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
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
A Formalization of Student Modeling.
ERIC Educational Resources Information Center
Danna, Frederic; Sebillot, Pascale
1997-01-01
Focuses on student modeling within an Intelligent Tutoring System. Describes three domain-independent properties that the formalism representing student knowledge and the processes synthesizing this knowledge must possess to build accurate student models for second-language learning. Notes when, how, and where hypothetical reasoning mechanisms…
Lee, Sang Ho; Ryu, Yasuji; Hayano, Koichi; Yoshida, Hiroyuki
2015-01-01
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. PMID:26236779
Formal modeling of virtual machines
NASA Technical Reports Server (NTRS)
Cremers, A. B.; Hibbard, T. N.
1978-01-01
Systematic software design can be based on the development of a 'hierarchy of virtual machines', each representing a 'level of abstraction' of the design process. The reported investigation presents the concept of 'data space' as a formal model for virtual machines. The presented model of a data space combines the notions of data type and mathematical machine to express the close interaction between data and control structures which takes place in a virtual machine. One of the main objectives of the investigation is to show that control-independent data type implementation is only of limited usefulness as an isolated tool of program development, and that the representation of data is generally dictated by the control context of a virtual machine. As a second objective, a better understanding is to be developed of virtual machine state structures than was heretofore provided by the view of the state space as a Cartesian product.
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.
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…
Kinetic theory of turbulence for parallel propagation revisited: Formal results
NASA Astrophysics Data System (ADS)
Yoon, Peter H.
2015-08-01
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.
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.
Formalizing Linguistic Conventions for Conceptual Models
NASA Astrophysics Data System (ADS)
Becker, Jörg; Delfmann, Patrick; Herwig, Sebastian; Lis, Łukasz; Stein, Armin
A precondition for the appropriate analysis of conceptual models is not only their syntactic correctness but also their semantic comparability. Assuring comparability is challenging especially when models are developed by different persons. Empirical studies show that such models can vary heavily, especially in model element naming, even if they express the same issue. In contrast to most ontology-driven approaches proposing the resolution of these differences ex-post, we introduce an approach that avoids naming differences in conceptual models already during modeling. Therefore we formalize naming conventions combining domain thesauri and phrase structures based on a lin-guistic grammar. This allows for guiding modelers automatically during the modeling process using standardized labels for model elements. Our approach is generic, making it applicable for any modeling language.
Multidimensional reactor kinetics modeling
Diamond, D.J.
1996-11-01
There is general agreement that for many light water reactor transient calculations, it is-necessary to use a multidimensional neutron kinetics model coupled to a thermal-hydraulics model for satisfactory results. These calculations are needed for a variety of applications for licensing safety analysis, probabilistic risk assessment (PRA), operational support, and training. The latter three applications have always required best-estimate models, but in the past applications for licensing could be satisfied with relatively simple models. By using more sophisticated best-estimate models, the consequences of these calculations are better understood, and the potential for gaining relief from restrictive operating limits increases. Hence, for all of the aforementioned applications, it is important to have the ability to do best-estimate calculations with multidimensional neutron kinetics models. coupled to sophisticated thermal-hydraulic models. Specifically, this paper reviews the status of multidimensional neutron kinetics modeling which would be used in conjunction with thermal-hydraulic models to do core dynamics calculations, either coupled to a complete NSSS representation or in isolation. In addition, the paper makes recommendations as to what should be the state-of-the-art for the next ten years. The review is an update to a previous review of the status as of ten years ago. The general requirements for a core dynamics code and the modeling available for such a code, discussed in that review, are still applicable. The emphasis in the current review is on the neutron kinetics assuming that the necessary thermal-hydraulic capability exists. In addition to discussing the basic neutron kinetics, discussion is given of related modeling (other than thermal- hydraulics). The capabilities and limitations of current computer codes are presented to understand the state-of-the-art and to help clarify the future direction of model development in this area.
On the relationship between kinetic and fluid formalisms for convection in the inner magnetosphere
NASA Astrophysics Data System (ADS)
Song, Yang; Sazykin, Stanislav; Wolf, Richard A.
2008-08-01
In the inner magnetosphere, the plasma flows are mostly slow compared to thermal or Alfvén speeds, but the convection is far away from the ideal magnetohydrodynamic regime since the gradient/curvature drifts become significant. Both kinetic (Wolf, 1983) and two-fluid (Peymirat and Fontaine, 1994; Heinemann, 1999) formalisms have been used to describe plasma dynamics, but it is not fully understood how they relate to each other. We explore the relations among kinetic, fluid, and recently developed "average" (Liu, 2006) models in an attempt to find the simplest yet realistic way to describe the convection. First, we prove analytically that the model of (Liu, 2006), when closed with the assumption of a Maxwellian distribution, is equivalent to the fluid model of (Heinemann, 1999). Second, we analyze the transport of both one-dimensional and two-dimensional Gaussian-shaped blob of hot plasma. For the kinetic case, it is known that the time evolution of such a blob is gradual spreading in time. For the fluid case, Heinemann and Wolf (2001a, 2001b) showed that in a one-dimensional idealized case, the blob separates into two drifting at different speeds. We present a fully nonlinear solution of this case, confirming this behavior but demonstrating what appears to be a shocklike steepening of the faster drifting secondary blob. A new, more realistic two-dimensional example using the dipole geometry with a uniform electric field confirms the one-dimensional solutions. Implications for the numerical simulations of magnetospheric dynamics are discussed.
Endorsement of formal leaders: an integrative model.
Michener, H A; Lawler, E J
1975-02-01
This experiment develops an integrative, path-analytic model for the endorsement accorded formal leaders. The model contains four independent variables reflecting aspects of group structure (i.e., group success-failure, the payoff distribution, the degree of support by others members for the leader, and the vulnerability of the leader). Also included are two intervening variables reflecting perceptual processes (attributed competence and attributed fairness), and one dependent variable endorsement). The results indicate that endorsement is greater when the group's success is high, when the payoff distribution is flat rather than hierarchial, and when the leader is not vulnerable to removal from office. Other support had no significant impact on endorsement. Analyses further demonstrate that the effect of success-failure on endorsement is mediated by attributed competence, while the effect of the payoff distributed is mediated by attributed fairness. These results suggest that moral and task evaluations are distinct bases of endorsement. PMID:1123712
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.
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
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.
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). PMID:25876164
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
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.
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
Kinetic models of hydrocarbon generation
Burnham, A.K.; Sweeney, J.J.
1990-10-25
We are carrying out an integrated program of laboratory experiments, kinetics modeling, and basin thermal history modeling in order to better understand the natural breakdown of organic matter into oil and gas. Our kinetic models of organic maturation are being used to better understand the coupling of generation, cracking, expulsion, and overpressuring in both the laboratory and geologic setting. Currently we are carrying out chemical experiments and developing more efficient chemical kinetic modeling schemes to obtain a better understanding of expulsion and cracking from lean source rocks and from hydrogen-poor (terrestrial) organic source material. We verify the chemical kinetic models by integrating them with thermal history models of hydrocarbon-producing sediments and comparing predicted and observed characteristics of the hydrocarbon occurrence in a variety of settings. We intend to apply this approach to evaluate the potential for deep gas resources in the Pacific Northwest and in the Louisiana Gulf Coast. 11 refs., 4 figs.
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
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.
An Operator Formalism for Unitary Matrix Models
NASA Astrophysics Data System (ADS)
Anagnostopoulos, K. N.; Bowick, M. J.; Ishibashi, N.
We analyze the double scaling limit of unitary matrix models in terms of trigonometric orthogonal polynomials on the circle. In particular we find a compact formulation of the string equation at the kth multicritical point in terms of pseudodifferential operators and a corresponding action principle. We also relate this approach to the mKdV hierarchy which appears in the analysis in terms of conventional orthogonal polynomials on the circle.
Hebenstreit, F.; Alkofer, R.; Gies, H.
2010-11-15
The nonperturbative electron-positron pair production (Schwinger effect) is considered for space- and time-dependent electric fields E-vector(x-vector,t). Based on the Dirac-Heisenberg-Wigner formalism, we derive a system of partial differential equations of infinite order for the 16 irreducible components of the Wigner function. In the limit of spatially homogeneous fields the Vlasov equation of quantum kinetic theory is rediscovered. It is shown that the quantum kinetic formalism can be exactly solved in the case of a constant electric field E(t)=E{sub 0} and the Sauter-type electric field E(t)=E{sub 0}sech{sup 2}(t/{tau}). These analytic solutions translate into corresponding expressions within the Dirac-Heisenberg-Wigner formalism and allow to discuss the effect of higher derivatives. We observe that spatial field variations typically exert a strong influence on the components of the Wigner function for large momenta or for late times.
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.
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.
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
Induced inflation from a 5D purely kinetic scalar field formalism on warped product spaces
NASA Astrophysics Data System (ADS)
Madriz Aguilar, J. E.
2008-01-01
Considering a separable and purely kinetic 5D scalar field we investigate the induction of 4D scalar potentials on a 4D constant foliation on the class of 5D warped product space-times. We obtain a quantum confinement of the inflaton modes given naturally from the model for at least a class of warping factors. We can recover a 4D inflationary scenario where the inflationary potential is geometrically induced from 5D and the effective equation of state in 4D that includes the effect of the inflaton field and the induced matter is Peff≃-ρeff.
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.
The help of formal models for healthcare security policies.
Trouessin, G; Barber, B
1997-01-01
This article is a personal contribution (i.e., from a strict security expert point of view) towards the help for specification, validation and/or evaluation of reliable, but also secure, healthcare security policies (HSP). The first part is dedicated to show, according to the various aspects of the security policy concept, that healthcare information systems (HIS) offer such a diversity of particularities and potential security needs, that it is necessary for healthcare security policies to be defined as flexible, but also as robust, as possible. Then the formal modelling approach, a wide area of solutions providing both flexibility (by means of modelling) and robustness (by means of formalization), is presented. The most well-known examples of security models are recalled. All of them try to use formal models as a security policy specification/validation tool, but none of them can be helpfully used in the very demanding context of HIS. Lastly, a new approach for the modelling of healthcare security policies, based on modal logic (i.e., epistemic and/or deontic logic) is proposed. It permits to take into account the flexibility (by means of high expressiveness due to modality) and the robustness (by means of high provability due to modelling) needs. PMID:10179775
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.
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.
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.
Formal versus heuristic modeling for multitarget Bayes filtering
NASA Astrophysics Data System (ADS)
Mahler, Ronald P. S.
2004-08-01
The multisensor-multitarget Bayes filter is the foundation for multi-sensor-multitarget detection, tracking, and identification. This paper addresses the question of principled implementation of this filter. Algorithms can always be cobbled together using catch-as-catch-can heuristic techniques. In formal Bayes modeling one instead derives statistically precise, implementation-independent equations from which principle approximations can then be derived. Indeed, this has become the accepted methodology for single-sensor, single-target tracking R&D. In the case of the multitarget filter, however, partisans of a so-called "plain-vanilla Bayesian approach" have disparaged formal Bayes modelling, and have protrayed specific, ad hoc implementations as completely general, "powerful and robust computational methods." In this and a companion paper I expose the speciousness of such claims. This paper reviews the elements of formal Bayes modeling and approximation, describes what they must look like in the multitarget case, and contrasts them with the "plain-vanilla Bayesian approach."
Los Alamos Center for Computer Security formal computer security model
Dreicer, J.S.; Hunteman, W.J.; Markin, J.T.
1989-01-01
This paper provides a brief presentation of the formal computer security model currently being developed at the Los Alamos Department of Energy (DOE) Center for Computer Security (CCS). The need to test and verify DOE computer security policy implementation first motivated this effort. The actual analytical model was a result of the integration of current research in computer security and previous modeling and research experiences. The model is being developed to define a generic view of the computer and network security domains, to provide a theoretical basis for the design of a security model, and to address the limitations of present formal mathematical models for computer security. The fundamental objective of computer security is to prevent the unauthorized and unaccountable access to a system. The inherent vulnerabilities of computer systems result in various threats from unauthorized access. The foundation of the Los Alamos DOE CCS model is a series of functionally dependent probability equations, relations, and expressions. The model is undergoing continued discrimination and evolution. We expect to apply the model to the discipline of the Bell and LaPadula abstract sets of objects and subjects. 6 refs.
A Formal Model for Real-Time Parallel Computation
Hui, Peter SY; Chikkagoudar, Satish
2012-12-29
The imposition of real-time constraints on a parallel computing environment--- specifically high-performance, cluster-computing systems--- introduces a variety of challenges with respect to the formal verification of the system's timing properties. In this paper, we briefly motivate the need for such a system, and we introduce an automaton-based method for performing such formal verification. We define the concept of a consistent parallel timing system: a hybrid system consisting of a set of timed automata (specifically, timed Buechi automata as well as a timed variant of standard finite automata), intended to model the timing properties of a well-behaved real-time parallel system. Finally, we give a brief case study to demonstrate the concepts in the paper: a parallel matrix multiplication kernel which operates within provable upper time bounds. We give the algorithm used, a corresponding consistent parallel timing system, and empirical results showing that the system operates under the specified timing constraints.
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.
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.
Modelling reaction kinetics inside cells
Grima, Ramon; Schnell, Santiago
2009-01-01
In the past decade, advances in molecular biology such as the development of non-invasive single molecule imaging techniques have given us a window into the intricate biochemical activities that occur inside cells. In this article we review four distinct theoretical and simulation frameworks: (1) non-spatial and deterministic, (2) spatial and deterministic, (3) non-spatial and stochastic and (4) spatial and stochastic. Each framework can be suited to modelling and interpreting intracellular reaction kinetics. By estimating the fundamental length scales, one can roughly determine which models are best suited for the particular reaction pathway under study. We discuss differences in prediction between the four modelling methodologies. In particular we show that taking into account noise and space does not simply add quantitative predictive accuracy but may also lead to qualitatively different physiological predictions, unaccounted for by classical deterministic models. PMID:18793122
Modeling and formal analysis of urban road traffic
NASA Astrophysics Data System (ADS)
Avram, Camelia; Machado, José; Aştilean, Adina
2013-10-01
Modern life in cities leads to complex urban traffic road and, sometimes, to go from one point to another, in a city, is a hard and very complex task. The use of assisted systems for helping drivers on their task of reaching the desired destination is being common, mainly systems like GPS location systems or other similar systems. The main gap of those systems is that they are not able to assist drivers when some unexpected changes occur, like accidents, or another unexpected situations. In this context, it would be desirable to have a dynamic system to inform the drivers, about everything that is happening "online". This work is inserted in this context and the work presented here is one part of a bigger project that has, as main goal, to be a dynamic system for assisting drivers under hard conditions of urban road traffic. In this paper is modeled, and formally analyzed, the intersection of four street segments, in order to take some considerations about this subject. This paper presents the model of the considered system, using timed automata formalism. The validation and verification of the road traffic model it is realized using UPPAAL model-checker.
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.
Elastic Network Models are Robust to Variations in Formalism.
Leioatts, Nicholas; Romo, Tod D; Grossfield, Alan
2012-07-10
Understanding the functions of biomolecules requires insight not only from structures, but from dynamics as well. Often, the most interesting processes occur on time scales too slow for exploration by conventional molecular dynamics (MD) simulations. For this reason, alternative computational methods such as elastic network models (ENMs) have become increasingly popular. These simple, coarse-grained models represent molecules as beads connected by harmonic springs; the system's motions are solved analytically by normal mode analysis. In the past few years, many different formalisms for performing ENM calculations have emerged, and several have been optimized using all-atom MD simulations. In contrast to other studies, we have compared the various formalisms in a systematic, quantitative way. In this study, we optimize many ENM functional forms using a uniform dataset containing only long (> 1 μs) all-atom MD simulations. Our results show that all models once optimized produce spring constants for immediate neighboring residues that are orders of magnitude stiffer than more distal contacts. In addition, the statistical significance of ENM performance varied with model resolution. We also show that fitting long trajectories does not improve ENM performance due to a problem inherent in all network models tested: they underestimate the relative importance of the most concerted motions. Finally, we characterize ENMs' resilience by tessellating the parameter space to show that broad ranges of parameters produce similar quality predictions. Taken together our data reveals that choice of spring function and parameters are not vital to performance of a network model and that simple parameters can by derived "by hand" when no data is available for fitting, thus illustrating the robustness of these models. PMID:22924033
Model Search: Formalizing and Automating Constraint Solving in MDE Platforms
NASA Astrophysics Data System (ADS)
Kleiner, Mathias; Del Fabro, Marcos Didonet; Albert, Patrick
Model Driven Engineering (MDE) and constraint programming (CP) have been widely used and combined in different applications. However, existing results are either ad-hoc, not fully integrated or manually executed. In this article, we present a formalization and an approach for automating constraint-based solving in a MDE platform. Our approach generalizes existing work by combining known MDE concepts with CP techniques into a single operation called model search. We present the theoretical basis for model search, as well as an automated process that details the involved operations. We validate our approach by comparing two implemented solutions (one based on Alloy/SAT, the other on OPL/CP), and by executing them over an academic use-case.
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
NASA Astrophysics Data System (ADS)
Gamba, Irene M.; Haack, Jeffrey R.; Motsch, Sebastien
2015-09-01
In this paper 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. We observe that the kinetic model captures key features such as vortex formation and traveling waves.
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 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. PMID:24028553
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…
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. PMID:27126601
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
Kinetic model for erythrocyte aggregation.
Bertoluzzo, S M; Bollini, A; Rasia, M; Raynal, A
1999-01-01
It is well known that light transmission through blood is the most widely utilized method for the study of erythrocyte aggregation. The curves obtained had been considered empirically as exponential functions. In consequence, the process becomes characterized by an only parameter that varies with all the process factors without discrimination. In the present paper a mathematical model for RBC aggregation process is deduced in accordance with von Smoluchowski's theory about the kinetics of colloidal particles agglomeration. The equation fitted the experimental pattern of the RBC suspension optical transmittance closely and contained two parameters that estimate the most important characteristics of the aggregation process separately, i.e., (1) average size of rouleaux at equilibrium and (2) aggregation rate. The evaluation of the method was assessed by some factors affecting erythrocyte aggregation, such as temperature, plasma dilutions, Dextran 500, Dextran 70 and PVP 360, at different media concentrations, cellular membrane alteration by the alkylating agent TCEA, and decrease of medium osmolarity. Results were interpreted considering the process characteristics estimated by the parameters, and there were also compared with similar studies carried out by other authors with other methods. This analysis allowed us to conclude that the equation proposed is reliable and useful to study erythrocyte aggregation. PMID:10660481
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…
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.
Solvation Phenomena in Dilute Solutions: Formal, Experimental Evidence, and Modeling Implications
Chialvo, Ariel A
2013-01-01
We review the fundamentals underlying a general molecular-based formalism for the microscopic interpretation of the solvation phenomena involving sparingly soluble solutes in compressible media, an approach that hinges around the unambiguous splitting of the species correlation function integrals into short-(finite) and long-ranged (diverging) contributions at infinite dilution, where this condition is taken as the reference system for the derivation of composition expansions. Then, we invoke the formalism (a) to illustrate the well-behaved nature of the solvation contributions to the mechanical partial molecular properties of solutes at infinite dilution, (b) to guide the development of, and provide molecular-based support to, the macroscopic modeling of high-temperature dilute aqueous-electrolyte solutions, (c) to study solvation effects on the kinetic rate constants of reactions in near-critical solvents in an attempt to understand from a microscopic perspective the macroscopic evidence regarding the thermodynamic pressure effects, and (d) to interpret the microscopic mechanism behind synergistic solvation effects involving either co-solutes or co-solvents, and provide a molecular argument on the unsuitability of the van der Waals one-fluid (vdW-1f) mixing rules for the 2 description of weakly attractive solutes in compressible solvents. Finally, we develop thermodynamically consistent perturbation expansions, around the infinite dilution reference, for the species residual properties in binary and ternary mixtures, and discuss the theoretical and modeling implications behind ad hoc first-order truncated expansions.
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
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.
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
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.
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”.
Constraint algebra of general relativity from a formal continuum limit of canonical tensor model
NASA Astrophysics Data System (ADS)
Sasakura, Naoki; Sato, Yuki
2015-10-01
Canonical tensor model (CTM for short below) is a rank-three tensor model formulated as a totally constrained system in the canonical formalism. In the classical case, the constraints form a first-class constraint Poisson algebra with structures similar to that of the ADM formalism of general relativity, qualifying CTM as a possible discrete formalism for quantum gravity. In this paper, we show that, in a formal continuum limit, the constraint Poisson algebra of CTM with no cosmological constant exactly reproduces that of the ADM formalism. To this end, we obtain the expression of the metric tensor field in general relativity in terms of one of the dynamical rank-three tensors in CTM, and determine the correspondence between the constraints of CTM and those of the ADM formalism. On the other hand, the cosmological constant term of CTM seems to induce non-local dynamics, and is inconsistent with an assumption about locality of the continuum limit.
Dynamics and kinetics of model biological systems
NASA Astrophysics Data System (ADS)
Mirigian, Stephen
In this work we study three systems of biological interest: the translocation of a heterogeneously charged polymer through an infinitely thin pore, the wrapped of a rigid particle by a soft vesicle and the modification of the dynamical properties of a gel due to the presence of rigid inclusions. We study the kinetics of translocation for a heterogeneously charged polyelectrolyte through an infinitely narrow pore using the Fokker-Planck formalism to compute mean first passage times, the probability of successful translocation, and the mean successful translocation time for a diblock copolymer. We find, in contrast to the homopolymer result, that details of the boundary conditions lead to qualitatively different behavior. Under experimentally relevant conditions for a diblock copolymer we find that there is a threshold length of the charged block, beyond which the probability of successful translocation is independent of charge fraction. Additionally, we find that mean successful translocation time exhibits non-monotonic behavior with increasing length of the charged fraction; there is an optimum length of the charged block where the mean successful translocation time is slowest and there can be a substantial range of charge fraction where it is slower than a minimally charged chain. For a fixed total charge on the chain, we find that finer distributions of the charge along the chain leads to a significant reduction in mean translocation time compared to the diblock distribution. Endocytosis is modeled using a simple geometrical model from the literature. We map the process of wrapping a rigid spherical bead onto a one-dimensional stochastic process described by the Fokker-Planck equation to compute uptake rates as a function of membrane properties and system geometry. We find that simple geometrical considerations pick an optimal particle size for uptake and a corresponding maximal uptake rate, which can be controlled by altering the material properties of the
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.
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.
Magnetic-sublevel atomic kinetics modeling for line polarization spectroscopy
Hakel, P.; Mancini, R. C.
2004-01-01
We discuss the mechanism of polarized X-ray line emission in plasmas, its connection to plasma anisotropy, and introduce an atomic kinetics model and code (POLAR) based on the population kinetics of magnetic sublevels. POLAR represents a multi-level, multi-process approach to the problem of polarized spectra in plasmas, and hence it is well suited for plasma applications where cascade effects and alignment transfer can become important. Polarization degrees of X-ray spectral lines computed with POLAR were successfully benchmarked against calculations done with other formalisms, and experimental results obtained at the EBIT facility of Lawrence Livermore National Laboratory. We also investigated the polarization of He-like Si X-ray satellite lines as spectral signatures of anisotropy in the electron distribution function. A comprehensive modeling study was performed taking into account hydrodynamics and electron kinetics. We find that two satellite lines connecting singlet states develop a noticeable polarization while the triplet lines remain unpolarized. These results suggest a scenario where triplet lines could be used as a reference while the singlets could be used as polarized markers of plasma anisotropy.
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…
Model-Independent Bounds on Kinetic Mixing
Hook, Anson; Izaguirre, Eder; Wacker, Jay G.
2011-01-01
New Abelimore » an vector bosons can kinetically mix with the hypercharge gauge boson of the Standard Model. This letter computes the model-independent limits on vector bosons with masses from 1 GeV to 1 TeV. The limits arise from the numerous e + e − experiments that have been performed in this energy range and bound the kinetic mixing by ϵ ≲ 0.03 for most of the mass range studied, regardless of any additional interactions that the new vector boson may have.« less
Model Independent Bounds on Kinetic Mixing
Hook, Anson; Izaguirre, Eder; Wacker, Jay G.; /SLAC
2011-08-22
New Abelian vector bosons can kinetically mix with the hypercharge gauge boson of the Standard Model. This letter computes the model independent limits on vector bosons with masses from 1 GeV to 1 TeV. The limits arise from the numerous e{sup +}e{sup -} experiments that have been performed in this energy range and bound the kinetic mixing by {epsilon} {approx}< 0.03 for most of the mass range studied, regardless of any additional interactions that the new vector boson may have.
Kinetic Analysis of Protein Folding Lattice Models
NASA Astrophysics Data System (ADS)
Chen, Hu; Zhou, Xin; Liaw, Chih Young; Koh, Chan Ghee
Based on two-dimensional square lattice models of proteins, the relation between folding time and temperature is studied by Monte Carlo simulation. The results can be represented by a kinetic model with three states — random coil, molten globule, and native state. The folding process is composed of nonspecific collapse and final searching for the native state. At high temperature, it is easy to escape from local traps in the folding process. With decreasing temperature, because of the trapping in local traps, the final searching speed decreases. Then the folding shows chevron rollover. Through the analysis of the fitted parameters of the kinetic model, it is found that the main difference between the energy landscapes of the HP model and the Go model is that the number of local minima of the Go model is less than that of the HP model.
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.
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.
KINETICS MODEL AND OZONE ISOPLETH PLOTTING PACKAGE
The Kinetics Model and Ozone Isopleth Plotting Package (OZIPP) computer program can be used to simulate ozone formation in urban atmospheres. OZIPP calculates maximum one-hour average ozone concentrations given a set of input assumptions about initial precursor concentrations, li...
Deterministic Modelling of BAK Activation Kinetics
NASA Astrophysics Data System (ADS)
Grills, C.; Chacko, A.; Crawford, N.; Johnston, P. G.; Fennell, D. A.; O'Rourke, S. F. C.
2009-08-01
The molecular mechanism underlying mitochondrial BAK activation during apoptosis remains highly controversial. Two seemingly conflicting models have been proposed. In the activation model, BAK requires so-called activating BH3 only proteins (aBH3) to initiate its conformation change. In the other, displacement from inhibitory pro-survival BCL-2 proteins (PBPs) and monomerization of BAK by PBP restricted dissociator BH3-only proteins (dBH3) is sufficient. To better understand the kinetic implications of these models and reconcile these conflicting but highly evidence-based models, we have employed dynamical systems analysis to explore the kinetics underlying BAK activation as a non-linear reaction system. Our findings accommodate both pure agonism and dissociation as mutually exclusive mechanisms capable of initiating BAK activation. In addition we find our work supports a modelling based approach for predicting resistance to therapeutically relevant small molecules BH3 mimetics.
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.
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.
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. PMID:22412853
Computational model for Halorhodopsin photocurrent kinetics
NASA Astrophysics Data System (ADS)
Bravo, Jaime; Stefanescu, Roxana; Talathi, Sachin
2013-03-01
Optogenetics is a rapidly developing novel optical stimulation technique that employs light activated ion channels to excite (using channelrhodopsin (ChR)) or suppress (using halorhodopsin (HR)) impulse activity in neurons with high temporal and spatial resolution. This technique holds enormous potential to externally control activity states in neuronal networks. The channel kinetics of ChR and HR are well understood and amenable for mathematical modeling. Significant progress has been made in recent years to develop models for ChR channel kinetics. To date however, there is no model to mimic photocurrents produced by HR. Here, we report the first model developed for HR photocurrents based on a four-state model of the HR photocurrent kinetics. The model provides an excellent fit (root-mean-square error of 3.1862x10-4, to an empirical profile of experimentally measured HR photocurrents. In combination, mathematical models for ChR and HR photocurrents can provide effective means to design test light based control systems to regulate neural activity, which in turn may have implications for the development of novel light based stimulation paradigms for brain disease control. I would like to thank the University of Florida and the Physics Research Experience for Undergraduates (REU) program, funded through NSF DMR-1156737. This research was also supported through start-up funds provided to Dr. Sachin Talathi
Urea kinetic modeling: comparing the options.
Hoenich, N A; Keir, M J; Hildreth, K; Woffindin, C; Goodall, R; Vanholder, R; Ward, M K
1993-09-01
In this study 6 commercially produced kinetic modeling packages utilizing a variable volume, single pool urea model, as well as formulae to determine the delivery of therapy, have been compared by applying to each the same set of rigorously collected data for a group of 12 patients. Comparison of the kinetically derived parameters (urea generation rate [G], urea distribution volume [V], delivery of therapy [Kt/V], and normalized protein catabolic rate [nPCR]) showed that the values obtained for both G and V differed between packages owing to the numerical methods and the clearance used in the solution of the differential equations. Although a broad agreement between the values established for Kt/V and nPCR was noted, the 95% limits of agreement indicated that it would be prudent to exercise caution when comparing results established by different modeling packages. PMID:8240076
Chemical kinetics models for semiconductor processing
Coltrin, M.E.; Creighton, J.R.; Meeks, E.; Grcar, J.F.; Houf, W.G.; Kee, R.J.
1997-12-31
Chemical reactions in the gas-phase and on surfaces are important in the deposition and etching of materials for microelectronic applications. A general software framework for describing homogeneous and heterogeneous reaction kinetics utilizing the Chemkin suite of codes is presented. Experimental, theoretical and modeling approaches to developing chemical reaction mechanisms are discussed. A number of TCAD application modules for simulating the chemically reacting flow in deposition and etching reactors have been developed and are also described.
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.
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 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.
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.
Compartmental model of leucine kinetics in humans.
Cobelli, C; Saccomani, M P; Tessari, P; Biolo, G; Luzi, L; Matthews, D E
1991-10-01
The complexity of amino acid and protein metabolism has limited the development of comprehensive, accurate whole body kinetic models. For leucine, simplified approaches are in use to measure in vivo leucine fluxes, but their domain of validity is uncertain. We propose here a comprehensive compartmental model of the kinetics of leucine and alpha-ketoisocaproate (KIC) in humans. Data from a multiple-tracer administration were generated with a two-stage (I and II) experiment. Six normal subjects were studied. In experiment I, labeled leucine and KIC were simultaneously injected into plasma. Four plasma leucine and KIC tracer concentration curves and label in the expired CO2 were measured. In experiment II, labeled bicarbonate was injected into plasma, and labeled CO2 in the expired air was measured. Radioactive (L-[1-14C]leucine, [4,5-3H]KIC, [14C]bicarbonate) and stable isotope (L-[1-13C]leucine, [5,5,5-2H3]KIC, [13C]bicarbonate) tracers were employed. The input format was a bolus (impulse) dose in the radioactive case and a constant infusion in the stable isotope case. A number of physiologically based, linear time-invariant compartmental models were proposed and tested against the data. The model finally chosen for leucine-KIC kinetics has 10 compartments: 4 for leucine, 3 for KIC, and 3 for bicarbonate. The model is a priori uniquely identifiable, and its parameters were estimated with precision from the five curves of experiment I. The separate assessment of bicarbonate kinetics (experiment II) was shown to be unnecessary. The model defines masses and fluxes of leucine in the organism, in particular its intracellular appearance from protein breakdown, its oxidation, and its incorporation into proteins. An important feature of the model is its ability to estimate leucine oxidation by resolving the bicarbonate model in each individual subject. Finally, the model allows the assessment of the domain of validity of the simpler commonly used models. PMID:1928344
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.
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.
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.
Cluster kinetics model for mixtures of glassformers.
Brenskelle, Lisa A; McCoy, Benjamin J
2007-10-14
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. PMID:17935407
Aggregation kinetics in a model colloidal suspension
Bastea, S
2005-08-08
The authors present molecular dynamics simulations of aggregation kinetics in a colloidal suspension modeled as a highly asymmetric binary mixture. Starting from a configuration with largely uncorrelated colloidal particles the system relaxes by coagulation-fragmentation dynamics to a structured state of low-dimensionality clusters with an exponential size distribution. The results show that short range repulsive interactions alone can give rise to so-called cluster phases. For the present model and probably other, more common colloids, the observed clusters appear to be equilibrium phase fluctuations induced by the entropic inter-colloidal attractions.
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.
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.
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.
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.
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.
Formal specification and analysis of intelligent agents for model-based medicine usage management.
Hoogendoorn, Mark; Klein, Michel C A; Memon, Zulfiqar A; Treur, Jan
2013-06-01
A model-based agent system model for medicine usage management is presented and formally analysed. The model incorporates an intelligent ambient agent model that has an explicit representation of a dynamical system model to estimate the medicine level in the patient's body by simulation, is able to analyse whether the patient intends to take the medicine too early or too late, and can take measures to prevent this. PMID:23566391
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…
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."…
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.
Brittle failure kinetics model for concrete
Silling, S.A.
1997-03-01
A new constitutive model is proposed for the modeling of penetration and large stress waves in concrete. Rate effects are incorporated explicitly into the damage evolution law, hence the term brittle failure kinetics. The damage variable parameterizes a family of Mohr-Coulomb strength curves. The model, which has been implemented in the CTH code, has been shown to reproduce some distinctive phenomena that occur in penetration of concrete targets. Among these are the sharp spike in deceleration of a rigid penetrator immediately after impact. Another is the size scale effect, which leads to a nonlinear scaling of penetration depth with penetrator size. This paper discusses the theory of the model and some results of an extensive validation effort.
Fillion-Gourdeau, F; Herrmann, H J; Mendoza, M; Palpacelli, S; Succi, S
2013-10-18
We point out a formal analogy between the Dirac equation in Majorana form and the discrete-velocity version of the Boltzmann kinetic equation. By a systematic analysis based on the theory of operator splitting, this analogy is shown to turn into a concrete and efficient computational method, providing a unified treatment of relativistic and nonrelativistic quantum mechanics. This might have potentially far-reaching implications for both classical and quantum computing, because it shows that, by splitting time along the three spatial directions, quantum information (Dirac-Majorana wave function) propagates in space-time as a classical statistical process (Boltzmann distribution). PMID:24182245
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.
The kinetic regime of the Vicsek model
NASA Astrophysics Data System (ADS)
Chepizhko, A. A.; Kulinskii, V. L.
2009-12-01
We consider the dynamics of the system of self-propelling particles modeled via the Vicsek algorithm in continuum time limit. It is shown that the alignment process for the velocities can be subdivided into two regimes: "fast" kinetic and "slow" hydrodynamic ones. In fast kinetic regime the alignment of the particle velocity to the local neighborhood takes place with characteristic relaxation time. So, that the bigger regions arise with the velocity alignment. These regions align their velocities thus giving rise to hydrodynamic regime of the dynamics. We propose the mean-field-like approach in which we take into account the correlations between density and velocity. The comparison of the theoretical predictions with the numerical simulations is given. The relation between Vicsek model in the zero velocity limit and the Kuramoto model is stated. The mean-field approach accounting for the dynamic change of the neighborhood is proposed. The nature of the discontinuity of the dependence of the order parameter in case of vectorial noise revealed in Gregorie and Chaite, Phys. Rev. Lett., 92, 025702 (2004) is discussed and the explanation of it is proposed.
Ryll, A; Bucher, J; Bonin, A; Bongard, S; Gonçalves, E; Saez-Rodriguez, J; Niklas, J; Klamt, S
2014-10-01
Systems biology has to increasingly cope with large- and multi-scale biological systems. Many successful in silico representations and simulations of various cellular modules proved mathematical modelling to be an important tool in gaining a solid understanding of biological phenomena. However, models spanning different functional layers (e.g. metabolism, signalling and gene regulation) are still scarce. Consequently, model integration methods capable of fusing different types of biological networks and various model formalisms become a key methodology to increase the scope of cellular processes covered by mathematical models. Here we propose a new integration approach to couple logical models of signalling or/and gene-regulatory networks with kinetic models of metabolic processes. The procedure ends up with an integrated dynamic model of both layers relying on differential equations. The feasibility of the approach is shown in an illustrative case study integrating a kinetic model of central metabolic pathways in hepatocytes with a Boolean logical network depicting the hormonally induced signal transduction and gene regulation events involved. In silico simulations demonstrate the integrated model to qualitatively describe the physiological switch-like behaviour of hepatocytes in response to nutritionally regulated changes in extracellular glucagon and insulin levels. A simulated failure mode scenario addressing insulin resistance furthermore illustrates the pharmacological potential of a model covering interactions between signalling, gene regulation and metabolism. PMID:25063553
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.
Kinetic model solves visbreaker constraint control problem
Iscovici, R.S. )
1994-05-01
A kinetic model of the visbreaking process was developed and used in an advanced control algorithm implemented in a distributed control system (DCS). During development, model predictions were checked against unit history data and compared to the actual unit performance with respect to fuel oil stability vs. cracking conversion. In the first stage, the algorithm was used in open-loop supervisory control. In the second stage the advanced control loop was closed and the visbreaking units was run automatically. The visbreaker control, based on process kinetics, is simple enough to be developed and implemented in a DCS, eliminating need for higher-power computers at the information system (IS) level, and reducing to a minimum data transfer from them to the process regulatory control level based on the DCS. The advanced control application led to profits estimated at $4.5 million annually, more than expected. The visbreaker advanced control showed how process engineering knowledge used in powerful and versatile DCSs could increase profit, shorten pay-out time and ease the workload on unit operators.
