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Sample records for formal kinetic models

  1. The Thermodynamic Flow-Force Interpretation of Root Nutrient Uptake Kinetics: A Powerful Formalism for Agronomic and Phytoplanktonic Models

    PubMed Central

    Le Deunff, Erwan; Tournier, Pierre-Henri; Malagoli, Philippe

    2016-01-01

    The ion influx isotherms obtained by measuring unidirectional influx across root membranes with radioactive or stable tracers are mostly interpreted by enzyme-substrate-like modeling. However, recent analyses from ion transporter mutants clearly demonstrate the inadequacy of the conventional interpretation of ion isotherms. Many genetically distinct carriers are involved in the root catalytic function. Parameters Vmax and Km deduced from this interpretation cannot therefore be regarded as microscopic parameters of a single transporter, but are instead macroscopic parameters (Vmapp and Kmapp, apparent maximum velocity and affinity constant) that depend on weighted activities of multiple transporters along the root. The flow-force interpretation based on the thermodynamic principle of irreversible processes is an alternative macroscopic modeling approach for ion influx isotherms in which macroscopic parameters Lj (overall conductance of the root system for the substrate j) and πj (thermodynamic parameter when Jj = 0) have a straightforward meaning with respect to the biological sample studied. They characterize the efficiency of the entire root catalytic structure without deducing molecular characteristics. Here we present the basic principles of this theory and how its use can be tested and improved by changing root pre- and post-wash procedures before influx measurements in order to come as close as possible to equilibrium conditions. In addition, the constant values of Vm and Km in the Michaelis-Menten (MM) formalism of enzyme-substrate interpretation do not reflect variations in response to temperature, nutrient status or nutrient regimes. The linear formalism of the flow-force approach, which integrates temperature effect on nutrient uptake, could usefully replace MM formalism in the 1-3-dimension models of plants and phytoplankton. This formalism offers a simplification of parametrization to help find more realistic analytical expressions and numerical

  2. The Thermodynamic Flow-Force Interpretation of Root Nutrient Uptake Kinetics: A Powerful Formalism for Agronomic and Phytoplanktonic Models.

    PubMed

    Le Deunff, Erwan; Tournier, Pierre-Henri; Malagoli, Philippe

    2016-01-01

    The ion influx isotherms obtained by measuring unidirectional influx across root membranes with radioactive or stable tracers are mostly interpreted by enzyme-substrate-like modeling. However, recent analyses from ion transporter mutants clearly demonstrate the inadequacy of the conventional interpretation of ion isotherms. Many genetically distinct carriers are involved in the root catalytic function. Parameters Vmax and Km deduced from this interpretation cannot therefore be regarded as microscopic parameters of a single transporter, but are instead macroscopic parameters (V[Formula: see text] and K[Formula: see text], apparent maximum velocity and affinity constant) that depend on weighted activities of multiple transporters along the root. The flow-force interpretation based on the thermodynamic principle of irreversible processes is an alternative macroscopic modeling approach for ion influx isotherms in which macroscopic parameters Lj (overall conductance of the root system for the substrate j) and πj (thermodynamic parameter when Jj = 0) have a straightforward meaning with respect to the biological sample studied. They characterize the efficiency of the entire root catalytic structure without deducing molecular characteristics. Here we present the basic principles of this theory and how its use can be tested and improved by changing root pre- and post-wash procedures before influx measurements in order to come as close as possible to equilibrium conditions. In addition, the constant values of Vm and Km in the Michaelis-Menten (MM) formalism of enzyme-substrate interpretation do not reflect variations in response to temperature, nutrient status or nutrient regimes. The linear formalism of the flow-force approach, which integrates temperature effect on nutrient uptake, could usefully replace MM formalism in the 1-3-dimension models of plants and phytoplankton. This formalism offers a simplification of parametrization to help find more realistic analytical

  3. Modeling formalisms in Systems Biology

    PubMed Central

    2011-01-01

    Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future. PMID:22141422

  4. Modeling formalisms in Systems Biology.

    PubMed

    Machado, Daniel; Costa, Rafael S; Rocha, Miguel; Ferreira, Eugénio C; Tidor, Bruce; Rocha, Isabel

    2011-01-01

    Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future. PMID:22141422

  5. Formal modeling of virtual machines

    NASA Technical Reports Server (NTRS)

    Cremers, A. B.; Hibbard, T. N.

    1978-01-01

    Systematic software design can be based on the development of a 'hierarchy of virtual machines', each representing a 'level of abstraction' of the design process. The reported investigation presents the concept of 'data space' as a formal model for virtual machines. The presented model of a data space combines the notions of data type and mathematical machine to express the close interaction between data and control structures which takes place in a virtual machine. One of the main objectives of the investigation is to show that control-independent data type implementation is only of limited usefulness as an isolated tool of program development, and that the representation of data is generally dictated by the control context of a virtual machine. As a second objective, a better understanding is to be developed of virtual machine state structures than was heretofore provided by the view of the state space as a Cartesian product.

  6. Experiences Using Formal Methods for Requirements Modeling

    NASA Technical Reports Server (NTRS)

    Easterbrook, Steve; Lutz, Robyn; Covington, Rick; Kelly, John; Ampo, Yoko; Hamilton, David

    1996-01-01

    This paper describes three cases studies in the lightweight application of formal methods to requirements modeling for spacecraft fault protection systems. The case studies differ from previously reported applications of formal methods in that formal methods were applied very early in the requirements engineering process, to validate the evolving requirements. The results were fed back into the projects, to improve the informal specifications. For each case study, we describe what methods were applied, how they were applied, how much effort was involved, and what the findings were. In all three cases, the formal modeling provided a cost effective enhancement of the existing verification and validation processes. We conclude that the benefits gained from early modeling of unstable requirements more than outweigh the effort needed to maintain multiple representations.

  7. Formal modeling of robot behavior with learning.

    PubMed

    Kirwan, Ryan; Miller, Alice; Porr, Bernd; Di Prodi, P

    2013-11-01

    We present formal specification and verification of a robot moving in a complex network, using temporal sequence learning to avoid obstacles. Our aim is to demonstrate the benefit of using a formal approach to analyze such a system as a complementary approach to simulation. We first describe a classical closed-loop simulation of the system and compare this approach to one in which the system is analyzed using formal verification. We show that the formal verification has some advantages over classical simulation and finds deficiencies our classical simulation did not identify. Specifically we present a formal specification of the system, defined in the Promela modeling language and show how the associated model is verified using the Spin model checker. We then introduce an abstract model that is suitable for verifying the same properties for any environment with obstacles under a given set of assumptions. We outline how we can prove that our abstraction is sound: any property that holds for the abstracted model will hold in the original (unabstracted) model.

  8. Formal Models of Language Learning.

    ERIC Educational Resources Information Center

    Pinker, Steven

    1979-01-01

    Research addressing development of mechanistic models capable of acquiring languages on the basis of exposure to linguistic data is reviewed. Research focuses on major issues in developmental psycholinguistics--in particular, nativism and empiricism, the role of semantics and pragmatics, cognitive development, and the importance of simplified…

  9. Formalization of an environmental model using formal concept analysis - FCA

    NASA Astrophysics Data System (ADS)

    Bourdon-García, Rubén D.; Burgos-Salcedo, Javier D.

    2016-08-01

    Nowadays, there is a huge necessity to generate novel strategies for social-ecological systems analyses for resolving global sustainability problems. This paper has as main purpose the application of the formal concept analysis to formalize the theory of Augusto Ángel Maya, who without a doubt, was one of the most important environmental philosophers in South America; Ángel Maya proposed and established that Ecosystem-Culture relations, instead Human-Nature ones, are determinants in our understanding and management of natural resources. Based on this, a concept lattice, formal concepts, subconcept-superconcept relations, partially ordered sets, supremum and infimum of the lattice and implications between attributes (Duquenne-Guigues base), were determined for the ecosystem-culture relations.

  10. Formal Problem Domain Modeling within MDA

    NASA Astrophysics Data System (ADS)

    Osis, Janis; Asnina, Erika; Grave, Andrejs

    The proposed approach called Topological Functioning Modeling for Model Driven Architecture (TFM4MDA) uses formal mathematical foundations of Topological Functioning Model (TFM). It introduces the main feature of MDA - Separation of Concerns by formal analysis of a business system, enables mapping to functional requirements and verifying whether those requirements are in conformity with the TFM of the problem domain. By using a goal-based method, a holistic behavior of the planned application can be decomposed in accordance with the goals. Graph transformation from the TFM to a conceptual model (or a domain object model) enables establishing the definition of domain concepts and their relations. The paper also suggests a concept of a tool for TFM4MDA, which is realized as an Eclipse plug-in.

  11. Kinetic theory of turbulence for parallel propagation revisited: Formal results

    SciTech Connect

    Yoon, Peter H.

    2015-08-15

    In a recent paper, Gaelzer et al. [Phys. Plasmas 22, 032310 (2015)] revisited the second-order nonlinear kinetic theory for turbulence propagating in directions parallel/anti-parallel to the ambient magnetic field. The original work was according to Yoon and Fang [Phys. Plasmas 15, 122312 (2008)], but Gaelzer et al. noted that the terms pertaining to discrete-particle effects in Yoon and Fang's theory did not enjoy proper dimensionality. The purpose of Gaelzer et al. was to restore the dimensional consistency associated with such terms. However, Gaelzer et al. was concerned only with linear wave-particle interaction terms. The present paper completes the analysis by considering the dimensional correction to nonlinear wave-particle interaction terms in the wave kinetic equation.

  12. Formalizing Linguistic Conventions for Conceptual Models

    NASA Astrophysics Data System (ADS)

    Becker, Jörg; Delfmann, Patrick; Herwig, Sebastian; Lis, Łukasz; Stein, Armin

    A precondition for the appropriate analysis of conceptual models is not only their syntactic correctness but also their semantic comparability. Assuring comparability is challenging especially when models are developed by different persons. Empirical studies show that such models can vary heavily, especially in model element naming, even if they express the same issue. In contrast to most ontology-driven approaches proposing the resolution of these differences ex-post, we introduce an approach that avoids naming differences in conceptual models already during modeling. Therefore we formalize naming conventions combining domain thesauri and phrase structures based on a lin-guistic grammar. This allows for guiding modelers automatically during the modeling process using standardized labels for model elements. Our approach is generic, making it applicable for any modeling language.

  13. Oxidative desulfurization: kinetic modelling.

    PubMed

    Dhir, S; Uppaluri, R; Purkait, M K

    2009-01-30

    Increasing environmental legislations coupled with enhanced production of petroleum products demand, the deployment of novel technologies to remove organic sulfur efficiently. This work represents the kinetic modeling of ODS using H(2)O(2) over tungsten-containing layered double hydroxide (LDH) using the experimental data provided by Hulea et al. [V. Hulea, A.L. Maciuca, F. Fajula, E. Dumitriu, Catalytic oxidation of thiophenes and thioethers with hydrogen peroxide in the presence of W-containing layered double hydroxides, Appl. Catal. A: Gen. 313 (2) (2006) 200-207]. The kinetic modeling approach in this work initially targets the scope of the generation of a superstructure of micro-kinetic reaction schemes and models assuming Langmuir-Hinshelwood (LH) and Eley-Rideal (ER) mechanisms. Subsequently, the screening and selection of above models is initially based on profile-based elimination of incompetent schemes followed by non-linear regression search performed using the Levenberg-Marquardt algorithm (LMA) for the chosen models. The above analysis inferred that Eley-Rideal mechanism describes the kinetic behavior of ODS process using tungsten-containing LDH, with adsorption of reactant and intermediate product only taking place on the catalyst surface. Finally, an economic index is presented that scopes the economic aspects of the novel catalytic technology with the parameters obtained during regression analysis to conclude that the cost factor for the catalyst is 0.0062-0.04759 US $ per barrel. PMID:18541367

  14. LLNL Chemical Kinetics Modeling Group

    SciTech Connect

    Pitz, W J; Westbrook, C K; Mehl, M; Herbinet, O; Curran, H J; Silke, E J

    2008-09-24

    The LLNL chemical kinetics modeling group has been responsible for much progress in the development of chemical kinetic models for practical fuels. The group began its work in the early 1970s, developing chemical kinetic models for methane, ethane, ethanol and halogenated inhibitors. Most recently, it has been developing chemical kinetic models for large n-alkanes, cycloalkanes, hexenes, and large methyl esters. These component models are needed to represent gasoline, diesel, jet, and oil-sand-derived fuels.

  15. A formal model of interpersonal inference

    PubMed Central

    Moutoussis, Michael; Trujillo-Barreto, Nelson J.; El-Deredy, Wael; Dolan, Raymond J.; Friston, Karl J.

    2014-01-01

    Introduction: We propose that active Bayesian inference—a general framework for decision-making—can equally be applied to interpersonal exchanges. Social cognition, however, entails special challenges. We address these challenges through a novel formulation of a formal model and demonstrate its psychological significance. Method: We review relevant literature, especially with regards to interpersonal representations, formulate a mathematical model and present a simulation study. The model accommodates normative models from utility theory and places them within the broader setting of Bayesian inference. Crucially, we endow people's prior beliefs, into which utilities are absorbed, with preferences of self and others. The simulation illustrates the model's dynamics and furnishes elementary predictions of the theory. Results: (1) Because beliefs about self and others inform both the desirability and plausibility of outcomes, in this framework interpersonal representations become beliefs that have to be actively inferred. This inference, akin to “mentalizing” in the psychological literature, is based upon the outcomes of interpersonal exchanges. (2) We show how some well-known social-psychological phenomena (e.g., self-serving biases) can be explained in terms of active interpersonal inference. (3) Mentalizing naturally entails Bayesian updating of how people value social outcomes. Crucially this includes inference about one's own qualities and preferences. Conclusion: We inaugurate a Bayes optimal framework for modeling intersubject variability in mentalizing during interpersonal exchanges. Here, interpersonal representations are endowed with explicit functional and affective properties. We suggest the active inference framework lends itself to the study of psychiatric conditions where mentalizing is distorted. PMID:24723872

  16. Bioreaction engineering. Vol. 1: Fundamentals, thermodynamics, formal kinetics, idealized reactor types and operation modes

    SciTech Connect

    Schugeri, K.

    1987-01-01

    This volume, provides view of the current state of bioreaction engineering, the science of the reaction engineering of cells and microorganisms. Topics covered include the modus operandi of bioreactors, basic types, reactors circuits, formal kinetics of cell growth and product formation, growth in idealized reactors, substrate-limited growth, operation modes in stirred reactors, discontinuous (batch) operation, continuous operation, dynamic behavior of open and closed loop reactors, and more.

  17. Animating Event B Models by Formal Data Models

    NASA Astrophysics Data System (ADS)

    Ait-Sadoune, Idir; Ait-Ameur, Yamine

    We present a formal approach allowing to animate event B formal models. Invariants, deadlock freeness properties are expressed and proved on these models. This paper presents an approach that suggests to complete the proof activity in the event B method by animation activity. The obtained animator may be used to check if the event B models obtained fulfill user requirements, or to provide a help to the developer when describing its formal event B models and particularly in defining event B invariants and guards. More precisely, event B models are translated into data models expressed in the EXPRESS formal data modeling technique. The obtained data models are instantiated and provide an animation of the original B models. Following this approach, it becomes possible to trigger event B models, which themselves trigger entity instantiation on the EXPRESS side. As a further step, we show that the B models can be used as a monitoring system raising alarms in case of incorrect systems behavior. The proposed approach is operationally implemented in the B2EXPRESS tool which handles animation of event B models. It has been experimented for the validation of multimodal human interfaces in the context of VERBATIM project.

  18. Formal Specification of the OpenMP Memory Model

    SciTech Connect

    Bronevetsky, G; de Supinski, B R

    2006-05-17

    OpenMP [1] is an important API for shared memory programming, combining shared memory's potential for performance with a simple programming interface. Unfortunately, OpenMP lacks a critical tool for demonstrating whether programs are correct: a formal memory model. Instead, the current official definition of the OpenMP memory model (the OpenMP 2.5 specification [1]) is in terms of informal prose. As a result, it is impossible to verify OpenMP applications formally since the prose does not provide a formal consistency model that precisely describes how reads and writes on different threads interact. This paper focuses on the formal verification of OpenMP programs through a proposed formal memory model that is derived from the existing prose model [1]. Our formalization provides a two-step process to verify whether an observed OpenMP execution is conformant. In addition to this formalization, our contributions include a discussion of ambiguities in the current prose-based memory model description. Although our formal model may not capture the current informal memory model perfectly, in part due to these ambiguities, our model reflects our understanding of the informal model's intent. We conclude with several examples that may indicate areas of the OpenMP memory model that need further refinement however it is specified. Our goal is to motivate the OpenMP community to adopt those refinements eventually, ideally through a formal model, in later OpenMP specifications.

  19. Chemical kinetics modeling

    SciTech Connect

    Westbrook, C.K.; Pitz, W.J.

    1993-12-01

    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.

  20. Kinetic Relaxation Models for Energy Transport

    NASA Astrophysics Data System (ADS)

    Aoki, Kazuo; Markowich, Peter; Takata, Shigeru

    2007-04-01

    Kinetic equations with relaxation collision kernels are considered under the basic assumption of two collision invariants, namely mass and energy. The collision kernels are of BGK-type with a general local Gibbs state, which may be quite different from the Gaussian. By the use of the diffusive length/time scales, energy transport systems consisting of two parabolic equations with the position density and the energy density as unknowns are derived on a formal level. The H theorem for the kinetic model is presented, and the entropy for the energy transport systems, which is inherited from the kinetic model, is derived. The energy transport systems for specific examples of the global Gibbs state, such as a power law with negative exponent, a cut-off power law with positive exponent, the Maxwellian, Bose-Einstein, and Fermi-Dirac distributions, arepresented.

  1. Multi-formalism modelling and simulation: application to cardiac modelling

    PubMed Central

    Defontaine, Antoine; Hernández, Alfredo; Carrault, Guy

    2004-01-01

    Cardiovascular modelling has been a major research subject for the last decades. Different cardiac models have been developed at a cellular level as well as at the whole organ level. Most of these models are defined by a comprehensive cellular modelling using continuous formalisms or by a tissue-level modelling often based on discrete formalisms. Nevertheless, both views still suffer from difficulties that reduce their clinical applications: the first approach requires heavy computational resources while the second one is not able to reproduce certain pathologies. This paper presents an original methodology trying to gather advantages from both approaches, by means of an hybrid model mixing discrete and continuous formalisms. This method has been applied to define a hybrid model of cardiac action potential propagation on a 2D grid of endocardial cells, combining cellular automata and a set of cells defined by the Beeler Reuter model. For simulations under physiologic and ischemic conditions, results show that the action potential propagation as well as electrogram reconstructions are consistent with clinical diagnosis. Finally, the interest of the proposed approach is discussed within the frame of cardiac modelling and simulation. PMID:15520534

  2. Modelling heart rate kinetics.

    PubMed

    Zakynthinaki, Maria S

    2015-01-01

    The objective of the present study was to formulate a simple and at the same time effective mathematical model of heart rate kinetics in response to movement (exercise). Based on an existing model, a system of two coupled differential equations which give the rate of change of heart rate and the rate of change of exercise intensity is used. The modifications introduced to the existing model are justified and discussed in detail, while models of blood lactate accumulation in respect to time and exercise intensity are also presented. The main modification is that the proposed model has now only one parameter which reflects the overall cardiovascular condition of the individual. The time elapsed after the beginning of the exercise, the intensity of the exercise, as well as blood lactate are also taken into account. Application of the model provides information regarding the individual's cardiovascular condition and is able to detect possible changes in it, across the data recording periods. To demonstrate examples of successful numerical fit of the model, constant intensity experimental heart rate data sets of two individuals have been selected and numerical optimization was implemented. In addition, numerical simulations provided predictions for various exercise intensities and various cardiovascular condition levels. The proposed model can serve as a powerful tool for a complete means of heart rate analysis, not only in exercise physiology (for efficiently designing training sessions for healthy subjects) but also in the areas of cardiovascular health and rehabilitation (including application in population groups for which direct heart rate recordings at intense exercises are not possible or not allowed, such as elderly or pregnant women).

  3. Modelling Heart Rate Kinetics

    PubMed Central

    Zakynthinaki, Maria S.

    2015-01-01

    The objective of the present study was to formulate a simple and at the same time effective mathematical model of heart rate kinetics in response to movement (exercise). Based on an existing model, a system of two coupled differential equations which give the rate of change of heart rate and the rate of change of exercise intensity is used. The modifications introduced to the existing model are justified and discussed in detail, while models of blood lactate accumulation in respect to time and exercise intensity are also presented. The main modification is that the proposed model has now only one parameter which reflects the overall cardiovascular condition of the individual. The time elapsed after the beginning of the exercise, the intensity of the exercise, as well as blood lactate are also taken into account. Application of the model provides information regarding the individual’s cardiovascular condition and is able to detect possible changes in it, across the data recording periods. To demonstrate examples of successful numerical fit of the model, constant intensity experimental heart rate data sets of two individuals have been selected and numerical optimization was implemented. In addition, numerical simulations provided predictions for various exercise intensities and various cardiovascular condition levels. The proposed model can serve as a powerful tool for a complete means of heart rate analysis, not only in exercise physiology (for efficiently designing training sessions for healthy subjects) but also in the areas of cardiovascular health and rehabilitation (including application in population groups for which direct heart rate recordings at intense exercises are not possible or not allowed, such as elderly or pregnant women). PMID:25876164

  4. Formal Specification of the OpenMP Memory Model

    SciTech Connect

    Bronevetsky, G; de Supinski, B

    2006-12-19

    OpenMP [2] is an important API for shared memory programming, combining shared memory's potential for performance with a simple programming interface. Unfortunately, OpenMP lacks a critical tool for demonstrating whether programs are correct: a formal memory model. Instead, the current official definition of the OpenMP memory model (the OpenMP 2.5 specification [2]) is in terms of informal prose. As a result, it is impossible to verify OpenMP applications formally since the prose does not provide a formal consistency model that precisely describes how reads and writes on different threads interact. We expand on our previous work that focused on the formal verification of OpenMP programs through a formal memory model [?]. As in that work, our formalization, which is derived from the existing prose model [2], provides a two-step process to verify whether an observed OpenMP execution is conformant. This paper extends the model to cover the entire specification. In addition to this formalization, our contributions include a discussion of ambiguities in the current prose-based memory model description. Although our formal model may not capture the current informal memory model perfectly, in part due to these ambiguities, our model reflects our understanding of the informal model's intent. We conclude with several examples that may indicate areas of the OpenMP memory model that need further refinement, however it is specified. Our goal is to motivate the OpenMP community to adopt those refinements eventually, ideally through a formal model, in later OpenMP specifications.

  5. Relaxation Kinetic Study of Eudragit® NM30D Film Based on Complex Modulus Formalism.

    PubMed

    Penumetcha, Sai Sumana; Byrn, Stephen R; Morris, Kenneth R

    2015-10-01

    This study is aimed at resolving and characterizing the primary (α) and secondary relaxations (β) in Eudragit® NM30D film based on apparent activation energies derived from complex modulus formalism using dielectric analysis (DEA). The glass transition (T g) of the film was determined using differential scanning calorimetry (DSC). The α relaxation corresponding to T g and the β relaxations occurring below T g were probed using DEA. The occurrence of α and β relaxations in Eudragit® NM30D film was elucidated using the complex modulus of the dielectric response employing loss modulus and permittivity data. Activation energies of these relaxations and the fundamental frequency so determined support the assignment of the relaxation pattern in the Eudragit® NM30D film. DEA methodology of the complex modulus formalism is a useful tool for differentiating the α and β relaxation kinetics in Eudragits® not easily studied using traditional thermal methods such as DSC. The kinetics associated with α and β relaxations so determined will provide formulation design support for solid orals that incorporate Eudragit® polymers. As mobility changes can affect stability and diffusion, the dipolar α and β relaxations revealed through DEA analysis may enable a better correlation to functionality of Eudragit® based pharmaceutical dosage forms.

  6. Symmetric Space σ-MODEL Dynamics:. Current Formalism

    NASA Astrophysics Data System (ADS)

    Yilmaz, Nejat T.

    After explicitly constructing the symmetric space sigma model Lagrangian in terms of the coset scalars of the solvable Lie algebra gauge in the current formalism, we derive the field equations of the theory.

  7. Experiences Using Lightweight Formal Methods for Requirements Modeling

    NASA Technical Reports Server (NTRS)

    Easterbrook, Steve; Lutz, Robyn; Covington, Rick; Kelly, John; Ampo, Yoko; Hamilton, David

    1997-01-01

    This paper describes three case studies in the lightweight application of formal methods to requirements modeling for spacecraft fault protection systems. The case studies differ from previously reported applications of formal methods in that formal methods were applied very early in the requirements engineering process, to validate the evolving requirements. The results were fed back into the projects, to improve the informal specifications. For each case study, we describe what methods were applied, how they were applied, how much effort was involved, and what the findings were. In all three cases, formal methods enhanced the existing verification and validation processes, by testing key properties of the evolving requirements, and helping to identify weaknesses. We conclude that the benefits gained from early modeling of unstable requirements more than outweigh the effort needed to maintain multiple representations.

  8. Formalisms for Specifying Markovian Population Models

    NASA Astrophysics Data System (ADS)

    Henzinger, Thomas A.; Jobstmann, Barbara; Wolf, Verena

    We compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. These languages —matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models— all describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, ease of use, and the support they provide for checking the well-formedness of a model and for analyzing a model.

  9. Formalized landscape models for surveying and modelling tasks

    NASA Astrophysics Data System (ADS)

    Löwner, Marc-Oliver

    2010-05-01

    We present a formalization of main geomorphic landscape models, mainly the concept of slopes, to clarify the needs and potentials of surveying technologies and modelling approaches. Using the Unified Modelling Language (UML) it is implemented as a exchangeable Geography Markup Language (GML3) -based application schema and therefore supports shared measurement campaigns. Today, knowledge in Geomorphology is given synoptically in textbooks in a more or less lyrical way. This knowledge is hard to implement for the use of modelling algorithms or data storage and sharing questions. On the other hand physical based numerical modelling and high resolution surveying technologies enable us to investigate case scenarios within small scales. Bringing together such approaches and organizing our data in an appropriate way will need the formalization of the concepts and knowledge that is archived in the science of geomorphology. The main problem of comparing research results in geomorphology but is that the objects under investigation are composed of 3-dimensional geometries that change in time due to processes of material fluxes, e. g. soil erosion or mass movements. They have internal properties, e. g. soil texture or bulk density, that determine the effectiveness of these processes but are under change as well. The presented application schema is available on the Internet and therefore a first step to enable researchers to share information using an OGC's Web feature service. In this vein comparing modelling results of landscape evolution with results of other scientist's observations is possible. Compared to prevalent data concepts the model presented makes it possible to store information about landforms, their geometry and the characteristics in more detail. It allows to represent the 3D-geometry, the set of material properties and the genesis of a landform by associating processes to a geoobject. Thus, time slices of a geomorphic system can be represented as well as

  10. Stochastic kinetic mean field model

    NASA Astrophysics Data System (ADS)

    Erdélyi, Zoltán; Pasichnyy, Mykola; Bezpalchuk, Volodymyr; Tomán, János J.; Gajdics, Bence; Gusak, Andriy M.

    2016-07-01

    This paper introduces a new model for calculating the change in time of three-dimensional atomic configurations. The model is based on the kinetic mean field (KMF) approach, however we have transformed that model into a stochastic approach by introducing dynamic Langevin noise. The result is a stochastic kinetic mean field model (SKMF) which produces results similar to the lattice kinetic Monte Carlo (KMC). SKMF is, however, far more cost-effective and easier to implement the algorithm (open source program code is provided on http://skmf.eu website). We will show that the result of one SKMF run may correspond to the average of several KMC runs. The number of KMC runs is inversely proportional to the amplitude square of the noise in SKMF. This makes SKMF an ideal tool also for statistical purposes.

  11. Schwinger pair production in space- and time-dependent electric fields: Relating the Wigner formalism to quantum kinetic theory

    SciTech Connect

    Hebenstreit, F.; Alkofer, R.; Gies, H.

    2010-11-15

    The nonperturbative electron-positron pair production (Schwinger effect) is considered for space- and time-dependent electric fields E-vector(x-vector,t). Based on the Dirac-Heisenberg-Wigner formalism, we derive a system of partial differential equations of infinite order for the 16 irreducible components of the Wigner function. In the limit of spatially homogeneous fields the Vlasov equation of quantum kinetic theory is rediscovered. It is shown that the quantum kinetic formalism can be exactly solved in the case of a constant electric field E(t)=E{sub 0} and the Sauter-type electric field E(t)=E{sub 0}sech{sup 2}(t/{tau}). These analytic solutions translate into corresponding expressions within the Dirac-Heisenberg-Wigner formalism and allow to discuss the effect of higher derivatives. We observe that spatial field variations typically exert a strong influence on the components of the Wigner function for large momenta or for late times.

  12. A Kinetic-fluid Model

    SciTech Connect

    First Author = C.Z. Cheng; Jay R. Johnson

    1998-07-10

    A nonlinear kinetic-fluid model for high-beta plasmas with multiple ion species which can be applied to multiscale phenomena is presented. The model embeds important kinetic effects due to finite ion Larmor radius (FLR), wave-particle resonances, magnetic particle trapping, etc. in the framework of simple fluid descriptions. When further restricting to low frequency phenomena with frequencies less than the ion cyclotron frequency the kinetic-fluid model takes a simpler form in which the fluid equations of multiple ion species collapse into single-fluid density and momentum equations and a low frequency generalized Ohm's law. The kinetic effects are introduced via plasma pressure tensors for ions and electrons which are computed from particle distribution functions that are governed by the Vlasov equation or simplified plasma dynamics equations such as the gyrokinetic equation. The ion FLR effects provide a finite parallel electric field, a perpendicular velocity that modifies the ExB drift, and a gyroviscosity tensor, all of which are neglected in the usual one-fluid MHD description. Eigenmode equations are derived which include magnetosphere-ionosphere coupling effects for low frequency waves (e.g., kinetic/inertial Alfven waves and ballooning-mirror instabilities).

  13. Chemical kinetics and combustion modeling

    SciTech Connect

    Miller, J.A.

    1993-12-01

    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.

  14. Modeling Cyber Conflicts Using an Extended Petri Net Formalism

    SciTech Connect

    Zakrzewska, Anita N; Ferragut, Erik M

    2011-01-01

    When threatened by automated attacks, critical systems that require human-controlled responses have difficulty making optimal responses and adapting protections in real- time and may therefore be overwhelmed. Consequently, experts have called for the development of automatic real-time reaction capabilities. However, a technical gap exists in the modeling and analysis of cyber conflicts to automatically understand the repercussions of responses. There is a need for modeling cyber assets that accounts for concurrent behavior, incomplete information, and payoff functions. Furthermore, we address this need by extending the Petri net formalism to allow real-time cyber conflicts to be modeled in a way that is expressive and concise. This formalism includes transitions controlled by players as well as firing rates attached to transitions. This allows us to model both player actions and factors that are beyond the control of players in real-time. We show that our formalism is able to represent situational aware- ness, concurrent actions, incomplete information and objective functions. These factors make it well-suited to modeling cyber conflicts in a way that allows for useful analysis. MITRE has compiled the Common Attack Pattern Enumera- tion and Classification (CAPEC), an extensive list of cyber attacks at various levels of abstraction. CAPEC includes factors such as attack prerequisites, possible countermeasures, and attack goals. These elements are vital to understanding cyber attacks and to generating the corresponding real-time responses. We demonstrate that the formalism can be used to extract precise models of cyber attacks from CAPEC. Several case studies show that our Petri net formalism is more expressive than other models, such as attack graphs, for modeling cyber conflicts and that it is amenable to exploring cyber strategies.

  15. Improving Project Management Using Formal Models and Architectures

    NASA Technical Reports Server (NTRS)

    Kahn, Theodore; Sturken, Ian

    2011-01-01

    This talk discusses the advantages formal modeling and architecture brings to project management. These emerging technologies have both great potential and challenges for improving information available for decision-making. The presentation covers standards, tools and cultural issues needing consideration, and includes lessons learned from projects the presenters have worked on.

  16. Kinetic Modeling of Biological Systems

    PubMed Central

    Petzold, Linda; Pettigrew, Michel F.

    2010-01-01

    The dynamics of how the constituent components of a natural system interact defines the spatio-temporal response of the system to stimuli. Modeling the kinetics of the processes that represent a biophysical system has long been pursued with the aim of improving our understanding of the studied system. Due to the unique properties of biological systems, in addition to the usual difficulties faced in modeling the dynamics of physical or chemical systems, biological simulations encounter difficulties that result from intrinsic multiscale and stochastic nature of the biological processes. This chapter discusses the implications for simulation of models involving interacting species with very low copy numbers, which often occur in biological systems and give rise to significant relative fluctuations. The conditions necessitating the use of stochastic kinetic simulation methods and the mathematical foundations of the stochastic simulation algorithms are presented. How the well-organized structural hierarchies often seen in biological systems can lead to multiscale problems, and possible ways to address the encountered computational difficulties are discussed. We present the details of the existing kinetic simulation methods, and discuss their strengths and shortcomings. A list of the publicly available kinetic simulation tools and our reflections for future prospects are also provided. PMID:19381542

  17. Formalization of hydrocarbon conversion scheme of catalytic cracking for mathematical model development

    NASA Astrophysics Data System (ADS)

    Nazarova, G.; Ivashkina, E.; Ivanchina, E.; Kiseleva, S.; Stebeneva, V.

    2015-11-01

    The issue of improving the energy and resource efficiency of advanced petroleum processing can be solved by the development of adequate mathematical model based on physical and chemical regularities of process reactions with a high predictive potential in the advanced petroleum refining. In this work, the development of formalized hydrocarbon conversion scheme of catalytic cracking was performed using thermodynamic parameters of reaction defined by the Density Functional Theory. The list of reaction was compiled according to the results of feedstock structural-group composition definition, which was done by the n-d-m-method, the Hazelvuda method, qualitative composition of feedstock defined by gas chromatography-mass spectrometry and individual composition of catalytic cracking gasoline fraction. Formalized hydrocarbon conversion scheme of catalytic cracking will become the basis for the development of the catalytic cracking kinetic model.

  18. Kinetic Modeling of Microbiological Processes

    SciTech Connect

    Liu, Chongxuan; Fang, Yilin

    2012-08-26

    Kinetic description of microbiological processes is vital for the design and control of microbe-based biotechnologies such as waste water treatment, petroleum oil recovery, and contaminant attenuation and remediation. Various models have been proposed to describe microbiological processes. This editorial article discusses the advantages and limiation of these modeling approaches in cluding tranditional, Monod-type models and derivatives, and recently developed constraint-based approaches. The article also offers the future direction of modeling researches that best suit for petroleum and environmental biotechnologies.

  19. Kinetic model of HIV infection

    SciTech Connect

    Zhdanov, V. P.

    2007-10-15

    Recent experiments clarifying the details of exhaustion of CD8 T cells specific to various strains of human immunodeficiency virus (HIV) are indicative of slow irreversible (on a one-year time scale) deterioration of the immune system. The conventional models of HIV kinetics do not take this effect into account. Removing this shortcoming, we show the likely influence of such changes on the escape of HIV from control of the immune system.

  20. Formal versus heuristic modeling for multitarget Bayes filtering

    NASA Astrophysics Data System (ADS)

    Mahler, Ronald P. S.

    2004-08-01

    The multisensor-multitarget Bayes filter is the foundation for multi-sensor-multitarget detection, tracking, and identification. This paper addresses the question of principled implementation of this filter. Algorithms can always be cobbled together using catch-as-catch-can heuristic techniques. In formal Bayes modeling one instead derives statistically precise, implementation-independent equations from which principle approximations can then be derived. Indeed, this has become the accepted methodology for single-sensor, single-target tracking R&D. In the case of the multitarget filter, however, partisans of a so-called "plain-vanilla Bayesian approach" have disparaged formal Bayes modelling, and have protrayed specific, ad hoc implementations as completely general, "powerful and robust computational methods." In this and a companion paper I expose the speciousness of such claims. This paper reviews the elements of formal Bayes modeling and approximation, describes what they must look like in the multitarget case, and contrasts them with the "plain-vanilla Bayesian approach."

  1. Los Alamos Center for Computer Security formal computer security model

    SciTech Connect

    Dreicer, J.S.; Hunteman, W.J.; Markin, J.T.

    1989-01-01

    This paper provides a brief presentation of the formal computer security model currently being developed at the Los Alamos Department of Energy (DOE) Center for Computer Security (CCS). The need to test and verify DOE computer security policy implementation first motivated this effort. The actual analytical model was a result of the integration of current research in computer security and previous modeling and research experiences. The model is being developed to define a generic view of the computer and network security domains, to provide a theoretical basis for the design of a security model, and to address the limitations of present formal mathematical models for computer security. The fundamental objective of computer security is to prevent the unauthorized and unaccountable access to a system. The inherent vulnerabilities of computer systems result in various threats from unauthorized access. The foundation of the Los Alamos DOE CCS model is a series of functionally dependent probability equations, relations, and expressions. The model is undergoing continued discrimination and evolution. We expect to apply the model to the discipline of the Bell and LaPadula abstract sets of objects and subjects. 6 refs.

  2. Formal representation of 3D structural geological models

    NASA Astrophysics Data System (ADS)

    Wang, Zhangang; Qu, Honggang; Wu, Zixing; Yang, Hongjun; Du, Qunle

    2016-05-01

    The development and widespread application of geological modeling methods has increased demands for the integration and sharing services of three dimensional (3D) geological data. However, theoretical research in the field of geological information sciences is limited despite the widespread use of Geographic Information Systems (GIS) in geology. In particular, fundamental research on the formal representations and standardized spatial descriptions of 3D structural models is required. This is necessary for accurate understanding and further applications of geological data in 3D space. In this paper, we propose a formal representation method for 3D structural models using the theory of point set topology, which produces a mathematical definition for the major types of geological objects. The spatial relationships between geologic boundaries, structures, and units are explained in detail using the 9-intersection model. Reasonable conditions for describing the topological space of 3D structural models are also provided. The results from this study can be used as potential support for the standardized representation and spatial quality evaluation of 3D structural models, as well as for specific needs related to model-based management, query, and analysis.

  3. Kinetic models of conjugated metabolic cycles

    NASA Astrophysics Data System (ADS)

    Ershov, Yu. A.

    2016-01-01

    A general method is developed for the quantitative kinetic analysis of conjugated metabolic cycles in the human organism. This method is used as a basis for constructing a kinetic graph and model of the conjugated citric acid and ureapoiesis cycles. The results from a kinetic analysis of the model for these cycles are given.

  4. Modelling reaction kinetics inside cells

    PubMed Central

    Grima, Ramon; Schnell, Santiago

    2009-01-01

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

  5. Kinetic models of immediate exchange

    NASA Astrophysics Data System (ADS)

    Heinsalu, Els; Patriarca, Marco

    2014-08-01

    We propose a novel kinetic exchange model differing from previous ones in two main aspects. First, the basic dynamics is modified in order to represent economies where immediate wealth exchanges are carried out, instead of reshufflings or uni-directional movements of wealth. Such dynamics produces wealth distributions that describe more faithfully real data at small values of wealth. Secondly, a general probabilistic trading criterion is introduced, so that two economic units can decide independently whether to trade or not depending on their profit. It is found that the type of the equilibrium wealth distribution is the same for a large class of trading criteria formulated in a symmetrical way with respect to the two interacting units. This establishes unexpected links between and provides a microscopic foundations of various kinetic exchange models in which the existence of a saving propensity is postulated. We also study the generalized heterogeneous version of the model in which units use different trading criteria and show that suitable sets of diversified parameter values with a moderate level of heterogeneity can reproduce realistic wealth distributions with a Pareto power law.

  6. Computational Modeling, Formal Analysis, and Tools for Systems Biology

    PubMed Central

    Bartocci, Ezio; Lió, Pietro

    2016-01-01

    As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science. PMID:26795950

  7. Computational Modeling, Formal Analysis, and Tools for Systems Biology.

    PubMed

    Bartocci, Ezio; Lió, Pietro

    2016-01-01

    As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science.

  8. A Formal Model of Partitioning for Integrated Modular Avionics

    NASA Technical Reports Server (NTRS)

    DiVito, Ben L.

    1998-01-01

    The aviation industry is gradually moving toward the use of integrated modular avionics (IMA) for civilian transport aircraft. An important concern for IMA is ensuring that applications are safely partitioned so they cannot interfere with one another. We have investigated the problem of ensuring safe partitioning and logical non-interference among separate applications running on a shared Avionics Computer Resource (ACR). This research was performed in the context of ongoing standardization efforts, in particular, the work of RTCA committee SC-182, and the recently completed ARINC 653 application executive (APEX) interface standard. We have developed a formal model of partitioning suitable for evaluating the design of an ACR. The model draws from the mathematical modeling techniques developed by the computer security community. This report presents a formulation of partitioning requirements expressed first using conventional mathematical notation, then formalized using the language of SRI'S Prototype Verification System (PVS). The approach is demonstrated on three candidate designs, each an abstraction of features found in real systems.

  9. Elastic Network Models are Robust to Variations in Formalism.

    PubMed

    Leioatts, Nicholas; Romo, Tod D; Grossfield, Alan

    2012-07-10

    Understanding the functions of biomolecules requires insight not only from structures, but from dynamics as well. Often, the most interesting processes occur on time scales too slow for exploration by conventional molecular dynamics (MD) simulations. For this reason, alternative computational methods such as elastic network models (ENMs) have become increasingly popular. These simple, coarse-grained models represent molecules as beads connected by harmonic springs; the system's motions are solved analytically by normal mode analysis. In the past few years, many different formalisms for performing ENM calculations have emerged, and several have been optimized using all-atom MD simulations. In contrast to other studies, we have compared the various formalisms in a systematic, quantitative way. In this study, we optimize many ENM functional forms using a uniform dataset containing only long (> 1 μs) all-atom MD simulations. Our results show that all models once optimized produce spring constants for immediate neighboring residues that are orders of magnitude stiffer than more distal contacts. In addition, the statistical significance of ENM performance varied with model resolution. We also show that fitting long trajectories does not improve ENM performance due to a problem inherent in all network models tested: they underestimate the relative importance of the most concerted motions. Finally, we characterize ENMs' resilience by tessellating the parameter space to show that broad ranges of parameters produce similar quality predictions. Taken together our data reveals that choice of spring function and parameters are not vital to performance of a network model and that simple parameters can by derived "by hand" when no data is available for fitting, thus illustrating the robustness of these models. PMID:22924033

  10. Elastic Network Models are Robust to Variations in Formalism.

    PubMed

    Leioatts, Nicholas; Romo, Tod D; Grossfield, Alan

    2012-07-10

    Understanding the functions of biomolecules requires insight not only from structures, but from dynamics as well. Often, the most interesting processes occur on time scales too slow for exploration by conventional molecular dynamics (MD) simulations. For this reason, alternative computational methods such as elastic network models (ENMs) have become increasingly popular. These simple, coarse-grained models represent molecules as beads connected by harmonic springs; the system's motions are solved analytically by normal mode analysis. In the past few years, many different formalisms for performing ENM calculations have emerged, and several have been optimized using all-atom MD simulations. In contrast to other studies, we have compared the various formalisms in a systematic, quantitative way. In this study, we optimize many ENM functional forms using a uniform dataset containing only long (> 1 μs) all-atom MD simulations. Our results show that all models once optimized produce spring constants for immediate neighboring residues that are orders of magnitude stiffer than more distal contacts. In addition, the statistical significance of ENM performance varied with model resolution. We also show that fitting long trajectories does not improve ENM performance due to a problem inherent in all network models tested: they underestimate the relative importance of the most concerted motions. Finally, we characterize ENMs' resilience by tessellating the parameter space to show that broad ranges of parameters produce similar quality predictions. Taken together our data reveals that choice of spring function and parameters are not vital to performance of a network model and that simple parameters can by derived "by hand" when no data is available for fitting, thus illustrating the robustness of these models.

  11. Spectral method for a kinetic swarming model

    DOE PAGESBeta

    Gamba, Irene M.; Haack, Jeffrey R.; Motsch, Sebastien

    2015-04-28

    Here we present the first numerical method for a kinetic description of the Vicsek swarming model. The kinetic model poses a unique challenge, as there is a distribution dependent collision invariant to satisfy when computing the interaction term. We use a spectral representation linked with a discrete constrained optimization to compute these interactions. To test the numerical scheme we investigate the kinetic model at different scales and compare the solution with the microscopic and macroscopic descriptions of the Vicsek model. Lastly, we observe that the kinetic model captures key features such as vortex formation and traveling waves.

  12. Electrostatics of a simple membrane model using Green's functions formalism.

    PubMed Central

    von Kitzing, E; Soumpasis, D M

    1996-01-01

    The electrostatics of a simple membrane model picturing a lipid bilayer as a low dielectric constant slab immersed in a homogeneous medium of high dielectric constant (water) can be accurately computed using the exact Green's functions obtainable for this geometry. We present an extensive discussion of the analysis and numerical aspects of the problem and apply the formalism and algorithms developed to the computation of the energy profiles of a test charge (e.g., ion) across the bilayer and a molecular model of the acetylcholine receptor channel embedded in it. The Green's function approach is a very convenient tool for the computer simulation of ionic transport across membrane channels and other membrane problems where a good and computationally efficient first-order treatment of dielectric polarization effects is crucial. PMID:8842218

  13. Appreciating Formal Similarities in the Kinetics of Homogeneous, Heterogeneous, and Enzyme Catalysis

    ERIC Educational Resources Information Center

    Ashby, Michael T.

    2007-01-01

    Because interest in catalysts is widespread, the kinetics of catalytic reactions have been investigated by widely diverse groups of individuals, including chemists, engineers, and biologists. This has lead to redundancy in theories, particularly with regard to the topics of homogeneous, heterogeneous, and enzyme catalysis. From a pedagogical…

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

    SciTech Connect

    Marinov, N.M.; Westbrook, C.K.; Cloutman, L.D.

    1995-09-01

    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.

  15. The Importance of Formalizing Computational Models of Face Adaptation Aftereffects

    PubMed Central

    Ross, David A.; Palmeri, Thomas J.

    2016-01-01

    Face adaptation is widely used as a means to probe the neural representations that support face recognition. While the theories that relate face adaptation to behavioral aftereffects may seem conceptually simple, our work has shown that testing computational instantiations of these theories can lead to unexpected results. Instantiating a model of face adaptation not only requires specifying how faces are represented and how adaptation shapes those representations but also specifying how decisions are made, translating hidden representational states into observed responses. Considering the high-dimensionality of face representations, the parallel activation of multiple representations, and the non-linearity of activation functions and decision mechanisms, intuitions alone are unlikely to succeed. If the goal is to understand mechanism, not simply to examine the boundaries of a behavioral phenomenon or correlate behavior with brain activity, then formal computational modeling must be a component of theory testing. To illustrate, we highlight our recent computational modeling of face adaptation aftereffects and discuss how models can be used to understand the mechanisms by which faces are recognized. PMID:27378960

  16. The Archival Photograph and Its Meaning: Formalisms for Modeling Images

    ERIC Educational Resources Information Center

    Benson, Allen C.

    2009-01-01

    This article explores ontological principles and their potential applications in the formal description of archival photographs. Current archival descriptive practices are reviewed and the larger question is addressed: do archivists who are engaged in describing photographs need a more formalized system of representation, or do existing encoding…

  17. Detecting Mode Confusion Through Formal Modeling and Analysis

    NASA Technical Reports Server (NTRS)

    Miller, Steven P.; Potts, James N.

    1999-01-01

    Aircraft safety has improved steadily over the last few decades. While much of this improvement can be attributed to the introduction of advanced automation in the cockpit, the growing complexity of these systems also increases the potential for the pilots to become confused about what the automation is doing. This phenomenon, often referred to as mode confusion, has been involved in several accidents involving modern aircraft. This report describes an effort by Rockwell Collins and NASA Langley to identify potential sources of mode confusion through two complementary strategies. The first is to create a clear, executable model of the automation, connect it to a simulation of the flight deck, and use this combination to review of the behavior of the automation and the man-machine interface with the designers, pilots, and experts in human factors. The second strategy is to conduct mathematical analyses of the model by translating it into a formal specification suitable for analysis with automated tools. The approach is illustrated by applying it to a hypothetical, but still realistic, example of the mode logic of a Flight Guidance System.

  18. Modeling of Reactor Kinetics and Dynamics

    SciTech Connect

    Matthew Johnson; Scott Lucas; Pavel Tsvetkov

    2010-09-01

    In order to model a full fuel cycle in a nuclear reactor, it is necessary to simulate the short time-scale kinetic behavior of the reactor as well as the long time-scale dynamics that occur with fuel burnup. The former is modeled using the point kinetics equations, while the latter is modeled by coupling fuel burnup equations with the kinetics equations. When the equations are solved simultaneously with a nonlinear equation solver, the end result is a code with the unique capability of modeling transients at any time during a fuel cycle.

  19. Physiologically based models of metal kinetics.

    PubMed

    O'Flaherty, E J

    1998-05-01

    The issues confronting the modeler of metals kinetics are somewhat different from those with which the modeler of organic chemical behavior is faced. Particularly important features of metals kinetics include metal-protein binding and metal-metal interactions. Reduction, and for some metals oxidation, is frequently an intrinsic part of metal metabolism. Alkylation/dealkylation reactions may or may not render the metal less active, and the behavior of alkylated or dealkylated metabolites must often be included in a complete kinetic model. Despite these complexities, the kinetics of metals are as amenable to the techniques of physiologically based modeling as are the kinetics of organic chemicals. Like all models, those for metals kinetics have the potential to organize a variety of observations, sometimes including apparently inconsistent observations, into a coherent framework of behavior, to identify needs for more complete experimental information, and to assist the risk assessor in making judgments concerning dose-response relationships. Development of physiologically based models of the kinetic behavior of metals is in its very early stages. The kinetics of only four metals, arsenic, chromium, mercury, and lead, have been modeled with any degree of completeness. Of these, the lead model is the most fully realized at the present time. The chromium and mercury models are still in the process of development, and experimental data are being gathered to support further development and refinement of the arsenic model. We may expect to see continued progress made on these models and their practical applications, as well as the development of new models for other toxicologically significant metals such as cadmium, manganese, nickel, and aluminum. PMID:9631283

  20. Beware the tail that wags the dog: informal and formal models in biology

    PubMed Central

    Gunawardena, Jeremy

    2014-01-01

    Informal models have always been used in biology to guide thinking and devise experiments. In recent years, formal mathematical models have also been widely introduced. It is sometimes suggested that formal models are inherently superior to informal ones and that biology should develop along the lines of physics or economics by replacing the latter with the former. Here I suggest to the contrary that progress in biology requires a better integration of the formal with the informal. PMID:25368417

  1. Viral kinetic modeling: state of the art

    DOE PAGESBeta

    Canini, Laetitia; Perelson, Alan S.

    2014-06-25

    Viral kinetic modeling has led to increased understanding of the within host dynamics of viral infections and the effects of therapy. Here we review recent developments in the modeling of viral infection kinetics with emphasis on two infectious diseases: hepatitis C and influenza. We review how viral kinetic modeling has evolved from simple models of viral infections treated with a drug or drug cocktail with an assumed constant effectiveness to models that incorporate drug pharmacokinetics and pharmacodynamics, as well as phenomenological models that simply assume drugs have time varying-effectiveness. We also discuss multiscale models that include intracellular events in viralmore » replication, models of drug-resistance, models that include innate and adaptive immune responses and models that incorporate cell-to-cell spread of infection. Overall, viral kinetic modeling has provided new insights into the understanding of the disease progression and the modes of action of several drugs. In conclusion, we expect that viral kinetic modeling will be increasingly used in the coming years to optimize drug regimens in order to improve therapeutic outcomes and treatment tolerability for infectious diseases.« less

  2. Viral kinetic modeling: state of the art

    SciTech Connect

    Canini, Laetitia; Perelson, Alan S.

    2014-06-25

    Viral kinetic modeling has led to increased understanding of the within host dynamics of viral infections and the effects of therapy. Here we review recent developments in the modeling of viral infection kinetics with emphasis on two infectious diseases: hepatitis C and influenza. We review how viral kinetic modeling has evolved from simple models of viral infections treated with a drug or drug cocktail with an assumed constant effectiveness to models that incorporate drug pharmacokinetics and pharmacodynamics, as well as phenomenological models that simply assume drugs have time varying-effectiveness. We also discuss multiscale models that include intracellular events in viral replication, models of drug-resistance, models that include innate and adaptive immune responses and models that incorporate cell-to-cell spread of infection. Overall, viral kinetic modeling has provided new insights into the understanding of the disease progression and the modes of action of several drugs. In conclusion, we expect that viral kinetic modeling will be increasingly used in the coming years to optimize drug regimens in order to improve therapeutic outcomes and treatment tolerability for infectious diseases.

  3. Chemical Kinetic Modeling of Advanced Transportation Fuels

    SciTech Connect

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

    2009-01-20

    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.

  4. Kinetic Modeling using BioPAX ontology

    PubMed Central

    Ruebenacker, Oliver; Moraru, Ion. I.; Schaff, James C.; Blinov, Michael L.

    2010-01-01

    Thousands of biochemical interactions are available for download from curated databases such as Reactome, Pathway Interaction Database and other sources in the Biological Pathways Exchange (BioPAX) format. However, the BioPAX ontology does not encode the necessary information for kinetic modeling and simulation. The current standard for kinetic modeling is the System Biology Markup Language (SBML), but only a small number of models are available in SBML format in public repositories. Additionally, reusing and merging SBML models presents a significant challenge, because often each element has a value only in the context of the given model, and information encoding biological meaning is absent. We describe a software system that enables a variety of operations facilitating the use of BioPAX data to create kinetic models that can be visualized, edited, and simulated using the Virtual Cell (VCell), including improved conversion to SBML (for use with other simulation tools that support this format). PMID:20862270

  5. Joint Non-kinetic Effects Model (JNEM)

    NASA Technical Reports Server (NTRS)

    Chamberlain, Robert G.; Metivier, Timothy

    2006-01-01

    This slide presentation reviews the development of the Joint Non-kinetic Effects Model (JNEM), which is tool to support Battle Command Training that links simulation-generated non-kinetic events and outcomes to Training Audience Command and Staff decisions. JNEM helps create the operating environment for the following population groups (P-groups): (1) Local Civilians on the Battlefield, (2) Inter-Governmental Organizations (3) Non-Governmental Organizations (4) Contractors on the battlefield.

  6. Algebraic operator approach to gas kinetic models

    NASA Astrophysics Data System (ADS)

    Il'ichov, L. V.

    1997-02-01

    Some general properties of the linear Boltzmann kinetic equation are used to present it in the form ∂ tϕ = - †Âϕ with the operators Âand† possessing some nontrivial algebraic properties. When applied to the Keilson-Storer kinetic model, this method gives an example of quantum ( q-deformed) Lie algebra. This approach provides also a natural generalization of the “kangaroo model”.

  7. A kinetic model for predicting biodegradation.

    PubMed

    Dimitrov, S; Pavlov, T; Nedelcheva, D; Reuschenbach, P; Silvani, M; Bias, R; Comber, M; Low, L; Lee, C; Parkerton, T; Mekenyan, O

    2007-01-01

    Biodegradation plays a key role in the environmental risk assessment of organic chemicals. The need to assess biodegradability of a chemical for regulatory purposes supports the development of a model for predicting the extent of biodegradation at different time frames, in particular the extent of ultimate biodegradation within a '10 day window' criterion as well as estimating biodegradation half-lives. Conceptually this implies expressing the rate of catabolic transformations as a function of time. An attempt to correlate the kinetics of biodegradation with molecular structure of chemicals is presented. A simplified biodegradation kinetic model was formulated by combining the probabilistic approach of the original formulation of the CATABOL model with the assumption of first order kinetics of catabolic transformations. Nonlinear regression analysis was used to fit the model parameters to OECD 301F biodegradation kinetic data for a set of 208 chemicals. The new model allows the prediction of biodegradation multi-pathways, primary and ultimate half-lives and simulation of related kinetic biodegradation parameters such as biological oxygen demand (BOD), carbon dioxide production, and the nature and amount of metabolites as a function of time. The model may also be used for evaluating the OECD ready biodegradability potential of a chemical within the '10-day window' criterion.

  8. Detailed chemical kinetic model for ethanol oxidation

    SciTech Connect

    Marinov, N.

    1997-04-01

    A detailed chemical kinetic model for ethanol oxidation has been developed and validated against a variety of experimental data sets. Laminar flame speed data obtained from a constant volume bomb, ignition delay data behind reflected shock waves, and ethanol oxidation product profiles from a turbulent flow reactor were used in this study. Very good agreement was found in modeling the data sets obtained from the three different experimental systems. The computational modeling results show that high temperature ethanol oxidation exhibits strong sensitivity to the fall-off kinetics of ethanol decomposition, branching ratio selection for c2h5oh+oh=products, and reactions involving the hydroperoxyl (HO2) radical.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  10. Model Independent Bounds on Kinetic Mixing

    SciTech Connect

    Hook, Anson; Izaguirre, Eder; Wacker, Jay G.; /SLAC

    2011-08-22

    New Abelian vector bosons can kinetically mix with the hypercharge gauge boson of the Standard Model. This letter computes the model independent limits on vector bosons with masses from 1 GeV to 1 TeV. The limits arise from the numerous e{sup +}e{sup -} experiments that have been performed in this energy range and bound the kinetic mixing by {epsilon} {approx}< 0.03 for most of the mass range studied, regardless of any additional interactions that the new vector boson may have.

  11. Automatic Generation of Integrated Formal Models Corresponding to UML System Models

    NASA Astrophysics Data System (ADS)

    Treharne, Helen; Turner, Edward; Paige, Richard F.; Kolovos, Dimitrios S.

    This paper presents a complex model transformation that takes two related UML models as input (class diagrams and state machines) and outputs an integrated formal model. The transformation is achieved using the Epsilon model management framework and has involved the definition of new CSP and B metamodels. The target model is a CSPB specification (a fusion of CSP and B) that can be used to analyse the source UML. Through a comparative study we conclude that the code written using Epsilon is more concise than the equivalent model-to-text transformation achieved using the iUML toolset.

  12. Kinetic Analysis of Protein Folding Lattice Models

    NASA Astrophysics Data System (ADS)

    Chen, Hu; Zhou, Xin; Liaw, Chih Young; Koh, Chan Ghee

    Based on two-dimensional square lattice models of proteins, the relation between folding time and temperature is studied by Monte Carlo simulation. The results can be represented by a kinetic model with three states — random coil, molten globule, and native state. The folding process is composed of nonspecific collapse and final searching for the native state. At high temperature, it is easy to escape from local traps in the folding process. With decreasing temperature, because of the trapping in local traps, the final searching speed decreases. Then the folding shows chevron rollover. Through the analysis of the fitted parameters of the kinetic model, it is found that the main difference between the energy landscapes of the HP model and the Go model is that the number of local minima of the Go model is less than that of the HP model.

  13. Formalization model of expert knowledge about a technical index level of engineering products

    NASA Astrophysics Data System (ADS)

    Zakharova, A. A.; Ostanin, V. V.

    2015-09-01

    The authors set a timely problem that concerns development of decision making models, which allow formalizing expert subjective ideas about technical index level of engineering products. The authors proposed a formalization model of expert knowledge about technical index level of engineering products on the basis of fuzzy sets. The model has a method of membership-function construction for linguistic variable terms on the basis of exponential functions.

  14. Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer

    PubMed Central

    Tareen, Samar H.K.; Siddiqa, Amnah; Bibi, Zurah; Ahmad, Jamil

    2016-01-01

    Background Breast cancer (BC) is one of the leading cause of death among females worldwide. The increasing incidence of BC is due to various genetic and environmental changes which lead to the disruption of cellular signaling network(s). It is a complex disease in which several interlinking signaling cascades play a crucial role in establishing a complex regulatory network. The logical modeling approach of René Thomas has been applied to analyze the behavior of estrogen receptor-alpha (ER-α) associated Biological Regulatory Network (BRN) for a small part of complex events that leads to BC metastasis. Methods A discrete model was constructed using the kinetic logic formalism and its set of logical parameters were obtained using the model checking technique implemented in the SMBioNet software which is consistent with biological observations. The discrete model was further enriched with continuous dynamics by converting it into an equivalent Petri Net (PN) to analyze the logical parameters of the involved entities. Results In-silico based discrete and continuous modeling of ER-α associated signaling network involved in BC provides information about behaviors and gene-gene interaction in detail. The dynamics of discrete model revealed, imperative behaviors represented as cyclic paths and trajectories leading to pathogenic states such as metastasis. Results suggest that the increased expressions of receptors ER-α, IGF-1R and EGFR slow down the activity of tumor suppressor genes (TSGs) such as BRCA1, p53 and Mdm2 which can lead to metastasis. Therefore, IGF-1R and EGFR are considered as important inhibitory targets to control the metastasis in BC. Conclusion The in-silico approaches allow us to increase our understanding of the functional properties of living organisms. It opens new avenues of investigations of multiple inhibitory targets (ER-α, IGF-1R and EGFR) for wet lab experiments as well as provided valuable insights in the treatment of cancers such as BC

  15. Investigation of the kinetic model equations

    NASA Astrophysics Data System (ADS)

    Liu, Sha; Zhong, Chengwen

    2014-03-01

    Currently the Boltzmann equation and its model equations are widely used in numerical predictions for dilute gas flows. The nonlinear integro-differential Boltzmann equation is the fundamental equation in the kinetic theory of dilute monatomic gases. By replacing the nonlinear fivefold collision integral term by a nonlinear relaxation term, its model equations such as the famous Bhatnagar-Gross-Krook (BGK) equation are mathematically simple. Since the computational cost of solving model equations is much less than that of solving the full Boltzmann equation, the model equations are widely used in predicting rarefied flows, multiphase flows, chemical flows, and turbulent flows although their predictions are only qualitatively right for highly nonequilibrium flows in transitional regime. In this paper the differences between the Boltzmann equation and its model equations are investigated aiming at giving guidelines for the further development of kinetic models. By comparing the Boltzmann equation and its model equations using test cases with different nonequilibrium types, two factors (the information held by nonequilibrium moments and the different relaxation rates of high- and low-speed molecules) are found useful for adjusting the behaviors of modeled collision terms in kinetic regime. The usefulness of these two factors are confirmed by a generalized model collision term derived from a mathematical relation between the Boltzmann equation and BGK equation that is also derived in this paper. After the analysis of the difference between the Boltzmann equation and the BGK equation, an attempt at approximating the collision term is proposed.

