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
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
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.
Hamiltonian formalism of two-dimensional Vlasov kinetic equation
Pavlov, Maxim V.
2014-01-01
In this paper, the two-dimensional Benney system describing long wave propagation of a finite depth fluid motion and the multi-dimensional Russo–Smereka kinetic equation describing a bubbly flow are considered. The Hamiltonian approach established by J. Gibbons for the one-dimensional Vlasov kinetic equation is extended to a multi-dimensional case. A local Hamiltonian structure associated with the hydrodynamic lattice of moments derived by D. J. Benney is constructed. A relationship between this hydrodynamic lattice of moments and the two-dimensional Vlasov kinetic equation is found. In the two-dimensional case, a Hamiltonian hydrodynamic lattice for the Russo–Smereka kinetic model is constructed. Simple hydrodynamic reductions are presented. PMID:25484603
Hamiltonian formalism of two-dimensional Vlasov kinetic equation.
Pavlov, Maxim V
2014-12-08
In this paper, the two-dimensional Benney system describing long wave propagation of a finite depth fluid motion and the multi-dimensional Russo-Smereka kinetic equation describing a bubbly flow are considered. The Hamiltonian approach established by J. Gibbons for the one-dimensional Vlasov kinetic equation is extended to a multi-dimensional case. A local Hamiltonian structure associated with the hydrodynamic lattice of moments derived by D. J. Benney is constructed. A relationship between this hydrodynamic lattice of moments and the two-dimensional Vlasov kinetic equation is found. In the two-dimensional case, a Hamiltonian hydrodynamic lattice for the Russo-Smereka kinetic model is constructed. Simple hydrodynamic reductions are presented.
On a Broken Formal Symmetry between Kinetic and Gravitational Energy
NASA Astrophysics Data System (ADS)
Nikkhah Shirazi, Armin
2011-03-01
Historically, the discovery of symmetries has played an important role in the progress of our fundamental understanding of nature. This paper will demonstrate that there exists in Newtonian theory in a spherical gravitational field a formal symmetry between the kinetic (KE) and gravitational potential energy (GPE) of a test mass. Put differently, there exists a way of expressing GPE such that the form of the mathematical expression remains invariant under an interchange of KE and GPE. When extended to relativity by a suitable assumption, it leads to a framework that bridges the general relativistic and Newtonian conceptions of gravitational energy, even though the symmetry is broken except in the infinitesimal limit. Recognizing this symmetry at infinitesimal scales makes it possible to write a relativistic equation of an individual graviton, the properties of which under under one interpretation may be unexpected.
Opinion dynamics model based on quantum formalism
Artawan, I. Nengah; Trisnawati, N. L. P.
2016-03-11
Opinion dynamics model based on quantum formalism is proposed. The core of the quantum formalism is on the half spin dynamics system. In this research the implicit time evolution operators are derived. The analogy between the model with Deffuant dan Sznajd models is discussed.
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.
Kiperman, S.L.
1995-01-01
The problems associated with the accuracy of kinetic models in heterogeneous catalysis and their adequacy to experimental data and reaction mechanisms are considered. The prospects for the further improvement and use of these models is also explored.
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…
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.
Workshop on Formal Models for Intelligent Control
1994-04-01
how and when to make these control law changes is the business of the sequential automaton. He went on to discuss a a uniform model of hybrid systems...computation complexity of simple questions concerning the behavior of such systems. Ramadge reviewed some of these models and results and speculated on...15 Reprenttlveysts A Formal Model for Heuristic Rules in DEDS 900 - 930 Yu Chi Ho What is Intelligent Control? Harvad University Shenke Sasy University
Kinetic theory of turbulence for parallel propagation revisited: Formal results
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.
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.
Some Formal Approaches to the Analysis of Kinetic Data in Terms of Linear Compartmental Systems
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
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.
Oxidative desulfurization: kinetic modelling.
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.
LLNL Chemical Kinetics Modeling Group
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.
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.
Time reversal invariance of quantum kinetic equations: Nonequilibrium Green functions formalism
NASA Astrophysics Data System (ADS)
Scharnke, Miriam; Schlünzen, Niclas; Bonitz, Michael
2017-06-01
Time reversal symmetry is a fundamental property of many quantum mechanical systems. The relation between statistical physics and time reversal is subtle and not all statistical theories conserve this particular symmetry, most notably hydrodynamic equations and kinetic equations such as the Boltzmann equation. In this article, it is shown analytically that quantum kinetic generalizations of the Boltzmann equation that are derived using the nonequilibrium Green functions formalism as well as all approximations that stem from Φ-derivable self-energies are time reversal invariant.
Starobinsky cosmological model in Palatini formalism
NASA Astrophysics Data System (ADS)
Stachowski, Aleksander; Szydłowski, Marek; Borowiec, Andrzej
2017-06-01
We classify singularities in FRW cosmologies, which dynamics can be reduced to the dynamical system of the Newtonian type. This classification is performed in terms of the geometry of a potential function if it has poles. At the sewn singularity, which is of a finite scale factor type, the singularity in the past meets the singularity in the future. We show that such singularities appear in the Starobinsky model in f({\\hat{R}})={\\hat{R}}+γ {\\hat{R}}^2 in the Palatini formalism, when dynamics is determined by the corresponding piecewise-smooth dynamical system. As an effect we obtain a degenerate singularity. Analytical calculations are given for the cosmological model with matter and the cosmological constant. The dynamics of model is also studied using dynamical system methods. From the phase portraits we find generic evolutionary scenarios of the evolution of the universe. For this model, the best fit value of Ω _γ =3γ H_0^2 is equal 9.70× 10^{-11}. We consider a model in both Jordan and Einstein frames. We show that after transition to the Einstein frame we obtain both the form of the potential of the scalar field and the decaying Lambda term.
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.
A formal model of interpersonal inference
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
Zakynthinaki, Maria S.
2015-01-01
The objective of the present study was to formulate a simple and at the same time effective mathematical model of heart rate kinetics in response to movement (exercise). Based on an existing model, a system of two coupled differential equations which give the rate of change of heart rate and the rate of change of exercise intensity is used. The modifications introduced to the existing model are justified and discussed in detail, while models of blood lactate accumulation in respect to time and exercise intensity are also presented. The main modification is that the proposed model has now only one parameter which reflects the overall cardiovascular condition of the individual. The time elapsed after the beginning of the exercise, the intensity of the exercise, as well as blood lactate are also taken into account. Application of the model provides information regarding the individual’s cardiovascular condition and is able to detect possible changes in it, across the data recording periods. To demonstrate examples of successful numerical fit of the model, constant intensity experimental heart rate data sets of two individuals have been selected and numerical optimization was implemented. In addition, numerical simulations provided predictions for various exercise intensities and various cardiovascular condition levels. The proposed model can serve as a powerful tool for a complete means of heart rate analysis, not only in exercise physiology (for efficiently designing training sessions for healthy subjects) but also in the areas of cardiovascular health and rehabilitation (including application in population groups for which direct heart rate recordings at intense exercises are not possible or not allowed, such as elderly or pregnant women). PMID:25876164
Modelling heart rate kinetics.
Zakynthinaki, Maria S
2015-01-01
The objective of the present study was to formulate a simple and at the same time effective mathematical model of heart rate kinetics in response to movement (exercise). Based on an existing model, a system of two coupled differential equations which give the rate of change of heart rate and the rate of change of exercise intensity is used. The modifications introduced to the existing model are justified and discussed in detail, while models of blood lactate accumulation in respect to time and exercise intensity are also presented. The main modification is that the proposed model has now only one parameter which reflects the overall cardiovascular condition of the individual. The time elapsed after the beginning of the exercise, the intensity of the exercise, as well as blood lactate are also taken into account. Application of the model provides information regarding the individual's cardiovascular condition and is able to detect possible changes in it, across the data recording periods. To demonstrate examples of successful numerical fit of the model, constant intensity experimental heart rate data sets of two individuals have been selected and numerical optimization was implemented. In addition, numerical simulations provided predictions for various exercise intensities and various cardiovascular condition levels. The proposed model can serve as a powerful tool for a complete means of heart rate analysis, not only in exercise physiology (for efficiently designing training sessions for healthy subjects) but also in the areas of cardiovascular health and rehabilitation (including application in population groups for which direct heart rate recordings at intense exercises are not possible or not allowed, such as elderly or pregnant women).
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.
Saa, Pedro A; Nielsen, Lars K
2017-09-12
Kinetic models are critical to predict the dynamic behaviour of metabolic networks. Mechanistic kinetic models for large networks remain uncommon due to the difficulty of fitting their parameters. Recent modelling frameworks promise new ways to overcome this obstacle while retaining predictive capabilities. In this review, we present an overview of the relevant mathematical frameworks for kinetic formulation, construction and analysis. Starting with kinetic formalisms, we next review statistical methods for parameter inference, as well as recent computational frameworks applied to the construction and analysis of kinetic models. Finally, we discuss opportunities and limitations hindering the development of larger kinetic reconstructions. Copyright © 2017. Published by Elsevier Inc.
Multi-formalism modelling and simulation: application to cardiac modelling
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
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.
Relaxation Kinetic Study of Eudragit® NM30D Film Based on Complex Modulus Formalism.
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.
Formal Specification of the OpenMP Memory Model
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.
Cellulose hydrolysis in evolving substrate morphologies I: A general modeling formalism.
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.
Incremental and unifying modelling formalism for biological interaction networks
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
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.
Formalized landscape models for surveying and modelling tasks
NASA Astrophysics Data System (ADS)
Löwner, Marc-Oliver
2010-05-01
We present a formalization of main geomorphic landscape models, mainly the concept of slopes, to clarify the needs and potentials of surveying technologies and modelling approaches. Using the Unified Modelling Language (UML) it is implemented as a exchangeable Geography Markup Language (GML3) -based application schema and therefore supports shared measurement campaigns. Today, knowledge in Geomorphology is given synoptically in textbooks in a more or less lyrical way. This knowledge is hard to implement for the use of modelling algorithms or data storage and sharing questions. On the other hand physical based numerical modelling and high resolution surveying technologies enable us to investigate case scenarios within small scales. Bringing together such approaches and organizing our data in an appropriate way will need the formalization of the concepts and knowledge that is archived in the science of geomorphology. The main problem of comparing research results in geomorphology but is that the objects under investigation are composed of 3-dimensional geometries that change in time due to processes of material fluxes, e. g. soil erosion or mass movements. They have internal properties, e. g. soil texture or bulk density, that determine the effectiveness of these processes but are under change as well. The presented application schema is available on the Internet and therefore a first step to enable researchers to share information using an OGC's Web feature service. In this vein comparing modelling results of landscape evolution with results of other scientist's observations is possible. Compared to prevalent data concepts the model presented makes it possible to store information about landforms, their geometry and the characteristics in more detail. It allows to represent the 3D-geometry, the set of material properties and the genesis of a landform by associating processes to a geoobject. Thus, time slices of a geomorphic system can be represented as well as
Stochastic kinetic mean field model
NASA Astrophysics Data System (ADS)
Erdélyi, Zoltán; Pasichnyy, Mykola; Bezpalchuk, Volodymyr; Tomán, János J.; Gajdics, Bence; Gusak, Andriy M.
2016-07-01
This paper introduces a new model for calculating the change in time of three-dimensional atomic configurations. The model is based on the kinetic mean field (KMF) approach, however we have transformed that model into a stochastic approach by introducing dynamic Langevin noise. The result is a stochastic kinetic mean field model (SKMF) which produces results similar to the lattice kinetic Monte Carlo (KMC). SKMF is, however, far more cost-effective and easier to implement the algorithm (open source program code is provided on http://skmf.eu website). We will show that the result of one SKMF run may correspond to the average of several KMC runs. The number of KMC runs is inversely proportional to the amplitude square of the noise in SKMF. This makes SKMF an ideal tool also for statistical purposes.
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.
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).
Chemical kinetics and combustion modeling
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.
Kinetic Modeling of Divertor Plasma
NASA Astrophysics Data System (ADS)
Ishiguro, Seiji; Hasegawa, Hiroki; Pianpanit, Theerasarn
2015-11-01
Particle-in-Cell (PIC) simulation with the Monte Carlo collisions and the cumulative scattering angle coulomb collision can present kinetic dynamics of divertor plasmas. We are developing two types of PIC codes. The first one is the three dimensional bounded PIC code where three dimensional kinetic dynamics of blob is studied and current flow structures related to sheath formation are unveiled. The second one is the one spatial three velocity space dimensional (1D3V) PIC code with the Monte Carlo collisions where formation of detach plasma is studied. First target of our research is to construct self-consistent full kinetic simulation modeling of the linear divertor simulation experiments. This work is performed with the support and under the auspices of NIFS Collaboration Research program (NIFS15KNSS059, NIFS14KNXN279, and NIFS13KNSS038) and the Research Cooperation Program on Hierarchy and Holism in Natural Science at NINS.
Kinetic Modeling of Biological Systems
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
Kinetic Modeling of Biological Systems
Resat, Haluk; Petzold, Linda; Pettigrew, Michel F.
2009-04-21
The dynamics of how its constituent components interact define the spatio-temporal response of a natural 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.
Models of fertilization kinetics
Lehtonen, Jussi
2015-01-01
Fertilization functions describe how the number of realized fertilizations depends on gamete numbers or density. They provide insight into the fertilization process, and are important components in models on the evolution of reproductive and sex-specific traits. Existing fertilization functions generally examine the proportion of fertilized eggs as a function of sperm numbers or density in a given fertilization environment. Because these functions have been developed for species with highly diverged gametes, there is an inbuilt (and well justified) asymmetry in them: they treat eggs and sperm, and therefore the two sexes, differently. Although very useful, such functions cannot therefore be used to consistently model early stages in the evolution of the two sexes, or extant species where sex-specific gamete sizes and numbers are similar. Here, I derive fertilization functions that describe the fertilization process without making prior assumptions about the two sexes, and are therefore consistent under any level of gamete dimorphism. These functions are compatible with simpler fertilization functions under appropriate conditions. Such functions can be particularly useful in understanding the early stages in the differentiation of the two sexes, as well as its consequences, where the gametes from the two sexes should be treated on an equal basis. PMID:26473043
Modeling Cyber Conflicts Using an Extended Petri Net Formalism
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.
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.
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…
Kinetic Modeling of Microbiological Processes
Liu, Chongxuan; Fang, Yilin
2012-08-26
Kinetic description of microbiological processes is vital for the design and control of microbe-based biotechnologies such as waste water treatment, petroleum oil recovery, and contaminant attenuation and remediation. Various models have been proposed to describe microbiological processes. This editorial article discusses the advantages and limiation of these modeling approaches in cluding tranditional, Monod-type models and derivatives, and recently developed constraint-based approaches. The article also offers the future direction of modeling researches that best suit for petroleum and environmental biotechnologies.
Kinetic model of HIV infection
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.
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 Fe^{2 +}-Fe^{3+} 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 Fe^{2+/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.
Dynamic decision modeling in medicine: a critique of existing formalisms.
Leong, T. Y.
1993-01-01
Dynamic decision models are frameworks for modeling and solving decision problems that take into explicit account the effects of time. These formalisms are based on structural and semantical extensions of conventional decision models, e.g., decision trees and influence diagrams, with the mathematical definitions of finite-state semi-Markov processes. This paper identifies the common theoretical basis of existing dynamic decision modeling formalisms, and compares and contrasts their applicability and efficiency. It also argues that a subclass of such dynamic decision problems can be formulated and solved more effectively with non-graphical techniques. Some insights gained from this exercise on automating the dynamic decision making process are summarized. PMID:8130519
Formal modeling of a system of chemical reactions under uncertainty.
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.
NASA Astrophysics Data System (ADS)
Nazarova, G.; Ivashkina, E.; Ivanchina, E.; Kiseleva, S.; Stebeneva, V.
2015-11-01
The issue of improving the energy and resource efficiency of advanced petroleum processing can be solved by the development of adequate mathematical model based on physical and chemical regularities of process reactions with a high predictive potential in the advanced petroleum refining. In this work, the development of formalized hydrocarbon conversion scheme of catalytic cracking was performed using thermodynamic parameters of reaction defined by the Density Functional Theory. The list of reaction was compiled according to the results of feedstock structural-group composition definition, which was done by the n-d-m-method, the Hazelvuda method, qualitative composition of feedstock defined by gas chromatography-mass spectrometry and individual composition of catalytic cracking gasoline fraction. Formalized hydrocarbon conversion scheme of catalytic cracking will become the basis for the development of the catalytic cracking kinetic model.
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.
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.
Kinetic models of immediate exchange
NASA Astrophysics Data System (ADS)
Heinsalu, Els; Patriarca, Marco
2014-08-01
We propose a novel kinetic exchange model differing from previous ones in two main aspects. First, the basic dynamics is modified in order to represent economies where immediate wealth exchanges are carried out, instead of reshufflings or uni-directional movements of wealth. Such dynamics produces wealth distributions that describe more faithfully real data at small values of wealth. Secondly, a general probabilistic trading criterion is introduced, so that two economic units can decide independently whether to trade or not depending on their profit. It is found that the type of the equilibrium wealth distribution is the same for a large class of trading criteria formulated in a symmetrical way with respect to the two interacting units. This establishes unexpected links between and provides a microscopic foundations of various kinetic exchange models in which the existence of a saving propensity is postulated. We also study the generalized heterogeneous version of the model in which units use different trading criteria and show that suitable sets of diversified parameter values with a moderate level of heterogeneity can reproduce realistic wealth distributions with a Pareto power law.
