of chemicals, and provides a holistic approach for prioritising chemical ingredients. The prioritisation exercise conducted in this study is shown to be strongly influenced by loss processes, such as the removal efficiencies of WWT plants and biotransformation.

  16. Using Physiologically-Based Pharmacokinetic Models to Incorporate Chemical and Non-Chemical Stressors into Cumulative Risk Assessment: A Case Study of Pesticide Exposures

    Directory of Open Access Journals (Sweden)

    Jonathan I. Levy


    Full Text Available Cumulative risk assessment has been proposed as an approach to evaluate the health risks associated with simultaneous exposure to multiple chemical and non-chemical stressors. Physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD models can allow for the inclusion and evaluation of multiple stressors, including non-chemical stressors, but studies have not leveraged PBPK/PD models to jointly consider these disparate exposures in a cumulative risk context. In this study, we focused on exposures to organophosphate (OP pesticides for children in urban low-income environments, where these children would be simultaneously exposed to other pesticides (including pyrethroids and non-chemical stressors that may modify the effects of these exposures (including diet. We developed a methodological framework to evaluate chemical and non-chemical stressor impacts on OPs, utilizing an existing PBPK/PD model for chlorpyrifos. We evaluated population-specific stressors that would influence OP doses or acetylcholinesterase (AChE inhibition, the relevant PD outcome. We incorporated the impact of simultaneous exposure to pyrethroids and dietary factors on OP dose through the compartments of metabolism and PD outcome within the PBPK model, and simulated combinations of stressors across multiple exposure ranges and potential body weights. Our analyses demonstrated that both chemical and non-chemical stressors can influence the health implications of OP exposures, with up to 5-fold variability in AChE inhibition across combinations of stressor values for a given OP dose. We demonstrate an approach for modeling OP risks in the presence of other population-specific environmental stressors, providing insight about co-exposures and variability factors that most impact OP health risks and contribute to children’s cumulative health risk from pesticides. More generally, this framework can be used to inform cumulative risk assessment for any compound impacted by

  17. In silico screening of estrogen-like chemicals based on different nonlinear classification models. (United States)

    Liu, Huanxiang; Papa, Ester; Walker, John D; Gramatica, Paola


    Increasing concern is being shown by the scientific community, government regulators, and the public about endocrine-disrupting chemicals that are adversely affecting human and wildlife health through a variety of mechanisms. There is a great need for an effective means of rapidly assessing endocrine-disrupting activity, especially estrogen-simulating activity, because of the large number of such chemicals in the environment. In this study, quantitative structure activity relationship (QSAR) models were developed to quickly and effectively identify possible estrogen-like chemicals based on 232 structurally-diverse chemicals (training set) by using several nonlinear classification methodologies (least-square support vector machine (LS-SVM), counter-propagation artificial neural network (CP-ANN), and k nearest neighbour (kNN)) based on molecular structural descriptors. The models were externally validated by 87 chemicals (prediction set) not included in the training set. All three methods can give satisfactory prediction results both for training and prediction sets, and the most accurate model was obtained by the LS-SVM approach through the comparison of performance. In addition, our model was also applied to about 58,000 discrete organic chemicals; about 76% were predicted not to bind to Estrogen Receptor. The obtained results indicate that the proposed QSAR models are robust, widely applicable and could provide a feasible and practical tool for the rapid screening of potential estrogens.

  18. Consequence and Resilience Modeling for Chemical Supply Chains (United States)

    Stamber, Kevin L.; Vugrin, Eric D.; Ehlen, Mark A.; Sun, Amy C.; Warren, Drake E.; Welk, Margaret E.


    The U.S. chemical sector produces more than 70,000 chemicals that are essential material inputs to critical infrastructure systems, such as the energy, public health, and food and agriculture sectors. Disruptions to the chemical sector can potentially cascade to other dependent sectors, resulting in serious national consequences. To address this concern, the U.S. Department of Homeland Security (DHS) tasked Sandia National Laboratories to develop a predictive consequence modeling and simulation capability for global chemical supply chains. This paper describes that capability , which includes a dynamic supply chain simulation platform called N_ABLE(tm). The paper also presents results from a case study that simulates the consequences of a Gulf Coast hurricane on selected segments of the U.S. chemical sector. The case study identified consequences that include impacted chemical facilities, cascading impacts to other parts of the chemical sector. and estimates of the lengths of chemical shortages and recovery . Overall. these simulation results can DHS prepare for and respond to actual disruptions.

  19. Identification of Chemical Reactor Plant’s Mathematical Model

    Directory of Open Access Journals (Sweden)

    Pyakillya Boris


    Full Text Available This work presents a solution of the identification problem of chemical reactor plant’s mathematical model. The main goal is to obtain a mathematical description of a chemical reactor plant from experimental data, which based on plant’s time response measurements. This data consists sequence of measurements for water jacket temperature and information about control input signal, which is used to govern plant’s behavior.

  20. Hydrogeochemical modeling of groundwater chemical environmental evolution in Hebei Plain

    Institute of Scientific and Technical Information of China (English)

    郭永海; 沈照理; 钟佐燊


    Using the hydrogeochemical modeling method, the groundwater chemical environmental problems of the Hebei Plain which involve increasing of hardness and total dissolved solids in piedmont area and mixing of saline water with fresh water in middle-eastern area are studied. The water-rock interactions and mass transfer along a ground-water flow path and in mixing processes are calculated. Thus the evolution mechanisms of the groundwater chemical environment are brought to light.

  1. Application of Detailed Chemical Kinetics to Combustion Instability Modeling (United States)


    under two different conditions corresponding to marginally stable and unstable operation in order to evaluate the performance of the chemical kinetics...instability is a complex interaction between acoustics and the heat release due to combustion.In rocket engines, which are acoustically compact, there is...and amplitudes remains a challenge. The present article is an attempt towards addressing such discrepancies by enhancing the chemical kinetics model

  2. Modelling Coagulation Systems: A Stochastic Approach

    CERN Document Server

    Ryazanov, V V


    A general stochastic approach to the description of coagulating aerosol system is developed. As the object of description one can consider arbitrary mesoscopic values (number of aerosol clusters, their size etc). The birth-and-death formalism for a number of clusters can be regarded as a partial case of the generalized storage model. An application of the storage model to the number of monomers in a cluster is discussed.

  3. Inverse modeling approach to allogenic karst system characterization. (United States)

    Dörfliger, N; Fleury, P; Ladouche, B


    Allogenic karst systems function in a particular way that is influenced by the type of water infiltrating through river water losses, by karstification processes, and by water quality. Management of this system requires a good knowledge of its structure and functioning, for which a new methodology based on an inverse modeling approach appears to be well suited. This approach requires both spring and river inflow discharge measurements and a continuous record of chemical parameters in the river and at the spring. The inverse model calculates unit hydrographs and the impulse responses of fluxes from rainfall hydraulic head at the spring or rainfall flux data, the purpose of which is hydrograph separation. Hydrograph reconstruction is done using rainfall and river inflow data as model input and enables definition at each time step of the ratio of each component. Using chemical data, representing event and pre-event water, as input, it is possible to determine the origin of spring water (either fast flow through the epikarstic zone or slow flow through the saturated zone). This study made it possible to improve a conceptual model of allogenic karst system functioning. The methodology is used to study the Bas-Agly and the Cent Font karst systems, two allogenic karst systems in Southern France.

  4. Sensitivity of chemical tracers to meteorological parameters in the MOZART-3 chemical transport model (United States)

    Kinnison, D. E.; Brasseur, G. P.; Walters, S.; Garcia, R. R.; Marsh, D. R.; Sassi, F.; Harvey, V. L.; Randall, C. E.; Emmons, L.; Lamarque, J. F.; Hess, P.; Orlando, J. J.; Tie, X. X.; Randel, W.; Pan, L. L.; Gettelman, A.; Granier, C.; Diehl, T.; Niemeier, U.; Simmons, A. J.


    The Model for Ozone and Related Chemical Tracers, version 3 (MOZART-3), which represents the chemical and physical processes from the troposphere through the lower mesosphere, was used to evaluate the representation of long-lived tracers and ozone using three different meteorological fields. The meteorological fields are based on (1) the Whole Atmosphere Community Climate Model, version 1b (WACCM1b), (2) the European Centre for Medium-Range Weather Forecasts (ECMWF) operational analysis, and (3) a new reanalysis for year 2000 from ECMWF called EXP471. Model-derived tracers (methane, water vapor, and total inorganic nitrogen) and ozone are compared to data climatologies from satellites. Model mean age of air was also derived and compared to in situ CO2 and SF6 data. A detailed analysis of the chemical fields simulated by MOZART-3 shows that even though the general features characterizing the three dynamical sets are rather similar, slight differences in winds and temperature can produce substantial differences in the calculated distributions of chemical tracers. The MOZART-3 simulations that use meteorological fields from WACCM1b and ECMWF EXP471 represented best the distribution of long-lived tracers and mean age of air in the stratosphere. There was a significant improvement using the ECMWF EXP471 reanalysis data product over the ECMWF operational data product. The effect of the quasi-biennial oscillation circulation on long-lived tracers and ozone is examined.

  5. A Multiple Model Approach to Modeling Based on LPF Algorithm

    Institute of Scientific and Technical Information of China (English)


    Input-output data fitting methods are often used for unknown-structure nonlinear system modeling. Based on model-on-demand tactics, a multiple model approach to modeling for nonlinear systems is presented. The basic idea is to find out, from vast historical system input-output data sets, some data sets matching with the current working point, then to develop a local model using Local Polynomial Fitting (LPF) algorithm. With the change of working points, multiple local models are built, which realize the exact modeling for the global system. By comparing to other methods, the simulation results show good performance for its simple, effective and reliable estimation.``

  6. Study of lattice QCD at finite chemical potential using canonical ensemble approach

    CERN Document Server

    Bornyakov, V G; Goy, V A; Molochkov, A V; Nakamura, Atsushi; Nikolaev, A A; Zakharov, V I


    New approach to computation of canonical partition functions in $N_f=2$ lattice QCD is presented. We compare results obtained by new method with results obtained by known method of hopping parameter expansion. We observe agreement between two methods indicating validity of the new method. We use results for the number density obtained in the confining and deconfining phases at imaginary chemical potential to determine the phase transition line at real chemical potential.

  7. A Networks Approach to Modeling Enzymatic Reactions. (United States)

    Imhof, P


    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.

  8. Post-16 Biology--Some Model Approaches? (United States)

    Lock, Roger


    Outlines alternative approaches to the teaching of difficult concepts in A-level biology which may help student learning by making abstract ideas more concrete and accessible. Examples include models, posters, and poems for illustrating meiosis, mitosis, genetic mutations, and protein synthesis. (DDR)

  9. Modelling of variability of the chemically peculiar star phi Draconis

    CERN Document Server

    Prvák, Milan; Krtička, Jiří; Mikulášek, Zdeněk; Lüftinger, T


    Context: The presence of heavier chemical elements in stellar atmospheres influences the spectral energy distribution (SED) of stars. An uneven surface distribution of these elements, together with flux redistribution and stellar rotation, are commonly believed to be the primary causes of the variability of chemically peculiar (CP) stars. Aims: We aim to model the photometric variability of the CP star PHI Dra based on the assumption of inhomogeneous surface distribution of heavier elements and compare it to the observed variability of the star. We also intend to identify the processes that contribute most significantly to its photometric variability. Methods: We use a grid of TLUSTY model atmospheres and the SYNSPEC code to model the radiative flux emerging from the individual surface elements of PHI Dra with different chemical compositions. We integrate the emerging flux over the visible surface of the star at different phases throughout the entire rotational period to synthesise theoretical light curves of...


    Grove, David B.; Stollenwerk, Kenneth G.


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

  11. Model reduction for stochastic chemical systems with abundant species

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Stephen; Cianci, Claudia; Grima, Ramon [School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH93JR, Scotland (United Kingdom)


    Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. We first identify the rate constant limits under which the concentrations of a given set of species will tend to infinity (the abundant species) while the concentrations of all other species remains constant (the non-abundant species). Subsequently, we prove that, in this limit, the fluctuations in the molecule numbers of non-abundant species are accurately described by a hybrid stochastic description consisting of a chemical master equation coupled to deterministic rate equations. This is a reduced description when compared to the conventional chemical master equation which describes the fluctuations in both abundant and non-abundant species. We show that the reduced master equation can be solved exactly for a number of biochemical networks involving gene expression and enzyme catalysis, whose conventional chemical master equation description is analytically impenetrable. We use the linear noise approximation to obtain approximate expressions for the difference between the variance of fluctuations in the non-abundant species as predicted by the hybrid approach and by the conventional chemical master equation. Furthermore, we show that surprisingly, irrespective of any separation in the mean molecule numbers of various species, the conventional and hybrid master equations exactly agree for a class of chemical systems.

  12. Decomposition approach to model smart suspension struts (United States)

    Song, Xubin


    Model and simulation study is the starting point for engineering design and development, especially for developing vehicle control systems. This paper presents a methodology to build models for application of smart struts for vehicle suspension control development. The modeling approach is based on decomposition of the testing data. Per the strut functions, the data is dissected according to both control and physical variables. Then the data sets are characterized to represent different aspects of the strut working behaviors. Next different mathematical equations can be built and optimized to best fit the corresponding data sets, respectively. In this way, the model optimization can be facilitated in comparison to a traditional approach to find out a global optimum set of model parameters for a complicated nonlinear model from a series of testing data. Finally, two struts are introduced as examples for this modeling study: magneto-rheological (MR) dampers and compressible fluid (CF) based struts. The model validation shows that this methodology can truly capture macro-behaviors of these struts.

  13. Environmental Pollution, Toxicity Profile and Treatment Approaches for Tannery Wastewater and Its Chemical Pollutants. (United States)

    Saxena, Gaurav; Chandra, Ram; Bharagava, Ram Naresh

    Leather industries are key contributors in the economy of many developing countries, but unfortunately they are facing serious challenges from the public and governments due to the associated environmental pollution. There is a public outcry against the industry due to the discharge of potentially toxic wastewater having alkaline pH, dark brown colour, unpleasant odour, high biological and chemical oxygen demand, total dissolved solids and a mixture of organic and inorganic pollutants. Various environment protection agencies have prioritized several chemicals as hazardous and restricted their use in leather processing however; many of these chemicals are used and discharged in wastewater. Therefore, it is imperative to adequately treat/detoxify the tannery wastewater for environmental safety. This paper provides a detail review on the environmental pollution and toxicity profile of tannery wastewater and chemicals. Furthermore, the status and advances in the existing treatment approaches used for the treatment and/or detoxification of tannery wastewater at both laboratory and pilot/industrial scale have been reviewed. In addition, the emerging treatment approaches alone or in combination with biological treatment approaches have also been considered. Moreover, the limitations of existing and emerging treatment approaches have been summarized and potential areas for further investigations have been discussed. In addition, the clean technologies for waste minimization, control and management are also discussed. Finally, the international legislation scenario on discharge limits for tannery wastewater and chemicals has also been discussed country wise with discharge standards for pollution prevention due to tannery wastewater.

  14. Nahoon: Time-dependent gas-phase chemical model (United States)

    Wakelam, V.


    Nahoon is a gas-phase chemical model that computes the chemical evolution in a 1D temperature and density structure. It uses chemical networks downloaded from the KInetic Database for Astrochemistry (KIDA) but the model can be adapted to any network. The program is written in Fortran 90 and uses the DLSODES (double precision) solver from the ODEPACK package to solve the coupled stiff differential equations. The solver computes the chemical evolution of gas-phase species at a fixed temperature and density and can be used in one dimension (1D) if a grid of temperature, density, and visual extinction is provided. Grains, both neutral and negatively charged, and electrons are considered as chemical species and their concentrations are computed at the same time as those of the other species. Nahoon contains a test to check the temperature range of the validity of the rate coefficients and avoid extrapolations outside this range. A test is also included to check for duplication of chemical reactions, defined over complementary ranges of temperature.

  15. A model for chemically-induced mechanical loading on MEMS

    DEFF Research Database (Denmark)

    Amiot, Fabien


    The development of full displacement field measurements as an alternative to the optical lever technique to measure the mechanical response for microelectro-mechanical systems components in their environment calls for a modeling of chemically-induced mechanical fields (stress, strain, and displac......The development of full displacement field measurements as an alternative to the optical lever technique to measure the mechanical response for microelectro-mechanical systems components in their environment calls for a modeling of chemically-induced mechanical fields (stress, strain...

  16. Combined physical and chemical nonequilibrium transport model for solution conduits. (United States)

    Field, Malcolm S; Leij, Feike J


    Solute transport in karst aquifers is primarily constrained to relatively complex and inaccessible solution conduits where transport is often rapid, turbulent, and at times constrictive. Breakthrough curves generated from tracer tests in solution conduits are typically positively-skewed with long tails evident. Physical nonequilibrium models to fit breakthrough curves for tracer tests in solution conduits are now routinely employed. Chemical nonequilibrium processes are likely important interactions, however. In addition to partitioning between different flow domains, there may also be equilibrium and nonequilibrium partitioning between the aqueous and solid phases. A combined physical and chemical nonequilibrium (PCNE) model was developed for an instantaneous release similar to that developed by Leij and Bradford (2009) for a pulse release. The PCNE model allows for partitioning open space in solution conduits into mobile and immobile flow regions with first-order mass transfer between the two regions to represent physical nonequilibrium in the conduit. Partitioning between the aqueous and solid phases proceeds either as an equilibrium process or as a first-order process and represents chemical nonequilibrium for both the mobile and immobile regions. Application of the model to three example breakthrough curves demonstrates the applicability of the combined physical and chemical nonequilibrium model to tracer tests conducted in karst aquifers, with exceptionally good model fits to the data. The three models, each from a different state in the United States, exhibit very different velocities, dispersions, and other transport properties with most of the transport occurring via the fraction of mobile water. Fitting the model suggests the potentially important interaction of physical and chemical nonequilibrium processes.

  17. Dynamic modeling of chemical fate and transport in multimedia environments at watershed scale-I: theoretical considerations and model implementation. (United States)

    Luo, Yuzhou; Gao, Qiong; Yang, Xiusheng


    A geo-referenced environmental fate model was developed for analyzing unsteady-state dispersion and distribution of chemicals in multimedia environmental systems. Chemical transport processes were formulated in seven environmental compartments of air, canopy, surface soil, root-zone soil, vadose-zone soil, surface water, and sediment. The model assumed that the compartments were completely mixed and chemical equilibrium was established instantaneously between the sub-compartments within each compartment. A fugacity approach was utilized to formulate the mechanisms of diffusion, advection, physical interfacial transport, and transformation reactions. The governing equations of chemical mass balances in the environmental compartments were solved simultaneously to reflect the interactions between the compartments. A geographic information system (GIS) database and geospatial analysis were integrated into the chemical transport simulation to provide spatially explicit estimations of model parameters at watershed scale. Temporal variations of the environmental properties and source emissions were also considered in the parameter estimations. The outputs of the model included time-dependent chemical concentrations in each compartment and its sub-compartments, and inter-media mass fluxes between adjacent compartments at daily time steps.

  18. A detailed chemical kinetic model for pyrolysis of the lignin model compound chroman

    Directory of Open Access Journals (Sweden)

    James Bland


    Full Text Available The pyrolysis of woody biomass, including the lignin component, is emerging as a potential technology for the production of renewable fuels and commodity chemicals. Here we describe the construction and implementation of an elementary chemical kinetic model for pyrolysis of the lignin model compound chroman and its reaction intermediate ortho-quinone methide (o-QM. The model is developed using both experimental and theoretical data, and represents a hybrid approach to kinetic modeling that has the potential to provide molecular level insight into reaction pathways and intermediates while accurately describing reaction rates and product formation. The kinetic model developed here can replicate all known aspects of chroman pyrolysis, and provides new information on elementary reaction steps. Chroman pyrolysis is found to proceed via an initial retro-Diels–Alder reaction to form o-QM + ethene (C2H4, followed by dissociation of o-QM to the C6H6 isomers benzene and fulvene (+ CO. At temperatures of around 1000–1200 K and above fulvene rapidly isomerizes to benzene, where an activation energy of around 270 kJ mol-1 is required to reproduce experimental observations. A new G3SX level energy surface for the isomerization of fulvene to benzene supports this result. Our modeling also suggests that thermal decomposition of fulvene may be important at around 950 K and above. This study demonstrates that theoretical protocols can provide a significant contribution to the development of kinetic models for biomass pyrolysis by elucidating reaction mechanisms, intermediates, and products, and also by supplying realistic rate coefficients and thermochemical properties.

  19. Multispecies QSAR modeling for predicting the aquatic toxicity of diverse organic chemicals for regulatory toxicology. (United States)

    Singh, Kunwar P; Gupta, Shikha; Kumar, Anuj; Mohan, Dinesh


    The research aims to develop multispecies quantitative structure-activity relationships (QSARs) modeling tools capable of predicting the acute toxicity of diverse chemicals in various Organization for Economic Co-operation and Development (OECD) recommended test species of different trophic levels for regulatory toxicology. Accordingly, the ensemble learning (EL) approach based classification and regression QSAR models, such as decision treeboost (DTB) and decision tree forest (DTF) implementing stochastic gradient boosting and bagging algorithms were developed using the algae (P. subcapitata) experimental toxicity data for chemicals. The EL-QSAR models were successfully applied to predict toxicities of wide groups of chemicals in other test species including algae (S. obliguue), daphnia, fish, and bacteria. Structural diversity of the selected chemicals and those of the end-point toxicity data of five different test species were tested using the Tanimoto similarity index and Kruskal-Wallis (K-W) statistics. Predictive and generalization abilities of the constructed QSAR models were compared using statistical parameters. The developed QSAR models (DTB and DTF) yielded a considerably high classification accuracy in complete data of model building (algae) species (97.82%, 99.01%) and ranged between 92.50%-94.26% and 92.14%-94.12% in four test species, respectively, whereas regression QSAR models (DTB and DTF) rendered high correlation (R(2)) between the measured and model predicted toxicity end-point values and low mean-squared error in model building (algae) species (0.918, 0.15; 0.905, 0.21) and ranged between 0.575 and 0.672, 0.18-0.51 and 0.605-0.689 and 0.20-0.45 in four different test species. The developed QSAR models exhibited good predictive and generalization abilities in different test species of varied trophic levels and can be used for predicting the toxicities of new chemicals for screening and prioritization of chemicals for regulation.

  20. Upper Secondary Teachers' Knowledge for Teaching Chemical Bonding Models (United States)

    Bergqvist, Anna; Drechsler, Michal; Rundgren, Shu-Nu Chang


    Researchers have shown a growing interest in science teachers' professional knowledge in recent decades. The article focuses on how chemistry teachers impart chemical bonding, one of the most important topics covered in upper secondary school chemistry courses. Chemical bonding is primarily taught using models, which are key for understanding science. However, many studies have determined that the use of models in science education can contribute to students' difficulties understanding the topic, and that students generally find chemical bonding a challenging topic. The aim of this study is to investigate teachers' knowledge of teaching chemical bonding. The study focuses on three essential components of pedagogical content knowledge (PCK): (1) the students' understanding, (2) representations, and (3) instructional strategies. We analyzed lesson plans about chemical bonding generated by 10 chemistry teachers with whom we also conducted semi-structured interviews about their teaching. Our results revealed that the teachers were generally unaware of how the representations of models they used affected student comprehension. The teachers had trouble specifying students' difficulties in understanding. Moreover, most of the instructional strategies described were generic and insufficient for promoting student understanding. Additionally, the teachers' rationale for choosing a specific representation or activity was seldom directed at addressing students' understanding. Our results indicate that both PCK components require improvement, and suggest that the two components should be connected. Implications for the professional development of pre-service and in-service teachers are discussed.

  1. A Bayesian Shrinkage Approach for AMMI Models. (United States)

    da Silva, Carlos Pereira; de Oliveira, Luciano Antonio; Nuvunga, Joel Jorge; Pamplona, Andrezza Kéllen Alves; Balestre, Marcio


    Linear-bilinear models, especially the additive main effects and multiplicative interaction (AMMI) model, are widely applicable to genotype-by-environment interaction (GEI) studies in plant breeding programs. These models allow a parsimonious modeling of GE interactions, retaining a small number of principal components in the analysis. However, one aspect of the AMMI model that is still debated is the selection criteria for determining the number of multiplicative terms required to describe the GE interaction pattern. Shrinkage estimators have been proposed as selection criteria for the GE interaction components. In this study, a Bayesian approach was combined with the AMMI model with shrinkage estimators for the principal components. A total of 55 maize genotypes were evaluated in nine different environments using a complete blocks design with three replicates. The results show that the traditional Bayesian AMMI model produces low shrinkage of singular values but avoids the usual pitfalls in determining the credible intervals in the biplot. On the other hand, Bayesian shrinkage AMMI models have difficulty with the credible interval for model parameters, but produce stronger shrinkage of the principal components, converging to GE matrices that have more shrinkage than those obtained using mixed models. This characteristic allowed more parsimonious models to be chosen, and resulted in models being selected that were similar to those obtained by the Cornelius F-test (α = 0.05) in traditional AMMI models and cross validation based on leave-one-out. This characteristic allowed more parsimonious models to be chosen and more GEI pattern retained on the first two components. The resulting model chosen by posterior distribution of singular value was also similar to those produced by the cross-validation approach in traditional AMMI models. Our method enables the estimation of credible interval for AMMI biplot plus the choice of AMMI model based on direct posterior

  2. A Bayesian Shrinkage Approach for AMMI Models.

    Directory of Open Access Journals (Sweden)

    Carlos Pereira da Silva

    Full Text Available Linear-bilinear models, especially the additive main effects and multiplicative interaction (AMMI model, are widely applicable to genotype-by-environment interaction (GEI studies in plant breeding programs. These models allow a parsimonious modeling of GE interactions, retaining a small number of principal components in the analysis. However, one aspect of the AMMI model that is still debated is the selection criteria for determining the number of multiplicative terms required to describe the GE interaction pattern. Shrinkage estimators have been proposed as selection criteria for the GE interaction components. In this study, a Bayesian approach was combined with the AMMI model with shrinkage estimators for the principal components. A total of 55 maize genotypes were evaluated in nine different environments using a complete blocks design with three replicates. The results show that the traditional Bayesian AMMI model produces low shrinkage of singular values but avoids the usual pitfalls in determining the credible intervals in the biplot. On the other hand, Bayesian shrinkage AMMI models have difficulty with the credible interval for model parameters, but produce stronger shrinkage of the principal components, converging to GE matrices that have more shrinkage than those obtained using mixed models. This characteristic allowed more parsimonious models to be chosen, and resulted in models being selected that were similar to those obtained by the Cornelius F-test (α = 0.05 in traditional AMMI models and cross validation based on leave-one-out. This characteristic allowed more parsimonious models to be chosen and more GEI pattern retained on the first two components. The resulting model chosen by posterior distribution of singular value was also similar to those produced by the cross-validation approach in traditional AMMI models. Our method enables the estimation of credible interval for AMMI biplot plus the choice of AMMI model based on direct

  3. Modeling Exposure to Persistent Chemicals in Hazard and Risk Assessment

    Energy Technology Data Exchange (ETDEWEB)

    Cowan-Ellsberry, Christina E.; McLachlan, Michael S.; Arnot, Jon A.; MacLeod, Matthew; McKone, Thomas E.; Wania, Frank


    Fate and exposure modeling has not thus far been explicitly used in the risk profile documents prepared to evaluate significant adverse effect of candidate chemicals for either the Stockholm Convention or the Convention on Long-Range Transboundary Air Pollution. However, we believe models have considerable potential to improve the risk profiles. Fate and exposure models are already used routinely in other similar regulatory applications to inform decisions, and they have been instrumental in building our current understanding of the fate of POP and PBT chemicals in the environment. The goal of this paper is to motivate the use of fate and exposure models in preparing risk profiles in the POP assessment procedure by providing strategies for incorporating and using models. The ways that fate and exposure models can be used to improve and inform the development of risk profiles include: (1) Benchmarking the ratio of exposure and emissions of candidate chemicals to the same ratio for known POPs, thereby opening the possibility of combining this ratio with the relative emissions and relative toxicity to arrive at a measure of relative risk. (2) Directly estimating the exposure of the environment, biota and humans to provide information to complement measurements, or where measurements are not available or are limited. (3) To identify the key processes and chemical and/or environmental parameters that determine the exposure; thereby allowing the effective prioritization of research or measurements to improve the risk profile. (4) Predicting future time trends including how quickly exposure levels in remote areas would respond to reductions in emissions. Currently there is no standardized consensus model for use in the risk profile context. Therefore, to choose the appropriate model the risk profile developer must evaluate how appropriate an existing model is for a specific setting and whether the assumptions and input data are relevant in the context of the application

  4. A multi-scale, multi-disciplinary approach for assessing the technological, economic and environmental performance of bio-based chemicals. (United States)

    Herrgård, Markus; Sukumara, Sumesh; Campodonico, Miguel; Zhuang, Kai


    In recent years, bio-based chemicals have gained interest as a renewable alternative to petrochemicals. However, there is a significant need to assess the technological, biological, economic and environmental feasibility of bio-based chemicals, particularly during the early research phase. Recently, the Multi-scale framework for Sustainable Industrial Chemicals (MuSIC) was introduced to address this issue by integrating modelling approaches at different scales ranging from cellular to ecological scales. This framework can be further extended by incorporating modelling of the petrochemical value chain and the de novo prediction of metabolic pathways connecting existing host metabolism to desirable chemical products. This multi-scale, multi-disciplinary framework for quantitative assessment of bio-based chemicals will play a vital role in supporting engineering, strategy and policy decisions as we progress towards a sustainable chemical industry.

  5. On matrix model partition functions for QCD with chemical potential

    CERN Document Server

    Akemann, G; Vernizzi, G


    Partition functions of two different matrix models for QCD with chemical potential are computed for an arbitrary number of quark and complex conjugate anti-quark flavors. In the large-N limit of weak nonhermiticity complete agreement is found between the two models. This supports the universality of such fermionic partition functions, that is of products of characteristic polynomials in the complex plane. In the strong nonhermiticity limit agreement is found for an equal number of quark and conjugate flavours. For a general flavor content the equality of partition functions holds only for small chemical potential. The chiral phase transition is analyzed for an arbitrary number of quarks, where the free energy presents a discontinuity of first order at a critical chemical potential. In the case of nondegenerate flavors there is first order phase transition for each separate mass scale.

  6. Scientific Theories, Models and the Semantic Approach

    Directory of Open Access Journals (Sweden)

    Décio Krause


    Full Text Available According to the semantic view, a theory is characterized by a class of models. In this paper, we examine critically some of the assumptions that underlie this approach. First, we recall that models are models of something. Thus we cannot leave completely aside the axiomatization of the theories under consideration, nor can we ignore the metamathematics used to elaborate these models, for changes in the metamathematics often impose restrictions on the resulting models. Second, based on a parallel between van Fraassen’s modal interpretation of quantum mechanics and Skolem’s relativism regarding set-theoretic concepts, we introduce a distinction between relative and absolute concepts in the context of the models of a scientific theory. And we discuss the significance of that distinction. Finally, by focusing on contemporary particle physics, we raise the question: since there is no general accepted unification of the parts of the standard model (namely, QED and QCD, we have no theory, in the usual sense of the term. This poses a difficulty: if there is no theory, how can we speak of its models? What are the latter models of? We conclude by noting that it is unclear that the semantic view can be applied to contemporary physical theories.

  7. Model Based Monitoring and Control of Chemical and Biochemical Processes

    DEFF Research Database (Denmark)

    Huusom, Jakob Kjøbsted

    This presentation will give an overview of the work performed at the department of Chemical and Biochemical Engineering related to process control. A research vision is formulated and related to a number of active projects at the department. In more detail a project describing model estimation...

  8. Modeling proteins using a super-secondary structure library and NMR chemical shift information. (United States)

    Menon, Vilas; Vallat, Brinda K; Dybas, Joseph M; Fiser, Andras


    A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available.