  16. Deterministic Modelling of BAK Activation Kinetics

    NASA Astrophysics Data System (ADS)

    Grills, C.; Chacko, A.; Crawford, N.; Johnston, P. G.; Fennell, D. A.; O'Rourke, S. F. C.

    2009-08-01

    The molecular mechanism underlying mitochondrial BAK activation during apoptosis remains highly controversial. Two seemingly conflicting models have been proposed. In the activation model, BAK requires so-called activating BH3 only proteins (aBH3) to initiate its conformation change. In the other, displacement from inhibitory pro-survival BCL-2 proteins (PBPs) and monomerization of BAK by PBP restricted dissociator BH3-only proteins (dBH3) is sufficient. To better understand the kinetic implications of these models and reconcile these conflicting but highly evidence-based models, we have employed dynamical systems analysis to explore the kinetics underlying BAK activation as a non-linear reaction system. Our findings accommodate both pure agonism and dissociation as mutually exclusive mechanisms capable of initiating BAK activation. In addition we find our work supports a modelling based approach for predicting resistance to therapeutically relevant small molecules BH3 mimetics.

  17. Modeling the enzyme kinetic reaction.

    PubMed

    Atangana, Abdon

    2015-09-01

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

  18. Using chemical kinetics to model biochemical pathways.

    PubMed

    Le Novère, Nicolas; Endler, Lukas

    2013-01-01

    Chemical kinetics is the study of the rate of reactions transforming some chemical entities into other chemical entities. Over the twentieth century it has become one of the cornerstones of biochemistry. When in the second half of the century basic knowledge of cellular processes became sufficient to understand quantitatively metabolic networks, chemical kinetics associated with systems theory led to the development of what would become an important branch of systems biology. In this chapter we introduce basic concepts of chemical and enzyme kinetics, and show how the temporal evolution of a reaction system can be described by ordinary differential equations. Finally we present a method to apply this type of approach to model any regulatory network.

  19. Chemical Kinetic Modeling of Hydrogen Combustion Limits

    SciTech Connect

    Pitz, W J; Westbrook, C K

    2008-04-02

    A detailed chemical kinetic model is used to explore the flammability and detonability of hydrogen mixtures. In the case of flammability, a detailed chemical kinetic mechanism for hydrogen is coupled to the CHEMKIN Premix code to compute premixed, laminar flame speeds. The detailed chemical kinetic model reproduces flame speeds in the literature over a range of equivalence ratios, pressures and reactant temperatures. A series of calculation were performed to assess the key parameters determining the flammability of hydrogen mixtures. Increased reactant temperature was found to greatly increase the flame speed and the flammability of the mixture. The effect of added diluents was assessed. Addition of water and carbon dioxide were found to reduce the flame speed and thus the flammability of a hydrogen mixture approximately equally well and much more than the addition of nitrogen. The detailed chemical kinetic model was used to explore the detonability of hydrogen mixtures. A Zeldovich-von Neumann-Doring (ZND) detonation model coupled with detailed chemical kinetics was used to model the detonation. The effectiveness on different diluents was assessed in reducing the detonability of a hydrogen mixture. Carbon dioxide was found to be most effective in reducing the detonability followed by water and nitrogen. The chemical action of chemical inhibitors on reducing the flammability of hydrogen mixtures is discussed. Bromine and organophosphorus inhibitors act through catalytic cycles that recombine H and OH radicals in the flame. The reduction in H and OH radicals reduces chain branching in the flame through the H + O{sub 2} = OH + O chain branching reaction. The reduction in chain branching and radical production reduces the flame speed and thus the flammability of the hydrogen mixture.

  20. Kinetics model development of cocoa bean fermentation

    NASA Astrophysics Data System (ADS)

    Kresnowati, M. T. A. P.; Gunawan, Agus Yodi; Muliyadini, Winny

    2015-12-01

    Although Indonesia is one of the biggest cocoa beans producers in the world, Indonesian cocoa beans are oftenly of low quality and thereby frequently priced low in the world market. In order to improve the quality, adequate post-harvest cocoa processing techniques are required. Fermentation is the vital stage in series of cocoa beans post harvest processing which could improve the quality of cocoa beans, in particular taste, aroma, and colours. During the fermentation process, combination of microbes grow producing metabolites that serve as the precursors for cocoa beans flavour. Microbial composition and thereby their activities will affect the fermentation performance and influence the properties of cocoa beans. The correlation could be reviewed using a kinetic model that includes unstructured microbial growth, substrate utilization and metabolic product formation. The developed kinetic model could be further used to design cocoa bean fermentation process to meet the expected quality. Further the development of kinetic model of cocoa bean fermentation also serve as a good case study of mixed culture solid state fermentation, that has rarely been studied. This paper presents the development of a kinetic model for solid-state cocoa beans fermentation using an empirical approach. Series of lab scale cocoa bean fermentations, either natural fermentations without starter addition or fermentations with mixed yeast and lactic acid bacteria starter addition, were used for model parameters estimation. The results showed that cocoa beans fermentation can be modelled mathematically and the best model included substrate utilization, microbial growth, metabolites production and its transport. Although the developed model still can not explain the dynamics in microbial population, this model can sufficiently explained the observed changes in sugar concentration as well as metabolic products in the cocoa bean pulp.

  1. Are improper kinetic models hampering drug development?

    PubMed Central

    2014-01-01

    Reproducibility of biological data is a significant problem in research today. One potential contributor to this, which has received little attention, is the over complication of enzyme kinetic inhibition models. The over complication of inhibitory models stems from the common use of the inhibitory term (1 + [I]/Ki), an equilibrium binding term that does not distinguish between inhibitor binding and inhibitory effect. Since its initial appearance in the literature, around a century ago, the perceived mechanistic methods used in its production have spurred countless inhibitory equations. These equations are overly complex and are seldom compared to each other, which has destroyed their usefulness resulting in the proliferation and regulatory acceptance of simpler models such as IC50s for drug characterization. However, empirical analysis of inhibitory data recognizing the clear distinctions between inhibitor binding and inhibitory effect can produce simple logical inhibition models. In contrast to the common divergent practice of generating new inhibitory models for every inhibitory situation that presents itself. The empirical approach to inhibition modeling presented here is broadly applicable allowing easy comparison and rational analysis of drug interactions. To demonstrate this, a simple kinetic model of DAPT, a compound that both activates and inhibits γ-secretase is examined using excel. The empirical kinetic method described here provides an improved way of probing disease mechanisms, expanding the investigation of possible therapeutic interventions. PMID:25374788

  2. Computational model for Halorhodopsin photocurrent kinetics

    NASA Astrophysics Data System (ADS)

    Bravo, Jaime; Stefanescu, Roxana; Talathi, Sachin

    2013-03-01

    Optogenetics is a rapidly developing novel optical stimulation technique that employs light activated ion channels to excite (using channelrhodopsin (ChR)) or suppress (using halorhodopsin (HR)) impulse activity in neurons with high temporal and spatial resolution. This technique holds enormous potential to externally control activity states in neuronal networks. The channel kinetics of ChR and HR are well understood and amenable for mathematical modeling. Significant progress has been made in recent years to develop models for ChR channel kinetics. To date however, there is no model to mimic photocurrents produced by HR. Here, we report the first model developed for HR photocurrents based on a four-state model of the HR photocurrent kinetics. The model provides an excellent fit (root-mean-square error of 3.1862x10-4, to an empirical profile of experimentally measured HR photocurrents. In combination, mathematical models for ChR and HR photocurrents can provide effective means to design test light based control systems to regulate neural activity, which in turn may have implications for the development of novel light based stimulation paradigms for brain disease control. I would like to thank the University of Florida and the Physics Research Experience for Undergraduates (REU) program, funded through NSF DMR-1156737. This research was also supported through start-up funds provided to Dr. Sachin Talathi

  3. Kinetic model for multidimensional opinion formation

    NASA Astrophysics Data System (ADS)

    Boudin, Laurent; Monaco, Roberto; Salvarani, Francesco

    2010-03-01

    In this paper, we deal with a kinetic model to describe the evolution of the opinion in a closed group with respect to a choice between multiple options (e.g., political parties), which takes into account two main mechanisms of opinion formation, namely, the interaction between individuals and the effect of the mass media. We numerically test the model in some relevant cases and eventually provide an existence and a uniqueness result for it.

  4. Viral kinetic modeling: state of the art.

    PubMed

    Canini, Laetitia; Perelson, Alan S

    2014-10-01

    Viral kinetic (VK) modeling has led to increased understanding of the within host dynamics of viral infections and the effects of therapy. Here we review recent developments in the modeling of viral infection kinetics with emphasis on two infectious diseases: hepatitis C and influenza. We review how VK modeling has evolved from simple models of viral infections treated with a drug or drug cocktail with an assumed constant effectiveness to models that incorporate drug pharmacokinetics and pharmacodynamics, as well as phenomenological models that simply assume drugs have time varying-effectiveness. We also discuss multiscale models that include intracellular events in viral replication, models of drug-resistance, models that include innate and adaptive immune responses and models that incorporate cell-to-cell spread of infection. Overall, VK modeling has provided new insights into the understanding of the disease progression and the modes of action of several drugs. We expect that VK modeling will be increasingly used in the coming years to optimize drug regimens in order to improve therapeutic outcomes and treatment tolerability for infectious diseases.

  5. A Formal Approach to Empirical Dynamic Model Optimization and Validation

    NASA Technical Reports Server (NTRS)

    Crespo, Luis G; Morelli, Eugene A.; Kenny, Sean P.; Giesy, Daniel P.

    2014-01-01

    A framework was developed for the optimization and validation of empirical dynamic models subject to an arbitrary set of validation criteria. The validation requirements imposed upon the model, which may involve several sets of input-output data and arbitrary specifications in time and frequency domains, are used to determine if model predictions are within admissible error limits. The parameters of the empirical model are estimated by finding the parameter realization for which the smallest of the margins of requirement compliance is as large as possible. The uncertainty in the value of this estimate is characterized by studying the set of model parameters yielding predictions that comply with all the requirements. Strategies are presented for bounding this set, studying its dependence on admissible prediction error set by the analyst, and evaluating the sensitivity of the model predictions to parameter variations. This information is instrumental in characterizing uncertainty models used for evaluating the dynamic model at operating conditions differing from those used for its identification and validation. A practical example based on the short period dynamics of the F-16 is used for illustration.

  6. Properties of a Formal Method to Model Emergence in Swarm-Based Systems

    NASA Technical Reports Server (NTRS)

    Rouff, Christopher; Vanderbilt, Amy; Truszkowski, Walt; Rash, James; Hinchey, Mike

    2004-01-01

    Future space missions will require cooperation between multiple satellites and/or rovers. Developers are proposing intelligent autonomous swarms for these missions, but swarm-based systems are difficult or impossible to test with current techniques. This viewgraph presentation examines the use of formal methods in testing swarm-based systems. The potential usefulness of formal methods in modeling the ANTS asteroid encounter mission is also examined.

  7. Formal analytical modeling of blog content as personal narrative

    NASA Astrophysics Data System (ADS)

    Coombs, Michael J.; Jaenisch, Holger M.; Handley, James W.

    2008-04-01

    This paper contrasts two techniques for analyzing blog content and making use of this information to model blog content. One method uses classical text content and analysis presented for human interpretation. The second method relies on a data mined list of descriptive words characterizing the blogs. We examine the use of different data mining tools, Kryltech's "Subject Search Summarizer", Leximancer, and QUEST, to provide orthogonal and independently generated key word lists. These lists are then converted into Data Models, enabling mathematical modeling of blog content.

  8. Building a Formal Model of a Human-Interactive System: Insights into the Integration of Formal Methods and Human Factors Engineering

    NASA Technical Reports Server (NTRS)

    Bolton, Matthew L.; Bass, Ellen J.

    2009-01-01

    Both the human factors engineering (HFE) and formal methods communities are concerned with finding and eliminating problems with safety-critical systems. This work discusses a modeling effort that leveraged methods from both fields to use model checking with HFE practices to perform formal verification of a human-interactive system. Despite the use of a seemingly simple target system, a patient controlled analgesia pump, the initial model proved to be difficult for the model checker to verify in a reasonable amount of time. This resulted in a number of model revisions that affected the HFE architectural, representativeness, and understandability goals of the effort. If formal methods are to meet the needs of the HFE community, additional modeling tools and technological developments are necessary.

  9. A kinetic model for chemical neurotransmission

    NASA Astrophysics Data System (ADS)

    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.

  10. A Model for Effective Professional Development of Formal Science Educators

    NASA Astrophysics Data System (ADS)

    Bleacher, L.; Jones, A. P.; Farrell, W. M.

    2015-12-01

    The Lunar Workshops for Educators (LWE) series was developed by the Lunar Reconnaissance Orbiter (LRO) education team in 2010 to provide professional development on lunar science and exploration concepts for grades 6-9 science teachers. Over 300 educators have been trained to date. The LWE model incorporates best practices from pedagogical research of science education, thoughtful integration of scientists and engineer subject matter experts for both content presentations and informal networking with educators, access to NASA-unique facilities, hands-on and data-rich activities aligned with education standards, exposure to the practice of science, tools for addressing common misconceptions, follow-up with participants, and extensive evaluation. Evaluation of the LWE model via pre- and post-assessments, daily workshop surveys, and follow-up surveys at 6-month and 1-year intervals indicate that the LWE are extremely effective in increasing educators' content knowledge, confidence in incorporating content into the classroom, understanding of the practice of science, and ability to address common student misconceptions. In order to address the efficacy of the LWE model for other science content areas, the Dynamic Response of Environments at Asteroids, the Moon, and moons of Mars (DREAM2) education team, funded by NASA's Solar System Exploration Research Virtual Institute, developed and ran a pilot workshop called Dream2Explore at NASA's Goddard Space Flight Center in June, 2015. Dream2Explore utilized the LWE model, but incorporated content related to the science and exploration of asteroids and the moons of Mars. Evaluation results indicate that the LWE model was effectively used for educator professional development on non-lunar content. We will present more detail on the LWE model, evaluation results from the Dream2Explore pilot workshop, and suggestions for the application of the model with other science content for robust educator professional development.

  11. A Model for Effective Professional Development of Formal Science Educators

    NASA Technical Reports Server (NTRS)

    Bleacher, L. V.; Jones, A. J. P.; Farrell, W. M.

    2015-01-01

    The Lunar Workshops for Educators (LWE) series was developed by the Lunar Reconnaissance Orbiter (LRO) education team in 2010 to provide professional development on lunar science and exploration concepts for grades 6-9 science teachers. Over 300 educators have been trained to date. The LWE model incorporates best practices from pedagogical research of science education, thoughtful integration of scientists and engineer subject matter experts for both content presentations and informal networking with educators, access to NASA-unique facilities, hands-on and data-rich activities aligned with education standards, exposure to the practice of science, tools for addressing common misconceptions, follow-up with participants, and extensive evaluation. Evaluation of the LWE model via pre- and post-assessments, daily workshop surveys, and follow-up surveys at 6-month and 1-year intervals indicate that the LWE are extremely effective in increasing educators' content knowledge, confidence in incorporating content into the classroom, understanding of the practice of science, and ability to address common student misconceptions. In order to address the efficacy of the LWE model for other science content areas, the Dynamic Response of Environments at Asteroids, the Moon, and moons of Mars (DREAM2) education team, funded by NASA's Solar System Exploration Research Virtual Institute, developed and ran a pilot workshop called Dream2Explore at NASA's Goddard Space Flight Center in June, 2015. Dream2Explore utilized the LWE model, but incorporated content related to the science and exploration of asteroids and the moons of Mars. Evaluation results indicate that the LWE model was effectively used for educator professional development on non-lunar content. We will present more detail on the LWE model, evaluation results from the Dream2Explore pilot workshop, and suggestions for the application of the model with other science content for robust educator professional development.

  12. Colored noise and memory effects on formal spiking neuron models.

    PubMed

    da Silva, L A; Vilela, R D

    2015-06-01

    Simplified neuronal models capture the essence of the electrical activity of a generic neuron, besides being more interesting from the computational point of view when compared to higher-dimensional models such as the Hodgkin-Huxley one. In this work, we propose a generalized resonate-and-fire model described by a generalized Langevin equation that takes into account memory effects and colored noise. We perform a comprehensive numerical analysis to study the dynamics and the point process statistics of the proposed model, highlighting interesting new features such as (i) nonmonotonic behavior (emergence of peak structures, enhanced by the choice of colored noise characteristic time scale) of the coefficient of variation (CV) as a function of memory characteristic time scale, (ii) colored noise-induced shift in the CV, and (iii) emergence and suppression of multimodality in the interspike interval (ISI) distribution due to memory-induced subthreshold oscillations. Moreover, in the noise-induced spike regime, we study how memory and colored noise affect the coherence resonance (CR) phenomenon. We found that for sufficiently long memory, not only is CR suppressed but also the minimum of the CV-versus-noise intensity curve that characterizes the presence of CR may be replaced by a maximum. The aforementioned features allow to interpret the interplay between memory and colored noise as an effective control mechanism to neuronal variability. Since both variability and nontrivial temporal patterns in the ISI distribution are ubiquitous in biological cells, we hope the present model can be useful in modeling real aspects of neurons.

  13. Colored noise and memory effects on formal spiking neuron models

    NASA Astrophysics Data System (ADS)

    da Silva, L. A.; Vilela, R. D.

    2015-06-01

    Simplified neuronal models capture the essence of the electrical activity of a generic neuron, besides being more interesting from the computational point of view when compared to higher-dimensional models such as the Hodgkin-Huxley one. In this work, we propose a generalized resonate-and-fire model described by a generalized Langevin equation that takes into account memory effects and colored noise. We perform a comprehensive numerical analysis to study the dynamics and the point process statistics of the proposed model, highlighting interesting new features such as (i) nonmonotonic behavior (emergence of peak structures, enhanced by the choice of colored noise characteristic time scale) of the coefficient of variation (CV) as a function of memory characteristic time scale, (ii) colored noise-induced shift in the CV, and (iii) emergence and suppression of multimodality in the interspike interval (ISI) distribution due to memory-induced subthreshold oscillations. Moreover, in the noise-induced spike regime, we study how memory and colored noise affect the coherence resonance (CR) phenomenon. We found that for sufficiently long memory, not only is CR suppressed but also the minimum of the CV-versus-noise intensity curve that characterizes the presence of CR may be replaced by a maximum. The aforementioned features allow to interpret the interplay between memory and colored noise as an effective control mechanism to neuronal variability. Since both variability and nontrivial temporal patterns in the ISI distribution are ubiquitous in biological cells, we hope the present model can be useful in modeling real aspects of neurons.

  14. A formal definition of data flow graph models

    NASA Technical Reports Server (NTRS)

    Kavi, Krishna M.; Buckles, Bill P.; Bhat, U. Narayan

    1986-01-01

    In this paper, a new model for parallel computations and parallel computer systems that is based on data flow principles is presented. Uninterpreted data flow graphs can be used to model computer systems including data driven and parallel processors. A data flow graph is defined to be a bipartite graph with actors and links as the two vertex classes. Actors can be considered similar to transitions in Petri nets, and links similar to places. The nondeterministic nature of uninterpreted data flow graphs necessitates the derivation of liveness conditions.

  15. Formalism Challenges of the Cougaar Model Driven Architecture

    NASA Technical Reports Server (NTRS)

    Bohner, Shawn A.; George, Boby; Gracanin, Denis; Hinchey, Michael G.

    2004-01-01

    The Cognitive Agent Architecture (Cougaar) is one of the most sophisticated distributed agent architectures developed today. As part of its research and evolution, Cougaar is being studied for application to large, logistics-based applications for the Department of Defense (DoD). Anticipiting future complex applications of Cougaar, we are investigating the Model Driven Architecture (MDA) approach to understand how effective it would be for increasing productivity in Cougar-based development efforts. Recognizing the sophistication of the Cougaar development environment and the limitations of transformation technologies for agents, we have systematically developed an approach that combines component assembly in the large and transformation in the small. This paper describes some of the key elements that went into the Cougaar Model Driven Architecture approach and the characteristics that drove the approach.

  16. Kinetic modeling in PET imaging of hypoxia

    PubMed Central

    Li, Fan; Joergensen, Jesper T; Hansen, Anders E; Kjaer, Andreas

    2014-01-01

    Tumor hypoxia is associated with increased therapeutic resistance leading to poor treatment outcome. Therefore the ability to detect and quantify intratumoral oxygenation could play an important role in future individual personalized treatment strategies. Positron Emission Tomography (PET) can be used for non-invasive mapping of tissue oxygenation in vivo and several hypoxia specific PET tracers have been developed. Evaluation of PET data in the clinic is commonly based on visual assessment together with semiquantitative measurements e.g. standard uptake value (SUV). However, dynamic PET contains additional valuable information on the temporal changes in tracer distribution. Kinetic modeling can be used to extract relevant pharmacokinetic parameters of tracer behavior in vivo that reflects relevant physiological processes. In this paper, we review the potential contribution of kinetic analysis for PET imaging of hypoxia. PMID:25250200

  17. Kinetic and hydrodynamic models of chemotactic aggregation

    NASA Astrophysics Data System (ADS)

    Chavanis, Pierre-Henri; Sire, Clément

    2007-10-01

    We derive general kinetic and hydrodynamic models of chemotactic aggregation that describe certain features of the morphogenesis of biological colonies (like bacteria, amoebae, endothelial cells or social insects). Starting from a stochastic model defined in terms of N coupled Langevin equations, we derive a nonlinear mean-field Fokker-Planck equation governing the evolution of the distribution function of the system in phase space. By taking the successive moments of this kinetic equation and using a local thermodynamic equilibrium condition, we derive a set of hydrodynamic equations involving a damping term. In the limit of small frictions, we obtain a hyperbolic model describing the formation of network patterns (filaments) and in the limit of strong frictions we obtain a parabolic model which is a generalization of the standard Keller-Segel model describing the formation of clusters (clumps). Our approach connects and generalizes several models introduced in the chemotactic literature. We discuss the analogy between bacterial colonies and self-gravitating systems and between the chemotactic collapse and the gravitational collapse (Jeans instability). We also show that the basic equations of chemotaxis are similar to nonlinear mean-field Fokker-Planck equations so that a notion of effective generalized thermodynamics can be developed.

  18. Cluster kinetics model for mixtures of glassformers

    NASA Astrophysics Data System (ADS)

    Brenskelle, Lisa A.; McCoy, Benjamin J.

    2007-10-01

    For glassformers we propose a binary mixture relation for parameters in a cluster kinetics model previously shown to represent pure compound data for viscosity and dielectric relaxation as functions of either temperature or pressure. The model parameters are based on activation energies and activation volumes for cluster association-dissociation processes. With the mixture parameters, we calculated dielectric relaxation times and compared the results to experimental values for binary mixtures. Mixtures of sorbitol and glycerol (seven compositions), sorbitol and xylitol (three compositions), and polychloroepihydrin and polyvinylmethylether (three compositions) were studied.

  19. Aggregation kinetics in a model colloidal suspension

    SciTech Connect

    Bastea, S

    2005-08-08

    The authors present molecular dynamics simulations of aggregation kinetics in a colloidal suspension modeled as a highly asymmetric binary mixture. Starting from a configuration with largely uncorrelated colloidal particles the system relaxes by coagulation-fragmentation dynamics to a structured state of low-dimensionality clusters with an exponential size distribution. The results show that short range repulsive interactions alone can give rise to so-called cluster phases. For the present model and probably other, more common colloids, the observed clusters appear to be equilibrium phase fluctuations induced by the entropic inter-colloidal attractions.

  20. Two Formal Gas Models For Multi-Agent Sweeping and Obstacle Avoidance

    NASA Technical Reports Server (NTRS)

    Kerr, Wesley; Spears, Diana; Spears, William; Thayer, David

    2004-01-01

    The task addressed here is a dynamic search through a bounded region, while avoiding multiple large obstacles, such as buildings. In the case of limited sensors and communication, maintaining spatial coverage - especially after passing the obstacles - is a challenging problem. Here, we investigate two physics-based approaches to solving this task with multiple simulated mobile robots, one based on artificial forces and the other based on the kinetic theory of gases. The desired behavior is achieved with both methods, and a comparison is made between them. Because both approaches are physics-based, formal assurances about the multi-robot behavior are straightforward, and are included in the paper.

  1. Modelling of Robotized Manufacturing Systems Using MultiAgent Formalism

    NASA Astrophysics Data System (ADS)

    Foit, K.; Gwiazda, A.; Banaś, W.

    2016-08-01

    The evolution of manufacturing systems has greatly accelerated due to development of sophisticated control systems. On top of determined, one way production flow the need of decision making has arisen as a result of growing product range that are manufactured simultaneously, using the same resources. On the other hand, the intelligent flow control could address the “bottleneck” problem caused by the machine failure. This sort of manufacturing systems uses advanced control algorithms that are introduced by the use of logic controllers. The complex algorithms used in the control systems requires to employ appropriate methods during the modelling process, like the agent-based one, which is the subject of this paper. The concept of an agent is derived from the object-based methodology of modelling, so it meets the requirements of representing the physical properties of the machines as well as the logical form of control systems. Each agent has a high level of autonomy and could be considered separately. The multi-agent system consists of minimum two agents that can interact and modify the environment, where they act. This may lead to the creation of self-organizing structure, what could be interesting feature during design and test of manufacturing system.

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

    SciTech Connect

    Pavanello, Michele; Neugebauer, Johannes

    2011-12-21

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

  3. Formal specification and analysis of intelligent agents for model-based medicine usage management.

    PubMed

    Hoogendoorn, Mark; Klein, Michel C A; Memon, Zulfiqar A; Treur, Jan

    2013-06-01

    A model-based agent system model for medicine usage management is presented and formally analysed. The model incorporates an intelligent ambient agent model that has an explicit representation of a dynamical system model to estimate the medicine level in the patient's body by simulation, is able to analyse whether the patient intends to take the medicine too early or too late, and can take measures to prevent this.

  4. Formal specification and analysis of intelligent agents for model-based medicine usage management.

    PubMed

    Hoogendoorn, Mark; Klein, Michel C A; Memon, Zulfiqar A; Treur, Jan

    2013-06-01

    A model-based agent system model for medicine usage management is presented and formally analysed. The model incorporates an intelligent ambient agent model that has an explicit representation of a dynamical system model to estimate the medicine level in the patient's body by simulation, is able to analyse whether the patient intends to take the medicine too early or too late, and can take measures to prevent this. PMID:23566391

  5. Learning Goal Orientation, Formal Mentoring, and Leadership Competence in HRD: A Conceptual Model

    ERIC Educational Resources Information Center

    Kim, Sooyoung

    2007-01-01

    Purpose: The purpose of this paper is to suggest a conceptual model of formal mentoring as a leadership development initiative including "learning goal orientation", "mentoring functions", and "leadership competencies" as key constructs of the model. Design/methodology/approach: Some empirical studies, though there are not many, will provide…

  6. Directly executable formal models of middleware for MANET and Cloud Networking and Computing

    NASA Astrophysics Data System (ADS)

    Pashchenko, D. V.; Sadeq Jaafar, Mustafa; Zinkin, S. A.; Trokoz, D. A.; Pashchenko, T. U.; Sinev, M. P.

    2016-04-01

    The article considers some “directly executable” formal models that are suitable for the specification of computing and networking in the cloud environment and other networks which are similar to wireless networks MANET. These models can be easily programmed and implemented on computer networks.

  7. A Formal Cognitive Model of the Go/No-Go Discrimination Task: Evaluation and Implications

    ERIC Educational Resources Information Center

    Yechiam, Eldad; Goodnight, Jackson; Bates, John E.; Busemeyer, Jerome R.; Dodge, Kenneth A.; Pettit, Gregory S.; Newman, Joseph P.

    2006-01-01

    This article proposes and tests a formal cognitive model for the go/no-go discrimination task. In this task, the performer chooses whether to respond to stimuli and receives rewards for responding to certain stimuli and punishments for responding to others. Three cognitive models were evaluated on the basis of data from a longitudinal study…

  8. Reasoning with Conditionals: A Test of Formal Models of Four Theories

    ERIC Educational Resources Information Center

    Oberauer, Klaus

    2006-01-01

    The four dominant theories of reasoning from conditionals are translated into formal models: The theory of mental models (Johnson-Laird, P. N., & Byrne, R. M. J. (2002). Conditionals: a theory of meaning, pragmatics, and inference. "Psychological Review," 109, 646-678), the suppositional theory (Evans, J. S. B. T., & Over, D. E. (2004). "If."…

  9. Chemical kinetics and modeling of planetary atmospheres

    NASA Technical Reports Server (NTRS)

    Yung, Yuk L.

    1990-01-01

    A unified overview is presented for chemical kinetics and chemical modeling in planetary atmospheres. The recent major advances in the understanding of the chemistry of the terrestrial atmosphere make the study of planets more interesting and relevant. A deeper understanding suggests that the important chemical cycles have a universal character that connects the different planets and ultimately link together the origin and evolution of the solar system. The completeness (or incompleteness) of the data base for chemical kinetics in planetary atmospheres will always be judged by comparison with that for the terrestrial atmosphere. In the latter case, the chemistry of H, O, N, and Cl species is well understood. S chemistry is poorly understood. In the atmospheres of Jovian planets and Titan, the C-H chemistry of simple species (containing 2 or less C atoms) is fairly well understood. The chemistry of higher hydrocarbons and the C-N, P-N chemistry is much less understood. In the atmosphere of Venus, the dominant chemistry is that of chlorine and sulfur, and very little is known about C1-S coupled chemistry. A new frontier for chemical kinetics both in the Earth and planetary atmospheres is the study of heterogeneous reactions. The formation of the ozone hole on Earth, the ubiquitous photochemical haze on Venus and in the Jovian planets and Titan all testify to the importance of heterogeneous reactions. It remains a challenge to connect the gas phase chemistry to the production of aerosols.

  10. Using Data-Driven Model-Brain Mappings to Constrain Formal Models of Cognition

    PubMed Central

    Borst, Jelmer P.; Nijboer, Menno; Taatgen, Niels A.; van Rijn, Hedderik; Anderson, John R.

    2015-01-01

    In this paper we propose a method to create data-driven mappings from components of cognitive models to brain regions. Cognitive models are notoriously hard to evaluate, especially based on behavioral measures alone. Neuroimaging data can provide additional constraints, but this requires a mapping from model components to brain regions. Although such mappings can be based on the experience of the modeler or on a reading of the literature, a formal method is preferred to prevent researcher-based biases. In this paper we used model-based fMRI analysis to create a data-driven model-brain mapping for five modules of the ACT-R cognitive architecture. We then validated this mapping by applying it to two new datasets with associated models. The new mapping was at least as powerful as an existing mapping that was based on the literature, and indicated where the models were supported by the data and where they have to be improved. We conclude that data-driven model-brain mappings can provide strong constraints on cognitive models, and that model-based fMRI is a suitable way to create such mappings. PMID:25747601

  11. Using data-driven model-brain mappings to constrain formal models of cognition.

    PubMed

    Borst, Jelmer P; Nijboer, Menno; Taatgen, Niels A; van Rijn, Hedderik; Anderson, John R

    2015-01-01

    In this paper we propose a method to create data-driven mappings from components of cognitive models to brain regions. Cognitive models are notoriously hard to evaluate, especially based on behavioral measures alone. Neuroimaging data can provide additional constraints, but this requires a mapping from model components to brain regions. Although such mappings can be based on the experience of the modeler or on a reading of the literature, a formal method is preferred to prevent researcher-based biases. In this paper we used model-based fMRI analysis to create a data-driven model-brain mapping for five modules of the ACT-R cognitive architecture. We then validated this mapping by applying it to two new datasets with associated models. The new mapping was at least as powerful as an existing mapping that was based on the literature, and indicated where the models were supported by the data and where they have to be improved. We conclude that data-driven model-brain mappings can provide strong constraints on cognitive models, and that model-based fMRI is a suitable way to create such mappings.

  12. Formal analogy between the Dirac equation in its Majorana form and the discrete-velocity version of the Boltzmann kinetic equation.

    PubMed

    Fillion-Gourdeau, F; Herrmann, H J; Mendoza, M; Palpacelli, S; Succi, S

    2013-10-18

    We point out a formal analogy between the Dirac equation in Majorana form and the discrete-velocity version of the Boltzmann kinetic equation. By a systematic analysis based on the theory of operator splitting, this analogy is shown to turn into a concrete and efficient computational method, providing a unified treatment of relativistic and nonrelativistic quantum mechanics. This might have potentially far-reaching implications for both classical and quantum computing, because it shows that, by splitting time along the three spatial directions, quantum information (Dirac-Majorana wave function) propagates in space-time as a classical statistical process (Boltzmann distribution).

  13. A kinetic model of plasma turbulence

    NASA Astrophysics Data System (ADS)

    Servidio, S.; Valentini, F.; Perrone, D.; Greco, A.; Califano, F.; Matthaeus, W. H.; Veltri, P.

    2015-01-01

    A Hybrid Vlasov-Maxwell (HVM) model is presented and recent results about the link between kinetic effects and turbulence are reviewed. Using five-dimensional (2D in space and 3D in the velocity space) simulations of plasma turbulence, it is found that kinetic effects (or non-fluid effects) manifest through the deformation of the proton velocity distribution function (DF), with patterns of non-Maxwellian features being concentrated near regions of strong magnetic gradients. The direction of the proper temperature anisotropy, calculated in the main reference frame of the distribution itself, has a finite probability of being along or across the ambient magnetic field, in general agreement with the classical definition of anisotropy T ⊥/T ∥ (where subscripts refer to the magnetic field direction). Adopting the latter conventional definition, by varying the global plasma beta (β) and fluctuation level, simulations explore distinct regions of the space given by T ⊥/T ∥ and β∥, recovering solar wind observations. Moreover, as in the solar wind, HVM simulations suggest that proton anisotropy is not only associated with magnetic intermittent events, but also with gradient-type structures in the flow and in the density. The role of alpha particles is reviewed using multi-ion kinetic simulations, revealing a similarity between proton and helium non-Maxwellian effects. The techniques presented here are applied to 1D spacecraft-like analysis, establishing a link between non-fluid phenomena and solar wind magnetic discontinuities. Finally, the dimensionality of turbulence is investigated, for the first time, via 6D HVM simulations (3D in both spaces). These preliminary results provide support for several previously reported studies based on 2.5D simulations, confirming several basic conclusions. This connection between kinetic features and turbulence open a new path on the study of processes such as heating, particle acceleration, and temperature

  14. Brittle failure kinetics model for concrete

    SciTech Connect

    Silling, S.A.

    1997-03-01

    A new constitutive model is proposed for the modeling of penetration and large stress waves in concrete. Rate effects are incorporated explicitly into the damage evolution law, hence the term brittle failure kinetics. The damage variable parameterizes a family of Mohr-Coulomb strength curves. The model, which has been implemented in the CTH code, has been shown to reproduce some distinctive phenomena that occur in penetration of concrete targets. Among these are the sharp spike in deceleration of a rigid penetrator immediately after impact. Another is the size scale effect, which leads to a nonlinear scaling of penetration depth with penetrator size. This paper discusses the theory of the model and some results of an extensive validation effort.

  15. Wealth redistribution in conservative linear kinetic models

    NASA Astrophysics Data System (ADS)

    Toscani, G.

    2009-10-01

    We introduce and discuss kinetic models for wealth distribution which include both taxation and uniform redistribution. The evolution of the continuous density of wealth obeys a linear Boltzmann equation where the background density represents the action of an external subject on the taxation mechanism. The case in which the mean wealth is conserved is analyzed in full details, by recovering the analytical form of the steady states. These states are probability distributions of convergent random series of a special structure, called perpetuities. Among others, Gibbs distribution appears as steady state in case of total taxation and uniform redistribution.

  16. The kinetic regime of the Vicsek model

    NASA Astrophysics Data System (ADS)

    Chepizhko, A. A.; Kulinskii, V. L.

    2009-12-01

    We consider the dynamics of the system of self-propelling particles modeled via the Vicsek algorithm in continuum time limit. It is shown that the alignment process for the velocities can be subdivided into two regimes: "fast" kinetic and "slow" hydrodynamic ones. In fast kinetic regime the alignment of the particle velocity to the local neighborhood takes place with characteristic relaxation time. So, that the bigger regions arise with the velocity alignment. These regions align their velocities thus giving rise to hydrodynamic regime of the dynamics. We propose the mean-field-like approach in which we take into account the correlations between density and velocity. The comparison of the theoretical predictions with the numerical simulations is given. The relation between Vicsek model in the zero velocity limit and the Kuramoto model is stated. The mean-field approach accounting for the dynamic change of the neighborhood is proposed. The nature of the discontinuity of the dependence of the order parameter in case of vectorial noise revealed in Gregorie and Chaite, Phys. Rev. Lett., 92, 025702 (2004) is discussed and the explanation of it is proposed.

  17. ADM Analysis of gravity models within the framework of bimetric variational formalism

    SciTech Connect

    Golovnev, Alexey; Karčiauskas, Mindaugas; Nyrhinen, Hannu J. E-mail: mindaugas.karciauskas@helsinki.fi

    2015-05-01

    Bimetric variational formalism was recently employed to construct novel bimetric gravity models. In these models an affine connection is generated by an additional tensor field which is independent of the physical metric. In this work we demonstrate how the ADM decomposition can be applied to study such models and provide some technical intermediate details. Using ADM decomposition we are able to prove that a linear model is unstable as has previously been indicated by perturbative analysis. Moreover, we show that it is also very difficult if not impossible to construct a non-linear model which is ghost-free within the framework of bimetric variational formalism. However, we demonstrate that viable models are possible along similar lines of thought. To this end, we consider a set up in which the affine connection is a variation of the Levi-Civita one. As a proof of principle we construct a gravity model with a massless scalar field obtained this way.

  18. A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.

    PubMed

    Ryll, A; Bucher, J; Bonin, A; Bongard, S; Gonçalves, E; Saez-Rodriguez, J; Niklas, J; Klamt, S

    2014-10-01

    Systems biology has to increasingly cope with large- and multi-scale biological systems. Many successful in silico representations and simulations of various cellular modules proved mathematical modelling to be an important tool in gaining a solid understanding of biological phenomena. However, models spanning different functional layers (e.g. metabolism, signalling and gene regulation) are still scarce. Consequently, model integration methods capable of fusing different types of biological networks and various model formalisms become a key methodology to increase the scope of cellular processes covered by mathematical models. Here we propose a new integration approach to couple logical models of signalling or/and gene-regulatory networks with kinetic models of metabolic processes. The procedure ends up with an integrated dynamic model of both layers relying on differential equations. The feasibility of the approach is shown in an illustrative case study integrating a kinetic model of central metabolic pathways in hepatocytes with a Boolean logical network depicting the hormonally induced signal transduction and gene regulation events involved. In silico simulations demonstrate the integrated model to qualitatively describe the physiological switch-like behaviour of hepatocytes in response to nutritionally regulated changes in extracellular glucagon and insulin levels. A simulated failure mode scenario addressing insulin resistance furthermore illustrates the pharmacological potential of a model covering interactions between signalling, gene regulation and metabolism. PMID:25063553

  19. A Kinetic Model of Active Extensile Bundles

    NASA Astrophysics Data System (ADS)

    Goldstein, Daniel; Chakraborty, Bulbul; Baskaran, Aparna

    Recent experiments in active filament networks reveal interesting rheological properties (Dan Chen: APS March Meeting 2015 D49.00001). This system consumes ATP to produce an extensile motion in bundles of microtubules. This extension then leads to self generated stresses and spontaneous flows. We propose a minimal model where the activity is modeled by self-extending bundles that are part of a cross linked network. This network can reorganize itself through buckling of extending filaments and merging events that alter the topology of the network. We numerically simulate this minimal kinetic model and examine the emergent rheological properties and determine how stresses are generated by the extensile activity. We will present results that focus on the effects of confinement and network connectivity of the bundles on stress fluctuations and response of an active gel.

  20. On Kinetics Modeling of Vibrational Energy Transfer

    NASA Technical Reports Server (NTRS)

    Gilmore, John O.; Sharma, Surendra P.; Cavolowsky, John A. (Technical Monitor)

    1996-01-01

    Two models of vibrational energy exchange are compared at equilibrium to the elementary vibrational exchange reaction for a binary mixture. The first model, non-linear in the species vibrational energies, was derived by Schwartz, Slawsky, and Herzfeld (SSH) by considering the detailed kinetics of vibrational energy levels. This model recovers the result demanded at equilibrium by the elementary reaction. The second model is more recent, and is gaining use in certain areas of computational fluid dynamics. This model, linear in the species vibrational energies, is shown not to recover the required equilibrium result. Further, this more recent model is inconsistent with its suggested rate constants in that those rate constants were inferred from measurements by using the SSH model to reduce the data. The non-linear versus linear nature of these two models can lead to significant differences in vibrational energy coupling. Use of the contemporary model may lead to significant misconceptions, especially when integrated in computer codes considering multiple energy coupling mechanisms.

  1. Basis of a formal language for facilitating communication among climate modelers

    NASA Astrophysics Data System (ADS)

    de Elía, Ramón

    2012-08-01

    The objective of this work is to present the basis for a formal language that aims to express in a concise way some fundamental beliefs held within the climate research community. The expression of this set of beliefs takes the form of relations, conjectures or propositions that describe characteristics of different aspects of climate modeling. Examples are constructed using topics that are much discussed within the climate modeling community. The article first introduces, as elements of this formal language, models considered a priori (the model as a code or algorithm) or a posteriori (the model as output), and then presents different relations between these elements. The most important relation is that of dominance, which helps to define the superiority of one model over another based on which model a rational agent will choose. Various kinds of dominance are considered. Also presented in a formal language are propositions and conjectures relating to model development, model calibration and climate change ensemble projections, each of which are held with diverse levels of acceptance within the climate modeling community. In addition, the relevance of defining elements—models—whose existence is improbable, such as bug-free model versions, is discussed. Although the potential value of this language is shown, there remains a need to improve the definitions presented here, as some of them remain unsatisfying. Still, we believe that this attempt may help us not only communicate more clearly but also to better distinguish different schools of thought that currently exist within the community.

  2. Canonical formalism for a 2n-dimensional model with topological mass generation

    NASA Astrophysics Data System (ADS)

    Deguchi, Shinichi

    2008-12-01

    The four-dimensional model with topological mass generation that was found by Dvali, Jackiw, and Pi has recently been generalized to any even number of dimensions (2n dimensions) in a nontrivial manner in which a Stückelberg-type mass term is introduced [S. Deguchi and S. Hayakawa, Phys. Rev. D 77, 045003 (2008)PRVDAQ0556-282110.1103/PhysRevD.77.045003]. The present paper deals with a self-contained model, called here a modified hybrid model, proposed in this 2n-dimensional generalization and considers the canonical formalism for this model. For the sake of convenience, the canonical formalism itself is studied for a model equivalent to the modified hybrid model by following the recipe for treating constrained Hamiltonian systems. This formalism is applied to the canonical quantization of the equivalent model in order to clarify observable and unobservable particles in the model. The equivalent model (with a gauge-fixing term) is converted to the modified hybrid model (with a corresponding gauge-fixing term) in a Becchi-Rouet-Stora-Tyutin-invariant manner. Thereby it is shown that the Chern-Pontryagin density behaves as an observable massive particle (or field). The topological mass generation is thus verified at the quantum-theoretical level.

  3. Canonical formalism for a 2n-dimensional model with topological mass generation

    SciTech Connect

    Deguchi, Shinichi

    2008-12-15

    The four-dimensional model with topological mass generation that was found by Dvali, Jackiw, and Pi has recently been generalized to any even number of dimensions (2n dimensions) in a nontrivial manner in which a Stueckelberg-type mass term is introduced [S. Deguchi and S. Hayakawa, Phys. Rev. D 77, 045003 (2008)]. The present paper deals with a self-contained model, called here a modified hybrid model, proposed in this 2n-dimensional generalization and considers the canonical formalism for this model. For the sake of convenience, the canonical formalism itself is studied for a model equivalent to the modified hybrid model by following the recipe for treating constrained Hamiltonian systems. This formalism is applied to the canonical quantization of the equivalent model in order to clarify observable and unobservable particles in the model. The equivalent model (with a gauge-fixing term) is converted to the modified hybrid model (with a corresponding gauge-fixing term) in a Becchi-Rouet-Stora-Tyutin-invariant manner. Thereby it is shown that the Chern-Pontryagin density behaves as an observable massive particle (or field). The topological mass generation is thus verified at the quantum-theoretical level.

  4. Open Learning and Formal Credentialing in Higher Education: Curriculum Models and Institutional Policies

    ERIC Educational Resources Information Center

    Reushle, Shirley, Ed.; Antonio, Amy, Ed.; Keppell, Mike, Ed.

    2016-01-01

    The discipline of education is a multi-faceted system that must constantly integrate new strategies and procedures to ensure successful learning experiences. Enhancements in education provide learners with greater opportunities for growth and advancement. "Open Learning and Formal Credentialing in Higher Education: Curriculum Models and…

  5. A formalism to generate probability distributions for performance-assessment modeling

    SciTech Connect

    Kaplan, P.G.

    1990-12-31

    A formalism is presented for generating probability distributions of parameters used in performance-assessment modeling. The formalism is used when data are either sparse or nonexistent. The appropriate distribution is a function of the known or estimated constraints and is chosen to maximize a quantity known as Shannon`s informational entropy. The formalism is applied to a parameter used in performance-assessment modeling. The functional form of the model that defines the parameter, data from the actual field site, and natural analog data are analyzed to estimate the constraints. A beta probability distribution of the example parameter is generated after finding four constraints. As an example of how the formalism is applied to the site characterization studies of Yucca Mountain, the distribution is generated for an input parameter in a performance-assessment model currently used to estimate compliance with disposal of high-level radioactive waste in geologic repositories, 10 CFR 60.113(a)(2), commonly known as the ground water travel time criterion. 8 refs., 2 figs.

  6. Kinetic modeling of non-ideal explosives

    SciTech Connect

    Fried, L E; Howard, W M; Souers, P C

    1999-03-01

    We have implemented a Wood-Kirkwood kinetic detonation model based on multi-species equations of state and multiple reaction rate laws. Finite rate laws are used for the slowest chemical reactions, while other reactions are given infinite rates and are kept in constant thermodynamic equilibrium. We model a wide range of ideal and non-ideal composite energetic materials. In addition, we develop an exp-6 equation of state for the product fluids that reproduces a wide range experimental shock Hugoniot and static compression data. For unreacted solids, including solid and liquid Al and Al{sub 2}O{sub 3}, we use a Murnaghan form for the equation of state. We find that we can replicate experimental detonation velocities to within a few per cent for a wide range of explosives, while obtaining good agreement with estimated reaction zone lengths. The detonation velocity as a function of charge radius is also correctly reproduced.

  7. Detailed Kinetic Modeling of Gasoline Surrogate Mixtures

    SciTech Connect

    Mehl, M; Curran, H J; Pitz, W J; Westbrook, C K

    2009-03-09

    Real fuels are complex mixtures of thousands of hydrocarbon compounds including linear and branched paraffins, naphthenes, olefins and aromatics. It is generally agreed that their behavior can be effectively reproduced by simpler fuel surrogates containing a limited number of components. In this work, a recently revised version of the kinetic model by the authors is used to analyze the combustion behavior of several components relevant to gasoline surrogate formulation. Particular attention is devoted to linear and branched saturated hydrocarbons (PRF mixtures), olefins (1-hexene) and aromatics (toluene). Model predictions for pure components, binary mixtures and multi-component gasoline surrogates are compared with recent experimental information collected in rapid compression machine, shock tube and jet stirred reactors covering a wide range of conditions pertinent to internal combustion engines. Simulation results are discussed focusing attention on the mixing effects of the fuel components.

  8. State Event Models for the Formal Analysis of Human-Machine Interactions

    NASA Technical Reports Server (NTRS)

    Combefis, Sebastien; Giannakopoulou, Dimitra; Pecheur, Charles

    2014-01-01

    The work described in this paper was motivated by our experience with applying a framework for formal analysis of human-machine interactions (HMI) to a realistic model of an autopilot. The framework is built around a formally defined conformance relation called "fullcontrol" between an actual system and the mental model according to which the system is operated. Systems are well-designed if they can be described by relatively simple, full-control, mental models for their human operators. For this reason, our framework supports automated generation of minimal full-control mental models for HMI systems, where both the system and the mental models are described as labelled transition systems (LTS). The autopilot that we analysed has been developed in the NASA Ames HMI prototyping tool ADEPT. In this paper, we describe how we extended the models that our HMI analysis framework handles to allow adequate representation of ADEPT models. We then provide a property-preserving reduction from these extended models to LTSs, to enable application of our LTS-based formal analysis algorithms. Finally, we briefly discuss the analyses we were able to perform on the autopilot model with our extended framework.

  9. Evaluation of a Guideline by Formal Modelling of Cruise Control System in Event-B

    NASA Technical Reports Server (NTRS)

    Yeganefard, Sanaz; Butler, Michael; Rezazadeh, Abdolbaghi

    2010-01-01

    Recently a set of guidelines, or cookbook, has been developed for modelling and refinement of control problems in Event-B. The Event-B formal method is used for system-level modelling by defining states of a system and events which act on these states. It also supports refinement of models. This cookbook is intended to systematize the process of modelling and refining a control problem system by distinguishing environment, controller and command phenomena. Our main objective in this paper is to investigate and evaluate the usefulness and effectiveness of this cookbook by following it throughout the formal modelling of cruise control system found in cars. The outcomes are identifying the benefits of the cookbook and also giving guidance to its future users.

  10. Equifinality of formal (DREAM) and informal (GLUE) bayesian approaches in hydrologic modeling?

    SciTech Connect

    Vrugt, Jasper A; Robinson, Bruce A; Ter Braak, Cajo J F; Gupta, Hoshin V

    2008-01-01

    In recent years, a strong debate has emerged in the hydrologic literature regarding what constitutes an appropriate framework for uncertainty estimation. Particularly, there is strong disagreement whether an uncertainty framework should have its roots within a proper statistical (Bayesian) context, or whether such a framework should be based on a different philosophy and implement informal measures and weaker inference to summarize parameter and predictive distributions. In this paper, we compare a formal Bayesian approach using Markov Chain Monte Carlo (MCMC) with generalized likelihood uncertainty estimation (GLUE) for assessing uncertainty in conceptual watershed modeling. Our formal Bayesian approach is implemented using the recently developed differential evolution adaptive metropolis (DREAM) MCMC scheme with a likelihood function that explicitly considers model structural, input and parameter uncertainty. Our results demonstrate that DREAM and GLUE can generate very similar estimates of total streamflow uncertainty. This suggests that formal and informal Bayesian approaches have more common ground than the hydrologic literature and ongoing debate might suggest. The main advantage of formal approaches is, however, that they attempt to disentangle the effect of forcing, parameter and model structural error on total predictive uncertainty. This is key to improving hydrologic theory and to better understand and predict the flow of water through catchments.

  11. Kinetic modelling of heterogeneous catalytic systems

    NASA Astrophysics Data System (ADS)

    Stamatakis, Michail

    2015-01-01

    The importance of heterogeneous catalysis in modern life is evidenced by the fact that numerous products and technologies routinely used nowadays involve catalysts in their synthesis or function. The discovery of catalytic materials is, however, a non-trivial procedure, requiring tedious trial-and-error experimentation. First-principles-based kinetic modelling methods have recently emerged as a promising way to understand catalytic function and aid in materials discovery. In particular, kinetic Monte Carlo (KMC) simulation is increasingly becoming more popular, as it can integrate several sources of complexity encountered in catalytic systems, and has already been used to successfully unravel the underlying physics of several systems of interest. After a short discussion of the different scales involved in catalysis, we summarize the theory behind KMC simulation, and present the latest KMC computational implementations in the field. Early achievements that transformed the way we think about catalysts are subsequently reviewed in connection to latest studies of realistic systems, in an attempt to highlight how the field has evolved over the last few decades. Present challenges and future directions and opportunities in computational catalysis are finally discussed.

  12. Kinetic modelling of coupled transport across biological membranes.

    PubMed

    Korla, Kalyani; Mitra, Chanchal K

    2014-04-01

    In this report, we have modelled a secondary active co-transporter (symport and antiport), based on the classical kinetics model. Michaelis-Menten model of enzyme kinetics for a single substrate, single intermediate enzyme catalyzed reaction was proposed more than a hundred years ago. However, no single model for the kinetics of co-transport of molecules across a membrane is available in the literature We have made several simplifying assumptions and have followed the basic Michaelis-Menten approach. The results have been simulated using GNU Octave. The results will be useful in general kinetic simulations and modelling.

  13. Kinetic model of excess activated sludge thermohydrolysis.

    PubMed

    Imbierowicz, Mirosław; Chacuk, Andrzej

    2012-11-01

    Thermal hydrolysis of excess activated sludge suspensions was carried at temperatures ranging from 423 K to 523 K and under pressure 0.2-4.0 MPa. Changes of total organic carbon (TOC) concentration in a solid and liquid phase were measured during these studies. At the temperature 423 K, after 2 h of the process, TOC concentration in the reaction mixture decreased by 15-18% of the initial value. At 473 K total organic carbon removal from activated sludge suspension increased to 30%. It was also found that the solubilisation of particulate organic matter strongly depended on the process temperature. At 423 K the transfer of TOC from solid particles into liquid phase after 1 h of the process reached 25% of the initial value, however, at the temperature of 523 K the conversion degree of 'solid' TOC attained 50% just after 15 min of the process. In the article a lumped kinetic model of the process of activated sludge thermohydrolysis has been proposed. It was assumed that during heating of the activated sludge suspension to a temperature in the range of 423-523 K two parallel reactions occurred. One, connected with thermal destruction of activated sludge particles, caused solubilisation of organic carbon and an increase of dissolved organic carbon concentration in the liquid phase (hydrolysate). The parallel reaction led to a new kind of unsolvable solid phase, which was further decomposed into gaseous products (CO(2)). The collected experimental data were used to identify unknown parameters of the model, i.e. activation energies and pre-exponential factors of elementary reactions. The mathematical model of activated sludge thermohydrolysis appropriately describes the kinetics of reactions occurring in the studied system. PMID:22951329

  14. Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes

    PubMed Central

    Gustafson, E. Hilary; Ciglar, Lucia; Junion, Guillaume; Gonzalez, Aitor; Girardot, Charles; Perrin, Laurent; Furlong, Eileen E. M.; Thieffry, Denis

    2016-01-01

    Given the complexity of developmental networks, it is often difficult to predict the effect of genetic perturbations, even within coding genes. Regulatory factors generally have pleiotropic effects, exhibit partially redundant roles, and regulate highly interconnected pathways with ample cross-talk. Here, we delineate a logical model encompassing 48 components and 82 regulatory interactions involved in mesoderm specification during Drosophila development, thereby providing a formal integration of all available genetic information from the literature. The four main tissues derived from mesoderm correspond to alternative stable states. We demonstrate that the model can predict known mutant phenotypes and use it to systematically predict the effects of over 300 new, often non-intuitive, loss- and gain-of-function mutations, and combinations thereof. We further validated several novel predictions experimentally, thereby demonstrating the robustness of model. Logical modelling can thus contribute to formally explain and predict regulatory outcomes underlying cell fate decisions. PMID:27599298

  15. Issues to be considered on obtaining plant models for formal verification purposes

    NASA Astrophysics Data System (ADS)

    Pacheco, R.; Gonzalez, L.; Intriago, M.; Machado, J.; Prisacaru, G.; Olaru, D.

    2016-08-01

    The development of dependable software for mechatronic systems can be a very complex and hard task. For facilitating the obtaining of dependable software for industrial controllers, some powerful software tools and analysis techniques can be used. Mainly, when using simulation and formal verification analysis techniques, it is necessary to develop plant models, in order to describe the plant behavior of those systems. However, developing a plant model implies that designer takes his (or her) decisions concerning granularity and level of abstraction of models; approach to consider for modeling (global or modular); and definition of strategies for simulation and formal verification tasks. This paper intends to highlight some aspects that can be considered for taking into account those decisions. For this purpose, it is presented a case study and there are illustrated and discussed very important aspects concerning above exposed issues.

  16. Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes.

    PubMed

    Mbodj, Abibatou; Gustafson, E Hilary; Ciglar, Lucia; Junion, Guillaume; Gonzalez, Aitor; Girardot, Charles; Perrin, Laurent; Furlong, Eileen E M; Thieffry, Denis

    2016-09-01

    Given the complexity of developmental networks, it is often difficult to predict the effect of genetic perturbations, even within coding genes. Regulatory factors generally have pleiotropic effects, exhibit partially redundant roles, and regulate highly interconnected pathways with ample cross-talk. Here, we delineate a logical model encompassing 48 components and 82 regulatory interactions involved in mesoderm specification during Drosophila development, thereby providing a formal integration of all available genetic information from the literature. The four main tissues derived from mesoderm correspond to alternative stable states. We demonstrate that the model can predict known mutant phenotypes and use it to systematically predict the effects of over 300 new, often non-intuitive, loss- and gain-of-function mutations, and combinations thereof. We further validated several novel predictions experimentally, thereby demonstrating the robustness of model. Logical modelling can thus contribute to formally explain and predict regulatory outcomes underlying cell fate decisions. PMID:27599298

  17. Formally verifying human-automation interaction as part of a system model: limitations and tradeoffs.

    PubMed

    Bolton, Matthew L; Bass, Ellen J

    2010-03-25

    Both the human factors engineering (HFE) and formal methods communities are concerned with improving the design of safety-critical systems. This work discusses a modeling effort that leveraged methods from both fields to perform formal verification of human-automation interaction with a programmable device. This effort utilizes a system architecture composed of independent models of the human mission, human task behavior, human-device interface, device automation, and operational environment. The goals of this architecture were to allow HFE practitioners to perform formal verifications of realistic systems that depend on human-automation interaction in a reasonable amount of time using representative models, intuitive modeling constructs, and decoupled models of system components that could be easily changed to support multiple analyses. This framework was instantiated using a patient controlled analgesia pump in a two phased process where models in each phase were verified using a common set of specifications. The first phase focused on the mission, human-device interface, and device automation; and included a simple, unconstrained human task behavior model. The second phase replaced the unconstrained task model with one representing normative pump programming behavior. Because models produced in the first phase were too large for the model checker to verify, a number of model revisions were undertaken that affected the goals of the effort. While the use of human task behavior models in the second phase helped mitigate model complexity, verification time increased. Additional modeling tools and technological developments are necessary for model checking to become a more usable technique for HFE.

  18. Aerosol kinetic code "AERFORM": Model, validation and simulation results

    NASA Astrophysics Data System (ADS)

    Gainullin, K. G.; Golubev, A. I.; Petrov, A. M.; Piskunov, V. N.

    2016-06-01

    The aerosol kinetic code "AERFORM" is modified to simulate droplet and ice particle formation in mixed clouds. The splitting method is used to calculate condensation and coagulation simultaneously. The method is calibrated with analytic solutions of kinetic equations. Condensation kinetic model is based on cloud particle growth equation, mass and heat balance equations. The coagulation kinetic model includes Brownian, turbulent and precipitation effects. The real values are used for condensation and coagulation growth of water droplets and ice particles. The model and the simulation results for two full-scale cloud experiments are presented. The simulation model and code may be used autonomously or as an element of another code.

  19. Kinetic Modeling of Esterification of Ethylene Glycol with Acetic Acid

    NASA Astrophysics Data System (ADS)

    Yadav, Vishnu P.; Mukherjee, Rudra Palash; Bantraj, Kandi; Maity, Sunil K.

    2010-10-01

    The reaction kinetics of the esterification of ethylene glycol with acetic acid in the presence of cation exchange resin has been studied and kinetic models based on empirical and Langmuir approach has been developed. The Langmuir based model involving eight kinetic parameters fits experimental data much better compared to empirical model involving four kinetic parameters. The effect of temperature and catalyst loading on the reaction system has been analyzed. Further, the activation energy and frequency factor of the rate constants for Langmuir based model has been estimated.

  20. Kinetic Modeling of Esterification of Ethylene Glycol with Acetic Acid

    SciTech Connect

    Yadav, Vishnu P.; Maity, Sunil K.; Mukherjee, Rudra Palash; Bantraj, Kandi

    2010-10-26

    The reaction kinetics of the esterification of ethylene glycol with acetic acid in the presence of cation exchange resin has been studied and kinetic models based on empirical and Langmuir approach has been developed. The Langmuir based model involving eight kinetic parameters fits experimental data much better compared to empirical model involving four kinetic parameters. The effect of temperature and catalyst loading on the reaction system has been analyzed. Further, the activation energy and frequency factor of the rate constants for Langmuir based model has been estimated.

  1. Chemical Kinetic Modeling of Biofuel Combustion

    NASA Astrophysics Data System (ADS)

    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

  2. Shear-Driven Reconnection in Kinetic Models

    NASA Astrophysics Data System (ADS)

    Black, C.; Antiochos, S. K.; Germaschewski, K.; Karpen, J. T.; DeVore, C. R.; Bessho, N.

    2015-12-01

    The explosive energy release in solar eruptive phenomena is believed to be due to magnetic reconnection. In the standard model for coronal mass ejections (CME) and/or solar flares, the free energy for the event resides in the strongly sheared magnetic field of a filament channel. The pre-eruption force balance consists of an upward force due to the magnetic pressure of the sheared field countered by a downward tension due to overlying unsheared field. Magnetic reconnection disrupts this force balance; therefore, it is critical for understanding CME/flare initiation, to model the onset of reconnection driven by the build-up of magnetic shear. In MHD simulations, the application of a magnetic-field shear is a trivial matter. However, kinetic effects are dominant in the diffusion region and thus, it is important to examine this process with PIC simulations as well. The implementation of such a driver in PIC methods is challenging, however, and indicates the necessity of a true multiscale model for such processes in the solar environment. The field must be sheared self-consistently and indirectly to prevent the generation of waves that destroy the desired system. Plasma instabilities can arise nonetheless. In the work presented here, we show that we can control this instability and generate a predicted out-of-plane magnetic flux. This material is based upon work supported by the National Science Foundation under Award No. AGS-1331356.