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.
Memory sparing, fast scattering formalism for rigorous diffraction modeling
NASA Astrophysics Data System (ADS)
Iff, W.; Kämpfe, T.; Jourlin, Y.; Tishchenko, A. V.
2017-07-01
The basics and algorithmic steps of a novel scattering formalism suited for memory sparing and fast electromagnetic calculations are presented. The formalism, called ‘S-vector algorithm’ (by analogy with the known scattering-matrix algorithm), allows the calculation of the collective scattering spectra of individual layered micro-structured scattering objects. A rigorous method of linear complexity is applied to model the scattering at individual layers; here the generalized source method (GSM) resorting to Fourier harmonics as basis functions is used as one possible method of linear complexity. The concatenation of the individual scattering events can be achieved sequentially or in parallel, both having pros and cons. The present development will largely concentrate on a consecutive approach based on the multiple reflection series. The latter will be reformulated into an implicit formalism which will be associated with an iterative solver, resulting in improved convergence. The examples will first refer to 1D grating diffraction for the sake of simplicity and intelligibility, with a final 2D application example.
Spectral method for a kinetic swarming model
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.
Spectral method for a kinetic swarming model
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.
Bridging the Semantic Gap Between Heterogeneous Modeling Formalisms and FMI
2014-04-25
the timed semantics of FMI. While in the case of encoding a discrete-event (DE) actor such as those used in Ptolemy [7, 12] as an FMU, we need to...in a number of languages and tools such as ns-3, VHDL, SimEvents, and Ptolemy [7]. The semantics of DE have been formalized in various papers, e.g...sense, since there are specialized tools (e.g., Ptolemy ) for SDF modeling and simulation. What is interesting about the above mapping, however, is that
Computational Modeling, Formal Analysis, and Tools for Systems Biology
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
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.
Chemical kinetic modeling of H{sub 2} applications
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.
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
Kinetic modelling of mitochondrial translation.
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.
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…
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…
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.
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.
Formal modeling and verification of fractional order linear systems.
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.
Modeling of Reactor Kinetics and Dynamics
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.
The Importance of Formalizing Computational Models of Face Adaptation Aftereffects
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
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…
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…
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.
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.
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.
Viral kinetic modeling: state of the art
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
Viral kinetic modeling: state of the art
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.
Kinetic-effect models and their applications.
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.
Beware the tail that wags the dog: informal and formal models in biology
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
Chemical Kinetic Modeling of Advanced Transportation Fuels
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.
Kinetic model for kraft pulping of hardwood
Giudici, R.; Park, S.W.
1996-03-01
A comprehensive model for the kraft pulping kinetics of Eucalyptus saligna hardwood is presented. Kinetic parameters were estimated by fitting the model to available experimental data taken from the literature over a range of process variables. The model takes into account the effect of hydroxide and sulfide concentration in the liquor as well as the temperature-time history of the cooking. Model predictions were successfully compared with an independent set of bench-scale plant data for lignin and carbohydrate dissolution. The model is able to predict quite well the trends of the process variables.
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.
Notes on the models of cadmium kinetics.
Yan, Xiong
2005-11-01
This paper identifies several drawbacks in the models of absorption and desorption of cadmium presented by [Garcia-Gomez, C., Carbonell, G., 2004. Modelling the absorption and desorption of cadmium on paper pulp using kinetic approaches. Chemosphere 55, 869-878]. It then provides suggestions on improving the effectiveness of the model.
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.
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 = - Â†Âϕ with the operators ÂandÂ† 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”.
Exact solutions for kinetic models of macromolecular dynamics.
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.
Algorithms, modelling and VO₂ kinetics.
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.
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.
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)
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)
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.
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.
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.
Chemical Kinetic Models for Advanced Engine Combustion
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.
Simple Model of Protein Folding Kinetics
NASA Astrophysics Data System (ADS)
Zwanzig, Robert
1995-10-01
A simple model of the kinetics of protein folding is presented. The reaction coordinate is the "correctness" of a configuration compared with the native state. The model has a gap in the energy spectrum, a large configurational entropy, a free energy barrier between folded and partially folded states, and a good thermodynamic folding transition. Folding kinetics is described by a master equation. The folding time is estimated by means of a local thermodynamic equilibrium assumption and then is calculated both numerically and analytically by solving the master equation. The folding time has a maximum near the folding transition temperature and can have a minimum at a lower temperature.
Modeling recrystallization kinetics during strip rolling
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.
Investigation of the kinetic model equations.
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.
Chiral Schwinger model based on the Batalin-Fradkin-Vilkovisky formalism
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.
Modeling the Medium: Effects of Formal Properties of Children's Television Programs.
ERIC Educational Resources Information Center
Huston-Stein, Aletha; Wright, John C.
This paper discusses research on the effects of formal features of television programs on children's attention, comprehension, and social behavior. Formal features are defined as visual and auditory events which are not primarily a part of the content or message. Three models of the influences of form and content are discussed: (1) the…
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.
Chemical Kinetic Modeling of Hydrogen Combustion Limits
Pitz, W J; Westbrook, C K
2008-04-02
A detailed chemical kinetic model is used to explore the flammability and detonability of hydrogen mixtures. In the case of flammability, a detailed chemical kinetic mechanism for hydrogen is coupled to the CHEMKIN Premix code to compute premixed, laminar flame speeds. The detailed chemical kinetic model reproduces flame speeds in the literature over a range of equivalence ratios, pressures and reactant temperatures. A series of calculation were performed to assess the key parameters determining the flammability of hydrogen mixtures. Increased reactant temperature was found to greatly increase the flame speed and the flammability of the mixture. The effect of added diluents was assessed. Addition of water and carbon dioxide were found to reduce the flame speed and thus the flammability of a hydrogen mixture approximately equally well and much more than the addition of nitrogen. The detailed chemical kinetic model was used to explore the detonability of hydrogen mixtures. A Zeldovich-von Neumann-Doring (ZND) detonation model coupled with detailed chemical kinetics was used to model the detonation. The effectiveness on different diluents was assessed in reducing the detonability of a hydrogen mixture. Carbon dioxide was found to be most effective in reducing the detonability followed by water and nitrogen. The chemical action of chemical inhibitors on reducing the flammability of hydrogen mixtures is discussed. Bromine and organophosphorus inhibitors act through catalytic cycles that recombine H and OH radicals in the flame. The reduction in H and OH radicals reduces chain branching in the flame through the H + O{sub 2} = OH + O chain branching reaction. The reduction in chain branching and radical production reduces the flame speed and thus the flammability of the hydrogen mixture.
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.
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.
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.
Modeling inhomogeneous DNA replication kinetics.
Gauthier, Michel G; Norio, Paolo; Bechhoefer, John
2012-01-01
In eukaryotic organisms, DNA replication is initiated at a series of chromosomal locations called origins, where replication forks are assembled proceeding bidirectionally to replicate the genome. The distribution and firing rate of these origins, in conjunction with the velocity at which forks progress, dictate the program of the replication process. Previous attempts at modeling DNA replication in eukaryotes have focused on cases where the firing rate and the velocity of replication forks are homogeneous, or uniform, across the genome. However, it is now known that there are large variations in origin activity along the genome and variations in fork velocities can also take place. Here, we generalize previous approaches to modeling replication, to allow for arbitrary spatial variation of initiation rates and fork velocities. We derive rate equations for left- and right-moving forks and for replication probability over time that can be solved numerically to obtain the mean-field replication program. This method accurately reproduces the results of DNA replication simulation. We also successfully adapted our approach to the inverse problem of fitting measurements of DNA replication performed on single DNA molecules. Since such measurements are performed on specified portion of the genome, the examined DNA molecules may be replicated by forks that originate either within the studied molecule or outside of it. This problem was solved by using an effective flux of incoming replication forks at the model boundaries to represent the origin activity outside the studied region. Using this approach, we show that reliable inferences can be made about the replication of specific portions of the genome even if the amount of data that can be obtained from single-molecule experiments is generally limited.
A kinetic model of precipitate evolution
Rohrer, C.L.; Hyland, R.W. Jr.; Asta, M.D.; Foiles, S.M.
1996-12-31
Chemical reaction rate theory is used to model the kinetics of precipitation reactions in Al alloys, including the effects of continuous cooling and thermally generated point defects. The computational method models the processes of nucleation, growth, and coarsening within a single framework. Calculated time and temperature dependent precipitate number densities and sizes during the homogeneous precipitation of the Al{sub 3}Sc phase in an Al-.11 at% Sc alloy are shown to compare favorably with experimental observations.
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.
Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer
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
Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer.
Khalid, Samra; Hanif, Rumeza; Tareen, Samar H K; Siddiqa, Amnah; Bibi, Zurah; Ahmad, Jamil
2016-01-01
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. 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. 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. 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.
Viral kinetic modeling: state of the art.
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.
Modeling the Kinetics of Root Gravireaction
NASA Astrophysics Data System (ADS)
Kondrachuk, Alexander V.; Starkov, Vyacheslav N.
2011-02-01
The known "sun-flower equation" (SFE), which was originally proposed to model root circumnutating, was used to describe the simplest tip root graviresponse. Two forms of the SFE (integro-differential and differential-delayed) were solved, analyzed and compared with each other. The numerical solutions of these equations were found to be matching with arbitrary accuracy. The analysis of the solutions focused on time-lag effects on the kinetics of tip root bending. The results of the modeling are in good correlation with an experiment at the initial stages of root tips graviresponse. Further development of the model calls for its systematic comparison with some specially designed experiments, which would include measuring the kinetics of root tip bending before gravistimulation over the period of time longer than the time lag.
A unified kinetic model for particle aggregation
Gardner, K.H.; Theis, T.L.
1996-06-01
Aggregation of submicrometer particles is a process with significant implications for the fate and transport of contaminants and major nutrients in many coastal, estuarine, and freshwater bodies as well as groundwater systems. A unified model has been developed that describes the kinetics of particle aggregation. The model is unique in the incorporation of surface chemical phenomena along with solution chemistry in the determination of the stability of a colloidal dispersion. The aggregation process is treated in a truly kinetic fashion, the main output from the model being the evolution of complete particle size distributions over time. The model was developed to interpret laboratory data and, as such, has the capacity to estimate a (variable) set of system parameters by fitting the size distribution over time data to that measured. It was found that the attachment distance, a parameter frequently approximated in practice, has a profound influence on the predicted aggregation kinetics as does the choice of a solid/solution interfacial model. Furthermore, simulation of relatively long-term aggregation, which was the principal focus of this work, indicates that values of the collision efficiency factor should be much smaller than those reported elsewhere in the literature.
Yavari, M.
2016-06-15
We generalize the results of Nesterenko [13, 14] and Gogilidze and Surovtsev [15] for DNA structures. Using the generalized Hamiltonian formalism, we investigate solutions of the equilibrium shape equations for the linear free energy model.
Fully analytical kinetic model of resonance dynamics in the Solar system
NASA Astrophysics Data System (ADS)
Cubrovic, M.
2006-05-01
We propose a fractional kinetic equation to model the transport in eccentricity of objects in the mean motion resonances in the Elliptic Planar Restricted Three-Body Problem. Making use of the renormalization group formalism, we show how the fractional exponents and the diffusion coefficient can be estimated analytically, making use of the degeneracy of the problem. We apply our model to selected Mean Motion Resonances in the Solar System and explain some basic properties of transport in these resonances.
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).
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.
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.
Kinetic modeling in PET imaging of hypoxia
Li, Fan; Joergensen, Jesper T; Hansen, Anders E; Kjaer, Andreas
2014-01-01
Tumor hypoxia is associated with increased therapeutic resistance leading to poor treatment outcome. Therefore the ability to detect and quantify intratumoral oxygenation could play an important role in future individual personalized treatment strategies. Positron Emission Tomography (PET) can be used for non-invasive mapping of tissue oxygenation in vivo and several hypoxia specific PET tracers have been developed. Evaluation of PET data in the clinic is commonly based on visual assessment together with semiquantitative measurements e.g. standard uptake value (SUV). However, dynamic PET contains additional valuable information on the temporal changes in tracer distribution. Kinetic modeling can be used to extract relevant pharmacokinetic parameters of tracer behavior in vivo that reflects relevant physiological processes. In this paper, we review the potential contribution of kinetic analysis for PET imaging of hypoxia. PMID:25250200
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.
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.
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.
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.
Psychological Screening for Weapons Use Suitability: A Formal Decision Model,
Psychological tests, *Military personnel, *Performance(Human), *Models, *Decision making, Scoring, Ratings, Data bases, Standardization, Personality ...tests, Psychology , Questionnaires, factor analysis, Diagnosis(General), Symposia
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.
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…
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…
Kinetic modeling of the polar wind
NASA Astrophysics Data System (ADS)
Tam, S. W. Y.; Chang, T.; Pierrard, V.
2007-11-01
The polar wind, a plasma outflow along open geomagnetic field lines from the Earth's ionosphere, has been the subject of many theoretical studies. Since the proposal of its existence more than 30 years ago, the polar wind has been described by various theoretical modeling approaches. In this paper, we first describe the two traditional modeling approaches for the classical polar wind: moment-based models and collisionless kinetic calculations; and discuss how other models of the outflow were formed by combining these two traditional approaches. We then discuss how kinetic calculations have been improved to take into account the effects of Coulomb collisions, which may contribute to the formation of double-peaked H+ velocity distributions in the polar wind. As observations of escaping O+ fluxes have guided theoreticians to go beyond the classical polar wind description, we discuss how models were modified or constructed in order to take into account the various non-classical effects, including those due to photoelectrons, which may also provide an explanation for the satellite observations of day night asymmetries in addition to the acceleration of the O+ ions.
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.
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.
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.
A Formal Comparison of Model Variants for Performance Prediction
2009-12-01
400 450 500 1 2 3 4 5 6 7 8 P e rf o rm a n c e S c o re s Mission Team Performance in UAS Predator Simulation CERI , 2005 Humans Model...Simulation CERI , 2005 Humans Model Team Performance in F-16 Simulator Missions DMO Testbd, Mesa Table 2. Cross-validation RMSD...Warfighter Readiness Research Division. The authors would like to thank the Cognitive Engineering Research Institute ( CERI ) and researchers from Mesa’s
Developing Formal Object-oriented Requirements Specifications: A Model, Tool and Technique.
ERIC Educational Resources Information Center
Jackson, Robert B.; And Others
1995-01-01
Presents a formal object-oriented specification model (OSS) for computer software system development that is supported by a tool that automatically generates a prototype from an object-oriented analysis model (OSA) instance, lets the user examine the prototype, and permits the user to refine the OSA model instance to generate a requirements…
Thermodynamic and kinetic modeling of transcriptional pausing.
Tadigotla, Vasisht R; O Maoiléidigh, Dáibhid; Sengupta, Anirvan M; Epshtein, Vitaly; Ebright, Richard H; Nudler, Evgeny; Ruckenstein, Andrei E
2006-03-21
We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA-DNA, DNA-RNA, and RNA-RNA base pairing associated with (i) the translocational and size fluctuations of the transcription bubble; (ii) changes in the associated DNA-RNA hybrid; and (iii) changes in the cotranscriptional RNA secondary structure upstream of the RNA exit channel. The calculations involve no adjustable parameters except for a cutoff used to discriminate paused from nonpaused complexes. When applied to 100 experimental pauses in transcription elongation by Escherichia coli RNA polymerase on 10 DNA templates, the approach produces statistically significant results. We also present a kinetic model for the rate of recovery of backtracked paused complexes. A crucial ingredient of our model is the incorporation of kinetic barriers to backtracking resulting from steric clashes of EC with the cotranscriptionally generated RNA secondary structure, an aspect not included explicitly in previous attempts at modeling the transcription elongation process.
Thermodynamic and kinetic modeling of transcriptional pausing
Tadigotla, Vasisht R.; Maoiléidigh, Dáibhid Ó; Sengupta, Anirvan M.; Epshtein, Vitaly; Ebright, Richard H.; Nudler, Evgeny; Ruckenstein, Andrei E.
2006-01-01
We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA–DNA, DNA–RNA, and RNA–RNA base pairing associated with (i) the translocational and size fluctuations of the transcription bubble; (ii) changes in the associated DNA–RNA hybrid; and (iii) changes in the cotranscriptional RNA secondary structure upstream of the RNA exit channel. The calculations involve no adjustable parameters except for a cutoff used to discriminate paused from nonpaused complexes. When applied to 100 experimental pauses in transcription elongation by Escherichia coli RNA polymerase on 10 DNA templates, the approach produces statistically significant results. We also present a kinetic model for the rate of recovery of backtracked paused complexes. A crucial ingredient of our model is the incorporation of kinetic barriers to backtracking resulting from steric clashes of EC with the cotranscriptionally generated RNA secondary structure, an aspect not included explicitly in previous attempts at modeling the transcription elongation process. PMID:16537373
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.
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.
Colored noise and memory effects on formal spiking neuron models.
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.
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.
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.
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.
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.
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.
Modeling cellular deformations using the level set formalism
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
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.
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.
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.
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.