  9. Animal models of temporomandibular joint disorders: implications for tissue engineering approaches. (United States)

    Almarza, Alejandro J; Hagandora, Catherine K; Henderson, Sarah E


    Animal models for temporomandibular joint disorder (TMD) or degradation are necessary for assessing the value of current and future tissue engineering therapies. After reviewing the literature, it is quite apparent that most TMD animal studies can be categorized into chemical approaches or surgical/mechanical approaches. Overall, it was found that the top five cited manuscripts for all chemical models were cited by almost 40% more manuscripts than the top five manuscripts for surgical/mechanical models. It is clear that the chemical approaches have focused on the inflammatory aspect of TMDs and its relationship to pain. However, chemical irritants must be tested in larger animal models, and the effect of short-term inflammation on the mechanical properties of the fibrocartilage must be examined. Nevertheless, therapeutic approaches aimed at reducing or controlling inflammation could use the established chemical methods. Surgical/mechanical methods can be used as negative controls for first generation TMJ tissue engineering approaches when the therapy is applied immediately after injury. Next generation tissue engineering approaches will require testing on tissues degenerated for a few months after the surgical/mechanical methods, with enhanced functional assessment techniques.

  10. Automated Physico-Chemical Cell Model Development through Information Theory

    Energy Technology Data Exchange (ETDEWEB)

    Peter J. Ortoleva


    The objective of this project was to develop predictive models of the chemical responses of microbial cells to variations in their surroundings. The application of these models is optimization of environmental remediation and energy-producing biotechnical processes.The principles on which our project is based are as follows: chemical thermodynamics and kinetics; automation of calibration through information theory; integration of multiplex data (e.g. cDNA microarrays, NMR, proteomics), cell modeling, and bifurcation theory to overcome cellular complexity; and the use of multiplex data and information theory to calibrate and run an incomplete model. In this report we review four papers summarizing key findings and a web-enabled, multiple module workflow we have implemented that consists of a set of interoperable systems biology computational modules.

  11. Multiscale Model Approach for Magnetization Dynamics Simulations

    CERN Document Server

    De Lucia, Andrea; Tretiakov, Oleg A; Kläui, Mathias


    Simulations of magnetization dynamics in a multiscale environment enable rapid evaluation of the Landau-Lifshitz-Gilbert equation in a mesoscopic sample with nanoscopic accuracy in areas where such accuracy is required. We have developed a multiscale magnetization dynamics simulation approach that can be applied to large systems with spin structures that vary locally on small length scales. To implement this, the conventional micromagnetic simulation framework has been expanded to include a multiscale solving routine. The software selectively simulates different regions of a ferromagnetic sample according to the spin structures located within in order to employ a suitable discretization and use either a micromagnetic or an atomistic model. To demonstrate the validity of the multiscale approach, we simulate the spin wave transmission across the regions simulated with the two different models and different discretizations. We find that the interface between the regions is fully transparent for spin waves with f...

  12. In situ chemical sensing for hydrothermal plume mapping and modeling (United States)

    Fukuba, T.; Kusunoki, T.; Maeda, Y.; Shitashima, K.; Kyo, M.; Fujii, T.; Noguchi, T.; Sunamura, M.


    Detection, monitoring, and mapping of biogeochemical anomalies in seawater such as temperature, salinity, turbidity, oxidation-reduction potential, and pH are essential missions to explore undiscovered hydrothermal sites and to understand distribution and behavior of hydrothermal plumes. Utilization of reliable and useful in situ sensors has been widely accepted as a promised approach to realize a spatiotemporally resolved mapping of anomalies without water sampling operations. Due to remarkable progresses of sensor technologies and its relatives, a number of highly miniaturized and robust chemical sensors have been proposed and developed. We have been developed, evaluated, and operated a compact ISFET (Ion-Sensitive Field-Effect Transistor)-based chemical sensors for ocean environmental sensing purposes. An ISFET has advantages against conventional glass-based electrodes on its faster response, robustness, and potential on miniaturization, and thus variety of chemical sensors has been already on the market. In this study, ISFET-based standalone pH sensors with a solid-state Cl-ISE as a reference electrode were mounted on various platforms and operated to monitor the pH anomalies in deep-sea environment at the Kairei, Edmond, and surrounding hydrothermal sites in the southern Central Indian Ridge area during KH10-06 scientific cruise (Nov. 2010), supported by project TAIGA (Trans-crustal Advection and In situ biogeochemical processes of Global sub-seafloor Aquifer). Up to three pH sensors were mounted on a wire-lined CTD/RMS (Rosette Multiple Sampler), dredge sampler, a series of MTD plankton nets, and VMPS (Vertical Multiple-operating Plankton Sampler). A standalone temperature sensor was bundled and operated with the pH sensor when they were mounted on the dredge sampler, MTD plankton nets, and VMPS. An AUV equipped with the pH sensor was also operated for hydrothermal activity survey operations. As a result of Tow-Yo intersect operations of the CTD

  13. A wet-chemical approach to perovskite and fluorite-type nanoceramics: synthesis and processing

    NARCIS (Netherlands)

    Veldhuis, Sjoerd Antonius


    In thesis the low-temperature, wet-chemical approach to various functional inorganic oxide materials is described. The main focus of this research is to control the material’s synthesis from liquid precursor to metal oxide powder or thin film; while understanding its formation mechanism. In addition

  14. Microwave-irradiation-assisted hybrid chemical approach for titanium dioxide nanoparticle synthesis: microbial and cytotoxicological evaluation. (United States)

    Ranjan, Shivendu; Dasgupta, Nandita; Rajendran, Bhavapriya; Avadhani, Ganesh S; Ramalingam, Chidambaram; Kumar, Ashutosh


    Titanium dioxide nanoparticles (TNPs) are widely used in the pharmaceutical and cosmetics industries. It is used for protection against UV exposure due to its light-scattering properties and high refractive index. Though TNPs are increasingly used, the synthesis of TNPs is tedious and time consuming; therefore, in the present study, microwave-assisted hybrid chemical approach was used for TNP synthesis. In the present study, we demonstrated that TNPs can be synthesized only in 2.5 h; however, the commonly used chemical approach using muffle furnace takes 5 h. The activity of TNP depends on the synthetic protocol; therefore, the present study also determined the effect of microwave-assisted hybrid chemical approach synthetic protocol on microbial and cytotoxicity. The results showed that TNP has the best antibacterial activity in decreasing order from Escherichia coli, Bacillus subtilis, and Staphylococcus aureus. The IC50 values of TNP for HCT116 and A549 were found to be 6.43 and 6.04 ppm, respectively. Cell death was also confirmed from trypan blue exclusion assay and membrane integrity loss was observed. Therefore, the study determines that the microwave-assisted hybrid chemical approach is time-saving; hence, this technique can be upgraded from lab scale to industrial scale via pilot plant scale. Moreover, it is necessary to find the mechanism of action at the molecular level to establish the reason for greater bacterial and cytotoxicological toxicity. Graphical abstract A graphical representation of TNP synthesis.

  15. Two Experiments to Approach the Boltzmann Factor: Chemical Reaction and Viscous Flow (United States)

    Fazio, Claudio; Battaglia, Onofrio R.; Guastella, Ivan


    In this paper we discuss a pedagogical approach aimed at pointing out the role played by the Boltzmann factor in describing phenomena usually perceived as regulated by different mechanisms of functioning. Experimental results regarding some aspects of a chemical reaction and of the viscous flow of some liquids are analysed and described in terms…

  16. Improving Students' Chemical Literacy Levels on Thermochemical and Thermodynamics Concepts through a Context-Based Approach (United States)

    Cigdemoglu, Ceyhan; Geban, Omer


    The aim of this study was to delve into the effect of context-based approach (CBA) over traditional instruction (TI) on students' chemical literacy level related to thermochemical and thermodynamics concepts. Four eleventh-grade classes with 118 students in total taught by two teachers from a public high school in 2012 fall semester were enrolled…

  17. Continuum modeling an approach through practical examples

    CERN Document Server

    Muntean, Adrian


    This book develops continuum modeling skills and approaches the topic from three sides: (1) derivation of global integral laws together with the associated local differential equations, (2) design of constitutive laws and (3) modeling boundary processes. The focus of this presentation lies on many practical examples covering aspects such as coupled flow, diffusion and reaction in porous media or microwave heating of a pizza, as well as traffic issues in bacterial colonies and energy harvesting from geothermal wells. The target audience comprises primarily graduate students in pure and applied mathematics as well as working practitioners in engineering who are faced by nonstandard rheological topics like those typically arising in the food industry.

  18. Interfacial Fluid Mechanics A Mathematical Modeling Approach

    CERN Document Server

    Ajaev, Vladimir S


    Interfacial Fluid Mechanics: A Mathematical Modeling Approach provides an introduction to mathematical models of viscous flow used in rapidly developing fields of microfluidics and microscale heat transfer. The basic physical effects are first introduced in the context of simple configurations and their relative importance in typical microscale applications is discussed. Then,several configurations of importance to microfluidics, most notably thin films/droplets on substrates and confined bubbles, are discussed in detail.  Topics from current research on electrokinetic phenomena, liquid flow near structured solid surfaces, evaporation/condensation, and surfactant phenomena are discussed in the later chapters. This book also:  Discusses mathematical models in the context of actual applications such as electrowetting Includes unique material on fluid flow near structured surfaces and phase change phenomena Shows readers how to solve modeling problems related to microscale multiphase flows Interfacial Fluid Me...

  19. The Coupled Chemical and Physical Dynamics Model of MALDI (United States)

    Knochenmuss, Richard


    The coupled physical and chemical dynamics model of ultraviolet matrix-assisted laser desorption/ionization (MALDI) has reproduced and explained a wide variety of MALDI phenomena. The rationale behind and elements of the model are reviewed, including the photophysics, kinetics, and thermodynamics of primary and secondary reaction steps. Experimental results are compared with model predictions to illustrate the foundations of the model, coupling of ablation and ionization, differences between and commonalities of matrices, secondary charge transfer reactions, ionization in both polarities, fluence and concentration dependencies, and suppression and enhancement effects.

  20. Determination of contact maps in proteins: A combination of structural and chemical approaches

    Energy Technology Data Exchange (ETDEWEB)

    Wołek, Karol; Cieplak, Marek, E-mail: [Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw (Poland); Gómez-Sicilia, Àngel [Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), Av. Doctor Arce, 37, 28002 Madrid (Spain); Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), C/Faraday 9, 28049 Cantoblanco (Madrid) (Spain)


    Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones — a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles.

  1. Chemical treatment of the intra-canal dentin surface: a new approach to modify dentin hydrophobicity

    Directory of Open Access Journals (Sweden)



    Full Text Available Objective This study evaluated the hydrophobicity of dentin surfaces that were modified through chemical silanization with octadecyltrichlorosilane (OTS. Material and Methods An in vitro experimental study was performed using 40 human permanent incisors that were divided into the following two groups: non-silanized and silanized. The specimens were pretreated and chemically modified with OTS. After the chemical modification, the dentin hydrophobicity was examined using a water contact angle measurement (WCA. The effectiveness of the modification of hydrophobicity was verified by the fluid permeability test (FPT. Results and Conclusions Statistically significant differences were found in the values of WCA and FPT between the two groups. After silanization, the hydrophobic intraradicular dentin surface exhibited in vitro properties that limit fluid penetration into the sealed root canal. This chemical treatment is a new approach for improving the sealing of the root canal system.

  2. Evolutionary modeling-based approach for model errors correction (United States)

    Wan, S. Q.; He, W. P.; Wang, L.; Jiang, W.; Zhang, W.


    The inverse problem of using the information of historical data to estimate model errors is one of the science frontier research topics. In this study, we investigate such a problem using the classic Lorenz (1963) equation as a prediction model and the Lorenz equation with a periodic evolutionary function as an accurate representation of reality to generate "observational data." On the basis of the intelligent features of evolutionary modeling (EM), including self-organization, self-adaptive and self-learning, the dynamic information contained in the historical data can be identified and extracted by computer automatically. Thereby, a new approach is proposed to estimate model errors based on EM in the present paper. Numerical tests demonstrate the ability of the new approach to correct model structural errors. In fact, it can actualize the combination of the statistics and dynamics to certain extent.

  3. A retroductive theoretical model of the pathway to chemical dependency in nurses. (United States)

    Burns, C M


    Much of the research on chemical dependency in nurses over the past 25 years has been a-theoretical and has tended to focus on descriptive characteristics of nurses. This field of study lacks systematic knowledge building and a useful theoretical base. This article focuses on the development of a middle range theory that begins to explicate the transactions of the chemically dependent nurse with the environment and the process through which nurses become addicted. Steiner's theory models approach using retroductive inference was the method selected to develop the theory. Theoretical work from Bandura, Jessor, and Pender were used as source theories to develop the middle range theory presented.

  4. Hydration of Portoguese cements, measurement and modelling of chemical shrinkage

    DEFF Research Database (Denmark)

    Maia, Lino; Geiker, Mette Rica; Figueiras, Joaquim A.


    form of the dispersion model. The development of hydration varied between the investigated cements; based on the measured data the degree of hydration after 24 h hydration at 20 C varied between 40 and 50%. This should be taken into account when comparing properties of concrete made from the different......Development of cement hydration was studied by measuring the chemical shrinkage of pastes. Five types of Portuguese Portland cement were used in cement pastes with . Chemical shrinkage was measured by gravimetry and dilatometry. In gravimeters results were recorded automatically during at least...

  5. Comparison of the 'chemical' and 'structural' approaches to the optimization of the thrombin-binding aptamer.

    Directory of Open Access Journals (Sweden)

    Olga Tatarinova

    Full Text Available Noncanonically structured DNA aptamers to thrombin were examined. Two different approaches were used to improve stability, binding affinity and biological activity of a known thrombin-binding aptamer. These approaches are chemical modification and the addition of a duplex module to the aptamer core structure. Several chemically modified aptamers and the duplex-bearing ones were all studied under the same conditions by a set of widely known and some relatively new methods. A number of the thrombin-binding aptamer analogs have demonstrated improved characteristics. Most importantly, the study allowed us to compare directly the two approaches to aptamer optimization and to analyze their relative advantages and disadvantages as well as their potential in drug design and fundamental studies.

  6. SDG-based Model Validation in Chemical Process Simulation

    Institute of Scientific and Technical Information of China (English)

    张贝克; 许欣; 马昕; 吴重光


    Signed direct graph (SDG) theory provides algorithms and methods that can be applied directly to chemical process modeling and analysis to validate simulation models, and is a basis for the development of a soft-ware environment that can automate the validation activity. This paper is concentrated on the pretreatment of the model validation. We use the validation scenarios and standard sequences generated by well-established SDG model to validate the trends fitted from the simulation model. The results are helpful to find potential problems, as-sess possible bugs in the simulation model and solve the problem effectively. A case study on a simulation model of boiler is presented to demonstrate the effectiveness of this method.

  7. Property Modelling for Applications in Chemical Product and Process Design

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    , polymers, mixtures as well as separation processes. The presentation will highlight the framework (ICAS software) for property modeling, the property models and issues such as prediction accuracy, flexibility, maintenance and updating of the database. Also, application issues related to the use of property......, they are not always available. Also, it may be too expensive to measure them or it may take too much time. In these situations and when repetitive calculations are involved (as in process simulation), it is useful to have appropriate models to reliably predict the needed properties. A collection of methods tools...... such as database, property model library, model parameter regression, and, property-model based product-process design will be presented. The database contains pure component and mixture data for a wide range of organic chemicals. The property models are based on the combined group contribution and atom...

  8. Regularization of turbulence - a comprehensive modeling approach (United States)

    Geurts, B. J.


    Turbulence readily arises in numerous flows in nature and technology. The large number of degrees of freedom of turbulence poses serious challenges to numerical approaches aimed at simulating and controlling such flows. While the Navier-Stokes equations are commonly accepted to precisely describe fluid turbulence, alternative coarsened descriptions need to be developed to cope with the wide range of length and time scales. These coarsened descriptions are known as large-eddy simulations in which one aims to capture only the primary features of a flow, at considerably reduced computational effort. Such coarsening introduces a closure problem that requires additional phenomenological modeling. A systematic approach to the closure problem, know as regularization modeling, will be reviewed. Its application to multiphase turbulent will be illustrated in which a basic regularization principle is enforced to physically consistently approximate momentum and scalar transport. Examples of Leray and LANS-alpha regularization are discussed in some detail, as are compatible numerical strategies. We illustrate regularization modeling to turbulence under the influence of rotation and buoyancy and investigate the accuracy with which particle-laden flow can be represented. A discussion of the numerical and modeling errors incurred will be given on the basis of homogeneous isotropic turbulence.

  9. Nonlocal Nambu-Jona-Lasinio model and chiral chemical potential

    CERN Document Server

    Frasca, Marco


    We derive the critical temperature in a nonlocal Nambu-Jona-Lasinio model with the presence of a chiral chemical potential. The model we consider uses a form factor derived from recent studies of the gluon propagator in Yang-Mills theory and has the property to fit in excellent way the form factor arising from the instanton liquid picture for the vacuum of the theory. Nambu-Jona-Lasinio model is derived form quantum chromodynamics providing all the constants of the theory without any need for fits. We show that the critical temperature in this case always exists and increases as the square of the chiral chemical potential. The expression we obtain for the critical temperature depends on the mass gap that naturally arises from Yang-Mills theory at low-energy as also confirmed by lattice computations.

  10. The chemical bond in inorganic chemistry the bond valence model

    CERN Document Server

    Brown, I David


    The bond valence model is a version of the ionic model in which the chemical constraints are expressed in terms of localized chemical bonds formed by the valence charge of the atoms. Theorems derived from the properties of the electrostatic flux predict the rules obeyed by both ionic and covalent bonds. They make quantitative predictions of coordination number, crystal structure, bond lengths and bond angles. Bond stability depends on the matching of the bonding strengths of the atoms, while the conflicting requirements of chemistry and space lead to the structural instabilities responsible for the unusual physical properties displayed by some materials. The model has applications in many fields ranging from mineralogy to molecular biology.

  11. A scalable machine-learning approach to recognize chemical names within large text databases

    Directory of Open Access Journals (Sweden)

    Wren Jonathan D


    Full Text Available Abstract Motivation The use or study of chemical compounds permeates almost every scientific field and in each of them, the amount of textual information is growing rapidly. There is a need to accurately identify chemical names within text for a number of informatics efforts such as database curation, report summarization, tagging of named entities and keywords, or the development/curation of reference databases. Results A first-order Markov Model (MM was evaluated for its ability to distinguish chemical names from words, yielding ~93% recall in recognizing chemical terms and ~99% precision in rejecting non-chemical terms on smaller test sets. However, because total false-positive events increase with the number of words analyzed, the scalability of name recognition was measured by processing 13.1 million MEDLINE records. The method yielded precision ranges from 54.7% to 100%, depending upon the cutoff score used, averaging 82.7% for approximately 1.05 million putative chemical terms extracted. Extracted chemical terms were analyzed to estimate the number of spelling variants per term, which correlated with the total number of times the chemical name appeared in MEDLINE. This variability in term construction was found to affect both information retrieval and term mapping when using PubMed and Ovid.

  12. A Modified Approach for Calculating Dressed Quark Propagator at Finite Chemical Potential

    Institute of Scientific and Technical Information of China (English)


    Based on the rainbow approximation of Dyson-Schwinger equation and the assumption that the full inverse quark propagator at finite chemical potential is analytic in the neighborhood of μ = 0, it is proved that the dressed From the dressed quark propagator at finite chemical potential μ can be written as (g0-1)[μ]=iγ·(p~)A((p~2))+B((p~2))with (p~)μ=((p),p4+iμ).From the dressed quark propagator at finite chemical potential in Munczek model the bag constant of a baryon and the scalar quark condensate are evaluated. A comparison with previous results is given.

  13. A moni-modelling approach to manage groundwater risk to pesticide leaching at regional scale. (United States)

    Di Guardo, Andrea; Finizio, Antonio


    Historically, the approach used to manage risk of chemical contamination of water bodies is based on the use of monitoring programmes, which provide a snapshot of the presence/absence of chemicals in water bodies. Monitoring is required in the current EU regulations, such as the Water Framework Directive (WFD), as a tool to record temporal variation in the chemical status of water bodies. More recently, a number of models have been developed and used to forecast chemical contamination of water bodies. These models combine information of chemical properties, their use, and environmental scenarios. Both approaches are useful for risk assessors in decision processes. However, in our opinion, both show flaws and strengths when taken alone. This paper proposes an integrated approach (moni-modelling approach) where monitoring data and modelling simulations work together in order to provide a common decision framework for the risk assessor. This approach would be very useful, particularly for the risk management of pesticides at a territorial level. It fulfils the requirement of the recent Sustainable Use of Pesticides Directive. In fact, the moni-modelling approach could be used to identify sensible areas where implement mitigation measures or limitation of use of pesticides, but even to effectively re-design future monitoring networks or to better calibrate the pedo-climatic input data for the environmental fate models. A case study is presented, where the moni-modelling approach is applied in Lombardy region (North of Italy) to identify groundwater vulnerable areas to pesticides. The approach has been applied to six active substances with different leaching behaviour, in order to highlight the advantages in using the proposed methodology.

  14. A Coupled Transport and Chemical Model for Durability Predictions of Cement Based Materials

    DEFF Research Database (Denmark)

    Jensen, Mads Mønster; Johannesson, Björn; Geiker, Mette Rica;

    initial and exposure conditions. Different numerical calcium silicate hydrate reaction approaches are studied and reactive transport modeling results using these are compared. Modeling results of ion ingress are compared with experimental results where mortar samples has been exposed to a NaCl solution...... are coupled by a sorption hysteresis function and the chemical equilibrium is solved in terms of mass actions laws using the geochemical code phreeqc. The overall durability model accounts for, ion diffusion, ion migration, two phase moisture transport including for hysteresis, ionic convection and chemical...... of the algorithm established. A calculated test example shows the model response to varying vapor content at the boundary, where saturated conditions occurs in periods and leaching of ions is only allowed in this period. The effect of the sorption hysteresis function is demonstrated in this test by a comparison...


    Directory of Open Access Journals (Sweden)

    H. Sadeq


    Full Text Available In this research different DSMs from different sources have been merged. The merging is based on a probabilistic model using a Bayesian Approach. The implemented data have been sourced from very high resolution satellite imagery sensors (e.g. WorldView-1 and Pleiades. It is deemed preferable to use a Bayesian Approach when the data obtained from the sensors are limited and it is difficult to obtain many measurements or it would be very costly, thus the problem of the lack of data can be solved by introducing a priori estimations of data. To infer the prior data, it is assumed that the roofs of the buildings are specified as smooth, and for that purpose local entropy has been implemented. In addition to the a priori estimations, GNSS RTK measurements have been collected in the field which are used as check points to assess the quality of the DSMs and to validate the merging result. The model has been applied in the West-End of Glasgow containing different kinds of buildings, such as flat roofed and hipped roofed buildings. Both quantitative and qualitative methods have been employed to validate the merged DSM. The validation results have shown that the model was successfully able to improve the quality of the DSMs and improving some characteristics such as the roof surfaces, which consequently led to better representations. In addition to that, the developed model has been compared with the well established Maximum Likelihood model and showed similar quantitative statistical results and better qualitative results. Although the proposed model has been applied on DSMs that were derived from satellite imagery, it can be applied to any other sourced DSMs.

  16. Merging Digital Surface Models Implementing Bayesian Approaches (United States)

    Sadeq, H.; Drummond, J.; Li, Z.


    In this research different DSMs from different sources have been merged. The merging is based on a probabilistic model using a Bayesian Approach. The implemented data have been sourced from very high resolution satellite imagery sensors (e.g. WorldView-1 and Pleiades). It is deemed preferable to use a Bayesian Approach when the data obtained from the sensors are limited and it is difficult to obtain many measurements or it would be very costly, thus the problem of the lack of data can be solved by introducing a priori estimations of data. To infer the prior data, it is assumed that the roofs of the buildings are specified as smooth, and for that purpose local entropy has been implemented. In addition to the a priori estimations, GNSS RTK measurements have been collected in the field which are used as check points to assess the quality of the DSMs and to validate the merging result. The model has been applied in the West-End of Glasgow containing different kinds of buildings, such as flat roofed and hipped roofed buildings. Both quantitative and qualitative methods have been employed to validate the merged DSM. The validation results have shown that the model was successfully able to improve the quality of the DSMs and improving some characteristics such as the roof surfaces, which consequently led to better representations. In addition to that, the developed model has been compared with the well established Maximum Likelihood model and showed similar quantitative statistical results and better qualitative results. Although the proposed model has been applied on DSMs that were derived from satellite imagery, it can be applied to any other sourced DSMs.

  17. Chemical, spectroscopic, and ab initio modelling approach to interfacial reactivity applied to anion retention by siderite; Approche couplee chimique, spectroscopique et de modelisation ab initio a la reactivite de surface: application a la retention des anions par la siderite

    Energy Technology Data Exchange (ETDEWEB)

    Badaut, V.


    Among the many radionuclides contained in high-level nuclear waste, {sup 79}Se was identified as a potential threat to the safety of long term underground storage. However, siderite (FeCO{sub 3}) is known to form upon corrosion of the waste container, and the impact of this mineral on the fate of selenium was not accounted for. In this work, the interactions between selenium oxyanions - selenate and selenite - and siderite were investigated. To this end, both experimental characterizations (solution chemistry, X-ray Absorption Spectroscopy - XAS) and theoretical studies (ab initio modelling using Density Functional Theory - DFT) were performed. Selenite and selenate ({<=} 10{sup 3} M) retention experiments by siderite suspensions (75 g/L) at neutral pH in reducing glovebox (5 % H{sub 2}) showed that selenite is quantitatively immobilized by siderite after 48 h of reaction time, when selenate is only partly immobilized after 10 days. In the selenite case, XAS showed that immobilized selenium is initially present as Se(IV) probably sorbed on siderite surface. After 10 days of reaction, selenite ions are quantitatively reduced and form poorly crystalline elementary selenium. Selenite retention and reduction kinetics are therefore distinct. On the other hand, the fraction of immobilized selenate retained in the solid fraction does not appear to be significantly reduced over the probed timescale (10 days). For a better understanding of the reduction mechanism of selenite ions by siderite, the properties of bulk and perfect surfaces of siderite were modelled using DFT. We suggest that the properties of the valence electrons can be correctly described only if the symmetry of the fundamental state electronic density is lower than the experimental crystallographic symmetry. We then show that the retention of simple molecules as O{sub 2} or H{sub 2}O on siderite and magnesite (10{sup -14}) perfect surfaces (perfect cleavage plane, whose surface energy is the lowest according

  18. A new approach for Bayesian model averaging

    Institute of Scientific and Technical Information of China (English)

    TIAN XiangJun; XIE ZhengHui; WANG AiHui; YANG XiaoChun


    Bayesian model averaging (BMA) is a recently proposed statistical method for calibrating forecast ensembles from numerical weather models.However,successful implementation of BMA requires accurate estimates of the weights and variances of the individual competing models in the ensemble.Two methods,namely the Expectation-Maximization (EM) and the Markov Chain Monte Carlo (MCMC) algorithms,are widely used for BMA model training.Both methods have their own respective strengths and weaknesses.In this paper,we first modify the BMA log-likelihood function with the aim of removing the additional limitation that requires that the BMA weights add to one,and then use a limited memory quasi-Newtonian algorithm for solving the nonlinear optimization problem,thereby formulating a new approach for BMA (referred to as BMA-BFGS).Several groups of multi-model soil moisture simulation experiments from three land surface models show that the performance of BMA-BFGS is similar to the MCMC method in terms of simulation accuracy,and that both are superior to the EM algorithm.On the other hand,the computational cost of the BMA-BFGS algorithm is substantially less than for MCMC and is almost equivalent to that for EM.

  19. Genetic Algorithm Approaches to Prebiobiotic Chemistry Modeling (United States)

    Lohn, Jason; Colombano, Silvano


    We model an artificial chemistry comprised of interacting polymers by specifying two initial conditions: a distribution of polymers and a fixed set of reversible catalytic reactions. A genetic algorithm is used to find a set of reactions that exhibit a desired dynamical behavior. Such a technique is useful because it allows an investigator to determine whether a specific pattern of dynamics can be produced, and if it can, the reaction network found can be then analyzed. We present our results in the context of studying simplified chemical dynamics in theorized protocells - hypothesized precursors of the first living organisms. Our results show that given a small sample of plausible protocell reaction dynamics, catalytic reaction sets can be found. We present cases where this is not possible and also analyze the evolved reaction sets.

  20. Expanding the applicability of multimedia fate models to polar organic chemicals. (United States)

    Breivik, Knut; Wania, Frank


    Reliable estimates of environmental phase partitioning are essential for accurate predictions of the environmental fate of organic chemicals. Current fate and transport models use single-parameter linear free energy relationships (SP-LFERs) to quantify equilibrium phase partitioning. The applicability of such SP-LFERs is limited because no single parameter is able to describe appropriately all the molecular interactions that contribute to environmental phase distribution processes. Environmental partitioning coefficients predicted by SP-LFERs may thus have errors of up to an order of magnitude. Ranges for several environmental partitioning equilibria are identified, where such errors can result in significantly different fate predictions for individual bulk model compartments. We propose that it is possible to reduce such errors and uncertainties by implementing polyparametric LFER (PP-LFER) approaches in multimedia fate models. A level III fugacity model was modified such that the partitioning properties of chemicals are characterized by five linear solvation energy parameters rather than vapor pressure, water solubility, and octanol-water partition coefficient. A comparison of modified and unmodified models for a set of organic chemicals shows that the approach chosen to simulate environmental phase partitioning can have a large impact on model results, including long-range transport potential, overall persistence, and concentrations in various media. It is argued that PP-LFER based environmental fate models are applicable to a much wider range of organic substances, in particular those with polar functional groups. Obstacles to the full implementation of PP-LFER in multimedia fate models are currently the lack of solute descriptors for some chemicals of environmental concern and suitable regression equations for some important environmental phase equilibria, in particular for the partitioning between gas and particle phase in the atmosphere.

  1. 2-D Chemical-Dynamical Modeling of Venus's Sulfur Variability (United States)

    Bierson, Carver J.; Zhang, Xi


    Over the last decade a combination of ground based and Venus Express observations have been made of the concentration of sulfur species in Venus's atmosphere, both above [1, 2] and below the clouds [3, 4]. These observations put constraints on both the vertical and meridional variations of the major sulfur species in Venus's atmosphere.. It has also been observed that SO2 concentrations varies on both timescales of hours and years [1,4]. The spatial and temporal distribution of tracer species is owing to two possibilities: mutual chemical interaction and dynamical tracer transport.Previous Chemical modeling of Venus's middle atmosphere has only been explored in 1-D. We will present the first 2-D (altitude and latitude) chemical-dynamical model for Venus's middle atmosphere. The sulfur chemistry is based on of the 1D model of Zhang et al. 2012 [5]. We do model runs over multiple Venus decades testing two scenarios: first one with varying sulfur fluxes from below, and second with secular dynamical perturbations in the atmosphere [6]. By comparing to Venus Express and ground based observations, we put constraints on the dynamics of Venus's middle atmosphere.References: [1] Belyaev et al. Icarus 2012 [2] Marcq et al. Nature geoscience, 2013 [3] Marcq et al. JGR:Planets, 2008 [4] Arney et al. JGR:Planets, 2014 [5] Zhang et al. Icarus 2012 [6] Parish et al. Icarus 2012

  2. Developing a multimedia model of chemical dynamics in an urban area. (United States)

    Diamond, M L; Priemer, D A; Law, N L


    A multimedia model has been developed to account for the movement of semi-volatile organic compounds (SOCs) in an urban environment. The model, based on a Level III fugacity model of D. Mackay (Multimedia Environmental Models: The Fugacity Approach, Lewis Publishers, Boca Raton, FL, 1991), consists of six compartments: air, surface water, sediment, soil, vegetation, and an organic film that coats impervious surfaces. The latter is a newly identified compartment into which gas-phase SOCs partition and particle-phase SOCs are believed to be efficiently captured (M.L. Diamond, S.E. Gingrich, K. Fertuck, B.E. McCarry, G.A. Stern, B. Billeck, B. Grift, D. Brooker, T.D. Yager, Environ. Sci. Technol., 34 (2000a), 2900-2908). The model, parameterized for downtown Toronto, Ontario, Canada, and run with an illustrative emission rate for selected polycyclic aromatic hydrocarbons and homologues of polychlorinated dibenzodioxins, indicates that the film achieves the highest concentrations among media but that soils are the greatest sink for all but the least hydrophobic chemicals. The film "reflects" the more volatile chemicals into air, facilitates removal to surface waters by wash-off, and provides a surface on which photolytic degradation can occur. As such, the film is a transient sink that increases chemical mobility in urban areas by increasing air concentrations and the cycling of these compounds between air and urban surfaces and increasing water concentrations. Vegetation also accumulates SOCs, a portion of which is transferred to soil that reduces chemical mobility.