  3. Kinetic modelling of krypton fluoride laser systems

    SciTech Connect

    Jancaitis, K.S.

    1983-11-01

    A kinetic model has been developed for the KrF* rare gas halide laser system, specifically for electron-beam pumped mixtures of krypton, fluorine, and either helium or argon. The excitation produced in the laser gas by the e-beam was calculated numerically using an algorithm checked by comparing the predicted ionization yields in the pure rare gases with their experimental values. The excitation of the laser media by multi-kilovolt x-rays was also modeled and shown to be similar to that produced by high energy electrons. A system of equations describing the transfer of the initial gas excitation into the laser upper level was assembled using reaction rate constants from both experiment and theory. A one-dimensional treatment of the interaction of the laser radiation with the gas was formulated which considered spontaneous and stimulated emission and absorption. The predictions of this model were in good agreement with the fluorescence signals and gain and absorption measured experimentally.

  4. Percolation in a kinetic opinion exchange model

    NASA Astrophysics Data System (ADS)

    Chandra, Anjan Kumar

    2012-02-01

    We study the percolation transition of the geometrical clusters in the square-lattice LCCC model [a kinetic opinion exchange model introduced by Lallouache, Chakrabarti, Chakraborti, and Chakrabarti, Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.82.056112 82, 056112 (2010)] with the change in conviction and influencing parameter. The cluster is comprised of the adjacent sites having an opinion value greater than or equal to a prefixed threshold value of opinion (Ω). The transition point is different from that obtained for the transition of the order parameter (average opinion value) found by Lallouache Although the transition point varies with the change in the threshold value of the opinion, the critical exponents for the percolation transition obtained from the data collapses of the maximum cluster size, the cluster size distribution, and the Binder cumulant remain the same. The exponents are also independent of the values of conviction and influencing parameters, indicating the robustness of this transition. The exponents do not match any other known percolation exponents (e.g., the static Ising, dynamic Ising, and standard percolation). This means that the LCCC model belongs to a separate universality class.

  5. Reflected kinetics model for nuclear space reactor kinetics and control scoping calculations

    SciTech Connect

    Washington, K.E.

    1986-05-01

    The objective of this research is to develop a model that offers an alternative to the point kinetics (PK) modelling approach in the analysis of space reactor kinetics and control studies. Modelling effort will focus on the explicit treatment of control drums as reactivity input devices so that the transition to automatic control can be smoothly done. The proposed model is developed for the specific integration of automatic control and the solution of the servo mechanism problem. The integration of the kinetics model with an automatic controller will provide a useful tool for performing space reactor scoping studies for different designs and configurations. Such a tool should prove to be invaluable in the design phase of a space nuclear system from the point of view of kinetics and control limitations.

  6. F-Nets and Software Cabling: Deriving a Formal Model and Language for Portable Parallel Programming

    NASA Technical Reports Server (NTRS)

    DiNucci, David C.; Saini, Subhash (Technical Monitor)

    1998-01-01

    Parallel programming is still being based upon antiquated sequence-based definitions of the terms "algorithm" and "computation", resulting in programs which are architecture dependent and difficult to design and analyze. By focusing on obstacles inherent in existing practice, a more portable model is derived here, which is then formalized into a model called Soviets which utilizes a combination of imperative and functional styles. This formalization suggests more general notions of algorithm and computation, as well as insights into the meaning of structured programming in a parallel setting. To illustrate how these principles can be applied, a very-high-level graphical architecture-independent parallel language, called Software Cabling, is described, with many of the features normally expected from today's computer languages (e.g. data abstraction, data parallelism, and object-based programming constructs).

  7. Formal Implementation of a Performance Evaluation Model for the Face Recognition System

    PubMed Central

    Shin, Yong-Nyuo; Kim, Jason; Lee, Yong-Jun; Shin, Woochang; Choi, Jin-Young

    2008-01-01

    Due to usability features, practical applications, and its lack of intrusiveness, face recognition technology, based on information, derived from individuals' facial features, has been attracting considerable attention recently. Reported recognition rates of commercialized face recognition systems cannot be admitted as official recognition rates, as they are based on assumptions that are beneficial to the specific system and face database. Therefore, performance evaluation methods and tools are necessary to objectively measure the accuracy and performance of any face recognition system. In this paper, we propose and formalize a performance evaluation model for the biometric recognition system, implementing an evaluation tool for face recognition systems based on the proposed model. Furthermore, we performed evaluations objectively by providing guidelines for the design and implementation of a performance evaluation system, formalizing the performance test process. PMID:18317524

  8. A kinetic model for subtractive hybridization.

    PubMed Central

    Milner, J J; Cecchini, E; Dominy, P J

    1995-01-01

    Nucleic acid sequences that differ in abundance between two populations (target sequences) can be cloned by multiple rounds of subtractive hybridization and amplification by PCR. These sequences can be cDNAs representing up-regulated mRNAs, or genomic DNAs from deletion mutants. We have derived an equation that describes the recovery of such sequences, and have used this to simulate the outcome of up to 10 rounds of subtractive hybridization and PCR amplification. When the model was tested by comparing its predictions with the published results from genomic and cDNA subtractions, the predictions of the model were generally in good agreement with the published data. We have modelled the outcomes of genomic subtractions, for a variety of genomes, and have used it to compare various strategies for enriching targets. The model predicts that for genomes of less than 5 x 10(8) bp, deletions of as small as 1 kbp should represent > 99% of the DNA after three to six rounds of hybridization (depending on the enrichment procedure). As genomes increase in size, the kinetics of hybridization become an important limiting factor. However, even for genomes as large as 3 x 10(9) bp, it should be possible to isolate deletions of 5 kbp using the appropriate conditions. These simulations suggest that such methods offer a realistic alternative to chromosome walking for identifying genomic deletions for which there are known phenotypes, thereby considerably reducing time and effort. For cDNA subtractive hybridization, the model predicts that after six rounds of hybridization, sequences that do not differ in abundance between the tester and driver populations (the background) will represent < 1% of the subtracted population, and even quite modestly upregulated cDNAs should be successfully enriched. Where several up-regulated cDNAs are present, the predicted final representation is dependent on both the initial abundance and the degree of up-regulation. PMID:7870584

  9. Formal modeling of Gene Ontology annotation predictions based on factor graphs

    NASA Astrophysics Data System (ADS)

    Spetale, Flavio; Murillo, Javier; Tapia, Elizabeth; Arce, Débora; Ponce, Sergio; Bulacio, Pilar

    2016-04-01

    Gene Ontology (GO) is a hierarchical vocabulary for gene product annotation. Its synergy with machine learning classification methods has been widely used for the prediction of protein functions. Current classification methods rely on heuristic solutions to check the consistency with some aspects of the underlying GO structure. In this work we formalize the GO is-a relationship through predicate logic. Moreover, an ontology model based on Forney Factor Graph (FFG) is shown on a general fragment of Cellular Component GO.

  10. Kinetic modeling of cell metabolism for microbial production.

    PubMed

    Costa, Rafael S; Hartmann, Andras; Vinga, Susana

    2016-02-10

    Kinetic models of cellular metabolism are important tools for the rational design of metabolic engineering strategies and to explain properties of complex biological systems. The recent developments in high-throughput experimental data are leading to new computational approaches for building kinetic models of metabolism. Herein, we briefly survey the available databases, standards and software tools that can be applied for kinetic models of metabolism. In addition, we give an overview about recently developed ordinary differential equations (ODE)-based kinetic models of metabolism and some of the main applications of such models are illustrated in guiding metabolic engineering design. Finally, we review the kinetic modeling approaches of large-scale networks that are emerging, discussing their main advantages, challenges and limitations. PMID:26724578

  11. Los Alamos CCS (Center for Computer Security) formal computer security model

    SciTech Connect

    Dreicer, J.S.; Hunteman, W.J. )

    1989-01-01

    This paper provides a brief presentation of the formal computer security model currently being developed at the Los Alamos Department of Energy (DOE) Center for Computer Security (CCS). The initial motivation for this effort was the need to provide a method by which DOE computer security policy implementation could be tested and verified. The actual analytical model was a result of the integration of current research in computer security and previous modeling and research experiences. The model is being developed to define a generic view of the computer and network security domains, to provide a theoretical basis for the design of a security model, and to address the limitations of present models. Formal mathematical models for computer security have been designed and developed in conjunction with attempts to build secure computer systems since the early 70's. The foundation of the Los Alamos DOE CCS model is a series of functionally dependent probability equations, relations, and expressions. The mathematical basis appears to be justified and is undergoing continued discrimination and evolution. We expect to apply the model to the discipline of the Bell-Lapadula abstract sets of objects and subjects. 5 refs.

  12. Reasoning with conditionals: a test of formal models of four theories.

    PubMed

    Oberauer, Klaus

    2006-11-01

    The four dominant theories of reasoning from conditionals are translated into formal models: The theory of mental models (Johnson-Laird, P. N., & Byrne, R. M. J. (2002). Conditionals: a theory of meaning, pragmatics, and inference. Psychological Review, 109, 646-678), the suppositional theory (Evans, J. S. B. T., & Over, D. E. (2004). If. Oxford: Oxford University Press), a dual-process variant of the model theory (Verschueren, N., Schaeken, W., & d'Ydewalle, G. (2005). A dual-process specification of causal conditional reasoning. Thinking &Reasoning, 11, 278-293), and the probabilistic theory (Oaksford, M., Chater, N., & Larkin, J. (2000). Probabilities and polarity biases in conditional inference. Journal of Experimental Psychology: Learning, Memory, and Cognition, 26, 883-899). The first three theories are formalized as multinomial models. The models are applied to the frequencies of patterns of acceptance or rejection across the four basic inferences modus ponens, acceptance of the consequent, denial of the antecedent, and modus tollens. Model fits are assessed for two large data sets, one representing reasoning with abstract, basic conditionals, the other reflecting reasoning with pseudo-realistic causal and non-causal conditionals. The best account of the data was provided by a modified version of the mental-model theory, augmented by directionality, and by the dual-process model.

  13. A Kinetic Model for the Radio CME

    NASA Astrophysics Data System (ADS)

    Lee, Jeongwoo; Gary, D. E.

    2009-05-01

    Current studies on Coronal Mass Ejections (CMEs) are mostly concentrated on their macroscopic properties as measured on White-Light images. On the other hand, radio emissions from CMEs carry the information of high energy particles associated with them, but usually without spatial information. In this regard, the rare radio maps of the 1998 April 20 CME obtained with the Nancay radioheliograph between 164 and 432 MHz (called a radio CME by Bastian et al. in 2001) offer an exceptional opportunity to explore the spatial distribution of high energy electrons inside the CME loop. We present a detailed kinetic model for the radio CME employing the lower hybrid (LH) waves excited by the CME shock as the primary electron acceleration mechanism, and magnetic mirroring and Coulomb collisions as the propagation effects inside the expanding loop. The main constraint in this modeling comes from the fact that the LH waves accelerate electrons parallel to the magnetic field and the accelerated electrons should gain, during propagation, sufficient amount of the perpendicular momentum to emit the synchrotron radiation as observed. The relative magnetic field variation responsible for the magnetic mirroring is inferred from the geometrical shape of the CME on the images of the Large Angle and Spectrometric Coronagraph Experiment (LASCO), and the field strength and the amplitude of the LH waves are determined from the observed radio spectra. The modeling is focused on the spatial distribution of the LH waves most plausible to explain the radio maps, and the result is discussed in relation to the associated shock property.

  14. A formally verified algorithm for interactive consistency under a hybrid fault model

    NASA Technical Reports Server (NTRS)

    Lincoln, Patrick; Rushby, John

    1993-01-01

    Consistent distribution of single-source data to replicated computing channels is a fundamental problem in fault-tolerant system design. The 'Oral Messages' (OM) algorithm solves this problem of Interactive Consistency (Byzantine Agreement) assuming that all faults are worst-cass. Thambidurai and Park introduced a 'hybrid' fault model that distinguished three fault modes: asymmetric (Byzantine), symmetric, and benign; they also exhibited, along with an informal 'proof of correctness', a modified version of OM. Unfortunately, their algorithm is flawed. The discipline of mechanically checked formal verification eventually enabled us to develop a correct algorithm for Interactive Consistency under the hybrid fault model. This algorithm withstands $a$ asymmetric, $s$ symmetric, and $b$ benign faults simultaneously, using $m+1$ rounds, provided $n is greater than 2a + 2s + b + m$, and $m\\geg a$. We present this algorithm, discuss its subtle points, and describe its formal specification and verification in PVS. We argue that formal verification systems such as PVS are now sufficiently effective that their application to fault-tolerance algorithms should be considered routine.

  15. Enskog-like kinetic models for vehicular traffic

    SciTech Connect

    Klar, A.; Wegener, R.

    1997-04-01

    In the present paper a general criticism of kinetic equations for vehicular traffic is given. The necessity of introducing an Enskog-type correction into these equations is shown. An Enskog-like kinetic traffic flow equation is presented and fluid dynamic equations are derived. This derivation yields new coefficients for the standard fluid dynamic equations of vehicular traffic. Numerical simulations for inhomogeneous traffic flow situations are shown together with a comparison between kinetic and fluid dynamics models.

  16. Reflected kinetics model for nuclear space reactor kinetics and control scoping calculations

    SciTech Connect

    Washington, K.E.

    1986-01-01

    Renewed interest in space nuclear applications has motivated the study of a specialized reactor kinetics model. Consideration of a kinetics model favorable for study of the feasibility of automatic control of these devices is warranted. The need to bridge this gap between reactor kinetics and automatic control in conjunction with the control drum design characteristic of next generation paper space reactors inspired the development of a new Reflected Kinetics (RK) model. An extension of the conventional point-kinetics (PK) model was done in order to explicitly correlate reactivity and the reflector/absorber control drums characteristic of space nuclear reactor designs. Open-loop computations and numerical comparison to analytic PK equations indicated that the RK model is a functional alternative to equivalent bare point kinetics in the analysis of moderate transients. Variations in the RK reflector-to-core transfer probabilities and coolant flow rate do indeed drive the transient differently than the lumped insertion of equivalent reactivity amounts in the core. These computations illustrated the potential importance of the utilization of variable coolant flow rate to aid control in space reactor systems limited by minimal drum reactivity worth. Additionally the Doppler reactivity shutdown mechanism was concluded to be the primarily reliable means of safety shutdown in such systems. The structure of the RK equations proved to be advantageous for integration of automatic control.

  17. Formalization, implementation, and modeling of institutional controllers for distributed robotic systems.

    PubMed

    Pereira, José N; Silva, Porfírio; Lima, Pedro U; Martinoli, Alcherio

    2014-01-01

    The work described is part of a long term program of introducing institutional robotics, a novel framework for the coordination of robot teams that stems from institutional economics concepts. Under the framework, institutions are cumulative sets of persistent artificial modifications made to the environment or to the internal mechanisms of a subset of agents, thought to be functional for the collective order. In this article we introduce a formal model of institutional controllers based on Petri nets. We define executable Petri nets-an extension of Petri nets that takes into account robot actions and sensing-to design, program, and execute institutional controllers. We use a generalized stochastic Petri net view of the robot team controlled by the institutional controllers to model and analyze the stochastic performance of the resulting distributed robotic system. The ability of our formalism to replicate results obtained using other approaches is assessed through realistic simulations of up to 40 e-puck robots. In particular, we model a robot swarm and its institutional controller with the goal of maintaining wireless connectivity, and successfully compare our model predictions and simulation results with previously reported results, obtained by using finite state automaton models and controllers. PMID:23373975

  18. Digital image watermarking: its formal model, fundamental properties and possible attacks

    NASA Astrophysics Data System (ADS)

    Nyeem, Hussain; Boles, Wageeh; Boyd, Colin

    2014-12-01

    While formal definitions and security proofs are well established in some fields like cryptography and steganography, they are not as evident in digital watermarking research. A systematic development of watermarking schemes is desirable, but at present, their development is usually informal, ad hoc, and omits the complete realization of application scenarios. This practice not only hinders the choice and use of a suitable scheme for a watermarking application, but also leads to debate about the state-of-the-art for different watermarking applications. With a view to the systematic development of watermarking schemes, we present a formal generic model for digital image watermarking. Considering possible inputs, outputs, and component functions, the initial construction of a basic watermarking model is developed further to incorporate the use of keys. On the basis of our proposed model, fundamental watermarking properties are defined and their importance exemplified for different image applications. We also define a set of possible attacks using our model showing different winning scenarios depending on the adversary capabilities. It is envisaged that with a proper consideration of watermarking properties and adversary actions in different image applications, use of the proposed model would allow a unified treatment of all practically meaningful variants of watermarking schemes.

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

    SciTech Connect

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

    2012-08-15

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

  20. End users transforming experiences into formal information and process models for personalised health interventions.

    PubMed

    Lindgren, Helena; Lundin-Olsson, Lillemor; Pohl, Petra; Sandlund, Marlene

    2014-01-01

    Five physiotherapists organised a user-centric design process of a knowledge-based support system for promoting exercise and preventing falls. The process integrated focus group studies with 17 older adults and prototyping. The transformation of informal medical and rehabilitation expertise and older adults' experiences into formal information and process models during the development was studied. As tool they used ACKTUS, a development platform for knowledge-based applications. The process became agile and incremental, partly due to the diversity of expectations and preferences among both older adults and physiotherapists, and the participatory approach to design and development. In addition, there was a need to develop the knowledge content alongside with the formal models and their presentations, which allowed the participants to test hands-on and evaluate the ideas, content and design. The resulting application is modular, extendable, flexible and adaptable to the individual end user. Moreover, the physiotherapists are able to modify the information and process models, and in this way further develop the application. The main constraint was found to be the lack of support for the initial phase of concept modelling, which lead to a redesigned user interface and functionality of ACKTUS.

  1. A formal model of asynchronous communication and its use in mechanically verifying a biphase mark protocol

    NASA Technical Reports Server (NTRS)

    Moore, J. Strother

    1992-01-01

    In this paper we present a formal model of asynchronous communication as a function in the Boyer-Moore logic. The function transforms the signal stream generated by one processor into the signal stream consumed by an independently clocked processor. This transformation 'blurs' edges and 'dilates' time due to differences in the phases and rates of the two clocks and the communications delay. The model can be used quantitatively to derive concrete performance bounds on asynchronous communications at ISO protocol level 1 (physical level). We develop part of the reusable formal theory that permits the convenient application of the model. We use the theory to show that a biphase mark protocol can be used to send messages of arbitrary length between two asynchronous processors. We study two versions of the protocol, a conventional one which uses cells of size 32 cycles and an unconventional one which uses cells of size 18. We conjecture that the protocol can be proved to work under our model for smaller cell sizes and more divergent clock rates but the proofs would be harder.

  2. Formal Modeling and Analysis of a Preliminary Small Aircraft Transportation System (SATS)Concept

    NASA Technical Reports Server (NTRS)

    Carrreno, Victor A.; Gottliebsen, Hanne; Butler, Ricky; Kalvala, Sara

    2004-01-01

    New concepts for automating air traffic management functions at small non-towered airports raise serious safety issues associated with the software implementations and their underlying key algorithms. The criticality of such software systems necessitates that strong guarantees of the safety be developed for them. In this paper we present a formal method for modeling and verifying such systems using the PVS theorem proving system. The method is demonstrated on a preliminary concept of operation for the Small Aircraft Transportation System (SATS) project at NASA Langley.

  3. Conceptual Model Formalization in a Semantic Interoperability Service Framework: Transforming Relational Database Schemas to OWL.

    PubMed

    Bravo, Carlos; Suarez, Carlos; González, Carolina; López, Diego; Blobel, Bernd

    2014-01-01

    Healthcare information is distributed through multiple heterogeneous and autonomous systems. Access to, and sharing of, distributed information sources are a challenging task. To contribute to meeting this challenge, this paper presents a formal, complete and semi-automatic transformation service from Relational Databases to Web Ontology Language. The proposed service makes use of an algorithm that allows to transform several data models of different domains by deploying mainly inheritance rules. The paper emphasizes the relevance of integrating the proposed approach into an ontology-based interoperability service to achieve semantic interoperability.

  4. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

    PubMed Central

    2013-01-01

    Background Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing. Results We present the Systems Biology Markup Language (SBML) Qualitative Models Package (“qual”), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models. Conclusions SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks. PMID:24321545

  5. Developing Quality Indicators and Auditing Protocols from Formal Guideline Models: Knowledge Representation and Transformations

    PubMed Central

    Advani, Aneel; Goldstein, Mary; Shahar, Yuval; Musen, Mark A.

    2003-01-01

    Automated quality assessment of clinician actions and patient outcomes is a central problem in guideline- or standards-based medical care. In this paper we describe a model representation and algorithm for deriving structured quality indicators and auditing protocols from formalized specifications of guidelines used in decision support systems. We apply the model and algorithm to the assessment of physician concordance with a guideline knowledge model for hypertension used in a decision-support system. The properties of our solution include the ability to derive automatically (1) context-specific and (2) case-mix-adjusted quality indicators that (3) can model global or local levels of detail about the guideline (4) parameterized by defining the reliability of each indicator or element of the guideline. PMID:14728124

  6. Determining the privacy policy deficiencies of health ICT applications through semi-formal modelling.

    PubMed

    Croll, Peter R

    2011-02-01

    To ensure that patient confidentiality is securely maintained, health ICT applications that contain sensitive personal information demand comprehensive privacy policies. Determining the adequacy of these policies to meet legal conformity together with clinical users and patient expectation is demanding in practice. Organisations and agencies looking to analyse their Privacy and Security policies can benefit from guidance provided by outside entities such as the Privacy Office of their State or Government together with law firms and ICT specialists. The advice given is not uniform and often open to different interpretations. Of greater concern is the possibility of overlooking any important aspects that later result in a data breach. Based on three case studies, this paper considers whether a more formal approach to privacy analysis could be taken that would help identify the full coverage of a Privacy Impact Analysis and determine the deficiencies with an organisation's current policies and approach. A diagrammatic model showing the relationships between Confidentiality, Privacy, Trust, Security and Safety is introduced. First the validity of this model is determined by mapping it against the real-world case studies taken from three healthcare services that depend on ICT. Then, by using software engineering methods, a formal mapping of the relationships is undertaken to identify a full set of policies needed to satisfy the model. How effective this approach may prove as a generic method for deriving a comprehensive set of policies in health ICT applications is finally discussed. PMID:21075675

  7. Determining the privacy policy deficiencies of health ICT applications through semi-formal modelling.

    PubMed

    Croll, Peter R

    2011-02-01

    To ensure that patient confidentiality is securely maintained, health ICT applications that contain sensitive personal information demand comprehensive privacy policies. Determining the adequacy of these policies to meet legal conformity together with clinical users and patient expectation is demanding in practice. Organisations and agencies looking to analyse their Privacy and Security policies can benefit from guidance provided by outside entities such as the Privacy Office of their State or Government together with law firms and ICT specialists. The advice given is not uniform and often open to different interpretations. Of greater concern is the possibility of overlooking any important aspects that later result in a data breach. Based on three case studies, this paper considers whether a more formal approach to privacy analysis could be taken that would help identify the full coverage of a Privacy Impact Analysis and determine the deficiencies with an organisation's current policies and approach. A diagrammatic model showing the relationships between Confidentiality, Privacy, Trust, Security and Safety is introduced. First the validity of this model is determined by mapping it against the real-world case studies taken from three healthcare services that depend on ICT. Then, by using software engineering methods, a formal mapping of the relationships is undertaken to identify a full set of policies needed to satisfy the model. How effective this approach may prove as a generic method for deriving a comprehensive set of policies in health ICT applications is finally discussed.

  8. Modeling of batch sorber system: kinetic, mechanistic, and thermodynamic modeling

    NASA Astrophysics Data System (ADS)

    Mishra, Vishal

    2016-09-01

    The present investigation has dealt with the biosorption of copper and zinc ions on the surface of egg-shell particles in the liquid phase. Various rate models were evaluated to elucidate the kinetics of copper and zinc biosorptions, and the results indicated that the pseudo-second-order model was more appropriate than the pseudo-first-order model. The curve of the initial sorption rate versus the initial concentration of copper and zinc ions also complemented the results of the pseudo-second-order model. Models used for the mechanistic modeling were the intra-particle model of pore diffusion and Bangham's model of film diffusion. The results of the mechanistic modeling together with the values of pore and film diffusivities indicated that the preferential mode of the biosorption of copper and zinc ions on the surface of egg-shell particles in the liquid phase was film diffusion. The results of the intra-particle model showed that the biosorption of the copper and zinc ions was not dominated by the pore diffusion, which was due to macro-pores with open-void spaces present on the surface of egg-shell particles. The thermodynamic modeling reproduced the fact that the sorption of copper and zinc was spontaneous, exothermic with the increased order of the randomness at the solid-liquid interface.

  9. Apatite Biomineralization: Model Studies of Composition and Kinetics

    NASA Astrophysics Data System (ADS)

    Tecklenburg, M. M. J.; Urbanawiz, S. A.; Derry, A. W.; Ling, M. L.; Zhou, D.; Pavan, B.

    2014-06-01

    Biomineralization of bone and teeth is modeled via studies of apatite crystallization to assess the effects of constituent ions and centrifugal force on kinetics of the amorphous to crystalline phase transition.

  10. Biomass torrefaction: modeling of volatile and solid product evolution kinetics.

    PubMed

    Bates, Richard B; Ghoniem, Ahmed F

    2012-11-01

    The aim of this work is the development of a kinetics model for the evolution of the volatile and solid product composition during torrefaction conditions between 200 and 300°C. Coupled to an existing two step solid mass loss kinetics mechanism, this model describes the volatile release kinetics in terms of a set of identifiable chemical components, permitting the solid product composition to be estimated by mass conservation. Results show that most of the volatiles released during the first stage include highly oxygenated species such as water, acetic acid, and carbon dioxide, while volatiles released during the second step are composed primarily of lactic acid, methanol, and acetic acid. This kinetics model will be used in the development of a model to describe reaction energy balance and heat release dynamics.

  11. Formal representation of a conceptual data model for the patient-based medical record.

    PubMed

    Gouveia-Oliveira, A; Lopes, L

    1993-01-01

    We present a general architecture for the patient-based medical record as it is being developed for the SAMS, a private social security system. The conceptual data model is described in a convenient formal notation, the entity-relationship diagram. Although following the original formulation of the problem-oriented medical record (POMR), the data model was designed with a level of generalization that, functionally, makes structural differences between conventional and POMR no longer apparent. The main features of this model are its adaptability to individual work practices and its problem-oriented structure, including the representation of problems' evolution. This structure will enable physicians to organize the data, mostly collected elsewhere, by explicitly relating the facts that constitute a particular patient record, which is a simple way to store context information and clinical knowledge that is not part of patient data.

  12. A formal model for measuring the effect of technological change on telecentre usage

    NASA Astrophysics Data System (ADS)

    Azizi, Azizi; Ahmad, Faudziah; Yusop, Nor Iadah; Aji, Zahurin Mat

    2016-08-01

    Technological change (TC), in general refers to continuous invention, innovation and diffusion of technology. In relation to telecentre, TC is seen as the driving force of the centre's operation. However, in recent years, telecentre's usage and operation is declining slowly and this leads to the question about the continued relevance of these centres as well as calls for evidence of impacts to justify further resources and program improvements. The paper aims to present the simulation results on an agent-based model that was developed to show the impact of TC on telecentre's usage. The model was constructed in four phases, Abstraction, Formalization, Simulation and Evaluation. Results showed that the computational model was able to show the effective usage of telecentre in different types of scenarios.

  13. Kinetic models in industrial biotechnology - Improving cell factory performance.

    PubMed

    Almquist, Joachim; Cvijovic, Marija; Hatzimanikatis, Vassily; Nielsen, Jens; Jirstrand, Mats

    2014-07-01

    An increasing number of industrial bioprocesses capitalize on living cells by using them as cell factories that convert sugars into chemicals. These processes range from the production of bulk chemicals in yeasts and bacteria to the synthesis of therapeutic proteins in mammalian cell lines. One of the tools in the continuous search for improved performance of such production systems is the development and application of mathematical models. To be of value for industrial biotechnology, mathematical models should be able to assist in the rational design of cell factory properties or in the production processes in which they are utilized. Kinetic models are particularly suitable towards this end because they are capable of representing the complex biochemistry of cells in a more complete way compared to most other types of models. They can, at least in principle, be used to in detail understand, predict, and evaluate the effects of adding, removing, or modifying molecular components of a cell factory and for supporting the design of the bioreactor or fermentation process. However, several challenges still remain before kinetic modeling will reach the degree of maturity required for routine application in industry. Here we review the current status of kinetic cell factory modeling. Emphasis is on modeling methodology concepts, including model network structure, kinetic rate expressions, parameter estimation, optimization methods, identifiability analysis, model reduction, and model validation, but several applications of kinetic models for the improvement of cell factories are also discussed.

  14. An integral representation of functions in gas-kinetic models

    NASA Astrophysics Data System (ADS)

    Perepelitsa, Misha

    2016-08-01

    Motivated by the theory of kinetic models in gas dynamics, we obtain an integral representation of lower semicontinuous functions on {{{R}}^d,} {d≥1}. We use the representation to study the problem of compactness of a family of the solutions of the discrete time BGK model for the compressible Euler equations. We determine sufficient conditions for strong compactness of moments of kinetic densities, in terms of the measures from their integral representations.

  15. Formal Modeling of Multi-Agent Systems using the Pi-Calculus and Epistemic Logic

    NASA Technical Reports Server (NTRS)

    Rorie, Toinette; Esterline, Albert

    1998-01-01

    Multi-agent systems have become important recently in computer science, especially in artificial intelligence (AI). We allow a broad sense of agent, but require at least that an agent has some measure of autonomy and interacts with other agents via some kind of agent communication language. We are concerned in this paper with formal modeling of multi-agent systems, with emphasis on communication. We propose for this purpose to use the pi-calculus, an extension of the process algebra CCS. Although the literature on the pi-calculus refers to agents, the term is used there in the sense of a process in general. It is our contention, however, that viewing agents in the AI sense as agents in the pi-calculus sense affords significant formal insight. One formalism that has been applied to agents in the AI sense is epistemic logic, the logic of knowledge. The success of epistemic logic in computer science in general has come in large part from its ability to handle concepts of knowledge that apply to groups. We maintain that the pi-calculus affords a natural yet rigorous means by which groups that are significant to epistemic logic may be identified, encapsulated, structured into hierarchies, and restructured in a principled way. This paper is organized as follows: Section 2 introduces the pi-calculus; Section 3 takes a scenario from the classical paper on agent-oriented programming [Sh93] and translates it into a very simple subset of the n-calculus; Section 4 then shows how more sophisticated features of the pi-calculus may bc brought into play; Section 5 discusses how the pi-calculus may be used to define groups for epistemic logic; and Section 6 is the conclusion.

  16. Detailed Chemical Kinetic Modeling of Cyclohexane Oxidation

    SciTech Connect

    Silke, E J; Pitz, W J; Westbrook, C K; Ribaucour, M

    2006-11-10

    A detailed chemical kinetic mechanism has been developed and used to study the oxidation of cyclohexane at both low and high temperatures. Reaction rate constant rules are developed for the low temperature combustion of cyclohexane. These rules can be used for in chemical kinetic mechanisms for other cycloalkanes. Since cyclohexane produces only one type of cyclohexyl radical, much of the low temperature chemistry of cyclohexane is described in terms of one potential energy diagram showing the reaction of cyclohexyl radical + O{sub 2} through five, six and seven membered ring transition states. The direct elimination of cyclohexene and HO{sub 2} from RO{sub 2} is included in the treatment using a modified rate constant of Cavallotti et al. Published and unpublished data from the Lille rapid compression machine, as well as jet-stirred reactor data are used to validate the mechanism. The effect of heat loss is included in the simulations, an improvement on previous studies on cyclohexane. Calculations indicated that the production of 1,2-epoxycyclohexane observed in the experiments can not be simulated based on the current understanding of low temperature chemistry. Possible 'alternative' H-atom isomerizations leading to different products from the parent O{sub 2}QOOH radical were included in the low temperature chemical kinetic mechanism and were found to play a significant role.

  17. Interval Predictor Models with a Formal Characterization of Uncertainty and Reliability

    NASA Technical Reports Server (NTRS)

    Crespo, Luis G.; Giesy, Daniel P.; Kenny, Sean P.

    2014-01-01

    This paper develops techniques for constructing empirical predictor models based on observations. By contrast to standard models, which yield a single predicted output at each value of the model's inputs, Interval Predictors Models (IPM) yield an interval into which the unobserved output is predicted to fall. The IPMs proposed prescribe the output as an interval valued function of the model's inputs, render a formal description of both the uncertainty in the model's parameters and of the spread in the predicted output. Uncertainty is prescribed as a hyper-rectangular set in the space of model's parameters. The propagation of this set through the empirical model yields a range of outputs of minimal spread containing all (or, depending on the formulation, most) of the observations. Optimization-based strategies for calculating IPMs and eliminating the effects of outliers are proposed. Outliers are identified by evaluating the extent by which they degrade the tightness of the prediction. This evaluation can be carried out while the IPM is calculated. When the data satisfies mild stochastic assumptions, and the optimization program used for calculating the IPM is convex (or, when its solution coincides with the solution to an auxiliary convex program), the model's reliability (that is, the probability that a future observation would be within the predicted range of outputs) can be bounded rigorously by a non-asymptotic formula.

  18. Weighed scalar averaging in LTB dust models: part II. A formalism of exact perturbations

    NASA Astrophysics Data System (ADS)

    Sussman, Roberto A.

    2013-03-01

    We examine the exact perturbations that arise from the q-average formalism that was applied in the preceding article (part I) to Lemaître-Tolman-Bondi (LTB) models. By introducing an initial value parametrization, we show that all LTB scalars that take an FLRW ‘look-alike’ form (frequently used in the literature dealing with LTB models) follow as q-averages of covariant scalars that are common to FLRW models. These q-scalars determine for every averaging domain a unique FLRW background state through Darmois matching conditions at the domain boundary, though the definition of this background does not require an actual matching with an FLRW region (Swiss cheese-type models). Local perturbations describe the deviation from the FLRW background state through the local gradients of covariant scalars at the boundary of every comoving domain, while non-local perturbations do so in terms of the intuitive notion of a ‘contrast’ of local scalars with respect to FLRW reference values that emerge from q-averages assigned to the whole domain or the whole time slice in the asymptotic limit. We derive fluid flow evolution equations that completely determine the dynamics of the models in terms of the q-scalars and both types of perturbations. A rigorous formalism of exact spherical nonlinear perturbations is defined over the FLRW background state associated with the q-scalars, recovering the standard results of linear perturbation theory in the appropriate limit. We examine the notion of the amplitude and illustrate the differences between local and non-local perturbations by qualitative diagrams and through an example of a cosmic density void that follows from the numeric solution of the evolution equations.

  19. Elimination kinetic model for organic chemicals in earthworms.

    PubMed

    Dimitrova, N; Dimitrov, S; Georgieva, D; Van Gestel, C A M; Hankard, P; Spurgeon, D; Li, H; Mekenyan, O

    2010-08-15

    Mechanistic understanding of bioaccumulation in different organisms and environments should take into account the influence of organism and chemical depending factors on the uptake and elimination kinetics of chemicals. Lipophilicity, metabolism, sorption (bioavailability) and biodegradation of chemicals are among the important factors that may significantly affect the bioaccumulation process in soil organisms. This study attempts to model elimination kinetics of organic chemicals in earthworms by accounting for the effects of both chemical and biological properties, including metabolism. The modeling approach that has been developed is based on the concept for simulating metabolism used in the BCF base-line model developed for predicting bioaccumulation in fish. Metabolism was explicitly accounted for by making use of the TIMES engine for simulation of metabolism and a set of principal transformations. Kinetic characteristics of transformations were estimated on the basis of observed kinetics data for the elimination of organic chemicals from earthworms. PMID:20185163

  20. Turbulent hydrocarbon combustions kinetics - Stochastic modeling and verification

    NASA Technical Reports Server (NTRS)

    Wang, T. S.; Farmer, R. C.; Tucker, Kevin

    1989-01-01

    Idealized reactors, that are designed to ensure perfect mixing and are used to generate the combustion kinetics for complex hydrocarbon fuels, may depart from the ideal and influence the kinetics model performance. A complex hydrocarbon kinetics model that was established by modeling a jet-stirred combustor (JSC) as a perfectly stirred reactor (PSR), is reevaluated with a simple stochastic process in order to introduce the unmixedness effect quantitatively into the reactor system. It is shown that the comparisons of the predictions and experimental data have improved dramatically with the inclusion of the unmixedness effect in the rich combustion region. The complex hydrocarbon kinetics is therefore verified to be mixing effect free and be applicable to general reacting flow calculations.

  1. An integrative formal model of motivation and decision making: The MGPM*.

    PubMed

    Ballard, Timothy; Yeo, Gillian; Loft, Shayne; Vancouver, Jeffrey B; Neal, Andrew

    2016-09-01

    We develop and test an integrative formal model of motivation and decision making. The model, referred to as the extended multiple-goal pursuit model (MGPM*), is an integration of the multiple-goal pursuit model (Vancouver, Weinhardt, & Schmidt, 2010) and decision field theory (Busemeyer & Townsend, 1993). Simulations of the model generated predictions regarding the effects of goal type (approach vs. avoidance), risk, and time sensitivity on prioritization. We tested these predictions in an experiment in which participants pursued different combinations of approach and avoidance goals under different levels of risk. The empirical results were consistent with the predictions of the MGPM*. Specifically, participants pursuing 1 approach and 1 avoidance goal shifted priority from the approach to the avoidance goal over time. Among participants pursuing 2 approach goals, those with low time sensitivity prioritized the goal with the larger discrepancy, whereas those with high time sensitivity prioritized the goal with the smaller discrepancy. Participants pursuing 2 avoidance goals generally prioritized the goal with the smaller discrepancy. Finally, all of these effects became weaker as the level of risk increased. We used quantitative model comparison to show that the MGPM* explained the data better than the original multiple-goal pursuit model, and that the major extensions from the original model were justified. The MGPM* represents a step forward in the development of a general theory of decision making during multiple-goal pursuit. (PsycINFO Database Record

  2. Formal Model for the Reduction of the Dynamic Energy Consumption in Multi-Layer Memory Subsystems

    NASA Astrophysics Data System (ADS)

    Zhu, Hongwei; Luican, Ilie I.; Balasa, Florin; Pradhan, Dhiraj K.

    In real-time data-dominated communication and multimedia processing applications, a multi-layer memory hierarchy is typically used to enhance the system performance and also to reduce the energy consumption. Savings of dynamic energy can be obtained by accessing frequently used data from smaller on-chip memories rather than from large background memories. This paper focuses on the reduction of the dynamic energy consumption in the memory subsystem of multidimensional signal processing systems, starting from the high-level algorithmic specification of the application. The paper presents a formal model which identifies those parts of arrays more intensely accessed, taking also into account the relative lifetimes of the signals. Tested on a two-layer memory hierarchy, this model led to savings of dynamic energy from 40% to over 70% relative to the energy used in the case of flat memory designs.

  3. Approximate Bayesian Computation in hydrologic modeling: equifinality of formal and informal approaches

    NASA Astrophysics Data System (ADS)

    Sadegh, M.; Vrugt, J. A.

    2013-04-01

    In recent years, a strong debate has emerged in the hydrologic literature how to properly treat non-traditional error residual distributions and quantify parameter and predictive uncertainty. Particularly, there is strong disagreement whether such uncertainty framework should have its roots within a proper statistical (Bayesian) context using Markov chain Monte Carlo (MCMC) simulation techniques, or whether such a framework should be based on a quite different philosophy and implement informal likelihood functions and simplistic search methods to summarize parameter and predictive distributions. In this paper we introduce an alternative framework, called Approximate Bayesian Computation (ABC) that summarizes the differing viewpoints of formal and informal Bayesian approaches. This methodology has recently emerged in the fields of biology and population genetics and relaxes the need for an explicit likelihood function in favor of one or multiple different summary statistics that measure the distance of each model simulation to the data. This paper is a follow up of the recent publication of Nott et al. (2012) and further studies the theoretical and numerical equivalence of formal (DREAM) and informal (GLUE) Bayesian approaches using data from different watersheds in the United States. We demonstrate that the limits of acceptability approach of GLUE is a special variant of ABC in which each discharge observation of the calibration data set is used as a summary diagnostic.

  4. Chemical Kinetic Models for HCCI and Diesel Combustion

    SciTech Connect

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

    2010-11-15

    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.

  5. Hybrid fluid/kinetic model for parallel heat conduction

    SciTech Connect

    Callen, J.D.; Hegna, C.C.; Held, E.D.

    1998-12-31

    It is argued that in order to use fluid-like equations to model low frequency ({omega} < {nu}) phenomena such as neoclassical tearing modes in low collisionality ({nu} < {omega}{sub b}) tokamak plasmas, a Chapman-Enskog-like approach is most appropriate for developing an equation for the kinetic distortion (F) of the distribution function whose velocity-space moments lead to the needed fluid moment closure relations. Further, parallel heat conduction in a long collision mean free path regime can be described through a combination of a reduced phase space Chapman-Enskog-like approach for the kinetics and a multiple-time-scale analysis for the fluid and kinetic equations.

  6. Phase-field Model for Interstitial Loop Growth Kinetics and Thermodynamic and Kinetic Models of Irradiated Fe-Cr Alloys

    SciTech Connect

    Li, Yulan; Hu, Shenyang Y.; Sun, Xin; Khaleel, Mohammad A.

    2011-06-15

    Microstructure evolution kinetics in irradiated materials has strongly spatial correlation. For example, void and second phases prefer to nucleate and grow at pre-existing defects such as dislocations, grain boundaries, and cracks. Inhomogeneous microstructure evolution results in inhomogeneity of microstructure and thermo-mechanical properties. Therefore, the simulation capability for predicting three dimensional (3-D) microstructure evolution kinetics and its subsequent impact on material properties and performance is crucial for scientific design of advanced nuclear materials and optimal operation conditions in order to reduce uncertainty in operational and safety margins. Very recently the meso-scale phase-field (PF) method has been used to predict gas bubble evolution, void swelling, void lattice formation and void migration in irradiated materials,. Although most results of phase-field simulations are qualitative due to the lake of accurate thermodynamic and kinetic properties of defects, possible missing of important kinetic properties and processes, and the capability of current codes and computers for large time and length scale modeling, the simulations demonstrate that PF method is a promising simulation tool for predicting 3-D heterogeneous microstructure and property evolution, and providing microstructure evolution kinetics for higher scale level simulations of microstructure and property evolution such as mean field methods. This report consists of two parts. In part I, we will present a new phase-field model for predicting interstitial loop growth kinetics in irradiated materials. The effect of defect (vacancy/interstitial) generation, diffusion and recombination, sink strength, long-range elastic interaction, inhomogeneous and anisotropic mobility on microstructure evolution kinetics is taken into account in the model. The model is used to study the effect of elastic interaction on interstitial loop growth kinetics, the interstitial flux, and sink

  7. Kinetic exchange models: From molecular physics to social science

    NASA Astrophysics Data System (ADS)

    Patriarca, Marco; Chakraborti, Anirban

    2013-08-01

    We discuss several multi-agent models that have their origin in the kinetic exchange theory of statistical mechanics and have been recently applied to a variety of problems in the social sciences. This class of models can be easily adapted for simulations in areas other than physics, such as the modeling of income and wealth distributions in economics and opinion dynamics in sociology.

  8. Kinetic model for the collisionless sheath of a collisional plasma

    NASA Astrophysics Data System (ADS)

    Tang, Xian-Zhu; Guo, Zehua

    2016-08-01

    Collisional plasmas typically have mean-free-path still much greater than the Debye length, so the sheath is mostly collisionless. Once the plasma density, temperature, and flow are specified at the sheath entrance, the profile variation of electron and ion density, temperature, flow speed, and conductive heat fluxes inside the sheath is set by collisionless dynamics, and can be predicted by an analytical kinetic model distribution. These predictions are contrasted here with direct kinetic simulations, showing good agreement.

  9. The Nonlinear Magnetosphere: Expressions in MHD and in Kinetic Models

    NASA Technical Reports Server (NTRS)

    Hesse, Michael; Birn, Joachim

    2011-01-01

    Like most plasma systems, the magnetosphere of the Earth is governed by nonlinear dynamic evolution equations. The impact of nonlinearities ranges from large scales, where overall dynamics features are exhibiting nonlinear behavior, to small scale, kinetic, processes, where nonlinear behavior governs, among others, energy conversion and dissipation. In this talk we present a select set of examples of such behavior, with a specific emphasis on how nonlinear effects manifest themselves in MHD and in kinetic models of magnetospheric plasma dynamics.

  10. On Accounting for the Interplay of Kinetic and Non-Kinetic Aspects in Population Mobility Models

    SciTech Connect

    Perumalla, Kalyan S; Bhaduri, Budhendra L

    2006-01-01

    Several important applications are placing demands on satisfactory characterization of the bi-directional interaction between kinetic and non-kinetic aspects in the mobility of people and commodities. Example applications include: emergency planning which needs to account for strong interplay of vehicular transport with inventory levels of critical supplies and/or people's psychologies; energy planning for normal day-to-day activities which considers the relation between travel patterns and energy usage; and, policy making for futuristic scenarios which examines the correlation between transportation behaviors and environmental/economic concerns. All these require new and holistic approaches for capturing the interplay of kinetic and non-kinetic aspects of mobility, as those aspects cannot be treated separately. Accurate characterization of such interplay requires proper integration of three distinct components, namely, data, models and computation. The availability of new sources of high-resolution data, and of detailed models together with recent advances in scalable computational methods now permits accurate capture of such an important interplay. This paper serves to highlight and argue that the interplay can in fact be captured in a high level of detail in simulations, enabled by the availability of new data, models and computational capabilities. Some of the challenges that are encountered in incorporating the interplay are outlined and plausible solution approaches are described in the context of large-scale scenarios involving mobility of people and commodities.

  11. Formal Individualized Teaching, a Differentiated Instructional Model, Effects on Student Learning in a High School ACT Preparation Course

    ERIC Educational Resources Information Center

    Donen, Tony

    2012-01-01

    The lack of clear and manageable implementation models for individualized instruction continued to exist in high schools. Formal individualized teaching (FIT), a differentiated instructional model, was studied to determine its impact on student learning. The FIT model included analyzing student data using a Pareto analysis to identify individual…

  12. Quantitative modeling of the Saccharomyces cerevisiae FLR1 regulatory network using an S-system formalism.

    PubMed

    Calçada, Dulce; Vinga, Susana; Freitas, Ana T; Oliveira, Arlindo L

    2011-10-01

    In this study we address the problem of finding a quantitative mathematical model for the genetic network regulating the stress response of the yeast Saccharomyces cerevisiae to the agricultural fungicide mancozeb. An S-system formalism was used to model the interactions of a five-gene network encoding four transcription factors (Yap1, Yrr1, Rpn4 and Pdr3) regulating the transcriptional activation of the FLR1 gene. Parameter estimation was accomplished by decoupling the resulting system of nonlinear ordinary differential equations into a larger nonlinear algebraic system, and using the Levenberg-Marquardt algorithm to fit the models predictions to experimental data. The introduction of constraints in the model, related to the putative topology of the network, was explored. The results show that forcing the network connectivity to adhere to this topology did not lead to better results than the ones obtained using an unrestricted network topology. Overall, the modeling approach obtained partial success when trained on the nonmutant datasets, although further work is required if one wishes to obtain more accurate prediction of the time courses. PMID:21976379

  13. Repopulation Kinetics and the Linear-Quadratic Model

    NASA Astrophysics Data System (ADS)

    O'Rourke, S. F. C.; McAneney, H.; Starrett, C.; O'Sullivan, J. M.

    2009-08-01

    The standard Linear-Quadratic (LQ) survival model for radiotherapy is used to investigate different schedules of radiation treatment planning for advanced head and neck cancer. We explore how these treament protocols may be affected by different tumour repopulation kinetics between treatments. The laws for tumour cell repopulation include the logistic and Gompertz models and this extends the work of Wheldon et al. [1], which was concerned with the case of exponential repopulation between treatments. Treatment schedules investigated include standarized and accelerated fractionation. Calculations based on the present work show, that even with growth laws scaled to ensure that the repopulation kinetics for advanced head and neck cancer are comparable, considerable variation in the survival fraction to orders of magnitude emerged. Calculations show that application of the Gompertz model results in a significantly poorer prognosis for tumour eradication. Gaps in treatment also highlight the differences in the LQ model with the effect of repopulation kinetics included.

  14. Theoretical study of gas hydrate decomposition kinetics: model predictions.

    PubMed

    Windmeier, Christoph; Oellrich, Lothar R

    2013-11-27

    In order to provide an estimate of intrinsic gas hydrate dissolution and dissociation kinetics, the Consecutive Desorption and Melting Model (CDM) was developed in a previous publication (Windmeier, C.; Oellrich, L. R. J. Phys. Chem. A 2013, 117, 10151-10161). In this work, an extensive summary of required model data is given. Obtained model predictions are discussed with respect to their temperature dependence as well as their significance for technically relevant areas of gas hydrate decomposition. As a result, an expression for determination of the intrinsic gas hydrate decomposition kinetics for various hydrate formers is given together with an estimate for the maximum possible rates of gas hydrate decomposition. PMID:24199870

  15. Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization

    PubMed Central

    Misirli, Goksel; Cavaliere, Matteo; Waites, William; Pocock, Matthew; Madsen, Curtis; Gilfellon, Owen; Honorato-Zimmer, Ricardo; Zuliani, Paolo; Danos, Vincent; Wipat, Anil

    2016-01-01

    Motivation: Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the form of metadata. The availability of computationally tractable metadata is especially important for the effective automated interpretation and processing of models. Metadata are typically represented as machine-readable annotations which enhance programmatic access to information about models. Rule-based languages have emerged as a modelling framework to represent the complexity of biological systems. Annotation approaches have been widely used for reaction-based formalisms such as SBML. However, rule-based languages still lack a rich annotation framework to add semantic information, such as machine-readable descriptions, to the components of a model. Results: We present an annotation framework and guidelines for annotating rule-based models, encoded in the commonly used Kappa and BioNetGen languages. We adapt widely adopted annotation approaches to rule-based models. We initially propose a syntax to store machine-readable annotations and describe a mapping between rule-based modelling entities, such as agents and rules, and their annotations. We then describe an ontology to both annotate these models and capture the information contained therein, and demonstrate annotating these models using examples. Finally, we present a proof of concept tool for extracting annotations from a model that can be queried and analyzed in a uniform way. The uniform representation of the annotations can be used to facilitate the creation, analysis, reuse and visualization of rule-based models. Although examples are given, using specific implementations the proposed techniques can be applied to rule-based models in general. Availability and implementation: The annotation ontology for rule-based models can be found at http

  16. Model-based analysis of coupled equilibrium-kinetic processes: indirect kinetic studies of thermodynamic parameters using the dynamic data.

    PubMed

    Emami, Fereshteh; Maeder, Marcel; Abdollahi, Hamid

    2015-05-01

    Thermodynamic studies of equilibrium chemical reactions linked with kinetic procedures are mostly impossible by traditional approaches. In this work, the new concept of generalized kinetic study of thermodynamic parameters is introduced for dynamic data. The examples of equilibria intertwined with kinetic chemical mechanisms include molecular charge transfer complex formation reactions, pH-dependent degradation of chemical compounds and tautomerization kinetics in micellar solutions. Model-based global analysis with the possibility of calculating and embedding the equilibrium and kinetic parameters into the fitting algorithm has allowed the complete analysis of the complex reaction mechanisms. After the fitting process, the optimal equilibrium and kinetic parameters together with an estimate of their standard deviations have been obtained. This work opens up a promising new avenue for obtaining equilibrium constants through the kinetic data analysis for the kinetic reactions that involve equilibrium processes.

  17. Hard-sphere kinetic models for inert and reactive mixtures.

    PubMed

    Polewczak, Jacek

    2016-10-19

    I consider stochastic variants of a simple reacting sphere (SRS) kinetic model (Xystris and Dahler 1978 J. Chem. Phys. 68 387-401, Qin and Dahler 1995 J. Chem. Phys. 103 725-50, Dahler and Qin 2003 J. Chem. Phys. 118 8396-404) for dense reacting mixtures. In contrast to the line-of-center models of chemical reactive models, in the SRS kinetic model, the microscopic reversibility (detailed balance) can be easily shown to be satisfied, and thus all mathematical aspects of the model can be fully justified. In the SRS model, the molecules behave as if they were single mass points with two internal states. Collisions may alter the internal states of the molecules, and this occurs when the kinetic energy associated with the reactive motion exceeds the activation energy. Reactive and non-reactive collision events are considered to be hard sphere-like. I consider a four component mixture A, B, A (*), B (*), in which the chemical reactions are of the type [Formula: see text], with A (*) and B (*) being distinct species from A and B. This work extends the joined works with George Stell to the kinetic models of dense inert and reactive mixtures. The idea of introducing smearing-type effect in the collisional process results in a new class of stochastic kinetic models for both inert and reactive mixtures. In this paper the important new mathematical properties of such systems of kinetic equations are proven. The new results for stochastic revised Enskog system for inert mixtures are also provided. PMID:27545341

  18. Hard-sphere kinetic models for inert and reactive mixtures

    NASA Astrophysics Data System (ADS)

    Polewczak, Jacek

    2016-10-01

    I consider stochastic variants of a simple reacting sphere (SRS) kinetic model (Xystris and Dahler 1978 J. Chem. Phys. 68 387-401, Qin and Dahler 1995 J. Chem. Phys. 103 725-50, Dahler and Qin 2003 J. Chem. Phys. 118 8396-404) for dense reacting mixtures. In contrast to the line-of-center models of chemical reactive models, in the SRS kinetic model, the microscopic reversibility (detailed balance) can be easily shown to be satisfied, and thus all mathematical aspects of the model can be fully justified. In the SRS model, the molecules behave as if they were single mass points with two internal states. Collisions may alter the internal states of the molecules, and this occurs when the kinetic energy associated with the reactive motion exceeds the activation energy. Reactive and non-reactive collision events are considered to be hard sphere-like. I consider a four component mixture A, B, A *, B *, in which the chemical reactions are of the type A+B\\rightleftharpoons {{A}\\ast}+{{B}\\ast} , with A * and B * being distinct species from A and B. This work extends the joined works with George Stell to the kinetic models of dense inert and reactive mixtures. The idea of introducing smearing-type effect in the collisional process results in a new class of stochastic kinetic models for both inert and reactive mixtures. In this paper the important new mathematical properties of such systems of kinetic equations are proven. The new results for stochastic revised Enskog system for inert mixtures are also provided.

  19. Hard-sphere kinetic models for inert and reactive mixtures.

    PubMed

    Polewczak, Jacek

    2016-10-19

    I consider stochastic variants of a simple reacting sphere (SRS) kinetic model (Xystris and Dahler 1978 J. Chem. Phys. 68 387-401, Qin and Dahler 1995 J. Chem. Phys. 103 725-50, Dahler and Qin 2003 J. Chem. Phys. 118 8396-404) for dense reacting mixtures. In contrast to the line-of-center models of chemical reactive models, in the SRS kinetic model, the microscopic reversibility (detailed balance) can be easily shown to be satisfied, and thus all mathematical aspects of the model can be fully justified. In the SRS model, the molecules behave as if they were single mass points with two internal states. Collisions may alter the internal states of the molecules, and this occurs when the kinetic energy associated with the reactive motion exceeds the activation energy. Reactive and non-reactive collision events are considered to be hard sphere-like. I consider a four component mixture A, B, A (*), B (*), in which the chemical reactions are of the type [Formula: see text], with A (*) and B (*) being distinct species from A and B. This work extends the joined works with George Stell to the kinetic models of dense inert and reactive mixtures. The idea of introducing smearing-type effect in the collisional process results in a new class of stochastic kinetic models for both inert and reactive mixtures. In this paper the important new mathematical properties of such systems of kinetic equations are proven. The new results for stochastic revised Enskog system for inert mixtures are also provided.

  20. Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism.

    PubMed

    Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em

    2015-12-28

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model. PMID:26723613

  1. Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism

    NASA Astrophysics Data System (ADS)

    Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em

    2015-12-01

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.

  2. Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism

    SciTech Connect

    Li, Zhen; Bian, Xin; Karniadakis, George Em; Li, Xiantao

    2015-12-28

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.

  3. Model formalism of liquid /sup 3/He-B at equilibrium

    SciTech Connect

    Goldstein, L.; Goldstein, J.C.

    1980-04-01

    The approximate formal treatment of the nuclear spin system of normal liquid /sup 3/He given some time ago is extended to the ordered /sup 3/He phase. The formalism leads to the prediction of normal thermal behavior of /sup 3/He-B at lower pressures and at temperatures approaching its phase-boundary temperatures. In contrast to the disordered normal liquid phase, which is thermally anomalous, the entropy of the /sup 3/He-B decreases on isothermal compression, or its isobaric volume expansion coefficient is positive. The equilibrium thermal behavior of ordered /sup 3/He-B is thus qualitatively different from that of disordered liquid /sup 3/He. Experimental control of these aspects of the liquid /sup 3/He phase transformation is lacking at the present time. Both early and new /sup 3/He-B paramagnetic susceptibility data, extended recently over a wide reduced-temperature range, disclose a fundamental competition between the spontaneous ordering mechanism responsible for the existence of /sup 3/He-B and the specific ordering process imposed upon this phase on application of an external constant and uniform magnetic field. As a consequence, magnetized /sup 3/He-B will be shown to increase its entropy on isothermal magnetization and to cool on adiabatic magnetization. The magnetocaloric effect is, however, only moderate. The competition of the ordering process leads to the delay or possibly even to the suppression of the formation of the ordered phase, a state of affairs foreseen in our earlier work. At low or moderate magnetic field strengths, the zero-field phase-boundary temperatures are shown to shift toward lower temperatures while, simultaneously, the order of the phase change decreases, from second order, in the absence of the field, to first order. Although of model-theoretic character, involving limitations of various types, the rich physical content of /sup 3/He-B at equilibrium clearly emerges in the present work.

  4. Kinetic modelling of phenol co-oxidation using horseradish peroxidase.

    PubMed

    Carvalho, R H; Lemos, F; Lemos, M A N D A; Vojinović, V; Fonseca, L P; Cabral, J M S

    2006-07-01

    Phenol is an industrial pollutant and its removal from industrial wastewaters is of great importance. In order to design optimised phenol removal procedures by using horseradish peroxidase-based systems, there are some points that have to be dealt with. One of the most important issues is the need for reliable kinetics as this is one of the difficulties found during process scale-up. Although simplified kinetics can be used for limited ranges of operating conditions, they are not usually reliable for the description of varying process conditions. The present work describes the implementation of a kinetic model, based on a mechanism, for the co-oxidation of phenol and 4-aminoantipyrine (Am-NH2), which is used as a chromogen agent, with hydrogen peroxide as the oxidant. The model covers not only the variation of the concentrations of all the species involved, but also the effect of temperature in the reaction. The estimation of kinetic rate constants and activation energies for the various steps in the mechanism is performed with a single optimisation procedure, and all the experimental results are described using a unique set of parameters, which, thus, is valid over an extended range of operating conditions. The mechanism allowed the determination of a reliable kinetic model which is appropriate for the range of experimental conditions used. The computational model was also tested with an independent set of experiments with different conditions from the ones for which the parameters were estimated. PMID:16612606

  5. Computer-Aided Construction of Chemical Kinetic Models

    SciTech Connect

    Green, William H.

    2014-12-31

    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. Inhibition of nickel precipitation by gluconate. 2: Kinetic modeling

    SciTech Connect

    Hu, H.L.; Nikolaidis, N.P.; Grasso, D.

    1998-08-01

    Gluconate has been shown to inhibit nickel precipitation. This can result in adverse system performance when treating nickel plating wastewater. A kinetic model based on the formation of major species was developed to simulate nickel precipitation in the absence and presence of gluconate. The model was calibrated and verified against batch kinetic experimental results. The model simulated the studied nickel-gluconate systems well. However, no universal mechanisms could be adopted to explain all of the phenomena observed in the kinetic study, indicating different controlling mechanisms in each system. The results of this study can be used to evaluate optimum conditions for nickel precipitation and to aid in the design of treatment processes enhancing the optimization of nickel recovery from metal finishing wastewaters.

  7. Kinetic modelling for zinc (II) ions biosorption onto Luffa cylindrica

    SciTech Connect

    Oboh, I.; Aluyor, E.; Audu, T.

    2015-03-30

    The biosorption of Zinc (II) ions onto a biomaterial - Luffa cylindrica has been studied. This biomaterial was characterized by elemental analysis, surface area, pore size distribution, scanning electron microscopy, and the biomaterial before and after sorption, was characterized by Fourier Transform Infra Red (FTIR) spectrometer. The kinetic nonlinear models fitted were Pseudo-first order, Pseudo-second order and Intra-particle diffusion. A comparison of non-linear regression method in selecting the kinetic model was made. Four error functions, namely coefficient of determination (R{sup 2}), hybrid fractional error function (HYBRID), average relative error (ARE), and sum of the errors squared (ERRSQ), were used to predict the parameters of the kinetic models. The strength of this study is that a biomaterial with wide distribution particularly in the tropical world and which occurs as waste material could be put into effective utilization as a biosorbent to address a crucial environmental problem.

  8. A Detailed Chemical Kinetic Model for TNT

    SciTech Connect

    Pitz, W J; Westbrook, C K

    2005-01-13

    A detailed chemical kinetic mechanism for 2,4,6-tri-nitrotoluene (TNT) has been developed to explore problems of explosive performance and soot formation during the destruction of munitions. The TNT mechanism treats only gas-phase reactions. Reactions for the decomposition of TNT and for the consumption of intermediate products formed from TNT are assembled based on information from the literature and on current understanding of aromatic chemistry. Thermodynamic properties of intermediate and radical species are estimated by group additivity. Reaction paths are developed based on similar paths for aromatic hydrocarbons. Reaction-rate constant expressions are estimated from the literature and from analogous reactions where the rate constants are available. The detailed reaction mechanism for TNT is added to existing reaction mechanisms for RDX and for hydrocarbons. Computed results show the effect of oxygen concentration on the amount of soot precursors that are formed in the combustion of RDX and TNT mixtures in N{sub 2}/O{sub 2} mixtures.

