Yuvan, Steven; Bier, Martin
2018-02-01
Two decades ago Bak et al. (1997) [3] proposed a reaction-diffusion model to describe market fluctuations. In the model buyers and sellers diffuse from opposite ends of a 1D interval that represents a price range. Trades occur when buyers and sellers meet. We show analytically and numerically that the model well reproduces the square-root relation between traded volumes and price changes that is observed in real-life markets. The result is remarkable as this relation has commonly been explained in terms of more elaborate trader strategies. We furthermore explain why the square-root relation is robust under model modifications and we show how real-life bond market data exhibit the square-root relation.
Method for preparing small volume reaction containers
Retterer, Scott T.; Doktycz, Mitchel J.
2017-04-25
Engineered reaction containers that can be physically and chemically defined to control the flux of molecules of different sizes and charge are disclosed. Methods for constructing small volume reaction containers through a combination of etching and deposition are also disclosed. The methods allow for the fabrication of multiple devices that possess features on multiple length scales, specifically small volume containers with controlled porosity on the nanoscale.
Numerical modelling of hydration reactions
Vrijmoed, Johannes C.; John, Timm
2017-04-01
Mineral reactions are generally accompanied by volume changes. Observations in rocks and thin section indicate that this often occurred by replacement reactions involving a fluid phase. Frequently, the volume of the original rock or mineral seems to be conserved. If the density of the solid reaction products is higher than the reactants, the associated solid volume decrease generates space for a fluid phase. In other words, porosity is created. The opposite is true for an increase in solid volume during reaction, which leads to a porosity reduction. This slows down and may even stop the reaction if it needs fluid as a reactant. Understanding the progress of reactions and their rates is important because reaction generally changes geophysical and rock mechanical properties which will therefore affect geodynamical processes and seismic properties. We studied the case of hydration of eclogite to blueschist in a subduction zone setting. Eclogitized pillow basalt structures from the Tian-Shan orogeny are transformed to blueschist on the rims of the pillow (van der Straaten et al., 2008). Fluid pathways existed between the pillow structures. The preferred hypothesis of blueschist formation is to supply the fluid for hydration from the pillow margins progressing inward. Using numerical modelling we simulate this coupled reaction-diffusion process. Porosity and fluid pressure evolution are coupled to local thermodynamic equilibrium and density changes. The first rim of blueschist that forms around the eclogite pillow increases volume to such a degree that the system is clogged and the reaction stops. Nevertheless, the field evidence suggests the blueschist formation continued. To prevent the system from clogging, a high incoming pore fluid pressure on the pillow boundaries is needed along with removal of mass from the system to accommodate the volume changes. The only other possibility is to form blueschist from any remaining fluid stored in the core of the pillow
Modelling Tethered Enzymatic Reactions
Solis Salas, Citlali; Goyette, Jesse; Coker-Gordon, Nicola; Bridge, Marcus; Isaacson, Samuel; Allard, Jun; Maini, Philip; Dushek, Omer
Enzymatic reactions are key to cell functioning, and whilst much work has been done in protein interaction in cases where diffusion is possible, interactions of tethered proteins are poorly understood. Yet, because of the large role cell membranes play in enzymatic reactions, several reactions may take place where one of the proteins is bound to a fixed point in space. We develop a model to characterize tethered signalling between the phosphatase SHP-1 interacting with a tethered, phosphorylated protein. We compare our model to experimental data obtained using surface plasmon resonance (SPR). We show that a single SPR experiment recovers 5 independent biophysical/biochemical constants. We also compare the results between a three dimensional model and a two dimensional model. The work gives the opportunity to use known techniques to learn more about signalling processes, and new insights into how enzyme tethering alters cellular signalling. With support from the Mexican Council for Science and Technology (CONACyT), the Public Education Secretariat (SEP), and the Mexican National Autonomous University's Foundation (Fundacion UNAM).
Models of spatially restricted biochemical reaction systems.
Neves, Susana R; Iyengar, Ravi
2009-02-27
Many reactions within the cell occur only in specific intracellular regions. Such local reaction networks give rise to microdomains of activated signaling components. The dynamics of microdomains can be visualized by live cell imaging. Computational models using partial differential equations provide mechanistic insights into the interacting factors that control microdomain dynamics. The mathematical models show that, for membrane-initiated signaling, the ratio of the surface area of the plasma membrane to the volume of the cytoplasm, the topology of the signaling network, the negative regulators, and kinetic properties of key components together define microdomain dynamics. Thus, patterns of locally restricted signaling reaction systems can be considered an emergent property of the cell.
Stochastic Modeling Of Biochemical Reactions
2006-11-01
STOCHASTIC MODELING OF BIOCHEMICAL REACTIONS Abhyudai Singh and João Pedro Hespanha* Department of Electrical and Computer Engineering University of...procedure for con- structing approximate stochastic models for chemical reactions used for modeling biochemical processes such as gene regulatory networks... biochemical reactions , the modeling tools developed in this paper can be applied to a very general class of stochastic systems, in particular
Reaction modeling in geothermal systems
Stefansson, A.
2012-12-01
Natural volcanic geothermal systems are open systems in term of matter and energy. Such systems are complex to model in terms of fluid chemistry, fluid flow and energy budget. Reaction modeling may be used to gain insight and possibly quantify chemical processes occurring within a system, for example fluid-fluid and fluid-rock interaction. Methods have been developed within the WATCH (Bjarnason, 1994; Arnórsson et al., 2007) and PHREEQC (Parkhurst and Appelo, 1999) programs to simulate reactions of multicomponent and multiphase systems to 300°C. The models include boiling and phase segregation (open system boiling), fluid-fluid mixing and fluid-rock interaction (gas-water-rock interaction). The models have been applied to quantify processes within the Hellisheidi geothermal system, Iceland. Open system boiling and fluid-rock interaction were simulated as a function of temperature, initial fluid composition and extent of reaction (T-X-ξ). In addition the interactions of magmatic gases with geothermal fluids and rocks were modeled. In this way various component behavior has been traced within the geothermal system and compared with observations of fluid composition and mineralogy. In addition, the reaction models have been used to evaluate the geochemical feasibility and best conditions of gas (CO2 and H2S) and waste water injection into geothermal system.
Modelling Students' Visualisation of Chemical Reaction
Cheng, Maurice M. W.; Gilbert, John K.
2017-01-01
This paper proposes a model-based notion of "submicro representations of chemical reactions". Based on three structural models of matter (the simple particle model, the atomic model and the free electron model of metals), we suggest there are two major models of reaction in school chemistry curricula: (a) reactions that are simple…
Modeling the enzyme kinetic reaction.
Atangana, Abdon
2015-09-01
The Enzymatic control reactions model was presented within the scope of fractional calculus. In order to accommodate the usual initial conditions, the fractional derivative used is in Caputo sense. The methodologies of the three analytical methods were used to derive approximate solution of the fractional nonlinear system of differential equations. Two methods use integral operator and the other one uses just an integral. Numerical results obtained exhibit biological behavior of real world problem.
Progress in microscopic direct reaction modeling of nucleon induced reactions
Energy Technology Data Exchange (ETDEWEB)
Dupuis, M.; Bauge, E.; Hilaire, S.; Lechaftois, F.; Peru, S.; Pillet, N.; Robin, C. [CEA, DAM, DIF, Arpajon (France)
2015-12-15
A microscopic nuclear reaction model is applied to neutron elastic and direct inelastic scatterings, and pre-equilibrium reaction. The JLM folding model is used with nuclear structure information calculated within the quasi-particle random phase approximation implemented with the Gogny D1S interaction. The folding model for direct inelastic scattering is extended to include rearrangement corrections stemming from both isoscalar and isovector density variations occurring during a transition. The quality of the predicted (n,n), (n,n{sup '}), (n,xn) and (n,n{sup '}γ) cross sections, as well as the generality of the present microscopic approach, shows that it is a powerful tool that can help improving nuclear reactions data quality. Short- and long-term perspectives are drawn to extend the present approach to more systems, to include missing reactions mechanisms, and to consistently treat both structure and reaction problems. (orig.)
Constrained reaction volume approach for studying chemical kinetics behind reflected shock waves
Hanson, Ronald K.
2013-09-01
We report a constrained-reaction-volume strategy for conducting kinetics experiments behind reflected shock waves, achieved in the present work by staged filling in a shock tube. Using hydrogen-oxygen ignition experiments as an example, we demonstrate that this strategy eliminates the possibility of non-localized (remote) ignition in shock tubes. Furthermore, we show that this same strategy can also effectively eliminate or minimize pressure changes due to combustion heat release, thereby enabling quantitative modeling of the kinetics throughout the combustion event using a simple assumption of specified pressure and enthalpy. We measure temperature and OH radical time-histories during ethylene-oxygen combustion behind reflected shock waves in a constrained reaction volume and verify that the results can be accurately modeled using a detailed mechanism and a specified pressure and enthalpy constraint. © 2013 The Combustion Institute.
Reaction Time for Trimolecular Reactions in Compartment-based Reaction-Diffusion Models
Li, F; Chen, M; Erban, R; Cao, Y
2016-01-01
Trimolecular reaction models are investigated in the compartment-based (lattice-based) framework for stochastic reaction-diffusion modelling. The formulae for the first collision time and the mean reaction time are derived for the case where three molecules are present in the solution.
A Numerical Study of Reaction Kinetics Model of Polymerization In ...
African Journals Online (AJOL)
The model which is a system of partial differential equations is analyzed numerically using the finite difference scheme to obtain results for1, 2, 3, 4, 10, 100, 1000 (where p is the order of reaction). Keywords: Frontal polymerization, Material diffusion. Journal of the Nigerian Association of Mathematical Physics, Volume 19 ...
DSMC Modeling of Flows with Recombination Reactions
2017-06-23
Reactions S. Gimelshein, I. Wysong Air Force Research Laboratory (AFMC) AFRL/RQRC 10 E. Saturn Blvd. Edwards AFB, CA 93524-7680 Air Force Research ...dis- sociation and exchange reactions for diatomic , and sometimes for polyatomic, molecules. The recombination reaction was largely avoided in the DSMC...believed to provide adequate accuracy to the VT energy exchange of diatomic molecules. As shown in Fig. 4(a), the use of that model results in good
Kinetics of Model Reactions for Interfacial Polymerization
Directory of Open Access Journals (Sweden)
Henry Hall
2012-02-01
Full Text Available To model the rates of interfacial polycondensations, the rates of reaction of benzoyl chloride and methyl chloroformate with various aliphatic monoamines in acetonitrile were determined at 25 °C. Buffering with picric acid slowed these extremely fast reactions so the rate constants could be determined from the rate of disappearance of picrate ion. The rates of the amine reactions correlated linearly with their Swain-Scott nucleophilicities.
Kinetics of Model Reactions for Interfacial Polymerization
Henry Hall; Robert Bates (Harvard University); Jeffrey Robertson; Anne Padias; Trevor Centeno-Hall
2012-01-01
To model the rates of interfacial polycondensations, the rates of reaction of benzoyl chloride and methyl chloroformate with various aliphatic monoamines in acetonitrile were determined at 25 °C. Buffering with picric acid slowed these extremely fast reactions so the rate constants could be determined from the rate of disappearance of picrate ion. The rates of the amine reactions correlated linearly with their Swain-Scott nucleophilicities.
Multicomponent modelling of Portland cement hydration reactions
Ukrainczyk, N.; Koenders, E.A.B.; Van Breugel, K.
2012-01-01
The prospect of cement and concrete technologies depends on more in depth understanding of cement hydration reactions. Hydration reaction models simulate the development of the microstructures that can finally be used to estimate the cement based material properties that influence performance and
A Full Disturbance Model for Reaction Wheels
Le, M.P.; Ellenbroek, Marcellinus Hermannus Maria; Seiler, R; van Put, P.; Cottaar, E.J.E.
2014-01-01
Reaction wheels are rotating devices used for the attitude control of spacecraft. However, reaction wheels also generate undesired disturbances in the form of vibrations, which may have an adverse effect on the pointing accuracy and stability of spacecraft (optical) payloads. A disturbance model for
Nonlinear control of the Salnikov model reaction
DEFF Research Database (Denmark)
Recke, Bodil; Jørgensen, Sten Bay
1999-01-01
This paper explores different nonlinear control schemes, applied to a simple model reaction. The model is the Salnikov model, consisting of two ordinary differential equations. The control strategies investigated are I/O-linearisation, Exact linearisation, exact linearisation combined with LQR...
Storm Water Management Model Reference Manual Volume ...
SWMM is a dynamic rainfall-runoff simulation model used for single event or long-term (continuous) simulation of runoff quantity and quality from primarily urban areas. The runoff component of SWMM operates on a collection of subcatchment areas that receive precipitation and generate runoff and pollutant loads. The routing portion of SWMM transports this runoff through a system of pipes, channels, storage/treatment devices, pumps, and regulators. SWMM tracks the quantity and quality of runoff generated within each subcatchment, and the flow rate, flow depth, and quality of water in each pipe and channel during a simulation period comprised of multiple time steps. The reference manual for this edition of SWMM is comprised of three volumes. Volume I describes SWMM’s hydrologic models, Volume II its hydraulic models, and Volume III its water quality and low impact development models. Reference manual presenting underlying mathematics of the Storm Water Management Model - Volume III Water Quality Modules
Spur Reaction Model of Positronium Formation
DEFF Research Database (Denmark)
Mogensen, O. E.
1974-01-01
A new model of positronium (Ps) formation is proposed. Positronium is assumed to be formed by a reaction between a positron and an electron in the positron spur. Ps formation must compete with electron‐ion recombination and electron or positron reactions with solvent molecules and scavenger...... impurities. It is also influenced by electron and positron solvation. The model correlates the measured Ps formation probabilities with the spur electron properties determined in radiation chemistry. The predictions of the model are shown to be in good agreement with experimental results for liquids...
Working Papers in Dialogue Modeling, Volume 2.
Mann, William C.; And Others
The technical working papers that comprise the two volumes of this document are related to the problem of creating a valid process model of human communication in dialogue. In Volume 2, the first paper concerns study methodology, and raises such issues as the choice between system-building and process-building, and the advantages of studying cases…
Propagation models for computing biochemical reaction networks
Henzinger, Thomas A; Mateescu, Maria
2011-01-01
We introduce propagation models, a formalism designed to support general and efficient data structures for the transient analysis of biochemical reaction networks. We give two use cases for propagation abstract data types: the uniformization method and numerical integration. We also sketch an implementation of a propagation abstract data type, which uses abstraction to approximate states.
Competing reaction model with many absorbing configurations.
de Andrade, M F; Figueiredo, W
2010-02-01
We study a competitive reaction model between two monomers A and B on a linear lattice. We assume that monomer A can react with a nearest-neighbor monomer A or B , but reactions between monomers of type B are prohibited. We include in our model lateral interactions between monomers as well as the effects of temperature of the catalyst. The model is considered in the adsorption controlled limit, where the reaction rate is infinitely larger than the adsorption rate of the monomers. We employ site and pair mean-field approximations as well as static Monte Carlo simulations. We determine the phase diagram of the model in the plane y_{A} versus temperature, where y_{A} is the probability that a monomer of the type A arrives at the surface. This phase diagram shows regions of active and absorbing states separated by a line of continuous phase transitions. Despite the absorbing state of the model to be strongly dependent on temperature, we show that the static critical exponents of the model belong to the same universality class of the directed percolation.
Reaction-diffusion pulses: a combustion model
Energy Technology Data Exchange (ETDEWEB)
Campos, Daniel [Grup de FIsica EstadIstica, Dept. de FIsica, Universitat Autonoma de Barcelona, E-08193 Bellaterrra (Spain); Llebot, Josep Enric [Grup de FIsica EstadIstica, Dept. de FIsica, Universitat Autonoma de Barcelona, E-08193 Bellaterrra (Spain); Fort, Joaquim [Dept. de FIsica, Univ. de Girona, Campus de Montilivi, 17071 Girona, Catalonia (Spain)
2004-07-02
We focus on a reaction-diffusion approach proposed recently for experiments on combustion processes, where the heat released by combustion follows first-order reaction kinetics. This case allows us to perform an exhaustive analytical study. Specifically, we obtain the exact expressions for the speed of the thermal pulses, their maximum temperature and the condition of self-sustenance. Finally, we propose two generalizations of the model, namely, the case of several reactants burning together, and that of time-delayed heat conduction. We find an excellent agreement between our analytical results and simulations.
Directory of Open Access Journals (Sweden)
Fan Zhang
2012-01-01
Full Text Available This paper describes details of an automatic matrix decomposition approach for a reaction-based stream water quality model. The method yields a set of equilibrium equations, a set of kinetic-variable transport equations involving kinetic reactions only, and a set of component transport equations involving no reactions. Partial decomposition of the system of water quality constituent transport equations is performed via Gauss-Jordan column reduction of the reaction network by pivoting on equilibrium reactions to decouple equilibrium and kinetic reactions. This approach minimizes the number of partial differential advective-dispersive transport equations and enables robust numerical integration. Complete matrix decomposition by further pivoting on linearly independent kinetic reactions allows some rate equations to be formulated individually and explicitly enforces conservation of component species when component transport equations are solved. The methodology is demonstrated for a case study involving eutrophication reactions in the Des Moines River in Iowa, USA and for two hypothetical examples to illustrate the ability of the model to simulate sediment and chemical transport with both mobile and immobile water phases and with complex reaction networks involving both kinetic and equilibrium reactions.
Reaction Wheel Disturbance Model Extraction Software - RWDMES
Blaurock, Carl
2009-01-01
The RWDMES is a tool for modeling the disturbances imparted on spacecraft by spinning reaction wheels. Reaction wheels are usually the largest disturbance source on a precision pointing spacecraft, and can be the dominating source of pointing error. Accurate knowledge of the disturbance environment is critical to accurate prediction of the pointing performance. In the past, it has been difficult to extract an accurate wheel disturbance model since the forcing mechanisms are difficult to model physically, and the forcing amplitudes are filtered by the dynamics of the reaction wheel. RWDMES captures the wheel-induced disturbances using a hybrid physical/empirical model that is extracted directly from measured forcing data. The empirical models capture the tonal forces that occur at harmonics of the spin rate, and the broadband forces that arise from random effects. The empirical forcing functions are filtered by a physical model of the wheel structure that includes spin-rate-dependent moments (gyroscopic terms). The resulting hybrid model creates a highly accurate prediction of wheel-induced forces. It accounts for variation in disturbance frequency, as well as the shifts in structural amplification by the whirl modes, as the spin rate changes. This software provides a point-and-click environment for producing accurate models with minimal user effort. Where conventional approaches may take weeks to produce a model of variable quality, RWDMES can create a demonstrably high accuracy model in two hours. The software consists of a graphical user interface (GUI) that enables the user to specify all analysis parameters, to evaluate analysis results and to iteratively refine the model. Underlying algorithms automatically extract disturbance harmonics, initialize and tune harmonic models, and initialize and tune broadband noise models. The component steps are described in the RWDMES user s guide and include: converting time domain data to waterfall PSDs (power spectral
Modelling of structural effects on chemical reactions in turbulent flows
Energy Technology Data Exchange (ETDEWEB)
Gammelsaeter, H.R.
1997-12-31
Turbulence-chemistry interactions are analysed using algebraic moment closure for the chemical reaction term. The coupling between turbulence and chemical length and time scales generate a complex interaction process. This interaction process is called structural effects in this work. The structural effects are shown to take place on all scales between the largest scale of turbulence and the scales of the molecular motions. The set of equations describing turbulent correlations involved in turbulent reacting flows are derived. Interactions are shown schematically using interaction charts. Algebraic equations for the turbulent correlations in the reaction rate are given using the interaction charts to include the most significant couplings. In the frame of fundamental combustion physics, the structural effects appearing on the small scales of turbulence are proposed modelled using a discrete spectrum of turbulent scales. The well-known problem of averaging the Arrhenius law, the specific reaction rate, is proposed solved using a presumed single variable probability density function and a sub scale model for the reaction volume. Although some uncertainties are expected, the principles are addressed. Fast chemistry modelling is shown to be consistent in the frame of algebraic moment closure when the turbulence-chemistry interaction is accounted for in the turbulent diffusion. The modelling proposed in this thesis is compared with experimental data for an laboratory methane flame and advanced probability density function modelling. The results show promising features. Finally it is shown a comparison with full scale measurements for an industrial burner. All features of the burner are captured with the model. 41 refs., 33 figs.
Noise Exposure Model MOD-5 : Volume 2
1971-06-01
The report contains three sections. The first two sections are contained in Volume 1. It contains an airport analysis which describes the noise exposure model MOD-5 from the perspective of analysing an airport in order to develop the program input mo...
Noise Exposure Model MOD-5 : Volume 1
1971-06-01
The report contains three sections. The first two sections are contained in Volume 1. It contains an airport analysis which describes the noise exposure model MOD-5 from the perspective of analysing an airport in order to develop the program input mo...
Modelling enzyme reaction mechanisms, specificity and catalysis.
Mulholland, Adrian J
2005-10-15
Modern modelling methods can now give uniquely detailed understanding of enzyme-catalyzed reactions, including the analysis of mechanisms and the identification of determinants of specificity and catalytic efficiency. A new field of computational enzymology has emerged that has the potential to contribute significantly to structure-based design and to develop predictive models of drug metabolism and, for example, of the effects of genetic polymorphisms. This review outlines important techniques in this area, including quantum-chemical model studies and combined quantum-mechanics and molecular-mechanics (QM/MM) methods. Some recent applications to enzymes of pharmacological interest are also covered, showing the types of problems that can be tackled and the insight they can give.
Reaction-diffusion models of decontamination
DEFF Research Database (Denmark)
Hjorth, Poul G.
A contaminant, which also contains a polymer is in the form of droplets on a solid surface. It is to be removed by the action of a decontaminant, which is applied in aqueous solution. The contaminant is only sparingly soluble in water, so the reaction mechanism is that it slowly dissolves...... in the aqueous solution and then is oxidized by the decontaminant. The polymer is insoluble in water, and so builds up near the interface, where its presence can impede the transport of contaminant. In these circumstances, Dstl wish to have mathematical models that give an understanding of the process, and can...
Modeling stochasticity in biochemical reaction networks
Constantino, P. H.; Vlysidis, M.; Smadbeck, P.; Kaznessis, Y. N.
2016-03-01
Small biomolecular systems are inherently stochastic. Indeed, fluctuations of molecular species are substantial in living organisms and may result in significant variation in cellular phenotypes. The chemical master equation (CME) is the most detailed mathematical model that can describe stochastic behaviors. However, because of its complexity the CME has been solved for only few, very small reaction networks. As a result, the contribution of CME-based approaches to biology has been very limited. In this review we discuss the approach of solving CME by a set of differential equations of probability moments, called moment equations. We present different approaches to produce and to solve these equations, emphasizing the use of factorial moments and the zero information entropy closure scheme. We also provide information on the stability analysis of stochastic systems. Finally, we speculate on the utility of CME-based modeling formalisms, especially in the context of synthetic biology efforts.
Comparison of DSMC Reaction Models with QCT Reaction Rates for Nitrogen
2016-07-17
include area code) N/A Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. 239.18 Comparison of DSMC Reaction Models with QCT Reaction Rates ...controls vibration coupling A is adjusted to match thermal reaction rate Simplest to implement, not tied to any other model Distribution A: Approved for...General trend: reaction rate increases with v • TCE, QK: lack of vibrational favoring results in much lower slope as compared to the benchmark QCT • VFD: φ
1988 DOE model conference proceedings: Volume 4
Energy Technology Data Exchange (ETDEWEB)
1988-01-01
These Proceedings of the October 3-7, 1988, DOE Model Conference are a compilation of the papers that were presented in the technical or poster sessions at the conference. Papers and posters not submitted for publication are not included in the Proceedings. The Table of Contents lists the titles of papers as well as the names of the presenters. These individuals are not, in all cases, the primary authors of the papers published. The actual title pages, appearing later with the papers, show the primary author(s) and all co-authors. The papers in all three volumes of the Proceedings appear as they were originally submitted for publication and have not been edited or changed in any way. Topics discussed in Volume 4 include site characterization and remediation projects, environmental monitoring and modeling; disposal site selection and facility design, risk assessment, safety and health issues, and site remediation technology.
Effects of uncertainty in model predictions of individual tree volume on large area volume estimates
Ronald E. McRoberts; James A. Westfall
2014-01-01
Forest inventory estimates of tree volume for large areas are typically calculated by adding model predictions of volumes for individual trees. However, the uncertainty in the model predictions is generally ignored with the result that the precision of the large area volume estimates is overestimated. The primary study objective was to estimate the effects of model...
Medical Countermeasure Models. Volume 8. Botulinum Neurotoxin
2013-04-12
of Internal Medicine . 129(221-228). 1998. Medical Countermeasure Models Volume 8: Botulinum Neurotoxin Gryphon Scientific, LLC 6 Figure...Sauteed Onions . Clinical and Epidemiological Observations.” Journal of the American Medical Association. 253(9). 1985. 23 Arnon SS et al. “Botulinum...Factors that Predict Outcome in Type A Foodborne Botulism.” The American Journal of Medicine . 76. 1984. 25 CDC. “Notice of CDC’s Discontinuation of
Modeling of Reaction Processes Controlled by Diffusion
Revelli, J
2003-01-01
Stochastic modeling is quite powerful in science and technology.The technics derived from this process have been used with great success in laser theory, biological systems and chemical reactions.Besides, they provide a theoretical framework for the analysis of experimental results on the field of particle's diffusion in ordered and disordered materials.In this work we analyze transport processes in one-dimensional fluctuating media, which are media that change their state in time.This fact induces changes in the movements of the particles giving rise to different phenomena and dynamics that will be described and analyzed in this work.We present some random walk models to describe these fluctuating media.These models include state transitions governed by different dynamical processes.We also analyze the trapping problem in a lattice by means of a simple model which predicts a resonance-like phenomenon.Also we study effective diffusion processes over surfaces due to random walks in the bulk.We consider differe...
Investigation and Modelling of Diesel Hydrotreating Reactions
DEFF Research Database (Denmark)
Boesen, Rasmus Risum
it has received increased attention within the last decade due to tightened legislations regarding the sulfur content, e.g. the demand for Ultra Low Sulfur Diesel (ULSD) with a maximum sulfur content of as low as 10 ppm S has increased. The process is complex, as the performance of a hydrotreating......This project consists of a series of studies, that are related to hydrotreating of diesel. Hy- drotreating is an important refinery process, in which the oil stream is upgraded to meet the required environmental specifications and physical properties. Although hydrotreating is a ma- ture technology...... due to a stronger adsorption on hydrogenation sites. Since feeds used in the hydrotreating process, usually gas-oils, are complex mixtures with a large number of compounds, analysis of the reactions of individual compounds can be difficult. In this work a model-diesel feed consisting of 13 different...
Model Experiment of Thermal Runaway Reactions Using the Aluminum-Hydrochloric Acid Reaction
Kitabayashi, Suguru; Nakano, Masayoshi; Nishikawa, Kazuyuki; Koga, Nobuyoshi
2016-01-01
A laboratory exercise for the education of students about thermal runaway reactions based on the reaction between aluminum and hydrochloric acid as a model reaction is proposed. In the introductory part of the exercise, the induction period and subsequent thermal runaway behavior are evaluated via a simple observation of hydrogen gas evolution and…
Modeling nuclear volume isotope effects in crystals
Schauble, Edwin A.
2013-01-01
Mass-independent isotope fractionations driven by differences in volumes and shapes of nuclei (the field shift effect) are known in several elements and are likely to be found in more. All-electron relativistic electronic structure calculations can predict this effect but at present are computationally intensive and limited to modeling small gas phase molecules and clusters. Density functional theory, using the projector augmented wave method (DFT-PAW), has advantages in greater speed and compatibility with a three-dimensional periodic boundary condition while preserving information about the effects of chemistry on electron densities within nuclei. These electron density variations determine the volume component of the field shift effect. In this study, DFT-PAW calculations are calibrated against all-electron, relativistic Dirac–Hartree–Fock, and coupled-cluster with single, double (triple) excitation methods for estimating nuclear volume isotope effects. DFT-PAW calculations accurately reproduce changes in electron densities within nuclei in typical molecules, when PAW datasets constructed with finite nuclei are used. Nuclear volume contributions to vapor–crystal isotope fractionation are calculated for elemental cadmium and mercury, showing good agreement with experiments. The nuclear-volume component of mercury and cadmium isotope fractionations between atomic vapor and montroydite (HgO), cinnabar (HgS), calomel (Hg2Cl2), monteponite (CdO), and the CdS polymorphs hawleyite and greenockite are calculated, indicating preferential incorporation of neutron-rich isotopes in more oxidized, ionically bonded phases. Finally, field shift energies are related to Mössbauer isomer shifts, and equilibrium mass-independent fractionations for several tin-bearing crystals are calculated from 119Sn spectra. Isomer shift data should simplify calculations of mass-independent isotope fractionations in other elements with Mössbauer isotopes, such as platinum and uranium
Modeling nuclear volume isotope effects in crystals.
Schauble, Edwin A
2013-10-29
Mass-independent isotope fractionations driven by differences in volumes and shapes of nuclei (the field shift effect) are known in several elements and are likely to be found in more. All-electron relativistic electronic structure calculations can predict this effect but at present are computationally intensive and limited to modeling small gas phase molecules and clusters. Density functional theory, using the projector augmented wave method (DFT-PAW), has advantages in greater speed and compatibility with a three-dimensional periodic boundary condition while preserving information about the effects of chemistry on electron densities within nuclei. These electron density variations determine the volume component of the field shift effect. In this study, DFT-PAW calculations are calibrated against all-electron, relativistic Dirac-Hartree-Fock, and coupled-cluster with single, double (triple) excitation methods for estimating nuclear volume isotope effects. DFT-PAW calculations accurately reproduce changes in electron densities within nuclei in typical molecules, when PAW datasets constructed with finite nuclei are used. Nuclear volume contributions to vapor-crystal isotope fractionation are calculated for elemental cadmium and mercury, showing good agreement with experiments. The nuclear-volume component of mercury and cadmium isotope fractionations between atomic vapor and montroydite (HgO), cinnabar (HgS), calomel (Hg2Cl2), monteponite (CdO), and the CdS polymorphs hawleyite and greenockite are calculated, indicating preferential incorporation of neutron-rich isotopes in more oxidized, ionically bonded phases. Finally, field shift energies are related to Mössbauer isomer shifts, and equilibrium mass-independent fractionations for several tin-bearing crystals are calculated from (119)Sn spectra. Isomer shift data should simplify calculations of mass-independent isotope fractionations in other elements with Mössbauer isotopes, such as platinum and uranium.
1988 DOE model conference proceedings: Volume 3
Energy Technology Data Exchange (ETDEWEB)
1988-01-01
These Proceedings of the October 3 - 7, 1988, DOE Model Conference are a compilation of the papers that were presented in the technical or poster sessions at the conference. Papers and posters not submitted for publication are not included in the Proceedings. The Table of Contents lists the titles of papers as well as the names of the presenters. These individuals are not, in all cases, the primary authors of the papers published. The actual title pages, appearing later with the papers, show the primary author(s) and all co-authors. The papers in all three volumes of the proceedings appear as they were originally submitted for publication and have not been edited or changed in any way. Topics included in Volume 3 include treatment of soils, waste characterization and certification, waste minimization site remediation management plans and programs, and training programs.
1988 DOE model conference proceedings: Volume 1
Energy Technology Data Exchange (ETDEWEB)
1988-01-01
These Proceedings of the October 3-7, 1988, DOE Model Conference are a compilation of the papers that were presented in the technical or poster sessions at the conference. Papers and posters not submitted for publication are not included in the Proceedings. The Table of Contents lists the titles of papers as well as the names of the presenters. These individuals are not, in all cases, the primary authors of the papers published. The actual title pages, appearing later with the papers, show the primary author(s) and all co-authors. The papers in all three volumes of the Proceedings appear as they were originally submitted for publication and have not been edited or changed in any way. Topics included in Volume 1 are Environmental Data Management, Site characterization technology, Wastewater treatment, Waste management in foreign countries, Transuranic waste management, and Groundwater characterization and treatment.
1988 DOE model conference proceedings: Volume 5
Energy Technology Data Exchange (ETDEWEB)
1988-01-01
These Proceedings of the October 3--7, 1988 DOE Model Conference are a compilation of the papers that were presented in the technical or poster sessions at the conference papers and posters not submitted for publication are not included in the Proceedings. The Table of Contents lists the titles of papers as well as the names of the presenters. These individuals are not, in all cases, the primary authors of the papers published. The actual title pages, appearing later with the papers, show the primary author(s) and all co-authors. The papers in all three volumes of the Proceedings appear as they were originally submitted for publication and have not been edited or changed in any way. Topics discussed in Volume 5 include environmental assessments and program strategies, waste treatment technologies, and regulations and compliance studies.
Model for reaction kinetics in pyrolysis of wood
Energy Technology Data Exchange (ETDEWEB)
Ahuja, P.; Singh, P.C.; Upadhyay, S.N.; Kumar, S. [Banaras Hindu Univ., Varanasi (India)
1996-12-31
A reaction model for the pyrolysis of small and large particles of wood Is developed. The chemical reactions that take place when biomass is pyrolyzed are the devolatilization reactions (primary) and due to the vapour-solid interactions (secondary). In the case of small particles, when the volatiles are immediately removed by the purge gas, only primary reactions occur and the reaction model is described by weight loss and char forming reactions. The of heterogeneous secondary reactions occur in the case of large particles due to the interaction between the volatiles and the hot nascent primary char. A chain reaction mechanism of secondary char formation is proposed. The model takes both the volatiles retention time and cracking and repolymerization reactions of the vapours with the decomposing solid as well as autocatalysis into consideration. 7 refs., 3 figs., 2 tabs.
Model for reaction kinetics in pyrolysis of wood
Energy Technology Data Exchange (ETDEWEB)
Ahuja, P.; Singh, P.C.; Upadhyay, S.N.; Kuma, S. [Banaras Hindu Univ., Varanasi (India)
1996-12-31
A reaction model for the pyrolysis of small and large particles of wood is developed. The chemical reactions that take place when biomass is pyrolyzed are the devolatilization reactions (primary) and due to the vapour-solid interactions (secondary). In the case of small particles, when the volatiles are immediately removed by the purge gas, only primary reactions occur and the reaction model is described by weight loss and char forming reactions. The heterogeneous secondary reactions occur in the case of large particles due to the interaction between the volatiles and the hot nascent primary char. A chain reaction mechanism of secondary char formation is proposed. The model takes both the volatiles retention time and cracking and repolymerization reactions of the vapours with the decomposing solid as well as autocatalysis into consideration. 6 refs., 3 figs., 2 tabs.
Kinetic modelling of the Maillard reaction between proteins and sugars
Brands, C.M.J.
2002-01-01
Keywords: Maillard reaction, sugar isomerisation, kinetics, multiresponse modelling, brown colour formation, lysine damage, mutagenicity, casein, monosaccharides, disaccharides, aldoses, ketoses
The aim of this thesis was to determine the kinetics of the Maillard reaction between
Vilkas, Marius J.; Zhan, Chang-Guo
2008-11-01
An efficient algorithm of the surface and volume polarization for electrostatics (SVPE) method in self-consistent reaction field (SCRF) theory, denoted by SV(1)PE, has been proposed to simulate direct volume polarization potential with a single layer of point charges outside the solute cavity while the indirect effects of volume polarization on surface polarization are still simulated with multiple layers of point charges. The free energies of solvation calculated using the SV(1)PE algorithm (implemented in GAUSSIAN03) reproduce the corresponding values calculated using the standard SVPE implementation within an error of only ˜0.1% when the solute cavity is defined by the standard 0.001e/a03 solute charge isodensity contour. The SV(1)PE results are much less sensitive to the used cavity size in comparison with the well-established surface and simulated volume polarization for electrostatics [SS(V)PE] method which simulates volume polarization through an additional surface charge distribution on the cavity surface. The SCRF calculations using the SV(1)PE method are more efficient than those using the original SVPE method.
Atmospheric Renewable Energy Research, Volume 5 (Solar Radiation Flux Model)
2017-09-01
ARL-TR-8155 ● SEP 2017 US Army Research Laboratory Atmospheric Renewable Energy Research, Volume 5 (Solar Radiation Flux Model... Energy Research, Volume 5 (Solar Radiation Flux Model) by Clayton Walker and Gail Vaucher Computational and Information Sciences Directorate, ARL...2017 June 28 4. TITLE AND SUBTITLE Atmospheric Renewable Energy Research, Volume 5 (Solar Radiation Flux Model) 5a. CONTRACT NUMBER ROTC Internship
Reactions of the students to integral volume problems and socio–psycho–mathematical relationship
Directory of Open Access Journals (Sweden)
Ergene Özkan
2016-01-01
Full Text Available In this research; how the changes in reactions which university students give integral volume problems before solution and after solution affect the solution processes is inspected. In the study adopting qualitative paradigm’s interpretive approach, case study is used as study design. Participants of the research are the 142 students which had been chosen from four different faculties of two universities in Istanbul, using nonprobability sampling. Semi-structured interviews were conducted with two students randomly chosen from every department and Integral Volume Pre Solution Test and Integral Volume Solution and After Solution Test were used as data collection tools. The data have been analyzed using descriptive analysis and presented by frequency and percentage tables. As a result of the research, it is concluded that the reactions of the students in the faculty, their familiarity to the mathematical statement and their attitude towards the problem and faculty based institutional differences such as professors, professional expectation causes the evolution of the socio-psycho-mathematical relationship between university students and problems and that affects the solution processes.
DEFF Research Database (Denmark)
Kemppainen, Erno; Halme, Janne; Hansen, Ole
2016-01-01
With electrocatalysts it is important to be able to distinguish between the effects of mass transport and reaction kinetics on the performance of the catalyst. When the hydrogen evolution reaction (HER) is considered, an additional and often neglected detail of mass transport in liquid...... the gas volume fraction is sufficiently high to facilitate H2 transfer to bubbles within a distance shorter than the diffusion layer thickness. At current densities below about 40 mA/cm2 the model reduces to an analytical approximation that has characteristics similar to the diffusion of H2. At higher...... current densities the increase in the gas volume fraction makes the H2 surface concentration nonlinear with respect to the current density. Compared to the typical diffusion layer model, our model is an extension that allows more detailed studies of reaction kinetics and mass transport in the electrolyte...
A Reaction-Diffusion Model of Cholinergic Retinal Waves
Lansdell, Benjamin; Ford, Kevin; Kutz, J. Nathan
2014-01-01
Prior to receiving visual stimuli, spontaneous, correlated activity in the retina, called retinal waves, drives activity-dependent developmental programs. Early-stage waves mediated by acetylcholine (ACh) manifest as slow, spreading bursts of action potentials. They are believed to be initiated by the spontaneous firing of Starburst Amacrine Cells (SACs), whose dense, recurrent connectivity then propagates this activity laterally. Their inter-wave interval and shifting wave boundaries are the result of the slow after-hyperpolarization of the SACs creating an evolving mosaic of recruitable and refractory cells, which can and cannot participate in waves, respectively. Recent evidence suggests that cholinergic waves may be modulated by the extracellular concentration of ACh. Here, we construct a simplified, biophysically consistent, reaction-diffusion model of cholinergic retinal waves capable of recapitulating wave dynamics observed in mice retina recordings. The dense, recurrent connectivity of SACs is modeled through local, excitatory coupling occurring via the volume release and diffusion of ACh. In addition to simulation, we are thus able to use non-linear wave theory to connect wave features to underlying physiological parameters, making the model useful in determining appropriate pharmacological manipulations to experimentally produce waves of a prescribed spatiotemporal character. The model is used to determine how ACh mediated connectivity may modulate wave activity, and how parameters such as the spontaneous activation rate and sAHP refractory period contribute to critical wave size variability. PMID:25474327
Disturbances in reaction wheels; from measurement to modelling
Le, M.P.; Ellenbroek, Marcellinus Hermannus Maria; Seiler, R; van Put, P.; Cottaar, E.J.E.
2014-01-01
Disturbances in reaction wheels have been long a crucial aspect for many scientific observation missions. An accurate and reliable disturbance model to understand and evaluate the influence of reaction wheel disturbances to the spacecraft is critically needed. Several reaction wheel disturbance
A computational study of pyrolysis reactions of lignin model compounds
Thomas Elder
2010-01-01
Enthalpies of reaction for the initial steps in the pyrolysis of lignin have been evaluated at the CBS-4m level of theory using fully substituted b-O-4 dilignols. Values for competing unimolecular decomposition reactions are consistent with results previously published for phenethyl phenyl ether models, but with lowered selectivity. Chain propagating reactions of free...
Including lateral interactions into microkinetic models of catalytic reactions
DEFF Research Database (Denmark)
Hellman, Anders; Honkala, Johanna Karoliina
2007-01-01
In many catalytic reactions lateral interactions between adsorbates are believed to have a strong influence on the reaction rates. We apply a microkinetic model to explore the effect of lateral interactions and how to efficiently take them into account in a simple catalytic reaction. Three...
DEFF Research Database (Denmark)
Kemppainen, Erno; Halme, Janne; Hansen, Ole
2016-01-01
With electrocatalysts it is important to be able to distinguish between the effects of mass transport and reaction kinetics on the performance of the catalyst. When the hydrogen evolution reaction (HER) is considered, an additional and often neglected detail of mass transport in liquid is the evo......With electrocatalysts it is important to be able to distinguish between the effects of mass transport and reaction kinetics on the performance of the catalyst. When the hydrogen evolution reaction (HER) is considered, an additional and often neglected detail of mass transport in liquid...... current densities the increase in the gas volume fraction makes the H2 surface concentration nonlinear with respect to the current density. Compared to the typical diffusion layer model, our model is an extension that allows more detailed studies of reaction kinetics and mass transport in the electrolyte...
Adverse reaction after hyaluronan injection for minimally invasive papilla volume augmentation
DEFF Research Database (Denmark)
Bertl, Kristina; Gotfredsen, Klaus; Jensen, Simon S
2017-01-01
tenderness with a burning sensation on the lip next to the injection area, after the second injection session. In one of the cases, a net-like skin discoloration (livedo reticularis) was also noted. The symptoms lasted for up to 7 days, and in both cases, symptoms resolved without any signs of skin......OBJECTIVES: To report two cases of adverse reaction after mucosal hyaluronan (HY) injection around implant-supported crowns, with the aim to augment the missing interdental papilla. MATERIAL AND METHODS: Two patients with single, non-neighbouring, implants in the anterior maxilla, who were treated...... within the frames of a randomized controlled clinical trial testing the effectiveness of HY gel injection to reconstruct missing papilla volume at single implants, presented an adverse reaction. Injection of HY was performed bilaterally using a 3-step technique: (i) creation of a reservoir in the mucosa...
Reaction Kinetics Model of Polymerization in the Absence of ...
African Journals Online (AJOL)
This paper is on reaction kinetics models for approximating diffuse propagation reaction fronts in one-dimensional gasless combustion type models. This study is carried out in the context of free-radical frontal polymerization (FP) via a propagating, self sustaining reacting front in the absence of material diffusion. The model ...
Reaction Wheel Disturbance Model Extraction Software Project
National Aeronautics and Space Administration — Reaction wheel mechanical noise is one of the largest sources of disturbance forcing on space-based observatories. Such noise arises from mass imbalance, bearing...
Reaction Wheel Disturbance Model Extraction Software Project
National Aeronautics and Space Administration — Reaction wheel disturbances are some of the largest sources of noise on sensitive telescopes. Such wheel-induced mechanical noises are not well characterized....
Modelling Chemical Reasoning to Predict and Invent Reactions.
Segler, Marwin H S; Waller, Mark P
2017-05-02
The ability to reason beyond established knowledge allows organic chemists to solve synthetic problems and invent novel transformations. Herein, we propose a model that mimics chemical reasoning, and formalises reaction prediction as finding missing links in a knowledge graph. We have constructed a knowledge graph containing 14.4 million molecules and 8.2 million binary reactions, which represents the bulk of all chemical reactions ever published in the scientific literature. Our model outperforms a rule-based expert system in the reaction prediction task for 180 000 randomly selected binary reactions. The data-driven model generalises even beyond known reaction types, and is thus capable of effectively (re-)discovering novel transformations (even including transition metal-catalysed reactions). Our model enables computers to infer hypotheses about reactivity and reactions by only considering the intrinsic local structure of the graph and because each single reaction prediction is typically achieved in a sub-second time frame, the model can be used as a high-throughput generator of reaction hypotheses for reaction discovery. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
A Gibbs Energy Minimization Approach for Modeling of Chemical Reactions in a Basic Oxygen Furnace
Kruskopf, Ari; Visuri, Ville-Valtteri
2017-12-01
In modern steelmaking, the decarburization of hot metal is converted into steel primarily in converter processes, such as the basic oxygen furnace. The objective of this work was to develop a new mathematical model for top blown steel converter, which accounts for the complex reaction equilibria in the impact zone, also known as the hot spot, as well as the associated mass and heat transport. An in-house computer code of the model has been developed in Matlab. The main assumption of the model is that all reactions take place in a specified reaction zone. The mass transfer between the reaction volume, bulk slag, and metal determine the reaction rates for the species. The thermodynamic equilibrium is calculated using the partitioning of Gibbs energy (PGE) method. The activity model for the liquid metal is the unified interaction parameter model and for the liquid slag the modified quasichemical model (MQM). The MQM was validated by calculating iso-activity lines for the liquid slag components. The PGE method together with the MQM was validated by calculating liquidus lines for solid components. The results were compared with measurements from literature. The full chemical reaction model was validated by comparing the metal and slag compositions to measurements from industrial scale converter. The predictions were found to be in good agreement with the measured values. Furthermore, the accuracy of the model was found to compare favorably with the models proposed in the literature. The real-time capability of the proposed model was confirmed in test calculations.
A Gibbs Energy Minimization Approach for Modeling of Chemical Reactions in a Basic Oxygen Furnace
Kruskopf, Ari; Visuri, Ville-Valtteri
2017-08-01
In modern steelmaking, the decarburization of hot metal is converted into steel primarily in converter processes, such as the basic oxygen furnace. The objective of this work was to develop a new mathematical model for top blown steel converter, which accounts for the complex reaction equilibria in the impact zone, also known as the hot spot, as well as the associated mass and heat transport. An in-house computer code of the model has been developed in Matlab. The main assumption of the model is that all reactions take place in a specified reaction zone. The mass transfer between the reaction volume, bulk slag, and metal determine the reaction rates for the species. The thermodynamic equilibrium is calculated using the partitioning of Gibbs energy (PGE) method. The activity model for the liquid metal is the unified interaction parameter model and for the liquid slag the modified quasichemical model (MQM). The MQM was validated by calculating iso-activity lines for the liquid slag components. The PGE method together with the MQM was validated by calculating liquidus lines for solid components. The results were compared with measurements from literature. The full chemical reaction model was validated by comparing the metal and slag compositions to measurements from industrial scale converter. The predictions were found to be in good agreement with the measured values. Furthermore, the accuracy of the model was found to compare favorably with the models proposed in the literature. The real-time capability of the proposed model was confirmed in test calculations.