  3. A stepwise approach for defining the applicability domain of SAR and QSAR models

    DEFF Research Database (Denmark)

    Dimitrov, Sabcho; Dimitrova, Gergana; Pavlov, Todor;


    parametric requirements are imposed in the first stage, specifying in the domain only those chemicals that fall in the range of variation of the physicochemical properties of the chemicals in the training set. The second stage defines the structural similarity between chemicals that are correctly predicted......A stepwise approach for determining the model applicability domain is proposed. Four stages are applied to account for the diversity and complexity of the current SAR/QSAR models, reflecting their mechanistic rationality (including metabolic activation of chemicals) and transparency. General...... by the model. The structural neighborhood of atom-centered fragments is used to determine this similarity. The third stage in defining the domain is based on a mechanistic understanding of the modeled phenomenon. Here, the model domain combines the reliability of specific reactive groups hypothesized to cause...

  4. Economic model predictive control theory, formulations and chemical process applications

    CERN Document Server

    Ellis, Matthew; Christofides, Panagiotis D


    This book presents general methods for the design of economic model predictive control (EMPC) systems for broad classes of nonlinear systems that address key theoretical and practical considerations including recursive feasibility, closed-loop stability, closed-loop performance, and computational efficiency. Specifically, the book proposes: Lyapunov-based EMPC methods for nonlinear systems; two-tier EMPC architectures that are highly computationally efficient; and EMPC schemes handling explicitly uncertainty, time-varying cost functions, time-delays and multiple-time-scale dynamics. The proposed methods employ a variety of tools ranging from nonlinear systems analysis, through Lyapunov-based control techniques to nonlinear dynamic optimization. The applicability and performance of the proposed methods are demonstrated through a number of chemical process examples. The book presents state-of-the-art methods for the design of economic model predictive control systems for chemical processes. In addition to being...

  5. Computer-Aided Construction of Chemical Kinetic Models

    Energy Technology Data Exchange (ETDEWEB)

    Green, William H. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)


    The combustion chemistry of even simple fuels can be extremely complex, involving hundreds or thousands of kinetically significant species. The most reasonable way to deal with this complexity is to use a computer not only to numerically solve the kinetic model, but also to construct the kinetic model in the first place. Because these large models contain so many numerical parameters (e.g. rate coefficients, thermochemistry) one never has sufficient data to uniquely determine them all experimentally. Instead one must work in “predictive” mode, using theoretical rather than experimental values for many of the numbers in the model, and as appropriate refining the most sensitive numbers through experiments. Predictive chemical kinetics is exactly what is needed for computer-aided design of combustion systems based on proposed alternative fuels, particularly for early assessment of the value and viability of proposed new fuels before those fuels are commercially available. This project was aimed at making accurate predictive chemical kinetics practical; this is a challenging goal which requires a range of science advances. The project spanned a wide range from quantum chemical calculations on individual molecules and elementary-step reactions, through the development of improved rate/thermo calculation procedures, the creation of algorithms and software for constructing and solving kinetic simulations, the invention of methods for model-reduction while maintaining error control, and finally comparisons with experiment. Many of the parameters in the models were derived from quantum chemistry calculations, and the models were compared with experimental data measured in our lab or in collaboration with others.

  6. Nuclear level density: Shell-model approach (United States)

    Sen'kov, Roman; Zelevinsky, Vladimir


    Knowledge of the nuclear level density is necessary for understanding various reactions, including those in the stellar environment. Usually the combinatorics of a Fermi gas plus pairing is used for finding the level density. Recently a practical algorithm avoiding diagonalization of huge matrices was developed for calculating the density of many-body nuclear energy levels with certain quantum numbers for a full shell-model Hamiltonian. The underlying physics is that of quantum chaos and intrinsic thermalization in a closed system of interacting particles. We briefly explain this algorithm and, when possible, demonstrate the agreement of the results with those derived from exact diagonalization. The resulting level density is much smoother than that coming from conventional mean-field combinatorics. We study the role of various components of residual interactions in the process of thermalization, stressing the influence of incoherent collision-like processes. The shell-model results for the traditionally used parameters are also compared with standard phenomenological approaches.

  7. Pedagogic process modeling: Humanistic-integrative approach

    Directory of Open Access Journals (Sweden)

    Boritko Nikolaj M.


    Full Text Available The paper deals with some current problems of modeling the dynamics of the subject-features development of the individual. The term "process" is considered in the context of the humanistic-integrative approach, in which the principles of self education are regarded as criteria for efficient pedagogic activity. Four basic characteristics of the pedagogic process are pointed out: intentionality reflects logicality and regularity of the development of the process; discreteness (stageability in dicates qualitative stages through which the pedagogic phenomenon passes; nonlinearity explains the crisis character of pedagogic processes and reveals inner factors of self-development; situationality requires a selection of pedagogic conditions in accordance with the inner factors, which would enable steering the pedagogic process. Offered are two steps for singling out a particular stage and the algorithm for developing an integrative model for it. The suggested conclusions might be of use for further theoretic research, analyses of educational practices and for realistic predicting of pedagogical phenomena. .

  8. Modeling Social Annotation: a Bayesian Approach

    CERN Document Server

    Plangprasopchok, Anon


    Collaborative tagging systems, such as, CiteULike, and others, allow users to annotate objects, e.g., Web pages or scientific papers, with descriptive labels called tags. The social annotations, contributed by thousands of users, can potentially be used to infer categorical knowledge, classify documents or recommend new relevant information. Traditional text inference methods do not make best use of socially-generated data, since they do not take into account variations in individual users' perspectives and vocabulary. In a previous work, we introduced a simple probabilistic model that takes interests of individual annotators into account in order to find hidden topics of annotated objects. Unfortunately, our proposed approach had a number of shortcomings, including overfitting, local maxima and the requirement to specify values for some parameters. In this paper we address these shortcomings in two ways. First, we extend the model to a fully Bayesian framework. Second, we describe an infinite ver...

  9. Studies on modelling of bubble driven flows in chemical reactors

    Energy Technology Data Exchange (ETDEWEB)

    Grevskott, Sverre


    Multiphase reactors are widely used in the process industry, especially in the petrochemical industry. They very often are characterized by very good thermal control and high heat transfer coefficients against heating and cooling surfaces. This thesis first reviews recent advances in bubble column modelling, focusing on the fundamental flow equations, drag forces, transversal forces and added mass forces. The mathematical equations for the bubble column reactor are developed, using an Eulerian description for the continuous and dispersed phase in tensor notation. Conservation equations for mass, momentum, energy and chemical species are given, and the k-{epsilon} and Rice-Geary models for turbulence are described. The different algebraic solvers used in the model are described, as are relaxation procedures. Simulation results are presented and compared with experimental values. Attention is focused on the modelling of void fractions and gas velocities in the column. The energy conservation equation has been included in the bubble column model in order to model temperature distributions in a heated reactor. The conservation equation of chemical species has been included to simulate absorption of CO{sub 2}. Simulated axial and radial mass fraction profiles for CO{sub 2} in the gas phase are compared with measured values. Simulations of the dynamic behaviour of the column are also presented. 189 refs., 124 figs., 1 tab.

  10. Chemical modeling of water deuteration in IRAS16293-2422

    CERN Document Server

    Wakelam, V; Aikawa, Y; Coutens, A; Bottinelli, S; Caux, E


    IRAS 16293-2422 is a well studied low-mass protostar characterized by a strong level of deuterium fractionation. In the line of sight of the protostellar envelope, an additional absorption layer, rich in singly and doubly deuterated water has been discovered by a detailed multiline analysis of HDO. To model the chemistry in this source, the gas-grain chemical code Nautilus has been used with an extended deuterium network. For the protostellar envelope, we solve the chemical reaction network in infalling fluid parcels in a protostellar core model. For the foreground cloud, we explored several physical conditions (density, cosmic ionization rate, C/O ratio). The main results of the paper are that gas-phase abundances of H2O, HDO and D2O observed in the inner regions of IRAS16293-2422 are lower than those predicted by a 1D dynamical/chemical (hot corino) model in which the ices are fully evaporated. The abundance in the outer part of the envelope present chaotic profiles due to adsorption/evaporation competition...

  11. Probabilistic consequence model of accidenal or intentional chemical releases.

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Y.-S.; Samsa, M. E.; Folga, S. M.; Hartmann, H. M.


    In this work, general methodologies for evaluating the impacts of large-scale toxic chemical releases are proposed. The potential numbers of injuries and fatalities, the numbers of hospital beds, and the geographical areas rendered unusable during and some time after the occurrence and passage of a toxic plume are estimated on a probabilistic basis. To arrive at these estimates, historical accidental release data, maximum stored volumes, and meteorological data were used as inputs into the SLAB accidental chemical release model. Toxic gas footprints from the model were overlaid onto detailed population and hospital distribution data for a given region to estimate potential impacts. Output results are in the form of a generic statistical distribution of injuries and fatalities associated with specific toxic chemicals and regions of the United States. In addition, indoor hazards were estimated, so the model can provide contingency plans for either shelter-in-place or evacuation when an accident occurs. The stochastic distributions of injuries and fatalities are being used in a U.S. Department of Homeland Security-sponsored decision support system as source terms for a Monte Carlo simulation that evaluates potential measures for mitigating terrorist threats. This information can also be used to support the formulation of evacuation plans and to estimate damage and cleanup costs.

  12. Universal Electrochemical/Chemical Simulator Based on an Exponentially Expanding Grid Network Approach

    Institute of Scientific and Technical Information of China (English)

    DENG,Zhao-Xiang(邓兆祥); LIN,Xiang-Qin(林祥钦); TONG,Zhong-Hua(童中华)


    A universal simulator capable of simulating virtually any user-defined electrochemical/chemical problems in one-dimensional diffusion geometry was developed based on an exponentially expanding grid modification of the existing network approach. Some generalized reaction-diffusion governing equations of an arbitrary electrochemical/chemical process were derived, and program controlled automatic generation of the corresponding PSPICE netlist file was realized. On the basis of the above techniques, a universal simulator package was realized, which is capable of dealing with arbitrarily complex electrochemical/chemical problems with one-dimensional diffusion geometry such as planar diffusion, spherical diffusion, cylindrical diffusion and rotational disk diffusion-convection processes. The building of such a simulator is easy and thus it would be very convenient to have it updated for simulations of newly raised electrochemical problems.

  13. Enhancing sewage sludge dewaterability by bioleaching approach with comparison to other physical and chemical conditioning methods

    Institute of Scientific and Technical Information of China (English)

    Fenwu Liu; Jun Zhou; Dianzhan Wang; Lixiang Zhou


    The sewage sludge conditioning process is critical to improve the sludge dewaterability prior to mechanical dewatering.Traditionally,sludge is conditioned by physical or chemical approaches,mostly with the addition of inorganic or organic chemicals.Here we report that bioleaching,an efficient and economical microbial method for the removal of sludge-borne heavy metals,also plays a significant role in enhancing sludge dewaterability.The effects of bioleaching and physical or chemical approaches on sludge dewaterability were compared.The conditioning result of bioleaching by Acidithiobacillus thiooxidans and Acidithiobacillus ferrooxidans on sludge dewatering was investigated and compared with the effects of hydrothermal(121 ℃ for 2 hr),microwave(1050 W for 50 sec),ultrasonic (250 W for 2 min),and chemical conditioning(24% ferric chloride and 68% calcium oxide; dry basis).The results show that the specific resistance to filtration(SRF)or capillary suction time(CST)of sludge is decreased by 93.1% or 74.1%,respectively,after fresh sludge is conditioned by bioleaching,which is similar to chemical conditioning treatment with ferric chloride and calcium oxide but much more effective than other conditioning approaches including hydrothermal,microwave,and ultrasonic conditioning.Furthermore,after sludge dewatering,bioleached sludge filtrate contains the lowest concentrations of chroma(18 times),COD(542 mg/L),total N(TN,300 mg/L),NH4+-N(208 mg/L),and total P(TP,2 mg/L)while the hydrothermal process resulted in the highest concentration of chroma(660 times),COD(18,155 mg/L),TN(472 mg/L),NH4+-N(381 mg/L),and TP(191 mg/L)among these selected conditioning methods.Moreover,unlike chemical conditioning,sludge bioleaching does not result in a significant reduction of organic matter,TN,and TP in the resulting dewatered sludge cake.Therefore,considering sludge dewaterability and the chemical properties of sludge filtrate and resulting dewatered sludge cakes,bioleaching has

  14. An Informatics Approach to Evaluating Combined Chemical Exposures from Consumer Products: A Case Study of Asthma-Associated Chemicals and Potential Endocrine Disruptors (United States)

    Gabb, Henry A.; Blake, Catherine


    Background: Simultaneous or sequential exposure to multiple environmental stressors can affect chemical toxicity. Cumulative risk assessments consider multiple stressors but it is impractical to test every chemical combination to which people are exposed. New methods are needed to prioritize chemical combinations based on their prevalence and possible health impacts. Objectives: We introduce an informatics approach that uses publicly available data to identify chemicals that co-occur in consumer products, which account for a significant proportion of overall chemical load. Methods: Fifty-five asthma-associated and endocrine disrupting chemicals (target chemicals) were selected. A database of 38,975 distinct consumer products and 32,231 distinct ingredient names was created from online sources, and PubChem and the Unified Medical Language System were used to resolve synonymous ingredient names. Synonymous ingredient names are different names for the same chemical (e.g., vitamin E and tocopherol). Results: Nearly one-third of the products (11,688 products, 30%) contained ≥ 1 target chemical and 5,229 products (13%) contained > 1. Of the 55 target chemicals, 31 (56%) appear in ≥ 1 product and 19 (35%) appear under more than one name. The most frequent three-way chemical combination (2-phenoxyethanol, methyl paraben, and ethyl paraben) appears in 1,059 products. Further work is needed to assess combined chemical exposures related to the use of multiple products. Conclusions: The informatics approach increased the number of products considered in a traditional analysis by two orders of magnitude, but missing/incomplete product labels can limit the effectiveness of this approach. Such an approach must resolve synonymy to ensure that chemicals of interest are not missed. Commonly occurring chemical combinations can be used to prioritize cumulative toxicology risk assessments. Citation: Gabb HA, Blake C. 2016. An informatics approach to evaluating combined chemical

  15. Regimes of chemical reaction waves initiated by nonuniform initial conditions for detailed chemical reaction models. (United States)

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


    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.

  16. CADASTER QSPR Models for Predictions of Melting and Boiling Points of Perfluorinated Chemicals. (United States)

    Bhhatarai, Barun; Teetz, Wolfram; Liu, Tao; Öberg, Tomas; Jeliazkova, Nina; Kochev, Nikolay; Pukalov, Ognyan; Tetko, Igor V; Kovarich, Simona; Papa, Ester; Gramatica, Paola


    Quantitative structure property relationship (QSPR) studies on per- and polyfluorinated chemicals (PFCs) on melting point (MP) and boiling point (BP) are presented. The training and prediction chemicals used for developing and validating the models were selected from Syracuse PhysProp database and literatures. The available experimental data sets were split in two different ways: a) random selection on response value, and b) structural similarity verified by self-organizing-map (SOM), in order to propose reliable predictive models, developed only on the training sets and externally verified on the prediction sets. Individual linear and non-linear approaches based models developed by different CADASTER partners on 0D-2D Dragon descriptors, E-state descriptors and fragment based descriptors as well as consensus model and their predictions are presented. In addition, the predictive performance of the developed models was verified on a blind external validation set (EV-set) prepared using PERFORCE database on 15 MP and 25 BP data respectively. This database contains only long chain perfluoro-alkylated chemicals, particularly monitored by regulatory agencies like US-EPA and EU-REACH. QSPR models with internal and external validation on two different external prediction/validation sets and study of applicability-domain highlighting the robustness and high accuracy of the models are discussed. Finally, MPs for additional 303 PFCs and BPs for 271 PFCs were predicted for which experimental measurements are unknown.

  17. The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches

    DEFF Research Database (Denmark)

    Ugelvig, Line; Drijfhout, Falko; Kronauer, Daniel;


    BACKGROUND: The invasive garden ant, Lasius neglectus, is the most recently detected pest ant and the first known invasive ant able to become established and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct the invasion history of this ant in Europe analysing 14...... populations with three complementary approaches: genetic microsatellite analysis, chemical analysis of cuticular hydrocarbon profiles and behavioural observations of aggression behaviour. We evaluate the relative informative power of the three methodological approaches and estimate both the number...... of independent introduction events from a yet unknown native range somewhere in the Black Sea area, and the invasive potential of the existing introduced populations. RESULTS: Three clusters of genetically similar populations were detected, and all but one population had a similar chemical profile. Aggression...

  18. En route to a multi-model scheme for clinker comminution with chemical grinding aids

    CERN Document Server

    Mishra, R K; Carmona, H A; Wittel, F K; Sawley, M L; Weibel, M; Gallucci, E; Herrmann, H J; Heinz, H; Flatt, R J


    We present a multi-model simulation approach, targeted at understanding the behavior of comminution and the effect of grinding aids (GAs) in industrial cement mills. On the atomistic scale we use Molecular Dynamics (MD) simulations with validated force field models to quantify elastic and structural properties, cleavage energies as well as the organic interactions with mineral surfaces. Simulations based on the Discrete Element Method (DEM) are used to integrate the information gained from MD simulations into the clinker particle behavior at larger scales. Computed impact energy distributions from DEM mill simulations can serve as a link between large-scale industrial and laboratory sized mills. They also provide the required input for particle impact fragmentation models. Such a multi-scale, multi-model methodology paves the way for a structured approach to the design of chemical additives aimed at improving mill performance.

  19. Physical/chemical modeling for photovoltaic module life prediction (United States)

    Moacanin, J.; Carroll, W. F.; Gupta, A.


    The paper presents a generalized methodology for identification and evaluation of potential degradation and failure of terrestrial photovoltaic encapsulation. Failure progression modeling and an interaction matrix are utilized to complement the conventional approach to failure degradation mode identification. Comparison of the predicted performance based on these models can produce: (1) constraints on system or component design, materials or operating conditions, (2) qualification (predicted satisfactory function), and (3) uncertainty. The approach has been applied to an investigation of an unexpected delamination failure; it is being used to evaluate thermomechanical interactions in photovoltaic modules and to study corrosion of contacts and interconnects.

  20. A local chemical potential approach within the variable charge method formalism (United States)

    Elsener, A.; Politano, O.; Derlet, P. M.; Van Swygenhoven, H.


    A new and computationally efficient implementation of the variable charge method of Streitz and Mintmire (1994 Phys. Rev. B 50 11996) is presented. In particular a local chemical potential approach that optimizes the charge on only those atoms expected to be ionic is developed. By doing so, the charge fluctuation problem experienced in regions far from any oxygen is solved, leading to a linear minimization problem of the electrostatic energy. In the dilute oxygen limit, such an approach can lead to at least an order of magnitude saving in computation.

  1. The Instanton-Dyon Liquid Model III: Finite Chemical Potential

    CERN Document Server

    Liu, Yizhuang; Zahed, Ismail


    We discuss an extension of the instanton-dyon liquid model that includes light quarks at finite chemical potential in the center symmetric phase. We develop the model in details for the case of SU_c(2)\\times SU_f(2) by mapping the theory on a 3-dimensional quantum effective theory. We analyze the different phases in the mean-field approximation. We extend this analysis to the general case of SU_c(N_c)\\times SU_f(N_f) and note that the chiral and diquark pairings are always comparable.

  2. Effective Model Approach to the Dense State of QCD Matter

    CERN Document Server

    Fukushima, Kenji


    The first-principle approach to the dense state of QCD matter, i.e. the lattice-QCD simulation at finite baryon density, is not under theoretical control for the moment. The effective model study based on QCD symmetries is a practical alternative. However the model parameters that are fixed by hadronic properties in the vacuum may have unknown dependence on the baryon chemical potential. We propose a new prescription to constrain the effective model parameters by the matching condition with the thermal Statistical Model. In the transitional region where thermal quantities blow up in the Statistical Model, deconfined quarks and gluons should smoothly take over the relevant degrees of freedom from hadrons and resonances. We use the Polyakov-loop coupled Nambu--Jona-Lasinio (PNJL) model as an effective description in the quark side and show how the matching condition is satisfied by a simple ansatz on the Polyakov loop potential. Our results favor a phase diagram with the chiral phase transition located at sligh...

  3. The introduction history of invasive garden ants in Europe: Integrating genetic, chemical and behavioural approaches


    Boomsma Jacobus J; Kronauer Daniel JC; Drijfhout Falko P; Ugelvig Line V; Pedersen Jes S; Cremer Sylvia


    Abstract Background The invasive garden ant, Lasius neglectus, is the most recently detected pest ant and the first known invasive ant able to become established and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct the invasion history of this ant in Europe analysing 14 populations with three complementary approaches: genetic microsatellite analysis, chemical analysis of cuticular hydrocarbon profiles and behavioural observations of aggression behaviour. We eva...

  4. Development of Computational Approaches for Simulation and Advanced Controls for Hybrid Combustion-Gasification Chemical Looping

    Energy Technology Data Exchange (ETDEWEB)

    Joshi, Abhinaya; Lou, Xinsheng; Neuschaefer, Carl; Chaudry, Majid; Quinn, Joseph


    This document provides the results of the project through September 2009. The Phase I project has recently been extended from September 2009 to March 2011. The project extension will begin work on Chemical Looping (CL) Prototype modeling and advanced control design exploration in preparation for a scale-up phase. The results to date include: successful development of dual loop chemical looping process models and dynamic simulation software tools, development and test of several advanced control concepts and applications for Chemical Looping transport control and investigation of several sensor concepts and establishment of two feasible sensor candidates recommended for further prototype development and controls integration. There are three sections in this summary and conclusions. Section 1 presents the project scope and objectives. Section 2 highlights the detailed accomplishments by project task area. Section 3 provides conclusions to date and recommendations for future work.

  5. Modeling thermal/chemical/mechanical response of energetic materials

    Energy Technology Data Exchange (ETDEWEB)

    Baer, M.R.; Hobbs, M.L.; Gross, R.J. [and others


    An overview of modeling at Sandia National Laboratories is presented which describes coupled thermal, chemical and mechanical response of energetic materials. This modeling addresses cookoff scenarios for safety assessment studies in systems containing energetic materials. Foundation work is discussed which establishes a method for incorporating chemistry and mechanics into multidimensional analysis. Finite element analysis offers the capabilities to simultaneously resolve reactive heat transfer and structural mechanics in complex geometries. Nonlinear conduction heat transfer, with multiple step finite-rate chemistry, is resolved using a thermal finite element code. Rate equations are solved element-by-element using a modified matrix-free stiff solver This finite element software was developed for the simulation of systems requiring large numbers of finite elements. An iterative implicit scheme, based on the conjugate gradient method, is used and a hemi-cube algorithm is employed for the determination of view factors in surface-to-surface radiation transfer The critical link between the reactive heat transfer and mechanics is the introduction of an appropriate constitutive material model providing a stress-strain relationship for quasi-static mechanics analysis. This model is formally derived from bubble nucleation theory, and parameter variations of critical model parameters indicate that a small degree of decomposition leads to significant mechanical response. Coupled thermal/chemical/mechanical analysis is presented which simulates experiments designed to probe cookoff thermal-mechanical response of energetic materials.

  6. Modelling Chemical Reasoning to Predict and Invent Reactions. (United States)

    Segler, Marwin H S; Waller, Mark P


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

  7. The introduction history of invasive garden ants in Europe: Integrating genetic, chemical and behavioural approaches

    Directory of Open Access Journals (Sweden)

    Boomsma Jacobus J


    Full Text Available Abstract Background The invasive garden ant, Lasius neglectus, is the most recently detected pest ant and the first known invasive ant able to become established and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct the invasion history of this ant in Europe analysing 14 populations with three complementary approaches: genetic microsatellite analysis, chemical analysis of cuticular hydrocarbon profiles and behavioural observations of aggression behaviour. We evaluate the relative informative power of the three methodological approaches and estimate both the number of independent introduction events from a yet unknown native range somewhere in the Black Sea area, and the invasive potential of the existing introduced populations. Results Three clusters of genetically similar populations were detected, and all but one population had a similar chemical profile. Aggression between populations could be predicted from their genetic and chemical distance, and two major clusters of non-aggressive groups of populations were found. However, populations of L. neglectus did not separate into clear supercolonial associations, as is typical for other invasive ants. Conclusion The three methodological approaches gave consistent and complementary results. All joint evidence supports the inference that the 14 introduced populations of L. neglectus in Europe likely arose from only very few independent introductions from the native range, and that new infestations were typically started through introductions from other invasive populations. This indicates that existing introduced populations have a very high invasive potential when the ants are inadvertently spread by human transport.

  8. A semiparametric approach to physiological flow models. (United States)

    Verotta, D; Sheiner, L B; Ebling, W F; Stanski, D R


    By regarding sampled tissues in a physiological model as linear subsystems, the usual advantages of flow models are preserved while mitigating two of their disadvantages, (i) the need for assumptions regarding intratissue kinetics, and (ii) the need to simultaneously fit data from several tissues. To apply the linear systems approach, both arterial blood and (interesting) tissue drug concentrations must be measured. The body is modeled as having an arterial compartment (A) distributing drug to different linear subsystems (tissues), connected in a specific way by blood flow. The response (CA, with dimensions of concentration) of A is measured. Tissues receive input from A (and optionally from other tissues), and send output to the outside or to other parts of the body. The response (CT, total amount of drug in the tissue (T) divided by the volume of T) from the T-th one, for example, of such tissues is also observed. From linear systems theory, CT can be expressed as the convolution of CA with a disposition function, F(t) (with dimensions 1/time). The function F(t) depends on the (unknown) structure of T, but has certain other constant properties: The integral integral infinity0 F(t) dt is the steady state ratio of CT to CA, and the point F(0) is the clearance rate of drug from A to T divided by the volume of T. A formula for the clearance rate of drug from T to outside T can be derived. To estimate F(t) empirically, and thus mitigate disadvantage (i), we suggest that, first, a nonparametric (or parametric) function be fitted to CA data yielding predicted values, CA, and, second, the convolution integral of CA with F(t) be fitted to CT data using a deconvolution method. By so doing, each tissue's data are analyzed separately, thus mitigating disadvantage (ii). A method for system simulation is also proposed. The results of applying the approach to simulated data and to real thiopental data are reported.

  9. Extension of the Dermal Sensitisation Threshold (DST) approach to incorporate chemicals classified as reactive. (United States)

    Safford, Robert J; Api, Anne Marie; Roberts, David W; Lalko, Jon F


    The evaluation of chemicals for their skin sensitising potential is an essential step in ensuring the safety of ingredients in consumer products. Similar to the Threshold of Toxicological Concern, the Dermal Sensitisation Threshold (DST) has been demonstrated to provide effective risk assessments for skin sensitisation in cases where human exposure is low. The DST was originally developed based on a Local Lymph Node Assay (LLNA) dataset and applied to chemicals that were not considered to be directly reactive to skin proteins, and unlikely to initiate the first mechanistic steps leading to the induction of sensitisation. Here we have extended the DST concept to protein reactive chemicals. A probabilistic assessment of the original DST dataset was conducted and a threshold of 64 μg/cm(2) was derived. In our accompanying publication, a set of structural chemistry based rules was developed to proactively identify highly reactive and potentially highly potent materials which should be excluded from the DST approach. The DST and rule set were benchmarked against a test set of chemicals with LLNA/human data. It is concluded that by combining the reactive DST with knowledge of chemistry a threshold can be established below which there is no appreciable risk of sensitisation for protein-reactive chemicals.

  10. Mining chemical reactions using neighborhood behavior and condensed graphs of reactions approaches. (United States)

    de Luca, Aurélie; Horvath, Dragos; Marcou, Gilles; Solov'ev, Vitaly; Varnek, Alexandre


    This work addresses the problem of similarity search and classification of chemical reactions using Neighborhood Behavior (NB) and Condensed Graphs of Reaction (CGR) approaches. The CGR formalism represents chemical reactions as a classical molecular graph with dynamic bonds, enabling descriptor calculations on this graph. Different types of the ISIDA fragment descriptors generated for CGRs in combination with two metrics--Tanimoto and Euclidean--were considered as chemical spaces, to serve for reaction dissimilarity scoring. The NB method has been used to select an optimal combination of descriptors which distinguish different types of chemical reactions in a database containing 8544 reactions of 9 classes. Relevance of NB analysis has been validated in generic (multiclass) similarity search and in clustering with Self-Organizing Maps (SOM). NB-compliant sets of descriptors were shown to display enhanced mapping propensities, allowing the construction of better Self-Organizing Maps and similarity searches (NB and classical similarity search criteria--AUC ROC--correlate at a level of 0.7). The analysis of the SOM clusters proved chemically meaningful CGR substructures representing specific reaction signatures.

  11. Coupling approaches used in atmospheric entry models (United States)

    Gritsevich, M. I.


    While a planet orbits the Sun, it is subject to impact by smaller objects, ranging from tiny dust particles and space debris to much larger asteroids and comets. Such collisions have taken place frequently over geological time and played an important role in the evolution of planets and the development of life on the Earth. Though the search for near-Earth objects addresses one of the main points of the Asteroid and Comet Hazard, one should not underestimate the useful information to be gleaned from smaller atmospheric encounters, known as meteors or fireballs. Not only do these events help determine the linkages between meteorites and their parent bodies; due to their relative regularity they provide a good statistical basis for analysis. For successful cases with found meteorites, the detailed atmospheric path record is an excellent tool to test and improve existing entry models assuring the robustness of their implementation. There are many more important scientific questions meteoroids help us to answer, among them: Where do these objects come from, what are their origins, physical properties and chemical composition? What are the shapes and bulk densities of the space objects which fully ablate in an atmosphere and do not reach the planetary surface? Which values are directly measured and which are initially assumed as input to various models? How to couple both fragmentation and ablation effects in the model, taking real size distribution of fragments into account? How to specify and speed up the recovery of a recently fallen meteorites, not letting weathering to affect samples too much? How big is the pre-atmospheric projectile to terminal body ratio in terms of their mass/volume? Which exact parameters beside initial mass define this ratio? More generally, how entering object affects Earth's atmosphere and (if applicable) Earth's surface? How to predict these impact consequences based on atmospheric trajectory data? How to describe atmospheric entry

  12. Modeling the chemical evolution of nitrogen oxides near roadways (United States)

    Wang, Yan Jason; DenBleyker, Allison; McDonald-Buller, Elena; Allen, David; Zhang, K. Max


    The chemical evolution of nitrogen dioxide (NO 2) and nitrogen monoxide (NO) in the vicinity of roadways is numerically investigated using a computational fluid dynamics model, CFD-VIT-RIT and a Gaussian-based model, CALINE4. CFD-VIT-RIT couples a standard k- ɛ turbulence model for turbulent mixing and the Finite-Rate model for chemical reactions. CALINE4 employs a discrete parcel method, assuming that chemical reactions are independent of the dilution process. The modeling results are compared to the field measurement data collected near two roadways in Austin, Texas, State Highway 71 (SH-71) and Farm to Market Road 973 (FM-973), under parallel and perpendicular wind conditions during the summer of 2007. In addition to ozone (O 3), other oxidants and reactive species including hydroperoxyl radical (HO 2), organic peroxyl radical (RO 2), formaldehyde (HCHO) and acetaldehyde (CH 3CHO) are considered in the transformation from NO to NO 2. CFD-VIT-RIT is shown to be capable of predicting both NO x and NO 2 profiles downwind. CALINE4 is able to capture the NO x profiles, but underpredicts NO 2 concentrations under high wind velocity. Our study suggests that the initial NO 2/NO x ratios have to be carefully selected based on traffic conditions in order to assess NO 2 concentrations near roadways. The commonly assumed NO 2/NO x ratio by volume of 5% may not be suitable for most roadways, especially those with a high fraction of heavy-duty truck traffic. In addition, high O 3 concentrations and high traffic volumes would lead to the peak NO 2 concentration occurring near roadways with elevated concentrations persistent over a long distance downwind.

  13. Fish population modeling approaches for assessing direct effects and recovery following mitigation of a pulp mill effluent in Jackfish Bay (United States)

    We present an approach to link chemically-induced alterations in molecular and biochemical endpoints to adverse outcomes in whole organisms and populations. A predictive population model was developed to translate changes in fecundity measures of white sucker (Catostomus commers...