Basis of a formal language for facilitating communication among climate modelers
NASA Astrophysics Data System (ADS)
de Elía, Ramón
2012-08-01
The objective of this work is to present the basis for a formal language that aims to express in a concise way some fundamental beliefs held within the climate research community. The expression of this set of beliefs takes the form of relations, conjectures or propositions that describe characteristics of different aspects of climate modeling. Examples are constructed using topics that are much discussed within the climate modeling community. The article first introduces, as elements of this formal language, models considered a priori (the model as a code or algorithm) or a posteriori (the model as output), and then presents different relations between these elements. The most important relation is that of dominance, which helps to define the superiority of one model over another based on which model a rational agent will choose. Various kinds of dominance are considered. Also presented in a formal language are propositions and conjectures relating to model development, model calibration and climate change ensemble projections, each of which are held with diverse levels of acceptance within the climate modeling community. In addition, the relevance of defining elements—models—whose existence is improbable, such as bug-free model versions, is discussed. Although the potential value of this language is shown, there remains a need to improve the definitions presented here, as some of them remain unsatisfying. Still, we believe that this attempt may help us not only communicate more clearly but also to better distinguish different schools of thought that currently exist within the community.
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.
Canonical formalism for a 2n-dimensional model with topological mass generation
Deguchi, Shinichi
2008-12-15
The four-dimensional model with topological mass generation that was found by Dvali, Jackiw, and Pi has recently been generalized to any even number of dimensions (2n dimensions) in a nontrivial manner in which a Stueckelberg-type mass term is introduced [S. Deguchi and S. Hayakawa, Phys. Rev. D 77, 045003 (2008)]. The present paper deals with a self-contained model, called here a modified hybrid model, proposed in this 2n-dimensional generalization and considers the canonical formalism for this model. For the sake of convenience, the canonical formalism itself is studied for a model equivalent to the modified hybrid model by following the recipe for treating constrained Hamiltonian systems. This formalism is applied to the canonical quantization of the equivalent model in order to clarify observable and unobservable particles in the model. The equivalent model (with a gauge-fixing term) is converted to the modified hybrid model (with a corresponding gauge-fixing term) in a Becchi-Rouet-Stora-Tyutin-invariant manner. Thereby it is shown that the Chern-Pontryagin density behaves as an observable massive particle (or field). The topological mass generation is thus verified at the quantum-theoretical level.
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…
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.
Probabilistic formalism and hierarchy of models for polydispersed turbulent two-phase flows
NASA Astrophysics Data System (ADS)
Peirano, Eric; Minier, Jean-Pierre
2002-04-01
This paper deals with a probabilistic approach to polydispersed turbulent two-phase flows following the suggestions of Pozorski and Minier [Phys. Rev. E 59, 855 (1999)]. A general probabilistic formalism is presented in the form of a two-point Lagrangian PDF (probability density function). A new feature of the present approach is that both phases, the fluid as well as the particles, are included in the PDF description. It is demonstrated how the formalism can be used to show that there exists a hierarchy between the classical approaches such as the Eulerian and Lagrangian methods. It is also shown that the Eulerian and Lagrangian models can be obtained in a systematic way from the PDF formalism. Connections with previous papers are discussed.
Monochloramination of resorcinol: mechanism and kinetic modeling.
Cimetiere, Nicolas; Dossier-Berne, Florence; De Laat, Joseph
2009-12-15
The kinetics of monochloramination of resorcinol, 4-chlororesorcinol, and 4,6-dichlororesorcinol have been investigated over the pH range of 5-12, at 23 +/- 2 degrees C. Monochloramine solutions were prepared with ammonia-to-chlorine ratios (N/Cl) ranging from 1.08 to 31 mol/mol. Under conditions that minimize free chlorine reactions (N/Cl > 2 mol/mol), the apparent second-order rate constants of monochloramination of resorcinol compounds show a maximum at pH values between 8.6 and 10.2. The intrinsic second-order rate constants for the reaction of monochloramine with the acid-base forms of the dihydroxybenzenes (Ar(OH)(2), Ar(OH)O(-), and Ar(O(-))(2)) were calculated from the apparent second-order rate constants. The stoichiometric coefficients for the formation of 4-chlororesorcinol by monochloramination of resorcinol and 4,6-dichlororesorcinol by monochloramination of 4-chlororesorcinol were found to be equal to 0.66 +/- 0.05 and 0.25 +/- 0.02 mol/mol, respectively at pH 8.6. A kinetic model that incorporates reactions of free chlorine and monochloramine with the different acid-base forms of resorcinol compounds simulated well the initial rates of degradation of resorcinol compounds and was useful to evaluate the contribution of free chlorine reactions to the overall rates of degradation of resorcinol at low N/Cl ratios. PMID:20000532
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.
On the adequacy of current empirical evaluations of formal models of categorization.
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. Progress in assessing the relative adequacy of formal categorization models has, to date, been limited because (a) formal model comparisons are narrow in the number of models and phenomena considered and (b) models do not often clearly define their explanatory scope. Progress is further hampered by the practice of fitting models with arbitrarily variable parameters to each data set independently. Reviewing examples of good practice in the literature, we conclude that model comparisons are most fruitful when relative adequacy is assessed by comparing well-defined models on the basis of the number and proportion of irreversible, ordinal, penetrable successes (principles of minimal flexibility, breadth, good-enough precision, maximal simplicity, and psychological focus). PMID:22061692
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.
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.
Mbodj, Abibatou; Gustafson, E Hilary; Ciglar, Lucia; Junion, Guillaume; Gonzalez, Aitor; Girardot, Charles; Perrin, Laurent; Furlong, Eileen E M; Thieffry, Denis
2016-09-01
Given the complexity of developmental networks, it is often difficult to predict the effect of genetic perturbations, even within coding genes. Regulatory factors generally have pleiotropic effects, exhibit partially redundant roles, and regulate highly interconnected pathways with ample cross-talk. Here, we delineate a logical model encompassing 48 components and 82 regulatory interactions involved in mesoderm specification during Drosophila development, thereby providing a formal integration of all available genetic information from the literature. The four main tissues derived from mesoderm correspond to alternative stable states. We demonstrate that the model can predict known mutant phenotypes and use it to systematically predict the effects of over 300 new, often non-intuitive, loss- and gain-of-function mutations, and combinations thereof. We further validated several novel predictions experimentally, thereby demonstrating the robustness of model. Logical modelling can thus contribute to formally explain and predict regulatory outcomes underlying cell fate decisions. PMID:27599298
Kinetic Modeling of Esterification of Ethylene Glycol with Acetic Acid
NASA Astrophysics Data System (ADS)
Yadav, Vishnu P.; Mukherjee, Rudra Palash; Bantraj, Kandi; Maity, Sunil K.
2010-10-01
The reaction kinetics of the esterification of ethylene glycol with acetic acid in the presence of cation exchange resin has been studied and kinetic models based on empirical and Langmuir approach has been developed. The Langmuir based model involving eight kinetic parameters fits experimental data much better compared to empirical model involving four kinetic parameters. The effect of temperature and catalyst loading on the reaction system has been analyzed. Further, the activation energy and frequency factor of the rate constants for Langmuir based model has been estimated.
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.
Kinetic Modeling of Esterification of Ethylene Glycol with Acetic Acid
Yadav, Vishnu P.; Maity, Sunil K.; Mukherjee, Rudra Palash; Bantraj, Kandi
2010-10-26
The reaction kinetics of the esterification of ethylene glycol with acetic acid in the presence of cation exchange resin has been studied and kinetic models based on empirical and Langmuir approach has been developed. The Langmuir based model involving eight kinetic parameters fits experimental data much better compared to empirical model involving four kinetic parameters. The effect of temperature and catalyst loading on the reaction system has been analyzed. Further, the activation energy and frequency factor of the rate constants for Langmuir based model has been estimated.
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.
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
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.
Percolation in a kinetic opinion exchange model
NASA Astrophysics Data System (ADS)
Chandra, Anjan Kumar
2012-02-01
We study the percolation transition of the geometrical clusters in the square-lattice LCCC model [a kinetic opinion exchange model introduced by Lallouache, Chakrabarti, Chakraborti, and Chakrabarti, Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.82.056112 82, 056112 (2010)] with the change in conviction and influencing parameter. The cluster is comprised of the adjacent sites having an opinion value greater than or equal to a prefixed threshold value of opinion (Ω). The transition point is different from that obtained for the transition of the order parameter (average opinion value) found by Lallouache Although the transition point varies with the change in the threshold value of the opinion, the critical exponents for the percolation transition obtained from the data collapses of the maximum cluster size, the cluster size distribution, and the Binder cumulant remain the same. The exponents are also independent of the values of conviction and influencing parameters, indicating the robustness of this transition. The exponents do not match any other known percolation exponents (e.g., the static Ising, dynamic Ising, and standard percolation). This means that the LCCC model belongs to a separate universality class.
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.
Fully implicit kinetic modelling of collisional plasmas
Mousseau, V.A.
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.
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.
Kinetic modeling of cell metabolism for microbial production.
Costa, Rafael S; Hartmann, Andras; Vinga, Susana
2016-02-10
Kinetic models of cellular metabolism are important tools for the rational design of metabolic engineering strategies and to explain properties of complex biological systems. The recent developments in high-throughput experimental data are leading to new computational approaches for building kinetic models of metabolism. Herein, we briefly survey the available databases, standards and software tools that can be applied for kinetic models of metabolism. In addition, we give an overview about recently developed ordinary differential equations (ODE)-based kinetic models of metabolism and some of the main applications of such models are illustrated in guiding metabolic engineering design. Finally, we review the kinetic modeling approaches of large-scale networks that are emerging, discussing their main advantages, challenges and limitations. PMID:26724578
Formal Implementation of a Performance Evaluation Model for the Face Recognition System
Shin, Yong-Nyuo; Kim, Jason; Lee, Yong-Jun; Shin, Woochang; Choi, Jin-Young
2008-01-01
Due to usability features, practical applications, and its lack of intrusiveness, face recognition technology, based on information, derived from individuals' facial features, has been attracting considerable attention recently. Reported recognition rates of commercialized face recognition systems cannot be admitted as official recognition rates, as they are based on assumptions that are beneficial to the specific system and face database. Therefore, performance evaluation methods and tools are necessary to objectively measure the accuracy and performance of any face recognition system. In this paper, we propose and formalize a performance evaluation model for the biometric recognition system, implementing an evaluation tool for face recognition systems based on the proposed model. Furthermore, we performed evaluations objectively by providing guidelines for the design and implementation of a performance evaluation system, formalizing the performance test process. PMID:18317524
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).
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.
Los Alamos CCS (Center for Computer Security) formal computer security model
Dreicer, J.S.; Hunteman, W.J. )
1989-01-01
This paper provides a brief presentation of the formal computer security model currently being developed at the Los Alamos Department of Energy (DOE) Center for Computer Security (CCS). The initial motivation for this effort was the need to provide a method by which DOE computer security policy implementation could be tested and verified. The actual analytical model was a result of the integration of current research in computer security and previous modeling and research experiences. The model is being developed to define a generic view of the computer and network security domains, to provide a theoretical basis for the design of a security model, and to address the limitations of present models. Formal mathematical models for computer security have been designed and developed in conjunction with attempts to build secure computer systems since the early 70's. The foundation of the Los Alamos DOE CCS model is a series of functionally dependent probability equations, relations, and expressions. The mathematical basis appears to be justified and is undergoing continued discrimination and evolution. We expect to apply the model to the discipline of the Bell-Lapadula abstract sets of objects and subjects. 5 refs.
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.
Chemical kinetic modeling of exhaust hydrocarbon oxidation
Wu, K.C.; Hochgreb, S.; Norris, M.B. . Dept. of Mechanical Engineering)
1995-01-01
Numerical simulations of the oxidation of unburned hydrocarbons from spark ignition engines were made based on full-chemistry, zero-dimensional models and compared with experiments for engine-out hydrocarbons and exhaust port oxidation. Simple correlations can be drawn between calculated results for hydrocarbon oxidation half-lives in plug or stirred reactors and measured hydrocarbon emissions. the extent of reaction through the exhaust port was simulated using calculated temperature histories for each burned gas mass element leaving the cylinder, coupled to detailed chemical kinetic rate equations. The results show that, for the fuels considered, the extent of oxidation of the remaining unburned fuel measured through the exhaust can be bracketed by the calculated results for the well-mixed (average) and core (adiabatically expanded) temperatures in the exhaust. Most of the oxidation is shown to occur at the very early exhaust times. For the paraffins considered, comparisons of simulations and experiments suggest that fuel oxidation is partially controlled by the mixing of cold gases at the initial stages of exhaust, where temperatures are high and the cold unburned mixture emerges from the wall layers into the exhaust jet. These conclusions are supported by the relatively small measured dependence on fuel type of the extent of oxidation in the exhaust, and by the resulting ratio of fuel to nonfuel hydrocarbons in the exhaust port exit.
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.
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.
A generalized kinetic model for heterogeneous gas-solid reactions.
Xu, Zhijie; Sun, Xin; Khaleel, Mohammad A
2012-08-21
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. PMID:22920132
A generalized kinetic model for heterogeneous gas-solid reactions
NASA Astrophysics Data System (ADS)
Xu, Zhijie; Sun, Xin; Khaleel, Mohammad A.
2012-08-01
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.
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.
Pereira, José N; Silva, Porfírio; Lima, Pedro U; Martinoli, Alcherio
2014-01-01
The work described is part of a long term program of introducing institutional robotics, a novel framework for the coordination of robot teams that stems from institutional economics concepts. Under the framework, institutions are cumulative sets of persistent artificial modifications made to the environment or to the internal mechanisms of a subset of agents, thought to be functional for the collective order. In this article we introduce a formal model of institutional controllers based on Petri nets. We define executable Petri nets-an extension of Petri nets that takes into account robot actions and sensing-to design, program, and execute institutional controllers. We use a generalized stochastic Petri net view of the robot team controlled by the institutional controllers to model and analyze the stochastic performance of the resulting distributed robotic system. The ability of our formalism to replicate results obtained using other approaches is assessed through realistic simulations of up to 40 e-puck robots. In particular, we model a robot swarm and its institutional controller with the goal of maintaining wireless connectivity, and successfully compare our model predictions and simulation results with previously reported results, obtained by using finite state automaton models and controllers. PMID:23373975
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. PMID:19210171
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
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.
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.
Advani, Aneel; Goldstein, Mary; Shahar, Yuval; Musen, Mark A.
2003-01-01
Automated quality assessment of clinician actions and patient outcomes is a central problem in guideline- or standards-based medical care. In this paper we describe a model representation and algorithm for deriving structured quality indicators and auditing protocols from formalized specifications of guidelines used in decision support systems. We apply the model and algorithm to the assessment of physician concordance with a guideline knowledge model for hypertension used in a decision-support system. The properties of our solution include the ability to derive automatically (1) context-specific and (2) case-mix-adjusted quality indicators that (3) can model global or local levels of detail about the guideline (4) parameterized by defining the reliability of each indicator or element of the guideline. PMID:14728124
A Formal Algorithm for Verifying the Validity of Clustering Results Based on Model Checking
Huang, Shaobin; Cheng, Yuan; Lang, Dapeng; Chi, Ronghua; Liu, Guofeng
2014-01-01
The limitations in general methods to evaluate clustering will remain difficult to overcome if verifying the clustering validity continues to be based on clustering results and evaluation index values. This study focuses on a clustering process to analyze crisp clustering validity. First, we define the properties that must be satisfied by valid clustering processes and model clustering processes based on program graphs and transition systems. We then recast the analysis of clustering validity as the problem of verifying whether the model of clustering processes satisfies the specified properties with model checking. That is, we try to build a bridge between clustering and model checking. Experiments on several datasets indicate the effectiveness and suitability of our algorithms. Compared with traditional evaluation indices, our formal method can not only indicate whether the clustering results are valid but, in the case the results are invalid, can also detect the objects that have led to the invalidity. PMID:24608823
Biomass torrefaction: modeling of volatile and solid product evolution kinetics.
Bates, Richard B; Ghoniem, Ahmed F
2012-11-01
The aim of this work is the development of a kinetics model for the evolution of the volatile and solid product composition during torrefaction conditions between 200 and 300°C. Coupled to an existing two step solid mass loss kinetics mechanism, this model describes the volatile release kinetics in terms of a set of identifiable chemical components, permitting the solid product composition to be estimated by mass conservation. Results show that most of the volatiles released during the first stage include highly oxygenated species such as water, acetic acid, and carbon dioxide, while volatiles released during the second step are composed primarily of lactic acid, methanol, and acetic acid. This kinetics model will be used in the development of a model to describe reaction energy balance and heat release dynamics. PMID:23026268
An integral representation of functions in gas-kinetic models
NASA Astrophysics Data System (ADS)
Perepelitsa, Misha
2016-08-01
Motivated by the theory of kinetic models in gas dynamics, we obtain an integral representation of lower semicontinuous functions on {{{R}}^d,} {d≥1}. We use the representation to study the problem of compactness of a family of the solutions of the discrete time BGK model for the compressible Euler equations. We determine sufficient conditions for strong compactness of moments of kinetic densities, in terms of the measures from their integral representations.
HCCI in a CFR engine: experiments and detailed kinetic modeling
Flowers, D; Aceves, S; Smith, R; Torres, J; Girard, J; Dibble, R
1999-11-05
Single cylinder engine experiments and chemical kinetic modeling have been performed to study the effect of variations in fuel, equivalence ratio, and intake charge temperature on the start of combustion and the heat release rate. Neat propane and a fuel blend of 15% dimethyl-ether in methane have been studied. The results demonstrate the role of these parameters on the start of combustion, efficiency, imep, and emissions. Single zone kinetic modeling results show the trends consistent with the experimental results.
Shen, Guang-Bin; Xia, Ke; Li, Xiu-Tao; Li, Jun-Ling; Fu, Yan-Hua; Yuan, Lin; Zhu, Xiao-Qing
2016-03-24
In this work, kinetic isotope effect (KIEself) values of 68 hydride self-exchange reactions, XH(D) + X(+) → X(+) + XH(D), in acetonitrile at 298 K were determined using a new experimental method. KIE values of 4556 hydride cross transfer reactions, XH(D) + Y(+) → X(+) + YH(D), in acetonitrile were estimated from the 68 determined KIEself values of hydride self-exchange reactions using a new KIE relation formula derived from Zhu's kinetic equation and the reliability of the estimations was verified using different experimental methods. A new KIE kinetic model to explain and predict KIE values was developed according to Zhu's kinetic model using two different Morse free energy curves instead of one Morse free energy curve in the traditional KIE theories to describe the free energy changes of X-H bond and X-D bond dissociation in chemical reactions. The most significant contribution of this paper to KIE theory is to build a new KIE kinetic model, which can be used to not only uniformly explain the various (normal, enormous and inverse) KIE values but also safely prodict KIE values of various chemical reactions. PMID:26938149
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.
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.
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.
Elimination kinetic model for organic chemicals in earthworms.
Dimitrova, N; Dimitrov, S; Georgieva, D; Van Gestel, C A M; Hankard, P; Spurgeon, D; Li, H; Mekenyan, O
2010-08-15
Mechanistic understanding of bioaccumulation in different organisms and environments should take into account the influence of organism and chemical depending factors on the uptake and elimination kinetics of chemicals. Lipophilicity, metabolism, sorption (bioavailability) and biodegradation of chemicals are among the important factors that may significantly affect the bioaccumulation process in soil organisms. This study attempts to model elimination kinetics of organic chemicals in earthworms by accounting for the effects of both chemical and biological properties, including metabolism. The modeling approach that has been developed is based on the concept for simulating metabolism used in the BCF base-line model developed for predicting bioaccumulation in fish. Metabolism was explicitly accounted for by making use of the TIMES engine for simulation of metabolism and a set of principal transformations. Kinetic characteristics of transformations were estimated on the basis of observed kinetics data for the elimination of organic chemicals from earthworms. PMID:20185163
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.
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.
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.
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
Kinetic Modelling of Macroscopic Properties Changes during Crosslinked Polybutadiene Oxidation
NASA Astrophysics Data System (ADS)
Audouin, Ludmila; Coquillat, Marie; Colin, Xavier; Verdu, Jacques; Nevière, Robert
2008-08-01
The thermal oxidation of additive free hydroxyl-terminated polybutadiene (HTPB) isocyanate crosslinked rubber bulk samples has been studied at 80, 100 and 120 °C in air. The oxidation kinetics has been monitored by gravimetry and thickness distribution of oxidation products was determined by FTIR mapping. Changes of elastic shear modulus G' during oxidation were followed during oxidation at the same temperatures. The kinetic model established previously for HTPB has been adapted for bulk sample oxidation using previously determined set of kinetic parameters. Oxygen diffusion control of oxidation has been introduced into the model. The mass changes kinetic curves and oxidation products profiles were simulated and adequate fit was obtained. Using the rubber elasticity theory the elastic modulus changes were simulated taking into account the elastically active chains concentration changes due to chain scission and crosslinking reactions. The reasonable fit of G' as a function of oxidation time experimental curves was obtained.
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. PMID:25019910
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.
EFFECTS OF PHOTOCHEMICAL KINETIC MECHANISMS ON OXIDANT MODEL PREDICTIONS
The comparative effects of kinetic mechanisms on oxidant model predictions have been tested using two different mechanisms (the Carbon-Bond Mechanism II (CBM-II) and the Demerjian Photochemical Box Model (DPBM) mechanism) in three air quality models (the OZIPM/EKMA, the Urban Air...
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 for the collisionless sheath of a collisional plasma
NASA Astrophysics Data System (ADS)
Tang, Xian-Zhu; Guo, Zehua
2016-08-01
Collisional plasmas typically have mean-free-path still much greater than the Debye length, so the sheath is mostly collisionless. Once the plasma density, temperature, and flow are specified at the sheath entrance, the profile variation of electron and ion density, temperature, flow speed, and conductive heat fluxes inside the sheath is set by collisionless dynamics, and can be predicted by an analytical kinetic model distribution. These predictions are contrasted here with direct kinetic simulations, showing good agreement.
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 of continuous-wave flow chemical lasers
NASA Astrophysics Data System (ADS)
Gao, Z.; X., E.
1982-02-01
A kinetic approach to modeling the gain in a chemical wave continuous laser when the lasing frequency is coincident with the center of the line shape is presented. Governing equations are defined for the relaxing behavior of an initially nonequilibrium distribution toward the local equilibrium Boltzmann-Maxwellian distribution. A new gain is introduced which is related to the thermal motion of the molecules and cold-reaction and premixed CW models are discussed. Coincidence of the lasing frequency with the line shape is demonstrated to result in a radiative intensity within the homogeneous broadening limit. The rate model predictions are compared with those of the kinetic model. It is found that when the broadening parameter is less than 0.2 the kinetic model more accurately describes the behavior of the CW chemical laser.
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. PMID:26479706
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
Chialvo, Ariel A; Chialvo, Sebastian; Simonson, J Michael {Mike}
2009-01-01
Truncated series expansions for the species partial molar fugacity coefficients in ternary dilute systems are derived for the systematic study of mixed solutes in highly compressible media. Then, explicit molecularbased expressions for the expansion coefficients are drawn in terms of direct and total correlation function integrals associated with the actual microstructure of the reference infinite dilute system. Finally, these selfconsistent formal expressions are used (a) to derive the corresponding expressions for special systems, (b) to highlight, and discuss with examples from the literature, some frequent pitfalls in the molecular modeling of these mixtures leading to serious thermodynamic inconsistencies, and (c) to illustrate how the proposed expressions reduce exactly, in the zero-density limit, to those for the partial molar properties of mixtures obeying the 1st-order truncated virial equation of state.
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.
Kinetic modeling of the Townsend breakdown in argon
NASA Astrophysics Data System (ADS)
Macheret, S. O.; Shneider, M. N.
2013-10-01
Kinetic modeling of the Townsend breakdown in argon was performed in the "forward-back" approximation. The kinetic model was found to adequately describe the left branch of the Paschen curve, and the important role of ionization by fast ions and atoms near the cathode, as well as the increase in secondary emission coefficient in strong electric fields described in the literature, was confirmed. The modeling also showed that the electron energy distribution function develops a beam of high-energy electrons and that the runaway effect, i.e., the monotonic increase of the mean electron energy with the distance from the cathode, occurs at the left branch of the Paschen curve.
Hard-sphere kinetic models for inert and reactive mixtures.
Polewczak, Jacek
2016-10-19
I consider stochastic variants of a simple reacting sphere (SRS) kinetic model (Xystris and Dahler 1978 J. Chem. Phys. 68 387-401, Qin and Dahler 1995 J. Chem. Phys. 103 725-50, Dahler and Qin 2003 J. Chem. Phys. 118 8396-404) for dense reacting mixtures. In contrast to the line-of-center models of chemical reactive models, in the SRS kinetic model, the microscopic reversibility (detailed balance) can be easily shown to be satisfied, and thus all mathematical aspects of the model can be fully justified. In the SRS model, the molecules behave as if they were single mass points with two internal states. Collisions may alter the internal states of the molecules, and this occurs when the kinetic energy associated with the reactive motion exceeds the activation energy. Reactive and non-reactive collision events are considered to be hard sphere-like. I consider a four component mixture A, B, A (*), B (*), in which the chemical reactions are of the type [Formula: see text], with A (*) and B (*) being distinct species from A and B. This work extends the joined works with George Stell to the kinetic models of dense inert and reactive mixtures. The idea of introducing smearing-type effect in the collisional process results in a new class of stochastic kinetic models for both inert and reactive mixtures. In this paper the important new mathematical properties of such systems of kinetic equations are proven. The new results for stochastic revised Enskog system for inert mixtures are also provided. PMID:27545341
Kinetic Modeling of the Moon-Solar Wind Plasma Interaction
NASA Astrophysics Data System (ADS)
Fatemi, S.; Poppe, A. R.; Halekas, J. S.; Delory, G. T.; Holmstrom, M.; Farrell, W. M.
2016-05-01
We use a three-dimensional self-consistent hybrid model of plasma (kinetic ions, fluid electrons) to study solar wind plasma interaction with the Moon. We have studied lunar wake, interaction with crustal fields, and lunar interior with our model.
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
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.
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.
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. PMID:26723613
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.
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.
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.
Microscopic kinetic model for polymer crystal growth
NASA Astrophysics Data System (ADS)
Hu, Wenbing
2011-03-01
Linear crystal growth rates characterize the net result of competition between growth and melting at the liquid-solid interfaces. The rate equation for polymer crystal growth can be derived with a barrier term for crystal growth and with a driving force term of excess lamellar thickness, provided that growth and melting share the same rate-determining steps at the growth front. Such an ansatz can be verified by the kinetic symmetry between growth and melting around the melting point of lamellar crystals, as made in our recent dynamic Monte Carlo simulations. The profile of the growth/melting front appears as wedge-shaped, with the free energy barrier for intramolecular secondary crystal nucleation at its top, and with the driving force gained via instant thickening at its bottom. Such a scenario explains unique phenomena on polymer crystal growth, such as chain folding, regime transitions, molecular segregation of polydisperse polymers, self-poisoning with integer-number chain-folding of short chains, and colligative growth rates of binary mixtures of two chain lengths. Financial support from NNSFC No. 20825415 and NBRPC No. 2011CB606100 is acknowledged.
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.
Model formalism of liquid /sup 3/He-B at equilibrium
Goldstein, L.; Goldstein, J.C.
1980-04-01
The approximate formal treatment of the nuclear spin system of normal liquid /sup 3/He given some time ago is extended to the ordered /sup 3/He phase. The formalism leads to the prediction of normal thermal behavior of /sup 3/He-B at lower pressures and at temperatures approaching its phase-boundary temperatures. In contrast to the disordered normal liquid phase, which is thermally anomalous, the entropy of the /sup 3/He-B decreases on isothermal compression, or its isobaric volume expansion coefficient is positive. The equilibrium thermal behavior of ordered /sup 3/He-B is thus qualitatively different from that of disordered liquid /sup 3/He. Experimental control of these aspects of the liquid /sup 3/He phase transformation is lacking at the present time. Both early and new /sup 3/He-B paramagnetic susceptibility data, extended recently over a wide reduced-temperature range, disclose a fundamental competition between the spontaneous ordering mechanism responsible for the existence of /sup 3/He-B and the specific ordering process imposed upon this phase on application of an external constant and uniform magnetic field. As a consequence, magnetized /sup 3/He-B will be shown to increase its entropy on isothermal magnetization and to cool on adiabatic magnetization. The magnetocaloric effect is, however, only moderate. The competition of the ordering process leads to the delay or possibly even to the suppression of the formation of the ordered phase, a state of affairs foreseen in our earlier work. At low or moderate magnetic field strengths, the zero-field phase-boundary temperatures are shown to shift toward lower temperatures while, simultaneously, the order of the phase change decreases, from second order, in the absence of the field, to first order. Although of model-theoretic character, involving limitations of various types, the rich physical content of /sup 3/He-B at equilibrium clearly emerges in the present work.
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.
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.
NASA Astrophysics Data System (ADS)
Tanizaki, Seiichiro; Feig, Michael
2005-03-01
Reliable computer simulations of complex biological environments such as integral membrane proteins with explicit water and lipid molecules remain a challenging task. We propose a modification of the standard generalized Born theory of homogeneous solvent for modeling the heterogeneous dielectric environments such as lipid/water interfaces. Our model allows the representation of biological membranes in the form of multiple layered dielectric regions with dielectric constants that are different from the solute cavity. The proposed new formalism is shown to predict the electrostatic component of solvation free energy with a relative error of 0.17% compared to exact finite-difference solutions of the Poisson equation for a transmembrane helix test system. Molecular dynamics simulations of melittin and bacteriorhodopsin are carried out and performed over 10ns and 7ns of simulation time, respectively. The center of melittin along the membrane normal in these stable simulations is in excellent agreement with the relevant experimental data. Simulations of bacteriorhodopsin started from the experimental structure remained stable and in close agreement with experiment. We also examined the free energy profiles of water and amino acid side chain analogs upon membrane insertion. The results with our implicit membrane model agree well with the experimental transfer free energy data from cyclohexane to water as well as explicit solvent simulations of water and selected side chain analogs.
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.…
An efficient chemical kinetics solver using high dimensional model representation
Shorter, J.A.; Ip, P.C.; Rabitz, H.A.
1999-09-09
A high dimensional model representation (HDMR) technique is introduced to capture the input-output behavior of chemical kinetic models. The HDMR expresses the output chemical species concentrations as a rapidly convergent hierarchical correlated function expansion in the input variables. In this paper, the input variables are taken as the species concentrations at time t{sub i} and the output is the concentrations at time t{sub i} + {delta}, where {delta} can be much larger than conventional integration time steps. A specially designed set of model runs is performed to determine the correlated functions making up the HDMR. The resultant HDMR can be used to (1) identify the key input variables acting independently or cooperatively on the output, and (2) create a high speed fully equivalent operational model (FEOM) serving to replace the original kinetic model and its differential equation solver. A demonstration of the HDMR technique is presented for stratospheric chemical kinetics. The FEOM proved to give accurate and stable chemical concentrations out to long times of many years. In addition, the FEOM was found to be orders of magnitude faster than a conventional stiff equation solver. This computational acceleration should have significance in many chemical kinetic applications.
Towards a principled way of making kinetic models from data
NASA Astrophysics Data System (ADS)
Presse, Steve
2012-02-01
Kinetic model extraction from noisy data is the basic route to mechanistic insight in biology. I will show how the tools of Maximum Caliber (the dynamical analog of Maximum Entropy) can be used to infer -and not fit- models in a way which is driven by the structure and limitations of the data. For instance, the typical output of an experiment in systems biology is the stochastic expression of one reporter gene. Master equations used to model the regulatory process underlying the stochastic gene expression require knowledge of a circuit topology and rates. However rates and topology are often fit as these are rarely all independently determinable from the limited data. Our goal is to build a kinetic model from the data available with no adjustable parameter using the tools of Maximum Caliber. We apply our method to infer the statistics of rare stochastic switching events in the genetic toggle switch from fluctuations on shorter measurable timescales. In addition, we discuss how these tools can be used to infer kinetic models from real single molecule data drawn from anomalous folding kinetics of phosphoglycerate kinase and RNA hairpin zipping-unzipping time traces.
Kinetics of steel slag leaching: Batch tests and modeling.
De Windt, Laurent; Chaurand, Perrine; Rose, Jerome
2011-02-01
Reusing steel slag as an aggregate for road construction requires to characterize the leaching kinetics and metal releases. In this study, basic oxygen furnace (BOF) steel slag were subjected to batch leaching tests at liquid to solid ratios (L/S) of 10 and 100 over 30 days; the leachate chemistry being regularly sampled in time. A geochemical model of the steel slag is developed and validated from experimental data, particularly the evolution with leaching of mineralogical composition of the slag and trace element speciation. Kinetics is necessary for modeling the primary phase leaching, whereas a simple thermodynamic equilibrium approach can be used for secondary phase precipitation. The proposed model simulates the kinetically-controlled dissolution (hydrolysis) of primary phases, the precipitation of secondary phases (C-S-H, hydroxide and spinel), the pH and redox conditions, and the progressive release of major elements as well as the metals Cr and V. Modeling indicates that the dilution effect of the L/S ratio is often coupled to solubility-controlled processes, which are sensitive to both the pH and the redox potential. A sensitivity analysis of kinetic uncertainties on the modeling of element releases is performed. PMID:20646922
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.
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
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
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.
Spin Kinetic Models of Plasmas - Semiclassical and Quantum Mechanical Theory
Brodin, Gert; Marklund, Mattias; Zamanian, Jens
2009-11-10
In this work a recently published semiclassical spin kinetic model, generalizing those of previous authors are discussed. Some previously described properties are reviewed, and a new example illustrating the theory is presented. The generalization to a fully quantum mechanical description is discussed, and the main features of such a theory is outlined. Finally, the main conclusions are presented.
Paradigms of Complexity in Modelling of Fluid and Kinetic Processes
NASA Astrophysics Data System (ADS)
Diamond, P. H.
2006-10-01
The need to discuss and compare a wide variety of models of fluid and kinetic processes is motivated by the astonishing wide variety of complex physical phenomena which occur in plasmas in nature. Such phenomena include, but are not limited to: turbulence, turbulent transport and mixing, reconnection and structure formation. In this talk, I will review how various fluid and kinetic models come to grips with the essential physics of these phenomena. For example, I will discuss how the idea of a turbulent cascade and the concept of an ``eddy'' are realized quite differently in fluid and Vlasov models. Attention will be placed primarily on physical processes, the physics content of various models, and the consequences of choices in model construction, rather than on the intrinsic mathematical structure of the theories. Examples will be chosen from fusion, laboratory, space and astrophysical plasmas.
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
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.
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.
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.
Modeling the Kinetics of Open Self-Assembly.
Verdier, Timothée; Foret, Lionel; Castelnovo, Martin
2016-07-01
In this work, we explore theoretically the kinetics of molecular self-assembly in the presence of constant monomer flux as an input, and a maximal size. The proposed model is supposed to reproduce the dynamics of viral self-assembly for enveloped virus. It turns out that the kinetics of open self-assembly is rather quantitatively different from the kinetics of similar closed assembly. In particular, our results show that the convergence toward the stationary state is reached through assembly waves. Interestingly, we show that the production of complete clusters is much more efficient in the presence of a constant input flux, rather than providing all monomers at the beginning of the self-assembly. PMID:27295398
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. PMID:25105267
Formal Models of the Network Co-occurrence Underlying Mental Operations.
Bzdok, Danilo; Varoquaux, Gaël; Grisel, Olivier; Eickenberg, Michael; Poupon, Cyril; Thirion, Bertrand
2016-06-01
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
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
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
Enhanced NLTE Atomic Kinetics Modeling Capabilities in HYDRA
NASA Astrophysics Data System (ADS)
Patel, Mehul V.; Scott, Howard A.; Marinak, Michael M.
2014-10-01
In radiation hydrodynamics modeling of ICF targets, an NLTE treatment of atomic kinetics is necessary for modeling high-Z hohlraum wall materials, high-Z dopants mixed in the central gas hotspot, and is potentially needed for accurate modeling of outer layers of the capsule ablator. Over the past several years, the NLTE DCA atomic physics capabilities in the 3D ICF radiation hydrodynamics code HYDRA have been significantly enhanced. The underlying atomic models have been improved, additional kinetics options including the ability to run DCA in cells with dynamic mixing of species has been added, and the computational costs have been significantly reduced using OpenMP threading. To illustrate the improved capabilities, we will show higher fidelity results from simulations of ICF hohlraum energetics, laser irradiated sphere experiments, and ICF capsule implosions. Prepared by LLNL under Contract DE-AC52-07NA27344.
A Structural, Kinetic Model of Soft Tissue Thermomechanics☆
Stylianopoulos, Triantafyllos; Aksan, Alptekin; Barocas, Victor H.
2008-01-01
Abstract A structure-based kinetic model was developed to predict the thermomechanical response of collagenous soft tissues. The collagen fibril was represented as an ensemble of molecular arrays with cross-links connecting the collagen molecules within the same array. A two-state kinetic model for protein folding was employed to represent the native and the denatured states of the collagen molecule. The Monte Carlo method was used to determine the state of the collagen molecule when subjected to thermal and mechanical loads. The model predictions were compared to existing experimental data for New Zealand white rabbit patellar tendons. The model predictions for one-dimensional tissue shrinkage and the corresponding mechanical property degradation agreed well with the experimental data, showing that the gross tissue behavior is dictated by molecular-level phenomena. PMID:17890379
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.