Effects of reaction-kinetic parameters on modeling reaction pathways in GaN MOVPE growth
Zhang, Hong; Zuo, Ran; Zhang, Guoyi
2017-11-01
In the modeling of the reaction-transport process in GaN MOVPE growth, the selections of kinetic parameters (activation energy Ea and pre-exponential factor A) for gas reactions are quite uncertain, which cause uncertainties in both gas reaction path and growth rate. In this study, numerical modeling of the reaction-transport process for GaN MOVPE growth in a vertical rotating disk reactor is conducted with varying kinetic parameters for main reaction paths. By comparisons of the molar concentrations of major Ga-containing species and the growth rates, the effects of kinetic parameters on gas reaction paths are determined. The results show that, depending on the values of the kinetic parameters, the gas reaction path may be dominated either by adduct/amide formation path, or by TMG pyrolysis path, or by both. Although the reaction path varies with different kinetic parameters, the predicted growth rates change only slightly because the total transport rate of Ga-containing species to the substrate changes slightly with reaction paths. This explains why previous authors using different chemical models predicted growth rates close to the experiment values. By varying the pre-exponential factor for the amide trimerization, it is found that the more trimers are formed, the lower the growth rates are than the experimental value, which indicates that trimers are poor growth precursors, because of thermal diffusion effect caused by high temperature gradient. The effective order for the contribution of major species to growth rate is found as: pyrolysis species > amides > trimers. The study also shows that radical reactions have little effect on gas reaction path because of the generation and depletion of H radicals in the chain reactions when NH2 is considered as the end species.
Albaugh, Matthew D; Orr, Catherine; Chaarani, Bader; Althoff, Robert R; Allgaier, Nicholas; D'Alberto, Nicholas; Hudson, Kelsey; Mackey, Scott; Spechler, Philip A; Banaschewski, Tobias; Brühl, Rüdiger; Bokde, Arun L W; Bromberg, Uli; Büchel, Christian; Cattrell, Anna; Conrod, Patricia J; Desrivières, Sylvane; Flor, Herta; Frouin, Vincent; Gallinat, Jürgen; Goodman, Robert; Gowland, Penny; Grimmer, Yvonne; Heinz, Andreas; Kappel, Viola; Martinot, Jean-Luc; Paillère Martinot, Marie-Laure; Nees, Frauke; Orfanos, Dimitri Papadopoulos; Penttila, Jani; Poustka, Luise; Paus, Tomáš; Smolka, Michael N; Struve, Maren; Walter, Henrik; Whelan, Robert; Schumann, Gunter; Garavan, Hugh; Potter, Alexandra S
2017-11-01
Neuroimaging studies of attention-deficit/hyperactivity disorder (ADHD) have most commonly reported volumetric abnormalities in the basal ganglia, cerebellum, and prefrontal cortices. Few studies have examined the relationship between ADHD symptomatology and brain structure in population-based samples. We investigated the relationship between dimensional measures of ADHD symptomatology, brain structure, and reaction time variability-an index of lapses in attention. We also tested for associations between brain structural correlates of ADHD symptomatology and maps of dopaminergic gene expression. Psychopathology and imaging data were available for 1538 youths. Parent ratings of ADHD symptoms were obtained using the Development and Well-Being Assessment and the Strengths and Difficulties Questionnaire (SDQ). Self-reports of ADHD symptoms were assessed using the youth version of the SDQ. Reaction time variability was available in a subset of participants. For each measure, whole-brain voxelwise regressions with gray matter volume were calculated. Parent ratings of ADHD symptoms (Development and Well-Being Assessment and SDQ), adolescent self-reports of ADHD symptoms on the SDQ, and reaction time variability were each negatively associated with gray matter volume in an overlapping region of the ventromedial prefrontal cortex. Maps of DRD1 and DRD2 gene expression were associated with brain structural correlates of ADHD symptomatology. This is the first study to reveal relationships between ventromedial prefrontal cortex structure and multi-informant measures of ADHD symptoms in a large population-based sample of adolescents. Our results indicate that ventromedial prefrontal cortex structure is a biomarker for ADHD symptomatology. These findings extend previous research implicating the default mode network and dopaminergic dysfunction in ADHD. Copyright © 2017 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.
Multi-criteria comparative evaluation of spallation reaction models
Andrianov, Andrey; Andrianova, Olga; Konobeev, Alexandr; Korovin, Yury; Kuptsov, Ilya
2017-09-01
This paper presents an approach to a comparative evaluation of the predictive ability of spallation reaction models based on widely used, well-proven multiple-criteria decision analysis methods (MAVT/MAUT, AHP, TOPSIS, PROMETHEE) and the results of such a comparison for 17 spallation reaction models in the presence of the interaction of high-energy protons with natPb.
Chen, Juhui; Yin, Weijie; Wang, Shuai; Meng, Cheng; Li, Jiuru; Qin, Bai; Yu, Guangbin
2016-07-01
Large-eddy simulation (LES) approach is used for gas turbulence, and eddy dissipation concept (EDC)-sub-grid scale (SGS) reaction model is employed for reactions in small eddies. The simulated gas molar fractions are in better agreement with experimental data with EDC-SGS reaction model. The effect of reactions in small eddies on biomass gasification is emphatically analyzed with EDC-SGS reaction model. The distributions of the SGS reaction rates which represent the reactions in small eddies with particles concentration and temperature are analyzed. The distributions of SGS reaction rates have the similar trend with those of total reactions rates and the values account for about 15% of the total reactions rates. The heterogeneous reaction rates with EDC-SGS reaction model are also improved during the biomass gasification process in bubbling fluidized bed. Copyright © 2016 Elsevier Ltd. All rights reserved.
Analysis and Simulation of Hybrid Models for Reaction Networks
Kreim, Michael
2014-01-01
The dynamics of biochemical reaction networks can be described by a variety of models, like the Reaction Rate equation (RRE), the Chemical Master equation (CME) or the Fokker-Planck equation (FPE). In this thesis, the behaviour of these different models is analysed. It is shown that the FPE can be motivated as an approximation of the CME and convergence is proven. Furthermore, two hybrid models are constructed by combining different approaches and convergence properties are proven and discussed.
Reading and a diffusion model analysis of reaction time.
Naples, Adam; Katz, Leonard; Grigorenko, Elena L
2012-01-01
Processing speed is associated with reading performance. However, the literature is not clear either on the definition of processing speed or on why and how it contributes to reading performance. In this study we demonstrated that processing speed, as measured by reaction time, is not a unitary construct. Using the diffusion model of two-choice reaction time, we assessed processing speed in a series of same-different reaction time tasks for letter and number strings. We demonstrated that the association between reaction time and reading performance is driven by processing speed for reading-related information, but not motor or sensory encoding speed.
The Sugar Model: Autocatalytic Activity of the Triose Ammonia Reaction
Weber, Arthur L.
2007-04-01
Reaction of triose sugars with ammonia under anaerobic conditions yielded autocatalytic products. The autocatalytic behavior of the products was examined by measuring the effect of the crude triose ammonia reaction product on the kinetics of a second identical triose ammonia reaction. The reaction product showed autocatalytic activity by increasing both the rate of disappearance of triose and the rate of formation of pyruvaldehyde, the product of triose dehydration. This synthetic process is considered a reasonable model of origin-of-life chemistry because it uses plausible prebiotic substrates, and resembles modern biosynthesis by employing the energized carbon groups of sugars to drive the synthesis of autocatalytic molecules.
Abelian Sandpile Model (ASM) and Infinite Volume Limit
Indian Academy of Sciences (India)
Abelian Sandpile Model (ASM) and. Infinite Volume Limit. Infinite volume limit for the stationary distribution of Abelian sandpile models. http://www.isid.ac.in/ athreya/Research. Joint work with Antal Jarai. To Appear in Communications in Mathematical Physics ...
A model reduction method for biochemical reaction networks
National Research Council Canada - National Science Library
Rao, Shodhan; van der Schaft, Arjan; van Eunen, Karen; Bakker, Barbara; Jayawardhana, Bayu
2014-01-01
Background: In this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill kinetics...
Turing patterns in a reaction-diffusion model with the Degn-Harrison reaction scheme
Li, Shanbing; Wu, Jianhua; Dong, Yaying
2015-09-01
In this paper, we consider a reaction-diffusion model with Degn-Harrison reaction scheme. Some fundamental analytic properties of nonconstant positive solutions are first investigated. We next study the stability of constant steady-state solution to both ODE and PDE models. Our result also indicates that if either the size of the reactor or the effective diffusion rate is large enough, then the system does not admit nonconstant positive solutions. Finally, we establish the global structure of steady-state bifurcations from simple eigenvalues by bifurcation theory and the local structure of the steady-state bifurcations from double eigenvalues by the techniques of space decomposition and implicit function theorem.
Gene dosage imbalances: action, reaction, and models.
Veitia, Reiner A; Potier, Marie Claude
2015-06-01
Single-gene deletions, duplications, and misregulation, as well as aneuploidy, can lead to stoichiometric imbalances within macromolecular complexes and cellular networks, causing their malfunction. Such alterations can be responsible for inherited or somatic genetic disorders including Mendelian diseases, aneuploid syndromes, and cancer. We review the effects of gene dosage alterations at the transcriptomic and proteomic levels, and the various responses of the cell to counteract their effects. Furthermore, we explore several biochemical models and ideas that can provide the rationale for treatments modulating the effects of gene dosage imbalances. Copyright © 2015 Elsevier Ltd. All rights reserved.
Knockout reactions on p-shell nuclei for tests of structure and reaction models
Kuchera, A. N.; Bazin, D.; Babo, M.; Baumann, T.; Bowry, M.; Bradt, J.; Brown, J.; Deyoung, P. A.; Elman, B.; Finck, J. E.; Gade, A.; Grinyer, G. F.; Jones, M. D.; Lunderberg, E.; Redpath, T.; Rogers, W. F.; Stiefel, K.; Thoennessen, M.; Weisshaar, D.; Whitmore, K.
2015-10-01
A series of knockout reactions on p-shell nuclei were studied to extract exclusive cross sections and to investigate the neutron knockout mechanism. The measured cross sections provide stringent tests of shell model and ab initio calculations while measurements of neutron+residual coincidences test the accuracy and validity of reaction models used to predict cross sections. Six different beams ranging from A = 7 to 12 were produced at the NSCL totaling measurements of nine different reaction settings. The reaction settings were determined by the magnetic field of the Sweeper magnet which bends the residues into charged particle detectors. The reaction target was surrounded by the high efficiency CsI array, CAESAR, to tag gamma rays for cross section measurements of low-lying excited states. Additionally, knocked out neutrons were detected with MoNA-LISA in coincidence with the charged residuals. Preliminary results will be discussed. This work is partially supported by the National Science Foundation under Grant No. PHY11-02511 and the Department of Energy National Nuclear Security Administration under Award No. DE-NA0000979.
1987 Oak Ridge model conference: Proceedings: Volume 2, Environmental protection
Energy Technology Data Exchange (ETDEWEB)
1987-01-01
See the abstract for Volume I for general information on the conference. Topics discussed in Volume II include data management techiques for environmental protection efforts, the use of models in environmental auditing, in emergency plans, chemical accident emergency response, risk assessment, monitoring of waste sites, air and water monitoring of waste sites, and in training programs. (TEM)
Storm Water Management Model Reference Manual Volume II ...
SWMM is a dynamic rainfall-runoff simulation model used for single event or long-term (continuous) simulation of runoff quantity and quality from primarily urban areas. The runoff component of SWMM operates on a collection of subcatchment areas that receive precipitation and generate runoff and pollutant loads. The routing portion of SWMM transports this runoff through a system of pipes, channels, storage/treatment devices, pumps, and regulators. SWMM tracks the quantity and quality of runoff generated within each subcatchment, and the flow rate, flow depth, and quality of water in each pipe and channel during a simulation period comprised of multiple time steps. The reference manual for this edition of SWMM is comprised of three volumes. Volume I describes SWMM’s hydrologic models, Volume II its hydraulic models, and Volume III its water quality and low impact development models. This document provides the underlying mathematics for the hydraulic calculations of the Storm Water Management Model (SWMM)
Model-order reduction of biochemical reaction networks
Rao, Shodhan; Schaft, Arjan van der; Eunen, Karen van; Bakker, Barbara M.; Jayawardhana, Bayu
2013-01-01
In this paper we propose a model-order reduction method for chemical reaction networks governed by general enzyme kinetics, including the mass-action and Michaelis-Menten kinetics. The model-order reduction method is based on the Kron reduction of the weighted Laplacian matrix which describes the
An Investigation of Model Catalyzed Hydrocarbon Formation Reactions
Energy Technology Data Exchange (ETDEWEB)
Tysoe, W. T.
2001-05-02
Work was focused on two areas aimed at understanding the chemistry of realistic catalytic systems: (1) The synthesis and characterization of model supported olefin metathesis catalysts. (2) Understanding the role of the carbonaceous layer present on Pd(111) single crystal model catalysts during reaction.
Definition and sensitivity analysis of a finite volume SOFC model for a tubular cell geometry
Campanari, S.; Iora, P.
A finite volume model of a solid oxide fuel cell has been developed. The model applies a detailed electrochemical and thermal analysis to a tubular SOFC of given geometry, material properties and assigned input flows. Electrochemical modeling includes an evaluation of ohmic, activation and diffusion losses as well as a kinetic model of hydrocarbon reactions, based on most recent literature experiences. Internal heat exchange coefficients have been calculated with a specific fluid-dynamic finite volume analysis. The model is calibrated on the available experimental data for atmospheric and pressurized tubular SOFCs, showing the capacity of predicting accurately the SOFC operating conditions. The model generates total cell balances and internal cell profiles for any relevant thermodynamic or electrochemical variable, giving the possibility of discussing the effects of different operating conditions on the internal FC behavior. A sensitivity analysis is carried out to investigate the effects of different assumptions on a selection of key model parameters involved in the calculation of cell losses, internal heat exchange process and reforming reactions. Among other results, it is shown that the importance of the adoption of appropriate parameters for the evaluation of activation polarization, as well as the relevance of a kinetic model for reforming reactions.
Disc volume reduction with percutaneous nucleoplasty in an animal model.
Directory of Open Access Journals (Sweden)
Richard Kasch
Full Text Available STUDY DESIGN: We assessed volume following nucleoplasty disc decompression in lower lumbar spines from cadaveric pigs using 7.1Tesla magnetic resonance imaging (MRI. PURPOSE: To investigate coblation-induced volume reductions as a possible mechanism underlying nucleoplasty. METHODS: We assessed volume following nucleoplastic disc decompression in pig spines using 7.1-Tesla MRI. Volumetry was performed in lumbar discs of 21 postmortem pigs. A preoperative image data set was obtained, volume was determined, and either disc decompression or placebo therapy was performed in a randomized manner. Group 1 (nucleoplasty group was treated according to the usual nucleoplasty protocol with coblation current applied to 6 channels for 10 seconds each in an application field of 360°; in group 2 (placebo group the same procedure was performed but without coblation current. After the procedure, a second data set was generated and volumes calculated and matched with the preoperative measurements in a blinded manner. To analyze the effectiveness of nucleoplasty, volumes between treatment and placebo groups were compared. RESULTS: The average preoperative nucleus volume was 0.994 ml (SD: 0.298 ml. In the nucleoplasty group (n = 21 volume was reduced by an average of 0.087 ml (SD: 0.110 ml or 7.14%. In the placebo group (n = 21 volume was increased by an average of 0.075 ml (SD: 0.075 ml or 8.94%. The average nucleoplasty-induced volume reduction was 0.162 ml (SD: 0.124 ml or 16.08%. Volume reduction in lumbar discs was significant in favor of the nucleoplasty group (p<0.0001. CONCLUSIONS: Our study demonstrates that nucleoplasty has a volume-reducing effect on the lumbar nucleus pulposus in an animal model. Furthermore, we show the volume reduction to be a coblation effect of nucleoplasty in porcine discs.
Thermodynamic properties derived from the free volume model of liquids
Miller, R. I.
1974-01-01
An equation of state and expressions for the isothermal compressibility, thermal expansion coefficient, heat capacity, and entropy of liquids have been derived from the free volume model partition function suggested by Turnbull. The simple definition of the free volume is used, and it is assumed that the specific volume is directly related to the cube of the intermolecular separation by a proportionality factor which is found to be a function of temperature and pressure as well as specific volume. When values of the proportionality factor are calculated from experimental data for real liquids, it is found to be approximately constant over ranges of temperature and pressure which correspond to the dense liquid phase. This result provides a single-parameter method for calculating dense liquid thermodynamic properties and is consistent with the fact that the free volume model is designed to describe liquids near the solidification point.
Modeling Electric Double-Layers Including Chemical Reaction Effects
DEFF Research Database (Denmark)
Paz-Garcia, Juan Manuel; Johannesson, Björn; Ottosen, Lisbeth M.
2014-01-01
for symmetric and asymmetric multi-species electrolytes and is not limited to a range of surface potentials. Numerical simulations are presented, for the case of a CaCO3 electrolyte solution in contact with a surface with rate-controlled protonation/deprotonation reactions. The surface charge and potential...... are determined by the surface reactions, and therefore they depends on the bulk solution composition and concentration......A physicochemical and numerical model for the transient formation of an electric double-layer between an electrolyte and a chemically-active flat surface is presented, based on a finite elements integration of the nonlinear Nernst-Planck-Poisson model including chemical reactions. The model works...
Edge of chaos in reaction diffusion CNN model
Directory of Open Access Journals (Sweden)
Slavova Angela
2017-02-01
Full Text Available In this paper, we study the dynamics of a reaction-diffusion Cellular Nonlinear Network (RD-CNN nodel in which the reaction term is represented by Brusselator cell. We investigate the RD-CNN dynamics by means of describing function method. Comparison with classical results for Brusselator equation is provided. Then we introduce a new RD-CNN model with memristor coupling, for which the edge of chaos regime in the parameter space is determined. Numerical simulations are presented for obtaining dynamic patterns in the RD-CNN model with memristor coupling.
Challenges in modelling the reaction chemistry of interstellar dust.
Bromley, S T; Goumans, T P M; Herbst, E; Jones, A P; Slater, B
2014-09-21
Studies aiming to understand the physicochemical properties of interstellar dust and the chemical reactions that occur on and in it have traditionally been the preserve of astronomical observation and experimental attempts to mimic astronomically relevant conditions in the laboratory. Increasingly, computational modelling in its various guises is establishing a complementary third pillar of support to this endeavour by providing detailed insights into the complexities of interstellar dust chemistry. Inherently, the basis of computational modelling is to be found in the details (e.g. atomic structure/composition, reaction barriers) that are difficult to probe accurately from observation and experiment. This bottom-up atom-based theoretical approach, often itself based on deeper quantum mechanical principles, although extremely powerful, also has limitations when systems become too large or complex. In this Perspective, after first providing a general background to the current state of observational-based knowledge, we introduce a number of computational modelling methods with reference to recent state-of-the-art studies, in order to highlight the capabilities of such approaches in this field. Specifically, we first outline the use of computational chemistry methods for dust nucleation, structure, and individual reactions on bare and icy dust surfaces. Later, we review kinetic modelling of networks of reactions relevant to dust chemistry and how to take into account quantum tunnelling effects in the low temperature reactions in the interstellar medium. Finally, we point to the future challenges that need to be overcome for computational modelling to provide even more detailed and encompassing perspectives on the nature and reaction chemistry of interstellar dust.
Modeling human behaviors and reactions under dangerous environment.
Kang, J; Wright, D K; Qin, S F; Zhao, Y
2005-01-01
This paper describes the framework of a real-time simulation system to model human behavior and reactions in dangerous environments. The system utilizes the latest 3D computer animation techniques, combined with artificial intelligence, robotics and psychology, to model human behavior, reactions and decision making under expected/unexpected dangers in real-time in virtual environments. The development of the system includes: classification on the conscious/subconscious behaviors and reactions of different people; capturing different motion postures by the Eagle Digital System; establishing 3D character animation models; establishing 3D models for the scene; planning the scenario and the contents; and programming within Virtools Dev. Programming within Virtools Dev is subdivided into modeling dangerous events, modeling character's perceptions, modeling character's decision making, modeling character's movements, modeling character's interaction with environment and setting up the virtual cameras. The real-time simulation of human reactions in hazardous environments is invaluable in military defense, fire escape, rescue operation planning, traffic safety studies, and safety planning in chemical factories, the design of buildings, airplanes, ships and trains. Currently, human motion modeling can be realized through established technology, whereas to integrate perception and intelligence into virtual human's motion is still a huge undertaking. The challenges here are the synchronization of motion and intelligence, the accurate modeling of human's vision, smell, touch and hearing, the diversity and effects of emotion and personality in decision making. There are three types of software platforms which could be employed to realize the motion and intelligence within one system, and their advantages and disadvantages are discussed.
Optimized volume models of earthquake-triggered landslides.
Xu, Chong; Xu, Xiwei; Shen, Lingling; Yao, Qi; Tan, Xibin; Kang, Wenjun; Ma, Siyuan; Wu, Xiyan; Cai, Juntao; Gao, Mingxing; Li, Kang
2016-07-12
In this study, we proposed three optimized models for calculating the total volume of landslides triggered by the 2008 Wenchuan, China Mw 7.9 earthquake. First, we calculated the volume of each deposit of 1,415 landslides triggered by the quake based on pre- and post-quake DEMs in 20 m resolution. The samples were used to fit the conventional landslide "volume-area" power law relationship and the 3 optimized models we proposed, respectively. Two data fitting methods, i.e. log-transformed-based linear and original data-based nonlinear least square, were employed to the 4 models. Results show that original data-based nonlinear least square combining with an optimized model considering length, width, height, lithology, slope, peak ground acceleration, and slope aspect shows the best performance. This model was subsequently applied to the database of landslides triggered by the quake except for two largest ones with known volumes. It indicates that the total volume of the 196,007 landslides is about 1.2 × 10(10) m(3) in deposit materials and 1 × 10(10) m(3) in source areas, respectively. The result from the relationship of quake magnitude and entire landslide volume related to individual earthquake is much less than that from this study, which reminds us the necessity to update the power-law relationship.
A model for reaction rates in turbulent reacting flows
Chinitz, W.; Evans, J. S.
1984-01-01
To account for the turbulent temperature and species-concentration fluctuations, a model is presented on the effects of chemical reaction rates in computer analyses of turbulent reacting flows. The model results in two parameters which multiply the terms in the reaction-rate equations. For these two parameters, graphs are presented as functions of the mean values and intensity of the turbulent fluctuations of the temperature and species concentrations. These graphs will facilitate incorporation of the model into existing computer programs which describe turbulent reacting flows. When the model was used in a two-dimensional parabolic-flow computer code to predict the behavior of an experimental, supersonic hydrogen jet burning in air, some improvement in agreement with the experimental data was obtained in the far field in the region near the jet centerline. Recommendations are included for further improvement of the model and for additional comparisons with experimental data.
Energy Technology Data Exchange (ETDEWEB)
NONE
1996-02-26
The Natural Gas Transmission and Distribution Model (NGTDM) of the National Energy Modeling System is developed and maintained by the Energy Information Administration (EIA), Office of Integrated Analysis and Forecasting. This report documents the archived version of the NGTDM that was used to produce the natural gas forecasts presented in the Annual Energy Outlook 1996, (DOE/EIA-0383(96)). The purpose of this report is to provide a reference document for model analysts, users, and the public that defines the objectives of the model, describes its basic approach, and provides detail on the methodology employed. Previously this report represented Volume I of a two-volume set. Volume II reported on model performance, detailing convergence criteria and properties, results of sensitivity testing, comparison of model outputs with the literature and/or other model results, and major unresolved issues.
A Multiple Reaction Modelling Framework for Microbial Electrochemical Technologies
Directory of Open Access Journals (Sweden)
Tolutola Oyetunde
2017-01-01
Full Text Available A mathematical model for the theoretical evaluation of microbial electrochemical technologies (METs is presented that incorporates a detailed physico-chemical framework, includes multiple reactions (both at the electrodes and in the bulk phase and involves a variety of microbial functional groups. The model is applied to two theoretical case studies: (i A microbial electrolysis cell (MEC for continuous anodic volatile fatty acids (VFA oxidation and cathodic VFA reduction to alcohols, for which the theoretical system response to changes in applied voltage and VFA feed ratio (anode-to-cathode as well as membrane type are investigated. This case involves multiple parallel electrode reactions in both anode and cathode compartments; (ii A microbial fuel cell (MFC for cathodic perchlorate reduction, in which the theoretical impact of feed flow rates and concentrations on the overall system performance are investigated. This case involves multiple electrode reactions in series in the cathode compartment. The model structure captures interactions between important system variables based on first principles and provides a platform for the dynamic description of METs involving electrode reactions both in parallel and in series and in both MFC and MEC configurations. Such a theoretical modelling approach, largely based on first principles, appears promising in the development and testing of MET control and optimization strategies.
A model reduction method for biochemical reaction networks
Rao, Shodhan; van der Schaft, Arjan; van Eunen, Karen; Bakker, Barbara; Jayawardhana, Bayu
2014-01-01
Background: In this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill kinetics. The method proceeds by a stepwise reduction in the number of
Python framework for kinetic modeling of electronically excited reaction pathways
Verboncoeur, John; Parsey, Guy; Guclu, Yaman; Christlieb, Andrew
2012-10-01
The use of plasma energy to enhance and control the chemical reactions during combustion, a technology referred to as ``plasma assisted combustion'' (PAC), can result in a variety of beneficial effects: e.g. stable lean operation, pollution reduction, and wider range of p-T operating conditions. While experimental evidence abounds, theoretical understanding of PAC is at best incomplete, and numerical tools still lack in reliable predictive capabilities. In the context of a joint experimental-numerical effort at Michigan State University, we present here an open-source modular Python framework dedicated to the dynamic optimization of non-equilibrium PAC systems. Multiple sources of experimental reaction data, e.g. reaction rates, cross-sections and oscillator strengths, are used in order to quantify the effect of data uncertainty and limiting assumptions. A collisional-radiative model (CRM) is implemented to organize reactions by importance and as a potential means of measuring a non-Maxwellian electron energy distribution function (EEDF), when coupled to optical emission spectroscopy data. Finally, we explore scaling laws in PAC parameter space using a kinetic global model (KGM) accelerated with CRM optimized reaction sequences and sparse stiff integrators.
Geometric Model Extraction from Magnetic Resonance Volume Data
Laidlaw, David H.
1995-01-01
This thesis presents a computational framework and new algorithms for creating geometric models and images of physical objects. Our framework combines magnetic resonance imaging (MRI) research with image processing and volume visualization. One focus is feedback of requirements from later stages of the framework to earlier ones. Within the framework we measure physical objects yielding vector-valued MRI volume datasets. We process these datasets to identify different materials, and from the c...
Melnikov, A. A.; Popov, S. G.; Nikolaev, D. V.; Vikulov, A. D.
2013-04-01
We have investigated the distribution of peripheral blood volumes in different regions of the body in response to the tilt-test in endurance trained athletes after aerobic exercise. Distribution of peripheral blood volumes (ml/beat) simultaneously in six regions of the body (two legs, two hands, abdomen, neck and ECG) was assessed in response to the tilt-test using the impedance method (the impedance change rate (dZ/dT). Before and after exercise session cardiac stroke (CSV) and blood volumes in legs, arms and neck were higher in athletes both in lying and standing positions. Before exercise the increase of heart rate and the decrease of a neck blood volume in response to tilting was lower (p athletes. The reactions in arms and abdomen blood volumes were similar. Also, the neck blood volumes as percentage of CSV (%/CSV) did not change in the control but increased in athletes (p athletes. The neck blood flow (%/CSV) did not change in athletes but decreased in control (pathletes both before and after exercise during fatigue which is due to effective distribution of blood flows aimed at maintaining cerebral blood flow.
The balance model for heat transport from hydrolytic reaction mixture
Directory of Open Access Journals (Sweden)
Janacova Dagmar
2017-01-01
Full Text Available The content of the paper is the industrial application of enzyme hydrolysis of tanning solids waste with a view to minimizing the price of enzyme hydrolysate product, which has widely used. On the base of the energy balance of the enzymatic hydrolysis we estimated the critical minimal charge of a tanning drum. We performed of the critical minimal on the basis of a balance model for heat transport from reaction mixture into the environment through reactor wall. Employing a tanning drum for hydrolytic reaction allows to process tanning wastes in the place of their origin. It means thus considerably to enhancing economics of the whole process.
Spatial Economics Model Predicting Transport Volume
Directory of Open Access Journals (Sweden)
Lu Bo
2016-10-01
Full Text Available It is extremely important to predict the logistics requirements in a scientific and rational way. However, in recent years, the improvement effect on the prediction method is not very significant and the traditional statistical prediction method has the defects of low precision and poor interpretation of the prediction model, which cannot only guarantee the generalization ability of the prediction model theoretically, but also cannot explain the models effectively. Therefore, in combination with the theories of the spatial economics, industrial economics, and neo-classical economics, taking city of Zhuanghe as the research object, the study identifies the leading industry that can produce a large number of cargoes, and further predicts the static logistics generation of the Zhuanghe and hinterlands. By integrating various factors that can affect the regional logistics requirements, this study established a logistics requirements potential model from the aspect of spatial economic principles, and expanded the way of logistics requirements prediction from the single statistical principles to an new area of special and regional economics.
Sadi, M; Dabir, B
2003-01-01
Monte Carlo Method is one of the most powerful techniques to model different processes, such as polymerization reactions. By this method, without any need to solve moment equations, a very detailed information on the structure and properties of polymers are obtained. The number of algorithm repetitions (selected volumes of reactor for modelling which represent the number of initial molecules) is very important in this method. In Monte Carlo method calculations are based on the random number of generations and reaction probability determinations. so the number of algorithm repetition is very important. In this paper, the initiation reaction was considered alone and the importance of number of initiator molecules on the result were studied. It can be concluded that Monte Carlo method will not give accurate results if the number of molecules is not satisfied to be big enough, because in that case , selected volume would not be representative of the whole system.
Modelling biochemical reaction systems by stochastic differential equations with reflection.
Niu, Yuanling; Burrage, Kevin; Chen, Luonan
2016-05-07
In this paper, we gave a new framework for modelling and simulating biochemical reaction systems by stochastic differential equations with reflection not in a heuristic way but in a mathematical way. The model is computationally efficient compared with the discrete-state Markov chain approach, and it ensures that both analytic and numerical solutions remain in a biologically plausible region. Specifically, our model mathematically ensures that species numbers lie in the domain D, which is a physical constraint for biochemical reactions, in contrast to the previous models. The domain D is actually obtained according to the structure of the corresponding chemical Langevin equations, i.e., the boundary is inherent in the biochemical reaction system. A variant of projection method was employed to solve the reflected stochastic differential equation model, and it includes three simple steps, i.e., Euler-Maruyama method was applied to the equations first, and then check whether or not the point lies within the domain D, and if not perform an orthogonal projection. It is found that the projection onto the closure D¯ is the solution to a convex quadratic programming problem. Thus, existing methods for the convex quadratic programming problem can be employed for the orthogonal projection map. Numerical tests on several important problems in biological systems confirmed the efficiency and accuracy of this approach. Copyright © 2016 Elsevier Ltd. All rights reserved.
KINETIC MODELS STUDY OF HYDRODESULPHURIZATION VACUUM DISTILLATE REACTION
Directory of Open Access Journals (Sweden)
AbdulMunem A. Karim
2013-05-01
Full Text Available This study deals with kinetics of hydrodesulphurization (HDS reaction of vacuum gas oil (611-833 K which was distillated from Kirkuk crude oil and which was obtained by blending the fractions, light vacuum gas oil (611 - 650 K, medium vacuum gas oil (650-690 K, heavy vacuum gas oil (690-727 K and very heavy vacuum gas oil (727-833 K. The vacuum gas oil was hydrotreated on a commercial cobalt-molybdenum alumina catalyst presulfied at specified conditions in a laboratory trickle bed reactor. The reaction temperature range (583-643 K,liquid hourly space velocity range (1.5-3.75 h-1 and hydrogen pressure was kept constant at 3.5 MPa with hydrogen to oil ratio about 250 lt/lt. The conversion results for desulphurization reaction appeared to obey the second order reaction. According to this model, the rate constants for desulphurization reaction were determined. Finally, the apparent activation energy (Ea, enthalpy of activation ( H* and entropy ( S* were calculated based on the values of rate constant (k2 and were equal 80.3792 KJ/mole, 75.2974 KJ/mole and 197.493 J/mole, respectively.
Morphological modeling of terrains and volume data
Comic, Lidija; Magillo, Paola; Iuricich, Federico
2014-01-01
This book describes the mathematical background behind discrete approaches to morphological analysis of scalar fields, with a focus on Morse theory and on the discrete theories due to Banchoff and Forman. The algorithms and data structures presented are used for terrain modeling and analysis, molecular shape analysis, and for analysis or visualization of sensor and simulation 3D data sets. It covers a variety of application domains including geography, geology, environmental sciences, medicine and biology. The authors classify the different approaches to morphological analysis which are all ba
Grima, R
2010-07-21
Chemical master equations provide a mathematical description of stochastic reaction kinetics in well-mixed conditions. They are a valid description over length scales that are larger than the reactive mean free path and thus describe kinetics in compartments of mesoscopic and macroscopic dimensions. The trajectories of the stochastic chemical processes described by the master equation can be ensemble-averaged to obtain the average number density of chemical species, i.e., the true concentration, at any spatial scale of interest. For macroscopic volumes, the true concentration is very well approximated by the solution of the corresponding deterministic and macroscopic rate equations, i.e., the macroscopic concentration. However, this equivalence breaks down for mesoscopic volumes. These deviations are particularly significant for open systems and cannot be calculated via the Fokker-Planck or linear-noise approximations of the master equation. We utilize the system-size expansion including terms of the order of Omega(-1/2) to derive a set of differential equations whose solution approximates the true concentration as given by the master equation. These equations are valid in any open or closed chemical reaction network and at both the mesoscopic and macroscopic scales. In the limit of large volumes, the effective mesoscopic rate equations become precisely equal to the conventional macroscopic rate equations. We compare the three formalisms of effective mesoscopic rate equations, conventional rate equations, and chemical master equations by applying them to several biochemical reaction systems (homodimeric and heterodimeric protein-protein interactions, series of sequential enzyme reactions, and positive feedback loops) in nonequilibrium steady-state conditions. In all cases, we find that the effective mesoscopic rate equations can predict very well the true concentration of a chemical species. This provides a useful method by which one can quickly determine the
Directory of Open Access Journals (Sweden)
David eGomez
2015-06-01
Full Text Available Molecular crowding is ubiquitous within cells and affects many biological processes including protein-protein binding, enzyme activities and gene regulation. Here we revisit some generic effects of crowding using a combination of lattice simulations and reaction-diffusion simulations with the program ReaDDy. Specifically, we implement three reactions, simple binding, a diffusion-limited reaction and a reaction with Michaelis-Menten kinetics. Histograms of binding and unbinding times provide a detailed picture how crowding affects these reactions and how the separate effects of crowding on binding equilibrium and on diffusion act together. In addition, we discuss how crowding affects processes related to gene expression such as RNA polymerase-promoter binding and translation elongation.
Shin, Jae Hong; Chung, Yongsug; Park, Joo Hyun
2017-02-01
The refractory-slag-metal-inclusion multiphase reaction model was developed by integrating the refractory-slag, slag-metal, and metal-inclusion elementary reactions in order to predict the evolution of inclusions during the secondary refining processes. The mass transfer coefficient in the metal and slag phase, and the mass transfer coefficient of MgO in the slag were employed in the present multiphase reactions modeling. The "Effective Equilibrium Reaction Zone (EERZ) Model" was basically employed. In this model, the reaction zone volume per unit step for metal and slag phase, which is dependent on the `effective reaction zone depth' in each phase, should be defined. Thus, we evaluated the effective reaction zone depth from the mass transfer coefficient in metal and slag phase at 1873 K (1600 °C) for the desulfurization reaction which was measured in the present study. Because the dissolution rate of MgO from the refractory to slag phase is one of the key factors affecting the slag composition, the mass transfer coefficient of MgO in the ladle slag was also experimentally determined. The calculated results for the variation of the composition of slag and molten steel as a function of reaction time were in good agreement with the experimental results. The MgAl2O4 spinel inclusion was observed at the early to middle stage of the reaction, whereas the liquid oxide inclusion was mainly observed at the final stage of the refining reaction. The content of CaO sharply increased, and the SiO2 content increased mildly with the increasing reaction time, while the content of Al2O3 in the inclusion drastically decreased. Even though there is slight difference between the calculated and measured results, the refractory-slag-metal multiphase reaction model constructed in the present study exhibited a good predictability of the inclusion evolution during ladle refining process.
Assessment of the hybrid propagation model, Volume 2: Comparison with the Integrated Noise Model
2012-08-31
This is the second of two volumes of the report on the Hybrid Propagation Model (HPM), an advanced prediction model for aviation noise propagation. This volume presents comparisons of the HPM and the Integrated Noise Model (INM) for conditions of une...
A model reduction method for biochemical reaction networks.
Rao, Shodhan; van der Schaft, Arjan; van Eunen, Karen; Bakker, Barbara M; Jayawardhana, Bayu
2014-05-03
In this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill kinetics. The method proceeds by a stepwise reduction in the number of complexes, defined as the left and right-hand sides of the reactions in the network. It is based on the Kron reduction of the weighted Laplacian matrix, which describes the graph structure of the complexes and reactions in the network. It does not rely on prior knowledge of the dynamic behaviour of the network and hence can be automated, as we demonstrate. The reduced network has fewer complexes, reactions, variables and parameters as compared to the original network, and yet the behaviour of a preselected set of significant metabolites in the reduced network resembles that of the original network. Moreover the reduced network largely retains the structure and kinetics of the original model. We apply our method to a yeast glycolysis model and a rat liver fatty acid beta-oxidation model. When the number of state variables in the yeast model is reduced from 12 to 7, the difference between metabolite concentrations in the reduced and the full model, averaged over time and species, is only 8%. Likewise, when the number of state variables in the rat-liver beta-oxidation model is reduced from 42 to 29, the difference between the reduced model and the full model is 7.5%. The method has improved our understanding of the dynamics of the two networks. We found that, contrary to the general disposition, the first few metabolites which were deleted from the network during our stepwise reduction approach, are not those with the shortest convergence times. It shows that our reduction approach performs differently from other approaches that are based on time-scale separation. The method can be used to facilitate fitting of the parameters or to embed a detailed model of interest in a more coarse
A stochastic modeling of isotope exchange reactions in glutamine synthetase
Kazmiruk, N. V.; Boronovskiy, S. E.; Nartsissov, Ya R.
2017-11-01
The model presented in this work allows simulation of isotopic exchange reactions at chemical equilibrium catalyzed by a glutamine synthetase. To simulate the functioning of the enzyme the algorithm based on the stochastic approach was applied. The dependence of exchange rates for 14C and 32P on metabolite concentration was estimated. The simulation results confirmed the hypothesis of the ascertained validity for preferred order random binding mechanism. Corresponding values of K0.5 were also obtained.
Diabatic models with transferrable parameters for generalized chemical reactions
Reimers, Jeffrey R.; McKemmish, Laura K.; McKenzie, Ross H.; Hush, Noel S.
2017-05-01
Diabatic models applied to adiabatic electron-transfer theory yield many equations involving just a few parameters that connect ground-state geometries and vibration frequencies to excited-state transition energies and vibration frequencies to the rate constants for electron-transfer reactions, utilizing properties of the conical-intersection seam linking the ground and excited states through the Pseudo Jahn-Teller effect. We review how such simplicity in basic understanding can also be obtained for general chemical reactions. The key feature that must be recognized is that electron-transfer (or hole transfer) processes typically involve one electron (hole) moving between two orbitals, whereas general reactions typically involve two electrons or even four electrons for processes in aromatic molecules. Each additional moving electron leads to new high-energy but interrelated conical-intersection seams that distort the shape of the critical lowest-energy seam. Recognizing this feature shows how conical-intersection descriptors can be transferred between systems, and how general chemical reactions can be compared using the same set of simple parameters. Mathematical relationships are presented depicting how different conical-intersection seams relate to each other, showing that complex problems can be reduced into an effective interaction between the ground-state and a critical excited state to provide the first semi-quantitative implementation of Shaik’s “twin state” concept. Applications are made (i) demonstrating why the chemistry of the first-row elements is qualitatively so different to that of the second and later rows, (ii) deducing the bond-length alternation in hypothetical cyclohexatriene from the observed UV spectroscopy of benzene, (iii) demonstrating that commonly used procedures for modelling surface hopping based on inclusion of only the first-derivative correction to the Born-Oppenheimer approximation are valid in no region of the chemical
Diffusion-controlled reactions modeling in Geant4-DNA
Karamitros, M.; Luan, S.; Bernal, M. A.; Allison, J.; Baldacchino, G.; Davidkova, M.; Francis, Z.; Friedland, W.; Ivantchenko, V.; Ivantchenko, A.; Mantero, A.; Nieminem, P.; Santin, G.; Tran, H. N.; Stepan, V.; Incerti, S.
2014-10-01
Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k-d tree data structure for quickly locating, for a given molecule, its closest reactants. The
Diffusion-controlled reactions modeling in Geant4-DNA
Energy Technology Data Exchange (ETDEWEB)
Karamitros, M., E-mail: matkara@gmail.com [CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, INCIA, UMR 5287, F-33400 Talence (France); Luan, S. [University of New Mexico, Department of Computer Science, Albuquerque, NM (United States); Bernal, M.A. [Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, SP (Brazil); Allison, J. [Geant4 Associates International Ltd (United Kingdom); Baldacchino, G. [CEA Saclay, IRAMIS, LIDYL, Radiation Physical Chemistry Group, F-91191 Gif sur Yvette Cedex (France); CNRS, UMR3299, SIS2M, F-91191 Gif sur Yvette Cedex (France); Davidkova, M. [Nuclear Physics Institute of the ASCR, Prague (Czech Republic); Francis, Z. [Saint Joseph University, Faculty of Sciences, Department of Physics, Mkalles, Beirut (Lebanon); Friedland, W. [Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Radiation Protection, Ingolstädter Landstr. 1, 85764 Neuherberg (Germany); Ivantchenko, V. [Ecoanalytica, 119899 Moscow (Russian Federation); Geant4 Associates International Ltd (United Kingdom); Ivantchenko, A. [Geant4 Associates International Ltd (United Kingdom); Mantero, A. [SwHaRD s.r.l., via Buccari 9, 16153 Genova (Italy); Nieminem, P.; Santin, G. [ESA-ESTEC, 2200 AG Noordwijk (Netherlands); Tran, H.N. [Division of Nuclear Physics and Faculty of Applied Sciences, Ton Duc Thang University, Tan Phong Ward, District 7, Ho Chi Minh City (Viet Nam); Stepan, V. [CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Nuclear Physics Institute of the ASCR, Prague (Czech Republic); Incerti, S., E-mail: incerti@cenbg.in2p3.fr [CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France)
2014-10-01
Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k–d tree data structure for quickly locating, for a given molecule, its closest reactants. The
The Data Model Resource Book Volume 3 Universal Patterns for Data Modeling
Silverston, Len
2011-01-01
This third volume of the best-selling "Data Model Resource Book" series revolutionizes the data modeling discipline by answering the question "How can you save significant time while improving the quality of any type of data modeling effort?" In contrast to the first two volumes, this new volume focuses on the fundamental, underlying patterns that affect over 50 percent of most data modeling efforts. These patterns can be used to considerably reduce modeling time and cost, to jump-start data modeling efforts, as standards and guidelines to increase data model consistency and quality, and as an
Sensitivity of Reaction Rates in X-Ray Burst Models
Borowiak, Jessica; Elliott, Jacob; Estrade, Alfredo; Jacobs, Adam; Schatz, Hendrik; Schmidt, Konrad
2017-09-01
We present a computational project on the rapid-proton capture process that occurs in accreting neutron stars. Our research involves conducting a sensitivity study of the rp-process to nuclear reaction rates in simulations using various compositions for the accreted material onto the neutron stars. In this research, we analyze the effects these variations of composition have on the resulting X-ray bursts simulated by a single-zone rp-process model. Current work is focused on modifying the initial abundances of accreted hydrogen and helium, including a range of values that correspond to the expected composition of X-ray burst sources with reliable observational data. Our objective is to determine which reaction rates have the largest effect on the modeled bursts. A second goal of the project is to implement a script to run the rp-process code in a distributed mode in a computer cluster. With this, we will be able to extend the sensitivity study to a finer grid of different chemical compositions of the accreted material. By running the sensitivity study and examining how the computational data compares with observational data, we can identify nuclear reactions that would need better experimental constraints to improve the accuracy of the rp-process model.
A volume-balance model for flow on porous media
Malaga, Carlos; Mandujano, Francisco; Becerra, Julian
2015-11-01
Volume-balance models are used by petroleum engineers for simulating multiphase and multicomponent flow phenomena in porous media and the extraction process in oil reservoirs. In these models, mass conservation equations and Darcy's law are supplemented by a balance condition for the pore and fluid volumes. This provides a pressure equation suitable for simulating a compressible flow within a compressible solid matrix. Here we present an alternative interpretation of the volume-balance condition that includes the advective transport within a consolidated porous media. We obtain a modified equation for the time evolution of the pressure field. Numerical tests for phase separation under gravity are presented for multiphase three dimensional flow in heterogeneous porous media. The authors acknowledge funding from Fondo Sectorial CONACYT-SENER grant number 42536 (DGAJ-SPI-34-170412-217).
