Science.gov

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

    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

  2. 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

  3. Feasibility of Single-Input Tracer Kinetic Modeling with Continuous-Time Formalism in Liver 4-Phase Dynamic Contrast-Enhanced CT.

    PubMed

    Lee, Sang Ho; Ryu, Yasuji; Hayano, Koichi; Yoshida, Hiroyuki

    2014-09-01

    The modeling of tracer kinetics with use of low-temporal-resolution data is of central importance for patient dose reduction in dynamic contrast-enhanced CT (DCE-CT) study. Tracer kinetic models of the liver vary according to the physiologic assumptions imposed on the model, and they can substantially differ in the ways how the input for blood supply and tissue compartments are modeled. In this study, single-input flow-limited (FL), Tofts-Kety (TK), extended TK (ETK), Hayton-Brady (HB), two compartment exchange (2CX), and adiabatic approximation to the tissue homogeneity (AATH) models were applied to the analysis of liver 4-phase DCE-CT data with fully continuous-time parameter formulation, including the bolus arrival time. The bolus arrival time for the 2CX and AATH models was described by modifying the vascular transport operator theory. Initial results indicate that single-input tracer kinetic modeling is feasible for distinguishing between hepatocellular carcinoma and normal liver parenchyma.

  4. 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.

  5. 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…

  6. 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.

  7. Formal Definition of Measures for BPMN Models

    NASA Astrophysics Data System (ADS)

    Reynoso, Luis; Rolón, Elvira; Genero, Marcela; García, Félix; Ruiz, Francisco; Piattini, Mario

    Business process models are currently attaining more relevance, and more attention is therefore being paid to their quality. This situation led us to define a set of measures for the understandability of BPMN models, which is shown in a previous work. We focus on understandability since a model must be well understood before any changes are made to it. These measures were originally informally defined in natural language. As is well known, natural language is ambiguous and may lead to misunderstandings and a misinterpretation of the concepts captured by a measure and the way in which the measure value is obtained. This has motivated us to provide the formal definition of the proposed measures using OCL (Object Constraint Language) upon the BPMN (Business Process Modeling Notation) metamodel presented in this paper. The main advantages and lessons learned (which were obtained both from the current work and from previous works carried out in relation to the formal definition of other measures) are also summarized.

  8. 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.

  9. Some Formal Approaches to the Analysis of Kinetic Data in Terms of Linear Compartmental Systems

    PubMed Central

    Berman, Mones; Shahn, Ezra; Weiss, Marjory F.

    1962-01-01

    A formal approach to the routine analysis of kinetic data in terms of linear compartmental systems is presented. The methods of analysis are general in that they include much of the theory in common use, such as direct solution of differential equations, integral equations, transfer functions, fitting of data to sums of exponentials, matrix solutions, etc. The key to the formalism presented lies in the fact that a basic operational unit—called “compartment”—has been defined, in terms of which physical and mathematical models as well as input and output functions can be expressed. Additional features for calculating linear combinations of functions and for setting linear dependence relations between parameters add to the versatility of this method. The actual computations for the values of model parameters to yield a least squares fit of the data are performed on a digital computer. A general computer program was developed that permits the routine fitting of data and the evolution of models. PMID:13867976

  10. Perturbative method for the derivation of quantum kinetic theory based on closed-time-path formalism.

    PubMed

    Koide, Jun

    2002-02-01

    Within the closed-time-path formalism, a perturbative method is presented, which reduces the microscopic field theory to the quantum kinetic theory. In order to make this reduction, the expectation value of a physical quantity must be calculated under the condition that the Wigner distribution function is fixed, because it is the independent dynamical variable in the quantum kinetic theory. It is shown that when a nonequilibrium Green function in the form of the generalized Kadanoff-Baym ansatz is utilized, this condition appears as a cancellation of a certain part of contributions in the diagrammatic expression of the expectation value. Together with the quantum kinetic equation, which can be derived in the closed-time-path formalism, this method provides a basis for the kinetic-theoretical description.

  11. 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.

  12. 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.

  13. Kinetic theory of hydromagnetic turbulence. I. Formal results for parallel propagation

    NASA Astrophysics Data System (ADS)

    Yoon, Peter H.

    2007-10-01

    Formal weak turbulence kinetic equations for magnetized collisionless plasmas are derived. The kinetic theory of plasma turbulence found in the literature is largely applicable for unmagnetized plasmas, and most of the available literature only deal with electrostatic Langmuir turbulence problem. However, real plasmas in nature and laboratory are usually immersed in magnetic fields. At present there is no practical kinetic theory for turbulence in magnetized plasmas. The present paper and a companion article [P. H. Yoon and T.-M. Fang, Phys. Plasmas 14, 102303 (2007)] constitute a first step in the formulation of general kinetic theory for magnetized plasmas. For the sake of simplicity, it is assumed that turbulent fluctuations predominantly propagate along the direction of ambient magnetic field vector, and that the characteristic frequency associated with the fluctuations is much lower than the electron gyrofrequency, i.e., hydromagnetic turbulence. The effects of spontaneous thermal fluctuation and spatial inhomogeneity are also ignored.

  14. 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.

  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. Extended sigma-model in nontrivially deformed field-antifield formalism

    NASA Astrophysics Data System (ADS)

    Batalin, Igor A.; Lavrov, Peter M.

    2015-08-01

    We propose an action for the extended sigma-models in the most general setting of the kinetic term allowed in the nontrivially deformed field-antifield formalism. We show that the classical motion equations do naturally take their desired canonical form.

  17. 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

  18. The power of integrating kinetic isotope effects into the formalism of the Michaelis-Menten equation.

    PubMed

    Klinman, Judith P

    2014-01-01

    The final arbiter of enzyme mechanism is the ability to establish and test a kinetic mechanism. Isotope effects play a major role in expanding the scope and insight derived from the Michaelis-Menten equation. The integration of isotope effects into the formalism of the Michaelis-Menten equation began in the 1970s and has continued until the present. This review discusses a family of eukaryotic copper proteins, including dopamine β-monooxygenase, tyramine β-monooxygenase and peptidylglycine α-amidating enzyme, which are responsible for the synthesis of neuroactive compounds, norepinephrine, octopamine and C-terminally carboxamidated peptides, respectively. The review highlights the results of studies showing how combining kinetic isotope effects with initial rate parameters permits the evaluation of: (a) the order of substrate binding to multisubstrate enzymes; (b) the magnitude of individual rate constants in complex, multistep reactions; (c) the identification of chemical intermediates; and (d) the role of nonclassical (tunnelling) behaviour in C-H activation.

  19. 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.

  20. 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.

  1. Cellulose hydrolysis in evolving substrate morphologies I: A general modeling formalism.

    PubMed

    Zhou, Wen; Schüttler, Heinz-Bernd; Hao, Zhiqian; Xu, Ying

    2009-10-01

    We develop a general framework for a realistic rate equation modeling of cellulose hydrolysis using non-complexed cellulase. Our proposed formalism, for the first time, takes into account explicitly the time evolution of the random substrate morphology resulting from the hydrolytic cellulose chain fragmentation and solubilization. This is achieved by integrating novel geometrical concepts to quantitatively capture the time-dependent random morphology, together with the enzymatic chain fragmentation, into a coupled morphology-plus-kinetics rate equation approach. In addition, an innovative site number representation, based on tracking available numbers of beta(1,4) glucosidic bonds, of different "site" types, exposed to attacks by different enzyme types, is presented. This site number representation results in an ordinary differential equation (ODE) system, with a substantially reduced ODE system size, compared to earlier chain fragmentation kinetics approaches. This formalism enables us to quantitatively simulate both the hydrolytically evolving random substrate morphology and the profound, and heretofore neglected, morphology effects on the hydrolysis kinetics. By incorporating the evolving morphology on an equal footing with the hydrolytic chain fragmentation, our formalism provides a framework for the realistic modeling of the entire solubilization process, beyond the short-time limit and through near-complete hydrolytic conversion. As part I of two companion papers, the present paper focuses on the development of the general modelling formalism. Results and testable experimental predictions from detailed numerical simulations are presented in part II.

  2. Bridging the Semantic Gap Between Heterogeneous Modeling Formalisms and FMI

    DTIC Science & Technology

    2014-04-25

    Bridging the Semantic Gap Between Heterogeneous Modeling Formalisms and FMI Stavros Tripakis David Broman Electrical Engineering and Computer...Modeling Formalisms and FMI 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f...SUPPLEMENTARY NOTES 14. ABSTRACT FMI (Functional Mockup Interface) is a standard for exchanging and co-simulating model components (called FMUs) coming

  3. Kinetics Modeling of Cancer Immunology.

    DTIC Science & Technology

    1986-05-09

    CANCER IMMUNOLOGY -1 DTICS ELECTED SEP 9 8 UNITED STATES NAVAL ACADEMY ANNAPOLIS, MARYLAND V ,1986 %,e docment ha le approved for public A." I and sale...1986 4. TITLE (and Subtitle) S. TYPE OF REPORT & PERIOD COVERED KINETICS MODELING OF CANCER IMMUNOLOGY Final: 1985/1986 6. PERFORMING ORG. REPORT...137 (1986) "Kinetics Modeling of Cancer Immunology " A Trident Scholar Project Report by Midn I/C Scott Helmers, Class of 1986 United States Naval

  4. Incremental and unifying modelling formalism for biological interaction networks

    PubMed Central

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

    2007-01-01

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

  5. 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.

  6. 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.

  7. 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).

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. A Formal Model for the Study of Communication Support Systems.

    ERIC Educational Resources Information Center

    Holsapple, Clyde W.; And Others

    1996-01-01

    Documents the lack of conceptual frameworks for integrating research on organizational computer-based communications technologies. Formalizes an integrated model for studying computer communication support phenomena in organizations using a knowledge management perspective and set-theoretic notation. Defines two types of communications support…

  13. Formalisms for Electron Exchange Kinetics in Aqueous Solution, and the Role of Ab Initio Techniques in Their Implementation

    SciTech Connect

    Newton, M. D.

    1980-01-01

    Formalisms suitable for calculating the rate of electron exchange between transition metal complexes in aqueous solution are reviewed and implemented in conjunction with ab initio quantum chemical calculations which provide crucial off-diagonal Hamiltonian matrix elements as well as other relevant electronic structural data. Rate constants and activation parameters are calculated for the hex-aquo Fe2 +-Fe3+ system, using a simple activated complex theory, a non-adiabatic semi-classical model which includes nuclear tunnelling, and a more detailed quantum mechanical method based on the Golden Rule. Comparisons are made between calculated results and those obtained by extrapolating experimental data to zero ionic strength. All methods yield similar values for the overall rate constant (∾ 0.1 L/(mol-sec)). The experimental activation parameters (δH and δS) are in somewhat better agreement with the semi classical and quantum mechanical results than with those from the simple activated complex theory, thereby providing some indication that non-adiabaticity and nuclear tunnelling may be important in the Fe2+/3+ exchange reaction. It is concluded that a model based on direct metal-metal overlap can account for the observed reaction kinetics provided the reactants are allowed to approach well within the traditional contact distance of 6.9 Å. 6 figures, 7 tables.

  14. 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.

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

    PubMed

    Ghosh, Krishnendu; Schlipf, John

    2014-10-01

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

  16. A Formal Environment Model for Multi-Agent Systems

    NASA Astrophysics Data System (ADS)

    da Silva, Paulo Salem; de Melo, Ana C. V.

    Multi-agent systems are employed to model complex systems which can be decomposed into several interacting pieces called agents. In such systems, agents exist, evolve and interact within an environment. In this paper we present a model for the specification of such environments. This Environment Model for Multi-Agent Systems (EMMAS), as we call it, defines both structural and dynamic aspects of environments. Structurally, EMMAS connects agents by a social network, in which the link between agents is specified as the capability that one agent has to act upon another. Dynamically, EMMAS provides operations that can be composed together in order to create a number of different environmental situations and to respond appropriately to agents' actions. These features are founded on a mathematical model that we provide and that defines rigorously what constitutes an environment. Formality is achieved by employing the π-calculus process algebra in order to give the semantics of this model. This allows, in particular, a simple characterization of the evolution of the environment structure. Moreover, owing to this formal semantics, it is possible to perform formal analyses on environments thus described. For the sake of illustration, a concrete example of environment specification using EMMAS is also given.

  17. 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.

  18. 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

  19. 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.

  20. Spectral method for a kinetic swarming model

    DOE PAGES

    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.

  1. 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

  2. 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.

  3. 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.

  4. Kinetic Modelling of Transcription Elongation

    NASA Astrophysics Data System (ADS)

    O'Maoileidigh, Daibhid; Tadigotla, Vasisht; Sengupta, Anirvan; Epshtein, Vitaly; Ebright, Richard; Nudler, Evgeny; Ruckenstein, Andrei

    2006-03-01

    Transcription is the first step in gene expression and it is at this stage that most of genetic regulation occurs. The enzyme RNA polymerase (RNAP) walks along DNA creating an RNA transcript at a highly non-uniform rate. We discuss how many non-intuitive features of the system may be experimentally and physically motivated and present first a model, which agrees qualitatively with a host of experimental evidence. We also examine intrinsic pauses where it is thought that the RNAP will move backwards along the DNA template without changing the length of the RNA transcript. We describe a simplified kinetic scheme for the recovery of intrinsic pauses with the same degree of predictive power as our thermodynamic model (presented separately). The separation of timescales between the movement of the RNAP and global changes in the RNA secondary structure is seen to be crucial for the function of RNAP. This is essentially a model of a Brownian ratchet where RNAP executes a 1D random walk in a sequence dependent potential over a range determined by the co-transcriptional RNA fold for each transcript length

  5. Kinetic modelling of mitochondrial translation.

    PubMed

    Korla, Kalyani; Mitra, Chanchal K

    2014-01-01

    Mitochondrial genome contains 13 protein coding genes, all being part of the oxidative phosphorylation complexes. The process of translation of these protein coding mRNAs in mitochondrial matrix is a good miniature model of translation in cytoplasm. In this work, we have simulated three phases of mitochondrial translation viz. initiation, elongation and termination (including ribosome recycling). The kinetic equations for these phases have been deduced based on the information available in literature. Various factors involved in the process have been included explicitly. Kinetic simulation was done using Octave, open source software. Scripts were written individually for each phase. Initiation begins with mitoribosome, mRNA, fMet-tRNA and initiation factors. The final product of the initiation script, the initiation complex, was introduced as the start point in the successive step, i.e. elongation. Elongation is a particular extensive process where the various aminoacyl-tRNAs already present in the matrix check for matching with the triplet codon in A-site of mitoribosome. This script consists of two parts: one with the time behaviour of the factors involved in the molecular process (using ordinary differential equation solver) and the other including the reading of triplet codon on the mRNA and incorporating the corresponding aminoacyl-tRNA, and then at each step elongating the peptide chain (using loops and conditions). The peptide chain thus formed in the elongation step (in the loops and conditions segment) was released in the termination step. This was followed by mitoribosome recycling where the mitoribosome reached the native state and was ready for the next cycle of translation.

  6. Formal description of aggregates of a generalised model of interaction processes in computer networks

    SciTech Connect

    Ratsin, Yu.V.

    1984-01-01

    The realisation using PL/1 of a formal description of a set of interaction process functions in computer networks using the language of discrete parallel processes is described. The formal description is intended for conducting computer modelling experiments. 4 references.

  7. 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…

  8. Stochastic effects in a discretized kinetic model of economic exchange

    NASA Astrophysics Data System (ADS)

    Bertotti, M. L.; Chattopadhyay, A. K.; Modanese, G.

    2017-04-01

    Linear stochastic models and discretized kinetic theory are two complementary analytical techniques used for the investigation of complex systems of economic interactions. The former employ Langevin equations, with an emphasis on stock trade; the latter is based on systems of ordinary differential equations and is better suited for the description of binary interactions, taxation and welfare redistribution. We propose a new framework which establishes a connection between the two approaches by introducing random fluctuations into the kinetic model based on Langevin and Fokker-Planck formalisms. Numerical simulations of the resulting model indicate positive correlations between the Gini index and the total wealth, that suggest a growing inequality with increasing income. Further analysis shows, in the presence of a conserved total wealth, a simultaneous decrease in inequality as social mobility increases, in conformity with economic data.

  9. Formal modeling and verification of fractional order linear systems.

    PubMed

    Zhao, Chunna; Shi, Likun; Guan, Yong; Li, Xiaojuan; Shi, Zhiping

    2016-05-01

    This paper presents a formalization of a fractional order linear system in a higher-order logic (HOL) theorem proving system. Based on the formalization of the Grünwald-Letnikov (GL) definition, we formally specify and verify the linear and superposition properties of fractional order systems. The proof provides a rigor and solid underpinnings for verifying concrete fractional order linear control systems. Our implementation in HOL demonstrates the effectiveness of our approach in practical applications.

  10. 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.

  11. 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

  12. 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…

  13. The development of a model of creative space and its potential for transfer from non-formal to formal education

    NASA Astrophysics Data System (ADS)

    White, Irene; Lorenzi, Francesca

    2016-12-01

    Creativity has been emerging as a key concept in educational policies since the mid-1990s, with many Western countries restructuring their education systems to embrace innovative approaches likely to stimulate creative and critical thinking. But despite current intentions of putting more emphasis on creativity in education policies worldwide, there is still a relative dearth of viable models which capture the complexity of creativity and the conditions for its successful infusion into formal school environments. The push for creativity is in direct conflict with the results-driven/competitive performance-oriented culture which continues to dominate formal education systems. The authors of this article argue that incorporating creativity into mainstream education is a complex task and is best tackled by taking a systematic and multifaceted approach. They present a multidimensional model designed to help educators in tackling the challenges of the promotion of creativity. Their model encompasses three distinct yet interrelated dimensions of a creative space - physical, social-emotional and critical. The authors use the metaphor of space to refer to the interplay of the three identified dimensions. Drawing on confluence approaches to the theorisation of creativity, this paper exemplifies the development of a model before the background of a growing trend of systems theories. The aim of the model is to be helpful in systematising creativity by offering parameters - derived from the evaluation of an example offered by a non-formal educational environment - for the development of creative environments within mainstream secondary schools.

  14. Kinetic model of network traffic

    NASA Astrophysics Data System (ADS)

    Antoniou, I.; Ivanov, V. V.; Kalinovsky, Yu. L.

    2002-05-01

    We present the first results on the application of the Prigogine-Herman kinetic approach (Kinetic Theory of Vehicular Traffic, American Elsevier Publishing Company, Inc., New York, 1971) to the network traffic. We discuss the solution of the kinetic equation for homogeneous time-independent situations and for the desired speed distribution function, obtained from traffic measurements analysis. For the log-normal desired speed distribution function the solution clearly shows two modes corresponding to individual flow patterns (low-concentration mode) and to collective flow patterns (traffic jam mode). For low-concentration situations we found almost linear dependence of the information flow versus the concentration and that the higher the average speed the lower the concentration at which the optimum flow takes place. When approaching the critical concentration there are no essential differences in the flow for different desired average speeds, whereas for the individual flow regions there are dramatic differences.

  15. 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.

  16. 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.

  17. Viral kinetic modeling: state of the art

    DOE PAGES

    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

  18. 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

  19. Kinetic-effect models and their applications.

    PubMed

    Grevel, J

    1987-04-01

    This article focuses on mathematical models that analyze the time course of drug effects in humans. Any such model, whether parametric or nonparametric, is termed a kinetic-effect model (KEM). These models serve to describe (interpolation) and to predict (extrapolation) the effect-time profile. KEMs are applicable to many problems in pharmaceutics, pharmacology, and clinical pharmacology.

  20. 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.

  1. Classical Antiferromagnetism in Kinetically Frustrated Electronic Models

    NASA Astrophysics Data System (ADS)

    Sposetti, C. N.; Bravo, B.; Trumper, A. E.; Gazza, C. J.; Manuel, L. O.

    2014-05-01

    We study, by means of the density matrix renormalization group, the infinite U Hubbard model—with one hole doped away from half filling—in triangular and square lattices with frustrated hoppings, which invalidate Nagaoka's theorem. We find that these kinetically frustrated models have antiferromagnetic ground states with classical local magnetization in the thermodynamic limit. We identify the mechanism of this kinetic antiferromagnetism with the release of the kinetic energy frustration, as the hole moves in the established antiferromagnetic background. This release can occur in two different ways: by a nontrivial spin Berry phase acquired by the hole, or by the effective vanishing of the hopping amplitude along the frustrating loops.

  2. Exact solutions for kinetic models of macromolecular dynamics.

    PubMed

    Chemla, Yann R; Moffitt, Jeffrey R; Bustamante, Carlos

    2008-05-15

    Dynamic biological processes such as enzyme catalysis, molecular motor translocation, and protein and nucleic acid conformational dynamics are inherently stochastic processes. However, when such processes are studied on a nonsynchronized ensemble, the inherent fluctuations are lost, and only the average rate of the process can be measured. With the recent development of methods of single-molecule manipulation and detection, it is now possible to follow the progress of an individual molecule, measuring not just the average rate but the fluctuations in this rate as well. These fluctuations can provide a great deal of detail about the underlying kinetic cycle that governs the dynamical behavior of the system. However, extracting this information from experiments requires the ability to calculate the general properties of arbitrarily complex theoretical kinetic schemes. We present here a general technique that determines the exact analytical solution for the mean velocity and for measures of the fluctuations. We adopt a formalism based on the master equation and show how the probability density for the position of a molecular motor at a given time can be solved exactly in Fourier-Laplace space. With this analytic solution, we can then calculate the mean velocity and fluctuation-related parameters, such as the randomness parameter (a dimensionless ratio of the diffusion constant and the velocity) and the dwell time distributions, which fully characterize the fluctuations of the system, both commonly used kinetic parameters in single-molecule measurements. Furthermore, we show that this formalism allows calculation of these parameters for a much wider class of general kinetic models than demonstrated with previous methods.

  3. 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”.

  4. 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.

  5. An Evaluation of the Preceptor Model versus the Formal Teaching Model.

    ERIC Educational Resources Information Center

    Shamian, Judith; Lemieux, Suzanne

    1984-01-01

    This study evaluated the effectiveness of two teaching methods to determine which is more effective in enhancing the knowledge base of participating nurses: the preceptor model embodies decentralized instruction by a member of the nursing staff, and the formal teaching model uses centralized teaching by the inservice education department. (JOW)

  6. Algorithms, modelling and VO₂ kinetics.

    PubMed

    Capelli, Carlo; Carlo, Capelli; Cautero, Michela; Michela, Cautero; Pogliaghi, Silvia; Silvia, Pogliaghi

    2011-03-01

    This article summarises the pros and cons of different algorithms developed for estimating breath-by-breath (B-by-B) alveolar O(2) transfer (VO 2A) in humans. VO 2A is the difference between O(2) uptake at the mouth and changes in alveolar O(2) stores (∆ VO(2s)), which for any given breath, are equal to the alveolar volume change at constant FAO2/FAiO2 ∆VAi plus the O(2) alveolar fraction change at constant volume [V Ai-1(F Ai - F Ai-1) O2, where V (Ai-1) is the alveolar volume at the beginning of a breath. Therefore, VO 2A can be determined B-by-B provided that V (Ai-1) is: (a) set equal to the subject's functional residual capacity (algorithm of Auchincloss, A) or to zero; (b) measured (optoelectronic plethysmography, OEP); (c) selected according to a procedure that minimises B-by-B variability (algorithm of Busso and Robbins, BR). Alternatively, the respiratory cycle can be redefined as the time between equal FO(2) in two subsequent breaths (algorithm of Grønlund, G), making any assumption of V (Ai-1) unnecessary. All the above methods allow an unbiased estimate of VO2 at steady state, albeit with different precision. Yet the algorithms "per se" affect the parameters describing the B-by-B kinetics during exercise transitions. Among these approaches, BR and G, by increasing the signal-to-noise ratio of the measurements, reduce the number of exercise repetitions necessary to study VO2 kinetics, compared to A approach. OEP and G (though technically challenging and conceptually still debated), thanks to their ability to track ∆VO(2s) changes during the early phase of exercise transitions, appear rather promising for investigating B-by-B gas exchange.

  7. Formal Languages as an Approach to Modelling Distance Education Fora

    NASA Astrophysics Data System (ADS)

    Patriarcheas, Kiriakos; Xenos, Michalis

    2011-09-01

    This paper presents the development of a formal language defined in mathematical terms to represent messages at distance education fora. This language has an alphabet for terminal symbols, an alphabet for non-terminal symbols, a grammar and a symbol where each sentence in the language is generated from this.

  8. Adsorption studies of molasse's wastewaters on activated carbon: modelling with a new fractal kinetic equation and evaluation of kinetic models.

    PubMed

    Figaro, S; Avril, J P; Brouers, F; Ouensanga, A; Gaspard, S

    2009-01-30

    Adsorption kinetic of molasses wastewaters after anaerobic digestion (MSWD) and melanoidin respectively on activated carbon was studied at different pH. The kinetic parameters could be determined using classical kinetic equations and a recently published fractal kinetic equation. A linear form of this equation can also be used to fit adsorption data. Even with lower correlation coefficients the fractal kinetic equation gives lower normalized standard deviation values than the pseudo-second order model generally used to fit adsorption kinetic data, indicating that the fractal kinetic model is much more accurate for describing the kinetic adsorption data than the pseudo-second order kinetic model.

  9. Nilpotent and absolutely anticommuting symmetries in the Freedman-Townsend model: Augmented superfield formalism

    NASA Astrophysics Data System (ADS)

    Shukla, A.; Krishna, S.; Malik, R. P.

    2014-12-01

    We derive the off-shell nilpotent and absolutely anticommuting Becchi-Rouet-Stora-Tyutin (BRST) and anti-BRST symmetry transformations, corresponding to the (1-form) Yang-Mills (YM) and (2-form) tensorial gauge symmetries of the four (3+1)-dimensional (4D) Freedman-Townsend (FT) model, by exploiting the augmented version of Bonora-Tonin's (BT) superfield approach to BRST formalism where the 4D flat Minkowskian theory is generalized onto the (4, 2)-dimensional supermanifold. One of the novel observations is the fact that we are theoretically compelled to go beyond the horizontality condition (HC) to invoke an additional set of gauge-invariant restrictions (GIRs) for the derivation of the full set of proper (anti-)BRST symmetries. To obtain the (anti-)BRST symmetry transformations, corresponding to the tensorial (2-form) gauge symmetries within the framework of augmented version of BT-superfield approach, we are logically forced to modify the FT-model to incorporate an auxiliary 1-form field and the kinetic term for the antisymmetric (2-form) gauge field. This is also a new observation in our present investigation. We point out some of the key differences between the modified FT-model and Lahiri-model (LM) of the dynamical non-Abelian 2-form gauge theories. We also briefly mention a few similarities.

  10. 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.

  11. Chemical Kinetic Models for Advanced Engine Combustion

    SciTech Connect

    Pitz, William J.; Mehl, Marco; Westbrook, Charles K.

    2014-10-22

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

  12. Chiral Schwinger model based on the Batalin-Fradkin-Vilkovisky formalism

    SciTech Connect

    Kim, Y.; Kim, S.; Kim, W.; Park, Y.; Kim, K.Y.; Kim, Y. )

    1992-11-15

    We quantize the bosonized chiral Schwinger model by using the systematic Batalin-Fradkin-Vilkovisky formalism. We derive a Becchi-Rouet-Stora-Tyutin gauge-fixed covariant action showing that the auxiliary fields introduced in the formalism turn into the Wess-Zumino scalar.

  13. Modeling recrystallization kinetics during strip rolling

    SciTech Connect

    Sun, W.P.; Hawbolt, E.B.; Meadowcroft, T.R.

    1995-01-01

    In order to simulate the microstructural evolution during hot strip rolling, double-hit compression tests have been carried out on plain carbon steels. Using the softening data obtained by these tests, mathematical models were developed to predict the overall kinetics of static recrystallization under roughing and finishing mill conditions. These models include the effects of deformation temperature, applied strain, strain rate and initial austenite grain size. Predictions based on these models are in reasonable agreement with the present experimental results.

  14. Investigation of the kinetic model equations.

    PubMed

    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.

  15. Non-Markovian closure models for large eddy simulations using the Mori-Zwanzig formalism

    NASA Astrophysics Data System (ADS)

    Parish, Eric J.; Duraisamy, Karthik

    2017-01-01

    This work uses the Mori-Zwanzig (M-Z) formalism, a concept originating from nonequilibrium statistical mechanics, as a basis for the development of coarse-grained models of turbulence. The mechanics of the generalized Langevin equation (GLE) are considered, and insight gained from the orthogonal dynamics equation is used as a starting point for model development. A class of subgrid models is considered which represent nonlocal behavior via a finite memory approximation [Stinis, arXiv:1211.4285 (2012)], the length of which is determined using a heuristic that is related to the spectral radius of the Jacobian of the resolved variables. The resulting models are intimately tied to the underlying numerical resolution and are capable of approximating non-Markovian effects. Numerical experiments on the Burgers equation demonstrate that the M-Z-based models can accurately predict the temporal evolution of the total kinetic energy and the total dissipation rate at varying mesh resolutions. The trajectory of each resolved mode in phase space is accurately predicted for cases where the coarse graining is moderate. Large eddy simulations (LESs) of homogeneous isotropic turbulence and the Taylor-Green Vortex show that the M-Z-based models are able to provide excellent predictions, accurately capturing the subgrid contribution to energy transfer. Last, LESs of fully developed channel flow demonstrate the applicability of M-Z-based models to nondecaying problems. It is notable that the form of the closure is not imposed by the modeler, but is rather derived from the mathematics of the coarse graining, highlighting the potential of M-Z-based techniques to define LES closures.