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…
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.
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 kinetic modeling of stimulated Raman scattering
NASA Astrophysics Data System (ADS)
Benisti, Didier
2011-10-01
Despite its importance for many applications, such as or Raman amplification or inertial confinement fusion, deriving a nonlinear estimate of Raman reflectivity in a plasma has remained quite a challenge for decades. This is mainly due to the nonlinear modification of the electron distribution function induced by the plasma wave (EPW), which, in turn, modifies the propagation of this wave. In this paper is derived an envelope equation for the EPW valid in 3D and which accounts for the nonlinear change of its collisionless (Landau-like) damping rate, group velocity, coupling to the electromagnetic drive, frequency and wave number. Our theoretical predictions for each of these terms are carefully compared against results from Vlasov simulations of stimulated Raman scattering (SRS), as well as with other theories. Moreover, our envelope model shows to be as accurate as a Vlasov code in predicting Raman threshold in 1D. Making comparisons with experimental results nevertheless requires including transverse dimensions and letting Raman start from noise. To this end, we performed a completely new derivation of the electrostatic fluctuations in a plasma, which accounts nonlinear effects. Moreover, based on our Multi-D simulations of Raman scattering with our envelope code BRAMA, we discuss the effect on SRS of wave front bowing, transverse detrapping and of a completely new defocussing effect due to the local change in the direction of the EPW group velocity induced by the nonlinear decrease of Landau damping.
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.
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.
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.
Kinetic model of DNA replication in eukaryotic organisms
NASA Astrophysics Data System (ADS)
Bechhoefer, John; Herrick, John; Bensimon, Aaron
2001-03-01
We introduce an analogy between DNA replication in eukaryotic organisms and crystal growth in one dimension. Drawing on models of crystallization kinetics developed in the 1930s to describe the freezing of metals, we formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. It allows one, for the first time, to determine the parameters governing the DNA replication program in a eukaryote on a genome-wide basis. In particular, we have determined the frequency of origin activation in time and space during the cell cycle. Although we focus on a specific stage of development, this model can easily be adapted to describe replication in many other organisms, including budding yeast.
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.
A chemical kinetic modeling study of chlorinated hydrocarbon combustion
Pitz, W.J.; Westbrook, C.K.
1990-09-05
The combustion of chloroethane is modeled as a stirred reactor so that we can study critical emission characteristics of the reactor as a function of residence time. We examine important operating conditions such as pressure, temperature, and equivalence ratio and their influence on destructive efficiency of chloroethane. The model uses a detailed chemical kinetic mechanism that we have developed previously for C{sub 3} hydrocarbons. We have added to this mechanism the chemical kinetic mechanism for C{sub 2} chlorinated hydrocarbons developed by Senkan and coworkers. In the modeling calculations, sensitivity coefficients are determined to find which reaction-rate constants have the largest effect on destructive efficiency. 24 refs., 6 figs., 1 tab.
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.
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.
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.
Kinetic models for historical processes of fast invasion and aggression.
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. PMID:25974546
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. PMID:27082268
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).
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.
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.
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.
Kinetic model of metabolic network for xiamenmycin biosynthetic optimisation.
Xu, Min-juan; Chen, Yong-cong; Xu, Jun; Ao, Ping; Zhu, Xiao-mei
2016-02-01
Xiamenmycins, a series of prenylated benzopyran compounds with anti-fibrotic bioactivities, were isolated from a mangrove-derived Streptomyces xiamenensis. To fulfil the requirements of pharmaceutical investigations, a high production of xiamenmycin is needed. In this study, the authors present a kinetic metabolic model to evaluate fluxes in an engineered Streptomyces lividans with xiamenmycin-oriented genetic modification based on generic enzymatic rate equations and stability constraints. Lyapunov function was used for a viability optimisation. From their kinetic model, the flux distributions for the engineered S. lividans fed on glucose and glycerol as carbon sources were calculated. They found that if the bacterium can utilise glucose simultaneously with glycerol, xiamenmycin production can be enhanced by 40% theoretically, while maintaining the same growth rate. Glycerol may increase the flux for phosphoenolpyruvate synthesis without interfering citric acid cycle. They therefore believe this study demonstrates a possible new direction for bioengineering of S. lividans. PMID:26816395
Polar Coordinate Lattice Boltzmann Kinetic Modeling of Detonation Phenomena
NASA Astrophysics Data System (ADS)
Lin, Chuan-Dong; Xu, Ai-Guo; Zhang, Guang-Cai; Li, Ying-Jun
2014-11-01
A novel polar coordinate lattice Boltzmann kinetic model for detonation phenomena is presented and applied to investigate typical implosion and explosion processes. In this model, the change of discrete distribution function due to local chemical reaction is dynamically coupled into the modified lattice Boltzmann equation which could recover the Navier—Stokes equations, including contribution of chemical reaction, via the Chapman—Enskog expansion. For the numerical investigations, the main focuses are the nonequilibrium behaviors in these processes. The system at the disc center is always in its thermodynamic equilibrium in the highly symmetric case. The internal kinetic energies in different degrees of freedom around the detonation front do not coincide. The dependence of the reaction rate on the pressure, influences of the shock strength and reaction rate on the departure amplitude of the system from its local thermodynamic equilibrium are probed.
Urban multitarget tracking via gas-kinetic dynamics models
NASA Astrophysics Data System (ADS)
Mahler, Ronald
2013-05-01
Multitarget tracking in urban environments presents a major theoretical and practical challenge. A recently suggested approach is that of modeling traffic dynamics using the fluid-kinetic methods of traffic-flow theory (TFT). I propose use of the newer, more general, gas-kinetic (GK) approach to TFT. In GK, traffic flow is modeled as a one- or two-dimensional constrained gas. The paper demonstrates the following. (1) The foundational concept in GK--the "phase-space density"--is the same thing as the probability hypothesis density (PHD) of multitarget tracking theory. (2) The theoretically best-that-one-can do approach to TFT-based tracking is a PHD filter. (3) Better performance can be obtained by augmenting this PHD filter as a cardinalized PHD (CPHD) filter. A simple example is presented to illustrate how PHD/CPHD filters can be integrated with conventional macroscopic, mesoscopic, and microscopic TFT.
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 models for socio-economic dynamics of speculative markets
NASA Astrophysics Data System (ADS)
Maldarella, Dario; Pareschi, Lorenzo
2012-02-01
In this paper we introduce a simple model for a financial market characterized by a single stock or good and an interplay between two different trader populations, chartists and fundamentalists, which determine the price dynamics of the stock. The model has been inspired by the microscopic Lux-Marchesi model (Lux and Marchesi (2000, 1999) [3,25]). The introduction of kinetic equations permits to study the asymptotic behavior of the investments and the price distributions and to characterize the regimes of lognormal behavior and the formation of power law tails.
NASA Astrophysics Data System (ADS)
Perla, Rocco J.; Carifio, James
In sharp contrast to the early positivist view of the nature of science and scientific knowledge, Kuhn argues that the scientific enterprise involves states of continuous, gradual development punctuated by comparatively rare instances of turmoil and change, which ultimately brings about a new stability and a qualitatively changed knowledge base. Although this discontinuous or nonlinear view of scientific knowledge is shared by a number of philosophers of science and science educators currently, Kuhn's description of how progress in science occurs has never been formally modeled from a nonlinear mathematical perspective. In this article, we represent aspects of Kuhn's main thesis and ideas as stated in his classic work The Structure of Scientific Revolutions using catastrophe theory, which is a particular instantiation of chaos theory capable of describing discontinuous phenomenon. Through this catastrophe theory representation we attempt to depict and develop a formal nonlinear model of scientific change. The pedagogical implications of the model developed and presented are discussed.
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
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
Modeling solute advection coupled with sorption kinetics in heterogeneous formations
NASA Astrophysics Data System (ADS)
Selroos, Jan-Olof; Cvetkovic, Vladimir
1992-05-01
A method for coupling sorption kinetics and solute advection in particle-tracking models is proposed; this method is efficient for the case where sorption rate coefficients can be assumed constant field scale parameters. A simulation example of reactive solute advection in two-dimensional heterogeneous porous media is presented. The effect of sorption kinetics on solute advection is investigated. Nonequilibrium effects are exhibited as enhanced tailing in the solute breakthrough. Because high variability in the hydraulic conductivity also yields enhanced tailing, the nonequilibrium effect is more pronounced for the case of low variability. Moreover, it may be difficult to distinguish cases of low variability with nonequilibrium sorption from cases of high variability with equilibrium sorption. A comparison of Monte Carlo ensemble results is made with an analytical model for the mass arrival of kinetically sorbing solute in heterogeneous porous media obtained using first-order perturbation. The comparison indicates that the analytical model provides reasonable approximations of the expected solute breakthrough if the variance of the natural logarithm of the hydraulic conductivity is smaller than 1.
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.
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.
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.
Multiensemble Markov models of molecular thermodynamics and kinetics.
Wu, Hao; Paul, Fabian; Wehmeyer, Christoph; Noé, Frank
2016-06-01
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
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. PMID:24231266
Kinetic and reactor models for HDT of middle distillates
Cotta, R.M.; Filho, R.M.
1996-12-31
Hydrodesulfurization (HDS) and hydrodenitrogenation (HDN) of middle distillates over a commercial Ni-Mo/y-Al{sub 2}O{sub 3} has been studied under wide operating conditions just as 340 to 380{degrees}C and 38 to 98 atm. A Power Law model was presented to each one of those reactions. The parameters of kinetic equations were estimated solving the ordinary differential equations by the 4 order Runge-Kutta-Gill algorithm and Marquardt method for searching of set of kinetic parameters (kinetic constants as well as the orders of reactions). An adiabatic diesel hydrotreating trickle-bed reactor packed with the same catalyst was simulated numerically in order to check up the behavior of this specific reaction system. One dimensional pseudo-homogeneous model was used in this work. For each feed, the mass and energy balance equations were integrated along the length of the catalytic bed using the 4th Runge-Kutta-Gill method. The performance of two industrial reactors was checked. 5 refs., 2 tabs.
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
Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.
Fleming, R M T; Thiele, I; Provan, G; Nasheuer, H P
2010-06-01
The quantitative analysis of biochemical reactions and metabolites is at frontier of biological sciences. The recent availability of high-throughput technology data sets in biology has paved the way for new modelling approaches at various levels of complexity including the metabolome of a cell or an organism. Understanding the metabolism of a single cell and multi-cell organism will provide the knowledge for the rational design of growth conditions to produce commercially valuable reagents in biotechnology. Here, we demonstrate how equations representing steady state mass conservation, energy conservation, the second law of thermodynamics, and reversible enzyme kinetics can be formulated as a single system of linear equalities and inequalities, in addition to linear equalities on exponential variables. Even though the feasible set is non-convex, the reformulation is exact and amenable to large-scale numerical analysis, a prerequisite for computationally feasible genome scale modelling. Integrating flux, concentration and kinetic variables in a unified constraint-based formulation is aimed at increasing the quantitative predictive capacity of flux balance analysis. Incorporation of experimental and theoretical bounds on thermodynamic and kinetic variables ensures that the predicted steady state fluxes are both thermodynamically and biochemically feasible. The resulting in silico predictions are tested against fluxomic data for central metabolism in Escherichia coli and compare favourably with in silico prediction by flux balance analysis. PMID:20230840
Kinetic models for in vivo interaction of radioligand and neuroreceptors
Holland, M.J.C. )
1990-02-26
Estimating the amount of nonspecifically bound ligand is required for the analysis of kinetic data derived from in vivo studies of radioligand-neuroreceptor interactions. Most models assume that nonspecific binding is nonsaturable and rapidly reversible and, therefore, represent nonspecific binding as a constant fraction of the radioligand present in a given tissue compartment. This treatment of nonspecific binding predicts that all brain regions will exhibit similar levels of nonspecific binding subject only to differences in blood flow, and is used to justify the practice of estimating specific binding in receptor-rich regions by subtracting the total radioligand in receptor-poor regions from that found in the receptor-rich region. In reality, however, nonspecific binding is probably heterogeneous in character. Some of it may not exhibit very rapid kinetics relative to specific binding to receptors; some of it may be irreversible. When computer simulations are performed using a model which treats nonspecific binding as a separate compartment with its own kinetic parameters rather than as a constant fraction of the radioligand in extracellular fluid, predicted levels of nonspecific binding differ in receptor-rich and receptor-poor regions, suggesting that using receptor-poor regions to estimate nonspecific binding may not be justified.
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.
Kinetic measurements of hydrocarbon conversion reactions on model metal surfaces.
Wilson, Jarod; Guo, Hansheng; Morales, Ricardo; Podgornov, Egor; Lee, Ilkeun; Zaera, Francisco
2007-08-01
Examples from recent studies in our laboratory are presented to illustrate the main tools available to surface scientists for the determination of the kinetics of surface reactions. Emphasis is given here to hydrocarbon conversions and studies that rely on the use of model systems, typically single crystals and controlled (ultrahigh vacuum) environments. A detailed discussion is provided on the use of temperature-programmed desorption for the determination of activation energies as well as for product identification and yield estimations. Isothermal kinetic measurements are addressed next by focusing on studies under vacuum using molecular beams and surface-sensitive spectroscopies. That is followed by a review of the usefulness of high-pressure cells and other reactor designs for the emulation of realistic catalytic conditions. Finally, an analysis of the power of isotope labeling and chemical substitutions in mechanistic research on surface reactions is presented. PMID:17637975
Modeling interface-controlled phase transformation kinetics in thin films
NASA Astrophysics Data System (ADS)
Pang, E. L.; Vo, N. Q.; Philippe, T.; Voorhees, P. W.
2015-05-01
The Johnson-Mehl-Avrami-Kolmogorov (JMAK) equation is widely used to describe phase transformation kinetics. This description, however, is not valid in finite size domains, in particular, thin films. A new computational model incorporating the level-set method is employed to study phase evolution in thin film systems. For both homogeneous (bulk) and heterogeneous (surface) nucleation, nucleation density and film thickness were systematically adjusted to study finite-thickness effects on the Avrami exponent during the transformation process. Only site-saturated nucleation with isotropic interface-kinetics controlled growth is considered in this paper. We show that the observed Avrami exponent is not constant throughout the phase transformation process in thin films with a value that is not consistent with the dimensionality of the transformation. Finite-thickness effects are shown to result in reduced time-dependent Avrami exponents when bulk nucleation is present, but not necessarily when surface nucleation is present.
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.
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
Isothermal crystallization kinetic modeling of poly(etherketoneketone) (PEKK)
NASA Astrophysics Data System (ADS)
Choupin, T.; Paris, C.; Cinquin, J.; Fayolle, B.; Régnier, G.
2016-05-01
Isothermal melt and cold crystallization kinetics of poly(etherketoneketone) (PEKK) have been investigated by differential scanning calorimetry. A modified Avrami model has been used to describe the two-stage crystallization of PEKK. The primary crystallization stage is assumed to be a two dimensional nucleation growth with an Avrami exponent of 2 whereas the secondary stage is assumed to be a one dimensional nucleation growth with an Avrami exponent of 1. The evolution of the crystallization constant rates depending on temperature has been modeled with the Hoffman and Lauritzen growth equation. The activation energy of nucleation constants Kg for both crystallizations are presented.
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.
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.
β-function formalism for inflationary models with a non minimal coupling with gravity
NASA Astrophysics Data System (ADS)
Pieroni, M.
2016-02-01
We discuss the introduction of a non minimal coupling between the inflaton and gravity in terms of our recently proposed β-function formalism for inflation. Via a field redefinition we reduce to the case of minimally coupled theories. The universal attractor at strong coupling has a simple explanation in terms of the new field. Generalizations are discussed and the possibility of evading the universal attractor is shown.
Kinetic energy for the nuclear Yang-Mills collective model
NASA Astrophysics Data System (ADS)
Rosensteel, George; Sparks, Nick
2015-10-01
The Bohr-Mottelson-Frankfurt model of nuclear rotations and quadrupole vibrations is a foundational model in nuclear structure physics. The model, also called the geometrical collective model or simply GCM, has two hidden mathematical structures, one Lie group theoretic and the other differential geometric. Although the group structure has been understood for some time, the geometric structure is a new unexplored feature that shares the same mathematical origin as Yang-Mills, viz., a vector bundle with a non-abelian structure group and a connection. Using the de Rham Laplacian ▵ = * d * d from differential geometry for the kinetic energy extends significantly the physical scope of the GCM model. This Laplacian contains a ``magnetic'' term due to the coupling between base manifold rotational and fiber vorticity degrees of freedom. When the connection specializes to irrotational flow, the Laplacian reduces to the Bohr-Mottelson kinetic energy operator. More generally, the connection yields a moment of inertia that is intermediate between the extremes of irrotational flow and rigid body motion.
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.
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.
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
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.
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.
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…
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
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).
A hybrid model describing ion induced kinetic electron emission
NASA Astrophysics Data System (ADS)
Hanke, S.; Duvenbeck, A.; Heuser, C.; Weidtmann, B.; Wucher, A.
2015-06-01
We present a model to describe the kinetic internal and external electron emission from an ion bombarded metal target. The model is based upon a molecular dynamics treatment of the nuclear degree of freedom, the electronic system is assumed as a quasi-free electron gas characterized by its Fermi energy, electron temperature and a characteristic attenuation length. In a series of previous works we have employed this model, which includes the local kinetic excitation as well as the rapid spread of the generated excitation energy, in order to calculate internal and external electron emission yields within the framework of a Richardson-Dushman-like thermionic emission model. However, this kind of treatment turned out to fail in the realistic prediction of experimentally measured internal electron yields mainly due to the restriction of the treatment of electronic transport to a diffusive manner. Here, we propose a slightly modified approach additionally incorporating the contribution of hot electrons which are generated in the bulk material and undergo ballistic transport towards the emitting interface.
Modeling anomalous radial transport in kinetic transport codes
NASA Astrophysics Data System (ADS)
Bodi, K.; Krasheninnikov, S. I.; Cohen, R. H.; Rognlien, T. D.
2009-11-01
Anomalous transport is typically the dominant component of the radial transport in magnetically confined plasmas, where the physical origin of this transport is believed to be plasma turbulence. A model is presented for anomalous transport that can be used in continuum kinetic edge codes like TEMPEST, NEO and the next-generation code being developed by the Edge Simulation Laboratory. The model can also be adapted to particle-based codes. It is demonstrated that the model with a velocity-dependent diffusion and convection terms can match a diagonal gradient-driven transport matrix as found in contemporary fluid codes, but can also include off-diagonal effects. The anomalous transport model is also combined with particle drifts and a particle/energy-conserving Krook collision operator to study possible synergistic effects with neoclassical transport. For the latter study, a velocity-independent anomalous diffusion coefficient is used to mimic the effect of long-wavelength ExB turbulence.
NASA Astrophysics Data System (ADS)
Duchemin, Ivan; Jacquemin, Denis; Blase, Xavier
2016-04-01
We have implemented the polarizable continuum model within the framework of the many-body Green's function GW formalism for the calculation of electron addition and removal energies in solution. The present formalism includes both ground-state and non-equilibrium polarization effects. In addition, the polarization energies are state-specific, allowing to obtain the bath-induced renormalisation energy of all occupied and virtual energy levels. Our implementation is validated by comparisons with ΔSCF calculations performed at both the density functional theory and coupled-cluster single and double levels for solvated nucleobases. The present study opens the way to GW and Bethe-Salpeter calculations in disordered condensed phases of interest in organic optoelectronics, wet chemistry, and biology.
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. PMID:27131530
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.
Equilibrium, kinetic, and reactive transport models for plutonium
NASA Astrophysics Data System (ADS)
Schwantes, Jon Michael
Equilibrium, kinetic, and reactive transport models for plutonium (Pu) have been developed to help meet environmental concerns posed by past war-related and present and future peacetime nuclear technologies. A thorough review of the literature identified several hurdles that needed to be overcome in order to develop capable predictive tools for Pu. These hurdles include: (1) missing or ill-defined chemical equilibrium and kinetic constants for environmentally important Pu species; (2) no adequate conceptual model describing the formation of Pu oxy/hydroxide colloids and solids; and (3) an inability of two-phase reactive transport models to adequately simulate Pu behavior in the presence of colloids. A computer program called INVRS K was developed that integrates the geochemical modeling software of PHREEQC with a nonlinear regression routine. This program provides a tool for estimating equilibrium and kinetic constants from experimental data. INVRS K was used to regress on binding constants for Pu sorbing onto various mineral and humic surfaces. These constants enhance the thermodynamic database for Pu and improve the capability of current predictive tools. Time and temperature studies of the Pu intrinsic colloid were also conducted and results of these studies were presented here. Formation constants for the fresh and aged Pu intrinsic colloid were regressed upon using INVRS K. From these results, it was possible to develop a cohesive diagenetic model that describes the formation of Pu oxy/hydroxide colloids and solids. This model provides for the first time a means of deciphering historically unexplained observations with respect to the Pu intrinsic colloid, as well as a basis for simulating the behavior within systems containing these solids. Discussion of the development and application of reactive transport models is also presented and includes: (1) the general application of a 1-D in flow, three-phase (i.e., dissolved, solid, and colloidal), reactive
Quantitative description of realistic wealth distributions by kinetic trading models.
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+alpha) at the high end, where, in general, alpha 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. PMID:18999570
Kinetic mixing effect in the 3 -3 -1 -1 model
NASA Astrophysics Data System (ADS)
Dong, P. V.; Si, D. T.
2016-06-01
We show that the mixing effect of the neutral gauge bosons in the 3 -3 -1 -1 model comes from two sources. The first one is due to the 3 -3 -1 -1 gauge symmetry breaking as usual, whereas the second one results from the kinetic mixing between the gauge bosons of U (1 )X and U (1 )N groups, which are used to determine the electric charge and baryon minus lepton numbers, respectively. Such mixings modify the ρ -parameter and the known couplings of Z with fermions. The constraints that arise from flavor-changing neutral currents due to the gauge boson mixings and nonuniversal fermion generations are also given.
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.
Bio-butanol: Combustion properties and detailed chemical kinetic model
Black, G.; Curran, H.J.; Pichon, S.; Simmie, J.M.; Zhukov, V.
2010-02-15
Autoignition delay time measurements were performed at equivalence ratios of 0.5, 1 and 2 for butan-1-ol at reflected shock pressures of 1, 2.6 and 8 atm at temperatures from 1100 to 1800 K. High-level ab initio calculations were used to determine enthalpies of formation and consequently bond dissociation energies for each bond in the alcohol. A detailed chemical kinetic model consisting of 1399 reactions involving 234 species was constructed and tested against the delay times and also against recent jet-stirred reactor speciation data with encouraging results. The importance of enol chemistry is highlighted. (author)
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 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/.
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.
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
Kinetic modeling and design of colloidal lock and key assembly.
Beltran-Villegas, Daniel J; Colón-Meléndez, Laura; Solomon, Michael J; Larson, Ronald G
2016-02-01
We investigate the kinetics of colloidal lock and key particle assembly by modeling transitions between free, non-specifically and specifically (dumbbells) bound pairs to enable the rapid formation of specific pairs. We expand on a model introduced in a previous publication (Colón-Meléndez et al., 2015) to account for the shape complementarity between the lock and the key particle. Specifically we develop a theory to predict free energy differences between specific and non-specific states based on the interaction potential between arbitrary surfaces and apply this to the interaction of a spherical key particle with the concave dimple surface. Our results show that a lock particle dimple slightly wider than the key particle radius results in optimal binding, but also show escape rates much smaller than those observed in experimental measurements described in the paper cited above. We assess the possible sources of error in experiments and in analysis, including spatial and temporal resolution of the confocal microscopy method used to measure kinetic coefficients, the polydispersity of the lock dimple size, and the sedimentation of the particles in a quasi-two-dimensional layer. We find that the largest sources of variation are in the limited temporal resolution of the experiments, which we account for in our theory, and in the quasi-two-dimensional nature of the experiment that leads to misidentification of non-specific pairs as specific ones. Accounting for these sources of variation results in very good quantitative agreement with experimental data. PMID:26550782
Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo
Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.
2000-10-10
Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.
Growth kinetics in a phase field model with continuous symmetry
NASA Astrophysics Data System (ADS)
Marini Bettolo Marconi, Umberto; Crisanti, Andrea
1996-07-01
We discuss the static and kinetic properties of a Ginzburg-Landau spherically symmetric O(N) model recently introduced [U. Marini Bettolo Marconi and A. Crisanti, Phys. Rev. Lett. 75, 2168 (1995)] in order to generalize the so-called phase field model of Langer [Rev. Mod. Phys. 52, 1 (1980); Science 243, 1150 (1989)]. The Hamiltonian contains two O(N) invariant fields φ and U bilinearly coupled. The order parameter field φ evolves according to a nonconserved dynamics, whereas the diffusive field U follows a conserved dynamics. In the limit N-->∞ we obtain an exact solution, which displays an interesting kinetic behavior characterized by three different growth regimes. In the early regime the system displays normal scaling and the average domain size grows as t1/2; in the intermediate regime one observes a finite wave-vector instability, which is related to the Mullins-Sekerka instability; finally, in the late stage the structure function has a multiscaling behavior, while the domain size grows as t1/4.
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
A general moment expansion method for stochastic kinetic models
NASA Astrophysics Data System (ADS)
Ale, Angelique; Kirk, Paul; Stumpf, Michael P. H.
2013-05-01
Moment approximation methods are gaining increasing attention for their use in the approximation of the stochastic kinetics of chemical reaction systems. In this paper we derive a general moment expansion method for any type of propensities and which allows expansion up to any number of moments. For some chemical reaction systems, more than two moments are necessary to describe the dynamic properties of the system, which the linear noise approximation is unable to provide. Moreover, also for systems for which the mean does not have a strong dependence on higher order moments, moment approximation methods give information about higher order moments of the underlying probability distribution. We demonstrate the method using a dimerisation reaction, Michaelis-Menten kinetics and a model of an oscillating p53 system. We show that for the dimerisation reaction and Michaelis-Menten enzyme kinetics system higher order moments have limited influence on the estimation of the mean, while for the p53 system, the solution for the mean can require several moments to converge to the average obtained from many stochastic simulations. We also find that agreement between lower order moments does not guarantee that higher moments will agree. Compared to stochastic simulations, our approach is numerically highly efficient at capturing the behaviour of stochastic systems in terms of the average and higher moments, and we provide expressions for the computational cost for different system sizes and orders of approximation. We show how the moment expansion method can be employed to efficiently quantify parameter sensitivity. Finally we investigate the effects of using too few moments on parameter estimation, and provide guidance on how to estimate if the distribution can be accurately approximated using only a few moments.
Simulation of carbon gasification kinetics using an edge recession model
Takashi Kyotani; Leon y Leon, C.A.L.; Radovic, L.R. )
1993-07-01
An edge recession modeling method is proposed as a new approach to the prediction of carbon gasification kinetics. Using this method, the variations in reactive surface area (RSA) and specific reactivity (R) with conversion were simulated for several polynuclear aromatic molecules adopted as models of carbon crystallites. The effects of crystallite size and shape, edge site reactivity and vacancies on the changes in RSA and R with conversion were investigated. As a result, RSA and R were found to be essentially independent of crystallite shape, but to depend on crystallite size and the presence of vacancies. Good agreement was obtained between model predictions and experimental data for several kinds of model carbon crystallites. In the case of structurally disordered carbons (such as chars), simultaneous gasification of model crystallites of two different sizes gave better predictions than that of single-size crystallites. The edge recession model is proposed as an alternative, or at least complementary, approach to the more conventional (and, arguably, less physically meaningful) pore structure development models.
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.
Kinetic model for colchicine inhibition of microtubule assembly
Sternlicht, H.; Ringel, I.; Szasz, J.
1980-10-01
Colchicine is a potent drug used to probe microtubule dependent processes. We have recently shown that substoichiometric concentrations of colchicine-tubulin complex (CD), a 1:1 tight binding complex of drug with tubulin, copolymerizes with tubulin to form microtubule copolymers. The affinity of the microtubule ends for tublin decreased as the CD mole fraction in the microtubule increased. Mole fraction ratios as small as 1 CD to approx. 50 to 100 tubulins in the copolymers were accompanied by a significant change in binding affinities and polymerization rates. We have further extended our investigation of the CD-tubulin copolymerization reaction. A kinetic model was derived which relates the composition of the microtubule copolymer to the composition of the reaction mixture. This model allowed a predictive correlation to be made between copolymer composition and the extent of assembly inhibition.
Fluid catalytic cracking catalyst for reformulated gasolines: Kinetic modeling
Gianetto, A. ); Farag, H.I. . Dept. of Chemical Engineering); Blasetti, A.P. . Dept. de Procesos); Lasa, H.I. de . Faculty of Engineering Science)
1994-12-01
Changes of the relative importance of intradiffusion on USY zeolite crystals were studied as a way of affecting selectivity of catalytic cracking reactions. Zeolite crystals were synthesized (Si/Al = 2.4), activated and stabilized using ion exchange and steam calcination to obtain USSY (Ultra Stable Submicron Y) zeolites. After the activation the zeolites were pelletized (45--60 [mu]m particles). USSYs were tested in a novel Riser Simulator. Results obtained show that total aromatics (BTX), benzene, C[sub 4] olefins, and coke were significantly affected with the change of zeolite crystal sizes. Gasolines produced with USSY zeolites contain less aromatics and particularly lower benzene levels. Experimental results were analyzed with a model including several lumps: unconverted gas oil, gasoline, light gases, and coke. This model also accounts for catalyst deactivation as a function of coke on catalyst. Various kinetic parameters were determined with their corresponding spans for the 95% level of confidence.
Immersed boundary method for Boltzmann model kinetic equations
NASA Astrophysics Data System (ADS)
Pekardan, Cem; Chigullapalli, Sruti; Sun, Lin; Alexeenko, Alina
2012-11-01
Three different immersed boundary method formulations are presented for Boltzmann model kinetic equations such as Bhatnagar-Gross-Krook (BGK) and Ellipsoidal statistical Bhatnagar-Gross-Krook (ESBGK) model equations. 1D unsteady IBM solution for a moving piston is compared with the DSMC results and 2D quasi-steady microscale gas damping solutions are verified by a conformal finite volume method solver. Transient analysis for a sinusoidally moving beam is also carried out for the different pressure conditions (1 atm, 0.1 atm and 0.01 atm) corresponding to Kn=0.05,0.5 and 5. Interrelaxation method (Method 2) is shown to provide a faster convergence as compared to the traditional interpolation scheme used in continuum IBM formulations. Unsteady damping in rarefied regime is characterized by a significant phase-lag which is not captured by quasi-steady approximations.
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.
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.
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 .
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.
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.
Discrete Kinetic Models from Funneled Energy Landscape Simulations
Burger, Anat; Craig, Patricio O.; Komives, Elizabeth A.; Wolynes, Peter G.
2012-01-01
A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an “inside-out”, nucleation-propagation like character. PMID:23251375
Constraining kinetic rates of mineral reactions using reactive transport models
NASA Astrophysics Data System (ADS)
Bolton, E. W.; Wang, Z.; Ague, J.; Bercovici, D.; Cai, Z.; Karato, S.; Oristaglio, M. L.; Qiu, L.
2012-12-01
We use a reactive transport model to better understand results of experiments to obtain kinetic rates of mineral reactions in closed systems. Closed system experiments pose special challenges in that secondary minerals may form that modify the fluid composition evolution and may grow on the dissolving minerals thus armoring the surface. Even so, such closed system experiments provide critical data for what minerals would actually form in field applications and how coupled dissolution and precipitation mineral reactions are strongly linked. Comparing to experimental observations can test the reactive transport model, and the experimental observations can be better understood by comparing the results to the modeling. We apply a 0D end member of the model to understand the dissolution of single crystals of forsterite in a variety of settings (low pH, high pH, or NaHCO3 initial fluids, at 100 C and 1 bar, or 200 C and 150 bar). Depending on the initial conditions, we observe the precipitation of talc, brucite, amorphous silica, chrysotile, or magnesite, in various combinations. We compare simulation results to fluid compositions and the presence of secondary minerals experimentally sampled at various times. Insight from the simulations helped create an inverse model to extract the rates of forsterite dissolution and to create a simple forward model useful for exploring the influence of system size, secondary mineral surface areas, etc. Our reactive transport model allows secondary minerals to armor the forsterite surface, which can strongly decrease the dissolution rate as the system evolves. Tuning our model with experimentally derived rates and assuring relevant processes are included so as to reproduce experimental observations is necessary before upscaling to heterogeneous field conditions. The reactive transport model will be used for field-scale sequestration simulations and coupled with a geomechanical model that includes the influence of deformation.
[Kinetics model for batch culture of white rot fungus].
Xiong, Xiao-ping; Wen, Xiang-hua; Xu, Kang-ning; Bian, Bing-hui
2008-02-01
In order to understand ligninolytic enzymes production process during culture of white rot fungus, accordingly to direct the design of fermentation process, a kinetics model was built for the batch culture of Phanerochaete chrysosporium. The parameters in the model were calibrated based on the experimental data from free and immobilized culture separately. The difference between each variable's values calculated based on kinetics model and experimental data is within 15%. Comparing parameters for the free and the immobilized culture, it is found that maximum biomass concentrations are both 1.78 g/L; growth rate ratio of immobilized culture (0.6683 d(-1)) is larger than that of free culture (0.5144 d(-1)); very little glucose is consumed for biomass growth in free culture while in immobilized culture much glucose is used and ammonium nitrogen is consumed at a greater rate. Ligninolytic enzymes production process is non-growth related; fungal pellets can produce MnP (231 U/L) in free culture with a production rate of 115.8 U x (g x d)(-1) before peak and 26.1 U x (g x d)(-1) after peak, thus fed-batch is a possible mode to improve MnP production and fermentation efficiency. MnP (410 U/L) and LiP (721 U/L) can be produced in immobilized culture, but MnP and LiP production rate decrease from 80.1 U x (g x d)(-1) and 248.9 U x (g x d)(-1) to 6.04 U x (g x d)(-1) and 0 U x (g x d)(-1), respectively, indicating a proper feed moment is before the enzymes peak during fed-batch culture. PMID:18613526
Photon kinetic modeling of laser pulse propagation in underdense plasma
Reitsma, A. J. W.; Trines, R. M. G. M.; Bingham, R.; Cairns, R. A.; Mendonca, J. T.; Jaroszynski, D. A.
2006-11-15
This paper discusses photon kinetic theory, which is a description of the electromagnetic field in terms of classical particles in coordinate and wave number phase space. Photon kinetic theory is applied to the interaction of laser pulses with underdense plasma and the transfer of energy and momentum between the laser pulse and the plasma is described in photon kinetic terms. A comparison is made between a one-dimensional full wave and a photon kinetic code for the same laser and plasma parameters. This shows that the photon kinetic simulations accurately reproduce the pulse envelope evolution for photon frequencies down to the plasma frequency.
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
Kinetic Modeling of Toluene Oxidation for Surrogate Fuel Applications
Frassoldati, A; Mehl, M; Fietzek, R; Faravelli, T; Pitz, W J; Ranzi, E
2009-04-21
New environmental issues, like the effect of combustion-generated greenhouse gases, provide motivation to better characterize oxidation of hydrocarbons. Transportation, in particular, significantly contributes to energy consumption and CO{sub 2} emissions. Kinetic studies about the combustion of fuels under conditions typical of internal combustion engines provides important support to improve mechanism formulation and to eventually provide better computational tools that can be used to increase the engine performance. It is foreseeable that at least in the next 30 years the main transportation fuels will be either gasoline or diesel. Unfortunately, these fuels are very complex mixtures of many components. Moreover, their specifications and performance requirements significantly change the composition of these fuels: gasoline and diesel mixtures are different if coming from different refineries or they are different from winter to summer. At the same time a fuel with a well defined and reproducible composition is needed for both experimental and modeling work. In response to these issues, surrogate fuels are proposed. Surrogate fuels are defined as mixtures of a small number of hydrocarbons whose relative concentrations is adjusted in order to approximate the chemical and physical properties of a real fuel. Surrogate fuels are then very useful both for the design of reproducible experimental tests and also for the development of reliable kinetic models. The primary reference fuels (PRF) are a typical and old example of surrogate fuel: n-heptane and iso-octane mixtures are used to reproduce antiknock propensity of complex mixtures contained in a gasoline. PRFs are not able to surrogate gasoline in operating conditions different from standard ones and new surrogates have been recently proposed. Toluene is included in all of them as a species able to represent the behavior of aromatic compounds. On the other side, the toluene oxidation chemistry is not so well
Calcite growth kinetics: Modeling the effect of solution stoichiometry
NASA Astrophysics Data System (ADS)
Wolthers, Mariëtte; Nehrke, Gernot; Gustafsson, Jon Petter; Van Cappellen, Philippe
2012-01-01
Until recently the influence of solution stoichiometry on calcite crystal growth kinetics has attracted little attention, despite the fact that in most aqueous environments calcite precipitates from non-stoichiometric solution. In order to account for the dependence of the calcite crystal growth rate on the cation to anion ratio in solution, we extend the growth model for binary symmetrical electrolyte crystals of Zhang and Nancollas (1998) by combining it with the surface complexation model for the chemical structure of the calcite-aqueous solution interface of Wolthers et al. (2008). To maintain crystal stoichiometry, the rate of attachment of calcium ions to step edges is assumed to equal the rate of attachment of carbonate plus bicarbonate ions. The model parameters are optimized by fitting the model to the step velocities obtained previously by atomic force microscopy (AFM, Teng et al., 2000; Stack and Grantham, 2010). A variable surface roughness factor is introduced in order to reconcile the new process-based growth model with bulk precipitation rates measured in seeded calcite growth experiments. For practical applications, we further present empirical parabolic rate equations fitted to bulk growth rates of calcite in common background electrolytes and in artificial seawater-type solutions. Both the process-based and empirical growth rate equations agree with measured calcite growth rates over broad ranges of ionic strength, pH, solution stoichiometry and degree of supersaturation.