Mathematical Model of Synthesis Catalyst with Local Reaction Centers
Directory of Open Access Journals (Sweden)
I. V. Derevich
2017-01-01
Full Text Available The article considers a catalyst granule with a porous ceramic passive substrate and point active centers on which an exothermic synthesis reaction occurs. A rate of the chemical reaction depends on the temperature according to the Arrhenius law. Heat is removed from the pellet surface in products of synthesis due to heat transfer. In our work we first proposed a model for calculating the steady-state temperature of a catalyst pellet with local reaction centers. Calculation of active centers temperature is based on the idea of self-consistent field (mean-field theory. At first, it is considered that powers of the reaction heat release at the centers are known. On the basis of the found analytical solution, which describes temperature distribution inside the granule, the average temperature of the reaction centers is calculated, which then is inserted in the formula for heat release. The resulting system of transcendental algebraic equations is transformed into a system of ordinary differential equations of relaxation type and solved numerically to achieve a steady-state value. As a practical application, the article considers a Fischer-Tropsch synthesis catalyst granule with active cobalt metallic micro-particles. Cobalt micro-particles are the centers of the exothermic reaction of hydrocarbons macromolecular synthesis. Synthesis occurs as a result of absorption of the components of the synthesis gas on metallic cobalt. The temperature distribution inside the granule for a single local center and reaction centers located on the same granule diameter is found. It was found that there is a critical temperature of reactor exceeding of which leads to significant local overheating of the centers - thermal explosion. The temperature distribution with the local reaction centers is qualitatively different from the granule temperature, calculated in the homogeneous approximation. It is shown that, in contrast to the homogeneous approximation, the
Modeling Bimolecular Reactions and Transport in Porous Media Via Particle Tracking
Energy Technology Data Exchange (ETDEWEB)
Dong Ding; David Benson; Amir Paster; Diogo Bolster
2012-01-01
We use a particle-tracking method to simulate several one-dimensional bimolecular reactive transport experiments. In this numerical method, the reactants are represented by particles: advection and dispersion dominate the flow, and molecular diffusion dictates, in large part, the reactions. The particle/particle reactions are determined by a combination of two probabilities dictated by the physics of transport and energetics of reaction. The first is that reactant particles occupy the same volume over a short time interval. The second is the conditional probability that two collocated particles favorably transform into a reaction. The first probability is a direct physical representation of the degree of mixing in an advancing displacement front, and as such lacks empirical parameters except for the user-defined number of particles. This number can be determined analytically from concentration autocovariance, if this type of data is available. The simulations compare favorably to two physical experiments. In one, the concentration of product, 1,2-naphthoquinoe-4-aminobenzene (NQAB) from reaction between 1,2-naphthoquinone-4-sulfonic acid (NQS) and aniline (AN), was measured at the outflow of a column filled with glass beads at different times. In the other, the concentration distribution of reactants (CuSO_4 and EDTA^{4-}) and products (CuEDTA^{4-}) were quantified by snapshots of transmitted light through a column packed with cryloite sand. The thermodynamic rate coefficient in the latter experiment was 10^7 times greater than the former experiment, making it essentially instantaneous. When compared to the solution of the advection-dispersion-reaction equation (ADRE) with the well-mixed reaction coefficient, the experiments and the particle-tracking simulations showed on the order of 20% to 40% less overall product, which is attributed to poor mixing. The poor mixing also leads to higher product concentrations on the edges of the mixing zones, which the particle
Developed Hybrid Model for Propylene Polymerisation at Optimum Reaction Conditions
Directory of Open Access Journals (Sweden)
Mohammad Jakir Hossain Khan
2016-02-01
Full Text Available A statistical model combined with CFD (computational fluid dynamic method was used to explain the detailed phenomena of the process parameters, and a series of experiments were carried out for propylene polymerisation by varying the feed gas composition, reaction initiation temperature, and system pressure, in a fluidised bed catalytic reactor. The propylene polymerisation rate per pass was considered the response to the analysis. Response surface methodology (RSM, with a full factorial central composite experimental design, was applied to develop the model. In this study, analysis of variance (ANOVA indicated an acceptable value for the coefficient of determination and a suitable estimation of a second-order regression model. For better justification, results were also described through a three-dimensional (3D response surface and a related two-dimensional (2D contour plot. These 3D and 2D response analyses provided significant and easy to understand findings on the effect of all the considered process variables on expected findings. To diagnose the model adequacy, the mathematical relationship between the process variables and the extent of polymer conversion was established through the combination of CFD with statistical tools. All the tests showed that the model is an excellent fit with the experimental validation. The maximum extent of polymer conversion per pass was 5.98% at the set time period and with consistent catalyst and co-catalyst feed rates. The optimum conditions for maximum polymerisation was found at reaction temperature (RT 75 °C, system pressure (SP 25 bar, and 75% monomer concentration (MC. The hydrogen percentage was kept fixed at all times. The coefficient of correlation for reaction temperature, system pressure, and monomer concentration ratio, was found to be 0.932. Thus, the experimental results and model predicted values were a reliable fit at optimum process conditions. Detailed and adaptable CFD results were capable
Forced thermal cycling of catalytic reactions: experiments and modelling
DEFF Research Database (Denmark)
Jensen, Søren; Olsen, Jakob Lind; Thorsteinsson, Sune
2007-01-01
Recent studies of catalytic reactions subjected to fast forced temperature oscillations have revealed a rate enhancement increasing with temperature oscillation frequency. We present detailed studies of the rate enhancement up to frequencies of 2.5 Hz. A maximum in the rate enhancement is observed...... at about 1 Hz. A model for the rate enhancement that includes the surface kinetics and the dynamic partial pressure variations in the reactor is introduced. The model predicts a levelling off of the rate enhancement with frequency at about 1 Hz. The experimentally observed decrease above 1 Hz is explained...
Bayesian inference of chemical kinetic models from proposed reactions
Galagali, Nikhil
2015-02-01
© 2014 Elsevier Ltd. Bayesian inference provides a natural framework for combining experimental data with prior knowledge to develop chemical kinetic models and quantify the associated uncertainties, not only in parameter values but also in model structure. Most existing applications of Bayesian model selection methods to chemical kinetics have been limited to comparisons among a small set of models, however. The significant computational cost of evaluating posterior model probabilities renders traditional Bayesian methods infeasible when the model space becomes large. We present a new framework for tractable Bayesian model inference and uncertainty quantification using a large number of systematically generated model hypotheses. The approach involves imposing point-mass mixture priors over rate constants and exploring the resulting posterior distribution using an adaptive Markov chain Monte Carlo method. The posterior samples are used to identify plausible models, to quantify rate constant uncertainties, and to extract key diagnostic information about model structure-such as the reactions and operating pathways most strongly supported by the data. We provide numerical demonstrations of the proposed framework by inferring kinetic models for catalytic steam and dry reforming of methane using available experimental data.
Measuring individual corrective reaction time using the intermittent illumination model.
Lin, Ray F; Hsu, Chih-Hsiang
2014-01-01
The corrective reaction time (tcr) is an essential motor property when modelling hand control movements. Many studies designed experiments to estimate tcr, but reported only group means with inconsistent definitions. This study proposes an alternative methodology using Drury's (1994) intermittent illumination model. A total of 24 participants performed circular tracking movements under five levels of visual information delay using a modified monitor in a darkened room. Measured movement speeds and the manipulated delays were used with the model to estimate tcr of individuals and test effects of gender and path width. The results showed excellent model fits and demonstrated individual differences of tcr, which was 273 ms on average and ranged from 87 to 441 ms. The wide range of tcr values was due to significant effects of gender and path width. Male participants required shorter tcr compared to female participants, especially for narrow path widths. This study reports the corrective reaction time (tcr) of individuals using a novel methodology. The estimated tcr ranged from 87 to 441 ms, helping model hand control movements, such as aiming and tracking. The methodology can be continuously applied to study tcr under conditions with various performers and movements.
A discrete model to study reaction-diffusion-mechanics systems.
Weise, Louis D; Nash, Martyn P; Panfilov, Alexander V
2011-01-01
This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.
Directory of Open Access Journals (Sweden)
Uraina S. Clark
2018-01-01
Full Text Available There is burgeoning evidence that, among HIV+ adults, exposure to high levels of early life stress (ELS is associated with increased cognitive impairment as well as brain volume abnormalities and elevated neuropsychiatric symptoms. Currently, we have a limited understanding of the degree to which cognitive difficulties observed in HIV+ High-ELS samples reflect underlying neural abnormalities rather than increases in neuropsychiatric symptoms. Here, we utilized a behavioral marker of cognitive function, reaction time intra-individual variability (RT-IIV, which is sensitive to both brain volume reductions and neuropsychiatric symptoms, to elucidate the unique contributions of brain volume abnormalities and neuropsychiatric symptoms to cognitive difficulties in HIV+ High-ELS adults. We assessed the relation of RT-IIV to neuropsychiatric symptom levels and total gray and white matter volumes in 44 HIV+ adults (26 with high ELS. RT-IIV was examined during a working memory task. Self-report measures assessed current neuropsychiatric symptoms (depression, stress, post-traumatic stress disorder. Magnetic resonance imaging was used to quantify total gray and white matter volumes. Compared to Low-ELS participants, High-ELS participants exhibited elevated RT-IIV, elevated neuropsychiatric symptoms, and reduced gray and white matter volumes. Across the entire sample, RT-IIV was significantly associated with gray and white matter volumes, whereas significant associations with neuropsychiatric symptoms were not observed. In the High-ELS group, despite the presence of elevated neuropsychiatric symptom levels, brain volume reductions explained more than 13% of the variance in RT-IIV, whereas neuropsychiatric symptoms explained less than 1%. Collectively, these data provide evidence that, in HIV+ High-ELS adults, ELS-related cognitive difficulties (as indexed by RT-IIV exhibit strong associations with global brain volumes, whereas ELS-related elevations in
Photophysical processes in models of reaction centers of photosynthesis
Energy Technology Data Exchange (ETDEWEB)
Solov`yov, K.N.; Losev, A.P.; Kuz`mitskii, V.A. [Academy of Sciences of Belarus (Russian Federation)] [and others
1995-11-01
Simulation modeling of photosynthesis remains an urgent problem for two reasons. First, the cognitive value of this approach has not been exhausted yet. Second, this should lead to practical use of solar energy with the yield of oxygen, organic products, and nitrogen compounds. At present it has been found that photochemical stages of photosynthesis occur in reaction centers. A greater part of chlorophyll or bacteriochlorophyll molecules function as a light-harvesting antenna. The energy of an absorbed quantum migrates over the antenna and reaches the reaction centers, where the charge is separated and a chemical potential is generated. These are followed by dark stages of photosynthesis. The authors have investigated the photophysical properties of chlorophyll-like molecules and have approached the problem of intramolecular photoinduced electron transfer (PET) in studies of nitroporphyrins.
Reactions of Lignin Model Compounds in Ionic Liquids
Energy Technology Data Exchange (ETDEWEB)
Holladay, John E.; Binder, Joseph B.; Gray, Michel J.; White, James F.; Zhang, Z. Conrad
2009-09-15
Lignin, a readily available form of biomass, awaits novel chemistry for converting it to valuable aromatic chemicals. Recent work has demonstrated that ionic liquids are excellent solvents for processing woody biomass and lignin. Seeking to exploit ionic liquids as media for depolymerization of lignin, we investigated reactions of lignin model compounds in these solvents. Using Brønsted acid catalysts in 1-ethyl-3-methylimidazolium triflate at moderate temperatures, we obtained up to 11.6% yield of the dealkylation product guaiacol from the model compound eugenol and cleaved phenethyl phenyl ether, a model for lignin ethers. Despite these successes, acid catalysis failed in dealkylation of the unsaturated model compound 4-ethylguaiacol and did not produce monomeric products from organosolv lignin, demonstrating that further work is required to understand the complex chemistry of lignin depolymerization.
Ruthig, Gregory R; Deridder, Benjamin P
2012-01-24
The fungal pathogen Batrachochytrium dendrobatidis threatens amphibian populations around the world. The ability to detect this pathogen on infected animals and in the environment is critical for understanding and controlling this pandemic. We tested several advances in quantitative PCR (qPCR) techniques to detect B. dendrobatidis DNA. We used a fast PCR thermocycler and enzymes that reduced the volume and the duration of the reaction. We also compared a conventional TaqMan minor groove binding (MGB) probe to an identical locked nucleic acid (LNA) counterpart. The fast qPCR reaction had a high degree of sensitivity to B. dendrobatidis DNA. The LNA probe was effective for detecting B. dendrobatidis DNA and produced results -similar to those of the MGB probe. The modifications that we tested can improve the cost, time efficiency and specificity of quantitative PCR as a tool for detecting pathogen DNA.
Reaction-Diffusion Modeling ERK- and STAT-Interaction Dynamics
Directory of Open Access Journals (Sweden)
Georgiev Nikola
2006-01-01
Full Text Available The modeling of the dynamics of interaction between ERK and STAT signaling pathways in the cell needs to establish the biochemical diagram of the corresponding proteins interactions as well as the corresponding reaction-diffusion scheme. Starting from the verbal description available in the literature of the cross talk between the two pathways, a simple diagram of interaction between ERK and STAT5a proteins is chosen to write corresponding kinetic equations. The dynamics of interaction is modeled in a form of two-dimensional nonlinear dynamical system for ERK—and STAT5a —protein concentrations. Then the spatial modeling of the interaction is accomplished by introducing an appropriate diffusion-reaction scheme. The obtained system of partial differential equations is analyzed and it is argued that the possibility of Turing bifurcation is presented by loss of stability of the homogeneous steady state and forms dissipative structures in the ERK and STAT interaction process. In these terms, a possible scaffolding effect in the protein interaction is related to the process of stabilization and destabilization of the dissipative structures (pattern formation inherent to the model of ERK and STAT cross talk.
DISCRETE VOLUME-ELEMENT METHOD FOR NETWORK WATER- QUALITY MODELS
An explicit dynamic water-quality modeling algorithm is developed for tracking dissolved substances in water-distribution networks. The algorithm is based on a mass-balance relation within pipes that considers both advective transport and reaction kinetics. Complete mixing of m...
Directory of Open Access Journals (Sweden)
E. I. Ponomareva
2013-01-01
Full Text Available Researches are devoted to identifying changes in the chemical composition of whole-grain wheat bread during baking and to forecasting of food value of bakery products by mathematical modeling of biochemical transformations. The received model represents the invariant composition, considering speed of biochemical reactions at a batch of bakery products, and allowing conduct virtual experiments to develop new types of bread for various categories of the population, including athletes. The offered way of modeling of biochemical transformations at a stage of heat treatment allows to predict food value of bakery products, without spending funds for raw materials and large volume of experiment that will provide possibility of economy of material resources at a stage of development of new types of bakery products and possibility of production efficiency increase.
Traffic Volume Data Outlier Recovery via Tensor Model
Directory of Open Access Journals (Sweden)
Huachun Tan
2013-01-01
Full Text Available Traffic volume data is already collected and used for a variety of purposes in intelligent transportation system (ITS. However, the collected data might be abnormal due to the problem of outlier data caused by malfunctions in data collection and record systems. To fully analyze and operate the collected data, it is necessary to develop a validate method for addressing the outlier data. Many existing algorithms have studied the problem of outlier recovery based on the time series methods. In this paper, a multiway tensor model is proposed for constructing the traffic volume data based on the intrinsic multilinear correlations, such as day to day and hour to hour. Then, a novel tensor recovery method, called ADMM-TR, is proposed for recovering outlier data of traffic volume data. The proposed method is evaluated on synthetic data and real world traffic volume data. Experimental results demonstrate the practicability, effectiveness, and advantage of the proposed method, especially for the real world traffic volume data.
Dynamical evolution of volume fractions in multipressure multiphase flow models.
Chang, C H; Ramshaw, J D
2008-06-01
Compared to single-pressure models, multipressure multiphase flow models require additional closure relations to determine the individual pressures of the different phases. These relations are often taken to be evolution equations for the volume fractions. We present a rigorous theoretical framework for constructing such equations for compressible multiphase mixtures in terms of submodels for the relative volumetric expansion rates DeltaE_{i} of the phases. These quantities are essentially the rates at which the phases dynamically expand or contract in response to pressure differences, and represent the general tendency of the volume fractions to relax toward values that produce local pressure equilibrium. We present a simple provisional model of this type in which DeltaE_{i} is proportional to pressure differences divided by the time required for sound waves to traverse an appropriate characteristic length. It is shown that the resulting approach to pressure equilibrium is monotonic rather than oscillatory, and occurs instantaneously in the incompressible limit.
Control volume based modelling of compressible flow in reciprocating machines
DEFF Research Database (Denmark)
Andersen, Stig Kildegård; Thomsen, Per Grove; Carlsen, Henrik
2004-01-01
An approach to modelling unsteady compressible flow that is primarily one dimensional is presented. The approach was developed for creating distributed models of machines with reciprocating pistons but it is not limited to this application. The approach is based on the integral form of the unsteady...... conservation laws for mass, energy, and momentum applied to a staggered mesh consisting of two overlapping strings of control volumes. Loss mechanisms can be included directly in the governing equations of models by including them as terms in the conservation laws. Heat transfer, flow friction......, and multidimensional effects must be calculated using empirical correlations; correlations for steady state flow can be used as an approximation. A transformation that assumes ideal gas is presented for transforming equations for masses and energies in control volumes into the corresponding pressures and temperatures...
Reaction times to weak test lights. [psychophysics biological model
Wandell, B. A.; Ahumada, P.; Welsh, D.
1984-01-01
Maloney and Wandell (1984) describe a model of the response of a single visual channel to weak test lights. The initial channel response is a linearly filtered version of the stimulus. The filter output is randomly sampled over time. Each time a sample occurs there is some probability increasing with the magnitude of the sampled response - that a discrete detection event is generated. Maloney and Wandell derive the statistics of the detection events. In this paper a test is conducted of the hypothesis that the reaction time responses to the presence of a weak test light are initiated at the first detection event. This makes it possible to extend the application of the model to lights that are slightly above threshold, but still within the linear operating range of the visual system. A parameter-free prediction of the model proposed by Maloney and Wandell for lights detected by this statistic is tested. The data are in agreement with the prediction.
Parametric pattern selection in a reaction-diffusion model.
Directory of Open Access Journals (Sweden)
Michael Stich
Full Text Available We compare spot patterns generated by Turing mechanisms with those generated by replication cascades, in a model one-dimensional reaction-diffusion system. We determine the stability region of spot solutions in parameter space as a function of a natural control parameter (feed-rate where degenerate patterns with different numbers of spots coexist for a fixed feed-rate. While it is possible to generate identical patterns via both mechanisms, we show that replication cascades lead to a wider choice of pattern profiles that can be selected through a tuning of the feed-rate, exploiting hysteresis and directionality effects of the different pattern pathways.
Souza, C A; Oliveira, T C; Crovella, S; Santos, S M; Rabêlo, K C N; Soriano, E P; Carvalho, M V D; Junior, A F Caldas; Porto, G G; Campello, R I C; Antunes, A A; Queiroz, R A; Souza, S M
2017-04-28
The use of Y chromosome haplotypes, important for the detection of sexual crimes in forensics, has gained prominence with the use of databases that incorporate these genetic profiles in their system. Here, we optimized and validated an amplification protocol for Y chromosome profile retrieval in reference samples using lesser materials than those in commercial kits. FTA(®) cards (Flinders Technology Associates) were used to support the oral cells of male individuals, which were amplified directly using the SwabSolution reagent (Promega). First, we optimized and validated the process to define the volume and cycling conditions. Three reference samples and nineteen 1.2 mm-diameter perforated discs were used per sample. Amplification of one or two discs (samples) with the PowerPlex(®) Y23 kit (Promega) was performed using 25, 26, and 27 thermal cycles. Twenty percent, 32%, and 100% reagent volumes, one disc, and 26 cycles were used for the control per sample. Thereafter, all samples (N = 270) were amplified using 27 cycles, one disc, and 32% reagents (optimized conditions). Data was analyzed using a study of equilibrium values between fluorophore colors. In the samples analyzed with 20% volume, an imbalance was observed in peak heights, both inside and in-between each dye. In samples amplified with 32% reagents, the values obtained for the intra-color and inter-color standard balance calculations for verification of the quality of the analyzed peaks were similar to those of samples amplified with 100% of the recommended volume. The quality of the profiles obtained with 32% reagents was suitable for insertion into databases.
A simplified approach to derive Cleland model for enzymatic reactions.
Saraswathi, Ganesan; Panda, Tapobrata; Basak, Tanmay
2013-05-01
Metabolic modeling can suggest which is the key enzyme activity that needs to be controlled or its activity enhanced for the required production of a metabolite in a pathway. It also helps to find possible drug targets (enzymes to be inhibited). In metabolic modeling, knowing the kinetics of the enzymes involved in a pathway is mandatory. Most enzymatic reactions involve multi-substrates and follow an ordered sequential or ping-pong mechanism. The kinetic parameters involved in the model are obtained by fitting experimental data using a model based on the mechanism. The Cleland model has been used for some years. The grouping of parameters, such as dissociation constant and Michaelis-Menten constant, makes the strategy meaningful and hence the Cleland model is still in use. Although other alternate methods, e.g., the King-Altman method, are available, derivation by determinants can be used to derive a rate expression for the sequential or ping-pong mechanism, they are tedious. Hence, a meaningful modification is suggested in this communication for deriving the enzyme mechanism which is based on Thilakavathi et al. (Biotech Lett 28:1889-1894, 2006) to obtain the Cleland model in an easier way.
Energy Technology Data Exchange (ETDEWEB)
NONE
1994-02-24
The Natural Gas Transmission and Distribution Model (NGTDM) is a component of the National Energy Modeling System (NEMS) used to represent the domestic natural gas transmission and distribution system. NEMS is the third in a series of computer-based, midterm energy modeling systems used since 1974 by the Energy Information Administration (EIA) and its predecessor, the Federal Energy Administration, to analyze domestic energy-economy markets and develop projections. This report documents the archived version of NGTDM that was used to produce the natural gas forecasts used in support of the Annual Energy Outlook 1994, DOE/EIA-0383(94). The purpose of this report is to provide a reference document for model analysts, users, and the public that defines the objectives of the model, describes its basic design, provides detail on the methodology employed, and describes the model inputs, outputs, and key assumptions. It is intended to fulfill the legal obligation of the EIA to provide adequate documentation in support of its models (Public Law 94-385, Section 57.b.2). This report represents Volume 1 of a two-volume set. (Volume 2 will report on model performance, detailing convergence criteria and properties, results of sensitivity testing, comparison of model outputs with the literature and/or other model results, and major unresolved issues.) Subsequent chapters of this report provide: (1) an overview of the NGTDM (Chapter 2); (2) a description of the interface between the National Energy Modeling System (NEMS) and the NGTDM (Chapter 3); (3) an overview of the solution methodology of the NGTDM (Chapter 4); (4) the solution methodology for the Annual Flow Module (Chapter 5); (5) the solution methodology for the Distributor Tariff Module (Chapter 6); (6) the solution methodology for the Capacity Expansion Module (Chapter 7); (7) the solution methodology for the Pipeline Tariff Module (Chapter 8); and (8) a description of model assumptions, inputs, and outputs (Chapter 9).
Excluded volume effect enhances the homology pairing of model chromosomes
Takamiya, Kazunori; Yamamoto, Keisuke; Isami, Shuhei; Nishimori, Hiraku; Awazu, Akinori
To investigate the structural dynamics of the homology pairing of polymers, we mod- eled the scenario of homologous chromosome pairings during meiosis in Schizosaccharomyces pombe, one of the simplest model organisms of eukaryotes. We consider a simple model consist- ing of pairs of homologous polymers with the same structures that are confined in a cylindrical container, which represents the local parts of chromosomes contained in an elongated nucleus of S. pombe. Brownian dynamics simulations of this model showed that the excluded volume effects among non-homological chromosomes and the transitional dynamics of nuclear shape serve to enhance the pairing of homologous chromosomes.
Surface models and gradually peeled volume model to explore hand structures.
Chung, Beom Sun; Kwon, Koojoo; Shin, Byeong-Seok; Chung, Min Suk
2017-05-01
This study was intended to confirm whether simultaneous examination of surface and volume models contributes to learning of hand structures. Outlines of the skin, muscles, and bones of the right hand were traced in sectioned images of a male cadaver to create surface models of the structures. After the outlines were filled with selected colors, the color-filled sectioned images were stacked to produce a volume model of the hand, from which the skin was gradually peeled. The surface models provided locational orientation of the hand structures such as extrinsic and intrinsic hand muscles, while the peeled volume model revealed the depth of the individual hand structures. In addition, the characteristic appearances of the radial artery and the wrist joint were confirmed. The exploration of the volume model accompanied by equivalent surface models is synergistically helpful for understanding the morphological properties of hand structures. Copyright © 2017 Elsevier GmbH. All rights reserved.
Becker, D. D.
1980-01-01
The orbiter subsystems and interfacing program elements which interact with the orbiter computer flight software are analyzed. The failure modes identified in the subsystem/element failure mode and effects analysis are examined. Potential interaction with the software is examined through an evaluation of the software requirements. The analysis is restricted to flight software requirements and excludes utility/checkout software. The results of the hardware/software interaction analysis for the forward reaction control system are presented.
Orbiter subsystem hardware/software interaction analysis. Volume 8: Forward reaction control system
Becker, D. D.
1980-01-01
The results of the orbiter hardware/software interaction analysis for the AFT reaction control system are presented. The interaction between hardware failure modes and software are examined in order to identify associated issues and risks. All orbiter subsystems and interfacing program elements which interact with the orbiter computer flight software are analyzed. The failure modes identified in the subsystem/element failure mode and effects analysis are discussed.
Stepwise kinetic equilibrium models of quantitative polymerase chain reaction.
Cobbs, Gary
2012-08-16
Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model the annealing phase and does not assume constant efficiency of amplification. Mechanistic models describing the annealing phase with kinetic theory offer the most potential for accurate interpretation of qPCR data. Even so, they have not been thoroughly investigated and are rarely used for interpretation of qPCR data. New results for kinetic modeling of qPCR are presented. Two models are presented in which the efficiency of amplification is based on equilibrium solutions for the annealing phase of the qPCR process. Model 1 assumes annealing of complementary targets strands and annealing of target and primers are both reversible reactions and reach a dynamic equilibrium. Model 2 assumes all annealing reactions are nonreversible and equilibrium is static. Both models include the effect of primer concentration during the annealing phase. Analytic formulae are given for the equilibrium values of all single and double stranded molecules at the end of the annealing step. The equilibrium values are then used in a stepwise method to describe the whole qPCR process. Rate constants of kinetic models are the same for solutions that are identical except for possibly having different initial target concentrations. Analysis of qPCR curves from such solutions are thus analyzed by simultaneous non-linear curve fitting with the same rate constant values applying to all curves and each curve having a unique value for initial target concentration. The models were fit to two data sets for which the true initial target concentrations are known. Both models give better fit to observed qPCR data than other kinetic models present in the literature. They also give better estimates of
Stepwise kinetic equilibrium models of quantitative polymerase chain reaction
Directory of Open Access Journals (Sweden)
Cobbs Gary
2012-08-01
Full Text Available Abstract Background Numerous models for use in interpreting quantitative PCR (qPCR data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model the annealing phase and does not assume constant efficiency of amplification. Mechanistic models describing the annealing phase with kinetic theory offer the most potential for accurate interpretation of qPCR data. Even so, they have not been thoroughly investigated and are rarely used for interpretation of qPCR data. New results for kinetic modeling of qPCR are presented. Results Two models are presented in which the efficiency of amplification is based on equilibrium solutions for the annealing phase of the qPCR process. Model 1 assumes annealing of complementary targets strands and annealing of target and primers are both reversible reactions and reach a dynamic equilibrium. Model 2 assumes all annealing reactions are nonreversible and equilibrium is static. Both models include the effect of primer concentration during the annealing phase. Analytic formulae are given for the equilibrium values of all single and double stranded molecules at the end of the annealing step. The equilibrium values are then used in a stepwise method to describe the whole qPCR process. Rate constants of kinetic models are the same for solutions that are identical except for possibly having different initial target concentrations. Analysis of qPCR curves from such solutions are thus analyzed by simultaneous non-linear curve fitting with the same rate constant values applying to all curves and each curve having a unique value for initial target concentration. The models were fit to two data sets for which the true initial target concentrations are known. Both models give better fit to observed qPCR data than other kinetic models present in the
In silico strain optimization by adding reactions to metabolic models.
Correia, Sara; Rocha, Miguel
2012-12-01
Nowadays, the concerns about the environment and the needs to increase the productivity at low costs, demand for the search of new ways to produce compounds with industrial interest. Based on the increasing knowledge of biological processes, through genome sequencing projects, and high-throughput experimental techniques as well as the available computational tools, the use of microorganisms has been considered as an approach to produce desirable compounds. However, this usually requires to manipulate these organisms by genetic engineering and/ or changing the enviromental conditions to make the production of these compounds possible. In many cases, it is necessary to enrich the genetic material of those microbes with hereologous pathways from other species and consequently adding the potential to produce novel compounds. This paper introduces a new plug-in for the OptFlux Metabolic Engineering platform, aimed at finding suitable sets of reactions to add to the genomes of selected microbes (wild type strain), as well as finding complementary sets of deletions, so that the mutant becomes able to overproduce compounds with industrial interest, while preserving their viability. The necessity of adding reactions to the metabolic model arises from existing gaps in the original model or motivated by the productions of new compounds by the organism. The optimization methods used are metaheuristics such as Evolutionary Algorithms and Simulated Annealing. The usefulness of this plug-in is demonstrated by a case study, regarding the production of vanillin by the bacterium E. coli.
A quantum constrained kinematic model for elementary chemical reactions
McCaffery, Anthony J.; Truhins, Kaspars; Whiteley, Thomas W. J.
1998-05-01
The model we have termed quantum constrained kinematics and found to give an accurate account of atom-diatom inelastic scattering is tested by application to elementary atom-molecule reactive collisions. The approach emphasizes the disposal of initial relative momentum into rotational angular momentum of the product diatomic via vector relations that are constrained by the internal quantum structure of the product diatomic. We introduce the concept of vibrational momentum of the atoms in a diatomic molecule in order to treat vibrational and rotational excitation of the product species. This representation is valuable in providing a realistic picture of the motion in a heteronuclear diatomic and also indicates how the enthalpy of a reaction may be disposed in momentum terms. It may also provide criteria for assessing the likelihood of particular reaction mechanisms. Comparison of results calculated using the quantum constrained kinematic model with experimental data indicates a number of simple, transferable rule-of-thumb guides to the outcome of reactive collisions. Most probable j values and distributions are accurately predicted using readily available data in parameter-free calculations. It is found that in reactive collisions, initial velocity distributions are mapped onto those of product rotational states via an effective impact parameter distribution that is sharply peaked around the half bond length of the product diatomic molecule.
Magnetic resonance image tissue classification using a partial volume model.
Shattuck, D W; Sandor-Leahy, S R; Schaper, K A; Rottenberg, D A; Leahy, R M
2001-05-01
We describe a sequence of low-level operations to isolate and classify brain tissue within T1-weighted magnetic resonance images (MRI). Our method first removes nonbrain tissue using a combination of anisotropic diffusion filtering, edge detection, and mathematical morphology. We compensate for image nonuniformities due to magnetic field inhomogeneities by fitting a tricubic B-spline gain field to local estimates of the image nonuniformity spaced throughout the MRI volume. The local estimates are computed by fitting a partial volume tissue measurement model to histograms of neighborhoods about each estimate point. The measurement model uses mean tissue intensity and noise variance values computed from the global image and a multiplicative bias parameter that is estimated for each region during the histogram fit. Voxels in the intensity-normalized image are then classified into six tissue types using a maximum a posteriori classifier. This classifier combines the partial volume tissue measurement model with a Gibbs prior that models the spatial properties of the brain. We validate each stage of our algorithm on real and phantom data. Using data from the 20 normal MRI brain data sets of the Internet Brain Segmentation Repository, our method achieved average kappa indices of kappa = 0.746 +/- 0.114 for gray matter (GM) and kappa = 0.798 +/- 0.089 for white matter (WM) compared to expert labeled data. Our method achieved average kappa indices kappa = 0.893 +/- 0.041 for GM and kappa = 0.928 +/- 0.039 for WM compared to the ground truth labeling on 12 volumes from the Montreal Neurological Institute's BrainWeb phantom. Copyright 2001 Academic Press.
Modelling and Simulation of Volume Controlled Mechanical Ventilation System
Directory of Open Access Journals (Sweden)
Yan Shi
2014-01-01
Full Text Available Volume controlled mechanical ventilation system is a typical time-delay system, which is applied to ventilate patients who cannot breathe adequately on their own. To illustrate the influences of key parameters of the ventilator on the dynamics of the ventilated respiratory system, this paper firstly derived a new mathematical model of the ventilation system; secondly, simulation and experimental results are compared to verify the mathematical model; lastly, the influences of key parameters of ventilator on the dynamics of the ventilated respiratory system are carried out. This study can be helpful in the VCV ventilation treatment and respiratory diagnostics.
Soldatov, A. P.
2017-05-01
As part of ongoing studies aimed at designing the next generation of nanosized membrane reactors (NMRs) with accumulated hydrogen, the noncatalytic hydrogenation of naphthalene in pores of ceramic membranes (TRUMEM ultrafiltration membranes with D av = 50 and 90 nm) is performed for the first time, using hydrogen preadsorbed in a hybrid carbon nanostructure: mono- and multilayered oriented carbon nanotubes with graphene walls (OCNTGs) that form on inner pore surfaces. In this technique, the reaction proceeds in the temperature range of 330-390°C at contact times of 10-16 h. The feedstock is an 8% naphthalene solution in decane. The products are analyzed via chromatography on a quartz capillary column coated with polydimethylsiloxane (SE-30). It is established for the first time that in NMRs, the noncatalytic hydrogenation of naphthalene occurs at 370-390°C, forming 1,2,3,4-tetrahydronaphthalene in amounts of up to 0.61%. The rate constants and activation energy (123.5 kJ/mol) of the noncatalytic hydrogenation reaction are determined for the first time. The possibility of designing an NMR with an adjustable reaction zone volume is explored. Changes in the pore structure of the membranes after their modification with pyrocarbon nanosized crystallites (PNCs) are therefore studied as well. It is shown that lengthening the process time reduces pore size: within 23 h after the deposition of PNCs, the average pore radius ( r av) falls from 25 to 3.1 nm. The proposed approach would allow us to design nanoreactors of molecular size and conduct hydrogenation reactions within certain guidelines to synthesize new chemical compounds.
A multi-pathway model for Photosynthetic reaction center
Qin, M; Yi, X X
2015-01-01
Charge separation in light-harvesting complexes occurs in a pair of tightly coupled chlorophylls at the heart of photosynthetic reaction centers of both plants and bacteria. Recently it has been shown that quantum coherence can, in principle, enhance the efficiency of a solar cell, working like a quantum heat engine (QHE). Here, we propose a biological quantum heat engine (BQHE) motivated by Photosystem {\\rm II} reaction center (PS{\\rm II} RC) to describe the charge separation. Our model mainly considers two charge-separation pathways more than that in the published literature. The two pathways can interfere via cross-couplings and work together to enhance the charge-separation yields. We explore how these cross-couplings increase the current and voltage of the charge separation and discuss the advantages of multiple pathways in terms of current and power. The robustness of the BQHE against the charge recombination in natural PS{\\rm II} RC and dephasing induced by environments is also explored, and extension ...
Antioxidative properties of Iberis amara extracts in biochemical model reactions.
Schempp, Harald; Toth, Angela; Weiser, Dieter; Elstner, Erich F
2003-01-01
Gastro-intestinal disorders such as the non-ulcer dyspepsia and irritable bowel syndrome expatiate on/with inflammatory processes of the gastro-intestinal mucosa. Iberogast is used in treatment of such disorders. Iberis amara L. extract (IAE) is one of nine components of the drug. There is increasing evidence that mediators of inflammation processes in the stomach and intestine include reactive oxygen species (ROS), arising from several enzymic reactions characteristic for inflammatory events. In this study it was shown that Iberis amara extract (STW 6) has the potential for scavenging ROS, dependent on the individual test system. Biochemical model reactions relevant for the formation of ROS in vivo at inflammatory sites were used. Inhibition of the formation of ROS could be shown to be excellent in test systems known to preferentially produce reactive species (myeloperoxidase-generated HOCl, peroxynitrite) with high affinities to sulfur-containing compounds, e.g. mustard oil glycosides such as glucoiberin. Furthermore ROS, generated during xanthine oxidase (XOD)-catalysed oxidation of xanthine into uric acid, were also efficiently decreased by IAE. However, an inhibition of XOD could be excluded, but chelation of metal ions (Fe, Cu) decreasing their redox-cycling activities seems to play a role. A major activity of IAE proved to represent inhibition of lipid peroxidation processes, shown as delay of the lag phase of the Cu(II)-induced LDL oxidation as well as protection of alpha-linolenic acid from peroxidation by singlet oxygen.
An Equilibrium-Based Model of Gas Reaction and Detonation
Energy Technology Data Exchange (ETDEWEB)
Trowbridge, L.D.
2000-04-01
During gaseous diffusion plant operations, conditions leading to the formation of flammable gas mixtures may occasionally arise. Currently, these could consist of the evaporative coolant CFC-114 and fluorinating agents such as F2 and ClF3. Replacement of CFC-114 with a non-ozone-depleting substitute is planned. Consequently, in the future, the substitute coolant must also be considered as a potential fuel in flammable gas mixtures. Two questions of practical interest arise: (1) can a particular mixture sustain and propagate a flame if ignited, and (2) what is the maximum pressure that can be generated by the burning (and possibly exploding) gas mixture, should it ignite? Experimental data on these systems, particularly for the newer coolant candidates, are limited. To assist in answering these questions, a mathematical model was developed to serve as a tool for predicting the potential detonation pressures and for estimating the composition limits of flammability for these systems based on empirical correlations between gas mixture thermodynamics and flammability for known systems. The present model uses the thermodynamic equilibrium to determine the reaction endpoint of a reactive gas mixture and uses detonation theory to estimate an upper bound to the pressure that could be generated upon ignition. The model described and documented in this report is an extended version of related models developed in 1992 and 1999.
Modeling of deformation phenomena in volume label during its operation
Directory of Open Access Journals (Sweden)
Svitlana Sheludko
2017-06-01
Full Text Available BIt was considered in the article the research of physical and mechanical properties of materials based on PVC film ORACAL and RITRAMA that used in the production of volume labels. In particular, it was shown the changes of dependences between linear deformation of printed and unprinted films and the value of stress with regard to their minimum and maximum values. It was also established that deformation properties of the films are different in the transverse and longitudinal directions, which should be considered when producing labels. It was conducted the modeling of stress-strain state of volume label when gluing it to the surfaces of various shapes. We considered the boundary conditions for displacement and stress of labels layer components with regard to the chemical structure of epoxy resins and their physical and mechanical characteristics.
Assessment of the hybrid propagation model, Volume 1: Analysis of noise propagation effects
2012-08-31
This is the first of two volumes of a report on the Hybrid Propagation Model (HPM), an advanced prediction model for aviation noise propagation. This volume presents the noise level predictions for eleven different sets of propagation conditions, run...
Easley, Christopher J; Legendre, Lindsay A; Roper, Michael G; Wavering, Thomas A; Ferrance, Jerome P; Landers, James P
2005-02-15
Optical fiber extrinsic Fabry-Perot interferometry (EFPI) was investigated as a noncontact temperature sensor and utilized for regulating the temperature of small-volume solutions in microchips. Interference pattern analysis determined the optical path lengths (OPL) associated with reflections from various surfaces on or in the microchip, in particular, from gold sputtered on the bottom of a microchannel. Since OPL is directly proportional to refractive index, which is dependent on solution temperature, the EFPI sensor was capable of noncontact monitoring of solution temperature simply from alterations in the measured path length. Calibration of the sensor against a thermocouple was performed while heating the microchip in a noncontact manner with an IR lamp. The combination of EFPI temperature sensor, IR-mediated heating, and air cooling allowed a fully noncontact system for small-volume temperature control in microchip structures, and its utility was illustrated by optimal digestion of DNA by a temperature-dependent restriction endonuclease in 320 nL. The functionality and simplicity of the microchip EFPI temperature sensor was enhanced by replacing the prebonding sputtered gold with a tunable, chemically plated semireflective silver coating created in situ after chip fabrication. This provided an 8-fold improvement in the lowest detectable temperature change (deltaT = 0.1 degrees C), facilitated primarily by enhanced reflection from both the bottom and top surfaces of the microchannel. This approach for controlling micro- and nanoscale reactions--with heating, cooling, and temperature control being carried out in a completely noncontact fashion--provides an accurate and sensitive method for executing chemical and biochemical reactions in microchips.
Flow of a mixture of reactive gases: H{sub 2}-air detonation with a model of 8 reactions
Energy Technology Data Exchange (ETDEWEB)
Rouboa, A. [Univ. of Evry val d`Essonne (France); Poissant, G. [I.U.T. d`Evry (France); Forestier, A. [L.T.M.E., St. Paul-lez-Durance (France); Gibert, R.J. [C.E.A. Saclay, Gif-sur-Yvette (France)
1995-11-01
This report deals with the modeling of a flow in the case of a reactive gas mixture submitted to a detonation wave. The system of Euler multispecies equations is coupled with a reactional model of eight reactions. In order to solve this system numerically, a finite volume formulation is used, based on the Van Leer method. In spite of the fact that the studied tests present some difficulties due to non regular structures and severe shock waves, the authors obtain satisfying results. In this paper, they present a monodimensional example. This paper is divided into four sections: in the first one, the authors have given Euler`s multispecies equations, in a second, they have proposed a kinetic model of the hydrogen-oxygen mixtures, in a third one, they have presented a resolution method and the results of a common numeric test (impact tube). Finally, they have explained the future prospects for the evolution of a more efficient model.
Kinetic study on pyrolytic process of oil-palm solid waste using two-step consecutive reaction model
Energy Technology Data Exchange (ETDEWEB)
Guo, J.; Lua, A.C. [Nanyang Technological University (Singapore). School of Mechanical and Production Engineering
2001-07-01
Pyrolysis of oil-palm (Elaeis guineensis Jacq.) shell, a cheap and abundantly available solid waste from palm oil producing process, was carried out using thermogravimetric analysis. The effects of raw material particle size and heating rate on the pyrolytic properties and kinetic parameters (activation energy, frequency factor and reaction order) were investigated. A one-step global model and a two-step consecutive reaction model were used to simulate the pyrolytic process and predict the weight loss during pyrolysis. The two-step model fitted the experimental data much better than the one-step model as the softening effect and formation of an intermediate during the pyrolytic process were taken into account. This two-stage reaction characteristic was confirmed by two obvious maxima in the derivative thermogram for pyrolysis of palm shells under different heating rates. The pyrolytic reactions at the low- and high-temperature regimes were found to be based on a first-order reaction mechanism and a contracting volume mechanism, respectively. (author)
Model reactions and natural occurrence of furans from hypersaline environments
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T. Krause
2014-05-01
Full Text Available Volatile organic compounds like furan and its derivatives are important for atmospheric properties and reactions. In this work the known abiotic formation of furan from catechol under Fenton-like conditions with Fe3+ sulfate was revised by the use of a bispidine Fe2+ complex as a model compound for iron with well-known characteristics. While total yields were comparable to those with the Fe3+ salt, the bispidine Fe2+ complex is a better catalyst as the turnover numbers of the active iron species were higher. Additionally, the role of iron and pH is discussed in relation to furan formation from model compounds and in natural sediment and water samples collected from the Dead Sea and several salt lakes in Western Australia. Various alkylated furans and even traces of halogenated furans (3-chlorofuran and 3-bromofuran were found in some Australian samples. 3-chlorofuran was found in three sediments and four water samples, whereas 3-bromofuran was detected in three water samples. Further, the emission of furans is compared to the abundance of several possible precursors such as isoprene and aromatic hydrocarbons as well as to the related thiophenes. It is deduced that the emissions of volatile organic compounds such as furans contribute to the formation of ultra-fine particles in the vicinity of salt lakes and are important for the local climate.
Konkoli, Zoran
2012-07-21
A novel computational method for modeling reaction noise characteristics has been suggested. The method can be classified as a moment closure method. The approach is based on the concept of correlation forms which are used for describing spatially extended many body problems where particle numbers change in space and time. In here, it was shown how the formalism of spatially extended correlation forms can be adapted to study well mixed reaction systems. Stochastic fluctuations in particle numbers are described by selectively capturing correlation effects up to the desired order, ξ. The method is referred to as the ξ-level Approximation Reaction Noise Estimator method (XARNES). For example, the ξ=1 description is equivalent to the mean field theory (first-order effects), the ξ=2 case corresponds to the previously developed PARNES method (pair effects), etc. The main idea is that inclusion of higher order correlation effects should lead to better (more accurate) results. Several models were used to test the method, two versions of a simple complex formation model, the Michaelis-Menten model of enzymatic kinetics, the smallest bistable reaction network, a gene expression network with negative feedback, and a random large network. It was explicitly demonstrated that increase in ξ indeed improves accuracy in all cases investigated. The approach has been implemented as automatic software using the Mathematica programming language. The user only needs to input reaction rates, stoichiometry coefficients, and the desired level of computation ξ. Copyright © 2012 Elsevier Ltd. All rights reserved.
Magnotti, F.; Diskin, G.; Matulaitis, J.; Chinitz, W.
1984-01-01
The use of silane (SiH4) as an effective ignitor and flame stabilizing pilot fuel is well documented. A reliable chemical kinetic mechanism for prediction of its behavior at the conditions encountered in the combustor of a SCRAMJET engine was calculated. The effects of hydrogen addition on hydrocarbon ignition and flame stabilization as a means for reduction of lengthy ignition delays and reaction times were studied. The ranges of applicability of chemical kinetic models of hydrogen-air combustors were also investigated. The CHARNAL computer code was applied to the turbulent reaction rate modeling.
Integrating model of the Project Independence Evaluation System. Volume IV. Model documentation
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Shaw, M L; Allen, B J; Gale, J E; Lutz, M S; O& #x27; Hara, N E; Wood, R K
1979-02-01
This volume is the fourth in a series of seven documenting the PIES Integrating Model. It contains detailed descriptions of the basic assumptions behind each of the components of PIES and how they interact with one another. Chapter II of this volume presents the methodology used to integrate supply and demand. It includes a discussion of both the interface between the Demand Model and the equilibrating mechanism and the various supply models via the equilibrating algorithm used by PIES. Chapters III through IX describe each supply submodel in turn: coal, oil, and natural gas supply, utilities, refineries, advanced technologies, and transportation. Code and data documentation are covered elsewhere in this series (Volumes V and VI respectively). PIES is an evolving system. As this document was being prepared, many parts of the model were being modified. This document describes the PIES Integrating Model as of January 1, 1978.
A Lumped-Parameter Subject-Specific Model of Blood Volume Response to Fluid Infusion
Ramin Bighamian; Andrew Reisner; Jin-Oh Hahn
2016-01-01
This paper presents a lumped-parameter model that can reproduce blood volume response to fluid infusion. The model represents the fluid shift between the intravascular and interstitial compartments as the output of a hypothetical feedback controller that regulates the ratio between the volume changes in the intravascular and interstitial fluid at a target value (called target volume ratio). The model is characterized by only three parameters: the target volume ratio, feedback gain (specifyi...
Winkelmann, Stefanie; Schütte, Christof
2017-09-21
Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations. For systems with multiple scales, there exist hybrid approaches that keep parts of the system discrete while another part is approximated either using Langevin dynamics or deterministically. This paper aims at giving a coherent overview of the different hybrid approaches, focusing on their basic concepts and the relation between them. We derive a novel general description of such hybrid models that allows expressing various forms by one type of equation. We also check in how far the approaches apply to model extensions of the CME for dynamics which do not comply with the central well-mixed condition and require some spatial resolution. A simple but meaningful gene expression system with negative self-regulation is analysed to illustrate the different approximation qualities of some of the hybrid approaches discussed. Especially, we reveal the cause of error in the case of small volume approximations.
Winkelmann, Stefanie; Schütte, Christof
2017-09-01
Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations. For systems with multiple scales, there exist hybrid approaches that keep parts of the system discrete while another part is approximated either using Langevin dynamics or deterministically. This paper aims at giving a coherent overview of the different hybrid approaches, focusing on their basic concepts and the relation between them. We derive a novel general description of such hybrid models that allows expressing various forms by one type of equation. We also check in how far the approaches apply to model extensions of the CME for dynamics which do not comply with the central well-mixed condition and require some spatial resolution. A simple but meaningful gene expression system with negative self-regulation is analysed to illustrate the different approximation qualities of some of the hybrid approaches discussed. Especially, we reveal the cause of error in the case of small volume approximations.
A reaction diffusion model of pattern formation in clustering of adatoms on silicon surfaces
Directory of Open Access Journals (Sweden)
Trilochan Bagarti
2012-12-01
Full Text Available We study a reaction diffusion model which describes the formation of patterns on surfaces having defects. Through this model, the primary goal is to study the growth process of Ge on Si surface. We consider a two species reaction diffusion process where the reacting species are assumed to diffuse on the two dimensional surface with first order interconversion reaction occuring at various defect sites which we call reaction centers. Two models of defects, namely a ring defect and a point defect are considered separately. As reaction centers are assumed to be strongly localized in space, the proposed reaction-diffusion model is found to be exactly solvable. We use Green's function method to study the dynamics of reaction diffusion processes. Further we explore this model through Monte Carlo (MC simulations to study the growth processes in the presence of a large number of defects. The first passage time statistics has been studied numerically.