  16. Determination of formal kinetic constants of thermal decomposition of aqueous hydrogen peroxide solution in a mixture of magnetic powder, based on experimental thermogram, obtained in adiabatic conditions

    NASA Astrophysics Data System (ADS)

    Zaripov, Jamshed; Borisov, Boris; Bondarchuk, Sergey

    2014-08-01

    Process of thermal decomposition of hydrogen peroxide aqueous solution with the addition of magnetic powder in the form of toner for printers and lanthanum manganite were considered. Obtained resulting from an experiment in the Dewar container conducted thermogram analyzed using mass balance equations and heat. Formal kinetic parameters determined, and conclude that the magnetic powder in the mixture does not have catalytic properties. The described technique is recommended as a rapid analysis of the kinetics of the various reactions to substances having predefined thermal and thermodynamic properties.

  17. Kinetic modeling of active plasma resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Oberrath, Jens

    2016-09-01

    The term ``active plasma resonance spectroscopy'' (APRS) refers to a plasma diagnostic method which employs the natural ability of plasmas to resonate close to the plasma frequency. Essential for this method is an appropriate model to determine the relation between the resonance parameters and demanded plasma parameters. Measurements with these probes in plasmas of a few Pa typically show a broadening of the spectrum that cannot be predicted by a fluid model. Thus, a kinetic model is necessary. A general kinetic model of APRS probes, which can be described in electorstatic approximation, valid for all pressures has been presented. This model is used to analyze the dynamic behavior of such probes by means of functional analytic methods. One of the main results is, that the system response function Y (ω) is given in terms of the matrix elements of the resolvent of the dynamic operator evaluated for values on the imaginary axis. The spectrum of this operator is continuous which implies a new phenomenon related to anomalous or non-collisional dissipation. Based on the scalar product, which is motivated by the kinetic free energy, the non-collisional damping can be interpreted: In a periodic state, the probe constantly emits plasma waves which propagate to ``infinity''. The free energy simply leaves the ``observation range'' of the probe which is recorded as damping. The kinetic damping, which depends on the mean kinetic energy of the electrons, is responsible for the broadening of a resonance peak in the measured spectrum of APRS probes. The ultimate goal is to determine explicit formulas for the relation between the broadening of the resonance peak and the ``equivalent electron temperature'', especially in the case of the spherical Impedance Probe and the Multipole Resonance Probe. Gratitude is expressed to the internal funding of Leuphana University, the BMBF via PluTO+, the DFG via Collaborative Research Center TR 87, and the Ruhr University Research School.

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. Kinetic Models with Randomly Perturbed Binary Collisions

    NASA Astrophysics Data System (ADS)

    Bassetti, Federico; Ladelli, Lucia; Toscani, Giuseppe

    2011-02-01

    We introduce a class of Kac-like kinetic equations on the real line, with general random collisional rules which, in some special cases, identify models for granular gases with a background heat bath (Carrillo et al. in Discrete Contin. Dyn. Syst. 24(1):59-81, 2009), and models for wealth redistribution in an agent-based market (Bisi et al. in Commun. Math. Sci. 7:901-916, 2009). Conditions on these collisional rules which guarantee both the existence and uniqueness of equilibrium profiles and their main properties are found. The characterization of these stationary states is of independent interest, since we show that they are stationary solutions of different evolution problems, both in the kinetic theory of rarefied gases (Cercignani et al. in J. Stat. Phys. 105:337-352, 2001; Villani in J. Stat. Phys. 124:781-822, 2006) and in the econophysical context (Bisi et al. in Commun. Math. Sci. 7:901-916, 2009).

  4. 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.

  5. Kinetic effects in edge plasma: kinetic modeling for edge plasma and detached divertor

    NASA Astrophysics Data System (ADS)

    Takizuka, T.

    2017-03-01

    Detached divertor is considered a solution for the heat control in magnetic-confinement fusion reactors. Numerical simulations using the comprehensive divertor codes based on the plasma fluid modeling are indispensable for the design of the detached divertor in future reactors. Since the agreement in the results between detached-divertor experiments and simulations has been rather fair but not satisfactory, further improvement of the modeling is required. The kinetic effect is one of key issues for improving the modeling. Complete kinetic behaviors are able to be simulated by the kinetic modeling. In this paper at first, major kinetic effects in edge plasma and detached divertor are listed. One of the most powerful kinetic models, particle-in-cell (PIC) model, is described in detail. Several results of PIC simulations of edge-plasma kinetic natures are presented. Future works on PIC modeling and simulation for the deeper understanding of edge plasma and detached divertor are discussed.

  6. Crowdsourced Formal Verification: A Business Case Analysis Toward a Human-Centered Business Model

    DTIC Science & Technology

    2015-06-01

    NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS CROWDSOURCED FORMAL VERIFICATION: A BUSINESS CASE ANALYSIS TOWARD A HUMAN -CENTERED BUSINESS...to 05-14-2015 4. TITLE AND SUBTITLE CROWDSOURCED FORMALVERIFICATION: A BUSINESS CASE ANALYSIS TO- WARD A HUMAN -CENTERED BUSINESS MODEL 5. FUNDING...formal verification of software by human experts. This business case analysis evaluates the results of the CSFV-project phase 1. Based on data of

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. A Formal Model of Capacity Limits in Working Memory

    ERIC Educational Resources Information Center

    Oberauer, Klaus; Kliegl, Reinhold

    2006-01-01

    A mathematical model of working-memory capacity limits is proposed on the key assumption of mutual interference between items in working memory. Interference is assumed to arise from overwriting of features shared by these items. The model was fit to time-accuracy data of memory-updating tasks from four experiments using nonlinear mixed effect…

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  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. 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.

  2. Modeling cellular deformations using the level set formalism

    PubMed Central

    Yang, Liu; Effler, Janet C; Kutscher, Brett L; Sullivan, Sarah E; Robinson, Douglas N; Iglesias, Pablo A

    2008-01-01

    Background Many cellular processes involve substantial shape changes. Traditional simulations of these cell shape changes require that grids and boundaries be moved as the cell's shape evolves. Here we demonstrate that accurate cell shape changes can be recreated using level set methods (LSM), in which the cellular shape is defined implicitly, thereby eschewing the need for updating boundaries. Results We obtain a viscoelastic model of Dictyostelium cells using micropipette aspiration and show how this viscoelastic model can be incorporated into LSM simulations to recreate the observed protrusion of cells into the micropipette faithfully. We also demonstrate the use of our techniques by simulating the cell shape changes elicited by the chemotactic response to an external chemoattractant gradient. Conclusion Our results provide a simple but effective means of incorporating cellular deformations into mathematical simulations of cell signaling. Such methods will be useful for simulating important cellular events such as chemotaxis and cytokinesis. PMID:18652669

  3. 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.

  4. 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.

  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. 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."…

  7. On the Adequacy of Current Empirical Evaluations of Formal Models of Categorization

    ERIC Educational Resources Information Center

    Wills, Andy J.; Pothos, Emmanuel M.

    2012-01-01

    Categorization is one of the fundamental building blocks of cognition, and the study of categorization is notable for the extent to which formal modeling has been a central and influential component of research. However, the field has seen a proliferation of noncomplementary models with little consensus on the relative adequacy of these accounts.…

  8. 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.

  9. 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…

  10. 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.

  11. 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.

  12. 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.

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

    PubMed

    Pavanello, Michele; Neugebauer, Johannes

    2011-12-21

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

  14. Representing Model Inadequacy in Combustion Kinetics

    NASA Astrophysics Data System (ADS)

    Morrison, Rebecca E.; Moser, Robert D.

    2014-11-01

    An accurate description of the chemical processes involved in the oxidation of hydrocarbons may include hundreds of reactions and thirty or more chemical species. Kinetics models of these chemical mechanisms are often embedded in a fluid dynamics solver to represent combustion. Because the computational cost of such detailed mechanisms is so high, it is common practice to use drastically reduced mechanisms. But, this introduces modeling errors which may render the model inadequate. In this talk, we present a formulation of the model inadequacy in reduced models of hydrogen-methane combustion. Our goal is to account for the discrepancy between the high-fidelity model and its reduced version by incorporating an additive, linear, probabilistic inadequacy model. In effect, it is a random matrix, whose entries are characterized by probability distributions and which displays interesting properties due to conservation constraints. The distributions are calibrated via Bayesian inference using a hierarchical modeling scheme and high-dimensional MCMC. We apply this technique to a stand-alone reaction and also incorporate it within a one-dimensional laminar flame problem.

  15. Systems immunology: a survey of modeling formalisms, applications and simulation tools.

    PubMed

    Narang, Vipin; Decraene, James; Wong, Shek-Yoon; Aiswarya, Bindu S; Wasem, Andrew R; Leong, Shiang Rong; Gouaillard, Alexandre

    2012-09-01

    Immunological studies frequently analyze individual components (e.g., signaling pathways) of immune systems in a reductionist manner. In contrast, systems immunology aims to give a synthetic understanding of how these components function together as a whole. While immunological research involves in vivo and in vitro experiments, systems immunology research can also be conducted in silico. With an increasing interest in systems-level studies spawned by high-throughput technologies, many immunologists are looking forward to insights provided by computational modeling and simulation. However, modeling and simulation research has mainly been conducted in computational fields, and therefore, little material is available or accessible to immunologists today. This survey is an attempt at bridging the gap between immunologists and systems immunology modeling and simulation. Modeling and simulation refer to building and executing an in silico replica of an immune system. Models are specified within a mathematical or algorithmic framework called formalism and then implemented using software tools. A plethora of modeling formalisms and software tools are reported in the literature for systems immunology. However, it is difficult for a new entrant to the field to know which of these would be suitable for modeling an immunological application at hand. This paper covers three aspects. First, it introduces the field of system immunology emphasizing on the modeling and simulation components. Second, it gives an overview of the principal modeling formalisms, each of which is illustrated with salient applications in immunological research. This overview of formalisms and applications is conducted not only to illustrate their power but also to serve as a reference to assist immunologists in choosing the best formalism for the problem at hand. Third, it lists major software tools, which can be used to practically implement models in these formalisms. Combined, these aspects can help

  16. 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.

  17. 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.

  18. Population balance modeling of antibodies aggregation kinetics.

    PubMed

    Arosio, Paolo; Rima, Simonetta; Lattuada, Marco; Morbidelli, Massimo

    2012-06-21

    The aggregates morphology and the aggregation kinetics of a model monoclonal antibody under acidic conditions have been investigated. Growth occurs via irreversible cluster-cluster coagulation forming compact, fractal aggregates with fractal dimension of 2.6. We measured the time evolution of the average radius of gyration, , and the average hydrodynamic radius, , by in situ light scattering, and simulated the aggregation kinetics by a modified Smoluchowski's population balance equations. The analysis indicates that aggregation does not occur under diffusive control, and allows quantification of effective intermolecular interactions, expressed in terms of the Fuchs stability ratio (W). In particular, by introducing a dimensionless time weighed on W, the time evolutions of measured under various operating conditions (temperature, pH, type and concentration of salt) collapse on a single master curve. The analysis applies also to data reported in the literature when growth by cluster-cluster coagulation dominates, showing a certain level of generality in the antibodies aggregation behavior. The quantification of the stability ratio gives important physical insights into the process, including the Arrhenius dependence of the aggregation rate constant and the relationship between monomer-monomer and cluster-cluster interactions. Particularly, it is found that the reactivity of non-native monomers is larger than that of non-native aggregates, likely due to the reduction of the number of available hydrophobic patches during aggregation.

  19. Model colloid system for interfacial sorption kinetics

    NASA Astrophysics Data System (ADS)

    Salipante, Paul; Hudson, Steven

    2014-11-01

    Adsorption kinetics of nanometer scale molecules, such as proteins at interfaces, is usually determined through measurements of surface coverage. Their small size limits the ability to directly observe individual molecule behavior. To better understand the behavior of nanometer size molecules and the effect on interfacial kinetics, we use micron size colloids with a weak interfacial interaction potential as a model system. Thus, the interaction strength is comparable to many nanoscale systems (less than 10 kBT). The colloid-interface interaction potential is tuned using a combination of depletion, electrostatic, and gravitational forces. The colloids transition between an entropically trapped adsorbed state and a desorbed state through Brownian motion. Observations are made using an LED-based Total Internal Reflection Microscopy (TIRM) setup. The observed adsorption and desorption rates are compared theoretical predictions based on the measured interaction potential and near wall particle diffusivity. This experimental system also allows for the study of more complex dynamics such as nonspherical colloids and collective effects at higher concentrations.

  20. Kinetic Models for the Trading of Goods

    NASA Astrophysics Data System (ADS)

    Toscani, Giuseppe; Brugna, Carlo; Demichelis, Stefano

    2013-05-01

    In this paper we introduce kinetic equations for the evolution of the probability distribution of two goods among a huge population of agents. The leading idea is to describe the trading of these goods by means of some fundamental rules in price theory, in particular by using Cobb-Douglas utility functions for the binary exchange, and the Edgeworth box for the description of the common exchange area in which utility is increasing for both agents. This leads to a Boltzmann-type equation in which the post-interaction variables depend in a nonlinear way from the pre-interaction ones. Other models will be derived, by suitably linearizing this Boltzmann equation. In presence of uncertainty in the exchanges, it is shown that the solution to some of the linearized kinetic equations develop Pareto tails, where the Pareto index depends on the ratio between the gain and the variance of the uncertainty. In particular, the result holds true for the solution of a drift-diffusion equation of Fokker-Planck type, obtained from the linear Boltzmann equation as the limit of quasi-invariant trades.

  1. A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks

    PubMed Central

    2009-01-01

    Background The study of biological networks has led to the development of increasingly large and detailed models. Computer tools are essential for the simulation of the dynamical behavior of the networks from the model. However, as the size of the models grows, it becomes infeasible to manually verify the predictions against experimental data or identify interesting features in a large number of simulation traces. Formal verification based on temporal logic and model checking provides promising methods to automate and scale the analysis of the models. However, a framework that tightly integrates modeling and simulation tools with model checkers is currently missing, on both the conceptual and the implementational level. Results We have developed a generic and modular web service, based on a service-oriented architecture, for integrating the modeling and formal verification of genetic regulatory networks. The architecture has been implemented in the context of the qualitative modeling and simulation tool GNA and the model checkers NUSMV and CADP. GNA has been extended with a verification module for the specification and checking of biological properties. The verification module also allows the display and visual inspection of the verification results. Conclusions The practical use of the proposed web service is illustrated by means of a scenario involving the analysis of a qualitative model of the carbon starvation response in E. coli. The service-oriented architecture allows modelers to define the model and proceed with the specification and formal verification of the biological properties by means of a unified graphical user interface. This guarantees a transparent access to formal verification technology for modelers of genetic regulatory networks. PMID:20042075

  2. 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.

  3. On the Formal Componential Structure of the Transformational-Generative Model of Grammar.

    ERIC Educational Resources Information Center

    Brew, P. J.

    1970-01-01

    This paper examines the relationship that exists between the syntactic and phonological components of the transformational-generative model insofar as their formal structures are concerned. It is demonstrated that the number and importance of the structural similarities between the syntax and the phonology make it necessary to provide for them in…

  4. 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.

  5. 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…

  6. Kinetic Global Modeling of Rare Gas Lasers

    NASA Astrophysics Data System (ADS)

    Parsey, Guy; Verboncoeur, John; Christlieb, Andrew

    2016-10-01

    Akin to diode-pumped alkali metal lasers, electronically excited states of rare gases (e.g. Ar and Kr) have been shown to operate as chemically inert three-level gain media for an optically pumped laser system. As opposed to vaporization heating, these systems rely on electric discharge to efficiently maintain a population of metastable states acting as the bottom laser level. We propose that a modified electron energy distribution (EEDF) in the electric heating can tune optically pumped rare gas laser (OPRGL) efficiencies. The EEDF factors into all plasma phase chemistry within the underlying reaction network, and is assumed to be maintained by discharge and electron sources. Using parameter scanning methods within the kinetic global modeling framework (KGMf), optimized EEDFs are found for metastable production and increasing OPRGL operational efficiencies. Finally, we investigate the feasibility of using a modified EEDF to drive a rare gas laser system without optical pumping. Supported by AFOSR and an MSU SPG.

  7. 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.

  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. Kinetic modelling of vinyl ester resin polymerization

    SciTech Connect

    Dhulipala, R.; Kreig. G.; Hawley, M.C.

    1993-12-31

    The study of kinetics offers a substantional incentive in the endeavor to manufacture polymer matrix composites at high speeds. The study enables one to optimize the curing cycle based on the specific curing characteristics of the resin and also makes it possible to simulate the curing process. This paper reports the results of the modelling of the thermal curing of the vinyl ester resin. The parameters for the proposed model have been calculated based on conversion-vs-data generated at various temperatures and Benzoyl peroxide (initiator) concentrations. The extent of cure of the resin mixture was determined using Fourier Transform Infrared Spectroscopy. In this model the termination rate constant is considered to drop with extent of cure until a limiting value is reached. The limiting value is a consequence of the active chain ends possessing a degree of mobility due to the propagation reaction even though the translational motion of the growing for radicals in increasingly restricted with conversion. Good agreements is observed between the model predictions and the experimental data.

  10. Towards a Mathematical Formalism for Semi-stochastic Cell-Level Computational Modeling of Tumor Initiation.

    PubMed

    Vermolen, F J; Meijden, R P van der; Es, M van; Gefen, A; Weihs, D

    2015-07-01

    A phenomenological model is formulated to model the early stages of tumor formation. The model is based on a cell-based formalism, where each cell is represented as a circle or sphere in two-and three dimensional simulations, respectively. The model takes into account constituent cells, such as epithelial cells, tumor cells, and T-cells that chase the tumor cells and engulf them. Fundamental biological processes such as random walk, haptotaxis/chemotaxis, contact mechanics, cell proliferation and death, as well as secretion of chemokines are taken into account. The developed formalism is based on the representation of partial differential equations in terms of fundamental solutions, as well as on stochastic processes and stochastic differential equations. We also take into account the likelihood of seeding of tumors. The model shows the initiation of tumors and allows to study a quantification of the impact of various subprocesses and possibly even of various treatments.

  11. 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.

  12. 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.

  13. Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic.

    PubMed

    Lee, B; Yen, J; Yang, L; Liao, J C

    1999-03-20

    Modeling of metabolic pathway dynamics requires detailed kinetic equations at the enzyme level. In particular, the kinetic equations must account for metabolite effectors that contribute significantly to the pathway regulation in vivo. Unfortunately, most kinetic rate laws available in the literature do not consider all the effectors simultaneously, and much kinetic information exists in a qualitative or semiquantitative form. In this article, we present a strategy to incorporate such information into the kinetic equation. This strategy uses fuzzy logic-based factors to modify algebraic rate laws that account for partial kinetic characteristics. The parameters introduced by the fuzzy factors are then optimized by use of a hybrid of simplex and genetic algorithms. The resulting model provides a flexible form that can simulate various kinetic behaviors. Such kinetic models are suitable for pathway modeling without complete enzyme mechanisms. Three enzymes in Escherichia coli central metabolism are used as examples: phosphoenolpyruvate carboxylase; phosphoenolpyruvate carboxykinase; and pyruvate kinase I. Results show that, with fuzzy logic-augmented models, the kinetic data can be much better described. In particular, complex behavior, such as allosteric inhibition, can be captured using fuzzy rules. The resulting models, even though they do not provide additional physical meaning in enzyme mechanisms, allow the model to incorporate semiquantitative information in metabolic pathway models.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. Formal Uncertainty and Dispersion of Single and Double Difference Models for GNSS-Based Attitude Determination.

    PubMed

    Chen, Wen; Yu, Chao; Dong, Danan; Cai, Miaomiao; Zhou, Feng; Wang, Zhiren; Zhang, Lei; Zheng, Zhengqi

    2017-02-20

    With multi-antenna synchronized global navigation satellite system (GNSS) receivers, the single difference (SD) between two antennas is able to eliminate both satellite and receiver clock error, thus it becomes necessary to reconsider the equivalency problem between the SD and double difference (DD) models. In this paper, we quantitatively compared the formal uncertainties and dispersions between multiple SD models and the DD model, and also carried out static and kinematic short baseline experiments. The theoretical and experimental results show that under a non-common clock scheme the SD and DD model are equivalent. Under a common clock scheme, if we estimate stochastic uncalibrated phase delay (UPD) parameters every epoch, this SD model is still equivalent to the DD model, but if we estimate only one UPD parameter for all epochs or take it as a known constant, the SD (here called SD2) and DD models are no longer equivalent. For the vertical component of baseline solutions, the formal uncertainties of the SD2 model are two times smaller than those of the DD model, and the dispersions of the SD2 model are even more than twice smaller than those of the DD model. In addition, to obtain baseline solutions, the SD2 model requires a minimum of three satellites, while the DD model requires a minimum of four satellites, which makes the SD2 more advantageous in attitude determination under sheltered environments.

  19. Formal Uncertainty and Dispersion of Single and Double Difference Models for GNSS-Based Attitude Determination

    PubMed Central

    Chen, Wen; Yu, Chao; Dong, Danan; Cai, Miaomiao; Zhou, Feng; Wang, Zhiren; Zhang, Lei; Zheng, Zhengqi

    2017-01-01

    With multi-antenna synchronized global navigation satellite system (GNSS) receivers, the single difference (SD) between two antennas is able to eliminate both satellite and receiver clock error, thus it becomes necessary to reconsider the equivalency problem between the SD and double difference (DD) models. In this paper, we quantitatively compared the formal uncertainties and dispersions between multiple SD models and the DD model, and also carried out static and kinematic short baseline experiments. The theoretical and experimental results show that under a non-common clock scheme the SD and DD model are equivalent. Under a common clock scheme, if we estimate stochastic uncalibrated phase delay (UPD) parameters every epoch, this SD model is still equivalent to the DD model, but if we estimate only one UPD parameter for all epochs or take it as a known constant, the SD (here called SD2) and DD models are no longer equivalent. For the vertical component of baseline solutions, the formal uncertainties of the SD2 model are two times smaller than those of the DD model, and the dispersions of the SD2 model are even more than twice smaller than those of the DD model. In addition, to obtain baseline solutions, the SD2 model requires a minimum of three satellites, while the DD model requires a minimum of four satellites, which makes the SD2 more advantageous in attitude determination under sheltered environments. PMID:28230753

  20. Formal models in animal-metacognition research: the problem of interpreting animals' behavior.

    PubMed

    Smith, J David; Zakrzewski, Alexandria C; Church, Barbara A

    2016-10-01

    Ongoing research explores whether animals have precursors to metacognition-that is, the capacity to monitor mental states or cognitive processes. Comparative psychologists have tested apes, monkeys, rats, pigeons, and a dolphin using perceptual, memory, foraging, and information-seeking paradigms. The consensus is that some species have a functional analog to human metacognition. Recently, though, associative modelers have used formal-mathematical models hoping to describe animals' "metacognitive" performances in associative-behaviorist ways. We evaluate these attempts to reify formal models as proof of particular explanations of animal cognition. These attempts misunderstand the content and proper application of models. They embody mistakes of scientific reasoning. They blur fundamental distinctions in understanding animal cognition. They impede theoretical development. In contrast, an energetic empirical enterprise is achieving strong success in describing the psychology underlying animals' metacognitive performances. We argue that this careful empirical work is the clear path to useful theoretical development. The issues raised here about formal modeling-in the domain of animal metacognition-potentially extend to biobehavioral research more broadly.

  1. A formalism for cosmic ray propagation studies. [model based on continuity equation of multiply charged nuclei

    NASA Technical Reports Server (NTRS)

    Golden, R. L.; Badhwar, G. D.; Stephens, S. A.

    1975-01-01

    The continuity equation for cosmic ray propagation is used to derive a set of linear equations interrelating the fluxes of multiply charged nuclei as observed at any particular part of the galaxy. The derivation leads to model independent definitions for cosmic ray storage time, mean density of target nuclei and effective mass traversed. The set of equations form a common framework for comparisons of theories and observations. As an illustration, it is shown that there exists a large class of propagation models which give the same result as the exponential path length model. The formalism is shown to accommodate dynamic as well as equilibrium models of production and propagation.

  2. Exact results in nonequilibrium statistical mechanics: Formalism and applications in chemical kinetics and single-molecule free energy estimation

    NASA Astrophysics Data System (ADS)

    Adib, Artur B.

    In the last two decades or so, a collection of results in nonequilibrium statistical mechanics that departs from the traditional near-equilibrium framework introduced by Lars Onsager in 1931 has been derived, yielding new fundamental insights into far-from-equilibrium processes in general. Apart from offering a more quantitative statement of the second law of thermodynamics, some of these results---typified by the so-called "Jarzynski equality"---have also offered novel means of estimating equilibrium quantities from nonequilibrium processes, such as free energy differences from single-molecule "pulling" experiments. This thesis contributes to such efforts by offering three novel results in nonequilibrium statistical mechanics: (a) The entropic analog of the Jarzynski equality; (b) A methodology for estimating free energies from "clamp-and-release" nonequilibrium processes; and (c) A directly measurable symmetry relation in chemical kinetics similar to (but more general than) chemical detailed balance. These results share in common the feature of remaining valid outside Onsager's near-equilibrium regime, and bear direct applicability in protein folding kinetics as well as in single-molecule free energy estimation.

  3. 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).

  4. 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.

  5. 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.

  6. A perturbative formalism for electronic transitions through conical intersections in a fully quadratic vibronic model.

    PubMed

    Endicott, Julia S; Joubert-Doriol, Loïc; Izmaylov, Artur F

    2014-07-21

    We consider a fully quadratic vibronic model Hamiltonian for studying photoinduced electronic transitions through conical intersections. Using a second order perturbative approximation for diabatic couplings, we derive an analytical expression for the time evolution of electronic populations at a given temperature. This formalism extends upon a previously developed perturbative technique for a linear vibronic coupling Hamiltonian. The advantage of the quadratic model Hamiltonian is that it allows one to use separate quadratic representations for potential energy surfaces of different electronic states and a more flexible representation of interstate couplings. We explore features introduced by the quadratic Hamiltonian in a series of 2D models, and then apply our formalism to the 2,6-bis(methylene) adamantyl cation and its dimethyl derivative. The Hamiltonian parameters for the molecular systems have been obtained from electronic structure calculations followed by a diabatization procedure. The evolution of electronic populations in the molecular systems using the perturbative formalism shows a good agreement with that from variational quantum dynamics.

  7. A perturbative formalism for electronic transitions through conical intersections in a fully quadratic vibronic model

    SciTech Connect

    Endicott, Julia S.; Joubert-Doriol, Loïc; Izmaylov, Artur F.

    2014-07-21

    We consider a fully quadratic vibronic model Hamiltonian for studying photoinduced electronic transitions through conical intersections. Using a second order perturbative approximation for diabatic couplings, we derive an analytical expression for the time evolution of electronic populations at a given temperature. This formalism extends upon a previously developed perturbative technique for a linear vibronic coupling Hamiltonian. The advantage of the quadratic model Hamiltonian is that it allows one to use separate quadratic representations for potential energy surfaces of different electronic states and a more flexible representation of interstate couplings. We explore features introduced by the quadratic Hamiltonian in a series of 2D models, and then apply our formalism to the 2,6-bis(methylene) adamantyl cation and its dimethyl derivative. The Hamiltonian parameters for the molecular systems have been obtained from electronic structure calculations followed by a diabatization procedure. The evolution of electronic populations in the molecular systems using the perturbative formalism shows a good agreement with that from variational quantum dynamics.

  8. Studying dissolution with a model integrating solid-liquid interface kinetics and diffusion kinetics.

    PubMed

    Gao, Jeff Y

    2012-12-18

    A dissolution model that integrates the solid-liquid interface kinetics and the mass transport kinetics is introduced. Such a model reduces to the Noyes-Whitney equation under special conditions, but offers expanded range of applicability and flexibility fitting dissolution profiles when interfacial kinetics and interfacial concentration deviate from the assumptions implied in the Noyes-Whitney equation. General solutions to the integrated dissolution model derived for noninteractive solutes as well as for solutes participating in ionization equilibrium are discussed. Parameters defining the integrated dissolution model are explained conceptually along with practical ways for their determinations. Conditions under which the model exhibits supersaturation features are elaborated. Simulated dissolution profiles using the integrated dissolution model for published experimental data exhibiting supersaturation features are illustrated.