  14. Unified Ion-chemical Model for the Middle Atmosphere (United States)

    Kamsali, Nagaraja; Kamsali, Nagaraja; Datta, Jayati; Prasad, Bsn

    The importance of ion-chemical model studies in our understanding of middle atmospheric regions needs no special emphasis. Present day knowledge of middle atmosphere (0-100 km) has come from two distinct experimental developments: first, in situ measurements of ion composition by balloons and sounding rockets and second, laboratory investigations on ionchemical reactions of importance at these heights, determination of reaction rate coefficients and their temperature dependence. Model studies act as an interface between these, to generate theoretical estimates of ion composition and their derivatives (e.g. electrical conductivity) by using as input the laboratory data on reaction rate coefficients and the data on neutral species density, ionization flux, temperature etc. Free electrons exist only in the mesosphere. Positive molecular ions dominate the upper mesospheric heights and heavy positive and negative cluster ions appearing at the lower mesospheric heights continue to dominate in strato and troposphere. The equilibrium density of electrons and ionic species is governed by: a) ionization of the atmospheric constituents producing electron-positive ion pair b)gas-phase ion-chemical reactions that convert the electrons and primary positive ions into heavy cluster ions of both polarity c)heterogeneous ion-chemical reactions for producing aerosol ions and d) loss mechanisms for small ions and aerosol ions through recombination of oppositely charged species. Physical entities that control the ion production and loss processes are not the same and vary vastly both in nature and magnitude in the middle atmosphere X-rays, Lymann-alpha and precipitating electrons are the dominant ionizing agents at the mesospheric heights. Cosmic ray ionization that is not so significant in the mesosphere is the sole ionizing agent at stratosphere and troposphere. At the ground level and up to a few tens of meters above the earth's surface, natural radioactivity induced ionization is

  15. Modeling Nonlinear Adsorption with a Single Chemical Parameter: Predicting Chemical Median Langmuir Binding Constants. (United States)

    Davis, Craig Warren; Di Toro, Dominic M


    Procedures for accurately predicting linear partition coefficients onto various sorbents (e.g., organic carbon, soils, clay) are reliable and well established. However, similar procedures for the prediction of sorption parameters of nonlinear isotherm models are not. The purpose of this paper is to present a procedure for predicting nonlinear isotherm parameters, specifically the median Langmuir binding constants, K̃L, obtained utilizing the single-chemical parameter log-normal Langmuir isotherm developed in the accompanying work. A reduced poly parameter linear free energy relationship (pp-LFER) is able to predict median Langmuir binding constants for graphite, charcoal, and Darco granular activated carbon (GAC) adsorption data. For the larger F400 GAC data set, a single pp-LFER model was insufficient, as a plateau is observed for the median Langmuir binding constants of larger molecular volume sorbates. This volumetric cutoff occurs in proximity to the median pore diameter for F400 GAC. A log-linear relationship exists between the aqueous solubility of these large compounds and their median Langmuir binding constants. Using this relationship for the chemicals above the volumetric cutoff and the pp-LFER below the cutoff, the median Langmuir binding constants can be predicted with a root-mean square error for graphite (n = 13), charcoal (n = 11), Darco GAC (n = 14), and F400 GAC (n = 44) of 0.129, 0.307, 0.407, and 0.424, respectively.

  16. Thermo-Chemical Modelling Strategies for the Pultrusion Process

    DEFF Research Database (Denmark)

    Baran, Ismet; Hattel, Jesper Henri; Tutum, Cem Celal


    In the present study, three dimensional (3D) numerical modeling strategies of a thermosetting pultrusion process are investigated considering both transient and steady state approaches. For the transient solution, an unconditionally stable alternating direction implicit Douglas-Gunn (ADI-DG) sche...

  17. Gompertz kinetics model of fast chemical neurotransmission currents. (United States)

    Easton, Dexter M


    At a chemical synapse, transmitter molecules ejected from presynaptic terminal(s) bind reversibly with postsynaptic receptors and trigger an increase in channel conductance to specific ions. This paper describes a simple but accurate predictive model for the time course of the synaptic conductance transient, based on Gompertz kinetics. In the model, two simple exponential decay terms set the rates of development and decline of transmitter action. The first, r, triggering conductance activation, is surrogate for the decelerated rate of growth of conductance, G. The second, r', responsible for Y, deactivation of the conductance, is surrogate for the decelerated rate of decline of transmitter action. Therefore, the differential equation for the net conductance change, g, triggered by the transmitter is dg/dt=g(r-r'). The solution of that equation yields the product of G(t), representing activation, and Y(t), which defines the proportional decline (deactivation) of the current. The model fits, over their full-time course, published records of macroscopic ionic current associated with fast chemical transmission. The Gompertz model is a convenient and accurate method for routine analysis and comparison of records of synaptic current and putative transmitter time course. A Gompertz fit requiring only three independent rate constants plus initial current appears indistinguishable from a Markov fit using seven rate constants.

  18. Modeling the role of microplastics in Bioaccumulation of organic chemicals to marine aquatic organisms. Critical Review

    NARCIS (Netherlands)

    Koelmans, A.A.


    It has been shown that ingestion of microplastics may increase bioaccumulation of organic chemicals by aquatic organisms. This paper critically reviews the literature on the effects of plastic ingestion on the bioaccumulation of organic chemicals, emphasizing quantitative approaches and mechanistic

  19. Approaches and models of intercultural education

    Directory of Open Access Journals (Sweden)

    Iván Manuel Sánchez Fontalvo


    Full Text Available Needed to be aware of the need to build an intercultural society, awareness must be assumed in all social spheres, where stands the role play education. A role of transcendental, since it must promote educational spaces to form people with virtues and powers that allow them to live together / as in multicultural contexts and social diversities (sometimes uneven in an increasingly globalized and interconnected world, and foster the development of feelings of civic belonging shared before the neighborhood, city, region and country, allowing them concern and critical judgement to marginalization, poverty, misery and inequitable distribution of wealth, causes of structural violence, but at the same time, wanting to work for the welfare and transformation of these scenarios. Since these budgets, it is important to know the approaches and models of intercultural education that have been developed so far, analysing their impact on the contexts educational where apply.   

  20. Chemical kinetic modeling of H{sub 2} applications

    Energy Technology Data Exchange (ETDEWEB)

    Marinov, N.M.; Westbrook, C.K.; Cloutman, L.D. [Lawrence Livermore National Lab., CA (United States)] [and others


    Work being carried out at LLNL has concentrated on studies of the role of chemical kinetics in a variety of problems related to hydrogen combustion in practical combustion systems, with an emphasis on vehicle propulsion. Use of hydrogen offers significant advantages over fossil fuels, and computer modeling provides advantages when used in concert with experimental studies. Many numerical {open_quotes}experiments{close_quotes} can be carried out quickly and efficiently, reducing the cost and time of system development, and many new and speculative concepts can be screened to identify those with sufficient promise to pursue experimentally. This project uses chemical kinetic and fluid dynamic computational modeling to examine the combustion characteristics of systems burning hydrogen, either as the only fuel or mixed with natural gas. Oxidation kinetics are combined with pollutant formation kinetics, including formation of oxides of nitrogen but also including air toxics in natural gas combustion. We have refined many of the elementary kinetic reaction steps in the detailed reaction mechanism for hydrogen oxidation. To extend the model to pressures characteristic of internal combustion engines, it was necessary to apply theoretical pressure falloff formalisms for several key steps in the reaction mechanism. We have continued development of simplified reaction mechanisms for hydrogen oxidation, we have implemented those mechanisms into multidimensional computational fluid dynamics models, and we have used models of chemistry and fluid dynamics to address selected application problems. At the present time, we are using computed high pressure flame, and auto-ignition data to further refine the simplified kinetics models that are then to be used in multidimensional fluid mechanics models. Detailed kinetics studies have investigated hydrogen flames and ignition of hydrogen behind shock waves, intended to refine the detailed reactions mechanisms.

  1. Quantum-chemical approach to defect formation processes in non-metallic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kotomin, E.A.; Shluger, A.L. (Latvijskij Gosudarstvennyj Univ., Riga (USSR))


    Results of the quantum-chemical simulation of the formation of structural and radiation defects are reviewed, using ice, silicon, and silicon dioxide as examples. The relationship between the structural elements of these crystals and the structural defects is analysed. Models of the main defects, their optical characteristics, and the activation energy of their migration are discussed. The relationship between the characteristics obtained by quantum-chemical calculations and the parameters of the macroscopic kinetics of the processes induced by defects in dielectric crystals is considered. (author).

  2. IGE Model: An Extension of the Ideal Gas Model to Include Chemical Composition as Part of the Equilibrium State

    Directory of Open Access Journals (Sweden)

    Christopher P. Paolini


    Full Text Available The ideal gas (IG model is probably the most well-known gas models in engineering thermodynamics. In this paper, we extend the IG model into an ideal gas equilibrium (IGE model mixture model by incorporating chemical equilibrium calculations as part of the state evaluation. Through a simple graphical interface, users can set the atomic composition of a gas mixture. We have integrated this model into a thermodynamic web portal TEST ( that contains Java applets for various models for properties of pure substances. In the state panel of the IGE model, the known thermodynamic properties are entered. For a given pressure and temperature, the mixture's Gibbs function is minimized subject to atomic constraints and the equilibrium composition along with thermodynamic properties of the mixture are calculated and displayed. What is unique about this approach is that equilibrium computations are performed in the background, without requiring any major change in the familiar user interface used in other state daemons. Properties calculated by this equilibrium state daemon are compared with results from other established applications such as NASA CEA and STANJAN. Also, two different algorithms, an iterative approach and a direct approach based on minimizing different thermodynamic functions in different situation, are compared.

  3. Modelling physico-chemical properties of (benzo)triazoles, and screening for environmental partitioning. (United States)

    Bhhatarai, B; Gramatica, P


    (Benzo)triazoles are distributed throughout the environment, mainly in water compartments, because of their wide use in industry where they are employed in pharmaceutical, agricultural and deicing products. They are hazardous chemicals that adversely affect humans and other non-target species, and are on the list of substances of very high concern (SVHC) in the new European regulation of chemicals - REACH (Registration, Evaluation, Authorization and Restriction of Chemical substances). Thus there is a vital need for further investigations to understand the behavior of these compounds in biota and the environment. In such a scenario, physico-chemical properties like aqueous solubility, hydrophobicity, vapor pressure and melting point can be useful. However, the limited availability and the high cost of lab testing prevents the acquisition of necessary experimental data that industry must submit for the registration of these chemicals. In such cases a preliminary analysis can be made using Quantitative Structure-Property Relationships (QSPR) models. For such an analysis, we propose Multiple Linear Regression (MLR) models based on theoretical molecular descriptors selected by Genetic Algorithm (GA). Training and prediction sets were prepared a priori by splitting the available experimental data, which were then used to derive statistically robust and predictive (both internally and externally) models. These models, after verification of their structural applicability domain (AD), were used to predict the properties of a total of 351 compounds, including those in the REACH preregistration list. Finally, Principal Component Analysis was applied to the predictions to rank the environmental partitioning properties (relevant for leaching and volatility) of new and untested (benzo)triazoles within the AD of each model. Our study using this approach highlighted compounds dangerous for the aquatic compartment. Similar analyses using predictions obtained by the EPI Suite and

  4. A new extension of the polarizable continuum model: Toward a quantum chemical description of chemical reactions at extreme high pressure. (United States)

    Cammi, Roberto


    A quantum chemical method for studying potential energy surfaces of reactive molecular systems at extreme high pressures is presented. The method is an extension of the standard Polarizable Continuum Model that is usually used for Quantum Chemical study of chemical reactions at a standard condition of pressure. The physical basis of the method and the corresponding computational protocol are described in necessary detail, and an application of the method to the dimerization of cyclopentadiene (up to 20 GPa) is reported.

  5. Modelling of structural effects on chemical reactions in turbulent flows

    Energy Technology Data Exchange (ETDEWEB)

    Gammelsaeter, H.R.


    Turbulence-chemistry interactions are analysed using algebraic moment closure for the chemical reaction term. The coupling between turbulence and chemical length and time scales generate a complex interaction process. This interaction process is called structural effects in this work. The structural effects are shown to take place on all scales between the largest scale of turbulence and the scales of the molecular motions. The set of equations describing turbulent correlations involved in turbulent reacting flows are derived. Interactions are shown schematically using interaction charts. Algebraic equations for the turbulent correlations in the reaction rate are given using the interaction charts to include the most significant couplings. In the frame of fundamental combustion physics, the structural effects appearing on the small scales of turbulence are proposed modelled using a discrete spectrum of turbulent scales. The well-known problem of averaging the Arrhenius law, the specific reaction rate, is proposed solved using a presumed single variable probability density function and a sub scale model for the reaction volume. Although some uncertainties are expected, the principles are addressed. Fast chemistry modelling is shown to be consistent in the frame of algebraic moment closure when the turbulence-chemistry interaction is accounted for in the turbulent diffusion. The modelling proposed in this thesis is compared with experimental data for an laboratory methane flame and advanced probability density function modelling. The results show promising features. Finally it is shown a comparison with full scale measurements for an industrial burner. All features of the burner are captured with the model. 41 refs., 33 figs.

  6. CFD modeling of reactive pollutant dispersion in simplified urban configurations with different chemical mechanisms (United States)

    Sanchez, Beatriz; Santiago, Jose-Luis; Martilli, Alberto; Palacios, Magdalena; Kirchner, Frank


    An accurate understanding of urban air quality requires considering a coupled behavior between the dispersion of reactive pollutants and atmospheric dynamics. Currently, urban air pollution is mostly dominated by traffic emission, where nitrogen oxides (NOx) and volatile organic compounds (VOCs) are the primary emitted pollutants. However, modeling reactive pollutants with a large set of chemical reactions, using a computational fluid dynamic (CFD) model, requires a large amount of computational (CPU) time. In this sense, the selection of the chemical reactions needed in different atmospheric conditions becomes essential in finding the best compromise between CPU time and accuracy. The purpose of this work is to assess the differences in NO and NO2 concentrations by considering three chemical approaches: (a) passive tracers (non-reactive), (b) the NOx-O3 photostationary state and (c) a reduced complex chemical mechanism based on 23 species and 25 reactions. The appraisal of the effects of chemical reactions focuses on studying the NO and NO2 dispersion in comparison with the tracer behavior within the street. In turn, the effect of including VOC reactions is also analyzed taking into account several VOC / NOx ratios of traffic emission. Given that the NO and NO2 dispersion can also be affected by atmospheric conditions, such as wind flow or the background concentration from season-dependent pollutants, in this work the influence of wind speeds and background O3 concentrations are studied. The results show that the presence of ozone in the street plays an important role in NO and NO2 concentrations. Therefore, greater differences linked to the chemical approach used are found with higher O3 concentrations and faster wind speeds. This bears relation to the vertical flux as a function of ambient wind speed since it increases the pollutant exchange between the street and the overlying air. This detailed study allows one to ascertain under which atmospheric conditions

  7. Meteorological and Chemical Urban Scale Modelling for Shanghai Metropolitan Area (United States)

    Mahura, Alexander; Nuterman, Roman; Gonzalez-Aparicio, Iratxe; Amstrup, Bjarne; Yang, Xiaohua; Baklanov, Alexander


    Urban air pollution is a serious problem in megacities and major industrial agglomerations of China. Therefore, air quality information is important for public. In particular, the Shanghai metropolitan area is well known as megacity having severe air pollution episodes. The Enviro-HIRLAM (Environment - HIgh Resolution Limited Area Model) is applied for on-line integrated meteorology and atmospheric composition forecasting for the Shanghai region of China. The model setup includes the urban Building Effects Parameterization module, describing different types of urban districts with its own morphological and aerodynamical characteristics. The model is running in downscaling chain from regional-to-urban scales for selected periods in summer and winter having both elevated pollution levels as well as unfavorable meteorological conditions. For these periods, the effects of urbanization are analyzed for spatio-temporal variability of atmospheric and chemical/aerosols patterns. The formation and development of meteorological (air and surface temperature, relative humidity, wind speed, cloud cover, boundary layer height) and chemical/aerosol patterns (concentration and deposition) due to influence of the metropolitan area is evaluated. The impact of Shanghai region on regional-to-urban scales as well as relationship between air pollution and meteorology are estimated.

  8. Mathematical models of thermal and chemical transport in geologic media

    Energy Technology Data Exchange (ETDEWEB)

    Lai, C.-H.


    Semi-analytical and numerical methods are used to investigate thermal and chemical transport processes in geologic media. The work is divided into two parts: (1) development of semi-analytical models for the analysis of uncoupled isothermal and nonisothermal fluid flow in naturally fractured media, and (2) development of a high resolution numerical code to address coupled nonisothermal chemical transport in geologic media. A semi-analytical model is developed for well test data analysis in naturally fractured reservoirs. A simple approximate analytical solution for pressure buildup and drawdown tests is developed. Methods based on the approximate solution are developed for the evaluation of important reservoir properties. Type curves for nonisothermal fluid flow in naturally fractured media are developed to design injection systems for maximum energy in hydrothermal systems. An accurate finite difference method for the solution of a convection-diffusion type equation is developed. The method is incorporated in a two-dimensional code to investigate free convection in a porous slab and kinetic silica-water reactions in geothermal systems. A multicomponent model considering the variations of pressure, temperature and silica concentration is developed to interpret the evolution of geothermal systems during exploitation.

  9. Hydrological budget of Lake Chad: assessment of lake-groundwater interaction by coupling Bayesian approach and chemical budget (United States)

    Bouchez, Camille; Goncalves, Julio; Deschamps, Pierre; Seidel, Jean-Luc; Doumnang, Jean-Claude; Sylvestre, Florence


    Estimation of lake-groundwater interactions is a crucial step to constrain water balance of lacustrine and aquifer systems. Located in the Sahel, the Lake Chad is at the center of an endorheic basin of 2,5.106 km2. One of the most remarkable features of this terminal lake is that, despite the semi-arid context and high evaporation rates of the area, its waters are fresh. It is proposed in the literature that the solutes are evacuated in the underlying quaternary aquifer bearing witness to the importance of surface water and groundwater exchanges for the chemical regulation of the lake. The water balance of this system is still not fully understood. The respective roles of evaporation versus infiltration into the quaternary aquifer are particularly under constrained. To assess lake-groundwater flows, we used the previous conceptual hydrological model of the lake Chad proposed by Bader et al. (Hydrological Sciences Journal, 2011). This model involves six parameters including infiltration rate. A probabilistic inversion of parameters, based on an exploration of the parameters space through a Metropolis algorithm (a Monte Carlo Markov Chain method), allows the construction of an a posteriori Probability Density Function of each parameter yielding to the best fits between observed lake levels and simulated. Then, a chemical budget of a conservative element, such as chloride, is introduced in the water balance model using the optimal parameters resulting from the Bayesian inverse approach. The model simulates lake level and chloride concentration variations of lake Chad from 1956 up to 2008. Simulated lake levels are in overall agreement with the observations, with a Nash-Sutcliffe efficiency coefficient above 0.94 for all sets of parameters retained. The infiltration value, obtained by such probabilistic inversion approach, accounts for 120±20 mm/yr, representing 5% of the total outputs of the lake. However, simulated chloride concentrations are overestimated in

  10. A novel approach: chemical relational databases, and the role of the ISSCAN database on assessing chemical carcinogenicity. (United States)

    Benigni, Romualdo; Bossa, Cecilia; Richard, Ann M; Yang, Chihae


    Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did not contain chemical structures. Concepts and technologies originated from the structure-activity relationships science have provided powerful tools to create new types of databases, where the effective linkage of chemical toxicity with chemical structure can facilitate and greatly enhance data gathering and hypothesis generation, by permitting: a) exploration across both chemical and biological domains; and b) structure-searchability through the data. This paper reviews the main public databases, together with the progress in the field of chemical relational databases, and presents the ISSCAN database on experimental chemical carcinogens.

  11. Chemical kinetics and combustion modelling with CFX 4

    Energy Technology Data Exchange (ETDEWEB)

    Stopford, P. [AEA Technology, Computational Fluid Dynamics Services Harwell, Oxfordshire (United Kingdom)


    The presentation describes some recent developments in combustion and kinetics models used in the CFX software of AEA Technology. Three topics are highlighted: the development of coupled solvers in a traditional `SIMPLE`-based CFD code, the use of detailed chemical kinetics mechanism via `look-up` tables and the application of CFD to large-scale multi-burner combustion plant. The aim is identify those physical approximations and numerical methods that are likely to be most useful in the future and those areas where further developments are required. (author) 6 refs.

  12. Analytical model of plasma-chemical etching in planar reactor (United States)

    Veselov, D. S.; Bakun, A. D.; Voronov, Yu A.; Kireev, V. Yu; Vasileva, O. V.


    The paper discusses an analytical model of plasma-chemical etching in planar diode- type reactor. Analytical expressions of etch rate and etch anisotropy were obtained. It is shown that etch anisotropy increases with increasing the ion current and ion energy. At the same time, etch selectivity of processed material decreases as compared with the mask. Etch rate decreases with the distance from the centre axis of the reactor. To decrease the loading effect, it is necessary to reduce the wafer temperature and pressure in the reactor, as well as increase the gas flow rate through the reactor.

  13. Tribo-chemical mechanisms of copper chemical mechanical planarization (CMP) - Fundamental investigations and integrated modeling (United States)

    Tripathi, Shantanu

    In this work, copper Chemical Mechanical Planarization is identified primarily as a wear enhanced corrosion process (as opposed to the corrosion enhanced wear process assumed in existing modeling work), where intermittent abrasive action enhances the local oxidation rate, and is followed by time-dependant passivation of copper. Based on this mechanism, an integrated tribo-chemical model of material removal at the abrasive scale was developed based on oxidation of copper. This considers abrasive and pad properties, process parameters, and slurry chemistry. Three important components of this model -- the passivation kinetics of copper in CMP slurry chemicals; the mechanical properties of passive films on copper; and the interaction frequency of copper and abrasives -- are introduced. The first two components, in particular the passivation kinetics of copper, are extensively studied experimentally, while the third component is addressed theoretically. The passivation kinetics of copper (i.e. decrease in oxidation currents as passive films form on bare copper) were investigated by potential step chronoamperometry. Low cost microelectrodes were developed (first of its kind for studying copper CMP) to reduce many of the problems of traditional macroelectrodes, such as interference from capacitive charging, IR drops and low diffusion limited current. Electrochemical impedance spectroscopy (EIS) was used on copper microelectrodes in CMP slurry constituents to obtain equivalent circuit elements associated with different electrochemical phenomena (capacitive, kinetics, diffusion etc.) at different polarization potentials. The circuit elements were used to simulate chronoamperometry in a system where copper actively corrodes at anodic potentials; from the simulation and the experimental results, the current decay in this system was attributed entirely to capacitive charging. The circuit elements were also used to explain the chronoamperometry results in passivating and

  14. Sensitivity of chemical reaction networks: a structural approach. 1. Examples and the carbon metabolic network. (United States)

    Mochizuki, Atsushi; Fiedler, Bernold


    In biological cells, chemical reaction pathways lead to complex network systems like metabolic networks. One experimental approach to the dynamics of such systems examines their "sensitivity": each enzyme mediating a reaction in the system is increased/decreased or knocked out separately, and the responses in the concentrations of chemicals or their fluxes are observed. In this study, we present a mathematical method, named structural sensitivity analysis, to determine the sensitivity of reaction systems from information on the network alone. We investigate how the sensitivity responses of chemicals in a reaction network depend on the structure of the network, and on the position of the perturbed reaction in the network. We establish and prove some general rules which relate the sensitivity response to the structure of the underlying network. We describe a hierarchical pattern in the flux response which is governed by branchings in the network. We apply our method to several hypothetical and real life chemical reaction networks, including the metabolic network of the Escherichia coli TCA cycle.

  15. Chemical entity recognition in patents by combining dictionary-based and statistical approaches. (United States)

    Akhondi, Saber A; Pons, Ewoud; Afzal, Zubair; van Haagen, Herman; Becker, Benedikt F H; Hettne, Kristina M; van Mulligen, Erik M; Kors, Jan A


    We describe the development of a chemical entity recognition system and its application in the CHEMDNER-patent track of BioCreative 2015. This community challenge includes a Chemical Entity Mention in Patents (CEMP) recognition task and a Chemical Passage Detection (CPD) classification task. We addressed both tasks by an ensemble system that combines a dictionary-based approach with a statistical one. For this purpose the performance of several lexical resources was assessed using Peregrine, our open-source indexing engine. We combined our dictionary-based results on the patent corpus with the results of tmChem, a chemical recognizer using a conditional random field classifier. To improve the performance of tmChem, we utilized three additional features, viz. part-of-speech tags, lemmas and word-vector clusters. When evaluated on the training data, our final system obtained an F-score of 85.21% for the CEMP task, and an accuracy of 91.53% for the CPD task. On the test set, the best system ranked sixth among 21 teams for CEMP with an F-score of 86.82%, and second among nine teams for CPD with an accuracy of 94.23%. The differences in performance between the best ensemble system and the statistical system separately were small.Database URL:

  16. Novel approaches to improving the chemical safety of the meat chain towards toxicants. (United States)

    Engel, E; Ratel, J; Bouhlel, J; Planche, C; Meurillon, M


    In addition to microbiological issues, meat chemical safety is a growing concern for the public authorities, chain stakeholders and consumers. Meat may be contaminated by various chemical toxicants originating from the environment, treatments of agricultural production or food processing. Generally found at trace levels in meat, these toxicants may harm human health during chronic exposure. This paper overviews the key issues to be considered to ensure better control of their occurrence in meat and assessment of the related health risk. We first describe potential contaminants of meat products. Strategies to move towards a more efficient and systematic control of meat chemical safety are then presented in a second part, with a focus on emerging approaches based on toxicogenomics. The third part presents mitigation strategies to limit the impact of process-induced toxicants in meat. Finally, the last part introduces methodological advances to refine chemical risk assessment related to the occurrence of toxicants in meat by quantifying the influence of digestion on the fraction of food contaminants that may be assimilated by the human body.

  17. Validation of N-myristoyltransferase as an antimalarial drug target using an integrated chemical biology approach (United States)

    Wright, Megan H.; Clough, Barbara; Rackham, Mark D.; Rangachari, Kaveri; Brannigan, James A.; Grainger, Munira; Moss, David K.; Bottrill, Andrew R.; Heal, William P.; Broncel, Malgorzata; Serwa, Remigiusz A.; Brady, Declan; Mann, David J.; Leatherbarrow, Robin J.; Tewari, Rita; Wilkinson, Anthony J.; Holder, Anthony A.; Tate, Edward W.


    Malaria is an infectious disease caused by parasites of the genus Plasmodium, which leads to approximately one million deaths per annum worldwide. Chemical validation of new antimalarial targets is urgently required in view of rising resistance to current drugs. One such putative target is the enzyme N-myristoyltransferase, which catalyses the attachment of the fatty acid myristate to protein substrates (N-myristoylation). Here, we report an integrated chemical biology approach to explore protein myristoylation in the major human parasite P. falciparum, combining chemical proteomic tools for identification of the myristoylated and glycosylphosphatidylinositol-anchored proteome with selective small-molecule N-myristoyltransferase inhibitors. We demonstrate that N-myristoyltransferase is an essential and chemically tractable target in malaria parasites both in vitro and in vivo, and show that selective inhibition of N-myristoylation leads to catastrophic and irreversible failure to assemble the inner membrane complex, a critical subcellular organelle in the parasite life cycle. Our studies provide the basis for the development of new antimalarials targeting N-myristoyltransferase.

  18. Modeling non-isothermal multiphase multi-species reactive chemical transport in geologic media

    Energy Technology Data Exchange (ETDEWEB)

    Tianfu Xu; Gerard, F.; Pruess, K.; Brimhall, G.


    The assessment of mineral deposits, the analysis of hydrothermal convection systems, the performance of radioactive, urban and industrial waste disposal, the study of groundwater pollution, and the understanding of natural groundwater quality patterns all require modeling tools that can consider both the transport of dissolved species as well as their interactions with solid (or other) phases in geologic media and engineered barriers. Here, a general multi-species reactive transport formulation has been developed, which is applicable to homogeneous and/or heterogeneous reactions that can proceed either subject to local equilibrium conditions or kinetic rates under non-isothermal multiphase flow conditions. Two numerical solution methods, the direct substitution approach (DSA) and sequential iteration approach (SIA) for solving the coupled complex subsurface thermo-physical-chemical processes, are described. An efficient sequential iteration approach, which solves transport of solutes and chemical reactions sequentially and iteratively, is proposed for the current reactive chemical transport computer code development. The coupled flow (water, vapor, air and heat) and solute transport equations are also solved sequentially. The existing multiphase flow code TOUGH2 and geochemical code EQ3/6 are used to implement this SIA. The flow chart of the coupled code TOUGH2-EQ3/6, required modifications of the existing codes and additional subroutines needed are presented.

  19. Modeling contact angle hysteresis on chemically patterned and superhydrophobic surfaces. (United States)

    Kusumaatmaja, H; Yeomans, J M


    We investigate contact angle hysteresis on chemically patterned and superhydrophobic surfaces, as the drop volume is quasistatically increased and decreased. We consider both two (cylindrical drops) and three (spherical drops) dimensions using analytical and numerical approaches to minimize the free energy of the drop. In two dimensions, we find, in agreement with other authors, a slip, jump, stick motion of the contact line. In three dimensions, this behavior persists, but the position and magnitude of the contact line jumps are sensitive to the details of the surface patterning. In two dimensions, we identify analytically the advancing and receding contact angles on the different surfaces, and we use numerical insights to argue that these provide bounds for the three-dimensional cases. We present explicit simulations to show that a simple average over the disorder is not sufficient to predict the details of the contact angle hysteresis and to support an explanation for the low contact angle hysteresis of suspended drops on superhydrophobic surfaces.

  20. Two-dimensional numerical and eco-toxicological modeling of chemical spills

    Institute of Scientific and Technical Information of China (English)

    Suiliang HUANG; Yafei JIA; Sam S. Y. WANG


    The effects of chemical spills on aquatic nontarget organisms were evaluated in this study. Based on a review of three types of current eco-toxicological models of chemicals, i.e., ACQUATOX model of the US-EPA, Hudson River Model of PCBs, and critical body residual (CBR) model and dynamic energy budget (DEBtox)model, this paper presents an uncoupled numerical ecotoxicological model. The transport and transformation of spilled chemicals were simulated by a chemical transport model (including flow and sediment transport), and the mortalities of an organism caused by the chemicals were simulated by the extended threshold damage model,separately. Due to extreme scarcity of data, this model was applied to two hypothetical cases of chemical spills happening upstream of a lake. Theoretical analysis and simulated results indicated that this model is capable of reasonably predicting the acute effects of chemical spills on aquatic ecosystems or organism killings.


    CERN Multimedia

    Medical Service


    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or Chemistry Service : TIS-GS-GC : 78546

  2. A generalized quantum chemical approach for elastic and inelastic electron transports in molecular electronics devices (United States)

    Jiang, Jun; Kula, Mathias; Luo, Yi


    A generalized quantum chemical approach for electron transport in molecular devices is developed. It allows one to treat devices where the metal electrodes and the molecule are either chemically or physically bonded on equal footing. An extension to include the vibration motions of the molecule has also been implemented which has produced the inelastic electron-tunneling spectroscopy of molecular electronics devices with unprecedented accuracy. Important information about the structure of the molecule and of metal-molecule contacts that are not accessible in the experiment are revealed. The calculated current-voltage (I-V) characteristics of different molecular devices, including benzene-1,4-dithiolate, octanemonothiolate [H(CH2)8S], and octanedithiolate [S(CH2)8S] bonded to gold electrodes, are in very good agreement with experimental measurements.


    Energy Technology Data Exchange (ETDEWEB)

    Laurence, T


    We are developing an alternative approach to optical probes that will ultimately allow us to measure chemical concentrations in microenvironments within cells and tissues. This approach is based on monitoring the surface-enhanced Raman scattering (SERS) response of functionalized metal nanoparticles (50-100 nm in diameter). SERS allows for the sensitive detection of changes in the state of chemical groups attached to individual nanoparticles and small clusters. We present the development of a nanoscale pH meter. The pH response of these nanoprobes is tested in a cell-free medium, measuring the pH of the solution immediately surrounding the nanoparticles. We developed and used SERS correlation spectroscopy and single particle/cluster SERS spectroscopy to characterize heterogeneities in the SERS signal, which result from the formation of small nanoparticle clusters. These heterogeneities have historically provided inconsistent response to pH, leading a poor sensitivity of {approx}1 pH unit. The response of the nanoscale pH meters is tested under a wide range of conditions to approach the complex environment encountered inside living cells and to optimize probe performance. We have also developed a rapid scanning technique to obtain pH information using confocal microscopic imaging. Together with the development of hollow gold nanoshells with collaborators, this project enables future cell-based studies of pH using SERS. This research will be continued as a collaboration with the Center for Biophotonics Science and Technology (CBST) at UC Davis Medical Center.