A kinetic model of adsorption on solid surfaces
NASA Astrophysics Data System (ADS)
Aoki, Kazuo; Giovangigli, Vincent; Hattori, Masanari
2016-11-01
A kinetic model describing physisorption and chemisorption of gas particles on a crystal surface is introduced. A single kinetic equation is used to model gas and physisorbed particles interacting with an average potential and colliding with phonons. This equation is coupled to a kinetic equation describing localized chemisorbed species. A modified kinetic entropy is introduced for the coupled system and the H theorem is established. Using a fluid scaling and the Chapman-Enskog asymptotic method, fluid boundary conditions for the physisorbed and chemisorbed species are derived from the kinetic model.
Modelling charge transfer reactions with the frozen density embedding formalism.
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.
Modelling charge transfer reactions with the frozen density embedding formalism
NASA Astrophysics Data System (ADS)
Pavanello, Michele; Neugebauer, Johannes
2011-12-01
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.
Modelling charge transfer reactions with the frozen density embedding formalism
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.
Kinetic models of tissue fusion processes
NASA Astrophysics Data System (ADS)
Pearce, John A.; Thomsen, Sharon L.
1992-06-01
Recent studies of tissue fusion (welding) processes have reported temperature ranges but have not carefully analyzed critical exposure time data. Electron microscopic (EM) studies suggest that the fusion process in blood vessels may be dominated by random re-entwinement of thermally dissociated adventitial collagen fibrils (Type I) during the end stage heating and early cooling phases. At the light microscopic level, this bonding process is reflected by the formation of an amorphous coagulum of thermally coagulated adventitial collagen at the anastomotic site. We have constructed a numerical model of the vessel welding process, assuming CO2 laser impingement, and used it to simulate quantitative histologic data obtained from successful welds of rat femoral and canine brachial arteries (unpublished data). The model estimates smooth muscle and collagen damage based on kinetic thermal damage analysis and water loss boundaries as a function of irradiation beam parameters and heating time. Both heating and cooling phases are simulated. The results illustrate the importance of the damage kinetics and local heat transfer phenomena to the weld characteristics realized.
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…
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.…
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.
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…
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."…
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…
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.…
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.
Glassy dynamics of kinetically constrained models
NASA Astrophysics Data System (ADS)
Ritort, F.; Sollich, P.
2003-06-01
We review the use of kinetically constrained models (KCMs) for the study of dynamics in glassy systems. The characteristic feature of KCMs is that they have trivial, often non-interacting, equilibrium behaviour but interesting slow dynamics due to restrictions on the allowed transitions between configurations. The basic question which KCMs ask is therefore how much glassy physics can be understood without an underlying 'equilibrium glass transition'. After a brief review of glassy phenomenology, we describe the main model classes, which include spin-facilitated (Ising) models, constrained lattice gases, models inspired by cellular structures such as soap froths, models obtained via mappings from interacting systems without constraints, and finally related models such as urn, oscillator, tiling and needle models. We then describe the broad range of techniques that have been applied to KCMs, including exact solutions, adiabatic approximations, projection and mode-coupling techniques, diagrammatic approaches and mappings to quantum systems or effective models. Finally, we give a survey of the known results for the dynamics of KCMs both in and out of equilibrium, including topics such as relaxation time divergences and dynamical transitions, nonlinear relaxation, ageing and effective temperatures, cooperativity and dynamical heterogeneities, and finally non-equilibrium stationary states generated by external driving. We conclude with a discussion of open questions and possibilities for future work.
Systems immunology: a survey of modeling formalisms, applications and simulation tools.
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
Detailed Kinetic Modeling of Gasoline Surrogate Mixtures
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.
Kinetic modeling of non-ideal explosives
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.
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.
Kinetic modelling of heterogeneous catalytic systems
NASA Astrophysics Data System (ADS)
Stamatakis, Michail
2015-01-01
The importance of heterogeneous catalysis in modern life is evidenced by the fact that numerous products and technologies routinely used nowadays involve catalysts in their synthesis or function. The discovery of catalytic materials is, however, a non-trivial procedure, requiring tedious trial-and-error experimentation. First-principles-based kinetic modelling methods have recently emerged as a promising way to understand catalytic function and aid in materials discovery. In particular, kinetic Monte Carlo (KMC) simulation is increasingly becoming more popular, as it can integrate several sources of complexity encountered in catalytic systems, and has already been used to successfully unravel the underlying physics of several systems of interest. After a short discussion of the different scales involved in catalysis, we summarize the theory behind KMC simulation, and present the latest KMC computational implementations in the field. Early achievements that transformed the way we think about catalysts are subsequently reviewed in connection to latest studies of realistic systems, in an attempt to highlight how the field has evolved over the last few decades. Present challenges and future directions and opportunities in computational catalysis are finally discussed.
Population balance modeling of antibodies aggregation kinetics.
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,
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.
ADM Analysis of gravity models within the framework of bimetric variational formalism
Golovnev, Alexey; Karčiauskas, Mindaugas; Nyrhinen, Hannu J. E-mail: mindaugas.karciauskas@helsinki.fi
2015-05-01
Bimetric variational formalism was recently employed to construct novel bimetric gravity models. In these models an affine connection is generated by an additional tensor field which is independent of the physical metric. In this work we demonstrate how the ADM decomposition can be applied to study such models and provide some technical intermediate details. Using ADM decomposition we are able to prove that a linear model is unstable as has previously been indicated by perturbative analysis. Moreover, we show that it is also very difficult if not impossible to construct a non-linear model which is ghost-free within the framework of bimetric variational formalism. However, we demonstrate that viable models are possible along similar lines of thought. To this end, we consider a set up in which the affine connection is a variation of the Levi-Civita one. As a proof of principle we construct a gravity model with a massless scalar field obtained this way.
Kinetic model of excess activated sludge thermohydrolysis.
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.
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
Logarithmic relaxation in a kinetically constrained model.
Moreno, Angel J; Colmenero, Juan
2006-07-07
We present Monte Carlo simulations on a coarse-grained model for relaxation in binary mixtures. The liquid structure is substituted by a three-dimensional array of cells. A spin variable is assigned to each cell, with values 0 or 1 denoting, respectively, unexcited and excited local states in a mobility field. Change in local mobility (spin flip) is permitted according to kinetic constraints determined by the mobilities of neighboring cells. We introduce two types of cells ("fast" and "slow") with very different rates for spin flip. Fast cells display anomalous relaxation, characterized by a concave-to-convex crossover in dynamic correlators by changing temperature or composition. At intermediate state points logarithmic relaxation is observed over three time decades. These results display striking analogies with dynamic correlators reported in recent simulations on polymer blends.
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.
Formal Analysis of Self-Efficacy in Job Interviewee’s Mental State Model
NASA Astrophysics Data System (ADS)
Ajoge, N. S.; Aziz, A. A.; Yusof, S. A. Mohd
2017-08-01
This paper presents a formal analysis approach for self-efficacy model of interviewee’s mental state during a job interview session. Self-efficacy is a construct that has been hypothesised to combine with motivation and interviewee anxiety to define state influence of interviewees. The conceptual model was built based on psychological theories and models related to self-efficacy. A number of well-known relations between events and the course of self-efficacy are summarized from the literature and it is shown that the proposed model exhibits those patterns. In addition, this formal model has been mathematically analysed to find out which stable situations exist. Finally, it is pointed out how this model can be used in a software agent or robot-based platform. Such platform can provide an interview coaching approach where support to the user is provided based on their individual metal state during interview sessions.
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.
Noncommutative geometry and the BV formalism: Application to a matrix model
NASA Astrophysics Data System (ADS)
Iseppi, Roberta A.; van Suijlekom, Walter D.
2017-10-01
We analyze a U(2) -matrix model derived from a finite spectral triple. By applying the BV formalism, we find a general solution to the classical master equation. To describe the BV formalism in the context of noncommutative geometry, we define two finite spectral triples: the BV spectral triple and the BV auxiliary spectral triple. These are constructed from the gauge fields, ghost fields and anti-fields that enter the BV construction. We show that their fermionic actions add up precisely to the BV action. This approach allows for a geometric description of the ghost fields and their properties in terms of the BV spectral triple.
A formalism to generate probability distributions for performance-assessment modeling
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.
A Use-Case Driven Approach to Formal Service-Oriented Modelling
NASA Astrophysics Data System (ADS)
Bocchi, Laura; Fiadeiro, José Luiz; Lopes, Antónia
We put forward a use-case based approach for SRML - a formal framework that is being defined by the SENSORIA consortium for service-oriented modelling. We expand on the way SRML contributes to the engineering of software systems and we propose a number of extensions to the UML for supporting that approach. We use a mortgage brokerage scenario for illustrating our approach.
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…
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…
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…
An insight into DVB-T system using formal modelling in Event-B
NASA Astrophysics Data System (ADS)
Krayem, Said; Pátíková, Zuzana
2017-07-01
Digital Video Broadcast - Terrestrial (DVB-T) can be seen as a complex system with many concrete features and aspects. This paper presents a simplified model and the first insight into this system from point of view of formal modelling methods. Using Event-B a start-up model concerning relations between signals, multiplexes and channels is introduced. As a background the standards for DVB-T in the Czech Republic are taken.
Kinetic modelling of vinyl ester resin polymerization
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.
Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic.
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.
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.
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.
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.
A formal approach to the analysis of clinical computer-interpretable guideline modeling languages.
Grando, M Adela; Glasspool, David; Fox, John
2012-01-01
To develop proof strategies to formally study the expressiveness of workflow-based languages, and to investigate their applicability to clinical computer-interpretable guideline (CIG) modeling languages. We propose two strategies for studying the expressiveness of workflow-based languages based on a standard set of workflow patterns expressed as Petri nets (PNs) and notions of congruence and bisimilarity from process calculus. Proof that a PN-based pattern P can be expressed in a language L can be carried out semi-automatically. Proof that a language L cannot provide the behavior specified by a PNP requires proof by exhaustion based on analysis of cases and cannot be performed automatically. The proof strategies are generic but we exemplify their use with a particular CIG modeling language, PROforma. To illustrate the method we evaluate the expressiveness of PROforma against three standard workflow patterns and compare our results with a previous similar but informal comparison. We show that the two proof strategies are effective in evaluating a CIG modeling language against standard workflow patterns. We find that using the proposed formal techniques we obtain different results to a comparable previously published but less formal study. We discuss the utility of these analyses as the basis for principled extensions to CIG modeling languages. Additionally we explain how the same proof strategies can be reused to prove the satisfaction of patterns expressed in the declarative language CIGDec. The proof strategies we propose are useful tools for analysing the expressiveness of CIG modeling languages. This study provides good evidence of the benefits of applying formal methods of proof over semi-formal ones. Copyright © 2011 Elsevier B.V. All rights reserved.
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
Equifinality of formal (DREAM) and informal (GLUE) bayesian approaches in hydrologic modeling?
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.
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.
Kinetic modelling of krypton fluoride laser systems
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.
Reflected kinetics model for nuclear space reactor kinetics and control scoping calculations
Washington, K.E.
1986-05-01
The objective of this research is to develop a model that offers an alternative to the point kinetics (PK) modelling approach in the analysis of space reactor kinetics and control studies. Modelling effort will focus on the explicit treatment of control drums as reactivity input devices so that the transition to automatic control can be smoothly done. The proposed model is developed for the specific integration of automatic control and the solution of the servo mechanism problem. The integration of the kinetics model with an automatic controller will provide a useful tool for performing space reactor scoping studies for different designs and configurations. Such a tool should prove to be invaluable in the design phase of a space nuclear system from the point of view of kinetics and control limitations.
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
Issues to be considered on obtaining plant models for formal verification purposes
NASA Astrophysics Data System (ADS)
Pacheco, R.; Gonzalez, L.; Intriago, M.; Machado, J.; Prisacaru, G.; Olaru, D.
2016-08-01
The development of dependable software for mechatronic systems can be a very complex and hard task. For facilitating the obtaining of dependable software for industrial controllers, some powerful software tools and analysis techniques can be used. Mainly, when using simulation and formal verification analysis techniques, it is necessary to develop plant models, in order to describe the plant behavior of those systems. However, developing a plant model implies that designer takes his (or her) decisions concerning granularity and level of abstraction of models; approach to consider for modeling (global or modular); and definition of strategies for simulation and formal verification tasks. This paper intends to highlight some aspects that can be considered for taking into account those decisions. For this purpose, it is presented a case study and there are illustrated and discussed very important aspects concerning above exposed issues.
Fully implicit kinetic modelling of collisional plasmas
Mousseau, Vincent Andrew
1996-05-01
This dissertation describes a numerical technique, Matrix-Free Newton Krylov, for solving a simplified Vlasov-Fokker-Planck equation. This method is both deterministic and fully implicit, and may not have been a viable option before current developments in numerical methods. Results are presented that indicate the efficiency of the Matrix-Free Newton Krylov method for these fully-coupled, nonlinear integro-differential equations. The use and requirement for advanced differencing is also shown. To this end, implementations of Chang-Cooper differencing and flux limited Quadratic Upstream Interpolation for Convective Kinematics (QUICK) are presented. Results are given for a fully kinetic ion-electron problem with a self consistent electric field calculated from the ion and electron distribution functions. This numerical method, including advanced differencing, provides accurate solutions, which quickly converge on workstation class machines. It is demonstrated that efficient steady-state solutions can be achieved to the non-linear integro-differential equation, obtaining quadratic convergence, without incurring the large memory requirements of an integral operator. Model problems are presented which simulate plasma impinging on a plate with both high and low neutral particle recycling typical of a divertor in a Tokamak device. These model problems demonstrate the performance of the new solution method.
Formally verifying human–automation interaction as part of a system model: limitations and tradeoffs
Bass, Ellen J.
2011-01-01
Both the human factors engineering (HFE) and formal methods communities are concerned with improving the design of safety-critical systems. This work discusses a modeling effort that leveraged methods from both fields to perform formal verification of human–automation interaction with a programmable device. This effort utilizes a system architecture composed of independent models of the human mission, human task behavior, human-device interface, device automation, and operational environment. The goals of this architecture were to allow HFE practitioners to perform formal verifications of realistic systems that depend on human–automation interaction in a reasonable amount of time using representative models, intuitive modeling constructs, and decoupled models of system components that could be easily changed to support multiple analyses. This framework was instantiated using a patient controlled analgesia pump in a two phased process where models in each phase were verified using a common set of specifications. The first phase focused on the mission, human-device interface, and device automation; and included a simple, unconstrained human task behavior model. The second phase replaced the unconstrained task model with one representing normative pump programming behavior. Because models produced in the first phase were too large for the model checker to verify, a number of model revisions were undertaken that affected the goals of the effort. While the use of human task behavior models in the second phase helped mitigate model complexity, verification time increased. Additional modeling tools and technological developments are necessary for model checking to become a more usable technique for HFE. PMID:21572930
Kinetic model for phenolic compound oxidation by Fenton's reagent.
De Heredia, J B; Torregrosa, J; Dominguez, J R; Peres, J A
2001-10-01
A kinetic model is developed for the oxidation of phenolic compounds by Fenton's reagent. In the first stage a rigorous kinetic model is applied to calculate the different kinetic rate constants for the oxidation process of p-hydroxybenzoic acid. In a second phase a competitive method is applied to calculate these kinetic constants for another 10 phenolic compounds present in agroindustrial and pulp paper wastewaters. These 10 phenolic compounds were: beta-resorcylic acid, 3-(4-hydroxyphenyl)-propionic acid, ferulic acid, protocatechuic acid, caffeic acid, p-coumaric acid, vanillic acid, syringic acid, veratric acid and 3,4,5-trimethoxybenzoic acid.
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.
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
Formal models in animal-metacognition research: the problem of interpreting animals' behavior.
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.
Ahmad, Jamil; Niazi, Umar; Mansoor, Sajid; Siddique, Umair; Bibby, Jaclyn
2012-01-01
The discrete modeling formalism of René Thomas is a well known approach for the modeling and analysis of Biological Regulatory Networks (BRNs). This formalism uses a set of parameters which reflect the dynamics of the BRN under study. These parameters are initially unknown but may be deduced from the appropriately chosen observed dynamics of a BRN. The discrete model can be further enriched by using the model checking tool HyTech along with delay parameters. This paves the way to accurately analyse a BRN and to make predictions about critical trajectories which lead to a normal or diseased response. In this paper, we apply the formal discrete and hybrid (discrete and continuous) modeling approaches to characterize behavior of the BRN associated with MyD88-adapter-like (MAL) – a key protein involved with innate immune response to infections. In order to demonstrate the practical effectiveness of our current work, different trajectories and corresponding conditions that may lead to the development of cerebral malaria (CM) are identified. Our results suggest that the system converges towards hyperinflammation if Bruton's tyrosine kinase (BTK) remains constitutively active along with pre-existing high cytokine levels which may play an important role in CM pathogenesis. PMID:22479409
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.
Enskog-like kinetic models for vehicular traffic
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.
Reflected kinetics model for nuclear space reactor kinetics and control scoping calculations
Washington, K.E.