  9. A new model test in high energy physics in frequentist and Bayesian statistical formalisms

    NASA Astrophysics Data System (ADS)

    Kamenshchikov, A.

    2017-01-01

    A problem of a new physical model test given observed experimental data is a typical one for modern experiments of high energy physics (HEP). A solution of the problem may be provided with two alternative statistical formalisms, namely frequentist and Bayesian, which are widely spread in contemporary HEP searches. A characteristic experimental situation is modeled from general considerations and both the approaches are utilized in order to test a new model. The results are juxtaposed, what demonstrates their consistency in this work. An effect of a systematic uncertainty treatment in the statistical analysis is also considered.

  10. 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.

  11. 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.

  12. Agreement of stochastic soliton formalism with second-quantized and configuration-space models

    NASA Astrophysics Data System (ADS)

    Fini, J. M.; Hagelstein, P. L.; Haus, H. A.

    1998-06-01

    The stochastic theory presented by Drummond, Gardiner, and Walls [Phys. Rev. A 24, 914 (1981)] is an interesting approach to problems in quantum optics. In this theory, an exact, quantum evolution is written in terms of classical functions (not operators) driven by explicit, quantum noise. We examine the origin of uncertainty in the formalism through the simple example of a single, nonlinear oscillator. We then test the stochastic theory applied to the problem of soliton propagation. We extend the linearized stochastic model by computing analytically quantum uncertainties in the four basic soliton parameters: photon number, momentum, phase, and position. Agreement with second-quantized and configuration-space soliton theories verifies the stochastic formalism.

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

    SciTech Connect

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

    2012-08-15

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

  14. Multiple temperature kinetic model and gas-kinetic method for hypersonic non-equilibrium flow computations

    NASA Astrophysics Data System (ADS)

    Xu, Kun; He, Xin; Cai, Chunpei

    2008-07-01

    It is well known that for increasingly rarefied flowfields, the predictions from continuum formulation, such as the Navier-Stokes equations lose accuracy. For the high speed diatomic molecular flow in the transitional regime, the inaccuracies are partially attributed to the single temperature approximations in the Navier-Stokes equations. Here, we propose a continuum multiple temperature model based on the Bhatnagar-Gross-Krook (BGK) equation for the non-equilibrium flow computation. In the current model, the Landau-Teller-Jeans relaxation model for the rotational energy is used to evaluate the energy exchange between the translational and rotational modes. Due to the multiple temperature approximation, the second viscosity coefficient in the Navier-Stokes equations is replaced by the temperature relaxation term. In order to solve the multiple temperature kinetic model, a multiscale gas-kinetic finite volume scheme is proposed, where the gas-kinetic equation is numerically solved for the fluxes to update the macroscopic flow variables inside each control volume. Since the gas-kinetic scheme uses a continuous gas distribution function at a cell interface for the fluxes evaluation, the moments of a gas distribution function can be explicitly obtained for the multiple temperature model. Therefore, the kinetic scheme is much more efficient than the DSMC method, especially in the near continuum flow regime. For the non-equilibrium flow computations, i.e., the nozzle flow and hypersonic rarefied flow over flat plate, the computational results are validated in comparison with experimental measurements and DSMC solutions.

  15. Formal reasoning on qualitative models of coinfection of HIV and Tuberculosis and HAART therapy

    PubMed Central

    2010-01-01

    Background Several diseases, many of which nowadays pandemic, consist of multifactorial pathologies. Paradigmatic examples come from the immune response to pathogens, in which cases the effects of different infections combine together, yielding complex mutual feedback, often a positive one that boosts infection progression in a scenario that can easily become lethal. HIV is one such infection, which weakens the immune system favouring the insurgence of opportunistic infections, amongst which Tuberculosis (TB). The treatment with antiretroviral therapies has shown effective in reducing mortality. An in-depth understanding of complex systems, like the one consisting of HIV, TB and related therapies, is an open great challenge, on the boundaries of bioinformatics, computational and systems biology. Results We present a simplified formalisation of the highly dynamic system consisting of HIV, TB and related therapies, at the cellular level. The progression of the disease (AIDS) depends hence on interactions between viruses, cells, chemokines, the high mutation rate of viruses, the immune response of individuals and the interaction between drugs and infection dynamics. We first discuss a deterministic model of dual infection (HIV and TB) which is able to capture the long-term dynamics of CD4 T cells, viruses and Tumour Necrosis Factor (TNF). We contrast this model with a stochastic approach which captures intrinsic fluctuations of the biological processes. Furthermore, we also integrate automated reasoning techniques, i.e. probabilistic model checking, in our formal analysis. Beyond numerical simulations, model checking allows general properties (effectiveness of anti-HIV therapies) to be verified against the models by means of an automated procedure. Our work stresses the growing importance and flexibility of model checking techniques in bioinformatics. In this paper we i) describe HIV as a complex case of infectious diseases; ii) provide a number of different formal

  16. 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.

  17. 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.

  18. 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.

  19. Model-free deconvolution of femtosecond kinetic data.

    PubMed

    Bányász, Akos; Keszei, Erno

    2006-05-18

    Though shorter laser pulses can also be produced, pulses of the 100 fs range are typically used in femtosecond kinetic measurements, which are comparable to characteristic times of the studied processes, making detection of the kinetic response functions inevitably distorted by convolution with the pulses applied. A description of this convolution in terms of experiments and measurable signals is given, followed by a detailed discussion of a large number of available methods to solve the convolution equation to get the undistorted kinetic signal, without any presupposed kinetic or photophysical model of the underlying processes. A thorough numerical test of several deconvolution methods is described, and two iterative time-domain methods (Bayesian and Jansson deconvolution) along with two inverse filtering frequency-domain methods (adaptive Wiener filtering and regularization) are suggested to use for the deconvolution of experimental femtosecond kinetic data sets. Adaptation of these methods to typical kinetic curve shapes is described in detail. We find that the model-free deconvolution gives satisfactory results compared to the classical "reconvolution" method where the knowledge of the kinetic and photophysical mechanism is necessary to perform the deconvolution. In addition, a model-free deconvolution followed by a statistical inference of the parameters of a model function gives less biased results for the relevant parameters of the model than simple reconvolution. We have also analyzed real-life experimental data and found that the model-free deconvolution methods can be successfully used to get undistorted kinetic curves in that case as well. A graphical computer program to perform deconvolution via inverse filtering and additional noise filters is also provided as Supporting Information. Though deconvolution methods described here were optimized for femtosecond kinetic measurements, they can be used for any kind of convolved data where measured

  20. 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.

  1. A master equation formalism for macroscopic modeling of asynchronous irregular activity states.

    PubMed

    El Boustani, Sami; Destexhe, Alain

    2009-01-01

    Many efforts have been devoted to modeling asynchronous irregular (AI) activity states, which resemble the complex activity states seen in the cerebral cortex of awake animals. Most of models have considered balanced networks of excitatory and inhibitory spiking neurons in which AI states are sustained through recurrent sparse connectivity, with or without external input. In this letter we propose a mesoscopic description of such AI states. Using master equation formalism, we derive a second-order mean-field set of ordinary differential equations describing the temporal evolution of randomly connected balanced networks. This formalism takes into account finite size effects and is applicable to any neuron model as long as its transfer function can be characterized. We compare the predictions of this approach with numerical simulations for different network configurations and parameter spaces. Considering the randomly connected network as a unit, this approach could be used to build large-scale networks of such connected units, with an aim to model activity states constrained by macroscopic measurements, such as voltage-sensitive dye imaging.

  2. 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.

  3. 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.

  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. 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.

  6. First-order formalism for flat branes in generalized N-field models

    NASA Astrophysics Data System (ADS)

    Bazeia, D.; Lobão, A. S., Jr.; Losano, L.; Menezes, R.

    2013-08-01

    This work deals with braneworld scenarios obtained from N real scalar fields, whose dynamics is generalized to include higher-order power in the derivative of the fields. For the scalar fields being driven by nonstandard dynamics, we show how a first-order formalism can be obtained for a flat brane in the presence of several fields. We then illustrate our findings, investigating distinct potentials with one and two fields, and obtaining stable standard and compact solutions in the braneworld theory. In particular, we have found different models describing the very same warp factor.

  7. Information cascade, Kirman's ant colony model, and kinetic Ising model

    NASA Astrophysics Data System (ADS)

    Hisakado, Masato; Mori, Shintaro

    2015-01-01

    In this paper, we discuss a voting model in which voters can obtain information from a finite number of previous voters. There exist three groups of voters: (i) digital herders and independent voters, (ii) analog herders and independent voters, and (iii) tanh-type herders. In our previous paper Hisakado and Mori (2011), we used the mean field approximation for case (i). In that study, if the reference number r is above three, phase transition occurs and the solution converges to one of the equilibria. However, the conclusion is different from mean field approximation. In this paper, we show that the solution oscillates between the two states. A good (bad) equilibrium is where a majority of r select the correct (wrong) candidate. In this paper, we show that there is no phase transition when r is finite. If the annealing schedule is adequately slow from finite r to infinite r, the voting rate converges only to the good equilibrium. In case (ii), the state of reference votes is equivalent to that of Kirman's ant colony model, and it follows beta binomial distribution. In case (iii), we show that the model is equivalent to the finite-size kinetic Ising model. If the voters are rational, a simple herding experiment of information cascade is conducted. Information cascade results from the quenching of the kinetic Ising model. As case (i) is the limit of case (iii) when tanh function becomes a step function, the phase transition can be observed in infinite size limit. We can confirm that there is no phase transition when the reference number r is finite.

  8. Thermo-magnetic nonlocal NJL model in the real and imaginary time formalisms

    NASA Astrophysics Data System (ADS)

    Márquez, F.; Zamora, R.

    2017-02-01

    In this paper, we study a nonlocal Nambu-Jona-Lasinio (nNJL) model with a Gaussian regulator in presence of a uniform magnetic field. We take a mixed approach to the incorporation of temperature in the model, and consider aspects of both real and imaginary time formalisms. We include confinement in the model through the quasiparticle interpretation of the poles of the propagator. By working in the real time formalism and computing the spectral density function, we find that the effect of the magnetic field on the poles of the propagator can be entirely absorbed within the mean field value of the scalar field. The analytic structure of our propagator is then preserved in the weak magnetic field limit. The effect of the magnetic field in the deconfinement phase transition is then studied. It is found that, like with chiral symmetry restoration, magnetic catalysis occurs for the deconfinement phase transition. It is also found that the magnetic field enhances the thermodynamical instability of the system. We work in the weak field limit, i.e. (eB) < 5mπ2. At this level there is no splitting of the critical temperatures for chiral and deconfinement phase transitions.

  9. 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.

  10. Discounting of reward sequences: a test of competing formal models of hyperbolic discounting.

    PubMed

    Zarr, Noah; Alexander, William H; Brown, Joshua W

    2014-01-01

    Humans are known to discount future rewards hyperbolically in time. Nevertheless, a formal recursive model of hyperbolic discounting has been elusive until recently, with the introduction of the hyperbolically discounted temporal difference (HDTD) model. Prior to that, models of learning (especially reinforcement learning) have relied on exponential discounting, which generally provides poorer fits to behavioral data. Recently, it has been shown that hyperbolic discounting can also be approximated by a summed distribution of exponentially discounted values, instantiated in the μAgents model. The HDTD model and the μAgents model differ in one key respect, namely how they treat sequences of rewards. The μAgents model is a particular implementation of a Parallel discounting model, which values sequences based on the summed value of the individual rewards whereas the HDTD model contains a non-linear interaction. To discriminate among these models, we observed how subjects discounted a sequence of three rewards, and then we tested how well each candidate model fit the subject data. The results show that the Parallel model generally provides a better fit to the human data.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. Formal Integrals and Nekhoroshev Stability in a Mapping Model for the Trojan Asteroids

    NASA Astrophysics Data System (ADS)

    Efthymiopoulos, Christos

    2005-04-01

    A symplectic mapping model for the co-orbital motion (Sándor et al., 2002, Cel. Mech. Dyn. Astr. 84, 355) in the circular restricted three body problem is used to derive Nekhoroshev stability estimates for the Sun Jupiter Trojans. Following a brief review of the analytical part of Nekhoroshev theory, a direct method is developed to construct formal integrals of motion in symplectic mappings without use of a normal form. Precise estimates are given for the region of effective stability based on the optimization of the size of the remainder of the formal series. The stability region found for t=1010 yrs corresponds to a libration amplitude Dp=10.6°. About 30% of asteroids with accurately known proper elements (Milani, 1993, Cel. Mech. Dyn. Astron. 57, 59), at low eccentricities and inclinations, are included within this region. This represents an improvement with respect to previous estimates given in the literature. The improvement is due partly to the choice of better variables, but also to the use of a mapping model, which is a simplification of the circular restricted three body problem.

  16. Development of the cyclic cluster model formalism for Kohn-Sham auxiliary density functional theory methods.

    PubMed

    Janetzko, Florian; Köster, Andreas M; Salahub, Dennis R

    2008-01-14

    The development of the cyclic cluster model (CCM) formalism for Kohn-Sham auxiliary density functional theory (KS-ADFT) methods is presented. The CCM is a direct space approach for the calculation of perfect and defective systems under periodic boundary conditions. Translational symmetry is introduced in the CCM by integral weighting. A consistent weighting scheme for all two-center and three-center interactions appearing in the KS-ADFT method is presented. For the first time, an approach for the numerical integration of the exchange-correlation potential within the cyclic cluster formalism is derived. The presented KS-ADFT CCM implementation was applied to covalent periodic systems. The results of cyclic and molecular cluster model (MCM) calculations for trans-polyacetylene, graphene, and diamond are discussed as examples for systems periodic in one, two, and three dimensions, respectively. All structures were optimized. It is shown that the CCM results represent the results of MCM calculations in the limit of infinite molecular clusters. By analyzing the electronic structure, we demonstrate that the symmetry of the corresponding periodic systems is retained in CCM calculations. The obtained geometric and electronic structures are compared with available data from the literature.

  17. 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.

  18. 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.

  19. 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.

  20. Detailed Chemical Kinetic Modeling of Hydrazine Decomposition

    NASA Technical Reports Server (NTRS)

    Meagher, Nancy E.; Bates, Kami R.

    2000-01-01

    The purpose of this research project is to develop and validate a detailed chemical kinetic mechanism for gas-phase hydrazine decomposition. Hydrazine is used extensively in aerospace propulsion, and although liquid hydrazine is not considered detonable, many fuel handling systems create multiphase mixtures of fuels and fuel vapors during their operation. Therefore, a thorough knowledge of the decomposition chemistry of hydrazine under a variety of conditions can be of value in assessing potential operational hazards in hydrazine fuel systems. To gain such knowledge, a reasonable starting point is the development and validation of a detailed chemical kinetic mechanism for gas-phase hydrazine decomposition. A reasonably complete mechanism was published in 1996, however, many of the elementary steps included had outdated rate expressions and a thorough investigation of the behavior of the mechanism under a variety of conditions was not presented. The current work has included substantial revision of the previously published mechanism, along with a more extensive examination of the decomposition behavior of hydrazine. An attempt to validate the mechanism against the limited experimental data available has been made and was moderately successful. Further computational and experimental research into the chemistry of this fuel needs to be completed.

  1. Kinetic model of excitatory synaptic transmission to cerebellar Purkinje cells.

    PubMed

    Marienhagen, J; Keller, B U; Zippelius, A

    1997-09-21

    We present a minimal kinetic model for excitatory synaptic transmission to cerebellar Purkinje cells. The main components are a kinetic model for a single glutamate receptor, which is calibrated with the help of patch clamp data, and a mean field approximation for the dynamics of a population of channels, which generate an EPSC. The resulting minimal model of the parallel fiber-Purkinje cell synapse is used to estimate the dynamics of glutamate in the synaptic cleft and to clarify the role of receptor desensitization in synaptic transmission. We also apply the model to different aspects of synaptic modulation, like long-term depression and potentiation by pharmacological application of ampakines. In the framework of the minimal model these effects can be understood as the result of modified receptor kinetics.

  2. 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.

  3. 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.

  4. Models of atoms in plasmas based on common formalism for bound and free electrons

    NASA Astrophysics Data System (ADS)

    Blenski, T.; Piron, R.; Caizergues, C.; Cichocki, B.

    2013-12-01

    Atom-in-plasma models: Thomas-Fermi (TF) and INFERNO, AJCI and VAAQP, that use the same formalism for all electrons are briefly described and analyzed from the point of view of their thermodynamic consistence. While the TF and VAAQP models may be derived from variational principle and respect the virial theorem, it appears that two earlier quantum extensions of the quasi-classical TF model, INFERNO and AJCI, are not fully variational. The problems of the two latter approaches are analyzed from the point of view of the VAAQP model. However all quantum models seem to give unrealistic description of atoms in plasma at low temperature and high plasma densities. These difficulties are connected with the Wigner-Seitz cavity approach to non-central ions that is present in all considered models. Comparison of some equation-of-state data from TF, INFERNO and VAAQP models are shown on a chosen example. We report also on the status of our research on the frequency-dependent linear-response theory of atoms in plasma. A new Ehrenfest-type sum rule, originally proposed in the quantum VAAQP model, was proven in the case of the response of the TF atom with the Bloch hydrodynamics (TFB) and checked by numerical example. The TFB case allows one to have a direct insight into the rather involved mathematics of the self-consistent linear response calculations in situations when both the central atom and its plasma vicinity are perturbed by an electric field.

  5. On relating the generalized equivalent uniform dose formalism to the linear-quadratic model.

    PubMed

    Djajaputra, David; Wu, Qiuwen

    2006-12-01

    Two main approaches are commonly used in the literature for computing the equivalent uniform dose (EUD) in radiotherapy. The first approach is based on the cell-survival curve as defined in the linear-quadratic model. The second approach assumes that EUD can be computed as the generalized mean of the dose distribution with an appropriate fitting parameter. We have analyzed the connection between these two formalisms by deriving explicit formulas for the EUD which are applicable to normal distributions. From these formulas we have established an explicit connection between the two formalisms. We found that the EUD parameter has strong dependence on the parameters that characterize the distribution, namely the mean dose and the standard deviation around the mean. By computing the corresponding parameters for clinical dose distributions, which in general do not follow the normal distribution, we have shown that our results are also applicable to actual dose distributions. Our analysis suggests that caution should be used in using generalized EUD approach for reporting and analyzing dose distributions.

  6. 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.

  7. 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

    2015-05-07

    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.

  8. 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.

  9. 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.

  10. The effects of the theoretical formalism and data selection on mantle models derived from waveform tomography

    NASA Astrophysics Data System (ADS)

    Mégnin, Charles; Romanowicz, Barbara

    1999-08-01

    Most global tomographic models to date are derived using a combination of surface wave (or normal-mode) data and body wave traveltime data. The traveltime approach limits the number of phases available for inversion by requiring them to be isolated on the seismogram. This may ultimately result in limiting the resolution of 3-D structure, at least in some depth ranges in the mantle. In a previous study, we successfully derived a degree 12 whole-mantle SH-velocity tomographic model (SAW12D) using exclusively waveform data. In that inversion, a normal-mode formalism suitable for body waveforms, the non-linear asymptotic coupling theory (NACT), was combined with a body wave windowing scheme, referred to as the `individual wavepacket' (IW) technique, which allows one to assign individual weights to different body wave energy packets. We here compare the relative merits of this choice of theoretical formalism and windowing scheme at different depth ranges in the mantle. Choosing as the reference a model obtained using 7500 transverse-component body wave and 8000 surface wave seismograms and the NACT and IW approaches, we discuss the relative performance of the path average approximation (PAVA), a zeroth-order theoretical approximation appropriate for single-mode surface waves, relative to NACT, and compare the IW windowing scheme with a more standard `full window' (FW) approach, in which a single time window is considered from the first body wave arrival to the fundamental-mode surface waves. The combination PAVA/FW is often used in global tomography to supplement the traveltime data. We show that although the quality of the image derived under the PAVA/FW formalism is very similar to that derived under NACT/IW in the first 300 km of the upper mantle, where the resolution is dominated by surface waves, it deteriorates at greater depths. Images of the lower mantle are shown to be strongly sensitive to the theoretical formalism. In contrast, the resolution of structure

  11. Toward a formalized account of attitudes: The Causal Attitude Network (CAN) model.

    PubMed

    Dalege, Jonas; Borsboom, Denny; van Harreveld, Frenk; van den Berg, Helma; Conner, Mark; van der Maas, Han L J

    2016-01-01

    This article introduces the Causal Attitude Network (CAN) model, which conceptualizes attitudes as networks consisting of evaluative reactions and interactions between these reactions. Relevant evaluative reactions include beliefs, feelings, and behaviors toward the attitude object. Interactions between these reactions arise through direct causal influences (e.g., the belief that snakes are dangerous causes fear of snakes) and mechanisms that support evaluative consistency between related contents of evaluative reactions (e.g., people tend to align their belief that snakes are useful with their belief that snakes help maintain ecological balance). In the CAN model, the structure of attitude networks conforms to a small-world structure: evaluative reactions that are similar to each other form tight clusters, which are connected by a sparser set of "shortcuts" between them. We argue that the CAN model provides a realistic formalized measurement model of attitudes and therefore fills a crucial gap in the attitude literature. Furthermore, the CAN model provides testable predictions for the structure of attitudes and how they develop, remain stable, and change over time. Attitude strength is conceptualized in terms of the connectivity of attitude networks and we show that this provides a parsimonious account of the differences between strong and weak attitudes. We discuss the CAN model in relation to possible extensions, implication for the assessment of attitudes, and possibilities for further study.

  12. Continuous surface charge polarizable continuum models of solvation. I. General formalism.

    PubMed

    Scalmani, Giovanni; Frisch, Michael J

    2010-03-21

    Continuum solvation models are appealing because of the simplified yet accurate description they provide of the solvent effect on a solute, described either by quantum mechanical or classical methods. The polarizable continuum model (PCM) family of solvation models is among the most widely used, although their application has been hampered by discontinuities and singularities arising from the discretization of the integral equations at the solute-solvent interface. In this contribution we introduce a continuous surface charge (CSC) approach that leads to a smooth and robust formalism for the PCM models. We start from the scheme proposed over ten years ago by York and Karplus and we generalize it in various ways, including the extension to analytic second derivatives with respect to atomic positions. We propose an optimal discrete representation of the integral operators required for the determination of the apparent surface charge. We achieve a clear separation between "model" and "cavity" which, together with simple generalizations of modern integral codes, is all that is required for an extensible and efficient implementation of the PCM models. Following this approach we are now able to introduce solvent effects on energies, structures, and vibrational frequencies (analytical first and second derivatives with respect to atomic coordinates), magnetic properties (derivatives with respect of magnetic field using GIAOs), and in the calculation more complex properties like frequency-dependent Raman activities, vibrational circular dichroism, and Raman optical activity.

  13. Model reduction for chemical kinetics: An optimization approach

    SciTech Connect

    Petzold, L.; Zhu, W.

    1999-04-01

    The kinetics of a detailed chemically reacting system can potentially be very complex. Although the chemist may be interested in only a few species, the reaction model almost always involves a much larger number of species. Some of those species are radicals, which are very reactive species and can be important intermediaries in the reaction scheme. A large number of elementary reactions can occur among the species; some of these reactions are fast and some are slow. The aim of simplified kinetics modeling is to derive the simplest reaction system which retains the essential features of the full system. An optimization-based method for reduction of the number of species and reactions in chemical kinetics model is described. Numerical results for several reaction mechanisms illustrate the potential of this approach.

  14. 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.

  15. Simulations of plasma sheaths using continuum kinetic models

    NASA Astrophysics Data System (ADS)

    Srinivasan, Bhuvana; Hakim, Ammar

    2015-11-01

    Understanding plasma sheath physics is important for the performance of devices such as Hall thrusters due to the effect of energetic particles on electrode erosion. Plasma sheath physics is studied using kinetic and multi-fluid models with relevance to secondary electron emissions and plasma-surface interactions. Continuum kinetic models are developed to directly solve the Vlasov-Poisson equation using the discontinuous Galerkin method for each of the ion and electron species. A steady-state sheath is simulated by including a simple model for a neutral fluid. Multi-fluid simulations for the plasma sheath are also performed using the discontinuous Galerkin method to solve a complete set of fluid equations for each of the ion and electron species. The kinetic plasma sheath is compared to a multi-fluid plasma sheath. Supported by Air Force Office of Scientific Research.

  16. 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.

  17. A Sparse Reformulation of the Green's Function Formalism Allows Efficient Simulations of Morphological Neuron Models.

    PubMed

    Wybo, Willem A M; Boccalini, Daniele; Torben-Nielsen, Benjamin; Gewaltig, Marc-Oliver

    2015-12-01

    We prove that when a class of partial differential equations, generalized from the cable equation, is defined on tree graphs and the inputs are restricted to a spatially discrete, well chosen set of points, the Green's function (GF) formalism can be rewritten to scale as O(n) with the number n of inputs locations, contrary to the previously reported O(n(2)) scaling. We show that the linear scaling can be combined with an expansion of the remaining kernels as sums of exponentials to allow efficient simulations of equations from the aforementioned class. We furthermore validate this simulation paradigm on models of nerve cells and explore its relation with more traditional finite difference approaches. Situations in which a gain in computational performance is expected are discussed.

  18. Comparison of kinetic theory models of laser ablation of carbon

    SciTech Connect

    Shusser, Michael

    2010-05-15

    The paper compares the predictions of three-dimensional kinetic theory models of laser ablation of carbon. All the models are based on the moment solution of the Boltzmann equation for arbitrary strong evaporation but use different approximations. Comparison of the model predictions demonstrated that the choice of the particular model has very little influence on the results. The influence of the heat conduction from the gas to the solid phase was also found to be negligible in this problem.

  19. 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.

  20. Formal Methods Tool Qualification

    NASA Technical Reports Server (NTRS)

    Wagner, Lucas G.; Cofer, Darren; Slind, Konrad; Tinelli, Cesare; Mebsout, Alain

    2017-01-01

    Formal methods tools have been shown to be effective at finding defects in safety-critical digital systems including avionics systems. The publication of DO-178C and the accompanying formal methods supplement DO-333 allows applicants to obtain certification credit for the use of formal methods without providing justification for them as an alternative method. This project conducted an extensive study of existing formal methods tools, identifying obstacles to their qualification and proposing mitigations for those obstacles. Further, it interprets the qualification guidance for existing formal methods tools and provides case study examples for open source tools. This project also investigates the feasibility of verifying formal methods tools by generating proof certificates which capture proof of the formal methods tool's claim, which can be checked by an independent, proof certificate checking tool. Finally, the project investigates the feasibility of qualifying this proof certificate checker, in the DO-330 framework, in lieu of qualifying the model checker itself.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Ab initio quantum chemical and kinetic modeling study of the pyrolysis kinetics of pyrrole

    SciTech Connect

    Martoprawiro, M.; Bacskay, G.B.; Mackie, J.C.

    1999-05-20

    The five-membered heterocyclic pyrrole moiety is an important structure in coals and derived tars, and the thermal decomposition reactions of pyrrole are important for production of precursors of the oxides of nitrogen, NO{sub x}, in the combustion of coals. The kinetics of pyrolysis of pyrrole have been investigated theoretically by ab initio quantum chemical techniques and by detailed chemical kinetic modeling of previously reported experimental results. The overall kinetics can be successfully modeled by a 117 step kinetic model that gives good agreement with temperature profiles of major products and also provides an acceptable fit for minor products. The thermochemistry and rate parameters of a number of key reactions have been obtained by ab initio calculations carried out at CASSCF, CASPT2, and G2(MP2) levels of theory. Several reaction pathways were investigated. The major product, HCN, arises principally from a hydrogen migration in pyrrole to form a cyclic carbene with the NH bond intact. Ring scission of this carbene leads to an allenic imine precursor of HCN and propyne. This is the decomposition pathway of lowest energy. Pyrolysis is preceded by the facile tautomerization of pyrrole to 2H-pyrrolenine. The latter can undergo CN fission to form an open chain biradical species, which is the precursor of the butenenitrile isomeric products, cis- and trans-crotononitrile and allyl cyanide. The biradical can also undergo facile H-fission to form cyanoallyl radical, which is an important precursor of acetylene, acetonitrile, and acrylonitrile, H{sub 2} also arises principally from H-fission of the biradical.

  7. 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.