  4. Introductory lecture: atmospheric organic aerosols: insights from the combination of measurements and chemical transport models. (United States)

    Pandis, Spyros N; Donahue, Neil M; Murphy, Benjamin N; Riipinen, Ilona; Fountoukis, Christos; Karnezi, Eleni; Patoulias, David; Skyllakou, Ksakousti


    The formation, atmospheric evolution, properties, and removal of organic particulate matter remain some of the least understood aspects of atmospheric chemistry despite the importance of organic aerosol (OA) for both human health and climate change. Here, we summarize our recent efforts to deal with the chemical complexity of the tens of thousands of organic compounds in the atmosphere using the volatility-oxygen content framework (often called the 2D-Volatility Basis Set, 2D-VBS). Our current ability to measure the ambient OA concentration as a function of its volatility and oxygen to carbon (O:C) ratio is evaluated. The combination of a thermodenuder, isothermal dilution and Aerosol Mass Spectrometry (AMS) together with a mathematical aerosol dynamics model is a promising approach. The development of computational modules based on the 2D-VBS that can be used in chemical transport models (CTMs) is described. Approaches of different complexity are tested against ambient observations, showing the challenge of simulating the complex chemical evolution of atmospheric OA. The results of the simplest approach describing the net change due to functionalization and fragmentation are quite encouraging, reproducing both the observed OA levels and O : C in a variety of conditions. The same CTM coupled with source-apportionment algorithms can be used to gain insights into the travel distances and age of atmospheric OA. We estimate that the average age of OA near the ground in continental locations is 1-2 days and most of it was emitted (either as precursor vapors or particles) hundreds of kilometers away. Condensation of organic vapors on fresh particles is critical for the growth of these new particles to larger sizes and eventually to cloud condensation nuclei (CCN) sizes. The semivolatile organics currently simulated by CTMs are too volatile to condense on these tiny particles with high curvature. We show that chemical aging reactions converting these semivolatile

  5. Students' learning approaches and their understanding of some chemical concepts in eighth-grade science (United States)

    Chin, Christine Hui Li

    The purpose of this study was to (a) investigate the relationship between students' learning approaches and their conceptual understanding of some chemical concepts, (b) describe the qualitative differences between a deep and surface learning approach to learning science, and (c) identify the kinds of cognitive and metacognitive strategies that students use as they construct their conceptual knowledge. One hundred and two eighth grade students were given the Learning Approach Questionnaire to measure their orientation to learn using a deep or surface approach. They also completed a Chemistry Questionnaire both before and after the teaching of a chemistry unit which lasted nine weeks. Six target students from one class were selected for more in-depth study. They represented learners using a deep or surface learning approach, and were identified by the Learning Approach Questionnaire and their teacher's evaluation. They worked in groups during hands-on laboratory activities and were audiotaped or videotaped. The students were also interviewed individually both before and after instruction of the chemistry unit about their responses on the Chemistry Questionnaire and their thoughts and actions during the laboratory activities. The correlation between the students' scores on the "meaningful orientation" scale of the Learning Approach Questionnaire and their gain scores from the pre-test to post-test on the Chemistry Questionnaire was.06, suggesting no relationship between the students' learning approach and their conceptual change. Several reasons were given to explain this finding. Analysis of the target students' discourse and actions during the group activities and their interview responses revealed differences between the deep and surface learning approaches regarding generative thinking, nature of explanations, asking questions, metacognitive activity, and approach to tasks. Strategies associated with a deep learning approach included generating mental images and

  6. High Temperature Chemical Kinetic Combustion Modeling of Lightly Methylated Alkanes

    Energy Technology Data Exchange (ETDEWEB)

    Sarathy, S M; Westbrook, C K; Pitz, W J; Mehl, M


    Conventional petroleum jet and diesel fuels, as well as alternative Fischer-Tropsch (FT) fuels and hydrotreated renewable jet (HRJ) fuels, contain high molecular weight lightly branched alkanes (i.e., methylalkanes) and straight chain alkanes (n-alkanes). Improving the combustion of these fuels in practical applications requires a fundamental understanding of large hydrocarbon combustion chemistry. This research project presents a detailed high temperature chemical kinetic mechanism for n-octane and three lightly branched isomers octane (i.e., 2-methylheptane, 3-methylheptane, and 2,5-dimethylhexane). The model is validated against experimental data from a variety of fundamental combustion devices. This new model is used to show how the location and number of methyl branches affects fuel reactivity including laminar flame speed and species formation.

  7. Reaction Networks For Interstellar Chemical Modelling: Improvements and Challenges

    CERN Document Server

    Wakelam, V; Herbst, E; Troe, J; Geppert, W; Linnartz, H; Oberg, K; Roueff, E; Agundez, M; Pernot, P; Cuppen, H M; Loison, J C; Talbi, D


    We survey the current situation regarding chemical modelling of the synthesis of molecules in the interstellar medium. The present state of knowledge concerning the rate coefficients and their uncertainties for the major gas-phase processes -- ion-neutral reactions, neutral-neutral reactions, radiative association, and dissociative recombination -- is reviewed. Emphasis is placed on those reactions that have been identified, by sensitivity analyses, as 'crucial' in determining the predicted abundances of the species observed in the interstellar medium. These sensitivity analyses have been carried out for gas-phase models of three representative, molecule-rich, astronomical sources: the cold dense molecular clouds TMC-1 and L134N, and the expanding circumstellar envelope IRC +10216. Our review has led to the proposal of new values and uncertainties for the rate coefficients of many of the key reactions. The impact of these new data on the predicted abundances in TMC-1 and L134N is reported. Interstellar dust p...

  8. Mass transport measurements and modeling for chemical vapor infiltration

    Energy Technology Data Exchange (ETDEWEB)

    Starr, T.L.; Chiang, D.Y.; Fiadzo, O.G.; Hablutzel, N. [Georgia Inst. of Tech., Atlanta, GA (United States). School of Materials Science and Engineering


    This project involves experimental and modeling investigation of densification behavior and mass transport in fiber preforms and partially densified composites, and application of these results to chemical vapor infiltration (CVI) process modeling. This supports work on-going at ORNL in process development for fabrication of ceramic matrix composite (CMC) tubes. Tube-shaped composite preforms are fabricated at ORNL with Nextel{trademark} 312 fiber (3M Corporation, St. Paul, MN) by placing and compressing several layers of braided sleeve on a tubular mandrel. In terms of fiber architecture these preforms are significantly different than those made previously with Nicalon{trademark} fiber (Nippon Carbon Corp., Tokyo, Japan) square weave cloth. The authors have made microstructure and permeability measurements on several of these preforms and a few partially densified composites so as to better understand their densification behavior during CVI.

  9. Development of a computationally efficient urban modeling approach

    DEFF Research Database (Denmark)

    Wolfs, Vincent; Murla, Damian; Ntegeka, Victor


    This paper presents a parsimonious and data-driven modelling approach to simulate urban floods. Flood levels simulated by detailed 1D-2D hydrodynamic models can be emulated using the presented conceptual modelling approach with a very short calculation time. In addition, the model detail can be a...

  10. X-rays in protoplanetary disks: their impact on the thermal and chemical structure, a grid of models.

    NARCIS (Netherlands)

    Aresu, G.; Kamp, I.; Meijerink, R.; Woitke, P.; Thi, W. F.; Spaans, M.


    X-rays impact protoplanetary disks hydrostatic, thermal and chemical structure. The range of efficiency of X-rays is explored using a grid modelling approach: different parameters affects the structure of the disk, this determines different contribution of the X-ray radiation to the chemistry and th

  11. X-rays in protoplanetary disks : Their impact on the thermal and chemical structure, a grid of models

    NARCIS (Netherlands)

    Aresu, G.; Kamp, I.; Meijerink, R.; Woitke, P.; Thi, W. F.; Spaans, M.C.


    X-rays impact protoplanetary disks hydrostatic, thermal and chemical structure. The range of efficiency of X-rays is explored using a grid modelling approach: different parameters affects the structure of the disk, this determines different contribution of the X-ray radiation to the chemistry and th

  12. Sorption kinetics and microbial biodegradation activity of hydrophobic chemicals in sewage sludge: Model and measurements based on free concentrations

    NARCIS (Netherlands)

    Artola-Garicano, E.; Borkent, I.; Damen, K.; Jager, T.; Vaes, W.H.J.


    In the current study, a new method is introduced with which the rate-limiting factor of biodegradation processes of hydrophobic chemicals in organic and aqueous systems can be determined. The novelty of this approach lies in the combination of a free concentration-based kinetic model with measuremen

  13. Models of cortical malformation--Chemical and physical. (United States)

    Luhmann, Heiko J


    Pharmaco-resistant epilepsies, and also some neuropsychiatric disorders, are often associated with malformations in hippocampal and neocortical structures. The mechanisms leading to these cortical malformations causing an imbalance between the excitatory and inhibitory system are largely unknown. Animal models using chemical or physical manipulations reproduce different human pathologies by interfering with cell generation and neuronal migration. The model of in utero injection of methylazoxymethanol (MAM) acetate mimics periventricular nodular heterotopia. The freeze lesion model reproduces (poly)microgyria, focal heterotopia and schizencephaly. The in utero irradiation model causes microgyria and heterotopia. Intraperitoneal injections of carmustine 1-3-bis-chloroethyl-nitrosurea (BCNU) to pregnant rats produces laminar disorganization, heterotopias and cytomegalic neurons. The ibotenic acid model induces focal cortical malformations, which resemble human microgyria and ulegyria. Cortical dysplasia can be also observed following prenatal exposure to ethanol, cocaine or antiepileptic drugs. All these models of cortical malformations are characterized by a pronounced hyperexcitability, few of them also produce spontaneous epileptic seizures. This dysfunction results from an impairment in GABAergic inhibition and/or an increase in glutamatergic synaptic transmission. The cortical region initiating or contributing to this hyperexcitability may not necessarily correspond to the site of the focal malformation. In some models wide-spread molecular and functional changes can be observed in remote regions of the brain, where they cause pathophysiological activities. This paper gives an overview on different animal models of cortical malformations, which are mostly used in rodents and which mimic the pathology and to some extent the pathophysiology of neuronal migration disorders associated with epilepsy in humans.

  14. Fuzzy-logic modeling of Fenton's strong chemical oxidation process treating three types of landfill leachates. (United States)

    Sari, Hanife; Yetilmezsoy, Kaan; Ilhan, Fatih; Yazici, Senem; Kurt, Ugur; Apaydin, Omer


    Three multiple input and multiple output-type fuzzy-logic-based models were developed as an artificial intelligence-based approach to model a novel integrated process (UF-IER-EDBM-FO) consisted of ultrafiltration (UF), ion exchange resins (IER), electrodialysis with bipolar membrane (EDBM), and Fenton's oxidation (FO) units treating young, middle-aged, and stabilized landfill leachates. The FO unit was considered as the key process for implementation of the proposed modeling scheme. Four input components such as H(2)O(2)/chemical oxygen demand ratio, H(2)O(2)/Fe(2+) ratio, reaction pH, and reaction time were fuzzified in a Mamdani-type fuzzy inference system to predict the removal efficiencies of chemical oxygen demand, total organic carbon, color, and ammonia nitrogen. A total of 200 rules in the IF-THEN format were established within the framework of a graphical user interface for each fuzzy-logic model. The product (prod) and the center of gravity (centroid) methods were performed as the inference operator and defuzzification methods, respectively, for the proposed prognostic models. Fuzzy-logic predicted results were compared to the outputs of multiple regression models by means of various descriptive statistical indicators, and the proposed methodology was tested against the experimental data. The testing results clearly revealed that the proposed prognostic models showed a superior predictive performance with very high determination coefficients (R (2)) between 0.930 and 0.991. This study indicated a simple means of modeling and potential of a knowledge-based approach for capturing complicated inter-relationships in a highly non-linear problem. Clearly, it was shown that the proposed prognostic models provided a well-suited and cost-effective method to predict removal efficiencies of wastewater parameters prior to discharge to receiving streams.

  15. Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteins. (United States)

    Liu, Jinfeng; Zhang, John Z H; He, Xiao


    Geometry optimization and vibrational spectra (infrared and Raman spectra) calculations of proteins are carried out by a quantum chemical approach using the EE-GMFCC (electrostatically embedded generalized molecular fractionation with conjugate caps) method (J. Phys. Chem. A, 2013, 117, 7149). The first and second derivatives of the EE-GMFCC energy are derived and employed in geometry optimization and vibrational frequency calculations for several test systems, including a polypeptide ((GLY)6), an α-helix (AKA), a β-sheet (Trpzip2) and ubiquitin (76 residues with 1231 atoms). Comparison of the present results with those obtained from full system QM (quantum mechanical) calculations shows that the EE-GMFCC approach can give accurate molecular geometries, vibrational frequencies and vibrational intensities. The EE-GMFCC method is also employed to simulate the amide I vibration of proteins, which has been widely used for the analysis of peptide and protein structures, and the results are in good agreement with the experimental observations.

  16. Connectivity of channelized reservoirs: a modelling approach

    Energy Technology Data Exchange (ETDEWEB)

    Larue, David K. [ChevronTexaco, Bakersfield, CA (United States); Hovadik, Joseph [ChevronTexaco, San Ramon, CA (United States)


    Connectivity represents one of the fundamental properties of a reservoir that directly affects recovery. If a portion of the reservoir is not connected to a well, it cannot be drained. Geobody or sandbody connectivity is defined as the percentage of the reservoir that is connected, and reservoir connectivity is defined as the percentage of the reservoir that is connected to wells. Previous studies have mostly considered mathematical, physical and engineering aspects of connectivity. In the current study, the stratigraphy of connectivity is characterized using simple, 3D geostatistical models. Based on these modelling studies, stratigraphic connectivity is good, usually greater than 90%, if the net: gross ratio, or sand fraction, is greater than about 30%. At net: gross values less than 30%, there is a rapid diminishment of connectivity as a function of net: gross. This behaviour between net: gross and connectivity defines a characteristic 'S-curve', in which the connectivity is high for net: gross values above 30%, then diminishes rapidly and approaches 0. Well configuration factors that can influence reservoir connectivity are well density, well orientation (vertical or horizontal; horizontal parallel to channels or perpendicular) and length of completion zones. Reservoir connectivity as a function of net: gross can be improved by several factors: presence of overbank sandy facies, deposition of channels in a channel belt, deposition of channels with high width/thickness ratios, and deposition of channels during variable floodplain aggradation rates. Connectivity can be reduced substantially in two-dimensional reservoirs, in map view or in cross-section, by volume support effects and by stratigraphic heterogeneities. It is well known that in two dimensions, the cascade zone for the 'S-curve' of net: gross plotted against connectivity occurs at about 60% net: gross. Generalizing this knowledge, any time that a reservoir can be regarded as &apos

  17. A microscopic model for chemically-powered Janus motors. (United States)

    Huang, Mu-Jie; Schofield, Jeremy; Kapral, Raymond


    Very small synthetic motors that make use of chemical reactions to propel themselves in solution hold promise for new applications in the development of new materials, science and medicine. The prospect of such potential applications, along with the fact that systems with many motors or active elements display interesting cooperative phenomena of fundamental interest, has made the study of synthetic motors an active research area. Janus motors, comprising catalytic and noncatalytic hemispheres, figure prominently in experimental and theoretical studies of these systems. While continuum models of Janus motor systems are often used to describe motor dynamics, microscopic models that are able to account for intermolecular interactions, many-body concentration gradients, fluid flows and thermal fluctuations provide a way to explore the dynamical behavior of these complex out-of-equilibrium systems that does not rely on approximations that are often made in continuum theories. The analysis of microscopic models from first principles provides a foundation from which the range of validity and limitations of approximate theories of the dynamics may be assessed. In this paper, a microscopic model for the diffusiophoretic propulsion of Janus motors, where motor interactions with the environment occur only through hard collisions, is constructed, analyzed and compared to theoretical predictions. Microscopic simulations of both single-motor and many-motor systems are carried out to illustrate the results.

  18. Comparison of chemical and thermal protein denaturation by combination of computational and experimental approaches. II (United States)

    Wang, Qian; Christiansen, Alexander; Samiotakis, Antonios; Wittung-Stafshede, Pernilla; Cheung, Margaret S.


    Chemical and thermal denaturation methods have been widely used to investigate folding processes of proteins in vitro. However, a molecular understanding of the relationship between these two perturbation methods is lacking. Here, we combined computational and experimental approaches to investigate denaturing effects on three structurally different proteins. We derived a linear relationship between thermal denaturation at temperature Tb and chemical denaturation at another temperature Tu using the stability change of a protein (ΔG). For this, we related the dependence of ΔG on temperature, in the Gibbs-Helmholtz equation, to that of ΔG on urea concentration in the linear extrapolation method, assuming that there is a temperature pair from the urea (Tu) and the aqueous (Tb) ensembles that produces the same protein structures. We tested this relationship on apoazurin, cytochrome c, and apoflavodoxin using coarse-grained molecular simulations. We found a linear correlation between the temperature for a particular structural ensemble in the absence of urea, Tb, and the temperature of the same structural ensemble at a specific urea concentration, Tu. The in silico results agreed with in vitro far-UV circular dichroism data on apoazurin and cytochrome c. We conclude that chemical and thermal unfolding processes correlate in terms of thermodynamics and structural ensembles at most conditions; however, deviations were found at high concentrations of denaturant.

  19. Principles for identification of High Potency Category Chemicals for which the Dermal Sensitisation Threshold (DST) approach should not be applied. (United States)

    Roberts, David W; Api, Anne Marie; Safford, Robert J; Lalko, Jon F


    An essential step in ensuring the toxicological safety of chemicals used in consumer products is the evaluation of their skin sensitising potential. The sensitising potency, coupled with information on exposure levels, can be used in a Quantitative Risk Assessment (QRA) to determine an acceptable level of a given chemical in a given product. Where consumer skin exposure is low, a risk assessment can be conducted using the Dermal Sensitisation Threshold (DST) approach, avoiding the need to determine potency experimentally. Since skin sensitisation involves chemical reaction with skin proteins, the first step in the DST approach is to assess, on the basis of the chemical structure, whether the chemical is expected to be reactive or not. Our accompanying publication describes the probabilistic derivation of a DST of 64 μg/cm(2) for chemicals assessed as reactive. This would protect against 95% of chemicals assessed as reactive, but the remaining 5% would include chemicals with very high potency. Here we discuss the chemical properties and structural features of high potency sensitisers, and derive an approach whereby they can be identified and consequently excluded from application of the DST.

  20. An active film-coating approach to enhance chemical stability of a potent drug molecule. (United States)

    Desai, Divyakant; Rao, Venkatramana; Guo, Hang; Li, Danping; Stein, Daniel; Hu, Frank Y; Kiesnowski, Chris


    Peliglitazar, a PPAR α/γ agonist, was found to undergo acid as well as base catalyzed degradation. The acid catalyzed degradation led to the formation of benzylic alcohol and glycine carbamate and the base catalyzed degradation led to formation of p-hydroxyanisole and an amine degradant. In capsule formulations, the capsules with the lowest drug-loading exhibited maximum instability even at 25 °C/60% RH storage condition. Incorporation of pH-modifiers to maintain 'micro-environmental pH' acidic did not prevent the formation of the base-catalyzed degradants. Traditional dry granulated tablet formulation which is qualitatively similar to the capsule formulations showed the presence of acid-catalyzed degradants even without the presence of an acidifying agent. On the other hand, traditional wet granulated tablet formulation showed mainly base-catalyzed degradants. Stability problems of the tablet formulation were aggravated because the potent molecule required low tablet strengths which resulted in low drug to excipient ratio. To stabilize the molecule, an active film-coating approach was explored. In this approach, the drug was sprayed with the coating material onto non-active containing tablet cores. This approach of trapping the drug particles into the coating material provided tablets with satisfactory chemical stability. The stability enhancement observed in the active coating approach is attributed to the higher drug to excipient ratio in the film coat of non-reactive coating material compared to that in the traditional dry or wet granulated formulations.

  1. Analysis and modelling of the energy consumption of chemical batch plants

    Energy Technology Data Exchange (ETDEWEB)

    Bieler, P.S.


    This report for the Swiss Federal Office of Energy (SFOE) describes two different approaches for the energy analysis and modelling of chemical batch plants. A top-down model consisting of a linear equation based on the specific energy consumption per ton of production output and the base consumption of the plant is postulated. The model is shown to be applicable to single and multi-product batches for batch plants with constant production mix and multi-purpose batch plants in which only similar chemicals are produced. For multipurpose batch plants with highly varying production processes and changing production mix, the top-down model produced inaccurate results. A bottom-up model is postulated for such plants. The results obtained are discussed that show that the electricity consumption for infrastructure equipment was significant and responsible for about 50% of total electricity consumption. The specific energy consumption for the different buildings was related to the degree of automation and the production processes. Analyses of the results of modelling are presented. More detailed analyses of the energy consumption of this apparatus group show that about 30 to 40% of steam energy is lost and thus a large potential for optimisation exists. Various potentials for making savings, ranging from elimination of reflux conditions to the development of a new heating/cooling-system for a generic batch reactor, are identified.

  2. Identifying New Candidate Genes and Chemicals Related to Prostate Cancer Using a Hybrid Network and Shortest Path Approach (United States)

    Yuan, Fei; Zhou, You; Wang, Meng; Yang, Jing; Wu, Kai; Lu, Changhong; Kong, Xiangyin; Cai, Yu-Dong


    Prostate cancer is a type of cancer that occurs in the male prostate, a gland in the male reproductive system. Because prostate cancer cells may spread to other parts of the body and can influence human reproduction, understanding the mechanisms underlying this disease is critical for designing effective treatments. The identification of as many genes and chemicals related to prostate cancer as possible will enhance our understanding of this disease. In this study, we proposed a computational method to identify new candidate genes and chemicals based on currently known genes and chemicals related to prostate cancer by applying a shortest path approach in a hybrid network. The hybrid network was constructed according to information concerning chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions. Many of the obtained genes and chemicals are associated with prostate cancer. PMID:26504486

  3. Upper D region chemical kinetic modeling of LORE relaxation times (United States)

    Gordillo-Vázquez, F. J.; Luque, A.; Haldoupis, C.


    The recovery times of upper D region electron density elevations, caused by lightning-induced electromagnetic pulses (EMP), are modeled. The work was motivated from the need to understand a recently identified narrowband VLF perturbation named LOREs, an acronym for LOng Recovery Early VLF events. LOREs associate with long-living electron density perturbations in the upper D region ionosphere; they are generated by strong EMP radiated from large peak current intensities of ±CG (cloud to ground) lightning discharges, known also to be capable of producing elves. Relaxation model scenarios are considered first for a weak enhancement in electron density and then for a much stronger one caused by an intense lightning EMP acting as an impulsive ionization source. The full nonequilibrium kinetic modeling of the perturbed mesosphere in the 76 to 92 km range during LORE-occurring conditions predicts that the electron density relaxation time is controlled by electron attachment at lower altitudes, whereas above 79 km attachment is balanced totally by associative electron detachment so that electron loss at these higher altitudes is controlled mainly by electron recombination with hydrated positive clusters H+(H2O)n and secondarily by dissociative recombination with NO+ ions, a process which gradually dominates at altitudes >88 km. The calculated recovery times agree fairly well with LORE observations. In addition, a simplified (quasi-analytic) model build for the key charged species and chemical reactions is applied, which arrives at similar results with those of the full kinetic model. Finally, the modeled recovery estimates for lower altitudes, that is <79 km, are in good agreement with the observed short recovery times of typical early VLF events, which are known to be associated with sprites.

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

    Energy Technology Data Exchange (ETDEWEB)

    Adomaitis, Raymond A., E-mail: [Department of Chemical and Biomolecular Engineering, Institute for Systems Research, University of Maryland, College Park, Maryland 20742 (United States)


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

  5. Modeling Chemical Mechanical Polishing with Couple Stress Fluids

    Institute of Scientific and Technical Information of China (English)

    张朝辉; 雒建斌; 温诗铸


    Chemical mechanical polishing (CMP) is a manufacturing process used to achieve high levels of global and local planarity.Currently, the slurries used in CMP usually contain nanoscale particles to accelerate the removal ratio and to optimize the planarity, whose rheological properties can no longer be accurately modeled with Newtonian fluids.The Reynolds equation, including the couple stress effects, was derived in this paper.The equation describes the mechanism to solve the CMP lubrication equation with the couple stress effects.The effects on load and moments resulting from the various parameters, such as pivot height, roll angle, and pitch angle, were subsequently simulated.The results show that the couple stress can provide higher load and angular moments.This study sheds some lights into the mechanism of the CMP process.

  6. On the convergence of complex Langevin dynamics: the three-dimensional XY model at finite chemical potential

    CERN Document Server

    Aarts, Gert


    The three-dimensional XY model is studied at finite chemical potential using complex Langevin dynamics. The validity of the approach is probed at small chemical potential using imaginary chemical potential and continuity arguments, and at larger chemical potential by comparison with the world line method. While complex Langevin works for larger beta, we find that it fails for smaller beta, in the region of the phase diagram corresponding to the disordered phase. Diagnostic tests are developed to identify symptoms correlated with incorrect convergence. We argue that the erroneous behaviour at smaller beta is not due to the sign problem, but rather resembles dynamics observed in complex Langevin simulations of simple models with complex noise.

  7. Modeling in applied sciences a kinetic theory approach

    CERN Document Server

    Pulvirenti, Mario


    Modeling complex biological, chemical, and physical systems, in the context of spatially heterogeneous mediums, is a challenging task for scientists and engineers using traditional methods of analysis Modeling in Applied Sciences is a comprehensive survey of modeling large systems using kinetic equations, and in particular the Boltzmann equation and its generalizations An interdisciplinary group of leading authorities carefully develop the foundations of kinetic models and discuss the connections and interactions between model theories, qualitative and computational analysis and real-world applications This book provides a thoroughly accessible and lucid overview of the different aspects, models, computations, and methodology for the kinetic-theory modeling process Topics and Features * Integrated modeling perspective utilized in all chapters * Fluid dynamics of reacting gases * Self-contained introduction to kinetic models * Becker–Doring equations * Nonlinear kinetic models with chemical reactions * Kinet...

  8. Material removal model for non-contact chemical mechanical polishing

    Institute of Scientific and Technical Information of China (English)

    ZHANG JianQun; ZHANG ChaoHui


    Material removal mechanism under non-contact condition between the pad and the wafer in the chemical mechanical polishing (CMP) process is investigated. Based on the assumption that almost all effective material removals take place due to the active abrasives which cut material through the plowing effects. A novel model is developed to predict the material removal rate (MRR) under non-contact condition between the pad and the wafer in CMP. Validated by the experimental data, the model is proved to be able to predict the change of MRR under non-contact condition. Numerical simulation of the model shows: the relative velocity u between the pad and the wafer and fluid viscosity η are the most important factors which impact MRR under non-contact condition; load changes of wafer also affects the MRR, but the effect is not as obvious as the relative velocity and fluid viscosity;when the radius of abrasive is not less than 50nm, the impact of MRR alone with the changes in the size of the abrasive can be ignored.

  9. A Novel Approach: Chemical Relational Databases, and the Role of the ISSCAN Database on Assessing Chemical Carcinogenity (United States)

    Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did no...

  10. Chemical Reaction and Flow Modeling in Fullerene and Nanotube Production (United States)

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


    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

  11. Modeling and optimization of a sequence of chemical cleaning cycles in dead-end ultrafiltration

    NARCIS (Netherlands)

    Zondervan, Edwin; Betlem, Ben H.L.; Blankert, Bastiaan; Roffel, Brian


    In this paper a chemical cleaning sequence model is proposed that can be used to predict the fouling status of a membrane during multiple chemical cleaning cycles. The proposed model is used to minimize the overall operating costs – based on chemicals consumption, energy consumption and investment c

  12. Iceland as a Model for Chemical Alteration on Mars (United States)

    Bishop, J. L.; Schiffman, P.; Murad, E.; Southard, R.


    Subglacial volcanic activity on Iceland has led to the formation of a variety of silicate and iron oxide-rich alteration products that may ressemble chemical alteration on Mars. The spectral and chemical properties of Icelandic samples are presented.

  13. Prioritization of chemicals in the aquatic environment based on risk assessment: analytical, modeling and regulatory perspective. (United States)

    Guillén, D; Ginebreda, A; Farré, M; Darbra, R M; Petrovic, M; Gros, M; Barceló, D


    The extensive and intensive use of chemicals in our developed, highly technological society includes more than 100,000 chemical substances. Significant scientific evidence has lead to the recognition that their improper use and release may result in undesirable and harmful side-effects on both the human and ecosystem health. To cope with them, appropriate risk assessment processes and related prioritization schemes have been developed in order to provide the necessary scientific support for regulatory procedures. In the present paper, two of the elements that constitute the core of risk assessment, namely occurrence and hazard effects, have been discussed. Recent advances in analytical chemistry (sample pre-treatment and instrumental equipment, etc.) have allowed for more comprehensive monitoring of environmental pollution reaching limits of detection up to sub ng L(-1). Alternative to analytical measurements, occurrence models can provide risk managers with a very interesting approach for estimating environmental concentrations from real or hypothetical scenarios. The most representative prioritization schemes used for issuing lists of concerning chemicals have also been examined and put in the context of existing environmental policies for protection strategies and regulations. Finally, new challenges in the field of risk-assessment have been outlined, including those posed by new materials (i.e., nanomaterials), transformation products, multi-chemical exposure, or extension of the risk assessment process to the whole ecosystem.

  14. Quantitative nucleation and growth kinetics of gold nanoparticles via model-assisted dynamic spectroscopic approach. (United States)

    Zhou, Yao; Wang, Huixuan; Lin, Wenshuang; Lin, Liqin; Gao, Yixian; Yang, Feng; Du, Mingming; Fang, Weiping; Huang, Jiale; Sun, Daohua; Li, Qingbiao


    Lacking of quantitative experimental data and/or kinetic models that could mathematically depict the redox chemistry and the crystallization issue, bottom-to-up formation kinetics of gold nanoparticles (GNPs) remains a challenge. We measured the dynamic regime of GNPs synthesized by l-ascorbic acid (representing a chemical approach) and/or foliar aqueous extract (a biogenic approach) via in situ spectroscopic characterization and established a redox-crystallization model which allows quantitative and separate parameterization of the nucleation and growth processes. The main results were simplified as the following aspects: (I) an efficient approach, i.e., the dynamic in situ spectroscopic characterization assisted with the redox-crystallization model, was established for quantitative analysis of the overall formation kinetics of GNPs in solution; (II) formation of GNPs by the chemical and the biogenic approaches experienced a slow nucleation stage followed by a growth stage which behaved as a mixed-order reaction, and different from the chemical approach, the biogenic method involved heterogeneous nucleation; (III) also, biosynthesis of flaky GNPs was a kinetic-controlled process favored by relatively slow redox chemistry; and (IV) though GNPs formation consists of two aspects, namely the redox chemistry and the crystallization issue, the latter was the rate-determining event that controls the dynamic regime of the whole physicochemical process.

  15. Approaches to advancing quantitative human health risk assessment of environmental chemicals in the post-genomic era

    Energy Technology Data Exchange (ETDEWEB)

    Chiu, Weihsueh A., E-mail: [National Center for Environmental Assessment, U.S. Environmental Protection Agency, Washington DC, 20460 (United States); Euling, Susan Y.; Scott, Cheryl Siegel; Subramaniam, Ravi P. [National Center for Environmental Assessment, U.S. Environmental Protection Agency, Washington DC, 20460 (United States)


    The contribution of genomics and associated technologies to human health risk assessment for environmental chemicals has focused largely on elucidating mechanisms of toxicity, as discussed in other articles in this issue. However, there is interest in moving beyond hazard characterization to making more direct impacts on quantitative risk assessment (QRA) — i.e., the determination of toxicity values for setting exposure standards and cleanup values. We propose that the evolution of QRA of environmental chemicals in the post-genomic era will involve three, somewhat overlapping phases in which different types of approaches begin to mature. The initial focus (in Phase I) has been and continues to be on “augmentation” of weight of evidence — using genomic and related technologies qualitatively to increase the confidence in and scientific basis of the results of QRA. Efforts aimed towards “integration” of these data with traditional animal-based approaches, in particular quantitative predictors, or surrogates, for the in vivo toxicity data to which they have been anchored are just beginning to be explored now (in Phase II). In parallel, there is a recognized need for “expansion” of the use of established biomarkers of susceptibility or risk of human diseases and disorders for QRA, particularly for addressing the issues of cumulative assessment and population risk. Ultimately (in Phase III), substantial further advances could be realized by the development of novel molecular and pathway-based biomarkers and statistical and in silico models that build on anticipated progress in understanding the pathways of human diseases and disorders. Such efforts would facilitate a gradual “reorientation” of QRA towards approaches that more directly link environmental exposures to human outcomes.