  9. A Formal Framework for Modelling the Developmental Course of Competence and Performance in the Distance, Speed, and Time Domain

    ERIC Educational Resources Information Center

    Albert, Dietrich; Kickmeier-Rust, Michael D.; Matsuda, Fumiko

    2008-01-01

    The developmental course in the distance-speed-time domain is still a matter of debate. Traditional stage models are contested by theories of continuous development and adaptive thinking. In the present work, we introduce a formal framework for modelling the developmental course in this domain, grounding on Competence-based Knowledge Space Theory.…

  10. Kinetic model for dilute traffic flow

    NASA Astrophysics Data System (ADS)

    Balouchi, Ashkan; Browne, Dana A.

    The flow of traffic represents a many-particle non-equilibrium problem with important practical consequences. Traffic behavior has been studied using a variety of approaches, including fluid dynamics models, Boltzmann equation, and recently cellular automata (CA). The CA model for traffic flow that Nagel and Schreckenberg (NS) introduced can successfully mimic many of the known features of the traffic flow. We show that in the dilute limit of the NS model, where vehicles exhibit free flow, cars show significant nearest neighbor correlation primarily via a short-range repulsion. introduce an approximate analytic model to describe this dilute limit. We show that the distribution of the distance between consecutive vehicles obeys a drift-diffusion equation. We compared this model with direct simulations. The steady state solution and relaxation of this model agrees well with direct simulations. We explore how this model breaks down as the transition to jams occurs.

  11. Pyrolysis of Sawdust, Rice Husk and Sugarcane Bagasse: Kinetic Modeling and Estimation of Kinetic Parameters using Different Optimization Tools

    NASA Astrophysics Data System (ADS)

    Khonde, Ruta Dhanram; Chaurasia, Ashish Subhash

    2015-04-01

    The present study provides the kinetic model to describe the pyrolysis of sawdust, rice-husk and sugarcane bagasse as biomass. The kinetic scheme used for modelling of primary pyrolysis consisting of the two parallel reactions giving gaseous volatiles and solid char. Estimation of kinetic parameters for pyrolysis process has been carried out for temperature range of 773-1,173 K. As there are serious issues regarding non-convergence of some of the methods or solutions converging to local-optima, the proposed kinetic model is optimized to predict the best values of kinetic parameters for the system using three approaches—Two-dimensional surface fitting non-linear regression technique, MS-Excel Solver Tool and COMSOL software. The model predictions are in agreement with experimental data over a wide range of pyrolysis conditions. The estimated value of kinetic parameters are compared with earlier researchers and found to be matching well.

  12. Soluble kinetic model for spinodal decomposition

    SciTech Connect

    Scheucher, M.; Spohn, H.

    1988-10-01

    We compare the two-dimensional vote model with approximate theories for spinodal decomposition. The cluster size distribution and the short-time dynamics of the voter model are studied by means of a Monte Carlo simulation. The time-dependent structure factors and the long-time scaling of the voter dynamics are known analytically.

  13. Monosaccharide production in an acid sulfite process: kinetic modeling.

    PubMed

    Rueda, C; Fernández-Rodríguez, J; Ruiz, G; Llano, T; Coz, A

    2015-02-13

    Spent sulfite liquor is a lignocellulosic waste obtained after the sulfite pulping process. It is mainly formed by sugars and lignosulfonates which are isolated from the pulp during the cooking process. The current work investigates the kinetic modeling of the sulfite process from a biorefinery point of view since monosaccharides present in the spent liquor can be used as a raw material in further biorefinery processes to produce other value-added products. Kinetic parameters of carbohydrate degradation have been determined following sugar and inhibitors from wood to spent liquor, using laboratory scale reactors and different temperatures, 130, 140 and 150 °C. Three types of reaction schemes were developed. Kinetic parameters were obtained for each one using first and n order reactions, using Aspen Custom Modeler. Results show that the best temperature to be used in the process is 130 °C, giving the maximum sugar conversion, 33.91 mol% and obtaining 13.81 mol% of decomposition products.

  14. Towards a principled way of making kinetic models from data

    NASA Astrophysics Data System (ADS)

    Presse, Steve

    2012-02-01

    Kinetic model extraction from noisy data is the basic route to mechanistic insight in biology. I will show how the tools of Maximum Caliber (the dynamical analog of Maximum Entropy) can be used to infer -and not fit- models in a way which is driven by the structure and limitations of the data. For instance, the typical output of an experiment in systems biology is the stochastic expression of one reporter gene. Master equations used to model the regulatory process underlying the stochastic gene expression require knowledge of a circuit topology and rates. However rates and topology are often fit as these are rarely all independently determinable from the limited data. Our goal is to build a kinetic model from the data available with no adjustable parameter using the tools of Maximum Caliber. We apply our method to infer the statistics of rare stochastic switching events in the genetic toggle switch from fluctuations on shorter measurable timescales. In addition, we discuss how these tools can be used to infer kinetic models from real single molecule data drawn from anomalous folding kinetics of phosphoglycerate kinase and RNA hairpin zipping-unzipping time traces.

  15. An efficient chemical kinetics solver using high dimensional model representation

    SciTech Connect

    Shorter, J.A.; Ip, P.C.; Rabitz, H.A.

    1999-09-09

    A high dimensional model representation (HDMR) technique is introduced to capture the input-output behavior of chemical kinetic models. The HDMR expresses the output chemical species concentrations as a rapidly convergent hierarchical correlated function expansion in the input variables. In this paper, the input variables are taken as the species concentrations at time t{sub i} and the output is the concentrations at time t{sub i} + {delta}, where {delta} can be much larger than conventional integration time steps. A specially designed set of model runs is performed to determine the correlated functions making up the HDMR. The resultant HDMR can be used to (1) identify the key input variables acting independently or cooperatively on the output, and (2) create a high speed fully equivalent operational model (FEOM) serving to replace the original kinetic model and its differential equation solver. A demonstration of the HDMR technique is presented for stratospheric chemical kinetics. The FEOM proved to give accurate and stable chemical concentrations out to long times of many years. In addition, the FEOM was found to be orders of magnitude faster than a conventional stiff equation solver. This computational acceleration should have significance in many chemical kinetic applications.

  16. Kinetics of steel slag leaching: Batch tests and modeling

    SciTech Connect

    De Windt, Laurent; Chaurand, Perrine; Rose, Jerome

    2011-02-15

    Reusing steel slag as an aggregate for road construction requires to characterize the leaching kinetics and metal releases. In this study, basic oxygen furnace (BOF) steel slag were subjected to batch leaching tests at liquid to solid ratios (L/S) of 10 and 100 over 30 days; the leachate chemistry being regularly sampled in time. A geochemical model of the steel slag is developed and validated from experimental data, particularly the evolution with leaching of mineralogical composition of the slag and trace element speciation. Kinetics is necessary for modeling the primary phase leaching, whereas a simple thermodynamic equilibrium approach can be used for secondary phase precipitation. The proposed model simulates the kinetically-controlled dissolution (hydrolysis) of primary phases, the precipitation of secondary phases (C-S-H, hydroxide and spinel), the pH and redox conditions, and the progressive release of major elements as well as the metals Cr and V. Modeling indicates that the dilution effect of the L/S ratio is often coupled to solubility-controlled processes, which are sensitive to both the pH and the redox potential. A sensitivity analysis of kinetic uncertainties on the modeling of element releases is performed.

  17. Kinetics of steel slag leaching: Batch tests and modeling.

    PubMed

    De Windt, Laurent; Chaurand, Perrine; Rose, Jerome

    2011-02-01

    Reusing steel slag as an aggregate for road construction requires to characterize the leaching kinetics and metal releases. In this study, basic oxygen furnace (BOF) steel slag were subjected to batch leaching tests at liquid to solid ratios (L/S) of 10 and 100 over 30 days; the leachate chemistry being regularly sampled in time. A geochemical model of the steel slag is developed and validated from experimental data, particularly the evolution with leaching of mineralogical composition of the slag and trace element speciation. Kinetics is necessary for modeling the primary phase leaching, whereas a simple thermodynamic equilibrium approach can be used for secondary phase precipitation. The proposed model simulates the kinetically-controlled dissolution (hydrolysis) of primary phases, the precipitation of secondary phases (C-S-H, hydroxide and spinel), the pH and redox conditions, and the progressive release of major elements as well as the metals Cr and V. Modeling indicates that the dilution effect of the L/S ratio is often coupled to solubility-controlled processes, which are sensitive to both the pH and the redox potential. A sensitivity analysis of kinetic uncertainties on the modeling of element releases is performed.

  18. Kinetic theory and models of the global heliosphere

    NASA Astrophysics Data System (ADS)

    Izmodenov, Vladislav

    2016-07-01

    Current state of art in the kinetic-MHD modeling of the solar/stellar wind interaction with the local interstellar medium (LISM) will be reviewed. New model results will be presented as well as compared with currently available observations from both Voyagers and Interstellar Boundary Explorer (IBEX). Differences between model and observations will be discussed. Especial discussion will be on the recently suggested (by M. Opher and J. Drake) two-jet structure of the heliosphere.

  19. A formal hybrid modeling scheme for handling discontinuities in physical system models

    SciTech Connect

    Mosterman, P.J.; Biswas, G.

    1996-12-31

    Physical systems are by nature continuous, but often exhibit nonlinearities that make behavior generation complex and hard to analyze. Complexity is often reduced by linearizing model constraints and by abstracting the time scale for behavior generation. In either case, the physical components are modeled to operate in multiple modes, with abrupt changes between modes. This paper discusses a hybrid modeling methodology and analysis algorithms that combine continuous energy flow modeling and localized discrete signal flow modeling to generate complex, multi-mode behavior in a consistent and correct manner. Energy phase space analysis is employed to demonstrate the correctness of the algorithm, and the reachability of a continuous mode.

  20. Gyrofluid turbulence models with kinetic effects

    SciTech Connect

    Dorland, W.; Hammett, G.W.

    1992-12-01

    Nonlinear gyrofluid equations are derived by taking moments of the nonlinear, electrostatic gyrokinetic equation. The principal model presented includes evolution equations for the guiding center n, u[parallel], T[parallel], and T[perpendicular] along with an equation expressing the quasineutrality constraint. Additional evolution equations for higher moments are derived which may be used if greater accuracy is desired. The moment hierarchy is closed with a Landau-damping model which is equivalent to a multi-pole approximation to the plasma dispersion function, extended to include finite Larmor radius effects. In particular, new dissipative, nonlinear terms are found which model the perpendicular phase-mixing of the distribution function along contours of constant electrostatic potential. These FLR phase-mixing'' terms introduce a hyperviscosity-like damping [proportional to] k[sub [perpendicular

  1. Optimization of Time-Course Experiments for Kinetic Model Discrimination

    PubMed Central

    Lages, Nuno F.; Cordeiro, Carlos; Sousa Silva, Marta; Ponces Freire, Ana; Ferreira, António E. N.

    2012-01-01

    Systems biology relies heavily on the construction of quantitative models of biochemical networks. These models must have predictive power to help unveiling the underlying molecular mechanisms of cellular physiology, but it is also paramount that they are consistent with the data resulting from key experiments. Often, it is possible to find several models that describe the data equally well, but provide significantly different quantitative predictions regarding particular variables of the network. In those cases, one is faced with a problem of model discrimination, the procedure of rejecting inappropriate models from a set of candidates in order to elect one as the best model to use for prediction. In this work, a method is proposed to optimize the design of enzyme kinetic assays with the goal of selecting a model among a set of candidates. We focus on models with systems of ordinary differential equations as the underlying mathematical description. The method provides a design where an extension of the Kullback-Leibler distance, computed over the time courses predicted by the models, is maximized. Given the asymmetric nature this measure, a generalized differential evolution algorithm for multi-objective optimization problems was used. The kinetics of yeast glyoxalase I (EC 4.4.1.5) was chosen as a difficult test case to evaluate the method. Although a single-substrate kinetic model is usually considered, a two-substrate mechanism has also been proposed for this enzyme. We designed an experiment capable of discriminating between the two models by optimizing the initial substrate concentrations of glyoxalase I, in the presence of the subsequent pathway enzyme, glyoxalase II (EC 3.1.2.6). This discriminatory experiment was conducted in the laboratory and the results indicate a two-substrate mechanism for the kinetics of yeast glyoxalase I. PMID:22403703

  2. Crystal growth kinetics of the two-step model

    NASA Astrophysics Data System (ADS)

    Tai, Clifford Y.; Lin, Chiu-Hsiung

    1987-03-01

    The single crystal technique was used to measure the growth rate of the potassium alum (111) face and the magnesium sulfate (110) face. The two-step model was found appropriate to describe the growth kinetics with the surface integration order of two for potassium alum crystal and of one for magnesium sulfate crystal. The individual rate constants, Kd and Kr, were determined accordingly.

  3. Towards cleaner combustion engines through groundbreaking detailed chemical kinetic models

    PubMed Central

    Battin-Leclerc, Frédérique; Blurock, Edward; Bounaceur, Roda; Fournet, René; Glaude, Pierre-Alexandre; Herbinet, Olivier; Sirjean, Baptiste; Warth, V.

    2013-01-01

    In the context of limiting the environmental impact of transportation, this paper reviews new directions which are being followed in the development of more predictive and more accurate detailed chemical kinetic models for the combustion of fuels. In the first part, the performance of current models, especially in terms of the prediction of pollutant formation, is evaluated. In the next parts, recent methods and ways to improve these models are described. An emphasis is given on the development of detailed models based on elementary reactions, on the production of the related thermochemical and kinetic parameters, and on the experimental techniques available to produce the data necessary to evaluate model predictions under well defined conditions. PMID:21597604

  4. Formal Models of the Network Co-occurrence Underlying Mental Operations

    PubMed Central

    Bzdok, Danilo; Varoquaux, Gaël; Grisel, Olivier; Eickenberg, Michael; Poupon, Cyril; Thirion, Bertrand

    2016-01-01

    Systems neuroscience has identified a set of canonical large-scale networks in humans. These have predominantly been characterized by resting-state analyses of the task-unconstrained, mind-wandering brain. Their explicit relationship to defined task performance is largely unknown and remains challenging. The present work contributes a multivariate statistical learning approach that can extract the major brain networks and quantify their configuration during various psychological tasks. The method is validated in two extensive datasets (n = 500 and n = 81) by model-based generation of synthetic activity maps from recombination of shared network topographies. To study a use case, we formally revisited the poorly understood difference between neural activity underlying idling versus goal-directed behavior. We demonstrate that task-specific neural activity patterns can be explained by plausible combinations of resting-state networks. The possibility of decomposing a mental task into the relative contributions of major brain networks, the "network co-occurrence architecture" of a given task, opens an alternative access to the neural substrates of human cognition. PMID:27310288

  5. Second-order kinetic Kohn-Sham lattice model

    NASA Astrophysics Data System (ADS)

    Solórzano, S.; Mendoza, M.; Herrmann, H. J.

    2016-06-01

    In this work, we introduce a semi-implicit second-order correction scheme to the kinetic Kohn-Sham lattice model. This approach is validated by performing realistic exchange-correlation energy calculations of atoms and dimers of the first two rows of the Periodic Table, finding good agreement with the expected values. Additionally, we simulate the ethane molecule, where we recover the bond lengths and compare the results with standard methods. Finally, we discuss the current applicability of pseudopotentials within the lattice kinetic Kohn-Sham approach.

  6. Kinetic modeling based probabilistic segmentation for molecular images.

    PubMed

    Saad, Ahmed; Hamarneh, Ghassan; Möller, Torsten; Smith, Ben

    2008-01-01

    We propose a semi-supervised, kinetic modeling based segmentation technique for molecular imaging applications. It is an iterative, self-learning algorithm based on uncertainty principles, designed to alleviate low signal-to-noise ratio (SNR) and partial volume effect (PVE) problems. Synthetic fluorodeoxyglucose (FDG) and simulated Raclopride dynamic positron emission tomography (dPET) brain images with excessive noise levels are used to validate our algorithm. We show, qualitatively and quantitatively, that our algorithm outperforms state-of-the-art techniques in identifying different functional regions and recovering the kinetic parameters.

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

    PubMed

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

    2002-11-01

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

  8. Gyrofluid turbulence models with kinetic effects

    SciTech Connect

    Dorland, W.; Hammett, G.W.

    1992-12-01

    Nonlinear gyrofluid equations are derived by taking moments of the nonlinear, electrostatic gyrokinetic equation. The principal model presented includes evolution equations for the guiding center n, u{parallel}, T{parallel}, and T{perpendicular} along with an equation expressing the quasineutrality constraint. Additional evolution equations for higher moments are derived which may be used if greater accuracy is desired. The moment hierarchy is closed with a Landau-damping model which is equivalent to a multi-pole approximation to the plasma dispersion function, extended to include finite Larmor radius effects. In particular, new dissipative, nonlinear terms are found which model the perpendicular phase-mixing of the distribution function along contours of constant electrostatic potential. These ``FLR phase-mixing`` terms introduce a hyperviscosity-like damping {proportional_to} k{sub {perpendicular}}{sup 2}{vert_bar}{Phi}{sub {rvec k}}{rvec k} {times}{rvec k}{prime}{vert_bar} which should provide a physics-based damping mechanism at high k{perpendicular}{rho} which is potentially as important as the usual polarization drift nonlinearity. The moments are taken in guiding center space to pick up the correct nonlinear FLR terms and the gyroaveraging of the shear. The equations are solved with a nonlinear, three dimensional initial value code. Linear results are presented, showing excellent agreement with linear gyrokinetic theory.

  9. Practical Formal Verification of Diagnosability of Large Models via Symbolic Model Checking

    NASA Technical Reports Server (NTRS)

    Cavada, Roberto; Pecheur, Charles

    2003-01-01

    This document reports on the activities carried out during a four-week visit of Roberto Cavada at the NASA Ames Research Center. The main goal was to test the practical applicability of the framework proposed, where a diagnosability problem is reduced to a Symbolic Model Checking problem. Section 2 contains a brief explanation of major techniques currently used in Symbolic Model Checking, and how these techniques can be tuned in order to obtain good performances when using Model Checking tools. Diagnosability is performed on large and structured models of real plants. Section 3 describes how these plants are modeled, and how models can be simplified to improve the performance of Symbolic Model Checkers. Section 4 reports scalability results. Three test cases are briefly presented, and several parameters and techniques have been applied on those test cases in order to produce comparison tables. Furthermore, comparison between several Model Checkers is reported. Section 5 summarizes the application of diagnosability verification to a real application. Several properties have been tested, and results have been highlighted. Finally, section 6 draws some conclusions, and outlines future lines of research.

  10. Modeling the Kinetics of Open Self-Assembly.

    PubMed

    Verdier, Timothée; Foret, Lionel; Castelnovo, Martin

    2016-07-01

    In this work, we explore theoretically the kinetics of molecular self-assembly in the presence of constant monomer flux as an input, and a maximal size. The proposed model is supposed to reproduce the dynamics of viral self-assembly for enveloped virus. It turns out that the kinetics of open self-assembly is rather quantitatively different from the kinetics of similar closed assembly. In particular, our results show that the convergence toward the stationary state is reached through assembly waves. Interestingly, we show that the production of complete clusters is much more efficient in the presence of a constant input flux, rather than providing all monomers at the beginning of the self-assembly.

  11. Non isothermal model free kinetics for pyrolysis of rice straw.

    PubMed

    Mishra, Garima; Bhaskar, Thallada

    2014-10-01

    The kinetics of thermal decomposition of rice straw was studied by thermogravimetry. Non-isothermal thermogravimetric data of rice straw decomposition in nitrogen atmosphere at six different heating rates of 5-40 °C/min was used for evaluating kinetics using several model free kinetic methods. The results showed that the decomposition process exhibited two zones of constant apparent activation energies. The values ranged from 142 to 170 kJ/mol (E(avg) = 155.787 kJ/mol), and 170 to 270 kJ/mol (E(avg) = 236.743 kJ/mol) in the conversion range of 5-60% and 61-90% respectively. These values were used to determine the reaction mechanism of process using master plots and compensation parameters. The results show that the reaction mechanism of whole process can be kinetically characterized by two successive reactions, a diffusion reaction followed by a third order rate equation. The kinetic results were validated using isothermal predictions. The results derived are useful for development and optimization of biomass thermochemical conversion systems. PMID:25105267

  12. A Social Partnership Model to Promote Educators' Development in Mauritius through Formal and Informal Capacity-Building Initiatives

    ERIC Educational Resources Information Center

    Santally, Mohammad Issack; Cooshna-Naik, Dorothy; Conruyt, Noel; Wing, Caroline Koa

    2015-01-01

    This paper describes a social partnership model based on the living lab concept to promote the professional development of educators through formal and informal capacity-building initiatives. The aim is to have a broader impact on society through community outreach educational initiatives. A Living Lab is an environment for user-centered…

  13. A spatially resolved surface kinetic model for forsterite dissolution

    NASA Astrophysics Data System (ADS)

    Maher, Kate; Johnson, Natalie C.; Jackson, Ariel; Lammers, Laura N.; Torchinsky, Abe B.; Weaver, Karrie L.; Bird, Dennis K.; Brown, Gordon E.

    2016-02-01

    The development of complex alteration layers on silicate mineral surfaces undergoing dissolution is a widely observed phenomenon. Given the complexity of these layers, most kinetic models used to predict rates of mineral-fluid interactions do not explicitly consider their formation. As a result, the relationship between the development of the altered layers and the final dissolution rate is poorly understood. To improve our understanding of the relationship between the alteration layer and the dissolution rate, we developed a spatially resolved surface kinetic model for olivine dissolution and applied it to a series of closed-system experiments consisting of three-phases (water (±NaCl), olivine, and supercritical CO2) at conditions relevant to in situ mineral carbonation (i.e. 60 °C, 100 bar CO2). We also measured the corresponding δ26/24Mg of the dissolved Mg during early stages of dissolution. Analysis of the solid reaction products indicates the formation of Mg-depleted layers on the olivine surface as quickly as 2 days after the experiment was started and before the bulk solution reached saturation with respect to amorphous silica. The δ26/24Mg of the dissolved Mg decreased by approximately 0.4‰ in the first stages of the experiment and then approached the value of the initial olivine (-0.35‰) as the steady-state dissolution rate was approached. We attribute the preferential release of 24Mg to a kinetic effect associated with the formation of a Mg-depleted layer that develops as protons exchange for Mg2+. We used experimental data to calibrate a surface kinetic model for olivine dissolution that includes crystalline olivine, a distinct "active layer" from which Mg can be preferentially removed, and secondary amorphous silica precipitation. By coupling the spatial arrangement of ions with the kinetics, this model is able to reproduce both the early and steady-state long-term dissolution rates, and the kinetic isotope fractionation. In the early stages of

  14. Vlasiator: Global Kinetic Magnetospheric Modeling Tool

    NASA Astrophysics Data System (ADS)

    Sandroos, A.; von Alfthan, S.; Hoilijoki, S.; Honkonen, I.; Kempf, Y.; Pokhotelov, D.; Palmroth, M.

    2015-10-01

    We present Vlasiator, a novel code based on Vlasov's equation, developed for modeling magnetospheric plasma on a global scale. We have parallelized the code to petascale supercomputers with a hybrid OpenMP-MPI approach to answer the high computational cost of propagating ion distribution functions in six dimensions. The accuracy of the numerical method is demonstrated by comparing simulated wave dispersion plots to analytical results. Simulations of Earth's bow shock region were able to reproduce many well-known plasma phenomena, such as compressional magnetosonic waves in the foreshock region, and mirror mode instability in the magnetosheath.

  15. Chemistry Resolved Kinetic Flow Modeling of TATB Based Explosives

    SciTech Connect

    Vitello, P A; Fried, L E; Howard, W M; Levesque, G; Souers, P C

    2011-07-21

    Detonation waves in insensitive, TATB based explosives are believed to have multi-time scale regimes. The initial burn rate of such explosives has a sub-microsecond time scale. However, significant late-time slow release in energy is believed to occur due to diffusion limited growth of carbon. In the intermediate time scale concentrations of product species likely change from being in equilibrium to being kinetic rate controlled. They use the thermo-chemical code CHEETAH linked to an ALE hydrodynamics code to model detonations. They term their model chemistry resolved kinetic flow as CHEETAH tracks the time dependent concentrations of individual species in the detonation wave and calculates EOS values based on the concentrations. A HE-validation suite of model simulations compared to experiments at ambient, hot, and cold temperatures has been developed. They present here a new rate model and comparison with experimental data.

  16. Chemical Kinetic Modeling of Combustion of Automotive Fuels

    SciTech Connect

    Pitz, W J; Westbrook, C K; Silke, E J

    2006-11-10

    The objectives of this report are to: (1) Develop detailed chemical kinetic reaction models for components of fuels, including olefins and cycloalkanes used in diesel, spark-ignition and HCCI engines; (2) Develop surrogate mixtures of hydrocarbon components to represent real fuels and lead to efficient reduced combustion models; and (3) Characterize the role of fuel composition on production of emissions from practical automotive engines.

  17. Kinetic modelling of molecular hydrogen transport in microporous carbon materials.

    SciTech Connect

    Hankel, M.; Zhang, H.; Nguyen, T. X.; Bhatia, S. K.; Gray, S. K.; Smith, S. C.

    2011-01-01

    The proposal of kinetic molecular sieving of hydrogen isotopes is explored by employing statistical rate theory methods to describe the kinetics of molecular hydrogen transport in model microporous carbon structures. A Lennard-Jones atom-atom interaction potential is utilized for the description of the interactions between H{sub 2}/D{sub 2} and the carbon framework, while the requisite partition functions describing the thermal flux of molecules through the transition state are calculated quantum mechanically in view of the low temperatures involved in the proposed kinetic molecular sieving application. Predicted kinetic isotope effects for initial passage from the gas phase into the first pore mouth are consistent with expectations from previous modeling studies, namely, that at sufficiently low temperatures and for sufficiently narrow pore mouths D{sub 2} transport is dramatically favored over H{sub 2}. However, in contrast to expectations from previous modeling, the absence of any potential barrier along the minimum energy pathway from the gas phase into the first pore mouth yields a negative temperature dependence in the predicted absolute rate coefficients - implying a negative activation energy. In pursuit of the effective activation barrier, we find that the minimum potential in the cavity is significantly higher than in the pore mouth for nanotube-shaped models, throwing into question the common assumption that passage through the pore mouths should be the rate-determining step. Our results suggest a new mechanism that, depending on the size and shape of the cavity, the thermal activation barrier may lie in the cavity rather than at the pore mouth. As a consequence, design strategies for achieving quantum-mediated kinetic molecular sieving of H{sub 2}/D{sub 2} in a microporous membrane will need, at the very least, to take careful account of cavity shape and size in addition to pore-mouth size in order to ensure that the selective step, namely passage

  18. Comparisons of kinetic ablation models for the capillary discharge

    SciTech Connect

    Li Rui; Li Xingwen; Jia Shenli; Murphy, Anthony B.

    2010-07-15

    The properties of kinetic ablation models are considered in this paper. The widely used kinetic ablation model (model-K) only considers monatomic vapor. A revised model (model-Z) was introduced by taking into account the polyatomic vapor's internal degrees of freedom, as well as the temperature dependence of the average particle mass. In this work, both temperature and pressure dependence of average particle mass and the specific heat ratio {gamma} are taken into account, producing an improved version of model-Z (denoted model-Z{sup *}). Ablation data calculated by model-K and model-Z* for two typical capillary materials are presented. Compared to model-K, model-Z* predicts an increased ablation rate at lower plasma temperature and higher plasma density, and a decreased rate for the opposite conditions. Finally, based on the plasma parameters in a typical discharge cycle, all three models are used to calculate the time-dependent ablation rate and the integrated ablated mass. It is found that the main difference between their results arises because of the different average particle masses near the wall surface, and model-Z* is the most accurate for the discharge cycle considered. Further, it is found that the ablation parameters are highly sensitive to the pressure, in particular, through the pressure dependence of average particle mass.

  19. Kinetic Model Development for Lignin Pyrolysis

    SciTech Connect

    Clark, J.; Robichaud, D.; Nimlos, M.

    2012-01-01

    Lignin pyrolysis poses a significant barrier to the formation of liquid fuel products from biomass. Lignin pyrolyzes at higher temperatures than other biomass components (e.g. cellulose and hemi-cellulose) and tends to form radicals species that lead to cross-linking and ultimately char formation. A first step in the advancement of biomass-to-fuel technology is to discover the underlying mechanisms that lead to the breakdown of lignin at lower temperatures into more stable and usable products. We have investigated the thermochemistry of the various inter-linkage units found in lignin (B-O4, a-O4, B-B, B-O5, etc) using electronic structure calculations at the M06-2x/6-311++G(d,p) on a series of dimer model compounds. In addition to bond homolysis reactions, a variety of concerted elimination pathways are under investigation that tend to produce closed-shell stable products. Such a bottom-up approach could aid in the targeted development of catalysts that produce more desirable products under less severe reactor conditions.

  20. Nonlinear kinetic modeling of stimulated Raman scattering

    NASA Astrophysics Data System (ADS)

    Benisti, Didier

    2011-10-01

    Despite its importance for many applications, such as or Raman amplification or inertial confinement fusion, deriving a nonlinear estimate of Raman reflectivity in a plasma has remained quite a challenge for decades. This is mainly due to the nonlinear modification of the electron distribution function induced by the plasma wave (EPW), which, in turn, modifies the propagation of this wave. In this paper is derived an envelope equation for the EPW valid in 3D and which accounts for the nonlinear change of its collisionless (Landau-like) damping rate, group velocity, coupling to the electromagnetic drive, frequency and wave number. Our theoretical predictions for each of these terms are carefully compared against results from Vlasov simulations of stimulated Raman scattering (SRS), as well as with other theories. Moreover, our envelope model shows to be as accurate as a Vlasov code in predicting Raman threshold in 1D. Making comparisons with experimental results nevertheless requires including transverse dimensions and letting Raman start from noise. To this end, we performed a completely new derivation of the electrostatic fluctuations in a plasma, which accounts nonlinear effects. Moreover, based on our Multi-D simulations of Raman scattering with our envelope code BRAMA, we discuss the effect on SRS of wave front bowing, transverse detrapping and of a completely new defocussing effect due to the local change in the direction of the EPW group velocity induced by the nonlinear decrease of Landau damping.

  1. Elementary solutions of coupled model equations in the kinetic theory of gases

    NASA Technical Reports Server (NTRS)

    Kriese, J. T.; Siewert, C. E.; Chang, T. S.

    1974-01-01

    The method of elementary solutions is employed to solve two coupled integrodifferential equations sufficient for determining temperature-density effects in a linearized BGK model in the kinetic theory of gases. Full-range completeness and orthogonality theorems are proved for the developed normal modes and the infinite-medium Green's function is constructed as an illustration of the full-range formalism. The appropriate homogeneous matrix Riemann problem is discussed, and half-range completeness and orthogonality theorems are proved for a certain subset of the normal modes. The required existence and uniqueness theorems relevant to the H matrix, basic to the half-range analysis, are proved, and an accurate and efficient computational method is discussed. The half-space temperature-slip problem is solved analytically, and a highly accurate value of the temperature-slip coefficient is reported.

  2. Kinetic models of CO oxidation on gold nanoparticles

    NASA Astrophysics Data System (ADS)

    Zhdanov, Vladimir P.

    2014-12-01

    Despite 27 years of experimental and theoretical studies, the mechanism and kinetics of CO oxidation on gold nanoparticles are still open for debate. One of the key features of this reaction is that the reaction turnover frequency rapidly drops with an increasing particle size presumably due to a crucial role of a small number of sites located at the perimeter of nanoparticles. This factor limits the applicability of the conventional mean-field kinetic models implying that the reaction steps occur in a Langmuir overlayer. To clarify this aspect, the conventional kinetics are herein compared with those calculated in the opposite limit implying the reaction to occur on kinetically independent pairs of sites. The results predicted by the models of these two categories are found to differ if the reaction itself is rapid compared to other steps. In the practically interesting case when the reaction is slow, the results are similar. The analysis of different reaction schemes indicates that for the low-temperature reaction regime the apparent reaction orders can be explained assuming cooperative CO and O2 adsorption at different sites. In addition, the scale of the apparent pre-exponential factor for this reaction has been rationalized on the basis of the conventional transition-state theory.

  3. Kinetic model of the Buyers’ market

    NASA Astrophysics Data System (ADS)

    Zhykharsky, Alexander V.

    2013-09-01

    In this work the following results are received. The closed mathematical apparatus describing the process of interaction of the Buyers’ market with retail Shop is created. The “statistical analogy” between the vacuum electrostatic diode and the Buyers’ market co-operating with retail Shop is considered. On the basis of the spent analysis the closed mathematical apparatus describing process of interaction of the Buyers’ market with retail Shop is created. The analytical expressions connecting a stream of Buyers, come to Shop, and a stream of the gain of Shop, with parameters of the Buyers’ market are received. For check of adequacy of the received model it is solved of some real “market” problems. On the basis of the spent researches principles of construction of Information-analytical Systems of new type which provide direct measurements of parameters of the Buyers’ market are developed. Actually these Systems are devices for measurement of parameters of this market. In this work it is shown that by means of the device developed for measurement of parameters of the Buyers’ market, creation of a new science-“demandodynamics” the Buyers’ market, is possible. Here the term “demandodynamics the Buyers’ market” is accepted by analogy to the term “thermodynamics” in physics. (In this work it is shown that for the Buyers’ market concept “demand” is similar to concept “temperature” in physics.) The construction methodology “demandodynamics” the Buyers’ market is defined and is shown that within the limits of this science working out of a technique of a direct control by a condition of the Buyers’ market is possible.

  4. Kinetic investigation and mathematical modeling of methanogenesis of glucose

    SciTech Connect

    Kalyuzhnyy, S.V.; Sklyar, V.I.; Varfolomeyev, S.D.; Gachok, V.P.

    1991-12-31

    The kinetic regularities of anaerobic conversion of glucose, and intermediates of its decomposition (ethanol, butyrate, and acetate) by a microbial methanogenic association from anaerobic digester were investigated. Kinetic scheme for conversion of glucose is suggested, and the mathematical model based on the scheme is evolved. The model includes growth and metabolism of three kinds of microorganisms-acid producents, and acetate- and hydrogen-utilizing methane producents; of cell lysis with consequent fermentation of {open_quotes}died biomass{close_quotes} to acetate, hydrogen, and carbon dioxide; of induction and repression of the enzyme responsible for decomposition of butyrate, and for a number of regulations depending on the concentrations of intermediates in glucose metabolism. The values of parameters of the model have been calculated, sufficiently describing the experimental regularities. The numerical experiments have enabled us to reveal and describe the principal regulating factors of glucose methanogenesis.

  5. Kinetic modeling of Nernst effect in magnetized hohlraums.

    PubMed

    Joglekar, A S; Ridgers, C P; Kingham, R J; Thomas, A G R

    2016-04-01

    We present nanosecond time-scale Vlasov-Fokker-Planck-Maxwell modeling of magnetized plasma transport and dynamics in a hohlraum with an applied external magnetic field, under conditions similar to recent experiments. Self-consistent modeling of the kinetic electron momentum equation allows for a complete treatment of the heat flow equation and Ohm's law, including Nernst advection of magnetic fields. In addition to showing the prevalence of nonlocal behavior, we demonstrate that effects such as anomalous heat flow are induced by inverse bremsstrahlung heating. We show magnetic field amplification up to a factor of 3 from Nernst compression into the hohlraum wall. The magnetic field is also expelled towards the hohlraum axis due to Nernst advection faster than frozen-in flux would suggest. Nonlocality contributes to the heat flow towards the hohlraum axis and results in an augmented Nernst advection mechanism that is included self-consistently through kinetic modeling.

  6. Kinetic modeling of Nernst effect in magnetized hohlraums.

    PubMed

    Joglekar, A S; Ridgers, C P; Kingham, R J; Thomas, A G R

    2016-04-01

    We present nanosecond time-scale Vlasov-Fokker-Planck-Maxwell modeling of magnetized plasma transport and dynamics in a hohlraum with an applied external magnetic field, under conditions similar to recent experiments. Self-consistent modeling of the kinetic electron momentum equation allows for a complete treatment of the heat flow equation and Ohm's law, including Nernst advection of magnetic fields. In addition to showing the prevalence of nonlocal behavior, we demonstrate that effects such as anomalous heat flow are induced by inverse bremsstrahlung heating. We show magnetic field amplification up to a factor of 3 from Nernst compression into the hohlraum wall. The magnetic field is also expelled towards the hohlraum axis due to Nernst advection faster than frozen-in flux would suggest. Nonlocality contributes to the heat flow towards the hohlraum axis and results in an augmented Nernst advection mechanism that is included self-consistently through kinetic modeling. PMID:27176417

  7. Kinetic models for historical processes of fast invasion and aggression

    NASA Astrophysics Data System (ADS)

    Aristov, Vladimir V.; Ilyin, Oleg V.

    2015-04-01

    In the last few decades many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological, and historical processes. In the present paper we suggest a model of the Nazi Germany invasion of Poland, France, and the USSR based on kinetic theory. We simulate this process with the Cauchy boundary problem for two-element kinetic equations. The solution of the problem is given in the form of a traveling wave. The propagation velocity of a front line depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solution of the model can be expressed in terms of quadratures and elementary functions. Finally it is shown that the front-line velocities agree with the historical data.

  8. Kinetic model of DNA replication in eukaryotic organisms

    NASA Astrophysics Data System (ADS)

    Bechhoefer, John; Herrick, John; Bensimon, Aaron

    2001-03-01

    We introduce an analogy between DNA replication in eukaryotic organisms and crystal growth in one dimension. Drawing on models of crystallization kinetics developed in the 1930s to describe the freezing of metals, we formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. It allows one, for the first time, to determine the parameters governing the DNA replication program in a eukaryote on a genome-wide basis. In particular, we have determined the frequency of origin activation in time and space during the cell cycle. Although we focus on a specific stage of development, this model can easily be adapted to describe replication in many other organisms, including budding yeast.

  9. Kinetic modeling of Nernst effect in magnetized hohlraums

    NASA Astrophysics Data System (ADS)

    Joglekar, A. S.; Ridgers, C. P.; Kingham, R. J.; Thomas, A. G. R.

    2016-04-01

    We present nanosecond time-scale Vlasov-Fokker-Planck-Maxwell modeling of magnetized plasma transport and dynamics in a hohlraum with an applied external magnetic field, under conditions similar to recent experiments. Self-consistent modeling of the kinetic electron momentum equation allows for a complete treatment of the heat flow equation and Ohm's law, including Nernst advection of magnetic fields. In addition to showing the prevalence of nonlocal behavior, we demonstrate that effects such as anomalous heat flow are induced by inverse bremsstrahlung heating. We show magnetic field amplification up to a factor of 3 from Nernst compression into the hohlraum wall. The magnetic field is also expelled towards the hohlraum axis due to Nernst advection faster than frozen-in flux would suggest. Nonlocality contributes to the heat flow towards the hohlraum axis and results in an augmented Nernst advection mechanism that is included self-consistently through kinetic modeling.

  10. Chemistry resolved kinetic flow modeling of TATB based explosives

    NASA Astrophysics Data System (ADS)

    Vitello, Peter; Fried, Laurence E.; William, Howard; Levesque, George; Souers, P. Clark

    2012-03-01

    Detonation waves in insensitive, TATB-based explosives are believed to have multiple time scale regimes. The initial burn rate of such explosives has a sub-microsecond time scale. However, significant late-time slow release in energy is believed to occur due to diffusion limited growth of carbon. In the intermediate time scale concentrations of product species likely change from being in equilibrium to being kinetic rate controlled. We use the thermo-chemical code CHEETAH linked to an ALE hydrodynamics code to model detonations. We term our model chemistry resolved kinetic flow, since CHEETAH tracks the time dependent concentrations of individual species in the detonation wave and calculates EOS values based on the concentrations. We present here two variants of our new rate model and comparison with hot, ambient, and cold experimental data for PBX 9502.

  11. Reproducing Phenomenology of Peroxidation Kinetics via Model Optimization

    NASA Astrophysics Data System (ADS)

    Ruslanov, Anatole D.; Bashylau, Anton V.

    2010-06-01

    We studied mathematical modeling of lipid peroxidation using a biochemical model system of iron (II)-ascorbate-dependent lipid peroxidation of rat hepatocyte mitochondrial fractions. We found that antioxidants extracted from plants demonstrate a high intensity of peroxidation inhibition. We simplified the system of differential equations that describes the kinetics of the mathematical model to a first order equation, which can be solved analytically. Moreover, we endeavor to algorithmically and heuristically recreate the processes and construct an environment that closely resembles the corresponding natural system. Our results demonstrate that it is possible to theoretically predict both the kinetics of oxidation and the intensity of inhibition without resorting to analytical and biochemical research, which is important for cost-effective discovery and development of medical agents with antioxidant action from the medicinal plants.

  12. Calculating and Understanding: Formal Models and Causal Explanations in Science, Common Reasoning and Physics Teaching

    NASA Astrophysics Data System (ADS)

    Besson, Ugo

    2010-03-01

    This paper presents an analysis of the different types of reasoning and physical explanation used in science, common thought, and physics teaching. It then reflects on the learning difficulties connected with these various approaches, and suggests some possible didactic strategies. Although causal reasoning occurs very frequently in common thought and daily life, it has long been the subject of debate and criticism among philosophers and scientists. In this paper, I begin by providing a description of some general tendencies of common reasoning that have been identified by didactic research. Thereafter, I briefly discuss the role of causality in science, as well as some different types of explanation employed in the field of physics. I then present some results of a study examining the causal reasoning used by students in solid and fluid mechanics. The differences found between the types of reasoning typical of common thought and those usually proposed during instruction can create learning difficulties and impede student motivation. Many students do not seem satisfied by the mere application of formal laws and functional relations. Instead, they express the need for a causal explanation, a mechanism that allows them to understand how a state of affairs has come about. I discuss few didactic strategies aimed at overcoming these problems, and describe, in general terms, two examples of mechanics teaching sequences which were developed and tested in different contexts. The paper ends with a reflection on the possible role to be played in physics learning by intuitive and imaginative thought, and the use of simple explanatory models based on physical analogies and causal mechanisms.

  13. Kinetic Modeling of Oxidative Coagulation for Arsenic Removal

    SciTech Connect

    Kim, Jin-Wook; Kramer, Timothy A.

    2004-03-31

    A model of oxidative coagulation consisting of Fenton's reagent (Fe(II)/H2O2 at pH 7.0) was established. The optimum condition was found when the mole ratio of As(III):H2O2:Fe(II)=1:15:20. In this optimum condition, all of Fe(II) was converted to HFO (am-Fe(OH)3) and precipitated to be used as the oxidized arsenic(V) adsorbent and particle coagulant. Two sorption models consisting of a surface complexation model and a kinetic model were developed and coupled. Using the coupled sorption model, the kinetics of HFO surface charge/potential during As(V) sorption was calculated. Further, during arsenic sorption, the colloid stability kinetics resulting from the perikinetic coagulation mechanism was calculated by considering interparticle forces. Colloid surface potential was decreased from 60 mv to 12 mv in proportion to the amount of arsenic adsorbed onto HFO and this surface potential directly affected the colloid stability (collision efficiency).

  14. Kinetic modelling of laccase mediated delignification of Lantana camara.

    PubMed

    Gujjala, Lohit K S; Bandyopadhyay, Tapas K; Banerjee, Rintu

    2016-07-01

    Enzymatic delignification is seen as a green step in biofuels production owing to its specificity towards lignin and its proper understanding requires a kinetic study to decipher intricate details of the process such as thermodynamic parameters viz., activation energy, entropy change and enthalpy change. A system of two coupled kinetic models has been constructed to model laccase mediated delignification of Lantana camara. From the simulated output, activation energy was predicted to be 45.56 and 56.06 kJ/mol, entropy change was observed to be 1.08 × 10(2) and 1.05 × 10(2)cal/mol-K and enthalpy change was determined to be 3.33 × 10(4) and 3.20 × 10(4)cal/mol, respectively from Tessier's and Michaelis Menten model. While comparing the prediction efficiency, it was noticed that Tessier's model gave better performance. Sensitivity analysis was also conducted and it was observed that the model was most sensitive towards temperature dependent kinetic constants. PMID:27082268

  15. Comparisons of hydrodynamic beam models with kinetic treatments

    NASA Astrophysics Data System (ADS)

    Boyd, J. K.; Mark, J. W.; Sharp, W. M.; Yu, S. S.

    1983-10-01

    Hydrodynamic models were derived to describe energetic self-pinched beams, such as those used in ion-beam fusion. The closure of the Mark-Yu model is obtained with adiabatic assumptions mathematically analogous to those of Chew, Goldberger, and Low for MHD. The other models treated here use an ideal gas closure and a closure by Newcomb based on an expansion in V/sub th//V/sub z/. Features of these hydrodynamic beam models are compared with a kinetic treatment.

  16. Progress in Chemical Kinetic Modeling for Surrogate Fuels

    SciTech Connect

    Pitz, W J; Westbrook, C K; Herbinet, O; Silke, E J

    2008-06-06

    Gasoline, diesel, and other alternative transportation fuels contain hundreds to thousands of compounds. It is currently not possible to represent all these compounds in detailed chemical kinetic models. Instead, these fuels are represented by surrogate fuel models which contain a limited number of representative compounds. We have been extending the list of compounds for detailed chemical models that are available for use in fuel surrogate models. Detailed models for components with larger and more complicated fuel molecular structures are now available. These advancements are allowing a more accurate representation of practical and alternative fuels. We have developed detailed chemical kinetic models for fuels with higher molecular weight fuel molecules such as n-hexadecane (C16). Also, we can consider more complicated fuel molecular structures like cyclic alkanes and aromatics that are found in practical fuels. For alternative fuels, the capability to model large biodiesel fuels that have ester structures is becoming available. These newly addressed cyclic and ester structures in fuels profoundly affect the reaction rate of the fuel predicted by the model. Finally, these surrogate fuel models contain large numbers of species and reactions and must be reduced for use in multi-dimensional models for spark-ignition, HCCI and diesel engines.

  17. Kinetic models of gene expression including non-coding RNAs

    NASA Astrophysics Data System (ADS)

    Zhdanov, Vladimir P.

    2011-03-01

    In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to the feedbacks between these processes, the kinetics of gene expression may be complex even in the simplest genetic networks. The corresponding models have already been reviewed in the literature. A new avenue in this field is related to the recognition that the conventional scenario of gene expression is fully applicable only to prokaryotes whose genomes consist of tightly packed protein-coding sequences. In eukaryotic cells, in contrast, such sequences are relatively rare, and the rest of the genome includes numerous transcript units representing non-coding RNAs (ncRNAs). During the past decade, it has become clear that such RNAs play a crucial role in gene expression and accordingly influence a multitude of cellular processes both in the normal state and during diseases. The numerous biological functions of ncRNAs are based primarily on their abilities to silence genes via pairing with a target mRNA and subsequently preventing its translation or facilitating degradation of the mRNA-ncRNA complex. Many other abilities of ncRNAs have been discovered as well. Our review is focused on the available kinetic models describing the mRNA, ncRNA and protein interplay. In particular, we systematically present the simplest models without kinetic feedbacks, models containing feedbacks and predicting bistability and oscillations in simple genetic networks, and models describing the effect of ncRNAs on complex genetic networks. Mathematically, the presentation is based primarily on temporal mean-field kinetic equations. The stochastic and spatio-temporal effects are also briefly discussed.

  18. Development of Detailed Kinetic Models for Fischer-Tropsch Fuels

    SciTech Connect

    Westbrook, C K; Pitz, W J; Carstensen, H; Dean, A M

    2008-10-28

    Fischer-Tropsch (FT) fuels can be synthesized from a syngas stream generated by the gasification of biomass. As such they have the potential to be a renewable hydrocarbon fuel with many desirable properties. However, both the chemical and physical properties are somewhat different from the petroleum-based hydrocarbons that they might replace, and it is important to account for such differences when considering using them as replacements for conventional fuels in devices such as diesel engines and gas turbines. FT fuels generally contain iso-alkanes with one or two substituted methyl groups to meet the pour-point specifications. Although models have been developed for smaller branched alkanes such as isooctane, additional efforts are required to properly capture the kinetics of the larger branched alkanes. Recently, Westbrook et al. developed a chemical kinetic model that can be used to represent the entire series of n-alkanes from C{sub 1} to C{sub 16} (Figure 1). In the current work, the model is extended to treat 2,2,4,4,6,8,8-heptamethylnonane (HMN), a large iso-alkane. The same reaction rate rules used in the iso-octane mechanism were incorporated in the HMN mechanism. Both high and low temperature chemistry was included so that the chemical kinetic model would be applicable to advanced internal combustion engines using low temperature combustion strategies. The chemical kinetic model consists of 1114 species and 4468 reactions. Concurrently with this effort, work is underway to improve the details of specific reaction classes in the mechanism, guided by high-level electronic structure calculations. Attention is focused upon development of accurate rate rules for abstraction of the tertiary hydrogens present in branched alkanes and properly accounting for the pressure dependence of the ?-scission, isomerization, and R + O{sub 2} reactions.

  19. Heat transfer-solidification kinetics modeling of solidification of castings

    NASA Astrophysics Data System (ADS)

    Stefanescu, Doru M.; Upadhya, G.; Bandyopadhyay, D.

    1990-03-01

    A close examination of the recent developments in the field of computer simulation of solidification process reveals that a combination of both macroscopic and microscopic models is necessary in order to accurately describe the solidification of castings. Currently available macroscopic models include models that describe heat transfer from metal to mold, fluid flow of liquid metal during mold filling, and stress field in the casting. At the microscopic level, the models should include more intricate issues such as solidification kinetics and fluid flow in the mushy zone. Although significant progress has been accomplished over the years in each field, the task of including all of these models into a comprehensive package is far from being complete. This paper describes the state of the art on coupling the macroscopic heat transfer (HT) and microscopic solidification kinetics (SK) models and introduces the latent heat method as a more accurate method for solving the heat source term in the heat conduction equation. A new method for calculation of fraction of solid evolved during solidification based on computer-aided cooling curve analysis (CA-CCA), as well as a method based on nucleation and growth kinetics laws, is discussed. A new nucleation model based on the concept of instantaneous nucleation, which is used to describe equiaxed eutectic solidification of commercial alloys, has been introduced. It is demonstrated that the instantaneous nucleation model agrees well with the experimental results in terms of cooling curves and of evolution of the fraction of solid during solidification. Validation results are also shown for SK models that are based on CA-CCA coupled with HT models for eutectic Al-Si and gray cast iron alloys.

  20. The Nature of Scientific Revolutions from the Vantage Point of Chaos Theory: Toward a Formal Model of Scientific Change

    NASA Astrophysics Data System (ADS)

    Perla, Rocco J.; Carifio, James

    In sharp contrast to the early positivist view of the nature of science and scientific knowledge, Kuhn argues that the scientific enterprise involves states of continuous, gradual development punctuated by comparatively rare instances of turmoil and change, which ultimately brings about a new stability and a qualitatively changed knowledge base. Although this discontinuous or nonlinear view of scientific knowledge is shared by a number of philosophers of science and science educators currently, Kuhn's description of how progress in science occurs has never been formally modeled from a nonlinear mathematical perspective. In this article, we represent aspects of Kuhn's main thesis and ideas as stated in his classic work The Structure of Scientific Revolutions using catastrophe theory, which is a particular instantiation of chaos theory capable of describing discontinuous phenomenon. Through this catastrophe theory representation we attempt to depict and develop a formal nonlinear model of scientific change. The pedagogical implications of the model developed and presented are discussed.

  1. Integrating Kinetic Effects into Global Models for Reconnection

    NASA Technical Reports Server (NTRS)

    Antiochos, S. K.

    2012-01-01

    Magnetic reconnection is the most striking example of how the coupling between global and kinetic scales can lead to fast energy release. Explosive solar activity, such as coronal mass ejections and flares for example, is widely believed to be due to the release of magnetic energy stored on global scales by magnetic reconnection operating on kinetic scales. Understanding how processes couple across spatial scales is one of the most difficult challenges in all of physics, and is undoubtedly the main obstacle to developing predictive models for the Sun's activity. Consequently, the NASA Living With a Star Program selected a Focused Science Team to attack the problem of cross-scale coupling in reconnection. In this talk I will present some of the results of the Team and review our latest theories and methods for modeling the global-local coupling in solar reconnection.

  2. Urban multitarget tracking via gas-kinetic dynamics models

    NASA Astrophysics Data System (ADS)

    Mahler, Ronald

    2013-05-01

    Multitarget tracking in urban environments presents a major theoretical and practical challenge. A recently suggested approach is that of modeling traffic dynamics using the fluid-kinetic methods of traffic-flow theory (TFT). I propose use of the newer, more general, gas-kinetic (GK) approach to TFT. In GK, traffic flow is modeled as a one- or two-dimensional constrained gas. The paper demonstrates the following. (1) The foundational concept in GK--the "phase-space density"--is the same thing as the probability hypothesis density (PHD) of multitarget tracking theory. (2) The theoretically best-that-one-can do approach to TFT-based tracking is a PHD filter. (3) Better performance can be obtained by augmenting this PHD filter as a cardinalized PHD (CPHD) filter. A simple example is presented to illustrate how PHD/CPHD filters can be integrated with conventional macroscopic, mesoscopic, and microscopic TFT.

  3. Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation

    PubMed Central

    2011-01-01

    Background Higher plants and algae are able to fix atmospheric carbon dioxide through photosynthesis and store this fixed carbon in large quantities as starch, which can be hydrolyzed into sugars serving as feedstock for fermentation to biofuels and precursors. Rational engineering of carbon flow in plant cells requires a greater understanding of how starch breakdown fluxes respond to variations in enzyme concentrations, kinetic parameters, and metabolite concentrations. We have therefore developed and simulated a detailed kinetic ordinary differential equation model of the degradation pathways for starch synthesized in plants and green algae, which to our knowledge is the most complete such model reported to date. Results Simulation with 9 internal metabolites and 8 external metabolites, the concentrations of the latter fixed at reasonable biochemical values, leads to a single reference solution showing β-amylase activity to be the rate-limiting step in carbon flow from starch degradation. Additionally, the response coefficients for stromal glucose to the glucose transporter kcat and KM are substantial, whereas those for cytosolic glucose are not, consistent with a kinetic bottleneck due to transport. Response coefficient norms show stromal maltopentaose and cytosolic glucosylated arabinogalactan to be the most and least globally sensitive metabolites, respectively, and β-amylase kcat and KM for starch to be the kinetic parameters with the largest aggregate effect on metabolite concentrations as a whole. The latter kinetic parameters, together with those for glucose transport, have the greatest effect on stromal glucose, which is a precursor for biofuel synthetic pathways. Exploration of the steady-state solution space with respect to concentrations of 6 external metabolites and 8 dynamic metabolite concentrations show that stromal metabolism is strongly coupled to starch levels, and that transport between compartments serves to lower coupling between metabolic

  4. A general kinetic model for the hydrothermal liquefaction of microalgae.

    PubMed

    Valdez, Peter J; Tocco, Vincent J; Savage, Phillip E

    2014-07-01

    We developed a general kinetic model for hydrothermal liquefaction (HTL) of microalgae. The model, which allows the protein, lipid, and carbohydrate fractions of the cell to react at different rates, successfully correlated experimental data for the hydrothermal liquefaction of Chlorella protothecoides, Scenedesmus sp., and Nannochloropsis sp. The model can faithfully account for the influence of time and temperature on the gravimetric yields of gas, solid, biocrude, and aqueous-phase products from isothermal HTL of a 15 wt% slurry. Examination of the rate constants shows that lipids and proteins are the major contributors to the biocrude, while other algal cell constituents contribute very little to the biocrude.

  5. Software Formal Inspections Guidebook

    NASA Technical Reports Server (NTRS)

    1993-01-01

    The Software Formal Inspections Guidebook is designed to support the inspection process of software developed by and for NASA. This document provides information on how to implement a recommended and proven method for conducting formal inspections of NASA software. This Guidebook is a companion document to NASA Standard 2202-93, Software Formal Inspections Standard, approved April 1993, which provides the rules, procedures, and specific requirements for conducting software formal inspections. Application of the Formal Inspections Standard is optional to NASA program or project management. In cases where program or project management decide to use the formal inspections method, this Guidebook provides additional information on how to establish and implement the process. The goal of the formal inspections process as documented in the above-mentioned Standard and this Guidebook is to provide a framework and model for an inspection process that will enable the detection and elimination of defects as early as possible in the software life cycle. An ancillary aspect of the formal inspection process incorporates the collection and analysis of inspection data to effect continual improvement in the inspection process and the quality of the software subjected to the process.

  6. Computation Molecular Kinetics Model of HZE Induced Cell Cycle Arrest

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Ren, Lei

    2004-01-01

    Cell culture models play an important role in understanding the biological effectiveness of space radiation. High energy and charge (HZE) ions produce prolonged cell cycle arrests at the G1/S and G2/M transition points in the cell cycle. A detailed description of these phenomena is needed to integrate knowledge of the expression of DNA damage in surviving cells, including the determination of relative effectiveness factors between different types of radiation that produce differential types of DNA damage and arrest durations. We have developed a hierarchical kinetics model that tracks the distribution of cells in various cell phase compartments (early G1, late G1, S, G2, and M), however with transition rates that are controlled by rate-limiting steps in the kinetics of cyclin-cdk's interactions with their families of transcription factors and inhibitor molecules. The coupling of damaged DNA molecules to the downstream cyclin-cdk inhibitors is achieved through a description of the DNA-PK and ATM signaling pathways. For HZE irradiations we describe preliminary results, which introduce simulation of the stochastic nature of the number of direct particle traversals per cell in the modulation of cyclin-cdk and cell cycle population kinetics. Comparison of the model to data for fibroblast cells irradiated photons or HZE ions are described.

  7. Chemistry Resolved Kinetic Flow Modeling of TATB Based Explosives

    NASA Astrophysics Data System (ADS)

    Vitello, Peter; Fried, Lawrence; Howard, Mike; Levesque, George; Souers, Clark

    2011-06-01

    Detonation waves in insensitive, TATB based explosives are believed to have multi-time scale regimes. The initial burn rate of such explosives has a sub-microsecond time scale. However, significant late-time slow release in energy is believed to occur due to diffusion limited growth of carbon. In the intermediate time scale concentrations of product species likely change from being in equilibrium to being kinetic rate controlled. We use the thermo-chemical code CHEETAH linked to ALE hydrodynamics codes to model detonations. We term our model chemistry resolved kinetic flow as CHEETAH tracks the time dependent concentrations of individual species in the detonation wave and calculate EOS values based on the concentrations. A validation suite of model simulations compared to recent high fidelity metal push experiments at ambient and cold temperatures has been developed. We present here a study of multi-time scale kinetic rate effects for these experiments. Prepared by LLNL under Contract DE-AC52-07NA27344.

  8. Kinetic Modeling of Sunflower Grain Filling and Fatty Acid Biosynthesis.

    PubMed

    Durruty, Ignacio; Aguirrezábal, Luis A N; Echarte, María M

    2016-01-01

    Grain growth and oil biosynthesis are complex processes that involve various enzymes placed in different sub-cellular compartments of the grain. In order to understand the mechanisms controlling grain weight and composition, we need mathematical models capable of simulating the dynamic behavior of the main components of the grain during the grain filling stage. In this paper, we present a non-structured mechanistic kinetic model developed for sunflower grains. The model was first calibrated for sunflower hybrid ACA855. The calibrated model was able to predict the theoretical amount of carbohydrate equivalents allocated to the grain, grain growth and the dynamics of the oil and non-oil fraction, while considering maintenance requirements and leaf senescence. Incorporating into the model the serial-parallel nature of fatty acid biosynthesis permitted a good representation of the kinetics of palmitic, stearic, oleic, and linoleic acids production. A sensitivity analysis showed that the relative influence of input parameters changed along grain development. Grain growth was mostly affected by the specific growth parameter (μ') while fatty acid composition strongly depended on their own maximum specific rate parameters. The model was successfully applied to two additional hybrids (MG2 and DK3820). The proposed model can be the first building block toward the development of a more sophisticated model, capable of predicting the effects of environmental conditions on grain weight and composition, in a comprehensive and quantitative way.

  9. Kinetic Modeling of Sunflower Grain Filling and Fatty Acid Biosynthesis

    PubMed Central

    Durruty, Ignacio; Aguirrezábal, Luis A. N.; Echarte, María M.

    2016-01-01

    Grain growth and oil biosynthesis are complex processes that involve various enzymes placed in different sub-cellular compartments of the grain. In order to understand the mechanisms controlling grain weight and composition, we need mathematical models capable of simulating the dynamic behavior of the main components of the grain during the grain filling stage. In this paper, we present a non-structured mechanistic kinetic model developed for sunflower grains. The model was first calibrated for sunflower hybrid ACA855. The calibrated model was able to predict the theoretical amount of carbohydrate equivalents allocated to the grain, grain growth and the dynamics of the oil and non-oil fraction, while considering maintenance requirements and leaf senescence. Incorporating into the model the serial-parallel nature of fatty acid biosynthesis permitted a good representation of the kinetics of palmitic, stearic, oleic, and linoleic acids production. A sensitivity analysis showed that the relative influence of input parameters changed along grain development. Grain growth was mostly affected by the specific growth parameter (μ′) while fatty acid composition strongly depended on their own maximum specific rate parameters. The model was successfully applied to two additional hybrids (MG2 and DK3820). The proposed model can be the first building block toward the development of a more sophisticated model, capable of predicting the effects of environmental conditions on grain weight and composition, in a comprehensive and quantitative way. PMID:27242809

  10. Kinetic models for nucleocytoplasmic transport of messenger RNA.

    PubMed

    Schröder, H C; Müller, W E; Agutter, P S

    1995-05-21

    Much is known about the mechanism by which mRNAs cross the nuclear envelope (the translocation stage of nucleocytoplasmic transport), but far less is known about the preceding (intranuclear migration/release) and succeeding (cytoplasmic binding) stages. Therefore, existing information suffices for articulating detailed kinetic models of translocation, but not models for the overall mRNA transport process. In this paper, we show that simple kinetic models of translocation can (i) accommodate data about nucleocytoplasmic distributions of endogenous transcripts; (ii) predict the overall effects on these distributions of effectors such as insulin and epidermal growth factor; (iii) throw some light on the mechanism(s) of action of the HIV-1 protein Rev and produce experimentally testable predictions about this mechanism; and (iv) account for the action of influenza virus NS1 protein. However, the simplest forms of translocation models apparently fail to account for some properties of viral regulators such as HIV Rev and adenovirus E1B-E4 complex. To elucidate these topics, less narrowly focused models of mRNA transport are required, describing intranuclear binding/release as well as translocation. On the basis of our examination of translocation models, we suggest some criteria that the requisite broadly based models must satisfy.