  8. 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.…

  9. Linguistics from the Perspective of the Theory of Models in Empirical Sciences: From Formal to Corpus Linguistics

    ERIC Educational Resources Information Center

    Grabinska, Teresa; Zielinska, Dorota

    2010-01-01

    The authors examine language from the perspective of models of empirical sciences, which discipline studies the relationship between reality, models, and formalisms. Such a perspective allows one to notice that linguistics approached within the classical framework share a number of problems with other experimental sciences studied initially…

  10. Kinetic model of particle-inhibited grain growth

    NASA Astrophysics Data System (ADS)

    Thompson, Gary Scott

    The effects of second phase particles on matrix grain growth kinetics were investigated using Al2O3-SiC as a model system. In particular, the validity of the conclusion drawn from a previous kinetic analysis that the kinetics of particle-inhibited grain growth in Al2 O3-SiC samples with an intermediate volume fraction of second phase could be well quantified by a modified-Zener model was investigated. A critical analysis of assumptions made during the previous kinetic analysis revealed oversimplifications which affect the validity of the conclusion. Specifically, the degree of interaction between particles and grain boundaries was assumed to be independent of the mean second phase particle size and size distribution. In contrast, current measurements indicate that the degree of interaction in Al2O3-SiC is dependent on these parameters. An improved kinetic model for particle-inhibited grain growth in Al 2O3-SiC was developed using a modified-Zener approach. The comparison of model predictions with experimental grain growth data indicated that significant discrepancies (as much as 4--5 orders of magnitude) existed. Based on this, it was concluded that particles had a much more significant effect on grain growth kinetics than that caused by a simple reduction of the boundary driving force due to the removal of boundary area. Consequently, it was also concluded that the conclusion drawn from the earlier kinetic analysis regarding the validity of a modified-Zener model was incorrect. Discrepancies between model and experiment were found to be the result of a significant decrease in experimental growth rate constant not predicted by the model. Possible physical mechanisms for such a decrease were investigated. The investigation of a small amount of SiO2 on grain growth in Al2O3 indicated that the decrease was not the result of a decrease in grain boundary mobility due to impurity contamination by particles. By process of elimination and based on previous observations

  11. 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

  12. Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling.

    PubMed

    Noé, Frank; Banisch, Ralf; Clementi, Cecilia

    2016-11-08

    Identification of the main reaction coordinates and building of kinetic models of macromolecular systems require a way to measure distances between molecular configurations that can distinguish slowly interconverting states. Here we define the commute distance that can be shown to be closely related to the expected commute time needed to go from one configuration to the other, and back. A practical merit of this quantity is that it can be easily approximated from molecular dynamics data sets when an approximation of the Markov operator eigenfunctions is available, which can be achieved by the variational approach to approximate eigenfunctions of Markov operators, also called variational approach of conformation dynamics (VAC) or the time-lagged independent component analysis (TICA). The VAC or TICA components can be scaled such that a so-called commute map is obtained in which Euclidean distance corresponds to the commute distance, and thus kinetic models such as Markov state models can be computed based on Euclidean operations, such as standard clustering. In addition, the distance metric gives rise to a quantity we call total kinetic content, which is an excellent score to rank input feature sets and kinetic model quality.

  13. A Kinetic Model for Vapor-liquid Flows

    DTIC Science & Technology

    2005-07-13

    A Kinetic Model for Vapor-liquid Flows Aldo Frezzotti, Livio Gibelli and Silvia Lorenzani Dipartimento di Matematica del Politecnico di Milano Piazza...ES) Dipartimento di Matematica del Politecnico di Milano Piazza Leonardo da Vinci 32 - 20133 Milano - Italy 8. PERFORMING ORGANIZATION REPORT NUMBER

  14. 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

  15. A novel multistage kinetic modeling of flotation for wastewater treatment.

    PubMed

    Ksenofontov, B S; Ivanov, M V

    2013-01-01

    This study develops a new model for description of flotation kinetics. It defines flotation as a process that consists of several stages: separated air bubbles and particles, air bubbles and particles forming an aggregate, aggregate rising to the froth layer. This description significantly differs from known models, which are much simplified. The multistage model gives a novel in-depth description and considers different aspects of flotation, i.e. aggregate formation, which is critically important for flotation to take place. Experimental approval of the new model resulted in its accuracy. The model is to be used for a description of kinetics of all flotation processes in wastewater treatment. It helps in accurate design of flotation treatment plants and may be used for further research of the flotation process.

  16. MODELING EUTROPHICATION KINETICS IN RESERVOIR MICROCOSMS

    EPA Science Inventory

    This study addresses the question of how a general seasonal eutrophication model, WASP5, can handle daily phytoplankton and nutrient dynamics in perturbed microcosms for 1-to 2-week periods of time. It is intended to explore both the interpretative and the predictive capabilities...

  17. 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.

  18. A kinetic model for flavonoid production in tea cell culture.

    PubMed

    Shibasaki-Kitakawa, Naomi; Iizuka, Yasuhiro; Takahashi, Atsushi; Yonemoto, Toshikuni

    2017-02-01

    As one of the strategies for efficient production of a metabolite from cell cultures, a kinetic model is very useful tool to predict productivity under various culture conditions. In this study, we propose a kinetic model for flavonoid production in tea cell culture based on the cell life cycle and expression of PAL, the gene encoding phenylalanine ammonia-lyase (PAL)-the key enzyme in flavonoid biosynthesis. The flavonoid production rate was considered to be related to the amount of active PAL. Synthesis of PAL was modelled based on a general gene expression/translation mechanism, including the transcription of DNA encoding PAL into mRNA and the translation of PAL mRNA into the PAL protein. The transcription of DNA was assumed to be promoted at high light intensity and suppressed by a feedback regulatory mechanism at high flavonoid concentrations. In the model, mRNA and PAL were considered to self-decompose and to be lost by cell rupture. The model constants were estimated by fitting the experimental results obtained from tea cell cultures under various light intensities. The model accurately described the kinetic behaviors of dry and fresh cell concentrations, glucose concentration, cell viability, PAL specific activity, and flavonoid content under a wide range of light intensities. The model simulated flavonoid productivity per medium under various culture conditions. Therefore, this model will be useful to predict optimum culture conditions for maximum flavonoid productivity in cultured tea cells.

  19. 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.

  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}}{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.

  1. 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

  2. Vlasov models for kinetic Weibel-type instabilities

    NASA Astrophysics Data System (ADS)

    Ghizzo, A.; Sarrat, M.; Del Sarto, D.

    2017-02-01

    The Weibel instability, driven by a temperature anisotropy, is investigated within different kinetic descriptions based on the semi-Lagrangian full kinetic and relativistic Vlasov-Maxwell model, on the multi-stream approach, which is based on a Hamiltonian reduction technique, and finally, with the full pressure tensor fluid-type description. Dispersion relations of the Weibel instability are derived using the three different models. A qualitatively different regime is observed in Vlasov numerical experiments depending on the excitation of a longitudinal plasma electric field driven initially by the combined action of the stream symmetry breaking and weak relativistic effects, in contrast with the existing theories of the Weibel instability based on their purely transverse characters. The multi-stream model offers an alternate way to simulate easily the coupling with the longitudinal electric field and particularly the nonlinear regime of saturation, making numerical experiments more tractable, when only a few moments of the distribution are considered. Thus a numerical comparison between the reduced Hamiltonian model (the multi-stream model) and full kinetic (relativistic) Vlasov simulations has been investigated in that regime. Although nonlinear simulations of the fluid model, including the dynamics of the pressure tensor, have not been carried out here, the model is strongly relevant even in the three-dimensional case.

  3. Kinetic model for the chlorination of power plant cooling waters

    SciTech Connect

    Johnson, J.D.; Qualls, R.G.

    1983-01-01

    Concern over the environmental effects of chlorination has prompted efforts to minimize the amount of chlorine necessary to prevent fouling of power-plant condensers. Kinetic expressions are developed for the short-term reactions of chlorine consumption by organic substances in natural freshwater. These expressions were developed to use in a kinetic model to predict the free and total available chlorine discharged in cooling water. This model uses commonly available water-quality data. It assumes that most of the chlorine-consuming substances are: (1) NH/sub 3/, (2) chloramine-forming organic-N, and (3) humic substances. It uses the Morris-Wei model of chlorine-ammonia reactions. Chloramine formation from organic-N was represented by a model compound, glycylglycine.

  4. 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.

  5. 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

  6. 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.

  7. Extraction of lycopene from tomato processing waste: kinetics and modelling.

    PubMed

    Poojary, Mahesha M; Passamonti, Paolo

    2015-04-15

    Lycopene, a nutraceutical compound, was extracted from tomato processing waste, an abundantly available food industry by-product in Italy. The extraction kinetics was mathematically described using the first order kinetic model, the mass transfer model and Peleg's model to understand the physicochemical behaviour of the extraction. Samples were extracted using acetone/n-hexane mixtures at different ratios (1:3, 2:2 and 3:1, v/v) and at different temperatures (30, 40 and 50 °C) and simultaneously analysed using UV-VIS spectrophotometry. The lycopene yield was in the range 3.47-4.03 mg/100g, which corresponds to a percentage recovery of 65.22-75.75. All kinetic models gave a good fit to the experimental data, but the best one was Peleg's model, having the highest RAdj(2) and the lowest RMSE, MBE and χ(2) values. All the models confirmed that a temperature of 30 °C and solvent mixture of acetone/n-hexane 1:3 (v/v) provided optimal conditions for extraction of lycopene.

  8. Reflectance spectroscopy in analysis of UO2 scale: derivation of a kinetic model of uranium oxidation.

    PubMed

    Chernia, Z

    2009-03-21

    In this study, we analyzed the development of a compact oxide scale built in course of Uranium surface oxidation. The process was monitored by an in-situ acquisition of the reflectance interference peaks in the NIR-MIR. Dielectric properties of the growing oxide scale were derived in accord to the oscillator model. We used effective media approach to simulate heterogeneous dielectric content in the oxide-metal interface. Following dielectric parameterization, structural properties (e.g., scale thickness) of the proposed multi-scale scheme were calculated. As scale's growth process quantified, a valid kinetic model was proposed. Analysis showed that oxidation dynamics is governed by a multi-parabolic, true diffusion-limited mechanism of activation energy conveniently equaling the known anion diffusion enthalpy of 26 kcal/mol. The applied kinetic model suggested a setup of two consecutive oxide scales, characterized by differing anion diffusion rates. Though mathematical formalism presented a similar to the paralinear, time-dependent solution, here, in contrast to the classic paralinear assumption, both scales consisted of a compact, diffusion limited oxide barriers. As a result, the difference in anion flow across the outer and inner scale barriers assigned the overall, pseudo-linear rate constant-kl, of a negative (in contrast to the paralinear approach) value. Next, Uranium oxidation has been studied in the post-elastic domain. Markedly, upon breakaway of the compact oxide scale, classic paralinear behavior was reestablished for scale thickness of > or = 0.5 microm.

  9. Construction of reduced transport model by gyro-kinetic simulation with kinetic electrons in helical plasmas

    NASA Astrophysics Data System (ADS)

    Toda, S.; Nakata, M.; Nunami, M.; Ishizawa, A.; Watanabe, T.-H.; Sugama, H.

    2016-10-01

    A reduced model of the turbulent ion heat diffusivity is proposed by the gyrokinetic simulation code (GKV-X) with the adiabatic electrons for the high-Ti Large Helical Device discharge. The plasma parameter region of the short poloidal wavelength is studied, where the ion temperature gradient mode becomes unstable. The ion heat diffusivity by the nonlinear simulation with the kinetic electrons is found to be several times larger than the simulation results using the adiabatic electrons in the radial region 0.46 <= r / a <= 0.80 . The electromagnetic contribution is about a several percent in the ion energy flux. The model of the turbulent diffusivity is derived as the function of the squared electrostatic potential fluctuation and the squared zonal flow potential. Next, the squared electrostatic potential fluctuation is approximated with the mixing length estimate. The squared zonal flow potential fluctuation is shown as the linear zonal flow response function. The reduced model of the turbulent diffusivity is derived as the function of the physical parameters by the linear GKV-X simulation with the kinetic electrons. This reduced model is applied to the transport code with the same procedure as.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Fluid and kinetic models of negative ion sheaths

    SciTech Connect

    Cavenago, M.

    2011-09-26

    Due to the presence of a large transverse magnetic field (B{sub x} and B{sub y} where z is the extraction axis), the extraction of electrons from a negative ion source is likely to happen with a large angle with respect to z axis. The negative ion and electron sheaths are here studied both with kinetic and with fluid models. First, Vlasov-Poisson models are reduced to one dimensional integrodifferential equations, discussing also trapped orbits. The integrodifferential equations for electron transport are analytically solved for a variety of extraction potentials (in 1D). Collision frequency dependency from electron flow speed and temperature is discussed. Then both ion and electron space charge and fluid motion are solved, using electron densities expression consistent with kinetic model. Results for the sheath charge profile and extraction field as a function of B{sub x} are shown.

  15. 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.

  16. Kinetic Modeling of Paraffin Aromatization over Zeolites: A Design Perspective

    NASA Astrophysics Data System (ADS)

    Bhan, Aditya; Katare, Santhoji; Caruthers, James; Lauterbach, Jochen; Venkatasubramanian, Venkat; Delgass, Nicholas

    2002-03-01

    A generic framework for catalyst design involving the solution of a forward predictive problem using hybrid models and the inverse problem using evolutionary algorithms has been proposed. In that context, we investigate the aromatization of light paraffins over HZSM-5 to obtain the catalyst descriptors and associated kinetic parameters that predict performance. A detailed kinetic model that can fundamentally quantify the catalytic properties of acid sites in terms of intrinsic parameters such as rate constants and activation energies of elementary steps is developed on the basis of the following types of reactions: adsorption/desorption, oligomerization/ beta-scission, hydride transfer, protolysis and aromatization. The reaction network so generated has been grouped under various reaction families taking into account the different stabilities and reactivities of the adsorbed carbenium/carbonium ions. The detailed parameterization of each reaction type, optimizing fits to data, linking catalyst descriptors to performance, and means of improving the robustness of the model will be presented.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Kinetic plasma modeling with quiet Monte Carlo direct simulation.

    SciTech Connect

    Albright, B. J.; Jones, M. E.; Lemons, D. S.; Winske, D.

    2001-01-01

    The modeling of collisions among particles in space plasma media poses a challenge for computer simulation. Traditional plasma methods are able to model well the extremes of highly collisional plasmas (MHD and Hall-MHD simulations) and collisionless plasmas (particle-in-cell simulations). However, neither is capable of trealing the intermediate, semi-collisional regime. The authors have invented a new approach to particle simulation called Quiet Monte Carlo Direct Simulation (QMCDS) that can, in principle, treat plasmas with arbitrary and arbitrarily varying collisionality. The QMCDS method will be described, and applications of the QMCDS method as 'proof of principle' to diffusion, hydrodynamics, and radiation transport will be presented. Of particular interest to the space plasma simulation community is the application of QMCDS to kinetic plasma modeling. A method for QMCDS simulation of kinetic plasmas will be outlined, and preliminary results of simulations in the limit of weak pitch-angle scattering will be presented.

  2. 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

  3. 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.

  4. 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).

  5. 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…

  6. An autocatalytic kinetic model for describing microbial growth during fermentation.

    PubMed

    Ibarz, Albert; Augusto, Pedro E D

    2015-01-01

    The mathematical modelling of the behaviour of microbial growth is widely desired in order to control, predict and design food and bioproduct processing, stability and safety. This work develops and proposes a new semi-empirical mathematical model, based on an autocatalytic kinetic, to describe the microbial growth through its biomass concentration. The proposed model was successfully validated using 15 microbial growth patterns, covering the three most important types of microorganisms in food and biotechnological processing (bacteria, yeasts and moulds). Its main advantages and limitations are discussed, as well as the interpretation of its parameters. It is shown that the new model can be used to describe the behaviour of microbial growth.

  7. Modelling on corrosion inhibitor kinetics in carbon steel pipe used in oil industry

    NASA Astrophysics Data System (ADS)

    Hasmi, A. N.; Nuraini, N.; Wahyuningrum, D.; Sumarti, N.; Bunjali, B.

    2014-02-01

    A model to explain the kinetics of corrosion inhibitor is proposed here. The model is based on Transition State Theory. Our model has many similarities with Michelis-Menten Kinetics. The kinetics difference between uninhibited corrosion and inhibited corrosion is presented. Our model showed the inhibitor could suppress the corrosion rate.

  8. 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.

  9. A review of the kinetic statistical strength model

    SciTech Connect

    Attia, A.V.

    1996-03-11

    This is a review of the Kinetic-Statistical Strength (KSS) model described in the report ``Models of Material Strength, Fracture and Failure`` by V. Kuropatenko and V. Bychenkov. The models for metals subjected to high strain rates (explosions) are focussed on. Model implementation appears possible in a hydrocode. Applying the model to the shock response of metals will require a data source for the Weibull parameter {alpha}{sub u}, short of measuing the strength of specimens of various sizes. Model validation will require more detail on the experiments successfully calculated by SPRUT. Evaluation of the KSS model is needed against other existing rate-dependent models for metals such as the Steinberg-Lund or MTS model on other shock experiments.

  10. 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.

  11. Modeling organic micro pollutant degradation kinetics during sewage sludge composting.

    PubMed

    Sadef, Yumna; Poulsen, Tjalfe Gorm; Bester, Kai

    2014-11-01

    Degradation of 13 different organic micro-pollutants in sewage sludge during aerobic composting at 5 different temperatures over a 52 day period was investigated. Adequacy of two kinetic models: a single first order, and a dual first order expression (using an early (first 7 days) and a late-time (last 45 days) degradation coefficient), for describing micro-pollutant degradation, and kinetic constant dependency on composting temperature were evaluated. The results showed that both models provide relatively good descriptions of the degradation process, with the dual first order model being most accurate. The single first order degradation coefficient was 0.025 d(-1) on average across all compounds and temperatures. At early times, degradation was about three times faster than at later times. Average values of the early and late time degradation coefficients for the dual first order model were 0.066 d(-1) and 0.022 d(-1), respectively. On average 30% of the initial micro-pollutant mass present in the compost was degraded rapidly during the early stages of the composting process. Single first order and late time dual first order kinetic constants were strongly dependent on composting temperature with maximum values at temperatures of 35-65°C. In contrast the early time degradation coefficients were relatively independent of composting temperature.

  12. Extended Hamiltonian Formalism of the Pure Space-Like Axial Gauge Schwinger Model. II

    NASA Astrophysics Data System (ADS)

    Nakawaki, Y.; McCartor, G.

    2004-06-01

    Canonical methods are not sufficient to properly quantize space-like axial gauges. In this paper, we obtain guiding principles that allow for the construction of an extended Hamiltonian formalism for pure space-like axial gauge fields. To do so, we clarify the general role that residual gauge fields play in the space-like axial gauge Schwinger model. In all the calculations, we fix the gauge using the rule n•A=0, where n is a space-like constant vector, and we refer to its direction as x-. Then, to begin with, we construct a formulation in which the quantization surface is space-like but not parallel to the direction of n. The quantization surface has a parameter that allows us to rotate it, but when we do so, we keep the gauge fixing direction fixed. In that formulation, we can use canonical methods. We bosonize the model to simplify the investigation. We find that the inverse differentiation, (∂-)-1, is ill-defined whatever quantization coordinates we use, as long as the direction of n is space-like. We find that the physical part of the dipole ghost field includes infrared divergences. However, we also find that if we introduce residual gauge fields in such a way that the dipole ghost field satisfies the canonical commutation relations, then the residual gauge fields are determined so as to regularize the infrared divergences contained in the physical part. The propagators then take the form prescribed by Mandelstam and Leibbrandt. We make use of these properties to develop guiding principles that allow us to construct consistent operator solutions in the pure space-like case, in which the quantization surface is parallel to the direction of n, and canonical methods do not suffice.

  13. 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.

  14. Modelling the cooking doneness via integrating sensory evaluation and kinetics.

    PubMed

    Li, Jingpeng; Deng, Li; Jin, Zhengyu; Yan, Yong

    2017-02-01

    The aim of the current work was to develop a novel method to model and quantitatively determine cooking doneness via integrating sensory evaluation and kinetics based on the maturity value (M value) which was redefined. The well-done food was first selected from a series of samples with different M values by sensory evaluation, the average termination maturity values (AMT values) were obtained in accordance with the weighted M values of the selected doneness samples. Among, the changes of M values were assumed to be accorded with the first-order reaction kinetic model and a specific zM value was set as well. The zM value was then obtained due to the rationality of the hypothesis, which was validated by rigorous data analysis. Results showed that maturity time values (MT values) were existing and stable for specific types of materials and a specific population. Quantitative determination of the degree of doneness has profound significance in industrial production.

  15. 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

  16. Kinetic modelling of pressure filtration of ceramic powder suspensions

    SciTech Connect

    Correia, L.A.; Salomoni, A.; Hey, A.W.

    1995-09-01

    A kinetic model developed for radial pressure filtration is described and used to study the casting behaviour of an Alumina (Al6SG) and a Zirconia (TZ3Ys) slip stabilized with Dolapix CE64. For the Zirconia slip no influence of pressure and curvature is found. The casting behaviour of the Alumina slip seems to be influenced by both the pressure and the curvature of the filtrating surface.

  17. Kinetic Model of Conduction Changes across Excitable Membranes*

    PubMed Central

    Jain, Mahendra K.; Marks, Richard H. L.; Cordes, E. H.

    1970-01-01

    A kinetic model describing conduction changes across excitable membranes is proposed. It assumes that a population of discrete membrane sites is distributed among several distinct functional states determined by the voltage across the membrane. Interconversion of these states is postulated to occur by first-order reactions. It provides a satisfactory description of the central aspects of excitable membrane behavior, including current-time and current-voltage relationships, action potential, and effects of inhibitors. PMID:5289023

  18. Controllability in Hybrid Kinetic Equations Modeling Nonequilibrium Multicellular Systems

    PubMed Central

    Bianca, Carlo

    2013-01-01

    This paper is concerned with the derivation of hybrid kinetic partial integrodifferential equations that can be proposed for the mathematical modeling of multicellular systems subjected to external force fields and characterized by nonconservative interactions. In order to prevent an uncontrolled time evolution of the moments of the solution, a control operator is introduced which is based on the Gaussian thermostat. Specifically, the analysis shows that the moments are solution of a Riccati-type differential equation. PMID:24191137

  19. 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.

  20. 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.

  1. A model to describe Cr(VI) kinetics biosorption.

    PubMed

    Poch, Jordi; Villaescusa, Isabel

    2010-03-15

    In this work, the effect of pH control on kinetics of Cr(VI) sorption onto grape stalks has been studied. A set of experiments were performed at a constant pH 3+/-0.1 which was assured by means of a Programmable Logic Controller (PLC). In a second set of experiments the initial pH was adjusted to pH 3 and then pH was allowed to freely evolve during the sorption process. Both sets of experiments were carried out at different temperatures within the range 5-50 degrees C. Constant temperature was assured by water recirculation from a thermostatic bath. Results demonstrated that pH has high influence on kinetics only at the lowest temperatures studied. A model based on a complex reaction sequence which takes into account Cr(VI) sorption, reduction of Cr(VI) to Cr(III), sorption of the formed Cr(III) which includes the pH variation during the sorption process has been proposed to model Cr(VI) kinetics sorption onto grape stalk waste. Furthermore, the robustness of the model has been tested.

  2. 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.

  3. 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.

  4. 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

  5. Multiensemble Markov models of molecular thermodynamics and kinetics.

    PubMed

    Wu, Hao; Paul, Fabian; Wehmeyer, Christoph; Noé, Frank

    2016-06-07

    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.

  6. 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.

  7. 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

    2011-05-07

    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.

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

    PubMed Central

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

    2010-01-01

    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 E. coli and compare favourably with in silico prediction by flux balance analysis. PMID:20230840

  9. 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.

  10. Dendritic growth shapes in kinetic Monte Carlo models

    NASA Astrophysics Data System (ADS)

    Krumwiede, Tim R.; Schulze, Tim P.

    2017-02-01

    For the most part, the study of dendritic crystal growth has focused on continuum models featuring surface energies that yield six pointed dendrites. In such models, the growth shape is a function of the surface energy anisotropy, and recent work has shown that considering a broader class of anisotropies yields a correspondingly richer set of growth morphologies. Motivated by this work, we generalize nanoscale models of dendritic growth based on kinetic Monte Carlo simulation. In particular, we examine the effects of extending the truncation radius for atomic interactions in a bond-counting model. This is done by calculating the model’s corresponding surface energy and equilibrium shape, as well as by running KMC simulations to obtain nanodendritic growth shapes. Additionally, we compare the effects of extending the interaction radius in bond-counting models to that of extending the number of terms retained in the cubic harmonic expansion of surface energy anisotropy in the context of continuum models.

  11. Kinetics Modeling and Numerical Simulation of Reactive Materials

    NASA Astrophysics Data System (ADS)

    Yoo, Sunhee; Stewart, D. Scott; Lambert, David E.; Choi, Sunjin

    2011-06-01

    Simulations with reduced kinetic models are used to study shock ignition and detonation in reactive materials that may support non-classical detonation. Porous aluminum Teflon oxidizer mixtures that support combustion reactions in air are considered, as a member of a class of materials with intrinsic interest. We recast a phenomenological theory with realistic kinetics with end products; AlF3, C and CO2. Intermediate products include at least thirty elementary reactions; a sub-set can be selected to simplify, but a hard problem remains. We use the multi-scale asymptotic ``G-scheme'' proposed by M. Valorani, S. Paolucci and reduce a dynamical system consisting of the intermediate reactions and rates, conservation laws and porosity evolution. Results of the multi-species evolution and its impact on rapid self-oxidizing combustion and possible detonation conditions and the computational methods are presented. Supported by AFRL/RW and DTRA.

  12. Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.

    PubMed

    Pinamonti, Giovanni; Zhao, Jianbo; Condon, David E; Paul, Fabian; Noè, Frank; Turner, Douglas H; Bussi, Giovanni

    2017-02-14

    Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time or spatial resolution. Here we use state-of-the-art computational techniques, namely, atomistic molecular dynamics and Markov state models, to provide insight into the rapid dynamics of short RNA oligonucleotides, to elucidate the kinetics of stacking interactions. Analysis of multiple microsecond-long simulations indicates that the main relaxation modes of such molecules can consist of transitions between alternative folded states, rather than between random coils and native structures. After properly removing structures that are artificially stabilized by known inaccuracies of the current RNA AMBER force field, the kinetic properties predicted are consistent with the time scales of previously reported relaxation experiments.

  13. 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.

  14. 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

  15. Kinetic model for microbial growth and desulphurisation with Enterobacter sp.

    PubMed

    Liu, Long; Guo, Zhiguo; Lu, Jianjiang; Xu, Xiaolin

    2015-02-01

    Biodesulphurisation was investigated by using Enterobacter sp. D4, which can selectively desulphurise and convert dibenzothiophene into 2-hydroxybiphenyl (2-HBP). The experimental values of growth, substrate consumption and product generation were obtained at 95 % confidence level of the fitted values using three models: Hinshelwood equation, Luedeking-Piret and Luedeking-Piret-like equations. The average error values between experimental values and fitted values were less than 10 %. These kinetic models describe all the experimental data with good statistical parameters. The production of 2-HBP in Enterobacter sp. was by "coupled growth".

  16. 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.

  17. Meanings Generated while Using Algebraic-Like Formalism to Construct and Control Animated Models

    ERIC Educational Resources Information Center

    Kynigos, Chronis; Psycharis, Giorgos; Moustaki, Foteini

    2010-01-01

    This paper reports on a design experiment conducted to explore the construction of meanings by 17 year old students, emerging from their interpretations and uses of algebraic like formalism. The students worked collaboratively in groups of two or three, using MoPiX, a constructionist computational environment with which they could create concrete…

  18. 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.

  19. 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

  20. Zero-inflated endogenous count in censored model: effects of informal family care on formal health care.

    PubMed

    Lee, Myoung-Jae; Kim, Young-Sook

    2012-09-01

    If informal family health care is a substitute for formal health care, then there is a scope to reduce formal health care cost by promoting informal family health care. With the use of Korean data for the elderly, this paper estimates the effects of informal family health care on formal health care, where the former is measured by the number of caregivers and the latter is measured by the formal health care expenditure. This task, however, poses a number of difficulties. The first is that the number of the family caregivers is an endogenous count regressor. The second is that there are too many zeros in the count (85%). The third is that the response variable also has a nontrivial proportion of zeros (14%). This paper overcomes these problems by combining 'control function approach', 'zero-inflated' counts, and a semiparametric estimator for censored models. The resulting procedure avoids strong parametric assumptions and behaves well computationally. Our main empirical finding is that informal family health care has a large substitute effect for diabetics and that there are also weak evidences that informal family health care has substitute effects for high blood pressure and mental diseases.

  1. Norepinephrine metabolism in humans. Kinetic analysis and model

    SciTech Connect

    Linares, O.A.; Jacquez, J.A.; Zech, L.A.; Smith, M.J.; Sanfield, J.A.; Morrow, L.A.; Rosen, S.G.; Halter, J.B.