  16. Low Pass Filter Model for Chemical Sensors in Response to Gases and Odors

    Directory of Open Access Journals (Sweden)

    Mahmoud Z. Iskandarani


    Full Text Available Design and Modeling multi-gap sensing odor system for the objectives of odor recognition, classification and correlation are carried out. The model illustrates the low pass functionality of the multi-gap sensor acting as a filter for odors. Problem statement: Odor filtering is an important issue in today's world. In addition knowing the original material that an odor belongs to even after being mixed with others is also of vital importance. In addition measuring quality of mixed odors in terms of their affinity and belonging to a specific category or is critical. Approach: Mathematical modeling using low pass filter is carried out. Results: Clear evidence of ability to filter components of an odor mixture as the multi-gap sensor is acting as a filter. Conclusion: The ability to custom design chemical sensors to indicate the presence of various odors.

  17. Hillslope chemical weathering across Paraná, Brazil: a data mining-GIS hybrid approach (United States)

    Iwashita, Fabio; Friedel, Michael J.; Filho, Carlos Roberto de Souza; Fraser, Stephen J.


    Self-organizing map (SOM) and geographic information system (GIS) models were used to investigate the nonlinear relationships associated with geochemical weathering processes at local (~100 km2) and regional (~50,000 km2) scales. The data set consisted of 1) 22 B-horizon soil variables: P, C, pH, Al, total acidity, Ca, Mg, K, total cation exchange capacity, sum of exchangeable bases, base saturation, Cu, Zn, Fe, B, S, Mn, gammaspectrometry (total count, potassium, thorium, and uranium) and magnetic susceptibility measures; and 2) six topographic variables: elevation, slope, aspect, hydrological accumulated flux, horizontal curvature and vertical curvature. It is characterized at 304 locations from a quasi-regular grid spaced about 24 km across the state of Paraná. This data base was split into two subsets: one for analysis and modeling (274 samples) and the other for validation (30 samples) purposes. The self-organizing map and clustering methods were used to identify and classify the relations among solid-phase chemical element concentrations and GIS derived topographic models. The correlation between elevation and k-means clusters related the relative position inside hydrologic macro basins, which was interpreted as an expression of the weathering process reaching a steady-state condition at the regional scale. Locally, the chemical element concentrations were related to the vertical curvature representing concave–convex hillslope features, where concave hillslopes with convergent flux tends to be a reducing environment and convex hillslopes with divergent flux, oxidizing environments. Stochastic cross validation demonstrated that the SOM produced unbiased classifications and quantified the relative amount of uncertainty in predictions. This work strengthens the hypothesis that, at B-horizon steady-state conditions, the terrain morphometry were linked with the soil geochemical weathering in a two-way dependent process: the topographic relief was a factor on

  18. Systematic lumping of complex tropospheric chemical mechanisms using a time-scale based approach

    Directory of Open Access Journals (Sweden)

    L. E. Whitehouse


    Full Text Available This paper presents a formal method of species lumping that can be applied automatically to intermediate compounds within detailed and complex tropospheric chemical reaction schemes. The method is based on grouping species with reference to their chemical lifetimes and reactivity structures. A method for determining the forward and reverse transformations between individual and lumped compounds is developed. Preliminary application to the Leeds Master Chemical Mechanism (MCMv2.0 has led to the removal of 734 species and 1777 reactions from the scheme, with minimal degradation of accuracy across a wide range of test trajectories relevant to polluted tropospheric conditions. The lumped groups are seen to relate to groups of peroxy acyl nitrates, nitrates, carbonates, oxepins, substituted phenols, oxeacids and peracids with similar lifetimes and reaction rates with OH. In combination with other reduction techniques, such as sensitivity analysis and the application of the quasi-steady state approximation (QSSA, a reduced mechanism has been developed that contains 35% of the number of species and 40% of the number of reactions compared to the full mechanism. This has led to a speed up of a factor of 8 in terms of computer calculation time within box model simulations.

  19. The Karyote physico-chemical genomic, proteomic, metabolic cell modeling system. (United States)

    Ortoleva, P; Berry, E; Brun, Y; Fan, J; Fontus, M; Hubbard, K; Jaqaman, K; Jarymowycz, L; Navid, A; Sayyed-Ahmad, A; Shreif, Z; Stanley, F; Tuncay, K; Weitzke, E; Wu, L-C


    Modeling approaches to the dynamics of a living cell are presented that are strongly based on its underlying physical and chemical processes and its hierarchical spatio-temporal organization. Through the inclusion of a broad spectrum of processes and a rigorous analysis of the multiple scale nature of cellular dynamics, we are attempting to advance cell modeling and its applications. The presentation focuses on our cell modeling system, which integrates data archiving and quantitative physico-chemical modeling and information theory to provide a seamless approach to the modeling/data analysis endeavor. Thereby the rapidly growing mess of genomic, proteomic, metabolic, and cell physiological data can be automatically used to develop and calibrate a predictive cell model. The discussion focuses on the Karyote cell modeling system and an introduction to the CellX and VirusX models. The Karyote software system integrates three elements: (1) a model-building and data archiving module that allows one to define a cell type to be modeled through its reaction network, structure, and transport processes as well as to choose the surrounding medium and other parameters of the phenomenon to be modeled; (2) a genomic, proteomic, metabolic cell simulator that solves the equations of metabolic reaction, transcription/translation polymerization and the exchange of molecules between parts of the cell and with the surrounding medium; and (3) an information theory module (ITM) that automates model calibration and development, and integrates a variety of data types with the cell dynamic computations. In Karyote, reactions may be fast (equilibrated) or slow (finite rate), and the special effects of enzymes and other minority species yielding steady-state cycles of arbitrary complexities are accounted for. These features of the dynamics are handled via rigorous multiple scale analysis. A user interface allows for an automated generation and solution of the equations of multiple timescale

  20. Amino Acids from Icy Amines: A Radiation-Chemical Approach to Extraterrestrial Synthesis (United States)

    Dworkin, J. P.; Moore, M. H.


    Detections of amino acids in meteorites go back several decades, with at least 100 such compounds being reported for the Murchison meteorite alone. The presence of these extraterrestrial molecules raises questions as to their formation, abundance, thermal stability, racemization, and possible subsequent reactions. Although all of these topics have been studied in laboratories, such work often involves many variables and unknowns. This has led us to seek out model systems with which to uncover reaction products, test chemical predictions, and sited light on underlying reaction mechanisms. This presentation will describe one such study, focusing on amino-acid formation in ices.

  1. Uncertainty in biology a computational modeling approach

    CERN Document Server

    Gomez-Cabrero, David


    Computational modeling of biomedical processes is gaining more and more weight in the current research into the etiology of biomedical problems and potential treatment strategies.  Computational modeling allows to reduce, refine and replace animal experimentation as well as to translate findings obtained in these experiments to the human background. However these biomedical problems are inherently complex with a myriad of influencing factors, which strongly complicates the model building and validation process.  This book wants to address four main issues related to the building and validation of computational models of biomedical processes: Modeling establishment under uncertainty Model selection and parameter fitting Sensitivity analysis and model adaptation Model predictions under uncertainty In each of the abovementioned areas, the book discusses a number of key-techniques by means of a general theoretical description followed by one or more practical examples.  This book is intended for graduate stude...

  2. Implementation of a vibrationally linked chemical reaction model for DSMC (United States)

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


    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.

  3. A Chemical Evolution Model for the Fornax Dwarf Spheroidal Galaxy

    CERN Document Server

    Yuan, Zhen; Jing, Y P


    Fornax is the brightest Milky Way (MW) dwarf spheroidal galaxy and its star formation history (SFH) has been derived from observations. We estimate the time evolution of its gas mass and net inflow and outflow rates from the SFH using a simple star formation law that relates the star formation rate to the gas mass. We present a chemical evolution model on a 2D mass grid with supernovae (SNe) as sources of metal enrichment. We find that a key parameter controlling the enrichment is the mass M_x of the gas to mix with the ejecta from each SN. The choice of M_x depends on the evolution of SN remnants and on the global gas dynamics. It differs between the two types of SNe involved and between the periods before and after Fornax became an MW satellite at time t = t_sat . Our results indicate that due to the global gas outflow at t > t_sat , part of the ejecta from each SN may directly escape from Fornax. Sample results from our model are presented and compared with data.

  4. On The Stability Of Model Flows For Chemical Vapour Deposition (United States)

    Miller, Robert


    The flow in a chemical vapour deposition (CVD) reactor is assessed. The reactor is modelled as a flow over an infinite-radius rotating disk, where the mean flow and convective instability of the disk boundary layer are measured. Temperature-dependent viscosity and enforced axial flow are used to model the steep temperature gradients present in CVD reactors and the pumping of the gas towards the disk, respectively. Increasing the temperature-dependence parameter of the fluid viscosity (ɛ) results in an overall narrowing of the fluid boundary layer. Increasing the axial flow strength parameter (Ts) accelerates the fluid both radially and axially, while also narrowing the thermal boundary layer. It is seen that when both effects are imposed, the effects of axial flow generally dominate those of the viscosity temperature dependence. A local stability analysis is performed and the linearized stability equations are solved using a Galerkin projection in terms of Chebyshev polynomials. The neutral stability curves are then plotted for a range of ɛ and Ts values. Preliminary results suggest that increasing Ts has a stabilising effect on both type I and type II stationary instabilities, while small increases in ɛ results in a significant reduction to the critical Reynolds number.

  5. A Chemical Evolution Model for the Fornax Dwarf Spheroidal Galaxy

    Directory of Open Access Journals (Sweden)

    Yuan Zhen


    Full Text Available Fornax is the brightest Milky Way (MW dwarf spheroidal galaxy and its star formation history (SFH has been derived from observations. We estimate the time evolution of its gas mass and net inflow and outflow rates from the SFH usinga simple star formation law that relates the star formation rate to the gas mass. We present a chemical evolution model on a 2D mass grid with supernovae (SNe as sources of metal enrichment. We find that a key parameter controlling the enrichment is the mass Mx of the gas to mix with the ejecta from each SN. The choice of Mx depends on the evolution of SN remnants and on the global gas dynamics. It differs between the two types of SNe involved and between the periods before and after Fornax became an MW satellite at time t = tsat. Our results indicate that due to the global gas outflow at t > tsat, part of the ejecta from each SN may directly escape from Fornax. Sample results from our model are presented and compared with data.

  6. A multiobjective optimization approach for combating Aedes aegypti using chemical and biological alternated step-size control. (United States)

    Dias, Weverton O; Wanner, Elizabeth F; Cardoso, Rodrigo T N


    Dengue epidemics, one of the most important viral disease worldwide, can be prevented by combating the transmission vector Aedes aegypti. In support of this aim, this article proposes to analyze the Dengue vector control problem in a multiobjective optimization approach, in which the intention is to minimize both social and economic costs, using a dynamic mathematical model representing the mosquitoes' population. It consists in finding optimal alternated step-size control policies combining chemical (via application of insecticides) and biological control (via insertion of sterile males produced by irradiation). All the optimal policies consists in apply insecticides just at the beginning of the season and, then, keep the mosquitoes in an acceptable level spreading into environment a few amount of sterile males. The optimization model analysis is driven by the use of genetic algorithms. Finally, it performs a statistic test showing that the multiobjective approach is effective in achieving the same effect of variations in the cost parameters. Then, using the proposed methodology, it is possible to find, in a single run, given a decision maker, the optimal number of days and the respective amounts in which each control strategy must be applied, according to the tradeoff between using more insecticide with less transmission mosquitoes or more sterile males with more transmission mosquitoes.

  7. Adaptation of fugacity models to treat speciating chemicals with constant species concentration ratios. (United States)

    Toose, Liisa K; Mackay, Donald


    A "multiplier" method is developed by which multimedia mass balance fugacity models designed to describe the fate of a single chemical species can be applied to chemicals that exist as several interconverting species. The method is applicable only when observed ratios of species concentrations in each phase are relatively constant and there is thus no need to define interspecies conversion rates. It involves the compilation of conventional transformation and intermedia transport rate expressions for a single, selected key species, and then a multiplier, Ri, is deduced for each of the other species. The total rate applicable to all species is calculated as the product of the rate for the single key species and a combined multiplier (1 + R2 + R3 + etc.). The theory is developed and illustrated by two examples. Limitations of the method are discussed, especially under conditions when conversion rates are uncertain. The advantage of this approach is that existing fugacity and concentration-based models that describe the fate of single-species chemicals can be readily adapted to estimate the fate of multispecies substances such as mercury which display relatively constant species proportions in each medium.

  8. ALREST High Fidelity Modeling Program Approach (United States)


    Gases and Mixtures of Redlich - Kwong and Peng- Robinson Fluids Assumed pdf Model based on k- ε-g Model in NASA/LaRc Vulcan code Level Set model...Potential Attractiveness Of Liquid Hydrocarbon Engines For Boost Applications • Propensity Of Hydrocarbon Engines For Combustion Instability • Air


    Energy Technology Data Exchange (ETDEWEB)

    Martino, C.; Herman, D.; Pike, J.; Peters, T.


    Filtration within the Actinide Removal Process (ARP) currently limits the throughput in interim salt processing at the Savannah River Site. In this process, batches of salt solution with Monosodium Titanate (MST) sorbent are concentrated by crossflow filtration. The filtrate is subsequently processed to remove cesium in the Modular Caustic Side Solvent Extraction Unit (MCU) followed by disposal in saltstone grout. The concentrated MST slurry is washed and sent to the Defense Waste Processing Facility (DWPF) for vitrification. During recent ARP processing, there has been a degradation of filter performance manifested as the inability to maintain high filtrate flux throughout a multi-batch cycle. The objectives of this effort were to characterize the feed streams, to determine if solids (in addition to MST) are precipitating and causing the degraded performance of the filters, and to assess the particle size and rheological data to address potential filtration impacts. Equilibrium modelling with OLI Analyzer{sup TM} and OLI ESP{sup TM} was performed to determine chemical components at risk of precipitation and to simulate the ARP process. The performance of ARP filtration was evaluated to review potential causes of the observed filter behavior. Task activities for this study included extensive physical and chemical analysis of samples from the Late Wash Pump Tank (LWPT) and the Late Wash Hold Tank (LWHT) within ARP as well as samples of the tank farm feed from Tank 49H. The samples from the LWPT and LWHT were obtained from several stages of processing of Salt Batch 6D, Cycle 6, Batch 16.

  10. Frequency Modulation Spectroscopy Modeling for Remote Chemical Detection

    Energy Technology Data Exchange (ETDEWEB)

    Sheen, David M.


    Frequency modulation (FM) spectroscopy techniques show promise for active infrared remote chemical sensing. FM spectroscopy techniques have reduced sensitivity to optical and electronic noise, and are relatively immune to the effects of various electronic and mechanical drifts. FM systems are responsive to sharp spectral features and can therefore reduce the effects of spectral clutter due to interfering chemicals in the plume or in the atmosphere. The relatively high modulation frequencies used for FM also reduces the effects of albedo (reflectance) and plume variations. Conventional differential absorption lidar (DIAL) systems are performance limited by the noise induced by speckle. Analysis presented in this report shows that FM based sensors may reduce the effects of speckle by one to two orders of magnitude. This can result in reduced dwell times and faster area searches, as well as reducing various forms of spatial clutter. FM systems will require a laser system that is continuously tunable at relatively high frequencies (0.1 to 20 MHz). One promising candidate is the quantum-cascade (QC) laser [1, 2]. The QC laser is potentially capable of power levels on the order of 1 Watt and frequency tuning on the order of 3 - 6 GHz, which is the performance level required for FM spectroscopy based remote sensing. In this report we describe a high-level numerical model for an FM spectroscopy based remote sensing system, and application to two unmanned airborne vehicle (UAV) scenarios. A Predator scenario operating at a slant range of 6.5 km with a 10 cm diameter telescope, and a Global Hawk scenario operating at a range of 30 km with a 20 cm diameter telescope, has been assumed to allow estimation of the performance of potential FM systems.

  11. An experimental design approach to the chemical characterisation of pectin polysaccharides extracted from Cucumis melo Inodorus. (United States)

    Denman, Laura J; Morris, Gordon A


    Extracted pectins have been utilised in a number of applications in both the food and pharmaceutical industries where they are generally used as gelling agents, thickeners and stabilisers, although a number of pectins have been shown to be bioactive. These functional properties will depend upon extraction conditions. A statistical experimental design approach was used to study the effects of extraction conditions pH, time and temperature on pectins extracted from Cucumis melo Inodorus. The results show that the chemical composition is very sensitive to these conditions and that this has a great influence on for example the degree of branching. Higher temperatures, lower pHs and longer extraction times lead to a loss of the more acid labile arabinofuranose residues present on the pectin side chain. The fitting of regression equations relating yield and composition to extraction conditions can therefore lead to tailor-made pectins for specific properties and/or applications.

  12. Approaches to assessing the risk of chemical contamination of Urban Soils (United States)

    Makarov, O. A.; Makarov, A. A.


    The existing approaches to studying the risk of chemical contamination of soils are analyzed. It is noted that the actual and critical loads of contaminants on the soil cover are often compared for estimating these risks. The insufficient use of economic tools and methods for assessing the risk of soil contamination is emphasized. The sanitary-hygienic standards are found out to be exceeded for lead, zinc, cadmium and copper content in soils in six localities, each of 6250 m2 in the area, situated in the industrial and transport zones of Podol'sk and Moscow. The values of actual and maximal permissible damage exerted by the heavy-metal contamination to the studied soils are calculated. The probable damage R and the degree of probable damage implementation (DPDI) are used as the indices of soil contamination risk.

  13. Epidemiologic approaches to assessing human cancer risk from consuming aquatic food resources from chemically contaminated water

    Energy Technology Data Exchange (ETDEWEB)

    Ozonoff, D. (Boston Univ. School of Public Health, MA (United States)); Longnecker, M.P. (UCLA School of Public Health, Los Angeles, CA (United States))


    Epidemiologic approaches to assessing human cancer risk from contaminated waters must confront the problems of long latency and rarity of the end point (cancer). The latency problem makes determination of diet history more difficult, while the low frequency of cancer as an end point reduces the statistical power of the study. These factors are discussed in relation to the study designs most commonly employed in epidemiology. It is suggested that the use of biomarkers for persistent chemicals may be useful to mitigate the difficulty of determining exposure, while the use of more prevalent and timely end points, such as carcinogen-DNA adducts or oncogene proteins, may make the latency and rarity problems more tractable.

  14. A Multivariate Approach to Functional Neuro Modeling

    DEFF Research Database (Denmark)

    Mørch, Niels J.S.


    , provides the basis for a generalization theoretical framework relating model performance to model complexity and dataset size. Briefly summarized the major topics discussed in the thesis include: - An introduction of the representation of functional datasets by pairs of neuronal activity patterns...... a generalization theoretical framework centered around measures of model generalization error. - Only few, if any, examples of the application of generalization theory to functional neuro modeling currently exist in the literature. - Exemplification of the proposed generalization theoretical framework...... as particularly important; optimal model flexibility is a function of both the complexity and the size of the dataset at hand. This is something that has not received appropriate attention by the functional neuro modeling community so far. The observation implies that optimal model performance rarely is achieved...

  15. PNe as observational constraints in chemical evolution models for NGC 6822

    CERN Document Server

    Hernandez-Martinez, Liliana; Peña, Miriam; Peimbert, Manuel


    Chemical evolution models are useful for understanding the formation and evolution of stars and galaxies. Model predictions will be more robust as more observational constraints are used. We present chemical evolution models for the dwarf irregular galaxy NGC 6822 using chemical abundances of old and young Planetary Nebulae (PNe) and \\ion{H}{ii} regions as observational constraints. Two sets of chemical abundances, one derived from collisionally excited lines (CELs) and one, from recombination lines (RLs), are used. We try to use our models as a tool to discriminate between both procedures for abundance determinations. In our chemical evolution code, the chemical contribution of low and intermediate mass stars is time delayed, while for the massive stars the chemical contribution follows the instantaneous recycling approximation. Our models have two main free parameters: the mass-loss rate of a well-mixed outflow and the upper mass limit, $M_{up}$, of the initial mass function (IMF). To reproduce the gaseous ...

  16. An approach to enhance self-compensation capability in paper-based devices for chemical sensing. (United States)

    Lo, Shih-Jie; Chen, Kuan-Hung; Yao, Da-Jeng


    This paper describes a simple design for increasing the tolerance of reagent dislocation on a paper-based platform using a combination of wax-treated paper and a vortex mixer. To date, massive budgetary funds are required in the biotechnological industry to develop new applications; a large part of that cost is attributable to the screening of specific chemical compounds. Here, we propose using a liquid-handling robot to automatically deposit selected reagents on a paper-based platform. We also present a preliminary concept approach for developing a reagent placing device with simple and inexpensive features. A defect of inaccuracy was observed between droplet location and test well location after viewing the performance of the liquid-handling robot on our paper-based platform. Because of dislocation error resulting from robotic reagent placement, we decided to apply an external, rotational force following droplet placement in order to compensate for the distance of reagent dislocation. Note, the largest distance of reagent dislocation was determined by examining the results of altering applied reagent volume, but not concentration, in volumes from 5 µL to 30 µL in a series of experiments. As a result of these experiments, we observed that dislocation was positively affected by an increase in applied volume. A colorimetric assay for nitrite detection was also performed to confirm the feasibility of this method. This work, we believe, can minimize the cost of chemical compound screening for the biotechnological industry.

  17. Metabolomic Approaches to Explore Chemical Diversity of Human Breast-Milk, Formula Milk and Bovine Milk. (United States)

    Qian, Linxi; Zhao, Aihua; Zhang, Yinan; Chen, Tianlu; Zeisel, Steven H; Jia, Wei; Cai, Wei


    Although many studies have been conducted on the components present in human breast milk (HM), research on the differences of chemical metabolites between HM, bovine milk (BM) and formula milk (FM) is limited. This study was to explore the chemical diversity of HM, BM and FM by metabolomic approaches. GC-TOFMS and UPLC-QTOFMS were applied to investigate the metabolic compositions in 30 HM samples, 20 FM samples and 20 BM samples. Metabolite profiling identified that most of the non-esterified fatty acids, which reflected the hydrolysis of triglycerides, were much more abundant in HM than those in FM and BM, except for palmitic acid and stearic acid. The levels of tricarboxylic acid (TCA) intermediates were much higher in FM and BM than those in HM. Each type of milk also showed its unique composition of free amino acids and free carbohydrates. In conclusion, higher levels of non-esterified saturated fatty acids with aliphatic tails <16 carbons, monounsaturated fatty acids and polyunsaturated fatty acids and lower levels of TCA intermediates are characteristic of HM, as compared with FM and BM. The content of non-esterified fatty acids may reflect the hydrolysis of triglycerides in different milk types.

  18. A model-based multisensor data fusion knowledge management approach (United States)

    Straub, Jeremy


    A variety of approaches exist for combining data from multiple sensors. The model-based approach combines data based on its support for or refutation of elements of the model which in turn can be used to evaluate an experimental thesis. This paper presents a collection of algorithms for mapping various types of sensor data onto a thesis-based model and evaluating the truth or falsity of the thesis, based on the model. The use of this approach for autonomously arriving at findings and for prioritizing data are considered. Techniques for updating the model (instead of arriving at a true/false assertion) are also discussed.

  19. Effectiveness of bone cleaning process using chemical and entomology approaches: time and cost. (United States)

    Lai, Poh Soon; Khoo, Lay See; Mohd Hilmi, Saidin; Ahmad Hafizam, Hasmi; Mohd Shah, Mahmood; Nurliza, Abdullah; Nazni, Wasi Ahmad


    Skeletal examination is an important aspect of forensic pathology practice, requiring effective bone cleaning with minimal artefact. This study was conducted to compare between chemical and entomology methods of bone cleaning. Ten subjects between 20 and 40 years old who underwent uncomplicated medico-legal autopsies at the Institute of Forensic Medicine Malaysia were randomly chosen for this descriptive cross sectional study. The sternum bone was divided into 4 parts, each part subjected to a different cleaning method, being two chemical approaches i.e. laundry detergent and a combination of 6% hydrogen peroxide and powder sodium bicarbonate and two entomology approaches using 2nd instar maggots of Chrysomyia rufifacies and Ophyra spinigera. A scoring system for grading the outcome of cleaning was used. The effectiveness of the methods was evaluated based on average weight reduction per day and median number of days to achieve the average score of less than 1.5 within 12 days of the bone cleaning process. Using maggots was the most time-effective and costeffective method, achieving an average weight reduction of 1.4 gm per day, a median of 11.3 days to achieve the desired score and an average cost of MYR 4.10 per case to reach the desired score within 12 days. This conclusion was supported by blind validation by forensic specialists achieving a 77.8% preference for maggots. Emission scanning electron microscopy evaluation also revealed that maggots especially Chrysomyia rufifacies preserved the original condition of the bones better allowing improved elucidation of bone injuries in future real cases.

  20. Comparison of two novel approaches to model fibre reinforced concrete

    NARCIS (Netherlands)

    Radtke, F.K.F.; Simone, A.; Sluys, L.J.


    We present two approaches to model fibre reinforced concrete. In both approaches, discrete fibre distributions and the behaviour of the fibre-matrix interface are explicitly considered. One approach employs the reaction forces from fibre to matrix while the other is based on the partition of unity f

  1. Extend of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

    CERN Document Server

    Rosenow, Phil


    The extent of hydrogen coverage of the Si(001)c(4x2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computationa...

  2. Modelling the World Wool Market: A Hybrid Approach



    We present a model of the world wool market that merges two modelling traditions: the partialequilibrium commodity-specific approach and the computable general-equilibrium approach. The model captures the multistage nature of the wool production system, and the heterogeneous nature of raw wool, processed wool and wool garments. It also captures the important wool producing and consuming regions of the world. We illustrate the utility of the model by estimating the effects of tariff barriers o...

  3. Microsolvated transition state models for improved insight into chemical properties and reaction mechanisms. (United States)

    Sunoj, Raghavan B; Anand, Megha


    Over the years, several methods have been developed to effectively represent the chemical behavior of solutes in solvents. The environmental effects arising due to solvation can generally be achieved either through inclusion of discrete solvent molecules or by inscribing into a cavity in a homogeneous and continuum dielectric medium. In both these approaches of computational origin, the perturbations on the solute induced by the surrounding solvent are at the focus of the problem. While the rigor and method of inclusion of solvent effects vary, such solvation models have found widespread applications, as evident from modern chemical literature. A hybrid method, commonly referred to as cluster-continuum model (CCM), brings together the key advantages of discrete and continuum models. In this perspective, we intend to highlight the latent potential of CCM toward obtaining accurate estimates on a number of properties as well as reactions of contemporary significance. The objective has generally been achieved by choosing illustrative examples from the literature, besides expending efforts to bring out the complementary advantages of CCM as compared to continuum or discrete solvation models. The majority of examples emanate from the prevalent applications of CCM to organic reactions, although a handful of interesting organometallic reactions have also been discussed. In addition, increasingly accurate computations of properties like pK(a) and solvation of ions obtained using the CCM protocol are also presented.

  4. Finite state projection based bounds to compare chemical master equation models using single-cell data (United States)

    Fox, Zachary; Neuert, Gregor; Munsky, Brian


    Emerging techniques now allow for precise quantification of distributions of biological molecules in single cells. These rapidly advancing experimental methods have created a need for more rigorous and efficient modeling tools. Here, we derive new bounds on the likelihood that observations of single-cell, single-molecule responses come from a discrete stochastic model, posed in the form of the chemical master equation. These strict upper and lower bounds are based on a finite state projection approach, and they converge monotonically to the exact likelihood value. These bounds allow one to discriminate rigorously between models and with a minimum level of computational effort. In practice, these bounds can be incorporated into stochastic model identification and parameter inference routines, which improve the accuracy and efficiency of endeavors to analyze and predict single-cell behavior. We demonstrate the applicability of our approach using simulated data for three example models as well as for experimental measurements of a time-varying stochastic transcriptional response in yeast.

  5. Measuring equilibrium models: a multivariate approach

    Directory of Open Access Journals (Sweden)

    Nadji RAHMANIA


    Full Text Available This paper presents a multivariate methodology for obtaining measures of unobserved macroeconomic variables. The used procedure is the multivariate Hodrick-Prescot which depends on smoothing param eters. The choice of these parameters is crucial. Our approach is based on consistent estimators of these parameters, depending only on the observed data.

  6. Regularization of turbulence - a comprehensive modeling approach

    NARCIS (Netherlands)

    Geurts, Bernard J.


    Turbulence readily arises in numerous flows in nature and technology. The large number of degrees of freedom of turbulence poses serious challenges to numerical approaches aimed at simulating and controlling such flows. While the Navier-Stokes equations are commonly accepted to precisely describe fl

  7. An algebraic approach to the Hubbard model

    CERN Document Server

    de Leeuw, Marius


    We study the algebraic structure of an integrable Hubbard-Shastry type lattice model associated with the centrally extended su(2|2) superalgebra. This superalgebra underlies Beisert's AdS/CFT worldsheet R-matrix and Shastry's R-matrix. The considered model specializes to the one-dimensional Hubbard model in a certain limit. We demonstrate that Yangian symmetries of the R-matrix specialize to the Yangian symmetry of the Hubbard model found by Korepin and Uglov. Moreover, we show that the Hubbard model Hamiltonian has an algebraic interpretation as the so-called secret symmetry. We also discuss Yangian symmetries of the A and B models introduced by Frolov and Quinn.

  8. A new approach of cascade utilization of the chemical energy of fuel

    Institute of Scientific and Technical Information of China (English)

    HAN Wei; JIN Hongguang; LIN Rumou


    The indirect release of chemical energy of fuel is investigated, and a new mechanism is proposed to identify the cascade utilization of chemical energy of fuel more clearly. Based on the concept of energy level, the internal phenomenon of the indirect chemical energy release is disclosed, and the equations of energy level describing the utilization of chemical energy and thermal energy during the indirect chemical energy release process are obtained. From theoretical analysis, we find that the superiority of the indirect chemical energy release of fuel comes from the cascade utilization of the fuel's chemical energy. Moreover, the cascade utilization of chemical energy is verified by the investigation of CRGT (chemically recuperated gas turbine). As a result, the thermal exergy obtained from the chemical energy release of fuel increases by 2 % -3 %. The results obtained here may help a deeper understanding of indirect chemical energy release of fuel and provide a theoretical basis for the synthesis of innovative energy systems.

  9. A geometrical approach to structural change modeling


    Stijepic, Denis


    We propose a model for studying the dynamics of economic structures. The model is based on qualitative information regarding structural dynamics, in particular, (a) the information on the geometrical properties of trajectories (and their domains) which are studied in structural change theory and (b) the empirical information from stylized facts of structural change. We show that structural change is path-dependent in this model and use this fact to restrict the number of future structural cha...

  10. A graphical approach to analogue behavioural modelling


    Moser, Vincent; Nussbaum, Pascal; Amann, Hans-Peter; Astier, Luc; Pellandini, Fausto


    In order to master the growing complexity of analogue electronic systems, modelling and simulation of analogue hardware at various levels is absolutely necessary. This paper presents an original modelling method based on the graphical description of analogue electronic functional blocks. This method is intended to be automated and integrated into a design framework: specialists create behavioural models of existing functional blocks, that can then be used through high-level selection and spec...

  11. Quasi-chemical approach for adsorption of mixtures with non-additive lateral interactions (United States)

    Pinto, O. A.; Pasinetti, P. M.; Ramirez-Pastor, A. J.