1986-01-01
Renewed interest in space nuclear applications has motivated the study of a specialized reactor kinetics model. Consideration of a kinetics model favorable for study of the feasibility of automatic control of these devices is warranted. The need to bridge this gap between reactor kinetics and automatic control in conjunction with the control drum design characteristic of next generation paper space reactors inspired the development of a new Reflected Kinetics (RK) model. An extension of the conventional point-kinetics (PK) model was done in order to explicitly correlate reactivity and the reflector/absorber control drums characteristic of space nuclear reactor designs. Open-loop computations and numerical comparison to analytic PK equations indicated that the RK model is a functional alternative to equivalent bare point kinetics in the analysis of moderate transients. Variations in the RK reflector-to-core transfer probabilities and coolant flow rate do indeed drive the transient differently than the lumped insertion of equivalent reactivity amounts in the core. These computations illustrated the potential importance of the utilization of variable coolant flow rate to aid control in space reactor systems limited by minimal drum reactivity worth. Additionally the Doppler reactivity shutdown mechanism was concluded to be the primarily reliable means of safety shutdown in such systems. The structure of the RK equations proved to be advantageous for integration of automatic control.
Fully Kinetic versus Reduced-kinetic Modeling of Collisionless Plasma Turbulence
NASA Astrophysics Data System (ADS)
Grošelj, Daniel; Cerri, Silvio S.; Bañón Navarro, Alejandro; Willmott, Christopher; Told, Daniel; Loureiro, Nuno F.; Califano, Francesco; Jenko, Frank
2017-09-01
We report the results of a direct comparison between different kinetic models of collisionless plasma turbulence in two spatial dimensions. The models considered include a first-principles fully kinetic (FK) description, two widely used reduced models (gyrokinetic (GK) and hybrid-kinetic (HK) with fluid electrons), and a novel reduced gyrokinetic approach (KREHM). Two different ion beta ({β }i) regimes are considered: 0.1 and 0.5. For {β }i=0.5, good agreement between the GK and FK models is found at scales ranging from the ion to the electron gyroradius, thus providing firm evidence for a kinetic Alfvén cascade scenario. In the same range, the HK model produces shallower spectral slopes, presumably due to the lack of electron Landau damping. For {β }i=0.1, a detailed analysis of spectral ratios reveals a slight disagreement between the GK and FK descriptions at kinetic scales, even though kinetic Alfvén fluctuations likely still play a significant role. The discrepancy can be traced back to scales above the ion gyroradius, where the FK and HK results seem to suggest the presence of fast magnetosonic and ion Bernstein modes in both plasma beta regimes, but with a more notable deviation from GK in the low-beta case. The identified practical limits and strengths of reduced-kinetic approximations, compared here against the FK model on a case-by-case basis, may provide valuable insight into the main kinetic effects at play in turbulent collisionless plasmas, such as the solar wind.
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.
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.
Formal models in animal-metacognition research: the problem of interpreting animals’ behavior
Smith, J. David; Zakrzewski, Alexandria C.; Church, Barbara A.
2015-01-01
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. PMID:26669600
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).
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.
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.
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.
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.
Kinetic modeling of phototrophic biofilms: the PHOBIA model.
Wolf, Gundula; Picioreanu, Cristian; van Loosdrecht, Mark C M
2007-08-01
A kinetic model for mixed phototrophic biofilms is introduced, which focuses on the interactions between photoautotrophic, heterotrophic, and chemoautotrophic (nitrifying) functional microbial groups. Biofilm-specific phenomena are taken into account, such as extracellular polymeric substances (EPS) production by phototrophs as well as gradients of substrates and light in the biofilm. Acid-base equilibria, in particular carbon speciation, are explicitly accounted for, allowing for the determination of pH profiles across the biofilm. Further to previous models reported in literature, the PHOBIA model combines a number of kinetic mechanisms specific to phototrophic microbial communities, such as internal polyglucose storage under dynamic light conditions, phototrophic growth in the darkness using internally stored reserves, photoadaptation and photoinhibition, preference for ammonia over nitrate as N-source and the ability to utilize bicarbonate as a carbon source in the absence of CO(2). The sensitivity of the PHOBIA model to a number of key parameters is analyzed. An example on the potential use of phototrophic biofilms in wastewater polishing is discussed, where their performance is compared with conventional algal ponds. The PHOBIA model is presented in a manner that is compatible with other reference models in the area of water treatment. Its current version forms a theoretical base which is readily extendable once further experimental observations become available. (c) 2007 Wiley Periodicals, Inc.
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.
Modeling and formal representation of geospatial knowledge for the Geospatial Semantic Web
NASA Astrophysics Data System (ADS)
Huang, Hong; Gong, Jianya
2008-12-01
GML can only achieve geospatial interoperation at syntactic level. However, it is necessary to resolve difference of spatial cognition in the first place in most occasions, so ontology was introduced to describe geospatial information and services. But it is obviously difficult and improper to let users to find, match and compose services, especially in some occasions there are complicated business logics. Currently, with the gradual introduction of Semantic Web technology (e.g., OWL, SWRL), the focus of the interoperation of geospatial information has shifted from syntactic level to Semantic and even automatic, intelligent level. In this way, Geospatial Semantic Web (GSM) can be put forward as an augmentation to the Semantic Web that additionally includes geospatial abstractions as well as related reasoning, representation and query mechanisms. To advance the implementation of GSM, we first attempt to construct the mechanism of modeling and formal representation of geospatial knowledge, which are also two mostly foundational phases in knowledge engineering (KE). Our attitude in this paper is quite pragmatical: we argue that geospatial context is a formal model of the discriminate environment characters of geospatial knowledge, and the derivation, understanding and using of geospatial knowledge are located in geospatial context. Therefore, first, we put forward a primitive hierarchy of geospatial knowledge referencing first order logic, formal ontologies, rules and GML. Second, a metamodel of geospatial context is proposed and we use the modeling methods and representation languages of formal ontologies to process geospatial context. Thirdly, we extend Web Process Service (WPS) to be compatible with local DLL for geoprocessing and possess inference capability based on OWL.
Application of Detailed Chemical Kinetics to Combustion Instability Modeling
2016-01-04
Briefing Charts 3. DATES COVERED (From - To) Nov 2015 – Jan 2016 4. TITLE AND SUBTITLE Application of Detailed Chemical Kinetics to Combustion Instability...Chemical Kinetics to Combustion Instability Modeling Matt Harvazinski, Doug Talley, Venke Sankaran Air Force Research Laboratory Edwards AFB, CA...Distribution A: approved for public release; distribution unlimited. 2 Challenges of Combustion Instability Damaged engine injector faceplate
Reasoning with conditionals: a test of formal models of four theories.
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.
A Generalized Kinetic Model for Heterogeneous Gas-Solid Reactions
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.
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.
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.
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.
Thermal nonlocal Nambu-Jona-Lasinio model in the real time formalism
Loewe, M.; Morales, P.; Villavicencio, C.
2011-05-01
The real time formalism at finite temperature and chemical potential for the nonlocal Nambu-Jona-Lasinio model is developed in the presence of a Gaussian covariant regulator. We construct the most general thermal propagator, by means of the spectral function. As a result, the model involves the propagation of massive quasiparticles. The appearance of complex poles is interpreted as a confinement signal, and, in this case, we have unstable quasiparticles with a finite decay width. An expression for the propagator along the critical line, where complex poles start to appear, is also obtained. A generalization to other covariant regulators is proposed.
NASA Astrophysics Data System (ADS)
Iotti, Rita Claudia; Dolcini, Fabrizio; Rossi, Fausto
2017-09-01
In designing and optimizing new-generation nanomaterials and related quantum devices, dissipation versus decoherence phenomena are often accounted for via local scattering models, such as relaxation-time and Boltzmann-like schemes. Here we show that the use of such local scattering approaches within the Wigner-function formalism may lead to unphysical results, namely anomalous suppression of intersubband relaxation, incorrect thermalization dynamics, and violation of probability-density positivity. Furthermore, we propose a quantum-mechanical generalization of relaxation-time and Boltzmann-like models, resulting in nonlocal scattering superoperators that enable one to overcome such limitations.
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.
Formal reasoning on qualitative models of coinfection of HIV and Tuberculosis and HAART therapy
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
Model-free deconvolution of femtosecond kinetic data.
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
Kinetic modeling of oxidation of antibacterial agents by manganese oxide.
Zhang, Huichun; Chen, Wan-Ru; Huang, Ching-Hua
2008-08-01
Several groups of popular antibacterial agents (i.e., phenols, fluoroquinolones, aromatic N-oxides, and tetracyclines) were demonstrated in earlier studies to be highly susceptible to oxidation by manganese oxides, a common oxidant in soils. However, because of the high complexity, the reaction kinetics were not fully characterized. A mechanism-based kinetic model has now been developed to successfully describe the entire range of kinetic data for a total of 21 compounds of varying structural characteristics (with R2 > 0.93). The model characterizes the reaction kinetics by two independent parameters, the reaction rate constant (k) and total reactive surface sites (S(rxn)). The model fitting indicates that the reaction kinetics of antibacterials with MnO2 are controlled by either the rate of surface precursor complex formation (for tetracyclines) or by the rate of electron transfer within the precursor complex (for phenols, fluoroquinolones, and aromatic N-oxides). The effect of reactant concentration, pH, and cosolutes on the reaction kinetics was evaluated and correlated to kand S(rxn). All the trends are consistent with the proposed rate-limiting steps. This new model improves the ability to quantitatively evaluate the kinetics of oxidative transformation of organic contaminants by manganese oxides in well-defined systems.
Apatite Biomineralization: Model Studies of Composition and Kinetics
NASA Astrophysics Data System (ADS)
Tecklenburg, M. M. J.; Urbanawiz, S. A.; Derry, A. W.; Ling, M. L.; Zhou, D.; Pavan, B.
2014-06-01
Biomineralization of bone and teeth is modeled via studies of apatite crystallization to assess the effects of constituent ions and centrifugal force on kinetics of the amorphous to crystalline phase transition.
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.
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.
Jellium-with-gap model applied to semilocal kinetic functionals
NASA Astrophysics Data System (ADS)
Constantin, Lucian A.; Fabiano, Eduardo; Śmiga, Szymon; Della Sala, Fabio
2017-03-01
We investigate a highly nonlocal generalization of the Lindhard function, given by the jellium-with-gap model. We find a band-gap-dependent gradient expansion of the kinetic energy, which performs noticeably well for large atoms. Using the static linear response theory and the simplest semilocal model for the local band gap, we derive a nonempirical generalized gradient approximation (GGA) of the kinetic energy. This GGA kinetic-energy functional is remarkably accurate for the description of weakly interacting molecular systems within the subsystem formulation of density functional theory.
Kinetic models in industrial biotechnology - Improving cell factory performance.
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. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.
Propyl propionate methanolysis kinetics: experiment and modeling.
Povarov, Vladimir G; Keresten, Andrey A
2013-09-26
In concentrated solutions, the reaction rate constant calculated from the law of mass action depends on a mixture composition. In this study, we suggest a new approach based on the dynamic equilibrium principle and modified equations of van Rysselberghe and de Donder. Experimental results obtained for propyl propionate methanolysis are in good agreement with calculated ones in the entire area of studied compositions. Such a method allows one to describe kinetics of reversible chemical reactions on both sides of the equilibrium.
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.
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.
A master equation formalism for macroscopic modeling of asynchronous irregular activity states.
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.
Detailed Chemical Kinetic Modeling of Cyclohexane Oxidation
Silke, E J; Pitz, W J; Westbrook, C K; Ribaucour, M
2006-11-10
A detailed chemical kinetic mechanism has been developed and used to study the oxidation of cyclohexane at both low and high temperatures. Reaction rate constant rules are developed for the low temperature combustion of cyclohexane. These rules can be used for in chemical kinetic mechanisms for other cycloalkanes. Since cyclohexane produces only one type of cyclohexyl radical, much of the low temperature chemistry of cyclohexane is described in terms of one potential energy diagram showing the reaction of cyclohexyl radical + O{sub 2} through five, six and seven membered ring transition states. The direct elimination of cyclohexene and HO{sub 2} from RO{sub 2} is included in the treatment using a modified rate constant of Cavallotti et al. Published and unpublished data from the Lille rapid compression machine, as well as jet-stirred reactor data are used to validate the mechanism. The effect of heat loss is included in the simulations, an improvement on previous studies on cyclohexane. Calculations indicated that the production of 1,2-epoxycyclohexane observed in the experiments can not be simulated based on the current understanding of low temperature chemistry. Possible 'alternative' H-atom isomerizations leading to different products from the parent O{sub 2}QOOH radical were included in the low temperature chemical kinetic mechanism and were found to play a significant role.
Detailed chemical kinetic modeling of cyclohexane oxidation.
Silke, Emma J; Pitz, William J; Westbrook, Charles K; Ribaucour, Marc
2007-05-17
A detailed chemical kinetic mechanism has been developed and used to study the oxidation of cyclohexane at both low and high temperatures. Rules for reaction rate constants are developed for the low-temperature combustion of cyclohexane. These rules can be used for in chemical kinetic mechanisms for other cycloalkanes. Because cyclohexane produces only one type of cyclohexyl radical, much of the low-temperature chemistry of cyclohexane is described in terms of one potential energy diagram showing the reaction of cyclohexyl radical with O2 through five-, six-, and seven-membered-ring transition states. The direct elimination of cyclohexene and HO2 from RO2 is included in the treatment using a modified rate constant of Cavallotti et al. (Proc. Combust. Inst. 2007, 31, 201). Published and unpublished data from the Lille rapid compression machine, as well as jet-stirred reactor data, are used to validate the mechanism. The effect of heat loss is included in the simulations, an improvement on previous studies on cyclohexane. Calculations indicated that the production of 1,2-epoxycyclohexane observed in the experiments cannot be simulated according to the current understanding of low-temperature chemistry. Possible "alternative" H-atom isomerizations leading to different products from the parent O2QOOH radical were included in the low-temperature chemical kinetic mechanism and were found to play a significant role.
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
Chaouiya, Claudine; Bérenguier, Duncan; Keating, Sarah M; Naldi, Aurélien; van Iersel, Martijn P; Rodriguez, Nicolas; Dräger, Andreas; Büchel, Finja; Cokelaer, Thomas; Kowal, Bryan; Wicks, Benjamin; Gonçalves, Emanuel; Dorier, Julien; Page, Michel; Monteiro, Pedro T; von Kamp, Axel; Xenarios, Ioannis; de Jong, Hidde; Hucka, Michael; Klamt, Steffen; Thieffry, Denis; Le Novère, Nicolas; Saez-Rodriguez, Julio; Helikar, Tomáš
2013-12-10
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. 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. 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.
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.
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.
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.
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.
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.
Discounting of reward sequences: a test of competing formal models of hyperbolic discounting.
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.
Chemical Kinetic Models for HCCI and Diesel Combustion
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.
Hybrid fluid/kinetic model for parallel heat conduction
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.
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
NASA Astrophysics Data System (ADS)
Reinisch, Guillaume; Leyssale, Jean-Marc; Vignoles, Gérard L.
2010-10-01
We present an extension of some popular hindered rotor (HR) models, namely, the one-dimensional HR (1DHR) and the degenerated two-dimensional HR (d2DHR) models, allowing for a simple and accurate treatment of internal rotations. This extension, based on the use of a variable kinetic function in the Hamiltonian instead of a constant reduced moment of inertia, is extremely suitable in the case of rocking/wagging motions involved in dissociation or atom transfer reactions. The variable kinetic function is first introduced in the framework of a classical 1DHR model. Then, an effective temperature and potential dependent constant is proposed in the cases of quantum 1DHR and classical d2DHR models. These methods are finally applied to the atom transfer reaction SiCl3+BCl3→SiCl4+BCl2. We show, for this particular case, that a proper accounting of internal rotations greatly improves the accuracy of thermodynamic and kinetic predictions. Moreover, our results confirm (i) that using a suitably defined kinetic function appears to be very adapted to such problems; (ii) that the separability assumption of independent rotations seems justified; and (iii) that a quantum mechanical treatment is not a substantial improvement with respect to a classical one.
Breakdown parameter for kinetic modeling of multiscale gas flows.
Meng, Jianping; Dongari, Nishanth; Reese, Jason M; Zhang, Yonghao
2014-06-01
Multiscale methods built purely on the kinetic theory of gases provide information about the molecular velocity distribution function. It is therefore both important and feasible to establish new breakdown parameters for assessing the appropriateness of a fluid description at the continuum level by utilizing kinetic information rather than macroscopic flow quantities alone. We propose a new kinetic criterion to indirectly assess the errors introduced by a continuum-level description of the gas flow. The analysis, which includes numerical demonstrations, focuses on the validity of the Navier-Stokes-Fourier equations and corresponding kinetic models and reveals that the new criterion can consistently indicate the validity of continuum-level modeling in both low-speed and high-speed flows at different Knudsen numbers.
Sampling Kinetic Protein Folding Pathways using All-Atom Models
NASA Astrophysics Data System (ADS)
Bolhuis, P. G.
This chapter summarizes several computational strategies to study the kinetics of two-state protein folding using all atom models. After explaining the background of two state folding using energy landscapes I introduce common protein models and computational tools to study folding thermodynamics and kinetics. Free energy landscapes are able to capture the thermodynamics of two-state protein folding, and several methods for efficient sampling of these landscapes are presented. An accurate estimate of folding kinetics, the main topic of this chapter, is more difficult to achieve. I argue that path sampling methods are well suited to overcome the problems connected to the sampling of folding kinetics. Some of the major issues are illustrated in the case study on the folding of the GB1 hairpin.
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.
Identifiability of steady-state chemical kinetic models
Shvetsova-Shilovskaya, T.N.; Gorskii, V.G.