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.
Incorporation of chemical kinetic models into process control
Herget, C.J.; Frazer, J.W.
1981-07-08
An important consideration in chemical process control is to determine the precise rationing of reactant streams, particularly when a large time delay exists between the mixing of the reactants and the measurement of the product. In this paper, a method is described for incorporating chemical kinetic models into the control strategy in order to achieve optimum operating conditions. The system is first characterized by determining a reaction rate surface as a function of all input reactant concentrations over a feasible range. A nonlinear constrained optimization program is then used to determine the combination of reactants which produces the specified yield at minimum cost. This operating condition is then used to establish the nominal concentrations of the reactants. The actual operation is determined through a feedback control system employing a Smith predictor. The method is demonstrated on a laboratory bench scale enzyme reactor.
Low pressure microplasmas enabled by field ionization: Kinetic modeling
NASA Astrophysics Data System (ADS)
Macheret, Sergey O.; Tholeti, Siva Sashank; Alexeenko, Alina A.
2016-05-01
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.
A phase-separation kinetic model for coke formation
Wiehe, I.A. . Corporate Research Lab.)
1993-11-01
Coke formation during the thermolysis of petroleum residua is postulated to occur by a mechanism that involves the liquid-liquid phase separation of reacted asphaltenes to form a phase that is lean in abstractable hydrogen. This mechanism provides the basis of a model that quantitatively describes the kinetics for the thermolysis of Cold Lake vacuum residuum and its deasphalted oil in an open-tube reactor at 400 C. The previously unreacted asphaltenes were found to be the fraction with the highest rate of thermal reaction but with the least extent of reaction. This not only described the appearance and disappearance of asphaltenes but also quantitatively described the variation in molecular weight and hydrogen content of the asphaltenes with reaction time. Further evidence of the liquid-liquid phase separation was the observation of spherical particles of liquid crystalline coke and the preferential conversion of the most associated asphaltenes to coke.
A phase separation kinetic model for coke formation
Wiehe, I.A.
1993-12-31
Coke formation during the thermolysis of petroleum residua is postulated to occur by a mechanism that involves the liquid-liquid phase separation of reacted asphaltenes to form a phase that is lean in abstractable hydrogen. This mechanism provides the basis of a model the quantitatively describes the kinetics for the thermolysis of Cold Lake vacuum residuum and its deasphalted oil in an open tube reactor at 400{degrees}C. The previously unreacted asphaltenes were found to be the fraction with the highest rate of thermal reaction but with the least extent of reaction. Further evidence of the liquid-liquid phase separation was the observation of spherical particles of liquid crystalline coke and the preferential conversion of the most associated asphaltenes to coke.
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.
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.
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.
A Model of the Kinetics of Insulin in Man
Sherwin, Robert S.; Kramer, Karl J.; Tobin, Jordan D.; Insel, Paul A.; Liljenquist, John E.; Berman, Mones; Andres, Reubin
1974-01-01
The design of the present study of the kinetics of insulin in man combines experimental features which obviate two of the major problems in previous insulin studies. (a) The use of radioiodinated insulin as a tracer has been shown to be inappropriate since its metabolism differs markedly from that of the native hormone. Therefore porcine insulin was administered by procedures which raised insulin levels in arterial plasma into the upper physiologic range. Hypoglycemia was prevented by adjusting the rate of an intravenous infusion of glucose in order to control the blood glucose concentration (the glucose-clamp technique). (b) Estimation of a single biological half-time of insulin after pulse injection of the hormone has been shown to be inappropriate since plasma insulin disappearance curves are multiexponential. Therefore the SAAM 25 computer program was used in order to define the parameters of a three compartment insulin model. The combined insulin mass of the three compartments (expressed as plasma equivalent volume) is equal to inulin space (15.7% body wt). Compartment 1 is apparently the plasma space (4.5%). The other two compartments are extra-vascular; compartment 2 is small (1.7%) and equilibrates rapidly with plasma, and compartment 3 is large (9.5%) and equilibrates slowly with plasma. The SAAM 25 program can simulate the buildup and decay of insulin in compartments 2 and 3 which cannot be assayed directly. Insulin in compartment 3 was found to correlate remarkably with the time-course of the servo-controlled glucose infusion. Under conditions of a steady-state arterial glucose level, glucose infusion is a measure of glucose utilization. We conclude that compartment 3 insulin (rather than plasma insulin) is a more direct determinant of glucose utilization. We suggest that the combined use of glucose-clamp and kinetic-modeling techniques should aid in the delineation of pathophysiologic states affecting glucose and insulin metabolism. Images PMID:4856884
Dayglow on Mars: Kinetic modelling with SPICAM UV limb data
NASA Astrophysics Data System (ADS)
Simon, C.; Witasse, O.; Leblanc, F.; Gronoff, G.; Bertaux, J.-L.
2009-07-01
The UV spectrometer experiment SPICAM onboard ESA Mars Express has been orbiting Mars since December 2003. We present here some comparisons between airglow data that have been newly interpreted with the advanced kinetic model Trans-Mars. A series of numerical one-dimensional kinetic models, in the Trans-* family [Lilensten, J., Blelly. P.L., 2002. The TEC and F2 parameters as tracers of the ionosphere and thermosphere. J. Atmos. Solar-Terrestrial Phys. 64, 775-793] has been developed over the last years to take into account of airglow processes and yield altitude line profiles in planetary upper atmospheres (Earth, Venus, Titan and Mars). Trans-Mars is the last evolution of these simulations, applied to Mars. Electron and photon cross sections have been recently updated. The computed model line profiles are comparable to those of Fox and Dalgarno [1979b. Ionization, luminosity, and heating of the upper atmosphere of Mars. J. Geophys. Res. 84, 7315-7333] and Shematovich et al. [2008. Monte Carlo model of electron transport for the calculation of Mars dayglow emissions. J. Geophys. Res. (Planets) 113(E12), 2011]. Nearly 70000 limb UV spectra recorded by SPICAM between October 2004 and May 2006 are analysed in order to obtain altitude emission profiles on the main dayglow emissions. A variable point spread function (PSF) determined statistically throughout the wavelength range is used to estimate precisely the intensity of the airglow. This includes the Cameron bands ( a3Π-X1Σ) of CO, the CO2+ ultraviolet doublet ( B2Σu+-X2Πg) at 289.0 nm and the oxygen emission at 297.2 nm. Instrumental uncertainties of the emissions remain under 15%. Five groups of comparable orbits are selected to prepare for the data interpretation. The seasonal and solar activity effects on the dayside CO 'Cameron Bands', CO2+ and OI(2972 Å) emissions are discussed in light of previous studies. These emissions exhibit for equatorial latitudes two maxima of intensity for LS=140∘ and 290
Kinetic modeling of the Saturn ring-ionosphere plasma environment
NASA Technical Reports Server (NTRS)
Wilson, G. R.; Waite, J. H., Jr.
1989-01-01
A time-independent kinetic plasma model was developed on the basis of the Li et al. (1988) semikinetic plasma model and was used to study the interaction of the Saturnian ionosphere and ring plasma. The model includes the gravitational magnetic mirror and centripetal and ambipolar electric forces, and the effect of the mixing of two plasma populations. The results obtained indicate that the density, temperature, and composition of plasma near the rings changing in the direction from the inner C ring to the outer A ring, due to the fact that the predominant source of plasma changes from the ionosphere to the rings. The model results also suggest that the outflow of hydrogen from the ionosphere to the rings may be shut off for field lines passing through the outer B and A ring, due to the ambipolar electric field set up by the warm ring plasma trapped near the ring plane by the centipetal force. In these regions, there will be a net flux of O(+) ions from the rings to the ionosphere.
Modeling Momentum Transfer from Kinetic Impacts: Implications for Redirecting Asteroids
Stickle, A. M.; Atchison, J. A.; Barnouin, O. S.; Cheng, A. F.; Crawford, D. A.; Ernst, C. M.; Fletcher, Z.; Rivkin, A. S.
2015-05-19
Kinetic impactors are one way to deflect a potentially hazardous object headed for Earth. The Asteroid Impact and Deflection Assessment (AIDA) mission is designed to test the effectiveness of this approach and is a joint effort between NASA and ESA. The NASA-led portion is the Double Asteroid Redirect Test (DART) and is composed of a ~300-kg spacecraft designed to impact the moon of the binary system 65803 Didymos. The deflection of the moon will be measured by the ESA-led Asteroid Impact Mission (AIM) (which will characterize the moon) and from ground-based observations. Because the material properties and internal structure of the target are poorly constrained, however, analytical models and numerical simulations must be used to understand the range of potential outcomes. Here, we describe a modeling effort combining analytical models and CTH simulations to determine possible outcomes of the DART impact. We examine a wide parameter space and provide predictions for crater size, ejecta mass, and momentum transfer following the impact into the moon of the Didymos system. For impacts into “realistic” asteroid types, these models produce craters with diameters on the order of 10 m, an imparted Δv of 0.5–2 mm/s and a momentum enhancement of 1.07 to 5 for a highly porous aggregate to a fully dense rock.
Modeling Momentum Transfer from Kinetic Impacts: Implications for Redirecting Asteroids
Stickle, A. M.; Atchison, J. A.; Barnouin, O. S.; Cheng, A. F.; Crawford, D. A.; Ernst, C. M.; Fletcher, Z.; Rivkin, A. S.
2015-05-19
Kinetic impactors are one way to deflect a potentially hazardous object headed for Earth. The Asteroid Impact and Deflection Assessment (AIDA) mission is designed to test the effectiveness of this approach and is a joint effort between NASA and ESA. The NASA-led portion is the Double Asteroid Redirect Test (DART) and is composed of a ~300-kg spacecraft designed to impact the moon of the binary system 65803 Didymos. The deflection of the moon will be measured by the ESA-led Asteroid Impact Mission (AIM) (which will characterize the moon) and from ground-based observations. Because the material properties and internal structure ofmore » the target are poorly constrained, however, analytical models and numerical simulations must be used to understand the range of potential outcomes. Here, we describe a modeling effort combining analytical models and CTH simulations to determine possible outcomes of the DART impact. We examine a wide parameter space and provide predictions for crater size, ejecta mass, and momentum transfer following the impact into the moon of the Didymos system. For impacts into “realistic” asteroid types, these models produce craters with diameters on the order of 10 m, an imparted Δv of 0.5–2 mm/s and a momentum enhancement of 1.07 to 5 for a highly porous aggregate to a fully dense rock.« less
Metabolic engineering with multi-objective optimization of kinetic models.
Villaverde, Alejandro F; Bongard, Sophia; Mauch, Klaus; Balsa-Canto, Eva; Banga, Julio R
2016-03-20
Kinetic models have a great potential for metabolic engineering applications. They can be used for testing which genetic and regulatory modifications can increase the production of metabolites of interest, while simultaneously monitoring other key functions of the host organism. This work presents a methodology for increasing productivity in biotechnological processes exploiting dynamic models. It uses multi-objective dynamic optimization to identify the combination of targets (enzymatic modifications) and the degree of up- or down-regulation that must be performed in order to optimize a set of pre-defined performance metrics subject to process constraints. The capabilities of the approach are demonstrated on a realistic and computationally challenging application: a large-scale metabolic model of Chinese Hamster Ovary cells (CHO), which are used for antibody production in a fed-batch process. The proposed methodology manages to provide a sustained and robust growth in CHO cells, increasing productivity while simultaneously increasing biomass production, product titer, and keeping the concentrations of lactate and ammonia at low values. The approach presented here can be used for optimizing metabolic models by finding the best combination of targets and their optimal level of up/down-regulation. Furthermore, it can accommodate additional trade-offs and constraints with great flexibility. PMID:26826510
A computational kinetic model of diffusion for molecular systems
Teo, Ivan; Schulten, Klaus
2013-01-01
Regulation of biomolecular transport in cells involves intra-protein steps like gating and passage through channels, but these steps are preceded by extra-protein steps, namely, diffusive approach and admittance of solutes. The extra-protein steps develop over a 10–100 nm length scale typically in a highly particular environment, characterized through the protein's geometry, surrounding electrostatic field, and location. In order to account for solute energetics and mobility of solutes in this environment at a relevant resolution, we propose a particle-based kinetic model of diffusion based on a Markov State Model framework. Prerequisite input data consist of diffusion coefficient and potential of mean force maps generated from extensive molecular dynamics simulations of proteins and their environment that sample multi-nanosecond durations. The suggested diffusion model can describe transport processes beyond microsecond duration, relevant for biological function and beyond the realm of molecular dynamics simulation. For this purpose the systems are represented by a discrete set of states specified by the positions, volumes, and surface elements of Voronoi grid cells distributed according to a density function resolving the often intricate relevant diffusion space. Validation tests carried out for generic diffusion spaces show that the model and the associated Brownian motion algorithm are viable over a large range of parameter values such as time step, diffusion coefficient, and grid density. A concrete application of the method is demonstrated for ion diffusion around and through the Eschericia coli mechanosensitive channel of small conductance ecMscS. PMID:24089741
A computational kinetic model of diffusion for molecular systems
NASA Astrophysics Data System (ADS)
Teo, Ivan; Schulten, Klaus
2013-09-01
Regulation of biomolecular transport in cells involves intra-protein steps like gating and passage through channels, but these steps are preceded by extra-protein steps, namely, diffusive approach and admittance of solutes. The extra-protein steps develop over a 10-100 nm length scale typically in a highly particular environment, characterized through the protein's geometry, surrounding electrostatic field, and location. In order to account for solute energetics and mobility of solutes in this environment at a relevant resolution, we propose a particle-based kinetic model of diffusion based on a Markov State Model framework. Prerequisite input data consist of diffusion coefficient and potential of mean force maps generated from extensive molecular dynamics simulations of proteins and their environment that sample multi-nanosecond durations. The suggested diffusion model can describe transport processes beyond microsecond duration, relevant for biological function and beyond the realm of molecular dynamics simulation. For this purpose the systems are represented by a discrete set of states specified by the positions, volumes, and surface elements of Voronoi grid cells distributed according to a density function resolving the often intricate relevant diffusion space. Validation tests carried out for generic diffusion spaces show that the model and the associated Brownian motion algorithm are viable over a large range of parameter values such as time step, diffusion coefficient, and grid density. A concrete application of the method is demonstrated for ion diffusion around and through the Eschericia coli mechanosensitive channel of small conductance ecMscS.
Detailed kinetic modeling study of n-pentanol oxidation
Heufer, K. Alexander; Sarathy, S. Mani; Curran, Henry J.; Davis, Alexander C.; Westbrook, Charles K.; Pitz, William J.
2012-09-28
To help overcome the world’s dependence upon fossil fuels, suitable biofuels are promising alternatives that can be used in the transportation sector. Recent research on internal combustion engines shows that short alcoholic fuels (e.g., ethanol or n-butanol) have reduced pollutant emissions and increased knock resistance compared to fossil fuels. Although higher molecular weight alcohols (e.g., n-pentanol and n-hexanol) exhibit higher reactivity that lowers their knock resistance, they are suitable for diesel engines or advanced engine concepts, such as homogeneous charge compression ignition (HCCI), where higher reactivity at lower temperatures is necessary for engine operation. The present study presents a detailedmore » kinetic model for n-pentanol based on modeling rules previously presented for n-butanol. This approach was initially validated using quantum chemistry calculations to verify the most stable n-pentanol conformation and to obtain C–H and C–C bond dissociation energies. In addition, the proposed model has been validated against ignition delay time data, speciation data from a jet-stirred reactor, and laminar flame velocity measurements. Overall, the model shows good agreement with the experiments and permits a detailed discussion of the differences between alcohols and alkanes.« less
The use of automated parameter searches to improve ion channel kinetics for neural modeling.
Hendrickson, Eric B; Edgerton, Jeremy R; Jaeger, Dieter
2011-10-01
The voltage and time dependence of ion channels can be regulated, notably by phosphorylation, interaction with phospholipids, and binding to auxiliary subunits. Many parameter variation studies have set conductance densities free while leaving kinetic channel properties fixed as the experimental constraints on the latter are usually better than on the former. Because individual cells can tightly regulate their ion channel properties, we suggest that kinetic parameters may be profitably set free during model optimization in order to both improve matches to data and refine kinetic parameters. To this end, we analyzed the parameter optimization of reduced models of three electrophysiologically characterized and morphologically reconstructed globus pallidus neurons. We performed two automated searches with different types of free parameters. First, conductance density parameters were set free. Even the best resulting models exhibited unavoidable problems which were due to limitations in our channel kinetics. We next set channel kinetics free for the optimized density matches and obtained significantly improved model performance. Some kinetic parameters consistently shifted to similar new values in multiple runs across three models, suggesting the possibility for tailored improvements to channel models. These results suggest that optimized channel kinetics can improve model matches to experimental voltage traces, particularly for channels characterized under different experimental conditions than recorded data to be matched by a model. The resulting shifts in channel kinetics from the original template provide valuable guidance for future experimental efforts to determine the detailed kinetics of channel isoforms and possible modulated states in particular types of neurons. PMID:21243419
Global Kinetic Modeling of Banded Electron Structures in the Plasmasphere
NASA Technical Reports Server (NTRS)
Liemohn, M. W.; Khazanov, G. V.
1997-01-01
Significant fluxes of 10 eV to 30 keV electrons have been detected in the plasmasphere, appearing as banded structures in energy with broad spatial extents and slowly evolving over several days. It is thought that these populations are decaying plasma sheet electrons injected into the corotating region of near-Earth space. This capture can occur when the convective electric field drops rapidly and the Alfven boundary suddenly outward, trapping the inner edge of the plasma sheet along closed drift paths. Our bounce-averaged kinetic model of superthermal electron transport is able to simulate this capture and the subsequent drift, diffusion, and decay of the plasma cloud. Results of this simulation will be shown and discussed, from the initial injection during the elevated convection to the final loss of the particles. It is thought that not only Coulomb collisions but also wave-particle interactions play a significant role in altering the plasma cloud. Quasilinear diffusion is currently being incorporated into the model and the importance of this mechanism will be examined. Also, the high anisotropy of the trapped population could be unstable and generate plasma waves. These and other processes will be investigated to determine the final fate of the cloud and to quantify where, how, and when the energy of the plasma cloud is deposited. Comparisons with CRRES observations of these events are shown to verify the model and explain the data.
Chemical Kinetic Modeling of HMX and TATB Laser Ignition Tests
Tarver, C M
2004-03-02
Recent laser ignition experiments on octahydro-1,3,5,7-tetranitro-1,3,5,7-terrazocine (HMX) and 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) subjected to laser fluxes ranging from 10 to 800 W/cm{sup 2} produced ignition times from seconds to milliseconds. Global chemical kinetic thermal decomposition models for HMX and TATB have been developed to calculate times to thermal explosion for experiments in the seconds to days time frame. These models are applied to the laser ignition experimental data in this paper. Excellent agreement was obtained for TATB, while the calculated ignition times were longer than experiment for HMX at lower laser fluxes. At the temperatures produced in the laser experiments, HMX melts. Melting generally increases condensed phase reaction rates so faster rates were used for three of the HMX reaction rates. This improved agreement with experiments at the lower laser fluxes but yielded very fast ignition at high fluxes. The calculated times to ignition are in reasonable agreement with the laser ignition experiments, and this justifies the use of these models for estimating reaction times at impact and shock ''hot spot'' temperatures.
Kinetic Modeling of Damage Repair, Genome Instability, and Neoplastic Transformation
Stewart, Robert D
2007-03-17
Inducible repair and pathway interactions may fundamentally alter the shape of dose-response curves because different mechanisms may be important under low- and high-dose exposure conditions. However, the significance of these phenomena for risk assessment purposes is an open question. This project developed new modeling tools to study the putative effects of DNA damage induction and repair on higher-level biological endpoints, including cell killing, neoplastic transformation and cancer. The project scope included (1) the development of new approaches to simulate the induction and base excision repair (BER) of DNA damage using Monte Carlo methods and (2) the integration of data from the Monte Carlo simulations with kinetic models for higher-level biological endpoints. Methods of calibrating and testing such multiscale biological simulations were developed. We also developed models to aid in the analysis and interpretation of data from experimental assays, such as the pulsed-field gel electrophoresis (PFGE) assay used to quantity the amount of DNA damage caused by ionizing radiation.
A kinetic model of rapidly reversible nonphotochemical quenching
Zaks, Julia; Amarnath, Kapil; Kramer, David M.; Niyogi, Krishna K.; Fleming, Graham R.
2012-01-01
Oxygen-evolving photosynthetic organisms possess nonphotochemical quenching (NPQ) pathways that protect against photo-induced damage. The majority of NPQ in plants is regulated on a rapid timescale by changes in the pH of the thylakoid lumen. In order to quantify the rapidly reversible component of NPQ, called qE, we developed a mathematical model of pH-dependent quenching of chlorophyll excitations in Photosystem II. Our expression for qE depends on the protonation of PsbS and the deepoxidation of violaxanthin by violaxanthin deepoxidase. The model is able to simulate the kinetics of qE at low and high light intensities. The simulations suggest that the pH of the lumen, which activates qE, is not itself affected by qE. Our model provides a framework for testing hypothesized qE mechanisms and for assessing the role of qE in improving plant fitness in variable light intensity. PMID:22891305
Chemical kinetic modeling of component mixtures relevant to gasoline
Mehl, M; Curran, H J; Pitz, W J; Dooley, S; Westbrook, C K
2008-05-29
Detailed kinetic models of pyrolysis and combustion of hydrocarbon fuels are nowadays widely used in the design of internal combustion engines and these models are effectively applied to help meet the increasingly stringent environmental and energetic standards. In previous studies by the combustion community, such models not only contributed to the understanding of pure component combustion, but also provided a deeper insight into the combustion behavior of complex mixtures. One of the major challenges in this field is now the definition and the development of appropriate surrogate models able to mimic the actual features of real fuels. Real fuels are complex mixtures of thousands of hydrocarbon compounds including linear and branched paraffins, naphthenes, olefins and aromatics. Their behavior can be effectively reproduced by simpler fuel surrogates containing a limited number of components. Aside the most commonly used surrogates containing iso-octane and n-heptane only, the so called Primary Reference Fuels (PRF), new mixtures have recently been suggested to extend the reference components in surrogate mixtures to also include alkenes and aromatics. It is generally agreed that, including representative species for all the main classes of hydrocarbons which can be found in real fuels, it is possible to reproduce very effectively in a wide range of operating conditions not just the auto-ignition propensity of gasoline or Diesel fuels, but also their physical properties and their combustion residuals [1]. In this work, the combustion behavior of several components relevant to gasoline surrogate formulation is computationally examined. The attention is focused on the autoignition of iso-octane, hexene and their mixtures. Some important issues relevant to the experimental and modeling investigation of such fuels are discussed with the help of rapid compression machine data and calculations. Following the model validation, the behavior of mixtures is discussed on the
A kinetic model for RNA-interference of focal adhesions
2013-01-01
Background Focal adhesions are integrin-based cell-matrix contacts that transduce and integrate mechanical and biochemical cues from the environment. They develop from smaller and more numerous focal complexes under the influence of mechanical force and are key elements for many physiological and disease-related processes, including wound healing and metastasis. More than 150 different proteins localize to focal adhesions and have been systematically classified in the adhesome project (http://www.adhesome.org). First RNAi-screens have been performed for focal adhesions and the effect of knockdown of many of these components on the number, size, shape and location of focal adhesions has been reported. Results We have developed a kinetic model for RNA interference of focal adhesions which represents some of its main elements: a spatially layered structure, signaling through the small GTPases Rac and Rho, and maturation from focal complexes to focal adhesions under force. The response to force is described by two complementary scenarios corresponding to slip and catch bond behavior, respectively. Using estimated and literature values for the model parameters, three time scales of the dynamics of RNAi-influenced focal adhesions are identified: a sub-minute time scale for the assembly of focal complexes, a sub-hour time scale for the maturation to focal adhesions, and a time scale of days that controls the siRNA-mediated knockdown. Our model shows bistability between states dominated by focal complexes and focal adhesions, respectively. Catch bonding strongly extends the range of stability of the state dominated by focal adhesions. A sensitivity analysis predicts that knockdown of focal adhesion components is more efficient for focal adhesions with slip bonds or if the system is in a state dominated by focal complexes. Knockdown of Rho leads to an increase of focal complexes. Conclusions The suggested model provides a kinetic description of the effect of RNA
Feldman, Olga; Korotkov, Vladimir N; Logofet, Dmitrii O
2005-10-01
The monoculture strategy of forest management, where the same tree species (e.g., Picea abies) is cultivated in a number of successive planting-growing-felling cycles, is generally considered to be economically efficient, yet not sustainable as it reduces biodiversity in the forest. The sound alternative suggests a long-term strategy of forest management in which different forest types rotate either with planting after clear cutting, or by natural forest succession, yet the commercial output remains dubious. We suggest an approach to formalization and modelling forest dynamics in the long-term by means of Markov chains, the monoculture strategy resulting in an absorbing chain and the rotation one in a regular chain. The approach is illustrated with a case study of Russkii Les, a managed forest located in the Moscow Region, Russia, and the nearby forest reserve having been used as a data source for undisturbed forest dynamics. Starting with conceptual schemes of transitions among certain forest types (states of the chain) in the monoculture and rotation cases, we estimated the transition probabilities by an original method based on average duration of the corresponding states and on the likelihood of alternative transitions from a state into the next one. Formal analysis of the regular chain reveals an opportunity to achieve particular management objectives within the rotation strategy, in particular, to get the distribution of forest types in accordance with an adopted hierarchy of their commercial values, i.e. more valuable types have greater shares. PMID:16111801
Heterogeneous kinetic modeling of the catalytic conversion of cycloparaffins
NASA Astrophysics Data System (ADS)
Al-Sabawi, Mustafa N.
catalytic conversions respectively, are reported. Using these data, heterogeneous kinetic models accounting for intracrystallite molecular transport, adsorption and thermal and catalytic cracking of both cycloparaffin reactants are established. Results show that undesirable hydrogen transfer reactions are more pronounced and selectively favoured against other reactions at lower reaction temperatures, while the desirable ring-opening and cracking reactions predominate at the higher reaction temperatures. Moreover, results of the present work show that while crystallite size may have an effect on the overall conversion in some situations, there is a definite effect on the selectivity of products obtained during the cracking of MCH and decalin and the cracking of MCH in a mixture with co-reactants such as 1,3,5-triisopropylbenzene. Keywords. cycloparaffins, naphthenes, fluid catalytic cracking, kinetic modeling, Y-zeolites, diffusion, adsorption, ring-opening, hydrogen transfer, catalyst selectivity.
Keeping the Faith: A Model of Cultural Transmission in Formal Organizations.
ERIC Educational Resources Information Center
Harrison, J. Richard; Carroll, Glenn R.
1991-01-01
Develops a cultural transmission model with the following variables: worker entry and exit rate, organization growth rate, recruiting selectivity, socialization intensity, and the rate that socialization decays if not reinforced. A computer simulation of the model found that cultural systems in organizations are highly robust and reach equilibrium…
Formal verification of AI software
NASA Technical Reports Server (NTRS)
Rushby, John; Whitehurst, R. Alan
1989-01-01
The application of formal verification techniques to Artificial Intelligence (AI) software, particularly expert systems, is investigated. Constraint satisfaction and model inversion are identified as two formal specification paradigms for different classes of expert systems. A formal definition of consistency is developed, and the notion of approximate semantics is introduced. Examples are given of how these ideas can be applied in both declarative and imperative forms.
Numerical modeling of radiation physics in kinetic plasmas [II
NASA Astrophysics Data System (ADS)
Paraschiv, Ioana; Sentoku, Yasuhiko; Mancini, Roberto
2014-10-01
X-ray radiation is an important feature of ultra-intense laser interactions with high Z materials. In order to take into account the radiation effects in the high energy density plasmas created by such interactions, we have modified the collisional particle-in-cell code PICLS to self-consistently model the x-ray radiation transport (RT). Solving the equation of radiation transport requires the creation of a non-LTE database of emissivities and opacities as functions of photon frequency for given densities, bulk electron temperatures, hot electron temperatures, and hot electron fractions. The database was generated using results computed by a non-equilibrium, collisional-radiative atomic kinetics code. Using the two-dimensional RT-PICLS code we have studied the X-ray transport in an ultrafast heated target and the dependence of the emitted K- α radiation on the fast electron dynamics in the solid target. The details of these results obtained from the implementation of the radiation transport model into the PICLS calculations will be reported in this presentation. Work supported by the DOE Office of Science Grant No. DE-SC0008827 and by the NNSA/DOE Grants No. DE-FC52-06NA27616 and DE-NA0002075.
Kinetic modeling of copper biosorption by immobilized biomass
Veglio, F.; Beolchini, F.; Toro, L.
1998-03-01
Biosorption of heavy metals is one of the most promising technologies involved in the removal of toxic metals from industrial waste streams and natural waters. The kinetic modeling of copper biosorption by Arthrobacter sp. immobilized in a hydroxyethyl methacrylate-based matrix is reported in this work. The resin-biomass complex (RBC) has been used for copper biosorption in different conditions according to a factorial experiment. Factors investigated were cross-linker (trimethylolpropane trimethacrylate) concentration, biomass concentration in the solid, and particles` granulometry. A maximum copper specific uptake of abut 7 mg of Cu/g of biomass (dry weight) has been observed, in the case of a RBC with the following characteristics: 2% (w/w) cross-linker concentration, 8% (w/w) biomass concentration, and 425--750 {micro}m granulometry. The shrinking core model has been used for the fitting of experimental data. A good fit has been found in the case of controlling intraparticle diffusion in all experimental trials. The copper diffusion coefficient in RBC has been estimated from the slope of the regression lines. Values obtained for the diffusion coefficients do not differ from one another with respect to the estimated standard error. An average apparent copper diffusion coefficient of about 3 {times} 10{sup {minus}6} cm{sup 2}/s has been found.
Kinetic Modeling of Combustion Characteristics of Real Biodiesel Fuels
Naik, C V; Westbrook, C K
2009-04-08
Biodiesel fuels are of much interest today either for replacing or blending with conventional fuels for automotive applications. Predicting engine effects of using biodiesel fuel requires accurate understanding of the combustion characteristics of the fuel, which can be acquired through analysis using reliable detailed reaction mechanisms. Unlike gasoline or diesel that consists of hundreds of chemical compounds, biodiesel fuels contain only a limited number of compounds. Over 90% of the biodiesel fraction is composed of 5 unique long-chain C{sub 18} and C{sub 16} saturated and unsaturated methyl esters. This makes modeling of real biodiesel fuel possible without the need for a fuel surrogate. To this end, a detailed chemical kinetic mechanism has been developed for determining the combustion characteristics of a pure biodiesel (B100) fuel, applicable from low- to high-temperature oxidation regimes. This model has been built based on reaction rate rules established in previous studies at Lawrence Livermore National Laboratory. Computed results are compared with the few fundamental experimental data that exist for biodiesel fuel and its components. In addition, computed results have been compared with experimental data for other long-chain hydrocarbons that are similar in structure to the biodiesel components.
Kinetic Modeling of a Heterogeneous Fenton Oxidative Treatment of Petroleum Refining Wastewater
Basheer Hasan, Diya'uddeen; Abdul Raman, Abdul Aziz; Wan Daud, Wan Mohd Ashri
2014-01-01
The mineralisation kinetics of petroleum refinery effluent (PRE) by Fenton oxidation were evaluated. Within the ambit of the experimental data generated, first-order kinetic model (FKM), generalised lumped kinetic model (GLKM), and generalized kinetic model (GKM) were tested. The obtained apparent kinetic rate constants for the initial oxidation step (k2′), their final oxidation step (k1′), and the direct conversion to endproducts step (k3′) were 10.12, 3.78, and 0.24 min−1 for GKM; 0.98, 0.98, and nil min−1 for GLKM; and nil, nil, and >0.005 min−1 for FKM. The findings showed that GKM is superior in estimating the mineralization kinetics. PMID:24592152
Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes.
Miskovic, Ljubisa; Tokic, Milenko; Fengos, Georgios; Hatzimanikatis, Vassily
2015-12-01
The overarching ambition of kinetic metabolic modeling is to capture the dynamic behavior of metabolism to such an extent that systems and synthetic biology strategies can reliably be tested in silico. The lack of kinetic data hampers the development of kinetic models, and most of the current models use ad hoc reduced stoichiometry or oversimplified kinetic rate expressions, which may limit their predictive strength. There is a need to introduce the community-level standards that will organize and accelerate the future developments in this area. We introduce here a set of requirements that will ensure the model quality, we examine the current kinetic models with respect to these requirements, and we propose a general workflow for constructing models that satisfy these requirements. PMID:26342586
Uniformly rigid spaces and Néron models of formally finite type
NASA Astrophysics Data System (ADS)
Kappen, Christian
A new innovative polymer pyrolysis method was proposed for creation of attractive carbon molecular sieve (CMS) membranes. Oxygen exposure at ppm levels during pyrolysis was hypothesized and demonstrated to make slit-like CMS structures more selective and less permeable, which I contrary to ones expectation. Indeed prior to this work, any exposure to oxygen was expected to result in removal of carbon mass and increase in permeability. The results of this study indicated that the separation performance and CMS structure may be optimized for various gas separations by careful tuning of the oxygen level. This finding represents a breakthrough in the field of CMS membranes. Simple replacement of pyrolysis atmospheres from vacuum to inert can enable scale-up. The deviation in CMS membrane performance was significantly reduced once oxygen levels were carefully monitored and controlled. The method was shown to be effective and repeatable not only with dense films but also with asymmetric hollow fiber membranes. As a result, this work led the development of the "inert" pyrolysis method which has overcome the challenges faced with previously studied pyrolysis method to prepare attractive CMS membranes. The effect of oxygen exposure during inert pyrolysis was evaluated by a series of well-controlled experiments using homogeneous CMS dense films. Results indicated that the oxygen "doping" process on selective pores is likely governed by equilibrium limited reaction rather than (i) an external or (ii) internal transport or (iii) kinetically limited reaction. This significant finding was validated with two polyimide precursors: synthesized 6FDA/BPDA-DAM and commercial MatrimidRTM, which implies a possibility of the "inert" pyrolysis method application extending towards various precursors. The investigation was further extended to prepare CMS fibers. Despite the challenge of two different morphologies between homogeneous films and asymmetric hollow fibers, the "inert" pyrolysis
Eguzkiza, Aitor; Trigo, Jesús Daniel; Martínez-Espronceda, Miguel; Serrano, Luis; Andonegui, José
2015-08-01
Most healthcare services use information and communication technologies to reduce and redistribute the workload associated with follow-up of chronic conditions. However, the lack of normalization of the information handled in and exchanged between such services hinders the scalability and extendibility. The use of medical standards for modelling and exchanging information, especially dual-model based approaches, can enhance the features of screening services. Hence, the approach of this paper is twofold. First, this article presents a generic methodology to model patient-centered clinical processes. Second, a proof of concept of the proposed methodology was conducted within the diabetic retinopathy (DR) screening service of the Health Service of Navarre (Spain) in compliance with a specific dual-model norm (openEHR). As a result, a set of elements required for deploying a model-driven DR screening service has been established, namely: clinical concepts, archetypes, termsets, templates, guideline definition rules, and user interface definitions. This model fosters reusability, because those elements are available to be downloaded and integrated in any healthcare service, and interoperability, since from then on such services can share information seamlessly. PMID:26049092
Microbial Kinetic Model for the Degradation of Poorly Soluble Organic Materials
A novel mechanistic model is presented that describes the aerobic biodegradation kinetics of soybean biodiesel and petroleum diesel in batch experiments. The model was built on the assumptions that biodegradation takes place in the aqueous phase according to Monod kinetics, and ...
A Model of Adding Relations in Multi-levels to a Formal Organization Structure with Two Subordinates
NASA Astrophysics Data System (ADS)
Sawada, Kiyoshi; Amano, Kazuyuki
2009-10-01
This paper proposes a model of adding relations in multi-levels to a formal organization structure with two subordinates such that the communication of information between every member in the organization becomes the most efficient. When edges between every pair of nodes with the same depth in L (L = 1, 2, …, H) levels are added to a complete binary tree of height H, an optimal set of depths {N1, N2, …, NL} (H⩾N1>N2> …>NL⩾1) is obtained by maximizing the total shortening path length which is the sum of shortening lengths of shortest paths between every pair of all nodes in the complete binary tree. It is shown that {N1, N2, …, NL}* = {H, H-1, …, H-L+1}.