    The statistical thermodynamics of binary mixtures with non-additive lateral interactions was developed on a generalization in the spirit of the lattice-gas model and the classical quasi-chemical approximation (QCA). The traditional assumption of a strictly pairwise additive nearest-neighbors interaction is replaced by a more general one, namely that the bond linking a certain atom with any of its neighbors depends considerably on how many of them are actually present (or absent) on the sites in the first coordination shell of the atom. The total and partial adsorption isotherms are given for both attractive and repulsive lateral interactions between the adsorbed species. Interesting behaviors are observed and discussed in terms of the low-temperature phases formed in the system. Comparisons with Monte Carlo simulations are performed in order to test the validity of the theoretical model.

  12. Optimization of chemical reactor feed by simulations based on a kinetic approach. (United States)

    Guinand, Charles; Dabros, Michal; Roduit, Bertrand; Meyer, Thierry; Stoessel, Francis


    Chemical incidents are typically caused by loss of control, resulting in runaway reactions or process deviations in different stages of the production. In the case of fed-batch reactors, the problem generally encountered is the accumulation of heat. This is directly related to the temperature of the process, the reaction kinetics and adiabatic temperature rise, which is the maximum temperature attainable in the event of cooling failure. The main possibility to control the heat accumulation is the use of a well-controlled adapted feed. The feed rate can be adjusted by using reaction and reactor dynamic models coupled to Model Predictive Control. Thereby, it is possible to predict the best feed profile respecting the safety constraints.

  13. Consumer preference models: fuzzy theory approach (United States)

    Turksen, I. B.; Wilson, I. A.


    Consumer preference models are widely used in new product design, marketing management, pricing and market segmentation. The purpose of this article is to develop and test a fuzzy set preference model which can represent linguistic variables in individual-level models implemented in parallel with existing conjoint models. The potential improvements in market share prediction and predictive validity can substantially improve management decisions about what to make (product design), for whom to make it (market segmentation) and how much to make (market share prediction).

  14. A New Approach for Magneto-Static Hysteresis Behavioral Modeling

    DEFF Research Database (Denmark)

    Astorino, Antonio; Swaminathan, Madhavan; Antonini, Giulio


    In this paper, a new behavioral modeling approach for magneto-static hysteresis is presented. Many accurate models are currently available, but none of them seems to be able to correctly reproduce all the possible B-H paths with low computational cost. By contrast, the approach proposed...... achieved when comparing the measured and simulated results....

  15. Modelling the chemical evolution of star forming filaments (United States)

    Seifried, D.; Walch, S.


    We present simulations of star forming filaments incorporating - to our knowledge - the largest chemical network used to date on-the-fly in a 3D-MHD simulation. The network contains 37 chemical species and about 300 selected reaction rates. For this we use the newly developed package KROME (Grassi et al. [4]). Our results demonstrate the feasibility of using such a complex chemical network in 3D-MHD simulations on modern supercomputers. We perform simulations with different strengths of the interstellar radiation field and the cosmic ray ionisation rate and find chemical and physical results in accordance with observations and other recent numerical work.

  16. Modelling the chemical evolution of star forming filaments

    CERN Document Server

    Seifried, D


    We present simulations of star forming filaments incorporating - to our knowledge - the largest chemical network used to date on-the-fly in a 3D-MHD simulation. The network contains 37 chemical species and about 300 selected reaction rates. For this we use the newly developed package KROME (Grassi et al. 2014). Our results demonstrate the feasibility of using such a complex chemical network in 3D-MHD simulations on modern supercomputers. We perform simulations with different strengths of the interstellar radiation field and the cosmic ray ionisation rate and find chemical and physical results in accordance with observations and other recent numerical work.

  17. Nucleon Spin Content in a Relativistic Quark Potential Model Approach

    Institute of Scientific and Technical Information of China (English)

    DONG YuBing; FENG QingGuo


    Based on a relativistic quark model approach with an effective potential U(r) = (ac/2)(1 + γ0)r2, the spin content of the nucleon is investigated. Pseudo-scalar interaction between quarks and Goldstone bosons is employed to calculate the couplings between the Goldstone bosons and the nucleon. Different approaches to deal with the center of mass correction in the relativistic quark potential model approach are discussed.

  18. Development of chemical kinetic models for lean NOx traps.

    Energy Technology Data Exchange (ETDEWEB)

    Larson, Richard S.


    Overall project goal: Obtain the fundamental surface chemistry knowledge needed for the design and optimal utilization of NOx trap catalysts, thereby helping to speed the widespread adoption of this technology. Relevance to VT Program goals: Effective, durable advanced aftertreatment systems for lean-burn engines must be available if the fuel economy advantages of these engines are to be realized. Specific current year objective: Identify and correct any deficiencies in the previously developed reaction mechanism describing normal storage/regeneration cycles, and complete development of a supplementary mechanism accounting for the effects of sulfation. A fundamental understanding of LNT chemistry is needed to realize the full potential of this aftertreatment technology, which could lead to greater use of fuel-efficient lean-burn engines. We have used a multi-tiered approach to developing an elementary chemical mechanism benchmarked against experimental data: (1) Simulate a set of steady flow experiments, with storage effects minimized, to infer a tentative mechanism for chemistry on precious metal sites (completed). (2) Simulate a set of long cycle experiments to infer a mechanism for NOx and oxygen storage sites while simultaneously finalizing precious metal chemistry (completed). (3) Simulate a simplified sulfation/desulfation protocol to obtain a supplementary set of reactions involving sulfur on all three kinds of sites (nearly completed). (4) Investigate the potential role of reductants other than CO and H{sub 2}. While simulation of isothermal experiments is the preferred way to extract kinetic parameters, simulation of realistic storage/regeneration cycles requires that exotherms be considered. Our ultimate goal is to facilitate improved designs for LNT-based aftertreatment systems and to assist in the development of improved catalysts.

  19. Geo-referenced multimedia environmental fate model (G-CIEMS): model formulation and comparison to the generic model and monitoring approaches. (United States)

    Suzuki, Noriyuki; Murasawa, Kaori; Sakurai, Takeo; Nansai, Keisuke; Matsuhashi, Keisuke; Moriguchi, Yuichi; Tanabe, Kiyoshi; Nakasugi, Osami; Morita, Masatoshi


    A spatially resolved and geo-referenced dynamic multimedia environmental fate model, G-CIEMS (Grid-Catchment Integrated Environmental Modeling System) was developed on a geographical information system (GIS). The case study for Japan based on the air grid cells of 5 x 5 km resolution and catchments with an average area of 9.3 km2, which corresponds to about 40,000 air grid cells and 38,000 river segments/catchment polygons, were performed for dioxins, benzene, 1,3-butadiene, and di-(2-ethyhexyl)phthalate. The averaged concentration of the model and monitoring output were within a factor of 2-3 for all the media. Outputs from G-CIEMS and the generic model were essentially comparable when identical parameters were employed, whereas the G-CIEMS model gave explicit information of distribution of chemicals in the environment. Exposure-weighted averaged concentrations (EWAC) in air were calculated to estimate the exposure ofthe population, based on the results of generic, G-CIEMS, and monitoring approaches. The G-CIEMS approach showed significantly better agreement with the monitoring-derived EWAC than the generic model approach. Implication for the use of a geo-referenced modeling approach in the risk assessment scheme is discussed as a generic-spatial approach, which can be used to provide more accurate exposure estimation with distribution information, using generally available data sources for a wide range of chemicals.

  20. An approach for activity-based DEVS model specification

    DEFF Research Database (Denmark)

    Alshareef, Abdurrahman; Sarjoughian, Hessam S.; Zarrin, Bahram


    activity-based behavior modeling of parallel DEVS atomic models. We consider UML activities and actions as fundamental units of behavior modeling, especially in the presence of recent advances in the UML 2.5 specifications. We describe in detail how to approach activity modeling with a set of elemental...

  1. A simple approach to modeling ductile failure.

    Energy Technology Data Exchange (ETDEWEB)

    Wellman, Gerald William


    Sandia National Laboratories has the need to predict the behavior of structures after the occurrence of an initial failure. In some cases determining the extent of failure, beyond initiation, is required, while in a few cases the initial failure is a design feature used to tailor the subsequent load paths. In either case, the ability to numerically simulate the initiation and propagation of failures is a highly desired capability. This document describes one approach to the simulation of failure initiation and propagation.

  2. Challenges and opportunities for integrating lake ecosystem modelling approaches (United States)

    Mooij, Wolf M.; Trolle, Dennis; Jeppesen, Erik; Arhonditsis, George; Belolipetsky, Pavel V.; Chitamwebwa, Deonatus B.R.; Degermendzhy, Andrey G.; DeAngelis, Donald L.; Domis, Lisette N. De Senerpont; Downing, Andrea S.; Elliott, J. Alex; Ruberto, Carlos Ruberto; Gaedke, Ursula; Genova, Svetlana N.; Gulati, Ramesh D.; Hakanson, Lars; Hamilton, David P.; Hipsey, Matthew R.; Hoen, Jochem 't; Hulsmann, Stephan; Los, F. Hans; Makler-Pick, Vardit; Petzoldt, Thomas; Prokopkin, Igor G.; Rinke, Karsten; Schep, Sebastiaan A.; Tominaga, Koji; Van Dam, Anne A.; Van Nes, Egbert H.; Wells, Scott A.; Janse, Jan H.


    A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and trait-based models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative

  3. Modeling regional secondary organic aerosol using the Master Chemical Mechanism (United States)

    Li, Jingyi; Cleveland, Meredith; Ziemba, Luke D.; Griffin, Robert J.; Barsanti, Kelley C.; Pankow, James F.; Ying, Qi


    A modified near-explicit Master Chemical Mechanism (MCM, version 3.2) with 5727 species and 16,930 reactions and an equilibrium partitioning module was incorporated into the Community Air Quality Model (CMAQ) to predict the regional concentrations of secondary organic aerosol (SOA) from volatile organic compounds (VOCs) in the eastern United States (US). In addition to the semi-volatile SOA from equilibrium partitioning, reactive surface uptake processes were used to simulate SOA formation due to isoprene epoxydiol, glyoxal and methylglyoxal. The CMAQ-MCM-SOA model was applied to simulate SOA formation during a two-week episode from August 28 to September 7, 2006. The southeastern US has the highest SOA, with a maximum episode-averaged concentration of ∼12 μg m-3. Primary organic aerosol (POA) and SOA concentrations predicted by CMAQ-MCM-SOA agree well with AMS-derived hydrocarbon-like organic aerosol (HOA) and oxygenated organic aerosol (OOA) urban concentrations at the Moody Tower at the University of Houston. Predicted molecular properties of SOA (O/C, H/C, N/C and OM/OC ratios) at the site are similar to those reported in other urban areas, and O/C values agree with measured O/C at the same site. Isoprene epoxydiol is predicted to be the largest contributor to total SOA concentration in the southeast US, followed by methylglyoxal and glyoxal. The semi-volatile SOA components are dominated by products from β-caryophyllene oxidation, but the major species and their concentrations are sensitive to errors in saturation vapor pressure estimation. A uniform decrease of saturation vapor pressure by a factor of 100 for all condensable compounds can lead to a 150% increase in total SOA. A sensitivity simulation with UNIFAC-calculated activity coefficients (ignoring phase separation and water molecule partitioning into the organic phase) led to a 10% change in the predicted semi-volatile SOA concentrations.

  4. Development of pure component property models for chemical product-process design and analysis

    DEFF Research Database (Denmark)

    Hukkerikar, Amol Shivajirao

    Property prediction models based on the group-contribution+ (GC+) approach have been developed to provide reliable predictions of pure component properties together with uncertainties of predicted property values which is much needed information in performing chemical product and process design...... the CAPEC database, the US Environmental Protection Agency (EPA) database, and the USEtox database are used. In total, 21 thermo-physical properties and 22 environmental-related properties of pure components which include normal boiling point, critical constants, standard enthalpy of formation, liquid...... be applied to a wide range of properties of pure components. pure components. In this work, however, the application of ‘molecular structural similarity criteria’ is illustrated by considering performance improvement of models for enthalpy of formation, enthalpy of fusion, and critical temperature. For all...


    Energy Technology Data Exchange (ETDEWEB)



    Atmospheric aerosols, suspensions of solid or liquid particles, are an important multi-phase system. Aerosols scatter and absorb shortwave (solar) radiation, affecting climate (Charlson et al., 1992; Schwartz, 1996) and visibility; nucleate cloud droplet formation, modifying the reflectivity of clouds (Twomey et al., 1984; Schwartz and Slingo, 1996) as well as contributing to composition of cloudwater and to wet deposition (Seinfeld and Pandis, 1998); and affect human health through inhalation (NRC, 1998). Existing and prospective air quality regulations impose standards on concentrations of atmospheric aerosols to protect human health and welfare (EPA, 1998). Chemical transport and transformation models representing the loading and geographical distribution of aerosols and precursor gases are needed to permit development of effective and efficient strategies for meeting air quality standards, and for examining aerosol effects on climate retrospectively and prospectively for different emissions scenarios. Important aerosol properties and processes depend on their size distribution: light scattering, cloud nucleating properties, dry deposition, and penetration into airways of lungs. The evolution of the mass loading itself depends on particle size because of the size dependence of growth and removal processes. For these reasons it is increasingly recognized that chemical transport and transformation models must represent not just the mass loading of atmospheric particulate matter but also the aerosol microphysical properties and the evolution of these properties if aerosols are to be accurately represented in these models. If the size distribution of the aerosol is known, a given property can be evaluated as the integral of the appropriate kernel function over the size distribution. This has motivated the approach of determining aerosol size distribution, and of explicitly representing this distribution and its evolution in chemical transport models.

  6. Machine Learning Approaches for Modeling Spammer Behavior

    CERN Document Server

    Islam, Md Saiful; Islam, Md Rafiqul


    Spam is commonly known as unsolicited or unwanted email messages in the Internet causing potential threat to Internet Security. Users spend a valuable amount of time deleting spam emails. More importantly, ever increasing spam emails occupy server storage space and consume network bandwidth. Keyword-based spam email filtering strategies will eventually be less successful to model spammer behavior as the spammer constantly changes their tricks to circumvent these filters. The evasive tactics that the spammer uses are patterns and these patterns can be modeled to combat spam. This paper investigates the possibilities of modeling spammer behavioral patterns by well-known classification algorithms such as Na\\"ive Bayesian classifier (Na\\"ive Bayes), Decision Tree Induction (DTI) and Support Vector Machines (SVMs). Preliminary experimental results demonstrate a promising detection rate of around 92%, which is considerably an enhancement of performance compared to similar spammer behavior modeling research.

  7. Infectious disease modeling a hybrid system approach

    CERN Document Server

    Liu, Xinzhi


    This volume presents infectious diseases modeled mathematically, taking seasonality and changes in population behavior into account, using a switched and hybrid systems framework. The scope of coverage includes background on mathematical epidemiology, including classical formulations and results; a motivation for seasonal effects and changes in population behavior, an investigation into term-time forced epidemic models with switching parameters, and a detailed account of several different control strategies. The main goal is to study these models theoretically and to establish conditions under which eradication or persistence of the disease is guaranteed. In doing so, the long-term behavior of the models is determined through mathematical techniques from switched systems theory. Numerical simulations are also given to augment and illustrate the theoretical results and to help study the efficacy of the control schemes.

  8. A rational approach to selecting and ranking some pharmaceuticals of concern for the aquatic environment and their relative importance compared with other chemicals. (United States)

    Donnachie, Rachel L; Johnson, Andrew C; Sumpter, John P


    Aquatic organisms can be exposed to thousands of chemicals discharged by the human population. Many of these chemicals are considered disruptive to aquatic wildlife, and the literature on the impacts of these chemicals grows daily. However, because time and resources are not infinite, research must focus on the chemicals that represent the greatest threat. One group of chemicals of increasing concern is pharmaceuticals, for which the primary challenge is to identify which represent the greatest threat. In the present study, a list of 12 pharmaceuticals was compiled based on scoring the prevalence of different compounds from previous prioritization reviews. These included rankings based on prescription data, environmental concentrations, predicted environmental concentration/predicted no-effect concentration (PEC/PNEC) ratios, persistency/bioaccumulation/(eco)toxicity (PBT), and fish plasma model approaches. The most frequently cited were diclofenac, paracetamol, ibuprofen, carbamazepine, naproxen, atenolol, ethinyl estradiol, aspirin, fluoxetine, propranolol, metoprolol, and sulfamethoxazole. For each pharmaceutical, literature on effect concentrations was compiled and compared with river concentrations in the United Kingdom. The pharmaceuticals were ranked by degree of difference between the median effect and median river concentrations. Ethinyl estradiol was ranked as the highest concern, followed by fluoxetine, propranolol, and paracetamol. The relative risk of these pharmaceuticals was compared with those of metals and some persistent organic pollutants. Pharmaceuticals appear to be less of a threat to aquatic organisms than some metals (Cu, Al, Zn) and triclosan, using this ranking approach.

  9. Second Quantization Approach to Stochastic Epidemic Models

    CERN Document Server

    Mondaini, Leonardo


    We show how the standard field theoretical language based on creation and annihilation operators may be used for a straightforward derivation of closed master equations describing the population dynamics of multivariate stochastic epidemic models. In order to do that, we introduce an SIR-inspired stochastic model for hepatitis C virus epidemic, from which we obtain the time evolution of the mean number of susceptible, infected, recovered and chronically infected individuals in a population whose total size is allowed to change.

  10. Models for risk assessment of reactive chemicals in aquatic toxicology

    NARCIS (Netherlands)

    Freidig, Andreas Peter


    A quantitative structure property relationship (QSPR) for a,b-unsaturated carboxylates (mainly acrylates and methacrylates) was established in chapter 2. Chemical reaction rate constants were measured for 12 different chemicals with three different nucleophiles, namely H 2 O, OH - and glutathione (G

  11. Rates and Mechanisms of Oil Shale Pyrolysis: A Chemical Structure Approach

    Energy Technology Data Exchange (ETDEWEB)

    Fletcher, Thomas; Pugmire, Ronald


    Three pristine Utah Green River oil shale samples were obtained and used for analysis by the combined research groups at the University of Utah and Brigham Young University. Oil shale samples were first demineralized and the separated kerogen and extracted bitumen samples were then studied by a host of techniques including high resolution liquid-state carbon-13 NMR, solid-state magic angle sample spinning 13C NMR, GC/MS, FTIR, and pyrolysis. Bitumen was extracted from the shale using methanol/dichloromethane and analyzed using high resolution 13C NMR liquid state spectroscopy, showing carbon aromaticities of 7 to 11%. The three parent shales and the demineralized kerogens were each analyzed with solid-state 13C NMR spectroscopy. Carbon aromaticity of the kerogen was 23-24%, with 10-12 aromatic carbons per cluster. Crushed samples of Green River oil shale and its kerogen extract were pyrolyzed at heating rates from 1 to 10 K/min at pressures of 1 and 40 bar and temperatures up to 1000°C. The transient pyrolysis data were fit with a first-order model and a Distributed Activation Energy Model (DAEM). The demineralized kerogen was pyrolyzed at 10 K/min in nitrogen at atmospheric pressure at temperatures up to 525°C, and the pyrolysis products (light gas, tar, and char) were analyzed using 13C NMR, GC/MS, and FTIR. Details of the kerogen pyrolysis have been modeled by a modified version of the chemical percolation devolatilization (CPD) model that has been widely used to model coal combustion/pyrolysis. This refined CPD model has been successful in predicting the char, tar, and gas yields of the three shale samples during pyrolysis. This set of experiments and associated modeling represents the most sophisticated and complete analysis available for a given set of oil shale samples.

  12. Flipped models in Trinification: A Comprehensive Approach

    CERN Document Server

    Rodríguez, Oscar; Ponce, William A; Rojas, Eduardo


    By considering the 3-3-1 and the left-right symmetric models as low energy effective theories of the trinification group, alternative versions of these models are found. The new neutral gauge bosons in the universal 3-3-1 model and its flipped versions are considered; also, the left-right symmetric model and the two flipped variants of it are also studied. For these models, the couplings of the $Z'$ bosons to the standard model fermions are reported. The explicit form of the null space of the vector boson mass matrix for an arbitrary Higgs tensor and gauge group is also presented. In the general framework of the trinification gauge group, and by using the LHC experimental results and EW precision data, limits on the $Z'$ mass and the mixing angle between $Z$ and the new gauge bosons $Z'$ are imposed. The general results call for very small mixing angles in the range $10^{-3}$ radians and $M_{Z'}$ > 2.5 TeV.

  13. Approaching models of nursing from a postmodernist perspective. (United States)

    Lister, P


    This paper explores some questions about the use of models of nursing. These questions make various assumptions about the nature of models of nursing, in general and in particular. Underlying these assumptions are various philosophical positions which are explored through an introduction to postmodernist approaches in philosophical criticism. To illustrate these approaches, a critique of the Roper et al. model is developed, and more general attitudes towards models of nursing are examined. It is suggested that postmodernism offers a challenge to many of the assumptions implicit in models of nursing, and that a greater awareness of these assumptions should lead to nursing care being better informed where such models are in use.

  14. 3 Lectures: "Lagrangian Models", "Numerical Transport Schemes", and "Chemical and Transport Models" (United States)

    Douglass, A.


    The topics for the three lectures for the Canadian Summer School are Lagrangian Models, numerical transport schemes, and chemical and transport models. In the first lecture I will explain the basic components of the Lagrangian model (a trajectory code and a photochemical code), the difficulties in using such a model (initialization) and show some applications in interpretation of aircraft and satellite data. If time permits I will show some results concerning inverse modeling which is being used to evaluate sources of tropospheric pollutants. In the second lecture I will discuss one of the core components of any grid point model, the numerical transport scheme. I will explain the basics of shock capturing schemes, and performance criteria. I will include an example of the importance of horizontal resolution to polar processes. We have learned from NASA's global modeling initiative that horizontal resolution matters for predictions of the future evolution of the ozone hole. The numerical scheme will be evaluated using performance metrics based on satellite observations of long-lived tracers. The final lecture will discuss the evolution of chemical transport models over the last decade. Some of the problems with assimilated winds will be demonstrated, using satellite data to evaluate the simulations.

  15. Modeling the Influence of Transport on Chemical Reactivity in Microbial Membranes: Mineral Precipitation/Dissolution Reactions. (United States)

    Felmy, A. R.; Liu, C.; Clark, S.; Straatsma, T.; Rustad, J.


    It has long been known that microorganisms can alter the chemical composition of their immediate surroundings and influence such processes as ion uptake or adsorption and mineral precipitation dissolution. However, only recently have molecular imaging and molecular modeling capabilities been developed that begin to shed light on the nature of these processes at the nm to um scale at the surface of bacterial membranes. In this presentation we will show the results of recent molecular simulations of microbial surface reactions and describe our efforts to develop accurate non-equilibrium thermodynamic models for the microbial surface that can describe ion uptake and surface induced mineral precipitation. The thermodynamic models include the influence of the bacterial electrical double layer on the uptake of ions from solution and the removal, or exclusion, of ions from the surface of the cell, non-equilibrium diffusion and chemical reaction within the membrane, as well as a new thermodynamic approach to representing ion activities within the microbial membrane. In the latter case, the variability in the water content within the microbial membrane has a significant influence on the calculated mineral saturation indices. In such cases, we will propose the use of recently developed mixed solvent-electrolyte formalisms. Recent experimental data for mixed-solvent electrolyte systems will also be presented to demonstrate the potential impact of the variable water content on calculated ion activities within the membrane.

  16. Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization. (United States)

    Huang, Ruili; Xia, Menghang; Sakamuru, Srilatha; Zhao, Jinghua; Shahane, Sampada A; Attene-Ramos, Matias; Zhao, Tongan; Austin, Christopher P; Simeonov, Anton


    Target-specific, mechanism-oriented in vitro assays post a promising alternative to traditional animal toxicology studies. Here we report the first comprehensive analysis of the Tox21 effort, a large-scale in vitro toxicity screening of chemicals. We test ∼ 10,000 chemicals in triplicates at 15 concentrations against a panel of nuclear receptor and stress response pathway assays, producing more than 50 million data points. Compound clustering by structure similarity and activity profile similarity across the assays reveals structure-activity relationships that are useful for the generation of mechanistic hypotheses. We apply structural information and activity data to build predictive models for 72 in vivo toxicity end points using a cluster-based approach. Models based on in vitro assay data perform better in predicting human toxicity end points than animal toxicity, while a combination of structural and activity data results in better models than using structure or activity data alone. Our results suggest that in vitro activity profiles can be applied as signatures of compound mechanism of toxicity and used in prioritization for more in-depth toxicological testing.

  17. Inquiry guided learning in a chemical engineering core curriculum: General instructional approach and specific application to the fluid mechanics case


    Atilhan, Mert; Eljack, Fadwa; Alfadala, Hassan; Froyd, Jeffrey E.; El-Halwagi, Mahmoud; Mahalec, Vladimir


    This paper presents results from a preliminary study of the effectiveness of using inquiry-guided learning instructional strategies both in chemical engineering classrooms and laboratories. For readers unfamiliar with the instructional strategy, the paper describes the general approach and then reports on results of its application for the fluid mechanics course taken by undergraduate students in the Chemical Engineering Department at Qatar University. Inquiry-guided activities were developed...

  18. Manufacturing Excellence Approach to Business Performance Model

    Directory of Open Access Journals (Sweden)

    Jesus Cruz Alvarez


    Full Text Available Six Sigma, lean manufacturing, total quality management, quality control, and quality function deployment are the fundamental set of tools to enhance productivity in organizations. There is some research that outlines the benefit of each tool into a particular context of firm´s productivity, but not into a broader context of firm´s competitiveness that is achieved thru business performance. The aim of this theoretical research paper is to contribute to this mean and propose a manufacturing excellence approach that links productivity tools into a broader context of business performance.

  19. A Bayesian Model Committee Approach to Forecasting Global Solar Radiation

    CERN Document Server

    Lauret, Philippe; Muselli, Marc; David, Mathieu; Diagne, Hadja; Voyant, Cyril


    This paper proposes to use a rather new modelling approach in the realm of solar radiation forecasting. In this work, two forecasting models: Autoregressive Moving Average (ARMA) and Neural Network (NN) models are combined to form a model committee. The Bayesian inference is used to affect a probability to each model in the committee. Hence, each model's predictions are weighted by their respective probability. The models are fitted to one year of hourly Global Horizontal Irradiance (GHI) measurements. Another year (the test set) is used for making genuine one hour ahead (h+1) out-of-sample forecast comparisons. The proposed approach is benchmarked against the persistence model. The very first results show an improvement brought by this approach.

  20. MDA based-approach for UML Models Complete Comparison

    CERN Document Server

    Chaouni, Samia Benabdellah; Mouline, Salma


    If a modeling task is distributed, it will frequently be necessary to integrate models developed by different team members. Problems occur in the models integration step and particularly, in the comparison phase of the integration. This issue had been discussed in several domains and various models. However, previous approaches have not correctly handled the semantic comparison. In the current paper, we provide a MDA-based approach for models comparison which aims at comparing UML models. We develop an hybrid approach which takes into account syntactic, semantic and structural comparison aspects. For this purpose, we use the domain ontology as well as other resources such as dictionaries. We propose a decision support system which permits the user to validate (or not) correspondences extracted in the comparison phase. For implementation, we propose an extension of the generic correspondence metamodel AMW in order to transform UML models to the correspondence model.

  1. Bringing Science and Pragmatism together - a Tiered Approach for Modelling Toxicological Impacts in LCA

    DEFF Research Database (Denmark)

    Guinée, J; De Koning, A; Pennington, David W.;


    , there is insufficient knowledge and/or resources to have high data availability as well as high data quality and high model quality at the same time. Results. The OMNIITOX project is developing two inter-related models in order to be able to provide LCA impact assessment characterisation factors for toxic releases...... for as broad a range of chemicals as possible: 1) A base model representing a state-of-the-art multimedia model and 2) a simple model derived from the base model using statistical tools. Discussion. A preliminary decision tree for using the OMNIITOX information system (IS) is presented. The decision tree aims...... categories. The OMNIITOX project is developing a tiered model approach for this. It is foreseen that a first version of the base model will be ready in late summer of 2004, whereas a first version of the simple base model is expected a few months later....

  2. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Directory of Open Access Journals (Sweden)

    Mihai V. Putz


    Full Text Available Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding and quantitative (for predicting mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD as the revived precursor for comparative molecular field analyses (CoMFA and comparative molecular similarity indices analysis (CoMSIA; all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy-methyl]-6-(phenylthiothymine congeners’ (HEPT ligands antiviral activity against Human Immunodeficiency Virus of first type (HIV-1 and new pharmacophores in treating severe genetic disorders (like depression and psychosis, respectively, all involving 3D pharmacophore interactions.

  3. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions (United States)

    Putz, Mihai V.; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta


    Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

  4. Chemical Atmosphere-Snow-Sea Ice Interactions: defining future research in the field, lab and modeling (United States)

    Frey, Markus


    The air-snow-sea ice system plays an important role in the global cycling of nitrogen, halogens, trace metals or carbon, including greenhouse gases (e.g. CO2 air-sea flux), and therefore influences also climate. Its impact on atmospheric composition is illustrated for example by dramatic ozone and mercury depletion events which occur within or close to the sea ice zone (SIZ) mostly during polar spring and are catalysed by halogens released from SIZ ice, snow or aerosol. Recent field campaigns in the high Arctic (e.g. BROMEX, OASIS) and Antarctic (Weddell sea cruises) highlight the importance of snow on sea ice as a chemical reservoir and reactor, even during polar night. However, many processes, participating chemical species and their interactions are still poorly understood and/or lack any representation in current models. Furthermore, recent lab studies provide a lot of detail on the chemical environment and processes but need to be integrated much better to improve our understanding of a rapidly changing natural environment. During a 3-day workshop held in Cambridge/UK in October 2013 more than 60 scientists from 15 countries who work on the physics, chemistry or biology of the atmosphere-snow-sea ice system discussed research status and challenges, which need to be addressed in the near future. In this presentation I will give a summary of the main research questions identified during this workshop as well as ways forward to answer them through a community-based interdisciplinary approach.

  5. Review of laboratory-based terrestrial bioaccumulation assessment approaches for organic chemicals: Current status and future possibilities. (United States)

    Hoke, Robert; Huggett, Duane; Brasfield, Sandra; Brown, Becky; Embry, Michelle; Fairbrother, Anne; Kivi, Michelle; Paumen, Miriam Leon; Prosser, Ryan; Salvito, Dan; Scroggins, Rick


    In the last decade, interest has been renewed in approaches for the assessment of the bioaccumulation potential of chemicals, principally driven by the need to evaluate large numbers of chemicals as part of new chemical legislation, while reducing vertebrate test organism use called for in animal welfare legislation. This renewed interest has inspired research activities and advances in bioaccumulation science for neutral organic chemicals in aquatic environments. In January 2013, ILSI Health and Environmental Sciences Institute convened experts to identify the state of the science and existing shortcomings in terrestrial bioaccumulation assessment of neutral organic chemicals. Potential modifications to existing laboratory methods were identified, including areas in which new laboratory approaches or test methods could be developed to address terrestrial bioaccumulation. The utility of "non-ecotoxicity" data (e.g., mammalian laboratory data) was also discussed. The highlights of the workshop discussions are presented along with potential modifications in laboratory approaches and new test guidelines that could be used for assessing the bioaccumulation of chemicals in terrestrial organisms.

  6. Improving chemical education from high school to college using a more hands-on approach (United States)

    Ruddick, Kristie Winfield

    In this work, various alternative teaching methods and activities for chemical education are developed, presented, and evaluated. In the first study, an original hands-on activity using LEGO® blocks to model ionic chemical formulas is presented together with quantitative and qualitative data regarding its educational effectiveness. Students explore cation to anion ratios using LEGO® blocks to represent trivalent, divalent and monovalent cations and anions. High school chemistry students who participated in the LEGO® lab showed significantly higher post-test scores than other students. The second study grows out of the creation of a computational lab module that is shown to significantly increase student learning in the subject of molecular orbital theory in first semester college General Chemistry. The third and final study presented is a course redesign project for college CHEM 1100, Preparation for General Chemistry. In this project the classroom is “flipped”. Students watch video lectures at home, and spend class time working with peers and the instructor on problem solving activities. The results presented here are one of the first quantitative studies showing the effectiveness of “flipping the classroom”. Students who were taught using the Reverse-Instruction (RI) method had significantly higher success in both the Preparation for General Chemistry course and traditionally taught General Chemistry I the following semester.