A model for primary and heterogeneuos secondary reactions of wood pyrolysis
Energy Technology Data Exchange (ETDEWEB)
Ahuja, P. [Dept. of Chemical Engineering and Technology, Inst. of Technology, Banaras Hindu Univ., Varanasi (India); Kumar, S. [Dept. of Chemical Engineering and Technology, Inst. of Technology, Banaras Hindu Univ., Varanasi (India); Singh, P.C. [Dept. of Chemical Engineering and Technology, Inst. of Technology, Banaras Hindu Univ., Varanasi (India)
1996-06-01
A chain growth model for heterogeneous secondary reactions is developed for the pyrolysis of large wood particles and the parameters determined by nonlinear optimization. The model takes both the volatile retention time and cracking and repolymerization reactions of the vapours with the decomposing solid as well as autocatalysis into consideration. The extent of the secondary reactions is strongly influenced by the time and the ratio of the autocatalytic (propagation) reaction rate to noncatalytic (initiation) reaction rate. The wood which has a higher value of the autocatalytic/noncatalytic ratio also has a higher exothermic heat of reaction and yields a higher amount of final char residue. This fact confirms that the heterogeneous secondary reactions lead to carbon enrichment of the final residue and are accompanied with an exothermic heat of reaction. The lower activation energies of the initiation and propagation reactions as compared to primary reactions (competitive reaction model consisting of weight loss and char forming reactions) confirm autocatalysis in large particles. The sealed reactor studies of small quantities of fine wood samples show that heterogeneous secondary reactions and not lower heating rates in large particles are the main source of char formed during the thermal decomposition of large wood particles. The model predictions are in agreement with the weight loss and temperature versus time curves over a wide range of particle size and furnace temperatures. (orig.)
Unravelling the Maillard reaction network by multiresponse kinetic modelling
Martins, S.I.F.S.
2003-01-01
The Maillard reaction is an important reaction in food industry. It is responsible for the formation of colour and aroma, as well as toxic compounds as the recent discovered acrylamide. The knowledge of kinetic parameters, such as rate constants and activation energy, is necessary to predict its
Kinetic modelling of reactions in heated disaccharide-casein systems
Brands, C.M.J.; Boekel, van M.A.J.S.
2003-01-01
The reactions occurring in disaccharide-casein reaction mixtures during heating at 120 degreesC and pH 6.8 were studied. The existence of two main degradation routes were established: (1) Isomerisation of the aldose sugars lactose and maltose in their ketose isomers lactulose and maltulose,
Molecular Modeling of an Electrophilic Addition Reaction with "Unexpected" Regiochemistry
Best, Katherine T.; Li, Diana; Helms, Eric D.
2017-01-01
The electrophilic addition of a hydrohalic acid (HX) to an alkene is often one of the first reactions learned in second-year undergraduate organic chemistry classes. During the ensuing discussion of the mechanism, it is shown that this reaction follows Markovnikov's rule, which states that the hydrogen atom will attach to the carbon with fewer…
Stability Analysis of a Reaction-Diffusion System Modeling Atherogenesis
Ibragimov, Akif
2010-01-01
This paper presents a linear, asymptotic stability analysis for a reaction-diffusionconvection system modeling atherogenesis, the initiation of atherosclerosis, as an inflammatory instability. Motivated by the disease paradigm articulated by Ross, atherogenesis is viewed as an inflammatory spiral with a positive feedback loop involving key cellular and chemical species interacting and reacting within the intimal layer of muscular arteries. The inflammatory spiral is initiated as an instability from a healthy state which is defined to be an equilibrium state devoid of certain key inflammatory markers. Disease initiation is studied through a linear, asymptotic stability analysis of a healthy equilibrium state. Various theorems are proved, giving conditions on system parameters guaranteeing stability of the health state, and a general framework is developed for constructing perturbations from a healthy state that exhibit blow-up, which are interpreted as corresponding to disease initiation. The analysis reveals key features that arterial geometry, antioxidant levels, and the source of inflammatory components (through coupled third-kind boundary conditions or through body sources) play in disease initiation. © 2010 Society for Industrial and Applied Mathematics.
INTRA/Mod3.2. Manual and Code Description. Volume I - Physical Modelling
Energy Technology Data Exchange (ETDEWEB)
Andersson, Jenny; Edlund, O.; Hermann, J.; Johansson, Lise-Lotte
1999-01-01
The INTRA Manual consists of two volumes. Volume I of the manual is a thorough description of the code INTRA, the Physical modelling of INTRA and the ruling numerical methods and volume II, the User`s Manual is an input description. This document, the Physical modelling of INTRA, contains code characteristics, integration methods and applications
Modelling of geochemical reactions and experimental cation exchange in MX 80 bentonite.
Montes-H, G; Fritz, B; Clement, A; Michau, N
2005-10-01
Bentonites are widely used for waste repository systems because of their hydrodynamic, surface and chemical-retention properties. MX 80 bentonite (bentonite of Wyoming) contains approximately 85% Na/Ca-montmorillonite and 15% accessory minerals. The dominant presence of Na/Ca-montmorillonite in this clay mineral could cause it to perform exceptionally well as an engineered barrier for a radioactive waste repository because this buffer material is expected to fill up by swelling the void between canisters containing waste and the surrounding ground. However, the Na/Ca-montmorillonite could be transformed to other clay minerals as a function of time under repository conditions. Previous modelling studies based on the hydrolysis reactions have shown that the Na/Ca-montmorillonite-to-Ca-montmorillonite conversion is the most significant chemical transformation. In fact, this chemical process appears to be a simple cation exchange into the engineered barrier. The purpose of the present study was two-fold. Firstly, it was hoped to predict the newly formed products of bentonite-fluid reactions under repository conditions by applying a thermokinetic hydrochemical code (KIRMAT: Kinetic Reactions and Mass Transport). The system modelled herein was considered to consist of a 1-m thick zone of water-saturated engineered barrier. This non-equilibrated system was placed in contact with a geological fluid on one side, which was then allowed to diffuse into the barrier, while the other side was kept in contact with iron-charged water. Reducing initial conditions ( [P(O)2 approximately equals 0] ; Eh=-200 mV) and a constant reaction temperature (100 degrees C) were considered. Secondly, it was hoped to estimate the influence of inter-layer cations (Ca and Na) on the swelling behaviour of the MX 80 bentonite by using an isothermal system of water vapour adsorption and an environmental scanning electron microscope (ESEM) coupled with a digital image analysis (DIA) program. Here, the
Constructing and Visualizing Chemical Reaction Networks from Pi-Calculus Models
John, Mathias; Schulz, Hans-Jörg; Schumann, Heidrun; Uhrmacher, Adelinde; Unger, Andrea
2012-01-01
International audience; The pi-calculus, in particular its stochastic version the stochastic pi-calculus, is a common modeling formalism to concisely describe the chemical reactions occurring in biochemical systems. However, it remains largely unexplored how to transform a biochemical model expressed in the stochastic pi-calculus back into a set of meaningful reactions. To this end, we present a two step approach of first translating model states to reaction sets and then visualizing sequence...
Chemical reaction model for oil and gas generation from type 1 and type 2 kerogen
Energy Technology Data Exchange (ETDEWEB)
Braun, R.L.; Burnham, A.K.
1993-06-01
A global model for the generation of oil and gas from petroleum source rocks is presented. The model consists of 13 chemical species and 10 reactions, including an alternate-pathway mechanism for kerogen pyrolysis. Reaction rate parameters and stoichiometry coefficients determined from a variety of pyrolysis data are given for both type I and type II kerogen. Use of the chemical reaction model is illustrated for typical geologic conditions.
Ares I Reaction Control System Propellant Feedline Decontamination Modeling
Pasch, James J.
2010-01-01
The objective of the work presented here is to quantify the effects of purge gas temperature, pressure, and mass flow rate on Hydrazine (Hz) decontamination rates of the Ares I Roll Control System and Reaction Control System. A survey of experts in this field revealed the absence of any decontamination rate prediction models. Three basic decontamination methods were identified for analysis and modeling. These include low pressure eduction, high flow rate purge, and pulse purge. For each method, an approach to predict the Hz mass transfer rate, as a function of system pressure, temperature, and purge gas mass flow rate, is developed based on the applicable physics. The models show that low pressure eduction is two orders of magnitude more effective than the high velocity purge, which in turn is two orders of magnitude more effective than the pure diffusion component of pulse purging of deadheads. Eduction subjects the system to low pressure conditions that promote the extraction of Hz vapors. At 120 F, Hz is saturated at approximately 1 psia. At lower pressures and 120 F, Hz will boil, which is an extremely efficient means to remove liquid Hz. The Hz boiling rate is predicted by equating the rate at which energy is added to the saturated liquid Hz through heaters at the tube outer wall with the energy removed from the liquid through evaporation. Boil-off fluxes were predicted by iterating through the range of local pressures with limits set by the minimum allowed pressure of 0.2 psia and maximum allowed wall temperature of 120 F established by the heaters, which gives a saturation pressure of approximately 1.0 psia. Figure 1 shows the resulting boil-off fluxes as a function of local eduction pressure. As depicted in figure 1, the flux is a strong inverse function of eduction pressure, and that minimizing the eduction pressure maximizes the boil-off flux. Also, higher outer wall temperatures lead to higher boil-off fluxes and allow for boil-off over a greater range
Modeling adsorption and reactions of organic molecules at metal surfaces.
Liu, Wei; Tkatchenko, Alexandre; Scheffler, Matthias
2014-11-18
CONSPECTUS: The understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid inorganic/organic systems (HIOS) are relevant for many applications in catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. Obviously, the predictive modeling and understanding of the structure and stability of such hybrid systems is an essential prerequisite for tuning their electronic properties and functions. At present, density-functional theory (DFT) is the most promising approach to study the structure, stability, and electronic properties of complex systems, because it can be applied to both molecules and solids comprising thousands of atoms. However, state-of-the-art approximations to DFT do not provide a consistent and reliable description for HIOS, which is largely due to two issues: (i) the self-interaction of the electrons with themselves arising from the Hartree term of the total energy that is not fully compensated in approximate exchange-correlation functionals, and (ii) the lack of long-range part of the ubiquitous van der Waals (vdW) interactions. The self-interaction errors sometimes lead to incorrect description of charge transfer and electronic level alignment in HIOS, although for molecules adsorbed on metals these effects will often cancel out in total energy differences. Regarding vdW interactions, several promising vdW-inclusive DFT-based methods have been recently demonstrated to yield remarkable accuracy for intermolecular interactions in the gas phase. However, the majority of these approaches neglect the nonlocal collective electron response in the vdW energy tail, an effect that is particularly strong in condensed phases and at interfaces between different materials. Here we show that the recently developed DFT+vdW(surf) method that accurately accounts for the collective electronic
Wide Temperature Range Kinetics of Elementary Combustion Reactions for Army Models
National Research Council Canada - National Science Library
Fontijn, Arthur
2002-01-01
The goals of this program are to provide accurate kinetic data on isolated elementary reactions at temperatures relevant to Army combustion models, particularly for propellant combustion dark zones...
Modeled Urea Distribution Volume and Mortality in the HEMO Study
Greene, Tom; Depner, Thomas A.; Levin, Nathan W.; Chertow, Glenn M.
2011-01-01
Summary Background and objectives In the Hemodialysis (HEMO) Study, observed small decreases in achieved equilibrated Kt/Vurea were noncausally associated with markedly increased mortality. Here we examine the association of mortality with modeled volume (Vm), the denominator of equilibrated Kt/Vurea. Design, setting, participants, & measurements Parameters derived from modeled urea kinetics (including Vm) and blood pressure (BP) were obtained monthly in 1846 patients. Case mix–adjusted time-dependent Cox regressions were used to relate the relative mortality hazard at each time point to Vm and to the change in Vm over the preceding 6 months. Mixed effects models were used to relate Vm to changes in intradialytic systolic BP and to other factors at each follow-up visit. Results Mortality was associated with Vm and change in Vm over the preceding 6 months. The association between change in Vm and mortality was independent of vascular access complications. In contrast, mortality was inversely associated with V calculated from anthropometric measurements (Vant). In case mix–adjusted analysis using Vm as a time-dependent covariate, the association of mortality with Vm strengthened after statistical adjustment for Vant. After adjustment for Vant, higher Vm was associated with slightly smaller reductions in intradialytic systolic BP and with risk factors for mortality including recent hospitalization and reductions in serum albumin concentration and body weight. Conclusions An increase in Vm is a marker for illness and mortality risk in hemodialysis patients. PMID:21511841
Alligator Rivers Analogue project. Hydrogeological modelling. Final Report - Volume 6
Energy Technology Data Exchange (ETDEWEB)
Townley, L.R.; Trefry, M.G.; Barr, A.D. [CSIRO Div of Water Resources, PO Wembley, WA (Australia); Braumiller, S. [Univ of Arizona, Tucson, AZ (United States). Dept of Hydrology and Water Resources; Kawanishi, M. [Central Research Institute of Electric Power Industry, Abiko-Shi, Chiba-Ken (Japan)] [and others
1992-12-31
This volume describes hydrogeological modelling carried out as part of the Alligator Rivers Analogue Project. Hydrogeology has played a key integrating role in the Project, largely because water movement is believed to have controlled the evolution of the Koongarra uranium Orebody and therefore affects field observations of all types at all scales. Aquifer testing described uses the concept of transmissivity in its interpretation of aquifer response to pumping. The concept of an aquifer, a layer transmitting significant quantities of water in a mainly horizontal direction, seems hard to accept in an environment as heterogeneous as that at Koongarra. But modelling of aquifers both in one dimension and two dimensionally in plan has contributed significantly to our understanding of the site. A one-dimensional model with three layers (often described as a quasi two dimensional model) was applied to flow between the Fault and Koongarra Creek. Being a transient model, this model was able to show that reverse flows can indeed occur back towards the Fault, but only if there is distributed recharge over the orebody as well as a mechanism for the Fault, or a region near the Fault, to remove water from the simulated cross-section. The model also showed clearly that the response of the three-layered system, consisting of a highly weathered zone, a fractured transmissive zone and a less conductive lower schist zone, is governed mainly by the transmissivity and storage coefficient of the middle layer. The storage coefficient of the higher layer has little effect. A two-dimensional model in plan used a description of anisotropy to show that reverse flows can also occur even without a conducting Fault. Modelling of a three-dimensional region using discrete fractures showed that it is certainly possible to simulate systems like that observed at Koongarra, but that large amounts of data are probably needed to obtain realistic descriptions of the fracture networks. Inverse modelling
Hua, Pei; Vasyukova, Ekaterina; Uhl, Wolfgang
2015-05-15
A second order kinetic model for simulating chlorine decay in bulk water due to the reaction with dissolved organic matter (DOM) was developed. It takes into account the decreasing reactivity of dissolved organic matter using a variable reaction rate coefficient (VRRC) which decreases with an increasing conversion. The concentration of reducing species is surrogated by the maximum chlorine demand. Temperature dependency, respectively, is described by the Arrhenius-relationship. The accuracy and adequacy of the proposed model to describe chlorine decay in bulk water were evaluated and shown for very different waters and different conditions such as water mixing or rechlorination by applying statistical tests. It is thus very well suited for application in water quality modeling for distribution systems. Copyright © 2015 Elsevier Ltd. All rights reserved.
The JigCell model builder: a spreadsheet interface for creating biochemical reaction network models.
Vass, Marc T; Shaffer, Clifford A; Ramakrishnan, Naren; Watson, Layne T; Tyson, John J
2006-01-01
Converting a biochemical reaction network to a set of kinetic rate equations is tedious and error prone. We describe known interface paradigms for inputing models of intracellular regulatory networks: graphical layout (diagrams), wizards, scripting languages, and direct entry of chemical equations. We present the JigCell Model Builder, which allows users to define models as a set of reaction equations using a spreadsheet (an example of direct entry of equations) and outputs model definitions in the Systems Biology Markup Language, Level 2. We present the results of two usability studies. The spreadsheet paradigm demonstrated its effectiveness in reducing the number of errors made by modelers when compared to hand conversion of a wiring diagram to differential equations. A comparison of representatives of the four interface paradigms for a simple model of the cell cycle was conducted which measured time, mouse clicks, and keystrokes to enter the model, and the number of screens needed to view the contents of the model. All four paradigms had similar data entry times. The spreadsheet and scripting language approaches require significantly fewer screens to view the models than do the wizard or graphical layout approaches.
Murray, K. E.
2016-12-01
Management of produced fluids has become an important issue in Oklahoma because large volumes of saltwater are co-produced with oil and gas, and disposed into saltwater disposal wells at high rates. Petroleum production increased from 2009-2015, especially in central and north-central Oklahoma where the Mississippian and Hunton zones were redeveloped using horizontal wells and dewatering techniques that have led to a disproportional increase in produced water volumes. Improved management of co-produced water, including desalination for beneficial reuse and decreased saltwater disposal volumes, is only possible if spatial and temporal trends can be defined and related to the producing zones. It is challenging to quantify the volumes of co-produced water by region or production zone because co-produced water volumes are generally not reported. Therefore, the goal of this research is to estimate co-produced water volumes for 2008-present with an approach that can be replicated as petroleum production shifts to other regions. Oil and gas production rates from subsurface zones were multiplied by ratios of H2O:oil and H2O:gas for the respective zones. Initial H2O:oil and H2O:gas ratios were adjusted/calibrated, by zone, to maximize correlation of county-scale produced H2O estimates versus saltwater disposal volumes from 2013-2015. These calibrated ratios were then used to compute saltwater disposal volumes from 2008-2012 because of apparent data gaps in reported saltwater disposal volumes during that timeframe. This research can be used to identify regions that have the greatest need for produced water treatment systems. The next step in management of produced fluids is to explore optimal energy-efficient strategies that reduce deleterious effects.
Transportation Sector Model of the National Energy Modeling System. Volume 2 -- Appendices: Part 1
Energy Technology Data Exchange (ETDEWEB)
NONE
1998-01-01
This volume contains input data and parameters used in the model of the transportation sector of the National Energy Modeling System. The list of Transportation Sector Model variables includes parameters for the following: Light duty vehicle modules (fuel economy, regional sales, alternative fuel vehicles); Light duty vehicle stock modules; Light duty vehicle fleet module; Air travel module (demand model and fleet efficiency model); Freight transport module; Miscellaneous energy demand module; and Transportation emissions module. Also included in these appendices are: Light duty vehicle market classes; Maximum light duty vehicle market penetration parameters; Aircraft fleet efficiency model adjustment factors; and List of expected aircraft technology improvements.
Pimpalgaonkar, H.G.; van Steijn, V.; Kreutzer, M.T.; Kleijn, C.R.; Simos, Theodore; Tsitouras, Charalambos
2016-01-01
We present a finite volume implementation of a phase field method in OpenFOAM as a tool to simulate reactive multiphase flows on heterogeneous surfaces. Using this tool, we simulate the formation and growth of a droplet due to a chemical reaction on a hydrophilic catalytic patch surrounded by a
Energy Technology Data Exchange (ETDEWEB)
Hoffman, R D; Dietrich, F S; Kelley, K; Escher, J; Bauer, R; Mustafa, M
2008-02-26
We have developed a set of modeled nuclear reaction cross sections for use in radiochemical diagnostics. Systematics for the input parameters required by the Hauser-Feshbach statistical model were developed and used to calculate neutron induced nuclear reaction cross sections for targets ranging from osmium (Z = 76) to gold (Z = 79). Of particular interest are the cross sections on Ir and Au including reactions on isomeric targets.
Directory of Open Access Journals (Sweden)
Ahmad Arabi Shamsabadi
2016-04-01
Full Text Available This paper presents an experimental study of the self-initiation reaction of n-butyl acrylate (n-BA in free-radical polymerization. For the first time, the frequency factor and activation energy of the monomer self-initiation reaction are estimated from measurements of n-BA conversion in free-radical homo-polymerization initiated only by the monomer. The estimation was carried out using a macroscopic mechanistic mathematical model of the reactor. In addition to already-known reactions that contribute to the polymerization, the model considers a n-BA self-initiation reaction mechanism that is based on our previous electronic-level first-principles theoretical study of the self-initiation reaction. Reaction rate equations are derived using the method of moments. The reaction-rate parameter estimates obtained from conversion measurements agree well with estimates obtained via our purely-theoretical quantum chemical calculations.
A Joint Modeling Approach for Reaction Time and Accuracy in Psycholinguistic Experiments
Loeys, T.; Rosseel, Y.; Baten, K.
2011-01-01
In the psycholinguistic literature, reaction times and accuracy can be analyzed separately using mixed (logistic) effects models with crossed random effects for item and subject. Given the potential correlation between these two outcomes, a joint model for the reaction time and accuracy may provide further insight. In this paper, a Bayesian…
Competitive reaction- and feedback effects based on VARX models of pooled store data
Horvath, C; Leeflang, PSH; Wieringa, JE; Wittink, DR
2005-01-01
We apply a model that accommodates dynamic phenomena in demand- and reaction functions. The latter functions capture reactions to actions as well as to consequences of actions. We estimate a fixed effects VARX model with dynamic and interactive effects for multiple brands based on pooled time series
Incorporation of fragmentation into a volume average solidification model
Zheng, Y.; Wu, M.; Kharicha, A.; Ludwig, A.
2018-01-01
In this study, a volume average solidification model was extended to consider fragmentation as a source of equiaxed crystals during mixed columnar-equiaxed solidification. The formulation suggested for fragmentation is based on two hypotheses: the solute-driven remelting is the dominant mechanism; and the transport of solute-enriched melt through an interdendritic flow in the columnar growth direction is favorable for solute-driven remelting and is the necessary condition for fragment transportation. Furthermore, a test case with Sn-10 wt%Pb melt solidifying vertically downward in a 2D domain (50 × 60 mm2) was calculated to demonstrate the model’s features. Solidification started from the top boundary, and a columnar structure developed initially with its tip growing downward. Furthermore, thermo-solutal convection led to fragmentation in the mushy zone near the columnar tip front. The fragments transported out of the columnar region continued to grow and sink, and finally settled down and piled up in the bottom domain. The growing columnar structure from the top and pile-up of equiaxed crystals from the bottom finally led to a mixed columnar-equiaxed structure, in turn leading to a columnar-to-equiaxed transition (CET). A special macrosegregation pattern was also predicted, in which negative segregation occurred in both columnar and equiaxed regions and a relatively strong positive segregation occurred in the middle domain near the CET line. A parameter study was performed to verify the model capability, and the uncertainty of the model assumption and parameter was discussed.
Tang, Youneng; Valocchi, Albert J.; Werth, Charles J.
2015-03-01
It is a challenge to upscale solute transport in porous media for multispecies bio-kinetic reactions because of incomplete mixing within the elementary volume and because biofilm growth can change porosity and affect pore-scale flow and diffusion. To address this challenge, we present a hybrid model that couples pore-scale subdomains to continuum-scale subdomains. While the pore-scale subdomains involving significant biofilm growth and reaction are simulated using pore-scale equations, the other subdomains are simulated using continuum-scale equations to save computational time. The pore-scale and continuum-scale subdomains are coupled using a mortar method to ensure continuity of solute concentration and flux at the interfaces. We present results for a simplified two-dimensional system, neglect advection, and use dual Monod kinetics for solute utilization and biofilm growth. The results based on the hybrid model are consistent with the results based on a pore-scale model for three test cases that cover a wide range of Damköhler (Da = reaction rate/diffusion rate) numbers for both homogeneous (spatially periodic) and heterogeneous pore structures. We compare results from the hybrid method with an upscaled continuum model and show that the latter is valid only for cases of small Damköhler numbers, consistent with other results reported in the literature.
Simple, Inexpensive Model Spirometer for Understanding Ventilation Volumes
Giuliodori, Mauricio J.; DiCarlo, Stephen E.
2004-01-01
Spirometers are useful for enhancing students' understanding of normal lung volumes, capacities, and flow rates. Spirometers are also excellent for understanding how lung diseases alter ventilation volumes. However, spirometers are expensive, complex, and not appropriate for programs with limited space and budgets. Therefore, we developed a…
A COMPATIBLE ESTIMATION MODEL OF STEM VOLUME AND TAPER FOR Acacia mangium Willd. PLANTATIONS
Directory of Open Access Journals (Sweden)
Haruni Krisnawati
2016-04-01
Full Text Available This study describes the establishment of a compatible volume estimation model for Acacia mangium Willd on the basis of 279 felled sample trees collected from the A. mangium plantation stands in South Sumatra, Indonesia. The model comprises of a total volume model and a stem taper model, which is compatible in the sense of the total volume obtained by integration of the taper model being equal to that computed by the total volume model. Several well-known total volume functions were evaluated including constant form factor, combined variable, generalized combine variable, logarithmic, generalized logarithmic and Honer transformed variables. A logarithmic model was determined to be the best and was then used as the basis for deriving the taper model. Appropriate statistical procedures were used in model fitting to account for the problems of heteroscedasticity and autocorrelation that are associated with the construction of volume and taper functions. The simultaneous fitting method of the Seemingly Unrelated Regression (SUR improved the parameter estimates and goodness-of-fit statistics while ensuring numeric consistency among the component models and reducing the total squared error obtained by an independent fitting method. The developed model can be used to estimate total stem volume, merchantable volume to any merchantability diameter limit at any height, and (possibly height of any diameter based on only easily measurable parameters such as diameter at breast height and total tree height for the species analysed.
Daniel J. Yelle; John Ralph; Charles R. Frihart
2011-01-01
To better understand adhesive interactions with wood, reactions between model compounds of wood and a model compound of polymeric methylene diphenyl diisocyanate (pMDI) were characterized by solution-state NMR spectroscopy. For comparison, finely ground loblolly pine sapwood, milled-wood lignin and holocellulose from the same wood were isolated and derivatized with...
A Lumped-Parameter Subject-Specific Model of Blood Volume Response to Fluid Infusion
Directory of Open Access Journals (Sweden)
Ramin Bighamian
2016-08-01
Full Text Available This paper presents a lumped-parameter model that can reproduce blood volume response to fluid infusion. The model represents the fluid shift between the intravascular and interstitial compartments as the output of a hypothetical feedback controller that regulates the ratio between the volume changes in the intravascular and interstitial fluid at a target value (called target volume ratio. The model is characterized by only three parameters: the target volume ratio, feedback gain (specifying the speed of fluid shift, and initial blood volume. This model can obviate the need to incorporate complex mechanisms involved in the fluid shift in reproducing blood volume response to fluid infusion. The ability of the model to reproduce real-world blood volume response to fluid infusion was evaluated by fitting it to a series of data reported in the literature. The model reproduced the data accurately with average error and root-mean-squared error (RMSE of 0.6 % and 9.5 % across crystalloid and colloid fluids when normalized by the underlying responses. Further, the parameters derived for the model showed physiologically plausible behaviors. It was concluded that this simple model may accurately reproduce a variety of blood volume responses to fluid infusion throughout different physiological states by fitting three parameters to a given dataset. This offers a tool that can quantify the fluid shift in a dataset given the measured fractional blood volumes.
A Lumped-Parameter Subject-Specific Model of Blood Volume Response to Fluid Infusion.
Bighamian, Ramin; Reisner, Andrew T; Hahn, Jin-Oh
2016-01-01
This paper presents a lumped-parameter model that can reproduce blood volume response to fluid infusion. The model represents the fluid shift between the intravascular and interstitial compartments as the output of a hypothetical feedback controller that regulates the ratio between the volume changes in the intravascular and interstitial fluid at a target value (called "target volume ratio"). The model is characterized by only three parameters: the target volume ratio, feedback gain (specifying the speed of fluid shift), and initial blood volume. This model can obviate the need to incorporate complex mechanisms involved in the fluid shift in reproducing blood volume response to fluid infusion. The ability of the model to reproduce real-world blood volume response to fluid infusion was evaluated by fitting it to a series of data reported in the literature. The model reproduced the data accurately with average error and root-mean-squared error (RMSE) of 0.6 and 9.5% across crystalloid and colloid fluids when normalized by the underlying responses. Further, the parameters derived for the model showed physiologically plausible behaviors. It was concluded that this simple model may accurately reproduce a variety of blood volume responses to fluid infusion throughout different physiological states by fitting three parameters to a given dataset. This offers a tool that can quantify the fluid shift in a dataset given the measured fractional blood volumes.
Cold-cap reactions in vitrification of nuclear waste glass: Experiments and modeling
Energy Technology Data Exchange (ETDEWEB)
Chun, Jaehun; Pierce, David A. [Pacific Northwest National Laboratory, Richland, WA 99352 (United States); Pokorný, Richard [Department of Chemical Engineering, Institute of Chemical Technology in Prague, Technická 5, 166 28 Prague 6 (Czech Republic); Hrma, Pavel, E-mail: pavelhrma@postech.ac.kr [Pacific Northwest National Laboratory, Richland, WA 99352 (United States); Division of Advanced Nuclear Engineering, Pohang University of Science and Technology, Pohang (Korea, Republic of)
2013-05-10
Highlights: ► We measured enthalpy-based conversion degree of overlapping reactions using DSC. ► We employed the run/rerun technique to obtain heat flow associated with reactions. ► Batch-to-glass conversion advances via multiple overlapping reactions. ► The kinetic model is intended for the source term in the energy transfer equation. ► The results are relevant for industrial glass making and nuclear waste vitrification. - Abstract: Cold-cap reactions are multiple overlapping reactions that occur in the waste-glass melter during the vitrification process when the melter feed is being converted to molten glass. In this study, we used simultaneous differential scanning calorimetry–thermogravimetry (DSC–TGA) to investigate cold-cap reactions in a high-alumina high-level waste melter feed. To separate the reaction heat from both the heat associated with the heat capacity of the feed and experimental artifacts, we employed the run/rerun method, which enabled us to define the degree of conversion based on the reaction heat and to estimate the heat capacity of the reacting feed. Assuming that the reactions are nearly independent and can be approximated by an nth order kinetic model, we obtained the kinetic parameters using the Kissinger method combined with least squares analysis. The resulting mathematical simulation of the cold-cap reactions provides a key element for the development of an advanced cold-cap model.
Modeling of Chemical Reactions in Afterburning for the Reduction of N2O
DEFF Research Database (Denmark)
Gustavsson, Lennart; Glarborg, Peter; Leckner, Bo
1996-01-01
Full scale tests in a 12 MW fluidized bed combustor on reduction of N2O by secondary fuel injection are analyzed in terms a model that involves a detailed reaction mechanism for the gas phase chemistry as well as a description of gas-solid reactions.......Full scale tests in a 12 MW fluidized bed combustor on reduction of N2O by secondary fuel injection are analyzed in terms a model that involves a detailed reaction mechanism for the gas phase chemistry as well as a description of gas-solid reactions....
Reaction Zone Models for Vortex Simulation of Turbulent Combustion
1993-10-01
extinctio n stain-• " ~tlltlon lram 110’ 0 0 0.78 0.8 0.82 0.84 0.86 0.88 0.9 Heat Release parameter (Tb-T_O)/T_b Figure 9 Extinction strain and...flow. Thus, while dynamic effects associated with the presence of an expansion field and the details of the chemical reaction pro - cess are omitted
Statistical shape modeling based renal volume measurement using tracked ultrasound
Pai Raikar, Vipul; Kwartowitz, David M.
2017-03-01
Autosomal dominant polycystic kidney disease (ADPKD) is the fourth most common cause of kidney transplant worldwide accounting for 7-10% of all cases. Although ADPKD usually progresses over many decades, accurate risk prediction is an important task.1 Identifying patients with progressive disease is vital to providing new treatments being developed and enable them to enter clinical trials for new therapy. Among other factors, total kidney volume (TKV) is a major biomarker predicting the progression of ADPKD. Consortium for Radiologic Imaging Studies in Polycystic Kidney Disease (CRISP)2 have shown that TKV is an early, and accurate measure of cystic burden and likely growth rate. It is strongly associated with loss of renal function.3 While ultrasound (US) has proven as an excellent tool for diagnosing the disease; monitoring short-term changes using ultrasound has been shown to not be accurate. This is attributed to high operator variability and reproducibility as compared to tomographic modalities such as CT and MR (Gold standard). Ultrasound has emerged as one of the standout modality for intra-procedural imaging and with methods for spatial localization has afforded us the ability to track 2D ultrasound in physical space which it is being used. In addition to this, the vast amount of recorded tomographic data can be used to generate statistical shape models that allow us to extract clinical value from archived image sets. In this work, we aim at improving the prognostic value of US in managing ADPKD by assessing the accuracy of using statistical shape model augmented US data, to predict TKV, with the end goal of monitoring short-term changes.
Wick, Christian R; Smith, David M
2018-02-07
The reactions catalyzed by coenzyme B12 dependent enzymes are formally initiated by the homolytic cleavage of a carbon-cobalt bond and a subsequent or concerted H-atom-transfer reaction. A reasonable model chemistry for describing those reactions should, therefore, account for an accurate description of both reactions. The inherent limitation due to the necessary system size renders the coenzyme B12 system a suitable candidate for DFT or hybrid QM/MM methods; however, the accurate description of both homolytic Co-C cleavage and H-atom-transfer reactions within this framework is challenging and can lead to controversial results with varying accuracy. We present an assessment study of 16 common density functionals applied to prototypical model systems for both reactions. H-abstraction reactions were modeled on the basis of four reference reactions designed to resemble a broad range of coenzyme B12 reactions. The Co-C cleavage reaction is treated by an ONIOM(QM/MM) setup that is in excellent agreement with solution-phase experimental data and is as accurate as full DFT calculations on the complete model system. We find that the meta-GGAs TPSS-D3 and M06L-D3 and the meta-hybrid M06-D3 give the best overall performance with MUEs for both types of reactions below 10 kJ mol-1. Our recommended model chemistry allows for a fast and accurate description of coenzyme B12 chemistry that is readily applicable to study the reactions in an enzymatic framework.
Cold-cap reactions in vitrification of nuclear waste glass: experiments and modeling
Energy Technology Data Exchange (ETDEWEB)
Chun, Jaehun [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Pierce, David A. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Pokorny, Richard [Inst. of Chemical Technology, Prague (Czech Republic); Hrma, Pavel R. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Pohang Univ. of Science and Techology (Korea, Republic of)
2013-05-01
Cold-cap reactions are multiple overlapping reactions that occur in the waste-glass melter during the vitrification process when the melter feed is being converted to molten glass. In this study, we used differential scanning calorimetry (DSC) to investigate cold-cap reactions in a high-alumina high-level waste melter feed. To separate the reaction heat from both sensible heat and experimental instability, we employed the run/rerun method, which enabled us to define the degree of conversion based on the reaction heat and to estimate the heat capacity of the reacting feed. Assuming that the reactions are nearly independent and can be approximated by the nth order kinetics, we obtained the kinetic parameters using the Kissinger method combined with least squares analysis. The resulting mathematical simulation of the cold-cap reactions provides a key element for the development of an advanced cold-cap model.
Stepwise kinetic equilibrium models of quantitative polymerase chain reaction
Cobbs, Gary
2012-01-01
Abstract Background Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model the annealing phase and does not assume constant efficiency of amplification. Mechanistic models describing the annealing phase with kinetic theory offer the most pote...
Energy Technology Data Exchange (ETDEWEB)
Sverjensky, D. [The John Hopkins Univ, Dept of Earth and Planetary Sciences, Baltimore (United States); Bennett, D.G.; Read, D. [W.S. Atkins Science and Technology, Epsom Surrey, (United Kingdom)
1992-12-31
The purpose of the present study was to establish how the uranyl phosphate zone at the Koongarra site was formed. The overall approach taken in the present study employed theoretical chemical mass transfer calculations and models that permit investigation and reconstruction of the kinds of waters that could produce the uranyl phosphate zone. These calculations have used the geological and mineralogical data for the Koongarra weathered zone (Volumes 2, 8, and 9 of this series), to constrain the initial compositions and reactions undergone by groundwater during the formation of the uranyl phosphate zone. In carrying out these calculations the present-day analyses of Koongarra waters are used only as a guide to the possible initial composition of the fluids associated with the formation of the phosphate zone. Aqueous speciation, saturation state and chemical mass transfer calculations were carried out using the computer programs EQ3NR and EQ6 (Wolery, 1983; Wolery et al., 1984) and a thermodynamic database generated at The Johns Hopkins University over the last eight years which is tabulated in the Appendix 1 to Volume 12 of this series. Despite uncertainties in the thermodynamic characterisation of species, all the above calculations suggest that the uranyl phosphate zone at Koongarra has not formed from present-day groundwaters (Volume 12 of this series). The present-day groundwaters in the weathered zone (eg. at 13 m depth) appear to be undersaturated with respect to saleeite. Furthermore, as present-day groundwaters descend below the water table they rapidly lose their atmospheric oxygen imprint, as is typical of most groundwaters, and become even more reducing in character. Under these circumstances, the groundwaters become more undersaturated with respect to saleeite than the shallow groundwaters. Because much of the phosphate zone is currently below the water table, under saturated zone conditions, it is suggested in the present study that the uranyl phosphate
Energy Technology Data Exchange (ETDEWEB)
Louis, J.F.; Tung, S.E.
1980-10-01
This document is the second of a seven volume series of our Phase II Final Report. This volume deals with detailed descriptions of the structure of each program member (subroutines and functions), the interrelation between the members of a submodel, and the interrelation between the various submodels as such. The systems model for fluidized bed combustors (FBC-II) consists of a systematic combination of the following interrelated areas: fluid mechanics and bubble growth, char combustion and associated kinetics for particle burnout, sulfur capture, NO/sub x/ formation and reduction, freeboard reactions, and heat transfer. Program outline is shown in Figure 1.1. Input variables (supplied by the user are inspected to check that they lie inside the allowed range of values and are input to the various routines as needed. The necessary physical and fluid mechanical properties are calculated and utilized in estimating char combustion and sulfur capture in the bed and the freeboard. NO/sub x/ and CO emissions are estimated by taking into account all relevant chemical reactions. A material and energy balance is made over the bed. Figure 1.1 shows a block diagram of the systems program. In this diagram, the overall structure of the FBC program is illustrated in terms of the various submodels that together constitute the systems program. A more detailed outline of the systems program is shown in Figure 1.2. In this figure, all important subroutine members of the FBC program are shown, and their linkage to each other, as well as to the main program is indicated. A description of the exact sequence in which these various routines are called at time of program execution is provided in Chapter 8 under the executive routine MAIN.
Performance of Frozen Density Embedding for Modeling Hole Transfer Reactions
Ramos, Pablo; Pavanello, Michele
2015-01-01
We have carried out a thorough benchmark of the FDE-ET method for calculating hole transfer couplings. We have considered 10 exchange-correlation functionals, 3 non-additive kinetic energy functionals and 3 basis sets. Overall, we conclude that with a 7% mean relative unsigned error, the PBE functional coupled with the PW91k non-additive Kinetic energy functional and a TZP basis set constitutes the most stable, and accurate level of theory for hole-transfer coupling calculations. The FDE-ET method is found to be an excellent tool for computing diabatic couplings for hole transfer reactions.
Guedry, F. E., Jr.; Gilson, R. D.; Stockwell, C. W.
1973-01-01
Modelling will become increasingly important as more knowledge is accumulated, because it offers advantages in predicting reactions of individuals in a variety of situations, including novel aerospace environments, and in specifying a few parameters which should have considerable clinical significance. However, the need for continuing experimental crosschecks of these models has been illustrated by several sets of results which would not have been predicted by any existing models.
2016-05-23
AFRL-AFOSR-VA-TR-2016-0200 Noise Propagation and Uncertainty Quantification in Hybrid Multiphysics Models Daniel Tartakovsky UNIVERSITY OF CALIFORNIA...2016 Title: Noise Propagation and Uncertainty Quantification in Hybrid Multi-Physics Models Subtitle: Initiation and Reaction Propagation in...and Uncertainty Quantification in Hybrid Multi-Physics Models Task: Initiation and Reaction Propagation in Energetic Materials AFOSR award: FA9550-12-1
An In Vitro Model of Skeletal Muscle Volume Regulation
Anna Wibberley; Staunton, Caroline A; Feetham, Claire H.; Vereninov, Alexey A.; Richard Barrett-Jolley
2015-01-01
Introduction Hypertonic media causes cells to shrink due to water loss through aquaporin channels. After acute shrinkage, cells either regulate their volume or, alternatively, undergo a number of metabolic changes which ultimately lead to cell death. In many cell types, hypertonic shrinkage is followed by apoptosis. Due to the complex 3D morphology of skeletal muscle and the difficulty in obtaining isolated human tissue, we have begun skeletal muscle volume regulation studies using the human ...
Structure-reactivity modeling using mixture-based representation of chemical reactions
Polishchuk, Pavel; Madzhidov, Timur; Gimadiev, Timur; Bodrov, Andrey; Nugmanov, Ramil; Varnek, Alexandre
2017-09-01
We describe a novel approach of reaction representation as a combination of two mixtures: a mixture of reactants and a mixture of products. In turn, each mixture can be encoded using an earlier reported approach involving simplex descriptors (SiRMS). The feature vector representing these two mixtures results from either concatenated product and reactant descriptors or the difference between descriptors of products and reactants. This reaction representation doesn't need an explicit labeling of a reaction center. The rigorous "product-out" cross-validation (CV) strategy has been suggested. Unlike the naïve "reaction-out" CV approach based on a random selection of items, the proposed one provides with more realistic estimation of prediction accuracy for reactions resulting in novel products. The new methodology has been applied to model rate constants of E2 reactions. It has been demonstrated that the use of the fragment control domain applicability approach significantly increases prediction accuracy of the models. The models obtained with new "mixture" approach performed better than those required either explicit (Condensed Graph of Reaction) or implicit (reaction fingerprints) reaction center labeling.
Okubo, Fumiya; Kobayashi, Satoshi; YOKOMORI, Takashi
2011-01-01
Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that feature (string) language acceptors with multiset manipulation as a computing mechanism, and show that reaction automata are computationally Turing universal. Further, some subclasses of reaction automata with space complexity are investigated and their la...
PhreeqcRM: A reaction module for transport simulators based on the geochemical model PHREEQC
Parkhurst, David L.; Wissmeier, Laurin
2015-01-01
PhreeqcRM is a geochemical reaction module designed specifically to perform equilibrium and kinetic reaction calculations for reactive transport simulators that use an operator-splitting approach. The basic function of the reaction module is to take component concentrations from the model cells of the transport simulator, run geochemical reactions, and return updated component concentrations to the transport simulator. If multicomponent diffusion is modeled (e.g., Nernst–Planck equation), then aqueous species concentrations can be used instead of component concentrations. The reaction capabilities are a complete implementation of the reaction capabilities of PHREEQC. In each cell, the reaction module maintains the composition of all of the reactants, which may include minerals, exchangers, surface complexers, gas phases, solid solutions, and user-defined kinetic reactants.PhreeqcRM assigns initial and boundary conditions for model cells based on standard PHREEQC input definitions (files or strings) of chemical compositions of solutions and reactants. Additional PhreeqcRM capabilities include methods to eliminate reaction calculations for inactive parts of a model domain, transfer concentrations and other model properties, and retrieve selected results. The module demonstrates good scalability for parallel processing by using multiprocessing with MPI (message passing interface) on distributed memory systems, and limited scalability using multithreading with OpenMP on shared memory systems. PhreeqcRM is written in C++, but interfaces allow methods to be called from C or Fortran. By using the PhreeqcRM reaction module, an existing multicomponent transport simulator can be extended to simulate a wide range of geochemical reactions. Results of the implementation of PhreeqcRM as the reaction engine for transport simulators PHAST and FEFLOW are shown by using an analytical solution and the reactive transport benchmark of MoMaS.
Modelling combustion reactions for gas flaring and its resulting emissions
Directory of Open Access Journals (Sweden)
O. Saheed Ismail
2016-07-01
Full Text Available Flaring of associated petroleum gas is an age long environmental concern which remains unabated. Flaring of gas maybe a very efficient combustion process especially steam/air assisted flare and more economical than utilization in some oil fields. However, it has serious implications for the environment. This study considered different reaction types and operating conditions for gas flaring. Six combustion equations were generated using the mass balance concept with varying air and combustion efficiency. These equations were coded with a computer program using 12 natural gas samples of different chemical composition and origin to predict the pattern of emission species from gas flaring. The effect of key parameters on the emission output is also shown. CO2, CO, NO, NO2 and SO2 are the anticipated non-hydrocarbon emissions of environmental concern. Results show that the quantity and pattern of these chemical species depended on percentage excess/deficiency of stoichiometric air, natural gas type, reaction type, carbon mass content, impurities, combustion efficiency of the flare system etc. These emissions degrade the environment and human life, so knowing the emission types, pattern and flaring conditions that this study predicts is of paramount importance to governments, environmental agencies and the oil and gas industry.
Applying ARIMA model for annual volume time series of the Magdalena River
Directory of Open Access Journals (Sweden)
Gloria Amaris
2017-04-01
Conclusions: The simulated results obtained with the ARIMA model compared to the observed data showed a fairly good adjustment of the minimum and maximum magnitudes. This allows concluding that it is a good tool for estimating minimum and maximum volumes, even though this model is not capable of simulating the exact behaviour of an annual volume time series.
Models for estimation of tree volume in the miombo woodlands of ...
African Journals Online (AJOL)
This study developed models for estimating total, merchantable stem and branches volume applicable for the entire miombo woodlands of Tanzania. ... The relative mean prediction error of the general total tree volume model with diameter at breast height and tree height was lower (0.6%) than those of the previously ...
Modeling of the symmetry factor of electrochemical proton discharge via the Volmer reaction
DEFF Research Database (Denmark)
Björketun, Mårten E.; Tripkovic, Vladimir; Skúlason, Egill
2013-01-01
A scheme for evaluating symmetry factors of elementary electrode reactions using a density functional theory (DFT) based model of the electrochemical double layer is presented. As an illustration, the symmetry factor is determined for hydrogen adsorption via the electrochemical Volmer reaction. T...
A mesoscopic reaction rate model for shock initiation of multi-component PBX explosives.
Liu, Y R; Duan, Z P; Zhang, Z Y; Ou, Z C; Huang, F L
2016-11-05
The primary goal of this research is to develop a three-term mesoscopic reaction rate model that consists of a hot-spot ignition, a low-pressure slow burning and a high-pressure fast reaction terms for shock initiation of multi-component Plastic Bonded Explosives (PBX). Thereinto, based on the DZK hot-spot model for a single-component PBX explosive, the hot-spot ignition term as well as its reaction rate is obtained through a "mixing rule" of the explosive components; new expressions for both the low-pressure slow burning term and the high-pressure fast reaction term are also obtained by establishing the relationships between the reaction rate of the multi-component PBX explosive and that of its explosive components, based on the low-pressure slow burning term and the high-pressure fast reaction term of a mesoscopic reaction rate model. Furthermore, for verification, the new reaction rate model is incorporated into the DYNA2D code to simulate numerically the shock initiation process of the PBXC03 and the PBXC10 multi-component PBX explosives, and the numerical results of the pressure histories at different Lagrange locations in explosive are found to be in good agreements with previous experimental data. Copyright © 2016 Elsevier B.V. All rights reserved.