Kinetics and fixed-bed reactor modeling of butane oxidation to maleic anhydride
Sharma, R.K.; Cresswell, D.L. ); Newson, E.J. )
1991-01-01
This paper reports on selective oxidation kinetics of n-butane to maleic anhydride in air studied over a commercial, fixed-bed vanadium-phosphor oxide catalyst. The temperature range was 573-653 K with butane concentrations up to 3 mol % in the feed, which is within flammability limits but below ignition temperatures. The rate data were modeled using power law kinetics with product inhibition and included total oxidation and decomposition reactions. Kinetic parameters were estimated using a multiresponse, nonlinear regression algorithm showing intercorrelation effects. The kinetics were combined with independent measurements of catalyst diffusivity and reactor heat transfer using a one- dimensional heterogeneous reactor model.
Multiscale Model for the Assembly Kinetics of Protein Complexes.
Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao
2016-02-01
The assembly of proteins into high-order complexes is a general mechanism for these biomolecules to implement their versatile functions in cells. Natural evolution has developed various assembling pathways for specific protein complexes to maintain their stability and proper activities. Previous studies have provided numerous examples of the misassembly of protein complexes leading to severe biological consequences. Although the research focusing on protein complexes has started to move beyond the static representation of quaternary structures to the dynamic aspect of their assembly, the current understanding of the assembly mechanism of protein complexes is still largely limited. To tackle this problem, we developed a new multiscale modeling framework. This framework combines a lower-resolution rigid-body-based simulation with a higher-resolution Cα-based simulation method so that protein complexes can be assembled with both structural details and computational efficiency. We applied this model to a homotrimer and a heterotetramer as simple test systems. Consistent with experimental observations, our simulations indicated very different kinetics between protein oligomerization and dimerization. The formation of protein oligomers is a multistep process that is much slower than dimerization but thermodynamically more stable. Moreover, we showed that even the same protein quaternary structure can have very diverse assembly pathways under different binding constants between subunits, which is important for regulating the functions of protein complexes. Finally, we revealed that the binding between subunits in a complex can be synergistically strengthened during assembly without considering allosteric regulation or conformational changes. Therefore, our model provides a useful tool to understand the general principles of protein complex assembly. PMID:26738810
Formal Verification of a Power Controller Using the Real-Time Model Checker UPPAAL
NASA Technical Reports Server (NTRS)
Havelund, Klaus; Larsen, Kim Guldstrand; Skou, Arne
1999-01-01
A real-time system for power-down control in audio/video components is modeled and verified using the real-time model checker UPPAAL. The system is supposed to reside in an audio/video component and control (read from and write to) links to neighbor audio/video components such as TV, VCR and remote-control. In particular, the system is responsible for the powering up and down of the component in between the arrival of data, and in order to do so in a safe way without loss of data, it is essential that no link interrupts are lost. Hence, a component system is a multitasking system with hard real-time requirements, and we present techniques for modeling time consumption in such a multitasked, prioritized system. The work has been carried out in a collaboration between Aalborg University and the audio/video company B&O. By modeling the system, 3 design errors were identified and corrected, and the following verification confirmed the validity of the design but also revealed the necessity for an upper limit of the interrupt frequency. The resulting design has been implemented and it is going to be incorporated as part of a new product line.
Coupled cluster expansions for the massive Schwinger model in the lattice Hamiltonian formalism
Fang, Xi-Yan; Schutte, D.; Wethkamp, V.; Wichmann, A.
2001-07-01
The coupled cluster method is used to study the lattice massive Schwinger model with staggered fermions. The vacuum energy and mass gaps are calculated. Good agreement is found between these calculations, the exact results in the continuum limit, and the results obtained by other approximation methods.
Applying Schema Theory to Mass Media Information Processing: Moving toward a Formal Model.
ERIC Educational Resources Information Center
Wicks, Robert H.
Schema theory may be significant in determining if and how news audiences process information. For any given news topic, people have from none to many schemata (cognitive structures that represent organized knowledge about a given concept or type of stimulus abstracted from prior experience) upon which to draw. Models of how schemata are used…
Freed by interaction kinetic states in the Harper model
NASA Astrophysics Data System (ADS)
Frahm, Klaus M.; Shepelyansky, Dima L.
2015-12-01
We study the problem of two interacting particles in a one-dimensional quasiperiodic lattice of the Harper model. We show that a short or long range interaction between particles leads to emergence of delocalized pairs in the non-interacting localized phase. The properties of these freed by interaction kinetic states (FIKS) are analyzed numerically including the advanced Arnoldi method. We find that the number of sites populated by FIKS pairs grows algebraically with the system size with the maximal exponent b = 1, up to a largest lattice size N = 10 946 reached in our numerical simulations, thus corresponding to a complete delocalization of pairs. For delocalized FIKS pairs the spectral properties of such quasiperiodic operators represent a deep mathematical problem. We argue that FIKS pairs can be detected in the framework of recent cold atom experiments [M. Schreiber et al., Science 349, 842 (2015)] by a simple setup modification. We also discuss possible implications of FIKS pairs for electron transport in the regime of charge-density wave and high T c superconductivity.
Kinetic modeling of spectra of flames with suppressants
Green, A.E.S.; Xue, Hui
1995-12-31
The phase out of halons in response to the Montreal Protocol and the quest for alternative fire suppressants has focused attention on the current lack of understanding of mechanisms of flame extinction. Challenges to the free-radical scavenging mechanism in which chemical chains in combustion are interrupted have raised serious questions as to why the halons are effective. Low-resolution ultraviolet computer spectroscopy can be used to observe the OH radical and other simple molecules when acted upon by halon or alternative suppressants. However, the physical and chemical interpretation of such observations requires reaction rates leading to the OH radical and other observable molecules in 3-6 eV electronic states. Using a simple kinetics model, the authors illustrate where major reaction rates to excited states would be helpful to the interpretation of the interaction of suppressants with flames. Quantum chemists could provide a valuable service by providing such rates and helping to assess whether or not flame suppression by free-radical scavenging is a significant mechanism. 29 refs., 5 figs.
Multifractal formalisms of human behavior.
Ihlen, Espen A F; Vereijken, Beatrix
2013-08-01
With the mounting realization that variability is an inevitable part of human behavior comes the need to integrate this phenomenon in concomitant models and theories of motor control. Among other things, this has resulted in a debate throughout the last decades about the origin of variability in behavior, the outcome of which has important implications for motor control theories. To date, a monofractal formalism of variability has been used as the basis for arguing for component- versus interaction-oriented theories of motor control. However, monofractal formalism alone cannot decide between the opposing sides of the debate. The present theoretical overview introduces multifractal formalisms as a necessary extension of the conventional monofractal formalism. In multifractal formalisms, the scale invariance of behavior is numerically defined as a spectrum of scaling exponents, rather than a single average exponent as in the monofractal formalism. Several methods to estimate the multifractal spectrum of scaling exponents - all within two multifractal formalisms called large deviation and Legendre formalism - are introduced and briefly discussed. Furthermore, the multifractal analyses within these two formalisms are applied to several performance tasks to illustrate how explanations of motor control vary with the methods used. The main section of the theoretical overview discusses the implications of multifractal extensions of the component- and interaction-oriented models for existing theories of motor control. PMID:24054900
Kinetic modelling of runaway electron avalanches in tokamak plasmas
NASA Astrophysics Data System (ADS)
Nilsson, E.; Decker, J.; Peysson, Y.; Granetz, R. S.; Saint-Laurent, F.; Vlainic, M.
2015-09-01
Runaway electrons can be generated in tokamak plasmas if the accelerating force from the toroidal electric field exceeds the collisional drag force owing to Coulomb collisions with the background plasma. In ITER, disruptions are expected to generate runaway electrons mainly through knock-on collisions (Hender et al 2007 Nucl. Fusion 47 S128-202), where enough momentum can be transferred from existing runaways to slow electrons to transport the latter beyond a critical momentum, setting off an avalanche of runaway electrons. Since knock-on runaways are usually scattered off with a significant perpendicular component of the momentum with respect to the local magnetic field direction, these particles are highly magnetized. Consequently, the momentum dynamics require a full 3D kinetic description, since these electrons are highly sensitive to the magnetic non-uniformity of a toroidal configuration. For this purpose, a bounce-averaged knock-on source term is derived. The generation of runaway electrons from the combined effect of Dreicer mechanism and knock-on collision process is studied with the code LUKE, a solver of the 3D linearized bounce-averaged relativistic electron Fokker-Planck equation (Decker and Peysson 2004 DKE: a fast numerical solver for the 3D drift kinetic equation Report EUR-CEA-FC-1736, Euratom-CEA), through the calculation of the response of the electron distribution function to a constant parallel electric field. The model, which has been successfully benchmarked against the standard Dreicer runaway theory now describes the runaway generation by knock-on collisions as proposed by Rosenbluth (Rosenbluth and Putvinski 1997 Nucl. Fusion 37 1355-62). This paper shows that the avalanche effect can be important even in non-disruptive scenarios. Runaway formation through knock-on collisions is found to be strongly reduced when taking place off the magnetic axis, since trapped electrons can not contribute to the runaway electron population. Finally, the
NASA Astrophysics Data System (ADS)
Pais, Helena; Providência, Constança
2016-07-01
The Vlasov formalism is extended to relativistic mean field hadron models with nonlinear terms up to fourth order and applied to the calculation of the crust-core transition density. The effect of the nonlinear ω ρ and σ ρ coupling terms on the crust-core transition density and pressure and on the macroscopic properties of some families of hadronic stars is investigated. For that purpose, six families of relativistic mean field models are considered. Within each family, the members differ in the symmetry energy behavior. For all the models, the dynamical spinodals are calculated, and the crust-core transition density and pressure and the neutron star mass-radius relations are obtained. The effect on the star radius of the inclusion of a pasta calculation in the inner crust is discussed. The set of six models that best satisfy terrestrial and observational constraints predicts a radius of 13.6 ±0.3 km and a crust thickness of 1.36 ±0.06 km for a 1.4 M⊙ star.
Sol-gel kinetics: /sup 29/SI NMR and a statistical reaction model
Assink, R.A.; Kay, B.D.
1988-01-01
Sol-gel processes allow one to prepare novel materials at low processing temperatures. A detailed understanding of the chemical kinetics of such systems is important to fully exploit the unique features of sol-gel processing. This paper describes a systematic approach to the study of sol-gel kinetics which employs /sup 29/Si NMR spectroscopy and kinetic modelling techniques. 2 figs., 1 tab.
Holod, I.; Lin, Z.
2013-03-15
The fluid-kinetic hybrid electron model is verified in global gyrokinetic particle simulation of linear electromagnetic drift-Alfvenic instabilities in tokamak. In particular, we have recovered the {beta}-stabilization of the ion temperature gradient mode, transition to collisionless trapped electron mode, and the onset of kinetic ballooning mode as {beta}{sub e} (ratio of electron kinetic pressure to magnetic pressure) increases.
Kinetic model of carbonate dissolution in Martian meteorite ALH84001
NASA Astrophysics Data System (ADS)
Kopp, R. E.; Humayun, M.
2003-09-01
The magnetites and sulfides located in the rims of carbonate globules in the Martian meteorite ALH84001 have been claimed as evidence of past life on Mars. Here, we consider the possibility that the rims were formed by dissolution and reprecipitation of the primary carbonate by the action of water. To estimate the rate of these solution-precipitation reactions, a kinetic model of magnesite-siderite carbonate dissolution was applied and used to examine the physicochemical conditions under which these rims might have formed. The results indicate that the formation of the rims could have taken place in < 50 yr of exposure to small amounts of aqueous fluids at ambient temperatures. Plausible conditions pertaining to reactions under a hypothetical ancient Martian atmosphere (1 bar CO 2), the modern Martian atmosphere (8 mbar CO 2), and the present terrestrial atmosphere (0.35 mbar CO 2) were explored to constrain the site of the process. The results indicated that such reactions likely occurred under the latter two conditions. The possibility of Antarctic weathering must be entertained, which, if correct, would imply that the plausibly biogenic minerals (single-domain magnetite of characteristic morphology and sulfide) reported from the rims may be the products of terrestrial microbial activity. This model is discussed in terms of the available isotope data and found to be compatible with the formation of ALH84001 rims. Particularly, anticorrelated variations of radiocarbon with δ 13C indicate that carbonate in ALH84001 was affected by solution-precipitation reactions immediately after its initial fall (˜13,000 yr ago) and then again during its recent exposure prior to collection.
Decarboxylation of Δ 9-tetrahydrocannabinol: Kinetics and molecular modeling
NASA Astrophysics Data System (ADS)
Perrotin-Brunel, Helene; Buijs, Wim; van Spronsen, Jaap; van Roosmalen, Maaike J. E.; Peters, Cor J.; Verpoorte, Rob; Witkamp, Geert-Jan
2011-02-01
Efficient tetrahydrocannabinol (Δ 9-THC) production from cannabis is important for its medical application and as basis for the development of production routes of other drugs from plants. This work presents one of the steps of Δ 9-THC production from cannabis plant material, the decarboxylation reaction, transforming the Δ 9-THC-acid naturally present in the plant into the psychoactive Δ 9-THC. Results of experiments showed pseudo-first order reaction kinetics, with an activation barrier of 85 kJ mol -1 and a pre-exponential factor of 3.7 × 10 8 s -1. Using molecular modeling, two options were identified for an acid catalyzed β-keto acid type mechanism for the decarboxylation of Δ 9-THC-acid. Each of these mechanisms might play a role, depending on the actual process conditions. Formic acid proved to be a good model for a catalyst of such a reaction. Also, the computational idea of catalysis by water to catalysis by an acid, put forward by Li and Brill, and Churchev and Belbruno was extended, and a new direct keto-enol route was found. A direct keto-enol mechanism catalyzed by formic acid seems to be the best explanation for the observed activation barrier and the pre-exponential factor of the decarboxylation of Δ 9-THC-acid. Evidence for this was found by performing an extraction experiment with Cannabis Flos. It revealed the presence of short chain carboxylic acids supporting this hypothesis. The presented approach is important for the development of a sustainable production of Δ 9-THC from the plant.
Extended Standard Model in multi-spinor field formalism: Visible and dark sectors
NASA Astrophysics Data System (ADS)
Sogami, Ikuo S.
2013-12-01
To generalize the Standard Model so as to include dark matter, we formulate a theory of multi-spinor fields on the basis of an algebra that consists of triple-tensor products of elements of the Dirac algebra. Chiral combinations of multi-spinor fields form reducible representations of the Lorentz group possessing component fields with spin 1/2, which we interpret as expressing three ordinary families and an additional fourth family of quarks and leptons. Apart from the gauge and Higgs fields of the Standard Model interacting with the fermions of the three ordinary families, we assume the existence of additional gauge and Higgs fields interacting exclusively with the fermions of the fourth family. While the fields of the Standard Model organize the "visible sector" of our universe, the fields related with the fourth family are presumed to generate a "dark sector" that can contain dark matter. The two sectors possess a channel of communication through the bi-quadratic interaction between visible and dark Higgs fields. After experiencing a common inflationary phase, the two sectors follow a reheating period and weak-coupling paths of thermal histories. We propose scenarios for dark matter that have a tendency to take relatively broad interstellar distributions and examine methods for the detection of the main candidate particles of dark matter. The exchange of superposed fields of the visible and dark Higgs bosons induces weak reaction processes between the fields of the visible and dark sectors, which enables us to have a glimpse of the dark sector.
Statistical model of dephasing in mesoscopic devices introduced in the scattering matrix formalism
NASA Astrophysics Data System (ADS)
Pala, Marco G.; Iannaccone, Giuseppe
2004-06-01
We propose a phenomenological model of dephasing in mesoscopic transport, based on the introduction of random-phase fluctuations in the computation of the scattering matrix of the system. A Monte Carlo averaging procedure allows us to extract electrical and microscopic device properties. We show that, in this picture, scattering matrix properties enforced by current conservation and time-reversal invariance still hold. In order to assess the validity of the proposed approach, we present simulations of conductance and magnetoconductance of Aharonov-Bohm rings that reproduce the behavior observed in experiments, in particular as far as aspects related to decoherence are concerned.
NASA Astrophysics Data System (ADS)
Huffman, L. T.; Lynds, S. E.; Rack, F. R.
2012-12-01
Through a NOAA Environmental Literacy grant, ANDRILL (ANtarctic geological DRILLing) created a unique opportunity for both formal and informal educators to engage their classrooms/audiences in understanding the complexities of climate change. The program, entitled C2S2: Climate Change Student Summits, included excellent geographical coverage through an exceptional two-workshop professional development series for teachers in each of nine different regions representing the U.S. National Climate Assessment regions defined by the U.S. Global Change Research Program. The program also included a creative, investigative science research and presentation experience for teams of students in each region, culminating in the Climate Change Student Summit, an on-site capstone event including a videoconference connecting all sites. The success of this program is based on combining multiple aspects, such as providing professional development for educators and encouraging the active involvement of research scientists, both in the professional development workshops and in the Student Summit. Another key factor is the close working relationships between informal and formal education entities, including the involvement of informal science learning facilities and informal science education leaders. The program includes the creation and use of cutting-edge curriculum materials available in the ELF, (Environmental Literacy Framework with a focus on climate change) and hands-on resources for teachers and students that provide an earth systems approach to climate change education, which have been successfully used in grades 5-12 as well as at numerous science museums. The C2S2 project has completed four years of activities with demonstrated positive impacts on both students and teachers. This presentation will share the lessons learned about implementing this climate change science education program and suggest that it is a successful model that can be used to scale up this project from
A formalism for modeling solid electrolyte/electrode interfaces using first principles methods
NASA Astrophysics Data System (ADS)
Lepley, Nicholas; Holzwarth, Natalie
We describe a scheme based on the interface energy for analyzing interfaces between crystalline solids, quantitatively including the effect of lattice strain. This scheme is applied to the modeling of likely interface geometries of several solid state battery materials including Li metal, Li3PO4, Li3PS4, Li2O, and Li2S. We find that all of the interfaces in this study are stable with the exception of Li3PS4/Li. For this chemically unstable interface, the partial density of states helps to identify mechanisms associated with the interface reactions. We also consider the case of charged defects at the interface, and show that accurately modeling them requires a careful treatment of the resulting electric fields. Our energetic measure of interfaces and our analysis of the band alignment between interface materials indicate multiple factors which may be predictors of interface stability, an important property of solid electrolyte systems. Supported by NSF Grant DMR-1105485 and DMR-1507942.
Extension of Standard Model in multi-spinor field formalism — Visible and dark sectors
NASA Astrophysics Data System (ADS)
Sogami, Ikuo S.
2016-06-01
With multi-spinor fields which behave as triple-tensor products of the Dirac spinors, the Standard Model is extended so as to embrace three families of ordinary quarks and leptons in the visible sector and an additional family of exotic quarks and leptons in the dark sector of our Universe. Apart from the gauge and Higgs fields of the Standard Model symmetry G, new gauge and Higgs fields of a symmetry isomorphic to G are postulated to exist in the dark sector. It is the bi-quadratic interaction between visible and dark Higgs fields that opens a main portal to the dark sector. Breakdowns of the visible and dark electroweak symmetries result in the Higgs boson with mass 125 GeV and a new boson which can be related to the diphoton excess around 750 GeV. Subsequent to a common inflationary phase and a reheating period, the visible and dark sectors follow weakly-interacting paths of thermal histories. We propose scenarios for dark matter in which no dark nuclear reaction takes place. A candidate for the main component of the dark matter is a stable dark hadron with spin 3/2, and the upper limit of its mass is estimated to be 15.1 GeV/c2.
Electrical and kinetic model of an atmospheric rf device for plasma aerodynamics applications
Pinheiro, Mario J.; Martins, Alexandre A.
2010-08-15
The asymmetrically mounted flat plasma actuator is investigated using a self-consistent two-dimensional fluid model at atmospheric pressure. The computational model assumes the drift-diffusion approximation and uses a simple plasma kinetic model. It investigated the electrical and kinetic properties of the plasma, calculated the charged species concentrations, surface charge density, electrohydrodynamic forces, and gas speed. The present computational model contributes to understand the main physical mechanisms, and suggests ways to improve its performance.
Modeling of hydrogen production methods: Single particle model and kinetics assessment
Miller, R.S.; Bellan, J.
1996-10-01
The investigation carried out by the Jet Propulsion Laboratory (JPL) is devoted to the modeling of biomass pyrolysis reactors producing an oil vapor (tar) which is a precursor to hydrogen. This is an informal collaboration with NREL whereby JPL uses the experimentally-generated NREL data both as initial and boundary conditions for the calculations, and as a benchmark for model validation. The goal of this investigation is to find drivers of biomass fast-pyrolysis in the low temperature regime. The rationale is that experimental observations produce sparse discrete conditions for model validation, and that numerical simulations produced with a validated model are an economic way to find control parameters and an optimal operation regime, thereby circumventing costly changes in hardware and tests. During this first year of the investigation, a detailed mathematical model has been formulated for the temporal and spatial accurate modeling of solid-fluid reactions in biomass particles. These are porous particles for which volumetric reaction rate data is known a priori and both the porosity and the permeability of the particle are large enough to allow for continuous gas phase flow. The methodology has been applied to the pyrolysis of spherically symmetric biomass particles by considering previously published kinetics schemes for both cellulose and wood. The results show that models which neglect the thermal and species boundary layers exterior to the particle will generally over predict both the pyrolysis rates and experimentally obtainable tar yields. An evaluation of the simulation results through comparisons with experimental data indicates that while the cellulose kinetics is reasonably accurate, the wood pyrolysis kinetics is not accurate; particularly at high reactor temperatures. Current effort in collaboration with NREL is aimed at finding accurate wood kinetics.
Chemical Kinetics Laboratory Discussion Worksheet
Demoin, Dustin Wayne; Jurisson, Silvia S.
2013-01-01
A laboratory discussion worksheet and its answer key provide instructors and students a discussion model to further the students’ understanding of chemical kinetics. This discussion worksheet includes a section for students to augment their previous knowledge about chemical kinetics measurements, an initial check on students’ understanding of basic concepts, a group participation model where students work on solving complex-conceptual problems, and a conclusion to help students connect this discussion to their laboratory or lecture class. Additionally, the worksheet has a detailed solution to a more advanced problem to help students understand how the concepts they have put together relate to problems they will encounter during later formal assessments. PMID:24092948
Kinetic modelling of RDF pyrolysis: Model-fitting and model-free approaches.
Çepelioğullar, Özge; Haykırı-Açma, Hanzade; Yaman, Serdar
2016-02-01
In this study, refuse derived fuel (RDF) was selected as solid fuel and it was pyrolyzed in a thermal analyzer from room temperature to 900°C at heating rates of 5, 10, 20, and 50°C/min in N2 atmosphere. The obtained thermal data was used to calculate the kinetic parameters using Coats-Redfern, Friedman, Flylnn-Wall-Ozawa (FWO) and Kissinger-Akahira-Sunose (KAS) methods. As a result of Coats-Redfern model, decomposition process was assumed to be four independent reactions with different reaction orders. On the other hand, model free methods demonstrated that activation energy trend had similarities for the reaction progresses of 0.1, 0.2-0.7 and 0.8-0.9. The average activation energies were found between 73-161kJ/mol and it is possible to say that FWO and KAS models produced closer results to the average activation energies compared to Friedman model. Experimental studies showed that RDF may be a sustainable and promising feedstock for alternative processes in terms of waste management strategies. PMID:26613830
Detailed Chemical Kinetic Modeling of Diesel Combustion with Oxygenated Fuels
Curran, H J; Fisher, E M; Glaude, P-A; Marinov, N M; Pitz, W J; Westbrook, C K; Flynn, P F; Durrett, R P; zur Loye, A O; Akinyemi, O C; Dryer, F L
2000-01-11
mixing model to study the premixed, rich ignition process. Using n-heptane as a representative diesel fuel, they showed that addition of an oxygenated additive, methanol, to the fuel reduced the concentrations of a number of hydrocarbon species in the products of the rich ignition. Specifically, methanol addition reduced the total concentrations of acetylene, ethylene and 1,3-butadiene, as well as propargyl and vinyl radicals, in the ignition products. These are the same species shown in a number of studies [4-6] to be responsible for formation of aromatic and polycyclic aromatic species in flames, species which lead eventually to production of soot. Flynn et al. did not, however, examine the kinetic processes responsible for the computed reduction in production of soot precursor species. At least two hypotheses have been advanced to explain the role that oxygenated species play in diesel ignition and the reduction in the concentrations of these species. The first is that the additive, methanol in the case of Flynn et al., does not contain any C-C bonds and cannot then produce significant levels of the species such as acetylene, ethylene or the unsaturated radicals which are known to lead to aromatic species. The second hypothesis is that the product distribution changes very naturally as oxygen is added and the overall equivalence ratio is reduced. In the present study, we repeat the ignition calculations of Flynn et al. and include a number of other oxygenated species to determine which of these theories is more applicable to this model.
Modelling of an EGSB treating sugarcane vinasse using first-order variable kinetics.
López, Iván; Borzacconi, Liliana
2011-01-01
An expanded granular sludge bed (EGSB) anaerobic reactor treating sugar cane vinasse was modelled using a simple model with two steps (acidogenesis and methanogenesis), two populations, two substrates and completely mixed conditions. A first-order kinetic equation for both steps with time-variant kinetic coefficients was used. An observer system was used to estimate the evolution of kinetic constants over time. The model was validated by comparing methane flow predictions with experimental values. An estimation of evolution of populations of microorganisms was also performed. This approach allows calculation of specific kinetic constants that reflect biological activity of microorganisms. Variation of specific kinetic constants reflects the influence of the fraction of raw vinasse in the feed. High salt concentrations in the reactor may have inhibited the process. PMID:22105132
NASA Astrophysics Data System (ADS)
Chen, Xiangjun; Xiao, Namin; Cai, Minghui; Li, Dianzhong; Li, Guangyao; Sun, Guangyong; Rolfe, Bernard F.
2016-09-01
An inverse model is proposed to construct the mathematical relationship between continuous cooling transformation (CCT) kinetics with constant rates and the isothermal one. The kinetic parameters in JMAK equations of isothermal kinetics can be deduced from the experimental CCT kinetics. Furthermore, a generalized model with a new additive rule is developed for predicting the kinetics of nucleation and growth during diffusional phase transformation with arbitrary cooling paths based only on CCT curve. A generalized contribution coefficient is introduced into the new additivity rule to describe the influences of current temperature and cooling rate on the incubation time of nuclei. Finally, then the reliability of the proposed model is validated using dilatometry experiments of a microalloy steel with fully bainitic microstructure based on various cooling routes.
Kinetic modeling of antimony(III) oxidation and sorption in soils.
Cai, Yongbing; Mi, Yuting; Zhang, Hua
2016-10-01
Kinetic batch and saturated column experiments were performed to study the oxidation, adsorption and transport of Sb(III) in two soils with contrasting properties. Kinetic and column experiment results clearly demonstrated the extensive oxidation of Sb(III) in soils, and this can in return influence the adsorption and transport of Sb. Both sorption capacity and kinetic oxidation rate were much higher in calcareous Huanjiang soil than in acid red Yingtan soil. The results indicate that soil serve as a catalyst in promoting oxidation of Sb(III) even under anaerobic conditions. A PHREEQC model with kinetic formulations was developed to simulate the oxidation, sorption and transport of Sb(III) in soils. The model successfully described Sb(III) oxidation and sorption data in kinetic batch experiment. It was less successful in simulating the reactive transport of Sb(III) in soil columns. Additional processes such as colloid facilitated transport need to be quantified and considered in the model. PMID:27214003
NASA Astrophysics Data System (ADS)
Chen, Xiangjun; Xiao, Namin; Cai, Minghui; Li, Dianzhong; Li, Guangyao; Sun, Guangyong; Rolfe, Bernard F.
2016-06-01
An inverse model is proposed to construct the mathematical relationship between continuous cooling transformation (CCT) kinetics with constant rates and the isothermal one. The kinetic parameters in JMAK equations of isothermal kinetics can be deduced from the experimental CCT kinetics. Furthermore, a generalized model with a new additive rule is developed for predicting the kinetics of nucleation and growth during diffusional phase transformation with arbitrary cooling paths based only on CCT curve. A generalized contribution coefficient is introduced into the new additivity rule to describe the influences of current temperature and cooling rate on the incubation time of nuclei. Finally, then the reliability of the proposed model is validated using dilatometry experiments of a microalloy steel with fully bainitic microstructure based on various cooling routes.
NASA Astrophysics Data System (ADS)
Kokorev, M. F.; Maleev, N. A.
2000-03-01
Non-uniform doping profiles are typical of modern microstructures. The conventional procedure used in computer simulation of capacitance-voltage (C -V ) characteristics and C -V profiling is a quasistatic method based on solving a nonlinear Boltzmann-Poisson equation. This method includes the free carrier thermal motion, which is very important for microstructures. At the same time, it is strictly formal and employs numerical derivatives. From a mathematical standpoint, it is an ill-posed problem. To eliminate the disadvantages of the method, we propose another theoretical approach to barrier capacitance, inspired by two sources: small-signal modelling of the capacitor response and an averaging method for calculating values used in physical kinetics. This kinetic approach permits closer physical analysis of the C -V characteristics. Furthermore, the computer simulation technique based on this approach offers a great advantage over the quasistatic method in accuracy and efficiency. The results of computer simulation demonstrate the possibility of developing a technique for forward and inverse modelling.
NASA Astrophysics Data System (ADS)
Race, M. S.; Lafayette Library; Learning Center Foundation (Lllcf)
2011-12-01
In these times of budget cuts, tight school schedules, and limited opportunities for student field trips and teacher professional development, it is especially difficult to expose elementary and middle school students to the latest STEM information-particularly in the space sciences. Using our library as a facilitator and catalyst, we built a volunteer-based, multi-faceted, curriculum-linked program for students and teachers in local middle schools (Grade 8) and showcased new astronomical and planetary science information using mainly NASA resources and volunteer effort. The project began with the idea of bringing free NASA photo exhibits (FETTU) to the Lafayette and Antioch Libraries for public display. Subsequently, the effort expanded by adding layers of activities that brought space and science information to teachers, students and the pubic at 5 libraries and schools in the 2 cities, one of which serves a diverse, underserved community. Overall, the effort (supported by a pilot grant from the Bechtel Foundation) included school and library based teacher workshops with resource materials; travelling space museum visits with hands-on activities (Chabot-to-Go); separate powerpoint presentations for students and adults at the library; and concurrent ancillary space-related themes for young children's programs at the library. This pilot project, based largely on the use of free government resources and online materials, demonstrated that volunteer-based, standards-linked STEM efforts can enhance curriculum at the middle school, with libraries serving a special role. Using this model, we subsequently also obtained a small NASA-Space Grant award to bring star parties and hand-on science activities to three libraries this Fall, linking with numerous Grade 5 teachers and students in two additional underserved areas of our county. It's not necessary to reinvent the wheel, you just collect the pieces and build on what you already have.
Results of Formal Evaluation of a Data and Modeling Driven Hydrology Learning Module
NASA Astrophysics Data System (ADS)
Ruddell, B. L.; Sanchez, C. A.; Schiesser, R.; Merwade, V.
2014-12-01
New hydrologists should not only develop a well-defined knowledgebase of basic hydrological concepts, but also synthesize this factual learning with more authentic 'real-world' knowledge gained from the interpretation and analysis of data from hydrological models (Merwade and Ruddell, 2012, Wagener et al., 2007). However, hydrological instruction is often implemented using a traditional teacher-centered approach (e.g., lectures) (Wagener, 2007). The emergence of rich and dynamic computer simulation techniques which allow students the opportunity for more authentic application of knowledge (Merwade & Ruddell, 2012). This study evaluates the efficacy of using such data-driven simulations to increase the understanding of the field of hydrology in the lower-division undergraduate geoscience classroom. In this study, 88 students at a local community college who were enrolled in an Introductory Earth Science class were evaluated on their learning performance in a unit on applying the Rational Method to estimate hydrographs and flooding for urban areas. Students were either presented with a data and visualization rich computer module (n=52), or with paper and pencil calculation activities (n=36). All conceptual material presented in lecture was consistent across these two conditions. Students were evaluated for not only changes in their knowledge and application of the concepts within the unit (e.g., effects of urbanization and impervious cover, discharge rates), but also for their broad "T-shaped" profile of professional knowledge and skills. While results showed significant (p<.05) increases from pre to post assessments in all learning areas for both groups, there is a significantly larger benefit for the data module group when it came to (1) understanding the effects of urbanization and impervious cover on flooding, (2) applying consistent vocabulary appropriately within context, and (3) explaining the roles and responsibilities of hydrologists and flood managers.
Acceleration of the KINETICS Integrated Dynamical/Chemical Computational Model Using MPI
NASA Technical Reports Server (NTRS)
Grossman, Max; Willacy, Karen; Allen, Mark
2011-01-01
Understanding the evolution of a planet's atmosphere not only provides a better theoretical understanding of planetary physics and the formation of planets, but also grants useful insight into Earth's own atmosphere. One of the tools used at JPL for the modeling of planetary atmospheres and protostellar disks is KINETICS. KINETICS can simulate years of complex dynamics and chemistry.
A KINETIC MODEL FOR CELL DENSITY DEPENDENT BACTERIAL TRANSPORT IN POROUS MEDIA
A kinetic transport model with the ability to account for variations in cell density of the aqueous and solid phases was developed for bacteria in porous media. Sorption kinetics in the advective-dispersive-sorptive equation was described by assuming that adsorption was proportio...
NASA Astrophysics Data System (ADS)
Nikièma, Norbert
2011-12-01
This paper documents the new trend towards a first-language-first multilingual model in formal education in three former French colonies of West Africa, namely Burkina Faso, Mali and Niger. It compares the sociolinguistic situations, the conditions of the development of multilingual education and the achievements of mother-tongue-medium education in all three countries. The evidence is that, contrary to common discourse in francophonie, a strong first-language-first model in formal education is the best guarantee of a good mastery of French and, more generally, of quality education in francophone countries.
Mieussens, Luc
2013-11-15
The unified gas kinetic scheme (UGKS) of K. Xu et al. (2010) [37], originally developed for multiscale gas dynamics problems, is applied in this paper to a linear kinetic model of radiative transfer theory. While such problems exhibit purely diffusive behavior in the optically thick (or small Knudsen) regime, we prove that UGKS is still asymptotic preserving (AP) in this regime, but for the free transport regime as well. Moreover, this scheme is modified to include a time implicit discretization of the limit diffusion equation, and to correctly capture the solution in case of boundary layers. Contrary to many AP schemes, this method is based on a standard finite volume approach, it does neither use any decomposition of the solution, nor staggered grids. Several numerical tests demonstrate the properties of the scheme.
Moskvin, A. S.
2015-09-15
We discuss the most prominent and intensively studied S = 1 pseudospin formalism for the extended bosonic Hubbard model (EBHM) with the on-site Hilbert space truncated to the three lowest occupation states n = 0, 1, 2. The EBHM Hamiltonian is a paradigmatic model for the highly topical field of ultracold gases in optical lattices. The generalized non-Heisenberg effective pseudospin Hamiltonian does provide a deep link with a boson system and a physically clear description of “the myriad of phases,” from uniform Mott insulating phases and density waves to two types of superfluids and supersolids. We argue that the 2D pseudospin system is prone to a topological phase separation and focus on several types of unconventional skyrmion-like topological structures in 2D boson systems, which have not been analyzed until now. The structures are characterized by a complicated interplay of insulating and two superfluid phases with a single- boson and two-boson condensation, respectively.
Chemical kinetic modeling of propane oxidation behind shock waves
NASA Technical Reports Server (NTRS)
Mclain, A. G.; Jachimowski, C. J.
1977-01-01
The stoichiometric combustion of propane behind incident shock waves was studied experimentally and analytically over a temperature range from 1700 K to 2600 K and a pressure range from 1.2 to 1.9 atm. Measurements of the concentrations of carbon monoxide (CO) and carbon dioxide (CO2) and the product of the oxygen atom and carbon dioxide concentrations (O)(CO) were made after passage of the incident shock wave. A kinetic mechanism was developed which, when used in a computer program for a flowing, reacting gas behind an incident shock wave predicted experimentally measured results quite well. Ignition delay times from the literature were also predicted quite well. The kinetic mechanism consisted of 59 individual kinetic steps.
Chattoraj, Sayantan; Bhugra, Chandan; Li, Zheng Jane; Sun, Changquan Calvin
2014-12-01
The nonisothermal crystallization kinetics of amorphous materials is routinely analyzed by statistically fitting the crystallization data to kinetic models. In this work, we systematically evaluate how the model-dependent crystallization kinetics is impacted by variations in the heating rate and the selection of the kinetic model, two key factors that can lead to significant differences in the crystallization activation energy (Ea ) of an amorphous material. Using amorphous felodipine, we show that the Ea decreases with increase in the heating rate, irrespective of the kinetic model evaluated in this work. The model that best describes the crystallization phenomenon cannot be identified readily through the statistical fitting approach because several kinetic models yield comparable R(2) . Here, we propose an alternate paired model-fitting model-free (PMFMF) approach for identifying the most suitable kinetic model, where Ea obtained from model-dependent kinetics is compared with those obtained from model-free kinetics. The most suitable kinetic model is identified as the one that yields Ea values comparable with the model-free kinetics. Through this PMFMF approach, nucleation and growth is identified as the main mechanism that controls the crystallization kinetics of felodipine. Using this PMFMF approach, we further demonstrate that crystallization mechanism from amorphous phase varies with heating rate. PMID:25351553
Salloum, Maher N.; Gharagozloo, Patricia E.