1995-01-01
The methodology for the local and global identifiability analysis of steady-state kinetic models of catalytic reactions is discussed. This methodology is based on the prior transformation of the model into the linear form so that the coefficients of the linear form are uniquely identifiable combinations of constants (observed parameters). Identifiability analysis is applied to several particular models.
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.
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.
Kinetic model for the collisionless sheath of a collisional plasma
Tang, Xian-Zhu Guo, Zehua
2016-08-15
Collisional plasmas typically have mean-free-path still much greater than the Debye length, so the sheath is mostly collisionless. Once the plasma density, temperature, and flow are specified at the sheath entrance, the profile variation of electron and ion density, temperature, flow speed, and conductive heat fluxes inside the sheath is set by collisionless dynamics, and can be predicted by an analytical kinetic model distribution. These predictions are contrasted here with direct kinetic simulations, showing good agreement.
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.
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.
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.
Kinetic model of excitatory synaptic transmission to cerebellar Purkinje cells.
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.
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.
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.
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.
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.
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.
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.
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.
Vibrational kinetics in CO electric discharge lasers - Modeling and experiments
NASA Technical Reports Server (NTRS)
Stanton, A. C.; Hanson, R. K.; Mitchner, M.
1980-01-01
A model of CO laser vibrational kinetics is developed, and predicted vibrational distributions are compared with measurements. The experimental distributions were obtained at various flow locations in a transverse CW discharge in supersonic (M = 3) flow. Good qualitative agreement is obtained in the comparisons, including the prediction of a total inversion at low discharge current densities. The major area of discrepancy is an observed loss in vibrational energy downstream of the discharge which is not predicted by the model. This discrepancy may be due to three-dimensional effects in the experiment which are not included in the model. Possible kinetic effects which may contribute to vibrational energy loss are also examined.
A coke oven model including thermal decomposition kinetics of tar
Munekane, Fuminori; Yamaguchi, Yukio; Tanioka, Seiichi
1997-12-31
A new one-dimensional coke oven model has been developed for simulating the amount and the characteristics of by-products such as tar and gas as well as coke. This model consists of both heat transfer and chemical kinetics including thermal decomposition of coal and tar. The chemical kinetics constants are obtained by estimation based on the results of experiments conducted to investigate the thermal decomposition of both coal and tar. The calculation results using the new model are in good agreement with experimental ones.
On relating the generalized equivalent uniform dose formalism to the linear-quadratic model.
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.
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.
Kinetic Modeling of Enzymatic Hydrolysis of Pretreated Creeping Wild Ryegrass
USDA-ARS?s Scientific Manuscript database
A semimechanistic multi-reaction kinetic model was developed to describe the enzymatic hydrolysis of a lignocellulosic biomass, creeping wild ryegrass (CWR; Leymus triticoides). This model incorporated one homogeneous reaction of cellobiose-to-glucose and two heterogeneous reactions of cellulose-to...
Kinetic models for wealth exchange on directed networks
NASA Astrophysics Data System (ADS)
Chatterjee, A.
2009-02-01
We propose some kinetic models of wealth exchange and investigate their behavior on directed networks though numerical simulations. We observe that network topology and directedness yields a variety of interesting features in these models. The nature of asset distribution in such directed networks show varied results, the degree of asset inequality increased with the degree of disorder in the graphs.
Computer-Aided Construction of Chemical Kinetic Models
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.
Kinetic modelling for zinc (II) ions biosorption onto Luffa cylindrica
NASA Astrophysics Data System (ADS)
Oboh, I.; Aluyor, E.; Audu, T.
2015-03-01
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 (R2), 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.
Kinetic modelling for zinc (II) ions biosorption onto Luffa cylindrica
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.
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.
Model reduction for chemical kinetics: An optimization approach
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.
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
Continuous surface charge polarizable continuum models of solvation. I. General formalism.
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.
Toward a formalized account of attitudes: The Causal Attitude Network (CAN) model.
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. (c) 2015 APA, all rights reserved).
A Detailed Chemical Kinetic Model for TNT
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.
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.
Comparison of kinetic theory models of laser ablation of carbon
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.
Computer models for kinetic equations of magnetically confined plasmas
Killeen, J.; Kerbel, G.D.; McCoy, M.G.; Mirin, A.A.; Horowitz, E.J.; Shumaker, D.E.
1987-01-01
This paper presents four working computer models developed by the computational physics group of the National Magnetic Fusion Energy Computer Center. All of the models employ a kinetic description of plasma species. Three of the models are collisional, i.e., they include the solution of the Fokker-Planck equation in velocity space. The fourth model is collisionless and treats the plasma ions by a fully three-dimensional particle-in-cell method.
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.
Plasma interfacial mixing layers: Comparisons of fluid and kinetic models
NASA Astrophysics Data System (ADS)
Vold, Erik; Yin, Lin; Taitano, William; Albright, B. J.; Chacon, Luis; Simakov, Andrei; Molvig, Kim
2016-10-01
We examine plasma transport across an initial discontinuity between two species by comparing fluid and kinetic models. The fluid model employs a kinetic theory approximation for plasma transport in the limit of small Knudsen number. The kinetic simulations include explicit particle-in-cell simulations (VPIC) and a new implicit Vlasov-Fokker-Planck code, iFP. The two kinetic methods are shown to be in close agreement for many aspects of the mixing dynamics at early times (to several hundred collision times). The fluid model captures some of the earliest time dynamic behavior seen in the kinetic results, and also generally agrees with iFP at late times when the total pressure gradient relaxes and the species transport is dominated by slow diffusive processes. The results show three distinct phases of the mixing: a pressure discontinuity forms across the initial interface (on times of a few collisions), the pressure perturbations propagate away from the interfacial mixing region (on time scales of an acoustic transit) and at late times the pressure relaxes in the mix region leaving a non-zero center of mass flow velocity. The center of mass velocity associated with the outward propagating pressure waves is required to conserve momentum in the rest frame. Work performed under the auspices of the U.S. DOE by the LANS, LLC, Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396. Funding provided by the Advanced Simulation and Computing (ASC) Program.
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.
Kinetic model of local droplet etching
NASA Astrophysics Data System (ADS)
Heyn, Christian
2011-04-01
The self-organized in situ drilling of nanoholes into semiconductor surfaces by using liquid metallic droplets during conventional molecular beam epitaxy represents a new degree of freedom for the design of heterostructure devices. A model of this local droplet etching is presented that is based on a core-shell droplet structure. With the model, the evolution of the droplet and substrate morphology is calculated. We demonstrate quantitative agreement between model results and measured morphologies. Furthermore, also the influence of the process temperature is correctly reproduced by the model.
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.
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
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism.
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.
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.
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism
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.
Ab initio quantum chemical and kinetic modeling study of the pyrolysis kinetics of pyrrole
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.
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.
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
Hoyermann, Karlheinz; Mauß, Fabian; Olzmann, Matthias; Welz, Oliver; Zeuch, Thomas
2017-07-19
Partially oxidized intermediates play a central role in combustion and atmospheric chemistry. In this perspective, we focus on the chemical kinetics of alkoxy radicals, peroxy radicals, and Criegee intermediates, which are key species in both combustion and atmospheric environments. These reactive intermediates feature a broad spectrum of chemical diversity. Their reactivity is central to our understanding of how volatile organic compounds are degraded in the atmosphere and converted into secondary organic aerosol. Moreover, they sensitively determine ignition timing in internal combustion engines. The intention of this perspective article is to provide the reader with information about the general mechanisms of reactions initiated by addition of atomic and molecular oxygen to alkyl radicals and ozone to alkenes. We will focus on critical branching points in the subsequent reaction mechanisms and discuss them from a consistent point of view. As a first example of our integrated approach, we will show how experiment, theory, and kinetic modeling have been successfully combined in the first infrared detection of Criegee intermediates during the gas phase ozonolysis. As a second example, we will examine the ignition timing of n-heptane/air mixtures at low and intermediate temperatures. Here, we present a reduced, fuel size independent kinetic model of the complex chemistry initiated by peroxy radicals that has been successfully applied to simulate standard n-heptane combustion experiments.
Crystal growth kinetics of the two-step model
NASA Astrophysics Data System (ADS)
Tai, Clifford Y.; Lin, Chiu-Hsiung
1987-03-01
The single crystal technique was used to measure the growth rate of the potassium alum (111) face and the magnesium sulfate (110) face. The two-step model was found appropriate to describe the growth kinetics with the surface integration order of two for potassium alum crystal and of one for magnesium sulfate crystal. The individual rate constants, Kd and Kr, were determined accordingly.
A Kinetic Model for Vapor-liquid Flows
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
Dynamical response function of the disordered kinetic Ising model
NASA Astrophysics Data System (ADS)
Hinrichsen, Haye
2008-02-01
Recently Baumann et al (2007 Preprint 0709.3228v1) studied the phase-ordering kinetics of the two-dimensional Ising model for T
Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling.
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.
Kinetic modeling of kraft delignification of Eucalyptus globulus
Santos, A.; Rodriguez, F.; Gilarranz, M.A.; Moreno, D.; Garcia-Ochoa, F.
1997-10-01
A kinetic model for the kraft pulping delignification of Eucalyptus globulus is proposed. This model is discriminated among some kinetic expressions often used in the literature, and the kinetic parameters are determined by fitting of experimental results. A total of 25 isothermal experiments at liquor-to-wood ratios of 50 and 5 L/kg have been carried out. Initial, bulk, and residual delignification stages have been observed during the lignin removal, the transitions being, referring to the lignin initial content, about 82 and 3%. Carbohydrate removal and effective alkali-metal and hydrosulfide consumption have been related with the lignin removal by means of effective stoichiometric coefficients for each stage, coefficients also being calculated by fitting of the experimental data. The kinetic model chosen has been used to simulate typical kraft pulping experiments carried out at nonisothermal conditions, using a temperature ramp. The model yields simulated values close to those obtained experimentally for the wood studied and also ably reproduces the trends of the literature data.
Improved Kinetic Models for High-Speed Combustion Simulation
2008-06-01
TYPE 3. DATES COVERED (From - To) June 2008 Final 18 May 2006 – 18 June 2008 4 . TITLE AND SUBTITLE IMPROVED KINETIC MODELS FOR HIGH-SPEED...44 4 Results and Discussion...19 4 . Multi-Step, Sequential Process Leading to Formation of Phenyl from Benzyl (Scheme 1) ....20 5. Generic Chemical Activation Reaction System
KINETIC MODELING OF COUNTERFLOW DIFFUSION FLAMES OF BUTADIENE. (R828193)
A comprehensive, semi-detailed kinetic scheme was used to simulate the chemical structures of counterflow diffusion and fuel-rich premixed 1,3-butadiene flames, to better understand the formation of polycyclic aromatic hydrocarbons (PAH). The results showed that model predicti...
Gyrofluid turbulence models with kinetic effects
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
Towards cleaner combustion engines through groundbreaking detailed chemical kinetic models
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
A novel multistage kinetic modeling of flotation for wastewater treatment.
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.
Towards cleaner combustion engines through groundbreaking detailed chemical kinetic models.
Battin-Leclerc, Frédérique; Blurock, Edward; Bounaceur, Roda; Fournet, René; Glaude, Pierre-Alexandre; Herbinet, Olivier; Sirjean, Baptiste; Warth, V
2011-09-01
In the context of limiting the environmental impact of transportation, this critical review discusses 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 (212 references). This journal is © The Royal Society of Chemistry 2011
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…
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.…
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.…
Second-order kinetic Kohn-Sham lattice model
NASA Astrophysics Data System (ADS)
Solórzano, S.; Mendoza, M.; Herrmann, H. J.
2016-06-01
In this work, we introduce a semi-implicit second-order correction scheme to the kinetic Kohn-Sham lattice model. This approach is validated by performing realistic exchange-correlation energy calculations of atoms and dimers of the first two rows of the Periodic Table, finding good agreement with the expected values. Additionally, we simulate the ethane molecule, where we recover the bond lengths and compare the results with standard methods. Finally, we discuss the current applicability of pseudopotentials within the lattice kinetic Kohn-Sham approach.
Kinetic modeling based probabilistic segmentation for molecular images.
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.
MODELING EUTROPHICATION KINETICS IN RESERVOIR MICROCOSMS
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...
A kinetic model for flavonoid production in tea cell culture.
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.
Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles
Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto
2012-01-01
Kinetic modeling of metabolic pathways has important applications in metabolic engineering, but significant challenges still remain. The difficulties faced vary from finding best-fit parameters in a highly multidimensional search space to incomplete parameter identifiability. To meet some of these challenges, an ensemble modeling method is developed for characterizing a subset of kinetic parameters that give statistically equivalent goodness-of-fit to time series concentration data. The method is based on the incremental identification approach, where the parameter estimation is done in a step-wise manner. Numerical efficacy is achieved by reducing the dimensionality of parameter space and using efficient random parameter exploration algorithms. The shift toward using model ensembles, instead of the traditional “best-fit” models, is necessary to directly account for model uncertainty during the application of such models. The performance of the ensemble modeling approach has been demonstrated in the modeling of a generic branched pathway and the trehalose pathway in Saccharomyces cerevisiae using generalized mass action (GMA) kinetics. PMID:24957767
Modeling the Kinetics of Open Self-Assembly.
Verdier, Timothée; Foret, Lionel; Castelnovo, Martin
2016-07-07
In this work, we explore theoretically the kinetics of molecular self-assembly in the presence of constant monomer flux as an input, and a maximal size. The proposed model is supposed to reproduce the dynamics of viral self-assembly for enveloped virus. It turns out that the kinetics of open self-assembly is rather quantitatively different from the kinetics of similar closed assembly. In particular, our results show that the convergence toward the stationary state is reached through assembly waves. Interestingly, we show that the production of complete clusters is much more efficient in the presence of a constant input flux, rather than providing all monomers at the beginning of the self-assembly.
Non isothermal model free kinetics for pyrolysis of rice straw.
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.
Gyrofluid turbulence models with kinetic effects
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.
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
New kinetic model for thermal decomposition of heterogeneous materials
Caballero, J.A.; Font, R.; Marcilla, A.; Conesa, J.A.
1995-03-01
In the kinetic studies of thermal decomposition of lignocellulosic materials using dynamic TG, relationships between the biomass fraction ``w`` and the time ``t`` of the form dw/dt = {minus}k(w {minus} w{sub {infinity}}){sup n} are usually admitted, and the residue fraction at infinite time (w{sub {infinity}}) is considered constant. However, in heterogeneous solids such as lignocellulosic materials, the different polymers decompose at different temperatures, and so the value of w{sub {infinity}} is not constant, Therefore, the previous equation must be considered approximate. To illustrate this feature, experiments with kraft lignin, which decomposes in an interval of temperatures between 150 and 750 C, have been carried out. A kinetic model is proposed, bearing in mind that there is a maximum pyrolyzable fraction at each temperature. This model considers that the thermal decomposition of a heterogeneous material occurs through a great number of reactions and that at a given temperature only some fractions can decompose. The kinetic parameters (activation energy and preexponential factor) can change during the decomposition process as function of the reactions taking place. Under some assumptions, it is deduced that this model is equivalent to assume the kinetic law dw/dt = {minus}k(w{minus}w{sub {infinity}}) for first-order reaction, where the residue yield w{sub {infinity}} is a function of the temperature.
A 3D unstructured grid nearshore hydrodynamic model based on the vortex force formalism
NASA Astrophysics Data System (ADS)
Zheng, Peng; Li, Ming; van der A, Dominic A.; van der Zanden, Joep; Wolf, Judith; Chen, Xueen; Wang, Caixia
2017-08-01
A new three-dimensional nearshore hydrodynamic model system is developed based on the unstructured-grid version of the third generation spectral wave model SWAN (Un-SWAN) coupled with the three-dimensional ocean circulation model FVCOM to enable the full representation of the wave-current interaction in the nearshore region. A new wave-current coupling scheme is developed by adopting the vortex-force (VF) scheme to represent the wave-current interaction. The GLS turbulence model is also modified to better reproduce wave-breaking enhanced turbulence, together with a roller transport model to account for the effect of surface wave roller. This new model system is validated first against a theoretical case of obliquely incident waves on a planar beach, and then applied to three test cases: a laboratory scale experiment of normal waves on a beach with a fixed breaker bar, a field experiment of oblique incident waves on a natural, sandy barred beach (Duck'94 experiment), and a laboratory study of normal-incident waves propagating around a shore-parallel breakwater. Overall, the model predictions agree well with the available measurements in these tests, illustrating the robustness and efficiency of the present model for very different spatial scales and hydrodynamic conditions. Sensitivity tests indicate the importance of roller effects and wave energy dissipation on the mean flow (undertow) profile over the depth. These tests further suggest to adopt a spatially varying value for roller effects across the beach. In addition, the parameter values in the GLS turbulence model should be spatially inhomogeneous, which leads to better prediction of the turbulent kinetic energy and an improved prediction of the undertow velocity profile.
A Kinetic Model Describing Injury-Burden in Team Sports.