Modeling Proton- and Light Ion-Induced Reactions at Low Energies in the MARS15 Code
Energy Technology Data Exchange (ETDEWEB)
Rakhno, I. L. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Mokhov, N. V. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Gudima, K. K. [National Academy of Sciences, Cisineu (Moldova)
2015-04-25
An implementation of both ALICE code and TENDL evaluated nuclear data library in order to describe nuclear reactions induced by low-energy projectiles in the Monte Carlo code MARS15 is presented. Comparisons between results of modeling and experimental data on reaction cross sections and secondary particle distributions are shown.
A model for void-induced back reaction between radiolytic products in NaCl
Turkin, A.A.; Dubinko, V.I.; Vainshtein, D.I.; Hartog, H.W. den
A kinetic model is formulated for the chemical reaction between radiolytic sodium colloids and gas bubbles, which are brought into contact with each other during the exposure to ionising radiation by the growing voids. The reaction starts with the evaporation of Na atoms into the void due to the
New tools in modulating Maillard reaction from model systems to food
Troise, A.D.
2015-01-01
Stochastic modeling of biochemical systems with multistep reactions using state-dependent time delay
Wu, Qianqian; Tian, Tianhai
2016-08-01
To deal with the growing scale of molecular systems, sophisticated modelling techniques have been designed in recent years to reduce the complexity of mathematical models. Among them, a widely used approach is delayed reaction for simplifying multistep reactions. However, recent research results suggest that a delayed reaction with constant time delay is unable to describe multistep reactions accurately. To address this issue, we propose a novel approach using state-dependent time delay to approximate multistep reactions. We first use stochastic simulations to calculate time delay arising from multistep reactions exactly. Then we design algorithms to calculate time delay based on system dynamics precisely. To demonstrate the power of proposed method, two processes of mRNA degradation are used to investigate the function of time delay in determining system dynamics. In addition, a multistep pathway of metabolic synthesis is used to explore the potential of the proposed method to simplify multistep reactions with nonlinear reaction rates. Simulation results suggest that the state-dependent time delay is a promising and accurate approach to reduce model complexity and decrease the number of unknown parameters in the models.
Angelis, Alessia De; Pancani, Luca; Steca, Patrizia; Colaceci, Sofia; Giusti, Angela; Tibaldi, Laura; Alvaro, Rosaria; Ausili, Davide; Vellone, Ercole
2017-05-01
To test an explanatory model of nurses' intention to report adverse drug reactions in hospital settings, based on the theory of planned behaviour. Under-reporting of adverse drug reactions is an important problem among nurses. A cross-sectional design was used. Data were collected with the adverse drug reporting nurses' questionnaire. Confirmatory factor analysis was performed to test the factor validity of the adverse drug reporting nurses' questionnaire, and structural equation modelling was used to test the explanatory model. The convenience sample comprised 500 Italian hospital nurses (mean age = 43.52). Confirmatory factor analysis supported the factor validity of the adverse drug reporting nurses' questionnaire. The structural equation modelling showed a good fit with the data. Nurses' intention to report adverse drug reactions was significantly predicted by attitudes, subjective norms and perceived behavioural control (R² = 0.16). The theory of planned behaviour effectively explained the mechanisms behind nurses' intention to report adverse drug reactions, showing how several factors come into play. In a scenario of organisational empowerment towards adverse drug reaction reporting, the major predictors of the intention to report are support for the decision to report adverse drug reactions from other health care practitioners, perceptions about the value of adverse drug reaction reporting and nurses' favourable self-assessment of their adverse drug reaction reporting skills. © 2017 John Wiley & Sons Ltd.
Energy Technology Data Exchange (ETDEWEB)
Cho, Jeong Yeon; Lee, Hak Jong; Kim, Sung Hyun [Samsung Seoul Hospital, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Kim, Seung Hyup [Seoul National University College of Medicine, Seoul (Korea, Republic of)
2002-03-15
To evaluate the accuracy of measuring the volume of the prostate using the prolate ellipsoid volume calculation method (antero-posterior (AP) diameter X length X width X {pi}6) when the antero-posterior diameter of the prostate was measured on midsagittal (sagittal volume) and axial plane (axial volume).The devil's tongue jelly was used for the creation of ultrasound model of the prostate (volume: 15-40 cc) by cutting and shaping the surface. The volume in 10 prostatic models and 30 patients was measured and calculated. First, the AP diameter and length of the prostate models in midsagittal plane, and the height and width of the models in axial plane were measured for 3 times. The volume was calculated in two ways, one using the AP diameter an midsagittal plane and the other using the AP diameter in axial plane. The true volume of the model was measured using mess cylinder. The calculated volume and true volume were compared, and the accuracy of two method of measuring the prostatic volume was evaluated by Friedman test. The intraobserver variation was evaluated by General Linear Model, Repeated Measure. The reproducibility was evaluated by Cronbach's {alpha}. In vivo study was also performed in 30 patients. The prostate volume was calculated in the same manner. These volume data were analyzed by statistical method, and the intraobeserver variation was evaluated. While there was a statistically significant difference between the sagittal and true volume of the models, there was no statistical significant difference between the axial and true volumes. There was no significant intraobserver variation between both methods. The reproducibility was high in both methods with Cronbach's {alpha} of 0.977 and 0.942. The sagittal volume was larger than the axial volume in 30 patients with a statistically significant difference. There was no significant intraobserver variation in both methods. The reproducibility was high in both methods Cronbach's {alpha
The DoD Enterprise Model. Volume 1. Strategic Activity and Data Models
1994-01-01
they are consistent and integrated within Department " chains -of- command," such as Combatant Commands and their Components. In this way, a "tree" of...capabilities. Options are assessed for their DEVOp PLAS suitability, feasibility, acceptability, consistency "with Joint Doctrine, and risk. Based on...structures and chains of command. This activity involves the evaluation of force readiness or The DoD Enterprise Model, Volume I Page 40 11 January 1994
The Sugar Model: Autocatalytic Activity of the Triose-Ammonia Reaction
Weber, Arthur L.
2006-01-01
Reaction of triose sugars with ammonia under anaerobic conditions yielded autocatalytic products. The autocatalytic behavior of the products was examined by measuring the effect of the crude triose-ammonia reaction product on the kinetics of a second identical triose-ammonia reaction. The reaction product showed autocatalytic activity by increasing both the rate of disappearance of triose and the rate formation of pyruvaldehyde, the product of triose dehydration. This synthetic process is considered a reasonable model of origin-of-life chemistry because it uses plausible prebiotic substrates, and resembles modern biosynthesis by employing the energized carbon groups of sugars to drive the synthesis of autocatalytic molecules.
Attractor for a Reaction-Diffusion System Modeling Cancer Network
Directory of Open Access Journals (Sweden)
Xueyong Chen
2014-01-01
Full Text Available A reaction-diffusion cancer network regulated by microRNA is considered in this paper. We study the asymptotic behavior of solution and show the existence of global uniformly bounded solution to the system in a bounded domain Ω⊂Rn. Some estimates and asymptotic compactness of the solutions are proved. As a result, we establish the existence of the global attractor in L2(Ω×L2(Ω and prove that the solution converges to stable steady states. These results can help to understand the dynamical character of cancer network and propose a new insight to study the mechanism of cancer. In the end, the numerical simulation shows that the analytical results agree with numerical simulation.
Beretta, G P; Al-Abbasi, Omar; von Spakovsky, M R
2017-04-01
The steepest entropy ascent (SEA) dynamical principle provides a general framework for modeling the dynamics of nonequilibrium (NE) phenomena at any level of description, including the atomistic one. It has recently been shown to provide a precise implementation and meaning to the maximum entropy production principle and to encompass many well-established theories of nonequilibrium thermodynamics into a single unifying geometrical framework. Its original formulation in the framework of quantum thermodynamics (QT) assumes the simplest and most natural Fisher-Rao metric to geometrize from a dynamical standpoint the manifold of density operators, which represent the thermodynamic NE states of the system. This simplest SEAQT formulation is used here to develop a general mathematical framework for modeling the NE time evolution of the quantum state of a chemically reactive mixture at an atomistic level. The method is illustrated for a simple two-reaction kinetic scheme of the overall reaction F+H_{2}⇔HF+F in an isolated tank of fixed volume. However, the general formalism is developed for a reactive system subject to multiple reaction mechanisms. To explicitly implement the SEAQT nonlinear law of evolution for the density operator, both the energy and the particle number eigenvalue problems are set up and solved analytically under the dilute gas approximation. The system-level energy and particle number eigenvalues and eigenstates are used in the SEAQT equation of motion to determine the time evolution of the density operator, thus effectively describing the overall kinetics of the reacting system as it relaxes toward stable chemical equilibrium. The predicted time evolution in the near-equilibrium limit is compared to the reaction rates given by a standard detailed kinetic model so as to extract the single time constant needed by the present SEA model.
Molecular mobility with respect to accessible volume in Monte Carlo lattice model for polymers
Diani, J.; Gilormini, P.
2017-02-01
A three-dimensional cubic Monte Carlo lattice model is considered to test the impact of volume on the molecular mobility of amorphous polymers. Assuming classic polymer chain dynamics, the concept of locked volume limiting the accessible volume around the polymer chains is introduced. The polymer mobility is assessed by its ability to explore the entire lattice thanks to reptation motions. When recording the polymer mobility with respect to the lattice accessible volume, a sharp mobility transition is observed as witnessed during glass transition. The model ability to reproduce known actual trends in terms of glass transition with respect to material parameters, is also tested.
Generic Model-Based Tailor-Made Design and Analysis of Biphasic Reaction Systems
DEFF Research Database (Denmark)
Anantpinijwatna, Amata
Biphasic reaction systems are composed of immiscible aqueous and organic liquid phases where reactants, products, and catalysts are partitioned. These biphasic conditions point to novel synthesis paths, higher yields, and faster reactions, as well as facilitate product separation. The biphasic...... systems have a broad range of application, such as the manufacture of petroleum based chemicals, pharmaceuticals, and agro-bio products. Major considerations in the design and analysis of biphasic reaction systems are physical and chemical equilibria, kinetic mechanisms, and reaction rates. The primary...... contribution of this thesis is the development of a systematic modelling framework for the biphasic reaction system. The developed framework consists of three modules describing phase equilibria, reactions and mass transfer, and material balances of such processes. Correlative and predictive thermodynamic...
Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics.
Chen, Minghan; Li, Fei; Wang, Shuo; Cao, Young
2017-03-14
Stochastic simulation of reaction-diffusion systems presents great challenges for spatiotemporal biological modeling and simulation. One widely used framework for stochastic simulation of reaction-diffusion systems is reaction diffusion master equation (RDME). Previous studies have discovered that for the RDME, when discretization size approaches zero, reaction time for bimolecular reactions in high dimensional domains tends to infinity. In this paper, we demonstrate that in the 1D domain, highly nonlinear reaction dynamics given by Hill function may also have dramatic change when discretization size is smaller than a critical value. Moreover, we discuss methods to avoid this problem: smoothing over space, fixed length smoothing over space and a hybrid method. Our analysis reveals that the switch-like Hill dynamics reduces to a linear function of discretization size when the discretization size is small enough. The three proposed methods could correctly (under certain precision) simulate Hill function dynamics in the microscopic RDME system.
Piecewise linear and Boolean models of chemical reaction networks.
Veliz-Cuba, Alan; Kumar, Ajit; Josić, Krešimir
2014-12-01
Models of biochemical networks are frequently complex and high-dimensional. Reduction methods that preserve important dynamical properties are therefore essential for their study. Interactions in biochemical networks are frequently modeled using Hill functions ([Formula: see text]). Reduced ODEs and Boolean approximations of such model networks have been studied extensively when the exponent [Formula: see text] is large. However, while the case of small constant [Formula: see text] appears in practice, it is not well understood. We provide a mathematical analysis of this limit and show that a reduction to a set of piecewise linear ODEs and Boolean networks can be mathematically justified. The piecewise linear systems have closed-form solutions that closely track those of the fully nonlinear model. The simpler, Boolean network can be used to study the qualitative behavior of the original system. We justify the reduction using geometric singular perturbation theory and compact convergence, and illustrate the results in network models of a toggle switch and an oscillator.
Pore-to-Darcy Scale Hybrid Multiscale Finite Volume Model for Reactive Flow and Transport
Barajas-Solano, D. A.; Tartakovsky, A. M.
2016-12-01
In the present work we develop a hybrid scheme for the coupling and temporal integration of grid-based, continuum models for pore-scale and Darcy-scale flow and reactive transport. The hybrid coupling strategy consists on applying Darcy-scale and pore-scale flow and reactive transport models over overlapping subdomains Ω C and Ω F, and enforcing continuity of state and fluxes by means of restriction and prolongation operations defined over the overlap subdomain Ω hs ≡ Ω C \\cap Ω F. For the pore-scale model, we use a Multiscale Finite Volume (MsFV) characterization of the pore-scale state in terms of Darcy-scale degrees of freedom and local functions defined as the solution of pore-scale problems. The hybrid MsFV coupling results in a local-global combination of effective mass balance relations for the Darcy-scale degrees of freedom and local problems for the pore-scale degrees of freedom that capture pore-scale behavior. Our scheme allows for the rapid coarsening of pore-scale models and the adaptive enrichment of Darcy-scale models with pore-scale information. Additionally, we propose a strategy for modeling the dynamics of the pore-scale solid-liquid boundary due to precipitation and dissolution phenomena, based on the Diffuse Domain method (DDM), which is incorporated into the MsFV approximation of pore-scale states. We apply the proposed hybrid scheme to a reactive flow and transport problem in porous media subject to heterogeneous reactions and the corresponding precipitation and dissolution phenomena.
Fluorination of an Alumina Surface: Modeling Aluminum-Fluorine Reaction Mechanisms.
Padhye, Richa; Aquino, Adelia J A; Tunega, Daniel; Pantoya, Michelle L
2017-07-19
Density functional theory (DFT) calculations were performed to examine exothermic surface chemistry between alumina and four fluorinated, fragmented molecules representing species from decomposing fluoropolymers: F(-), HF, CH3F, and CF4. The analysis has strong implications for the reactivity of aluminum (Al) particles passivated by an alumina shell. It was hypothesized that the alumina surface structure could be transformed due to hydrogen bonding effects from the environment that promote surface reactions with fluorinated species. In this study, the alumina surface was analyzed using model clusters as isolated systems embedded in a polar environment (i.e., acetone). The conductor-like screening model (COSMO) was used to mimic environmental effects on the alumina surface. Four defect models for specific active -OH sites were investigated including two terminal hydroxyl groups and two hydroxyl bridge groups. Reactions involving terminal bonds produce more energy than bridge bonds. Also, surface exothermic reactions between terminal -OH bonds and fluorinated species produce energy in decreasing order with the following reactant species: CF4 > HF > CH3F. Additionally, experiments were performed on aluminum powders using thermal equilibrium analysis techniques that complement the calculations. Consistently, the experimental results show a linear relationship between surface exothermic reactions and the main fluorination reaction for Al powders. These results connect molecular level reaction kinetics to macroscopic measurements of surface energy and show that optimizing energy available in surface reactions linearly correlates to maximizing energy in the main reaction.
An in vitro model of skeletal muscle volume regulation.
Directory of Open Access Journals (Sweden)
Anna Wibberley
Full Text Available Hypertonic media causes cells to shrink due to water loss through aquaporin channels. After acute shrinkage, cells either regulate their volume or, alternatively, undergo a number of metabolic changes which ultimately lead to cell death. In many cell types, hypertonic shrinkage is followed by apoptosis. Due to the complex 3D morphology of skeletal muscle and the difficulty in obtaining isolated human tissue, we have begun skeletal muscle volume regulation studies using the human skeletal muscle cell line TE671RD. In this study we investigated whether hypertonic challenge of the human skeletal muscle cell line TE671RD triggered cell death or evoked a cell volume recovery response.The cellular volume of TE671RD cells was calculated from the 2D surface area. Cell death was assessed by both the trypan blue live/dead assay and the TUNEL assay.Medium osmolality was increased by addition of up to 200 mM sucrose. Addition of 200 mM sucrose resulted in mean cell shrinkage of 44±1% after 30 mins. At later time points (2 and 4 hrs two separate cell subpopulations with differing mean cell volume became apparent. The first subpopulation (15±2% of the total cell number continued to shrink whereas the second subpopulation had an increased cell volume. Cell death was observed in a small proportion of cells (approximately 6-8%.We have established that a substantial proportion of TE671RD cells respond to hypertonic challenge with RVI, but that these cells are resistant to hypertonicity triggered cell death.
An in vitro model of skeletal muscle volume regulation.
Wibberley, Anna; Staunton, Caroline A; Feetham, Claire H; Vereninov, Alexey A; Barrett-Jolley, Richard
2015-01-01
Hypertonic media causes cells to shrink due to water loss through aquaporin channels. After acute shrinkage, cells either regulate their volume or, alternatively, undergo a number of metabolic changes which ultimately lead to cell death. In many cell types, hypertonic shrinkage is followed by apoptosis. Due to the complex 3D morphology of skeletal muscle and the difficulty in obtaining isolated human tissue, we have begun skeletal muscle volume regulation studies using the human skeletal muscle cell line TE671RD. In this study we investigated whether hypertonic challenge of the human skeletal muscle cell line TE671RD triggered cell death or evoked a cell volume recovery response. The cellular volume of TE671RD cells was calculated from the 2D surface area. Cell death was assessed by both the trypan blue live/dead assay and the TUNEL assay. Medium osmolality was increased by addition of up to 200 mM sucrose. Addition of 200 mM sucrose resulted in mean cell shrinkage of 44±1% after 30 mins. At later time points (2 and 4 hrs) two separate cell subpopulations with differing mean cell volume became apparent. The first subpopulation (15±2% of the total cell number) continued to shrink whereas the second subpopulation had an increased cell volume. Cell death was observed in a small proportion of cells (approximately 6-8%). We have established that a substantial proportion of TE671RD cells respond to hypertonic challenge with RVI, but that these cells are resistant to hypertonicity triggered cell death.
RELAP5/MOD3 code manual. Volume 4, Models and correlations
Energy Technology Data Exchange (ETDEWEB)
NONE
1995-08-01
The RELAP5 code has been developed for best-estimate transient simulation of light water reactor coolant systems during postulated accidents. The code models the coupled behavior of the reactor coolant system and the core for loss-of-coolant accidents and operational transients such as anticipated transient without scram, loss of offsite power, loss of feedwater, and loss of flow. A generic modeling approach is used that permits simulating a variety of thermal hydraulic systems. Control system and secondary system components are included to permit modeling of plant controls, turbines, condensers, and secondary feedwater systems. RELAP5/MOD3 code documentation is divided into seven volumes: Volume I presents modeling theory and associated numerical schemes; Volume II details instructions for code application and input data preparation; Volume III presents the results of developmental assessment cases that demonstrate and verify the models used in the code; Volume IV discusses in detail RELAP5 models and correlations; Volume V presents guidelines that have evolved over the past several years through the use of the RELAP5 code; Volume VI discusses the numerical scheme used in RELAP5; and Volume VII presents a collection of independent assessment calculations.
Statistical Texture Modeling for Medical Volume Using Linear Tensor Coding
Directory of Open Access Journals (Sweden)
Junping Deng
2013-01-01
Full Text Available We introduced a compact representation method named Linear Tensor Coding (LTC for medical volume. With LTC, medical volumes can be represented by a linear combination of bases which are mutually independent. Furthermore, it is possible to choose the distinctive basis for classification. Before classification, correlations between category labels and the coefficients of LTC basis are used to choose the basis. Then we use the selected basis for classification. The classification accuracy can be significantly improved by the use of selected distinctive basis.
Modeling reaction front propagation from preferential flow pathways in fractured media
Myint, P. C.; Walsh, S. D.; Carroll, S.; Firoozabadi, A.
2013-12-01
We present analytical results and numerical models describing the growth and propagation of reaction fronts around fluid flow pathways in fractured rock, and explore how the front geometry influences both the propagation of the reaction fronts and changes in the solution chemistry. We compare model results to core-flood experiments conducted on mated wellbore cement/caprock half-cores, and demonstrate that the model accurately reproduces the observed solution chemistry. In particular the simulations provide a physical explanation for the apparent 'super-diffusive' reaction zone growth suggested by the brine chemistry. We conclude by discussing the implications of the model for long-term behavior of single and multiple reaction fronts.
Modifications of the optimal velocity traffic model to include delay due to driver reaction time
Davis, L. C.
2003-03-01
Straightforward inclusion of a delay time due to driver reaction time in the optimal velocity (OV) model reveals an unphysical sensitivity to driver reaction times. For delay times of nearly 1 s, which are typical for most drivers, oscillations in vehicle velocity induced by encountering a slower vehicle grow until limited by non-linear effects. Simulations demonstrate that unrealistically small delay times are needed for lengthy platoons of vehicles to avoid collisions. This is a serious limitation of the OV model. Other models, such as the inertial car-following model, allow somewhat larger delay times, but also show unphysical effects. Modifications of the OV model to overcome this deficiency are demonstrated. In addition, unphysical short-period oscillations of vehicle velocity are eliminated by introducing partial car-following into the model. Traffic jams are caused primarily by the delay due to driver reaction time in the modified OV model.
Analyzing Reaction Rates with the Distortion/Interaction‐Activation Strain Model
2017-01-01
Abstract The activation strain or distortion/interaction model is a tool to analyze activation barriers that determine reaction rates. For bimolecular reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction energies between the two distorted molecules. The energy required to distort the molecules is called the activation strain or distortion energy. This energy is the principal contributor to the activation barrier. The transition state occurs when this activation strain is overcome by the stabilizing interaction energy. Following the changes in these energies along the reaction coordinate gives insights into the factors controlling reactivity. This model has been applied to reactions of all types in both organic and inorganic chemistry, including substitutions and eliminations, cycloadditions, and several types of organometallic reactions. PMID:28447369
Analyzing Reaction Rates with the Distortion/Interaction-Activation Strain Model.
Bickelhaupt, F Matthias; Houk, Kendall N
2017-08-14
The activation strain or distortion/interaction model is a tool to analyze activation barriers that determine reaction rates. For bimolecular reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction energies between the two distorted molecules. The energy required to distort the molecules is called the activation strain or distortion energy. This energy is the principal contributor to the activation barrier. The transition state occurs when this activation strain is overcome by the stabilizing interaction energy. Following the changes in these energies along the reaction coordinate gives insights into the factors controlling reactivity. This model has been applied to reactions of all types in both organic and inorganic chemistry, including substitutions and eliminations, cycloadditions, and several types of organometallic reactions. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
Transportation Sector Model of the National Energy Modeling System. Volume 2 -- Appendices: Part 3
Energy Technology Data Exchange (ETDEWEB)
NONE
1998-01-01
This Appendix consists of two unpublished reports produced by Energy and Environmental Analysis, Inc., under contract to Oak Ridge National Laboratory. These two reports formed the basis for the subsequent development of the Fuel Economy Model described in Volume 1. They are included in order to document more completely the efforts undertaken to construct a comprehensive model of automobile fuel economy. The supplemental reports are as follows: Supplement 1--Documentation Attributes of Technologies to Improve Automotive Fuel Economy; Supplement 2--Analysis of the Fuel Economy Boundary for 2010 and Comparison to Prototypes.
Dynamical Coupled-Channel Model of Meson Production Reactions in the Nucleon Resonance Region
Energy Technology Data Exchange (ETDEWEB)
T.-S. H. Lee; A. Matsuyama; T. Sato
2006-11-15
A dynamical coupled-channel model is presented for investigating the nucleon resonances (N*) in the meson production reactions induced by pions and photons. Our objective is to extract the N* parameters and to investigate the meson production reaction mechanisms for mapping out the quark-gluon substructure of N* from the data. The model is based on an energy-independent Hamiltonian which is derived from a set of Lagrangians by using a unitary transformation method.
Fisher, Ian; Kastl, George; Sathasivan, Arumugam
2017-11-15
Accurate modelling of chlorine concentrations throughout a drinking water system needs sound mathematical descriptions of decay mechanisms in bulk water and at pipe walls. Wall-reaction rates along pipelines in three different systems were calculated from differences between field chlorine profiles and accurately modelled bulk decay. Lined pipes with sufficiently large diameters (>500 mm) and higher chlorine concentrations (>0.5 mg/L) had negligible wall-decay rates, compared with bulk-decay rates. Further downstream, wall-reaction rate consistently increased (peaking around 0.15 mg/dm 2 /h) as chlorine concentration decreased, until mass-transport to the wall was controlling wall reaction. These results contradict wall-reaction models, including those incorporated in the EPANET software, which assume wall decay is of either zero-order (constant decay rate) or first-order (wall-decay rate reduces with chlorine concentration). Instead, results are consistent with facilitation of the wall reaction by biofilm activity, rather than surficial chemical reactions. A new model of wall reaction combines the effect of biofilm activity moderated by chlorine concentration and mass-transport limitation. This wall reaction model, with an accurate bulk chlorine decay model, is essential for sufficiently accurate prediction of chlorine residuals towards the end of distribution systems and therefore control of microbial contamination. Implementing this model in EPANET-MSX (or similar) software enables the accurate chlorine modelling required for improving disinfection strategies in drinking water networks. New insight into the effect of chlorine on biofilm can also assist in controlling biofilm to maintain chlorine residuals. Copyright © 2017 Elsevier Ltd. All rights reserved.
Lazarev, V.; Geidmanis, D.
2016-02-01
The theoretical problem solved in this article is the calculation of thermodynamic parameters such as final temperature, distribution of the liquid and dry saturated vapour phases of the substance that are considered to be in thermodynamic equilibrium, and pressure of the system of several reaction products after adding to the system a certain amount of heat or the thermal effect released during rapid exothermic reaction in a closed volume that occurs so fast that it can be considered to be adiabatic, and when the volume of liquid reagents is several orders of magnitude less than the volume of the reactor. The general multi-substance problem is reduced to a theoretical problem for one substance of calculation thermodynamic parameters of system after adding a certain amount of heat that gives theoretically rigorous isochoric calculation. In this article, we substantiate our view that isochoric pass of calculation is more robust compared to seemingly more natural isobaric pass of calculation, if the later involves quite not trivial calculation of the adiabatic compression of a two-phase system (liquid - dry saturated vapour) that can pass itself into another kind of state (liquid - wet saturated vapour), which requires, apparently, more complex descriptions compared with isochoric calculation because the specific heat capacity of wet saturated vapour can be negative. The solved theoretical problem relates to a practical problem that has been a driver for our research as part of a design of the reactor of the titanium reduction from magnesium and titanium tetrachloride supplied into atmosphere of the reactor at high temperatures when both reagents are in gaseous state. The reaction is known to be exothermic with a high thermal effect, and estimate of the final temperature and pressure of the products of reaction, for instance, designing the reactor allows eliminating the possibility of the reaction products to penetrate backwards into supply tracts of the reagents
Xu, Lingshun; Wu, Zongfang; Jin, Yuekang; Ma, Yunsheng; Huang, Weixin
2013-08-07
We have employed XPS and TDS to study the adsorption and surface reactions of H2O, CO and HCOOH on an FeO(111)/Pt(111) inverse model catalyst. The FeO(111)-Pt(111) interface of the FeO(111)/Pt(111) inverse model catalyst exposes coordination-unsaturated Fe(II) cations (Fe(II)CUS) and the Fe(II)CUS cations are capable of modifying the reactivity of neighbouring Pt sites. Water facilely dissociates on the Fe(II)CUS cations at the FeO(111)-Pt(111) interface to form hydroxyls that react to form both water and H2 upon heating. Hydroxyls on the Fe(II)CUS cations can react with CO(a) on the neighbouring Pt(111) sites to produce CO2 at low temperatures. Hydroxyls act as the co-catalyst in the CO oxidation by hydroxyls to CO2 (PROX reaction), while they act as one of the reactants in the CO oxidation by hydroxyls to CO2 and H2 (WGS reaction), and the recombinative reaction of hydroxyls to produce H2 is the rate-limiting step in the WGS reaction. A comparison of reaction behaviors between the interfacial CO(a) + OH reaction and the formate decomposition reaction suggest that formate is the likely surface intermediate of the CO(a) + OH reaction. These results provide some solid experimental evidence for the associative reaction mechanism of WGS and PROX reactions catalyzed by Pt/oxide catalysts.
Periodic Anderson model with Holstein phonons for the description of the Cerium volume collapse
Li, Enzhi; Tam, Ka-Ming; Moreno, Juana; Jarrell, Mark
The volume collapse transition of Cerium has intrigued physicists since its discovery several decades ago. Various models and mechanisms have been proposed, the most prominent scenarios are based on the Mott transition and the Kondo volume collapse transition. In this study, we explore the volume collapse by a dynamical mean field theory (DMFT) study of the periodic Anderson model with phonons in the conduction band. This allows us to study the effect of the electron-phonon interaction on the volume collapse. In order to faithfully account for the volume collapse, we also include the effects due to the volume and temperature dependent bulk modulus. We find that as the electron-phonon interaction strength increases, the volume collapse effect is enhanced, which is consistent with the suggestion that the phonons have an important contribution in the volume collapse transition. Although we start with the canonical model for the Kondo volume collapse scenario, our results have some of the characteristics of the Mott scenario.
Predicting Complex Organic Mixture Atmospheric Chemistry Using Computer-Generated Reaction Models
Klein, M. T.; Broadbelt, L. J.; Mazurek, M. A.
2001-12-01
New measurement and chemical characterization technologies now offer unprecedented capabilities for detecting and describing atmospheric organic matter at the molecular level. As a result, very detailed and extensive chemical inventories are produced routinely in atmospheric field measurements of organic compounds found in the vapor and condensed phases (particles, cloud and fog droplets). Hundreds of organic compounds can constitute the complex chemical mixtures observed for these types of samples, exhibiting a wide spectrum of physical properties such as molecular weight, polarity, pH, and chemical reactivity. The central challenge is describing chemically the complex organic aerosol mixture in a useable fashion that can be linked to predictive models. However, the great compositional complexity of organic aerosols engenders a need for the modeling of the reaction chemistry of these compounds in atmospheric chemical models. On a mechanistic level, atmospheric reactions of organic compounds can involve a network of a very large number of chemical species and reactions. Deriving such large molecular kinetic models by hand is a tedious and time-consuming process. However, such models are usually built upon a few basic chemical principles tempered with the model builder's observations, experience, and intuition that can be summarized as a set of rules. This suggests that given an algorithmic framework, computers (information technology) may be used to apply these chemical principles and rules, thereby building a kinetic model. The framework for this model building process has been developed by means of graph theory. A molecule, which is a set of atoms connected by bonds, may be conceptualized as a set of vertices connected by edges, or to be more precise, a graph. The bond breaking and forming for a reaction can be represented compactly in the form of a matrix operator formally called the "reaction matrix". The addition of the reaction matrix operator to the reduced
Nicolin, Douglas J.; Jorge, Regina Maria M.; Jorge, Luiz Mario M.
2015-01-01
Several studies have taken into account the volume change of foods that undergo hydration or drying. However, the simplest boundary condition at the surface is usually considered to facilitate the solution of variable volume models. This paper presents a model of moisture diffusion in soybean grains that considers the volume change of these grains when absorbing water and also the dependence of diffusivity on moisture content. The boundary condition of equality of diffusive and convective flows on the surface was used and compared with two other approaches commonly found in the literature of grain hydration. This boundary condition was also applied to the case of constant volume of the grains and it was concluded that there are significant differences when the change in volume is taken into account. An analysis of the diffusion coefficients determined as functions of moisture content, temperature, and hydration time is presented for the best model.
Transportation Sector Model of the National Energy Modeling System. Volume 2 -- Appendices: Part 2
Energy Technology Data Exchange (ETDEWEB)
NONE
1998-01-01
The attachments contained within this appendix provide additional details about the model development and estimation process which do not easily lend themselves to incorporation in the main body of the model documentation report. The information provided in these attachments is not integral to the understanding of the model`s operation, but provides the reader with opportunity to gain a deeper understanding of some of the model`s underlying assumptions. There will be a slight degree of replication of materials found elsewhere in the documentation, made unavoidable by the dictates of internal consistency. Each attachment is associated with a specific component of the transportation model; the presentation follows the same sequence of modules employed in Volume 1. The following attachments are contained in Appendix F: Fuel Economy Model (FEM)--provides a discussion of the FEM vehicle demand and performance by size class models; Alternative Fuel Vehicle (AFV) Model--describes data input sources and extrapolation methodologies; Light-Duty Vehicle (LDV) Stock Model--discusses the fuel economy gap estimation methodology; Light Duty Vehicle Fleet Model--presents the data development for business, utility, and government fleet vehicles; Light Commercial Truck Model--describes the stratification methodology and data sources employed in estimating the stock and performance of LCT`s; Air Travel Demand Model--presents the derivation of the demographic index, used to modify estimates of personal travel demand; and Airborne Emissions Model--describes the derivation of emissions factors used to associate transportation measures to levels of airborne emissions of several pollutants.
Nicotiana tabacum as model for ozone - plant surface reactions
Jud, Werner; Fischer, Lukas; Wohlfahrt, Georg; Tissier, Alain; Canaval, Eva; Hansel, Armin
2015-04-01
Elevated tropospheric ozone concentrations are considered a toxic threat to plants, responsible for global crop losses with associated economic costs of several billion dollars per year. The ensuing injuries have been related to the uptake of ozone through the stomatal pores and oxidative effects damaging the internal leaf tissue. A striking question of current research is the environment and plant specific partitioning of ozone loss between gas phase, stomatal or plant surface sink terms. Here we show results from ozone fumigation experiments using various Nicotiana Tabacum varieties, whose surfaces are covered with different amounts of unsaturated diterpenoids exuded by their glandular trichomes. Exposure to elevated ozone levels (50 to 150 ppbv) for 5 to 15 hours in an exceptionally clean cuvette system did neither result in a reduction of photosynthesis nor caused any visible leaf damage. Both these ozone induced stress effects have been observed previously in ozone fumigation experiments with the ozone sensitive tobacco line Bel-W3. In our case ozone fumigation was accompanied by a continuous release of oxygenated volatile organic compounds, which could be clearly associated to their condensed phase precursors for the first time. Gas phase reactions of ozone were avoided by choosing a high enough gas exchange rate of the plant cuvette system. In the case of the Ambalema variety, that is known to exude only the diterpenoid cis-abienol, ozone fumigation experiments yield the volatiles formaldehyde and methyl vinyl ketone (MVK). The latter could be unequivocally separated from isomeric methacrolein (MACR) by the aid of a Selective Reagent Ion Time-of-Flight Mass Spectrometer (SRI-ToF-MS), which was switched every six minutes from H3O+ to NO+ primary ion mode and vice versa. Consistent with the picture of an ozone protection mechanism caused by reactive diterpenoids at the leaf surface are the results from dark-light experiments. The ozone loss obtained from the
A Predictive Model for the Diagnosis of Allergic Drug Reactions According to the Medical History.
Hierro Santurino, Beatriz; Mateos Conde, Javier; Cabero Morán, María Teresa; Mirón Canelo, José Antonio; Armentia Medina, Alicia
2016-01-01
Quantification of the risk of an allergic drug reaction through the medical history is essential in clinical decision making. However, in normal clinical practice, this evaluation is generally entirely subjective. The objective of this study was to construct a mathematical model to predict the risk of allergic drug reactions using the data collected in the medical history. A total of 696 active principles, corresponding to 466 patients aged more than 14 years attending the Allergy Service of the University Hospital of Salamanca, were included. Simple binary logistic regression was used to determine associations between variables from the medical history and the final diagnosis, to construct a predictive model. Variables useful in predicting a final diagnosis of allergic drug reaction were age, sex, drug class, number of active principles, time to the reaction, number of doses, clinical presentation suggestive of allergic disease, and time to medical consultation. True adverse drug reactions were estimated to occur in 20% of active principles. However, possible allergic reactions could only be ruled out in 52.2%. The use of mathematical models could greatly improve the discriminatory capacity of the medical history. Both the overdiagnosis and underdiagnosis of allergic drug reactions should be considered a public health problem. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.
Volume-area scaling approach versus flowline model in glacier volume projections
Radic, V.; Hock, Regine; Oerlemans, J.
2007-01-01
Volume–area scaling provides a practical alternative to ice-flow modelling to account for glacier size changes when modelling the future evolution of glaciers; however, uncertainties remain as to the validity of this approach under non-steady conditions. We address these uncertainties by deriving
Antarctic ice volume for the last 740 ka calculated with a simple ice sheet model
Oerlemans, J.
2005-01-01
Fluctuations in the volume of the Antarctic ice sheet for the last 740 ka are calculated by forcing a simple ice sheet model with a sea-level history (from a composite deep sea δ18O record) and a temperature history (from the Dome C deuterium record). Antarctic ice volume reaches maximum values of
Umur, Asli; van Gemert, Martin J. C.; Ross, Michael G.
2002-01-01
Clinical evidence suggests that increased amniotic fluid volume due to polyhydrarnnios increases placental vascular resistance. We have sought to model the possible effects of an increased amniotic fluid volume oil the net fetofetal transfusion in monochorionic twin pregnancies. We wanted to compare
BL-5255. I. Activity in animal models of immediate hypersensitivity reactions.
Siminoff, P; Reed, F C; Schurig, J E
1982-01-01
BL-5255 exhibited potent activity in several models of antigen-induced immediate hypersensitivity reactions in rats and guinea pigs. The compound was effective whether administered by oral or parenteral routes and in passively and actively sensitized animals. It appeared to be readily absorbed when given orally. Localized skin and bronchoconstriction reactions in rats were inhibited by the compound by oral doses at 0.014 and 1 mg/kg, respectively. BL-5255 was protective against both IgE- and IgG-mediated reactions in the rat and guinea pig. Its effectiveness versus the systemic anaphylaxis reaction in the guinea pig appears to be due to BL-5255's ability to inhibit both the IgE and IgG1 components of the reaction.
Ragavendar, M S; Anmol, Chopra M
2012-01-01
Lateral flow immunoassay (LFIA) platform is one of the most relevant technologies for screening and diagnosing clinical conditions. However due to low sensitivity and poor repeatability of the platform it has been used only for limited and non-critical tests. Mathematical models have been used to understand the principles of capillary flow and antibody antigen based immunoreactions in nitrocellulose membrane typically seen in LFIA. The model presented in this paper predicts the optimized location of test line on LFIA strip, sample volume and total reaction time that is needed to achieve the required sensitivity for different analytes on a case to case basis. The membrane properties like capillary flow time (s/cm), concentration and affinity constants of antibodies can be varied and the corresponding effect on strip design can be found. Hence this model can be used as a design tool to optimize the LFIA strip construction and reagent development processes.
Thermodynamic Models for Aqueous Alteration Coupled with Volume and Pressure Changes in Asteroids
Mironenko, M. V.; Zolotov, M. Y.
2005-01-01
All major classes of chondrites show signs of alteration on their parent bodies (asteroids). The prevalence of oxidation and hydration in alteration pathways implies that water was the major reactant. Sublimation and melting of water ice, generation of gases, formation of aqueous solutions, alteration of primary minerals and glasses and formation of secondary solids in interior parts of asteroids was likely to be driven by heat from the radioactive decay of short-lived radionuclides. Progress of alteration reactions should have affected masses and volumes of solids, and aqueous and gas phases. In turn, pressure evolution should have been controlled by changes in volumes and temperatures, escape processes, and production/ consumption of gases.
Droplet Reaction and Evaporation of Agents Model (DREAM). Glass model results; Sand model plans
Hin, A.R.T.
2006-01-01
The Agent Fate Program is generating an extensive set of quality agent fate data which is being used to develop highly accurate secondary evaporation predictive models. Models are being developed that cover a wide range of traditional chemical warfare agents deposited onto surfaces routinely found
Simple dissolution-reaction model for enzymatic conversion of suspension of solid substrate.
Wolff, A; Zhu, L; Kielland, V; Straathof, A J; Jongejan, J A; Heijnen, J J
1997-11-20
Although reactions in substrate suspension are employed in industry for several bioconversion processes, there appears to be no quantitative model available in the literature to rationalize the optimization of these processes. We present a simple model that incorporates the kinetics of substrate dissolution and a simultaneous enzymatic reaction. The model was tested in the alpha-chymotrypsin-catalyzed hydrolysis of an aqueous suspension of dimethyl benzylmethylmalonate to a homogeneous solution of enantiomerically pure monoester. This reaction occurs in the bulk phase, so catalysis by enzyme absorbed at the solid-liquid interface plays no role. The value of the parameters in the model (i.e., the mass transfer coefficient of substrate dissolution (k(L)), the substrate solubility, and the rate constant for the enzymatic reaction) were determined in separate experiments. Using these parameter values, the model gave a good quantitative prediction of the rate of the overall dissolution-reaction process. When the particle size distribution is known, k(L) may also be calculated instead. The model seems to be applicable also for other poorly soluble substrates, other enzymes, and other solvents. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 433-440, 1997.
Frazier, Zachary
2012-01-01
Abstract Particle-based Brownian dynamics simulations offer the opportunity to not only simulate diffusion of particles but also the reactions between them. They therefore provide an opportunity to integrate varied biological data into spatially explicit models of biological processes, such as signal transduction or mitosis. However, particle based reaction-diffusion methods often are hampered by the relatively small time step needed for accurate description of the reaction-diffusion framework. Such small time steps often prevent simulation times that are relevant for biological processes. It is therefore of great importance to develop reaction-diffusion methods that tolerate larger time steps while maintaining relatively high accuracy. Here, we provide an algorithm, which detects potential particle collisions prior to a BD-based particle displacement and at the same time rigorously obeys the detailed balance rule of equilibrium reactions. We can show that for reaction-diffusion processes of particles mimicking proteins, the method can increase the typical BD time step by an order of magnitude while maintaining similar accuracy in the reaction diffusion modelling. PMID:22697237
Flash Vacuum Pyrolysis of Lignin Model Compounds: Reaction Pathways of Aromatic Methoxy Groups
Energy Technology Data Exchange (ETDEWEB)
Britt, P.F.; Buchanan, A.C., III; Martineau, D.R.
1999-03-21
Currently, there is interest in utilizing lignin, a major constituent of biomass, as a renewable source of chemicals and fuels. High yields of liquid products can be obtained from the flash or fast pyrolysis of biomass, but the reaction pathways that lead to product formation are not understood. To provide insight into the primary reaction pathways under process relevant conditions, we are investigating the flash vacuum pyrolysis (FVP) of lignin model compounds at 500 C. This presentation will focus on the FVP of {beta}-ether linkages containing aromatic methoxy groups and the reaction pathways of methoxy-substituted phenoxy radicals.
Fixed site neutralization model programmer's manual. Volume II
Energy Technology Data Exchange (ETDEWEB)
Engi, D.; Chapman, L.D.; Judnick, W.; Blum, R.; Broegler, L.; Lenz, J.; Weinthraub, A.; Ballard, D.
1979-12-01
This report relates to protection of nuclear materials at nuclear facilities. This volume presents the source listings for the Fixed Site Neutralization Model and its supporting modules, the Plex Preprocessor and the Data Preprocessor. (DLC)
Directory of Open Access Journals (Sweden)
R. Atkinson
2008-08-01
Full Text Available This article, the fourth in the series, presents kinetic and photochemical data sheets evaluated by the IUPAC Subcommittee on Gas Kinetic Data Evaluation for Atmospheric Chemistry. It covers the gas phase and photochemical reactions of organic halogen species, which were last published in 1997, and were updated on the IUPAC website in 2006/07. The article consists of a summary sheet, containing the recommended kinetic parameters for the evaluated reactions, and four appendices containing the data sheets, which provide information upon which the recommendations are made.
Directory of Open Access Journals (Sweden)
R. Atkinson
2004-01-01
Full Text Available This article, the first in the series, presents kinetic and photochemical data evaluated by the IUPAC Subcommittee on GasKinetic Data Evaluation for Atmospheric Chemistry. It covers the gas phase and photochemical reactions of Ox, HOx, NOx and SOx species, which were last published in 1997, and were updated on the IUPAC website in late 2001. The article consists of a summary sheet, containing the recommended kinetic parameters for the evaluated reactions, and five appendices containing the data sheets, which provide information upon which the recommendations are made.
Directory of Open Access Journals (Sweden)
R. Atkinson
2006-01-01
Full Text Available This article, the second in the series, presents kinetic and photochemical data evaluated by the IUPAC Subcommittee on Gas Kinetic Data Evaluation for Atmospheric Chemistry. It covers the gas phase and photochemical reactions of Organic species, which were last published in 1999, and were updated on the IUPAC website in late 2002, and subsequently during the preparation of this article. The article consists of a summary table of the recommended rate coefficients, containing the recommended kinetic parameters for the evaluated reactions, and eight appendices containing the data sheets, which provide information upon which the recommendations are made.
Dynamic Analysis of a Reaction-Diffusion Rumor Propagation Model
Zhao, Hongyong; Zhu, Linhe
2016-06-01
The rapid development of the Internet, especially the emergence of the social networks, leads rumor propagation into a new media era. Rumor propagation in social networks has brought new challenges to network security and social stability. This paper, based on partial differential equations (PDEs), proposes a new SIS rumor propagation model by considering the effect of the communication between the different rumor infected users on rumor propagation. The stabilities of a nonrumor equilibrium point and a rumor-spreading equilibrium point are discussed by linearization technique and the upper and lower solutions method, and the existence of a traveling wave solution is established by the cross-iteration scheme accompanied by the technique of upper and lower solutions and Schauder’s fixed point theorem. Furthermore, we add the time delay to rumor propagation and deduce the conditions of Hopf bifurcation and stability switches for the rumor-spreading equilibrium point by taking the time delay as the bifurcation parameter. Finally, numerical simulations are performed to illustrate the theoretical results.
A robust methodology for kinetic model parameter estimation for biocatalytic reactions
DEFF Research Database (Denmark)
Al-Haque, Naweed; Andrade Santacoloma, Paloma de Gracia; Lima Afonso Neto, Watson
2012-01-01
Effective estimation of parameters in biocatalytic reaction kinetic expressions are very important when building process models to enable evaluation of process technology options and alternative biocatalysts. The kinetic models used to describe enzyme-catalyzed reactions generally include several...... lead to globally optimized parameter values. In this article, a robust methodology to estimate parameters for biocatalytic reaction kinetic expressions is proposed. The methodology determines the parameters in a systematic manner by exploiting the best features of several of the current approaches....... The parameter estimation problem is decomposed into five hierarchical steps, where the solution of each of the steps becomes the input for the subsequent step to achieve the final model with the corresponding regressed parameters. The model is further used for validating its performance and determining...
Directory of Open Access Journals (Sweden)
Fazle Mabood
2015-01-01
Full Text Available The heat flow patterns profiles are required for heat transfer simulation in each type of the thermal insulation. The exothermic reaction models in porous medium can prescribe the problems in the form of nonlinear ordinary differential equations. In this research, the driving force model due to the temperature gradients is considered. A governing equation of the model is restricted into an energy balance equation that provides the temperature profile in conduction state with constant heat source on the steady state. The proposed optimal homotopy asymptotic method (OHAM is used to compute the solutions of the exothermic reactions equation.