  11. Study on kinetic model of microwave thermocatalytic treatment of biomass tar model compound.

    PubMed

    Anis, Samsudin; Zainal, Z A

    2014-01-01

    Kinetic model parameters for toluene conversion under microwave thermocatalytic treatment were evaluated. The kinetic rate constants were determined using integral method based on experimental data and coupled with Arrhenius equation for obtaining the activation energies and pre-exponential factors. The model provides a good agreement with the experimental data. The kinetic model was also validated with standard error of 3% on average. The extrapolation of the model showed a reasonable trend to predict toluene conversion and product yield both in thermal and catalytic treatments. Under microwave irradiation, activation energy of toluene conversion was lower in the range of 3-27 kJ mol(-1) compared to those of conventional heating reported in the literatures. The overall reaction rate was six times higher compared to conventional heating. As a whole, the kinetic model works better for tar model removal in the absence of gas reforming within a level of reliability demonstrated in this study. PMID:24231266

  12. Markov models of molecular kinetics: generation and validation.

    PubMed

    Prinz, Jan-Hendrik; Wu, Hao; Sarich, Marco; Keller, Bettina; Senne, Martin; Held, Martin; Chodera, John D; Schütte, Christof; Noé, Frank

    2011-05-01

    Markov state models of molecular kinetics (MSMs), in which the long-time statistical dynamics of a molecule is approximated by a Markov chain on a discrete partition of configuration space, have seen widespread use in recent years. This approach has many appealing characteristics compared to straightforward molecular dynamics simulation and analysis, including the potential to mitigate the sampling problem by extracting long-time kinetic information from short trajectories and the ability to straightforwardly calculate expectation values and statistical uncertainties of various stationary and dynamical molecular observables. In this paper, we summarize the current state of the art in generation and validation of MSMs and give some important new results. We describe an upper bound for the approximation error made by modeling molecular dynamics with a MSM and we show that this error can be made arbitrarily small with surprisingly little effort. In contrast to previous practice, it becomes clear that the best MSM is not obtained by the most metastable discretization, but the MSM can be much improved if non-metastable states are introduced near the transition states. Moreover, we show that it is not necessary to resolve all slow processes by the state space partitioning, but individual dynamical processes of interest can be resolved separately. We also present an efficient estimator for reversible transition matrices and a robust test to validate that a MSM reproduces the kinetics of the molecular dynamics data.

  13. Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.

    PubMed

    Fleming, R M T; Thiele, I; Provan, G; Nasheuer, H P

    2010-06-01

    The quantitative analysis of biochemical reactions and metabolites is at frontier of biological sciences. The recent availability of high-throughput technology data sets in biology has paved the way for new modelling approaches at various levels of complexity including the metabolome of a cell or an organism. Understanding the metabolism of a single cell and multi-cell organism will provide the knowledge for the rational design of growth conditions to produce commercially valuable reagents in biotechnology. Here, we demonstrate how equations representing steady state mass conservation, energy conservation, the second law of thermodynamics, and reversible enzyme kinetics can be formulated as a single system of linear equalities and inequalities, in addition to linear equalities on exponential variables. Even though the feasible set is non-convex, the reformulation is exact and amenable to large-scale numerical analysis, a prerequisite for computationally feasible genome scale modelling. Integrating flux, concentration and kinetic variables in a unified constraint-based formulation is aimed at increasing the quantitative predictive capacity of flux balance analysis. Incorporation of experimental and theoretical bounds on thermodynamic and kinetic variables ensures that the predicted steady state fluxes are both thermodynamically and biochemically feasible. The resulting in silico predictions are tested against fluxomic data for central metabolism in Escherichia coli and compare favourably with in silico prediction by flux balance analysis.

  14. Formal specification and verification of a fault-masking and transient-recovery model for digital flight-control systems

    NASA Technical Reports Server (NTRS)

    Rushby, John

    1991-01-01

    The formal specification and mechanically checked verification for a model of fault-masking and transient-recovery among the replicated computers of digital flight-control systems are presented. The verification establishes, subject to certain carefully stated assumptions, that faults among the component computers are masked so that commands sent to the actuators are the same as those that would be sent by a single computer that suffers no failures.

  15. Kinetic model of impurity poisoning during growth of calcite

    SciTech Connect

    DeYoreo, J; Wasylenki, L; Dove, P; Wilson, D; Han, N

    2004-05-18

    The central role of the organic component in biologically controlled mineralization is widely recognized. These proteins are characterized by a high proportion of acidic amino acid residues, especially aspartate, Asp. At the same time, biomineralization takes place in the presence of a number of naturally-occurring, inorganic impurities, particularly Mg and Sr. In an attempt to decipher the controls on calcite growth imposed by both classes of modifiers, we have used in situ AFM to investigate the dependence of growth morphology and step kinetics on calcite in the presence of Sr{sup 2+}, as well as a wide suite of Aspartic acid-bearing polypeptides. In each case, we observe a distinct and step-specific modification. Most importantly, we find that the step speed exhibits a characteristic dependence on impurity concentration not predicted by existing crystal growth models. While all of the impurities clearly induce appearance of a 'dead zone,' neither the width of that dead zone nor the dependence of step speed on activity or impurity content can be explained by invoking the Gibbs-Thomson effect, which is the basis for the Cabrera-Vermilyea model of impurity poisoning. Common kink-blocking models also fail to explain the observed dependencies. Here we propose a kinetic model of inhibition based on a 'cooperative' effect of impurity adsorption at adjacent kink sites. The model is in qualitative agreement with the experimental results in that it predicts a non-linear dependence of dead zone width on impurity concentration, as well as a sharp drop in step speed above a certain impurity content. However, a detailed model of impurity adsorption kinetics that give quantitative agreement with the data has yet to be developed.

  16. A neural model of border-ownership from kinetic occlusion.

    PubMed

    Layton, Oliver W; Yazdanbakhsh, Arash

    2015-01-01

    Camouflaged animals that have very similar textures to their surroundings are difficult to detect when stationary. However, when an animal moves, humans readily see a figure at a different depth than the background. How do humans perceive a figure breaking camouflage, even though the texture of the figure and its background may be statistically identical in luminance? We present a model that demonstrates how the primate visual system performs figure-ground segregation in extreme cases of breaking camouflage based on motion alone. Border-ownership signals develop as an emergent property in model V2 units whose receptive fields are nearby kinetically defined borders that separate the figure and background. Model simulations support border-ownership as a general mechanism by which the visual system performs figure-ground segregation, despite whether figure-ground boundaries are defined by luminance or motion contrast. The gradient of motion- and luminance-related border-ownership signals explains the perceived depth ordering of the foreground and background surfaces. Our model predicts that V2 neurons, which are sensitive to kinetic edges, are selective to border-ownership (magnocellular B cells). A distinct population of model V2 neurons is selective to border-ownership in figures defined by luminance contrast (parvocellular B cells). B cells in model V2 receive feedback from neurons in V4 and MT with larger receptive fields to bias border-ownership signals toward the figure. We predict that neurons in V4 and MT sensitive to kinetically defined figures play a crucial role in determining whether the foreground surface accretes, deletes, or produces a shearing motion with respect to the background.

  17. β-function formalism for inflationary models with a non minimal coupling with gravity

    NASA Astrophysics Data System (ADS)

    Pieroni, M.

    2016-02-01

    We discuss the introduction of a non minimal coupling between the inflaton and gravity in terms of our recently proposed β-function formalism for inflation. Via a field redefinition we reduce to the case of minimally coupled theories. The universal attractor at strong coupling has a simple explanation in terms of the new field. Generalizations are discussed and the possibility of evading the universal attractor is shown.

  18. Multiensemble Markov models of molecular thermodynamics and kinetics

    PubMed Central

    Wu, Hao; Paul, Fabian; Noé, Frank

    2016-01-01

    We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models—clustering of high-dimensional spaces and modeling of complex many-state systems—with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein–ligand binding model. PMID:27226302

  19. Modeling transport kinetics in clinoptilolite-phosphate rock systems

    NASA Technical Reports Server (NTRS)

    Allen, E. R.; Ming, D. W.; Hossner, L. R.; Henninger, D. L.

    1995-01-01

    Nutrient release in clinoptilolite-phosphate rock (Cp-PR) systems occurs through dissolution and cation-exchange reactions. Investigating the kinetics of these reactions expands our understanding of nutrient release processes. Research was conducted to model transport kinetics of nutrient release in Cp-PR systems. The objectives were to identify empirical models that best describe NH4, K, and P release and define diffusion-controlling processes. Materials included a Texas clinoptilolite (Cp) and North Carolina phosphate rock (PR). A continuous-flow thin-disk technique was used. Models evaluated included zero order, first order, second order, parabolic diffusion, simplified Elovich, Elovich, and power function. The power-function, Elovich, and parabolic-diffusion models adequately described NH4, K, and P release. The power-function model was preferred because of its simplicity. Models indicated nutrient release was diffusion controlled. Primary transport processes controlling nutrient release for the time span observed were probably the result of a combination of several interacting transport mechanisms.

  20. Modeling the turbulent kinetic energy equation for compressible, homogeneous turbulence

    NASA Technical Reports Server (NTRS)

    Aupoix, B.; Blaisdell, G. A.; Reynolds, William C.; Zeman, Otto

    1990-01-01

    The turbulent kinetic energy transport equation, which is the basis of turbulence models, is investigated for homogeneous, compressible turbulence using direct numerical simulations performed at CTR. It is shown that the partition between dilatational and solenoidal modes is very sensitive to initial conditions for isotropic decaying turbulence but not for sheared flows. The importance of the dilatational dissipation and of the pressure-dilatation term is evidenced from simulations and a transport equation is proposed to evaluate the pressure-dilatation term evolution. This transport equation seems to work well for sheared flows but does not account for initial condition sensitivity in isotropic decay. An improved model is proposed.

  1. Kinetic modeling of non-ideal explosives with CHEETAH

    SciTech Connect

    Fried, L E; Howard, W M; Souers, P C

    1998-08-06

    We report an implementation of the Wood-Kirkwood kinetic detonation model based on multi-species equations of state and multiple reaction rate laws. Finite rate laws are used for the slowest chemical reactions. Other reactions are given infinite rates and are kept in constant thermodynamic equilibrium. We model a wide range of ideal and non-ideal composite energetic materials. We find that we can replicate experimental detonation velocities to within a few per cent, while obtaining good agreement with estimated reaction zone lengths. The detonation velocity as a function of charge radius is also correctly reproduced.

  2. Rethinking Formalisms in Formal Education

    ERIC Educational Resources Information Center

    Nathan, Mitchell J.

    2012-01-01

    I explore a belief about learning and teaching that is commonly held in education and society at large that nonetheless is deeply flawed. The belief asserts that mastery of "formalisms"--specialized representations such as symbolic equations and diagrams with no inherent meaning except that which is established by convention--is prerequisite to…

  3. Kinetic energy for the nuclear Yang-Mills collective model

    NASA Astrophysics Data System (ADS)

    Rosensteel, George; Sparks, Nick

    2015-10-01

    The Bohr-Mottelson-Frankfurt model of nuclear rotations and quadrupole vibrations is a foundational model in nuclear structure physics. The model, also called the geometrical collective model or simply GCM, has two hidden mathematical structures, one Lie group theoretic and the other differential geometric. Although the group structure has been understood for some time, the geometric structure is a new unexplored feature that shares the same mathematical origin as Yang-Mills, viz., a vector bundle with a non-abelian structure group and a connection. Using the de Rham Laplacian ▵ = * d * d from differential geometry for the kinetic energy extends significantly the physical scope of the GCM model. This Laplacian contains a ``magnetic'' term due to the coupling between base manifold rotational and fiber vorticity degrees of freedom. When the connection specializes to irrotational flow, the Laplacian reduces to the Bohr-Mottelson kinetic energy operator. More generally, the connection yields a moment of inertia that is intermediate between the extremes of irrotational flow and rigid body motion.

  4. Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

    PubMed Central

    Mannan, Ahmad A.; Toya, Yoshihiro; Shimizu, Kazuyuki; McFadden, Johnjoe; Kierzek, Andrzej M.; Rocco, Andrea

    2015-01-01

    An understanding of the dynamics of the metabolic profile of a bacterial cell is sought from a dynamical systems analysis of kinetic models. This modelling formalism relies on a deterministic mathematical description of enzyme kinetics and their metabolite regulation. However, it is severely impeded by the lack of available kinetic information, limiting the size of the system that can be modelled. Furthermore, the subsystem of the metabolic network whose dynamics can be modelled is faced with three problems: how to parameterize the model with mostly incomplete steady state data, how to close what is now an inherently open system, and how to account for the impact on growth. In this study we address these challenges of kinetic modelling by capitalizing on multi-‘omics’ steady state data and a genome-scale metabolic network model. We use these to generate parameters that integrate knowledge embedded in the genome-scale metabolic network model, into the most comprehensive kinetic model of the central carbon metabolism of E. coli realized to date. As an application, we performed a dynamical systems analysis of the resulting enriched model. This revealed bistability of the central carbon metabolism and thus its potential to express two distinct metabolic states. Furthermore, since our model-informing technique ensures both stable states are constrained by the same thermodynamically feasible steady state growth rate, the ensuing bistability represents a temporal coexistence of the two states, and by extension, reveals the emergence of a phenotypically heterogeneous population. PMID:26469081

  5. Langrangian model of nitrogen kinetics in the Chattahoochee river

    USGS Publications Warehouse

    Jobson, H.E.

    1987-01-01

    A Lagrangian reference frame is used to solve the convection-dispersion equation and interpret water-quality obtained from the Chattahoochee River. The model was calibrated using unsteady concentrations of organic nitrogen, ammonia, and nitrite plus nitrate obtained during June 1977 and verified using data obtained during August 1976. Reaction kinetics of the cascade type are shown to provide a reasonable description of the nitrogen-species processes in the Chattahoochee River. The conceptual model is easy to visualize in the physical sense and the output includes information that is not easily determined from an Eulerian approach, but which is very helpful in model calibration and data interpretation. For example, the model output allows one to determine which data are of most value in model calibration or verification.

  6. Kinetic equations modelling wealth redistribution: A comparison of approaches

    NASA Astrophysics Data System (ADS)

    Düring, Bertram; Matthes, Daniel; Toscani, Giuseppe

    2008-11-01

    Kinetic equations modelling the redistribution of wealth in simple market economies is one of the major topics in the field of econophysics. We present a unifying approach to the qualitative study for a large variety of such models, which is based on a moment analysis in the related homogeneous Boltzmann equation, and on the use of suitable metrics for probability measures. In consequence, we are able to classify the most important feature of the steady wealth distribution, namely the fatness of the Pareto tail, and the dynamical stability of the latter in terms of the model parameters. Our results apply, e.g., to the market model with risky investments [S. Cordier, L. Pareschi, and G. Toscani, J. Stat. Phys. 120, 253 (2005)], and to the model with quenched saving propensities [A. Chatterjee, B. K. Chakrabarti, and S. S. Manna, Physica A 335, 155 (2004)]. Also, we present results from numerical experiments that confirm the theoretical predictions.

  7. Kinetic modeling of virus transport at the field scale.

    PubMed

    Schijven, Jack F; Simůnek, Jirí

    2002-03-01

    Bacteriophage removal by soil passage in two field studies was re-analyzed with the goal to investigate differences between one- and two-dimensional modeling approaches, differences between one- and two-site kinetic sorption models, and the role of heterogeneities in the soil properties. The first study involved removal of bacteriophages MS2 and PRDI by dune recharge, while the second study represented removal of MS2 by deep well injection. In both studies, removal was higher during the first meters of soil passage than thereafter. The software packages HYDRUS-ID and HYDRUS-2D, which simulate water flow and solute transport in one- and two-dimensional variably saturated porous media, respectively, were used. The two codes were modified by incorporating reversible adsorption to two types of kinetic sites. Tracer concentrations were used first to calibrate flow and transport parameters of both models before analyzing transport of bacteriophages. The one-dimensional one-site model did not fully describe the tails of the measured breakthrough curves of MS2 and PRD1 from the dune recharge study. While the one-dimensional one-site model predicted a sudden decrease in virus concentrations immediately after the peaks, measured data displayed much smoother decline and tailing. The one-dimensional two-site model simulated the overall behavior of the breakthrough curves very well. The two-dimensional one-site model predicted a more gradual decrease in virus concentrations after the peaks than the one-dimensional one-site model, but not as good as the one-dimensional two-site model. The dimensionality of the problem hence can partly explain the smooth decrease in concentration after peak breakthrough. The two-dimensional two-site model provided the best results. Values for k(att2) and k(det2) could not be determined at the last two of four monitoring wells, thus suggesting that either a second type of kinetic sites is present in the first few meters of dune passage and not

  8. Beyond formalism

    NASA Technical Reports Server (NTRS)

    Denning, Peter J.

    1991-01-01

    The ongoing debate over the role of formalism and formal specifications in software features many speakers with diverse positions. Yet, in the end, they share the conviction that the requirements of a software system can be unambiguously specified, that acceptable software is a product demonstrably meeting the specifications, and that the design process can be carried out with little interaction between designers and users once the specification has been agreed to. This conviction is part of a larger paradigm prevalent in American management thinking, which holds that organizations are systems that can be precisely specified and optimized. This paradigm, which traces historically to the works of Frederick Taylor in the early 1900s, is no longer sufficient for organizations and software systems today. In the domain of software, a new paradigm, called user-centered design, overcomes the limitations of pure formalism. Pioneered in Scandinavia, user-centered design is spreading through Europe and is beginning to make its way into the U.S.

  9. Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

    NASA Astrophysics Data System (ADS)

    Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.

    2014-12-01

    Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

  10. Combining the GW formalism with the polarizable continuum model: A state-specific non-equilibrium approach

    NASA Astrophysics Data System (ADS)

    Duchemin, Ivan; Jacquemin, Denis; Blase, Xavier

    2016-04-01

    We have implemented the polarizable continuum model within the framework of the many-body Green's function GW formalism for the calculation of electron addition and removal energies in solution. The present formalism includes both ground-state and non-equilibrium polarization effects. In addition, the polarization energies are state-specific, allowing to obtain the bath-induced renormalisation energy of all occupied and virtual energy levels. Our implementation is validated by comparisons with ΔSCF calculations performed at both the density functional theory and coupled-cluster single and double levels for solvated nucleobases. The present study opens the way to GW and Bethe-Salpeter calculations in disordered condensed phases of interest in organic optoelectronics, wet chemistry, and biology.

  11. Coupling of chemical kinetics, gas dynamics, and charged particle kinetics models for the analysis of NO reduction from flue gases

    SciTech Connect

    Eichwald, O.; Yousfi, M.; Hennad, A.; Benabdessadok, M.D.

    1997-11-01

    A chemical kinetics model is developed to analyze the time evolution of the different main species involved in a flue gas initially stressed by a pulsed corona discharge at the atmospheric pressure and including N{sub 2}, O{sub 2}, H{sub 2}O, and CO{sub 2} with a few ppm of NO. The present chemical kinetics model is coupled to a gas dynamics model used to analyze the radial expansion of the gas in the ionized channel created during the discharge phase. It is also meant to analyze the gas heating due to the Joule effect. This chemical kinetics model is also coupled to charged particle kinetics models based on a Boltzmann equation model to calculate the electron-molecule reaction coefficients in the flue gas and on a Monte Carlo code to estimate the energy and momentum transfer terms relative to ion-molecule collisions which are the input data for the gas dynamics model. It is shown, in particular, that the evolution of the radicals and the oxides is substantially affected by the gas temperature rise (from the initial value of 300 K up to 750 K near the anode) thus emphasizing the present coupling between gas dynamics, charged particle, and chemical kinetics models. {copyright} {ital 1997 American Institute of Physics.}

  12. Coupling of chemical kinetics, gas dynamics, and charged particle kinetics models for the analysis of NO reduction from flue gases

    NASA Astrophysics Data System (ADS)

    Eichwald, O.; Yousfi, M.; Hennad, A.; Benabdessadok, M. D.

    1997-11-01

    A chemical kinetics model is developed to analyze the time evolution of the different main species involved in a flue gas initially stressed by a pulsed corona discharge at the atmospheric pressure and including N2, O2, H2O, and CO2 with a few ppm of NO. The present chemical kinetics model is coupled to a gas dynamics model used to analyze the radial expansion of the gas in the ionized channel created during the discharge phase. It is also meant to analyze the gas heating due to the Joule effect. This chemical kinetics model is also coupled to charged particle kinetics models based on a Boltzmann equation model to calculate the electron-molecule reaction coefficients in the flue gas and on a Monte Carlo code to estimate the energy and momentum transfer terms relative to ion-molecule collisions which are the input data for the gas dynamics model. It is shown, in particular, that the evolution of the radicals and the oxides is substantially affected by the gas temperature rise (from the initial value of 300 K up to 750 K near the anode) thus emphasizing the present coupling between gas dynamics, charged particle, and chemical kinetics models.

  13. A kinetic approach to modeling the manufacture of high density strucutral foam: Foaming and polymerization

    SciTech Connect

    Rao, Rekha R.; Mondy, Lisa Ann; Noble, David R.; Brunini, Victor; Roberts, Christine Cardinal; Long, Kevin Nicholas; Soehnel, Melissa Marie; Celina, Mathias C.; Wyatt, Nicholas B.; Thompson, Kyle R.; Tinsley, James

    2015-09-01

    We are studying PMDI polyurethane with a fast catalyst, such that filling and polymerization occur simultaneously. The foam is over-packed to tw ice or more of its free rise density to reach the density of interest. Our approach is to co mbine model development closely with experiments to discover new physics, to parameterize models and to validate the models once they have been developed. The model must be able to repres ent the expansion, filling, curing, and final foam properties. PMDI is chemically blown foam, wh ere carbon dioxide is pr oduced via the reaction of water and isocyanate. The isocyanate also re acts with polyol in a competing reaction, which produces the polymer. A new kinetic model is developed and implemented, which follows a simplified mathematical formalism that decouple s these two reactions. The model predicts the polymerization reaction via condensation chemis try, where vitrification and glass transition temperature evolution must be included to correctly predict this quantity. The foam gas generation kinetics are determined by tracking the molar concentration of both water and carbon dioxide. Understanding the therma l history and loads on the foam due to exothermicity and oven heating is very important to the results, since the kinetics and ma terial properties are all very sensitive to temperature. The conservation eq uations, including the e quations of motion, an energy balance, and thr ee rate equations are solved via a stabilized finite element method. We assume generalized-Newtonian rheology that is dependent on the cure, gas fraction, and temperature. The conservation equations are comb ined with a level set method to determine the location of the free surface over time. Results from the model are compared to experimental flow visualization data and post-te st CT data for the density. Seve ral geometries are investigated including a mock encapsulation part, two configur ations of a mock stru ctural part, and a bar geometry to

  14. Kinetic Model for 1D aggregation of yeast ``prions''

    NASA Astrophysics Data System (ADS)

    Kunes, Kay; Cox, Daniel; Singh, Rajiv

    2004-03-01

    Mammalian prion proteins (PrP) are of public health interest because of mad cow and chronic wasting diseases. Yeast have proteins which can undergo similar reconformation and aggregation processes to PrP; yeast forms are simpler to experimentally study and model. Recent in vitro studies of the SUP35 protein(1), showed long aggregates and pure exponential growth of the misfolded form. To explain this data, we have extended a previous model of aggregation kinetics(2). The model assumes reconformation only upon aggregation, and includes aggregate fissioning and an initial nucleation barrier. We find for sufficiently small nucleation rates or seeding by small dimer concentrations that we can achieve the requisite exponential growth and long aggregates. We will compare to a more realistic stochastic kinetics model and present prelimary attempts to describe recent experiments on SUP35 strains. *-Supported by U.S. Army Congressionally Mandated Research Fund. 1) P. Chien and J.S. Weissman, Nature 410, 223 (2001); http://online.kitp.ucsb.edu/online/bionet03/collins/. 2) J. Masel, V.A.> Jansen, M.A. Nowak, Biophys. Chem. 77, 139 (1999).

  15. A hybrid model describing ion induced kinetic electron emission

    NASA Astrophysics Data System (ADS)

    Hanke, S.; Duvenbeck, A.; Heuser, C.; Weidtmann, B.; Wucher, A.

    2015-06-01

    We present a model to describe the kinetic internal and external electron emission from an ion bombarded metal target. The model is based upon a molecular dynamics treatment of the nuclear degree of freedom, the electronic system is assumed as a quasi-free electron gas characterized by its Fermi energy, electron temperature and a characteristic attenuation length. In a series of previous works we have employed this model, which includes the local kinetic excitation as well as the rapid spread of the generated excitation energy, in order to calculate internal and external electron emission yields within the framework of a Richardson-Dushman-like thermionic emission model. However, this kind of treatment turned out to fail in the realistic prediction of experimentally measured internal electron yields mainly due to the restriction of the treatment of electronic transport to a diffusive manner. Here, we propose a slightly modified approach additionally incorporating the contribution of hot electrons which are generated in the bulk material and undergo ballistic transport towards the emitting interface.

  16. Effect of formal and informal likelihood functions on uncertainty assessment in a single event rainfall-runoff model

    NASA Astrophysics Data System (ADS)

    Nourali, Mahrouz; Ghahraman, Bijan; Pourreza-Bilondi, Mohsen; Davary, Kamran

    2016-09-01

    In the present study, DREAM(ZS), Differential Evolution Adaptive Metropolis combined with both formal and informal likelihood functions, is used to investigate uncertainty of parameters of the HEC-HMS model in Tamar watershed, Golestan province, Iran. In order to assess the uncertainty of 24 parameters used in HMS, three flood events were used to calibrate and one flood event was used to validate the posterior distributions. Moreover, performance of seven different likelihood functions (L1-L7) was assessed by means of DREAM(ZS)approach. Four likelihood functions, L1-L4, Nash-Sutcliffe (NS) efficiency, Normalized absolute error (NAE), Index of agreement (IOA), and Chiew-McMahon efficiency (CM), is considered as informal, whereas remaining (L5-L7) is represented in formal category. L5 focuses on the relationship between the traditional least squares fitting and the Bayesian inference, and L6, is a hetereoscedastic maximum likelihood error (HMLE) estimator. Finally, in likelihood function L7, serial dependence of residual errors is accounted using a first-order autoregressive (AR) model of the residuals. According to the results, sensitivities of the parameters strongly depend on the likelihood function, and vary for different likelihood functions. Most of the parameters were better defined by formal likelihood functions L5 and L7 and showed a high sensitivity to model performance. Posterior cumulative distributions corresponding to the informal likelihood functions L1, L2, L3, L4 and the formal likelihood function L6 are approximately the same for most of the sub-basins, and these likelihood functions depict almost a similar effect on sensitivity of parameters. 95% total prediction uncertainty bounds bracketed most of the observed data. Considering all the statistical indicators and criteria of uncertainty assessment, including RMSE, KGE, NS, P-factor and R-factor, results showed that DREAM(ZS) algorithm performed better under formal likelihood functions L5 and L7

  17. Modeling anomalous radial transport in kinetic transport codes

    NASA Astrophysics Data System (ADS)

    Bodi, K.; Krasheninnikov, S. I.; Cohen, R. H.; Rognlien, T. D.

    2009-11-01

    Anomalous transport is typically the dominant component of the radial transport in magnetically confined plasmas, where the physical origin of this transport is believed to be plasma turbulence. A model is presented for anomalous transport that can be used in continuum kinetic edge codes like TEMPEST, NEO and the next-generation code being developed by the Edge Simulation Laboratory. The model can also be adapted to particle-based codes. It is demonstrated that the model with a velocity-dependent diffusion and convection terms can match a diagonal gradient-driven transport matrix as found in contemporary fluid codes, but can also include off-diagonal effects. The anomalous transport model is also combined with particle drifts and a particle/energy-conserving Krook collision operator to study possible synergistic effects with neoclassical transport. For the latter study, a velocity-independent anomalous diffusion coefficient is used to mimic the effect of long-wavelength ExB turbulence.

  18. Tracer kinetic modelling in MRI: estimating perfusion and capillary permeability

    NASA Astrophysics Data System (ADS)

    Sourbron, S. P.; Buckley, D. L.

    2012-01-01

    The tracer-kinetic models developed in the early 1990s for dynamic contrast-enhanced MRI (DCE-MRI) have since become a standard in numerous applications. At the same time, the development of MRI hardware has led to increases in image quality and temporal resolution that reveal the limitations of the early models. This in turn has stimulated an interest in the development and application of a second generation of modelling approaches. They are designed to overcome these limitations and produce additional and more accurate information on tissue status. In particular, models of the second generation enable separate estimates of perfusion and capillary permeability rather than a single parameter Ktrans that represents a combination of the two. A variety of such models has been proposed in the literature, and development in the field has been constrained by a lack of transparency regarding terminology, notations and physiological assumptions. In this review, we provide an overview of these models in a manner that is both physically intuitive and mathematically rigourous. All are derived from common first principles, using concepts and notations from general tracer-kinetic theory. Explicit links to their historical origins are included to allow for a transfer of experience obtained in other fields (PET, SPECT, CT). A classification is presented that reveals the links between all models, and with the models of the first generation. Detailed formulae for all solutions are provided to facilitate implementation. Our aim is to encourage the application of these tools to DCE-MRI by offering researchers a clearer understanding of their assumptions and requirements.

  19. Quantitative description of realistic wealth distributions by kinetic trading models

    NASA Astrophysics Data System (ADS)

    Lammoglia, Nelson; Muñoz, Víctor; Rogan, José; Toledo, Benjamín; Zarama, Roberto; Valdivia, Juan Alejandro

    2008-10-01

    Data on wealth distributions in trading markets show a power law behavior x-(1+α) at the high end, where, in general, α is greater than 1 (Pareto’s law). Models based on kinetic theory, where a set of interacting agents trade money, yield power law tails if agents are assigned a saving propensity. In this paper we are solving the inverse problem, that is, in finding the saving propensity distribution which yields a given wealth distribution for all wealth ranges. This is done explicitly for two recently published and comprehensive wealth datasets.

  20. Kinetic mixing effect in the 3 -3 -1 -1 model

    NASA Astrophysics Data System (ADS)

    Dong, P. V.; Si, D. T.

    2016-06-01

    We show that the mixing effect of the neutral gauge bosons in the 3 -3 -1 -1 model comes from two sources. The first one is due to the 3 -3 -1 -1 gauge symmetry breaking as usual, whereas the second one results from the kinetic mixing between the gauge bosons of U (1 )X and U (1 )N groups, which are used to determine the electric charge and baryon minus lepton numbers, respectively. Such mixings modify the ρ -parameter and the known couplings of Z with fermions. The constraints that arise from flavor-changing neutral currents due to the gauge boson mixings and nonuniversal fermion generations are also given.

  1. Myosin-V stepping kinetics: a molecular model for processivity.

    PubMed

    Rief, M; Rock, R S; Mehta, A D; Mooseker, M S; Cheney, R E; Spudich, J A

    2000-08-15

    Myosin-V is a molecular motor that moves processively along its actin track. We have used a feedback-enhanced optical trap to examine the stepping kinetics of this movement. By analyzing the distribution of time periods separating discrete approximately 36-nm mechanical steps, we characterize the number and duration of rate-limiting biochemical transitions preceding each such step. These data show that myosin-V is a tightly coupled motor whose cycle time is limited by ADP release. On the basis of these results, we propose a model for myosin-V processivity.

  2. Detailed kinetics modeling of indium phosphide films in MOCVD reactors

    SciTech Connect

    Masi, M.; Cavallotti, C.; Radaelli, G.; Carra, S.

    1998-12-31

    The deposition kinetics of InP in MOCVD reactors is presented. The proposed chemical mechanism involves both gas phase and surface reactions. The fundamental hypothesis adopted in deriving the mechanism was a dual site dissociative adsorption of the precursors on the growing surface. In any case, all the rate constants either were taken from the literature or estimated through thermochemical methods. In addition, the deposition reactor was simulated by means of a monodimensional model that accounts for the main reactor features through the boundary layer theory.

  3. A generic 3D kinetic model of gene expression

    NASA Astrophysics Data System (ADS)

    Zhdanov, Vladimir P.

    2012-04-01

    Recent experiments show that mRNAs and proteins can be localized both in prokaryotic and eukaryotic cells. To describe such situations, I present a 3D mean-field kinetic model aimed primarily at gene expression in prokaryotic cells, including the formation of mRNA, its translation into protein, and slow diffusion of these species. Under steady-state conditions, the mRNA and protein spatial distribution is described by simple exponential functions. The protein concentration near the gene transcribed into mRNA is shown to depend on the protein and mRNA diffusion coefficients and degradation rate constants.

  4. Antipersistent dynamics in kinetic models of wealth exchange

    NASA Astrophysics Data System (ADS)

    Goswami, Sanchari; Chatterjee, Arnab; Sen, Parongama

    2011-11-01

    We investigate the detailed dynamics of gains and losses made by agents in some kinetic models of wealth exchange. An earlier work suggested that a walk in an abstract gain-loss space can be conceived for the agents. For models in which agents do not save, or save with uniform saving propensity, the walk has diffusive behavior. For the case in which the saving propensity λ is distributed randomly (0≤λ<1), the resultant walk showed a ballistic nature (except at a particular value of λ*≈0.47). Here we consider several other features of the walk with random λ. While some macroscopic properties of this walk are comparable to a biased random walk, at microscopic level, there are gross differences. The difference turns out to be due to an antipersistent tendency toward making a gain (loss) immediately after making a loss (gain). This correlation is in fact present in kinetic models without saving or with uniform saving as well, such that the corresponding walks are not identical to ordinary random walks. In the distributed saving case, antipersistence occurs with a simultaneous overall bias.

  5. A new kinetic model for human iodine metabolism

    SciTech Connect

    Ficken, V.J.; Allen, E.W.; Adams, G.D.

    1985-05-01

    A new kinetic model of iodine metabolism incorporating preferential organification of tyrosil (TYR) residues of thyroglobulin is developed and evaluated for euthyroid (n=5) and hyperthyroid (n=11) subjects. Iodine and peripheral T4 metabolims were measured with oral /sup 131/I-NaI and intravenous /sup 125/I-74 respectively. Data (obtained over 10 days) and kinetic model are analyzed using the SAAM27 program developed by Berman (1978). Compartment rate constants (mean rate per hour +- ISD) are tabulated in this paper. Thyroid and renal iodide clearance compare favorably with values reported in the literature. TYR rate constants were not unique; however, values obtained are within the range of rate constants determined from the invitro data reported by others. Intraluminal iodine as coupled TYR is predicted to be 21% for euthyroid and 59% for hyperthyroid subjects compared to analytical chemical methods of 30% and 51% respectively determined elsewhere. The authors plan to evaluate this model as a method of predicting the thyroid radiation dose from orally administered I/sup 131/.

  6. The redefinition of the familialist home care model in France: the complex formalization of care through cash payment.

    PubMed

    Le Bihan, Blanche

    2012-05-01

    This article investigates the impact of policy measures on the organisation of home-based care for older people in France, by examining the balance between formal and informal care and the redefinition of the initial familialist model. It focuses on the specific cash for care scheme (the Allocation personnalisée d'autonomie - Personalised allowance for autonomy) which is at the core of the French home-based care policy. The author argues that in a redefined context of 'welfare mix', the French public strategy for supporting home-based care in France is articulated around two major objectives, which can appear contradictory. It aims to formalise a professional care sector, with respect to the employment policy while allowing the development of new forms of informal care, which cannot be considered to be formal employment. The data collection is two-fold. Firstly, a detailed analysis was made of different policy documents and public reports, together with a systematic review of existing studies. Secondly, statistical analysis on home-based care resources were collected, which was not easy, as home-care services for older people in France are part of a larger sector of activity, 'personal services' (services à la personne). The article exposes three main findings. First, it highlights the complexity of the formalisation process related to the introduction of the French care allowance and demonstrates that formalisation, which facilitates the recognition of care as work, does not necessarily mean professionalisation. Second, it outlines the diversity of the resources available: heterogeneous professional care, semi-formal forms of care work with the possibility to employ a relative and informal family care. Finally, the analysis outlines the importance of the regulation of cash payments on the reshaping of formal and informal care and comments on its impact on the redefinition of informal caring activities. PMID:22225951

  7. The redefinition of the familialist home care model in France: the complex formalization of care through cash payment.

    PubMed

    Le Bihan, Blanche

    2012-05-01

    This article investigates the impact of policy measures on the organisation of home-based care for older people in France, by examining the balance between formal and informal care and the redefinition of the initial familialist model. It focuses on the specific cash for care scheme (the Allocation personnalisée d'autonomie - Personalised allowance for autonomy) which is at the core of the French home-based care policy. The author argues that in a redefined context of 'welfare mix', the French public strategy for supporting home-based care in France is articulated around two major objectives, which can appear contradictory. It aims to formalise a professional care sector, with respect to the employment policy while allowing the development of new forms of informal care, which cannot be considered to be formal employment. The data collection is two-fold. Firstly, a detailed analysis was made of different policy documents and public reports, together with a systematic review of existing studies. Secondly, statistical analysis on home-based care resources were collected, which was not easy, as home-care services for older people in France are part of a larger sector of activity, 'personal services' (services à la personne). The article exposes three main findings. First, it highlights the complexity of the formalisation process related to the introduction of the French care allowance and demonstrates that formalisation, which facilitates the recognition of care as work, does not necessarily mean professionalisation. Second, it outlines the diversity of the resources available: heterogeneous professional care, semi-formal forms of care work with the possibility to employ a relative and informal family care. Finally, the analysis outlines the importance of the regulation of cash payments on the reshaping of formal and informal care and comments on its impact on the redefinition of informal caring activities.

  8. Kinetic and Stochastic Models of 1D yeast ``prions"

    NASA Astrophysics Data System (ADS)

    Kunes, Kay

    2005-03-01

    Mammalian prion proteins (PrP) are of public health interest because of mad cow and chronic wasting diseases. Yeasts have proteins, which can undergo similar reconformation and aggregation processes to PrP; yeast ``prions" are simpler to experimentally study and model. Recent in vitro studies of the SUP35 protein (1), showed long aggregates and pure exponential growth of the misfolded form. To explain this data, we have extended a previous model of aggregation kinetics along with our own stochastic approach (2). Both models assume reconformation only upon aggregation, and include aggregate fissioning and an initial nucleation barrier. We find for sufficiently small nucleation rates or seeding by small dimer concentrations that we can achieve the requisite exponential growth and long aggregates.

  9. Kinetic modeling can describe in vivo glycolysis in Entamoeba histolytica.

    PubMed

    Saavedra, Emma; Marín-Hernández, Alvaro; Encalada, Rusely; Olivos, Alfonso; Mendoza-Hernández, Guillermo; Moreno-Sánchez, Rafael

    2007-09-01

    Glycolysis in the human parasite Entamoeba histolytica is characterized by the absence of cooperative modulation and the prevalence of pyrophosphate-dependent (over ATP-dependent) enzymes. To determine the flux-control distribution of glycolysis and understand its underlying control mechanisms, a kinetic model of the pathway was constructed by using the software gepasi. The model was based on the kinetic parameters determined in the purified recombinant enzymes, and the enzyme activities, and steady-state fluxes and metabolite concentrations determined in amoebal trophozoites. The model predicted, with a high degree of accuracy, the flux and metabolite concentrations found in trophozoites, but only when the pyrophosphate concentration was held constant; at variable pyrophosphate, the model was not able to completely account for the ATP production/consumption balance, indicating the importance of the pyrophosphate homeostasis for amoebal glycolysis. Control analysis by the model revealed that hexokinase exerted the highest flux control (73%), as a result of its low cellular activity and strong AMP inhibition. 3-Phosphoglycerate mutase also exhibited significant flux control (65%) whereas the other pathway enzymes showed little or no control. The control of the ATP concentration was also mainly exerted by ATP consuming processes and 3-phosphoglycerate mutase and hexokinase (in the producing block). The model also indicated that, in order to diminish the amoebal glycolytic flux by 50%, it was required to decrease hexokinase or 3-phosphoglycerate mutase by 24% and 55%, respectively, or by 18% for both enzymes. By contrast, to attain the same reduction in flux by inhibiting the pyrophosphate-dependent enzymes pyrophosphate-phosphofructokinase and pyruvate phosphate dikinase, they should be decreased > 70%. On the basis of metabolic control analysis, steps whose inhibition would have stronger negative effects on the energy metabolism of this parasite were identified

  10. Kinetic model of sucrose accumulation in maturing sugarcane culm tissue.

    PubMed

    Uys, Lafras; Botha, Frederik C; Hofmeyr, Jan-Hendrik S; Rohwer, Johann M

    2007-01-01

    Biochemically, it is not completely understood why or how commercial varieties of sugarcane (Saccharum officinarum) are able to accumulate sucrose in high concentrations. Such concentrations are obtained despite the presence of sucrose synthesis/breakdown cycles (futile cycling) in the culm of the storage parenchyma. Given the complexity of the process, kinetic modelling may help to elucidate the factors governing sucrose accumulation or direct the design of experimental optimisation strategies. This paper describes the extension of an existing model of sucrose accumulation (Rohwer, J.M., Botha, F.C., 2001. Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem. J. 358, 437-445) to account for isoforms of sucrose synthase and fructokinase, carbon partitioning towards fibre formation, and the glycolytic enzymes phosphofructokinase (PFK), pyrophosphate-dependent PFK and aldolase. Moreover, by including data on the maximal activity of the enzymes as measured in different internodes, a growth model was constructed that describes the metabolic behaviour as sugarcane parenchymal tissue matures from internodes 3-10. While there was some discrepancy between modelled and experimentally determined steady-state sucrose concentrations in the cytoplasm, steady-state fluxes showed a better fit. The model supports a hypothesis of vacuolar sucrose accumulation against a concentration gradient. A detailed metabolic control analysis of sucrose synthase showed that each isoform has a unique control profile. Fructose uptake by the cell and sucrose uptake by the vacuole had a negative control on the futile cycling of sucrose and a positive control on sucrose accumulation, while the control profile for neutral invertase was reversed. When the activities of these three enzymes were changed from their reference values, the effects on futile cycling and sucrose accumulation were amplified. The model can be run online at the JWS Online

  11. Upper D region chemical kinetic modeling of LORE relaxation times

    NASA Astrophysics Data System (ADS)

    Gordillo-Vázquez, F. J.; Luque, A.; Haldoupis, C.

    2016-04-01

    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.

  12. Kinetic modeling and design of colloidal lock and key assembly.

    PubMed

    Beltran-Villegas, Daniel J; Colón-Meléndez, Laura; Solomon, Michael J; Larson, Ronald G

    2016-02-01

    We investigate the kinetics of colloidal lock and key particle assembly by modeling transitions between free, non-specifically and specifically (dumbbells) bound pairs to enable the rapid formation of specific pairs. We expand on a model introduced in a previous publication (Colón-Meléndez et al., 2015) to account for the shape complementarity between the lock and the key particle. Specifically we develop a theory to predict free energy differences between specific and non-specific states based on the interaction potential between arbitrary surfaces and apply this to the interaction of a spherical key particle with the concave dimple surface. Our results show that a lock particle dimple slightly wider than the key particle radius results in optimal binding, but also show escape rates much smaller than those observed in experimental measurements described in the paper cited above. We assess the possible sources of error in experiments and in analysis, including spatial and temporal resolution of the confocal microscopy method used to measure kinetic coefficients, the polydispersity of the lock dimple size, and the sedimentation of the particles in a quasi-two-dimensional layer. We find that the largest sources of variation are in the limited temporal resolution of the experiments, which we account for in our theory, and in the quasi-two-dimensional nature of the experiment that leads to misidentification of non-specific pairs as specific ones. Accounting for these sources of variation results in very good quantitative agreement with experimental data.

  13. Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo

    SciTech Connect

    Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.

    2000-10-10

    Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.

  14. Kinetics of the monomer-monomer surface reaction model

    SciTech Connect

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

    1993-02-01

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

  15. Non-Markovian coarse-grained modeling of polymeric fluids based on the Mori-Zwanzig formalism

    NASA Astrophysics Data System (ADS)

    Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables based on the Mori-Zwanzig formalism. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons on both static and dynamic properties between the CG models with Markovian and non-Markovian approximations will be presented. Supported by the DOE Center on Mathematics for Mesoscopic Modeling of Materials (CM4) and an INCITE grant.

  16. Formal Relations and an Empirical Comparison among the Bi-Factor, the Testlet, and a Second-Order Multidimensional IRT Model

    ERIC Educational Resources Information Center

    Rijmen, Frank

    2010-01-01

    Testlet effects can be taken into account by incorporating specific dimensions in addition to the general dimension into the item response theory model. Three such multidimensional models are described: the bi-factor model, the testlet model, and a second-order model. It is shown how the second-order model is formally equivalent to the testlet…

  17. A study of the kinetic energy generation with general circulation models

    NASA Technical Reports Server (NTRS)

    Chen, T.-C.; Lee, Y.-H.

    1983-01-01

    The history data of winter simulation by the GLAS climate model and the NCAR community climate model are used to examine the generation of atmospheric kinetic energy. The contrast between the geographic distributions of the generation of kinetic energy and divergence of kinetic energy flux shows that kinetic energy is generated in the upstream side of jets, transported to the downstream side and destroyed there. The contributions from the time-mean and transient modes to the counterbalance between generation of kinetic energy and divergence of kinetic energy flux are also investigated. It is observed that the kinetic energy generated by the time-mean mode is essentially redistributed by the time-mean flow, while that generated by the transient flow is mainly responsible for the maintenance of the kinetic energy of the entire atmospheric flow.

  18. A general moment expansion method for stochastic kinetic models

    NASA Astrophysics Data System (ADS)

    Ale, Angelique; Kirk, Paul; Stumpf, Michael P. H.

    2013-05-01

    Moment approximation methods are gaining increasing attention for their use in the approximation of the stochastic kinetics of chemical reaction systems. In this paper we derive a general moment expansion method for any type of propensities and which allows expansion up to any number of moments. For some chemical reaction systems, more than two moments are necessary to describe the dynamic properties of the system, which the linear noise approximation is unable to provide. Moreover, also for systems for which the mean does not have a strong dependence on higher order moments, moment approximation methods give information about higher order moments of the underlying probability distribution. We demonstrate the method using a dimerisation reaction, Michaelis-Menten kinetics and a model of an oscillating p53 system. We show that for the dimerisation reaction and Michaelis-Menten enzyme kinetics system higher order moments have limited influence on the estimation of the mean, while for the p53 system, the solution for the mean can require several moments to converge to the average obtained from many stochastic simulations. We also find that agreement between lower order moments does not guarantee that higher moments will agree. Compared to stochastic simulations, our approach is numerically highly efficient at capturing the behaviour of stochastic systems in terms of the average and higher moments, and we provide expressions for the computational cost for different system sizes and orders of approximation. We show how the moment expansion method can be employed to efficiently quantify parameter sensitivity. Finally we investigate the effects of using too few moments on parameter estimation, and provide guidance on how to estimate if the distribution can be accurately approximated using only a few moments.

  19. Numerical Simulation of SNCR Technology with Simplified Chemical Kinetics Model

    NASA Astrophysics Data System (ADS)

    Blejchař, T.; Dolníčková, D.

    2013-04-01

    The paper deals with numerical simulation of SNCR method. For numerical modelling was used CFD code Ansys/CFX. SNCR method was described by dominant chemical reaction, which were look up NIST Chemical database. The reactions including reduction of NOx and concentration change of pollutants, like N2O and CO in flue gas too. Proposed chemical kinetics and CFD model was applied to two boilers. Both simulations were compared with experimental measurements. First simulation was used to validation of chemical mechanism. Second simulation was based on first simulation and it was used to verification of compiled SNCR chemical mechanism. Next the new variant of the reagent penetration lance was proposed and compared with the original variants.

  20. Fluid catalytic cracking catalyst for reformulated gasolines: Kinetic modeling

    SciTech Connect

    Gianetto, A. ); Farag, H.I. . Dept. of Chemical Engineering); Blasetti, A.P. . Dept. de Procesos); Lasa, H.I. de . Faculty of Engineering Science)

    1994-12-01

    Changes of the relative importance of intradiffusion on USY zeolite crystals were studied as a way of affecting selectivity of catalytic cracking reactions. Zeolite crystals were synthesized (Si/Al = 2.4), activated and stabilized using ion exchange and steam calcination to obtain USSY (Ultra Stable Submicron Y) zeolites. After the activation the zeolites were pelletized (45--60 [mu]m particles). USSYs were tested in a novel Riser Simulator. Results obtained show that total aromatics (BTX), benzene, C[sub 4] olefins, and coke were significantly affected with the change of zeolite crystal sizes. Gasolines produced with USSY zeolites contain less aromatics and particularly lower benzene levels. Experimental results were analyzed with a model including several lumps: unconverted gas oil, gasoline, light gases, and coke. This model also accounts for catalyst deactivation as a function of coke on catalyst. Various kinetic parameters were determined with their corresponding spans for the 95% level of confidence.

  1. Developing a computational model of human hand kinetics using AVS

    SciTech Connect

    Abramowitz, Mark S.

    1996-05-01

    As part of an ongoing effort to develop a finite element model of the human hand at the Institute for Scientific Computing Research (ISCR), this project extended existing computational tools for analyzing and visualizing hand kinetics. These tools employ a commercial, scientific visualization package called AVS. FORTRAN and C code, originally written by David Giurintano of the Gillis W. Long Hansen`s Disease Center, was ported to a different computing platform, debugged, and documented. Usability features were added and the code was made more modular and readable. When the code is used to visualize bone movement and tendon paths for the thumb, graphical output is consistent with expected results. However, numerical values for forces and moments at the thumb joints do not yet appear to be accurate enough to be included in ISCR`s finite element model. Future work includes debugging the parts of the code that calculate forces and moments and verifying the correctness of these values.

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

    SciTech Connect

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

    2011-03-01

    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.

  3. Chemical kinetic modeling of component mixtures relevant to gasoline

    SciTech Connect

    Mehl, M; Curran, H J; Pitz, W J; Westbrook, C K

    2009-02-13

    Real fuels are complex mixtures of thousands of hydrocarbon compounds including linear and branched paraffins, naphthenes, olefins and aromatics. It is generally agreed that their behavior can be effectively reproduced by simpler fuel surrogates containing a limited number of components. In this work, a recently revised version of the kinetic model by the authors is used to analyze the combustion behavior of several components relevant to gasoline surrogate formulation. Particular attention is devoted to linear and branched saturated hydrocarbons (PRF mixtures), olefins (1-hexene) and aromatics (toluene). Model predictions for pure components, binary mixtures and multi-component gasoline surrogates are compared with recent experimental information collected in rapid compression machine, shock tube and jet stirred reactors covering a wide range of conditions pertinent to internal combustion engines. Simulation results are discussed focusing attention on the mixing effects of the fuel components.

  4. Kinetic model for colchicine inhibition of microtubule assembly

    SciTech Connect

    Sternlicht, H.; Ringel, I.; Szasz, J.

    1980-10-01

    Colchicine is a potent drug used to probe microtubule dependent processes. We have recently shown that substoichiometric concentrations of colchicine-tubulin complex (CD), a 1:1 tight binding complex of drug with tubulin, copolymerizes with tubulin to form microtubule copolymers. The affinity of the microtubule ends for tublin decreased as the CD mole fraction in the microtubule increased. Mole fraction ratios as small as 1 CD to approx. 50 to 100 tubulins in the copolymers were accompanied by a significant change in binding affinities and polymerization rates. We have further extended our investigation of the CD-tubulin copolymerization reaction. A kinetic model was derived which relates the composition of the microtubule copolymer to the composition of the reaction mixture. This model allowed a predictive correlation to be made between copolymer composition and the extent of assembly inhibition.

  5. Working memory in children: tracing age differences and special educational needs to parameters of a formal model.

    PubMed

    Göthe, Katrin; Esser, Günther; Gendt, Anja; Kliegl, Reinhold

    2012-03-01

    Parameters of a formal working-memory model were estimated for verbal and spatial memory updating of children. The model proposes interference though feature overwriting and through confusion of whole elements as the primary cause of working-memory capacity limits. We tested 2 age groups each containing 1 group of normal intelligence and 1 deficit group. For young children the deficit was developmental dyslexia; for older children it was a general learning difficulty. The interference model predicts less interference through overwriting but more through confusion of whole elements for the dyslexic children than for their age-matched controls. Older children exhibited less interference through confusion of whole elements and a higher processing rate than young children, but general learning difficulty was associated with slower processing than in the age-matched control group. Furthermore, the difference between verbal and spatial updating mapped onto several meaningful dissociations of model parameters.

  6. Parameter estimation for models of ligninolytic and cellulolytic enzyme kinetics

    SciTech Connect

    Wang, Gangsheng; Post, Wilfred M; Mayes, Melanie; Frerichs, Joshua T; Jagadamma, Sindhu

    2012-01-01

    While soil enzymes have been explicitly included in the soil organic carbon (SOC) decomposition models, there is a serious lack of suitable data for model parameterization. This study provides well-documented enzymatic parameters for application in enzyme-driven SOC decomposition models from a compilation and analysis of published measurements. In particular, we developed appropriate kinetic parameters for five typical ligninolytic and cellulolytic enzymes ( -glucosidase, cellobiohydrolase, endo-glucanase, peroxidase, and phenol oxidase). The kinetic parameters included the maximum specific enzyme activity (Vmax) and half-saturation constant (Km) in the Michaelis-Menten equation. The activation energy (Ea) and the pH optimum and sensitivity (pHopt and pHsen) were also analyzed. pHsen was estimated by fitting an exponential-quadratic function. The Vmax values, often presented in different units under various measurement conditions, were converted into the same units at a reference temperature (20 C) and pHopt. Major conclusions are: (i) Both Vmax and Km were log-normal distributed, with no significant difference in Vmax exhibited between enzymes originating from bacteria or fungi. (ii) No significant difference in Vmax was found between cellulases and ligninases; however, there was significant difference in Km between them. (iii) Ligninases had higher Ea values and lower pHopt than cellulases; average ratio of pHsen to pHopt ranged 0.3 0.4 for the five enzymes, which means that an increase or decrease of 1.1 1.7 pH units from pHopt would reduce Vmax by 50%. (iv) Our analysis indicated that the Vmax values from lab measurements with purified enzymes were 1 2 orders of magnitude higher than those for use in SOC decomposition models under field conditions.

  7. Ultralocal models of modified gravity without kinetic term

    NASA Astrophysics Data System (ADS)

    Brax, Philippe; Rizzo, Luca Alberto; Valageas, Patrick

    2016-08-01

    We present a class of modified-gravity theories which we call ultralocal models. We add a scalar field, with negligible kinetic terms, to the Einstein-Hilbert action. We also introduce a conformal coupling to matter. This gives rise to a new screening mechanism which is not entirely due to the nonlinearity of the scalar-field potential or the coupling function but to the absence of the kinetic term. As a result this removes any fifth force between isolated objects in vacuum. It turns out that these models are similar to chameleon-type theories with a large mass when considered outside the Compton wavelength but differ on shorter scales. The predictions of these models only depend on a single free function, as the potential and the coupling function are degenerate, with an amplitude given by a parameter α ≲10-6 , whose magnitude springs from requiring a small modification of Newton's potential astrophysically and cosmologically. This singles out a redshift zα˜α-1 /3≳100 where the fifth force is the greatest. The cosmological background follows the Λ cold dark matter (Λ CDM ) history within a 10-6 accuracy, while cosmological perturbations are significantly enhanced (or damped) on small scales, k ≳2 h Mpc-1 at z =0 . The spherical collapse and the halo mass function are modified in the same manner. We find that the modifications of gravity are greater for galactic or subgalactic structures. We also present a thermodynamic analysis of the nonlinear and inhomogeneous fifth-force regime where we find that the Universe is not made more inhomogeneous before zα when the fifth force dominates, and does not lead to the existence of clumped matter on extra small scales inside halos for large masses while this possibility exists for masses M ≲1 011M⊙ where the phenomenology of ultralocal models would be most different from Λ CDM .

  8. Lorentz lattice-gas and kinetic-walk model

    NASA Astrophysics Data System (ADS)

    Ziff, Robert M.; Kong, X. P.; Cohen, E. G. D.

    1991-08-01

    The Ruijgrok-Cohen (RC) mirror model [Phys. Lett. A 133, 415 (1988)] of a Lorentz lattice gas, in which particles are reflected by left and right diagonally oriented mirrors randomly placed on the sites of a square lattice, is further investigated. Extensive computer simulations of individual trajectories up to 224 steps in length, on a lattice of 65 536×65 536 sites, are carried out. This model generates particle trajectories that are related to a variety of kinetic growth and ``smart'' (nontrapping) walks, and provides a kinetic interpretation of them. When all sites are covered with mirrors of both orientations with equal probability, the trajectories are equivalent to smart kinetic walks that effectively generate the hulls of bond percolation clusters at criticality. For this case, 106 trajectories were generated, yielding with unprecedented accuracy an orbit size-distribution exponent of τ=2.1423+/-0.0003 and a fractal dimension of df=1.750 47+/-0.000 24 (without correcting for finite-size effects), compared with theoretical predictions of 15/7=2.142 857. . . and 7/4, respectively. When the total concentration of mirrors C is less than unity, so that the trajectories can cross, the size distribution of the closed orbits does not follow a power law, but appears to be described by a logarithmic function. This function implies that all trajectories eventually close. The geometry of the trajectories does not show clear self-similar or fractal behavior in that the dependence of the mean-square displacement upon the time also appears to follow a logarithmic function. These trajectories are related to the growing self-avoiding trail (GSAT) introduced by Lyklema [J. Phys. A 18, L617 (1985)], and the present work supports the conjecture of Bradley [Phys. Rev. A 41, 914 (1990)] that the GSAT (the RC model with C=2/3) is not at a critical point. It is observed that when C<1, the trajectories behave asymptotically like an unrestricted random walk, and so for comparison

  9. Rigorous valid ranges for optimally reduced kinetic models

    SciTech Connect

    Oluwole, Oluwayemisi O.; Bhattacharjee, Binita; Tolsma, John E.; Barton, Paul I.; Green, William H.

    2006-07-15

    Reduced chemical kinetic models are often used in place of a detailed mechanism because of the computational expense of solving the complete set of equations describing the reacting system. Mathematical methods for model reduction are usually associated with a nominal set of reaction conditions for which the model is reduced. The important effects of variability in these nominal conditions are often ignored because there is no convenient way to deal with them. In this work, we introduce a method to identify rigorous valid ranges for reduced models; i.e., the reduced models are guaranteed to replicate the full model to within an error tolerance under all conditions in the identified valid range. Previous methods have estimated valid ranges using a limited set of variables (usually temperature and a few species compositions) and cannot guarantee that the reduced model is accurate at all points in the estimated range. The new method is demonstrated by identifying valid ranges for models reduced from the GRI-Mech 3.0 mechanism with 53 species and 325 reactions, and a truncated propane mechanism with 94 species and 505 reactions based on the comprehensive mechanism of Marinov et al. A library of reduced models is also generated for several prespecified ranges composing a desired state space. The use of these reduced models with error control in reacting flow simulations is demonstrated through an Adaptive Chemistry example. By using the reduced models in the simulation only when they are valid the Adaptive Chemistry solution matches the solution obtained using the detailed mechanism. (author)

  10. Integration Strategies for Efficient Multizone Chemical Kinetics Models

    SciTech Connect

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

    2009-10-15

    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.

  11. Photon kinetic modeling of laser pulse propagation in underdense plasma

    SciTech Connect

    Reitsma, A. J. W.; Trines, R. M. G. M.; Bingham, R.; Cairns, R. A.; Mendonca, J. T.; Jaroszynski, D. A.

    2006-11-15

    This paper discusses photon kinetic theory, which is a description of the electromagnetic field in terms of classical particles in coordinate and wave number phase space. Photon kinetic theory is applied to the interaction of laser pulses with underdense plasma and the transfer of energy and momentum between the laser pulse and the plasma is described in photon kinetic terms. A comparison is made between a one-dimensional full wave and a photon kinetic code for the same laser and plasma parameters. This shows that the photon kinetic simulations accurately reproduce the pulse envelope evolution for photon frequencies down to the plasma frequency.