2013-10-01
Metal particle beds have recently become a major technique for hydrogen storage. In order to extract hydrogen from such beds, it is crucial to understand the decomposition kinetics of the metal hydride. We are interested in obtaining a a better understanding of the uranium hydride (UH3) decomposition kinetics. We first developed an empirical model by fitting data compiled from different experimental studies in the literature and quantified the uncertainty resulting from the scattered data. We found that the decomposition time range predicted by the obtained kinetics was in a good agreement with published experimental results. Secondly, we developed a physics based mathematical model to simulate the rate of hydrogen diffusion in a hydride particle during the decomposition. We used this model to simulate the decomposition of the particles for temperatures ranging from 300K to 1000K while propagating parametric uncertainty and evaluated the kinetics from the results. We compared the kinetics parameters derived from the empirical and physics based models and found that the uncertainty in the kinetics predicted by the physics based model covers the scattered experimental data. Finally, we used the physics-based kinetics parameters to simulate the effects of boundary resistances and powder morphological changes during decomposition in a continuum level model. We found that the species change within the bed occurring during the decomposition accelerates the hydrogen flow by increasing the bed permeability, while the pressure buildup and the thermal barrier forming at the wall significantly impede the hydrogen extraction.
Evaluation of kinetic uncertainty in numerical models of petroleum generation
Peters, K.E.; Walters, C.C.; Mankiewicz, P.J.
2006-01-01
Oil-prone marine petroleum source rocks contain type I or type II kerogen having Rock-Eval pyrolysis hydrogen indices greater than 600 or 300-600 mg hydrocarbon/g total organic carbon (HI, mg HC/g TOC), respectively. Samples from 29 marine source rocks worldwide that contain mainly type II kerogen (HI = 230-786 mg HC/g TOC) were subjected to open-system programmed pyrolysis to determine the activation energy distributions for petroleum generation. Assuming a burial heating rate of 1??C/m.y. for each measured activation energy distribution, the calculated average temperature for 50% fractional conversion of the kerogen in the samples to petroleum is approximately 136 ?? 7??C, but the range spans about 30??C (???121-151??C). Fifty-two outcrop samples of thermally immature Jurassic Oxford Clay Formation were collected from five locations in the United Kingdom to determine the variations of kinetic response for one source rock unit. The samples contain mainly type I or type II kerogens (HI = 230-774 mg HC/g TOC). At a heating rate of 1??C/m.y., the calculated temperatures for 50% fractional conversion of the Oxford Clay kerogens to petroleum differ by as much as 23??C (127-150??C). The data indicate that kerogen type, as defined by hydrogen index, is not systematically linked to kinetic response, and that default kinetics for the thermal decomposition of type I or type II kerogen can introduce unacceptable errors into numerical simulations. Furthermore, custom kinetics based on one or a few samples may be inadequate to account for variations in organofacies within a source rock. We propose three methods to evaluate the uncertainty contributed by kerogen kinetics to numerical simulations: (1) use the average kinetic distribution for multiple samples of source rock and the standard deviation for each activation energy in that distribution; (2) use source rock kinetics determined at several locations to describe different parts of the study area; and (3) use a weighted
Kinetic Potential Model of the Cloud-to-Drizzle Transition
NASA Astrophysics Data System (ADS)
McGraw, Robert; Liu, Yangang; Luke, Edward; Senum, Gunnar
2013-03-01
It has been nearly a decade since the kinetic potential theory of drizzle formation in warm clouds was introduced [McGraw and Liu, Phys. Rev. Letts. 90, 018501 (2003)], and much progress in understanding the cloud-drizzle transition, especially regarding the role of turbulence, has been achieved within its framework. This poster will begin with an introduction to the kinetic potential idea, working up to the method it provides for predicting drizzle threshold conditions and rates, and concludes with an analysis this year of DOE/ARM cloud parcel vertical velocity measurements - discussing their implications for assessing turbulence fluctuations in water vapor saturation ratio and cloud droplet size.
Bordon, Jure; Moskon, Miha; Zimic, Nikolaj; Mraz, Miha
2015-01-01
Quantitative modelling of biological systems has become an indispensable computational approach in the design of novel and analysis of existing biological systems. However, kinetic data that describe the system's dynamics need to be known in order to obtain relevant results with the conventional modelling techniques. These data are often hard or even impossible to obtain. Here, we present a quantitative fuzzy logic modelling approach that is able to cope with unknown kinetic data and thus produce relevant results even though kinetic data are incomplete or only vaguely defined. Moreover, the approach can be used in the combination with the existing state-of-the-art quantitative modelling techniques only in certain parts of the system, i.e., where kinetic data are missing. The case study of the approach proposed here is performed on the model of three-gene repressilator. PMID:26451831
Westbrook, C K; Pitz, W J; Curran, H J; Herbinet, O; Mehl, M
2009-03-30
n-Hexadecane and 2,2,4,4,6,8,8-heptamethylnonane represent the primary reference fuels for diesel that are used to determine cetane number, a measure of the ignition property of diesel fuel. With the development of chemical kinetics models for these two primary reference fuels for diesel, a new capability is now available to model diesel fuel ignition. Also, we have developed chemical kinetic models for a whole series of large n-alkanes and a large iso-alkane to represent these chemical classes in fuel surrogates for conventional and future fuels. Methyl decanoate and methyl stearate are large methyl esters that are closely related to biodiesel fuels, and kinetic models for these molecules have also been developed. These chemical kinetic models are used to predict the effect of the fuel molecule size and structure on ignition characteristics under conditions found in internal combustion engines.
NASA Astrophysics Data System (ADS)
Kotasidis, F. A.; Matthews, J. C.; Reader, A. J.; Angelis, G. I.; Zaidi, H.
2014-10-01
Parametric imaging in thoracic and abdominal PET can provide additional parameters more relevant to the pathophysiology of the system under study. However, dynamic data in the body are noisy due to the limiting counting statistics leading to suboptimal kinetic parameter estimates. Direct 4D image reconstruction algorithms can potentially improve kinetic parameter precision and accuracy in dynamic PET body imaging. However, construction of a common kinetic model is not always feasible and in contrast to post-reconstruction kinetic analysis, errors in poorly modelled regions may spatially propagate to regions which are well modelled. To reduce error propagation from erroneous model fits, we implement and evaluate a new approach to direct parameter estimation by incorporating a recently proposed kinetic modelling strategy within a direct 4D image reconstruction framework. The algorithm uses a secondary more general model to allow a less constrained model fit in regions where the kinetic model does not accurately describe the underlying kinetics. A portion of the residuals then is adaptively included back into the image whilst preserving the primary model characteristics in other well modelled regions using a penalty term that trades off the models. Using fully 4D simulations based on dynamic [15O]H2O datasets, we demonstrate reduction in propagation-related bias for all kinetic parameters. Under noisy conditions, reductions in bias due to propagation are obtained at the cost of increased noise, which in turn results in increased bias and variance of the kinetic parameters. This trade-off reflects the challenge of separating the residuals arising from poor kinetic modelling fits from the residuals arising purely from noise. Nonetheless, the overall root mean square error is reduced in most regions and parameters. Using the adaptive 4D image reconstruction improved model fits can be obtained in poorly modelled regions, leading to reduced errors potentially propagating
Kotasidis, F A; Matthews, J C; Reader, A J; Angelis, G I; Zaidi, H
2014-10-21
Parametric imaging in thoracic and abdominal PET can provide additional parameters more relevant to the pathophysiology of the system under study. However, dynamic data in the body are noisy due to the limiting counting statistics leading to suboptimal kinetic parameter estimates. Direct 4D image reconstruction algorithms can potentially improve kinetic parameter precision and accuracy in dynamic PET body imaging. However, construction of a common kinetic model is not always feasible and in contrast to post-reconstruction kinetic analysis, errors in poorly modelled regions may spatially propagate to regions which are well modelled. To reduce error propagation from erroneous model fits, we implement and evaluate a new approach to direct parameter estimation by incorporating a recently proposed kinetic modelling strategy within a direct 4D image reconstruction framework. The algorithm uses a secondary more general model to allow a less constrained model fit in regions where the kinetic model does not accurately describe the underlying kinetics. A portion of the residuals then is adaptively included back into the image whilst preserving the primary model characteristics in other well modelled regions using a penalty term that trades off the models. Using fully 4D simulations based on dynamic [(15)O]H2O datasets, we demonstrate reduction in propagation-related bias for all kinetic parameters. Under noisy conditions, reductions in bias due to propagation are obtained at the cost of increased noise, which in turn results in increased bias and variance of the kinetic parameters. This trade-off reflects the challenge of separating the residuals arising from poor kinetic modelling fits from the residuals arising purely from noise. Nonetheless, the overall root mean square error is reduced in most regions and parameters. Using the adaptive 4D image reconstruction improved model fits can be obtained in poorly modelled regions, leading to reduced errors potentially propagating
Growth Kinetics and Modeling of ZnO Nanoparticles
ERIC Educational Resources Information Center
Hale, Penny S.; Maddox, Leone M.; Shapter, Joe G.; Voelcker, Nico H.; Ford, Michael J.; Waclawik, Eric R.
2005-01-01
The technique for producing quantum-sized zinc oxide (ZnO) particles is much safer than a technique that used hydrogen sulfide gas to produce cadmium sulfide and zinc sulfide nanoparticles. A further advantage of this method is the ability to sample the solution over time and hence determine the growth kinetics.
Isotope exchange kinetics in metal hydrides I : TPLUG model.
Larson, Rich; James, Scott Carlton; Nilson, Robert H.
2011-05-01
A one-dimensional isobaric reactor model is used to simulate hydrogen isotope exchange processes taking place during flow through a powdered palladium bed. This simple model is designed to serve primarily as a platform for the initial development of detailed chemical mechanisms that can then be refined with the aid of more complex reactor descriptions. The one-dimensional model is based on the Sandia in-house code TPLUG, which solves a transient set of governing equations including an overall mass balance for the gas phase, material balances for all of the gas-phase and surface species, and an ideal gas equation of state. An energy equation can also be solved if thermodynamic properties for all of the species involved are known. The code is coupled with the Chemkin package to facilitate the incorporation of arbitrary multistep reaction mechanisms into the simulations. This capability is used here to test and optimize a basic mechanism describing the surface chemistry at or near the interface between the gas phase and a palladium particle. The mechanism includes reversible dissociative adsorptions of the three gas-phase species on the particle surface as well as atomic migrations between the surface and the bulk. The migration steps are more general than those used previously in that they do not require simultaneous movement of two atoms in opposite directions; this makes possible the creation and destruction of bulk vacancies and thus allows the model to account for variations in the bulk stoichiometry with isotopic composition. The optimization code APPSPACK is used to adjust the mass-action rate constants so as to achieve the best possible fit to a given set of experimental data, subject to a set of rigorous thermodynamic constraints. When data for nearly isothermal and isobaric deuterium-to-hydrogen (D {yields} H) and hydrogen-to-deuterium (H {yields} D) exchanges are fitted simultaneously, results for the former are excellent, while those for the latter show
Ghosh, Erina; Shmuylovich, Leonid; Kovacs, Sandor J
2009-01-01
The filling (diastolic) function of the human left ventricle is most commonly assessed by echocardiography, a non-invasive imaging modality. To quantify diastolic function (DF) empiric indices are obtained from the features (height, duration, area) of transmitral flow velocity contour, obtained by echocardiography. The parameterized diastolic filling (PDF) formalism is a kinematic model developed by Kovács et. al. which incorporates the suction pump attribute of the left ventricle and facilitates DF quantitation by analysis of echocardiographic transmitral flow velocity contours in terms of stiffness (k), relaxation (c) and load (x(0)). A complementary approach developed by Gharib et. al., uses fluid mechanics and characterizes DF in terms of vortex formation time (T*) derived from streamline features formed by the jet of blood aspirated into the ventricle. Both of these methods characterize DF using a causality-based approach. In this paper, we derive T*'s kinematic analogue T*(kinematic) in terms of k, c and x(0). A comparison between T*(kinematic) and T*(fluid) (mechanic) obtained from averaged transmitral velocity and mitral annulus diameter, is presented. We found that T* calculated by the two methods were comparable and T*(kinematic) correlated with the peak LV recoil driving force kx(0). PMID:19964049
Singh, Jasmeet; Ranganathan, Radha; Hajdu, Joseph
2009-01-01
Activity at micellar interfaces of bacterial phospholipase C from Bacillus cereus on phospholipids solubilized in micelles was investigated with the goal of elucidating the role of the interface microstructure and developing further an existing kinetic model. Enzyme kinetics and physicochemical characterization of model substrate aggregates were combined; thus enabling the interpretation of kinetics in the context of the interface. Substrates were diacylphosphatidylcholine of different acyl chain lengths in the form of mixed micelles with dodecyldimethylammoniopropanesulfonate. An early kinetic model, reformulated to reflect the interfacial nature of the kinetics, was applied to the kinetic data. A better method of data treatment is proposed, use of which makes the presence of microstructure effects quite transparent. Models for enzyme-micelle binding and enzyme-lipid binding are developed and expressions incorporating the microstructural properties are derived for the enzyme-micelle dissociation constant KS and the interface Michaelis-Menten constant, KM. Use of these expressions in the interface kinetic model brings excellent agreement between the kinetic data and the model. Numerical values for the thermodynamic and kinetic parameters are determined. Enzyme-lipid binding is found to be an activated process with an acyl chain length dependent free energy of activation that decreases with micelle lipid molar fraction with a coefficient of about −15 RT and correlates with the tightness of molecular packing in the substrate aggregate. Thus the physical insight obtained includes a model for the kinetic parameters that shows that these parameters depend on the substrate concentration and acyl chain length of the lipid. Enzyme-micelle binding is indicated to be hydrophobic and solvent mediated with a dissociation constant of 1.2 mM. PMID:19367944
Modelling rainfall kinetic energy: a novel approach to erosion prediction and management
NASA Astrophysics Data System (ADS)
Nissan, H.; Toumi, R.
2013-12-01
Soil erosion is already a major global problem. Climate change and the rising world population will exert growing pressure on our land to deliver food and stability. This study presents a new and innovative application of a cloud resolving model, for use in soil erosion prediction studies. Rainfall kinetic energy flux is an important variable in erosion prediction, but is generally parameterized from intensity due to measurement difficulties. Instead, we show that a cloud resolving model can be used to dynamically simulate the kinetic energy of rain from basic physics, using four commonly used microphysics schemes. Rainfall kinetic energy flux is modelled during an idealized supercell storm with the Weather Research and Forecasting model. Results are within the range of observations and also capture the observed variability in kinetic energy flux for a given rainfall intensity, where current methods fail. Large raindrops are shown to contribute disproportionately to total kinetic energy flux compared with their number, suggesting that several existing relations between terminal velocity and size of raindrops are poorly suited for kinetic energy modelling. Treatment of raindrop size is tested and compared between the schemes, and factors influencing the erosive potential of rainfall will also be discussed. This work demonstrates the potential for conducting erosion prediction studies using a regional climate model. The method presented here may be easily extended for use in a full regional climate model with a microphysics parameterization scheme. This paves the way for full climate, and climate change, simulations of rainfall erosivity on regional to global scales and may contribute towards the ultimate integration of an erosion prediction scheme into climate models to allow coupled interactions with the atmosphere. Reference: Geophys. Res. Lett., 40, doi:10.1002/grl.50622 Schematic showing raindrop number density, rain mass flux and kinetic energy flux as
Chemical kinetic modeling of H{sub 2} applications
Westbrook, C.K.; Marinov, N.; Pitz, W.J.; Curran, H.
1996-10-01
This project is intended to develop detailed and simplified kinetic reaction mechanisms for the combustion of practical systems fueled by hydrogen, and then to use those mechanisms to examine the performance, efficiency, pollutant emissions, and other characteristics of those systems. During the last year, a H2/NOx mechanism has been developed that gives much improved predictions of NOx emissions compared to experimental data. Preliminary chemical kinetic and equilibrium calculations have been performed in support of Br2-H2O experiments to be conducted at NREL. Hydrogen, hydrogen/methane and hydrogen/natural gas mixtures have been investigated in a knock-rating engine to assess their automotive knock characteristics. The authors are currently developing the simplified analog reaction mechanisms that are computationally simple, yet still reproduce many of the macroscopic features of flame propagation.
Experimental and Kinetic Modeling Study of 2-Methyl-2-Butene: Allylic Hydrocarbon Kinetics.
Westbrook, Charles K; Pitz, William J; Mehl, Marco; Glaude, Pierre-Alexandre; Herbinet, Olivier; Bax, Sarah; Battin-Leclerc, Frederique; Mathieu, Olivier; Petersen, Eric L; Bugler, John; Curran, Henry J
2015-07-16
Two experimental studies have been carried out on the oxidation of 2-methyl-2-butene, one measuring ignition delay times behind reflected shock waves in a stainless steel shock tube, and the other measuring fuel, intermediate, and product species mole fractions in a jet-stirred reactor (JSR). The shock tube ignition experiments were carried out at three different pressures, approximately 1.7, 11.2, and 31 atm, and at each pressure, fuel-lean (ϕ = 0.5), stoichiometric (ϕ = 1.0), and fuel-rich (ϕ = 2.0) mixtures were examined, with each fuel/oxygen mixture diluted in 99% Ar, for initial postshock temperatures between 1330 and 1730 K. The JSR experiments were performed at nearly atmospheric pressure (800 Torr), with stoichiometric fuel/oxygen mixtures with 0.01 mole fraction of 2M2B fuel, a residence time in the reactor of 1.5 s, and mole fractions of 36 different chemical species were measured over a temperature range from 600 to 1150 K. These JSR experiments represent the first such study reporting detailed species measurements for an unsaturated, branched hydrocarbon fuel larger than iso-butene. A detailed chemical kinetic reaction mechanism was developed to study the important reaction pathways in these experiments, with particular attention on the role played by allylic C-H bonds and allylic pentenyl radicals. The results show that, at high temperatures, this olefinic fuel reacts rapidly, similar to related alkane fuels, but the pronounced thermal stability of the allylic pentenyl species inhibits low temperature reactivity, so 2M2B does not produce "cool flames" or negative temperature coefficient behavior. The connections between olefin hydrocarbon fuels, resulting allylic fuel radicals, the resulting lack of low-temperature reactivity, and the gasoline engine concept of octane sensitivity are discussed. PMID:25822578
NASA Technical Reports Server (NTRS)
Brat, Guillaume P.; Martinie, Celia; Palanque, Philippe
2013-01-01
During early phases of the development of an interactive system, future system properties are identified (through interaction with end users in the brainstorming and prototyping phase of the application, or by other stakehold-ers) imposing requirements on the final system. They can be specific to the application under development or generic to all applications such as usability principles. Instances of specific properties include visibility of the aircraft altitude, speed… in the cockpit and the continuous possibility of disengaging the autopilot in whatever state the aircraft is. Instances of generic properties include availability of undo (for undoable functions) and availability of a progression bar for functions lasting more than four seconds. While behavioral models of interactive systems using formal description techniques provide complete and unambiguous descriptions of states and state changes, it does not provide explicit representation of the absence or presence of properties. Assessing that the system that has been built is the right system remains a challenge usually met through extensive use and acceptance tests. By the explicit representation of properties and the availability of tools to support checking these properties, it becomes possible to provide developers with means for systematic exploration of the behavioral models and assessment of the presence or absence of these properties. This paper proposes the synergistic use two tools for checking both generic and specific properties of interactive applications: Petshop and Java PathFinder. Petshop is dedicated to the description of interactive system behavior. Java PathFinder is dedicated to the runtime verification of Java applications and as an extension dedicated to User Interfaces. This approach is exemplified on a safety critical application in the area of interactive cockpits for large civil aircrafts.
Formal descriptions for formulation.
This, Hervé
2007-11-01
Two formalisms used to describe the physical microstructure and the organization of formulated products are given. The first, called "complex disperse systems formalism" (CDS formalism) is useful for the description of the physical nature of disperse matter. The second, called "non periodical organizational space formalism" (NPOS formalism) has the same operators as the CDS formalism, but different elements; it is useful to describe the arrangement of any objects in space. Both formalisms can be viewed as the same, applied to different orders of magnitude for spatial size. PMID:17875375
NASA Astrophysics Data System (ADS)
Vu, H. X.; Bezzerides, B.; Dubois, D. F.
1998-11-01
A fully kinetic, reduced-description particle-in-cell (RPIC) model is presented in which deviations from quasineutrality, electron and ion kinetic effects, and nonlinear interactions between low-frequency and high-frequency parametric instabilities are modeled correctly. The model is based on a reduced description where the electromagnetic field is represented by three separate temporal WKB envelopes in order to model low-frequency and high-frequency parametric instabilities. Because temporal WKB approximations are invoked, the simulation can be performed on the electron time scale instead of the time scale of the light waves. The electrons and ions are represented by discrete finite-size particles, permitting electron and ion kinetic effects to be modeled properly. The Poisson equation is utilized to ensure that space-charge effects are included. Although RPIC is fully three dimensional, it has been implemented in only two dimensions on a CRAY-T3D with 512 processors and on the Accelerated Strategic Computing Initiative (ASCI) parallel computer at Los Alamos National Laboratory, and the resulting simulation code has been named ASPEN. Given the current computers available to the authors, one and two dimensional simulations are feasible to, and have been, performed. Three dimensional simulations are much more expensive, and are not feasible at this time. However, with rapidly advancing computer technologies, three dimensional simulations may be feasible in the near future. We believe this code is the first PIC code capable of simulating the interaction between low-frequency and high-frequency parametric instabilites in multiple dimensions. Test simulations of stimulated Raman scattering (SRS), stimulated Brillouin scattering (SBS), and Langmuir decay instability (LDI), are presented.
NASA Astrophysics Data System (ADS)
Morin, José A.; Ibarra, Borja; Cao, Francisco J.
2016-05-01
Single-molecule manipulation experiments of molecular motors provide essential information about the rate and conformational changes of the steps of the reaction located along the manipulation coordinate. This information is not always sufficient to define a particular kinetic cycle. Recent single-molecule experiments with optical tweezers showed that the DNA unwinding activity of a Phi29 DNA polymerase mutant presents a complex pause behavior, which includes short and long pauses. Here we show that different kinetic models, considering different connections between the active and the pause states, can explain the experimental pause behavior. Both the two independent pause model and the two connected pause model are able to describe the pause behavior of a mutated Phi29 DNA polymerase observed in an optical tweezers single-molecule experiment. For the two independent pause model all parameters are fixed by the observed data, while for the more general two connected pause model there is a range of values of the parameters compatible with the observed data (which can be expressed in terms of two of the rates and their force dependencies). This general model includes models with indirect entry and exit to the long-pause state, and also models with cycling in both directions. Additionally, assuming that detailed balance is verified, which forbids cycling, this reduces the ranges of the values of the parameters (which can then be expressed in terms of one rate and its force dependency). The resulting model interpolates between the independent pause model and the indirect entry and exit to the long-pause state model
ERIC Educational Resources Information Center
Moe, Owen; Cornelius, Richard
1988-01-01
Conveys an appreciation of enzyme kinetic analysis by using a practical and intuitive approach. Discusses enzyme assays, kinetic models and rate laws, the kinetic constants (V, velocity, and Km, Michaels constant), evaluation of V and Km from experimental data, and enzyme inhibition. (CW)
Kinetic modelling and simulation of laccase catalyzed degradation of reactive textile dyes.
Cristóvão, Raquel O; Tavares, Ana P M; Ribeiro, Adriano S; Loureiro, José M; Boaventura, Rui A R; Macedo, Eugénia A
2008-07-01
A kinetic model based on Michaelis-Menten equation was developed to simulate the dye decolourisation of Reactive Black 5 (RB5), Reactive Blue 114 (RB114), Reactive Yellow 15 (RY15), Reactive Red 239 (RR239) and Reactive Red 180 (RR180) dyes by commercial laccase. The unusual kinetic behavior of some of these reactions suggests that the kinetic model must consider the activation of the laccase-mediator system. Several reactions at different concentrations of each dye were performed in batch reactors and time courses were obtained. A LSODE code to solve the differential equation obtained from the batch reactor was combined with an optimization Fortran program to obtain the theoretical time courses. The time courses obtained from the developed program were compared with the experimentally obtained ones to estimate the kinetic constants that minimized the difference between them. The close correlation between the predicted and the experimental results seems to support the reliability of the established models. PMID:17986393
Skwarchuk, Sheri-Lynn; Sowinski, Carla; LeFevre, Jo-Anne
2014-05-01
The purpose of this study was to propose and test a model of children's home numeracy experience based on Sénéchal and LeFevre's home literacy model (Child Development, 73 (2002) 445-460). Parents of 183 children starting kindergarten in the fall (median child age=58 months) completed an early home learning experiences questionnaire. Most of the children whose parents completed the questionnaire were recruited for numeracy and literacy testing 1 year later (along with 32 children from the inner city). Confirmatory factor analyses were used to reduce survey items, and hierarchical regression analyses were used to predict the relation among parents' attitudes, academic expectations for their children, reports of formal and informal numeracy, and literacy home practices on children's test scores. Parental reports of formal home numeracy practices (e.g., practicing simple sums) predicted children's symbolic number system knowledge, whereas reports of informal exposure to games with numerical content (measured indirectly through parents' knowledge of children's games) predicted children's non-symbolic arithmetic, as did numeracy attitudes (e.g., parents' enjoyment of numeracy). The home literacy results replicated past findings; parental reports of formal literacy practices (e.g., helping their children to read words) predicted children's word reading, whereas reports of informal experiences (i.e., frequency of shared reading measured indirectly through parents' storybook knowledge) predicted children's vocabulary. These findings support a multifaceted model of children's early numeracy environment, with different types of early home experiences (formal and informal) predicting different numeracy outcomes. PMID:24462995
Lin Feng Meyer, Christian
2009-04-15
A hydration kinetics model for Portland cement is formulated based on thermodynamics of multiphase porous media. The mechanism of cement hydration is discussed based on literature review. The model is then developed considering the effects of chemical composition and fineness of cement, water-cement ratio, curing temperature and applied pressure. The ultimate degree of hydration of Portland cement is also analyzed and a corresponding formula is established. The model is calibrated against the experimental data for eight different Portland cements. Simple relations between the model parameters and cement composition are obtained and used to predict hydration kinetics. The model is used to reproduce experimental results on hydration kinetics, adiabatic temperature rise, and chemical shrinkage of different cement pastes. The comparisons between the model reproductions and the different experimental results demonstrate the applicability of the proposed model, especially for cement hydration at elevated temperature and high pressure.
Solar Wind Modelling: MHD And Kinetic Treatments with Kappa Distributions for the Electrons
NASA Astrophysics Data System (ADS)
Moschou, S. P.; Pierrard, V.; Keppens, R.; Pomoell, J.
2015-12-01
We want to constrain a kinetic solar wind model with Kappa-distributed electrons using observation-driven magnetohydrodynamics (MHD) modelling and in-situ data.Solar wind modelling efforts are presented using MHD - based modelling as well as a kinetic approach. In the fluid approach, photospheric magnetograms serve as observational input in semi-empirical coronal models that are used for estimating the plasma characteristics up to a heliocentric distance of 0.1AU. From there on a full MHD model which computes the three-dimensional time-dependent evolution of the macroscopic variables of the solar wind up to the orbit of the Earth is recruited. In the kinetic approach, an exospheric kinetic solar wind model based on the assumption of Maxwell and Kappa velocity distributions functions for protons and electrons respectively is used to determine appropriate boundary conditions to obtain the best comparison with available observations at the Earth's orbit. This will provide insight on more physically detailed processes, such as coronal heating and solar wind acceleration, that naturally arise by inclusion of suprathermal electrons in the model. We are interested in the profile of the solar wind speed and density at 1 AU, in characterising the slow and fast source regions of the wind and in comparing the features of that with results of exospheric models in similar conditions. We start from similar boundary conditions at the exobase and propagate the solution up to 1AU to compare MHD and kinetic treatments with observations.
Burnham, A K
2006-05-17
Chemical kinetic modeling has been used for many years in process optimization, estimating real-time material performance, and lifetime prediction. Chemists have tended towards developing detailed mechanistic models, while engineers have tended towards global or lumped models. Many, if not most, applications use global models by necessity, since it is impractical or impossible to develop a rigorous mechanistic model. Model fitting acquired a bad name in the thermal analysis community after that community realized a decade after other disciplines that deriving kinetic parameters for an assumed model from a single heating rate produced unreliable and sometimes nonsensical results. In its place, advanced isoconversional methods (1), which have their roots in the Friedman (2) and Ozawa-Flynn-Wall (3) methods of the 1960s, have become increasingly popular. In fact, as pointed out by the ICTAC kinetics project in 2000 (4), valid kinetic parameters can be derived by both isoconversional and model fitting methods as long as a diverse set of thermal histories are used to derive the kinetic parameters. The current paper extends the understanding from that project to give a better appreciation of the strengths and weaknesses of isoconversional and model-fitting approaches. Examples are given from a variety of sources, including the former and current ICTAC round-robin exercises, data sets for materials of interest, and simulated data sets.
Validity of Various Approaches to Global Kinetic Modeling of Material Lifetimes
Burnham, A K; Dinh, L N
2006-09-11
Chemical kinetic modeling has been used for many years in process optimization, estimating real-time material performance, and lifetime prediction. Chemists have tended towards developing detailed mechanistic models, while engineers have tended towards global or lumped models. Many, if not most, applications use global models by necessity, since it is impractical or impossible to develop a rigorous mechanistic model. Model fitting acquired a bad connotation in the thermal analysis community after that community realized a decade after other disciplines that deriving kinetic parameters for an assumed model from a single heating rate produced unreliable and sometimes nonsensical results. In its place, advanced isoconversional methods, which have their roots in the Friedman and Ozawa-Flynn-Wall methods of the 1960s, have become increasingly popular. In fact, as pointed out by the ICTAC kinetics project in 2000, valid kinetic parameters can be derived by both isoconversional and model fitting methods as long as a diverse set of thermal histories are used to derive the kinetic parameters. The current paper extends the understanding from that project to give a better appreciation of the strengths and weaknesses of isoconversional and model-fitting approaches. Examples are given from a variety of data sets.
Matsui, Yoshihiko; Ando, Naoya; Yoshida, Tomoaki; Kurotobi, Ryuji; Matsushita, Taku; Ohno, Koichi
2011-02-01
The capacity to adsorb natural organic matter (NOM) and polystyrene sulfonates (PSSs) on small particle-size activated carbon (super-powdered activated carbon, SPAC) is higher than that on larger particle-size activated carbon (powdered-activated carbon, PAC). Increased adsorption capacity is likely attributable to the larger external surface area because the NOM and PSS molecules do not completely penetrate the adsorbent particle; they preferentially adsorb near the outer surface of the particle. In this study, we propose a new isotherm equation, the Shell Adsorption Model (SAM), to explain the higher adsorption capacity on smaller adsorbent particles and to describe quantitatively adsorption isotherms of activated carbons of different particle sizes: PAC and SPAC. The SAM was verified with the experimental data of PSS adsorption kinetics as well as equilibrium. SAM successfully characterized PSS adsorption isotherm data for SPACs and PAC simultaneously with the same model parameters. When SAM was incorporated into an adsorption kinetic model, kinetic decay curves for PSSs adsorbing onto activated carbons of different particle sizes could be simultaneously described with a single kinetics parameter value. On the other hand, when SAM was not incorporated into such an adsorption kinetic model and instead isotherms were described by the Freundlich model, the kinetic decay curves were not well described. The success of the SAM further supports the adsorption mechanism of PSSs preferentially adsorbing near the outer surface of activated carbon particles. PMID:21172719
Nonlinear evolution of the magnetized Kelvin-Helmholtz instability: From fluid to kinetic modeling
Henri, P.; Université de Nice Sophia Antipolis, CNRS, Observatoire de la Côte d'Azur, BP 4229 06304, Nice Cedex 4 ; Cerri, S. S.; Max-Planck-Institut für Plasmaphysik, EURATOM Association, D-85748 Garching ; Califano, F.; Pegoraro, F.; Rossi, C.; LPP-CNRS, Ecole Polytechnique, UPMC, Université Paris VI, Université Paris XI, route de Saclay, 91128 Palaiseau ; Faganello, M. [International Institute for Fusion Science Šebek, O. [Astronomical Institute and Institute of Atmospheric Physics, AS CR Bocni II Trávníček, P. M. [Space Sciences Laboratory, University of California Berkeley, 7 Gauss Way, Berkeley, California 94720, USA and Astronomical Institute and Institute of Atmospheric Physics, AS CR Bocni II Hellinger, P. [Astronomical Institute and Institute of Atmospheric Physics, AS CR Bocni II and others
2013-10-15
The nonlinear evolution of collisionless plasmas is typically a multi-scale process, where the energy is injected at large, fluid scales and dissipated at small, kinetic scales. Accurately modelling the global evolution requires to take into account the main micro-scale physical processes of interest. This is why comparison of different plasma models is today an imperative task aiming at understanding cross-scale processes in plasmas. We report here the first comparative study of the evolution of a magnetized shear flow, through a variety of different plasma models by using magnetohydrodynamic (MHD), Hall-MHD, two-fluid, hybrid kinetic, and full kinetic codes. Kinetic relaxation effects are discussed to emphasize the need for kinetic equilibriums to study the dynamics of collisionless plasmas in non trivial configurations. Discrepancies between models are studied both in the linear and in the nonlinear regime of the magnetized Kelvin-Helmholtz instability, to highlight the effects of small scale processes on the nonlinear evolution of collisionless plasmas. We illustrate how the evolution of a magnetized shear flow depends on the relative orientation of the fluid vorticity with respect to the magnetic field direction during the linear evolution when kinetic effects are taken into account. Even if we found that small scale processes differ between the different models, we show that the feedback from small, kinetic scales to large, fluid scales is negligible in the nonlinear regime. This study shows that the kinetic modeling validates the use of a fluid approach at large scales, which encourages the development and use of fluid codes to study the nonlinear evolution of magnetized fluid flows, even in the collisionless regime.
SU-E-T-05: A 2D EPID Transit Dosimetry Model Based On An Empirical Quadratic Formalism
Tan, Y; Metwaly, M; Glegg, M; Baggarley, S; Elliott, A
2014-06-01
Purpose: To describe a 2D electronic portal imaging device (EPID) transit dosimetry model, based on an empirical quadratic formalism, that can predict either EPID or in-phantom dose distribution for comparisons with EPID captured image or treatment planning system (TPS) dose respectively. Methods: A quadratic equation can be used to relate the reduction in intensity of an exit beam to the equivalent path length of the attenuator. The calibration involved deriving coefficients from a set of dose planes measured for homogeneous phantoms with known thicknesses under reference conditions. In this study, calibration dose planes were measured with EPID and ionisation chamber (IC) in water for the same reference beam (6MV, 100mu, 20×20cm{sup 2}) and set of thicknesses (0–30cm). Since the same calibration conditions were used, the EPID and IC measurements can be related through the quadratic equation. Consequently, EPID transit dose can be predicted from TPS exported dose planes and in-phantom dose can be predicted using EPID distribution captured during treatment as an input. The model was tested with 4 open fields, 6 wedge fields, and 7 IMRT fields on homogeneous and heterogeneous phantoms. Comparisons were done using 2D absolute gamma (3%/3mm) and results were validated against measurements with a commercial 2D array device. Results: The gamma pass rates for comparisons between EPID measured and predicted ranged from 93.6% to 100.0% for all fields and phantoms tested. Results from this study agreed with 2D array measurements to within 3.1%. Meanwhile, comparisons in-phantom between TPS computed and predicted ranged from 91.6% to 100.0%. Validation with 2D array device was not possible for inphantom comparisons. Conclusion: A 2D EPID transit dosimetry model for treatment verification was described and proven to be accurate. The model has the advantage of being generic and allows comparisons at the EPID plane as well as multiple planes in-phantom.
Feisther, Vódice Amoroz; Ulson de Souza, Antônio Augusto; Trigueros, Daniela Estelita Goes; de Mello, Josiane Maria Muneronde; de Oliveira, Déborade; Guelli Ulson de Souza, Selene M A
2015-07-01
The biodegradation kinetics of BTX compounds (benzene, toluene, and xylene) individually and as mixtures was studied using models with different levels of sophistication. To compare the performance of the unstructured models applied in this work we used experimental data obtained here and some results published in the literature. The system description was based on the material balances of key components for batch operations, where the Monod and Andrews models were applied to predict the biodegradation of individual substrates. To simulate the biodegradation kinetics of substrate mixtures, models of substrate inhibition were applied along with the Sum Kinetics with Interaction Parameters (SKIP) models, where for two-component association toluene-xylene SKIP model presented better performance and for tri-component association benzene-toluene-xylene, the uncompetitive inhibition model was better. The kinetic parameters were estimated via a global search method known as Particle Swarm Optimization (PSO). The main result of this study is that the sophisticated biodegradation kinetics of BTX mixtures can be successfully described by applying the SKIP model, with the main advantage being the consideration of the substrate interactions. PMID:25627469
Kinetic model of product distribution over Fe catalyst for Fischer-Tropsch synthesis
Rongle Zhang; Jie Chang; Yuanyuan Xu; Liren Cao; Yongwang Li; Jinglai Zhou
2009-09-15
A new kinetic model of the Fischer-Tropsch synthesis (FTS) is proposed to describe the non-Anderson-Schulz-Flory (ASF) product distribution. The model is based on the double-polymerization monomers hypothesis, in which the surface C{sub 2}{asterisk} species acts as a chain-growth monomer in the light-product range, while C{sub 1}{asterisk} species acts as a chain-growth monomer in the heavy-product range. The detailed kinetic model in the Langmuir-Hinshelwood-Hougen-Watson type based on the elementary reactions is derived for FTS and the water-gas-shift reaction. Kinetic model candidates are evaluated by minimization of multiresponse objective functions with a genetic algorithm approach. The model of hydrocarbon product distribution is consistent with experimental data (
Novel Kinetic Theory of the Classical Isotropic Oscillator Gas, the Flexible Shell Model
NASA Astrophysics Data System (ADS)
Schruben, Dale
2013-12-01
Ever since Chapman and Enskog first used the hard sphere model to evaluate the collision integral in the Boltzmann equation, more sophisticated models for molecular encounters have been sought. Rotation of molecules in kinetic theory has been pursued with a number of models, such as the spherocylinder or loaded sphere, to account for that aspect. As these efforts continued, more workers started to incorporate quantum mechanics methods in pursuit of solutions to the Boltzmann equation. Progress there with both rotational and vibrational features of molecules has been attained. Until now though, there has been no classical vibration model for molecules in kinetic theory. Far from standard kinetic theory, here a simple classical mechanics isotropic oscillator is combined, through a flexible shell, with the hard sphere model in a full Chapman Enskog procedure. The intent here has been to introduce the model, so items like translational-vibrational coupling have not been included. Still, the results compliment literature.