Fuller, Colin W
2017-06-01
Injuries in team sports are normally characterised by the incidence, severity, and location and type of injuries sustained: these measures, however, do not provide an insight into the variable injury-burden experienced during a season. Injury burden varies according to the team's match and training loads, the rate at which injuries are sustained and the time taken for these injuries to resolve. At the present time, this time-based variation of injury burden has not been modelled. To develop a kinetic model describing the time-based injury burden experienced by teams in elite team sports and to demonstrate the model's utility. Rates of injury were quantified using a large eight-season database of rugby injuries (5253) and exposure (60,085 player-match-hours) in English professional rugby. Rates of recovery from injury were quantified using time-to-recovery analysis of the injuries. The kinetic model proposed for predicting a team's time-based injury burden is based on a composite rate equation developed from the incidence of injury, a first-order rate of recovery from injury and the team's playing load. The utility of the model was demonstrated by examining common scenarios encountered in elite rugby. The kinetic model developed describes and predicts the variable injury-burden arising from match play during a season of rugby union based on the incidence of match injuries, the rate of recovery from injury and the playing load. The model is equally applicable to other team sports and other scenarios.
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.
Kinetic model for the chlorination of power plant cooling waters
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.
Chemistry Resolved Kinetic Flow Modeling of TATB Based Explosives
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.
Kinetic modelling of molecular hydrogen transport in microporous carbon materials.
Hankel, Marlies; Zhang, Hong; Nguyen, Thanh X; Bhatia, Suresh K; Gray, Stephen K; Smith, Sean C
2011-05-07
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(2)/D(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(2) transport is dramatically favored over H(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(2)/D(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 through the pore mouth, is also
Kinetic modelling of molecular hydrogen transport in microporous carbon materials.
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
Nonlinear models for in vitro kill kinetics of antibiotics.
Lee, M L; DuBois, A; Ross, R A; Onderdonk, A B
1999-05-01
In this study, we developed nonlinear regression models to analyze the data generated from an in vitro continuous culture system to assess the kinetics of metronidazole and trovafloxacin in inhibiting the growth of Bacteroides fragilis. The model includes parameters describing the initial shock effect of an antibiotic pulse, the overall antibiotic wash-out rate from the system, and the long-term toxicity of the antibiotic in the environment after one pulse and before the next pulse.
Chemical Kinetic Modeling of Combustion of Automotive Fuels
Pitz, W J; Westbrook, C K; Silke, E J
2006-11-10
The objectives of this report are to: (1) Develop detailed chemical kinetic reaction models for components of fuels, including olefins and cycloalkanes used in diesel, spark-ignition and HCCI engines; (2) Develop surrogate mixtures of hydrocarbon components to represent real fuels and lead to efficient reduced combustion models; and (3) Characterize the role of fuel composition on production of emissions from practical automotive engines.
Extraction of lycopene from tomato processing waste: kinetics and modelling.
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.
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.
Kinetic modeling of nicotine in mainstream cigarette smoking.
Kibet, Joshua; Kurgat, Caren; Limo, Samuel; Rono, Nicholas; Bosire, Josephate
2016-01-01
The attempt to understand the kinetic behavior of nicotine in tobacco will provide a basis for unraveling its energetics in tobacco burning and the formation of free radicals considered harmful to the cigarette smoking community. To the best of our knowledge, the high temperature destruction kinetic characteristics of nicotine have not been investigated before; hence this study is necessary especially at a time addiction science and tobacco research in general is gaining intense attention. The pyrolysis of tobacco under conditions simulating cigarette smoking in the temperature region 200-700 °C has been investigated for the evolution of nicotine and pyridine from two commercial cigarettes coded ES1 and SM1 using gas chromatography hyphenated to a mass selective detector (MSD). Moreover, a kinetic model on the thermal destruction of nicotine within a temperature window of 673 and 973 K is proposed using pseudo-first order reaction kinetics. A reaction time of 2.0 s was employed in line with the average puff time in cigarette smoking. Nonetheless, various reaction times were considered for the formation kinetics of nicotine. GC-MS results showed the amount of nicotine evolved decreased with increase in the puff time. This observation was remarkably consistent with UV-Vis data reported in this investigation. Generally, the temperature dependent rate constants for the destruction of nicotine were found to be [Formula: see text] s(-1) and [Formula: see text] s(-1) for ES1 and SM1 cigarettes respectively. In addition, the amount of nicotine evolved by ES1 cigarette was ~10 times more than the amount of nicotine released by SM1 cigarette. The suggested mechanistic model for the formation of pyridine from the thermal degradation of nicotine in tobacco has been found to be agreement with the kinetic model proposed in this investigation. Consequently, the concentration of radical intermediates of tobacco smoke such as pyridinyl radical can be determined indirectly
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.
Kinetic Model Development for Lignin Pyrolysis
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.
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.
Modeling the kinetic diversity of dopamine in the dorsal striatum.
Walters, Seth H; Robbins, Elaine M; Michael, Adrian C
2015-08-19
Dopamine is an important neurotransmitter that exhibits numerous functions in the healthy, injured, and diseased brain. Fast scan cyclic voltammetry paired with electrical stimulation of dopamine axons is a popular and powerful method for investigating the dynamics of dopamine in the extracellular space. Evidence now suggests that the heterogeneity of electrically evoked dopamine responses reflects the inherent kinetic diversity of dopamine systems, which might contribute to their diversity of physiological function. Dopamine measurements by fast scan cyclic voltammetry are affected by the adsorption of dopamine to carbon fiber electrodes. The temporal distortion caused by dopamine adsorption is correctable by a straightforward mathematical procedure. The corrected responses exhibit excellent agreement with a dopamine kinetic model cast to provide a generic description of restricted diffusion, short-term plasticity of dopamine release, and first-order dopamine clearance. The new DA kinetic model brings to light the rich kinetic information content of electrically evoked dopamine responses recorded via fast scan cyclic voltammetry in the rat dorsal striatum.
A kinetic-MHD model for low frequency phenomena
Cheng, C.Z.
1991-07-01
A hybrid kinetic-MHD model for describing low-frequency phenomena in high beta anisotropic plasmas that consist of two components: a low energy core component and an energetic component with low density. The kinetic-MHD model treats the low energy core component by magnetohydrodynamic (MHD) description, the energetic component by kinetic approach such as the gyrokinetic equation, and the coupling between the dynamics of these two components through plasma pressure in the momentum equation. The kinetic-MHD model optimizes both the physics contents and the theoretical efforts in studying low frequency MHD waves and transport phenomena in general magnetic field geometries, and can be easily modified to include the core plasma kinetic effects if necessary. It is applicable to any magnetized collisionless plasma system where the parallel electric field effects are negligibly small. In the linearized limit two coupled eigenmode equations for describing the coupling between the transverse Alfven type and the compressional Alfven type waves are derived. The eigenmode equations are identical to those derived from the full gyrokinetic equation in the low frequency limit and were previously analyzed both analytically nd numerically to obtain the eigenmode structure of the drift mirror instability which explains successfully the multi-satellite observation of antisymmetric field-aligned structure of the compressional magnetic field of Pc 5 waves in the magnetospheric ring current plasma. Finally, a quadratic form is derived to demonstrate the stability of the low-frequency transverse and compressional Alfven type instabilities in terms of the pressure anisotropy parameter {tau} and the magnetic field curvature-pressure gradient parameter. A procedure for determining the stability of a marginally stable MHD wave due to wave-particle resonances is also presented.
A formal hybrid modeling scheme for handling discontinuities in physical system models
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.
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.
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.
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.
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.
Kinetic modeling of Nernst effect in magnetized hohlraums.
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.
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.
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.
Fluid and kinetic models of negative ion sheaths
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.
Kinetic plasma modeling with quiet Monte Carlo direct simulation.
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.
Kinetic Modeling of Oxidative Coagulation for Arsenic Removal
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).
Kinetic modelling of laccase mediated delignification of Lantana camara.
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.
Modelling reactive CAH transport using batch experiment degradation kinetics.
Haest, Pieter J; Springael, Dirk; Smolders, Erik
2010-05-01
Models describing transport of degradable organic substances in a porous medium require parameters of the biodegradation kinetics that can be obtained from batch degradation assays. It is rarely assessed if liquid batch biodegradation rates allow extrapolation to reactive transport in a porous medium, i.e. if the cell specific activity in a porous medium with flow-through is identical to that of pelagic cells in liquid cultures. Failure of model predictions can be used to identify the rate-limiting processes in the reactive transport. Column data of anaerobic trichloroethene (TCE) transport and degradation at three flow rates were predicted with a model using biodegradation kinetics derived from a liquid culture. The extent of dechlorination at the column outlet was very well predicted within a factor 1.4 if the specific microbial biomass in the columns was used as an input parameter. This suggests that potential mass transfer limitations in biofilms or differences in microbial ecology between batch and column had minor effects on dechlorination. The model was subsequently extended with Monod kinetics to predict both biomass growth and chlorinated aliphatic hydrocarbon (CAH) degradation in the columns using liquid batch data. These models largely overestimated CAH dechlorination unless microbial transport with cell elution was included and unless a slight batch to column adjustment was made to better predict microbial biomass. With 4 adjustable parameters the model succeeded in predicting the microbial numbers within a factor 4.3 and the extent of dechlorination within a factor 1.2. Our analysis validates the batch to column extrapolation for this dedicated set-up provided that the microbial biomass in columns is well predicted. The sensitivity analysis shows that the extent of dechlorination in the reactive transport is most sensitive to the parameters of TCE degradation kinetics, including microbial growth followed by the residence time. Copyright (c) 2010
Formal Models of the Network Co-occurrence Underlying Mental Operations
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
An autocatalytic kinetic model for describing microbial growth during fermentation.
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.
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.
Stepwise kinetic equilibrium models of quantitative polymerase chain reaction
2012-01-01
Background Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model the annealing phase and does not assume constant efficiency of amplification. Mechanistic models describing the annealing phase with kinetic theory offer the most potential for accurate interpretation of qPCR data. Even so, they have not been thoroughly investigated and are rarely used for interpretation of qPCR data. New results for kinetic modeling of qPCR are presented. Results Two models are presented in which the efficiency of amplification is based on equilibrium solutions for the annealing phase of the qPCR process. Model 1 assumes annealing of complementary targets strands and annealing of target and primers are both reversible reactions and reach a dynamic equilibrium. Model 2 assumes all annealing reactions are nonreversible and equilibrium is static. Both models include the effect of primer concentration during the annealing phase. Analytic formulae are given for the equilibrium values of all single and double stranded molecules at the end of the annealing step. The equilibrium values are then used in a stepwise method to describe the whole qPCR process. Rate constants of kinetic models are the same for solutions that are identical except for possibly having different initial target concentrations. Analysis of qPCR curves from such solutions are thus analyzed by simultaneous non-linear curve fitting with the same rate constant values applying to all curves and each curve having a unique value for initial target concentration. The models were fit to two data sets for which the true initial target concentrations are known. Both models give better fit to observed qPCR data than other kinetic models present in the literature. They also give
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…
A review of the kinetic statistical strength model
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.
Progress in Chemical Kinetic Modeling for Surrogate Fuels
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.
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.
Development of Detailed Kinetic Models for Fischer-Tropsch Fuels
Westbrook, C K; Pitz, W J; Carstensen, H; Dean, A M
2008-10-28
Fischer-Tropsch (FT) fuels can be synthesized from a syngas stream generated by the gasification of biomass. As such they have the potential to be a renewable hydrocarbon fuel with many desirable properties. However, both the chemical and physical properties are somewhat different from the petroleum-based hydrocarbons that they might replace, and it is important to account for such differences when considering using them as replacements for conventional fuels in devices such as diesel engines and gas turbines. FT fuels generally contain iso-alkanes with one or two substituted methyl groups to meet the pour-point specifications. Although models have been developed for smaller branched alkanes such as isooctane, additional efforts are required to properly capture the kinetics of the larger branched alkanes. Recently, Westbrook et al. developed a chemical kinetic model that can be used to represent the entire series of n-alkanes from C{sub 1} to C{sub 16} (Figure 1). In the current work, the model is extended to treat 2,2,4,4,6,8,8-heptamethylnonane (HMN), a large iso-alkane. The same reaction rate rules used in the iso-octane mechanism were incorporated in the HMN mechanism. Both high and low temperature chemistry was included so that the chemical kinetic model would be applicable to advanced internal combustion engines using low temperature combustion strategies. The chemical kinetic model consists of 1114 species and 4468 reactions. Concurrently with this effort, work is underway to improve the details of specific reaction classes in the mechanism, guided by high-level electronic structure calculations. Attention is focused upon development of accurate rate rules for abstraction of the tertiary hydrogens present in branched alkanes and properly accounting for the pressure dependence of the ?-scission, isomerization, and R + O{sub 2} reactions.
Kinetic models of gene expression including non-coding RNAs
NASA Astrophysics Data System (ADS)
Zhdanov, Vladimir P.
2011-03-01
In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to the feedbacks between these processes, the kinetics of gene expression may be complex even in the simplest genetic networks. The corresponding models have already been reviewed in the literature. A new avenue in this field is related to the recognition that the conventional scenario of gene expression is fully applicable only to prokaryotes whose genomes consist of tightly packed protein-coding sequences. In eukaryotic cells, in contrast, such sequences are relatively rare, and the rest of the genome includes numerous transcript units representing non-coding RNAs (ncRNAs). During the past decade, it has become clear that such RNAs play a crucial role in gene expression and accordingly influence a multitude of cellular processes both in the normal state and during diseases. The numerous biological functions of ncRNAs are based primarily on their abilities to silence genes via pairing with a target mRNA and subsequently preventing its translation or facilitating degradation of the mRNA-ncRNA complex. Many other abilities of ncRNAs have been discovered as well. Our review is focused on the available kinetic models describing the mRNA, ncRNA and protein interplay. In particular, we systematically present the simplest models without kinetic feedbacks, models containing feedbacks and predicting bistability and oscillations in simple genetic networks, and models describing the effect of ncRNAs on complex genetic networks. Mathematically, the presentation is based primarily on temporal mean-field kinetic equations. The stochastic and spatio-temporal effects are also briefly discussed.
Modeling organic micro pollutant degradation kinetics during sewage sludge composting.
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.
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.
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.
Modelling the cooking doneness via integrating sensory evaluation and kinetics.
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.
Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation
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
Kinetic modelling of pressure filtration of ceramic powder suspensions
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.
Kinetic Model of Conduction Changes across Excitable Membranes*
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
Controllability in Hybrid Kinetic Equations Modeling Nonequilibrium Multicellular Systems
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
A general kinetic model for the hydrothermal liquefaction of microalgae.
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.
Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics.
Bisaria, Namita; Greenfeld, Max; Limouse, Charles; Mabuchi, Hideo; Herschlag, Daniel
2017-09-12
Decades of study of the architecture and function of structured RNAs have led to the perspective that RNA tertiary structure is modular, made of locally stable domains that retain their structure across RNAs. We formalize a hypothesis inspired by this modularity-that RNA folding thermodynamics and kinetics can be quantitatively predicted from separable energetic contributions of the individual components of a complex RNA. This reconstitution hypothesis considers RNA tertiary folding in terms of ΔGalign, the probability of aligning tertiary contact partners, and ΔGtert, the favorable energetic contribution from the formation of tertiary contacts in an aligned state. This hypothesis predicts that changes in the alignment of tertiary contacts from different connecting helices and junctions (ΔGHJH) or from changes in the electrostatic environment (ΔG+/-) will not affect the energetic perturbation from a mutation in a tertiary contact (ΔΔGtert). Consistent with these predictions, single-molecule FRET measurements of folding of model RNAs revealed constant ΔΔGtert values for mutations in a tertiary contact embedded in different structural contexts and under different electrostatic conditions. The kinetic effects of these mutations provide further support for modular behavior of RNA elements and suggest that tertiary mutations may be used to identify rate-limiting steps and dissect folding and assembly pathways for complex RNAs. Overall, our model and results are foundational for a predictive understanding of RNA folding that will allow manipulation of RNA folding thermodynamics and kinetics. Conversely, the approaches herein can identify cases where an independent, additive model cannot be applied and so require additional investigation.
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.
Kinetics and specificity of nickel hypersensitivity in the murine model.
Siller, G M; Seymour, G J
1994-01-01
Nickel contact dermatitis appears to be almost exclusively a disease of females despite the increasing exposure of males to nickel. Successful murine models of nickel allergic contact dermatitis have been described. The purpose of this study is to investigate the kinetics and specificity of the response in this model and to examine if any differences exist between male and female. Mice were sensitised epicutaneously with nickel sulphate in aqueous solution of varying concentration, volume and duration of application. Following intradermal challenge, dose dependent response kinetics which approximated linearity were demonstrated upto the point of toxicity. Sensitised mice were challenged with Cobaltous chloride, Chromic chloride and Cupric sulphate and demonstrated no evidence of cross sensitivity to cobalt or chrome. Copper produced an irritant response making interpretation difficult. Earlier and stronger responses were observed in female mice, however these differences fell short of statistical significance. The results of the present study therefore establishes a reliable model for nickel hypersensitivity, that demonstrates both specificity and dose dependent kinetics without significant sex differences.
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.
A model to describe Cr(VI) kinetics biosorption.
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.
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.
Kinetic Modeling of Sunflower Grain Filling and Fatty Acid Biosynthesis.
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.