  12. Kinetic Modeling of Toluene Oxidation for Surrogate Fuel Applications

    SciTech Connect

    Frassoldati, A; Mehl, M; Fietzek, R; Faravelli, T; Pitz, W J; Ranzi, E

    2009-04-21

    New environmental issues, like the effect of combustion-generated greenhouse gases, provide motivation to better characterize oxidation of hydrocarbons. Transportation, in particular, significantly contributes to energy consumption and CO{sub 2} emissions. Kinetic studies about the combustion of fuels under conditions typical of internal combustion engines provides important support to improve mechanism formulation and to eventually provide better computational tools that can be used to increase the engine performance. It is foreseeable that at least in the next 30 years the main transportation fuels will be either gasoline or diesel. Unfortunately, these fuels are very complex mixtures of many components. Moreover, their specifications and performance requirements significantly change the composition of these fuels: gasoline and diesel mixtures are different if coming from different refineries or they are different from winter to summer. At the same time a fuel with a well defined and reproducible composition is needed for both experimental and modeling work. In response to these issues, surrogate fuels are proposed. Surrogate fuels are defined as mixtures of a small number of hydrocarbons whose relative concentrations is adjusted in order to approximate the chemical and physical properties of a real fuel. Surrogate fuels are then very useful both for the design of reproducible experimental tests and also for the development of reliable kinetic models. The primary reference fuels (PRF) are a typical and old example of surrogate fuel: n-heptane and iso-octane mixtures are used to reproduce antiknock propensity of complex mixtures contained in a gasoline. PRFs are not able to surrogate gasoline in operating conditions different from standard ones and new surrogates have been recently proposed. Toluene is included in all of them as a species able to represent the behavior of aromatic compounds. On the other side, the toluene oxidation chemistry is not so well

  13. Kinetic modeling and sensitivity analysis of plasma-assisted combustion

    NASA Astrophysics Data System (ADS)

    Togai, Kuninori

    Plasma-assisted combustion (PAC) is a promising combustion enhancement technique that shows great potential for applications to a number of different practical combustion systems. In this dissertation, the chemical kinetics associated with PAC are investigated numerically with a newly developed model that describes the chemical processes induced by plasma. To support the model development, experiments were performed using a plasma flow reactor in which the fuel oxidation proceeds with the aid of plasma discharges below and above the self-ignition thermal limit of the reactive mixtures. The mixtures used were heavily diluted with Ar in order to study the reactions with temperature-controlled environments by suppressing the temperature changes due to chemical reactions. The temperature of the reactor was varied from 420 K to 1250 K and the pressure was fixed at 1 atm. Simulations were performed for the conditions corresponding to the experiments and the results are compared against each other. Important reaction paths were identified through path flux and sensitivity analyses. Reaction systems studied in this work are oxidation of hydrogen, ethylene, and methane, as well as the kinetics of NOx in plasma. In the fuel oxidation studies, reaction schemes that control the fuel oxidation are analyzed and discussed. With all the fuels studied, the oxidation reactions were extended to lower temperatures with plasma discharges compared to the cases without plasma. The analyses showed that radicals produced by dissociation of the reactants in plasma plays an important role of initiating the reaction sequence. At low temperatures where the system exhibits a chain-terminating nature, reactions of HO2 were found to play important roles on overall fuel oxidation. The effectiveness of HO2 as a chain terminator was weakened in the ethylene oxidation system, because the reactions of C 2H4 + O that have low activation energies deflects the flux of O atoms away from HO2. For the

  14. Kinetic modeling of methyl butanoate in shock tube.

    PubMed

    Huynh, Lam K; Lin, Kuang C; Violi, Angela

    2008-12-25

    An increased necessity for energy independence and heightened concern about the effects of rising carbon dioxide levels have intensified the search for renewable fuels that could reduce our current consumption of petrol and diesel. One such fuel is biodiesel, which consists of the methyl esters of fatty acids. Methyl butanoate (MB) contains the essential chemical structure of the long-chain fatty acids and a shorter, but similar, alkyl chain. This paper reports on a detailed kinetic mechanism for MB that is assembled using theoretical approaches. Thirteen pathways that include fuel decomposition, isomerization, and propagation steps were computed using ab initio calculations [J. Org. Chem. 2008, 73, 94]. Rate constants from first principles for important reactions in CO(2) formation, namely CH(3)OCO=CH(3) + CO(2) (R1) and CH(3)OCO=CH(3)O + CO (R2) reactions, are computed at high levels of theory and implemented in the mechanism. Using the G3B3 potential energy surface together with the B3LYP/6-31G(d) gradient, Hessian and geometries, the rate constants for reactions R1 and R2 are calculated using the Rice-Ramsperger-Kassel-Marcus theory with corrections from treatments for tunneling, hindered rotation, and variational effects. The calculated rate constants of reaction R1 differ from the data present in the literature by at most 20%, while those of reaction R2 are about a factor of 4 lower than the available values. The new kinetic model derived from ab initio simulations is combined with the kinetic mechanism presented by Fisher et al. [Proc. Combust. Inst. 2000, 28, 1579] together with the addition of the newly found six-centered unimolecular elimination reaction that yields ethylene and methyl acetate, MB = C(2)H(4) + CH(3)COOCH(3). This latter pathway requires the inclusion of the CH(3)COOCH(3) decomposition model suggested by Westbrook et al. [Proc. Combust. Inst. 2008, accepted]. The newly composed kinetic mechanism for MB is used to study the CO(2) formation

  15. Calcite growth kinetics: Modeling the effect of solution stoichiometry

    NASA Astrophysics Data System (ADS)

    Wolthers, Mariëtte; Nehrke, Gernot; Gustafsson, Jon Petter; Van Cappellen, Philippe

    2012-01-01

    Until recently the influence of solution stoichiometry on calcite crystal growth kinetics has attracted little attention, despite the fact that in most aqueous environments calcite precipitates from non-stoichiometric solution. In order to account for the dependence of the calcite crystal growth rate on the cation to anion ratio in solution, we extend the growth model for binary symmetrical electrolyte crystals of Zhang and Nancollas (1998) by combining it with the surface complexation model for the chemical structure of the calcite-aqueous solution interface of Wolthers et al. (2008). To maintain crystal stoichiometry, the rate of attachment of calcium ions to step edges is assumed to equal the rate of attachment of carbonate plus bicarbonate ions. The model parameters are optimized by fitting the model to the step velocities obtained previously by atomic force microscopy (AFM, Teng et al., 2000; Stack and Grantham, 2010). A variable surface roughness factor is introduced in order to reconcile the new process-based growth model with bulk precipitation rates measured in seeded calcite growth experiments. For practical applications, we further present empirical parabolic rate equations fitted to bulk growth rates of calcite in common background electrolytes and in artificial seawater-type solutions. Both the process-based and empirical growth rate equations agree with measured calcite growth rates over broad ranges of ionic strength, pH, solution stoichiometry and degree of supersaturation.

  16. Adaptation of the microdosimetric kinetic model to hypoxia

    NASA Astrophysics Data System (ADS)

    Bopp, C.; Hirayama, R.; Inaniwa, T.; Kitagawa, A.; Matsufuji, N.; Noda, K.

    2016-11-01

    Ion beams present a potential advantage in terms of treatment of lesions with hypoxic regions. In order to use this potential, it is important to accurately model the cell survival of oxic as well as hypoxic cells. In this work, an adaptation of the microdosimetric kinetic (MK) model making it possible to account for cell hypoxia is presented. The adaptation relies on the modification of damage quantity (double strand breaks and more complex lesions) due to the radiation. Model parameters such as domain size and nucleus size are then adapted through a fitting procedure. We applied this approach to two cell lines, HSG and V79 for helium, carbon and neon ions. A similar behaviour of the parameters was found for the two cell lines, namely a reduction of the domain size and an increase in the sensitive nuclear volume of hypoxic cells compared to those of oxic cells. In terms of oxygen enhancement ratio (OER), the experimental data behaviour can be reproduced, including dependence on particle type at the same linear energy transfer (LET). Errors on the cell survival prediction are of the same order of magnitude than for the original MK model. Our adaptation makes it possible to account for hypoxia without modelling the OER as a function of the LET of the particles, but directly accounting for hypoxic cell survival data.

  17. A general kinetic-flow coupling model for FCC riser flow simulation.

    SciTech Connect

    Chang, S. L.

    1998-05-18

    A computational fluid dynamic (CFD) code has been developed for fluid catalytic cracking (FCC) riser flow simulation. Depending on the application of interest, a specific kinetic model is needed for the FCC flow simulation. This paper describes a method to determine a kinetic model based on limited pilot-scale test data. The kinetic model can then be used with the CFD code as a tool to investigate optimum operating condition ranges for a specific FCC unit.

  18. Thermogravimetric and model-free kinetic studies on CO2 gasification of low-quality, high-sulphur Indian coals

    NASA Astrophysics Data System (ADS)

    Das, Tonkeswar; Saikia, Ananya; Mahanta, Banashree; Choudhury, Rahul; Saikia, Binoy K.

    2016-10-01

    Coal gasification with CO2 has emerged as a cleaner and more efficient way for the production of energy, and it offers the advantages of CO2 mitigation policies through simultaneous CO2 sequestration. In the present investigation, a feasibility study on the gasification of three low-quality, high-sulphur coals from the north-eastern region (NER) of India in a CO2 atmosphere using thermogravimetric analysis (TGA-DTA) has been made in order to have a better understanding of the physical and chemical characteristics in the process of gasification of coal. Model-free kinetics was applied to determine the activation energies (E) and pre-exponential factors (A) of the CO2 gasification process of the coals. Multivariate non-linear regression analyses were performed to find out the formal mechanisms, kinetic model, and the corresponding kinetic triplets. The results revealed that coal gasification with CO2 mainly occurs in the temperature range of 800∘-1400∘C and a maximum of at around 1100∘C. The reaction mechanisms responsible for CO2 gasification of the coals were observed to be of the `nth order with autocatalysis (CnB)' and `nth order (Fn) mechanism'. The activation energy of the CO2 gasification was found to be in the range 129.07-146.81 kJ mol-1.

  19. An Experimental and Kinetic Modeling Study of Methyl Decanoate Combustion

    SciTech Connect

    Sarathy, S M; Thomson, M J; Pitz, W J; Lu, T

    2010-02-19

    Biodiesel is typically a mixture of long chain fatty acid methyl esters for use in compression ignition engines. Improving biofuel engine performance requires understanding its fundamental combustion properties and the pathways of combustion. This research study presents new combustion data for methyl decanoate in an opposed-flow diffusion flame. An improved detailed chemical kinetic model for methyl decanoate combustion is developed, which serves as the basis for deriving a skeletal mechanism via the direct relation graph method. The novel skeletal mechanism consists of 648 species and 2998 reactions. This mechanism well predicts the methyl decanoate opposed-flow diffusion flame data. The results from the flame simulations indicate that methyl decanoate is consumed via abstraction of hydrogen atoms to produce fuel radicals, which lead to the production of alkenes. The ester moiety in methyl decanoate leads to the formation of low molecular weight oxygenated compounds such as carbon monoxide, formaldehyde, and ketene.

  20. Prediction of contaminant retention and transport in soils using kinetic multireaction models.

    PubMed Central

    Selim, H M

    1989-01-01

    Mathematical models that describe the retention reactions of contaminants in the soil system are presented. Single and multireaction-type models for simultaneous retention and transport in the soil profile are discussed. Single retention models are classified into two types: equilibrium and kinetic models. Emphasis is given to the nonlinearity and kinetic behavior of solute retention processes in soils. Two-site models that include the equilibrium-kinetic types as well as the fully kinetic type are also examined. A multireaction-type model is also presented, which includes reversible and irreversible retention processes of the equilibrium and kinetic types. Advantages of the multireaction approach over the single or two-site models are discussed. The predictive capability of the two-site model and the multireaction model for their description of experimental results for phosphorus and two heavy metals (Cd and Cr) are examined. PMID:2695326

  1. Growth kinetic model that describes the inhibitory and lytic effects of phenol on Candida tropicalis yeast.

    PubMed

    Ruiz-Ordaz, N; Hernández-Manzano, E; Ruiz-Lagúnez, J C; Cristiani-Urbina, E; Galíndez-Mayer, J

    1998-01-01

    The object of this work was to carry out a kinetic study on the Candida tropicalis cell lysis and to obtain a kinetic model that would describe the inhibitory and lytic effects of phenol on the yeast growth. From the experiments, a model for the growth kinetic behavior of the yeast was evolved. The proposed model describes satisfactorily the inhibitory and lytic effects of phenol on yeast cultures. From the kinetic model constants, it was found that C. tropicalis showed high affinity and tolerance toward phenol. The overall growth yields decreased when the initial phenol concentration increased, and it may be due to an increased maintenance coefficient and to cell lysis.

  2. A computational kinetic model of diffusion for molecular systems.

    PubMed

    Teo, Ivan; Schulten, Klaus

    2013-09-28

    Regulation of biomolecular transport in cells involves intra-protein steps like gating and passage through channels, but these steps are preceded by extra-protein steps, namely, diffusive approach and admittance of solutes. The extra-protein steps develop over a 10-100 nm length scale typically in a highly particular environment, characterized through the protein's geometry, surrounding electrostatic field, and location. In order to account for solute energetics and mobility of solutes in this environment at a relevant resolution, we propose a particle-based kinetic model of diffusion based on a Markov State Model framework. Prerequisite input data consist of diffusion coefficient and potential of mean force maps generated from extensive molecular dynamics simulations of proteins and their environment that sample multi-nanosecond durations. The suggested diffusion model can describe transport processes beyond microsecond duration, relevant for biological function and beyond the realm of molecular dynamics simulation. For this purpose the systems are represented by a discrete set of states specified by the positions, volumes, and surface elements of Voronoi grid cells distributed according to a density function resolving the often intricate relevant diffusion space. Validation tests carried out for generic diffusion spaces show that the model and the associated Brownian motion algorithm are viable over a large range of parameter values such as time step, diffusion coefficient, and grid density. A concrete application of the method is demonstrated for ion diffusion around and through the Eschericia coli mechanosensitive channel of small conductance ecMscS.

  3. Improved Estimation of Human Lipoprotein Kinetics with Mixed Effects Models

    PubMed Central

    Berglund, Martin; Adiels, Martin; Taskinen, Marja-Riitta; Borén, Jan; Wennberg, Bernt

    2015-01-01

    Context Mathematical models may help the analysis of biological systems by providing estimates of otherwise un-measurable quantities such as concentrations and fluxes. The variability in such systems makes it difficult to translate individual characteristics to group behavior. Mixed effects models offer a tool to simultaneously assess individual and population behavior from experimental data. Lipoproteins and plasma lipids are key mediators for cardiovascular disease in metabolic disorders such as diabetes mellitus type 2. By the use of mathematical models and tracer experiments fluxes and production rates of lipoproteins may be estimated. Results We developed a mixed effects model to study lipoprotein kinetics in a data set of 15 healthy individuals and 15 patients with type 2 diabetes. We compare the traditional and the mixed effects approach in terms of group estimates at various sample and data set sizes. Conclusion We conclude that the mixed effects approach provided better estimates using the full data set as well as with both sparse and truncated data sets. Sample size estimates showed that to compare lipoprotein secretion the mixed effects approach needed almost half the sample size as the traditional method. PMID:26422201

  4. Metabolic engineering with multi-objective optimization of kinetic models.

    PubMed

    Villaverde, Alejandro F; Bongard, Sophia; Mauch, Klaus; Balsa-Canto, Eva; Banga, Julio R

    2016-03-20

    Kinetic models have a great potential for metabolic engineering applications. They can be used for testing which genetic and regulatory modifications can increase the production of metabolites of interest, while simultaneously monitoring other key functions of the host organism. This work presents a methodology for increasing productivity in biotechnological processes exploiting dynamic models. It uses multi-objective dynamic optimization to identify the combination of targets (enzymatic modifications) and the degree of up- or down-regulation that must be performed in order to optimize a set of pre-defined performance metrics subject to process constraints. The capabilities of the approach are demonstrated on a realistic and computationally challenging application: a large-scale metabolic model of Chinese Hamster Ovary cells (CHO), which are used for antibody production in a fed-batch process. The proposed methodology manages to provide a sustained and robust growth in CHO cells, increasing productivity while simultaneously increasing biomass production, product titer, and keeping the concentrations of lactate and ammonia at low values. The approach presented here can be used for optimizing metabolic models by finding the best combination of targets and their optimal level of up/down-regulation. Furthermore, it can accommodate additional trade-offs and constraints with great flexibility. PMID:26826510

  5. Gompertz kinetics model of fast chemical neurotransmission currents.

    PubMed

    Easton, Dexter M

    2005-10-01

    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.

  6. Detailed kinetic modeling study of n-pentanol oxidation

    DOE PAGESBeta

    Heufer, K. Alexander; Sarathy, S. Mani; Curran, Henry J.; Davis, Alexander C.; Westbrook, Charles K.; Pitz, William J.

    2012-09-28

    To help overcome the world’s dependence upon fossil fuels, suitable biofuels are promising alternatives that can be used in the transportation sector. Recent research on internal combustion engines shows that short alcoholic fuels (e.g., ethanol or n-butanol) have reduced pollutant emissions and increased knock resistance compared to fossil fuels. Although higher molecular weight alcohols (e.g., n-pentanol and n-hexanol) exhibit higher reactivity that lowers their knock resistance, they are suitable for diesel engines or advanced engine concepts, such as homogeneous charge compression ignition (HCCI), where higher reactivity at lower temperatures is necessary for engine operation. The present study presents a detailedmore » kinetic model for n-pentanol based on modeling rules previously presented for n-butanol. This approach was initially validated using quantum chemistry calculations to verify the most stable n-pentanol conformation and to obtain C–H and C–C bond dissociation energies. In addition, the proposed model has been validated against ignition delay time data, speciation data from a jet-stirred reactor, and laminar flame velocity measurements. Overall, the model shows good agreement with the experiments and permits a detailed discussion of the differences between alcohols and alkanes.« less

  7. Modeling Momentum Transfer from Kinetic Impacts: Implications for Redirecting Asteroids

    DOE PAGESBeta

    Stickle, A. M.; Atchison, J. A.; Barnouin, O. S.; Cheng, A. F.; Crawford, D. A.; Ernst, C. M.; Fletcher, Z.; Rivkin, A. S.

    2015-05-19

    Kinetic impactors are one way to deflect a potentially hazardous object headed for Earth. The Asteroid Impact and Deflection Assessment (AIDA) mission is designed to test the effectiveness of this approach and is a joint effort between NASA and ESA. The NASA-led portion is the Double Asteroid Redirect Test (DART) and is composed of a ~300-kg spacecraft designed to impact the moon of the binary system 65803 Didymos. The deflection of the moon will be measured by the ESA-led Asteroid Impact Mission (AIM) (which will characterize the moon) and from ground-based observations. Because the material properties and internal structure ofmore » the target are poorly constrained, however, analytical models and numerical simulations must be used to understand the range of potential outcomes. Here, we describe a modeling effort combining analytical models and CTH simulations to determine possible outcomes of the DART impact. We examine a wide parameter space and provide predictions for crater size, ejecta mass, and momentum transfer following the impact into the moon of the Didymos system. For impacts into “realistic” asteroid types, these models produce craters with diameters on the order of 10 m, an imparted Δv of 0.5–2 mm/s and a momentum enhancement of 1.07 to 5 for a highly porous aggregate to a fully dense rock.« less

  8. Modeling Momentum Transfer from Kinetic Impacts: Implications for Redirecting Asteroids

    SciTech Connect

    Stickle, A. M.; Atchison, J. A.; Barnouin, O. S.; Cheng, A. F.; Crawford, D. A.; Ernst, C. M.; Fletcher, Z.; Rivkin, A. S.

    2015-05-19

    Kinetic impactors are one way to deflect a potentially hazardous object headed for Earth. The Asteroid Impact and Deflection Assessment (AIDA) mission is designed to test the effectiveness of this approach and is a joint effort between NASA and ESA. The NASA-led portion is the Double Asteroid Redirect Test (DART) and is composed of a ~300-kg spacecraft designed to impact the moon of the binary system 65803 Didymos. The deflection of the moon will be measured by the ESA-led Asteroid Impact Mission (AIM) (which will characterize the moon) and from ground-based observations. Because the material properties and internal structure of the target are poorly constrained, however, analytical models and numerical simulations must be used to understand the range of potential outcomes. Here, we describe a modeling effort combining analytical models and CTH simulations to determine possible outcomes of the DART impact. We examine a wide parameter space and provide predictions for crater size, ejecta mass, and momentum transfer following the impact into the moon of the Didymos system. For impacts into “realistic” asteroid types, these models produce craters with diameters on the order of 10 m, an imparted Δv of 0.5–2 mm/s and a momentum enhancement of 1.07 to 5 for a highly porous aggregate to a fully dense rock.

  9. Metabolic engineering with multi-objective optimization of kinetic models.

    PubMed

    Villaverde, Alejandro F; Bongard, Sophia; Mauch, Klaus; Balsa-Canto, Eva; Banga, Julio R

    2016-03-20

    Kinetic models have a great potential for metabolic engineering applications. They can be used for testing which genetic and regulatory modifications can increase the production of metabolites of interest, while simultaneously monitoring other key functions of the host organism. This work presents a methodology for increasing productivity in biotechnological processes exploiting dynamic models. It uses multi-objective dynamic optimization to identify the combination of targets (enzymatic modifications) and the degree of up- or down-regulation that must be performed in order to optimize a set of pre-defined performance metrics subject to process constraints. The capabilities of the approach are demonstrated on a realistic and computationally challenging application: a large-scale metabolic model of Chinese Hamster Ovary cells (CHO), which are used for antibody production in a fed-batch process. The proposed methodology manages to provide a sustained and robust growth in CHO cells, increasing productivity while simultaneously increasing biomass production, product titer, and keeping the concentrations of lactate and ammonia at low values. The approach presented here can be used for optimizing metabolic models by finding the best combination of targets and their optimal level of up/down-regulation. Furthermore, it can accommodate additional trade-offs and constraints with great flexibility.

  10. Does attainment of Piaget's formal operational level of cognitive development predict student understanding of scientific models?

    NASA Astrophysics Data System (ADS)

    Lahti, Richard Dennis, II

    Knowledge of scientific models and their uses is a concept that has become a key benchmark in many of the science standards of the past 30 years, including the proposed Next Generation Science Standards. Knowledge of models is linked to other important nature of science concepts such as theory change which are also rising in prominence in newer standards. Effective methods of instruction will need to be developed to enable students to achieve these standards. The literature reveals an inconsistent history of success with modeling education. These same studies point to a possible cognitive development component which might explain why some students succeeded and others failed. An environmental science course, rich in modeling experiences, was used to test both the extent to which knowledge of models and modeling could be improved over the course of one semester, and more importantly, to identify if cognitive ability was related to this improvement. In addition, nature of science knowledge, particularly related to theories and theory change, was also examined. Pretest and posttest results on modeling (SUMS) and nature of science (SUSSI), as well as data from the modeling activities themselves, was collected. Cognitive ability was measured (CTSR) as a covariate. Students' gain in six of seven categories of modeling knowledge was at least medium (Cohen's d >.5) and moderately correlated to CTSR for two of seven categories. Nature of science gains were smaller, although more strongly correlated with CTSR. Student success at creating a model was related to CTSR, significantly in three of five sub-categories. These results suggest that explicit, reflective experience with models can increase student knowledge of models and modeling (although higher cognitive ability students may have more success), but successfully creating models may depend more heavily on cognitive ability. This finding in particular has implications in the grade placement of modeling standards and

  11. Kinetic models of laser-tissue fusion processes.

    PubMed

    Pearce, J A; Thomsen, S

    1993-01-01

    Laser tissue fusion processes depend primarily on thermal denaturization of tissue collagen: the fibrils of apposed collagen strands apparently unravel under sufficient heat and re-entwine during the cooling phase. Excessive heating desiccates the fibers to a brittle state unsuitable for fusion while inadequate heating results in weak bonds. In all cases local heat transfer processes significantly affect, and may dominate, the thermal damage realized. Consequently, in addition to spot size power and beam activation time, the choice of laser wavelength is critically dependent on the particular vessel or tissue geometry (chiefly the thickness). We have conducted parametric studies on tissue welding laser activation protocols in transient finite difference numerical models which include tissue water vaporization processes in parallel with kinetic models of collagen and smooth muscle thermal damage. The results show the complex inter-relationship between laser parameters and tissue geometry which determines whether successful fusion may be obtained. The advantage of the numerical modeling approach is that individual physical processes may be studied singly to determine their relative importance.

  12. Kinetic modelling of runaway electrons in dynamic scenarios

    NASA Astrophysics Data System (ADS)

    Stahl, A.; Embréus, O.; Papp, G.; Landreman, M.; Fülöp, T.

    2016-11-01

    Improved understanding of runaway-electron formation and decay processes are of prime interest for the safe operation of large tokamaks, and the dynamics of the runaway electrons during dynamical scenarios such as disruptions are of particular concern. In this paper, we present kinetic modelling of scenarios with time-dependent plasma parameters; in particular, we investigate hot-tail runaway generation during a rapid drop in plasma temperature. With the goal of studying runaway-electron generation with a self-consistent electric-field evolution, we also discuss the implementation of a collision operator that conserves momentum and energy and demonstrate its properties. An operator for avalanche runaway-electron generation, which takes the energy dependence of the scattering cross section and the runaway distribution into account, is investigated. We show that the simplified avalanche model of Rosenbluth and Putvinskii (1997 Nucl. Fusion 37 1355) can give inaccurate results for the avalanche growth rate (either lower or higher) for many parameters, especially when the average runaway energy is modest, such as during the initial phase of the avalanche multiplication. The developments presented pave the way for improved modelling of runaway-electron dynamics during disruptions or other dynamic events.

  13. Kinetic Modeling of Damage Repair, Genome Instability, and Neoplastic Transformation

    SciTech Connect

    Stewart, Robert D

    2007-03-17

    Inducible repair and pathway interactions may fundamentally alter the shape of dose-response curves because different mechanisms may be important under low- and high-dose exposure conditions. However, the significance of these phenomena for risk assessment purposes is an open question. This project developed new modeling tools to study the putative effects of DNA damage induction and repair on higher-level biological endpoints, including cell killing, neoplastic transformation and cancer. The project scope included (1) the development of new approaches to simulate the induction and base excision repair (BER) of DNA damage using Monte Carlo methods and (2) the integration of data from the Monte Carlo simulations with kinetic models for higher-level biological endpoints. Methods of calibrating and testing such multiscale biological simulations were developed. We also developed models to aid in the analysis and interpretation of data from experimental assays, such as the pulsed-field gel electrophoresis (PFGE) assay used to quantity the amount of DNA damage caused by ionizing radiation.

  14. Chemical Kinetic Modeling of HMX and TATB Laser Ignition Tests

    SciTech Connect

    Tarver, C M

    2004-03-02

    Recent laser ignition experiments on octahydro-1,3,5,7-tetranitro-1,3,5,7-terrazocine (HMX) and 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) subjected to laser fluxes ranging from 10 to 800 W/cm{sup 2} produced ignition times from seconds to milliseconds. Global chemical kinetic thermal decomposition models for HMX and TATB have been developed to calculate times to thermal explosion for experiments in the seconds to days time frame. These models are applied to the laser ignition experimental data in this paper. Excellent agreement was obtained for TATB, while the calculated ignition times were longer than experiment for HMX at lower laser fluxes. At the temperatures produced in the laser experiments, HMX melts. Melting generally increases condensed phase reaction rates so faster rates were used for three of the HMX reaction rates. This improved agreement with experiments at the lower laser fluxes but yielded very fast ignition at high fluxes. The calculated times to ignition are in reasonable agreement with the laser ignition experiments, and this justifies the use of these models for estimating reaction times at impact and shock ''hot spot'' temperatures.

  15. A kinetic model of rapidly reversible nonphotochemical quenching

    PubMed Central

    Zaks, Julia; Amarnath, Kapil; Kramer, David M.; Niyogi, Krishna K.; Fleming, Graham R.

    2012-01-01

    Oxygen-evolving photosynthetic organisms possess nonphotochemical quenching (NPQ) pathways that protect against photo-induced damage. The majority of NPQ in plants is regulated on a rapid timescale by changes in the pH of the thylakoid lumen. In order to quantify the rapidly reversible component of NPQ, called qE, we developed a mathematical model of pH-dependent quenching of chlorophyll excitations in Photosystem II. Our expression for qE depends on the protonation of PsbS and the deepoxidation of violaxanthin by violaxanthin deepoxidase. The model is able to simulate the kinetics of qE at low and high light intensities. The simulations suggest that the pH of the lumen, which activates qE, is not itself affected by qE. Our model provides a framework for testing hypothesized qE mechanisms and for assessing the role of qE in improving plant fitness in variable light intensity. PMID:22891305

  16. A kinetic model for RNA-interference of focal adhesions

    PubMed Central

    2013-01-01

    Background Focal adhesions are integrin-based cell-matrix contacts that transduce and integrate mechanical and biochemical cues from the environment. They develop from smaller and more numerous focal complexes under the influence of mechanical force and are key elements for many physiological and disease-related processes, including wound healing and metastasis. More than 150 different proteins localize to focal adhesions and have been systematically classified in the adhesome project (http://www.adhesome.org). First RNAi-screens have been performed for focal adhesions and the effect of knockdown of many of these components on the number, size, shape and location of focal adhesions has been reported. Results We have developed a kinetic model for RNA interference of focal adhesions which represents some of its main elements: a spatially layered structure, signaling through the small GTPases Rac and Rho, and maturation from focal complexes to focal adhesions under force. The response to force is described by two complementary scenarios corresponding to slip and catch bond behavior, respectively. Using estimated and literature values for the model parameters, three time scales of the dynamics of RNAi-influenced focal adhesions are identified: a sub-minute time scale for the assembly of focal complexes, a sub-hour time scale for the maturation to focal adhesions, and a time scale of days that controls the siRNA-mediated knockdown. Our model shows bistability between states dominated by focal complexes and focal adhesions, respectively. Catch bonding strongly extends the range of stability of the state dominated by focal adhesions. A sensitivity analysis predicts that knockdown of focal adhesion components is more efficient for focal adhesions with slip bonds or if the system is in a state dominated by focal complexes. Knockdown of Rho leads to an increase of focal complexes. Conclusions The suggested model provides a kinetic description of the effect of RNA

  17. Chemical kinetic modeling of component mixtures relevant to gasoline

    SciTech Connect

    Mehl, M; Curran, H J; Pitz, W J; Dooley, S; Westbrook, C K

    2008-05-29

    Detailed kinetic models of pyrolysis and combustion of hydrocarbon fuels are nowadays widely used in the design of internal combustion engines and these models are effectively applied to help meet the increasingly stringent environmental and energetic standards. In previous studies by the combustion community, such models not only contributed to the understanding of pure component combustion, but also provided a deeper insight into the combustion behavior of complex mixtures. One of the major challenges in this field is now the definition and the development of appropriate surrogate models able to mimic the actual features of real fuels. Real fuels are complex mixtures of thousands of hydrocarbon compounds including linear and branched paraffins, naphthenes, olefins and aromatics. Their behavior can be effectively reproduced by simpler fuel surrogates containing a limited number of components. Aside the most commonly used surrogates containing iso-octane and n-heptane only, the so called Primary Reference Fuels (PRF), new mixtures have recently been suggested to extend the reference components in surrogate mixtures to also include alkenes and aromatics. It is generally agreed that, including representative species for all the main classes of hydrocarbons which can be found in real fuels, it is possible to reproduce very effectively in a wide range of operating conditions not just the auto-ignition propensity of gasoline or Diesel fuels, but also their physical properties and their combustion residuals [1]. In this work, the combustion behavior of several components relevant to gasoline surrogate formulation is computationally examined. The attention is focused on the autoignition of iso-octane, hexene and their mixtures. Some important issues relevant to the experimental and modeling investigation of such fuels are discussed with the help of rapid compression machine data and calculations. Following the model validation, the behavior of mixtures is discussed on the

  18. A Model-Fitting Approach to Characterizing Polymer Decomposition Kinetics

    SciTech Connect

    Burnham, A K; Weese, R K

    2004-07-20

    The use of isoconversional, sometimes called model-free, kinetic analysis methods have recently gained favor in the thermal analysis community. Although these methods are very useful and instructive, the conclusion that model fitting is a poor approach is largely due to improper use of the model fitting approach, such as fitting each heating rate separately. The current paper shows the ability of model fitting to correlate reaction data over very wide time-temperature regimes, including simultaneous fitting of isothermal and constant heating rate data. Recently published data on cellulose pyrolysis by Capart et al. (TCA, 2004) with a combination of an autocatalytic primary reaction and an nth-order char pyrolysis reaction is given as one example. Fits for thermal decomposition of Estane, Viton-A, and Kel-F over very wide ranges of heating rates is also presented. The Kel-F required two parallel reactions--one describing a small, early decomposition process, and a second autocatalytic reaction describing the bulk of pyrolysis. Viton-A and Estane also required two parallel reactions for primary pyrolysis, with the first Viton-A reaction also being a minor, early process. In addition, the yield of residue from these two polymers depends on the heating rate. This is an example of a competitive reaction between volatilization and char formation, which violates the basic tenet of the isoconversional approach and is an example of why it has limitations. Although more complicated models have been used in the literature for this type of process, we described our data well with a simple addition to the standard model in which the char yield is a function of the logarithm of the heating rate.

  19. From a hybrid model to a fully kinetic model: On the modeling of planetary plasma environments by a fully kinetic electromagnetic global model HYB-em

    NASA Astrophysics Data System (ADS)

    Pohjola, Valter; Kallio, Esa; Jarvinen, Riku

    We have developed a fully kinetic electromagnetic model to study instabilities and waves in planetary plasma environments. In the particle-in-a-cell (PIC) model both ions and electrons are modeled as particles. An important feature of the developed global kinetic model, called HYB-em, compared to other electromagnetic codes is that it is built up on an earlier quasi-neutral hybrid simulation platform called HYB and that it can be used in conjunction with earlier hybrid models. The HYB models have been used during the past ten years to study globally the flowing plasma interaction with various Solar System objects: Mercury, Venus, the Moon, Mars, Saturnian moon Titan and asteroids. The new model enables us to (1) study the stability of various planetary plasma regions in three dimensional space, (2) analyze the propa-gation of waves in a plasma environment derived from the other global HYB models. All particle processes in a multi-ion plasma which are implemented on the HYB platform(e.g. ion-neutral collisions, chemical processes, particle loss and production processes) are also automatically included in HYB-em model. In this presentation we study the developed approach by analyzing the propagation of high frequency electromagnetic waves in non-magnetized plasma in two cases: We study (1) expan-sion of a spherical wave generated from a point source and (2) propagation of a plane wave in plasma. We demonstrate that the HYB-em model is capable of describing these space plasma situations successfully. The analysis suggests the potential of the developed model to study both high density-high magnetic field plasma environments, such as Mercury, and low density-low magnetic field plasma environments, such as Venus and Mars.

  20. From a hybrid model to a fully kinetic model: On the modeling of planetary plasma environments by a fully kinetic electromagnetic global model HYB-em

    NASA Astrophysics Data System (ADS)

    Pohjola, Valter; Kallio, Esa

    2010-05-01

    We have developed a fully kinetic electromagnetic model to study instabilities and waves in planetary plasma environments. In the particle-in-a-cell (PIC) model both ions and electrons are modeled as particles. An important feature of the developed global kinetic model, called HYB-em, compared to other electromagnetic codes is that it is built up on an earlier quasi-neutral hybrid simulation platform called HYB and that it can be used in conjunction with earlier hybrid models. The HYB models have been used during the past ten years to study globally the flowing plasma interaction with various Solar System objects: Mercury, Venus, the Moon, Mars, Saturnian moon Titan and asteroids. The new model enables us to (1) study the stability of various planetary plasma regions in three dimensional space, (2) analyze the propagation of waves in a plasma environment derived from the other global HYB models. All particle processes in a multi-ion plasma which are implemented on the HYB platform (e.g. ion-neutral-collisions, chemical processes, particle loss and production processes) are also automatically included in HYB-em model. In this presentation we study the developed approach by analyzing the propagation of high frequency electromagnetic waves in non-magnetized plasma in two cases: We study (1) expansion of a spherical wave generated from a point source and (2) propagation of a plane wave in plasma. We demonstrate that the HYB-em model is capable of describing these space plasma situations successfully. The analysis suggests the potential of the developed model to study both high density-high magnetic field plasma environments, such as Mercury, and low density-low magnetic field plasma environments, such as Venus and Mars.

  1. Kinetic Modeling of the Lunar Dust-Plasma Environment

    NASA Astrophysics Data System (ADS)

    Kallio, Esa; Alho, Markku; Alvarez, Francisco; Barabash, Stas; Dyadechkin, Sergey; Fernandes, Vera; Futaana, Yoshifumi; Harri, Ari-Matti; Haunia, Touko; Heilimo, Jyri; Holmström, Mats; Jarvinen, Riku; Lue, Charles; Makela, Jakke; Porjo, Niko; Schmidt, Walter; Shahab, Fatemi; Siili, Tero; Wurz, Peter

    2014-05-01

    Modeling of the lunar dust and plasma environment is a challenging task because a self-consistent model should include ions, electrons and dust particles and numerous other factors. However, most of the parameters are not well established or constrained by measurements in the lunar environment. More precisely, a comprehensive model should contain electrons originating from 1) the solar wind, 2) the lunar material (photoelectrons, secondary electrons) and 3) the lunar dust. Ions originate from the solar wind, the lunar material, the lunar exosphere and the dust. To model the role of the dust in the lunar plasma environment is a highly complex task since the properties of the dust particles in the exosphere are poorly known (e.g. mass, size, shape, conductivity) or not known (e.g. charge and photoelectron emission) and probably are time dependent. Models should also include the effects of interactions between the surface and solar wind and energetic particles, and micrometeorites. Largely different temporal and spatial scales are also a challenge for the numerical models. In addition, the modeling of a region on the Moon - for example on the South Pole - at a given time requires also knowledge of the solar illumination conditions at that time, mineralogical and electric properties of the local lunar surface, lunar magnetic anomalies, solar UV flux and the properties of the solar wind. Harmful effects of lunar dust to technical devices and to human health as well as modeling of the properties of the lunar plasma and dust environment have been topics of two ESA funded projects L-DEPP and DPEM. In the presentation we will summarize some basic results and characteristics of plasma and fields near and around the Moon as studied and discovered in these projects. Especially, we analyse three different space and time scales by kinetic models: [1] the "microscale" region near surface with an electrostatic PIC (ions and electrons are particles) model, [2] the "mesoscale

  2. Formal verification of AI software

    NASA Technical Reports Server (NTRS)

    Rushby, John; Whitehurst, R. Alan

    1989-01-01

    The application of formal verification techniques to Artificial Intelligence (AI) software, particularly expert systems, is investigated. Constraint satisfaction and model inversion are identified as two formal specification paradigms for different classes of expert systems. A formal definition of consistency is developed, and the notion of approximate semantics is introduced. Examples are given of how these ideas can be applied in both declarative and imperative forms.

  3. A hybrid method for hydrodynamic-kinetic flow - Part II - Coupling of hydrodynamic and kinetic models

    NASA Astrophysics Data System (ADS)

    Alaia, Alessandro; Puppo, Gabriella

    2012-06-01

    In this work we present a non stationary domain decomposition algorithm for multiscale hydrodynamic-kinetic problems, in which the Knudsen number may span from equilibrium to highly rarefied regimes. Our approach is characterized by using the full Boltzmann equation for the kinetic regime, the Compressible Euler equations for equilibrium, with a buffer zone in which the BGK-ES equation is used to represent the transition between fully kinetic to equilibrium flows. In this fashion, the Boltzmann solver is used only when the collision integral is non-stiff, and the mean free path is of the same order as the mesh size needed to capture variations in macroscopic quantities. Thus, in principle, the same mesh size and time steps can be used in the whole computation. Moreover, the time step is limited only by convective terms. Since the Boltzmann solver is applied only in wholly kinetic regimes, we use the reduced noise DSMC scheme we have proposed in Part I of the present work. This ensures a smooth exchange of information across the different domains, with a natural way to construct interface numerical fluxes. Several tests comparing our hybrid scheme with full Boltzmann DSMC computations show the good agreement between the two solutions, on a wide range of Knudsen numbers.

  4. Heterogeneous kinetic modeling of the catalytic conversion of cycloparaffins

    NASA Astrophysics Data System (ADS)

    Al-Sabawi, Mustafa N.

    catalytic conversions respectively, are reported. Using these data, heterogeneous kinetic models accounting for intracrystallite molecular transport, adsorption and thermal and catalytic cracking of both cycloparaffin reactants are established. Results show that undesirable hydrogen transfer reactions are more pronounced and selectively favoured against other reactions at lower reaction temperatures, while the desirable ring-opening and cracking reactions predominate at the higher reaction temperatures. Moreover, results of the present work show that while crystallite size may have an effect on the overall conversion in some situations, there is a definite effect on the selectivity of products obtained during the cracking of MCH and decalin and the cracking of MCH in a mixture with co-reactants such as 1,3,5-triisopropylbenzene. Keywords. cycloparaffins, naphthenes, fluid catalytic cracking, kinetic modeling, Y-zeolites, diffusion, adsorption, ring-opening, hydrogen transfer, catalyst selectivity.

  5. Formalize clinical processes into electronic health information systems: Modelling a screening service for diabetic retinopathy.

    PubMed

    Eguzkiza, Aitor; Trigo, Jesús Daniel; Martínez-Espronceda, Miguel; Serrano, Luis; Andonegui, José

    2015-08-01

    Most healthcare services use information and communication technologies to reduce and redistribute the workload associated with follow-up of chronic conditions. However, the lack of normalization of the information handled in and exchanged between such services hinders the scalability and extendibility. The use of medical standards for modelling and exchanging information, especially dual-model based approaches, can enhance the features of screening services. Hence, the approach of this paper is twofold. First, this article presents a generic methodology to model patient-centered clinical processes. Second, a proof of concept of the proposed methodology was conducted within the diabetic retinopathy (DR) screening service of the Health Service of Navarre (Spain) in compliance with a specific dual-model norm (openEHR). As a result, a set of elements required for deploying a model-driven DR screening service has been established, namely: clinical concepts, archetypes, termsets, templates, guideline definition rules, and user interface definitions. This model fosters reusability, because those elements are available to be downloaded and integrated in any healthcare service, and interoperability, since from then on such services can share information seamlessly.

  6. Formalize clinical processes into electronic health information systems: Modelling a screening service for diabetic retinopathy.

    PubMed

    Eguzkiza, Aitor; Trigo, Jesús Daniel; Martínez-Espronceda, Miguel; Serrano, Luis; Andonegui, José

    2015-08-01

    Most healthcare services use information and communication technologies to reduce and redistribute the workload associated with follow-up of chronic conditions. However, the lack of normalization of the information handled in and exchanged between such services hinders the scalability and extendibility. The use of medical standards for modelling and exchanging information, especially dual-model based approaches, can enhance the features of screening services. Hence, the approach of this paper is twofold. First, this article presents a generic methodology to model patient-centered clinical processes. Second, a proof of concept of the proposed methodology was conducted within the diabetic retinopathy (DR) screening service of the Health Service of Navarre (Spain) in compliance with a specific dual-model norm (openEHR). As a result, a set of elements required for deploying a model-driven DR screening service has been established, namely: clinical concepts, archetypes, termsets, templates, guideline definition rules, and user interface definitions. This model fosters reusability, because those elements are available to be downloaded and integrated in any healthcare service, and interoperability, since from then on such services can share information seamlessly. PMID:26049092

  7. Kinetic Modeling of a Heterogeneous Fenton Oxidative Treatment of Petroleum Refining Wastewater

    PubMed Central

    Basheer Hasan, Diya'uddeen; Abdul Raman, Abdul Aziz; Wan Daud, Wan Mohd Ashri

    2014-01-01

    The mineralisation kinetics of petroleum refinery effluent (PRE) by Fenton oxidation were evaluated. Within the ambit of the experimental data generated, first-order kinetic model (FKM), generalised lumped kinetic model (GLKM), and generalized kinetic model (GKM) were tested. The obtained apparent kinetic rate constants for the initial oxidation step (k2′), their final oxidation step (k1′), and the direct conversion to endproducts step (k3′) were 10.12, 3.78, and 0.24 min−1 for GKM; 0.98, 0.98, and nil min−1 for GLKM; and nil, nil, and >0.005 min−1 for FKM. The findings showed that GKM is superior in estimating the mineralization kinetics. PMID:24592152

  8. Kinetic modeling of a heterogeneous Fenton oxidative treatment of petroleum refining wastewater.

    PubMed

    Hasan, Diya'uddeen Basheer; Abdul Raman, Abdul Aziz; Daud, Wan Mohd Ashri Wan

    2014-01-01

    The mineralisation kinetics of petroleum refinery effluent (PRE) by Fenton oxidation were evaluated. Within the ambit of the experimental data generated, first-order kinetic model (FKM), generalised lumped kinetic model (GLKM), and generalized kinetic model (GKM) were tested. The obtained apparent kinetic rate constants for the initial oxidation step (k'2), their final oxidation step (k'1), and the direct conversion to endproducts step (k3') were 10.12, 3.78, and 0.24 min(-1) for GKM; 0.98, 0.98, and nil min(-1) for GLKM; and nil, nil, and >0.005 min(-1) for FKM. The findings showed that GKM is superior in estimating the mineralization kinetics.

  9. Kinetic Modeling of Combustion Characteristics of Real Biodiesel Fuels

    SciTech Connect

    Naik, C V; Westbrook, C K

    2009-04-08

    Biodiesel fuels are of much interest today either for replacing or blending with conventional fuels for automotive applications. Predicting engine effects of using biodiesel fuel requires accurate understanding of the combustion characteristics of the fuel, which can be acquired through analysis using reliable detailed reaction mechanisms. Unlike gasoline or diesel that consists of hundreds of chemical compounds, biodiesel fuels contain only a limited number of compounds. Over 90% of the biodiesel fraction is composed of 5 unique long-chain C{sub 18} and C{sub 16} saturated and unsaturated methyl esters. This makes modeling of real biodiesel fuel possible without the need for a fuel surrogate. To this end, a detailed chemical kinetic mechanism has been developed for determining the combustion characteristics of a pure biodiesel (B100) fuel, applicable from low- to high-temperature oxidation regimes. This model has been built based on reaction rate rules established in previous studies at Lawrence Livermore National Laboratory. Computed results are compared with the few fundamental experimental data that exist for biodiesel fuel and its components. In addition, computed results have been compared with experimental data for other long-chain hydrocarbons that are similar in structure to the biodiesel components.

  10. Kinetic modeling of copper biosorption by immobilized biomass

    SciTech Connect

    Veglio, F.; Beolchini, F.; Toro, L.

    1998-03-01

    Biosorption of heavy metals is one of the most promising technologies involved in the removal of toxic metals from industrial waste streams and natural waters. The kinetic modeling of copper biosorption by Arthrobacter sp. immobilized in a hydroxyethyl methacrylate-based matrix is reported in this work. The resin-biomass complex (RBC) has been used for copper biosorption in different conditions according to a factorial experiment. Factors investigated were cross-linker (trimethylolpropane trimethacrylate) concentration, biomass concentration in the solid, and particles` granulometry. A maximum copper specific uptake of abut 7 mg of Cu/g of biomass (dry weight) has been observed, in the case of a RBC with the following characteristics: 2% (w/w) cross-linker concentration, 8% (w/w) biomass concentration, and 425--750 {micro}m granulometry. The shrinking core model has been used for the fitting of experimental data. A good fit has been found in the case of controlling intraparticle diffusion in all experimental trials. The copper diffusion coefficient in RBC has been estimated from the slope of the regression lines. Values obtained for the diffusion coefficients do not differ from one another with respect to the estimated standard error. An average apparent copper diffusion coefficient of about 3 {times} 10{sup {minus}6} cm{sup 2}/s has been found.

  11. Amylolysis of maize mutant starches described with a fractal-like kinetics model.

    PubMed

    Kansou, Kamal; Buléon, Alain; Gérard, Catherine; Rolland-Sabaté, Agnès

    2015-06-01

    Two empirical models, a conventional first-order kinetics and a fractal-like first-order kinetic model were tested for analysing the hydrolysis of 13 wild type, single and double mutants of maize starch by porcine pancreatic α-amylase (PPA). The major difference between the two models is an additional parameter, the fractal kinetics exponent h, which enables to characterise a decrease of the reaction rate coefficient over time. The fractal-like kinetic model should be preferred to characterise the amylolysis for 10 mutants out of 13 as sugary-2 and amylose-extender curves exhibit clear reaction rate retardation, unlike normal maize and waxy maize. Analysis of the model parameter values reveals two groups of kinetics for the maize mutants: amylose-extender, normal and waxy on one hand, sugary-2 on the other hand. Possible relations between the parameters of the model and granule composition and structure are discussed.

  12. A Model of Adding Relations in Multi-levels to a Formal Organization Structure with Two Subordinates

    NASA Astrophysics Data System (ADS)

    Sawada, Kiyoshi; Amano, Kazuyuki

    2009-10-01

    This paper proposes a model of adding relations in multi-levels to a formal organization structure with two subordinates such that the communication of information between every member in the organization becomes the most efficient. When edges between every pair of nodes with the same depth in L (L = 1, 2, …, H) levels are added to a complete binary tree of height H, an optimal set of depths {N1, N2, …, NL} (H⩾N1>N2> …>NL⩾1) is obtained by maximizing the total shortening path length which is the sum of shortening lengths of shortest paths between every pair of all nodes in the complete binary tree. It is shown that {N1, N2, …, NL}* = {H, H-1, …, H-L+1}.

  13. A modified cable formalism for modeling neuronal membranes at high frequencies.

    PubMed

    Bédard, Claude; Destexhe, Alain

    2008-02-15

    Intracellular recordings of cortical neurons in vivo display intense subthreshold membrane potential (V(m)) activity. The power spectral density of the V(m) displays a power-law structure at high frequencies (>50 Hz) with a slope of approximately -2.5. This type of frequency scaling cannot be accounted for by traditional models, as either single-compartment models or models based on reconstructed cell morphologies display a frequency scaling with a slope close to -4. This slope is due to the fact that the membrane resistance is short-circuited by the capacitance for high frequencies, a situation which may not be realistic. Here, we integrate nonideal capacitors in cable equations to reflect the fact that the capacitance cannot be charged instantaneously. We show that the resulting nonideal cable model can be solved analytically using Fourier transforms. Numerical simulations using a ball-and-stick model yield membrane potential activity with similar frequency scaling as in the experiments. We also discuss the consequences of using nonideal capacitors on other cellular properties such as the transmission of high frequencies, which is boosted in nonideal cables, or voltage attenuation in dendrites. These results suggest that cable equations based on nonideal capacitors should be used to capture the behavior of neuronal membranes at high frequencies. PMID:17921220

  14. A Modified Cable Formalism for Modeling Neuronal Membranes at High Frequencies

    PubMed Central

    Bédard, Claude; Destexhe, Alain

    2008-01-01

    Intracellular recordings of cortical neurons in vivo display intense subthreshold membrane potential (Vm) activity. The power spectral density of the Vm displays a power-law structure at high frequencies (>50 Hz) with a slope of ∼−2.5. This type of frequency scaling cannot be accounted for by traditional models, as either single-compartment models or models based on reconstructed cell morphologies display a frequency scaling with a slope close to −4. This slope is due to the fact that the membrane resistance is short-circuited by the capacitance for high frequencies, a situation which may not be realistic. Here, we integrate nonideal capacitors in cable equations to reflect the fact that the capacitance cannot be charged instantaneously. We show that the resulting nonideal cable model can be solved analytically using Fourier transforms. Numerical simulations using a ball-and-stick model yield membrane potential activity with similar frequency scaling as in the experiments. We also discuss the consequences of using nonideal capacitors on other cellular properties such as the transmission of high frequencies, which is boosted in nonideal cables, or voltage attenuation in dendrites. These results suggest that cable equations based on nonideal capacitors should be used to capture the behavior of neuronal membranes at high frequencies. PMID:17921220

  15. Kinetic theories for spin models for cooperative relaxation dynamics

    NASA Astrophysics Data System (ADS)

    Pitts, Steven Jerome

    The facilitated kinetic Ising models with asymmetric spin flip constraints introduced by Jackle and co-workers [J. Jackle, S. Eisinger, Z. Phys. B 84, 115 (1991); J. Reiter, F. Mauch, J. Jackle, Physica A 184, 458 (1992)] exhibit complex relaxation behavior in their associated spin density time correlation functions. This includes the growth of relaxation times over many orders of magnitude when the thermodynamic control parameter is varied, and, in some cases, ergodic-nonergodic transitions. Relaxation equations for the time dependence of the spin density autocorrelation function for a set of these models are developed that relate this autocorrelation function to the irreducible memory function of Kawasaki [K. Kawasaki, Physica A 215, 61 (1995)] using a novel diagrammatic series approach. It is shown that the irreducible memory function in a theory of the relaxation of an autocorrelation function in a Markov model with detailed balance plays the same role as the part of the memory function approximated by a polynomial function of the autocorrelation function with positive coefficients in schematic simple mode coupling theories for supercooled liquids [W. Gotze, in Liquids, Freezing and the Glass Transition, D. Levesque, J. P. Hansen, J. Zinn-Justin eds., 287 (North Holland, New York, 1991)]. Sets of diagrams in the series for the irreducible memory function are summed which lead to approximations of this type. The behavior of these approximations is compared with known results from previous analytical calculations and from numerical simulations. For the simplest one dimensional model, relaxation equations that are closely related to schematic extended mode coupling theories [W. Gotze, ibid] are also derived using the diagrammatic series. Comparison of the results of these approximate theories with simulation data shows that these theories improve significantly on the results of the theories of the simple schematic mode coupling theory type. The potential

  16. Intrinsic radio-sensitivity of tumours to low let radiations: a mathematical model in LQ formalism.

    PubMed

    Mohammed, Sk Ayasuddin

    2013-12-01

    Intrinsic radio-sensitivity is the determinant of differential response of tumours to low LET ionising radiations. The probabilistic DNA fibril both model shows intrinsic radio-sensitivity factor [I] as function of nuclear diameter (Nd) and intra cellular hydrogen ion concentration [H+]. Linking probabilities of lethal and sub-lethal events to [I] further results in equations which show the LQ parameters namely alpha and beta are functions of (Nd), [H+] and repair constant (μ) mu. This model is able to explain radiobiological phenomena of OER and Do value of lymphocytes.

  17. Microbial Kinetic Model for the Degradation of Poorly Soluble Organic Materials

    EPA Science Inventory

    A novel mechanistic model is presented that describes the aerobic biodegradation kinetics of soybean biodiesel and petroleum diesel in batch experiments. The model was built on the assumptions that biodegradation takes place in the aqueous phase according to Monod kinetics, and ...

  18. Formal Verification of a Power Controller Using the Real-Time Model Checker UPPAAL

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus; Larsen, Kim Guldstrand; Skou, Arne

    1999-01-01

    A real-time system for power-down control in audio/video components is modeled and verified using the real-time model checker UPPAAL. The system is supposed to reside in an audio/video component and control (read from and write to) links to neighbor audio/video components such as TV, VCR and remote-control. In particular, the system is responsible for the powering up and down of the component in between the arrival of data, and in order to do so in a safe way without loss of data, it is essential that no link interrupts are lost. Hence, a component system is a multitasking system with hard real-time requirements, and we present techniques for modeling time consumption in such a multitasked, prioritized system. The work has been carried out in a collaboration between Aalborg University and the audio/video company B&O. By modeling the system, 3 design errors were identified and corrected, and the following verification confirmed the validity of the design but also revealed the necessity for an upper limit of the interrupt frequency. The resulting design has been implemented and it is going to be incorporated as part of a new product line.

  19. Formalizing the Role of Agent-Based Modeling in Causal Inference and Epidemiology

    PubMed Central

    Marshall, Brandon D. L.; Galea, Sandro

    2015-01-01

    Calls for the adoption of complex systems approaches, including agent-based modeling, in the field of epidemiology have largely centered on the potential for such methods to examine complex disease etiologies, which are characterized by feedback behavior, interference, threshold dynamics, and multiple interacting causal effects. However, considerable theoretical and practical issues impede the capacity of agent-based methods to examine and evaluate causal effects and thus illuminate new areas for intervention. We build on this work by describing how agent-based models can be used to simulate counterfactual outcomes in the presence of complexity. We show that these models are of particular utility when the hypothesized causal mechanisms exhibit a high degree of interdependence between multiple causal effects and when interference (i.e., one person's exposure affects the outcome of others) is present and of intrinsic scientific interest. Although not without challenges, agent-based modeling (and complex systems methods broadly) represent a promising novel approach to identify and evaluate complex causal effects, and they are thus well suited to complement other modern epidemiologic methods of etiologic inquiry. PMID:25480821

  20. Kinetics and fixed-bed reactor modeling of butane oxidation to maleic anhydride

    SciTech Connect

    Sharma, R.K.; Cresswell, D.L. ); Newson, E.J. )

    1991-01-01

    This paper reports on selective oxidation kinetics of n-butane to maleic anhydride in air studied over a commercial, fixed-bed vanadium-phosphor oxide catalyst. The temperature range was 573-653 K with butane concentrations up to 3 mol % in the feed, which is within flammability limits but below ignition temperatures. The rate data were modeled using power law kinetics with product inhibition and included total oxidation and decomposition reactions. Kinetic parameters were estimated using a multiresponse, nonlinear regression algorithm showing intercorrelation effects. The kinetics were combined with independent measurements of catalyst diffusivity and reactor heat transfer using a one- dimensional heterogeneous reactor model.

  1. Bootstrapping in a language of thought: a formal model of numerical concept learning.

    PubMed

    Piantadosi, Steven T; Tenenbaum, Joshua B; Goodman, Noah D

    2012-05-01

    In acquiring number words, children exhibit a qualitative leap in which they transition from understanding a few number words, to possessing a rich system of interrelated numerical concepts. We present a computational framework for understanding this inductive leap as the consequence of statistical inference over a sufficiently powerful representational system. We provide an implemented model that is powerful enough to learn number word meanings and other related conceptual systems from naturalistic data. The model shows that bootstrapping can be made computationally and philosophically well-founded as a theory of number learning. Our approach demonstrates how learners may combine core cognitive operations to build sophisticated representations during the course of development, and how this process explains observed developmental patterns in number word learning.

  2. Vlasov formalism for extended relativistic mean field models: The crust-core transition and the stellar matter equation of state

    NASA Astrophysics Data System (ADS)

    Pais, Helena; Providência, Constança

    2016-07-01

    The Vlasov formalism is extended to relativistic mean field hadron models with nonlinear terms up to fourth order and applied to the calculation of the crust-core transition density. The effect of the nonlinear ω ρ and σ ρ coupling terms on the crust-core transition density and pressure and on the macroscopic properties of some families of hadronic stars is investigated. For that purpose, six families of relativistic mean field models are considered. Within each family, the members differ in the symmetry energy behavior. For all the models, the dynamical spinodals are calculated, and the crust-core transition density and pressure and the neutron star mass-radius relations are obtained. The effect on the star radius of the inclusion of a pasta calculation in the inner crust is discussed. The set of six models that best satisfy terrestrial and observational constraints predicts a radius of 13.6 ±0.3 km and a crust thickness of 1.36 ±0.06 km for a 1.4 M⊙ star.

  3. Freed by interaction kinetic states in the Harper model

    NASA Astrophysics Data System (ADS)

    Frahm, Klaus M.; Shepelyansky, Dima L.

    2015-12-01

    We study the problem of two interacting particles in a one-dimensional quasiperiodic lattice of the Harper model. We show that a short or long range interaction between particles leads to emergence of delocalized pairs in the non-interacting localized phase. The properties of these freed by interaction kinetic states (FIKS) are analyzed numerically including the advanced Arnoldi method. We find that the number of sites populated by FIKS pairs grows algebraically with the system size with the maximal exponent b = 1, up to a largest lattice size N = 10 946 reached in our numerical simulations, thus corresponding to a complete delocalization of pairs. For delocalized FIKS pairs the spectral properties of such quasiperiodic operators represent a deep mathematical problem. We argue that FIKS pairs can be detected in the framework of recent cold atom experiments [M. Schreiber et al., Science 349, 842 (2015)] by a simple setup modification. We also discuss possible implications of FIKS pairs for electron transport in the regime of charge-density wave and high T c superconductivity.

  4. PLASMAKIN: A chemical kinetics library for plasma physics modeling

    NASA Astrophysics Data System (ADS)

    Pinhao, Nuno

    2007-10-01

    PLASMAKIN is a package to handle physical and chemical data used in plasma physics modeling and to compute kinetics data from the reactions taking place in the gas or at the surfaces: particle production and loss rates, photon spectra and energy exchange rates. It has no limits on the number of species and reactions that can be handled, is independent of problem dimensions and can be used in both steady-state and time-dependent problems. A broad range of species properties and reaction types are supported: gas or electron temperature dependent rate coefficients, vibrational and cascade levels, branching ratios, superelastic and other reverse processes, three-body collisions, radiation imprisonment and photoelectric emission. Non-standard rate coefficient functions can be handled by a user-supplied shared library. Reaction data is supplied in text files and is independent of the user's program. Recent additions include the simulation of emission spectra taking line broadening into account; reactions with excited ionic species; 3-body reactions with species with different efficiencies as 3rd body; a species properties database and a Python interface for rapid scripting and debugging.

  5. The rise and fall of a networked society: A formal model

    PubMed Central

    Marsili, Matteo; Vega-Redondo, Fernando; Slanina, František

    2004-01-01

    In a well networked community, there is intense social interaction, and information disseminates briskly and broadly. This is important if the environment is volatile (i.e., keeps changing) and individuals never stop searching for fresh opportunities. Here, we present a simple model that attributes the rise of a dynamic society to the emergence of some key features in its social network. We also explain the apparently paradoxical observation that although such features do not necessarily materialize even under favorable conditions they display a significant resilience to deteriorating conditions. We interpret these findings as a discontinuous phase transition in the network formation process. PMID:14745030

  6. Statistical model of dephasing in mesoscopic devices introduced in the scattering matrix formalism

    NASA Astrophysics Data System (ADS)

    Pala, Marco G.; Iannaccone, Giuseppe

    2004-06-01

    We propose a phenomenological model of dephasing in mesoscopic transport, based on the introduction of random-phase fluctuations in the computation of the scattering matrix of the system. A Monte Carlo averaging procedure allows us to extract electrical and microscopic device properties. We show that, in this picture, scattering matrix properties enforced by current conservation and time-reversal invariance still hold. In order to assess the validity of the proposed approach, we present simulations of conductance and magnetoconductance of Aharonov-Bohm rings that reproduce the behavior observed in experiments, in particular as far as aspects related to decoherence are concerned.

  7. Kinetic modelling of runaway electron avalanches in tokamak plasmas

    NASA Astrophysics Data System (ADS)

    Nilsson, E.; Decker, J.; Peysson, Y.; Granetz, R. S.; Saint-Laurent, F.; Vlainic, M.