    1987-11-01

    The present study was undertaken to quantify more precisely and to begin to address the problem of heterogeneity of the kinetics of distribution and metabolism of norepinephrine (NE) in humans, by using compartmental analysis. Steady-state NE specific activity in arterialized plasma during (/sup 3/H)NE infusion and postinfusion plasma disappearance of (/sup 3/H)NE were measured in eight healthy subjects in the supine and upright positions. Two exponentials were clearly identified in the plasma (/sup 3/H)NE disappearance curves of each subject studied in the supine (r = 0.94-1.00, all P less than 0.01) and upright (r = 0.90-0.98, all P less than 0.01) positions. A two-compartment model was the minimal model necessary to simultaneously describe the kinetics of NE in the supine and upright positions. The NE input rate into the extravascular compartment 2, estimated with the minimal model, increased with upright posture (1.87 +/- 0.08 vs. 3.25 +/- 0.2 micrograms/min per m2, P less than 0.001). Upright posture was associated with a fall in the volume of distribution of NE in compartment 1 (7.5 +/- 0.6 vs. 4.7 +/- 0.3 liters, P less than 0.001), and as a result of that, there was a fall in the metabolic clearance rate of NE from compartment 1 (1.80 +/- 0.11 vs. 1.21 +/- 0.08 liters/min per m2, P less than 0.001). We conclude that a two-compartment model is the minimal model that can accurately describe the kinetics of distribution and metabolism of NE in humans.

  2. A Detailed Level Kinetics Model of NO Vibrational Energy Distributions

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

    Several contemporary problems have pointed to the desirability of a detailed level kinetics approach to modeling the distribution of vibrational energy in NO. Such a model is necessary when vibrational redistribution reactions are insufficient to maintain a Boltzmann distribution over the vibrational energy states. Recent calculations of the rate constant for the first reaction of the Zeldovich mechanism (N2 + O (goes to) NO + N) have suggested that the product NO is formed in high vibrational states. In shock layer flowfields, the product NO molecules may experience an insufficient number of collisions to establish a Boltzmann distribution over vibrational states, thus necessitating a level kinetics model. In other flows, such as expansions of high temperature air, fast, near-resonance vibrational energy exchanges with N2 and O2 may also require a level specific model for NO because of the relative rates of vibrational exchange and redistribution. The proposed report will integrate computational and experimental components to construct such a model for the NO molecule.

  3. 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.

  4. 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.

  5. Kinetic equations modelling wealth redistribution: a comparison of approaches.

    PubMed

    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.

  6. 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

  7. 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

  8. Kinetic model for astaxanthin aggregation in water-methanol mixtures

    NASA Astrophysics Data System (ADS)

    Giovannetti, Rita; Alibabaei, Leila; Pucciarelli, Filippo

    2009-07-01

    The aggregation of astaxanthin in hydrated methanol was kinetically studied in the temperature range from 10 °C to 50 °C, at different astaxanthin concentrations and solvent composition. A kinetic model for the formation and transformation of astaxanthin aggregated has been proposed. Spectrophotometric studies showed that monomeric astaxanthin decayed to H-aggregates that after-wards formed J-aggregates when water content was 50% and the temperature lower than 20 °C; at higher temperatures, very stable J-aggregates were formed directly. Monomer formed very stable H-aggregates when the water content was greater than 60%; in these conditions H-aggregates decayed into J-aggregates only when the temperature was at least 50 °C. Through these findings it was possible to establish that the aggregation reactions took place through a two steps consecutive reaction with first order kinetic constants and that the values of these depended on the solvent composition and temperature.

  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. A cardiac muscle model relating sarcomere dynamics to calcium kinetics.

    PubMed

    Negroni, J A; Lascano, E C

    1996-05-01

    A muscle model establishing the link between cross-bridge dynamics and intracellular Ca2+ kinetics was assessed by simulation of experiments performed in isolated cardiac muscle. The model is composed by the series arrangement of muscle units formed by inextensible thick and thin filaments in parallel with an elastic element. Attached cross-bridges act as independent force generators whose force is linearly related to the elongation of their elastic structure. Ca2+ kinetics is described by a four-state system of sites on the thin filament associated with troponin C: sites with free troponin C (T), sites with Ca2+ bound to troponin C (TCa); sites with Ca2+ bound to troponin C and attached cross-bridges (TCa*); and sites with troponin C not associated with Ca2+ and attached cross-bridges (T*). The intracellular Ca2+ concentration ([Ca2+]) is controlled solely by the sarcoplasmic reticulum through an inflow function and a saturated outflow pump function. All the simulations were performed using the same set of parameters. The model was able to reproduce the following experiments in cardiac muscle: (a) time course of isometric force (peak force: 46.5 mN/mm2), intracellular [Ca2+] (peak [Ca2+]: 1.5 microM); (b) force-length-[Ca2+] relations; (c) transient response of force to step changes in length; (d) force-velocity relation (maximum velocity: 3 microns/s); (e) the force response to length pulses to estimate the time course of [TCa]; (f) force response to quick releases showing the superactivating and deactivating effects of shortening; (g) stiffness response to sinusoidal length changes; and (h) time course of active state. The good accordance of the simulations with experimental results indicates that the model is an adequate representation of the link between cross-bridge dynamic behaviour and Ca2+ kinetics.

  11. 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.

  12. Economic inequality and mobility in kinetic models for social sciences

    NASA Astrophysics Data System (ADS)

    Letizia Bertotti, Maria; Modanese, Giovanni

    2016-10-01

    Statistical evaluations of the economic mobility of a society are more difficult than measurements of the income distribution, because they require to follow the evolution of the individuals' income for at least one or two generations. In micro-to-macro theoretical models of economic exchanges based on kinetic equations, the income distribution depends only on the asymptotic equilibrium solutions, while mobility estimates also involve the detailed structure of the transition probabilities of the model, and are thus an important tool for assessing its validity. Empirical data show a remarkably general negative correlation between economic inequality and mobility, whose explanation is still unclear. It is therefore particularly interesting to study this correlation in analytical models. In previous work we investigated the behavior of the Gini inequality index in kinetic models in dependence on several parameters which define the binary interactions and the taxation and redistribution processes: saving propensity, taxation rates gap, tax evasion rate, welfare means-testing etc. Here, we check the correlation of mobility with inequality by analyzing the mobility dependence from the same parameters. According to several numerical solutions, the correlation is confirmed to be negative.

  13. Kinetic models for the VASIMR thruster helicon plasma source

    NASA Astrophysics Data System (ADS)

    Batishchev, Oleg; Molvig, Kim

    2001-10-01

    Helicon gas discharge [1] is widely used by industry because of its remarkable efficiency [2]. High energy and fuel efficiencies make it very attractive for space electrical propulsion applications. For example, helicon plasma source is used in the high specific impulse VASIMR [3] plasma thruster, including experimental prototypes VX-3 and upgraded VX-10 [4] configurations, which operate with hydrogen (deuterium) and helium plasmas. We have developed a set of models for the VASIMR helicon discharge. Firstly, we use zero-dimensional energy and mass balance equations to characterize partially ionized gas condition/composition. Next, we couple it to one-dimensional hybrid model [6] for gas flow in the quartz tube of the helicon. We compare hybrid model results to a purely kinetic simulation of propellant flow in gas feed + helicon source subsystem. Some of the experimental data [3-4] are explained. Lastly, we discuss full-scale kinetic modeling of coupled gas and plasmas [5-6] in the helicon discharge. [1] M.A.Lieberman, A.J.Lihtenberg, 'Principles of ..', Wiley, 1994; [2] F.F.Chen, Plas. Phys. Contr. Fus. 33, 339, 1991; [3] F.Chang-Diaz et al, Bull. APS 45 (7) 129, 2000; [4] J.Squire et al., Bull. APS 45 (7) 130, 2000; [5] O.Batishchev et al, J. Plasma Phys. 61, part II, 347, 1999; [6] O.Batishchev, K.Molvig, AIAA technical paper 2000-3754, -14p, 2001.

  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. Kinetic modelling of cytochrome c adsorption on SBA-15.

    PubMed

    Yokogawa, Yoshiyuki; Yamauchi, Rie; Saito, Akira; Yamato, Yuta; Toma, Takeshi

    2017-01-01

    The adsorption capacity of mesoporous silicate (MPS) materials as an adsorbent for protein adsorption from the aqueous phase and the mechanism of the adsorption processes by comparative analyses of the applicability of five kinetic transfer models, pseudo-first-order model, pseudo-second-order model, Elovich kinetic model, Bangham's equation model, and intraparticle diffusion model, were investigated. A mixture of tetraethyl orthosilicate (TEOS) and triblock copolymer as a template was stirred, hydrothermally treated to form the mesoporous SBA-15 structure, and heat-treated at 550°C to form the MPS material, SBA-15. The synthesized SBA-15 was immersed in a phosphate buffered saline (PBS) solution containing cytochrome c for 2, 48, and 120 hours at 4°C. The TEM observations of proteins on/in mesoporous SBA-15 revealed the protein behaviors. The holes of the MPS materials were observed to overlap those of the stained proteins for the first 2 hours of immersion. The stained proteins were observed between primary particles and partly inside the mesoporous channels in the MPS material when it had been immersed for 48 hours. For MPS when it had been immersed for 120 hours, stained proteins were observed in almost all meso-scale channels of MPS. The time profiles for adsorption of proteins can be described well by Bangham's equation model and the intraparticle diffusion model. The Bangham's equation model is based on the assumption that pore diffusion was the only rate controlling step during adsorption, whose contribution to the overall mechanism of cytochrome c adsorption on SBA-15 should not be neglected. The kinetic curves obtained from the experiment for cytochrome c adsorption on SBA-15 could show the three steps: the initial rapid increase of the adsorbed amount of cytochrome c, the second gradual increase, and the final equilibrium stage. These three adsorption steps can be interpreted well by the multi-linearity of the intraparticle diffusion model

  16. Adequacy indices for dialysis in acute renal failure: kinetic modeling.

    PubMed

    Debowska, Malgorzata; Lindholm, Bengt; Waniewski, Jacek

    2010-05-01

    Many aspects of the management of renal replacement therapy in acute renal failure (ARF), including the appropriate assessment of dialysis adequacy, remain unresolved, because ARF patients often are not in a metabolic steady state. The aim of this study was to evaluate a system of adequacy indices for dialysis in ARF patients using urea and creatinine kinetic modeling. Kinetic modeling was performed for two different fictitious patients (A and B) with characteristics described by the average parameters for two patient groups and for two blood purification treatments: sustained low efficiency daily dialysis (SLEDD) in Patient A and continuous venovenous hemofiltration (CVVH) in Patient B, based on data from a clinical report. Urea and creatinine generation rates were estimated according to the clinical data on the solute concentrations in blood. Then, using estimated generation rates, two hypothetical treatments were simulated, CVVH in Patient A and SLEDD in Patient B. KT/V, fractional solute removal (FSR) and equivalent renal clearance (EKR) were calculated according to the definitions developed for metabolically unstable patients. CVVH appeared as being more effective than SLEDD because KT/V, FSR, and EKR were higher for CVVH than SLEDD in Patients A and B. Creatinine KT/V, FSR, and EKR were lower and well correlated to the respective indices for urea. Urea and creatinine generation rates were overestimated more than twice in Patient A and by 30-40% in Patient B if calculated assuming the metabolically stable state than if estimated by kinetic modeling. Adequacy indices and solute generation rates for ARF patients should be estimated using the definition for unsteady metabolic state. EKR and FSR were higher for urea and creatinine with CVVH than with SLEDD, because of higher K.T and minimized compartmental effects for CVVH.

  17. 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.

  18. Integrating kinetic effects in fluid models for magnetic reconnection

    NASA Astrophysics Data System (ADS)

    Wang, L.; Hakim, A.; Bhattacharjee, A.; Germaschewski, K.

    2014-12-01

    The integration of kinetic effects in global fluid models is a grand challenge in space plasma physics, and has implication for our ability to model space weather in collisionless plasma environments such as the Earth's magnetosphere. We propose an extensible multi-fluid moment model, with focus on the physics of magnetic reconnection. This model evolves the full Maxwell equations, and simultaneously moments of the Vlasov-Maxwell equation for each species in the plasma. Effects like the Hall effect, the electron inertia, and the pressure gradient are self-consistently embedded in the resulting multi-fluid moment equations, without the need to explicitly solving a generalized Ohm's law. Two limits of the multi-fluid moment model are discussed, namely, the five-moment limit that evolves a scalar pressure for each species, and the ten-moment limit that evolves the full anisotropic, non-gyrotropic pressure tensor. Particularly, the five-moment model reduces to the widely used Hall Magnetohydrodynamics (Hall MHD) model under the assumptions of vanishing electron inertia, infinite speed of light, and quasi-neutrality. In this presentation, we first compare ten-moment and fully kinetic Particle-In-Cell (PIC) simulations of a large scale Harris sheet reconnection problem, where the ten-moment equations are closed with a local linear collisionless approximation for the heat flux. The ten-moment simulation gives reasonable agreement with the PIC results, regarding the structures and magnitudes of the electron flows, the polarities and magnitudes of elements of the electron pressure tensor, and the decomposition of the generalized Ohm's law. Preliminary results of application of the multi-fluid moment model to Ganymede are also discussed.

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

    SciTech Connect

    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.

  20. Large Scale Simulations of the Kinetic Ising Model

    NASA Astrophysics Data System (ADS)

    Münkel, Christian

    We present Monte Carlo simulation results for the dynamical critical exponent z of the two- and three-dimensional kinetic Ising model. The z-values were calculated from the magnetization relaxation from an ordered state into the equilibrium state at Tc for very large systems with up to (169984)2 and (3072)3 spins. To our knowledge, these are the largest Ising-systems simulated todate. We also report the successful simulation of very large lattices on a massively parallel MIMD computer with high speedups of approximately 1000 and an efficiency of about 0.93.

  1. Kinetic modeling of 3D equilibria in a tokamak

    NASA Astrophysics Data System (ADS)

    Albert, C. G.; Heyn, M. F.; Kasilov, S. V.; Kernbichler, W.; Martitsch, A. F.; Runov, A. M.

    2016-11-01

    External resonant magnetic perturbations (RMPs) can modify the magnetic topology in a tokamak. In this case the magnetic field cannot generally be described by ideal MHD equilibrium equations in the vicinity of resonant magnetic surfaces where parallel and perpendicular relaxation timescales are comparable. Usually, resistive MHD models are used to describe these regions. In the present work, a kinetic model is used for this purpose. Within this model, plasma response, current and charge density are computed with help of a Monte Carlo method, where guiding center orbit equations are solved using a semianalytical geometrical integrator. Besides its higher efficiency in comparison to usual integrators this method is not sensitive to noise in field quantities. The computed charges and currents are used to calculate the electromagnetic field with help of a finite element solver. A preconditioned iterative scheme is applied to search for a self-consistent solution. The discussed method is aimed at the nonlinear kinetic description of RMPs in experiments on Edge Localized Mode (ELM) mitigation by external perturbation coil systems without simplification of the device geometry.

  2. 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/.

  3. Probabilistic multicompartmental model for interpreting DGT kinetics in sediments.

    PubMed

    Ciffroy, P; Nia, Y; Garnier, J M

    2011-11-15

    Extensive research has been performed on the use of the DIFS (DGT-Induced Fluxes in Soils and Sediments) model to interpret diffusive gradients in thin-film, or DGT, measurements in soils and sediments. The current report identifies some areas where the DIFS model has been shown to yield poor results and proposes a model to address weaknesses. In particular, two major flaws in the current approaches are considered: (i) many studies of accumulation kinetics in DGT exhibit multiple kinetic stages and (ii) several combinations of the two fitted DIFS parameters can yield identical results, leaving the question of how to select the 'best' combination. Previously, problem (i) has been addressed by separating the experimental data sets into distinct time segments. To overcome these problems, a model considering two types of particulate binding sites is proposed, instead of the DIFS model which assumed one single particulate pool. A probabilistic approach is proposed to fit experimental data and to determine the range of possible physical parameters using Probability Distribution Functions (PDFs), as opposed to single values without any indication of their uncertainty. The new probabilistic model, called DGT-PROFS, was tested on three different formulated sediments which mainly differ in the presence or absence of iron oxides. It was shown that a good fit can be obtained for the complete set of data (instead of DIFS-2D) and that a range of uncertainty values for each modeling parameter can be obtained. The interpretation of parameter PDFs allows one to distinguish between a variety of geochemical behaviors, providing useful information on metal dynamics in sediments.

  4. Integrating kinetic effects in fluid models for magnetic reconnection

    NASA Astrophysics Data System (ADS)

    Wang, Liang

    The integration of kinetic effects in global fluid models is a grand challenge in space plasma physics, and has implication for our ability to model space weather in collisionless plasma environments such as the Earth's magnetosphere. We propose an extensible multi-fluid moment model, with focus on the physics of magnetic reconnection. This model evolves the full Maxwell equations, and simultaneously moments of the Vlasov-Maxwell equation for each species in the plasma. Effects like the Hall effect, the electron inertia, and the pressure gradient are self-consistently embedded in the resulting multi-fluid moment equations, without the need to explicitly solving a generalized Ohm's law. Two limits of the multi-fluid moment model are discussed, namely, the five-moment limit that evolves a scalar pressures for each species, and the ten-moment limit that evolves the full anisotropic, non-gyrotropic pressure tensor. Particularly, the five-moment model reduces to the widely used Hall Magnetohydrodynamics (Hall MHD) model under the assumptions of vanishing electron inertia, infinite speed of light, and quasi-neutrality. In this thesis, we first numerically confirm the reduction of five-moment to Hall MHD under the limit of vanishing electron inertia. Then, we compare ten-moment and fully kinetic Particle-In-Cell (PIC) simulations of a large scale Harris sheet reconnection problem, where the ten-moment equations are closed with a local linear collisionless approximation for the heat flux. The ten-moment simulation gives reasonable agreement with the PIC results, regarding the structures and magnitudes of the electron flows, the polarities and magnitudes of elements of the electron pressure tensor, and the decomposition of the generalized Ohm's law. Possible ways to improve the simple closure towards a non-local, fully three-dimensional description are also discussed.

  5. Kinetic models of sub-ion cylindrical magnetic hole

    NASA Astrophysics Data System (ADS)

    Shustov, P. I.; Artemyev, A. V.; Vasko, I. Y.; Yushkov, E. V.

    2016-12-01

    Magnetic holes are magnetoplasma structures very similar to the classical θ-pinch. They are widely observed in the space plasma and identified by the substantial magnetic field depressions on scales from magnetohydrodynamic range to electron scales. In this paper, we develop the kinetic models of cylindrically symmetric magnetic holes with sub-ion scales using two types of charged particle distribution functions (both current-carrying and background plasma populations are included). We demonstrate that developed magnetic holes have configurations very similar to those revealed in the recent spacecraft observations in the Earth magnetosphere: both localized electron currents and strong radial electric fields are found at the magnetic hole boundary. We demonstrate that for realistic plasma parameters, the inclusion of ion currents into the model produces magnetic holes with double-scale magnetic field profile. We find that the magnetic hole depth (amplitude of the magnetic field depression) depends on the magnetic hole typical radius. Possible applications of developed models are discussed.

  6. 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.

  7. Kinetic modeling of the adsorption of basic dyes by kudzu.

    PubMed

    Allen, Stephen J; Gan, Quan; Matthews, Ronan; Johnson, Pauline A

    2005-06-01

    The use of kudzu, a rapidly growing, high-climbing perennial leguminous vine, for the adsorption of basic dyes from aqueous solution has been investigated at various initial dye concentrations, masses of kudzu, and agitation rates. The extent and rate of adsorption of the three basic dyes (Basic Red 22, Basic Yellow 21, and Basic Blue 3) were analyzed using a pseudo-first-order and a pseudo-second-order kinetic model. While both rate mechanisms provided an acceptable degree of correlation with the experimental sorption rate data, the pseudo-second-order model gave a much higher degree of correlation, suggesting that this model could be used in design and simulation applications.

  8. 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…

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

    PubMed

    Duchemin, Ivan; Jacquemin, Denis; Blase, Xavier

    2016-04-28

    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.

  10. 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.

  11. 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

  12. 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.

  13. Modeling the kinetics of carbon coagulation in explosives detonation

    NASA Astrophysics Data System (ADS)

    Ree, F. H.; Viecelli, J. A.; Glosli, J. N.

    1998-05-01

    A typical insensitive high explosive such as LX-17 has a large carbon content. The detonation behavior of these explosives is affected by a slow coagulation of carbon atoms by diffusion and their possible transformation from one chemical bonding type to another. We have used the Brenner bond order potential to compute the melting line of diamond at high pressure and high temperature by molecular dynamics and Monte Carlo simulations, with the goal to refine the potential for the study of the kinetics of the graphite diamond transition. The slow diffusion-controlled kinetics of carbon clusters has been examined by including a time-dependent surface correction to the Gibbs free energy of these clusters in the nonequilibrium CHEQ code. We also propose a new explosive burn model which incorporates a partial release of the heat of detonation in a fast reaction zone, followed by a diffusion-limited release of the remaining energy. Hydrodynamic applications of the new burn model to LX-17 show that computed expansion and compression results both agree closely with experimental data.

  14. Kinetic model of mass exchange with dynamic Arrhenius transition rates

    NASA Astrophysics Data System (ADS)

    Hristopulos, Dionissios T.; Muradova, Aliki

    2016-02-01

    We study a nonlinear kinetic model of mass exchange between interacting grains. The transition rates follow the Arrhenius equation with an activation energy that depends dynamically on the grain mass. We show that the activation parameter can be absorbed in the initial conditions for the grain masses, and that the total mass is conserved. We obtain numerical solutions of the coupled, nonlinear, ordinary differential equations of mass exchange for the two-grain system, and we compare them with approximate theoretical solutions in specific neighborhoods of the phase space. Using phase plane methods, we determine that the system exhibits regimes of diffusive and growth-decay (reverse diffusion) kinetics. The equilibrium states are determined by the mass equipartition and separation nullcline curves. If the transfer rates are perturbed by white noise, numerical simulations show that the system maintains the diffusive and growth-decay regimes; however, the noise can reverse the sign of equilibrium mass difference. Finally, we present theoretical analysis and numerical simulations of a system with many interacting grains. Diffusive and growth-decay regimes are established as well, but the approach to equilibrium is considerably slower. Potential applications of the mass exchange model involve coarse-graining during sintering and wealth exchange in econophysics.

  15. Multiple-relaxation-time lattice Boltzmann kinetic model for combustion

    NASA Astrophysics Data System (ADS)

    Xu, Aiguo; Lin, Chuandong; Zhang, Guangcai; Li, Yingjun

    2015-04-01

    To probe both the hydrodynamic nonequilibrium (HNE) and thermodynamic nonequilibrium (TNE) in the combustion process, a two-dimensional multiple-relaxation-time (MRT) version of lattice Boltzmann kinetic model (LBKM) for combustion phenomena is presented. The chemical energy released in the progress of combustion is dynamically coupled into the system by adding a chemical term to the LB kinetic equation. Aside from describing the evolutions of the conserved quantities, the density, momentum, and energy, which are what the Navier-Stokes model describes, the MRT-LBKM presents also a coarse-grained description on the evolutions of some nonconserved quantities. The current model works for both subsonic and supersonic flows with or without chemical reaction. In this model, both the specific-heat ratio and the Prandtl number are flexible, the TNE effects are naturally presented in each simulation step. The model is verified and validated via well-known benchmark tests. As an initial application, various nonequilibrium behaviors, including the complex interplays between various HNEs, between various TNEs, and between the HNE and TNE, around the detonation wave in the unsteady and steady one-dimensional detonation processes are preliminarily probed. It is found that the system viscosity (or heat conductivity) decreases the local TNE, but increases the global TNE around the detonation wave, that even locally, the system viscosity (or heat conductivity) results in two kinds of competing trends, to increase and to decrease the TNE effects. The physical reason is that the viscosity (or heat conductivity) takes part in both the thermodynamic and hydrodynamic responses.

  16. Multiple-relaxation-time lattice Boltzmann kinetic model for combustion.

    PubMed

    Xu, Aiguo; Lin, Chuandong; Zhang, Guangcai; Li, Yingjun

    2015-04-01

    To probe both the hydrodynamic nonequilibrium (HNE) and thermodynamic nonequilibrium (TNE) in the combustion process, a two-dimensional multiple-relaxation-time (MRT) version of lattice Boltzmann kinetic model (LBKM) for combustion phenomena is presented. The chemical energy released in the progress of combustion is dynamically coupled into the system by adding a chemical term to the LB kinetic equation. Aside from describing the evolutions of the conserved quantities, the density, momentum, and energy, which are what the Navier-Stokes model describes, the MRT-LBKM presents also a coarse-grained description on the evolutions of some nonconserved quantities. The current model works for both subsonic and supersonic flows with or without chemical reaction. In this model, both the specific-heat ratio and the Prandtl number are flexible, the TNE effects are naturally presented in each simulation step. The model is verified and validated via well-known benchmark tests. As an initial application, various nonequilibrium behaviors, including the complex interplays between various HNEs, between various TNEs, and between the HNE and TNE, around the detonation wave in the unsteady and steady one-dimensional detonation processes are preliminarily probed. It is found that the system viscosity (or heat conductivity) decreases the local TNE, but increases the global TNE around the detonation wave, that even locally, the system viscosity (or heat conductivity) results in two kinds of competing trends, to increase and to decrease the TNE effects. The physical reason is that the viscosity (or heat conductivity) takes part in both the thermodynamic and hydrodynamic responses.

  17. Modeling aerosol surface chemistry and gas-particle interaction kinetics with K2-SURF: PAH oxidation

    NASA Astrophysics Data System (ADS)

    Shiraiwa, M.; Garland, R.; Pöschl, U.

    2009-04-01

    Atmospheric aerosols are ubiquitous in the atmosphere. They have the ability to impact cloud properties, radiative balance and provide surfaces for heterogeneous reactions. The uptake of gaseous species on aerosol surfaces impacts both the aerosol particles and the atmospheric budget of trace gases. These subsequent changes to the aerosol can in turn impact the aerosol chemical and physical properties. However, this uptake, as well as the impact on the aerosol, is not fully understood. This uncertainty is due not only to limited measurement data, but also a dearth of comprehensive and applicable modeling formalizations used for the analysis, interpretation and description of these heterogeneous processes. Without a common model framework, comparing and extrapolating experimental data is difficult. In this study, a novel kinetic surface model (K2-SURF) [Ammann & Pöschl, 2007; Pöschl et al., 2007] was used to describe the oxidation of a variety of polycyclic aromatic hydrocarbons (PAHs). Integrated into this consistent and universally applicable kinetic and thermodynamic process model are the concepts, terminologies and mathematical formalizations essential to the description of atmospherically relevant physicochemical processes involving organic and mixed organic-inorganic aerosols. Within this process model framework, a detailed master mechanism, simplified mechanism and parameterizations of atmospheric aerosol chemistry are being developed and integrated in analogy to existing mechanisms and parameterizations of atmospheric gas-phase chemistry. One of the key aspects to this model is the defining of a clear distinction between various layers of the particle and surrounding gas phase. The processes occurring at each layer can be fully described using known fluxes and kinetic parameters. Using this system there is a clear separation of gas phase, gas-surface and surface bulk transport and reactions. The partitioning of compounds can be calculated using the flux

  18. 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.

  19. Kinetic model of acetate metabolism in healthy and hyperinsulinaemic humans

    PubMed Central

    Fernandes, Judlyn; Vogt, Janet; Wolever, Thomas MS

    2014-01-01

    Background/objectives The short chain fatty acid acetate (AC), may play a role in increasing insulin sensitivity, thus lowering risk for obesity and type 2 diabetes mellitus. It is unclear if AC kinetics is similar in normal and hyperinsulinaemic participants. Therefore, we studied AC absorption from the distal colon in participants with normal (<40 pmol/L, NI) and high (≥40 pmol/L, HI) plasma-insulin. This work was part of a series of studies conceived to compute a kinetic model for acetate. Kinetic parameters such as estimates of rate of entry into peripheral blood, hepatic uptake and endogenous/exogenous production were compared in the groups. Subjects/methods Overnight fasted NI (n = 9) and HI (n = 8) participants were given rectal infusions containing sodium acetate (90 mmol/L). The solutions were retained for 40 min, then voided for AC measurement. Total amount of AC infused was 27 mmols. Results Acetate absorption from the distal colon (279±103 vs 322±91 μmol/min, P = 0.76) and hepatic uptake of AC (155±101 vs 146±85 μmol/min, P = 0.94) were similar in the groups. Endogenous and exogenous AC production was significantly higher in NI than HI participants. Plasma AC was inversely proportional to plasma insulin concentrations in the entire cohort (y=k/x, where k = 1813). Conclusions There was low power to detect differences in AC absorption rate and hepatic AC uptake in NI vs HI. The rate of entry of AC into peripheral blood was similar in NI and HI participants. However, hyperinsulinaemia may alter endogenous and exogenous AC metabolism. PMID:25052228

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. The cleft ion fountain - A two-dimensional kinetic model

    NASA Technical Reports Server (NTRS)

    Horwitz, J. L.; Lockwood, M.