Wu, Zeng-Qiang; Du, Wen-Bin; Li, Jin-Yi; Xia, Xing-Hua; Fang, Qun
2015-08-01
Numerical simulation can provide valuable insights for complex microfluidic phenomena coupling mixing and diffusion processes. Herein, a novel finite element model (FEM) has been established to extract chemical reaction kinetics in a microfluidic flow injection analysis (micro-FIA) system using high throughput sample introduction. To reduce the computation burden, the finite element mesh generation is performed with different scales based on the different geometric sizes of micro-FIA. In order to study the contribution of chemical reaction kinetics under non-equilibrium condition, a pseudo-first-order chemical kinetics equation is adopted in the numerical simulations. The effect of reactants diffusion on reaction products is evaluated, and the results demonstrate that the Taylor dispersion plays a determining role in the micro-FIA system. In addition, the effects of flow velocity and injection volume on the reaction product are also simulated. The simulated results agree well with the ones from experiments. Although gravity driven flow is used to the numerical model in the present study, the FEM model also can be applied into the systems with other driving forces such as pressure. Therefore, the established FEM model will facilitate the understanding of reaction mechanism in micro-FIA systems and help us to optimize the manifold of micro-FIA systems. Copyright © 2015 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
IVAN GUTMAN
1999-08-01
Full Text Available A simple explanation is offered for the recently discovered chiral amplification in the alkylation reaction of benzaldehyde by means of dialkylzinc, catalyzed by (dimethylaminoisoborneol. The model presentd is similar to, yet somewhat simpler than, the model put forward by Noyori et al.
Bifurcation Analysis of Gene Propagation Model Governed by Reaction-Diffusion Equations
Directory of Open Access Journals (Sweden)
Guichen Lu
2016-01-01
Full Text Available We present a theoretical analysis of the attractor bifurcation for gene propagation model governed by reaction-diffusion equations. We investigate the dynamical transition problems of the model under the homogeneous boundary conditions. By using the dynamical transition theory, we give a complete characterization of the bifurcated objects in terms of the biological parameters of the problem.
Jensen, L; van Duijnen, PT; Snijders, JG
2003-01-01
We present a discrete solvent reaction field (DRF) model for the calculation of frequency-dependent hyperpolarizabilities of molecules in solution. In this model the solute is described using density functional theory (DFT) and the discrete solvent molecules are described with a classical
The hydration of slag, part 2: reaction models for blended cement
Chen, Wei; Brouwers, Jos
2007-01-01
The hydration of slag-blended cement is studied by considering the interaction between the hydrations of slag and Portland cement clinker. Three reaction models for the slag-blended cement are developed based on stoichiometric calculations. These models correlate the compositions of the unhydrated
Tissue reactions to lead samples in a late infection rat model
VanWachem, PB; VanLuyn, MJA; DeWit, AW; Raatjes, D; Verhoeven, MLPM; Hendriks, M; Cahalan, PT
Tissue reactions to rat lead samples, model ii ng for clinically used leads, were investigated in a late infection model, in which injection of bacteria was performed after a 3-week encapsulation process. At the site of injection, detachment of the original fibrous capsule, wound fluid infiltration,
Alteration of the Martian Surface Through Time: A Reaction Path Modeling Approach
Ridley, W. I.; Plumlee, G. S.; Debraal, J. D.; Reed, M. H.
1995-09-01
We have performed preliminary geochemical reaction path calculations [1] that attempt to model reasonable martian geologic processes under various climatic conditions postulated for Mars during its planetary evolution [2]. Weathering and fluid evaporation and freezing are discussed here. Under current Earth conditions, 25 degrees C rainwater in equilibrium with the atmosphere has a calculated pH=5.66, dissolved O2=2.5x10^-4 mole/kg, and dissolved CO2=1.3x10^-5 mole/kg. In contrast, martian rainwater in a postulated early, warm and wet climate would have lower pH,, higher dissolved CO2, and lower dissolved oxygen. For instance, in a martian atmosphere with pCO2=2.2 bar [3] and pO2=10^-5 bar, rainwater is calculated to have pH=3.96, dissolved CO2 of 7.5x10^-2 mole/kg, and dissolved O2=1.3x10^-8 mole/kg. If, under these climatic conditions, there was also extensive basaltic volcanism, then rainwater would be further modified chemically by solution of volcanic gases to form acid rain. For example, we can model this process using a Kilauea gas composition, in mole percent (H2O=57.8; HCl=0.9; SO2=17.4; CO2=21.6; H2S=0.2; H2=1.0), and assume the resultant fluid is buffered by atmospheric CO2. Addition of only 0.1 gram of gas to 1 kgram of ancient rainwater reduces the pH to 3.07 and dramatically increases dissolved SO4- (3.8x10^-4 mole/kg), H2S[aq] (1.3x10^-4 mole/kg) and Cl- (4.4x10^-5 mole/kg). Weathering minerals formed by reaction of the above fluid types with martian basalts can vary significantly depending upon initial fluid acidity and solute content. Acid rain and "normal" rain (buffered under high pCO2 conditions) initially alter martian basalt (modeled as the Chassigny parent composition [4]) to, in order of decreasing abundance: Fe-smectite (+/- ferrihydrite), Mn hydroxide, kaolinite, apatite, chalcedony at pH 5 then dolomite, calcite, K-feldspar, and dawsonite also precipitate. An important aspect of this modeling is that acid rain can produce larger volumes
Energy Technology Data Exchange (ETDEWEB)
None
1996-12-01
Volume VII of the documentation for the Phase I Data Analysis Task performed in support of the current Regional Flow Model, Transport Model, and Risk Assessment for the Nevada Test Site Underground Test Area Subproject contains the tritium transport model documentation. Because of the size and complexity of the model area, a considerable quantity of data was collected and analyzed in support of the modeling efforts. The data analysis task was consequently broken into eight subtasks, and descriptions of each subtask's activities are contained in one of the eight volumes that comprise the Phase I Data Analysis Documentation.
DEFF Research Database (Denmark)
Thorborg, Jesper
, however, is constituted by the implementation of the $J_2$ flow theory in the control volume method. To apply the control volume formulation on the process of hardening concrete viscoelastic stress-strain models has been examined in terms of various rheological models. The generalized 3D models are based...... in connection with the thermal model to describe the general process of hardening concrete, i.e release of energy during hardening, creep in early age concrete and maturity dependent material properties. Generally the work presented in this thesis is motivated by the intention of using numerical modelling...
Energy Technology Data Exchange (ETDEWEB)
None
1996-11-01
Volume VI of the documentation for the Phase I Data Analysis Task performed in support of the current Regional Flow Model, Transport Model, and Risk Assessment for the Nevada Test Site Underground Test Area Subproject contains the groundwater flow model data. Because of the size and complexity of the model area, a considerable quantity of data was collected and analyzed in support of the modeling efforts. The data analysis task was consequently broken into eight subtasks, and descriptions of each subtask's activities are contained in one of the eight volumes that comprise the Phase I Data Analysis Documentation.
Statistical Modeling of Ultrawideband Body-Centric Wireless Channels Considering Room Volume
Directory of Open Access Journals (Sweden)
Miyuki Hirose
2012-01-01
Full Text Available This paper presents the results of a statistical modeling of onbody ultrawideband (UWB radio channels for wireless body area network (WBAN applications. Measurements were conducted in five different rooms. A measured delay profile can be divided into two domains; in the first domain (04 ns has multipath components that are dominant and dependent on room volume. The first domain was modeled with a conventional power decay law model, and the second domain with a modified Saleh-Valenzuela model considering the room volume. Realizations of the impulse responses are presented based on the composite model and compared with the measured average power delay profiles.
2015-01-01
The intracellular environment in which biological reactions occur is crowded with macromolecules and subdivided into microenvironments that differ in both physical properties and chemical composition. The work described here combines experimental and computational model systems to help understand the consequences of this heterogeneous reaction media on the outcome of coupled enzyme reactions. Our experimental model system for solution heterogeneity is a biphasic polyethylene glycol (PEG)/sodium citrate aqueous mixture that provides coexisting PEG-rich and citrate-rich phases. Reaction kinetics for the coupled enzyme reaction between glucose oxidase (GOX) and horseradish peroxidase (HRP) were measured in the PEG/citrate aqueous two-phase system (ATPS). Enzyme kinetics differed between the two phases, particularly for the HRP. Both enzymes, as well as the substrates glucose and H2O2, partitioned to the citrate-rich phase; however, the Amplex Red substrate necessary to complete the sequential reaction partitioned strongly to the PEG-rich phase. Reactions in ATPS were quantitatively described by a mathematical model that incorporated measured partitioning and kinetic parameters. The model was then extended to new reaction conditions, i.e., higher enzyme concentration. Both experimental and computational results suggest mass transfer across the interface is vital to maintain the observed rate of product formation, which may be a means of metabolic regulation in vivo. Although outcomes for a specific system will depend on the particulars of the enzyme reactions and the microenvironments, this work demonstrates how coupled enzymatic reactions in complex, heterogeneous media can be understood in terms of a mathematical model. PMID:24517887
Modelling of chalcopyrite oxidation reactions in the Outokumpu flash smelting process
Energy Technology Data Exchange (ETDEWEB)
Ahokainen, T.; Jokilaakso, A. [Helsinki Univ. of Technology, Otaniemi (Finland)
1996-12-31
A mathematical model for simulating oxidation reactions of chalcopyrite particles together with momentum, heat and mass transfer between particle and gas phase in a flash smelting furnace reaction shaft is presented. In simulation, the equations governing the gas flow are solved numerically with a commercial fluid flow package, Phoenics. The particle phase is introduced into the gas flow by a Particle Source In Cell (PSIC) - technique, where a number of discrete particles is tracked in a gas flow and the relevant source terms for momentum, mass, and heat transfer are added to the gas phase equations. The gas phase equations used are elliptic in nature and the fluid turbulence is described by the (k-{epsilon}) -model. Thermal gas phase radiation is simulated with a six-flux radiation model. The chemical reactions of concentrate particles are assumed to happen at two sharp interfaces, and a shrinking core model is applied to describe the mass transfer of chemical species through the reaction product layer. In a molten state, the oxygen consumption is controlled by a film penetration concept. The reacting concentrate particles are a mixture of chalcopyrite and silica. Also a certain amount of pure inert silica is fed to the process as flux. In the simulations the calculation domain includes the concentrate burner and a cylindrical reaction shaft of an industrial scale flash smelting furnace. Some examples about the simulations carried out by the combustion model are presented. (author)
Basilevsky, M V; Odinokov, A V; Titov, S V; Mitina, E A
2013-12-21
The algorithm for a theoretical calculation of transfer reaction rates for light quantum particles (i.e., the electron and H-atom transfers) in non-polar solid matrices is formulated and justified. The mechanism postulated involves a local mode (an either intra- or inter-molecular one) serving as a mediator which accomplishes the energy exchange between the reacting high-frequency quantum mode and the phonon modes belonging to the environment. This approach uses as a background the Fermi golden rule beyond the usually applied spin-boson approximation. The dynamical treatment rests on the one-dimensional version of the standard quantum relaxation equation for the reduced density matrix, which describes the frequency fluctuation spectrum for the local mode under consideration. The temperature dependence of a reaction rate is controlled by the dimensionless parameter ξ0 = ℏω0/k(B)T where ω0 is the frequency of the local mode and T is the temperature. The realization of the computational scheme is different for the high/intermediate (ξ0 kinetic regime, the Redfield approximation to the solution of the relaxation equation proved to be sufficient and efficient in practical applications. The study of the essentially quantum-mechanical low-temperature kinetic regime in its asymptotic limit requires the implementation of the exact relaxation equation. The coherent mechanism providing a non-vanishing reaction rate has been revealed when T → 0. An accurate computational methodology for the cross-over kinetic regime needs a further elaboration. The original model of the hopping mechanism for electronic conduction in photosensitive organic materials is considered, based on the above techniques. The electron transfer (ET) in active centers of such systems proceeds via local intra- and intermolecular modes. The active modes, as a rule, operate beyond the kinetic regimes, which are usually postulated in the existing theories of the ET. Our alternative dynamic ET model for
Multiphysics modelling of volume phase transition of ionic hydrogels responsive to thermal stimulus.
Li, Hua; Wang, Xiaogui; Wang, Zijie; Lam, K Y
2005-09-16
This paper presents the analysis of the volume phase transition of ionic thermo-sensitive hydrogels to thermal stimulus through mathematical modelling. The model is termed the multi-effect-coupling thermal-stimulus (MECtherm) model and it considers the effects of multi-phases and multi-physics. Its application to steady-state analysis of the hydrogels in swelling equilibrium is validated against available experimental data for the relation between volume swelling ratio and temperature, in which very good agreement is achieved. The phenomenon of volume phase transition is studied for the thermal-stimulus responsive hydrogel. The numerical studies predict well the influences of initially fixed charge density and initial volume fraction of polymeric network on the swelling equilibrium of the hydrogels.
Phase transitions in a holographic s + p model with back-reaction
Energy Technology Data Exchange (ETDEWEB)
Nie, Zhang-Yu [Kunming University of Science and Technology, Kunming (China); Chinese Academy of Sciences, State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Beijing (China); Shanghai Jiao Tong University, INPAC, Department of Physics, and Shanghai Key Laboratory of Particle Physics and Cosmology, Shanghai (China); Cai, Rong-Gen [Chinese Academy of Sciences, State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Beijing (China); Gao, Xin [Virginia Tech, Department of Physics, Blacksburg, VA (United States); Li, Li [University of Crete, Department of Physics, Crete Center for Theoretical Physics, Heraklion (Greece); Zeng, Hui [Kunming University of Science and Technology, Kunming (China); Chinese Academy of Sciences, State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Beijing (China)
2015-11-15
In a previous paper (Nie et al. in JHEP 1311:087, arXiv:1309.2204 [hep-th], 2013), we presented a holographic s + p superconductor model with a scalar triplet charged under an SU(2) gauge field in the bulk. We also study the competition and coexistence of the s-wave and p-wave orders in the probe limit. In this work we continue to study the model by considering the full back-reaction. The model shows a rich phase structure and various condensate behaviors such as the ''n-type'' and ''u-type'' ones, which are also known as reentrant phase transitions in condensed matter physics. The phase transitions to the p-wave phase or s + p coexisting phase become first order in strong back-reaction cases. In these first order phase transitions, the free energy curve always forms a swallow tail shape, in which the unstable s + p solution can also play an important role. The phase diagrams of this model are given in terms of the dimension of the scalar order and the temperature in the cases of eight different values of the back-reaction parameter, which show that the region for the s + p coexisting phase is enlarged with a small or medium back-reaction parameter but is reduced in the strong back-reaction cases. (orig.)
DEFF Research Database (Denmark)
Jeong, Cheol-Ho
2011-01-01
resistivity and the absorber thickness on the difference between the two surface reaction models are examined and discussed. For a porous absorber backed by a rigid surface, the local reaction models give errors of less than 10% if the thickness exceeds 120 mm for a flow resistivity of 5000 Nm-4s. As the flow...... resistivity doubles, a decrease in the required thickness by 25 mm is observed to achieve the same amount of error. For an absorber backed by an air gap, the thickness ratio between the material and air cavity is important. If the absorber thickness is approximately 40% of the cavity depth, the local reaction...... models give errors below 10% even for a low flow resistivity case....
Stimulation model for lenticular sands: Volume 2, Users manual
Energy Technology Data Exchange (ETDEWEB)
Rybicki, E.F.; Luiskutty, C.T.; Sutrick, J.S.; Palmer, I.D.; Shah, G.H.; Tomutsa, L.
1987-07-01
This User's Manual contains information for four fracture/proppant models. TUPROP1 contains a Geertsma and de Klerk type fracture model. The section of the program utilizing the proppant fracture geometry data from the pseudo three-dimensional highly elongated fracture model is called TUPROPC. The analogous proppant section of the program that was modified to accept fracture shape data from SA3DFRAC is called TUPROPS. TUPROPS also includes fracture closure. Finally there is the penny fracture and its proppant model, PENNPROP. In the first three chapters, the proppant sections are based on the same theory for determining the proppant distribution but have modifications to support variable height fractures and modifications to accept fracture geometry from three different fracture models. Thus, information about each proppant model in the User's Manual builds on information supplied in the previous chapter. The exception to the development of combined treatment models is the penny fracture and its proppant model. In this case, a completely new proppant model was developed. A description of how to use the combined treatment model for the penny fracture is contained in Chapter 4. 2 refs.
Directory of Open Access Journals (Sweden)
Jyotishkumar Parameswaranpillai
2013-01-01
Full Text Available The cure reaction, rheology, volume shrinkage, and thermomechanical behavior of epoxy-TiO2 nanocomposites based on diglycidyl ether of bisphenol A cured with 4,4′-diaminodiphenylsulfone have been investigated. The FTIR results show that, at the initial curing stage, TiO2 acts as a catalyst and facilitates the curing. The catalytic effect of TiO2 was further confirmed by the decrease in maximum exothermal peak temperature (DSC results; however, it was also found that the addition of TiO2 decreases the overall degree of cure, as evidenced by lower total heat of reaction of the cured composites compared to neat epoxy. The importance of cure rheology in the microstructure formation during curing was explored by using rheometry. From the PVT studies, it was found that TiO2 decreases the volume shrinkage behavior of the epoxy matrix. The mechanical properties of the cured epoxy composites, such as tensile strength, tensile modulus, flexural strength, flexural modulus, impact strength, and fracture toughness of the polymer composites, were examined. The nanocomposites exhibited good improvement in dimensional, thermal, and mechanical properties with respect to neat cross-linked epoxy system. FESEM micrographs of fractured surfaces were examined to understand the toughening mechanism.
Frazer, D G; Lindsley, W G; McKinney, W; Reynolds, J S; Franz, G N; Jackson, M; Goldsmith, W T
2013-03-01
The role of the recruitment-derecruitment of small structures in the lung (lung units) as the lung increases and decreases in volume has been debated. The objective of this study was to develop a model to estimate the change in the number and volume of open lung units as an excised lung is inflated-deflated between minimum and maximum lung volume. The model was formulated based on the observation that the compliance of the slowly changing quasi-static pressure-volume (P-V) curve of an excised rat lung can differ from the compliance of a faster changing small sinusoidal pressure volume perturbations superimposed on the curve. In those regions of the curve where differences in compliance occur, the lung tissue properties exhibit nonlinear characteristics, which cannot be linearized using "incremental" or "small signal" analysis. The model attributes the differences between the perturbation and quasi-static compliance to an additional nonlinear compliance term that results from the sequential opening and closing of lung units. Using this approach, it was possible to calculate the normalized average volume and the normalized number of open units as the lung is slowly inflated-deflated. Results indicate that the normalized average volume and the normalized number of open units are not linearly related to normalized lung volume, and at equal lung volumes the normalized number of open units is greater and the normalized average lung unit volume is smaller during lung deflation when compared to lung inflation. In summary, a model was developed to describe the recruitment-derecruitment process in excised lungs based on the differences between small signal perturbation compliance and quasi-static compliance. Values of normalized lung unit volume and the normalized number of open lung units were shown to be nonlinear functions of both transpulmonary pressure and normalized lung volume.
Study of the Deformation/Interaction Model: How Interactions Increase the Reaction Barrier
Directory of Open Access Journals (Sweden)
Zhiling Liang
2018-01-01
Full Text Available The interactions (including weak interactions between dienophiles and dienes play an important role in the Diels-Alder reaction. To elucidate the influence of these interactions on the reactivity, a popular DFT functional and a variational DFT functional corrected with dispersion terms are used to investigate different substituent groups incorporated on the dienophiles and dienes. The bond order is used to track the trajectory of the cycloaddition reaction. The deformation/interaction model is used to obtain the interaction energy from the reactant complex to the inflection point until reaching the saddle point. The interaction energy initially increases with a decrease in the interatomic distance, reaching a maximum value, but then decreases when the dienophiles and dienes come closer. Reduced density gradient and chemical energy component analysis are used to analyse the interaction. Traditional transition state theory and variational transition state theory are used to obtain the reaction rates. The influence of tunneling on the reaction rate is also discussed.
Predicting template-based catalysis rates in a simple catalytic reaction model.
Hordijk, Wim; Steel, Mike
2012-02-21
We show that in a particular model of catalytic reaction systems, known as the binary polymer model, there is a mathematical concordance between two versions of the model: (1) random catalysis and (2) template-based catalysis. In particular, we derive an analytical calculation that allows us to accurately predict the (observed) required level of catalysis in one version of the model from that in the other version, for a given probability of having self-sustaining autocatalytic sets exist in instances of both model versions. This provides a tractable connection between two models that have been investigated in theoretical origin-of-life studies. Copyright © 2011 Elsevier Ltd. All rights reserved.
Darmana, D.; Deen, N.G.; Kuipers, J.A.M.
2004-01-01
A 3D discrete bubble model is adopted to investigate complex behavior involving hydrodynamics, mass transfer and chemical reactions in a gas-liquid bubble column reactor. In this model a continuum description is adopted for the liquid phase and additionally each individual bubble is tracked in a
Darmana, D.; Deen, N.G.; Kuipers, J.A.M.
2005-01-01
A 3D discrete bubble model is adopted to investigate complex behavior involving hydrodynamics, mass transfer and chemical reactions in a gas¿liquid bubble column reactor. In this model a continuum description is adopted for the liquid phase and additionally each individual bubble is tracked in a
Energy Technology Data Exchange (ETDEWEB)
Contreras, Anthony Marshall [Univ. of California, Berkeley, CA (United States)
2006-05-20
In order to better understand the fundamental components that govern catalytic activity, two-dimensional model platinum nanocatalyst arrays have been designed and fabricated. These catalysts arrays are meant to model the interplay of the metal and support important to industrial heterogeneous catalytic reactions. Photolithography and sub-lithographic techniques such as electron beam lithography, size reduction lithography and nanoimprint lithography have been employed to create these platinum nanoarrays. Both in-situ and ex-situ surface science techniques and catalytic reaction measurements were used to correlate the structural parameters of the system to catalytic activity.
DEFF Research Database (Denmark)
Sayar, N.A.; Chen, B.H.; Lye, G.J.
2009-01-01
In this paper we have used a proposed mathematical model, describing the carbon-carbon bond format ion reaction between beta-hydroxypyruvate and glycolaldehyde to synthesise L-erythrulose, catalysed by the enzyme transketolase, for the analysis of the sensitivity of the process to its kinetic...... parameters. The model was validated with experimental data. As a conclusion, kinetic parameters with a possible positive impact on reaction performance were identified and assessed in relation to operating conditions. This resulted in the identification of suitable catalyst and process development targets...
A hybrid ARIMA and neural network model applied to forecast catch volumes of Selar crumenophthalmus
Aquino, Ronald L.; Alcantara, Nialle Loui Mar T.; Addawe, Rizavel C.
2017-11-01
The Selar crumenophthalmus with the English name big-eyed scad fish, locally known as matang-baka, is one of the fishes commonly caught along the waters of La Union, Philippines. The study deals with the forecasting of catch volumes of big-eyed scad fish for commercial consumption. The data used are quarterly caught volumes of big-eyed scad fish from 2002 to first quarter of 2017. This actual data is available from the open stat database published by the Philippine Statistics Authority (PSA)whose task is to collect, compiles, analyzes and publish information concerning different aspects of the Philippine setting. Autoregressive Integrated Moving Average (ARIMA) models, Artificial Neural Network (ANN) model and the Hybrid model consisting of ARIMA and ANN were developed to forecast catch volumes of big-eyed scad fish. Statistical errors such as Mean Absolute Errors (MAE) and Root Mean Square Errors (RMSE) were computed and compared to choose the most suitable model for forecasting the catch volume for the next few quarters. A comparison of the results of each model and corresponding statistical errors reveals that the hybrid model, ARIMA-ANN (2,1,2)(6:3:1), is the most suitable model to forecast the catch volumes of the big-eyed scad fish for the next few quarters.
Software Modeling Studies. Volume 1. Summary of Technical Progress
1978-01-01
of software modeling problems, and.in addition to develop models that truly reflect the actual software development process, and thus provide more...X - - Students Kenneth Apperley - - X - Marek Babinski X X - - Eli Berlinger - - X X John Casey - - X - Daniel Kaufman - - X - Ronald Karam - - X
Volume and aboveground biomass models for dry Miombo woodland in Tanzania
DEFF Research Database (Denmark)
Mwakalukwa, Ezekiel Edward; Meilby, Henrik; Treue, Thorsten
2014-01-01
Tools to accurately estimate tree volume and biomass are scarce for most forest types in East Africa, including Tanzania. Based on a sample of 142 trees and 57 shrubs from a 6,065 ha area of dry miombo woodland in Iringa rural district in Tanzania, regression models were developed for volume...... and biomass of three important species, Brachystegia spiciformis Benth. (n=40), Combretum molle G. Don (n=41), and Dalbergia arbutifolia Baker (n=37) separately, and for broader samples of trees (28 species, n=72), shrubs (16 species, n=31), and trees and shrubs combined (44 species, n=104). Applied...... of the predictions tended to increase from general to species-specific models. Except for a few volume and biomass models developed for shrubs, all models had R2 values of 96–99%. Thus, the models appear robust and should be applicable to forests with similar site conditions, species, and diameter ranges....
Supercritical water oxidation of quinazoline: Reaction kinetics and modeling.
Gong, Yanmeng; Guo, Yang; Wang, Shuzhong; Song, Wenhan; Xu, Donghai
2017-03-01
This paper presents a first quantitative kinetic model for supercritical water oxidation (SCWO) of quinazoline that describes the formation and interconversion of intermediates and final products at 673-873 K. The set of 11 reaction pathways for phenol, pyrimidine, naphthalene, NH3, etc, involved in the simplified reaction network proved sufficient for fitting the experimental results satisfactorily. We validated the model prediction ability on CO2 yields at initial quinazoline loading not used in the parameter estimation. Reaction rate analysis and sensitivity analysis indicate that nearly all reactions reach their thermodynamic equilibrium within 300 s. The pyrimidine yielding from quinazoline is the dominant ring-opening pathway and provides a significant contribution to CO2 formation. Low sensitivity of NH3 decomposition rate to concentration confirms its refractory nature in SCWO. Nitrogen content in liquid products decreases whereas that in gaseous phase increases as reaction time prolonged. The nitrogen predicted by the model in gaseous phase combined with the experimental nitrogen in liquid products gives an accurate nitrogen balance of conversion process. Copyright © 2016 Elsevier Ltd. All rights reserved.
Directory of Open Access Journals (Sweden)
Shim S.M.
2012-01-01
Full Text Available The performance of the CO2 absorber column using mono-ethanolamine (MEA solution as chemical solvent are predicted by a One-Dimensional (1-D rate based model in the present study. 1-D Mass and heat balance equations of vapor and liquid phase are coupled with interfacial mass transfer model and vapor-liquid equilibrium model. The two-film theory is used to estimate the mass transfer between the vapor and liquid film. Chemical reactions in MEA-CO2-H2O system are considered to predict the equilibrium pressure of CO2 in the MEA solution. The mathematical and reaction kinetics models used in this work are calculated by using in-house code. The numerical results are validated in the comparison of simulation results with experimental and simulation data given in the literature. The performance of CO2 absorber column is evaluated by the 1-D rate based model using various reaction rate coefficients suggested by various researchers. When the rate of liquid to gas mass flow rate is about 8.3, 6.6, 4.5 and 3.1, the error of CO2 loading and the CO2 removal efficiency using the reaction rate coefficients of Aboudheir et al. is within about 4.9 % and 5.2 %, respectively. Therefore, the reaction rate coefficient suggested by Aboudheir et al. among the various reaction rate coefficients used in this study is appropriate to predict the performance of CO2 absorber column using MEA solution. [Acknowledgement. This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF, funded by the Ministry of Education, Science and Technology (2011-0017220].
Measurement and modeling of advanced coal conversion processes, Volume III
Energy Technology Data Exchange (ETDEWEB)
Ghani, M.U.; Hobbs, M.L.; Hamblen, D.G. [and others
1993-08-01
A generalized one-dimensional, heterogeneous, steady-state, fixed-bed model for coal gasification and combustion is presented. The model, FBED-1, is a design and analysis tool that can be used to simulate a variety of gasification, devolatilization, and combustion processes. The model considers separate gas and solid temperatures, axially variable solid and gas flow rates, variable bed void fraction, coal drying, devolatilization based on chemical functional group composition, depolymerization, vaporization and crosslinking, oxidation, and gasification of char, and partial equilibrium in the gas phase.
Measurement and modeling of advanced coal conversion processes, Volume II
Energy Technology Data Exchange (ETDEWEB)
Solomon, P.R.; Serio, M.A.; Hamblen, D.G. [and others
1993-06-01
A two dimensional, steady-state model for describing a variety of reactive and nonreactive flows, including pulverized coal combustion and gasification, is presented. The model, referred to as 93-PCGC-2 is applicable to cylindrical, axi-symmetric systems. Turbulence is accounted for in both the fluid mechanics equations and the combustion scheme. Radiation from gases, walls, and particles is taken into account using a discrete ordinates method. The particle phase is modeled in a lagrangian framework, such that mean paths of particle groups are followed. A new coal-general devolatilization submodel (FG-DVC) with coal swelling and char reactivity submodels has been added.
Reactions of aqueous chlorine and chlorine dioxide with model food compounds.
Fukayama, M Y; Tan, H; Wheeler, W B; Wei, C I
1986-01-01
Chlorine and chlorine dioxide (ClO2), common disinfecting and bleaching chemicals used in the food industry, are potent oxidizing and chlorinating agents. Unfortunately, little is known about the nature of the reactions of chlorine with organic food constituents. This presentation reviews published information concerning the reactions of chlorine gas (Cl2[g]), aqueous chlorine, and ClO2 with model food compounds, the fate of chlorine during the chlorination of specific food products, and the potential toxicity of the reaction products. Fatty acids and their methyl esters react with chlorine with the degree of incorporation corresponding to their degree of unsaturation. Aqueous chlorine oxidizes and chlorinates lipids and amino acids much more readily than ClO2. Several amino acids are highly susceptible to oxidation and chlorination by chlorine compounds. Reactions of chlorine and ClO2 with several food products, including flour and shrimp, have also been characterized. In one model system, 99% of Cl2(g) either reacted with components of flour or was consumed by oxidation/chlorination reactions. The lipids extracted from the chlorinated flour contained significant amounts of chlorine. Exposure of shrimp to hypochlorous acid (HOCl) solution resulted in significant incorporation of chlorine into the edible portion. Although significant quantities of chlorine can be incorporated into specific model compounds and food products, the health risks associated with exposure to chlorinated organic products are unknown. Preliminary studies using the Ames Salmonella/microsome mutagenicity assay indicate that the reaction products from mixtures of aqueous chlorine and various lipids or tryptophan are nonmutagenic. Nevertheless, additional studies are warranted, so that the toxicological significance of these reaction products can be understood more fully. PMID:3545804
Forest growth modeling and prediction (Volumes 1 & 2).
Alan R. Ek; Stephen R. Shifley; Thomas E. Burk
1988-01-01
Proceedings of the August 23-27 IUFRO Conference, Minneapolis, Minnesota. Includes 143 manuscripts dealing with growth and yield modeling; regeneration; site characterization; effects of fertilization, genetics, and disturbance; density management; evaluation; estimation; inventory; and application.
Directory of Open Access Journals (Sweden)
Arschang eValipour
2012-10-01
Full Text Available Rationale: In clinical trials, homogeneous emphysema patients have responded well to upper lobe volume reduction but not lower lobe volume reduction. Materials/Methods: To understand the physiological basis for this observation, a computer model was developed to simulate the effects of upper and lower lobe lung volume reduction on RV/TLC and lung recoil in homogeneous emphysema.Results: Patients with homogeneous emphysema received either upper or lower lobe volume reduction therapy based on findings of radionucleotide scintigraphy scanning. CT analysis of lobar volumes showed that patients undergoing upper (n=18; -265 mL/site and lower lobe treatment (n=11; -217 mL/site experienced similar reductions in lung volume. However, only upper lobe treatment improved FEV1 (+11.1±14.7% vs -4.4±15.8% and RV/TLC (-5.4± 8.1% vs -2.4±8.6%. Model simulations provided an unexpected explanation for this response. Increases in transpulmonary pressure subsequent to volume reduction increased RV/TLC in upper lobe alveoli, while caudal shifts in airway closure decreased RV/TLC in lower lobe alveoli. Upper lobe treatment, which eliminates apical alveoli with high RV/TLC values, lowers the average RV/TLC of the lung. Conversely, lower lobe treatment, which eliminates caudal alveoli with low RV/TLC values, has less effect. Conclusions: Lower lobe treatment in homogeneous emphysema is uniformly less effective than upper lobe treatment.
Developing a stochastic traffic volume prediction model for public-private partnership projects
Phong, Nguyen Thanh; Likhitruangsilp, Veerasak; Onishi, Masamitsu
2017-11-01
Transportation projects require an enormous amount of capital investment resulting from their tremendous size, complexity, and risk. Due to the limitation of public finances, the private sector is invited to participate in transportation project development. The private sector can entirely or partially invest in transportation projects in the form of Public-Private Partnership (PPP) scheme, which has been an attractive option for several developing countries, including Vietnam. There are many factors affecting the success of PPP projects. The accurate prediction of traffic volume is considered one of the key success factors of PPP transportation projects. However, only few research works investigated how to predict traffic volume over a long period of time. Moreover, conventional traffic volume forecasting methods are usually based on deterministic models which predict a single value of traffic volume but do not consider risk and uncertainty. This knowledge gap makes it difficult for concessionaires to estimate PPP transportation project revenues accurately. The objective of this paper is to develop a probabilistic traffic volume prediction model. First, traffic volumes were estimated following the Geometric Brownian Motion (GBM) process. Monte Carlo technique is then applied to simulate different scenarios. The results show that this stochastic approach can systematically analyze variations in the traffic volume and yield more reliable estimates for PPP projects.
Phase-segregated model for plant cell culture: The effect of cell volume fraction
Energy Technology Data Exchange (ETDEWEB)
Zhang, W. [Univ. of Adelaide, Adelaide (Australia). Dept. of Chemical Engineering]|[Tokyo Univ. (Japan)hinese Academy of Sciences, Dalian (China). Dalian Inst. of Chemical Physics; Furusaki, S. [Tokyo Univ. (Japan)] Middelberg, A. [Univ. of Adelaide, Adelaide (Australia). Dept. of Chemical Engineering
1998-06-01
Plant cells are characterized by low water content, so the fraction of cell volume (volume fraction) in a vessel is large compared with other cell systems, even if the cell concentrations are the same. Therefore, concentration of plant cells should preferably be expressed by the liquid volume basis rather than by the total vessel volume basis. In this paper, a new model is proposed to analyze behavior of a plant cell culture by dividing the cell suspension into the biotic- and abiotic-phases. Using this model, we analyzed the cell-growth and the alkaloid production by Catharanthus roseus. Large errors in the simulated results were observed if the phase-segregation was not considered. 12 refs., 3 figs.
Salvage, Karen M.; Yeh, Gour-Tsyh
1998-08-01
This paper presents the conceptual and mathematical development of the numerical model titled BIOKEMOD, and verification simulations performed using the model. BIOKEMOD is a general computer model for simulation of geochemical and microbiological reactions in batch aqueous solutions. BIOKEMOD may be coupled with hydrologic transport codes for simulation of chemically and biologically reactive transport. The chemical systems simulated may include any mixture of kinetic and equilibrium reactions. The pH, pe, and ionic strength may be specified or simulated. Chemical processes included are aqueous complexation, adsorption, ion-exchange and precipitation/dissolution. Microbiological reactions address growth of biomass and degradation of chemicals by microbial metabolism of substrates, nutrients, and electron acceptors. Inhibition or facilitation of growth due to the presence of specific chemicals and a lag period for microbial acclimation to new substrates may be simulated if significant in the system of interest. Chemical reactions controlled by equilibrium are solved using the law of mass action relating the thermodynamic equilibrium constant to the activities of the products and reactants. Kinetic chemical reactions are solved using reaction rate equations based on collision theory. Microbiologically mediated reactions for substrate removal and biomass growth are assumed to follow Monod kinetics modified for the potentially limiting effects of substrate, nutrient, and electron acceptor availability. BIOKEMOD solves the ordinary differential and algebraic equations of mixed geochemical and biogeochemical reactions using the Newton-Raphson method with full matrix pivoting. Simulations may be either steady state or transient. Input to the program includes the stoichiometry and parameters describing the relevant chemical and microbiological reactions, initial conditions, and sources/sinks for each chemical species. Output includes the chemical and biomass concentrations
A Series Solution of the Cauchy Problem for Turing Reaction-diffusion Model
Directory of Open Access Journals (Sweden)
L. Päivärinta
2011-12-01
Full Text Available In this paper, the series pattern solution of the Cauchy problem for Turing reaction-diffusion model is obtained by using the homotopy analysis method (HAM. Turing reaction-diffusion model is nonlinear reaction-diffusion system which usually has power-law nonlinearities or may be rewritten in the form of power-law nonlinearities. Using the HAM, it is possible to find the exact solution or an approximate solution of the problem. This technique provides a series of functions which converges rapidly to the exact solution of the problem. The efficiency of the approach will be shown by applying the procedure on two problems. Furthermore, the so-called homotopy-Pade technique (HPT is applied to enlarge the convergence region and rate of solution series given by the HAM.
Kocadağlı, Tolgahan; Gökmen, Vural
2016-11-15
The study describes the kinetics of the formation and degradation of α-dicarbonyl compounds in glucose/wheat flour system heated under low moisture conditions. Changes in the concentrations of glucose, fructose, individual free amino acids, lysine and arginine residues, glucosone, 1-deoxyglucosone, 3-deoxyglucosone, 3,4-dideoxyglucosone, 5-hydroxymethyl-2-furfural, glyoxal, methylglyoxal and diacetyl concentrations were determined to form a multiresponse kinetic model for isomerisation and degradation reactions of glucose. Degradation of Amadori product mainly produced 1-deoxyglucosone. Formation of 3-deoxyglucosone proceeded directly from glucose and also Amadori product degradation. Glyoxal formation was predominant from glucosone while methylglyoxal and diacetyl originated from 1-deoxyglucosone. Formation of 5-hydroxymethyl-2-furfural from fructose was found to be a key step. Multi-response kinetic modelling of Maillard reaction and caramelisation simultaneously indicated quantitatively predominant parallel and consecutive pathways and rate limiting steps by estimating the reaction rate constants. Copyright © 2016 Elsevier Ltd. All rights reserved.
Pharmacodynamic modeling of propofol-induced tidal volume depression in children.
Hahn, Jin-Oh; Khosravi, Sara; Dosani, Maryam; Dumont, Guy A; Mark Ansermino, J
2011-08-01
This investigation aimed to develop a pediatric pharmacodynamic model of propofol-induced tidal volume depression towards an ultimate goal of developing a dosing schedule that would preserve spontaneous breathing following a loading dose of propofol. Fifty two ASA 1 and 2 children aged 6-15 year presenting for gastrointestinal endoscopy were enrolled. Subjects were administered a loading dose of 4 mg/kg of propofol intravenously at a constant infusion rate determined by a randomization schedule. Respiratory parameters including tidal volume, respiratory rate, minute volume, and end-tidal CO(2) were recorded at 5 s intervals. Using the predicted plasma concentration, based on the Paedfusor pharmacokinetic model, propofol-induced tidal volume depression was modeled by 3 different approaches (2-stage, pooled, and mixed effects) and results were compared using prediction residual, median percentage errors, median absolute percentage errors, and root-mean-squared normalized errors. The effects of age and body weight as covariates were examined. Respiratory rate and end-tidal CO(2) did not show clear dependence on the predicted plasma concentration. The pharmacodynamic models for tidal volume derived from different modeling approaches were highly consistent. The 2-stage, pooled, and mixed effects approaches yielded k(e0) of 1.06, 1.24, and 0.72 min(-1); γ of 1.10, 0.83, and 0.93; EC50 of 3.18, 3.44, and 3.00 mcg/ml. Including age and body weight as covariates did not significantly improve the predictive performance of the models. A pediatric pharmacodynamic model of propofol-induced tidal volume depression was developed. Models derived from 3 different approaches were shown to be consistent with each other; however, the individual pharmacodynamic parameters exhibited significant inter-individual variability without strong dependence on age and body weight. This would suggest the desirability of adapting the pharmacodynamic model to each subject in real time.
Hash, David B.; Govindan, T. R.; Meyyappan, M.
2004-01-01
In many plasma simulations, ion-molecule reactions are modeled using ion energy independent reaction rate coefficients that are taken from low temperature selected-ion flow tube experiments. Only exothermic or nearly thermoneutral reactions are considered. This is appropriate for plasma applications such as high-density plasma sources in which sheaths are collisionless and ion temperatures 111 the bulk p!asma do not deviate significantly from the gas temperature. However, for applications at high pressure and large sheath voltages, this assumption does not hold as the sheaths are collisional and ions gain significant energy in the sheaths from Joule heating. Ion temperatures and thus reaction rates vary significantly across the discharge, and endothermic reactions become important in the sheaths. One such application is plasma enhanced chemical vapor deposition of carbon nanotubes in which dc discharges are struck at pressures between 1-20 Torr with applied voltages in the range of 500-700 V. The present work investigates The importance of the inclusion of ion energy dependent ion-molecule reaction rates and the role of collision induced dissociation in generating radicals from the feedstock used in carbon nanotube growth.
Parallel plate model for trabecular bone exhibits volume fraction-dependant bias
DEFF Research Database (Denmark)
Day, J; Ding, Ming; Odgaard, A
2000-01-01
, canine distal femur, rat tail, and pig spine and scanned in a micro-CT scanner. Trabecular thickness, trabecular spacing, and trabecular number were calculated using the parallel plate model. Direct thickness, and spacing and connectivity density were calculated using unbiased three-dimensional methods....... Both thickness and spacing calculated using the plate model were well correlated to the direct three-dimensional measures (r(2) = 0. 77-0.92). The correlation between trabecular number and connectivity density varied greatly (r(2) = 0.41-0.94). Whereas trabecular thickness was consistently...... underestimated using the plate model, trabecular spacing was underestimated at low volume fractions and overestimated at high volume fractions. Use of the plate model resulted in a volume-dependent bias in measures of thickness and spacing (p
A volume averaged global model for inductively coupled HBr/Ar plasma discharge
Chung, Sang-Young; Kwon, Deuk-Chul; Choi, Heechol; Song, Mi-Young
2015-09-01
A global model for inductively coupled HBr/Ar plasma was developed. The model was based on a self-consistent global model had been developed by Kwon et al., and a set of chemical reactions in the HBr/Ar plasma was compiled by surveying theoretical, experimental and evaluative researches. In this model vibrational excitations of bi-atomic molecules and electronic excitations of hydrogen atom were taken into account. Neutralizations by collisions between positive and negative ions were considered with Hakman's approximate formula achieved by fitting of theoretical result. For some reactions that were not supplied from literatures the reaction parameters of Cl2 and HCl were adopted as them Br2 and HBr, respectively. For validation calculation results using this model were compared with experimental results from literatures for various plasma discharge parameters and it showed overall good agreement.
Recreation of architectural structures using procedural modeling based on volumes
Directory of Open Access Journals (Sweden)
Santiago Barroso Juan
2013-11-01
Full Text Available While the procedural modeling of buildings and other architectural structures has evolved very significantly in recent years, there is noticeable absence of high-level tools that allow a designer, an artist or an historian, creating important buildings or architectonic structures in a particular city. In this paper we present a tool for creating buildings in a simple and clear, following rules that use the language and methodology of creating their own buildings, and hiding the user the algorithmic details of the creation of the model.
Multiphasic Reaction Modeling for Polypropylene Production in a Pilot-Scale Catalytic Reactor
Directory of Open Access Journals (Sweden)
Mohammad Jakir Hossain Khan
2016-06-01
Full Text Available In this study, a novel multiphasic model for the calculation of the polypropylene production in a complicated hydrodynamic and the physiochemical environments has been formulated, confirmed and validated. This is a first research attempt that describes the development of the dual-phasic phenomena, the impact of the optimal process conditions on the production rate of polypropylene and the fluidized bed dynamic details which could be concurrently obtained after solving the model coupled with the CFD (computational fluid dynamics model, the basic mathematical model and the moment equations. Furthermore, we have established the quantitative relationship between the operational condition and the dynamic gas–solid behavior in actual reaction environments. Our results state that the proposed model could be applied for generalizing the production rate of the polymer from a chemical procedure to pilot-scale chemical reaction engineering. However, it was assumed that the solids present in the bubble phase and the reactant gas present in the emulsion phase improved the multiphasic model, thus taking into account that the polymerization took place mutually in the emulsion besides the bubble phase. It was observed that with respect to the experimental extent of the superficial gas velocity and the Ziegler-Natta feed rate, the ratio of the polymer produced as compared to the overall rate of production was approximately in the range of 9%–11%. This is a significant amount and it should not be ignored. We also carried out the simulation studies for comparing the data of the CFD-dependent dual-phasic model, the emulsion phase model, the dynamic bubble model and the experimental results. It was noted that the improved dual-phasic model and the CFD model were able to predict more constricted and safer windows at similar conditions as compared to the experimental results. Our work is unique, as the integrated developed model is able to offer clearer ideas
Towards a unified model of neutrino-nucleus reactions for neutrino oscillation experiments
Nakamura, S. X.; Kamano, H.; Hayato, Y.; Hirai, M.; Horiuchi, W.; Kumano, S.; Murata, T.; Saito, K.; Sakuda, M.; Sato, T.; Suzuki, Y.
2017-05-01
A precise description of neutrino-nucleus reactions will play a key role in addressing fundamental questions such as the leptonic CP violation and the neutrino mass hierarchy through analyzing data from next-generation neutrino oscillation experiments. The neutrino energy relevant to the neutrino-nucleus reactions spans a broad range and, accordingly, the dominant reaction mechanism varies across the energy region from quasi-elastic scattering through nucleon resonance excitations to deep inelastic scattering. This corresponds to transitions of the effective degree of freedom for theoretical description from nucleons through meson-baryon to quarks. The main purpose of this review is to report our recent efforts towards a unified description of the neutrino-nucleus reactions over the wide energy range; recent overall progress in the field is also sketched. Starting with an overview of the current status of neutrino-nucleus scattering experiments, we formulate the cross section to be commonly used for the reactions over all the energy regions. A description of the neutrino-nucleon reactions follows and, in particular, a dynamical coupled-channels model for meson productions in and beyond the Δ (1232) region is discussed in detail. We then discuss the neutrino-nucleus reactions, putting emphasis on our theoretical approaches. We start the discussion with electroweak processes in few-nucleon systems studied with the correlated Gaussian method. Then we describe quasi-elastic scattering with nuclear spectral functions, and meson productions with a Δ -hole model. Nuclear modifications of the parton distribution functions determined through a global analysis are also discussed. Finally, we discuss issues to be addressed for future developments.
Influence of heat and chemical reactions on the Sisko fluid model for ...
African Journals Online (AJOL)
The present article studies the effects of heat and chemical reactions on the blood flow through tapered artery with a stenosis. The model incorporates Sisko fluid representation for the blood flow through an axially non-symmetrical but radially symmetric stenosis. Symmetry of the distribution of the wall shearing stress and ...
Rothe, Erhard W.; Zygmunt, William E.