Systematic construction of kinetic models from genome-scale metabolic networks.
Stanford, Natalie J; Lubitz, Timo; Smallbone, Kieran; Klipp, Edda; Mendes, Pedro; Liebermeister, Wolfram
2013-01-01
The quantitative effects of environmental and genetic perturbations on metabolism can be studied in silico using kinetic models. We present a strategy for large-scale model construction based on a logical layering of data such as reaction fluxes, metabolite concentrations, and kinetic constants. The resulting models contain realistic standard rate laws and plausible parameters, adhere to the laws of thermodynamics, and reproduce a predefined steady state. These features have not been simultaneously achieved by previous workflows. We demonstrate the advantages and limitations of the workflow by translating the yeast consensus metabolic network into a kinetic model. Despite crudely selected data, the model shows realistic control behaviour, a stable dynamic, and realistic response to perturbations in extracellular glucose concentrations. The paper concludes by outlining how new data can continuously be fed into the workflow and how iterative model building can assist in directing experiments. PMID:24324546
First Results of PIC Modeling of Kinetic Alfven Wave Dissipation
NASA Technical Reports Server (NTRS)
Chulaki, Anna; Hesse, Michael; Zenitani, Seiji
2007-01-01
We present first results of an investigation of the kinetic damping of Alfven wave turbulence. The methodology is based on a fully electromagnetic, three-dimensional, particle in cell code. The calculation is initialized by an Alfven wave spectrum. Subsequently, a cascade develops, and damping by coupling to both ions and electrons is observed. We discuss results of these calculations, and present first estimates of damping rates and of the effects of energy transfer on ion and electron distributions. The results pertain to solar wind heating and acceleration.
Group-kinetic theory and modeling of atmospheric turbulence
NASA Technical Reports Server (NTRS)
Tchen, C. M.
1989-01-01
A group kinetic method is developed for analyzing eddy transport properties and relaxation to equilibrium. The purpose is to derive the spectral structure of turbulence in incompressible and compressible media. Of particular interest are: direct and inverse cascade, boundary layer turbulence, Rossby wave turbulence, two phase turbulence; compressible turbulence, and soliton turbulence. Soliton turbulence can be found in large scale turbulence, turbulence connected with surface gravity waves and nonlinear propagation of acoustical and optical waves. By letting the pressure gradient represent the elementary interaction among fluid elements and by raising the Navier-Stokes equation to higher dimensionality, the master equation was obtained for the description of the microdynamical state of turbulence.
ENZO: A Web Tool for Derivation and Evaluation of Kinetic Models of Enzyme Catalyzed Reactions
Bevc, Staš; Konc, Janez; Stojan, Jure; Hodošček, Milan; Penca, Matej; Praprotnik, Matej; Janežič, Dušanka
2011-01-01
We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions. ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme. These differential equations are processed by a numerical solver and a regression algorithm which fits the coefficients of differential equations to experimentally observed time course curves. ENZO allows rapid evaluation of rival reaction schemes and can be used for routine tests in enzyme kinetics. It is freely available as a web tool, at http://enzo.cmm.ki.si. PMID:21818304
Kinetics of the iron α -ɛ phase transition at high-strain rates: Experiment and model
NASA Astrophysics Data System (ADS)
Amadou, N.; de Resseguier, T.; Brambrink, E.; Vinci, T.; Benuzzi-Mounaix, A.; Huser, G.; Morard, G.; Guyot, F.; Miyanishi, K.; Ozaki, N.; Kodama, R.; Koenig, M.
2016-06-01
In this article, we investigate the kinetics of the iron α -ɛ transition under laser-driven ramp compression for deformation rates ranging from 3 to 9 ×107s-1 . As in previous work, we observe a plateau in the rear surface velocity profile at the transition. With increasing deformation rate the transition onset pressure raises from 11 to 25 GPa, while the plateau duration decreases. These kinetic effects are well reproduced by an Avrami-type kinetics model of nucleation and growth with a constant, nanosecond scale completion time, which suggests an isokinetic regime over the explored range of strain rates.
Autoignition chemistry of the hexane isomers: An experimental and kinetic modeling study
Curran, H.J.; Gaffuri, P.; Pitz, W.J.; Westbrook, C.K.; Leppard, W.R.
1995-06-01
Autoignition of the five distinct isomers of hexane is studied experimentally under motored engine conditions and computationally using a detailed chemical kinetic reaction mechanism. Computed and experimental results are compared and used to help understand the chemical factors leading to engine knock in spark-ignited engines and the molecular structure factors contributing to octane rating for hydrocarbon fuels. The kinetic model reproduces observed variations in critical compression ratio with fuel structure, and it also provides intermediate and final product species concentrations in very dose agreement with observed results. In addition, the computed results provide insights into the kinetic origins of fuel octane sensitive.
Modeling capsid kinetics assembly from the steady state distribution of multi-sizes aggregates
NASA Astrophysics Data System (ADS)
Hozé, Nathanaël; Holcman, David
2014-01-01
The kinetics of aggregation for particles of various sizes depends on their diffusive arrival and fusion at a specific nucleation site. We present here a mean-field approximation and a stochastic jump model for aggregates at equilibrium. This approach is an alternative to the classical Smoluchowski equations that do not have a close form and are not solvable in general. We analyze these mean-field equations and obtain the kinetics of a cluster formation. Our approach provides a simplified theoretical framework to study the kinetics of viral capsid formation, such as HIV from the self-assembly of the structural proteins Gag.
A Model for the Interfacial Kinetics of Phospholipase D Activity on Long-Chain Lipids
Majd, Sheereen; Yusko, Erik C.; Yang, Jerry; Sept, David; Mayer, Michael
2013-01-01
The membrane-active enzyme phospholipase D (PLD) catalyzes the hydrolysis of the phosphodiester bond in phospholipids and plays a critical role in cell signaling. This catalytic reaction proceeds on lipid-water interfaces and is an example of heterogeneous catalysis in biology. Recently we showed that planar lipid bilayers, a previously unexplored model membrane for these kinetic studies, can be used for monitoring interfacial catalytic reactions under well-defined experimental conditions with chemical and electrical access to both sides of the lipid membrane. Employing an assay that relies on the conductance of the pore-forming peptide gramicidin A to monitor PLD activity, the work presented here reveals the kinetics of hydrolysis of long-chain phosphatidylcholine lipids in situ. We have developed an extension of a basic kinetic model for interfacial catalysis that includes product activation and substrate depletion. This model describes the kinetic behavior very well and reveals two kinetic parameters, the specificity constant and the interfacial quality constant. This approach results in a simple and general model to account for product accumulation in interfacial enzyme kinetics. PMID:23823233
NASA Astrophysics Data System (ADS)
Isenberg, P. A.; Vasquez, B. J.
2015-12-01
We have constructed a kinetic model of coronal hole protons heated in the directions perpendicular to the magnetic field according to the turbulent stochastic heating mechanism of Chandran et al. The kinetic heating is modeled by a proton diffusion in v_perp. The protons additionally respond to the coronal hole forces of gravity, charge-separation electric field, and the mirror force as described in our previous kinetic guiding-center models. We have further extended this kinetic model to include wave growth and damping by the anisotropic protons through the quasilinear cyclotron-resonant interaction. We solve the coupled equations for the kinetic proton behavior and for the self-consistent development of ion-cyclotron wave spectra propagating within 60˚ of the magnetic field direction. We seek to obtain a steady-state solution, showing the evolution of the proton distribution and the wave spectra with increasing heliocentric radial position due to the combined effects of heating, resonant scattering coupled to the wave generation, and the kinetic response to the large-scale forces of the inhomogeneous coronal hole. We will report on our results and the implications for the measurements to be made by the Solar Probe Plus mission.
An experimental and kinetic modeling study of n-propanol and iso-propanol combustion
Frassoldati, Alessio; Cuoci, Alberto; Faravelli, Tiziano; Ranzi, Eliseo; Niemann, Ulrich; Seiser, Reinhard; Seshadri, Kalyanasundaram
2010-01-15
A kinetic model is developed to describe combustion of n-propanol and iso-propanol. It is validated by comparing predictions made using this kinetic model with new experimental data on structures of counterflow non-premixed flames and previously reported data over a wide range of configurations and conditions. The elementary pyrolysis reactions of methanol and ethanol are well-known and were used as a starting point for extension to propanol. A detailed description leading to evaluation of rate constants for initiation reactions, metathesis reactions, decomposition reactions, and four-center molecular dehydration reactions are given. Decomposition and oxidation of primary intermediate products are described using a previously developed semi-detailed kinetic model for hydrocarbon fuels. The kinetic mechanism is made up of more than 7000 reactions among 300 species. The structures of counterflow non-premixed flames were measured by removing gas samples from the flame and analyzing the samples using a gas chromatograph. The flame structures were measured under similar conditions for both fuels to elucidate the similarities and differences in combustion characteristics of the two isomers. The profiles measured include those of formaldehyde, acetaldehyde, propanal, and acetone. These species are considered to be pollutants. Validation of the kinetic model was first performed by comparing predictions with experimental data reported in the literature obtained in flow reactors and shock tubes. In these configurations, combustion is not influenced by molecular transport. The agreement between the kinetic model and experimental data was satisfactory. The predictions of the kinetic model were then compared with new and previously reported experimental data on structures of counterflow non-premixed flames of both isomers. The agreement between the kinetic model and experimental data was again satisfactory. Satisfactory agreement was also obtained when the predictions of the
MODELING OF SIMULATED PHOTOCHEMICAL SMOG WITH KINETIC MECHANISMS. VOLUME 1. INTERIM REPORT
Computer modeling of smog chamber data is discussed in three parts. First, a series of detailed chemical mechanisms were developed to describe the photochemical formation of ozone from nitrogen oxides and the following organic compounds (alone and in various combinations): formal...
MODELING OF SIMULATED PHOTOCHEMICAL SMOG WITH KINETIC MECHANISMS. VOLUME 2. INTERIM REPORT APPENDIX
Computer modeling of smog chamber data is discussed in three parts. First, a series of detailed chemical mechanisms were developed to describe the photochemical formation of ozone from nitrogen oxides and the following organic compounds (alone and in various combinations): formal...
NASA Astrophysics Data System (ADS)
Yano, Ryosuke; Matsumoto, Jun; Suzuki, Kojiro
2011-06-01
Thermally relativistic flow with dissipation was analyzed by solving the rarefied supersonic flow of thermally relativistic matter around a triangle prism by Yano and Suzuki [Phys. Rev. DPRVDAQ1550-7998 83, 023517 (2011)10.1103/PhysRevD.83.023517], where the Anderson-Witting (AW) model was used as a solver. In this paper, we solve the same problem, which was analyzed by Yano and Suzuki, using the relativistic Boltzmann equation (RBE). To solve the RBE, the conventional direct simulation Monte Carlo method for the nonrelativistic Boltzmann equation is extended to a new direct simulation Monte Carlo method for the RBE. Additionally, we solve the modified Marle (MM) model proposed by Yano-Suzuki-Kuroda for comparisons. The solution of the thermally relativistic shock layer around the triangle prism obtained using the relativistic Boltzmann equation is considered by focusing on profiles of macroscopic quantities, such as the density, velocity, temperature, heat flux and dynamic pressure along the stagnation streamline (SSL). Differences among profiles of the number density, velocity and temperature along the SSL obtained using the RBE, the AW and MM. models are described in the framework of the relativistic Navier-Stokes-Fourier law. Finally, distribution functions on the SSL obtained using the RBE are compared with those obtained using the AW and MM models. The distribution function inside the shock wave obtained using the RBE does not indicate a bimodal form, which is obtained using the AW and MM models, but a smooth deceleration of thermally relativistic matter inside a shock wave.
Gering, Kevin L.
2013-01-01
A system includes an electrochemical cell, monitoring hardware, and a computing system. The monitoring hardware samples performance characteristics of the electrochemical cell. The computing system determines cell information from the performance characteristics. The computing system also analyzes the cell information of the electrochemical cell with a Butler-Volmer (BV) expression modified to determine exchange current density of the electrochemical cell by including kinetic performance information related to pulse-time dependence, electrode surface availability, or a combination thereof. A set of sigmoid-based expressions may be included with the modified-BV expression to determine kinetic performance as a function of pulse time. The determined exchange current density may be used with the modified-BV expression, with or without the sigmoid expressions, to analyze other characteristics of the electrochemical cell. Model parameters can be defined in terms of cell aging, making the overall kinetics model amenable to predictive estimates of cell kinetic performance along the aging timeline.
Continuum Kinetic Modeling of the Tokamak Plasma Edge
NASA Astrophysics Data System (ADS)
Dorf, Mikhail
2015-11-01
The problem of edge plasma transport provides substantial challenges for analytical or numerical analysis due to (a) complex magnetic geometry including both open and closed magnetic field lines B, (b) steep radial gradients comparable to ion drift-orbit excursions, and (c) a variation in the collision mean-free path along B from long to short compared to the magnetic connection length. Here, the first 4D continuum drift-kinetic transport simulations that span the magnetic separatrix of a tokamak are presented, motivated in part by the success of continuum kinetic codes for core physics and in part by the potential for high accuracy. The calculations include fully-nonlinear Fokker-Plank collisions and electrostatic potential variations. The problem of intrinsic toroidal rotation driven by ion orbit loss is addressed in detail. The code, COGENT, developed by the Edge Simulation Laboratory collaboration, is distinguished by a fourth-order finite-volume discretization combined with mapped multiblock grid technology to handle the strong anisotropy of plasma transport and the complex magnetic X-point divertor geometry with high accuracy. Previously, successful performance of high-order algorithms has been demonstrated in a simpler closed magnetic-flux-surface geometry for the problems of neoclassical transport and collisionless relaxation of geodesic acoustic modes in a tokamak pedestal, including the effects of a strong radial electric field under H-mode conditions. Work performed for USDOE, at LLNL under contract DE-AC52-07NA27344.
Gardner, Shea Nicole
2007-10-23
A method and system for tailoring treatment regimens to individual patients with diseased cells exhibiting evolution of resistance to such treatments. A mathematical model is provided which models rates of population change of proliferating and quiescent diseased cells using cell kinetics and evolution of resistance of the diseased cells, and pharmacokinetic and pharmacodynamic models. Cell kinetic parameters are obtained from an individual patient and applied to the mathematical model to solve for a plurality of treatment regimens, each having a quantitative efficacy value associated therewith. A treatment regimen may then be selected from the plurlaity of treatment options based on the efficacy value.
Malaguerra, Flavio; Chambon, Julie C; Bjerg, Poul L; Scheutz, Charlotte; Binning, Philip J
2011-10-01
A fully kinetic biogeochemical model of sequential reductive dechlorination (SERD) occurring in conjunction with lactate and propionate fermentation, iron reduction, sulfate reduction, and methanogenesis was developed. Production and consumption of molecular hydrogen (H(2)) by microorganisms have been modeled using modified Michaelis-Menten kinetics and has been implemented in the geochemical code PHREEQC. The model have been calibrated using a Shuffled Complex Evolution Metropolis algorithm to observations of chlorinated solvents, organic acids, and H(2) concentrations in laboratory batch experiments of complete trichloroethene (TCE) degradation in natural sediments. Global sensitivity analysis was performed using the Morris method and Sobol sensitivity indices to identify the most influential model parameters. Results show that the sulfate concentration and fermentation kinetics are the most important factors influencing SERD. The sensitivity analysis also suggests that it is not possible to simplify the model description if all system behaviors are to be well described. PMID:21877704
NASA Astrophysics Data System (ADS)
Stökl, A.
2008-11-01
Context: In spite of all the advances in multi-dimensional hydrodynamics, investigations of stellar evolution and stellar pulsations still depend on one-dimensional computations. This paper devises an alternative to the mixing-length theory or turbulence models usually adopted in modelling convective transport in such studies. Aims: The present work attempts to develop a time-dependent description of convection, which reflects the essential physics of convection and that is only moderately dependent on numerical parameters and far less time consuming than existing multi-dimensional hydrodynamics computations. Methods: Assuming that the most extensive convective patterns generate the majority of convective transport, the convective velocity field is described using two parallel, radial columns to represent up- and downstream flows. Horizontal exchange, in the form of fluid flow and radiation, over their connecting interface couples the two columns and allows a simple circulating motion. The main parameters of this convective description have straightforward geometrical meanings, namely the diameter of the columns (corresponding to the size of the convective cells) and the ratio of the cross-section between up- and downdrafts. For this geometrical setup, the time-dependent solution of the equations of radiation hydrodynamics is computed from an implicit scheme that has the advantage of being unaffected by the Courant-Friedrichs-Lewy time-step limit. This implementation is part of the TAPIR-Code (short for The adaptive, implicit RHD-Code). Results: To demonstrate the approach, results for convection zones in Cepheids are presented. The convective energy transport and convective velocities agree with expectations for Cepheids and the scheme reproduces both the kinetic energy flux and convective overshoot. A study of the parameter influence shows that the type of solution derived for these stars is in fact fairly robust with respect to the constitutive numerical
ERIC Educational Resources Information Center
Brown, Eleanor J.
2015-01-01
This paper presents comparative case studies of non-formal development education by non-profit organisations in two European countries. The study aimed to explore the extent to which such activities provide opportunities for transformative learning. The research was qualitative and began with interviews with educators across 14 organisations in…
A model for lignin alteration - Part I: A kinetic reaction-network model
Payne, D.F.; Ortoleva, P.J.
2001-01-01
A new quantitative model is presented which simulates the maturation of lignin-derived sedimentary organic matter under geologic conditions. In this model, compositionally specific reactants evolve to specific intermediate and mobile products through balanced, nth order processes, by way of a network of sequential and parallel reactions. The chemical kinetic approach is based primarily on published observed structural transformations of naturally matured, lignin-derived, sedimentary organic matter. Assuming that Upper Cretaceous Williams Fork coal in the Piceance Basin is primarily lignin-derived, the model is calibrated for the Multi-Well Experiment(MWX) Site in this basin. This kind of approach may be applied to other selectively preserved chemical components of sedimentary organic matter. ?? 2001 Elsevier Science Ltd. All rights reserved.
Kumar, B Shiva; Venkateswarlu, Ch
2014-08-01
The complex nature of biological reactions in biofilm reactors often poses difficulties in analyzing such reactors experimentally. Mathematical models could be very useful for their design and analysis. However, application of biofilm reactor models to practical problems proves somewhat ineffective due to the lack of knowledge of accurate kinetic models and uncertainty in model parameters. In this work, we propose an inverse modeling approach based on tabu search (TS) to estimate the parameters of kinetic and film thickness models. TS is used to estimate these parameters as a consequence of the validation of the mathematical models of the process with the aid of measured data obtained from an experimental fixed-bed anaerobic biofilm reactor involving the treatment of pharmaceutical industry wastewater. The results evaluated for different modeling configurations of varying degrees of complexity illustrate the effectiveness of TS for accurate estimation of kinetic and film thickness model parameters of the biofilm process. The results show that the two-dimensional mathematical model with Edward kinetics (with its optimum parameters as mu(max)rho(s)/Y = 24.57, Ks = 1.352 and Ki = 102.36) and three-parameter film thickness expression (with its estimated parameters as a = 0.289 x 10(-5), b = 1.55 x 10(-4) and c = 15.2 x 10(-6)) better describes the biofilm reactor treating the industry wastewater. PMID:25306783
Formally verifying Ada programs which use real number types
NASA Technical Reports Server (NTRS)
Sutherland, David
1986-01-01
Formal verification is applied to programs which use real number arithmetic operations (mathematical programs). Formal verification of a program P consists of creating a mathematical model of F, stating the desired properties of P in a formal logical language, and proving that the mathematical model has the desired properties using a formal proof calculus. The development and verification of the mathematical model are discussed.
A dynamic void growth model governed by dislocation kinetics
NASA Astrophysics Data System (ADS)
Wilkerson, J. W.; Ramesh, K. T.
2014-10-01
Here we examine the role of dislocation kinetics and substructure evolution on the dynamic growth of voids under very high strain rates, and develop a methodology for accounting for these effects in a computationally efficient manner. In particular, we account for the combined effects of relativistic dislocation drag and an evolving mobile dislocation density on the dynamics of void growth. We compare these effects to the constraints imposed by micro-inertia and discuss the conditions under which each mechanism governs the rate of void growth. The consequences of these constraints may be seen in a number of experimental observations associated with dynamic tensile failure, including the extreme rate-sensitivity of spall strength observed in laser shock experiments, an apparent anomalous temperate dependence of spall strength, and some particular features of void size distributions on spall surfaces.
Explicit equilibria in a kinetic model of gambling
NASA Astrophysics Data System (ADS)
Bassetti, F.; Toscani, G.
2010-06-01
We introduce and discuss a nonlinear kinetic equation of Boltzmann type which describes the evolution of wealth in a pure gambling process, where the entire sum of wealths of two agents is up for gambling, and randomly shared between the agents. For this equation the analytical form of the steady states is found for various realizations of the random fraction of the sum which is shared to the agents. Among others, the exponential distribution appears as steady state in case of a uniformly distributed random fraction, while Gamma distribution appears for a random fraction which is Beta distributed. The case in which the gambling game is only conservative-in-the-mean is shown to lead to an explicit heavy tailed distribution.
Interdependence of Formal Reasoning
ERIC Educational Resources Information Center
Berzonsky, Michael D.; And Others
1975-01-01
Investigated the intercorrelations among tasks that appear to require Piagetian formal reasoning to determine whether formal reasoning is used selectively or all-pervasively. Subjects were 60 undergraduate females. (SDH)
Dynamic nuclear renography kinetic analysis: Four-compartment model for assessing kidney function
Raswan, T. R. Haryanto, F.
2014-09-30
Dynamic nuclear renography method produces TACs of kidneys and bladder. Multiple TACs data can be further analyzed to obtain the overview of urinary system's condition. Tracer kinetic analysis was performed using four-compartment models. The system's model consist of four irreversible compartment with four transport constants (k1, k2, k3 and k4). The mathematical expressions of tracer's distributions is fitted to experimental data (TACs) resulting in model constants. This transport constants represent the urinary system behavior, and later can be used for analyzing system's condition. Different intervals of kinetics parameter are clearly shown by abnormal system with respect to the normal one. Furthermore, the system with delayed uptake has 82% lower uptake parameters (k1 and k2) than normal one. Meanwhile, the system with prolonged clearance time has its kinetics parameters k3 or k4 lower than the others. This model is promising for quantitatively describe urinary system's function especially if supplied with more data.
Evaluation and modeling of thermal kinetic degradation for PVA doped PbS quantum dot
Mahmoud, Waleed E.; Al-Heniti, S.H.
2011-09-15
Highlights: {yields} Synthesis of PVA doped PbS quantum dots. {yields} Data fitting using integral and differential thermal kinetic models for calculating activation energy. {yields} Prediction of thermal degradation using iso-conversion model. -- Abstract: The kinetic analysis of the thermogravimetric curves for the thermal decomposition processes of PVA/PbS was performed. The samples were heated in nitrogen, with three different heating rates: 10, 20 and 30 {sup o}C min{sup -1}. Various forms of non-isothermal methods of analysis for determining the kinetic parameters were used. The differential and integral models were used to calculate the activation energies. Comparing with pure PVA, the results showed that the maximum activation energy of thermal degradation is achieved for PVA/PbS nanocomposite. Isoconversion model is used for predicting the thermal degradation acceleration. The results showed that the acceleration of thermal degradation for pure PVA was faster than PVA/PbS nanocomposite.
Fokker–Planck kinetic modeling of suprathermal α-particles in a fusion plasma
Peigney, B.E.
2014-12-01
We present an ion kinetic model describing the transport of suprathermal α-particles in inertial fusion targets. The analysis of the underlying physical model enables us to develop efficient numerical methods to simulate the creation, transport and collisional relaxation of fusion reaction products (α-particles) at a kinetic level. The model assumes spherical symmetry in configuration space and axial symmetry in velocity space around the mean flow velocity. A two-energy-scale approach leads to a self-consistent modeling of the coupling between suprathermal α-particles and the thermal bulk of the imploding plasma. This method provides an accurate numerical treatment of energy deposition and transport processes involving suprathermal particles. The numerical tools presented here are then validated against known analytical results. This enables us to investigate the potential role of ion kinetic effects on the physics of ignition and thermonuclear burn in inertial confinement fusion schemes.
A detailed kinetic model for the hydrothermal decomposition process of sewage sludge.
Yin, Fengjun; Chen, Hongzhen; Xu, Guihua; Wang, Guangwei; Xu, Yuanjian
2015-12-01
A detailed kinetic model for the hydrothermal decomposition (HTD) of sewage sludge was developed based on an explicit reaction scheme considering exact intermediates including protein, saccharide, NH4(+)-N and acetic acid. The parameters were estimated by a series of kinetic data at a temperature range of 180-300°C. This modeling framework is capable of revealing stoichiometric relationships between different components by determining the conversion coefficients and identifying the reaction behaviors by determining rate constants and activation energies. The modeling work shows that protein and saccharide are the primary intermediates in the initial stage of HTD resulting from the fast reduction of biomass. The oxidation processes of macromolecular products to acetic acid are highly dependent on reaction temperature and dramatically restrained when temperature is below 220°C. Overall, this detailed model is meaningful for process simulation and kinetic analysis. PMID:26409104
Dynamic nuclear renography kinetic analysis: Four-compartment model for assessing kidney function
NASA Astrophysics Data System (ADS)
Raswan, T. R.; Haryanto, F.
2014-09-01
Dynamic nuclear renography method produces TACs of kidneys and bladder. Multiple TACs data can be further analyzed to obtain the overview of urinary system's condition. Tracer kinetic analysis was performed using four-compartment models. The system's model consist of four irreversible compartment with four transport constants (k1, k2, k3 and k4). The mathematical expressions of tracer's distributions is fitted to experimental data (TACs) resulting in model constants. This transport constants represent the urinary system behavior, and later can be used for analyzing system's condition. Different intervals of kinetics parameter are clearly shown by abnormal system with respect to the normal one. Furthermore, the system with delayed uptake has 82% lower uptake parameters (k1 and k2) than normal one. Meanwhile, the system with prolonged clearance time has its kinetics parameters k3 or k4 lower than the others. This model is promising for quantitatively describe urinary system's function especially if supplied with more data.
Njikam, Eloh; Schiewer, Silke
2012-04-30
Citrus peel biosorbents are efficient in removing heavy metals from wastewater. Heavy metal recovery and sorbent regeneration are important for the financial competitiveness of biosorption with other processes. The desorbing agents HNO(3), NaNO(3), Ca(NO(3))(2), EDTA, S, S-EDDS, and Na-Citrate were studied at different concentrations to optimize cadmium elution from orange or grapefruit peels. In most cases, desorption was fast, being over 90% complete within 50 min. However sodium nitrate and 0.001 M nitric acid were less efficient. Several new models for desorption kinetics were developed. While zero-, first- and second-order kinetics are commonly applied for modeling adsorption kinetics, the present study adapts these models to describe desorption kinetics. The proposed models relate to the number of metal-filled binding sites as the rate-determining reactant concentration. A model based on first order kinetics with respect to the remaining metal bound performed best. Cd bound in subsequent adsorption after desorption was similar to the original amount bound for desorption by nitric acid, but considerably lower for calcium nitrate as the desorbent. While complexing agents were effective desorbents, their cost is higher than that of common mineral acids. Thus 0.01-0.1 M acids are the most promising desorbing agents for efficient sorbent regeneration. PMID:22342899
Comparison of the kinetics of different Markov models for ligand binding under varying conditions
Martini, Johannes W. R.; Habeck, Michael
2015-03-07
We recently derived a Markov model for macromolecular ligand binding dynamics from few physical assumptions and showed that its stationary distribution is the grand canonical ensemble [J. W. R. Martini, M. Habeck, and M. Schlather, J. Math. Chem. 52, 665 (2014)]. The transition probabilities of the proposed Markov process define a particular Glauber dynamics and have some similarity to the Metropolis-Hastings algorithm. Here, we illustrate that this model is the stochastic analog of (pseudo) rate equations and the corresponding system of differential equations. Moreover, it can be viewed as a limiting case of general stochastic simulations of chemical kinetics. Thus, the model links stochastic and deterministic approaches as well as kinetics and equilibrium described by the grand canonical ensemble. We demonstrate that the family of transition matrices of our model, parameterized by temperature and ligand activity, generates ligand binding kinetics that respond to changes in these parameters in a qualitatively similar way as experimentally observed kinetics. In contrast, neither the Metropolis-Hastings algorithm nor the Glauber heat bath reflects changes in the external conditions correctly. Both converge rapidly to the stationary distribution, which is advantageous when the major interest is in the equilibrium state, but fail to describe the kinetics of ligand binding realistically. To simulate cellular processes that involve the reversible stochastic binding of multiple factors, our pseudo rate equation model should therefore be preferred to the Metropolis-Hastings algorithm and the Glauber heat bath, if the stationary distribution is not of only interest.
Kinetic modelling of anaerobic hydrolysis of solid wastes, including disintegration processes
García-Gen, Santiago; Sousbie, Philippe; Rangaraj, Ganesh; Lema, Juan M.; Rodríguez, Jorge; Steyer, Jean-Philippe; Torrijos, Michel
2015-01-15
Highlights: • Fractionation of solid wastes into readily and slowly biodegradable fractions. • Kinetic coefficients estimation from mono-digestion batch assays. • Validation of kinetic coefficients with a co-digestion continuous experiment. • Simulation of batch and continuous experiments with an ADM1-based model. - Abstract: A methodology to estimate disintegration and hydrolysis kinetic parameters of solid wastes and validate an ADM1-based anaerobic co-digestion model is presented. Kinetic parameters of the model were calibrated from batch reactor experiments treating individually fruit and vegetable wastes (among other residues) following a new protocol for batch tests. In addition, decoupled disintegration kinetics for readily and slowly biodegradable fractions of solid wastes was considered. Calibrated parameters from batch assays of individual substrates were used to validate the model for a semi-continuous co-digestion operation treating simultaneously 5 fruit and vegetable wastes. The semi-continuous experiment was carried out in a lab-scale CSTR reactor for 15 weeks at organic loading rate ranging between 2.0 and 4.7 g VS/L d. The model (built in Matlab/Simulink) fit to a large extent the experimental results in both batch and semi-continuous mode and served as a powerful tool to simulate the digestion or co-digestion of solid wastes.
Comparison of the kinetics of different Markov models for ligand binding under varying conditions.
Martini, Johannes W R; Habeck, Michael
2015-03-01
We recently derived a Markov model for macromolecular ligand binding dynamics from few physical assumptions and showed that its stationary distribution is the grand canonical ensemble [J. W. R. Martini, M. Habeck, and M. Schlather, J. Math. Chem. 52, 665 (2014)]. The transition probabilities of the proposed Markov process define a particular Glauber dynamics and have some similarity to the Metropolis-Hastings algorithm. Here, we illustrate that this model is the stochastic analog of (pseudo) rate equations and the corresponding system of differential equations. Moreover, it can be viewed as a limiting case of general stochastic simulations of chemical kinetics. Thus, the model links stochastic and deterministic approaches as well as kinetics and equilibrium described by the grand canonical ensemble. We demonstrate that the family of transition matrices of our model, parameterized by temperature and ligand activity, generates ligand binding kinetics that respond to changes in these parameters in a qualitatively similar way as experimentally observed kinetics. In contrast, neither the Metropolis-Hastings algorithm nor the Glauber heat bath reflects changes in the external conditions correctly. Both converge rapidly to the stationary distribution, which is advantageous when the major interest is in the equilibrium state, but fail to describe the kinetics of ligand binding realistically. To simulate cellular processes that involve the reversible stochastic binding of multiple factors, our pseudo rate equation model should therefore be preferred to the Metropolis-Hastings algorithm and the Glauber heat bath, if the stationary distribution is not of only interest. PMID:25747058
Comparison of the kinetics of different Markov models for ligand binding under varying conditions
NASA Astrophysics Data System (ADS)
Martini, Johannes W. R.; Habeck, Michael
2015-03-01
We recently derived a Markov model for macromolecular ligand binding dynamics from few physical assumptions and showed that its stationary distribution is the grand canonical ensemble [J. W. R. Martini, M. Habeck, and M. Schlather, J. Math. Chem. 52, 665 (2014)]. The transition probabilities of the proposed Markov process define a particular Glauber dynamics and have some similarity to the Metropolis-Hastings algorithm. Here, we illustrate that this model is the stochastic analog of (pseudo) rate equations and the corresponding system of differential equations. Moreover, it can be viewed as a limiting case of general stochastic simulations of chemical kinetics. Thus, the model links stochastic and deterministic approaches as well as kinetics and equilibrium described by the grand canonical ensemble. We demonstrate that the family of transition matrices of our model, parameterized by temperature and ligand activity, generates ligand binding kinetics that respond to changes in these parameters in a qualitatively similar way as experimentally observed kinetics. In contrast, neither the Metropolis-Hastings algorithm nor the Glauber heat bath reflects changes in the external conditions correctly. Both converge rapidly to the stationary distribution, which is advantageous when the major interest is in the equilibrium state, but fail to describe the kinetics of ligand binding realistically. To simulate cellular processes that involve the reversible stochastic binding of multiple factors, our pseudo rate equation model should therefore be preferred to the Metropolis-Hastings algorithm and the Glauber heat bath, if the stationary distribution is not of only interest.
The LANL atomic kinetics modeling effort and its application to W plasmas
Colgan, James; Abdallah, Joseph; Fontes, Christopher; Zhang, Honglin
2010-12-10
This is the work of the LANL group on atomic kinetics modelling. There are various levels of detail in the LANL suite of atomic physics codes: (1) Non-relativistic configuration average kinetics (nl{sup w}) + UTA spectra, (2) Relativistic configuration average kinetics (nlj{sup w}) + UTA spectra, (3) Mixed UTA (MUTA) - configuration average kinetics and spectra composed of mixture of UTAs and fine-structure features and (4) Fine-structure levels. The LANL suite of atomic physics codes consists of 5 codes: (1) CATS/RATS atomic structure codes (semi-relativistic Cowan code or Dirac-Fock-Slater code), (2) ACE collisional excitation code (Plane-wave Born, Columb-Born and distorted-wave methods) and (3) GIPPER ionization code (scaled-hydrogenic and distorted-wave methods). An on-line version of the codes is available at http://aphysics2.lanl.gov/tempweb. ATOMIC kinetics modelling code uses the atomic data for LTE or NLTE population kinetics models and spectral modelling of a broad range of plasma applications. The mixed UTA (MUTA) approach was developed for the spectra of complex ions and the results are in very good agreement with the Sandia-Z Iron opacity experiments. The LANL configuration-average/MUTA calculations were applied to tungsten problems of the non-LTE kinetics code comparison workshops. The LANL group plans to perform much larger calculations to assess the accuracy of the older results and to investigate low-temperature tungsten processes relevant to the divertor modelling.
A phase-field model coupled with lattice kinetics solver for modeling crystal growth in furnaces
Lin, Guang; Bao, Jie; Xu, Zhijie; Tartakovsky, Alexandre M.; Henager, Charles H.
2014-02-02
In this study, we present a new numerical model for crystal growth in a vertical solidification system. This model takes into account the buoyancy induced convective flow and its effect on the crystal growth process. The evolution of the crystal growth interface is simulated using the phase-field method. Two novel phase-field models are developed to model the crystal growth interface in vertical gradient furnaces with two temperature profile setups: 1) fixed wall temperature profile setup and 2) time-dependent temperature profile setup. A semi-implicit lattice kinetics solver based on the Boltzmann equation is employed to model the unsteady incompressible flow. This model is used to investigate the effect of furnace operational conditions on crystal growth interface profiles and growth velocities. For a simple case of macroscopic radial growth, the phase-field model is validated against an analytical solution. Crystal growth in vertical gradient furnaces with two temperature profile setups have been also investigated using the developed model. The numerical simulations reveal that for a certain set of temperature boundary conditions, the heat transport in the melt near the phase interface is diffusion dominant and advection is suppressed.