Kinetic Modeling of Sunflower Grain Filling and Fatty Acid Biosynthesis
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
NASA Astrophysics Data System (ADS)
Besson, Ugo
2010-03-01
This paper presents an analysis of the different types of reasoning and physical explanation used in science, common thought, and physics teaching. It then reflects on the learning difficulties connected with these various approaches, and suggests some possible didactic strategies. Although causal reasoning occurs very frequently in common thought and daily life, it has long been the subject of debate and criticism among philosophers and scientists. In this paper, I begin by providing a description of some general tendencies of common reasoning that have been identified by didactic research. Thereafter, I briefly discuss the role of causality in science, as well as some different types of explanation employed in the field of physics. I then present some results of a study examining the causal reasoning used by students in solid and fluid mechanics. The differences found between the types of reasoning typical of common thought and those usually proposed during instruction can create learning difficulties and impede student motivation. Many students do not seem satisfied by the mere application of formal laws and functional relations. Instead, they express the need for a causal explanation, a mechanism that allows them to understand how a state of affairs has come about. I discuss few didactic strategies aimed at overcoming these problems, and describe, in general terms, two examples of mechanics teaching sequences which were developed and tested in different contexts. The paper ends with a reflection on the possible role to be played in physics learning by intuitive and imaginative thought, and the use of simple explanatory models based on physical analogies and causal mechanisms.
Multiensemble Markov models of molecular thermodynamics and kinetics.
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.
Study on kinetic model of microwave thermocatalytic treatment of biomass tar model compound.
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.
Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.
Fleming, R M T; Thiele, I; Provan, G; Nasheuer, H P
2010-06-07
The quantitative analysis of biochemical reactions and metabolites is at frontier of biological sciences. The recent availability of high-throughput technology data sets in biology has paved the way for new modelling approaches at various levels of complexity including the metabolome of a cell or an organism. Understanding the metabolism of a single cell and multi-cell organism will provide the knowledge for the rational design of growth conditions to produce commercially valuable reagents in biotechnology. Here, we demonstrate how equations representing steady state mass conservation, energy conservation, the second law of thermodynamics, and reversible enzyme kinetics can be formulated as a single system of linear equalities and inequalities, in addition to linear equalities on exponential variables. Even though the feasible set is non-convex, the reformulation is exact and amenable to large-scale numerical analysis, a prerequisite for computationally feasible genome scale modelling. Integrating flux, concentration and kinetic variables in a unified constraint-based formulation is aimed at increasing the quantitative predictive capacity of flux balance analysis. Incorporation of experimental and theoretical bounds on thermodynamic and kinetic variables ensures that the predicted steady state fluxes are both thermodynamically and biochemically feasible. The resulting in silico predictions are tested against fluxomic data for central metabolism in Escherichia coli and compare favourably with in silico prediction by flux balance analysis.
Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism
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
Markov models of molecular kinetics: generation and validation.
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.
Hydrothermal alteration of granite rock cores: experiments and kinetic modelling
NASA Astrophysics Data System (ADS)
Kuesters, T.; Mueller, T.; Renner, J.
2016-12-01
The kinetics of water-rock interactions at elevated temperatures is key for understanding the dynamic evolution of porosity and permeability in natural and industrial systems. The implementation of rate data in numerical models simulating reactive transport is crucial to reliably predict subsurface fluid flow. The vast majority of data are constrained by single phase powder experiments inhering unrealistically high surface areas and hampering consideration of microstructural effects on reaction progress. We present experimental results of batch experiments conducted at 200 °C for up to 60 days on a quartz-monzodiorite and pure water that bridge the gap between powder experiments and complex natural systems. The effect of reactive surface area was modelled by using bulk-rock powders, intact, and thermally cracked rock cubes. Fluid composition was monitored (ICP-MS) and solid products were analysed after each experiment (SEM, EMPA). The evolution of fluid and solid compositions was compared to a self-coded geochemical transport model accounting for dissolution, nucleation, growth and reactive surface area. Experimental and modelling results indicate a fast increase of Na, Ca, K and Si in the fluid related to kinetically controlled dissolution of feldspar (plg and kfs) and quartz. Maximum concentrations of Al, Mg, and Fe are reached within two days followed by a rapid decrease induced by secondary mineral precipitation. The amount and type of secondary phases strongly depend on the host substrate indicating that local fluid composition and substrate surface are the controlling parameters. Observed reaction rates differ strongly between powder and rock cube experiments due to differences in reactive surface area. Combining kinetic data, gained by modelling the experimental results, with new information on substrate-precipitate relationship will aid large scale-transport models to realistically predict chemo-mechanical changes and fluid flow in subsurface systems.
Kinetic model of impurity poisoning during growth of calcite
DeYoreo, J; Wasylenki, L; Dove, P; Wilson, D; Han, N
2004-05-18
The central role of the organic component in biologically controlled mineralization is widely recognized. These proteins are characterized by a high proportion of acidic amino acid residues, especially aspartate, Asp. At the same time, biomineralization takes place in the presence of a number of naturally-occurring, inorganic impurities, particularly Mg and Sr. In an attempt to decipher the controls on calcite growth imposed by both classes of modifiers, we have used in situ AFM to investigate the dependence of growth morphology and step kinetics on calcite in the presence of Sr{sup 2+}, as well as a wide suite of Aspartic acid-bearing polypeptides. In each case, we observe a distinct and step-specific modification. Most importantly, we find that the step speed exhibits a characteristic dependence on impurity concentration not predicted by existing crystal growth models. While all of the impurities clearly induce appearance of a 'dead zone,' neither the width of that dead zone nor the dependence of step speed on activity or impurity content can be explained by invoking the Gibbs-Thomson effect, which is the basis for the Cabrera-Vermilyea model of impurity poisoning. Common kink-blocking models also fail to explain the observed dependencies. Here we propose a kinetic model of inhibition based on a 'cooperative' effect of impurity adsorption at adjacent kink sites. The model is in qualitative agreement with the experimental results in that it predicts a non-linear dependence of dead zone width on impurity concentration, as well as a sharp drop in step speed above a certain impurity content. However, a detailed model of impurity adsorption kinetics that give quantitative agreement with the data has yet to be developed.
A neural model of border-ownership from kinetic occlusion.
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.
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.
Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.
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.
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.
Multiensemble Markov models of molecular thermodynamics and kinetics
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
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.
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.
Modeling the turbulent kinetic energy equation for compressible, homogeneous turbulence
NASA Technical Reports Server (NTRS)
Aupoix, B.; Blaisdell, G. A.; Reynolds, William C.; Zeman, Otto
1990-01-01
The turbulent kinetic energy transport equation, which is the basis of turbulence models, is investigated for homogeneous, compressible turbulence using direct numerical simulations performed at CTR. It is shown that the partition between dilatational and solenoidal modes is very sensitive to initial conditions for isotropic decaying turbulence but not for sheared flows. The importance of the dilatational dissipation and of the pressure-dilatation term is evidenced from simulations and a transport equation is proposed to evaluate the pressure-dilatation term evolution. This transport equation seems to work well for sheared flows but does not account for initial condition sensitivity in isotropic decay. An improved model is proposed.
Kinetic model for microbial growth and desulphurisation with Enterobacter sp.
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".
Obtaining kinetics from MBMS and modeling of propene flame structure
Westmoreland, P.R.; Thomas, S.D.; Bhargava, A.
1995-03-01
Molecular-beam mass spectrometry is being used to map hydrocarbon flat flames for subsequent modeling. The paper focuses on describing the authors` apparatus and its use. Difficulties and solutions for modeling MBMS flame data are discussed using the particular case of a fuel-lean flat flame of propene, oxygen, and argon ({phi} = 0.229, 30 Torr, v{sub o} = 57.5 cm/s at 298 K). Here, the MBMS technique has led to the identification of new kinetics for allyl + O{sub 2} at high temperatures.
Moisture desorption rates from TATB formulations: experiments and kinetic models.
Glascoe, Elizabeth A; Dinh, Long N; Small, Ward; Overturf, George E
2012-06-07
The rate of water desorption from PBX-9502, a formulation containing 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), is measured using temperature-programmed desorption and modeled using conventional kinetic modeling methods. The results of these studies show two stages of moisture release. At lower temperatures, the release is likely assisted by thermal expansion of the TATB and melting of the Kel-F binder. At higher temperatures, a considerable amount of water is released and is attributed to sublimation of the TATB, which exposes new surfaces for water desorption.
Kinetic modeling of non-ideal explosives with CHEETAH
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.
Reduction of Fe(III) colloids by Shewanella putrefaciens: A kinetic model
NASA Astrophysics Data System (ADS)
Bonneville, Steeve; Behrends, Thilo; van Cappellen, Philippe; Hyacinthe, Christelle; Röling, Wilfred F. M.
2006-12-01
A kinetic model for the microbial reduction of Fe(III) oxyhydroxide colloids in the presence of excess electron donor is presented. The model assumes a two-step mechanism: (1) attachment of Fe(III) colloids to the cell surface and (2) reduction of Fe(III) centers at the surface of attached colloids. The validity of the model is tested using Shewanella putrefaciens and nanohematite as model dissimilatory iron reducing bacteria and Fe(III) colloidal particles, respectively. Attachment of nanohematite to the bacteria is formally described by a Langmuir isotherm. Initial iron reduction rates are shown to correlate linearly with the relative coverage of the cell surface by nanohematite particles, hence supporting a direct electron transfer from membrane-bound reductases to mineral particles attached to the cells. Using internally consistent parameter values for the maximum attachment capacity of Fe(III) colloids to the cells, Mmax, the attachment constant, KP, and the first-order Fe(III) reduction rate constant, k, the model reproduces the initial reduction rates of a variety of fine-grained Fe(III) oxyhydroxides by S. putrefaciens. The model explains the observed dependency of the apparent Fe(III) half-saturation constant, Km∗, on the solid to cell ratio, and it predicts that initial iron reduction rates exhibit saturation with respect to both the cell density and the abundance of the Fe(III) oxyhydroxide substrate.
Norepinephrine metabolism in humans. Kinetic analysis and model
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.
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…
Formal Models of Continuity, Discontinuity, and Partial Discontinuity for Behavioral Development.
ERIC Educational Resources Information Center
Brainerd, Charles J.
The purpose of this paper is to provide a formal three-step explication of a question that has been traditionally viewed as fundamental to developmental theory construction and explanation: Is behavioral development continous or discontinuous, or is it both? First, a preliminary structural definition of behavioral development involving a certain…
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
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.
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.
Kinetic equations modelling wealth redistribution: a comparison of approaches.
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.
Langrangian model of nitrogen kinetics in the Chattahoochee river
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.
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.
Kinetic modeling of virus transport at the field scale.
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
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.
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.
Modeling Large Zinc Isotope Fractionations Associated with Reaction Kinetics
NASA Astrophysics Data System (ADS)
Black, J. R.; John, S.; Kavner, A.
2009-12-01
Often multiple processes govern isotope fractionation during a chemical reaction, such as the mass-transport, equilibrium and reaction kinetics between reactants and products. Here we use experimental electrochemical techniques to control the mass-transport and reaction kinetics of the electrodeposition reaction: Zn2+ + 2e- = Zn(s); and model the isotopic fractionation measured to resolve the underlying mechanisms of fractionation. Zn was plated on a rotating disc electrode at various applied overpotentials, rotation rates and temperatures. Electroplated Zn was recovered in acid for analysis of the stable isotope composition by multi-collector ICP-MS. The isotopic composition (66Zn/64Zn) of plated metal is reported relative to the stock solution. A large range of Δ66Znsample-stock is observed, with increasing fractionation at higher rotation rates (Fig. 1A), and lower overpotentials (Fig. 1B). Models of electrochemical kinetics, show that these variables control the relative rates of precipitation and diffusion, as defined by the Koutecky-Levich equation [Bard and Faulkner (2001), Electrochemical Methods, John Wiley & Sons]. Using this equation to interpret our data shows that all the data fall along a systematic trend (Fig. 1C) with smaller fractionations in the mass-transport limited regime and larger fractionations produced under electrochemical kinetic control. We extend the Koutecky-Levich model to predict isotope fractionation during electrochemical processes as a function of mass-dependent diffusion (Fig. 2A); standard rate constant (Fig. 2B); and transfer coefficient, describing reaction barrier symmetry (Fig. 2C). A comparison of the model and our data shows that diffusive and equilibrium fractionation alone (Fig. 2A-B) cannot reproduce the trends in our data, but a mass-dependence in α can explain our observations. However, the predicted fractionation is very sensitive to the magnitude of k0 (Fig. 2C). This model predicts how isotope fractionation
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.
Modelling proteins: conformational sampling and reconstruction of folding kinetics.
Klenin, Konstantin; Strodel, Birgit; Wales, David J; Wenzel, Wolfgang
2011-08-01
In the last decades biomolecular simulation has made tremendous inroads to help elucidate biomolecular processes in-silico. Despite enormous advances in molecular dynamics techniques and the available computational power, many problems involve long time scales and large-scale molecular rearrangements that are still difficult to sample adequately. In this review we therefore summarise recent efforts to fundamentally improve this situation by decoupling the sampling of the energy landscape from the description of the kinetics of the process. Recent years have seen the emergence of many advanced sampling techniques, which permit efficient characterisation of the relevant family of molecular conformations by dispensing with the details of the short-term kinetics of the process. Because these methods generate thermodynamic information at best, they must be complemented by techniques to reconstruct the kinetics of the process using the ensemble of relevant conformations. Here we review recent advances for both types of methods and discuss their perspectives to permit efficient and accurate modelling of large-scale conformational changes in biomolecules. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches. Copyright © 2010 Elsevier B.V. All rights reserved.
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.
A cardiac muscle model relating sarcomere dynamics to calcium kinetics.
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.
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
Stochastic Kinetic Modeling of Vesicular Stomatitis Virus Intracellular Growth
Hensel, Sebastian C.; Rawlings, James B.; Yin, John
2011-01-01
By building kinetic models of biological networks one may advance the development of new modeling approaches while gaining insights into the biology. We focus here on building a stochastic kinetic model for the intracellular growth of vesicular stomatitis virus (VSV), a well-studied virus that encodes five genes. The essential network of VSV reactions creates challenges to stochastic simulation owing to (i) delayed reactions associated with transcription and genome replication, (ii) production of large numbers of intermediate proteins by translation, and (iii) the presence of highly reactive intermediates that rapidly fluctuate in their intracellular levels. We address these issues by developing a hybrid implementation of the model that combines a delayed stochastic simulation algorithm (DSSA) with Langevin equations to simulate the reactions that produce species in high numbers. Further, we employ a quasi-steady state approximation (QSSA) to overcome the computational burden of small time steps caused by highly reactive species. The simulation is able to capture experimentally observed patterns of viral gene expression. Moreover, the simulation suggests that early levels of a low-abundance species, VSV L mRNA, play a key role in determining the production level of VSV genomes, transcripts, and proteins within an infected cell. Ultimately, these results suggest that stochastic gene expression contribute to the distribution of virus progeny yields from infected cells. PMID:19459014
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).
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.
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.
Kinetic modelling of cytochrome c adsorption on SBA-15.
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
Renormalization of the O(N) model in the 1/N expansion in the auxiliary field formalism
Jakovac, A.
2008-10-15
We study the renormalization of the O(N) model using the auxiliary field formalism (Hubbard-Stratonovich transformation) in the 1/N expansion at finite temperature. We provide the general strategy of renormalization for arbitrary order and make a calculation up to next-to-leading order. We show that renormalization is possible for any values of the condensates, prove the temperature independence of the counterterms, and determine the cutoff dependence of the first nontrivial counterterm parts.
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.
Adequacy indices for dialysis in acute renal failure: kinetic modeling.
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.
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.
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.
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.
Quantitative description of realistic wealth distributions by kinetic trading models
NASA Astrophysics Data System (ADS)
Lammoglia, Nelson; Muñoz, Víctor; Rogan, José; Toledo, Benjamín; Zarama, Roberto; Valdivia, Juan Alejandro
2008-10-01
Data on wealth distributions in trading markets show a power law behavior x-(1+α) at the high end, where, in general, α is greater than 1 (Pareto’s law). Models based on kinetic theory, where a set of interacting agents trade money, yield power law tails if agents are assigned a saving propensity. In this paper we are solving the inverse problem, that is, in finding the saving propensity distribution which yields a given wealth distribution for all wealth ranges. This is done explicitly for two recently published and comprehensive wealth datasets.
A generic 3D kinetic model of gene expression
NASA Astrophysics Data System (ADS)
Zhdanov, Vladimir P.
2012-04-01
Recent experiments show that mRNAs and proteins can be localized both in prokaryotic and eukaryotic cells. To describe such situations, I present a 3D mean-field kinetic model aimed primarily at gene expression in prokaryotic cells, including the formation of mRNA, its translation into protein, and slow diffusion of these species. Under steady-state conditions, the mRNA and protein spatial distribution is described by simple exponential functions. The protein concentration near the gene transcribed into mRNA is shown to depend on the protein and mRNA diffusion coefficients and degradation rate constants.
Kinetic Relations for a Lattice Model of Phase Transitions
NASA Astrophysics Data System (ADS)
Schwetlick, Hartmut; Zimmer, Johannes
2012-11-01
The aim of this article is to analyse travelling waves for a lattice model of phase transitions, specifically the Fermi-Pasta-Ulam chain with piecewise quadratic interaction potential. First, for fixed, sufficiently large subsonic wave speeds, we rigorously prove the existence of a family of travelling wave solutions. Second, it is shown that this family of solutions gives rise to a kinetic relation which depends on the jump in the oscillatory energy in the solution tails. Third, our constructive approach provides a very good approximate travelling wave solution.