    2015-09-01

    Runaway electrons can be generated in tokamak plasmas if the accelerating force from the toroidal electric field exceeds the collisional drag force owing to Coulomb collisions with the background plasma. In ITER, disruptions are expected to generate runaway electrons mainly through knock-on collisions (Hender et al 2007 Nucl. Fusion 47 S128-202), where enough momentum can be transferred from existing runaways to slow electrons to transport the latter beyond a critical momentum, setting off an avalanche of runaway electrons. Since knock-on runaways are usually scattered off with a significant perpendicular component of the momentum with respect to the local magnetic field direction, these particles are highly magnetized. Consequently, the momentum dynamics require a full 3D kinetic description, since these electrons are highly sensitive to the magnetic non-uniformity of a toroidal configuration. For this purpose, a bounce-averaged knock-on source term is derived. The generation of runaway electrons from the combined effect of Dreicer mechanism and knock-on collision process is studied with the code LUKE, a solver of the 3D linearized bounce-averaged relativistic electron Fokker-Planck equation (Decker and Peysson 2004 DKE: a fast numerical solver for the 3D drift kinetic equation Report EUR-CEA-FC-1736, Euratom-CEA), through the calculation of the response of the electron distribution function to a constant parallel electric field. The model, which has been successfully benchmarked against the standard Dreicer runaway theory now describes the runaway generation by knock-on collisions as proposed by Rosenbluth (Rosenbluth and Putvinski 1997 Nucl. Fusion 37 1355-62). This paper shows that the avalanche effect can be important even in non-disruptive scenarios. Runaway formation through knock-on collisions is found to be strongly reduced when taking place off the magnetic axis, since trapped electrons can not contribute to the runaway electron population. Finally, the

  8. One-dimensional model of interacting-step fluctuations on vicinal surfaces: Analytical formulas and kinetic Monte-Carlo simulations

    NASA Astrophysics Data System (ADS)

    Patrone, Paul; Einstein, T. L.; Margetis, Dionisios

    2011-03-01

    We study a 1+1D, stochastic, Burton-Cabrera-Frank (BCF) model of interacting steps fluctuating on a vicinal crystal. The step energy accounts for entropic and nearest-neighbor elastic-dipole interactions. Our goal is to formulate and validate a self-consistent mean-field (MF) formalism to approximately solve the system of coupled, nonlinear stochastic differential equations (SDEs) governing fluctuations in surface motion. We derive formulas for the time-dependent terrace width distribution (TWD) and its steady-state limit. By comparison with kinetic Monte-Carlo simulations, we show that our MF formalism improves upon models in which step interactions are linearized. We also indicate how fitting parameters of our steady state MF TWD may be used to determine the mass transport regime and step interaction energy of certain experimental systems. PP and TLE supported by NSF MRSEC under Grant DMR 05-20471 at U. of Maryland; DM supported by NSF under Grant DMS 08-47587.

  9. Extension of Standard Model in multi-spinor field formalism — Visible and dark sectors

    NASA Astrophysics Data System (ADS)

    Sogami, Ikuo S.

    2016-06-01

    With multi-spinor fields which behave as triple-tensor products of the Dirac spinors, the Standard Model is extended so as to embrace three families of ordinary quarks and leptons in the visible sector and an additional family of exotic quarks and leptons in the dark sector of our Universe. Apart from the gauge and Higgs fields of the Standard Model symmetry G, new gauge and Higgs fields of a symmetry isomorphic to G are postulated to exist in the dark sector. It is the bi-quadratic interaction between visible and dark Higgs fields that opens a main portal to the dark sector. Breakdowns of the visible and dark electroweak symmetries result in the Higgs boson with mass 125 GeV and a new boson which can be related to the diphoton excess around 750 GeV. Subsequent to a common inflationary phase and a reheating period, the visible and dark sectors follow weakly-interacting paths of thermal histories. We propose scenarios for dark matter in which no dark nuclear reaction takes place. A candidate for the main component of the dark matter is a stable dark hadron with spin 3/2, and the upper limit of its mass is estimated to be 15.1 GeV/c2.

  10. A model for climate change education in formal and informal settings--C2S2 Climate Change Student Summit

    NASA Astrophysics Data System (ADS)

    Huffman, L. T.; Lynds, S. E.; Rack, F. R.

    2012-12-01

    Through a NOAA Environmental Literacy grant, ANDRILL (ANtarctic geological DRILLing) created a unique opportunity for both formal and informal educators to engage their classrooms/audiences in understanding the complexities of climate change. The program, entitled C2S2: Climate Change Student Summits, included excellent geographical coverage through an exceptional two-workshop professional development series for teachers in each of nine different regions representing the U.S. National Climate Assessment regions defined by the U.S. Global Change Research Program. The program also included a creative, investigative science research and presentation experience for teams of students in each region, culminating in the Climate Change Student Summit, an on-site capstone event including a videoconference connecting all sites. The success of this program is based on combining multiple aspects, such as providing professional development for educators and encouraging the active involvement of research scientists, both in the professional development workshops and in the Student Summit. Another key factor is the close working relationships between informal and formal education entities, including the involvement of informal science learning facilities and informal science education leaders. The program includes the creation and use of cutting-edge curriculum materials available in the ELF, (Environmental Literacy Framework with a focus on climate change) and hands-on resources for teachers and students that provide an earth systems approach to climate change education, which have been successfully used in grades 5-12 as well as at numerous science museums. The C2S2 project has completed four years of activities with demonstrated positive impacts on both students and teachers. This presentation will share the lessons learned about implementing this climate change science education program and suggest that it is a successful model that can be used to scale up this project from

  11. Verification of electromagnetic fluid-kinetic hybrid electron model in global gyrokinetic particle simulation

    NASA Astrophysics Data System (ADS)

    Holod, I.; Lin, Z.

    2013-03-01

    The fluid-kinetic hybrid electron model is verified in global gyrokinetic particle simulation of linear electromagnetic drift-Alfvénic instabilities in tokamak. In particular, we have recovered the β-stabilization of the ion temperature gradient mode, transition to collisionless trapped electron mode, and the onset of kinetic ballooning mode as βe (ratio of electron kinetic pressure to magnetic pressure) increases.

  12. Shear viscosities from Kubo formalism in a large-Nc Nambu-Jona-Lasinio model

    NASA Astrophysics Data System (ADS)

    Lang, Robert; Kaiser, Norbert; Weise, Wolfram

    2015-10-01

    In this work the shear viscosity of strongly interacting matter is calculated within a two-flavor Nambu-Jona-Lasinio model as a function of temperature and chemical potential. The general Kubo formula is applied, incorporating the full Dirac structure of the thermal quark spectral function and avoiding commonly used on-shell approximations. Mesonic fluctuations contributing via Fock diagrams provide the dominant dissipative processes. The resulting ratio η/ s (shear viscosity over entropy density) decreases with temperature and chemical potential. Interpolating between our NJL results at low temperatures and hard thermal loop results at high temperatures a minimum slightly above the AdS/CFT benchmark η/ s = 1/4 τ is obtained.

  13. Kinetic models of current sheets with a sheared magnetic field

    SciTech Connect

    Mingalev, O. V.; Mingalev, I. V.; Mel'nik, M. N.; Artemyev, A. V.; Malova, H. V.; Popov, V. Yu.; Chao, Shen; Zelenyi, L. M.

    2012-04-15

    Thin current sheets, whose existence in the Earth's magnetotail is confirmed by numerous spacecraft measurements, are studied analytically and numerically. The thickness of such sheets is on the order of the ion Larmor radius, and the normal component of the magnetic field (B{sub z}) in the sheet is almost constant, while the tangential (B{sub x}) and shear (B{sub y}) components depend on the transverse coordinate z. The current density in the sheet also has two self-consistent components (j{sub x} and j{sub y}, respectively), and the magnetic field lines are deformed and do not lie in a single plane. To study such quasi-one-dimensional current configurations, two kinetic models are used, in particular, a numerical model based on the particle-in-cell method and an analytical model. The calculated results show that two different modes of the self-consistent shear magnetic field B{sub y} and, accordingly, two thin current sheet configurations can exist for the same input parameters. For the mode with an antisymmetric z profile of the B{sub y} component, the magnetic field lines within the sheet are twisted, whereas the profiles of the plasma density, current density component j{sub y}, and magnetic field component B{sub x} differ slightly from those in the case of a shearless magnetic field (B{sub y} = 0). For the symmetric B{sub y} mode, the magnetic field lines lie in a curved surface. In this case, the plasma density in the sheet varies slightly and the current sheet is two times thicker. Analysis of the dependence of the current sheet structure on the flow anisotropy shows that the sheet thickness decreases significantly with decreasing ratio between the thermal and drift plasma velocities, which is caused by the dynamics of quasi-adiabatic ions. It is shown that the results of the analytical and numerical models are in good agreement. The problems of application of these models to describe current sheets at the magnetopause and near magnetic reconnection regions

  14. Decarboxylation of Δ 9-tetrahydrocannabinol: Kinetics and molecular modeling

    NASA Astrophysics Data System (ADS)

    Perrotin-Brunel, Helene; Buijs, Wim; van Spronsen, Jaap; van Roosmalen, Maaike J. E.; Peters, Cor J.; Verpoorte, Rob; Witkamp, Geert-Jan

    2011-02-01

    Efficient tetrahydrocannabinol (Δ 9-THC) production from cannabis is important for its medical application and as basis for the development of production routes of other drugs from plants. This work presents one of the steps of Δ 9-THC production from cannabis plant material, the decarboxylation reaction, transforming the Δ 9-THC-acid naturally present in the plant into the psychoactive Δ 9-THC. Results of experiments showed pseudo-first order reaction kinetics, with an activation barrier of 85 kJ mol -1 and a pre-exponential factor of 3.7 × 10 8 s -1. Using molecular modeling, two options were identified for an acid catalyzed β-keto acid type mechanism for the decarboxylation of Δ 9-THC-acid. Each of these mechanisms might play a role, depending on the actual process conditions. Formic acid proved to be a good model for a catalyst of such a reaction. Also, the computational idea of catalysis by water to catalysis by an acid, put forward by Li and Brill, and Churchev and Belbruno was extended, and a new direct keto-enol route was found. A direct keto-enol mechanism catalyzed by formic acid seems to be the best explanation for the observed activation barrier and the pre-exponential factor of the decarboxylation of Δ 9-THC-acid. Evidence for this was found by performing an extraction experiment with Cannabis Flos. It revealed the presence of short chain carboxylic acids supporting this hypothesis. The presented approach is important for the development of a sustainable production of Δ 9-THC from the plant.

  15. Kinetic model of carbonate dissolution in Martian meteorite ALH84001

    NASA Astrophysics Data System (ADS)

    Kopp, R. E.; Humayun, M.

    2003-09-01

    The magnetites and sulfides located in the rims of carbonate globules in the Martian meteorite ALH84001 have been claimed as evidence of past life on Mars. Here, we consider the possibility that the rims were formed by dissolution and reprecipitation of the primary carbonate by the action of water. To estimate the rate of these solution-precipitation reactions, a kinetic model of magnesite-siderite carbonate dissolution was applied and used to examine the physicochemical conditions under which these rims might have formed. The results indicate that the formation of the rims could have taken place in < 50 yr of exposure to small amounts of aqueous fluids at ambient temperatures. Plausible conditions pertaining to reactions under a hypothetical ancient Martian atmosphere (1 bar CO 2), the modern Martian atmosphere (8 mbar CO 2), and the present terrestrial atmosphere (0.35 mbar CO 2) were explored to constrain the site of the process. The results indicated that such reactions likely occurred under the latter two conditions. The possibility of Antarctic weathering must be entertained, which, if correct, would imply that the plausibly biogenic minerals (single-domain magnetite of characteristic morphology and sulfide) reported from the rims may be the products of terrestrial microbial activity. This model is discussed in terms of the available isotope data and found to be compatible with the formation of ALH84001 rims. Particularly, anticorrelated variations of radiocarbon with δ 13C indicate that carbonate in ALH84001 was affected by solution-precipitation reactions immediately after its initial fall (˜13,000 yr ago) and then again during its recent exposure prior to collection.

  16. A Formal Analysis of the Feedback Concept in Climate Models. Part I: Exclusive and Inclusive Feedback Analyses

    NASA Astrophysics Data System (ADS)

    Lahellec, Alain; Dufresne, Jean-Louis

    2013-12-01

    Climate sensitivity and feedback are key concepts if the complex behavior of climate response to perturbation is to be interpreted in a simple way. They have also become an essential tool for comparing global circulation models and assessing the reason for the spread in their results. The authors introduce a formal basic model to analyze the practical methods used to infer climate feedbacks and sensitivity from GCMs. The tangent linear model is used first to critically review the standard methods of feedback analyses that have been used in the GCM community for 40 years now. This leads the authors to distinguish between exclusive feedback analyses as in the partial radiative perturbation approach and inclusive analyses as in the "feedback suppression" methods. This review explains the hypotheses needed to apply these methods with confidence. Attention is paid to the more recent regression technique applied to the abrupt 2-CO2 experiment. A numerical evaluation of it is given, related to the Lyapunov analysis of the dynamical feature of the regression. It is applied to the Planck response, determined in its most strict definition within the GCM. In this approach, the Planck feedback becomes a dynamical feedback among others and, as such, also has a fast response differing from its steady-state profile.

  17. Impact of kinetic parameters on heat transfer modeling for a pultrusion process

    NASA Astrophysics Data System (ADS)

    Gorthala, R.; Roux, J. A.; Vaughan, J. G.; Donti, R. P.; Hassouneh, A.

    An examination is conducted of pultrusion heat model predictions for various parameters of resin chemical kinetics; these parameters' values affect model heat-transfer results and model predictions. Attention is given to the applicability of DSC kinetic parameters to resin cure modeling, by comparing the predicted product cure temperature profiles and resin degree-of-cure values with pultrusion experiment results obtained for both carbon and glass reinforcements, different pull speeds and fiber volumes, and various die temperature profiles.

  18. Electrical and kinetic model of an atmospheric rf device for plasma aerodynamics applications

    SciTech Connect

    Pinheiro, Mario J.; Martins, Alexandre A.

    2010-08-15

    The asymmetrically mounted flat plasma actuator is investigated using a self-consistent two-dimensional fluid model at atmospheric pressure. The computational model assumes the drift-diffusion approximation and uses a simple plasma kinetic model. It investigated the electrical and kinetic properties of the plasma, calculated the charged species concentrations, surface charge density, electrohydrodynamic forces, and gas speed. The present computational model contributes to understand the main physical mechanisms, and suggests ways to improve its performance.

  19. Modeling of hydrogen production methods: Single particle model and kinetics assessment

    SciTech Connect

    Miller, R.S.; Bellan, J.

    1996-10-01

    The investigation carried out by the Jet Propulsion Laboratory (JPL) is devoted to the modeling of biomass pyrolysis reactors producing an oil vapor (tar) which is a precursor to hydrogen. This is an informal collaboration with NREL whereby JPL uses the experimentally-generated NREL data both as initial and boundary conditions for the calculations, and as a benchmark for model validation. The goal of this investigation is to find drivers of biomass fast-pyrolysis in the low temperature regime. The rationale is that experimental observations produce sparse discrete conditions for model validation, and that numerical simulations produced with a validated model are an economic way to find control parameters and an optimal operation regime, thereby circumventing costly changes in hardware and tests. During this first year of the investigation, a detailed mathematical model has been formulated for the temporal and spatial accurate modeling of solid-fluid reactions in biomass particles. These are porous particles for which volumetric reaction rate data is known a priori and both the porosity and the permeability of the particle are large enough to allow for continuous gas phase flow. The methodology has been applied to the pyrolysis of spherically symmetric biomass particles by considering previously published kinetics schemes for both cellulose and wood. The results show that models which neglect the thermal and species boundary layers exterior to the particle will generally over predict both the pyrolysis rates and experimentally obtainable tar yields. An evaluation of the simulation results through comparisons with experimental data indicates that while the cellulose kinetics is reasonably accurate, the wood pyrolysis kinetics is not accurate; particularly at high reactor temperatures. Current effort in collaboration with NREL is aimed at finding accurate wood kinetics.

  20. Chemical Kinetics Laboratory Discussion Worksheet.

    PubMed

    Demoin, Dustin Wayne; Jurisson, Silvia S

    2013-09-10

    A laboratory discussion worksheet and its answer key provide instructors and students a discussion model to further the students' understanding of chemical kinetics. This discussion worksheet includes a section for students to augment their previous knowledge about chemical kinetics measurements, an initial check on students' understanding of basic concepts, a group participation model where students work on solving complex-conceptual problems, and a conclusion to help students connect this discussion to their laboratory or lecture class. Additionally, the worksheet has a detailed solution to a more advanced problem to help students understand how the concepts they have put together relate to problems they will encounter during later formal assessments.

  1. Results of Formal Evaluation of a Data and Modeling Driven Hydrology Learning Module

    NASA Astrophysics Data System (ADS)

    Ruddell, B. L.; Sanchez, C. A.; Schiesser, R.; Merwade, V.

    2014-12-01

    New hydrologists should not only develop a well-defined knowledgebase of basic hydrological concepts, but also synthesize this factual learning with more authentic 'real-world' knowledge gained from the interpretation and analysis of data from hydrological models (Merwade and Ruddell, 2012, Wagener et al., 2007). However, hydrological instruction is often implemented using a traditional teacher-centered approach (e.g., lectures) (Wagener, 2007). The emergence of rich and dynamic computer simulation techniques which allow students the opportunity for more authentic application of knowledge (Merwade & Ruddell, 2012). This study evaluates the efficacy of using such data-driven simulations to increase the understanding of the field of hydrology in the lower-division undergraduate geoscience classroom. In this study, 88 students at a local community college who were enrolled in an Introductory Earth Science class were evaluated on their learning performance in a unit on applying the Rational Method to estimate hydrographs and flooding for urban areas. Students were either presented with a data and visualization rich computer module (n=52), or with paper and pencil calculation activities (n=36). All conceptual material presented in lecture was consistent across these two conditions. Students were evaluated for not only changes in their knowledge and application of the concepts within the unit (e.g., effects of urbanization and impervious cover, discharge rates), but also for their broad "T-shaped" profile of professional knowledge and skills. While results showed significant (p<.05) increases from pre to post assessments in all learning areas for both groups, there is a significantly larger benefit for the data module group when it came to (1) understanding the effects of urbanization and impervious cover on flooding, (2) applying consistent vocabulary appropriately within context, and (3) explaining the roles and responsibilities of hydrologists and flood managers.

  2. Linking Formal and Informal Science Education: A Successful Model using Libraries, Volunteers and NASA Resources

    NASA Astrophysics Data System (ADS)

    Race, M. S.; Lafayette Library; Learning Center Foundation (Lllcf)

    2011-12-01

    In these times of budget cuts, tight school schedules, and limited opportunities for student field trips and teacher professional development, it is especially difficult to expose elementary and middle school students to the latest STEM information-particularly in the space sciences. Using our library as a facilitator and catalyst, we built a volunteer-based, multi-faceted, curriculum-linked program for students and teachers in local middle schools (Grade 8) and showcased new astronomical and planetary science information using mainly NASA resources and volunteer effort. The project began with the idea of bringing free NASA photo exhibits (FETTU) to the Lafayette and Antioch Libraries for public display. Subsequently, the effort expanded by adding layers of activities that brought space and science information to teachers, students and the pubic at 5 libraries and schools in the 2 cities, one of which serves a diverse, underserved community. Overall, the effort (supported by a pilot grant from the Bechtel Foundation) included school and library based teacher workshops with resource materials; travelling space museum visits with hands-on activities (Chabot-to-Go); separate powerpoint presentations for students and adults at the library; and concurrent ancillary space-related themes for young children's programs at the library. This pilot project, based largely on the use of free government resources and online materials, demonstrated that volunteer-based, standards-linked STEM efforts can enhance curriculum at the middle school, with libraries serving a special role. Using this model, we subsequently also obtained a small NASA-Space Grant award to bring star parties and hand-on science activities to three libraries this Fall, linking with numerous Grade 5 teachers and students in two additional underserved areas of our county. It's not necessary to reinvent the wheel, you just collect the pieces and build on what you already have.

  3. Modelling of an EGSB treating sugarcane vinasse using first-order variable kinetics.

    PubMed

    López, Iván; Borzacconi, Liliana

    2011-01-01

    An expanded granular sludge bed (EGSB) anaerobic reactor treating sugar cane vinasse was modelled using a simple model with two steps (acidogenesis and methanogenesis), two populations, two substrates and completely mixed conditions. A first-order kinetic equation for both steps with time-variant kinetic coefficients was used. An observer system was used to estimate the evolution of kinetic constants over time. The model was validated by comparing methane flow predictions with experimental values. An estimation of evolution of populations of microorganisms was also performed. This approach allows calculation of specific kinetic constants that reflect biological activity of microorganisms. Variation of specific kinetic constants reflects the influence of the fraction of raw vinasse in the feed. High salt concentrations in the reactor may have inhibited the process. PMID:22105132

  4. Kinetic modeling of antimony(III) oxidation and sorption in soils.

    PubMed

    Cai, Yongbing; Mi, Yuting; Zhang, Hua

    2016-10-01

    Kinetic batch and saturated column experiments were performed to study the oxidation, adsorption and transport of Sb(III) in two soils with contrasting properties. Kinetic and column experiment results clearly demonstrated the extensive oxidation of Sb(III) in soils, and this can in return influence the adsorption and transport of Sb. Both sorption capacity and kinetic oxidation rate were much higher in calcareous Huanjiang soil than in acid red Yingtan soil. The results indicate that soil serve as a catalyst in promoting oxidation of Sb(III) even under anaerobic conditions. A PHREEQC model with kinetic formulations was developed to simulate the oxidation, sorption and transport of Sb(III) in soils. The model successfully described Sb(III) oxidation and sorption data in kinetic batch experiment. It was less successful in simulating the reactive transport of Sb(III) in soil columns. Additional processes such as colloid facilitated transport need to be quantified and considered in the model.

  5. Kinetic modeling of antimony(III) oxidation and sorption in soils.

    PubMed

    Cai, Yongbing; Mi, Yuting; Zhang, Hua

    2016-10-01

    Kinetic batch and saturated column experiments were performed to study the oxidation, adsorption and transport of Sb(III) in two soils with contrasting properties. Kinetic and column experiment results clearly demonstrated the extensive oxidation of Sb(III) in soils, and this can in return influence the adsorption and transport of Sb. Both sorption capacity and kinetic oxidation rate were much higher in calcareous Huanjiang soil than in acid red Yingtan soil. The results indicate that soil serve as a catalyst in promoting oxidation of Sb(III) even under anaerobic conditions. A PHREEQC model with kinetic formulations was developed to simulate the oxidation, sorption and transport of Sb(III) in soils. The model successfully described Sb(III) oxidation and sorption data in kinetic batch experiment. It was less successful in simulating the reactive transport of Sb(III) in soil columns. Additional processes such as colloid facilitated transport need to be quantified and considered in the model. PMID:27214003

  6. A Modified Approach to Modeling of Diffusive Transformation Kinetics from Nonisothermal Data and Experimental Verification

    NASA Astrophysics Data System (ADS)

    Chen, Xiangjun; Xiao, Namin; Cai, Minghui; Li, Dianzhong; Li, Guangyao; Sun, Guangyong; Rolfe, Bernard F.

    2016-09-01

    An inverse model is proposed to construct the mathematical relationship between continuous cooling transformation (CCT) kinetics with constant rates and the isothermal one. The kinetic parameters in JMAK equations of isothermal kinetics can be deduced from the experimental CCT kinetics. Furthermore, a generalized model with a new additive rule is developed for predicting the kinetics of nucleation and growth during diffusional phase transformation with arbitrary cooling paths based only on CCT curve. A generalized contribution coefficient is introduced into the new additivity rule to describe the influences of current temperature and cooling rate on the incubation time of nuclei. Finally, then the reliability of the proposed model is validated using dilatometry experiments of a microalloy steel with fully bainitic microstructure based on various cooling routes.

  7. A first-language-first multilingual model to meet the quality imperative in formal basic education in three `francophone' West African countries

    NASA Astrophysics Data System (ADS)

    Nikièma, Norbert

    2011-12-01

    This paper documents the new trend towards a first-language-first multilingual model in formal education in three former French colonies of West Africa, namely Burkina Faso, Mali and Niger. It compares the sociolinguistic situations, the conditions of the development of multilingual education and the achievements of mother-tongue-medium education in all three countries. The evidence is that, contrary to common discourse in francophonie, a strong first-language-first model in formal education is the best guarantee of a good mastery of French and, more generally, of quality education in francophone countries.

  8. Detailed Chemical Kinetic Modeling of Diesel Combustion with Oxygenated Fuels

    SciTech Connect

    Curran, H J; Fisher, E M; Glaude, P-A; Marinov, N M; Pitz, W J; Westbrook, C K; Flynn, P F; Durrett, R P; zur Loye, A O; Akinyemi, O C; Dryer, F L

    2000-01-11

    mixing model to study the premixed, rich ignition process. Using n-heptane as a representative diesel fuel, they showed that addition of an oxygenated additive, methanol, to the fuel reduced the concentrations of a number of hydrocarbon species in the products of the rich ignition. Specifically, methanol addition reduced the total concentrations of acetylene, ethylene and 1,3-butadiene, as well as propargyl and vinyl radicals, in the ignition products. These are the same species shown in a number of studies [4-6] to be responsible for formation of aromatic and polycyclic aromatic species in flames, species which lead eventually to production of soot. Flynn et al. did not, however, examine the kinetic processes responsible for the computed reduction in production of soot precursor species. At least two hypotheses have been advanced to explain the role that oxygenated species play in diesel ignition and the reduction in the concentrations of these species. The first is that the additive, methanol in the case of Flynn et al., does not contain any C-C bonds and cannot then produce significant levels of the species such as acetylene, ethylene or the unsaturated radicals which are known to lead to aromatic species. The second hypothesis is that the product distribution changes very naturally as oxygen is added and the overall equivalence ratio is reduced. In the present study, we repeat the ignition calculations of Flynn et al. and include a number of other oxygenated species to determine which of these theories is more applicable to this model.

  9. Dynamic disorder in single-molecule Michaelis-Menten kinetics: The reaction-diffusion formalism in the Wilemski-Fixman approximation

    NASA Astrophysics Data System (ADS)

    Chaudhury, Srabanti; Cherayil, Binny J.

    2007-09-01

    Single-molecule equations for the Michaelis-Menten [Biochem. Z. 49, 333 (1913)] mechanism of enzyme action are analyzed within the Wilemski-Fixman [J. Chem. Phys. 58, 4009 (1973); 60, 866 (1974)] approximation after the effects of dynamic disorder—modeled by the anomalous diffusion of a particle in a harmonic well—are incorporated into the catalytic step of the reaction. The solution of the Michaelis-Menten equations is used to calculate the distribution of waiting times between successive catalytic turnovers in the enzyme β-galactosidase. The calculated distribution is found to agree qualitatively with experimental results on this enzyme obtained at four different substrate concentrations. The calculations are also consistent with measurements of correlations in the fluctuations of the fluorescent light emitted during the course of catalysis, and with measurements of the concentration dependence of the randomness parameter.

  10. Pseudospin S = 1 formalism and skyrmion-like excitations in the three-body constrained extended Bose–Hubbard model

    SciTech Connect

    Moskvin, A. S.

    2015-09-15

    We discuss the most prominent and intensively studied S = 1 pseudospin formalism for the extended bosonic Hubbard model (EBHM) with the on-site Hilbert space truncated to the three lowest occupation states n = 0, 1, 2. The EBHM Hamiltonian is a paradigmatic model for the highly topical field of ultracold gases in optical lattices. The generalized non-Heisenberg effective pseudospin Hamiltonian does provide a deep link with a boson system and a physically clear description of “the myriad of phases,” from uniform Mott insulating phases and density waves to two types of superfluids and supersolids. We argue that the 2D pseudospin system is prone to a topological phase separation and focus on several types of unconventional skyrmion-like topological structures in 2D boson systems, which have not been analyzed until now. The structures are characterized by a complicated interplay of insulating and two superfluid phases with a single- boson and two-boson condensation, respectively.

  11. A KINETIC MODEL FOR CELL DENSITY DEPENDENT BACTERIAL TRANSPORT IN POROUS MEDIA

    EPA Science Inventory

    A kinetic transport model with the ability to account for variations in cell density of the aqueous and solid phases was developed for bacteria in porous media. Sorption kinetics in the advective-dispersive-sorptive equation was described by assuming that adsorption was proportio...

  12. Acceleration of the KINETICS Integrated Dynamical/Chemical Computational Model Using MPI

    NASA Technical Reports Server (NTRS)

    Grossman, Max; Willacy, Karen; Allen, Mark

    2011-01-01

    Understanding the evolution of a planet's atmosphere not only provides a better theoretical understanding of planetary physics and the formation of planets, but also grants useful insight into Earth's own atmosphere. One of the tools used at JPL for the modeling of planetary atmospheres and protostellar disks is KINETICS. KINETICS can simulate years of complex dynamics and chemistry.

  13. Ion Dynamics during Substorm Events Modeled with Coupled Global MHD and Kinetic Models

    NASA Astrophysics Data System (ADS)

    Lapenta, G.; Ashour-Abdalla, M.; Walker, R. J.; El-Alaoui, M.

    2014-12-01

    We have studied ion dynamics during a substorm by using a coupled fluid-kinetic approach. The UCLA global magnetospheric model was applied first and its results in a region encompassing a magnetotail reconnection site and earthward propagating dipolarization fronts was selected as input state for a full kinetic simulation based on the iPic3D code [1]. The coupling is one-way: the MHD result is used to create a full kinetic initial state by using the approach described by [2] and to force the boundary conditions. The kinetic results are not fed back into the MHD run. This approach previously has been shown [3] to provide correctly the large scale picture for a kinetic approach when the duration of the kinetic run is not so long as to alter significantly the macroscopic state captured by MHD. Here we focus especially on the ions. The electrons were described in [3]. Three aspects are analyzed. First, the ions are accelerated during the event and we track the localization of the energy exchanged, separating the contributions to the directed energy and those to the thermal energy. Second, we consider the ion motion to identify the regions where the finite Larmor radius effects violate the drift approximation and the frozen-in condition, thereby identifying the ion diffusion region. Our approach follows individual electrons and ions fully kinetically and no approximation is made in the particle orbit, so our code is equipped to study accurately the regions where the drift approximation is valid. Finally, we consider the ion distribution as a possible source of instabilities, focusing especially on temperature anisotropy instabilities and on the firehose instability. The novelty of the approach is this kinetic study is done for a specific substorm by using the global state of the magnetosphere as provided by a global MHD simulation. This differs sharply from previous approaches based on analytical approximations such as the Harris or the (quasi)-parabolic equilibria. [1

  14. On the asymptotic preserving property of the unified gas kinetic scheme for the diffusion limit of linear kinetic models

    SciTech Connect

    Mieussens, Luc

    2013-11-15

    The unified gas kinetic scheme (UGKS) of K. Xu et al. (2010) [37], originally developed for multiscale gas dynamics problems, is applied in this paper to a linear kinetic model of radiative transfer theory. While such problems exhibit purely diffusive behavior in the optically thick (or small Knudsen) regime, we prove that UGKS is still asymptotic preserving (AP) in this regime, but for the free transport regime as well. Moreover, this scheme is modified to include a time implicit discretization of the limit diffusion equation, and to correctly capture the solution in case of boundary layers. Contrary to many AP schemes, this method is based on a standard finite volume approach, it does neither use any decomposition of the solution, nor staggered grids. Several numerical tests demonstrate the properties of the scheme.

  15. Effect of heating rate and kinetic model selection on activation energy of nonisothermal crystallization of amorphous felodipine.

    PubMed

    Chattoraj, Sayantan; Bhugra, Chandan; Li, Zheng Jane; Sun, Changquan Calvin

    2014-12-01

    The nonisothermal crystallization kinetics of amorphous materials is routinely analyzed by statistically fitting the crystallization data to kinetic models. In this work, we systematically evaluate how the model-dependent crystallization kinetics is impacted by variations in the heating rate and the selection of the kinetic model, two key factors that can lead to significant differences in the crystallization activation energy (Ea ) of an amorphous material. Using amorphous felodipine, we show that the Ea decreases with increase in the heating rate, irrespective of the kinetic model evaluated in this work. The model that best describes the crystallization phenomenon cannot be identified readily through the statistical fitting approach because several kinetic models yield comparable R(2) . Here, we propose an alternate paired model-fitting model-free (PMFMF) approach for identifying the most suitable kinetic model, where Ea obtained from model-dependent kinetics is compared with those obtained from model-free kinetics. The most suitable kinetic model is identified as the one that yields Ea values comparable with the model-free kinetics. Through this PMFMF approach, nucleation and growth is identified as the main mechanism that controls the crystallization kinetics of felodipine. Using this PMFMF approach, we further demonstrate that crystallization mechanism from amorphous phase varies with heating rate.

  16. Empirical and physics based mathematical models of uranium hydride decomposition kinetics with quantified uncertainties.

    SciTech Connect

    Salloum, Maher N.; Gharagozloo, Patricia E.

    2013-10-01

    Metal particle beds have recently become a major technique for hydrogen storage. In order to extract hydrogen from such beds, it is crucial to understand the decomposition kinetics of the metal hydride. We are interested in obtaining a a better understanding of the uranium hydride (UH3) decomposition kinetics. We first developed an empirical model by fitting data compiled from different experimental studies in the literature and quantified the uncertainty resulting from the scattered data. We found that the decomposition time range predicted by the obtained kinetics was in a good agreement with published experimental results. Secondly, we developed a physics based mathematical model to simulate the rate of hydrogen diffusion in a hydride particle during the decomposition. We used this model to simulate the decomposition of the particles for temperatures ranging from 300K to 1000K while propagating parametric uncertainty and evaluated the kinetics from the results. We compared the kinetics parameters derived from the empirical and physics based models and found that the uncertainty in the kinetics predicted by the physics based model covers the scattered experimental data. Finally, we used the physics-based kinetics parameters to simulate the effects of boundary resistances and powder morphological changes during decomposition in a continuum level model. We found that the species change within the bed occurring during the decomposition accelerates the hydrogen flow by increasing the bed permeability, while the pressure buildup and the thermal barrier forming at the wall significantly impede the hydrogen extraction.

  17. Kinetic modelling of nitrogen and organics removal in vertical and horizontal flow wetlands.

    PubMed

    Saeed, Tanveer; Sun, Guangzhi

    2011-05-01

    This paper provides a comparative evaluation of the kinetic models that were developed to describe the biodegradation of nitrogen and organics removal in wetland systems. Reaction kinetics that were considered in the model development included first order kinetics, Monod and multiple Monod kinetics; these kinetics were combined with continuous-stirred tank reactor (CSTR) or plug flow pattern to produce equations to link inlet and outlet concentrations of each key pollutants across a single wetland. Using three statistical parameters, a critical evaluation of five potential models was made for vertical and horizontal flow wetlands. The results recommended the models that were developed based on Monod models, for predicting the removal of nitrogen and organics in a vertical and horizontal flow wetland system. No clear correlation was observed between influent BOD/COD values and kinetic coefficients of BOD(5) in VF and HF wetlands, illustrating that the removal of biodegradable organics was insensitive to the nature of organic matter. Higher effluent COD/TN values coincided with greater denitrification kinetic coefficients, signifying the dependency of denitrification on the availability of COD in VF wetland systems. In contrast, the trend was opposite in HF wetlands, indicating that availability of NO(3)-N was the main limiting step for nitrogen removal. Overall, the results suggested the possible application of the developed alternative predictive models, for understanding the complex biodegradation routes of nitrogen and organics removal in VF and HF wetland systems.

  18. Generalizing a unified model of dark matter, dark energy, and inflation with a noncanonical kinetic term

    SciTech Connect

    De-Santiago, Josue; Cervantes-Cota, Jorge L.

    2011-03-15

    We study a unification model for dark energy, dark matter, and inflation with a single scalar field with noncanonical kinetic term. In this model, the kinetic term of the Lagrangian accounts for the dark matter and dark energy, and at early epochs, a quadratic potential accounts for slow roll inflation. The present work is an extension to the work by Bose and Majumdar [Phys. Rev. D 79, 103517 (2009).] with a more general kinetic term that was proposed by Chimento in Phys. Rev. D 69, 123517 (2004). We demonstrate that the model is viable at the background and linear perturbation levels.

  19. Detailed chemical kinetic modeling of diesel combustion with oxygenated fuels

    SciTech Connect

    Pitz, W J; Curran, H J; Fisher, E; Glaude, P A; Marinov, N M; Westbrook, C K

    1999-10-28

    The influence of oxygenated hydrocarbons as additives to diesel fuels on ignition, NOx emissions and soot production has been examined using a detailed chemical kinetic reaction mechanism. N-heptane was used as a representative diesel fuel, and methanol, ethanol, dimethyl ether and dimethoxymethane were used as oxygenated fuel additives. It was found that addition of oxygenated hydrocarbons reduced NOx levels and reduced the production of soot precursors. When the overall oxygen content in the fuel reached approximately 25% by mass, production of soot precursors fell effectively to zero, in agreement with experimental studies. The kinetic factors responsible for these observations are discussed.

  20. Evaluation of kinetic uncertainty in numerical models of petroleum generation

    USGS Publications Warehouse

    Peters, K.E.; Walters, C.C.; Mankiewicz, P.J.

    2006-01-01

    Oil-prone marine petroleum source rocks contain type I or type II kerogen having Rock-Eval pyrolysis hydrogen indices greater than 600 or 300-600 mg hydrocarbon/g total organic carbon (HI, mg HC/g TOC), respectively. Samples from 29 marine source rocks worldwide that contain mainly type II kerogen (HI = 230-786 mg HC/g TOC) were subjected to open-system programmed pyrolysis to determine the activation energy distributions for petroleum generation. Assuming a burial heating rate of 1??C/m.y. for each measured activation energy distribution, the calculated average temperature for 50% fractional conversion of the kerogen in the samples to petroleum is approximately 136 ?? 7??C, but the range spans about 30??C (???121-151??C). Fifty-two outcrop samples of thermally immature Jurassic Oxford Clay Formation were collected from five locations in the United Kingdom to determine the variations of kinetic response for one source rock unit. The samples contain mainly type I or type II kerogens (HI = 230-774 mg HC/g TOC). At a heating rate of 1??C/m.y., the calculated temperatures for 50% fractional conversion of the Oxford Clay kerogens to petroleum differ by as much as 23??C (127-150??C). The data indicate that kerogen type, as defined by hydrogen index, is not systematically linked to kinetic response, and that default kinetics for the thermal decomposition of type I or type II kerogen can introduce unacceptable errors into numerical simulations. Furthermore, custom kinetics based on one or a few samples may be inadequate to account for variations in organofacies within a source rock. We propose three methods to evaluate the uncertainty contributed by kerogen kinetics to numerical simulations: (1) use the average kinetic distribution for multiple samples of source rock and the standard deviation for each activation energy in that distribution; (2) use source rock kinetics determined at several locations to describe different parts of the study area; and (3) use a weighted

  1. Fuzzy Logic as a Computational Tool for Quantitative Modelling of Biological Systems with Uncertain Kinetic Data.

    PubMed

    Bordon, Jure; Moskon, Miha; Zimic, Nikolaj; Mraz, Miha

    2015-01-01

    Quantitative modelling of biological systems has become an indispensable computational approach in the design of novel and analysis of existing biological systems. However, kinetic data that describe the system's dynamics need to be known in order to obtain relevant results with the conventional modelling techniques. These data are often hard or even impossible to obtain. Here, we present a quantitative fuzzy logic modelling approach that is able to cope with unknown kinetic data and thus produce relevant results even though kinetic data are incomplete or only vaguely defined. Moreover, the approach can be used in the combination with the existing state-of-the-art quantitative modelling techniques only in certain parts of the system, i.e., where kinetic data are missing. The case study of the approach proposed here is performed on the model of three-gene repressilator. PMID:26451831

  2. Recent Advances in Detailed Chemical Kinetic Models for Large Hydrocarbon and Biodiesel Transportation Fuels

    SciTech Connect

    Westbrook, C K; Pitz, W J; Curran, H J; Herbinet, O; Mehl, M

    2009-03-30

    n-Hexadecane and 2,2,4,4,6,8,8-heptamethylnonane represent the primary reference fuels for diesel that are used to determine cetane number, a measure of the ignition property of diesel fuel. With the development of chemical kinetics models for these two primary reference fuels for diesel, a new capability is now available to model diesel fuel ignition. Also, we have developed chemical kinetic models for a whole series of large n-alkanes and a large iso-alkane to represent these chemical classes in fuel surrogates for conventional and future fuels. Methyl decanoate and methyl stearate are large methyl esters that are closely related to biodiesel fuels, and kinetic models for these molecules have also been developed. These chemical kinetic models are used to predict the effect of the fuel molecule size and structure on ignition characteristics under conditions found in internal combustion engines.

  3. Fuzzy Logic as a Computational Tool for Quantitative Modelling of Biological Systems with Uncertain Kinetic Data.

    PubMed

    Bordon, Jure; Moskon, Miha; Zimic, Nikolaj; Mraz, Miha

    2015-01-01

    Quantitative modelling of biological systems has become an indispensable computational approach in the design of novel and analysis of existing biological systems. However, kinetic data that describe the system's dynamics need to be known in order to obtain relevant results with the conventional modelling techniques. These data are often hard or even impossible to obtain. Here, we present a quantitative fuzzy logic modelling approach that is able to cope with unknown kinetic data and thus produce relevant results even though kinetic data are incomplete or only vaguely defined. Moreover, the approach can be used in the combination with the existing state-of-the-art quantitative modelling techniques only in certain parts of the system, i.e., where kinetic data are missing. The case study of the approach proposed here is performed on the model of three-gene repressilator.

  4. Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints.

    PubMed

    Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher; Hatzimanikatis, Vassily

    2013-09-01

    Mathematical modeling is an essential tool for the comprehensive understanding of cell metabolism and its interactions with the environmental and process conditions. Recent developments in the construction and analysis of stoichiometric models made it possible to define limits on steady-state metabolic behavior using flux balance analysis. However, detailed information on enzyme kinetics and enzyme regulation is needed to formulate kinetic models that can accurately capture the dynamic metabolic responses. The use of mechanistic enzyme kinetics is a difficult task due to uncertainty in the kinetic properties of enzymes. Therefore, the majority of recent works considered only mass action kinetics for reactions in metabolic networks. Herein, we applied the optimization and risk analysis of complex living entities (ORACLE) framework and constructed a large-scale mechanistic kinetic model of optimally grown Escherichia coli. We investigated the complex interplay between stoichiometry, thermodynamics, and kinetics in determining the flexibility and capabilities of metabolism. Our results indicate that enzyme saturation is a necessary consideration in modeling metabolic networks and it extends the feasible ranges of metabolic fluxes and metabolite concentrations. Our results further suggest that enzymes in metabolic networks have evolved to function at different saturation states to ensure greater flexibility and robustness of cellular metabolism.

  5. Application of adaptive kinetic modelling for bias propagation reduction in direct 4D image reconstruction

    NASA Astrophysics Data System (ADS)

    Kotasidis, F. A.; Matthews, J. C.; Reader, A. J.; Angelis, G. I.; Zaidi, H.

    2014-10-01

    Parametric imaging in thoracic and abdominal PET can provide additional parameters more relevant to the pathophysiology of the system under study. However, dynamic data in the body are noisy due to the limiting counting statistics leading to suboptimal kinetic parameter estimates. Direct 4D image reconstruction algorithms can potentially improve kinetic parameter precision and accuracy in dynamic PET body imaging. However, construction of a common kinetic model is not always feasible and in contrast to post-reconstruction kinetic analysis, errors in poorly modelled regions may spatially propagate to regions which are well modelled. To reduce error propagation from erroneous model fits, we implement and evaluate a new approach to direct parameter estimation by incorporating a recently proposed kinetic modelling strategy within a direct 4D image reconstruction framework. The algorithm uses a secondary more general model to allow a less constrained model fit in regions where the kinetic model does not accurately describe the underlying kinetics. A portion of the residuals then is adaptively included back into the image whilst preserving the primary model characteristics in other well modelled regions using a penalty term that trades off the models. Using fully 4D simulations based on dynamic [15O]H2O datasets, we demonstrate reduction in propagation-related bias for all kinetic parameters. Under noisy conditions, reductions in bias due to propagation are obtained at the cost of increased noise, which in turn results in increased bias and variance of the kinetic parameters. This trade-off reflects the challenge of separating the residuals arising from poor kinetic modelling fits from the residuals arising purely from noise. Nonetheless, the overall root mean square error is reduced in most regions and parameters. Using the adaptive 4D image reconstruction improved model fits can be obtained in poorly modelled regions, leading to reduced errors potentially propagating

  6. The connection-set algebra--a novel formalism for the representation of connectivity structure in neuronal network models.

    PubMed

    Djurfeldt, Mikael

    2012-07-01

    The connection-set algebra (CSA) is a novel and general formalism for the description of connectivity in neuronal network models, from small-scale to large-scale structure. The algebra provides operators to form more complex sets of connections from simpler ones and also provides parameterization of such sets. CSA is expressive enough to describe a wide range of connection patterns, including multiple types of random and/or geometrically dependent connectivity, and can serve as a concise notation for network structure in scientific writing. CSA implementations allow for scalable and efficient representation of connectivity in parallel neuronal network simulators and could even allow for avoiding explicit representation of connections in computer memory. The expressiveness of CSA makes prototyping of network structure easy. A C+ + version of the algebra has been implemented and used in a large-scale neuronal network simulation (Djurfeldt et al., IBM J Res Dev 52(1/2):31-42, 2008b) and an implementation in Python has been publicly released.

  7. Growth Kinetics and Modeling of ZnO Nanoparticles

    ERIC Educational Resources Information Center

    Hale, Penny S.; Maddox, Leone M.; Shapter, Joe G.; Voelcker, Nico H.; Ford, Michael J.; Waclawik, Eric R.

    2005-01-01

    The technique for producing quantum-sized zinc oxide (ZnO) particles is much safer than a technique that used hydrogen sulfide gas to produce cadmium sulfide and zinc sulfide nanoparticles. A further advantage of this method is the ability to sample the solution over time and hence determine the growth kinetics.

  8. A kinetic model for human blood concentrations of gaseous halocarbon fire-extinguishing agents.

    PubMed

    Lyon, Richard E; Speitel, Louise C

    2010-12-01

    A simple kinetic model for calculating the blood concentration history of humans exposed to time-varying concentrations of gaseous, halocarbon fire-extinguishing agents is described. The kinetic model was developed to extend experimental physiologically based pharmacokinetic (PBPK) models for arterial blood concentration of halocarbons, obtained from constant concentration exposure of dogs to time-varying exposure conditions for humans. In the present work, the simplified kinetic model was calibrated using published PBPK-derived arterial concentration histories for constant concentration exposure to several common fire-extinguishing agents. The calibrated kinetic model was then used to predict the blood concentration histories of humans exposed to time-varying concentrations of these fire-extinguishing agents in ventilated compartments and the results were compared with PBPK-derived data for the agents. It was found that the properly calibrated kinetic model predicts human arterial blood concentration histories for time-varying exposures as well as the PBPK models. Consequently, the kinetic model represents an economical methodology for calculating safe human exposure limits for time-varying concentrations of gaseous halocarbon fire-extinguishing agents when only PBPK-derived human arterial blood concentration histories for constant exposure conditions are available.

  9. Isotope exchange kinetics in metal hydrides I : TPLUG model.

    SciTech Connect

    Larson, Rich; James, Scott Carlton; Nilson, Robert H.

    2011-05-01

    A one-dimensional isobaric reactor model is used to simulate hydrogen isotope exchange processes taking place during flow through a powdered palladium bed. This simple model is designed to serve primarily as a platform for the initial development of detailed chemical mechanisms that can then be refined with the aid of more complex reactor descriptions. The one-dimensional model is based on the Sandia in-house code TPLUG, which solves a transient set of governing equations including an overall mass balance for the gas phase, material balances for all of the gas-phase and surface species, and an ideal gas equation of state. An energy equation can also be solved if thermodynamic properties for all of the species involved are known. The code is coupled with the Chemkin package to facilitate the incorporation of arbitrary multistep reaction mechanisms into the simulations. This capability is used here to test and optimize a basic mechanism describing the surface chemistry at or near the interface between the gas phase and a palladium particle. The mechanism includes reversible dissociative adsorptions of the three gas-phase species on the particle surface as well as atomic migrations between the surface and the bulk. The migration steps are more general than those used previously in that they do not require simultaneous movement of two atoms in opposite directions; this makes possible the creation and destruction of bulk vacancies and thus allows the model to account for variations in the bulk stoichiometry with isotopic composition. The optimization code APPSPACK is used to adjust the mass-action rate constants so as to achieve the best possible fit to a given set of experimental data, subject to a set of rigorous thermodynamic constraints. When data for nearly isothermal and isobaric deuterium-to-hydrogen (D {yields} H) and hydrogen-to-deuterium (H {yields} D) exchanges are fitted simultaneously, results for the former are excellent, while those for the latter show

  10. A First-Language-First Multilingual Model to Meet the Quality Imperative in Formal Basic Education in Three "Francophone" West African Countries

    ERIC Educational Resources Information Center

    Nikiema, Norbert

    2011-01-01

    This paper documents the new trend towards a first-language-first multilingual model in formal education in three former French colonies of West Africa, namely Burkina Faso, Mali and Niger. It compares the sociolinguistic situations, the conditions of the development of multilingual education and the achievements of mother-tongue-medium education…

  11. The models of cosmological inflation in the context of kinetic approximation

    NASA Astrophysics Data System (ADS)

    Fomin, I.

    2016-07-01

    In this work the building of models of cosmological inflation with approximate linear dependence of the scalar field kinetic energy on the state parameter is considered. The key parameters of cosmological perturbations are also calculated.

  12. Kinetic models as a route to control acrylamide formation in food.

    PubMed

    Wedzicha, Bronislaw L; Mottram, Donald S; Elmore, J Stephen; Koutsidis, Georgios; Dodson, Andrew T

    2005-01-01

    A kinetic model for the formation of acrylamide in potato, rye and wheat products has been derived, and kinetic parameters calculated for potato by multi-response modeling of reducing sugar (glucose and fructose), amino acid, asparagine and acrylamide concentrations with time. The kinetic mechanism shares, with Maillard browning, a rate limiting (probably dicarbonylic) intermediate, and includes reaction steps of this intermediate which are competitive with respect to acrylamide formation. A pathway representing physical and/or chemical losses of acrylamide accounts for the measured reduction of acrylamide yield at long reaction times. A mechanistic hypothesis regarding the competing reactions of Strecker aldehyde formation and tautomerization followed by beta-elimination to give acrylamide, features in the kinetic model and can be used to determine the factors which steer the reaction towards acrylamide. A predictive application of this model is for 'what-if' experiments to explore the conditions which lead to reduced acrylamide yields. PMID:16438302

  13. Kinetics of Nanochain Formation in a Simplified Model of Amelogenin Biomacromolecules

    PubMed Central

    Li, Wei; Liu, Ya; Perez, Toni; Gunton, J.D.; Sorensen, C.M.; Chakrabarti, A.

    2011-01-01

    We show that the kinetics of nanochain formation of amelogenin molecules is well described by a combination of translational and rotational diffusion of a simplified anisotropic bipolar model consisting of hydrophobic spherical colloid particles and a point charge located on each particle surface. The colloid particles interact via a standard depletion attraction whereas the point charges interact through a screened Coulomb repulsion. We study the kinetics via a Brownian dynamics simulation of both translational and rotational motions and show that the anisotropy brought in by the charge dramatically affects the kinetic pathway of cluster formation and our simple model captures the main features of the experimental observations. PMID:22098749

  14. V and V of Lexical, Syntactic and Semantic Properties for Interactive Systems Through Model Checking of Formal Description of Dialog

    NASA Technical Reports Server (NTRS)

    Brat, Guillaume P.; Martinie, Celia; Palanque, Philippe

    2013-01-01

    During early phases of the development of an interactive system, future system properties are identified (through interaction with end users in the brainstorming and prototyping phase of the application, or by other stakehold-ers) imposing requirements on the final system. They can be specific to the application under development or generic to all applications such as usability principles. Instances of specific properties include visibility of the aircraft altitude, speed… in the cockpit and the continuous possibility of disengaging the autopilot in whatever state the aircraft is. Instances of generic properties include availability of undo (for undoable functions) and availability of a progression bar for functions lasting more than four seconds. While behavioral models of interactive systems using formal description techniques provide complete and unambiguous descriptions of states and state changes, it does not provide explicit representation of the absence or presence of properties. Assessing that the system that has been built is the right system remains a challenge usually met through extensive use and acceptance tests. By the explicit representation of properties and the availability of tools to support checking these properties, it becomes possible to provide developers with means for systematic exploration of the behavioral models and assessment of the presence or absence of these properties. This paper proposes the synergistic use two tools for checking both generic and specific properties of interactive applications: Petshop and Java PathFinder. Petshop is dedicated to the description of interactive system behavior. Java PathFinder is dedicated to the runtime verification of Java applications and as an extension dedicated to User Interfaces. This approach is exemplified on a safety critical application in the area of interactive cockpits for large civil aircrafts.

  15. Thermal conductivity of zirconia based inert matrix fuel: use and abuse of the formal models for testing new experimental data

    NASA Astrophysics Data System (ADS)

    Degueldre, C.; Arima, T.; Lee, Y. W.

    2003-06-01

    An inert matrix fuel material based on yttria-stabilized cubic zirconia: Er xY yPu zZr 1- x- y- zO 2-( x + y)/2 ( x+ y=0.15, z: [0.05-0.15]) was proposed for burning excess plutonium in light water reactors. The studied inert matrix fuel is made of cubic stabilized zirconia. The limited number of experimental thermal conductivity data justifies this formal and intensive study. Approaches derived from Klemens theory were revisited and the derived conductivity model applied for zirconia, accounting the effects of phononic scattering centers. The hyperbolic thermal conductivity trend with temperature known for pure zirconia, is reduced by isotopes, impurities, dopants and oxygen vacancies, which act as scattering centers and contribute to conductivity reduction to a flat plot with temperature for stabilized zirconia. It is experimentally observed that the thermal conductivity derived from laser flash measurements for Er xY yM zZr 1- x- y- zO 2-( x + y)/2 (with M=Ce or Pu, z=0 or ˜0.1 and x+ y=0.15) is rather constant as a function of temperature in the range 300-1000 K. The thermal conductivity was observed to depend on the concentration of dopants such as YO 1.5 and/or ErO 1.5, CeO 2 (analogous of PuO 2) or PuO 2. The bulk material conductivity of Er 0.05Y 0.10Pu 0.10Zr 0.75O 1.925 is about 2 W m -1 K -1. In this study, the thermal conductivity data of both monoclinic and stabilized cubic zirconia based IMF are tested with the model approach in order to understand the experimental data in a semi-quantitative way.

  16. Kinetics of bacterial phospholipase C activity at micellar interfaces: effect of substrate aggregate microstructure and a model for the kinetic parameters.

    PubMed

    Singh, Jasmeet; Ranganathan, Radha; Hajdu, Joseph

    2008-12-25

    Activity at micellar interfaces of bacterial phospholipase C from Bacillus cereus on phospholipids solubilized in micelles was investigated with the goal of elucidating the role of the interface microstructure and developing further an existing kinetic model. Enzyme kinetics and physicochemical characterization of model substrate aggregates were combined, thus enabling the interpretation of kinetics in the context of the interface. Substrates were diacylphosphatidylcholine of different acyl chain lengths in the form of mixed micelles with dodecyldimethylammoniopropanesulfonate. An early kinetic model, reformulated to reflect the interfacial nature of the kinetics, was applied to the kinetic data. A better method of data treatment is proposed, use of which makes the presence of microstructure effects quite transparent. Models for enzyme-micelle binding and enzyme-lipid binding are developed, and expressions incorporating the microstructural properties are derived for the enzyme-micelle dissociation constant K(s) and the interface Michaelis-Menten constant, K(M). Use of these expressions in the interface kinetic model brings excellent agreement between the kinetic data and the model. Numerical values for the thermodynamic and kinetic parameters are determined. Enzyme-lipid binding is found to be an activated process with an acyl chain length dependent free energy of activation that decreases with micelle lipid molar fraction with a coefficient of about -15RT and correlates with the tightness of molecular packing in the substrate aggregate. Thus, the physical insight obtained includes a model for the kinetic parameters that shows that these parameters depend on the substrate concentration and acyl chain length of the lipid. Enzyme-micelle binding is indicated to be hydrophobic and solvent mediated with a dissociation constant of 1.2 mM.

  17. Multicompartment kinetic models for lead. II. Linear kinetics and variable absorption in humans without excessive lead exposures

    SciTech Connect

    Marcus, A.H.

    1985-04-01

    Multicompartment models with constant fractional transfer rates have been fitted to experimental data on lead metabolism in four subjects studied by M.B. Rabinowitz, G.W. Wetherill, and J.D. Kopple. Long-term retention is estimated for blood, soft tissue, cortical and trabecular bone pools, and for facial hair. The absorption of lead from diet is shown to change with time, but no evidence was found for other variable or nonlinear kinetic mechanisms of lead metabolism in humans without excessive lead exposure.

  18. [Kinetic model of enhanced biological phosphorus removal with mixed acetic and propionic acids as carbon sources. (I): Model constitution].

    PubMed

    Zhang, Chao; Chen, Yin-Guang

    2013-03-01

    Based on activated sludge model No. 2 (ASM2), the anaerobic/aerobic kinetic model of phosphorus-accumulating organisms (PAO) was established with mixed short-chain fatty acids (SCFAs) as the base substance in enhanced biological phosphorus removal process. The characteristic of the PAO model was that the anaerobic metabolism rates of glycogen degradation, poly-beta-hydroxyalkanoates synthesis and polyphosphate hydrolysis were expressed by SCFAs uptake equation, and the effects of anaerobic maintenance on kinetics and stoichiometry were considered. The PAO kinetic model was composed of 3 soluble components, 4 particulate components and a pH parameter, which constituted the matrix of stoichiometric coefficients. On the basis of PAO model, the GAO kinetic model was established, which included 7 processes, and phosphorus content influenced the aerobic metabolism only.

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

    SciTech Connect

    Westbrook, C.K.; Marinov, N.; Pitz, W.J.; Curran, H.

    1996-10-01

    This project is intended to develop detailed and simplified kinetic reaction mechanisms for the combustion of practical systems fueled by hydrogen, and then to use those mechanisms to examine the performance, efficiency, pollutant emissions, and other characteristics of those systems. During the last year, a H2/NOx mechanism has been developed that gives much improved predictions of NOx emissions compared to experimental data. Preliminary chemical kinetic and equilibrium calculations have been performed in support of Br2-H2O experiments to be conducted at NREL. Hydrogen, hydrogen/methane and hydrogen/natural gas mixtures have been investigated in a knock-rating engine to assess their automotive knock characteristics. The authors are currently developing the simplified analog reaction mechanisms that are computationally simple, yet still reproduce many of the macroscopic features of flame propagation.

  20. Formal and informal home learning activities in relation to children's early numeracy and literacy skills: the development of a home numeracy model.

    PubMed

    Skwarchuk, Sheri-Lynn; Sowinski, Carla; LeFevre, Jo-Anne

    2014-05-01

    The purpose of this study was to propose and test a model of children's home numeracy experience based on Sénéchal and LeFevre's home literacy model (Child Development, 73 (2002) 445-460). Parents of 183 children starting kindergarten in the fall (median child age=58 months) completed an early home learning experiences questionnaire. Most of the children whose parents completed the questionnaire were recruited for numeracy and literacy testing 1 year later (along with 32 children from the inner city). Confirmatory factor analyses were used to reduce survey items, and hierarchical regression analyses were used to predict the relation among parents' attitudes, academic expectations for their children, reports of formal and informal numeracy, and literacy home practices on children's test scores. Parental reports of formal home numeracy practices (e.g., practicing simple sums) predicted children's symbolic number system knowledge, whereas reports of informal exposure to games with numerical content (measured indirectly through parents' knowledge of children's games) predicted children's non-symbolic arithmetic, as did numeracy attitudes (e.g., parents' enjoyment of numeracy). The home literacy results replicated past findings; parental reports of formal literacy practices (e.g., helping their children to read words) predicted children's word reading, whereas reports of informal experiences (i.e., frequency of shared reading measured indirectly through parents' storybook knowledge) predicted children's vocabulary. These findings support a multifaceted model of children's early numeracy environment, with different types of early home experiences (formal and informal) predicting different numeracy outcomes.

  1. Formal and informal home learning activities in relation to children's early numeracy and literacy skills: the development of a home numeracy model.