Mathematical modelling of thermal and kinetic phenomena in electron-beam technologies
NASA Astrophysics Data System (ADS)
Knyazeva, A. G.; Pobol, I. L.; Demidov, V. N.
2016-07-01
The article presents a scheme for constructing models using kinetic laws for additional parameters. The work describes the example of the model of electro-beam treatment of a material with a coating. The study uses the simple kinetic law for powder layer evolution due to shrinkage. The model takes into account the melting of powder layer and substrate. The numerical solution gives the temperature field, evolution of the molten pool, the heat affected zone and the surface relief for different moments of time. The results depend on the treatment rate and electron beam energy.
A generalised enzyme kinetic model for predicting the behaviour of complex biochemical systems
Wong, Martin Kin Lok; Krycer, James Robert; Burchfield, James Geoffrey; James, David Ernest; Kuncic, Zdenka
2015-01-01
Quasi steady-state enzyme kinetic models are increasingly used in systems modelling. The Michaelis Menten model is popular due to its reduced parameter dimensionality, but its low-enzyme and irreversibility assumption may not always be valid in the in vivo context. Whilst the total quasi-steady state assumption (tQSSA) model eliminates the reactant stationary assumptions, its mathematical complexity is increased. Here, we propose the differential quasi-steady state approximation (dQSSA) kinetic model, which expresses the differential equations as a linear algebraic equation. It eliminates the reactant stationary assumptions of the Michaelis Menten model without increasing model dimensionality. The dQSSA was found to be easily adaptable for reversible enzyme kinetic systems with complex topologies and to predict behaviour consistent with mass action kinetics in silico. Additionally, the dQSSA was able to predict coenzyme inhibition in the reversible lactate dehydrogenase enzyme, which the Michaelis Menten model failed to do. Whilst the dQSSA does not account for the physical and thermodynamic interactions of all intermediate enzyme-substrate complex states, it is proposed to be suitable for modelling complex enzyme mediated biochemical systems. This is due to its simpler application, reduced parameter dimensionality and improved accuracy. PMID:25859426
Parameter Estimates in Differential Equation Models for Chemical Kinetics
ERIC Educational Resources Information Center
Winkel, Brian
2011-01-01
We discuss the need for devoting time in differential equations courses to modelling and the completion of the modelling process with efforts to estimate the parameters in the models using data. We estimate the parameters present in several differential equation models of chemical reactions of order n, where n = 0, 1, 2, and apply more general…
The Application of Global Kinetic Models to HMX Beta-Delta Transition and Cookoff Processes
Wemhoff, A P; Burnham, A K; Nichols III, A L
2006-12-07
The reduction of the number of reactions in kinetic models for both the HMX beta-delta phase transition and thermal cookoff provides an attractive alternative to traditional multi-stage kinetic models due to reduced calibration effort requirements. In this study, we use the LLNL code ALE3D to provide calibrated kinetic parameters for a two-reaction bidirectional beta-delta HMX phase transition model based on Sandia Instrumented Thermal Ignition (SITI) and Scaled Thermal Explosion (STEX) temperature history curves, and a Prout-Tompkins cookoff model based on One-Dimensional Time to Explosion (ODTX) data. Results show that the two-reaction bidirectional beta-delta transition model presented here agrees as well with STEX and SITI temperature history curves as a reversible four-reaction Arrhenius model, yet requires an order of magnitude less computational effort. In addition, a single-reaction Prout-Tompkins model calibrated to ODTX data provides better agreement with ODTX data than a traditional multi-step Arrhenius model, and can contain up to 90% less chemistry-limited time steps for low-temperature ODTX simulations. Manual calibration methods for the Prout-Tompkins kinetics provide much better agreement with ODTX experimental data than parameters derived from Differential Scanning Calorimetry (DSC) measurements at atmospheric pressure. The predicted surface temperature at explosion for STEX cookoff simulations is a weak function of the cookoff model used, and a reduction of up to 15% of chemistry-limited time steps can be achieved by neglecting the beta-delta transition for this type of simulation. Finally, the inclusion of the beta-delta transition model in the overall kinetics model can affect the predicted time to explosion by 1% for the traditional multi-step Arrhenius approach, while up to 11% using a Prout-Tompkins cookoff model.
A MATHEMATICAL MODEL FOR THE KINETICS OF THE MALE REPRODUCTIVE ENDOCRINE SYSTEM
In this presentation a model for the hormonal regulation of the reproductive endocrine system in the adult male rat will be discussed. The model includes a description of the kinetics of the androgenic hormones testosterone and dihydrotestosterone, as well as the receptor-mediate...
Equilibrium and kinetic models for colloid release under transient solution chemistry conditions
Technology Transfer Automated Retrieval System (TEKTRAN)
We present continuum models to describe colloid release in the subsurface during transient physicochemical conditions. Our modeling approach relates the amount of colloid release to changes in the fraction of the solid surface area that contributes to retention. Equilibrium, kinetic, equilibrium and...
A Multi Water Bag model of drift kinetic electron plasmaa
NASA Astrophysics Data System (ADS)
Morel, Pierre; Ghiro, Florent Dreydemy; Berionni, Vincent; Coulette, David; Besse, Nicolas; Gürcan, Özgür D.
2014-08-01
A Multi Water Bag model is proposed for describing drift kinetic plasmas in a magnetized cylindrical geometry, relevant for various experimental devices, solar wind modeling... The Multi Water Bag (MWB) model is adapted to the description of a plasma with kinetic electrons as well as an arbitrary number of kinetic ions. This allows to describe the kinetic dynamics of the electrons, making possible the study of electron temperature gradient (ETG) modes, in addition to the effects of non adiabatic electrons on the ion temperature gradient (ITG) modes, that are of prime importance in the magnetized plasmas micro-turbulence [X. Garbet, Y. Idomura, L. Villard, T.H. Watanabe, Nucl. Fusion 50, 043002 (2010); J.A. Krommes, Ann. Rev. Fluid Mech. 44, 175 (2012)]. The MWB model is shown to link kinetic and fluid descriptions, depending on the number of bags considered. Linear stability of the ETG modes is presented and compared to the existing results regarding cylindrical ITG modes [P. Morel, E. Gravier, N. Besse, R. Klein, A. Ghizzo, P. Bertrand, W. Garbet, Ph. Ghendrih, V. Grandgirard, Y. Sarazin, Phys. Plasmas 14, 112109 (2007)].
A new hybrid kinetic electron model for full-f gyrokinetic simulations
NASA Astrophysics Data System (ADS)
Idomura, Y.
2016-05-01
A new hybrid kinetic electron model is developed for electrostatic full-f gyrokinetic simulations of the ion temperature gradient driven trapped electron mode (ITG-TEM) turbulence at the ion scale. In the model, a full kinetic electron model is applied to the full-f gyrokinetic equation, the multi-species linear Fokker-Planck collision operator, and an axisymmetric part of the gyrokinetic Poisson equation, while in a non-axisymmetric part of the gyrokinetic Poisson equation, turbulent fluctuations are determined only by kinetic trapped electrons responses. By using this approach, the so-called ωH mode is avoided with keeping important physics such as the ITG-TEM, the neoclassical transport, the ambipolar condition, and particle trapping and detrapping processes. The model enables full-f gyrokinetic simulations of ITG-TEM turbulence with a reasonable computational cost. Comparisons between flux driven ITG turbulence simulations with kinetic and adiabatic electrons are presented. Although the similar ion temperature gradients with nonlinear upshift from linear critical gradients are sustained in quasi-steady states, parallel flows and radial electric fields are qualitatively different with kinetic electrons.
Analysis of the importance of sorption kinetics to PCB fate modeling
Connolly, J.; Dean, M.
1995-12-31
A considerable amount of literature exists describing the importance of slow kinetics and resistantly bound fractions to the sorption process for hydrophobic organics such as PCBs. The frequently observed deviations of field measured partition coefficients from the presumed relationship between the organic carbon normalized partition coefficient (K{sub oc}) and octanol-water partition coefficient (K{sub ow}) may be evidence of slow sorption kinetics. Of note are the observations in Green Bay and New Bedford Harbor of increases in PCB partition coefficients along a gradient from high concentration to low concentration. These changes in partitioning were evaluated by incorporating a kinetic model derived from experiments with Hudson River sediment into a model of PCB fate in lower Green Bay. The kinetic model successfully described the observed changes in PCB partition coefficient. The results of this work support the conclusion that sorption kinetics are important to the transport and fate of PCBs. An implication of these results is that the resistant fraction of the sorbed PCBs increases with time. This may result in a decrease in bioavailability that could be significant to the use of models to protect future concentrations and ecological or human health risk.
Whitten, G.Z.; Hogo, H.
1980-02-01
Mechanisms that describe the formation of photochemical smog are developed using a computer modeling technique directed toward the simulation of data collected in two smog chambers: an indoor chamber and a dual outdoor chamber. Individual compounds for which specific experiments were simulated and mechanisms developed include the following: formaldehyde, acetaldehyde, ethylene, propylene, butane, and toluene. Volume 2 contains the user's manual and coding for a chemical kinetics computer program, CHEMK.
Mean kinetic energy budget of wakes within an array of model wind turbines and porous discs
NASA Astrophysics Data System (ADS)
Cal, Raúl Bayoán; Camp, Elizabeth
2015-11-01
Wind turbines are often modeled as porous actuator discs within computational studies. In this wind tunnel study, stereo particle image velocimetry (SPIV) is used to characterize the wakes within a 4 ×3 model wind turbine array and an analogous array of porous disks. The SPIV measurements are performed upstream between - 2 . 9 <= x / D <= - 0 . 3 and downstream between 0 . 7 <= x / D <= 5 . 6 of the center turbine in the fourth row. To provide context, the similarities and differences in the flow fields as well as the mean and turbulent stresses are found. The primary analysis revolves around the mean kinetic energy budget in the wakes for both cases, model turbines and discs, obtained by the computation of mean kinetic energy, production of turbulence and flux of kinetic energy as these are equivalent to a measure of extracted power.
Evolution kinetics of interstitial loops in irradiated materials: a phase-field model
Hu, Shenyang Y.; Henager, Charles H.; Li, Yulan; Gao, Fei; Sun, Xin; Khaleel, Mohammad A.
2012-01-01
Interstitial loops are one of the principal evolving defects in irradiated materials. The evolution of interstitial loops, including spatial and size distributions, affects both vacancy and interstitial accumulations in the matrix, hence, void formation and volumetric swelling. In this work, a phase-field model to simulate the growth kinetics of interstitial loops in irradiated materials during aging is developed. The diffusion of vacancies and interstitials and the elastic interaction between interstitial loops and point defects are accounted in the model. The effects of interstitial concentration, chemical potential, and elastic interaction on the growth kinetics and stability of interstitial loops are investigated in two and three dimensions. It is found that the elastic interaction enhances the growth kinetics of interstitial loops. The elastic interaction also affects the stability of a small interstitial loop adjacent to a larger loop. The model predicts linear growth rates for interstitial loops that is in agreement with the previous theoretical predictions and experimental observations.
NASA Astrophysics Data System (ADS)
de-Santiago, Josue; Cervantes-Cota, Jorge L.
2011-03-01
We study a unification model for dark energy, dark matter, and inflation with a single scalar field with noncanonical kinetic term. In this model, the kinetic term of the Lagrangian accounts for the dark matter and dark energy, and at early epochs, a quadratic potential accounts for slow roll inflation. The present work is an extension to the work by Bose and Majumdar [Phys. Rev. DPRVDAQ1550-7998 79, 103517 (2009).10.1103/PhysRevD.79.103517] with a more general kinetic term that was proposed by Chimento in Phys. Rev. DPRVDAQ0556-2821 69, 123517 (2004).10.1103/PhysRevD.69.123517 We demonstrate that the model is viable at the background and linear perturbation levels.
Formal Methods at Intel - An Overview
NASA Technical Reports Server (NTRS)
Harrison, John
2010-01-01
Since the 1990s, Intel has invested heavily in formal methods, which are now deployed in several domains: hardware, software, firmware, protocols etc. Many different formal methods tools and techniques are in active use, including symbolic trajectory evaluation, temporal logic model checking, SMT-style combined decision procedures, and interactive higher-order logic theorem proving. I will try to give a broad overview of some of the formal methods activities taking place at Intel, and describe the challenges of extending formal verification to new areas and of effectively using multiple formal techniques in combination
Detailed and global chemical kinetics model for hydrogen
Marinov, N.M.; Westbrook, C.K.; Pitz, W.J.
1995-03-01
Detailed and global chemical kinetic computations for hydrogen-air mixtures have been performed to describe flame propagation, flame structure and ignition phenomena. Simulations of laminar flame speeds, flame compositions and shock tube ignition delay times have been successfully performed. Sensitivity analysis was applied to determine the governing rate-controlling reactions for the experimental data sets examined. In the flame propagation and structure studies, the reactions, OH + H{sub 2} = H{sub 2}0 + H, 0 + H{sub 2} = OH + H and 0 + OH = 0{sub 2} + H were the most important in flames. The shock tube ignition delay time study indicated the H + 0{sub 2} + M = H0{sub 2} + M (M = N{sub 2}, H{sub 2}) and 0 + OH = 0{sub 2} + H reactions controlled ignition. A global rate expression for a one-step overall reaction was developed and validated against experimental hydrogen-air laminar flame speed data. The global reaction expression was determined to be 1.8 {times} 10{sup 13} exp({minus}17614K/T)[H{sub 2}]{sup 1.0}[O{sub 2}]{sup 0.5} for the single step reaction H{sub 2} + 1/2O{sub 2} = H{sub 2}O.
Modeling and simulation of cement hydration kinetics and microstructure development
Thomas, Jeffrey J.; Biernacki, Joseph J.; Bullard, Jeffrey W.; Bishnoi, Shashank; Dolado, Jorge S.; Scherer, George W.; Luttge, Andreas
2011-12-15
Efforts to model and simulate the highly complex cement hydration process over the past 40 years are reviewed, covering different modeling approaches such as single particle models, mathematical nucleation and growth models, and vector and lattice-based approaches to simulating microstructure development. Particular attention is given to promising developments that have taken place in the past few years. Recent applications of molecular-scale simulation methods to understanding the structure and formation of calcium-silicate-hydrate phases, and to understanding the process of dissolution of cement minerals in water are also discussed, as these topics are highly relevant to the future development of more complete and fundamental hydration models.
Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters.
Liu, Fei; Heiner, Monika; Yang, Ming
2016-01-01
Stochastic Petri nets (SPNs) have been widely used to model randomness which is an inherent feature of biological systems. However, for many biological systems, some kinetic parameters may be uncertain due to incomplete, vague or missing kinetic data (often called fuzzy uncertainty), or naturally vary, e.g., between different individuals, experimental conditions, etc. (often called variability), which has prevented a wider application of SPNs that require accurate parameters. Considering the strength of fuzzy sets to deal with uncertain information, we apply a specific type of stochastic Petri nets, fuzzy stochastic Petri nets (FSPNs), to model and analyze biological systems with uncertain kinetic parameters. FSPNs combine SPNs and fuzzy sets, thereby taking into account both randomness and fuzziness of biological systems. For a biological system, SPNs model the randomness, while fuzzy sets model kinetic parameters with fuzzy uncertainty or variability by associating each parameter with a fuzzy number instead of a crisp real value. We introduce a simulation-based analysis method for FSPNs to explore the uncertainties of outputs resulting from the uncertainties associated with input parameters, which works equally well for bounded and unbounded models. We illustrate our approach using a yeast polarization model having an infinite state space, which shows the appropriateness of FSPNs in combination with simulation-based analysis for modeling and analyzing biological systems with uncertain information. PMID:26910830
Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters
Liu, Fei; Heiner, Monika; Yang, Ming
2016-01-01
Stochastic Petri nets (SPNs) have been widely used to model randomness which is an inherent feature of biological systems. However, for many biological systems, some kinetic parameters may be uncertain due to incomplete, vague or missing kinetic data (often called fuzzy uncertainty), or naturally vary, e.g., between different individuals, experimental conditions, etc. (often called variability), which has prevented a wider application of SPNs that require accurate parameters. Considering the strength of fuzzy sets to deal with uncertain information, we apply a specific type of stochastic Petri nets, fuzzy stochastic Petri nets (FSPNs), to model and analyze biological systems with uncertain kinetic parameters. FSPNs combine SPNs and fuzzy sets, thereby taking into account both randomness and fuzziness of biological systems. For a biological system, SPNs model the randomness, while fuzzy sets model kinetic parameters with fuzzy uncertainty or variability by associating each parameter with a fuzzy number instead of a crisp real value. We introduce a simulation-based analysis method for FSPNs to explore the uncertainties of outputs resulting from the uncertainties associated with input parameters, which works equally well for bounded and unbounded models. We illustrate our approach using a yeast polarization model having an infinite state space, which shows the appropriateness of FSPNs in combination with simulation-based analysis for modeling and analyzing biological systems with uncertain information. PMID:26910830
Calibration of Chemical Kinetic Models Using Simulations of Small-Scale Cookoff Experiments
Wemhoff, A P; Becker, R C; Burnham, A K
2008-02-26
Establishing safe handling limits for explosives in elevated temperature environments is a difficult problem that often requires extensive simulation. The largest influence on predicting thermal cookoff safety lies in the chemical kinetic model used in these simulations, and these kinetic model reaction sequences often contain multiple steps. Several small-scale cookoff experiments, notably Differential Scanning Calorimetry (DSC), Thermogravimetric Analysis (TGA), One-Dimensional Time-to-Explosion (ODTX), and the Scaled Thermal Explosion (STEX) have been performed on various explosives to aid in cookoff behavior determination. Past work has used a single test from this group to create a cookoff model, which does not guarantee agreement with the other experiments. In this study, we update the kinetic parameters of an existing model for the common explosive 2,4,6-Trinitrotoluene (TNT) using DSC and ODTX experimental data at the same time by minimizing a global Figure of Merit based on hydrodynamic simulated data. We then show that the new kinetic model maintains STEX agreement, reduces DSC agreement, and improves ODTX and TGA agreement when compared to the original model. In addition, we describe a means to use implicit hydrodynamic simulations of DSC experiments to develop a reaction model for TNT melting.
Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics.
Chiu, See Hong; Xie, Lei
2016-06-27
One of the unaddressed challenges in drug discovery is that drug potency determined in vitro is not a reliable indicator of drug activity in vivo. Accumulated evidence suggests that in vivo activity is more strongly correlated with the binding/unbinding kinetics than the equilibrium thermodynamics of protein-ligand interactions (PLIs). However, existing experimental and computational techniques are insufficient in studying the molecular details of kinetics processes of PLIs on a large scale. Consequently, we not only have limited mechanistic understanding of the kinetic processes but also lack a practical platform for high-throughput screening and optimization of drug leads on the basis of their kinetic properties. For the first time, we address this unmet need by integrating coarse-grained normal mode analysis with multitarget machine learning (MTML). To test our method, HIV-1 protease is used as a model system. We find that computational models based on the residue normal mode directionality displacement of PLIs can not only recapitulate the results from all-atom molecular dynamics simulations but also predict protein-ligand binding/unbinding kinetics accurately. When this is combined with energetic features, the accuracy of combined kon and koff prediction reaches 74.35%. Furthermore, our integrated model provides us with new insights into the molecular determinants of the kinetics of PLIs. We propose that the coherent coupling of conformational dynamics and thermodynamic interactions between the receptor and the ligand may play a critical role in determining the kinetic rate constants of PLIs. In conclusion, we demonstrate that residue normal mode directionality displacement can serve as a kinetic fingerprint to capture long-time-scale conformational dynamics of the binding/unbinding kinetics. When this is coupled with MTML, it is possible to screen and optimize compounds on the basis of their binding/unbinding kinetics in a high-throughput fashion. The further
Exploring growth kinetics of carbon nanotube arrays by in situ optical diagnostics and modeling
Puretzky, Alexander A; Geohegan, David B; Pannala, Sreekanth; Rouleau, Christopher
2014-01-01
Simple kinetic models of carbon nanotube growth have been able to successfully link together many experimental parameters involved in the growth of carbon nanotubes for practical applications including the prediction of growth rates, terminal lengths, number of walls, activation energies, and their dependences on the growth environment. The implications of recent experiments utilizing in situ monitoring of carbon nanotube growth on our past kinetic model are first reviewed. Then, sub-second pulsed feedstock gas introduction is discussed to explore the nucleation and initial growth of carbon nanotubes in the context of the kinetic model. Moreover, kinetic effects in "pulsed CVD" - using repeated pulsed gas introduction to stop and restart nanotube growth - are explored to understand renucleation, the origin of alignment in nanotube arrays, and incremental growth. Time-resolved reflectivity of the surface is used to remotely understand the kinetics of nucleation and the coordinated growth of arrays. This approach demonstrates that continuous vertically aligned single wall carbon nanotubes can be grown incrementally by pulsed CVD, and that the first exposure of fresh catalyst to feedstock gas is critical to nanotubes site density required for coordinated growth. Aligned nanotube arrays (as short as 60 nm) are shown to nucleate and grow within single, sub-second gas pulses. The multiple-pulse growth experiments (> 100 pulses) show that a high fraction of nanotubes renucleate on subsequent gas pulses.
Gleeson, Michael R.; Sheridan, John T.
2009-09-15
The photochemical processes present during free-radical-based holographic grating formation are examined. A kinetic model is presented, which includes, in a more nearly complete and physically realistic way, most of the major photochemical and nonlocal photopolymerization-driven diffusion effects. These effects include: (i) non-steady-state kinetics (ii) spatially and temporally nonlocal polymer chain growth (iii) time varying photon absorption (iv) diffusion controlled viscosity effects (v) multiple termination mechanisms, and (vi) inhibition. The convergence of the predictions of the resulting model is then examined. Comparisons with experimental results are carried out in Part II of this series of papers [J. Opt. Soc. Am. B 26, 1746 (2009)].
Capitelli, M.; De Pascale, O.; Diomede, P.; Gorse, C.; Longo, S.; Pagano, D.; Gicquel, A.; Hassouni, K.
2005-04-06
Different approaches to study vibrational kinetics coupled to electron one for modeling different kinds of negative ion sources are presented. In particular two types of sources are investigated. The first one is a classical negative ion source in which the plasma is generated by thermoemitted electrons; in the second one, electrons already present in the mixture are accelerated by an RF field to sufficiently high energy to ionize the gas molecules. For the first kind of ion source a new computational scheme is presented to couple heavy particle and electron kinetics. Moreover models developed for an RF inductive discharge and for a parallel plate discharge are described.
State to State and Charged Particle Kinetic Modeling of Time Filtering and Cs Addition
Capitelli, M.; Gorse, C.; Longo, S.; Diomede, P.; Pagano, D.
2007-08-10
We present here an account on the progress of kinetic simulation of non equilibrium plasmas in conditions of interest for negative ion production by using the 1D Bari code for hydrogen plasma simulation. The model includes the state to state kinetics of the vibrational level population of hydrogen molecules, plus a PIC/MCC module for the multispecies dynamics of charged particles. In particular we present new results for the modeling of two issues of great interest: the time filtering and the Cs addition via surface coverage.
Kinetics of Oxygen Reduction in Aprotic Li-O2 Cells: A Model-Based Study.
Safari, M; Adams, B D; Nazar, L F
2014-10-16
A comprehensive and general kinetic model is developed for the oxygen reduction reaction in aprotic Li-O2 cells. The model is based on the competitive uptake of lithium superoxide by the surface and solution. A demonstrative kinetic study is provided to demystify the origin of curvature in Tafel plots as well as the current dependency and aberrant diversity of the nature and morphology of discharge products in these systems. Our results are general and extend to any system where solubilization of superoxide is favored, such as where phase-transfer catalysts play an important role. PMID:26278597
Wang, Xu; Ding, Jie; Guo, Wan-Qian; Ren, Nan-Qi
2010-12-01
Investigating how a bioreactor functions is a necessary precursor for successful reactor design and operation. Traditional methods used to investigate flow-field cannot meet this challenge accurately and economically. Hydrodynamics model can solve this problem, but to understand a bioreactor in sufficient depth, it is often insufficient. In this paper, a coupled hydrodynamics-reaction kinetics model was formulated from computational fluid dynamics (CFD) code to simulate a gas-liquid-solid three-phase biotreatment system for the first time. The hydrodynamics model is used to formulate prediction of the flow field and the reaction kinetics model then portrays the reaction conversion process. The coupled model is verified and used to simulate the behavior of an expanded granular sludge bed (EGSB) reactor for biohydrogen production. The flow patterns were visualized and analyzed. The coupled model also demonstrates a qualitative relationship between hydrodynamics and biohydrogen production. The advantages and limitations of applying this coupled model are discussed. PMID:20727741
Perelson, Alan S; Shudo, Emi; Ribeiro, Ruy M
2008-01-01
Mathematical models have proven helpful in analyzing the virological response to antiviral therapy in hepatitis C virus (HCY) infected subjects. Objective: To summarize the uses and limitations of different models for analyzing HCY kinetic data under pegylated interferon therapy. Methods: We formulate mathematical models and fit them by nonlinear least square regression to patient data in order estimate model parameters. We compare the goodness of fit and parameter values estimated by different models statistically. Results/Conclusion: The best model for parameter estimation depends on the availability and the quality of data as well as the therapy used. We also discuss the mathematical models that will be needed to analyze HCV kinetic data from clinical trials with new antiviral drugs.
A kinetic model for molecular diffusion through pores.
D'Agostino, Tommaso; Salis, Samuele; Ceccarelli, Matteo
2016-07-01
The number of pathogens developing multiple drug resistance is ever increasing. The impact on healthcare systems is huge and the need for novel antibiotics as well a new way to develop them is urgent, especially against Gram-negative bacteria. The first defense of these bacteria is the outer membrane, where unspecific protein channels (porins) modulate nutrients passive diffusion. Also polar antibiotics enter through this path and down-regulation and/or mutation of porins are very common in drug resistant strains. Our inability to come up with novel effective antibiotics mostly relies upon the insufficient comprehension of the key molecular features enabling better penetration through porins. Molecular dynamics simulations offer an extraordinary tool in the study of the dynamics of biological systems; however, one of the major drawbacks of this method is that its use is currently restricted to study time scales of the order of microsecond. Enhanced sampling methods like Metadynamics have been recently used to investigate the diffusion of antibiotics through bacterial porins. The main limitation is that dynamical properties cannot be estimated because of the different potential that the systems under study are experiencing. Recently, the scope of Metadynamics has been extended. By applying an a posteriori analysis one can obtain rates of transitions and rate-limiting steps of the process under study, directly comparable with kinetic data extracted from electrophysiology experiments. In this work, we apply this method to the study of the permeability of Escherichia coli's OmpF with respect to Meropenem, finding good agreement with the residence time obtained analyzing experimental current noise. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. PMID:26796683
Passalía, Claudio; Alfano, Orlando M; Brandi, Rodolfo J
2012-04-15
A methodology for modeling photocatalytic reactors for their application in indoor air pollution control is carried out. The methodology implies, firstly, the determination of intrinsic reaction kinetics for the removal of formaldehyde. This is achieved by means of a simple geometry, continuous reactor operating under kinetic control regime and steady state. The kinetic parameters were estimated from experimental data by means of a nonlinear optimization algorithm. The second step was the application of the obtained kinetic parameters to a very different photoreactor configuration. In this case, the reactor is a corrugated wall type using nanosize TiO(2) as catalyst irradiated by UV lamps that provided a spatially uniform radiation field. The radiative transfer within the reactor was modeled through a superficial emission model for the lamps, the ray tracing method and the computation of view factors. The velocity and concentration fields were evaluated by means of a commercial CFD tool (Fluent 12) where the radiation model was introduced externally. The results of the model were compared experimentally in a corrugated wall, bench scale reactor constructed in the laboratory. The overall pollutant conversion showed good agreement between model predictions and experiments, with a root mean square error less than 4%. PMID:22030272
Kinetic models of the interference of gene transcription to ncRNA and mRNA
NASA Astrophysics Data System (ADS)
Zhdanov, Vladimir P.
2011-06-01
The experiments indicate that the transcription of genes into ncRNA can positively or negatively interfere with transcription into mRNA. We propose two kinetic models describing this effect. The first model is focused on the ncRNA-induced chromatin modification facilitating the transcription of the downstream gene into mRNA. The second model includes the competition between the transcription into ncRNA and the binding of activator to a regulatory site of the downstream gene transcribed into mRNA. Our analysis based on the mean-field kinetic equations and Monte Carlo simulations shows the likely dependences of the transcription rate on RNA polymerase concentration in situations with different rate-limiting steps. Our models can also be used to scrutinize the dependence of the transcription rate on other kinetic parameters. Our kinetic Monte Carlo simulations show that the first model predicts stochastic bursts in the mRNA formation provided that the transcription into ncRNA is slow, while the second model predicts in addition anti-phase stochastic bursts in the mRNA and ncRNA formation provided that that the protein attachment to and detachment from a regulatory site is slow.
NASA Astrophysics Data System (ADS)
Franz, Silvio; Gradenigo, Giacomo; Spigler, Stefano
2016-03-01
We study how the thermodynamic properties of the triangular plaquette model (TPM) are influenced by the addition of extra interactions. The thermodynamics of the original TPM is trivial, while its dynamics is glassy, as usual in kinetically constrained models. As soon as we generalize the model to include additional interactions, a thermodynamic phase transition appears in the system. The additional interactions we consider are either short ranged, forming a regular lattice in the plane, or long ranged of the small-world kind. In the case of long-range interactions we call the new model the random-diluted TPM. We provide arguments that the model so modified should undergo a thermodynamic phase transition, and that in the long-range case this is a glass transition of the "random first-order" kind. Finally, we give support to our conjectures studying the finite-temperature phase diagram of the random-diluted TPM in the Bethe approximation. This corresponds to the exact calculation on the random regular graph, where free energy and configurational entropy can be computed by means of the cavity equations.
Franz, Silvio; Gradenigo, Giacomo; Spigler, Stefano
2016-03-01
We study how the thermodynamic properties of the triangular plaquette model (TPM) are influenced by the addition of extra interactions. The thermodynamics of the original TPM is trivial, while its dynamics is glassy, as usual in kinetically constrained models. As soon as we generalize the model to include additional interactions, a thermodynamic phase transition appears in the system. The additional interactions we consider are either short ranged, forming a regular lattice in the plane, or long ranged of the small-world kind. In the case of long-range interactions we call the new model the random-diluted TPM. We provide arguments that the model so modified should undergo a thermodynamic phase transition, and that in the long-range case this is a glass transition of the "random first-order" kind. Finally, we give support to our conjectures studying the finite-temperature phase diagram of the random-diluted TPM in the Bethe approximation. This corresponds to the exact calculation on the random regular graph, where free energy and configurational entropy can be computed by means of the cavity equations. PMID:27078408
KINETIC MODELING OF NOX FORMATION AND DESTRUCTION AND COMBUSTIBLES BURNOUT
The report describes a model of the gas-phase chemistry involved in the combustion of simple hydrocarbon fuels and the interconversion of fixed nitrogen species. One focus of the work was on modeling the chemistry involved in reburning and other advanced NOx control strategies. A...
Approximate models for the ion-kinetic regime in inertial-confinement-fusion capsule implosions
Hoffman, Nelson M.; Zimmerman, George B.; Molvig, Kim; Rinderknecht, Hans G.; Rosenberg, Michael J.; Albright, B. J.; Simakov, Andrei N.; Sio, Hong; Zylstra, Alex B.; Johnson, Maria Gatu; Séguin, Fredrick H.; Frenje, Johan A.; Li, C. K.; Petrasso, Richard D.; Higdon, David M.; Srinivasan, Gowri; Glebov, Vladimir Yu.; Stoeckl, Christian; Seka, Wolf; Sangster, T. Craig
2015-05-19
“Reduced” (i.e., simplified or approximate) ion-kinetic (RIK) models in radiation-hydrodynamic simulations permit a useful description of inertial-confinement-fusion (ICF) implosions where kinetic deviations from hydrodynamic behavior are important. For implosions in or near the kinetic regime (i.e., when ion mean free paths are comparable to the capsule size), simulations using a RIK model give a detailed picture of the time- and space-dependent structure of imploding capsules, allow an assessment of the relative importance of various kinetic processes during the implosion, enable explanations of past and current observations, and permit predictions of the results of future experiments. The RIK simulation method described here uses moment-based reduced kinetic models for transport of mass, momentum, and energy by long-mean-free-path ions, a model for the decrease of fusion reactivity owing to the associated modification of the ion distribution function, and a model of hydrodynamic turbulent mixing. The transport models are based on local gradient-diffusion approximations for the transport of moments of the ion distribution functions, with coefficients to impose flux limiting or account for transport modification. After calibration against a reference set of ICF implosions spanning the hydrodynamic-to-kinetic transition, the method has useful, quantifiable predictive ability over a broad range of capsule parameter space. Calibrated RIK simulations show that an important contributor to ion species separation in ICF capsule implosions is the preferential flux of longer-mean-free-path species out of the fuel and into the shell, leaving the fuel relatively enriched in species with shorter mean free paths. Also, the transport of ion thermal energy is enhanced in the kinetic regime, causing the fuel region to have a more uniform, lower ion temperature, extending over a larger volume, than implied by clean simulations. We expect that the success of our simple approach
Approximate models for the ion-kinetic regime in inertial-confinement-fusion capsule implosions
Hoffman, Nelson M.; Zimmerman, George B.; Molvig, Kim; Rinderknecht, Hans G.; Rosenberg, Michael J.; Albright, B. J.; Simakov, Andrei N.; Sio, Hong; Zylstra, Alex B.; Johnson, Maria Gatu; et al
2015-05-19
“Reduced” (i.e., simplified or approximate) ion-kinetic (RIK) models in radiation-hydrodynamic simulations permit a useful description of inertial-confinement-fusion (ICF) implosions where kinetic deviations from hydrodynamic behavior are important. For implosions in or near the kinetic regime (i.e., when ion mean free paths are comparable to the capsule size), simulations using a RIK model give a detailed picture of the time- and space-dependent structure of imploding capsules, allow an assessment of the relative importance of various kinetic processes during the implosion, enable explanations of past and current observations, and permit predictions of the results of future experiments. The RIK simulation method describedmore » here uses moment-based reduced kinetic models for transport of mass, momentum, and energy by long-mean-free-path ions, a model for the decrease of fusion reactivity owing to the associated modification of the ion distribution function, and a model of hydrodynamic turbulent mixing. The transport models are based on local gradient-diffusion approximations for the transport of moments of the ion distribution functions, with coefficients to impose flux limiting or account for transport modification. After calibration against a reference set of ICF implosions spanning the hydrodynamic-to-kinetic transition, the method has useful, quantifiable predictive ability over a broad range of capsule parameter space. Calibrated RIK simulations show that an important contributor to ion species separation in ICF capsule implosions is the preferential flux of longer-mean-free-path species out of the fuel and into the shell, leaving the fuel relatively enriched in species with shorter mean free paths. Also, the transport of ion thermal energy is enhanced in the kinetic regime, causing the fuel region to have a more uniform, lower ion temperature, extending over a larger volume, than implied by clean simulations. We expect that the success of our simple
Approximate models for the ion-kinetic regime in inertial-confinement-fusion capsule implosions
NASA Astrophysics Data System (ADS)
Hoffman, Nelson M.; Zimmerman, George B.; Molvig, Kim; Rinderknecht, Hans G.; Rosenberg, Michael J.; Albright, B. J.; Simakov, Andrei N.; Sio, Hong; Zylstra, Alex B.; Gatu Johnson, Maria; Séguin, Fredrick H.; Frenje, Johan A.; Li, C. K.; Petrasso, Richard D.; Higdon, David M.; Srinivasan, Gowri; Glebov, Vladimir Yu.; Stoeckl, Christian; Seka, Wolf; Sangster, T. Craig
2015-05-01
"Reduced" (i.e., simplified or approximate) ion-kinetic (RIK) models in radiation-hydrodynamic simulations permit a useful description of inertial-confinement-fusion (ICF) implosions where kinetic deviations from hydrodynamic behavior are important. For implosions in or near the kinetic regime (i.e., when ion mean free paths are comparable to the capsule size), simulations using a RIK model give a detailed picture of the time- and space-dependent structure of imploding capsules, allow an assessment of the relative importance of various kinetic processes during the implosion, enable explanations of past and current observations, and permit predictions of the results of future experiments. The RIK simulation method described here uses moment-based reduced kinetic models for transport of mass, momentum, and energy by long-mean-free-path ions, a model for the decrease of fusion reactivity owing to the associated modification of the ion distribution function, and a model of hydrodynamic turbulent mixing. The transport models are based on local gradient-diffusion approximations for the transport of moments of the ion distribution functions, with coefficients to impose flux limiting or account for transport modification. After calibration against a reference set of ICF implosions spanning the hydrodynamic-to-kinetic transition, the method has useful, quantifiable predictive ability over a broad range of capsule parameter space. Calibrated RIK simulations show that an important contributor to ion species separation in ICF capsule implosions is the preferential flux of longer-mean-free-path species out of the fuel and into the shell, leaving the fuel relatively enriched in species with shorter mean free paths. Also, the transport of ion thermal energy is enhanced in the kinetic regime, causing the fuel region to have a more uniform, lower ion temperature, extending over a larger volume, than implied by clean simulations. We expect that the success of our simple approach