A simplified kinetic model for an autopoietic synthesis of micelles
NASA Astrophysics Data System (ADS)
Chizmadzhew, Yuri A.; Maestro, Marco; Mavelli, Fabio
1994-08-01
Recently, some chemical systems have been implemented which have an autopoietic behaviour according to Varela and Maturana's definition. They consist of micelles or reversed micelles which are able to produce their building material inside themselves, and, in such a way reproduce themselves. For one of these systems we have elaborated a kinetic model to rationalize the long lag phase and the abrupt rate increase displayed during the autopietic process of micellar self-replication. The theoretical predictions are in good agreement with the experimental observations available to date.
β-function formalism for inflationary models with a non minimal coupling with gravity
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.
Formal and Informal Work Group Relationships With Performance: A Moderation Model Using Social
2006-03-01
performance (Baldwin et. al., 1997; Sparrowe et. al., 2001; Yang & Tang, 2004). This idea is consistent with a group research phenomenon termed “social...performance of members of project teams in an academic setting. This research - 9 - expects to find a similar relationship between centrality and...the Casciaro and Lobo (2005) study, they closely resemble the idea of formal and informal social interaction respectively, as defined in social
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.
A new kinetic model for human iodine metabolism
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/.
Probabilistic multicompartmental model for interpreting DGT kinetics in sediments.
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.
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.
Formal reasoning about systems biology using theorem proving
Hasan, Osman; Siddique, Umair; Tahar, Sofiène
2017-01-01
System biology provides the basis to understand the behavioral properties of complex biological organisms at different levels of abstraction. Traditionally, analysing systems biology based models of various diseases have been carried out by paper-and-pencil based proofs and simulations. However, these methods cannot provide an accurate analysis, which is a serious drawback for the safety-critical domain of human medicine. In order to overcome these limitations, we propose a framework to formally analyze biological networks and pathways. In particular, we formalize the notion of reaction kinetics in higher-order logic and formally verify some of the commonly used reaction based models of biological networks using the HOL Light theorem prover. Furthermore, we have ported our earlier formalization of Zsyntax, i.e., a deductive language for reasoning about biological networks and pathways, from HOL4 to the HOL Light theorem prover to make it compatible with the above-mentioned formalization of reaction kinetics. To illustrate the usefulness of the proposed framework, we present the formal analysis of three case studies, i.e., the pathway leading to TP53 Phosphorylation, the pathway leading to the death of cancer stem cells and the tumor growth based on cancer stem cells, which is used for the prognosis and future drug designs to treat cancer patients. PMID:28671950
Kinetic modeling of the adsorption of basic dyes by kudzu.
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.
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.
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.
Chemical Kinetic Models for HCCI and Diesel Combustion
Pitz, W J; Westbook, C K; Mehl, M
2008-10-30
Hydrocarbon fuels for advanced combustion engines consist of complex mixtures of hundreds or even thousands of different components. These components can be grouped into a number of chemically distinct classes, consisting of n-paraffins, branched paraffins, cyclic paraffins, olefins, oxygenates, and aromatics. Biodiesel contains its own unique chemical class called methyl esters. The fractional amounts of these chemical classes are quite different in gasoline, diesel fuel, oil-sand derived fuels and bio-derived fuels, which contributes to the very different combustion characteristics of each of these types of combustion systems. The objectives of this project are: (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.
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.
Kinetic model of sucrose accumulation in maturing sugarcane culm tissue.
Uys, Lafras; Botha, Frederik C; Hofmeyr, Jan-Hendrik S; Rohwer, Johann M
2007-01-01
Biochemically, it is not completely understood why or how commercial varieties of sugarcane (Saccharum officinarum) are able to accumulate sucrose in high concentrations. Such concentrations are obtained despite the presence of sucrose synthesis/breakdown cycles (futile cycling) in the culm of the storage parenchyma. Given the complexity of the process, kinetic modelling may help to elucidate the factors governing sucrose accumulation or direct the design of experimental optimisation strategies. This paper describes the extension of an existing model of sucrose accumulation (Rohwer, J.M., Botha, F.C., 2001. Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem. J. 358, 437-445) to account for isoforms of sucrose synthase and fructokinase, carbon partitioning towards fibre formation, and the glycolytic enzymes phosphofructokinase (PFK), pyrophosphate-dependent PFK and aldolase. Moreover, by including data on the maximal activity of the enzymes as measured in different internodes, a growth model was constructed that describes the metabolic behaviour as sugarcane parenchymal tissue matures from internodes 3-10. While there was some discrepancy between modelled and experimentally determined steady-state sucrose concentrations in the cytoplasm, steady-state fluxes showed a better fit. The model supports a hypothesis of vacuolar sucrose accumulation against a concentration gradient. A detailed metabolic control analysis of sucrose synthase showed that each isoform has a unique control profile. Fructose uptake by the cell and sucrose uptake by the vacuole had a negative control on the futile cycling of sucrose and a positive control on sucrose accumulation, while the control profile for neutral invertase was reversed. When the activities of these three enzymes were changed from their reference values, the effects on futile cycling and sucrose accumulation were amplified. The model can be run online at the JWS Online
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…
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…
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.
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.
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.
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.
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.
Multiple-relaxation-time lattice Boltzmann kinetic model for combustion.
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.
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
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.
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.
The Routine Fitting of Kinetic Data to Models
Berman, Mones; Shahn, Ezra; Weiss, Marjory F.
1962-01-01
A mathematical formalism is presented for use with digital computers to permit the routine fitting of data to physical and mathematical models. Given a set of data, the mathematical equations describing a model, initial conditions for an experiment, and initial estimates for the values of model parameters, the computer program automatically proceeds to obtain a least squares fit of the data by an iterative adjustment of the values of the parameters. When the experimental measures are linear combinations of functions, the linear coefficients for a least squares fit may also be calculated. The values of both the parameters of the model and the coefficients for the sum of functions may be unknown independent variables, unknown dependent variables, or known constants. In the case of dependence, only linear dependencies are provided for in routine use. The computer program includes a number of subroutines, each one of which performs a special task. This permits flexibility in choosing various types of solutions and procedures. One subroutine, for example, handles linear differential equations, another, special non-linear functions, etc. The use of analytic or numerical solutions of equations is possible. PMID:13867975
Kinetic model of acetate metabolism in healthy and hyperinsulinaemic humans
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
Quantum kinetics and thermalization in a particle bath model.
Alamoudi, S M; Boyanovsky, D; de Vega, H J
1999-07-01
We study the dynamics of relaxation and thermalization in an exactly solvable model of a particle interacting with a harmonic oscillator bath. Our goal is to understand the effects of non-Markovian processes on the relaxational dynamics and to compare the exact evolution of the distribution function with approximate Markovian and non-Markovian quantum kinetics. There are two different cases that are studied in detail: (i) a quasiparticle (resonance) when the renormalized frequency of the particle is above the frequency threshold of the bath and (ii) a stable renormalized "particle" state below this threshold. The time evolution of the occupation number for the particle is evaluated exactly using different approaches that yield to complementary insights. The exact solution allows us to investigate the concept of the formation time of a quasiparticle and to study the difference between the relaxation of the distribution of bare particles and that of quasiparticles. For the case of quasiparticles, the exact occupation number asymptotically tends to a statistical equilibrium distribution that differs from a simple Bose-Einstein form as a result of off-shell processes whereas in the stable particle case, the distribution of particles does not thermalize with the bath. We derive a non-Markovian quantum kinetic equation which resums the perturbative series and includes off-shell effects. A Markovian approximation that includes off-shell contributions and the usual Boltzmann equation (energy conserving) are obtained from the quantum kinetic equation in the limit of wide separation of time scales upon different coarse-graining assumptions. The relaxational dynamics predicted by the non-Markovian, Markovian, and Boltzmann approximations are compared to the exact result. The Boltzmann approach is seen to fail in the case of wide resonances and when threshold and renormalization effects are important.
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
High Temperature Chemical Kinetic Combustion Modeling of Lightly Methylated Alkanes
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.
Chemical kinetic modeling of component mixtures relevant to gasoline
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.
Developing a computational model of human hand kinetics using AVS
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.
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.
A Global Modeling Framework for Plasma Kinetics: Development and Applications
NASA Astrophysics Data System (ADS)
Parsey, Guy Morland
The modern study of plasmas, and applications thereof, has developed synchronously with com- puter capabilities since the mid-1950s. Complexities inherent to these charged-particle, many- body, systems have resulted in the development of multiple simulation methods (particle-in-cell, fluid, global modeling, etc.) in order to both explain observed phenomena and predict outcomes of plasma applications. Recognizing that different algorithms are chosen to best address specific topics of interest, this thesis centers around the development of an open-source global model frame- work for the focused study of non-equilibrium plasma kinetics. After verification and validation of the framework, it was used to study two physical phenomena: plasma-assisted combustion and the recently proposed optically-pumped rare gas metastable laser. Global models permeate chemistry and plasma science, relying on spatial averaging to focus attention on the dynamics of reaction networks. Defined by a set of species continuity and energy conservation equations, the required data and constructed systems are conceptually similar across most applications, providing a light platform for exploratory and result-search parameter scan- ning. Unfortunately, it is common practice for custom code to be developed for each application-- an enormous duplication of effort which negatively affects the quality of the software produced. Presented herein, the Python-based Kinetic Global Modeling framework (KGMf) was designed to support all modeling phases: collection and analysis of reaction data, construction of an exportable system of model ODEs, and a platform for interactive evaluation and post-processing analysis. A symbolic ODE system is constructed for interactive manipulation and generation of a Jacobian, both of which are compiled as operation-optimized C-code. Plasma-assisted combustion and ignition (PAC/PAI) embody the modernization of burning fuel by opening up new avenues of control and optimization
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.
Ab initio determination of kinetics for atomic layer deposition modeling
NASA Astrophysics Data System (ADS)
Remmers, Elizabeth M.
A first principles model is developed to describe the kinetics of atomic layer deposition (ALD) systems. This model requires no fitting parameters, as it is based on the reaction pathways, structures, and energetics obtained from quantum-chemical studies. Using transition state theory and partition functions from statistical mechanics, equilibrium constants and reaction rates can be calculated. Several tools were created in Python to aid in the calculation of these quantities, and this procedure was applied to two systems- zinc oxide deposition from diethyl zinc (DEZ) and water, and alumina deposition from trimethyl aluminum (TMA) and water. A Gauss-Jordan factorization is used to decompose the system dynamics, and the resulting systems of equations are solved numerically to obtain the temporal concentration profiles of these two deposition systems.
Parameter estimation for models of ligninolytic and cellulolytic enzyme kinetics
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.
Modeling of chemical inhibition from amyloid protein aggregation kinetics
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
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 .
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.
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.
Integration Strategies for Efficient Multizone Chemical Kinetics Models
McNenly, M J; Havstad, M A; Aceves, S M; Pitz, W J
2009-10-15
Three integration strategies are developed and tested for the stiff, ordinary differential equation (ODE) integrators used to solve the fully coupled multizone chemical kinetics model. Two of the strategies tested are found to provide more than an order of magnitude of improvement over the original, basic level of usage for the stiff ODE solver. One of the faster strategies uses a decoupled, or segregated, multizone model to generate an approximate Jacobian. This approach yields a 35-fold reduction in the computational cost for a 20 zone model. Using the same approximate Jacobian as a preconditioner for an iterative Krylov-type linear system solver, the second improved strategy achieves a 75-fold reduction in the computational cost for a 20 zone model. The faster strategies achieve their cost savings with no significant loss of accuracy. The pressure, temperature and major species mass fractions agree with the solution from the original integration approach to within six significant digits; and the radical mass fractions agree with the original solution to within four significant digits. The faster strategies effectively change the cost scaling of the multizone model from cubic to quadratic, with respect to the number of zones. As a consequence of the improved scaling, the 40 zone model offers more than a 250-fold cost savings over the basic calculation.
How informative is your kinetic model?: using resampling methods for model invalidation
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
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
Kinetic Modeling of Incremental Ambulatory Peritoneal Dialysis Exchanges.
Guest, Steven; Leypoldt, John K; Cassin, Michelle; Schreiber, Martin
2017-01-01
♦ BACKGROUND: Incremental peritoneal dialysis (PD), the gradual introduction of dialysate exchanges at less than full-dose therapy, has been infrequently described in clinical reports. One concern with less than full-dose dialysis is whether urea clearance targets are achievable with an incremental regimen. In this report, we used a large database of PD patients, across all membrane transport types, and performed urea kinetic modeling determinations of possible incremental regimens for an individual membrane type. ♦ METHODS: Using a modified 3-pore model of peritoneal transport, various incremental manual continuous ambulatory PD (CAPD) exchanges employing glucose and/or icodextrin were evaluated. Peritoneal urea clearances from those simulations were added to residual kidney urea clearance for patients with various glomerular filtration rates (GFRs), and the total weekly urea clearance was then compared to the total weekly urea Kt/V target of 1.7. All 4 peritoneal membrane types were modeled. For each simulated prescription, net ultrafiltration and carbohydrate absorption were also calculated. ♦ RESULTS: Incremental CAPD regimens of 2 exchanges a day met adequacy targets if the GFR was 6 mL/min/1.73 m(2) in all membrane types. For regimens employing 3 exchanges a day, Kt/V targets were achieved at GFR levels of 4 to 5 mL/min/1.73 m(2) in high transporters to low transporters but higher tonicity 2.5% glucose solutions or icodextrin were required in some regimens. ♦ CONCLUSIONS: This work demonstrates that with incremental CAPD regimens, urea kinetic targets are achievable in most new starts to PD with residual kidney function. Incremental PD may be a less intrusive, better accepted initial treatment regime and a cost-effective way to initiate chronic dialysis in the incident patient. The key role of intrinsic kidney function in incremental regimens is highlighted in this analysis and would warrant conscientious monitoring. Copyright © 2017 International
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
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.
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.
A general kinetic-flow coupling model for FCC riser flow simulation.
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.
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…
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…
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.
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.
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.
An Experimental and Kinetic Modeling Study of Methyl Decanoate Combustion
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.
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.
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.
Positron Emission Tomography - Tracer Kinetic Modelling in Drug Development
NASA Astrophysics Data System (ADS)
Cunningham, Vincent J.; Gunn, Roger N.
2006-04-01
There is a growing interest in the application of imaging techniques to drug discovery and development to enable earlier decisions to be made on the suitability of a given drug for the treatment of disease in humans. PET has the ability to image pharmacological functions in vivo in conscious humans and is ideally suited to this task. Either the drug itself can be radiolabelled and its biodistribution in tissues measured directly, or alternatively, a given pharmacological target can be labelled, enabling quantification of exogenous drug interaction. A wide range of mathematical modelling techniques may be applied to the spatial and kinetic PET data giving rise to functional images or regional parameter values that reflect the pharmacology of the drug under study. Examples will be shown and some of the mathematical techniques behind quantification will be discussed.
Low pressure microplasmas enabled by field ionization: Kinetic modeling
Macheret, Sergey O. Tholeti, Siva Sashank; Alexeenko, Alina A.
2016-05-09
A principle of microplasma generation that utilizes field emission of electrons at the cathode and field ionization producing ions at the anode, both processes relying on nanorods or nanotubes, is explored theoretically. In this plasma generation concept, collisional ionization of atoms and molecules by electron impact would play a negligible role. Analytical estimates as well as plasma kinetic modeling by particle-in-cell method with Monte Carlo collisions in argon confirm that this principle can enable substantial plasma densities at near-collisionless microgaps, while requiring relatively low voltages, less than 100 V. An order of magnitude increase in electron number density can be achieved due to enhancement of field emission at the cathode by positive space charge at high field ionization ion current densities.
Kinetic modelling of isometamidium chloride (Samorin) uptake by Trypanosoma congolense.
Sutherland, I A; Mounsey, A; Eisler, M; Holmes, P H
1992-08-01
Clones of Trypanosoma congolense which express resistance to the widely used trypanocide isometamidium chloride accumulate less of the drug than clones which are sensitive to drug treatment. A mathematical model has been developed which was able to predict theoretical lines representing the uptake kinetics in trypanosomes which were sensitive to isometamidium, as well as for resistant trypanosomes in which reduced accumulation was a result of either reduced uptake or enhanced efflux of the drug. Data from drug uptake experiments were then fitted to these theoretical lines. While the value for drug efflux could not be separated from the dissociation constant of the trypanosomes for isometamidium, it was demonstrated that reduced accumulation is not a result of reduced uptake of isometamidium by drug-resistant trypanosomes.
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.
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.
Kinetic effects of adriamycin and bleomycin on two osteosarcoma models.
Bell, D F; Bell, R S; Mankin, H J; Gebhardt, M C; Weltie, F; O'Brien, T
1988-01-01
Although chemotherapeutic drugs are frequently administered to patients with osteosarcoma, there has been little research into the effect of cytotoxic drugs on osteosarcoma cell biology. The effect of two drugs (Adriamycin and bleomycin) on cell cycle kinetics was investigated in vitro in an established line of human osteosarcoma cells and in vivo using the Dunn osteosarcoma model. The cell cycle changes were consistent with G2 arrest for both drugs in vivo and in vitro. The alteration in cell cycle distribution was correlated with inhibition of 3H-thymidine incorporation in vitro. In vivo, the greater change in cell cycle distribution caused by Adriamycin was reflected in the increased inhibition of tumor growth found with this drug.