    PubMed

    Skwarchuk, Sheri-Lynn; Sowinski, Carla; LeFevre, Jo-Anne

    2014-05-01

    The purpose of this study was to propose and test a model of children's home numeracy experience based on Sénéchal and LeFevre's home literacy model (Child Development, 73 (2002) 445-460). Parents of 183 children starting kindergarten in the fall (median child age=58 months) completed an early home learning experiences questionnaire. Most of the children whose parents completed the questionnaire were recruited for numeracy and literacy testing 1 year later (along with 32 children from the inner city). Confirmatory factor analyses were used to reduce survey items, and hierarchical regression analyses were used to predict the relation among parents' attitudes, academic expectations for their children, reports of formal and informal numeracy, and literacy home practices on children's test scores. Parental reports of formal home numeracy practices (e.g., practicing simple sums) predicted children's symbolic number system knowledge, whereas reports of informal exposure to games with numerical content (measured indirectly through parents' knowledge of children's games) predicted children's non-symbolic arithmetic, as did numeracy attitudes (e.g., parents' enjoyment of numeracy). The home literacy results replicated past findings; parental reports of formal literacy practices (e.g., helping their children to read words) predicted children's word reading, whereas reports of informal experiences (i.e., frequency of shared reading measured indirectly through parents' storybook knowledge) predicted children's vocabulary. These findings support a multifaceted model of children's early numeracy environment, with different types of early home experiences (formal and informal) predicting different numeracy outcomes. PMID:24462995

  2. Experimental and Kinetic Modeling Study of 2-Methyl-2-Butene: Allylic Hydrocarbon Kinetics.

    PubMed

    Westbrook, Charles K; Pitz, William J; Mehl, Marco; Glaude, Pierre-Alexandre; Herbinet, Olivier; Bax, Sarah; Battin-Leclerc, Frederique; Mathieu, Olivier; Petersen, Eric L; Bugler, John; Curran, Henry J

    2015-07-16

    Two experimental studies have been carried out on the oxidation of 2-methyl-2-butene, one measuring ignition delay times behind reflected shock waves in a stainless steel shock tube, and the other measuring fuel, intermediate, and product species mole fractions in a jet-stirred reactor (JSR). The shock tube ignition experiments were carried out at three different pressures, approximately 1.7, 11.2, and 31 atm, and at each pressure, fuel-lean (ϕ = 0.5), stoichiometric (ϕ = 1.0), and fuel-rich (ϕ = 2.0) mixtures were examined, with each fuel/oxygen mixture diluted in 99% Ar, for initial postshock temperatures between 1330 and 1730 K. The JSR experiments were performed at nearly atmospheric pressure (800 Torr), with stoichiometric fuel/oxygen mixtures with 0.01 mole fraction of 2M2B fuel, a residence time in the reactor of 1.5 s, and mole fractions of 36 different chemical species were measured over a temperature range from 600 to 1150 K. These JSR experiments represent the first such study reporting detailed species measurements for an unsaturated, branched hydrocarbon fuel larger than iso-butene. A detailed chemical kinetic reaction mechanism was developed to study the important reaction pathways in these experiments, with particular attention on the role played by allylic C-H bonds and allylic pentenyl radicals. The results show that, at high temperatures, this olefinic fuel reacts rapidly, similar to related alkane fuels, but the pronounced thermal stability of the allylic pentenyl species inhibits low temperature reactivity, so 2M2B does not produce "cool flames" or negative temperature coefficient behavior. The connections between olefin hydrocarbon fuels, resulting allylic fuel radicals, the resulting lack of low-temperature reactivity, and the gasoline engine concept of octane sensitivity are discussed. PMID:25822578

  3. ASPEN: A Fully Kinetic, Reduced-Description Particle-in-Cell Model for Modeling Parametric Instabilities

    NASA Astrophysics Data System (ADS)

    Vu, H. X.; Bezzerides, B.; Dubois, D. F.

    1998-11-01

    A fully kinetic, reduced-description particle-in-cell (RPIC) model is presented in which deviations from quasineutrality, electron and ion kinetic effects, and nonlinear interactions between low-frequency and high-frequency parametric instabilities are modeled correctly. The model is based on a reduced description where the electromagnetic field is represented by three separate temporal WKB envelopes in order to model low-frequency and high-frequency parametric instabilities. Because temporal WKB approximations are invoked, the simulation can be performed on the electron time scale instead of the time scale of the light waves. The electrons and ions are represented by discrete finite-size particles, permitting electron and ion kinetic effects to be modeled properly. The Poisson equation is utilized to ensure that space-charge effects are included. Although RPIC is fully three dimensional, it has been implemented in only two dimensions on a CRAY-T3D with 512 processors and on the Accelerated Strategic Computing Initiative (ASCI) parallel computer at Los Alamos National Laboratory, and the resulting simulation code has been named ASPEN. Given the current computers available to the authors, one and two dimensional simulations are feasible to, and have been, performed. Three dimensional simulations are much more expensive, and are not feasible at this time. However, with rapidly advancing computer technologies, three dimensional simulations may be feasible in the near future. We believe this code is the first PIC code capable of simulating the interaction between low-frequency and high-frequency parametric instabilites in multiple dimensions. Test simulations of stimulated Raman scattering (SRS), stimulated Brillouin scattering (SBS), and Langmuir decay instability (LDI), are presented.

  4. Enzyme Kinetics.

    ERIC Educational Resources Information Center

    Moe, Owen; Cornelius, Richard

    1988-01-01

    Conveys an appreciation of enzyme kinetic analysis by using a practical and intuitive approach. Discusses enzyme assays, kinetic models and rate laws, the kinetic constants (V, velocity, and Km, Michaels constant), evaluation of V and Km from experimental data, and enzyme inhibition. (CW)

  5. Kinetic modeling of molecular motors: pause model and parameter determination from single-molecule experiments

    NASA Astrophysics Data System (ADS)

    Morin, José A.; Ibarra, Borja; Cao, Francisco J.

    2016-05-01

    Single-molecule manipulation experiments of molecular motors provide essential information about the rate and conformational changes of the steps of the reaction located along the manipulation coordinate. This information is not always sufficient to define a particular kinetic cycle. Recent single-molecule experiments with optical tweezers showed that the DNA unwinding activity of a Phi29 DNA polymerase mutant presents a complex pause behavior, which includes short and long pauses. Here we show that different kinetic models, considering different connections between the active and the pause states, can explain the experimental pause behavior. Both the two independent pause model and the two connected pause model are able to describe the pause behavior of a mutated Phi29 DNA polymerase observed in an optical tweezers single-molecule experiment. For the two independent pause model all parameters are fixed by the observed data, while for the more general two connected pause model there is a range of values of the parameters compatible with the observed data (which can be expressed in terms of two of the rates and their force dependencies). This general model includes models with indirect entry and exit to the long-pause state, and also models with cycling in both directions. Additionally, assuming that detailed balance is verified, which forbids cycling, this reduces the ranges of the values of the parameters (which can then be expressed in terms of one rate and its force dependency). The resulting model interpolates between the independent pause model and the indirect entry and exit to the long-pause state model

  6. SU-E-T-05: A 2D EPID Transit Dosimetry Model Based On An Empirical Quadratic Formalism

    SciTech Connect

    Tan, Y; Metwaly, M; Glegg, M; Baggarley, S; Elliott, A

    2014-06-01

    Purpose: To describe a 2D electronic portal imaging device (EPID) transit dosimetry model, based on an empirical quadratic formalism, that can predict either EPID or in-phantom dose distribution for comparisons with EPID captured image or treatment planning system (TPS) dose respectively. Methods: A quadratic equation can be used to relate the reduction in intensity of an exit beam to the equivalent path length of the attenuator. The calibration involved deriving coefficients from a set of dose planes measured for homogeneous phantoms with known thicknesses under reference conditions. In this study, calibration dose planes were measured with EPID and ionisation chamber (IC) in water for the same reference beam (6MV, 100mu, 20×20cm{sup 2}) and set of thicknesses (0–30cm). Since the same calibration conditions were used, the EPID and IC measurements can be related through the quadratic equation. Consequently, EPID transit dose can be predicted from TPS exported dose planes and in-phantom dose can be predicted using EPID distribution captured during treatment as an input. The model was tested with 4 open fields, 6 wedge fields, and 7 IMRT fields on homogeneous and heterogeneous phantoms. Comparisons were done using 2D absolute gamma (3%/3mm) and results were validated against measurements with a commercial 2D array device. Results: The gamma pass rates for comparisons between EPID measured and predicted ranged from 93.6% to 100.0% for all fields and phantoms tested. Results from this study agreed with 2D array measurements to within 3.1%. Meanwhile, comparisons in-phantom between TPS computed and predicted ranged from 91.6% to 100.0%. Validation with 2D array device was not possible for inphantom comparisons. Conclusion: A 2D EPID transit dosimetry model for treatment verification was described and proven to be accurate. The model has the advantage of being generic and allows comparisons at the EPID plane as well as multiple planes in-phantom.

  7. Kinetic modelling and simulation of laccase catalyzed degradation of reactive textile dyes.

    PubMed

    Cristóvão, Raquel O; Tavares, Ana P M; Ribeiro, Adriano S; Loureiro, José M; Boaventura, Rui A R; Macedo, Eugénia A

    2008-07-01

    A kinetic model based on Michaelis-Menten equation was developed to simulate the dye decolourisation of Reactive Black 5 (RB5), Reactive Blue 114 (RB114), Reactive Yellow 15 (RY15), Reactive Red 239 (RR239) and Reactive Red 180 (RR180) dyes by commercial laccase. The unusual kinetic behavior of some of these reactions suggests that the kinetic model must consider the activation of the laccase-mediator system. Several reactions at different concentrations of each dye were performed in batch reactors and time courses were obtained. A LSODE code to solve the differential equation obtained from the batch reactor was combined with an optimization Fortran program to obtain the theoretical time courses. The time courses obtained from the developed program were compared with the experimentally obtained ones to estimate the kinetic constants that minimized the difference between them. The close correlation between the predicted and the experimental results seems to support the reliability of the established models.

  8. Hydration kinetics modeling of Portland cement considering the effects of curing temperature and applied pressure

    SciTech Connect

    Lin Feng Meyer, Christian

    2009-04-15

    A hydration kinetics model for Portland cement is formulated based on thermodynamics of multiphase porous media. The mechanism of cement hydration is discussed based on literature review. The model is then developed considering the effects of chemical composition and fineness of cement, water-cement ratio, curing temperature and applied pressure. The ultimate degree of hydration of Portland cement is also analyzed and a corresponding formula is established. The model is calibrated against the experimental data for eight different Portland cements. Simple relations between the model parameters and cement composition are obtained and used to predict hydration kinetics. The model is used to reproduce experimental results on hydration kinetics, adiabatic temperature rise, and chemical shrinkage of different cement pastes. The comparisons between the model reproductions and the different experimental results demonstrate the applicability of the proposed model, especially for cement hydration at elevated temperature and high pressure.

  9. Validity of Various Approaches to Global Kinetic Modeling of Material Lifetimes

    SciTech Connect

    Burnham, A K; Dinh, L N

    2006-09-11

    Chemical kinetic modeling has been used for many years in process optimization, estimating real-time material performance, and lifetime prediction. Chemists have tended towards developing detailed mechanistic models, while engineers have tended towards global or lumped models. Many, if not most, applications use global models by necessity, since it is impractical or impossible to develop a rigorous mechanistic model. Model fitting acquired a bad connotation in the thermal analysis community after that community realized a decade after other disciplines that deriving kinetic parameters for an assumed model from a single heating rate produced unreliable and sometimes nonsensical results. In its place, advanced isoconversional methods, which have their roots in the Friedman and Ozawa-Flynn-Wall methods of the 1960s, have become increasingly popular. In fact, as pointed out by the ICTAC kinetics project in 2000, valid kinetic parameters can be derived by both isoconversional and model fitting methods as long as a diverse set of thermal histories are used to derive the kinetic parameters. The current paper extends the understanding from that project to give a better appreciation of the strengths and weaknesses of isoconversional and model-fitting approaches. Examples are given from a variety of data sets.

  10. A Comparison of Isoconversional and Model-Fitting Approaches to Kinetic Parameter Estimation and Application Predictions

    SciTech Connect

    Burnham, A K

    2006-05-17

    Chemical kinetic modeling has been used for many years in process optimization, estimating real-time material performance, and lifetime prediction. Chemists have tended towards developing detailed mechanistic models, while engineers have tended towards global or lumped models. Many, if not most, applications use global models by necessity, since it is impractical or impossible to develop a rigorous mechanistic model. Model fitting acquired a bad name in the thermal analysis community after that community realized a decade after other disciplines that deriving kinetic parameters for an assumed model from a single heating rate produced unreliable and sometimes nonsensical results. In its place, advanced isoconversional methods (1), which have their roots in the Friedman (2) and Ozawa-Flynn-Wall (3) methods of the 1960s, have become increasingly popular. In fact, as pointed out by the ICTAC kinetics project in 2000 (4), valid kinetic parameters can be derived by both isoconversional and model fitting methods as long as a diverse set of thermal histories are used to derive the kinetic parameters. The current paper extends the understanding from that project to give a better appreciation of the strengths and weaknesses of isoconversional and model-fitting approaches. Examples are given from a variety of sources, including the former and current ICTAC round-robin exercises, data sets for materials of interest, and simulated data sets.

  11. Ammonium removal from aqueous solutions by clinoptilolite: determination of isotherm and thermodynamic parameters and comparison of kinetics by the double exponential model and conventional kinetic models.

    PubMed

    Tosun, Ismail

    2012-03-01

    The adsorption isotherm, the adsorption kinetics, and the thermodynamic parameters of ammonium removal from aqueous solution by using clinoptilolite in aqueous solution was investigated in this study. Experimental data obtained from batch equilibrium tests have been analyzed by four two-parameter (Freundlich, Langmuir, Tempkin and Dubinin-Radushkevich (D-R)) and four three-parameter (Redlich-Peterson (R-P), Sips, Toth and Khan) isotherm models. D-R and R-P isotherms were the models that best fitted to experimental data over the other two- and three-parameter models applied. The adsorption energy (E) from the D-R isotherm was found to be approximately 7 kJ/mol for the ammonium-clinoptilolite system, thereby indicating that ammonium is adsorbed on clinoptilolite by physisorption. Kinetic parameters were determined by analyzing the nth-order kinetic model, the modified second-order model and the double exponential model, and each model resulted in a coefficient of determination (R(2)) of above 0.989 with an average relative error lower than 5%. A Double Exponential Model (DEM) showed that the adsorption process develops in two stages as rapid and slow phase. Changes in standard free energy (∆G°), enthalpy (∆H°) and entropy (∆S°) of ammonium-clinoptilolite system were estimated by using the thermodynamic equilibrium coefficients.

  12. Ammonium Removal from Aqueous Solutions by Clinoptilolite: Determination of Isotherm and Thermodynamic Parameters and Comparison of Kinetics by the Double Exponential Model and Conventional Kinetic Models

    PubMed Central

    Tosun, İsmail

    2012-01-01

    The adsorption isotherm, the adsorption kinetics, and the thermodynamic parameters of ammonium removal from aqueous solution by using clinoptilolite in aqueous solution was investigated in this study. Experimental data obtained from batch equilibrium tests have been analyzed by four two-parameter (Freundlich, Langmuir, Tempkin and Dubinin-Radushkevich (D-R)) and four three-parameter (Redlich-Peterson (R-P), Sips, Toth and Khan) isotherm models. D-R and R-P isotherms were the models that best fitted to experimental data over the other two- and three-parameter models applied. The adsorption energy (E) from the D-R isotherm was found to be approximately 7 kJ/mol for the ammonium-clinoptilolite system, thereby indicating that ammonium is adsorbed on clinoptilolite by physisorption. Kinetic parameters were determined by analyzing the nth-order kinetic model, the modified second-order model and the double exponential model, and each model resulted in a coefficient of determination (R2) of above 0.989 with an average relative error lower than 5%. A Double Exponential Model (DEM) showed that the adsorption process develops in two stages as rapid and slow phase. Changes in standard free energy (∆G°), enthalpy (∆H°) and entropy (∆S°) of ammonium-clinoptilolite system were estimated by using the thermodynamic equilibrium coefficients. PMID:22690177

  13. Modeling high adsorption capacity and kinetics of organic macromolecules on super-powdered activated carbon.

    PubMed

    Matsui, Yoshihiko; Ando, Naoya; Yoshida, Tomoaki; Kurotobi, Ryuji; Matsushita, Taku; Ohno, Koichi

    2011-02-01

    The capacity to adsorb natural organic matter (NOM) and polystyrene sulfonates (PSSs) on small particle-size activated carbon (super-powdered activated carbon, SPAC) is higher than that on larger particle-size activated carbon (powdered-activated carbon, PAC). Increased adsorption capacity is likely attributable to the larger external surface area because the NOM and PSS molecules do not completely penetrate the adsorbent particle; they preferentially adsorb near the outer surface of the particle. In this study, we propose a new isotherm equation, the Shell Adsorption Model (SAM), to explain the higher adsorption capacity on smaller adsorbent particles and to describe quantitatively adsorption isotherms of activated carbons of different particle sizes: PAC and SPAC. The SAM was verified with the experimental data of PSS adsorption kinetics as well as equilibrium. SAM successfully characterized PSS adsorption isotherm data for SPACs and PAC simultaneously with the same model parameters. When SAM was incorporated into an adsorption kinetic model, kinetic decay curves for PSSs adsorbing onto activated carbons of different particle sizes could be simultaneously described with a single kinetics parameter value. On the other hand, when SAM was not incorporated into such an adsorption kinetic model and instead isotherms were described by the Freundlich model, the kinetic decay curves were not well described. The success of the SAM further supports the adsorption mechanism of PSSs preferentially adsorbing near the outer surface of activated carbon particles. PMID:21172719

  14. Systematic construction of kinetic models from genome-scale metabolic networks.

    PubMed

    Stanford, Natalie J; Lubitz, Timo; Smallbone, Kieran; Klipp, Edda; Mendes, Pedro; Liebermeister, Wolfram

    2013-01-01

    The quantitative effects of environmental and genetic perturbations on metabolism can be studied in silico using kinetic models. We present a strategy for large-scale model construction based on a logical layering of data such as reaction fluxes, metabolite concentrations, and kinetic constants. The resulting models contain realistic standard rate laws and plausible parameters, adhere to the laws of thermodynamics, and reproduce a predefined steady state. These features have not been simultaneously achieved by previous workflows. We demonstrate the advantages and limitations of the workflow by translating the yeast consensus metabolic network into a kinetic model. Despite crudely selected data, the model shows realistic control behaviour, a stable dynamic, and realistic response to perturbations in extracellular glucose concentrations. The paper concludes by outlining how new data can continuously be fed into the workflow and how iterative model building can assist in directing experiments. PMID:24324546

  15. A kinetics modeling study on the inhibition of glucose on cellulosome of Clostridium thermocellum.

    PubMed

    Zhang, Pengcheng; Wang, Buyun; Xiao, Qunfang; Wu, Shan

    2015-08-01

    A simplified kinetics model was built to study the inhibition of glucose on cellulosome of Clostridium thermocellum. Suitable reaction conditions were adopted to evaluate the model. The model was evaluated at different temperatures and further with various activated carbon additions as adsorbent for glucose. Investigation results revealed that the model could describe the hydrolysis kinetics of cellulose by cellulosome quite well. Glucose was found to be an inhibitor for cellulosome based on the kinetics analysis. Inhibition increased with the increase in temperature. Activated carbon as adsorbent could lower the inhibition. Parameters in the model were further discussed based on the experiment. The model might also be used to describe the strong inhibition of cellobiose on cellulosome. Saccharification of cellulose by both cellulosome and C. thermocellum could be enhanced efficiently by activated carbon addition.

  16. Autoignition chemistry of the hexane isomers: An experimental and kinetic modeling study

    SciTech Connect

    Curran, H.J.; Gaffuri, P.; Pitz, W.J.; Westbrook, C.K.; Leppard, W.R.

    1995-06-01

    Autoignition of the five distinct isomers of hexane is studied experimentally under motored engine conditions and computationally using a detailed chemical kinetic reaction mechanism. Computed and experimental results are compared and used to help understand the chemical factors leading to engine knock in spark-ignited engines and the molecular structure factors contributing to octane rating for hydrocarbon fuels. The kinetic model reproduces observed variations in critical compression ratio with fuel structure, and it also provides intermediate and final product species concentrations in very dose agreement with observed results. In addition, the computed results provide insights into the kinetic origins of fuel octane sensitive.

  17. Modeling capsid kinetics assembly from the steady state distribution of multi-sizes aggregates

    NASA Astrophysics Data System (ADS)

    Hozé, Nathanaël; Holcman, David

    2014-01-01

    The kinetics of aggregation for particles of various sizes depends on their diffusive arrival and fusion at a specific nucleation site. We present here a mean-field approximation and a stochastic jump model for aggregates at equilibrium. This approach is an alternative to the classical Smoluchowski equations that do not have a close form and are not solvable in general. We analyze these mean-field equations and obtain the kinetics of a cluster formation. Our approach provides a simplified theoretical framework to study the kinetics of viral capsid formation, such as HIV from the self-assembly of the structural proteins Gag.

  18. Group-kinetic theory and modeling of atmospheric turbulence

    NASA Technical Reports Server (NTRS)

    Tchen, C. M.

    1989-01-01

    A group kinetic method is developed for analyzing eddy transport properties and relaxation to equilibrium. The purpose is to derive the spectral structure of turbulence in incompressible and compressible media. Of particular interest are: direct and inverse cascade, boundary layer turbulence, Rossby wave turbulence, two phase turbulence; compressible turbulence, and soliton turbulence. Soliton turbulence can be found in large scale turbulence, turbulence connected with surface gravity waves and nonlinear propagation of acoustical and optical waves. By letting the pressure gradient represent the elementary interaction among fluid elements and by raising the Navier-Stokes equation to higher dimensionality, the master equation was obtained for the description of the microdynamical state of turbulence.

  19. First Results of PIC Modeling of Kinetic Alfven Wave Dissipation

    NASA Technical Reports Server (NTRS)

    Chulaki, Anna; Hesse, Michael; Zenitani, Seiji

    2007-01-01

    We present first results of an investigation of the kinetic damping of Alfven wave turbulence. The methodology is based on a fully electromagnetic, three-dimensional, particle in cell code. The calculation is initialized by an Alfven wave spectrum. Subsequently, a cascade develops, and damping by coupling to both ions and electrons is observed. We discuss results of these calculations, and present first estimates of damping rates and of the effects of energy transfer on ion and electron distributions. The results pertain to solar wind heating and acceleration.

  20. An experimental and kinetic modeling study of n-propanol and iso-propanol combustion

    SciTech Connect

    Frassoldati, Alessio; Cuoci, Alberto; Faravelli, Tiziano; Ranzi, Eliseo; Niemann, Ulrich; Seiser, Reinhard; Seshadri, Kalyanasundaram

    2010-01-15

    A kinetic model is developed to describe combustion of n-propanol and iso-propanol. It is validated by comparing predictions made using this kinetic model with new experimental data on structures of counterflow non-premixed flames and previously reported data over a wide range of configurations and conditions. The elementary pyrolysis reactions of methanol and ethanol are well-known and were used as a starting point for extension to propanol. A detailed description leading to evaluation of rate constants for initiation reactions, metathesis reactions, decomposition reactions, and four-center molecular dehydration reactions are given. Decomposition and oxidation of primary intermediate products are described using a previously developed semi-detailed kinetic model for hydrocarbon fuels. The kinetic mechanism is made up of more than 7000 reactions among 300 species. The structures of counterflow non-premixed flames were measured by removing gas samples from the flame and analyzing the samples using a gas chromatograph. The flame structures were measured under similar conditions for both fuels to elucidate the similarities and differences in combustion characteristics of the two isomers. The profiles measured include those of formaldehyde, acetaldehyde, propanal, and acetone. These species are considered to be pollutants. Validation of the kinetic model was first performed by comparing predictions with experimental data reported in the literature obtained in flow reactors and shock tubes. In these configurations, combustion is not influenced by molecular transport. The agreement between the kinetic model and experimental data was satisfactory. The predictions of the kinetic model were then compared with new and previously reported experimental data on structures of counterflow non-premixed flames of both isomers. The agreement between the kinetic model and experimental data was again satisfactory. Satisfactory agreement was also obtained when the predictions of the

  1. A two-column formalism for time-dependent modelling of stellar convection. I. Description of the method

    NASA Astrophysics Data System (ADS)

    Stökl, A.

    2008-11-01

    Context: In spite of all the advances in multi-dimensional hydrodynamics, investigations of stellar evolution and stellar pulsations still depend on one-dimensional computations. This paper devises an alternative to the mixing-length theory or turbulence models usually adopted in modelling convective transport in such studies. Aims: The present work attempts to develop a time-dependent description of convection, which reflects the essential physics of convection and that is only moderately dependent on numerical parameters and far less time consuming than existing multi-dimensional hydrodynamics computations. Methods: Assuming that the most extensive convective patterns generate the majority of convective transport, the convective velocity field is described using two parallel, radial columns to represent up- and downstream flows. Horizontal exchange, in the form of fluid flow and radiation, over their connecting interface couples the two columns and allows a simple circulating motion. The main parameters of this convective description have straightforward geometrical meanings, namely the diameter of the columns (corresponding to the size of the convective cells) and the ratio of the cross-section between up- and downdrafts. For this geometrical setup, the time-dependent solution of the equations of radiation hydrodynamics is computed from an implicit scheme that has the advantage of being unaffected by the Courant-Friedrichs-Lewy time-step limit. This implementation is part of the TAPIR-Code (short for The adaptive, implicit RHD-Code). Results: To demonstrate the approach, results for convection zones in Cepheids are presented. The convective energy transport and convective velocities agree with expectations for Cepheids and the scheme reproduces both the kinetic energy flux and convective overshoot. A study of the parameter influence shows that the type of solution derived for these stars is in fact fairly robust with respect to the constitutive numerical

  2. Systems, methods and computer-readable media to model kinetic performance of rechargeable electrochemical devices

    DOEpatents

    Gering, Kevin L.

    2013-01-01

    A system includes an electrochemical cell, monitoring hardware, and a computing system. The monitoring hardware samples performance characteristics of the electrochemical cell. The computing system determines cell information from the performance characteristics. The computing system also analyzes the cell information of the electrochemical cell with a Butler-Volmer (BV) expression modified to determine exchange current density of the electrochemical cell by including kinetic performance information related to pulse-time dependence, electrode surface availability, or a combination thereof. A set of sigmoid-based expressions may be included with the modified-BV expression to determine kinetic performance as a function of pulse time. The determined exchange current density may be used with the modified-BV expression, with or without the sigmoid expressions, to analyze other characteristics of the electrochemical cell. Model parameters can be defined in terms of cell aging, making the overall kinetics model amenable to predictive estimates of cell kinetic performance along the aging timeline.

  3. Models of Transformative Learning for Social Justice: Comparative Case Studies of Non-Formal Development Education in Britain and Spain

    ERIC Educational Resources Information Center

    Brown, Eleanor J.

    2015-01-01

    This paper presents comparative case studies of non-formal development education by non-profit organisations in two European countries. The study aimed to explore the extent to which such activities provide opportunities for transformative learning. The research was qualitative and began with interviews with educators across 14 organisations in…

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

    SciTech Connect

    Kowalsky, Michael B.; Moridis, George J.

    2006-11-29

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

  5. Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws--a promising method for speeding up the kinetic modelling of complex metabolic networks.

    PubMed

    Bulik, Sascha; Grimbs, Sergio; Huthmacher, Carola; Selbig, Joachim; Holzhütter, Hermann G

    2009-01-01

    Kinetic modelling of complex metabolic networks - a central goal of computational systems biology - is currently hampered by the lack of reliable rate equations for the majority of the underlying biochemical reactions and membrane transporters. On the basis of biochemically substantiated evidence that metabolic control is exerted by a narrow set of key regulatory enzymes, we propose here a hybrid modelling approach in which only the central regulatory enzymes are described by detailed mechanistic rate equations, and the majority of enzymes are approximated by simplified(non mechanistic) rate equations (e.g. mass action, LinLog, Michaelis-Menten and power law) capturing only a few basic kinetic features and hence containing only a small number of parameters to be experimentally determined. To check the reliability of this approach, we have applied it to two different metabolic networks, the energy and redox metabolism of red blood cells, and the purine metabolism of hepatocytes, using in both cases available comprehensive mechanistic models as reference standards. Identification of the central regulatory enzymes was performed by employing only information on network topology and the metabolic data for a single reference state of the network [Grimbs S, Selbig J, Bulik S, Holzhutter HG & Steuer R (2007) Mol Syst Biol 3, 146, doi:10.1038/msb4100186].Calculations of stationary and temporary states under various physiological challenges demonstrate the good performance of the hybrid models. We propose the hybrid modelling approach as a means to speed up the development of reliable kinetic models for complex metabolic networks.

  6. Computational model, method, and system for kinetically-tailoring multi-drug chemotherapy for individuals

    DOEpatents

    Gardner, Shea Nicole

    2007-10-23

    A method and system for tailoring treatment regimens to individual patients with diseased cells exhibiting evolution of resistance to such treatments. A mathematical model is provided which models rates of population change of proliferating and quiescent diseased cells using cell kinetics and evolution of resistance of the diseased cells, and pharmacokinetic and pharmacodynamic models. Cell kinetic parameters are obtained from an individual patient and applied to the mathematical model to solve for a plurality of treatment regimens, each having a quantitative efficacy value associated therewith. A treatment regimen may then be selected from the plurlaity of treatment options based on the efficacy value.

  7. Kinetic model of the inner magnetosphere with arbitrary magnetic field

    NASA Astrophysics Data System (ADS)

    Ilie, Raluca; Liemohn, Michael W.; Toth, Gabor; Skoug, Ruth M.

    2012-04-01

    Theoretical and numerical modifications to an inner magnetosphere model—Hot Electron Ion Drift Integrator (HEIDI)—were implemented, in order to accommodate for a nondipolar arbitrary magnetic field. While the dipolar solution for the geomagnetic field during quiet times represents a reasonable assumption in the near-Earth closed field region, during storm activity this assumption becomes invalid. HEIDI solves the time-dependent, gyration- and bounce-averaged kinetic equation for the phase space density of one or more ring current species. New equations are derived for the bounce-averaged coefficients for the distribution function, and their numerical implementation is discussed. Also, numerically solving all the bounce-averaged coefficients for the dipole case does not change the results significantly from the analytical approximation of Ejiri (1978). However, distorting the magnetic field changes all bounce-averaged coefficients that make up the kinetic equation. Initial simulations show that changing the magnetic field changes the whole topology of the ring current. This is because the drifts are altered due to dayside compression and nightside stretching of the field. Therefore, at certain locations, the nondipolar magnetic drifts can dominate the convective drifts, considerably altering the pressure distribution in the equatorial plane.

  8. KINETICS AND SCALING OF METABOLIC BIOTRANSFORMATION IN FISH: EFFECTS ON BIOACCUMULATION PREDICTED BY INCORPORATING IN VITRO DATA INTO TWO KINETIC MODELS

    EPA Science Inventory

    Metabolism data reported in these two abstracts will advance EPA's ability to extrapolate toxicological data among fish species. This information can be used to improve ecological risk assessments for metabolized compounds, parameterize chemical kinetic models, and optimize the d...

  9. A kinetic model for the sodium conductance system in squid axon.

    PubMed Central

    Moore, J W; Cox, E B

    1976-01-01

    We describe a kinetic reaction sequence for the sodium conductance system in the squid axon. It closely matches the original Hodgkin and Huxley model for voltage clamp experiments but it generates an action potential without a bump on the falling phase. When calcium ions are included in the reaction, this model faithfully reproduces the experimental observations of Frankenhaeuser and Hodgkin on the effects of altered calcium in the medium. The fit to experiment is much better than when a voltage shift in rate constants is assumed. The gating currents recently observed by Armstrong and Bezanilla are not compatible with the Hodgkin and Huxley model but can be reprocuced in considerable detail by the kinetic model. Thus it appears that the kinetic model differs from that of Hodgkin and Huxley perhaps in an important and fundamental way that makes it more realistic. PMID:1247646

  10. Adsorption rate of phenol from aqueous solution onto organobentonite: surface diffusion and kinetic models.

    PubMed

    Ocampo-Perez, Raul; Leyva-Ramos, Roberto; Mendoza-Barron, Jovita; Guerrero-Coronado, Rosa M

    2011-12-01

    The concentration decay curves for the adsorption of phenol on organobentonite were obtained in an agitated tank batch adsorber. The experimental adsorption rate data were interpreted with diffusional models as well as first-order, second-order and Langmuir kinetic models. The surface diffusion model adjusted the data quite well, revealing that the overall rate of adsorption was controlled by surface diffusion. Furthermore, the surface diffusion coefficient increased raising the mass of phenol adsorbed at equilibrium and was independent of the particle diameter in the range 0.042-0.0126 cm. It was demonstrated that the overall rate of adsorption was essentially not affected by the external mass transfer. The second-order and the Langmuir kinetic models fitted the experimental data quite well; however, the kinetic constants of both models varied without any physical meaning while increasing the particle size and the mass of phenol adsorbed at equilibrium.

  11. GEOMETRY, HEAT REMOVAL AND KINETICS SCOPING MODELS FOR HYDROGEN STORAGE SYSTEMS

    SciTech Connect

    Hardy, B

    2007-11-16

    It is recognized that detailed models of proposed hydrogen storage systems are essential to gain insight into the complex processes occurring during the charging and discharging processes. Such insight is an invaluable asset for both assessing the viability of a particular system and/or for improving its design. The detailed models, however, require time to develop and run. Clearly, it is much more efficient to begin a modeling effort with a good system design and to progress from that point. To facilitate this approach, it is useful to have simplified models that can quickly estimate optimal loading and discharge kinetics, effective hydrogen capacities, system dimensions and heat removal requirements. Parameters obtained from these models can then be input to the detailed models to obtain an accurate assessment of system performance that includes more complete integration of the physical processes. This report describes three scoping models that assess preliminary system design prior to invoking a more detailed finite element analysis. The three models address the kinetics, the scaling and heat removal parameters of the system, respectively. The kinetics model is used to evaluate the effect of temperature and hydrogen pressure on the loading and discharge kinetics. As part of the kinetics calculations, the model also determines the mass of stored hydrogen per mass of hydride (in a particular reference form). As such, the model can determine the optimal loading and discharge rates for a particular hydride and the maximum achievable loading (over an infinite period of time). The kinetics model developed with the Mathcad{reg_sign} solver, runs in a mater of seconds and can quickly be used to identify the optimal temperature and pressure for either the loading or discharge processes. The geometry scoping model is used to calculate the size of the system, the optimal placement of heat transfer elements, and the gravimetric and volumetric capacities for a particular

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

    USGS Publications Warehouse

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

    2001-01-01

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

  13. Inverse modeling approach for evaluation of kinetic parameters of a biofilm reactor using tabu search.

    PubMed

    Kumar, B Shiva; Venkateswarlu, Ch

    2014-08-01

    The complex nature of biological reactions in biofilm reactors often poses difficulties in analyzing such reactors experimentally. Mathematical models could be very useful for their design and analysis. However, application of biofilm reactor models to practical problems proves somewhat ineffective due to the lack of knowledge of accurate kinetic models and uncertainty in model parameters. In this work, we propose an inverse modeling approach based on tabu search (TS) to estimate the parameters of kinetic and film thickness models. TS is used to estimate these parameters as a consequence of the validation of the mathematical models of the process with the aid of measured data obtained from an experimental fixed-bed anaerobic biofilm reactor involving the treatment of pharmaceutical industry wastewater. The results evaluated for different modeling configurations of varying degrees of complexity illustrate the effectiveness of TS for accurate estimation of kinetic and film thickness model parameters of the biofilm process. The results show that the two-dimensional mathematical model with Edward kinetics (with its optimum parameters as mu(max)rho(s)/Y = 24.57, Ks = 1.352 and Ki = 102.36) and three-parameter film thickness expression (with its estimated parameters as a = 0.289 x 10(-5), b = 1.55 x 10(-4) and c = 15.2 x 10(-6)) better describes the biofilm reactor treating the industry wastewater.

  14. Explicit equilibria in a kinetic model of gambling

    NASA Astrophysics Data System (ADS)

    Bassetti, F.; Toscani, G.

    2010-06-01

    We introduce and discuss a nonlinear kinetic equation of Boltzmann type which describes the evolution of wealth in a pure gambling process, where the entire sum of wealths of two agents is up for gambling, and randomly shared between the agents. For this equation the analytical form of the steady states is found for various realizations of the random fraction of the sum which is shared to the agents. Among others, the exponential distribution appears as steady state in case of a uniformly distributed random fraction, while Gamma distribution appears for a random fraction which is Beta distributed. The case in which the gambling game is only conservative-in-the-mean is shown to lead to an explicit heavy tailed distribution.

  15. C. botulinum inactivation kinetics implemented in a computational model of a high-pressure sterilization process.

    PubMed

    Juliano, Pablo; Knoerzer, Kai; Fryer, Peter J; Versteeg, Cornelis

    2009-01-01

    High-pressure, high-temperature (HPHT) processing is effective for microbial spore inactivation using mild preheating, followed by rapid volumetric compression heating and cooling on pressure release, enabling much shorter processing times than conventional thermal processing for many food products. A computational thermal fluid dynamic (CTFD) model has been developed to model all processing steps, including the vertical pressure vessel, an internal polymeric carrier, and food packages in an axis-symmetric geometry. Heat transfer and fluid dynamic equations were coupled to four selected kinetic models for the inactivation of C. botulinum; the traditional first-order kinetic model, the Weibull model, an nth-order model, and a combined discrete log-linear nth-order model. The models were solved to compare the resulting microbial inactivation distributions. The initial temperature of the system was set to 90 degrees C and pressure was selected at 600 MPa, holding for 220 s, with a target temperature of 121 degrees C. A representation of the extent of microbial inactivation throughout all processing steps was obtained for each microbial model. Comparison of the models showed that the conventional thermal processing kinetics (not accounting for pressure) required shorter holding times to achieve a 12D reduction of C. botulinum spores than the other models. The temperature distribution inside the vessel resulted in a more uniform inactivation distribution when using a Weibull or an nth-order kinetics model than when using log-linear kinetics. The CTFD platform could illustrate the inactivation extent and uniformity provided by the microbial models. The platform is expected to be useful to evaluate models fitted into new C. botulinum inactivation data at varying conditions of pressure and temperature, as an aid for regulatory filing of the technology as well as in process and equipment design.

  16. A formal statistical approach to representing uncertainty in rainfall-runoff modelling with focus on residual analysis and probabilistic output evaluation - Distinguishing simulation and prediction

    NASA Astrophysics Data System (ADS)

    Breinholt, Anders; Møller, Jan Kloppenborg; Madsen, Henrik; Mikkelsen, Peter Steen

    2012-11-01

    SummaryWhile there seems to be consensus that hydrological model outputs should be accompanied with an uncertainty estimate the appropriate method for uncertainty estimation is not agreed upon and a debate is ongoing between advocators of formal statistical methods who consider errors as stochastic and GLUE advocators who consider errors as epistemic, arguing that the basis of formal statistical approaches that requires the residuals to be stationary and conform to a statistical distribution is unrealistic. In this paper we take a formal frequentist approach to parameter estimation and uncertainty evaluation of the modelled output, and we attach particular importance to inspecting the residuals of the model outputs and improving the model uncertainty description. We also introduce the probabilistic performance measures sharpness, reliability and interval skill score for model comparison and for checking the reliability of the confidence bounds. Using point rainfall and evaporation data as input and flow measurements from a sewer system for model conditioning, a state space model is formulated that accounts for three different flow contributions: wastewater from households, and fast rainfall-runoff from paved areas and slow rainfall-dependent infiltration-inflow from unknown sources. We consider two different approaches to evaluate the model output uncertainty, the output error method that lumps all uncertainty into the observation noise term, and a method based on Stochastic Differential Equations (SDEs) that separates input and model structure uncertainty from observation uncertainty and allows updating of model states in real-time. The results show that the optimal simulation (off-line) model is based on the output error method whereas the optimal prediction (on-line) model is based on the SDE method and the skill scoring criterion proved that significant predictive improvements of the output can be gained from updating the states continuously. In an effort to

  17. The Cognitive Processes Underlying Event-Based Prospective Memory In School Age Children and Young Adults: A Formal Model-Based Study

    PubMed Central

    Smith, Rebekah E.; Bayen, Ute Johanna; Martin, Claudia

    2010-01-01

    Fifty 7-year-olds (29 female), 53 10-year-olds (29 female), and 36 young adults (19 female), performed a computerized event-based prospective memory task. All three groups differed significantly in prospective memory performance with adults showing the best performance and 7-year-olds the poorest performance. We used a formal multinomial process tree model of event-based prospective memory to decompose age differences in cognitive processes that jointly contribute to prospective memory performance. The formal modeling results demonstrated that adults differed significantly from the 7-year-olds and 10-year-olds on both the prospective component and the retrospective component of the task. The 7-year-olds and 10-year-olds differed only in the ability to recognize prospective memory target events. The prospective memory task imposed a cost to ongoing activities in all three age groups. PMID:20053020

  18. Fokker–Planck kinetic modeling of suprathermal α-particles in a fusion plasma

    SciTech Connect

    Peigney, B.E.

    2014-12-01

    We present an ion kinetic model describing the transport of suprathermal α-particles in inertial fusion targets. The analysis of the underlying physical model enables us to develop efficient numerical methods to simulate the creation, transport and collisional relaxation of fusion reaction products (α-particles) at a kinetic level. The model assumes spherical symmetry in configuration space and axial symmetry in velocity space around the mean flow velocity. A two-energy-scale approach leads to a self-consistent modeling of the coupling between suprathermal α-particles and the thermal bulk of the imploding plasma. This method provides an accurate numerical treatment of energy deposition and transport processes involving suprathermal particles. The numerical tools presented here are then validated against known analytical results. This enables us to investigate the potential role of ion kinetic effects on the physics of ignition and thermonuclear burn in inertial confinement fusion schemes.

  19. Dynamic nuclear renography kinetic analysis: Four-compartment model for assessing kidney function

    SciTech Connect

    Raswan, T. R. Haryanto, F.

    2014-09-30

    Dynamic nuclear renography method produces TACs of kidneys and bladder. Multiple TACs data can be further analyzed to obtain the overview of urinary system's condition. Tracer kinetic analysis was performed using four-compartment models. The system's model consist of four irreversible compartment with four transport constants (k1, k2, k3 and k4). The mathematical expressions of tracer's distributions is fitted to experimental data (TACs) resulting in model constants. This transport constants represent the urinary system behavior, and later can be used for analyzing system's condition. Different intervals of kinetics parameter are clearly shown by abnormal system with respect to the normal one. Furthermore, the system with delayed uptake has 82% lower uptake parameters (k1 and k2) than normal one. Meanwhile, the system with prolonged clearance time has its kinetics parameters k3 or k4 lower than the others. This model is promising for quantitatively describe urinary system's function especially if supplied with more data.

  20. Effect of wall growth on the kinetic modeling of nitrite oxidation in a CSTR.

    PubMed

    Dokianakis, Spiros N; Kornaros, Michael; Lyberatos, Gerasimos

    2006-03-01

    A simple kinetic model was developed for describing nitrite oxidation by autotrophic aerobic nitrifiers in a continuous stirred tank reactor (CSTR), in which mixed (suspended and attached) growth conditions prevail. The CSTR system was operated under conditions of constant nitrite feed concentration and varying volumetric flow rates. Experimental data from steady-state conditions in the CSTR system and from batch experiments were used for the determination of the model's kinetic parameters. Model predictions were verified against experimental data obtained under transient operating conditions, when volumetric flow rate and nitrite feed concentration disturbances were imposed on the CSTR. The presented kinetic modeling procedure is quite simple and general and therefore can also be applied to other mixed growth biological systems.

  1. Evaluation and modeling of thermal kinetic degradation for PVA doped PbS quantum dot

    SciTech Connect

    Mahmoud, Waleed E.; Al-Heniti, S.H.

    2011-09-15

    Highlights: {yields} Synthesis of PVA doped PbS quantum dots. {yields} Data fitting using integral and differential thermal kinetic models for calculating activation energy. {yields} Prediction of thermal degradation using iso-conversion model. -- Abstract: The kinetic analysis of the thermogravimetric curves for the thermal decomposition processes of PVA/PbS was performed. The samples were heated in nitrogen, with three different heating rates: 10, 20 and 30 {sup o}C min{sup -1}. Various forms of non-isothermal methods of analysis for determining the kinetic parameters were used. The differential and integral models were used to calculate the activation energies. Comparing with pure PVA, the results showed that the maximum activation energy of thermal degradation is achieved for PVA/PbS nanocomposite. Isoconversion model is used for predicting the thermal degradation acceleration. The results showed that the acceleration of thermal degradation for pure PVA was faster than PVA/PbS nanocomposite.

  2. Comparison of the kinetics of different Markov models for ligand binding under varying conditions

    SciTech Connect

    Martini, Johannes W. R.; Habeck, Michael

    2015-03-07

    We recently derived a Markov model for macromolecular ligand binding dynamics from few physical assumptions and showed that its stationary distribution is the grand canonical ensemble [J. W. R. Martini, M. Habeck, and M. Schlather, J. Math. Chem. 52, 665 (2014)]. The transition probabilities of the proposed Markov process define a particular Glauber dynamics and have some similarity to the Metropolis-Hastings algorithm. Here, we illustrate that this model is the stochastic analog of (pseudo) rate equations and the corresponding system of differential equations. Moreover, it can be viewed as a limiting case of general stochastic simulations of chemical kinetics. Thus, the model links stochastic and deterministic approaches as well as kinetics and equilibrium described by the grand canonical ensemble. We demonstrate that the family of transition matrices of our model, parameterized by temperature and ligand activity, generates ligand binding kinetics that respond to changes in these parameters in a qualitatively similar way as experimentally observed kinetics. In contrast, neither the Metropolis-Hastings algorithm nor the Glauber heat bath reflects changes in the external conditions correctly. Both converge rapidly to the stationary distribution, which is advantageous when the major interest is in the equilibrium state, but fail to describe the kinetics of ligand binding realistically. To simulate cellular processes that involve the reversible stochastic binding of multiple factors, our pseudo rate equation model should therefore be preferred to the Metropolis-Hastings algorithm and the Glauber heat bath, if the stationary distribution is not of only interest.

  3. Kinetic modelling of anaerobic hydrolysis of solid wastes, including disintegration processes

    SciTech Connect

    García-Gen, Santiago; Sousbie, Philippe; Rangaraj, Ganesh; Lema, Juan M.; Rodríguez, Jorge; Steyer, Jean-Philippe; Torrijos, Michel

    2015-01-15

    Highlights: • Fractionation of solid wastes into readily and slowly biodegradable fractions. • Kinetic coefficients estimation from mono-digestion batch assays. • Validation of kinetic coefficients with a co-digestion continuous experiment. • Simulation of batch and continuous experiments with an ADM1-based model. - Abstract: A methodology to estimate disintegration and hydrolysis kinetic parameters of solid wastes and validate an ADM1-based anaerobic co-digestion model is presented. Kinetic parameters of the model were calibrated from batch reactor experiments treating individually fruit and vegetable wastes (among other residues) following a new protocol for batch tests. In addition, decoupled disintegration kinetics for readily and slowly biodegradable fractions of solid wastes was considered. Calibrated parameters from batch assays of individual substrates were used to validate the model for a semi-continuous co-digestion operation treating simultaneously 5 fruit and vegetable wastes. The semi-continuous experiment was carried out in a lab-scale CSTR reactor for 15 weeks at organic loading rate ranging between 2.0 and 4.7 g VS/L d. The model (built in Matlab/Simulink) fit to a large extent the experimental results in both batch and semi-continuous mode and served as a powerful tool to simulate the digestion or co-digestion of solid wastes.

  4. Comparison between hybrid and fully kinetic models of asymmetric magnetic reconnection: Coplanar and guide field configurations

    SciTech Connect

    Aunai, Nicolas; Hesse, Michael; Kuznetsova, Maria; Black, Carrie; Evans, Rebekah; Zenitani, Seiji; Smets, Roch

    2013-02-15

    Magnetic reconnection occurring in collisionless environments is a multi-scale process involving both ion and electron kinetic processes. Because of their small mass, the electron scales are difficult to resolve in numerical and satellite data, it is therefore critical to know whether the overall evolution of the reconnection process is influenced by the kinetic nature of the electrons, or is unchanged when assuming a simpler, fluid, electron model. This paper investigates this issue in the general context of an asymmetric current sheet, where both the magnetic field amplitude and the density vary through the discontinuity. A comparison is made between fully kinetic and hybrid kinetic simulations of magnetic reconnection in coplanar and guide field systems. The models share the initial condition but differ in their electron modeling. It is found that the overall evolution of the system, including the reconnection rate, is very similar between both models. The best agreement is found in the guide field system, which confines particle better than the coplanar one, where the locality of the moments is violated by the electron bounce motion. It is also shown that, contrary to the common understanding, reconnection is much faster in the guide field system than in the coplanar one. Both models show this tendency, indicating that the phenomenon is driven by ion kinetic effects and not electron ones.

  5. The LANL atomic kinetics modeling effort and its application to W plasmas

    SciTech Connect

    Colgan, James; Abdallah, Joseph; Fontes, Christopher; Zhang, Honglin

    2010-12-10

    This is the work of the LANL group on atomic kinetics modelling. There are various levels of detail in the LANL suite of atomic physics codes: (1) Non-relativistic configuration average kinetics (nl{sup w}) + UTA spectra, (2) Relativistic configuration average kinetics (nlj{sup w}) + UTA spectra, (3) Mixed UTA (MUTA) - configuration average kinetics and spectra composed of mixture of UTAs and fine-structure features and (4) Fine-structure levels. The LANL suite of atomic physics codes consists of 5 codes: (1) CATS/RATS atomic structure codes (semi-relativistic Cowan code or Dirac-Fock-Slater code), (2) ACE collisional excitation code (Plane-wave Born, Columb-Born and distorted-wave methods) and (3) GIPPER ionization code (scaled-hydrogenic and distorted-wave methods). An on-line version of the codes is available at http://aphysics2.lanl.gov/tempweb. ATOMIC kinetics modelling code uses the atomic data for LTE or NLTE population kinetics models and spectral modelling of a broad range of plasma applications. The mixed UTA (MUTA) approach was developed for the spectra of complex ions and the results are in very good agreement with the Sandia-Z Iron opacity experiments. The LANL configuration-average/MUTA calculations were applied to tungsten problems of the non-LTE kinetics code comparison workshops. The LANL group plans to perform much larger calculations to assess the accuracy of the older results and to investigate low-temperature tungsten processes relevant to the divertor modelling.

  6. A phase-field model coupled with lattice kinetics solver for modeling crystal growth in furnaces

    SciTech Connect

    Lin, Guang; Bao, Jie; Xu, Zhijie; Tartakovsky, Alexandre M.; Henager, Charles H.

    2014-02-02

    In this study, we present a new numerical model for crystal growth in a vertical solidification system. This model takes into account the buoyancy induced convective flow and its effect on the crystal growth process. The evolution of the crystal growth interface is simulated using the phase-field method. Two novel phase-field models are developed to model the crystal growth interface in vertical gradient furnaces with two temperature profile setups: 1) fixed wall temperature profile setup and 2) time-dependent temperature profile setup. A semi-implicit lattice kinetics solver based on the Boltzmann equation is employed to model the unsteady incompressible flow. This model is used to investigate the effect of furnace operational conditions on crystal growth interface profiles and growth velocities. For a simple case of macroscopic radial growth, the phase-field model is validated against an analytical solution. Crystal growth in vertical gradient furnaces with two temperature profile setups have been also investigated using the developed model. The numerical simulations reveal that for a certain set of temperature boundary conditions, the heat transport in the melt near the phase interface is diffusion dominant and advection is suppressed.

  7. Mathematical modelling of thermal and kinetic phenomena in electron-beam technologies

    NASA Astrophysics Data System (ADS)

    Knyazeva, A. G.; Pobol, I. L.; Demidov, V. N.

    2016-07-01

    The article presents a scheme for constructing models using kinetic laws for additional parameters. The work describes the example of the model of electro-beam treatment of a material with a coating. The study uses the simple kinetic law for powder layer evolution due to shrinkage. The model takes into account the melting of powder layer and substrate. The numerical solution gives the temperature field, evolution of the molten pool, the heat affected zone and the surface relief for different moments of time. The results depend on the treatment rate and electron beam energy.

  8. The use of kinetic modelling as a fast way to screen thermal endurance of space materials

    NASA Astrophysics Data System (ADS)

    Moser, M.; Heltzel, S.; Semprimoschnig, C.; Garcia Martin, G.

    2003-09-01

    Currently planned missions of ESA (European Space Agency) to the inner part of the solar system will require the use of materials at an extreme radiation and temperature environment. A major concern regarding the selection of these materials is the thermal behaviour and the thermal stability. In this paper two kinetic models, the one following the ASTM E 1641 and ASTM E 1877 standards and the other following the Model Free Kinetics (MFK) approach, are presented. These models allow an easy and fast way to screen the thermal endurance of organic materials by running Thermo Gravimetric Analyses (TGA) temperature scans.

  9. A generalised enzyme kinetic model for predicting the behaviour of complex biochemical systems.

    PubMed

    Wong, Martin Kin Lok; Krycer, James Robert; Burchfield, James Geoffrey; James, David Ernest; Kuncic, Zdenka

    2015-01-01

    Quasi steady-state enzyme kinetic models are increasingly used in systems modelling. The Michaelis Menten model is popular due to its reduced parameter dimensionality, but its low-enzyme and irreversibility assumption may not always be valid in the in vivo context. Whilst the total quasi-steady state assumption (tQSSA) model eliminates the reactant stationary assumptions, its mathematical complexity is increased. Here, we propose the differential quasi-steady state approximation (dQSSA) kinetic model, which expresses the differential equations as a linear algebraic equation. It eliminates the reactant stationary assumptions of the Michaelis Menten model without increasing model dimensionality. The dQSSA was found to be easily adaptable for reversible enzyme kinetic systems with complex topologies and to predict behaviour consistent with mass action kinetics in silico. Additionally, the dQSSA was able to predict coenzyme inhibition in the reversible lactate dehydrogenase enzyme, which the Michaelis Menten model failed to do. Whilst the dQSSA does not account for the physical and thermodynamic interactions of all intermediate enzyme-substrate complex states, it is proposed to be suitable for modelling complex enzyme mediated biochemical systems. This is due to its simpler application, reduced parameter dimensionality and improved accuracy.

  10. Kinetics of interaction of vanillin with amino acids and peptides in model systems.

    PubMed

    Chobpattana, W; Jeon, I J; Smith, J S

    2000-09-01

    Model systems were used to study the reaction kinetics of vanillin and pentalysine, lysine, glutathione, cysteine, aspartame, or phenylalanine (molar ratio 1:1) in phosphate buffer. The buffer pH was adjusted to the pK(a)(2) of the available alpha-amino group of each amino acid or peptide. Reductions of vanillin followed first-order kinetics at 55, 65, and 75 degrees C in the presence of each of the amino acids or peptides used. The reaction rates were accelerated as the temperature increased. The rate constants were highest for pentalysine followed by lysine, phenylalanine, glutathione/cysteine, and aspartame. The reduction of phenylalanine followed first-order kinetics, whereas the formation of its reaction product followed zero-order kinetics. The activation energy (E(a)) for the reaction ranged from 5.6 to 14.5 kcal/mol.

  11. Parameter Estimates in Differential Equation Models for Chemical Kinetics

    ERIC Educational Resources Information Center

    Winkel, Brian

    2011-01-01

    We discuss the need for devoting time in differential equations courses to modelling and the completion of the modelling process with efforts to estimate the parameters in the models using data. We estimate the parameters present in several differential equation models of chemical reactions of order n, where n = 0, 1, 2, and apply more general…

  12. Multicompartment kinetic models for lead. 2. Linear kinetics and variable absorption in humans without excessive lead exposures

    SciTech Connect

    Marcus, A.H.

    1985-01-01

    Multicompartment models with constant fractional transfer rates were fitted to experimental data on lead metabolism in four subjects studied by M. B. Rabinowitz, G. W. Wetherill, and J. D. Kopple (Science 182, 725-727, 1973; Environ. Health Perspect. 7, 145-153, 1974; Arch. Environ. Health 31, 220-223, 1976; J. Clin. Invest. 58, 260-270, 1976; J. Lab Clin. Med. 90, 238-248, 1977). Long-term retention is estimated for blood, soft tissue, cortical and trabecular bone pools, and for facial hair. The absorption of lead from diet is shown to change with time, but no evidence was found for other variable or nonlinear kinetic mechanisms of lead metabolism in humans without excessive lead exposure.

  13. The Application of Global Kinetic Models to HMX Beta-Delta Transition and Cookoff Processes

    SciTech Connect

    Wemhoff, A P; Burnham, A K; Nichols III, A L

    2006-12-07

    The reduction of the number of reactions in kinetic models for both the HMX beta-delta phase transition and thermal cookoff provides an attractive alternative to traditional multi-stage kinetic models due to reduced calibration effort requirements. In this study, we use the LLNL code ALE3D to provide calibrated kinetic parameters for a two-reaction bidirectional beta-delta HMX phase transition model based on Sandia Instrumented Thermal Ignition (SITI) and Scaled Thermal Explosion (STEX) temperature history curves, and a Prout-Tompkins cookoff model based on One-Dimensional Time to Explosion (ODTX) data. Results show that the two-reaction bidirectional beta-delta transition model presented here agrees as well with STEX and SITI temperature history curves as a reversible four-reaction Arrhenius model, yet requires an order of magnitude less computational effort. In addition, a single-reaction Prout-Tompkins model calibrated to ODTX data provides better agreement with ODTX data than a traditional multi-step Arrhenius model, and can contain up to 90% less chemistry-limited time steps for low-temperature ODTX simulations. Manual calibration methods for the Prout-Tompkins kinetics provide much better agreement with ODTX experimental data than parameters derived from Differential Scanning Calorimetry (DSC) measurements at atmospheric pressure. The predicted surface temperature at explosion for STEX cookoff simulations is a weak function of the cookoff model used, and a reduction of up to 15% of chemistry-limited time steps can be achieved by neglecting the beta-delta transition for this type of simulation. Finally, the inclusion of the beta-delta transition model in the overall kinetics model can affect the predicted time to explosion by 1% for the traditional multi-step Arrhenius approach, while up to 11% using a Prout-Tompkins cookoff model.

  14. Formal Methods at Intel - An Overview

    NASA Technical Reports Server (NTRS)

    Harrison, John

    2010-01-01

    Since the 1990s, Intel has invested heavily in formal methods, which are now deployed in several domains: hardware, software, firmware, protocols etc. Many different formal methods tools and techniques are in active use, including symbolic trajectory evaluation, temporal logic model checking, SMT-style combined decision procedures, and interactive higher-order logic theorem proving. I will try to give a broad overview of some of the formal methods activities taking place at Intel, and describe the challenges of extending formal verification to new areas and of effectively using multiple formal techniques in combination

  15. Equilibrium and kinetic models for colloid release under transient solution chemistry conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We present continuum models to describe colloid release in the subsurface during transient physicochemical conditions. Our modeling approach relates the amount of colloid release to changes in the fraction of the solid surface area that contributes to retention. Equilibrium, kinetic, equilibrium and...

  16. Kinetic Models for Adiabatic Reversible Expansion of a Monatomic Ideal Gas.

    ERIC Educational Resources Information Center

    Chang, On-Kok

    1983-01-01

    A fixed amount of an ideal gas is confined in an adiabatic cylinder and piston device. The relation between temperature and volume in initial/final phases can be derived from the first law of thermodynamics. However, the relation can also be derived based on kinetic models. Several of these models are discussed. (JN)

  17. A MATHEMATICAL MODEL FOR THE KINETICS OF THE MALE REPRODUCTIVE ENDOCRINE SYSTEM

    EPA Science Inventory

    In this presentation a model for the hormonal regulation of the reproductive endocrine system in the adult male rat will be discussed. The model includes a description of the kinetics of the androgenic hormones testosterone and dihydrotestosterone, as well as the receptor-mediate...

  18. Analysis of the importance of sorption kinetics to PCB fate modeling

    SciTech Connect

    Connolly, J.; Dean, M.

    1995-12-31

    A considerable amount of literature exists describing the importance of slow kinetics and resistantly bound fractions to the sorption process for hydrophobic organics such as PCBs. The frequently observed deviations of field measured partition coefficients from the presumed relationship between the organic carbon normalized partition coefficient (K{sub oc}) and octanol-water partition coefficient (K{sub ow}) may be evidence of slow sorption kinetics. Of note are the observations in Green Bay and New Bedford Harbor of increases in PCB partition coefficients along a gradient from high concentration to low concentration. These changes in partitioning were evaluated by incorporating a kinetic model derived from experiments with Hudson River sediment into a model of PCB fate in lower Green Bay. The kinetic model successfully described the observed changes in PCB partition coefficient. The results of this work support the conclusion that sorption kinetics are important to the transport and fate of PCBs. An implication of these results is that the resistant fraction of the sorbed PCBs increases with time. This may result in a decrease in bioavailability that could be significant to the use of models to protect future concentrations and ecological or human health risk.

  19. Model discrimination and mechanistic interpretation of kinetic data in protein aggregation studies.

    PubMed

    Bernacki, Joseph P; Murphy, Regina M

    2009-04-01

    Given the importance of protein aggregation in amyloid diseases and in the manufacture of protein pharmaceuticals, there has been increased interest in measuring and modeling the kinetics of protein aggregation. Several groups have analyzed aggregation data quantitatively, typically measuring aggregation kinetics by following the loss of protein monomer over time and invoking a nucleated growth mechanism. Such analysis has led to mechanistic conclusions about the size and nature of the nucleus, the aggregation pathway, and/or the physicochemical properties of aggregation-prone proteins. We have examined some of the difficulties that arise when extracting mechanistic meaning from monomer-loss kinetic data. Using literature data on the aggregation of polyglutamine, a mutant beta-clam protein, and protein L, we determined parameter values for 18 different kinetic models. We developed a statistical model discrimination method to analyze protein aggregation data in light of competing mechanisms; a key feature of the method is that it penalizes overparameterization. We show that, for typical monomer-loss kinetic data, multiple models provide equivalent fits, making mechanistic determination impossible. We also define the type and quality of experimental data needed to make more definitive conclusions about the mechanism of aggregation. Specifically, we demonstrate how direct measurement of fibril size provides robust discrimination. PMID:19348769

  20. An investigation on the modelling of kinetics of thermal decomposition of hazardous mercury wastes.

    PubMed

    Busto, Yailen; M G Tack, Filip; Peralta, Luis M; Cabrera, Xiomara; Arteaga-Pérez, Luis E

    2013-09-15

    The kinetics of mercury removal from solid wastes generated by chlor-alkali plants were studied. The reaction order and model-free method with an isoconversional approach were used to estimate the kinetic parameters and reaction mechanism that apply to the thermal decomposition of hazardous mercury wastes. As a first approach to the understanding of thermal decomposition for this type of systems (poly-disperse and multi-component), a novel scheme of six reactions was proposed to represent the behaviour of mercury compounds in the solid matrix during the treatment. An integration-optimization algorithm was used in the screening of nine mechanistic models to develop kinetic expressions that best describe the process. The kinetic parameters were calculated by fitting each of these models to the experimental data. It was demonstrated that the D₁-diffusion mechanism appeared to govern the process at 250°C and high residence times, whereas at 450°C a combination of the diffusion mechanism (D₁) and the third order reaction mechanism (F3) fitted the kinetics of the conversions. The developed models can be applied in engineering calculations to dimension the installations and determine the optimal conditions to treat a mercury containing sludge.