2016-01-01
We inserted a self-taught molecular modeling project into an otherwise conventional undergraduate chemical-reaction-engineering course. Our objectives were that students should (a) learn with minimal instructor intervention, (b) gain an appreciation for the relationship between molecular structure and, first, macroscopic state functions in…
The hydration of slag, part 1: reaction models for blended cement
Chen, Wei; Brouwers, Jos
2007-01-01
Reaction models are proposed to quantify the hydration products and to determine the composition of C–S–H from alkali-activated slags (AAS). Products of the slag hydration are first summarized from observations in literature. The main hydration products include C–S–H, hydrotalcite, hydrogarnet, AFm
Toward a Kinetic Model for Acrylamide Formation in a Glucose-Asparagine Reaction System
Knol, J.J.; Loon, W.A.M.; Linssen, J.P.H.; Ruck, A.L.; Boekel, van M.A.J.S.
2005-01-01
A kinetic model for the formation of acrylamide in a glucose-asparagine reaction system is pro-posed. Equimolar solutions (0.2 M) of glucose and asparagine were heated at different tempera-tures (120-200 C) at pH 6.8. Besides the reactants, acrylamide, fructose, and melanoidins were quantified after
Deeper Insight into the Diels-Alder Reaction through the Activation Strain Model
Fernandez, I.; Bickelhaupt, F.M.
2016-01-01
The Diels–Alder (DA) cycloaddition reaction has the ability to significantly increase molecular complexity regioselectively and stereospecifically in a single synthetic step. In this review it is discussed how the activation strain model of chemical reactivity reveals the physical factors that
satl model lesson for teaching effect of temperature on rate of reaction
African Journals Online (AJOL)
IICBA01
SATL MODEL LESSON FOR TEACHING EFFECT OF TEMPERATURE. ON RATE OF REACTION. Shazia Summer, Anam Shafi and Iftikhar Imam Naqvi*. Department of Chemistry, Jinnah University for women, 5C Nazimabad, 74600, Karachi. Pakistan. *Corresponding author email: shaziasamar@hotmail.com. ABSTRACT.
Directory of Open Access Journals (Sweden)
Aaron Smith
2014-12-01
Full Text Available The accurate characterization of three-dimensional (3D root architecture, volume, and biomass is important for a wide variety of applications in forest ecology and to better understand tree and soil stability. Technological advancements have led to increasingly more digitized and automated procedures, which have been used to more accurately and quickly describe the 3D structure of root systems. Terrestrial laser scanners (TLS have successfully been used to describe aboveground structures of individual trees and stand structure, but have only recently been applied to the 3D characterization of whole root systems. In this study, 13 recently harvested Norway spruce root systems were mechanically pulled from the soil, cleaned, and their volumes were measured by displacement. The root systems were suspended, scanned with TLS from three different angles, and the root surfaces from the co-registered point clouds were modeled with the 3D Quantitative Structure Model to determine root architecture and volume. The modeling procedure facilitated the rapid derivation of root volume, diameters, break point diameters, linear root length, cumulative percentages, and root fraction counts. The modeled root systems underestimated root system volume by 4.4%. The modeling procedure is widely applicable and easily adapted to derive other important topological and volumetric root variables.
Estimating Reaction Rate Coefficients Within a Travel-Time Modeling Framework
Energy Technology Data Exchange (ETDEWEB)
Gong, R [Georgia Institute of Technology; Lu, C [Georgia Institute of Technology; Luo, Jian [Georgia Institute of Technology; Wu, Wei-min [Stanford University; Cheng, H. [Stanford University; Criddle, Craig [Stanford University; Kitanidis, Peter K. [Stanford University; Gu, Baohua [ORNL; Watson, David B [ORNL; Jardine, Philip M [ORNL; Brooks, Scott C [ORNL
2011-03-01
A generalized, efficient, and practical approach based on the travel-time modeling framework is developed to estimate in situ reaction rate coefficients for groundwater remediation in heterogeneous aquifers. The required information for this approach can be obtained by conducting tracer tests with injection of a mixture of conservative and reactive tracers and measurements of both breakthrough curves (BTCs). The conservative BTC is used to infer the travel-time distribution from the injection point to the observation point. For advection-dominant reactive transport with well-mixed reactive species and a constant travel-time distribution, the reactive BTC is obtained by integrating the solutions to advective-reactive transport over the entire travel-time distribution, and then is used in optimization to determine the in situ reaction rate coefficients. By directly working on the conservative and reactive BTCs, this approach avoids costly aquifer characterization and improves the estimation for transport in heterogeneous aquifers which may not be sufficiently described by traditional mechanistic transport models with constant transport parameters. Simplified schemes are proposed for reactive transport with zero-, first-, nth-order, and Michaelis-Menten reactions. The proposed approach is validated by a reactive transport case in a two-dimensional synthetic heterogeneous aquifer and a field-scale bioremediation experiment conducted at Oak Ridge, Tennessee. The field application indicates that ethanol degradation for U(VI)-bioremediation is better approximated by zero-order reaction kinetics than first-order reaction kinetics.
Reaction reversibility in α-pinene thermal isomerization: improving the kinetic model
Chibiryaev, A. M.; Ermakova, A.; Kozhevnikov, I. V.
2011-08-01
Revision of the experimental data on α-pinene thermal isomerization attained in supercritical ethanol allowed us to expand the reaction scheme, which includes now six main products and eleven reversible reactions. The equilibrium constants of every reaction ( K T, j and K Φ, j) were calculated to allow for reversibility of reactions. The thermochemical data of the pure compounds required to calculate constants K T, j and K Φ, j (standard enthalpy and entropy of formation Δf H° (298.15 K), Δf S° (298.15 K), heat capacity C p ( T), critical parameters T cr and p cr, boiling point T b, and the acentric factor ω) were preliminary estimated using the empirical Joback and Benson methods. A kinetic model based on the new expanded scheme of reversible reactions was successfully identified and its kinetic parameters k j (600 K) and E j were determined. Detailed examination of the new kinetic model allowed us to refine the generally accepted mechanism of α-pinene thermal isomerization and to distinguish additional features of the multistep process.
Volume Sculpting: Intuitive, Interactive 3D Shape Modelling
DEFF Research Database (Denmark)
Bærentzen, Jakob Andreas
A system for interactive modelling of 3D shapes on a computer is presented. The system is intuitive and has a flat learning curve. It is especially well suited to the creation of organic shapes and shapes of complex topology. The interaction is simple; the user can either add new shape features...
Development and validation of stem volume models for Pinus kesiya ...
African Journals Online (AJOL)
80% of the data set) and validation (20% of the data set). The performance of the different models was evaluated using evaluation statistics: fit index (FI), root mean square error (RMSE), bias (E), absolute mean difference (AMD) and coefficient of ...
Storm Water Management Model Reference Manual Volume II – Hydraulics
SWMM is a dynamic rainfall-runoff simulation model used for single event or long-term (continuous) simulation of runoff quantity and quality from primarily urban areas. The runoff component of SWMM operates on a collection of subcatchment areas that receive precipitation and gene...
Storm Water Management Model Reference Manual Volume I, Hydrology
SWMM is a dynamic rainfall-runoff simulation model used for single event or long-term (continuous) simulation of runoff quantity and quality from primarily urban areas. The runoff component of SWMM operates on a collection of subcatchment areas that receive precipitation and gene...
Modeling Degradation in Solid Oxide Electrolysis Cells - Volume II
Energy Technology Data Exchange (ETDEWEB)
Manohar Motwani
2011-09-01
Idaho National Laboratory has an ongoing project to generate hydrogen from steam using solid oxide electrolysis cells (SOECs). To accomplish this, technical and degradation issues associated with the SOECs will need to be addressed. This report covers various approaches being pursued to model degradation issues in SOECs. An electrochemical model for degradation of SOECs is presented. The model is based on concepts in local thermodynamic equilibrium in systems otherwise in global thermodynamic non-equilibrium. It is shown that electronic conduction through the electrolyte, however small, must be taken into account for determining local oxygen chemical potential,, within the electrolyte. The within the electrolyte may lie out of bounds in relation to values at the electrodes in the electrolyzer mode. Under certain conditions, high pressures can develop in the electrolyte just near the oxygen electrode/electrolyte interface, leading to oxygen electrode delamination. These predictions are in accordance with the reported literature on the subject. Development of high pressures may be avoided by introducing some electronic conduction in the electrolyte. By combining equilibrium thermodynamics, non-equilibrium (diffusion) modeling, and first-principles, atomic scale calculations were performed to understand the degradation mechanisms and provide practical recommendations on how to inhibit and/or completely mitigate them.
Reaction rates of ozone and terpenes adsorbed to model indoor surfaces.
Springs, M; Wells, J R; Morrison, G C
2011-08-01
Reaction rates and reaction probabilities have been quantified on model indoor surfaces for the reaction of ozone with two monoterpenes (Δ(3) -carene and d-limonene). Molar surface loadings were obtained by performing breakthrough experiments in a plug-flow reactor (PFR) packed with beads of glass, polyvinylchloride or zirconium silicate. Reaction rates and probabilities were determined by equilibrating the PFR with both the terpene and the ozone and measuring the ozone consumption rate. To mimic typical indoor conditions, temperatures of 20, 25, and 30°C were used in both types of experiments along with a relative humidity ranging from 10% to 80%. The molar surface loading decreased with increased relative humidity, especially on glass, suggesting that water competed with the terpenes for adsorption sites. The ozone reactivity experiments indicate that higher surface loadings correspond with higher ozone uptake. The reaction probability for Δ(3) -carene with ozone ranged from 2.9 × 10(-6) to 3.0 × 10(-5) while reaction probabilities for d-limonene ranged from 2.8 × 10(-5) to 3.0 × 10(-4) . These surface reaction probabilities are roughly 10-100 times greater than the corresponding gas-phase values. Extrapolation of these results to typical indoor conditions suggests that surface conversion rates may be substantial relative to gas-phase rates, especially for lower volatility terpenoids. At present, it is unclear how important heterogeneous reactions will be in influencing indoor concentrations of terpenes, ozone and their reaction products. We observe that surface reaction probabilities were 10 to 100 times greater than their corresponding gas-phase values. Thus indoor surfaces do enhance effective reaction rates and adsorption of terpenes will increase ozone flux to otherwise low-reactivity surfaces. Extrapolation of these results to typical indoor conditions suggests that surface conversion rates may be substantial relative to gas-phase rates, especially
Modeling finite-volume effects and chiral symmetry breaking in two-flavor QCD thermodynamics
Klein, Bertram
2017-11-01
Finite-volume effects in Quantum Chromodynamics (QCD) have been a subject of much theoretical interest for more than two decades. They are in particular important for the analysis and interpretation of QCD simulations on a finite, discrete space-time lattice. Most of these effects are closely related to the phenomenon of spontaneous breaking of the chiral flavor symmetry and the emergence of pions as light Goldstone bosons. These long-range fluctuations are strongly affected by putting the system into a finite box, and an analysis with different methods can be organized according to the interplay between pion mass and box size. The finite volume also affects critical behavior at the chiral phase transition in QCD. In the present review, I will be mainly concerned with modeling such finite volume effects as they affect the thermodynamics of the chiral phase transition for two quark flavors. I review recent work on the analysis of finite-volume effects which makes use of the quark-meson model for dynamical chiral symmetry breaking. To account for the effects of critical long-range fluctuations close to the phase transition, most of the calculations have been performed using non-perturbative Renormalization Group (RG) methods. I give an overview over the application of these methods to a finite volume. The method, the model and the results are put into the context of related work in random matrix theory for very small volumes, chiral perturbation theory for larger volumes, and related methods and approaches. They are applied towards the analysis of finite-volume effects in lattice QCD simulations and their interpretation, mainly in the context of the chiral phase transition for two quark flavors.
Directory of Open Access Journals (Sweden)
Syed Imran A. Shah
2012-01-01
Full Text Available There are two classes of mixing sensitive reactions: competitive-consecutive and competitive-parallel. The yield of desired product from these coupled reactions depends on how fast the reactants are brought together. Recent experimental results have suggested that the mixing effect may depend strongly on the stoichiometry of the reactions. To investigate this, a 1D, dimensionless, reaction-diffusion model at the micromixing scale was developed. Assuming constant mass concentration and mass diffusivities, systems of PDE's were derived on a mass fraction basis for both types of reactions. Two dimensionless reaction rate ratios and a single general Damköhler number emerged from the analysis. The resulting dimensionless equations were used to investigate the effects of mixing, reaction rate ratio, and reaction stoichiometry. As expected, decreasing either the striation thickness or the dimensionless rate ratio maximizes yield, the reaction stoichiometry has a considerable effect on yield, and all three variables interact strongly.
Traveling Wave Solutions of Reaction-Diffusion Equations Arising in Atherosclerosis Models
Directory of Open Access Journals (Sweden)
Narcisa Apreutesei
2014-05-01
Full Text Available In this short review article, two atherosclerosis models are presented, one as a scalar equation and the other one as a system of two equations. They are given in terms of reaction-diffusion equations in an infinite strip with nonlinear boundary conditions. The existence of traveling wave solutions is studied for these models. The monostable and bistable cases are introduced and analyzed.
Energy Technology Data Exchange (ETDEWEB)
Canudas de Wit, C. [Ecole Nationale Superieure d' Ingenieurs de Genie Chimique, ENSIGC, 31 - Toulouse (France)
2000-07-01
This first volume deals with the problems of control of asynchronous motors in industrial environments: industrial environment, variable speed, asynchronous motors and power supplies, modeling, direct torque control laws, control by controlled limit cycles under frequency constraints. (J.S.)
Energy Technology Data Exchange (ETDEWEB)
Wang, Jing [Iowa State Univ., Ames, IA (United States)
2013-01-11
We analyze the spatiotemporal behavior of species concentrations in a diffusion-mediated conversion reaction which occurs at catalytic sites within linear pores of nanometer diameter. A strict single-file (no passing) constraint occurs in the diffusion within such narrow pores. Both transient and steady-state behavior is precisely characterized by kinetic Monte Carlo simulations of a spatially discrete lattice–gas model for this reaction–diffusion process considering various distributions of catalytic sites. Exact hierarchical master equations can also be developed for this model. Their analysis, after application of mean-field type truncation approximations, produces discrete reaction–diffusion type equations (mf-RDE). For slowly varying concentrations, we further develop coarse-grained continuum hydrodynamic reaction–diffusion equations (h-RDE) incorporating a precise treatment of single-file diffusion (SFD) in this multispecies system. Noting the shortcomings of mf-RDE and h-RDE, we then develop a generalized hydrodynamic (GH) formulation of appropriate gh-RDE which incorporates an unconventional description of chemical diffusion in mixed-component quasi-single-file systems based on a refined picture of tracer diffusion for finite-length pores. The gh-RDE elucidate the non-exponential decay of the steady-state reactant concentration into the pore and the non-mean-field scaling of the reactant penetration depth. Then an extended model of a catalytic conversion reaction within a functionalized nanoporous material is developed to assess the effect of varying the reaction product – pore interior interaction from attractive to repulsive. The analysis is performed utilizing the generalized hydrodynamic formulation of the reaction-diffusion equations which can reliably capture the complex interplay between reaction and restricted transport for both irreversible and reversible reactions.
Geometric Modeling Applications Interface Program (GMAP). Volume 1. Executive Overview
1989-09-01
342f CI FTR560240OOlU September 1989 SECTION 2 SCOPE OF GMAP GMAP focused on the generacion , control, and exchange of computer information to replace...embraced the idea of PDD and product models that had come out of the PDDI program. As part of the GMAP contract, it was necessay to establish the minimum... ideas and concepts that result from this research and be appropriately motivated to develop commercial products. 5.5 INTEGRATE PD WITH SUPPLIER BASE The
Haque, Md Mazharul; Washington, Simon
2014-01-01
The use of mobile phones while driving is more prevalent among young drivers-a less experienced cohort with elevated crash risk. The objective of this study was to examine and better understand the reaction times of young drivers to a traffic event originating in their peripheral vision whilst engaged in a mobile phone conversation. The CARRS-Q advanced driving simulator was used to test a sample of young drivers on various simulated driving tasks, including an event that originated within the driver's peripheral vision, whereby a pedestrian enters a zebra crossing from a sidewalk. Thirty-two licensed drivers drove the simulator in three phone conditions: baseline (no phone conversation), hands-free and handheld. In addition to driving the simulator each participant completed questionnaires related to driver demographics, driving history, usage of mobile phones while driving, and general mobile phone usage history. The participants were 21-26 years old and split evenly by gender. Drivers' reaction times to a pedestrian in the zebra crossing were modelled using a parametric accelerated failure time (AFT) duration model with a Weibull distribution. Also tested where two different model specifications to account for the structured heterogeneity arising from the repeated measures experimental design. The Weibull AFT model with gamma heterogeneity was found to be the best fitting model and identified four significant variables influencing the reaction times, including phone condition, driver's age, license type (provisional license holder or not), and self-reported frequency of usage of handheld phones while driving. The reaction times of drivers were more than 40% longer in the distracted condition compared to baseline (not distracted). Moreover, the impairment of reaction times due to mobile phone conversations was almost double for provisional compared to open license holders. A reduction in the ability to detect traffic events in the periphery whilst distracted
STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies.
Hepburn, Iain; Chen, Weiliang; Wils, Stefan; De Schutter, Erik
2012-05-10
Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. We describe STEPS, a stochastic reaction-diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction-diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. STEPS simulates models of cellular reaction-diffusion systems with complex
Noise-and delay-induced phase transitions of the dimer-monomer surface reaction model
Energy Technology Data Exchange (ETDEWEB)
Zeng Chunhua, E-mail: zchh2009@126.com [Faculty of Science, Kunming University of Science and Technology, Kunming 650093 (China) and Center of Metallurgical Energy Conservation and Emission Reduction, Ministry of Education, Kunming University of Science and Technology, Kunming 650093 (China); Wang Hua, E-mail: wanghuaheat@hotmail.com [Center of Metallurgical Energy Conservation and Emission Reduction, Ministry of Education, Kunming University of Science and Technology, Kunming 650093 (China)
2012-06-19
Highlights: Black-Right-Pointing-Pointer We study the dimer-monomer surface reaction model. Black-Right-Pointing-Pointer We show that noise induces first-order irreversible phase transition (IPT). Black-Right-Pointing-Pointer Combination of noise and time-delayed feedback induce first- and second-order IPT. Black-Right-Pointing-Pointer First- and second-order IPT is viewed as noise-and delay-induced phase transitions. - Abstract: The effects of noise and time-delayed feedback in the dimer-monomer (DM) surface reaction model are investigated. Applying small delay approximation, we construct a stochastic delayed differential equation and its Fokker-Planck equation to describe the state evolution of the DM reaction model. We show that the noise can only induce first-order irreversible phase transition (IPT) characteristic of the DM model, however the combination of the noise and time-delayed feedback can simultaneously induce first- and second-order IPT characteristics of the DM model. Therefore, it is shown that the well-known first- and second-order IPT characteristics of the DM model may be viewed as noise-and delay-induced phase transitions.
Jung, Minseok; Kihara, Hisashi; Abe, Ken-ichi; Takahashi, Yusuke
2018-01-01
A numerical simulation model of plasma flows and electromagnetic waves around a vehicle was developed to predict a radio frequency blackout. Plasma flows in the shock layer and the wake region were calculated using a computational fluid dynamics technique with a three-dimensional model. A finite-catalytic wall condition known to affect plasma properties, such as the number density of electrons, was considered for accurate prediction. A parametric study was performed to investigate the effect of uncertainty in the chemical reaction rate model on evaluating a radio frequency blackout. The behavior of electromagnetic waves in plasma was investigated using a frequency-dependent finite-difference time-domain method. Numerical simulations of reentry blackout were performed for the Atmospheric Reentry Demonstrator mission at various altitudes. The plasma flows and the complex movement of electromagnetic waves around the Atmospheric Reentry Demonstrator vehicle were clarified. The predicted signal loss profile was then directly compared with the experimental flight data to validate the present models. The numerical results generally reproduced the trends over altitudes of the measured data. It is suggested that the present simulation model can be used to investigate the radio frequency blackout and signal loss of electromagnetic waves in the communication of a reentry vehicle. It was confirmed that high associative ionization reaction rates contribute to reducing the electron density in the wake region and radio frequency blackout. It is suggested that the accuracy of predicting the signal loss improved when considering the uncertainty in the chemical reaction model for associative ionizations.
DEFF Research Database (Denmark)
Gaspar, Jozsef; Fosbøl, Philip Loldrup
2017-01-01
industrially relevant reaction regimes must be developed and validated against experimental measurements.In a previous work, we presented the general model (GM) enhancement factor model for (m+n)-th order reversible reactions and validated it against the numerical solution of the two-film model for absorption.......23 and 0.41 mol CO2/2 mol PZ. We show that overall second order kinetics describes well the reaction between CO2 and PZ accounting for the carbamate and bicarbamate reactions. Here we prove the GM model for piperazine and MEA but we expect that this practical approach is applicable for various amines...
Teraguchi, Shunsuke; Kumagai, Yutaro; Vandenbon, Alexis; Akira, Shizuo; Standley, Daron M
2011-12-01
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic process, while reducing each biochemical quantity to a binary value at the level of individual cells. The system can be analytically represented by a finite set of ordinary linear differential equations, which provides a continuous time course prediction of each molecular state. Here we introduce our formalism and demonstrate it with several examples.
Pre-equilibrium (exciton) model and the heavy-ion reactions with cluster emission
Betak, E
2015-01-01
We bring the possibility to include the cluster emission into the statistical pre-equilibrium (exciton) model enlarged for considering also the heavy ion collisions. At this moment, the calculations have been done without treatment of angular momentum variables, but all the approach can be straightforwardly applied to heavy-ion reactions with cluster emission including the angular momentum variables. The direct motivation of this paper is a possibility of producing the superdeformed nuclei, which are easier to be detected in heavy-ion reactions than in those induced by light projectiles (nucleons, deuterons, $\\alpha$-particles).
Gamma emission in precompound reactions: 1, Statistical model and collective gamma decay
Energy Technology Data Exchange (ETDEWEB)
Hoering, A. (Max-Planck-Institut fuer Kernphysik, Heidelberg (Germany) Washington Univ., Seattle, WA (United States). Inst. for Nuclear Theory); Weidenmueller, H.A. (Max-Planck-Institut fuer Kernphysik, Heidelberg (Germany))
1992-01-01
We extend the theory of particle-induced precompound reactions by including gamma decay. We use the Brink-Axel hypothesis and consider the gamma emission of giant dipole resonances built on the ground state and on the excited states of the composite system. The latter are modeled as multiparticle multi-hole excitations. In this way, we combine the statistical ansatz and the chaining hypothesis typical for precompound reaction theories, with the collective aspects of gamma decay. Formulas for average S-matrix and average cross section are derived in this framework.
Gamma emission in precompound reactions: 1, Statistical model and collective gamma decay
Energy Technology Data Exchange (ETDEWEB)
Hoering, A. [Max-Planck-Institut fuer Kernphysik, Heidelberg (Germany)]|[Washington Univ., Seattle, WA (United States). Inst. for Nuclear Theory; Weidenmueller, H.A. [Max-Planck-Institut fuer Kernphysik, Heidelberg (Germany)
1992-09-01
We extend the theory of particle-induced precompound reactions by including gamma decay. We use the Brink-Axel hypothesis and consider the gamma emission of giant dipole resonances built on the ground state and on the excited states of the composite system. The latter are modeled as multiparticle multi-hole excitations. In this way, we combine the statistical ansatz and the chaining hypothesis typical for precompound reaction theories, with the collective aspects of gamma decay. Formulas for average S-matrix and average cross section are derived in this framework.
Modeling radical edge-site reactions of biochar in CO2/water solution under ultrasonic treatment
Zubatiuk, Tetiana; Sajjadi, Baharak; Hill, Glake; Leszczynska, Danuta; Chen, Wei-Yin; Leszczynski, Jerzy
2017-12-01
We report results of theoretical evaluation of the mechanisms of possible radical reactions on the edge-site of biochar with CO2,SUP>·-, OH ˙ , and H ˙ in irradiated aqueous solution. The computational studies were performed for model poly aromatic systems. Obtained mechanisms reflect one of the routes of the oxygen loss accompanied by increase of hydrogen content, as observed in photochemical experiment. The reaction of CO2·- with the edge site of biochar mainly leads to reduced rather than oxidized products. The mechanism of CO2 capturing is mapped by different routes of one-electron reduction and radical addition to the aromatic ring.
Deeper Insight into the Diels-Alder Reaction through the Activation Strain Model.
Fernández, Israel; Bickelhaupt, F Matthias
2016-12-06
In this Focus Review, we present the application of the so-called Activation Strain Model of chemical reactivity to the Diels-Alder cycloaddition reaction. To this end, representative recent examples have been selected to illustrate the power of this new computational approach to gain a deeper quantitative understanding of this fundamental process in chemistry. We cover a wide range of issues, such as, the "endo-rule", reactivity trends emerging from systematic variation in the reactants' strain, and cycloaddition reactions involving relevant species in material science, that is, fullerenes, polycyclic aromatic hydrocarbons and nanotubes. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Combining 3d Volume and Mesh Models for Representing Complicated Heritage Buildings
Tsai, F.; Chang, H.; Lin, Y.-W.
2017-08-01
This study developed a simple but effective strategy to combine 3D volume and mesh models for representing complicated heritage buildings and structures. The idea is to seamlessly integrate 3D parametric or polyhedral models and mesh-based digital surfaces to generate a hybrid 3D model that can take advantages of both modeling methods. The proposed hybrid model generation framework is separated into three phases. Firstly, after acquiring or generating 3D point clouds of the target, these 3D points are partitioned into different groups. Secondly, a parametric or polyhedral model of each group is generated based on plane and surface fitting algorithms to represent the basic structure of that region. A "bare-bones" model of the target can subsequently be constructed by connecting all 3D volume element models. In the third phase, the constructed bare-bones model is used as a mask to remove points enclosed by the bare-bones model from the original point clouds. The remaining points are then connected to form 3D surface mesh patches. The boundary points of each surface patch are identified and these boundary points are projected onto the surfaces of the bare-bones model. Finally, new meshes are created to connect the projected points and original mesh boundaries to integrate the mesh surfaces with the 3D volume model. The proposed method was applied to an open-source point cloud data set and point clouds of a local historical structure. Preliminary results indicated that the reconstructed hybrid models using the proposed method can retain both fundamental 3D volume characteristics and accurate geometric appearance with fine details. The reconstructed hybrid models can also be used to represent targets in different levels of detail according to user and system requirements in different applications.
COMBINING 3D VOLUME AND MESH MODELS FOR REPRESENTING COMPLICATED HERITAGE BUILDINGS
Directory of Open Access Journals (Sweden)
F. Tsai
2017-08-01
Full Text Available This study developed a simple but effective strategy to combine 3D volume and mesh models for representing complicated heritage buildings and structures. The idea is to seamlessly integrate 3D parametric or polyhedral models and mesh-based digital surfaces to generate a hybrid 3D model that can take advantages of both modeling methods. The proposed hybrid model generation framework is separated into three phases. Firstly, after acquiring or generating 3D point clouds of the target, these 3D points are partitioned into different groups. Secondly, a parametric or polyhedral model of each group is generated based on plane and surface fitting algorithms to represent the basic structure of that region. A “bare-bones” model of the target can subsequently be constructed by connecting all 3D volume element models. In the third phase, the constructed bare-bones model is used as a mask to remove points enclosed by the bare-bones model from the original point clouds. The remaining points are then connected to form 3D surface mesh patches. The boundary points of each surface patch are identified and these boundary points are projected onto the surfaces of the bare-bones model. Finally, new meshes are created to connect the projected points and original mesh boundaries to integrate the mesh surfaces with the 3D volume model. The proposed method was applied to an open-source point cloud data set and point clouds of a local historical structure. Preliminary results indicated that the reconstructed hybrid models using the proposed method can retain both fundamental 3D volume characteristics and accurate geometric appearance with fine details. The reconstructed hybrid models can also be used to represent targets in different levels of detail according to user and system requirements in different applications.
Energy Technology Data Exchange (ETDEWEB)
Ma, Qiang [China University of Mining and Technology, Beijing (China); Harpalani, Satya; Liu, Shimin [Southern Illinois University, Carbondale (United States)
2011-01-01
Significant changes occur in the absolute permeability of coalbed methane (CBM) reservoirs during primary depletion or enhanced recovery/CO{sub 2} sequestration operations. In order to project gas production, several analytical models have been developed to predict changes in coal permeability as a function of stress/porosity and sorption. Although these models are more transparent and less complicated than the coupled numerical models, there are differences between the various analytical models and there are several uncertainties. These are discussed briefly in this paper. A new model is then proposed, which is based on the volumetric balance between the bulk coal, and solid grains and pores, using the constant volume theory. It incorporates primarily the changes in grain and cleat volumes and is, therefore, different from the other models that lay heavy emphasis on the pore volume/cleat compressibility values. Finally, in order to demonstrate the simplicity of the proposed model, a history matching exercise is carried out using field data in order to compare the different models. The modeling results suggest that the agreement between the predicted permeability using the existing models and the one proposed here is very good. The merit of the proposed model is its simplicity, and the fact that all input parameters are easily measurable for any coal type with no uncertainties. (author)
Volume-Targeted Ventilation in the Neonate: Benchmarking Ventilators on an Active Lung Model.
Krieger, Tobias J; Wald, Martin
2017-03-01
Mechanically ventilated neonates have been observed to receive substantially different ventilation after switching ventilator models, despite identical ventilator settings. This study aims at establishing the range of output variability among 10 neonatal ventilators under various breathing conditions. Relative benchmarking test of 10 neonatal ventilators on an active neonatal lung model. Neonatal ICU. Ten current neonatal ventilators. Ventilators were set identically to flow-triggered, synchronized, volume-targeted, pressure-controlled, continuous mandatory ventilation and connected to a neonatal lung model. The latter was configured to simulate three patients (500, 1,500, and 3,500 g) in three breathing modes each (passive breathing, constant active breathing, and variable active breathing). Averaged across all weight conditions, the included ventilators delivered between 86% and 110% of the target tidal volume in the passive mode, between 88% and 126% during constant active breathing, and between 86% and 120% under variable active breathing. The largest relative deviation occurred during the 500 g constant active condition, where the highest output machine produced 147% of the tidal volume of the lowest output machine. All machines deviate significantly in volume output and ventilation regulation. These differences depend on ventilation type, respiratory force, and patient behavior, preventing the creation of a simple conversion table between ventilator models. Universal neonatal tidal volume targets for mechanical ventilation cannot be transferred from one ventilator to another without considering necessary adjustments.
An advective volume-balance model for flow in porous media
Malaga, Carlos; Mandujano, Francisco; Becerra, Julian
2016-11-01
Volume-balance models are used by petroleum engineers to simulate multiphase and multicomponent flow phenomena in porous media and the extraction process in oil reservoirs. In these models, mass conservation equations and Darcy's law are supplemented by a balance condition for the pore and fluid volumes. This provides a pressure equation suitable for simulating a compressible flow within a compressible solid matrix. Here we present an alternative interpretation of the volume-balance condition that includes the advective transport within a consolidated porous media. We obtain a modified equation for the time evolution of the pressure field. Preliminary numerical tests of phase separation due to gravity suggest the model reproduces qualitatively the physical phenomena. Fondo Sectorial CONACYT-SENER Grant Number 42536 (DGAJ-SPI-34-170412-217).
Directory of Open Access Journals (Sweden)
Sang-Eun Park
2012-05-01
Full Text Available In this paper, the three-component power decomposition for polarimetric SAR (PolSAR data with an adaptive volume scattering model is proposed. The volume scattering model is assumed to be reflection-symmetric but parameterized. For each image pixel, the decomposition first starts with determining the adaptive parameter based on matrix similarity metric. Then, a respective scattering power component is retrieved with the established procedure. It has been shown that the proposed method leads to complete elimination of negative powers as the result of the adaptive volume scattering model. Experiments with the PolSAR data from both the NASA/JPL (National Aeronautics and Space Administration/Jet Propulsion Laboratory Airborne SAR (AIRSAR and the JAXA (Japan Aerospace Exploration Agency ALOS-PALSAR also demonstrate that the proposed method not only obtains similar/better results in vegetated areas as compared to the existing Freeman-Durden decomposition but helps to improve discrimination of the urban regions.
Prescott, Thomas P; Papachristodoulou, Antonis
2014-09-07
Biochemical reaction networks tend to exhibit behaviour on more than one timescale and they are inevitably modelled by stiff systems of ordinary differential equations. Singular perturbation is a well-established method for approximating stiff systems at a given timescale. Standard applications of singular perturbation partition the state variable into fast and slow modules and assume a quasi-steady state behaviour in the fast module. In biochemical reaction networks, many reactants may take part in both fast and slow reactions; it is not necessarily the case that the reactants themselves are fast or slow. Transformations of the state space are often required in order to create fast and slow modules, which thus no longer model the original species concentrations. This paper introduces a layered decomposition, which is a natural choice when reaction speeds are separated in scale. The new framework ensures that model reduction can be carried out without seeking state space transformations, and that the effect of the fast dynamics on the slow timescale can be described directly in terms of the original species. Copyright © 2014 Elsevier Ltd. All rights reserved.
A Stefan model for mass transfer in a rotating disk reaction vessel
BOHUN, C. S.
2015-05-04
Copyright © Cambridge University Press 2015. In this paper, we focus on the process of mass transfer in the rotating disk apparatus formulated as a Stefan problem with consideration given to both the hydrodynamics of the process and the specific chemical reactions occurring in the bulk. The wide range in the reaction rates of the underlying chemistry allows for a natural decoupling of the problem into a simplified set of weakly coupled convective-reaction-diffusion equations for the slowly reacting chemical species and a set of algebraic relations for the species that react rapidly. An analysis of the chemical equilibrium conditions identifies an expansion parameter and a reduced model that remains valid for arbitrarily large times. Numerical solutions of the model are compared to an asymptotic analysis revealing three distinct time scales and chemical diffusion boundary layer that lies completely inside the hydrodynamic layer. Formulated as a Stefan problem, the model generalizes the work of Levich (Levich and Spalding (1962) Physicochemical hydrodynamics, vol. 689, Prentice-Hall Englewood Cliffs, NJ) and will help better understand the natural limitations of the rotating disk reaction vessel when consideration is made for the reacting chemical species.
Fliege, R; Metzler, M
2000-05-01
The mycotoxin patulin (PAT) is believed to exert its cytotoxic and chromosome-damaging effects by forming covalent adducts with essential cellular thiols. Since the chemical structures of such adducts are unknown to date, we have studied the reaction of PAT and its O-acetylated derivative with the monofunctional thiol model compound 4-bromothiophenol (BTP), which was chosen due to analytical advantages. By means of analytical and preparative high-performance liquid chromatography, 16 adducts of PAT and 3 adducts of acetyl-PAT were isolated and their chemical structures elucidated by (1)H and (13)C NMR, IR, and UV spectroscopy. Time course studies and analysis of daughter product formation from isolated intermediate adducts led to a detailed scheme for the reaction of PAT with BTP. The structures of adducts of PAT formed with other model nucleophiles, e. g., the aliphatic thiol 2-mercaptoethanol and the aromatic amine 4-bromoaniline, were also elucidated and found to corroborate the reaction scheme. In addition, one further reaction pathway was observed with 2-mercaptoethanol, which appears to be independent from those found for BTP. Our study with model nucleophiles provides insights into the electrophilic reactivity of PAT and proved to be useful for the structure elucidation of PAT adducts with biological nucleophiles of toxicological relevance, as will be reported by Fliege and Metzler [(2000) Chem. Res. Toxicol. 13, 373-381].
A mathematical model for the adenylosuccinate synthetase reaction involved in purine biosynthesis
Directory of Open Access Journals (Sweden)
Likhoshvai Vitalii A
2007-02-01
Full Text Available Abstract Background Development of the mathematical models that adequately describe biochemical reactions and molecular-genetic mechanisms is one of the most important tasks in modern bioinformatics. Because the enzyme adenylosuccinate synthetase (AdSS has long been extensively studied, a wealth of kinetic data has been accumulated. Results We describe a mathematical model for the reaction catalyzed by AdSS. The model's parameters were fitted to experimental data obtained from published literature. The advantage of our model is that it includes relationships between the reaction rate, the concentrations of three substrates (GTP, IMP and ASP, the effects of five inhibitors (GMP, GDP, AMP, ASUC and SUCC, and the influence of Mg2+ ions. Conclusion Our model describes the reaction catalyzed by AdSS as a fully random process. The model structure implies that each of the inhibitors included in it is only competitive to one of the substrates. The model was tested for adequacy using experimental data published elsewhere. The values obtained for the parameters are as follows: Vmax = 1.35·10-3 mM/min, KmGTP = 0.023 mM, KmIMP = 0.02 mM, KmASP = 0.3 mM, KiGMP = 0.024 mM, KiGDP = 8·10-3 mM, KiAMP = 0.01 mM, KiASUC = 7.5·10-3 mM, KiSUCC = 8 mM, KmMg = 0.08 mM.
Energy Technology Data Exchange (ETDEWEB)
NONE
1995-02-17
The Natural Gas Transmission and Distribution Model (NGTDM) is the component of the National Energy Modeling System (NEMS) that is used to represent the domestic natural gas transmission and distribution system. NEMS was developed in the Office of integrated Analysis and Forecasting of the Energy information Administration (EIA). NEMS is the third in a series of computer-based, midterm energy modeling systems used since 1974 by the EIA and its predecessor, the Federal Energy Administration, to analyze domestic energy-economy markets and develop projections. The NGTDM is the model within the NEMS that represents the transmission, distribution, and pricing of natural gas. The model also includes representations of the end-use demand for natural gas, the production of domestic natural gas, and the availability of natural gas traded on the international market based on information received from other NEMS models. The NGTDM determines the flow of natural gas in an aggregate, domestic pipeline network, connecting domestic and foreign supply regions with 12 demand regions. The methodology employed allows the analysis of impacts of regional capacity constraints in the interstate natural gas pipeline network and the identification of pipeline capacity expansion requirements. There is an explicit representation of core and noncore markets for natural gas transmission and distribution services, and the key components of pipeline tariffs are represented in a pricing algorithm. Natural gas pricing and flow patterns are derived by obtaining a market equilibrium across the three main elements of the natural gas market: the supply element, the demand element, and the transmission and distribution network that links them. The NGTDM consists of four modules: the Annual Flow Module, the Capacity F-expansion Module, the Pipeline Tariff Module, and the Distributor Tariff Module. A model abstract is provided in Appendix A.
Energy Technology Data Exchange (ETDEWEB)
Ahmadi, A.; Meyer, M.; Rouzineau, D.; Prevost, M. [Universite de Toulouse, INPT, ENSIACET, Laboratoire de Genie Chimique, UMR 5503, 31 - Toulouse (France); Alix, P.; Laloue, N. [IFP Energies nouvelles-Lyon, 69 - Solaize (France)
2010-09-15
This paper gives the first step of the development of a rigorous multicomponent reactive separation model. Such a model is highly essential to further the optimization of acid gases removal plants (CO{sub 2} capture, gas treating, etc.) in terms of size and energy consumption, since chemical solvents are conventionally used. Firstly, two main modelling approaches are presented: the equilibrium-based and the rate-based approaches. Secondly, an extended rate-based model with rigorous modelling methodology for diffusion-reaction phenomena is proposed. The film theory and the generalized Maxwell-Stefan equations are used in order to characterize multicomponent interactions. The complete chain of chemical reactions is taken into account. The reactions can be kinetically controlled or at chemical equilibrium, and they are considered for both liquid film and liquid bulk. Thirdly, the method of numerical resolution is described. Coupling the generalized Maxwell-Stefan equations with chemical equilibrium equations leads to a highly non-linear Differential-Algebraic Equations system known as DAE index 3. The set of equations is discretized with finite-differences as its integration by Gear method is complex. The resulting algebraic system is resolved by the Newton- Raphson method. Finally, the present model and the associated methods of numerical resolution are validated for the example of esterification of methanol. This archetype non-electrolytic system permits an interesting analysis of reaction impact on mass transfer, especially near the phase interface. The numerical resolution of the model by Newton-Raphson method gives good results in terms of calculation time and convergence. The simulations show that the impact of reactions at chemical equilibrium and that of kinetically controlled reactions with high kinetics on mass transfer is relatively similar. Moreover, the Fick's law is less adapted for multicomponent mixtures where some abnormalities such as counter
A reaction-diffusion model of CO2 influx into an oocyte.
Somersalo, Erkki; Occhipinti, Rossana; Boron, Walter F; Calvetti, Daniela
2012-09-21
We have developed and implemented a novel mathematical model for simulating transients in surface pH (pH(S)) and intracellular pH (pH(i)) caused by the influx of carbon dioxide (CO(2)) into a Xenopus oocyte. These transients are important tools for studying gas channels. We assume that the oocyte is a sphere surrounded by a thin layer of unstirred fluid, the extracellular unconvected fluid (EUF), which is in turn surrounded by the well-stirred bulk extracellular fluid (BECF) that represents an infinite reservoir for all solutes. Here, we assume that the oocyte plasma membrane is permeable only to CO(2). In both the EUF and intracellular space, solute concentrations can change because of diffusion and reactions. The reactions are the slow equilibration of the CO(2) hydration-dehydration reactions and competing equilibria among carbonic acid (H(2)CO(3))/bicarbonate (HCO(3)(-)) and a multitude of non-CO(2)/HCO(3)(-) buffers. Mathematically, the model is described by a coupled system of reaction-diffusion equations that-assuming spherical radial symmetry-we solved using the method of lines with appropriate stiff solvers. In agreement with experimental data [Musa-Aziz et al. 2009, PNAS 106 5406-5411], the model predicts that exposing the cell to extracellular 1.5% CO(2)/10 mM HCO(3)(-) (pH 7.50) causes pH(i) to fall and pH(S) to rise rapidly to a peak and then decay. Moreover, the model provides insights into the competition between diffusion and reaction processes when we change the width of the EUF, membrane permeability to CO(2), native extra- and intracellular carbonic anhydrase-like activities, the non-CO(2)/HCO(3)(-) (intrinsic) intracellular buffering power, or mobility of intrinsic intracellular buffers. Copyright © 2012 Elsevier Ltd. All rights reserved.
In-human subject-specific evaluation of a control-theoretic plasma volume regulation model.
Bighamian, Ramin; Kinsky, Michael; Kramer, George; Hahn, Jin-Oh
2017-12-01
The goal of this study was to conduct a subject-specific evaluation of a control-theoretic plasma volume regulation model in humans. We employed a set of clinical data collected from nine human subjects receiving fluid bolus with and without co-administration of an inotrope agent, including fluid infusion rate, plasma volume, and urine output. Once fitted to the data associated with each subject, the model accurately reproduced the fractional plasma volume change responses in all subjects: the error between actual versus model-reproduced fractional plasma volume change responses was only 1.4 ± 1.6% and 1.2 ± 0.3% of the average fractional plasma volume change responses in the absence and presence of inotrope co-administration. In addition, the model parameters determined by the subject-specific fitting assumed physiologically plausible values: (i) initial plasma volume was estimated to be 36 ± 11 mL/kg and 37 ± 10 mL/kg in the absence and presence of inotrope infusion, respectively, which was comparable to its actual counterpart of 37 ± 4 mL/kg and 43 ± 6 mL/kg; (ii) volume distribution ratio, specifying the ratio with which the inputted fluid is distributed in the intra- and extra-vascular spaces, was estimated to be 3.5 ± 2.4 and 1.9 ± 0.5 in the absence and presence of inotrope infusion, respectively, which accorded with the experimental observation that inotrope could enhance plasma volume expansion in response to fluid infusion. We concluded that the model was equipped with the ability to reproduce plasma volume response to fluid infusion in humans with physiologically plausible model parameters, and its validity may persist even under co-administration of inotropic agents. Copyright © 2017 Elsevier Ltd. All rights reserved.
Classical and recent free-volume models for polymer solutions: A comparative evaluation
DEFF Research Database (Denmark)
Radfarnia, H.R.; Kontogeorgis, Georgios; Ghotbi, C.
2007-01-01
for aqueous and alcohol solutions, based on the physical values of the van der Waals volume and surface areas for both FV-combinatorial and residual contributions. The prediction results of both "recent" and "classical" FV models using the new regressed energy parameters are significantly better, compared......In this work, two "classical" (UNIFAC-FV, Entropic-FV) and two "recent" free-volume (FV) models (Kannan-FV, Freed-FV) are comparatively evaluated for polymer-solvent vapor-liquid equilibria including both aqueous and non-aqueous solutions. Moreover, some further developments are presented here...... by the modified Freed-FV model for athermal and non-athermal polymer systems are compared to other "recent" and "classical" FV models, indicating an improvement for the modified Freed-FV model for aqueous polymer solutions. Second, for the original Freed-FV model, new UNIFAC group energy parameters are regressed...
Formulation of consumables management models. Volume 1: Mission planning
Torian, J. G.; Zamora, M. A.
1978-01-01
Development of an STS (Space Transportation System) interactive computer program MPP (Mission Planning Processor) working model was conducted. A summary of the computer program development and those supporting tasks conducted is presented. Development of the MPP Computer Program is discussed. This development was supported by several parallel tasks. These tasks either directly supported the program development, or provided information for future application and/or modification to the program in relation to the flight planning and flight operations of the STS and advanced spacecraft. The supporting tasks also included development of a Space Station MPP to demonstrate the applicability of the analytical methods developed under this RTOP to more advanced spacecraft than the STS.
Nonlinear electromechanical modelling and dynamical behavior analysis of a satellite reaction wheel
Aghalari, Alireza; Shahravi, Morteza
2017-12-01
The present research addresses the satellite reaction wheel (RW) nonlinear electromechanical coupling dynamics including dynamic eccentricity of brushless dc (BLDC) motor and gyroscopic effects, as well as dry friction of shaft-bearing joints (relative small slip) and bearing friction. In contrast to other studies, the rotational velocity of the flywheel is considered to be controllable, so it is possible to study the reaction wheel dynamical behavior in acceleration stages. The RW is modeled as a three-phases BLDC motor as well as flywheel with unbalances on a rigid shaft and flexible bearings. Improved Lagrangian dynamics for electromechanical systems is used to obtain the mathematical model of the system. The developed model can properly describe electromechanical nonlinear coupled dynamical behavior of the satellite RW. Numerical simulations show the effectiveness of the presented approach.
Extended Parker-Sochacki method for Michaelis-Menten enzymatic reaction model.
Abdelrazik, Ismail M; Elkaranshawy, Hesham A
2016-03-01
In this article, a new approach--namely, the extended Parker-Sochacki method (EPSM)--is presented for solving the Michaelis-Menten nonlinear enzymatic reaction model. The Parker-Sochacki method (PSM) is combined with a new resummation method called the Sumudu-Padé resummation method to obtain approximate analytical solutions for the model. The obtained solutions by the proposed approach are compared with the solutions of PSM and the Runge-Kutta numerical method (RKM). The comparison proves the practicality, efficiency, and correctness of the presented approach. It serves as a basis for solving other nonlinear biochemical reaction models in the future. Copyright © 2015 Elsevier Inc. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Wampler, William R.; Myers, Samuel Maxwell,
2014-02-01
A model is presented for recombination of charge carriers at displacement damage in gallium arsenide, which includes clustering of the defects in atomic displacement cascades produced by neutron or ion irradiation. The carrier recombination model is based on an atomistic description of capture and emission of carriers by the defects with time evolution resulting from the migration and reaction of the defects. The physics and equations on which the model is based are presented, along with details of the numerical methods used for their solution. The model uses a continuum description of diffusion, field-drift and reaction of carriers and defects within a representative spherically symmetric cluster. The initial radial defect profiles within the cluster were chosen through pair-correlation-function analysis of the spatial distribution of defects obtained from the binary-collision code MARLOWE, using recoil energies for fission neutrons. Charging of the defects can produce high electric fields within the cluster which may influence transport and reaction of carriers and defects, and which may enhance carrier recombination through band-to-trap tunneling. Properties of the defects are discussed and values for their parameters are given, many of which were obtained from density functional theory. The model provides a basis for predicting the transient response of III-V heterojunction bipolar transistors to pulsed neutron irradiation.