  7. Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach. (United States)

    van Roekel, Hendrik W H; Rosier, Bas J H M; Meijer, Lenny H H; Hilbers, Peter A J; Markvoort, Albert J; Huck, Wilhelm T S; de Greef, Tom F A


    Living cells are able to produce a wide variety of biological responses when subjected to biochemical stimuli. It has become apparent that these biological responses are regulated by complex chemical reaction networks (CRNs). Unravelling the function of these circuits is a key topic of both systems biology and synthetic biology. Recent progress at the interface of chemistry and biology together with the realisation that current experimental tools are insufficient to quantitatively understand the molecular logic of pathways inside living cells has triggered renewed interest in the bottom-up development of CRNs. This builds upon earlier work of physical chemists who extensively studied inorganic CRNs and showed how a system of chemical reactions can give rise to complex spatiotemporal responses such as oscillations and pattern formation. Using purified biochemical components, in vitro synthetic biologists have started to engineer simplified model systems with the goal of mimicking biological responses of intracellular circuits. Emulation and reconstruction of system-level properties of intracellular networks using simplified circuits are able to reveal key design principles and molecular programs that underlie the biological function of interest. In this Tutorial Review, we present an accessible overview of this emerging field starting with key studies on inorganic CRNs followed by a discussion of recent work involving purified biochemical components. Finally, we review recent work showing the versatility of programmable biochemical reaction networks (BRNs) in analytical and diagnostic applications.

  8. Mixture modeling approach to flow cytometry data. (United States)

    Boedigheimer, Michael J; Ferbas, John


    Flow Cytometry has become a mainstay technique for measuring fluorescent and physical attributes of single cells in a suspended mixture. These data are reduced during analysis using a manual or semiautomated process of gating. Despite the need to gate data for traditional analyses, it is well recognized that analyst-to-analyst variability can impact the dataset. Moreover, cells of interest can be inadvertently excluded from the gate, and relationships between collected variables may go unappreciated because they were not included in the original analysis plan. A multivariate non-gating technique was developed and implemented that accomplished the same goal as traditional gating while eliminating many weaknesses. The procedure was validated against traditional gating for analysis of circulating B cells in normal donors (n = 20) and persons with Systemic Lupus Erythematosus (n = 42). The method recapitulated relationships in the dataset while providing for an automated and objective assessment of the data. Flow cytometry analyses are amenable to automated analytical techniques that are not predicated on discrete operator-generated gates. Such alternative approaches can remove subjectivity in data analysis, improve efficiency and may ultimately enable construction of large bioinformatics data systems for more sophisticated approaches to hypothesis testing.

  9. A consortium approach to glass furnace modeling.

    Energy Technology Data Exchange (ETDEWEB)

    Chang, S.-L.; Golchert, B.; Petrick, M.


    Using computational fluid dynamics to model a glass furnace is a difficult task for any one glass company, laboratory, or university to accomplish. The task of building a computational model of the furnace requires knowledge and experience in modeling two dissimilar regimes (the combustion space and the liquid glass bath), along with the skill necessary to couple these two regimes. Also, a detailed set of experimental data is needed in order to evaluate the output of the code to ensure that the code is providing proper results. Since all these diverse skills are not present in any one research institution, a consortium was formed between Argonne National Laboratory, Purdue University, Mississippi State University, and five glass companies in order to marshal these skills into one three-year program. The objective of this program is to develop a fully coupled, validated simulation of a glass melting furnace that may be used by industry to optimize the performance of existing furnaces.

  10. The Ehrenfest force topology: a physically intuitive approach for analyzing chemical interactions. (United States)

    Maza, Julio R; Jenkins, Samantha; Kirk, Steven R; Anderson, James S M; Ayers, Paul W


    Modified ANO-RCC basis sets are used to determine twelve molecular graphs of the Ehrenfest force for H2, CH4, CH2O, CH3NO, C2H2, C2H4, C3H3NO, N4H4, H2O, (H2O)2, (H2O)4 and (H2O)6. The molecular graphs include all types of topological critical points and a mix of bonding types is chosen to include sigma-, π- and hydrogen-bonding. We then compare a wide range of point properties: charge density, trace of the Hessian, eigenvalues, ellipticity, stiffness, total local energy and the eigenvectors are calculated at the bond critical points (BCPs) and compared for the Ehrenfest, QTAIM and stress tensor schemes. QTAIM is found to be the only partitioning scheme that can differentiate between shared- and closed-shell chemical bond types. Only the results from the Ehrenfest force partitioning, however, are demonstrated to be physically intuitive. This is demonstrated for the water molecule, the water-dimer and the water clusters (H2O)4 and (H2O)6. In particular, both the stiffness and the trace of the Hessians of the appropriate quantities of the sigma-bond BCPs for the water clusters are found to depend on the quantum topology dimension of the molecular graph. The behavior of all the stress tensor point properties is found to be erratic. This is explained by the ambiguity in the theoretical definition of the stress tensor. As a complementary approach the Ehrenfest force provides a new indicator of the mixed chemical character of the hydrogen-bond BCP, which arises from the collinear donor sigma-bond donating a degree of covalent character to the hydrogen-bond. This indicator takes the form of the relative orientation of the shallowest direction of the Ehrenfest potential of the hydrogen-bond BCPs and the corresponding direction for the collinear sigma-bond BCP.

  11. Thermochemical model for shock-induced chemical reactions in porous thermite: The heat detonation model

    Energy Technology Data Exchange (ETDEWEB)

    Boslough, M.B.


    A thermochemical model has been developed that treats a shock-induced solid state chemical reaction as a special type of detonation, called a ''heat detonation'' to distinguish it from an ordinary explosive detonation and describe the final form that the chemical energy takes. According to shock temperature measurements, chemical energy can be released from porous reactive solids on a time scale shorter than shock-transit times in laboratory samples. By comparing the experimental shock temperature for porous thermite to that calculated by the model, the amount of thermite reacted when shocked to about 4 GPa was estimated to be between 60 and 70%. Calculated shock temperatures are extremely strong functions of the extent of reaction, but are relatively insensitive to the initial porosity and amount of volatile impurities. Thus, shock temperature measurements are the most useful for real-time studies of shock-induced exothermic chemical reactions in solids. 11 refs., 5 figs., 1 tab.


    Energy Technology Data Exchange (ETDEWEB)

    Offner, Stella S. R. [Department of Astronomy, Yale University, New Haven, CT 06511 (United States); Bisbas, Thomas G.; Viti, Serena [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6B (United Kingdom); Bell, Tom A., E-mail: [Centro de Astrobiologia (CSIC-INTA), Carretera de Ajalvir, km 4, E-28850 Madrid (Spain)


    We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C{sup +}, C, H{sub 2}, and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric problems. We compare our results with the work of Glover et al., who self-consistently followed the time evolution of molecule formation in hydrodynamic simulations using a reduced chemical network. In general, we find good agreement with this in situ approach for C and CO abundances. However, the temperature and H{sub 2} abundances are discrepant in the boundary regions (A{sub v} {<=} 5), which is due to the different number of rays used by the two approaches.

  13. Use of comparative genomics approaches to characterize interspecies differences in response to environmental chemicals: Challenges, opportunities, and research needs

    Energy Technology Data Exchange (ETDEWEB)

    Burgess-Herbert, Sarah L., E-mail: [American Association for the Advancement of Science (AAAS) Science and Technology Policy Fellow at the US Environmental Protection Agency (EPA), 2009–10 (United States); Euling, Susan Y. [National Center for Environmental Assessment, Office of Research and Development, US Environmental Protection Agency, Washington, DC 20460 (United States)


    A critical challenge for environmental chemical risk assessment is the characterization and reduction of uncertainties introduced when extrapolating inferences from one species to another. The purpose of this article is to explore the challenges, opportunities, and research needs surrounding the issue of how genomics data and computational and systems level approaches can be applied to inform differences in response to environmental chemical exposure across species. We propose that the data, tools, and evolutionary framework of comparative genomics be adapted to inform interspecies differences in chemical mechanisms of action. We compare and contrast existing approaches, from disciplines as varied as evolutionary biology, systems biology, mathematics, and computer science, that can be used, modified, and combined in new ways to discover and characterize interspecies differences in chemical mechanism of action which, in turn, can be explored for application to risk assessment. We consider how genetic, protein, pathway, and network information can be interrogated from an evolutionary biology perspective to effectively characterize variations in biological processes of toxicological relevance among organisms. We conclude that comparative genomics approaches show promise for characterizing interspecies differences in mechanisms of action, and further, for improving our understanding of the uncertainties inherent in extrapolating inferences across species in both ecological and human health risk assessment. To achieve long-term relevance and consistent use in environmental chemical risk assessment, improved bioinformatics tools, computational methods robust to data gaps, and quantitative approaches for conducting extrapolations across species are critically needed. Specific areas ripe for research to address these needs are recommended.

  14. A moving approach for the Vector Hysteron Model

    Energy Technology Data Exchange (ETDEWEB)

    Cardelli, E. [Department of Engineering, University of Perugia, Via G. Duranti 93, 06125 Perugia (Italy); Faba, A., E-mail: [Department of Engineering, University of Perugia, Via G. Duranti 93, 06125 Perugia (Italy); Laudani, A. [Department of Engineering, Roma Tre University, Via V. Volterra 62, 00146 Rome (Italy); Quondam Antonio, S. [Department of Engineering, University of Perugia, Via G. Duranti 93, 06125 Perugia (Italy); Riganti Fulginei, F.; Salvini, A. [Department of Engineering, Roma Tre University, Via V. Volterra 62, 00146 Rome (Italy)


    A moving approach for the VHM (Vector Hysteron Model) is here described, to reconstruct both scalar and rotational magnetization of electrical steels with weak anisotropy, such as the non oriented grain Silicon steel. The hysterons distribution is postulated to be function of the magnetization state of the material, in order to overcome the practical limitation of the congruency property of the standard VHM approach. By using this formulation and a suitable accommodation procedure, the results obtained indicate that the model is accurate, in particular in reproducing the experimental behavior approaching to the saturation region, allowing a real improvement respect to the previous approach.

  15. Nonperturbative approach to the modified statistical model

    Energy Technology Data Exchange (ETDEWEB)

    Magdy, M.A.; Bekmezci, A.; Sever, R. [Middle East Technical Univ., Ankara (Turkey)


    The modified form of the statistical model is used without making any perturbation. The mass spectra of the lowest S, P and D levels of the (Q{bar Q}) and the non-self-conjugate (Q{bar q}) mesons are studied with the Song-Lin potential. The authors results are in good agreement with the experimental and theoretical findings.

  16. "Dispersion modeling approaches for near road (United States)

    Roadway design and roadside barriers can have significant effects on the dispersion of traffic-generated pollutants, especially in the near-road environment. Dispersion models that can accurately simulate these effects are needed to fully assess these impacts for a variety of app...

  17. Similarity transformation approach for ferromagnetic mixed convection flow in the presence of chemically reactive magnetic dipole (United States)

    Hayat, Tasawar; Ijaz Khan, Muhammad; Imtiaz, Maria; Alsaedi, Ahmed; Waqas, Muhammad


    A simple model of chemical reactions for two dimensional ferrofluid flows is constructed. The impact of magnetic dipole and mixed convection is further analyzed. Flow is caused by linear stretching of the sheet. Similarity transformation is adopted to convert the partial differential equations into ordinary differential equations and then solved by Euler's explicit method. The characteristics of sundry parameters on the velocity, temperature, and concentration fields are graphically elaborated. It is noted that the impact of magneto-thermomechanical interaction is to slow down the fluid motion. The skin friction coefficient enhances and affects the rate of heat transfer. For higher values of ferrohydrodynamics, the interaction velocity shows decreasing behavior. Further the Prandtl number on temperature has opposite behavior when compared with thermal radiation and ferrohydrodynamics interaction.

  18. National, holistic, watershed-scale approach to understand the sources, transport, and fate of agricultural chemicals (United States)

    Capel, P.D.; McCarthy, K.A.; Barbash, J.E.


    This paper is an introduction to the following series of papers that report on in-depth investigations that have been conducted at five agricultural study areas across the United States in order to gain insights into how environmental processes and agricultural practices interact to determine the transport and fate of agricultural chemicals in the environment. These are the first study areas in an ongoing national study. The study areas were selected, based on the combination of cropping patterns and hydrologic setting, as representative of nationally important agricultural settings to form a basis for extrapolation to unstudied areas. The holistic, watershed-scale study design that involves multiple environmental compartments and that employs both field observations and simulation modeling is presented. This paper introduces the overall study design and presents an overview of the hydrology of the five study areas. Copyright ?? 2008 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

  19. A thermodynamic approach of the mechano-chemical coupling during the oxidation of uranium dioxide

    CERN Document Server

    Creton, Nicolas; Montesin, Tony; Garruchet, Sébastien; Desgranges, Lionel; 10.4028/


    The aim of the present work is to introduce a thermodynamic model to describe the growth of an oxide layer on a metallic substrate. More precisely, this paper offers a study of oxygen dissolution into a solid, and its consequences on the apparition of mechanical stresses. They strongly influence the oxidation processes and may be, in some materials, responsible for cracking. To realize this study, mechanical considerations are introduced into the classical diffusion laws. Simulations were made for the particular case of uranium dioxide, which undergoes the chemical fragmentation. According to our simulations, the hypothesis of a compression stress field into the oxidised UO2 compound near the internal interface is consistent with the interpretation of the mechanisms of oxidation observed experimentally.

  20. Integration models: multicultural and liberal approaches confronted (United States)

    Janicki, Wojciech


    European societies have been shaped by their Christian past, upsurge of international migration, democratic rule and liberal tradition rooted in religious tolerance. Boosting globalization processes impose new challenges on European societies, striving to protect their diversity. This struggle is especially clearly visible in case of minorities trying to resist melting into mainstream culture. European countries' legal systems and cultural policies respond to these efforts in many ways. Respecting identity politics-driven group rights seems to be the most common approach, resulting in creation of a multicultural society. However, the outcome of respecting group rights may be remarkably contradictory to both individual rights growing out from liberal tradition, and to reinforced concept of integration of immigrants into host societies. The hereby paper discusses identity politics upturn in the context of both individual rights and integration of European societies.

  1. Inflow, Outflow, Yields, and Stellar Population Mixing in Chemical Evolution Models (United States)

    Andrews, Brett H.; Weinberg, David H.; Schönrich, Ralph; Johnson, Jennifer A.


    Chemical evolution models are powerful tools for interpreting stellar abundance surveys and understanding galaxy evolution. However, their predictions depend heavily on the treatment of inflow, outflow, star formation efficiency (SFE), the stellar initial mass function, the SN Ia delay time distribution, stellar yields, and stellar population mixing. Using flexCE, a flexible one-zone chemical evolution code, we investigate the effects of and trade-offs between parameters. Two critical parameters are SFE and the outflow mass-loading parameter, which shift the knee in [O/Fe]–[Fe/H] and the equilibrium abundances that the simulations asymptotically approach, respectively. One-zone models with simple star formation histories follow narrow tracks in [O/Fe]–[Fe/H] unlike the observed bimodality (separate high-α and low-α sequences) in this plane. A mix of one-zone models with inflow timescale and outflow mass-loading parameter variations, motivated by the inside-out galaxy formation scenario with radial mixing, reproduces the two sequences better than a one-zone model with two infall epochs. We present [X/Fe]–[Fe/H] tracks for 20 elements assuming three different supernova yield models and find some significant discrepancies with solar neighborhood observations, especially for elements with strongly metallicity-dependent yields. We apply principal component abundance analysis to the simulations and existing data to reveal the main correlations among abundances and quantify their contributions to variation in abundance space. For the stellar population mixing scenario, the abundances of α-elements and elements with metallicity-dependent yields dominate the first and second principal components, respectively, and collectively explain 99% of the variance in the model. flexCE is a python package available at

  2. Chemical equilibrium modeling of organic acids, pH, aluminum, and iron in Swedish surface waters. (United States)

    Sjöstedt, Carin S; Gustafsson, Jon Petter; Köhler, Stephan J


    A consistent chemical equilibrium model that calculates pH from charge balance constraints and aluminum and iron speciation in the presence of natural organic matter is presented. The model requires input data for total aluminum, iron, organic carbon, fluoride, sulfate, and charge balance ANC. The model is calibrated to pH measurements (n = 322) by adjusting the fraction of active organic matter only, which results in an error of pH prediction on average below 0.2 pH units. The small systematic discrepancy between the analytical results for the monomeric aluminum fractionation and the model results is corrected for separately for two different fractionation techniques (n = 499) and validated on a large number (n = 3419) of geographically widely spread samples all over Sweden. The resulting average error for inorganic monomeric aluminum is around 1 µM. In its present form the model is the first internally consistent modeling approach for Sweden and may now be used as a tool for environmental quality management. Soil gibbsite with a log *Ks of 8.29 at 25°C together with a pH dependent loading function that uses molar Al/C ratios describes the amount of aluminum in solution in the presence of organic matter if the pH is roughly above 6.0.

  3. Approaches for externally validated QSAR modelling of Nitrated Polycyclic Aromatic Hydrocarbon mutagenicity. (United States)

    Gramatica, P; Pilutti, P; Papa, E


    Nitrated Polycyclic Aromatic Hydrocarbons (nitro-PAHs), ubiquitous environmental pollutants, are recognized mutagens and carcinogens. A set of mutagenicity data (TA100) for 48 nitro-PAHs was modeled by the Quantitative Structure-Activity Relationships (QSAR) regression method, and OECD principles for QSAR model validation were applied. The proposed Multiple Linear Regression (MLR) models are based on two topological molecular descriptors. The models were validated for predictivity by both internal and external validation. For the external validation, three different splitting approaches, D-optimal Experimental Design, Self Organizing Maps (SOM) and Random Selection by activity sampling, were applied to the original data set in order to compare these methodologies and to select the best descriptors able to model each prediction set chemicals independently of the splitting method applied. The applicability domain was verified by the leverage approach.

  4. Chemical Potential Dependence of the Dressed-Quark Propagator in a Simple Confining QCD Model

    Institute of Scientific and Technical Information of China (English)

    ZONG Hong-Shi; HOU Feng-Yao; CHEN Xiang-Song; LIU Yu-Xin


    Based on the Dyson-Schwinger approach, a method for obtaining the chemical potential dependence of the dressed quark propagator in the ‘Nambu-Goldstone' and the ‘Wigner' phase is developed. The bag constant in the presence of the non-zero chemical potential is analysed.

  5. Quantum Machine and SR Approach: a Unified Model

    CERN Document Server

    Garola, C; Sozzo, S; Garola, Claudio; Pykacz, Jaroslav; Sozzo, Sandro


    The Geneva-Brussels approach to quantum mechanics (QM) and the semantic realism (SR) nonstandard interpretation of QM exhibit some common features and some deep conceptual differences. We discuss in this paper two elementary models provided in the two approaches as intuitive supports to general reasonings and as a proof of consistency of general assumptions, and show that Aerts' quantum machine can be embodied into a macroscopic version of the microscopic SR model, overcoming the seeming incompatibility between the two models. This result provides some hints for the construction of a unified perspective in which the two approaches can be properly placed.

  6. ISM Approach to Model Offshore Outsourcing Risks

    Directory of Open Access Journals (Sweden)

    Sunand Kumar


    Full Text Available In an effort to achieve a competitive advantage via cost reductions and improved market responsiveness, organizations are increasingly employing offshore outsourcing as a major component of their supply chain strategies. But as evident from literature number of risks such as Political risk, Risk due to cultural differences, Compliance and regulatory risk, Opportunistic risk and Organization structural risk, which adversely affect the performance of offshore outsourcing in a supply chain network. This also leads to dissatisfaction among different stake holders. The main objective of this paper is to identify and understand the mutual interaction among various risks which affect the performance of offshore outsourcing.  To this effect, authors have identified various risks through extant review of literature.  From this information, an integrated model using interpretive structural modelling (ISM for risks affecting offshore outsourcing is developed and the structural relationships between these risks are modeled.  Further, MICMAC analysis is done to analyze the driving power and dependency of risks which shall be helpful to managers to identify and classify important criterions and to reveal the direct and indirect effects of each criterion on offshore outsourcing. Results show that political risk and risk due to cultural differences are act as strong drivers.

  7. Fate Model for Organic Chemicals in Sewage Treatment Plants

    DEFF Research Database (Denmark)

    Mikkelsen, J.

    Miljøprojekt, 308; I tilknytning til hovedrapporten Environmental Exposure Assessment of Chemicals (Miljøprojekt, 306) er udgivet i alt 5 tekniske bilagsrapporter, alle i serien Miljøprojekt.......Miljøprojekt, 308; I tilknytning til hovedrapporten Environmental Exposure Assessment of Chemicals (Miljøprojekt, 306) er udgivet i alt 5 tekniske bilagsrapporter, alle i serien Miljøprojekt....

  8. A market model for stochastic smile: a conditional density approach

    NARCIS (Netherlands)

    Zilber, A.


    The purpose of this paper is to introduce a new approach that allows to construct no-arbitrage market models of for implied volatility surfaces (in other words, stochastic smile models). That is to say, the idea presented here allows us to model prices of liquidly traded vanilla options as separate

  9. A modular approach to numerical human body modeling

    NARCIS (Netherlands)

    Forbes, P.A.; Griotto, G.; Rooij, L. van


    The choice of a human body model for a simulated automotive impact scenario must take into account both accurate model response and computational efficiency as key factors. This study presents a "modular numerical human body modeling" approach which allows the creation of a customized human body mod


    NARCIS (Netherlands)



    The behavioral approach to system theory provides a parameter-free framework for the study of the general problem of linear exact modeling and recursive modeling. The main contribution of this paper is the solution of the (continuous-time) polynomial-exponential time series modeling problem. Both re

  11. A simple model for the distribution and fate of organic chemicals in a landfill: MOCLA

    DEFF Research Database (Denmark)

    Kjeldsen, Peter; Christensen, Thomas Højlund


    of degradation and transformation in the landfill. Local equilibrium is assumed for the distribution of the chemicals in the landfill as expressed by Henry’s Law for the leachate-gas interface, and by the linear partition coefficient based on the waste solid organic carbon content for the waste......A simple mathematical model (MOCLA: Model for Organic Chemicals in Landfills) is presented, describing the distribution of organic chemicals between leachate, gas and solid waste. The model also predicts the fate of the chemicals in terms of emissions with leachate and landfill gas and in terms......-leachate interface. Degradation of the chemicals is expressed as a first order reaction. Annual specific leachate and gas generation data in combination with data on landfill area and volume allow for prediction of main emission routes. Model simulations involving two landfill scenarios for a number of chemicals...

  12. Generalized Ginzburg–Landau approach to inhomogeneous phases in nonlocal chiral quark models

    Energy Technology Data Exchange (ETDEWEB)

    Carlomagno, J.P. [IFLP, CONICET – Dpto. de Física, FCE, Universidad Nacional de La Plata, C.C. 67, 1900 La Plata (Argentina); CONICET, Rivadavia 1917, 1033 Buenos Aires (Argentina); Gómez Dumm, D., E-mail: [IFLP, CONICET – Dpto. de Física, FCE, Universidad Nacional de La Plata, C.C. 67, 1900 La Plata (Argentina); CONICET, Rivadavia 1917, 1033 Buenos Aires (Argentina); Scoccola, N.N. [CONICET, Rivadavia 1917, 1033 Buenos Aires (Argentina); Physics Department, Comisión Nacional de Energía Atómica, Av. Libertador 8250, 1429 Buenos Aires (Argentina); Universidad Favaloro, Solís 453, 1078 Buenos Aires (Argentina)


    We analyze the presence of inhomogeneous phases in the QCD phase diagram within the framework of nonlocal chiral quark models. We concentrate in particular in the positions of the tricritical (TCP) and Lifshitz (LP) points, which are studied in a general context using a generalized Ginzburg–Landau approach. We find that for all the phenomenologically acceptable model parametrizations considered the TCP is located at a higher temperature and a lower chemical potential in comparison with the LP. Consequently, these models seem to favor a scenario in which the onset of the first order transition between homogeneous phases is not covered by an inhomogeneous, energetically favored phase.

  13. Setting safe acute exposure limits for halon replacement chemicals using physiologically based pharmacokinetic modeling. (United States)

    Vinegar, A; Jepson, G W; Cisneros, M; Rubenstein, R; Brock, W J


    Most proposed replacements for Halon 1301 as a fire suppressant are halogenated hydrocarbons. The acute toxic endpoint of concern for these agents is cardiac sensitization. An approach is described that links the cardiac endpoint as assessed in dogs to a target arterial concentration in humans. Linkage was made using a physiologically based pharmacokinetic (PBPK) model. Monte Carlo simulations, which account for population variability, were used to establish safe exposure times at different exposure concentrations for Halon 1301 (bromotrifluoromethane), CF(3)I (trifluoroiodomethane), HFC-125 (pentafluoroethane), HFC-227ea (1,1,1,2,3,3,3-heptafluoropropane), and HFC-236fa (1,1,1,3,3,3-hexafluoropropane). Application of the modeling technique described here not only makes use of the conservative cardiac sensitization endpoint, but also uses an understanding of the pharmacokinetics of the chemical agents to better establish standards for safe exposure. The combined application of cardiac sensitization data and physiologically based modeling provides a quantitative approach, which can facilitate the selection and effective use of halon replacement candidates.

  14. The potential of computer-based quantitative structure activity approaches for predicting acute toxicity of chemicals

    NARCIS (Netherlands)

    Zvinavashe, E.


    Within the EU, the management of the risks of chemicals currently falls under a new legislation called Registration, Evaluation, and Authorization of Chemicals (REACH). Within the next 10 years, existing (eco)toxicological data gaps for the more than 100 000 chemicals on the European Inventory of E

  15. Dynamic Metabolic Model Building Based on the Ensemble Modeling Approach

    Energy Technology Data Exchange (ETDEWEB)

    Liao, James C. [Univ. of California, Los Angeles, CA (United States)


    Ensemble modeling of kinetic systems addresses the challenges of kinetic model construction, with respect to parameter value selection, and still allows for the rich insights possible from kinetic models. This project aimed to show that constructing, implementing, and analyzing such models is a useful tool for the metabolic engineering toolkit, and that they can result in actionable insights from models. Key concepts are developed and deliverable publications and results are presented.

  16. Thermoplasmonics modeling: A Green's function approach (United States)

    Baffou, Guillaume; Quidant, Romain; Girard, Christian


    We extend the discrete dipole approximation (DDA) and the Green’s dyadic tensor (GDT) methods—previously dedicated to all-optical simulations—to investigate the thermodynamics of illuminated plasmonic nanostructures. This extension is based on the use of the thermal Green’s function and a original algorithm that we named Laplace matrix inversion. It allows for the computation of the steady-state temperature distribution throughout plasmonic systems. This hybrid photothermal numerical method is suited to investigate arbitrarily complex structures. It can take into account the presence of a dielectric planar substrate and is simple to implement in any DDA or GDT code. Using this numerical framework, different applications are discussed such as thermal collective effects in nanoparticles assembly, the influence of a substrate on the temperature distribution and the heat generation in a plasmonic nanoantenna. This numerical approach appears particularly suited for new applications in physics, chemistry, and biology such as plasmon-induced nanochemistry and catalysis, nanofluidics, photothermal cancer therapy, or phase-transition control at the nanoscale.

  17. A coupled model between mechanical deformation and chemical diffusion: An explanation for the preservation of chemical zonation in plagioclase at high temperatures (United States)

    Zhong, Xin; Vrijmoed, Johannes; Moulas, Evangelos; Tajcmanová, Lucie


    Compositional zoning in metamorphic minerals have been generally recognized as an important geological feature to decipher the metamorphic history of rocks. The observed chemical zoning of, e.g. garnet, is commonly interpreted as disequilibrium between the fractionated inner core and the surrounding matrix. However, chemically zoned minerals were also observed in high grade rocks (T>800 degree C) where the duration of metamorphic processes was independently dated to take several Ma. This implies that temperature may not be the only factor that controls diffusion timescales, and grain scale pressure variation was proposed to be a complementary factor that may significantly contribute to the formation and preservation of chemical zoning in high temperature metamorphic minerals [Tajcmanová 2013, 2015]. Here, a coupled model is developed to simulate viscous deformation and chemical diffusion. The numerical approach considers the conservation of mass, momentum, and a constitutive relation developed from equilibrium thermodynamics. A compressible viscoelastic rheology is applied, which associates the volumetric change triggered by deformation and diffusion to a change of pressure. The numerical model is applied to the chemically zoned plagioclase rim described by [Tajcmanová 2014]. The diffusion process operating during the plagioclase rim formation can lead to a development of a pressure gradient. Such a pressure gradient, if maintained during ongoing viscous relaxation, can lead to the preservation of the observed chemical zonation in minerals. An important dimensionless number, the Deborah number, is defined as the ratio between the Maxwell viscoelastic relaxation time and the characteristic diffusion time. It characterizes the relative influence between the maintenance of grain scale pressure variation and chemical diffusion. Two extreme regimes are shown: the mechanically-controlled regime (high Deborah number) and diffusion-controlled regime (low Deborah number

  18. CPUF - a chemical-structure-based polyurethane foam decomposition and foam response model.

    Energy Technology Data Exchange (ETDEWEB)

    Fletcher, Thomas H. (Brigham Young University, Provo, UT); Thompson, Kyle Richard; Erickson, Kenneth L.; Dowding, Kevin J.; Clayton, Daniel (Brigham Young University, Provo, UT); Chu, Tze Yao; Hobbs, Michael L.; Borek, Theodore Thaddeus III


    A Chemical-structure-based PolyUrethane Foam (CPUF) decomposition model has been developed to predict the fire-induced response of rigid, closed-cell polyurethane foam-filled systems. The model, developed for the B-61 and W-80 fireset foam, is based on a cascade of bondbreaking reactions that produce CO2. Percolation theory is used to dynamically quantify polymer fragment populations of the thermally degrading foam. The partition between condensed-phase polymer fragments and gas-phase polymer fragments (i.e. vapor-liquid split) was determined using a vapor-liquid equilibrium model. The CPUF decomposition model was implemented into the finite element (FE) heat conduction codes COYOTE and CALORE, which support chemical kinetics and enclosure radiation. Elements were removed from the computational domain when the calculated solid mass fractions within the individual finite element decrease below a set criterion. Element removal, referred to as ?element death,? creates a radiation enclosure (assumed to be non-participating) as well as a decomposition front, which separates the condensed-phase encapsulant from the gas-filled enclosure. All of the chemistry parameters as well as thermophysical properties for the CPUF model were obtained from small-scale laboratory experiments. The CPUF model was evaluated by comparing predictions to measurements. The validation experiments included several thermogravimetric experiments at pressures ranging from ambient pressure to 30 bars. Larger, component-scale experiments were also used to validate the foam response model. The effects of heat flux, bulk density, orientation, embedded components, confinement and pressure were measured and compared to model predictions. Uncertainties in the model results were evaluated using a mean value approach. The measured mass loss in the TGA experiments and the measured location of the decomposition front were within the 95% prediction limit determined using the CPUF model for all of the

  19. Applied Regression Modeling A Business Approach

    CERN Document Server

    Pardoe, Iain


    An applied and concise treatment of statistical regression techniques for business students and professionals who have little or no background in calculusRegression analysis is an invaluable statistical methodology in business settings and is vital to model the relationship between a response variable and one or more predictor variables, as well as the prediction of a response value given values of the predictors. In view of the inherent uncertainty of business processes, such as the volatility of consumer spending and the presence of market uncertainty, business professionals use regression a

  20. Development of a computationally efficient urban modeling approach

    DEFF Research Database (Denmark)

    Wolfs, Vincent; Murla, Damian; Ntegeka, Victor;


    This paper presents a parsimonious and data-driven modelling approach to simulate urban floods. Flood levels simulated by detailed 1D-2D hydrodynamic models can be emulated using the presented conceptual modelling approach with a very short calculation time. In addition, the model detail can...... be adjust-ed, allowing the modeller to focus on flood-prone locations. This results in efficiently parameterized models that can be tailored to applications. The simulated flood levels are transformed into flood extent maps using a high resolution (0.5-meter) digital terrain model in GIS. To illustrate...... the developed methodology, a case study for the city of Ghent in Belgium is elaborated. The configured conceptual model mimics the flood levels of a detailed 1D-2D hydrodynamic InfoWorks ICM model accurately, while the calculation time is an order of magnitude of 106 times shorter than the original highly...