    1985-01-01

    The transport of ionospheric ions from a source in the polar cleft ionosphere through the polar magnetosphere is investigated using a two-dimensional, kinetic, trajectory-based code. The transport model includes the effects of gravitation, longitudinal magnetic gradient force, convection electric fields, and parallel electric fields. Individual ion trajectories as well as distribution functions and resulting bulk parameters of density, parallel average energy, and parallel flux for a presumed cleft ionosphere source distribution are presented for various conditions to illustrate parametrically the dependences on source energies, convection electric field strengths, ion masses, and parallel electric field strengths. The essential features of the model are consistent with the concept of a cleft-based ion fountain supplying ionospheric ions to the polar magnetosphere, and the resulting plasma distributions and parameters are in general agreement with recent low-energy ion measurements from the DE 1 satellite.

  5. 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.

  6. Modeling of chemical inhibition from amyloid protein aggregation kinetics

    PubMed Central

    2014-01-01

    Backgrounds The process of amyloid proteins aggregation causes several human neuropathologies. In some cases, e.g. fibrillar deposits of insulin, the problems are generated in the processes of production and purification of protein and in the pump devices or injectable preparations for diabetics. Experimental kinetics and adequate modelling of chemical inhibition from amyloid aggregation are of practical importance in order to study the viable processing, formulation and storage as well as to predict and optimize the best conditions to reduce the effect of protein nucleation. Results In this manuscript, experimental data of insulin, Aβ42 amyloid protein and apomyoglobin fibrillation from recent bibliography were selected to evaluate the capability of a bivariate sigmoid equation to model them. The mathematical functions (logistic combined with Weibull equation) were used in reparameterized form and the effect of inhibitor concentrations on kinetic parameters from logistic equation were perfectly defined and explained. The surfaces of data were accurately described by proposed model and the presented analysis characterized the inhibitory influence on the protein aggregation by several chemicals. Discrimination between true and apparent inhibitors was also confirmed by the bivariate equation. EGCG for insulin (working at pH = 7.4/T = 37°C) and taiwaniaflavone for Aβ42 were the compounds studied that shown the greatest inhibition capacity. Conclusions An accurate, simple and effective model to investigate the inhibition of chemicals on amyloid protein aggregation has been developed. The equation could be useful for the clear quantification of inhibitor potential of chemicals and rigorous comparison among them. PMID:24572069

  7. 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.

  8. 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 .

  9. 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.

  10. Assessment of two-temperature kinetic model for ionizing air

    NASA Technical Reports Server (NTRS)

    Park, Chul

    1987-01-01

    A two-temperature chemical-kinetic model for air is assessed by comparing theoretical results with existing experimental data obtained in shock-tubes, ballistic ranges, and flight experiments. In the model, named the TTv model, one temperature (T) is assumed to characterize the heavy-particle translational and molecular rotational energies, and another temperature (Tv) to characterize the molecular vibrational, electron translational, and electronic excitation energies. The theoretical results for nonequilibrium air flow in shock tubes are obtained using the computer code STRAP (Shock-Tube Radiation Program), and for flow along the stagnation streamline in the shock layer over spherical bodies using the newly developed code STRAP (Stagnation-Point Radiation Program). Substantial agreement is shown between the theoretical and experimental results for relaxation times and radiative heat fluxes. At very high temperatures the spectral calculations need further improvement. The present agreement provides strong evidence that the two-temperature model characterizes principal features of nonequilibrium air flow. New theoretical results using the model are presented for the radiative heat fluxes at the stagnation point of a 6-m-radius sphere, representing an aeroassisted orbital transfer vehicle, over a range of free-stream conditions. Assumptions, approximations, and limitations of the model are discussed.

  11. How informative is your kinetic model?: using resampling methods for model invalidation

    PubMed Central

    2014-01-01

    Background Kinetic models can present mechanistic descriptions of molecular processes within a cell. They can be used to predict the dynamics of metabolite production, signal transduction or transcription of genes. Although there has been tremendous effort in constructing kinetic models for different biological systems, not much effort has been put into their validation. In this study, we introduce the concept of resampling methods for the analysis of kinetic models and present a statistical model invalidation approach. Results We based our invalidation approach on the evaluation of a kinetic model’s predictive power through cross validation and forecast analysis. As a reference point for this evaluation, we used the predictive power of an unsupervised data analysis method which does not make use of any biochemical knowledge, namely Smooth Principal Components Analysis (SPCA) on the same test sets. Through a simulations study, we showed that too simple mechanistic descriptions can be invalidated by using our SPCA-based comparative approach until high amount of noise exists in the experimental data. We also applied our approach on an eicosanoid production model developed for human and concluded that the model could not be invalidated using the available data despite its simplicity in the formulation of the reaction kinetics. Furthermore, we analysed the high osmolarity glycerol (HOG) pathway in yeast to question the validity of an existing model as another realistic demonstration of our method. Conclusions With this study, we have successfully presented the potential of two resampling methods, cross validation and forecast analysis in the analysis of kinetic models’ validity. Our approach is easy to grasp and to implement, applicable to any ordinary differential equation (ODE) type biological model and does not suffer from any computational difficulties which seems to be a common problem for approaches that have been proposed for similar purposes. Matlab files

  12. 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…

  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 sodium in the exosphere of Mercury

    NASA Astrophysics Data System (ADS)

    Tenishev, V.; Rubin, M.; Combi, M. R.; Slavin, J. A.; Raines, J. M.

    2012-12-01

    Discovered more that 20 years ago Mercury's sodium exosphere is characterized by rapid variations determined by planet's orbital motion and rotation. Because collisions are rare, the sodium atom velocity distribution is determined by a unique combination of radiation pressure, source and loss processes, and the interaction with the surface. Neutral sodium atoms injected into the exosphere can be photo-ionized by solar radiation. These ions have been recently observed by FIPS instrument onboard of MESSENGER, and can help in a better understanding of the nature of the source processes as well as the structure of the neutral exosphere itself. A detailed theoretical study of the sodium distribution in the exosphere requires numerical modeling. Having kinetic theory as a physical basis, our exospheric Monte Carlo model preserves the kinetic nature of these exospheric processes. The distinctive features of the model include accounting for the planet's rotation and motion along its orbit, the realistic distribution of the sources, an accurate calculation of the g-factor, and simulation of the photolytic reactions in the exosphere and tail. Here we describe the results of our numerical study of the neutral sodium environment around Mercury. The primary goal of this work was to combine, in a self-consistent manner, models of different surface processes, the planet's orbital motion and rotation, and time-dependent dynamics of sodium atoms in the exosphere. Using ground based and in situ observations obtained at different times to constrain our model allows us to get a more comprehensive picture of Mercury's exosphere including the source and loss rates of sodium. We discuss relative importance of the source processes in the sodium exosphere, the effect of solar radiation pressure on the structure of the tail, and the effect of the surface sticking as well as of the planetary rotation and orbital motion on the sodium surface abundance. Presented simulations cover a domain

  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. A Kinetic Model for the Ruhrstahl Heraeus (RH) Degassing Process

    NASA Astrophysics Data System (ADS)

    van Ende, Marie-Aline; Kim, Young-Min; Cho, Mun-Kyu; Choi, Juhan; Jung, In-Ho

    2011-06-01

    A kinetic model (effective equilibrium reaction zone model) was developed to simulate the decarburization reaction in the Ruhrstahl Heraeus (RH) degassing process. The model assumes that the chemical reactions reach equilibrium in the designated effective reaction volumes near the reaction interfaces. After the RH degassing process was divided into various reaction zones, the effective reaction volumes of each reaction zone were expressed as a function of the process conditions based on the physical descriptions of the reaction mechanisms. The influence of the chemical reaction between the RH slag and the RH steel to the decarburization phenomena was considered for the first time. The calculated C and O profiles by the present model are in good agreement with the industrial operation data for various steel compositions and process conditions. RH slag can serve as an oxygen reservoir to supply O during the RH decarburization process, which induces the observed deviation of the C and O contents from their ideal stoichiometric trajectory. The present model provides an efficient tool to understand the RH degassing process.

  17. 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.

  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. Molecular modeling of mechanical stresses on proteins in glassy matrices: Formalism

    NASA Astrophysics Data System (ADS)

    Hatch, Harold W.; Debenedetti, Pablo G.

    2012-07-01

    We present an expression for the calculation of microscopic stresses in molecular simulation, which is compatible with the use of electrostatic lattice sums such as the Ewald sum, with the presence of many-body interactions, and which allows local stresses to be calculated on surfaces of arbitrarily complex shape. The ultimate goal of this work is to investigate microscopic stresses on proteins in glassy matrices, which are used in the pharmaceutical industry for the long-term storage and stabilization of labile biomolecules. We demonstrate the formalism's usefulness through selected results on ubiquitin and an α-keratin fragment, in liquid and glassy states. We find that atomic-level normal stresses on hydrophilic side-chains exhibit a similar fingerprint in both proteins, and protein-level normal stresses increase upon vitrification. Both proteins experience compressive stresses of the order of 102 bar in the glassy state.

  20. 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.

  1. Estimation of homogeneous nucleation flux via a kinetic model

    NASA Technical Reports Server (NTRS)

    Wilcox, C. F.; Bauer, S. H.

    1991-01-01

    The proposed kinetic model for condensation under homogeneous conditions, and the onset of unidirectional cluster growth in supersaturated gases, does not suffer from the conceptual flaws that characterize classical nucleation theory. When a full set of simultaneous rate equation is solved, a characteristic time emerges, for each cluster size, at which the production rate, and its rate of conversion to the next size (n + 1) are equal. Procedures for estimating the essential parameters are proposed; condensation fluxes J(kin) exp ss are evaluated. Since there are practical limits to the cluster size that can be incorporated in the set of simultaneous first-order differential equations, a code was developed for computing an approximate J(th) exp ss based on estimates of a 'constrained equilibrium' distribution, and identification of its minimum.

  2. 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.

  3. Kinetic modeling of an IBr solar pumped laser

    NASA Technical Reports Server (NTRS)

    Harries, W. L.; Meador, W. E.

    1983-01-01

    The possibility of using an IBr laser as a solar-energy converter is examined theoretically, and reasons for its choice are given. Broadband absorption results in dissociation with the formation of excited metastable Br atoms, some of which then lase to the ground state Br. The ground state is depopulated by three-body recombination and, more importantly, by exchange reactions which more than compensate for the high quenching in heteronuclear halogen systems. Kinetic modeling indicates lasing is possible in the pulsed mode and possibly in the steady state with a cooled gas flow system. Temperature effects are discussed. The efficiency of the laser approaches 1.2 percent at optical thicknesses large enough for complete absorption of the photons.

  4. Validation and Verification with Applications to a Kinetic Global Model

    NASA Astrophysics Data System (ADS)

    Verboncoeur, J. P.

    2014-10-01

    As scientific software matures, verification, validation, benchmarking, and error estimation are becoming increasingly important to ensure predictable operation. Having well-described and consistent data is critical for consistent results. This presentation briefly addresses the motivation for V&V, the history and goals of the workshop series. A roadmap of the current workshop is presented. Finally, examples of V&V are applied to a novel kinetic global model for a series of low temperature plasma problems ranging from verification of specific rate equations to benchmarks and validation with other codes and experimental data for Penning breakdown and hydrocarbon plasmas. The results are included in the code release to ensure repeatability following code modifications. In collaboration with G. Parsey, J. Kempf, and A. Christlieb, Michigan State University. This work is supported in part by a U.S. Air Force Office of Scientific Research Basic Research Initiative and a Michigan State University Strategic Partnership grant.

  5. Effects of turbulence on a kinetic auroral arc model

    NASA Technical Reports Server (NTRS)

    Cornwall, J. M.; Chiu, Y. T.

    1981-01-01

    A plasma kinetic model of an inverted-V auroral arc structure which includes the effects of electrostatic turbulence is proposed. In the absence of turbulence, a parallel potential drop is supported by magnetic mirror forces and charge quasi neutrality, with energetic auroral ions penetrating to low altitudes; relative to the electrons, the ions' pitch angle distribution is skewed toward smaller pitch angles. The electrons energized by the potential drop form a current which excites electrostatic turbulence. In equilibrium the plasma is marginally stable. The conventional anomalous resistivity contribution to the potential drop is very small. Anomalous resistivity processes are far too dissipative to be powered by auroral particles. It is concluded that under certain circumstances equilibrium may be impossible and relaxation oscillations set in.

  6. Dayglow on Mars: Kinetic modelling with SPICAM UV limb data

    NASA Astrophysics Data System (ADS)

    Simon, C.; Witasse, O.; Leblanc, F.; Gronoff, G.; Bertaux, J.-L.

    2009-07-01

    The UV spectrometer experiment SPICAM onboard ESA Mars Express has been orbiting Mars since December 2003. We present here some comparisons between airglow data that have been newly interpreted with the advanced kinetic model Trans-Mars. A series of numerical one-dimensional kinetic models, in the Trans-* family [Lilensten, J., Blelly. P.L., 2002. The TEC and F2 parameters as tracers of the ionosphere and thermosphere. J. Atmos. Solar-Terrestrial Phys. 64, 775-793] has been developed over the last years to take into account of airglow processes and yield altitude line profiles in planetary upper atmospheres (Earth, Venus, Titan and Mars). Trans-Mars is the last evolution of these simulations, applied to Mars. Electron and photon cross sections have been recently updated. The computed model line profiles are comparable to those of Fox and Dalgarno [1979b. Ionization, luminosity, and heating of the upper atmosphere of Mars. J. Geophys. Res. 84, 7315-7333] and Shematovich et al. [2008. Monte Carlo model of electron transport for the calculation of Mars dayglow emissions. J. Geophys. Res. (Planets) 113(E12), 2011]. Nearly 70000 limb UV spectra recorded by SPICAM between October 2004 and May 2006 are analysed in order to obtain altitude emission profiles on the main dayglow emissions. A variable point spread function (PSF) determined statistically throughout the wavelength range is used to estimate precisely the intensity of the airglow. This includes the Cameron bands ( a3Π-X1Σ) of CO, the CO2+ ultraviolet doublet ( B2Σu+-X2Πg) at 289.0 nm and the oxygen emission at 297.2 nm. Instrumental uncertainties of the emissions remain under 15%. Five groups of comparable orbits are selected to prepare for the data interpretation. The seasonal and solar activity effects on the dayside CO 'Cameron Bands', CO2+ and OI(2972 Å) emissions are discussed in light of previous studies. These emissions exhibit for equatorial latitudes two maxima of intensity for LS=140∘ and 290

  7. Mechanistic kinetic models of enzymatic cellulose hydrolysis-a review.

    PubMed

    Jeoh, Tina; Cardona, Maria J; Karuna, Nardrapee; Mudinoor, Akshata R; Nill, Jennifer

    2017-02-28

    Bioconversion of lignocellulose forms the basis for renewable, advanced biofuels, and bioproducts. Mechanisms of hydrolysis of cellulose by cellulases have been actively studied for nearly 70 years with significant gains in understanding of the cellulolytic enzymes. Yet, a full mechanistic understanding of the hydrolysis reaction has been elusive. We present a review to highlight new insights gained since the most recent comprehensive review of cellulose hydrolysis kinetic models by Bansal et al. () Biotechnol Adv 27:833-848. Recent models have taken a two-pronged approach to tackle the challenge of modeling the complex heterogeneous reaction-an enzyme-centric modeling approach centered on the molecularity of the cellulase-cellulose interactions to examine rate limiting elementary steps and a substrate-centric modeling approach aimed at capturing the limiting property of the insoluble cellulose substrate. Collectively, modeling results suggest that at the molecular-scale, how rapidly cellulases can bind productively (complexation) and release from cellulose (decomplexation) is limiting, while the overall hydrolysis rate is largely insensitive to the catalytic rate constant. The surface area of the insoluble substrate and the degrees of polymerization of the cellulose molecules in the reaction both limit initial hydrolysis rates only. Neither enzyme-centric models nor substrate-centric models can consistently capture hydrolysis time course at extended reaction times. Thus, questions of the true reaction limiting factors at extended reaction times and the role of complexation and decomplexation in rate limitation remain unresolved. Biotechnol. Bioeng. 2017;9999: 1-16. © 2017 Wiley Periodicals, Inc.

  8. 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.

  9. A computational kinetic model of diffusion for molecular systems

    NASA Astrophysics Data System (ADS)

    Teo, Ivan; Schulten, Klaus

    2013-09-01

    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.

  10. Scale-up and kinetic modeling for bioethanol production.

    PubMed

    Imamoglu, Esra; Sukan, Fazilet Vardar

    2013-09-01

    Bioethanol was produced from acidic hydrolysate of rice hulls using recombinant Escherichia coli KO11. Two different issues (scale-up and kinetic modeling) were evaluated simultaneously and concomitantly for bioethanol production. During the step-wise scale-up process from 100 mL shaken flask to 10 L stirred-tank bioreactor, the constant Reynolds number and the constant impeller tip speed were evaluated as scale-up methodologies under laboratory conditions. It was determined that the volumetric bioethanol productivity was 88% higher in 10 L bioreactor in comparison to the value of 0.21 g L(-1) h(-1) in shaken flask. The modified Monod and Luedeking-Piret models provided an accurate approach for the modeling of the experimental data. Ethanol concentration reached the maximum level of 29.03 g/L, which was 5% higher than the value of model prediction in 10 L bioreactor. The findings of this research could contribute to the industrial scale productions especially from lignocellulosic raw materials.

  11. Kinetics and modeling of hexavalent chromium reduction in Enterobacter cloacae

    SciTech Connect

    Yamamoto, Koji; Kato, Junichi; Yano, Takuo; Ohtake, Hisao )

    1993-01-05

    Kinetics of bacterial reduction of toxic hexavalent chromium (chromate: CrO[sub 4][sup [minus]2]) was investigated using batch and fed-batch cultures of Enterobacter cloacae strain HO1. In fed-batch cultures, the CrO[sub 4][sup [minus]2] feed was controlled on the basis of the rate of pH change. This control strategy has proven to be useful for avoiding toxic CrO[sub 3][sup [minus]2] overload. A simple mathematical model was developed to describe the bacterial process of CrO[sub 4][sup [minus]2] reduction. In this model, two types of bacterial cells were considered: induced, CrO[sub 4][sup [minus]2]-resistant cells and uninduced, sensitive ones. Only resistant cells were assumed to be able to reduce CrO[sub 4][sup [minus]2]. These fundamental ideas were supported by the model predictions which well approximated all experimental data. In a simulation study, the model was also used to optimize fed-batch cultures, instead of lengthy and expensive laboratory experiments.

  12. 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.

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

    DOE PAGES

    Stickle, A. M.; Atchison, J. A.; Barnouin, O. 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

  14. 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.

  15. Detailed kinetic modeling study of n-pentanol oxidation

    DOE PAGES

    Heufer, K. Alexander; Sarathy, S. Mani; Curran, Henry 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

  16. A computational kinetic model of diffusion for molecular systems

    PubMed Central

    Teo, Ivan; Schulten, Klaus

    2013-01-01

    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. PMID:24089741

  17. 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.

  18. 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.

  19. Hopping electron model with geometrical frustration: kinetic Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Terao, Takamichi

    2016-09-01

    The hopping electron model on the Kagome lattice was investigated by kinetic Monte Carlo simulations, and the non-equilibrium nature of the system was studied. We have numerically confirmed that aging phenomena are present in the autocorrelation function C ({t,tW )} of the electron system on the Kagome lattice, which is a geometrically frustrated lattice without any disorder. The waiting-time distributions p(τ ) of hopping electrons of the system on Kagome lattice has been also studied. It is confirmed that the profile of p (τ ) obtained at lower temperatures obeys the power-law behavior, which is a characteristic feature of continuous time random walk of electrons. These features were also compared with the characteristics of the Coulomb glass model, used as a model of disordered thin films and doped semiconductors. This work represents an advance in the understanding of the dynamics of geometrically frustrated systems and will serve as a basis for further studies of these physical systems.

  20. Global Kinetic Modeling of Banded Electron Structures in the Plasmasphere

    NASA Technical Reports Server (NTRS)

    Liemohn, M. W.; Khazanov, G. V.

    1997-01-01

    Significant fluxes of 10 eV to 30 keV electrons have been detected in the plasmasphere, appearing as banded structures in energy with broad spatial extents and slowly evolving over several days. It is thought that these populations are decaying plasma sheet electrons injected into the corotating region of near-Earth space. This capture can occur when the convective electric field drops rapidly and the Alfven boundary suddenly outward, trapping the inner edge of the plasma sheet along closed drift paths. Our bounce-averaged kinetic model of superthermal electron transport is able to simulate this capture and the subsequent drift, diffusion, and decay of the plasma cloud. Results of this simulation will be shown and discussed, from the initial injection during the elevated convection to the final loss of the particles. It is thought that not only Coulomb collisions but also wave-particle interactions play a significant role in altering the plasma cloud. Quasilinear diffusion is currently being incorporated into the model and the importance of this mechanism will be examined. Also, the high anisotropy of the trapped population could be unstable and generate plasma waves. These and other processes will be investigated to determine the final fate of the cloud and to quantify where, how, and when the energy of the plasma cloud is deposited. Comparisons with CRRES observations of these events are shown to verify the model and explain the data.

  1. 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.

  2. 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

  3. A theoretical compartment model for antigen kinetics in the skin.

    PubMed

    Römgens, Anne M; Bader, Dan L; Bouwstra, Joke A; Oomens, Cees W J

    2016-03-10

    The skin is a promising location for vaccination with its abundant population of antigen capturing and presenting cells. The development of new techniques, such as the use of microneedles, can facilitate the delivery of vaccines into the skin. In recent years, many different types of microneedle arrays have been designed. However, their geometry and arrangement within an array may be optimized to trigger sufficient antigen presenting cells. A computational model can support the rational design of microneedle arrays. Therefore, the aim of the current study was to describe the distribution and kinetics of a delivered antigen within the skin using a theoretical compartment model, which included binding of antigens to receptors and their uptake by cells, and to determine which parameters should be measured to validate the model for a specific application. Multiple simulations were performed using a high and low antigen delivery dose and a range of values for the rate constants. The results indicated that the cells were highly saturated when a high dose was applied, while for a low dose saturation was only reached in 5% of the simulations. This was caused by the difference in the ratio between the administered dose and the available binding sites and suggests the dose should be adapted to the number of cells and receptors for a specific compound. The sensitivity analysis of the model parameters confirmed that the initial dose and receptor concentrations were indeed the two parameters that had the largest influence on the variance in antigen concentrations within the cells and circulation at equilibrium. Hence, these parameters are important to be measured in vivo. The presented pharmacokinetics model can be used in future computational models to predict the influence of microneedle array geometry to optimize their design.

  4. 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

  5. Development of DEM formalism to modeling the dynamic response of brittle solids

    NASA Astrophysics Data System (ADS)

    Grigoriev, Aleksandr S.; Shilko, Eugeny V.; Psakhie, Sergey G.

    2016-11-01

    The paper presents a numerical model of the response for brittle materials to dynamic mechanical loading and implementation of the model within the discrete element method (DEM) by the example of the movable cellular automaton method (MCA). Verification of the model was carried out using the numerical modeling of the uniaxial compression tests of concrete and sandstone samples at various strain rates. It is shown that the developed model is correct and adequately describes the behavior of brittle materials under dynamic loading.

  6. Chemical kinetic model uncertainty minimization through laminar flame speed measurements.

    PubMed

    Park, Okjoo; Veloo, Peter S; Sheen, David A; Tao, Yujie; Egolfopoulos, Fokion N; Wang, Hai

    2016-10-01

    Laminar flame speed measurements were carried for mixture of air with eight C3-4 hydrocarbons (propene, propane, 1,3-butadiene, 1-butene, 2-butene, iso-butene, n-butane, and iso-butane) at the room temperature and ambient pressure. Along with C1-2 hydrocarbon data reported in a recent study, the entire dataset was used to demonstrate how laminar flame speed data can be utilized to explore and minimize the uncertainties in a reaction model for foundation fuels. The USC Mech II kinetic model was chosen as a case study. The method of uncertainty minimization using polynomial chaos expansions (MUM-PCE) (D.A. Sheen and H. Wang, Combust. Flame 2011, 158, 2358-2374) was employed to constrain the model uncertainty for laminar flame speed predictions. Results demonstrate that a reaction model constrained only by the laminar flame speed values of methane/air flames notably reduces the uncertainty in the predictions of the laminar flame speeds of C3 and C4 alkanes, because the key chemical pathways of all of these flames are similar to each other. The uncertainty in model predictions for flames of unsaturated C3-4 hydrocarbons remain significant without considering fuel specific laminar flames speeds in the constraining target data set, because the secondary rate controlling reaction steps are different from those in the saturated alkanes. It is shown that the constraints provided by the laminar flame speeds of the foundation fuels could reduce notably the uncertainties in the predictions of laminar flame speeds of C4 alcohol/air mixtures. Furthermore, it is demonstrated that an accurate prediction of the laminar flame speed of a particular C4 alcohol/air mixture is better achieved through measurements for key molecular intermediates formed during the pyrolysis and oxidation of the parent fuel.

  7. A Kinetic Muti-Plume Model of the Enceladus’ Atmosphere

    NASA Astrophysics Data System (ADS)

    Tenishev, Valeriy; Combi, M.; Teolis, B.; Waite, H.

    2009-09-01

    In addition of being the major source of neutral gas and dust particles for the Saturnian E-ring and, ultimately, heavy ions for the Saturnian inner magnetosphere, Enceladus exhibits geological activity that made it an object of recent intensive study. The interest has significantly increased after Cassini flybys in 2005 that have provided a detailed map of its surface, showing that most of activity occurs in a region around the south pole of the satellite. Dust jets that were discovered during the flybys can be related to a set of localized gas sources that dominate in supplying material into the rarefied atmosphere of Enceladus. A comprehensive data analysis requires developing of physical models that include all major processes occurring in the atmosphere. Such models can be used not only for calibration and understanding of already available data but also could have a practical application for planning of the coming flybys and predicting of expected results. This work presents a kinetic model of Enceladus’ atmosphere with plumes located at positions determined with CIRS observations and described by local Maxwellian distribution functions. The model parameters include production rate, temperature and bulk velocity of a gas near a vent. Assuming collision frequency being negligible outside of the vents, density distribution in the atmosphere is obtained by solving a Louwville equation. The parameters are optimized to fit various combinations of sets of Cassini data from INMS and UVIS. Here we present results of fitting the multi-plume model to UVIS E2, and INMS E3 and E5 flyby data and place estimates of source rates from some plumes as well as upper limits from others. This work was partially supported by NASA Cassini Data Analysis grant NNX08AP94G.

  8. 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.

  9. 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

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

    PubMed

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

    2015-06-05

    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.

  11. Detailed Kinetic Modeling of Processes Relevant To Fusion Energy

    NASA Astrophysics Data System (ADS)

    Mehl, Marco; Armstrong, Michael; Zaug, Joseph; Crowhurst, Jonathan; Radousky, Harry; Stavrou, Elissaios

    2016-10-01

    Carbon based materials have been proposed as candidates for the fabrication of plasma-facing components in the design of fusion energy devices. Although these components are not supposed to be in direct contact with the core fusion plasma, plasma instabilities and the harsh environment they are exposed to can cause the degradation of plasma-exposed components and the transfer of contaminants into the plasma followed by deposition of byproducts. In order to investigate the chemistry involved in these processes and to assist the development of models suitable to understand the long term consequences of the carbon ablation/deposition cycle, an inductively coupled plasma flow reactor (ICPFR) has been developed. The ICPFR allows the atomization of carbon containing precursors to high temperatures (in the order of 10000K) and the characterization of the gas and solid species formed downsteam from the plasma source through spectroscopic techniques. In parallel to the experimental analysis a comprehensive set of fluid dynamic and detailed kinetic simulations are used to analyze the data. The combination of these two approaches resulted in a validated and comprehensive chemical model for the formation of carbon deposits in carbon contaminated cooling plasmas. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  12. 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.

  13. A particle dynamic model of red blood cell aggregation kinetics.

    PubMed

    Fenech, Marianne; Garcia, Damien; Meiselman, Herbert J; Cloutier, Guy

    2009-11-01

    To elucidate the relationship between microscopic red blood cell (RBC) interactions and macroscopic rheological behavior, we propose a two-dimensional particle model capable of mimicking the main characteristics of RBC aggregation kinetics. The mechanical model of RBCs sheared in Couette flow is based on Newton law. We assumed a hydrodynamic force to move particles, a force to describe aggregation and an elasticity force. The role of molecular mass and concentration of neutral polymers on aggregation [Neu, B., and H. J. Meiselman. Biophys. J. 83:2482-2490, 2002] could be mimicked. Specifically, it was shown that for any shear rate (SR), the mean aggregate size (MAS) grew with time until it reached a constant value, which is consistent with in vitro experiments. It was also demonstrated that we could mimic the modal relationship between MAS and SR and the occurrence of maximum aggregation at about 0.1 s(-1). As anticipated, simulations indicated that an increase in aggregation force augmented MAS. Further, augmentation of the depletion layer thickness influenced MAS only for SR close to zero, which is a new finding. To conclude, our contribution reveals that the aggregation force intensity and SR influence the steady state MAS, and that the depletion and layer thickness affect the aggregation speed.

  14. Mesoscopic kinetic Monte Carlo modeling of organic photovoltaic device characteristics

    NASA Astrophysics Data System (ADS)

    Kimber, Robin G. E.; Wright, Edward N.; O'Kane, Simon E. J.; Walker, Alison B.; Blakesley, James C.

    2012-12-01

    Measured mobility and current-voltage characteristics of single layer and photovoltaic (PV) devices composed of poly{9,9-dioctylfluorene-co-bis[N,N'-(4-butylphenyl)]bis(N,N'-phenyl-1,4-phenylene)diamine} (PFB) and poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT) have been reproduced by a mesoscopic model employing the kinetic Monte Carlo (KMC) approach. Our aim is to show how to avoid the uncertainties common in electrical transport models arising from the need to fit a large number of parameters when little information is available, for example, a single current-voltage curve. Here, simulation parameters are derived from a series of measurements using a self-consistent “building-blocks” approach, starting from data on the simplest systems. We found that site energies show disorder and that correlations in the site energies and a distribution of deep traps must be included in order to reproduce measured charge mobility-field curves at low charge densities in bulk PFB and F8BT. The parameter set from the mobility-field curves reproduces the unipolar current in single layers of PFB and F8BT and allows us to deduce charge injection barriers. Finally, by combining these disorder descriptions and injection barriers with an optical model, the external quantum efficiency and current densities of blend and bilayer organic PV devices can be successfully reproduced across a voltage range encompassing reverse and forward bias, with the recombination rate the only parameter to be fitted, found to be 1×107 s-1. These findings demonstrate an approach that removes some of the arbitrariness present in transport models of organic devices, which validates the KMC as an accurate description of organic optoelectronic systems, and provides information on the microscopic origins of the device behavior.

  15. 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 ...

  16. 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

  17. 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.

  18. Model-based formalization of medical knowledge for context-aware assistance in laparoscopic surgery

    NASA Astrophysics Data System (ADS)

    Katić, Darko; Wekerle, Anna-Laura; Gärtner, Fabian; Kenngott, Hannes G.; Müller-Stich, Beat P.; Dillmann, Rüdiger; Speidel, Stefanie

    2014-03-01

    The increase of technological complexity in surgery has created a need for novel man-machine interaction techniques. Specifically, context-aware systems which automatically adapt themselves to the current circumstances in the OR have great potential in this regard. To create such systems, models of surgical procedures are vital, as they allow analyzing the current situation and assessing the context. For this purpose, we have developed a Surgical Process Model based on Description Logics. It incorporates general medical background knowledge as well as intraoperatively observed situational knowledge. The representation consists of three parts: the Background Knowledge Model, the Preoperative Process Model and the Integrated Intraoperative Process Model. All models depend on each other and create a concise view on the surgery. As a proof of concept, we applied the system to a specific intervention, the laparoscopic distal pancreatectomy.

  19. A Formal Modelling Language Extending SysML for Simulation of Continuous and Discrete System

    DTIC Science & Technology

    2012-11-01

    Nick Luckman2 1Block Software and 2Weapons Systems Division, DSTO Abstract MBSE tools and techniques in a broad sense provide a structured approach...aims to support the broader modelling needs of SE, hence the term MBSE . However, engineering has at its disposal another type of modelling that is...more precisely iterative algorithms. The challenge therefore for MBSE is to develop general purpose graphical modelling views that transition naturally

  20. Multiscale Model for the Assembly Kinetics of Protein Complexes.

    PubMed

    Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

    2016-02-04

    The assembly of proteins into high-order complexes is a general mechanism for these biomolecules to implement their versatile functions in cells. Natural evolution has developed various assembling pathways for specific protein complexes to maintain their stability and proper activities. Previous studies have provided numerous examples of the misassembly of protein complexes leading to severe biological consequences. Although the research focusing on protein complexes has started to move beyond the static representation of quaternary structures to the dynamic aspect of their assembly, the current understanding of the assembly mechanism of protein complexes is still largely limited. To tackle this problem, we developed a new multiscale modeling framework. This framework combines a lower-resolution rigid-body-based simulation with a higher-resolution Cα-based simulation method so that protein complexes can be assembled with both structural details and computational efficiency. We applied this model to a homotrimer and a heterotetramer as simple test systems. Consistent with experimental observations, our simulations indicated very different kinetics between protein oligomerization and dimerization. The formation of protein oligomers is a multistep process that is much slower than dimerization but thermodynamically more stable. Moreover, we showed that even the same protein quaternary structure can have very diverse assembly pathways under different binding constants between subunits, which is important for regulating the functions of protein complexes. Finally, we revealed that the binding between subunits in a complex can be synergistically strengthened during assembly without considering allosteric regulation or conformational changes. Therefore, our model provides a useful tool to understand the general principles of protein complex assembly.

  1. Model for Strain-Induced Precipitation Kinetics in Microalloyed Steels

    NASA Astrophysics Data System (ADS)

    Medina, Sebastian F.; Quispe, Alberto; Gomez, Manuel

    2013-10-01

    Based on Dutta and Sellars's expression for the start of strain-induced precipitation in microalloyed steels, a new model has been constructed which takes into account the influence of variables such as microalloying element percentages, strain, temperature, strain rate, and grain size. Although the equation given by these authors reproduces the typical "C" shape of the precipitation start time (P s) curve well, the expression is not reliable for all cases. Recrystallization-precipitation-time-temperature diagrams have been plotted thanks to a new experimental study carried out by means of hot torsion tests on approximately twenty microalloyed steels with different Nb, V, and Ti contents. Mathematical analysis of the results recommends the modification of some parameters such as the supersaturation ratio (K s) and constant B, which is no longer a constant, but a function of K s when the latter is calculated at the nose temperature (T N) of the P s curve. The value of parameter B is deduced from the minimum point or nose of the P s curve, where ∂t 0.05/∂T is equal to zero, and it can be demonstrated that B cannot be a constant. The new expressions for these parameters are derived from the latest studies undertaken by the authors and this work represents an attempt to improve the model. The expressions are now more consistent and predict the precipitation-time-temperature curves with remarkable accuracy. The model for strain-induced precipitation kinetics is completed by means of Avrami's equation.

  2. The dilute rheology of swimming suspensions: A simple kinetic model

    NASA Astrophysics Data System (ADS)

    Saintillan, David

    2009-11-01

    A simple kinetic model is presented for the shear rheology of a dilute suspension of particles swimming at low Reynolds number. If interparticle hydrodynamic interactions are neglected, the configuration of the suspension is characterized by the particle orientation distribution, which satisfies a Fokker-Planck equation including the effects of the external shear flow, rotary diffusion, and particle tumbling. The orientation distribution then determines the leading-order term in the particle extra stress in the suspension, which can be evaluated based on the classic theory of Hinch and Leal [J. Fluid. Mech. 52(4):683-712 (1972)], and involves an additional contribution arising from the permanent force dipole exerted by the particles as they propel themselves through the fluid. Numerical solutions of the steady-state Fokker-Planck equation were obtained using a spectral method, and results are reported for the shear viscosity and normal stress differences in terms of flow strength, rotary diffusivity, and correlation time for tumbling. It is found that the rheology is characterized by much stronger normal stress differences than for passive suspensions, and that tail-actuated swimmers result in a strong decrease in the effective shear viscosity of the fluid.

  3. Exact solutions of kinetic equations in an autocatalytic growth model.

    PubMed

    Jędrak, Jakub

    2013-02-01

    Kinetic equations are introduced for the transition-metal nanocluster nucleation and growth mechanism, as proposed by Watzky and Finke [J. Am. Chem. Soc. 119, 10382 (1997)]. Equations of this type take the form of Smoluchowski coagulation equations supplemented with the terms responsible for the chemical reactions. In the absence of coagulation, we find complete analytical solutions of the model equations for the autocatalytic rate constant both proportional to the cluster mass, and the mass-independent one. In the former case, ξ(k)=s(k)(ξ(1))[proportionality]ξ(1)(k)/k was obtained, while in the latter, the functional form of s(k)(ξ(1)) is more complicated. In both cases, ξ(1)(t)=h(μ)(M(μ)(t)) is a function of the moments of the mass distribution. Both functions, s(k)(ξ(1)) and h(μ)(M(μ)), depend on the assumed mechanism of autocatalytic growth and monomer production, and not on other chemical reactions present in a system.

  4. 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.

  5. Kinetic modeling study of toluene pyrolysis at low pressure

    SciTech Connect

    Zhang, Lidong; Cai, Jianghuai; Zhang, Taichang; Qi, Fei

    2010-09-15

    A detailed kinetic model, consisting of 137 species and 530 reactions, was developed to simulate toluene pyrolysis at low pressure within the temperature range from 1270 to 1870 K. The mole fraction profiles predicted for pyrolysis species up to phenanthrene were in good agreement with the experiment. The decomposition pathways of toluene and the growth pathways to polycyclic aromatic hydrocarbons (PAHs) were discussed from reaction flux analysis. Toluene decomposes through the reaction sequence C{sub 6}H{sub 5}CH{sub 3}{yields} C{sub 6}H{sub 5}CH{sub 2}{yields}C{sub 7}H{sub 6}{yields}c-C{sub 5}H{sub 5}{yields}C{sub 3}H{sub 3}, which also has a predominant contribution to the production of acetylene. Furthermore, sensitivity analysis showed that the primary decomposition reactions of toluene, C{sub 6}H{sub 5}CH{sub 3}=C{sub 6}H{sub 5}CH{sub 2}+H and C{sub 6}H{sub 5}CH{sub 3}=C{sub 6}H{sub 5}+CH{sub 3}, have great influences on the formation of small molecules, such as phenyl radical, benzyl radical, C2- and C3-species, which are critical to the formation of PAHs in the pyrolysis of toluene. (author)

  6. The appropriateness of ignorance in the inverse kinetic Ising model

    NASA Astrophysics Data System (ADS)

    Dunn, Benjamin; Battistin, Claudia

    2017-03-01

    We develop efficient ways to consider and correct for the effects of hidden units for the paradigmatic case of the inverse kinetic Ising model with fully asymmetric couplings. We identify two sources of error in reconstructing the connectivity among the observed units while ignoring part of the network. One leads to a systematic bias in the inferred parameters, whereas the other involves correlations between the visible and hidden populations and has a magnitude that depends on the coupling strength. We estimate these two terms using a mean field approach and derive self-consistent equations for the couplings accounting for the systematic bias. Through application of these methods on simple networks of varying relative population size and connectivity strength, we assess how and under what conditions the hidden portion can influence inference and to what degree it can be crudely estimated. We find that for weak to moderately coupled systems, the effects of the hidden units is a simple rotation that can be easily corrected for. For strongly coupled systems, the non-systematic term becomes large and can no longer be safely ignored, further highlighting the importance of understanding the average strength of couplings for a given system of interest.

  7. Modeling of vibrational kinetics in CO2 dielectric barrier discharges

    NASA Astrophysics Data System (ADS)

    Ponduri, S.; Becker, M. M.; Loffhagen, D.; Welzel, S.; Sanden, M. C. M. Van De; Engeln, R.

    2014-10-01

    CO2 reduction to CO is considered to improve the prospects of CO2 recycling which in turn could mitigate the greenhouse effect and serve as energy storage. Non equilibrium plasmas were used in the past to achieve high energy efficiencies in dissociating CO2. Non equilibrium distribution in asymmetric stretch modes of CO2, driven by vibrational up-pumping (VV process), has been suggested as key for achieving such high energy efficiencies. In this work, a time-dependent, one dimensional fluid model taking into account balance equations for the densities of all relevant species and electron mean energy is used to investigate the kinetics of VV process in a pure CO2 dielectric barrier discharge. A Treanor like distribution has been observed in CO2 asymmetric modes and the rates of dissociation have been obtained from these distributions. The rates thus obtained have proved to be significantly lower than the rates of other dissociating processes such as electron impact dissociation. The effect of power in-coupling, duration of plasma and pressure on the vibrational distributions and CO production rate is also studied.

  8. Formal Modeling of Diffie-Hellman Derivability for Exploratory Automated Analysis

    DTIC Science & Technology

    2013-06-01

    model to a weaker one which does not capture exponent addition or group multiplication. This would seem to be a problematic model: it seems to deny the...protocol analysis for Diffie-Hellman. CoRR, abs/1202.2168, 2012. [5] Catherine Meadows and Paliath Narendran. A unification algorithm for the group

  9. 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

  10. Kinetic modeling of a multiple immobilized enzyme system. I. Development and testing of the model

    SciTech Connect

    Mercer, D.G.; O'Driscoll, K.F.

    1981-11-01

    A kinetic model for the reaction sequence catalyzed by coimmobilized invertase and glucose oxidase with a sucrose substrate in a tubular reactor has been developed. The computerized mathematical model employs an orthogonal collocation technique for solving the set of simultaneous equations generated by this treatment. The invertase and glucose oxidase were coimmobilized in poly(2-hydroxyethylmethacrylate) gels and used in a continuous flow packed-bed tubular reactor system. In addition to describing the development of the kinetic model, this article compares experimentally determined reactor effluent concentrations for various sucrose feed solutions to those predicted by the model. Variations between experimental and predicted reactor effluent concentrations were found to be on the micromolar level for sucrose feed concentrations as low as 1.38mM. (Refs. 27).

  11. Uniformly rigid spaces and Néron models of formally finite type

    NASA Astrophysics Data System (ADS)

    Kappen, Christian

    A new innovative polymer pyrolysis method was proposed for creation of attractive carbon molecular sieve (CMS) membranes. Oxygen exposure at ppm levels during pyrolysis was hypothesized and demonstrated to make slit-like CMS structures more selective and less permeable, which I contrary to ones expectation. Indeed prior to this work, any exposure to oxygen was expected to result in removal of carbon mass and increase in permeability. The results of this study indicated that the separation performance and CMS structure may be optimized for various gas separations by careful tuning of the oxygen level. This finding represents a breakthrough in the field of CMS membranes. Simple replacement of pyrolysis atmospheres from vacuum to inert can enable scale-up. The deviation in CMS membrane performance was significantly reduced once oxygen levels were carefully monitored and controlled. The method was shown to be effective and repeatable not only with dense films but also with asymmetric hollow fiber membranes. As a result, this work led the development of the "inert" pyrolysis method which has overcome the challenges faced with previously studied pyrolysis method to prepare attractive CMS membranes. The effect of oxygen exposure during inert pyrolysis was evaluated by a series of well-controlled experiments using homogeneous CMS dense films. Results indicated that the oxygen "doping" process on selective pores is likely governed by equilibrium limited reaction rather than (i) an external or (ii) internal transport or (iii) kinetically limited reaction. This significant finding was validated with two polyimide precursors: synthesized 6FDA/BPDA-DAM and commercial MatrimidRTM, which implies a possibility of the "inert" pyrolysis method application extending towards various precursors. The investigation was further extended to prepare CMS fibers. Despite the challenge of two different morphologies between homogeneous films and asymmetric hollow fibers, the "inert" pyrolysis

  12. Combining the Many-Body GW Formalism with Classical Polarizable Models: Insights on the Electronic Structure of Molecular Solids.

    PubMed

    Li, Jing; D'Avino, Gabriele; Duchemin, Ivan; Beljonne, David; Blase, Xavier

    2016-07-21

    We present an original hybrid QM/MM scheme merging the many-body Green's function GW formalism with classical discrete polarizable models and its application to the paradigmatic case of a pentacene crystal. Our calculated transport gap is found to be in excellent agreement with reference periodic bulk GW calculations, together with properly parametrized classical microelectrostatic calculations, and with photoionization measurements at crystal surfaces. More importantly, we prove that the gap is insensitive to the partitioning of pentacene molecules in QM and MM subsystems, as a result of the mutual compensation of quantum and classical polarizabilities, clarifying the relation between polarization energy and delocalization. The proposed hybrid method offers a computationally attractive strategy to compute the full spectrum of charged excitations in complex molecular environments, accounting for both QM and MM contributions to the polarization energy, a crucial requirement in the limit of large QM subsystems.

  13. 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.

  14. Chemical Kinetics Laboratory Discussion Worksheet

    PubMed Central

    Demoin, Dustin Wayne; Jurisson, Silvia S.

    2013-01-01

    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. PMID:24092948

  15. Formal and Informal Work Group Relationships With Performance: A Moderation Model Using Social

    DTIC Science & Technology

    2006-03-01

    McGrath, 1984) with the most common model being that proposed by Tuckman (1965). Tuckman’s model shows four stages of group development: forming...social and psychological consequences of the long-wall method of coal-getting. Human Relations, 4: 1-38. Tuckman , B.W. (1965). Developmental...sequences in small groups. Psychological Bulletin, 63: 384-399. Tuckman , B.W. & Jensen, M.C. (1977). Stages of small group development

  16. 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.

  17. 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.

  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. Analysis of “On/Off” Kinetics of a CETP Inhibitor Using a Mechanistic Model of Lipoprotein Metabolism and Kinetics

    PubMed Central

    Lu, J; Cleary, Y; Maugeais, C; Kiu Weber, CI; Mazer, NA

    2015-01-01

    RG7232 is a potent inhibitor of cholesteryl-ester transfer protein (CETP). Daily oral administration of RG7232 produces a dose- and time-dependent increase in high-density lipoprotein-cholesterol (HDL-C) and apolipoproteinA-I (ApoA-I) levels and a corresponding decrease in low-density lipoprotein-cholesterol (LDL-C) and apolipoproteinB (ApoB) levels. Due to its short plasma half-life (∼3 hours), RG7232 transiently inhibits CETP activity during each dosing interval (“on/off” kinetics), as reflected by the temporal effects on HDL-C and LDL-C. The influence of RG7232 on lipid-poor ApoA-I (i.e., pre-β1) levels and reverse cholesterol transport rates is unclear. To investigate this, a published model of lipoprotein metabolism and kinetics was combined with a pharmacokinetic model of RG7232. After calibration and validation of the combined model, the effect of RG7232 on pre-β1 levels was simulated. A dose-dependent oscillation of pre-β1, driven by the “on/off” kinetics of RG7232 was observed. The possible implications of these findings are discussed. PMID:26380155

  20. A Variational Formalism for the Radiative Transfer Equation: Prelude to Model 3

    NASA Technical Reports Server (NTRS)

    Achtemeier, Gary L.

    1991-01-01

    The MODEL III variational data assimilation model is the third of four general assimilation models designed to blend weather data measured from space based platforms in the meteorological data mainstream in a way that maximizes the information content of the satellite data. Because there are many different observation locations and there are many instruments with different measurement error characteristics, it is also necessary to require that the blending be done to maximize the information content of the data and simultaneously to retain a dynamically consistent and reasonably accurate description of the state of the atmosphere. This is ideally a variational problem for which the data receive relative weights that are inversely proportional to measurement error and are adjusted to satisfy a set of dynamical equations that govern atmospheric processes. The advantage of MODEL III over the previous two models is that radiance, the atmospheric variable measured by satellite, becomes a dependent variable. In the previous versions, mean layer temperatures that had been retrieved from the radiances by some method, were included in the assimilation by substituting them in place of the rawinsonde temperatures. Now both rawinsonde temperatures and satellite radiances are included independently in the assimilation.

  1. 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.

  2. A BDMI-VSK-T logic-based formal model in war simulation

    NASA Astrophysics Data System (ADS)

    Li, Biao; Tang, Jinguo

    2012-01-01

    With the cross-disciplinary development of agent technology and war simulation technology, there are many problems when classical BDI logic is used in war simulation. Aiming at the characteristic of agent in war simulation, the BDMIVSK- T model frame is built, which combines with classic BDI-VSK-T model and imports a non-normal modal operator mission. Basic axioms and interaction axioms in BDMI-VSK-T logic are discussed and its soundness and completeness are proved. It is also proved that operator mission avoid the side-effect and the logical omniscience problem.

  3. Formalizing the role of agent-based modeling in causal inference and epidemiology.

    PubMed

    Marshall, Brandon D L; Galea, Sandro

    2015-01-15

    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.

  4. 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.

  5. Applying Schema Theory to Mass Media Information Processing: Moving toward a Formal Model.

    ERIC Educational Resources Information Center

    Wicks, Robert H.

    Schema theory may be significant in determining if and how news audiences process information. For any given news topic, people have from none to many schemata (cognitive structures that represent organized knowledge about a given concept or type of stimulus abstracted from prior experience) upon which to draw. Models of how schemata are used…

  6. Kinetic modelling of RDF pyrolysis: Model-fitting and model-free approaches.

    PubMed

    Çepelioğullar, Özge; Haykırı-Açma, Hanzade; Yaman, Serdar

    2016-02-01

    In this study, refuse derived fuel (RDF) was selected as solid fuel and it was pyrolyzed in a thermal analyzer from room temperature to 900°C at heating rates of 5, 10, 20, and 50°C/min in N2 atmosphere. The obtained thermal data was used to calculate the kinetic parameters using Coats-Redfern, Friedman, Flylnn-Wall-Ozawa (FWO) and Kissinger-Akahira-Sunose (KAS) methods. As a result of Coats-Redfern model, decomposition process was assumed to be four independent reactions with different reaction orders. On the other hand, model free methods demonstrated that activation energy trend had similarities for the reaction progresses of 0.1, 0.2-0.7 and 0.8-0.9. The average activation energies were found between 73-161kJ/mol and it is possible to say that FWO and KAS models produced closer results to the average activation energies compared to Friedman model. Experimental studies showed that RDF may be a sustainable and promising feedstock for alternative processes in terms of waste management strategies.

  7. Kinetic modeling of antimony(III) oxidation and sorption in soils.

    PubMed

    Cai, Yongbing; Mi, Yuting; Zhang, Hua

    2016-10-05

    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.

  8. 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.

  9. Kinetic parameter estimation model for anaerobic co-digestion of waste activated sludge and microalgae.

    PubMed

    Lee, Eunyoung; Cumberbatch, Jewel; Wang, Meng; Zhang, Qiong

    2017-03-01

    Anaerobic co-digestion has a potential to improve biogas production, but limited kinetic information is available for co-digestion. This study introduced regression-based models to estimate the kinetic parameters for the co-digestion of microalgae and Waste Activated Sludge (WAS). The models were developed using the ratios of co-substrates and the kinetic parameters for the single substrate as indicators. The models were applied to the modified first-order kinetics and Monod model to determine the rate of hydrolysis and methanogenesis for the co-digestion. The results showed that the model using a hyperbola function was better for the estimation of the first-order kinetic coefficients, while the model using inverse tangent function closely estimated the Monod kinetic parameters. The models can be used for estimating kinetic parameters for not only microalgae-WAS co-digestion but also other substrates' co-digestion such as microalgae-swine manure and WAS-aquatic plants.

  10. 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...

  11. 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.

  12. Cooperativity and saturation in biochemical networks: a saturable formalism using Taylor series approximations.

    PubMed

    Sorribas, Albert; Hernández-Bermejo, Benito; Vilaprinyo, Ester; Alves, Rui

    2007-08-01

    Cooperative and saturable systems are common in molecular biology. Nevertheless, common canonical formalisms for kinetic modeling that are theoretically well justified do not have a saturable form. Modeling and fitting data from saturable systems are widely done using Hill-like equations. In practice, there is no theoretical justification for the generalized use of these equations, other than their ability to fit experimental data. Thus it is important to find a canonical formalism that is (a) theoretically well supported, (b) has a saturable functional form, and (c) can be justifiably applicable to any biochemical network. Here we derive such a formalism using Taylor approximations in a special transformation space defined by power-inverses and logarithms of power-inverses. This formalism is generalized for processes with n-variables, leading to a useful mathematical representation for molecular biology: the Saturable and Cooperative Formalism (SC formalism). This formalism provides an appropriate representation that can be used for modeling processes with cooperativity and saturation. We also show that the Hill equation can be seen as a special case within this formalism. Parameter estimation for the SC formalism requires information that is also necessary to build Power-Law models, Metabolic Control Analysis descriptions or (log)linear and Lin-log models. In addition, the saturation fraction of the relevant processes at the operating point needs to be considered. The practical use of the SC formalism for modeling is illustrated with a few examples. Similar models are built using different formalisms and compared to emphasize advantages and limitations of the different approaches.

  13. 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.

  14. Goldstino and sgoldstino in microscopic models and the constrained superfields formalism

    NASA Astrophysics Data System (ADS)

    Antoniadis, I.; Dudas, E.; Ghilencea, D. M.

    2012-04-01

    We examine the exact relation between the superconformal symmetry breaking chiral superfield ( X) and the goldstino superfield in microscopic models of an arbitrary Kahler potential ( K) and in the presence of matter fields. We investigate the decoupling of the massive sgoldstino and scalar matter fields and the offshell/onshell-SUSY expressions of their superfields in terms of the fermions composites. For general K of two superfields, we study the properties of the superfield X after integrating out these scalar fields, to show that in the infrared it satisfies (offshell) the condition X=0 and X≠0. We then compare our results to those of the well-known method of constrained superfields discussed in the literature, based on the conjecture X=0. Our results can be used in applications, to couple offshell the (s)goldstino fields to realistic models such as the MSSM.

  15. 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

  16. Thermal degradation studies and kinetic modeling of cardoon (Cynara cardunculus) pyrolysis using thermogravimetric analysis (TGA).

    PubMed

    Damartzis, Th; Vamvuka, D; Sfakiotakis, S; Zabaniotou, A

    2011-05-01

    A key element in the design of sustainable pyrolysis processes is the thermal degradation kinetics of biomass. In this work, pyrolysis tests for cardoon (Cynara carduculus) stems and leaves were performed in a non-isothermal thermogravimetric analyzer (TGA) in order to determine the thermal degradation behavior of both stems and leaves. The kinetic parameters of the process were evaluated using three different kinetic models, the independent parallel reaction model, KAS and OFW iso-conversional model. Good agreement with the experimental TGA data was observed for all models, the best being with the independent parallel reaction model. A variance in the activation energy with conversion was observed when the KAS and OFW models were employed, which reveals that the pyrolysis of cardoon progresses through more complex and multi-step kinetics.

  17. 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

  18. 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.

  19. Introduction to Wave Turbulence Formalisms for Incoherent Optical Waves

    NASA Astrophysics Data System (ADS)

    Picozzi, Antonio; Garnier, Josselin; Xu, Gang; Rica, Sergio

    We provide an introduction to different wave turbulence formalisms describing the propagation of partially incoherent optical waves in nonlinear media. We consider the nonlinear Schrödinger equation as a representative model accounting for a nonlocal or a noninstantaneous nonlinearity, as well as higher-order dispersion effects. We discuss the wave turbulence kinetic equation describing, e.g., wave condensation or wave thermalization through supercontinuum generation; the Vlasov formalism describing incoherent modulational instabilities and the formation of large scale incoherent localized structures in analogy with long-range gravitational systems; and the weak Langmuir turbulence formalism describing spectral incoherent solitons, as well as spectral shock or collapse singularities. Finally, recent developments and some open questions are discussed, in particular in relation with a wave turbulence formulation of laser systems and different mechanisms of breakdown of thermalization.

  20. 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.

  1. An Extensible and Scalable Framework for Formal Modeling, Analysis, and Development of Distributed Systems

    DTIC Science & Technology

    2008-11-30

    Tempo model shown in Code I and 2 descrihes the entire syste: i as a single Timed I/O Automaton. The vocabulary section declares the data types used in... declared to have the value 5, and /2 is declared to have the value 2. Then /I and /2 are used 3Ciirrcii(Iy only uf type Nat. VF.ROMODO, In Final...may be used instead. The node types of a deployment musl be declared with the keywords node types followed by comma-separated list of node names and

  2. 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

  3. 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.

  4. 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.

  5. Advanced Kinetic-Based Modeling Applied to Plasma and Neutral Flows

    DTIC Science & Technology

    2012-09-01

    Advanced Kinetic-Based Modeling Applied to Plasma and Neutral Flows Briefers: Andrew Ketsdever Sergey Gimelshein PIs: Andrew Ketsdever...number. 1. REPORT DATE SEP 2012 2. REPORT TYPE 3. DATES COVERED 00-00-2012 to 00-00-2012 4. TITLE AND SUBTITLE Advanced Kinetic-Based Modeling ...magnetic field in opposite direction of applied field Extreme pressure tends to drive plasma out of discharge chamber Difficulties in modeling FRCs High

  6. Hybrid kinetic/fluid modeling of silicon nanoparticles dynamics in silane plasma discharges

    NASA Astrophysics Data System (ADS)

    Orlac'h, J.-M.; Giovangigli, V.; Novikova, T.; Cabarrocas, P. Roca i.

    2016-11-01

    We present a fully coupled self-consistent model for the evolution of nanoparticles in a plasma-enhanced chemical vapor deposition (PECVD) reactor. The plasma is treated as a fluid while the nanoparticles are handled kinetically. The plasma fluid model is derived from kinetic theory applied to multicomponent two-temperature chemically reactive polyatomic plasmas. The model has been implemented numerically for a silane-hydrogen plasma in the early stage of nanoparticles generation.

  7. Extension of Standard Model in Multi-spinor Field Formalism - Visible and Dark Sectors

    NASA Astrophysics Data System (ADS)

    Sogami, Ikuo S.

    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 inationary 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.

  8. Coupling Kinetic and Hydrodynamic Models for Simulations of Gas Flows and Weakly Ionized Plasmas

    NASA Astrophysics Data System (ADS)

    Kolobov, V. I.; Arslanbekov, R. R.

    2011-10-01

    This paper presents adaptive kinetic/fluid models for simulations of gases and weakly ionized plasmas. We first describe a Unified Flow Solver (UFS), which combines Adaptive Mesh Refinement with automatic selection of kinetic or hydrodynamic models for different parts of flows. This Adaptive Mesh and Algorithm Refinement (AMAR) technique limits expensive atomistic-scale solutions only to the regions where they are needed. We present examples of plasma simulations with fluid models and describe kinetic solvers for electrons which are currently being incorporated into AMAR techniques for plasma simulations.

  9. 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.

  10. A hot-atom reaction kinetic model for H abstraction from solid surfaces

    NASA Astrophysics Data System (ADS)

    Kammler, Th.; Kolovos-Vellianitis, D.; Küppers, J.

    2000-07-01

    Measurements of the abstraction reaction kinetics in the interaction of gaseous H atoms with D adsorbed on metal and semiconductor surfaces, H(g)+D(ad)/S→ products, have shown that the kinetics of the HD products are at variance with the expectations drawn from the operation of Eley-Rideal mechanisms. Furthermore, in addition to HD product molecules, D 2 products were observed which are not expected in an Eley-Rideal scenario. Products and kinetics of abstraction reactions on Ni(100), Pt(111), and Cu(111) surfaces were recently explained by a random-walk model based solely on the operation of hot-atom mechanistic steps. Based on the same reaction scenario, the present work provides numerical solutions of the appropriate kinetic equations in the limit of the steady-state approximation for hot-atom species. It is shown that the HD and D 2 product kinetics derived from global kinetic rate constants are the same as those obtained from local probabilities in the random walk model. The rate constants of the hot-atom kinetics provide a background for the interpretation of measured data, which was missing up to now. Assuming that reconstruction affects the competition between hot-atom sticking and hot-atom reaction, the application of the present model at D abstraction from Cu(100) surfaces reproduces the essential characteristics of the experimentally determined kinetics.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Application of adaptive kinetic modelling for bias propagation reduction in direct 4D image reconstruction.

    PubMed

    Kotasidis, F A; Matthews, J C; Reader, A J; Angelis, G I; Zaidi, H

    2014-10-21

    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 [(15)O]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

  17. Dynamic disorder in single-molecule Michaelis-Menten kinetics: the reaction-diffusion formalism in the Wilemski-Fixman approximation.

    PubMed

    Chaudhury, Srabanti; Cherayil, Binny J

    2007-09-14

    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 beta-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.

  18. [Study on simplification of extraction kinetics model and adaptability of total flavonoids model of Scutellariae radix].

    PubMed

    Chen, Yang; Zhang, Jin; Ni, Jian; Dong, Xiao-Xu; Xu, Meng-Jie; Dou, Hao-Ran; Shen, Ming-Rui; Yang, Bo-Di; Fu, Jing

    2014-01-01

    Because of irregular shapes of Chinese herbal pieces, we simplified the previously deduced general extraction kinetic model for TCMs, and integrated particle diameters of Chinese herbs that had been hard to be determined in the final parameter "a". The reduction of the direct determination of particle diameters of Chinese herbs was conducive to increase the accuracy of the model, expand the application scope of the model, and get closer to the actual production conditions. Finally, a simplified model was established, with its corresponding experimental methods and data processing methods determined. With total flavonoids in Scutellariae Radix as the determination index, we conducted a study on the adaptability of total flavonoids extracted from Scutellariae Radix with the water decoction method in the model. The results showed a good linear correlation among the natural logarithm value of the mass concentration of total flavonoids in Scutellariae Radix, the time and the changes in the natural logarithm of solvent multiple. Through calculating and fitting, efforts were made to establish the kinetic model of extracting total flavonoids from Scutellariae Radix with the water decoction method, and verify the model, with a good degree of fitting and deviation within the range of the industrial production requirements. This indicated that the model established by the method has a good adaptability.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. Chemical kinetic modeling study of the effects of oxygenated hydrocarbons on soot emissions from diesel engines.

    PubMed

    Westbrook, Charles K; Pitz, William J; Curran, Henry J

    2006-06-01

    A detailed chemical kinetic modeling approach is used to examine the phenomenon of suppression of sooting in diesel engines by the addition of oxygenated hydrocarbon species to the fuel. This suppression, which has been observed experimentally for a few years, is explained kinetically as a reduction in concentrations of soot precursors present in the hot products of a fuel-rich diesel ignition zone when oxygenates are included. The kinetic model is also used to show how different oxygenates, ester structures in particular, can have different soot-suppression efficiencies due to differences in the molecular structure of the oxygenated species.

  4. The Application of Discontinuous Galerkin Space and Velocity Discretization to Model Kinetic Equations (PREPRINT)

    DTIC Science & Technology

    2009-10-07

    relative velocity of colliding molecules, and b and ε are geometric impact parameters. The Boltzmann equation is a nonlinear integro - differential equation ...Space and Velocity Discretization to Model Kinetic Equations (PREPRINT) 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Alexander...Galerkin discretization is proposed for the Bhatnagar-Gross-Krook model kinetic equation . This approach allows for a high order polynomial approximation of

  5. Modelling rainfall kinetic energy: a novel approach to erosion prediction and management

    NASA Astrophysics Data System (ADS)

    Nissan, H.; Toumi, R.

    2013-12-01

    Soil erosion is already a major global problem. Climate change and the rising world population will exert growing pressure on our land to deliver food and stability. This study presents a new and innovative application of a cloud resolving model, for use in soil erosion prediction studies. Rainfall kinetic energy flux is an important variable in erosion prediction, but is generally parameterized from intensity due to measurement difficulties. Instead, we show that a cloud resolving model can be used to dynamically simulate the kinetic energy of rain from basic physics, using four commonly used microphysics schemes. Rainfall kinetic energy flux is modelled during an idealized supercell storm with the Weather Research and Forecasting model. Results are within the range of observations and also capture the observed variability in kinetic energy flux for a given rainfall intensity, where current methods fail. Large raindrops are shown to contribute disproportionately to total kinetic energy flux compared with their number, suggesting that several existing relations between terminal velocity and size of raindrops are poorly suited for kinetic energy modelling. Treatment of raindrop size is tested and compared between the schemes, and factors influencing the erosive potential of rainfall will also be discussed. This work demonstrates the potential for conducting erosion prediction studies using a regional climate model. The method presented here may be easily extended for use in a full regional climate model with a microphysics parameterization scheme. This paves the way for full climate, and climate change, simulations of rainfall erosivity on regional to global scales and may contribute towards the ultimate integration of an erosion prediction scheme into climate models to allow coupled interactions with the atmosphere. Reference: Geophys. Res. Lett., 40, doi:10.1002/grl.50622 Schematic showing raindrop number density, rain mass flux and kinetic energy flux as

  6. TChem - A Software Toolkit for the Analysis of Complex Kinetic Models

    SciTech Connect

    Safta, Cosmin; Najm, Habib N.; Knio, Omar

    2011-05-01

    The TChem toolkit is a software library that enables numerical simulations using complex chemistry and facilitates the analysis of detailed kinetic models. The toolkit provide capabilities for thermodynamic properties based on NASA polynomials and species production/consumption rates. It incorporates methods that can selectively modify reaction parameters for sensitivity analysis. The library contains several functions that provide analytically computed Jacobian matrices necessary for the efficient time advancement and analysis of detailed kinetic models.

  7. Macrotransport-solidification kinetics modeling of equiaxed dendritic growth. Part 1: Model development and discussion

    SciTech Connect

    Nastac, L.; Stefanescu, D.M.

    1996-12-01

    An analytical model that describes solidification of equiaxed dendrites has been developed for use in solidification kinetics-macrotransport modeling. It relaxes some of the assumptions made in previous models, such as the Dustin-Kurz, Rappaz-Thevoz, and Kanetkar-Stefanescu models. It is assumed that nuclei grow as unperturbed spheres until the radius of the sphere becomes larger than the minimum radius of instability. Then, growth of the dendrites is related to morphological instability and is calculated as a function of melt undercooling around the dendrite tips, which is controlled by the bulk temperature and the intrinsic volume average concentration of the liquid phase. When the general morphology of equiaxed dendrites is considered, the evolution of the fraction of solid is related to the interdendritic branching and dynamic coarsening (through the evolution of the specific interfacial areas) and to the topology and movement of the dendrite envelope (through the tip growth velocity and dendrite shape factor). The particular case of this model is the model for globulitic an overall solute and thermal balance around a growing equiaxed dendrite grain within a spherical closed system. Overall solute balance in the integral form is obtained by a complete analytical solution of the diffusion field in both liquid and solid phases. The bulk temperature is obtained from the solution of the macrotransport-solidification kinetics problem.

  8. [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.

  9. Application of a hybrid kinetic-continuum solver to the near wall modelling

    NASA Astrophysics Data System (ADS)

    Rovenskaya, O.; Croce, G.

    2014-11-01

    A hybrid method dynamically coupling the direct numerical solution of the S-model kinetic equation and Navier-Stokes equations is applied to a numerical simulation of the flow through the channel of a finite length due to arbitrarily pressure ratios and for a wide range of Knudsen number. The decomposition of the physical domain into kinetic and hydrodynamic sub-domains is updated at each time step. The solution is advanced in time simultaneously in both kinetic and hydrodynamic domains: the coupling is achieved by matching half fluxes at the interface of the kinetic and Navier-Stokes domains, thus taking care of the conservation of momentum, energy and mass through the interface. Solver efficiency is increased via MPI (Message Passing Interface) parallelization. Accuracy and reliability of the method, for different decomposition criteria, are assessed via comparison with a pure kinetic solution.

  10. 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.

  11. 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)

  12. 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.

  13. Analysis of pion production data in electron-hadron scattering at JLAB using the TMD Parton Model Formalism

    NASA Astrophysics Data System (ADS)

    Warmate, Tamuno-Negiyeofori; Gamberg, Leonard; Prokudin, Alexei

    2016-09-01

    I have performed a phenomenological analysis of pion production data from Jefferson Laboratory in semi-inclusive deep inelastic scattering of electrons on unpolarized nucleons and deuterium using the transverse momentum dependent (TMD) parton model formalism. We parameterize the data in terms of TMD parton distribution functions that describe the three-dimensional (3-D) partonic structure of the nucleon. One of the main enigmas of data analysis is how to reliably estimate the errors of the parameters that describe some particular physical process. A common method is to use Hessian matrix or vary the delta chi-square of the corresponding fits to the data. In this particular project we use the so-called bootstrap method that is very robust for error estimation. This method has not been extensively used in the description of the TMD distributions that describe the 3-D nucleon structure. The reliable estimate of the errors and thus reliable predictions for future experiments is of great scientific interest. We are using Python and modern methods of data analysis in this project. The results of the project will be useful for understanding the effects of internal motion of quarks and gluons inside of the proton and will be reported in a forthcoming publication.

  14. Weibull mixture model for isoconversional kinetic analysis of biomass oxidative pyrolysis

    NASA Astrophysics Data System (ADS)

    Cai, J. M.; Chen, S. Y.

    2010-03-01

    In this work, the possibility of applying the weighted sum of three cumulative Weibull distribution functions for the fitting of the kinetic conversion data of biomass oxidative pyrolysis has been investigated. The kinetic conversion data of the thermal decomposition of olive oil solid waste in oxygen atmosphere for different heating rates have been analyzed. The results have shown that the experimental data can be perfectly reproduced by the general fitting function. Therefore, it is possible to obtain the corresponding conversion rate values of biomass oxidative pyrolysis by differentiating directly the fitted kinetic conversion data. Additionally, the logistic mixture model has been applied to the same experimental data. It can be found that the newly proposed function can provide a better fit of the data than the logistic mixture model. Based on the fitting of Weibull mixture model, the kinetic triples (E, A and f(α)) of oxidative pyrolysis of olive solid waste were obtained by means of Friedman's differential isoconversional method.

  15. 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

  16. 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.

  17. 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…

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. A kinetic model for the transport of electrons in a graphene layer

    NASA Astrophysics Data System (ADS)

    Fermanian Kammerer, Clotilde; Méhats, Florian

    2016-12-01

    In this article, we propose a new numerical scheme for the computation of the transport of electrons in a graphene device. The underlying quantum model for graphene is a massless Dirac equation, whose eigenvalues display a conical singularity responsible for non-adiabatic transitions between the two modes. We first derive a kinetic model which takes the form of two Boltzmann equations coupled by a collision operator modeling the non-adiabatic transitions. This collision term includes a Landau-Zener transfer term and a jump operator whose presence is essential in order to ensure a good energy conservation during the transitions. We propose an algorithmic realization of the semi-group solving the kinetic model, by a particle method. We give analytic justification of the model and propose a series of numerical experiments studying the influences of the various sources of errors between the quantum and the kinetic models.

  3. 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.

  4. 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.

  5. 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.

  6. Unanimous Model for Describing the Fast Bioluminescence Kinetics of Ca(2+) -regulated Photoproteins of Different Organisms.

    PubMed

    Eremeeva, Elena V; Bartsev, Sergey I; van Berkel, Willem J H; Vysotski, Eugene S

    2017-03-01

    Upon binding their metal ion cofactors, Ca(2+) -regulated photoproteins display a rapid increase of light signal, which reaches its peak within milliseconds. In the present study, we investigate bioluminescence kinetics of the entire photoprotein family. All five recombinant hydromedusan Ca(2+) -regulated photoproteins-aequorin from Aequorea victoria, clytin from Clytia gregaria, mitrocomin from Mitrocoma cellularia and obelins from Obelia longissima and Obelia geniculata-demonstrate the same bioluminescent kinetics pattern. Based on these findings, for the first time we propose a unanimous kinetic model describing the bioluminescence mechanism of Ca(2+) -regulated photoproteins.

  7. Kinetic viscoelasticity modeling applied to degradation during carbon-carbon composite processing

    NASA Astrophysics Data System (ADS)

    Drakonakis, Vassilis M.; Seferis, James C.; Wardle, Brian L.; Nam, Jae-Do; Papanicolaou, George C.; Doumanidis, Charalambos C.

    2010-04-01

    Kinetic viscoelasticity modeling has been successfully utilized to describe phenomena during cure of thermoset based carbon fiber reinforced matrices. The basic difference from classic viscoelasticity is that the fundamental material descriptors change as a result of reaction kinetics. Accordingly, we can apply the same concept for different kinetic phenomena with simultaneous curing and degradation. The application of this concept can easily be utilized in processing and manufacturing of carbon-carbon composites, where phenolic resin matrices are cured degraded and reinfused in a carbon fiber bed. This work provides a major step towards understanding complex viscoelastic phenomena that go beyond simple thermomechanical descriptors.

  8. 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.

  9. Kinetic Model of Coronal Hole Protons Undergoing Turbulent Stochastic Heating and Quasilinear Wave Generation

    NASA Astrophysics Data System (ADS)

    Isenberg, P. A.; Vasquez, B. J.

    2015-12-01

    We have constructed a kinetic model of coronal hole protons heated in the directions perpendicular to the magnetic field according to the turbulent stochastic heating mechanism of Chandran et al. The kinetic heating is modeled by a proton diffusion in v_perp. The protons additionally respond to the coronal hole forces of gravity, charge-separation electric field, and the mirror force as described in our previous kinetic guiding-center models. We have further extended this kinetic model to include wave growth and damping by the anisotropic protons through the quasilinear cyclotron-resonant interaction. We solve the coupled equations for the kinetic proton behavior and for the self-consistent development of ion-cyclotron wave spectra propagating within 60˚ of the magnetic field direction. We seek to obtain a steady-state solution, showing the evolution of the proton distribution and the wave spectra with increasing heliocentric radial position due to the combined effects of heating, resonant scattering coupled to the wave generation, and the kinetic response to the large-scale forces of the inhomogeneous coronal hole. We will report on our results and the implications for the measurements to be made by the Solar Probe Plus mission.

  10. A model for the interfacial kinetics of phospholipase D activity on long-chain lipids.

    PubMed

    Majd, Sheereen; Yusko, Erik C; Yang, Jerry; Sept, David; Mayer, Michael

    2013-07-02

    The membrane-active enzyme phospholipase D (PLD) catalyzes the hydrolysis of the phosphodiester bond in phospholipids and plays a critical role in cell signaling. This catalytic reaction proceeds on lipid-water interfaces and is an example of heterogeneous catalysis in biology. Recently we showed that planar lipid bilayers, a previously unexplored model membrane for these kinetic studies, can be used for monitoring interfacial catalytic reactions under well-defined experimental conditions with chemical and electrical access to both sides of the lipid membrane. Employing an assay that relies on the conductance of the pore-forming peptide gramicidin A to monitor PLD activity, the work presented here reveals the kinetics of hydrolysis of long-chain phosphatidylcholine lipids in situ. We have developed an extension of a basic kinetic model for interfacial catalysis that includes product activation and substrate depletion. This model describes the kinetic behavior very well and reveals two kinetic parameters, the specificity constant and the interfacial quality constant. This approach results in a simple and general model to account for product accumulation in interfacial enzyme kinetics.

  11. Mathematical Formalism of Nonequilibrium Thermodynamics for Nonlinear Chemical Reaction Systems with General Rate Law

    NASA Astrophysics Data System (ADS)

    Ge, Hao; Qian, Hong

    2017-01-01

    This paper studies a mathematical formalism of nonequilibrium thermodynamics for chemical reaction models with N species, M reactions, and general rate law. We establish a mathematical basis for J. W. Gibbs' macroscopic chemical thermodynamics under G. N. Lewis' kinetic law of entire equilibrium (detailed balance in nonlinear chemical kinetics). In doing so, the equilibrium thermodynamics is then naturally generalized to nonequilibrium settings without detailed balance. The kinetic models are represented by a Markovian jumping process. A generalized macroscopic chemical free energy function and its associated balance equation with nonnegative source and sink are the major discoveries. The proof is based on the large deviation principle of this type of Markov processes. A general fluctuation dissipation theorem for stochastic reaction kinetics is also proved. The mathematical theory illustrates how a novel macroscopic dynamic law can emerges from the mesoscopic kinetics in a multi-scale system.

  12. Gas-kinetic model of heat conduction of heterogeneous substances

    NASA Astrophysics Data System (ADS)

    Gladkov, S. O.

    2008-07-01

    A theoretical approach is proposed for calculating thermal conductivity κ of an arbitrary type of porous structures as a function of porosity ξ, temperature T, density ρ, and a number of other parameters. The general computational algorithm is based on the theory of nonequilibrium processes. Its modification in the language of gas-kinetic approximation makes it possible to derive compact relations for κ and to easily estimate the corresponding dependences. Theoretical formulas are compared to experimental results and their good agreement is demonstrated for a specific example of refractory concrete, which is a very important substance for practical applications.

  13. 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.

  14. Kinetic model of turbulence in an incompressible fluid

    NASA Technical Reports Server (NTRS)

    Tchen, C. M.

    1978-01-01

    A statistical description of turbulence in an incompressible fluid obeying the Navier-Stokes equations is proposed, where pressure is regarded as a potential for the interaction between fluid elements. A scaling procedure divides a fluctuation into three ranks representing the three transport processes of macroscopic evolution, transport property, and relaxation. Closure is obtained by relaxation, and a kinetic equation is obtained for the fluctuation of the macroscopic rank of the distribution function. The solution gives the transfer function and eddy viscosity. When applied to the inertia subrange of the energy spectrum the analysis recovers the Kolmogorov law and its numerical coefficient.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Exact results for parallel-chain kinetic models of biological transport

    NASA Astrophysics Data System (ADS)

    Kolomeisky, Anatoly B.

    2001-10-01

    In order to describe the observed behavior of single motor proteins moving along linear molecular tracks, a class of stochastic models is studied which recognizes the possibility of parallel biochemical pathways. Extending the theoretical analysis of Derrida [J. Stat. Phys. 31, 433 (1983)], exact results are derived for the velocity and dispersion of a discrete one-dimensional kinetic model which consists of two parallel chains of N states and M states, respectively, with arbitrary forward and backward rates. Generalizations of this approach for g>2 parallel chains models are briefly sketched. These results and other properties of parallel-chain kinetic models are illustrated by various examples.

  20. 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.

  1. First-principle based modeling of urea decomposition kinetics in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Nicolle, André; Cagnina, Stefania; de Bruin, Theodorus

    2016-11-01

    This study aims at validating a multi-scale modeling methodology based on an implicit solvent model for urea thermal decomposition pathways in aqueous solutions. The influence of the number of cooperative water molecules on kinetics was highlighted. The obtained kinetic model is able to accurately reproduce urea decomposition in aqueous phase under a variety of experimental conditions from different research groups. The model also highlights the competition between HNCO desorption to gas phase and hydrolysis in aqueous phase, which may influence SCR depollution process operation.

  2. 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.

  3. Continuum Kinetic Modeling of the Tokamak Plasma Edge

    NASA Astrophysics Data System (ADS)

    Dorf, Mikhail

    2015-11-01

    The problem of edge plasma transport provides substantial challenges for analytical or numerical analysis due to (a) complex magnetic geometry including both open and closed magnetic field lines B, (b) steep radial gradients comparable to ion drift-orbit excursions, and (c) a variation in the collision mean-free path along B from long to short compared to the magnetic connection length. Here, the first 4D continuum drift-kinetic transport simulations that span the magnetic separatrix of a tokamak are presented, motivated in part by the success of continuum kinetic codes for core physics and in part by the potential for high accuracy. The calculations include fully-nonlinear Fokker-Plank collisions and electrostatic potential variations. The problem of intrinsic toroidal rotation driven by ion orbit loss is addressed in detail. The code, COGENT, developed by the Edge Simulation Laboratory collaboration, is distinguished by a fourth-order finite-volume discretization combined with mapped multiblock grid technology to handle the strong anisotropy of plasma transport and the complex magnetic X-point divertor geometry with high accuracy. Previously, successful performance of high-order algorithms has been demonstrated in a simpler closed magnetic-flux-surface geometry for the problems of neoclassical transport and collisionless relaxation of geodesic acoustic modes in a tokamak pedestal, including the effects of a strong radial electric field under H-mode conditions. Work performed for USDOE, at LLNL under contract DE-AC52-07NA27344.

  4. [A simple kinetic model of myocardium contraction: calcium-mechanics coupling].

    PubMed

    Semin, F A

    2014-01-01

    A kinetic model of cardiac muscle contraction is suggested. It is based on our earlier simplified model of the kinetics of the actin-myosin interaction. We examined the kinetics of formation of calcium-troponin complexes that open the binding sites-on actin for myosin heads. The model also takes into account the cooperativity of this process and the influence of myosin heads on it. It was shown that with proper choice of its parameters the model appropriately describes the dependence of myocardium activation.on sarcomeres length that underlies the Frank-Starling law of the heart. The model fits both steady state experiments on myocardial specimens with permeable membrane and twitch contractions of intact cardiac muscle. It also describes well the myocardium load-dependent relaxation.

  5. Development and sensitivity analysis of a fully kinetic model of sequential reductive dechlorination in groundwater.

    PubMed

    Malaguerra, Flavio; Chambon, Julie C; Bjerg, Poul L; Scheutz, Charlotte; Binning, Philip J

    2011-10-01

    A fully kinetic biogeochemical model of sequential reductive dechlorination (SERD) occurring in conjunction with lactate and propionate fermentation, iron reduction, sulfate reduction, and methanogenesis was developed. Production and consumption of molecular hydrogen (H(2)) by microorganisms have been modeled using modified Michaelis-Menten kinetics and has been implemented in the geochemical code PHREEQC. The model have been calibrated using a Shuffled Complex Evolution Metropolis algorithm to observations of chlorinated solvents, organic acids, and H(2) concentrations in laboratory batch experiments of complete trichloroethene (TCE) degradation in natural sediments. Global sensitivity analysis was performed using the Morris method and Sobol sensitivity indices to identify the most influential model parameters. Results show that the sulfate concentration and fermentation kinetics are the most important factors influencing SERD. The sensitivity analysis also suggests that it is not possible to simplify the model description if all system behaviors are to be well described.

  6. 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.

  7. 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.

  8. 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

  9. A general model for kinetics of heavy metal adsorption and desorption on soils.

    PubMed

    Shi, Zhenqing; Di Toro, Dominic M; Allen, Herbert E; Sparks, Donald L

    2013-04-16

    In this study, we propose a general kinetics model for heavy metal adsorption and desorption reactions in soils when soil organic matter (SOM) is the dominant adsorbent. The kinetics model, integrated with the equilibrium speciation model WHAM VI, specifically considers metal reactions with SOM and dissolved organic matter (DOM) and accounts for the variations of solution chemistry. Metal reactions with SOM are associated with two groups of sites, one from the monodentate sites and another one from the bidentate and tridentate sites. There are three model parameters, desorption rate coefficients of the two groups of SOM sites for each metal and reactive organic carbon (ROC) for each soil. The applicability of the kinetics model was mainly examined with three elements, Cu, Pb, and Zn, which demonstrate different binding ability with organic matter. The kinetic data were collected with a stirred-flow reactor covering a wide range of experimental conditions, including varying SOM, DOM, Ca, and metal concentrations, reaction pHs, and different flow rates. The kinetics model has been successfully applied to describe heavy metal adsorption and desorption on soils under various reaction conditions.

  10. Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis.

    PubMed

    Zhou, Y; Karplus, M

    1999-11-05

    The kinetics and thermodynamics of an off-lattice model for a three-helix bundle protein are investigated as a function of a bias gap parameter that determines the energy difference between native and non-native contacts. A simple dihedral potential is used to introduce the tendency to form right-handed helices. For each value of the bias parameter, 100 trajectories of up to one microsecond are performed. Such statistically valid sampling of the kinetics is made possible by the use of the discrete molecular dynamics method with square-well interactions. This permits much faster simulations for off-lattice models than do continuous potentials. It is found that major folding pathways can be defined, although ensembles with considerable structural variation are involved. The large gap models generally fold faster than those with a smaller gap. For the large gap models, the kinetic intermediates are non-obligatory, while both obligatory and non-obligatory intermediates are present for small gap models. Certain large gap intermediates have a two-helix microdomain with one helix extended outward (as in domain-swapped dimers); the small gap intermediates have more diverse structures. The importance of studying the kinetic, as well as the thermodynamics, of folding for an understanding of the mechanism is discussed and the relation between kinetic and equilibrium intermediates is examined. It is found that the behavior of this model system has aspects that encompass both the "new" view and the "old" view of protein folding.

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

    USGS Publications Warehouse

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

    2001-01-01

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

  12. 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.

  13. Effect of wall growth on the kinetic modeling of nitrite oxidation in a CSTR.

    PubMed

    Dokianakis, Spiros N; Kornaros, Michael; Lyberatos, Gerasimos

    2006-03-05

    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.

  14. Dynamic nuclear renography kinetic analysis: Four-compartment model for assessing kidney function

    NASA Astrophysics Data System (ADS)

    Raswan, T. R.; Haryanto, F.

    2014-09-01

    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.

  15. 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.

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

    PubMed

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

    2011-02-01

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

  17. A detailed kinetic model for the hydrothermal decomposition process of sewage sludge.

    PubMed

    Yin, Fengjun; Chen, Hongzhen; Xu, Guihua; Wang, Guangwei; Xu, Yuanjian

    2015-12-01

    A detailed kinetic model for the hydrothermal decomposition (HTD) of sewage sludge was developed based on an explicit reaction scheme considering exact intermediates including protein, saccharide, NH4(+)-N and acetic acid. The parameters were estimated by a series of kinetic data at a temperature range of 180-300°C. This modeling framework is capable of revealing stoichiometric relationships between different components by determining the conversion coefficients and identifying the reaction behaviors by determining rate constants and activation energies. The modeling work shows that protein and saccharide are the primary intermediates in the initial stage of HTD resulting from the fast reduction of biomass. The oxidation processes of macromolecular products to acetic acid are highly dependent on reaction temperature and dramatically restrained when temperature is below 220°C. Overall, this detailed model is meaningful for process simulation and kinetic analysis.

  18. 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.

  19. 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.

  20. 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.