Research on the model reactions of ClONO 2 with HCl on water clusters
Xu, Si Chuan; Guo, Rui; Wang, Sheng Long
1999-11-01
The reaction of ClONO 2 with HCl on ice or on PSC surfaces occurs readily. However, the rate of ClONO 2 reacting with HCl in pure gas phase is small. In order to understand the reaction conditions of ClONO 2 with HCl, several model reactions of ClONO 2 with the (H 2O) n·HCl clusters for n=0,1,2,3,4 have been theoretically studied at the MP2//HF/6-31G(d) level and for n=0,1 at the MP2/6-31G(d) level. One of the reactions for n=3 has been further calculated at the MP2//HF/6-31G(d,p), MP2//HF/6-311G(d,p), and MP2//HF/6-311+G(d,p) levels. Numerical results show that the reaction of ClONO 2 with HCl on a three- or four-water cluster proceeds faster with a low-energy barrier. The implication for ozone holes in the Antartic and Artic stratosphere is discussed.
Özkan, N.; Güray, R. T.; Yalçın, C.; Tan, W. P.; Aprahamian, A.; Beard, M.; deBoer, R. J.; Almaraz-Calderon, S.; Falahat, S.; Görres, J.; Li, Q.; Sauerwein, A.; Sonnabend, K.; Wiescher, M.; Fülöp, Zs.; Gyürky, Gy.; Somorjai, E.; Greene, J.
2017-10-01
It is crucial to measure reaction cross sections relevant to the astrophysical γ process so that theoretical reaction rates can be tested and validated with experimental data. The total cross sections for the 162Er(p ,γ )163Tm and the 162Er(p ,n )162Tm reactions have been measured by the activation method in center-of-mass energies from 3.973 to 8.944 MeV and from 5.962 to 8.944 MeV, respectively. The nucleus 162Er is the heaviest p nuclide to be measured by the activation method using γ -ray spectroscopy, so far. It is important to note that the energy range for the (p ,γ ) reaction measurement covers a large fraction of the astrophysically relevant energy region between 2.71 and 5.34 MeV. The targets were prepared by evaporating 28.2 % isotopically enriched Er1622O3 powder onto carbon backing foils, and bombarded with proton beams provided by the FN Tandem Accelerator at the University of Notre Dame. The reaction yields have been determined by the observed activity of produced radioactive isotopes, which was detected offline by a high-purity germanium detector. The results are presented and compared with calculations from two statistical model codes: non-smoker and talys.
Computing homogeneous models with finite volume upwind schemes
Energy Technology Data Exchange (ETDEWEB)
Herard, J.M. [Electricite de France (EDF/DRD/DMFTT), 78 - Chatou (France); Universite de Provence, Centre de Mathematiques et d' Informatique, L.A.T.P. - UMR CNRS 6632, 13 - Marseille (France); Kokh, S. [CEA Saclay, Dir. de l' Energie Nucleaire (DEN/SFME), 91 - Gif sur Yvette (France)
2003-07-01
We provide in this paper some algorithms to deal with homogeneous equilibrium models on any type of mesh. These schemes rely on the exact Godunov scheme or on some rough Godunov schemes. We first recall some basic ideas which were recently introduced in the 1D framework. We then turn to the 2D framework, and define a class of first order schemes which enable to improve the accuracy on coarse unstructured 2D meshes. We have also tried to underline that current computing power does not enable to perform accurate enough computations for reasonable CPU time, in a few situations including sharp contact discontinuities; this is due in some sense to some kind of loss of pressure consistency between PDE and numerical schemes in conservative form. We have also indicated that some specific remedies available in the literature are not adequate for nuclear safety problems, both in a one dimensional framework (owing to EOS), and in the two dimensional framework (due to differences between mesh interfaces and waves fronts). Comments pertaining to other hybrid schemes are then made. The last part of the paper will focus on computations of three dimensional gas-liquid flows including sharp interfaces. (authors)
Joint modelling of flood peaks and volumes: A copula application for the Danube River
Directory of Open Access Journals (Sweden)
Papaioannou George
2016-12-01
Full Text Available Flood frequency analysis is usually performed as a univariate analysis of flood peaks using a suitable theoretical probability distribution of the annual maximum flood peaks or peak over threshold values. However, other flood attributes, such as flood volume and duration, are necessary for the design of hydrotechnical projects, too. In this study, the suitability of various copula families for a bivariate analysis of peak discharges and flood volumes has been tested. Streamflow data from selected gauging stations along the whole Danube River have been used. Kendall’s rank correlation coefficient (tau quantifies the dependence between flood peak discharge and flood volume settings. The methodology is applied to two different data samples: 1 annual maximum flood (AMF peaks combined with annual maximum flow volumes of fixed durations at 5, 10, 15, 20, 25, 30 and 60 days, respectively (which can be regarded as a regime analysis of the dependence between the extremes of both variables in a given year, and 2 annual maximum flood (AMF peaks with corresponding flood volumes (which is a typical choice for engineering studies. The bivariate modelling of the extracted peak discharge - flood volume couples is achieved with the use of the Ali-Mikhail-Haq (AMH, Clayton, Frank, Joe, Gumbel, Hüsler-Reiss, Galambos, Tawn, Normal, Plackett and FGM copula families. Scatterplots of the observed and simulated peak discharge - flood volume pairs and goodness-of-fit tests have been used to assess the overall applicability of the copulas as well as observing any changes in suitable models along the Danube River. The results indicate that for the second data sampling method, almost all of the considered Archimedean class copula families perform better than the other copula families selected for this study, and that for the first method, only the upper-tail-flat copulas excel (except for the AMH copula due to its inability to model stronger relationships.
Directory of Open Access Journals (Sweden)
Sayed Ameenuddin Irfan
2017-03-01
Full Text Available A mathematical model for the reaction-diffusion equation is developed to describe the nutrient release profiles and degradation of poly(lactic acid (PLA-coated controlled-release fertilizer. A multi-diffusion model that consists of coupled partial differential equations is used to study the diffusion and chemical reaction (autocatalytic degradation simultaneously. The model is solved using an analytical-numerical method. Firstly, the model equation is transformed using the Laplace transformation as the Laplace transform cannot be inverted analytically. Numerical inversion of the Laplace transform is used by employing the Zakian method. The solution is useful in predicting the nutrient release profiles at various diffusivity, concentration of extraction medium, and reaction rates. It also helps in explaining the transformation of autocatalytic concentration in the coating material for various reaction rates, times of reaction, and reaction-multi diffusion. The solution is also applicable to the other biodegradable polymer-coated controlled-release fertilizers.
A Semi-Empirical Two Step Carbon Corrosion Reaction Model in PEM Fuel Cells
Energy Technology Data Exchange (ETDEWEB)
Young, Alan; Colbow, Vesna; Harvey, David; Rogers, Erin; Wessel, Silvia
2013-01-01
The cathode CL of a polymer electrolyte membrane fuel cell (PEMFC) was exposed to high potentials, 1.0 to 1.4 V versus a reversible hydrogen electrode (RHE), that are typically encountered during start up/shut down operation. While both platinum dissolution and carbon corrosion occurred, the carbon corrosion effects were isolated and modeled. The presented model separates the carbon corrosion process into two reaction steps; (1) oxidation of the carbon surface to carbon-oxygen groups, and (2) further corrosion of the oxidized surface to carbon dioxide/monoxide. To oxidize and corrode the cathode catalyst carbon support, the CL was subjected to an accelerated stress test cycled the potential from 0.6 VRHE to an upper potential limit (UPL) ranging from 0.9 to 1.4 VRHE at varying dwell times. The reaction rate constants and specific capacitances of carbon and platinum were fitted by evaluating the double layer capacitance (Cdl) trends. Carbon surface oxidation increased the Cdl due to increased specific capacitance for carbon surfaces with carbon-oxygen groups, while the second corrosion reaction decreased the Cdl due to loss of the overall carbon surface area. The first oxidation step differed between carbon types, while both reaction rate constants were found to have a dependency on UPL, temperature, and gas relative humidity.
Integrated Approach to Mathematical Modelling of Atrazine Degradation in Different Reaction Systems
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Marijan Bošnjak
2010-01-01
Full Text Available Based on the known approaches and published mathematical models, as well as on theoretical consideration using our experimental data, the integrated approach to mathematical modelling of atrazine biodegradation processes has been employed and sophisticated mathematical models for different reaction systems have been developed. The applicability of these models which take into account physical, chemical, biochemical and biological complexity of atrazine biodegradation was further analyzed in comparison with mathematical models describing simple consecutive reaction systems using first-order kinetics. Kinetics of atrazine degradation in liquid media and soil contaminated with atrazine at the temperatures of 10 and 30 °C was assessed and compared. Biodegradation experiments in liquid media were conducted at atrazine concentrations ranging from 0.14 to 25 mmol/L, while the experiments in soil were conducted at atrazine concentration of approx. 0.44 μmol/g. Computer simulations were applied to explain experimental results and test the adequacy of mathematical models. Detailed analysis of computer simulation data showed that the developed integrated mathematical models could be considered as the most convenient for describing kinetics of atrazine biotransformation in both liquid media and contaminated soil, although even simple mathematical models are suitable for explaining some experimental results, especially when evaluating the temperature effects on biodegradation efficacy of the applied mixed bacterial culture.
DEFF Research Database (Denmark)
Zubov, Alexandr; Sin, Gürkan
2018-01-01
process based on hybrid Monte Carlo approach, and (iii) mesoscopic public domain model of polymer chain reptation dynamics. Based on the input reaction conditions, the macro-scale model predicts L,L-lactide conversion and averaged molar mass of PLLA, while the micro-scale and meso-scale simulations allow......Abstract Poly(L-lactic acid) (PLLA) is a fully biodegradable bioplastic with promising market potential. The paper deals with systematic development and analysis of the modeling framework allowing direct mapping between PLLA production process conditions and rheological properties of the polymer...
Glass Property Data and Models for Estimating High-Level Waste Glass Volume
Energy Technology Data Exchange (ETDEWEB)
Vienna, John D.; Fluegel, Alexander; Kim, Dong-Sang; Hrma, Pavel R.
2009-10-05
This report describes recent efforts to develop glass property models that can be used to help estimate the volume of high-level waste (HLW) glass that will result from vitrification of Hanford tank waste. The compositions of acceptable and processable HLW glasses need to be optimized to minimize the waste-form volume and, hence, to save cost. A database of properties and associated compositions for simulated waste glasses was collected for developing property-composition models. This database, although not comprehensive, represents a large fraction of data on waste-glass compositions and properties that were available at the time of this report. Glass property-composition models were fit to subsets of the database for several key glass properties. These models apply to a significantly broader composition space than those previously publised. These models should be considered for interim use in calculating properties of Hanford waste glasses.
ATHENA code manual. Volume 1. Code structure, system models, and solution methods
Energy Technology Data Exchange (ETDEWEB)
Carlson, K.E.; Roth, P.A.; Ransom, V.H.
1986-09-01
The ATHENA (Advanced Thermal Hydraulic Energy Network Analyzer) code has been developed to perform transient simulation of the thermal hydraulic systems which may be found in fusion reactors, space reactors, and other advanced systems. A generic modeling approach is utilized which permits as much of a particular system to be modeled as necessary. Control system and secondary system components are included to permit modeling of a complete facility. Several working fluids are available to be used in one or more interacting loops. Different loops may have different fluids with thermal connections between loops. The modeling theory and associated numerical schemes are documented in Volume I in order to acquaint the user with the modeling base and thus aid effective use of the code. The second volume contains detailed instructions for input data preparation.
Sutiani, Ani; Silitonga, Mei Y.
2017-08-01
This research focused on the effect of learning models and emotional intelligence in students' chemistry learning outcomes on reaction rate teaching topic. In order to achieve the objectives of the research, with 2x2 factorial research design was used. There were two factors tested, namely: the learning models (factor A), and emotional intelligence (factor B) factors. Then, two learning models were used; problem-based learning/PBL (A1), and project-based learning/PjBL (A2). While, the emotional intelligence was divided into higher and lower types. The number of population was six classes containing 243 grade X students of SMAN 10 Medan, Indonesia. There were 15 students of each class were chosen as the sample of the research by applying purposive sampling technique. The data were analyzed by applying two-ways analysis of variance (2X2) at the level of significant α = 0.05. Based on hypothesis testing, there was the interaction between learning models and emotional intelligence in students' chemistry learning outcomes. Then, the finding of the research showed that students' learning outcomes in reaction rate taught by using PBL with higher emotional intelligence is higher than those who were taught by using PjBL. There was no significant effect between students with lower emotional intelligence taught by using both PBL and PjBL in reaction rate topic. Based on the finding, the students with lower emotional intelligence were quite hard to get in touch with other students in group discussion.
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Kansuporn eSriyudthsak
2016-05-01
Full Text Available The high-throughput acquisition of metabolome data is greatly anticipated for the complete understanding of cellular metabolism in living organisms. A variety of analytical technologies have been developed to acquire large-scale metabolic profiles under different biological or environmental conditions. Time series data are useful for predicting the most likely metabolic pathways because they provide important information regarding the accumulation of metabolites, which implies causal relationships in the metabolic reaction network. Considerable effort has been undertaken to utilize these data for constructing a mathematical model merging system properties and quantitatively characterizing a whole metabolic system in toto. However, there are technical difficulties between benchmarking the provision and utilization of data. Although hundreds of metabolites can be measured, which provide information on the metabolic reaction system, simultaneous measurement of thousands of metabolites is still challenging. In addition, it is nontrivial to logically predict the dynamic behaviors of unmeasurable metabolite concentrations without sufficient information on the metabolic reaction network. Yet, consolidating the advantages of advancements in both metabolomics and mathematical modeling remain to be accomplished. This review outlines the conceptual basis of and recent advances in technologies in both the research fields. It also highlights the potential for constructing a large-scale mathematical model by estimating model parameters from time series metabolome data in order to comprehensively understand metabolism at the systems level.
Sriyudthsak, Kansuporn; Shiraishi, Fumihide; Hirai, Masami Yokota
2016-01-01
The high-throughput acquisition of metabolome data is greatly anticipated for the complete understanding of cellular metabolism in living organisms. A variety of analytical technologies have been developed to acquire large-scale metabolic profiles under different biological or environmental conditions. Time series data are useful for predicting the most likely metabolic pathways because they provide important information regarding the accumulation of metabolites, which implies causal relationships in the metabolic reaction network. Considerable effort has been undertaken to utilize these data for constructing a mathematical model merging system properties and quantitatively characterizing a whole metabolic system in toto. However, there are technical difficulties between benchmarking the provision and utilization of data. Although, hundreds of metabolites can be measured, which provide information on the metabolic reaction system, simultaneous measurement of thousands of metabolites is still challenging. In addition, it is nontrivial to logically predict the dynamic behaviors of unmeasurable metabolite concentrations without sufficient information on the metabolic reaction network. Yet, consolidating the advantages of advancements in both metabolomics and mathematical modeling remain to be accomplished. This review outlines the conceptual basis of and recent advances in technologies in both the research fields. It also highlights the potential for constructing a large-scale mathematical model by estimating model parameters from time series metabolome data in order to comprehensively understand metabolism at the systems level.
MELSAR: a mesoscale air quality model for complex terrain. Volume 2. Appendices
Energy Technology Data Exchange (ETDEWEB)
Allwine, K.J.; Whiteman, C.D.
1985-04-01
This final report is submitted as part of the Green River Ambient Model Assessment (GRAMA) project conducted at the US Department of Energy's Pacific Northwest Laboratory for the US Environmental Protection Agency. The GRAMA Program has, as its ultimate goal, the development of validated air quality models that can be applied to the complex terrain of the Green River Formation of western Colorado, eastern Utah and southern Wyoming. The Green River Formation is a geologic formation containing large reserves of oil shale, coal, and other natural resources. Development of these resources may lead to a degradation of the air quality of the region. Air quality models are needed immediately for planning and regulatory purposes to assess the magnitude of these regional impacts. This report documents one of the models being developed for this purpose within GRAMA - specifically a model to predict short averaging time (less than or equal to 24 h) pollutant concentrations resulting from the mesoscale transport of pollutant releases from multiple sources. MELSAR has not undergone any rigorous operational testing, sensitivity analyses, or validation studies. Testing and evaluation of the model are needed to gain a measure of confidence in the model's performance. This report consists of two volumes. This volume contains the Appendices, which include listings of the FORTRAN code and Volume 1 contains the model overview, technical description, and user's guide. 13 figs., 10 tabs.
A KLM-circuit model of a multi-layer transducer for acoustic bladder volume measurements.
Merks, E J W; Borsboom, J M G; Bom, N; van der Steen, A F W; de Jong, N
2006-12-22
In a preceding study a new technique to non-invasively measure the bladder volume on the basis of non-linear wave propagation was validated. It was shown that the harmonic level generated at the posterior bladder wall increases for larger bladder volumes. A dedicated transducer is needed to further verify and implement this approach. This transducer must be capable of both transmission of high-pressure waves at fundamental frequency and reception of up to the third harmonic. For this purpose, a multi-layer transducer was constructed using a single element PZT transducer for transmission and a PVDF top-layer for reception. To determine feasibility of the multi-layer concept for bladder volume measurements, and to ensure optimal performance, an equivalent mathematical model on the basis of KLM-circuit modeling was generated. This model was obtained in two subsequent steps. Firstly, the PZT transducer was modeled without PVDF-layer attached by means of matching the model with the measured electrical input impedance. It was validated using pulse-echo measurements. Secondly, the model was extended with the PVDF-layer. The total model was validated by considering the PVDF-layer as a hydrophone on the PZT transducer surface and comparing the measured and simulated PVDF responses on a wave transmitted by the PZT transducer. The obtained results indicated that a valid model for the multi-layer transducer was constructed. The model showed feasibility of the multi-layer concept for bladder volume measurements. It also allowed for further optimization with respect to electrical matching and transmit waveform. Additionally, the model demonstrated the effect of mechanical loading of the PVDF-layer on the PZT transducer.
A 3-D Finite-Volume Non-hydrostatic Icosahedral Model (NIM)
Lee, Jin
2013-11-01
The Nonhydrostatic Icosahedral Model (NIM) formulates the latest numerical innovation of the three-dimensional finite-volume control volume on the quasi-uniform icosahedral grid suitable for ultra-high resolution simulations. NIM's modeling goal is to improve numerical accuracy for weather and climate simulations as well as to utilize the state-of-art computing architecture such as massive parallel CPUs and GPUs to deliver routine high-resolution forecasts in timely manner. NIM uses innovations in model formulation similar to its hydrostatic version of the Flow-following Icosahedral Model (FIM) developed by Earth System Research Laboratory (ESRL) which has been tested and accepted for future use by the National Weather Service as part of their operational global prediction ensemble. Innovations from the FIM used in the NIM include: * A local coordinate system remapped spherical surface to plane for numerical accuracy (Lee and MacDonald, 2009), * Grid points in a table-driven horizontal loop that allow any horizontal point sequence (A.E. MacDonald et al., 2010), * Flux-Corrected Transport formulated on finite-volume operators to maintain conservative positive definite transport (J.-L, Lee, et al., 2010), * All differentials evaluated as finite-volume integrals around the cells, *Icosahedral grid optimization (Wang and Lee, 2011) NIM extends the two-dimensional finite-volume operators used in FIM into the three-dimensional finite-volume solvers designed to improve pressure gradient calculation and orographic precipitation over complex terrain. The NIM dynamical core has been successfully verified with various non-hydrostatic benchmark test cases such as warm bubble, density current, internal gravity wave, and mountain waves. Physical parameterizations have been incorporated into the NIM dynamic core and successfully tested with multimonth aqua-planet simulations. Recent results from NIM simulations will be presented at the Symposium.
Directory of Open Access Journals (Sweden)
Qinghua Xie
2017-01-01
Full Text Available Recently, a general polarimetric model-based decomposition framework was proposed by Chen et al., which addresses several well-known limitations in previous decomposition methods and implements a simultaneous full-parameter inversion by using complete polarimetric information. However, it only employs four typical models to characterize the volume scattering component, which limits the parameter inversion performance. To overcome this issue, this paper presents two general polarimetric model-based decomposition methods by incorporating the generalized volume scattering model (GVSM or simplified adaptive volume scattering model, (SAVSM proposed by Antropov et al. and Huang et al., respectively, into the general decomposition framework proposed by Chen et al. By doing so, the final volume coherency matrix structure is selected from a wide range of volume scattering models within a continuous interval according to the data itself without adding unknowns. Moreover, the new approaches rely on one nonlinear optimization stage instead of four as in the previous method proposed by Chen et al. In addition, the parameter inversion procedure adopts the modified algorithm proposed by Xie et al. which leads to higher accuracy and more physically reliable output parameters. A number of Monte Carlo simulations of polarimetric synthetic aperture radar (PolSAR data are carried out and show that the proposed method with GVSM yields an overall improvement in the final accuracy of estimated parameters and outperforms both the version using SAVSM and the original approach. In addition, C-band Radarsat-2 and L-band AIRSAR fully polarimetric images over the San Francisco region are also used for testing purposes. A detailed comparison and analysis of decomposition results over different land-cover types are conducted. According to this study, the use of general decomposition models leads to a more accurate quantitative retrieval of target parameters. However, there
Krantz, William B
2007-01-01
This book is unique as the first effort to expound on the subject of systematic scaling analysis. Not written for a specific discipline, the book targets any reader interested in transport phenomena and reaction processes. The book is logically divided into chapters on the use of systematic scaling analysis in fluid dynamics, heat transfer, mass transfer, and reaction processes. An integrating chapter is included that considers more complex problems involving combined transport phenomena. Each chapter includes several problems that are explained in considerable detail. These are followed by several worked examples for which the general outline for the scaling is given. Each chapter also includes many practice problems. This book is based on recognizing the value of systematic scaling analysis as a pedagogical method for teaching transport and reaction processes and as a research tool for developing and solving models and in designing experiments. Thus, the book can serve as both a textbook and a reference boo...
Energy Technology Data Exchange (ETDEWEB)
Patisson, F
2005-09-15
Gas-solid reactions control a great number of major industrial processes involving matter transformation. This dissertation aims at showing that mathematical modelling is a useful tool for both understanding phenomena and optimising processes. First, the physical processes associated with a gas-solid reaction are presented in detail for a single particle, together with the corresponding available kinetic grain models. A second part is devoted to the modelling of multiparticle reactors. Different approaches, notably for coupling grain models and reactor models, are illustrated through various case studies: coal pyrolysis in a rotary kiln, production of uranium tetrafluoride in a moving bed furnace, on-grate incineration of municipal solid wastes, thermogravimetric apparatus, nuclear fuel making, steel-making electric arc furnace. (author)
Directory of Open Access Journals (Sweden)
Dong Sup Lee
2011-04-01
Full Text Available Although real-time monitoring of bladder volume together with intravesical pressure can provide more information for understanding the functional changes of the urinary bladder, it still entails difficulties in the accurate prediction of real-time bladder volume in urodynamic studies with small animal models. We studied a new implantable bladder volume monitoring device with eight rats. During cystometry, microelectrodes prepared by the microelectromechanical systems process were placed symmetrically on both lateral walls of the bladder, and the expanded bladder volume was calculated. Immunohistological study was done after 1 week and after 4 weeks to evaluate the biocompatibility of the microelectrode. From the point that infused saline volume into the bladder was higher than 0.6 mL, estimated bladder volume was statistically correlated with the volume of saline injected (p<0.01. Additionally, the microelectromechanical system microelectrodes used in this study showed reliable biocompatibility. Therefore, the device can be used to evaluate changes in bladder volume in studies with small animals, and it may help to provide more information about functional changes in the bladder in laboratory studies. Furthermore, owing to its biocompatibility, the device could be chronically implanted in conscious ambulating animals, thus allowing a novel longitudinal study to be performed for a specific purpose.
Veldsink, J.W.; Veldsink, J.W.; van Damme, Rudolf M.J.; Versteeg, Geert; van Swaaij, Willibrordus Petrus Maria
1995-01-01
In the present study, mass transport accompanied by chemical reactions in porous media is studied according to the Fick model and the dusty-gas model. For mass transport accompanied by a chemical reaction in catalyst structures showing a plane, line, or point of symmetry, the approximate analytical
Directory of Open Access Journals (Sweden)
Wim Hordijk
2011-05-01
Full Text Available The formation of a self-sustaining autocatalytic chemical network is a necessary but not sufficient condition for the origin of life. The question of whether such a network could form “by chance” within a sufficiently complex suite of molecules and reactions is one that we have investigated for a simple chemical reaction model based on polymer ligation and cleavage. In this paper, we extend this work in several further directions. In particular, we investigate in more detail the levels of catalysis required for a self-sustaining autocatalytic network to form. We study the size of chemical networks within which we might expect to find such an autocatalytic subset, and we extend the theoretical and computational analyses to models in which catalysis requires template matching.
Energy Technology Data Exchange (ETDEWEB)
Al-Abyad, M., E-mail: alabyad_m@yahoo.com [Experimental Nuclear Physics Department (Cyclotron Facility), Nuclear Research Center, AEA, Postal Code 13759, Cairo (Egypt); Abdel-Hamid, A.S. [Experimental Nuclear Physics Department (Cyclotron Facility), Nuclear Research Center, AEA, Postal Code 13759, Cairo (Egypt); Tarkanyi, F.; Ditroi, F.; Takacs, S. [Institute of Nuclear Research, Hungarian Academy of Sciences, H-4026 Debrecen (Hungary); Seddik, U. [Experimental Nuclear Physics Department (Cyclotron Facility), Nuclear Research Center, AEA, Postal Code 13759, Cairo (Egypt); Bashter, I.I. [Physics Department, Faculty of Science, Zagazig University, Zagazig (Egypt)
2012-01-15
Proton induced nuclear reactions were measured with stacked-foil technique on natural zirconium targets up to 16.7 MeV. Excitation functions were measured for the production of {sup 90,92m,95m,95g,96}Nb and {sup 88}Y. Cumulative cross-section, thick target yields and activation functions were deduced and compared with the available experimental data, as well as with the nuclear models codes; ALICE-IPPE, EMPIRE and TALYS. The integral yields for thick targets were deduced from the measured excitation function of the produced radionuclides. - Highlights: Black-Right-Pointing-Pointer We measured the excitation functions for proton induced reactions on Zr for the production of {sup 90.92m,95m,95g,96}Nb and {sup 88}Y. Black-Right-Pointing-Pointer Results compared with the experimental data, as well as with nuclear models codes. Black-Right-Pointing-Pointer Integral yields for thick targets were deduced .
Research on surveying technology applied for DTM modelling and volume computation in open pit mines
Directory of Open Access Journals (Sweden)
Jaroslaw Wajs
2016-01-01
Full Text Available The spatial information systems of mining company can be used for monitoring of mining activity, excavation planning, calculations of the ore volume and decision making. Nowadays, data base has to be updated by sources such as surveying positioning technologies and remote sensed photogrammetry data. The presented paper contains review of the methodology for the digital terrain model, i.e. DTM, modelling and obtaining data from surveying technologies in an open pit mine or quarry. This paper reviews the application of GPS, total station measurements, and ground photogrammetry for the volume accuracy assessment of a selected object. The testing field was situated in Belchatow lignite open pit mine. A suitable object had been selected. The testing layer of coal seam was located at 8’th pit sidewall excavation area. The data were acquired two times within one month period and it was connected with monthly DTM actualization of excavation. This paper presents the technological process and the results of the research of using digital photogrammetry for opencast mining purposes in the scope of numerical volume computation and monitoring the mines by comparison of different sources. The results shows that the presented workflow allow to build DTM manually and remote sensed and the accuracy assessment was presented by the volume computation pathway. Major advantages of the techniques are presented illustrating how a terrestrial photogrammetry techniques provide rapid spatial measurements of breaklines 3D data utilized to volume calculation.
Sensitivity Analysis of Wavelet Neural Network Model for Short-Term Traffic Volume Prediction
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Jinxing Shen
2013-01-01
Full Text Available In order to achieve a more accurate and robust traffic volume prediction model, the sensitivity of wavelet neural network model (WNNM is analyzed in this study. Based on real loop detector data which is provided by traffic police detachment of Maanshan, WNNM is discussed with different numbers of input neurons, different number of hidden neurons, and traffic volume for different time intervals. The test results show that the performance of WNNM depends heavily on network parameters and time interval of traffic volume. In addition, the WNNM with 4 input neurons and 6 hidden neurons is the optimal predictor with more accuracy, stability, and adaptability. At the same time, a much better prediction record will be achieved with the time interval of traffic volume are 15 minutes. In addition, the optimized WNNM is compared with the widely used back-propagation neural network (BPNN. The comparison results indicated that WNNM produce much lower values of MAE, MAPE, and VAPE than BPNN, which proves that WNNM performs better on short-term traffic volume prediction.
Impact of particle density and initial volume on mathematical compression models
DEFF Research Database (Denmark)
Sonnergaard, Jørn
2000-01-01
In the calculation of the coefficients of compression models for powders either the initial volume or the particle density is introduced as a normalising factor. The influence of these normalising factors is, however, widely different on coefficients derived from the Kawakita, Walker and Heckel e...
Modelling dynamic liquid-gas systems: Extensions to the volume-of-fluid solver
CSIR Research Space (South Africa)
Heyns, Johan A
2013-06-01
Full Text Available This study presents the extension of the volume-of-fluid solver, interFoam, for improved accuracy and efficiency when modelling dynamic liquid-gas systems. Examples of these include the transportation of liquids, such as in the case of fuel carried...
On the minimum volume simplex enclosure problem for estimating a linear mixing model
Hendrix, E.M.T.; Gracía, I.; Plaza, J.; Plaza, A.
2013-01-01
We describe the minimum volume simplex enclosure problem (MVSEP), which is known to be a global optimization problem, and further investigate its multimodality. The problem is a basis for several (unmixing) methods that estimate so-called endmembers and fractional values in a linear mixing model. We
Conditions for the critical phenomena in a dynamic model of an electrocatalytic reaction
Firstova, Natalia; Shchepakina, Elena
2017-02-01
In the paper, a detailed study of the critical phenomena mechanism in a model of an electrocatalytic reaction is carried out. The use of the geometric theory of integral manifolds allows us to show the relationship between the critical regime and the stability loss delay of the slow integral manifold of the corresponding differential system. The asymptotic formula for the critical value of the control parameter is obtained.
DL-ADR: a novel deep learning model for classifying genomic variants into adverse drug reactions.
Liang, Zhaohui; Huang, Jimmy Xiangji; Zeng, Xing; Zhang, Gang
2016-08-10
Genomic variations are associated with the metabolism and the occurrence of adverse reactions of many therapeutic agents. The polymorphisms on over 2000 locations of cytochrome P450 enzymes (CYP) due to many factors such as ethnicity, mutations, and inheritance attribute to the diversity of response and side effects of various drugs. The associations of the single nucleotide polymorphisms (SNPs), the internal pharmacokinetic patterns and the vulnerability of specific adverse reactions become one of the research interests of pharmacogenomics. The conventional genomewide association studies (GWAS) mainly focuses on the relation of single or multiple SNPs to a specific risk factors which are a one-to-many relation. However, there are no robust methods to establish a many-to-many network which can combine the direct and indirect associations between multiple SNPs and a serial of events (e.g. adverse reactions, metabolic patterns, prognostic factors etc.). In this paper, we present a novel deep learning model based on generative stochastic networks and hidden Markov chain to classify the observed samples with SNPs on five loci of two genes (CYP2D6 and CYP1A2) respectively to the vulnerable population of 14 types of adverse reactions. A supervised deep learning model is proposed in this study. The revised generative stochastic networks (GSN) model with transited by the hidden Markov chain is used. The data of the training set are collected from clinical observation. The training set is composed of 83 observations of blood samples with the genotypes respectively on CYP2D6*2, *10, *14 and CYP1A2*1C, *1 F. The samples are genotyped by the polymerase chain reaction (PCR) method. A hidden Markov chain is used as the transition operator to simulate the probabilistic distribution. The model can perform learning at lower cost compared to the conventional maximal likelihood method because the transition distribution is conditional on the previous state of the hidden Markov
Holme, Petter; Huss, Mikael; Lee, Sang Hoon
2011-05-06
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species). For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection.
Establishing the 3-D finite element solid model of femurs in partial by volume rendering.
Zhang, Yinwang; Zhong, Wuxue; Zhu, Haibo; Chen, Yun; Xu, Lingjun; Zhu, Jianmin
2013-01-01
It remains rare to report three-dimensional (3-D) finite element solid model of femurs in partial by volume rendering method, though several methods of femoral 3-D finite element modeling are already available. We aim to analyze the advantages of the modeling method by establishing the 3-D finite element solid model of femurs in partial by volume rendering. A 3-D finite element model of the normal human femurs, made up of three anatomic structures: cortical bone, cancellous bone and pulp cavity, was constructed followed by pretreatment of the CT original image. Moreover, the finite-element analysis was carried on different material properties, three types of materials given for cortical bone, six assigned for cancellous bone, and single for pulp cavity. The established 3-D finite element of femurs contains three anatomical structures: cortical bone, cancellous bone, and pulp cavity. The compressive stress primarily concentrated in the medial surfaces of femur, especially in the calcar femorale. Compared with whole modeling by volume rendering method, the 3-D finite element solid model created in partial is more real and fit for finite element analysis. Copyright © 2013 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.
Comparison of Moving Boundary and Finite-Volume Heat Exchanger Models in the Modelica Language
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Adriano Desideri
2016-05-01
Full Text Available When modeling low capacity energy systems, such as a small size (5–150 kWel organic Rankine cycle unit, the governing dynamics are mainly concentrated in the heat exchangers. As a consequence, the accuracy and simulation speed of the higher level system model mainly depend on the heat exchanger model formulation. In particular, the modeling of thermo-flow systems characterized by evaporation or condensation requires heat exchanger models capable of handling phase transitions. To this aim, the finite volume (FV and the moving boundary (MB approaches are the most widely used. The two models are developed and included in the open-source ThermoCycle Modelica library. In this contribution, a comparison between the two approaches is presented. An integrity and accuracy test is designed to evaluate the performance of the FV and MB models during transient conditions. In order to analyze how the two modeling approaches perform when integrated at a system level, two organic Rankine cycle (ORC system models are built using the FV and the MB evaporator model, and their responses are compared against experimental data collected on an 11 kWel ORC power unit. Additionally, the effect of the void fraction value in the MB evaporator model and of the number of control volumes (CVs in the FV one is investigated. The results allow drawing general guidelines for the development of heat exchanger dynamic models involving two-phase flows.
Reaction-diffusion model of TGA gasification experiments for estimating diffusional effects
Energy Technology Data Exchange (ETDEWEB)
A. Gomez-Barea; P. Ollero; R. Arjona [Escuela Superior de Ingenieros (University of Seville), Seville (Spain). Department of Chemical and Environmental Engineering
2005-09-01
A 2D non-isothermal and non-equimolar reaction-diffusion model is developed in order to assess the diffusional effects that may take place during the CO{sub 2} gasification of a biomass char contained in the cylindrical crucible of a horizontal-arm thermogravimetric apparatus (TGA). The model takes into account the chemical reaction rate and the effective transport properties as a function of the local conversion and therefore as a function of time and position within the char bed. Intraparticle diffusion and structural changes of the char bed during the gasification are also included. The model results showed good agreement with the experimental ones obtained at different temperatures and CO{sub 2} partial pressures, and points out the relevant role of diffusional effects in TGA experiments. The effectiveness factor defined as the ratio of the measured to the intrinsic reaction rates at the same gas conditions strongly depends on temperature and CO{sub 2} partial pressure and may be as low as 0.2 at 950{sup o}C and 50% char conversion. The marked variation found for the effectiveness factor at different conversions suggests the necessity of a complementary analysis of the variation of the diffusional effects with conversion when TGA experiments for kinetic determination are carried out. 36 refs., 7 figs., 1 tab.
Jalali Farahani, R.; Li, S.; Mohammed, F.; Astill, S.; Williams, C. R.; Lee, R.; Wilson, P. S.; Srinvias, B.
2014-12-01
Six transoceanic historical tsunami events including Japan Tohoku tsunami (2011), Chile Maule tsunami (2010), Indian Ocean tsunami (2004), Japan Nankai tsunami (1946), Chile Valdivia tsunami (1960), and Alaska tsunami (1964) have been modeled using a 2D well-balanced shallow water numerical model. The model solves the nonlinear 2D shallow water equations using an upwind finite volume method and is shown in this study to be capable of modeling the tsunami waves and resulting inundations over complex topography and bathymetry. The finite volume method is capable of modeling the wetting and drying of the bed surface at the coastline with no numerical instabilities and the inundation is modeled by allowing the computational cells to dynamically change from dry to wet. The numerical model implements parallel computations on Graphics Processing Units (GPUs), which enables the model to implement detailed modeling of inundation of small-scale coastal regions in a short simulation time. The slip distribution and seismic moment of the six earthquake driven tsunami events are introduced to the model as the initial condition including coastal uplift and subsidence. Both local regions and far-field regions affected by these tsunami waves are numerically studied and the resulting run-up and tsunami inundations are compared with the recorded observation data provided by National Oceanic and Atmospheric Administration (NOAA) including coastal tide gauges and eyewitness observation data. The GPU-based finite volume model indicates accuracy and robustness as well as short simulation time that can be used for transoceanic tsunami waves modeling including real-time numerical modeling of tsunami events and their inland inundations.
RELAP5/MOD3 code manual: Code structure, system models, and solution methods. Volume 1
Energy Technology Data Exchange (ETDEWEB)
NONE
1995-08-01
The RELAP5 code has been developed for best estimate transient simulation of light water reactor coolant systems during postulated accidents. The code models the coupled behavior of the reactor coolant system and the core for loss-of-coolant accidents, and operational transients, such as anticipated transient without scram, loss of offsite power, loss of feedwater, and loss of flow. A generic modeling, approach is used that permits simulating a variety of thermal hydraulic systems. Control system and secondary system components are included to permit modeling of plant controls, turbines, condensers, and secondary feedwater systems. RELAP5/MOD3 code documentation is divided into seven volumes: Volume I provides modeling theory and associated numerical schemes.
van Hout, G P J; de Jong, R; Vrijenhoek, J E P; Timmers, L; Duckers, H J; Hoefer, I E
2013-11-01
The aim of this study was to validate admittance-based pressure-volume (PV) loop measurements for the assessment of cardiac function in a porcine model of chronic myocardial infarction. The traditional PV loop measurement technique requires hypertonic saline injections for parallel conductance correction prior to signal conversion into volume. Furthermore, it assumes a linear relationship between conductance and volume. More recently, an admittance-based technique has been developed, which continuously measures parallel conductance and uses a non-linear equation for volume calculation. This technique has not yet been evaluated in a large-animal model of myocardial ischaemia. Eleven pigs underwent invasive PV measurements with the admittance system (AS) and the traditional conductance system followed by three-dimensional echocardiography (3DE). After baseline measurements, pigs were subjected to 90 min left anterior descending coronary artery occlusion, followed by the same measurements at 8 weeks follow-up. In the healthy heart, the AS showed good agreement with 3DE for left ventricular volumes and a reasonable correlation for ejection fraction (r = 0.756, P = 0.007). At follow-up, an increase in end-systolic volume was observed with 3DE (+15.4 ± 14.4 ml, P = 0.005) and the AS (+34.6 ± 36.1 ml, P = 0.010). The ejection fraction measured with 3DE (-13.2 ± 5.2%, P infarction and provides comparable results to 3DE, rendering it a useful tool for functional testing in large-animal cardiac models.
ezBioNet: A modeling and simulation system for analyzing biological reaction networks
Yu, Seok Jong; Tung, Thai Quang; Park, Junho; Lim, Jongtae; Yoo, Jaesoo
2012-10-01
To achieve robustness against living environments, a living organism is composed of complicated regulatory mechanisms ranging from gene regulations to signal transduction. If such life phenomena are to be understand, an integrated analysis tool that should have modeling and simulation functions for biological reactions, as well as new experimental methods for measuring biological phenomena, is fundamentally required. We have designed and implemented modeling and simulation software (ezBioNet) for analyzing biological reaction networks. The software can simultaneously perform an integrated modeling of various responses occurring in cells, ranging from gene expressions to signaling processes. To support massive analysis of biological networks, we have constructed a server-side simulation system (VCellSim) that can perform ordinary differential equations (ODE) analysis, sensitivity analysis, and parameter estimates. ezBioNet integrates the BioModel database by connecting the european bioinformatics institute (EBI) servers through Web services APIs and supports the handling of systems biology markup language (SBML) files. In addition, we employed eclipse RCP (rich client platform) which is a powerful modularity framework allowing various functional expansions. ezBioNet is intended to be an easy-to-use modeling tool, as well as a simulation system, to understand the control mechanism by monitoring the change of each component in a biological network. A researcher may perform the kinetic modeling and execute the simulation. The simulation result can be managed and visualized on ezBioNet, which is freely available at http://ezbionet.cbnu.ac.kr.
Hybrid approaches for multiple-species stochastic reaction-diffusion models
Spill, Fabian; Alarcon, Tomas; Maini, Philip K; Byrne, Helen
2015-01-01
Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains ...
Huang, Jinbao; He, Chao; Li, Xinsheng; Pan, Guiying; Tong, Hong
2018-01-01
Density functional theory methods (DFT) M062X have been used to investigate the thermal degradation processes of model compound of bisphenol A polycarbonate (MPC) and to identify the optimal reaction paths in the thermal decomposition of bisphenol A polycarbonate (PC). The bond dissociation energies of main bonds in MPC were calculated, and it is found that the weakest bond in MPC is the single bond between the methylic carbon and carbon atom and the second weakest bond in MPC is the single bond between oxygen atom and the carbonyl carbon. On the basis of computational results of kinetic parameters, a mechanism is proposed where the hydrolysis (or alcoholysis) reaction is the main degradation pathways for the formation of the evolved products, and the homolytic cleavage and rearrangement reactions are the competitive reaction pathways in the thermal degradation of PC. The proposed mechanism is consistent with experimental observations of CO2, bisphenol A and 1,1-bis(4-hydroxyphenyl)-ethane as the main degradation products, together with a small amount of CO, alkyl phenol and diphenyl carbonate. Copyright © 2017 Elsevier Ltd. All rights reserved.
Valocchi, A. J.; Werth, C. J.; Yoon, H.; Tang, Y.
2012-12-01
Several studies have demonstrated the important role played by mixing-controlled reactions in porous media. For example, transverse mixing of nutrients along the fringes of a contaminant plume is often the limiting step that controls overall degradation rate during natural or engineered in situ bioremediation. Similar mixing processes can promote precipitation/dissolution reactions during geological sequestration of carbon dioxide. Field and laboratory investigations have demonstrated that the length scale of transverse mixing zones can be very small, often on the order of centimeters or less. To study dispersion, mixing and reaction at this scale, we use pore-scale numerical simulation models and micro-fluidics laboratory experiments. An overview of our methods and findings, including comparisons between direct numerical simulations and laboratory experiments will be presented. The presentation will emphasize recent results including: (a) coupling of precipitation/dissolution with porosity reduction under different geochemical conditions, and (b) impact of pore structure on biodegradation and biofilm growth patterns. Our work has improved understanding of coupled flow, transport and reaction processes; however, there remain significant challenges in extending the results to larger field scales.
Grief reaction model of families who experienced acute bereavement in Japan.
Tatsuno, Junko; Yamase, Hiroaki; Yamase, Yoshie
2012-06-01
The present study clarified the structure of factors that affect grief reactions of families who experienced acute bereavement in critical care settings in Japan. Sixty-four families who experienced acute bereavement answered a questionnaire. The questionnaire included the Miyabayashi Grief Measurement, recognition of bereavement, Multidimensional Scale of Perceived Social Support, and the Tri-Axial Coping Scale. We analyzed the causal structure regarding the relationship of stress recognition, coping, and grief reactions using structural equation modeling. The greatest influence on grief reactions of bereaved families was stress recognition. Factors that influenced stress recognition were subjective degree of sadness, acceptance of bereavement, regret for bereavement, and recognition of a peaceful death. These results show that the quality of end-of-life care in critical care settings is an important factor that affects bereaved families' stress recognition and grief reactions. Nurses and medical staff must provide end-of-life care to help family members accept the death of their loved one and reduce regrets as much as possible. © 2012 Blackwell Publishing Asia Pty Ltd.
Catalytic Reactions on Model Gold Surfaces: Effect of Surface Steps and of Surface Doping
Directory of Open Access Journals (Sweden)
Maria Natália D. S. Cordeiro
2011-11-01
Full Text Available The adsorption energies and the activation energy barriers for a series of reactions catalyzed by gold surfaces and obtained theoretically through density functional theory (DFT based calculations were considered to clarify the role of the low coordinated gold atoms and the role of doping in the catalytic activity of gold. The effect of the surface steps was introduced by comparison of the activation energy barriers and of the adsorption energies on flat gold surfaces such as the Au(111 surface with those on stepped surfaces such as the Au(321 or the Au(110 surfaces. It is concluded that the presence of low coordinated atoms on the latter surfaces increases the adsorption energies of the reactants and decreases the activation energy barriers. Furthermore, the increasing of the adsorption energy of the reaction products can lead to lower overall reaction rates in the presence of low gold coordinated atoms due to desorption limitations. On the other hand, the effect of doping gold surfaces with other transition metal atoms was analyzed using the dissociation reaction of molecular oxygen as a test case. The calculations showed that increasing the silver content in some gold surfaces was related to a considerable increment of the reactivity of bimetallic systems toward the oxygen dissociation. Importantly, that increment in the reactivity was enhanced by the presence of low coordinated atoms in the catalytic surface models considered.
Kinetic Modeling of the Reaction Rate for Quartz and Carbon Pellet
Li, Fei; Tangstad, Merete
2018-01-01
Kinetic modeling of quartz and carbon pellet at temperatures of 1898 K, 1923 K, and 1948 K (1625 °C, 1650 °C, and 1675 °C) was investigated in this study. The carbon materials used were charcoal, coke, coal, and preheated coal. The overall SiC producing reaction can be described by the reaction SiO2 + 3C = SiC + 2CO. In the SiC-producing step, the reaction rate of quartz and carbon pellet can be expressed as {d{ pct}}/dt = ( {1 - 0.40 × X_{fix - C}^{ - 0.86} × FC × {pct}} ) × A × \\exp ( { - E/{{RT}}} ) The carbon factor F C was used to describe the influence of different carbon materials that effect the gas-solid interface reaction. For charcoal, coke, coal, and preheated coal, the F C values were 0.83, 0.80, 0.94, and 0.83, respectively. The pre-exponential factor A values for the preceding four carbon materials were 1.06 × 1016 min-1, 4.21 × 1015 min-1, 3.85 × 109 min-1, and 1.00 × 1025 min-1, respectively. The activation energies E for the SiC-producing step were 570, 563, 336, and 913 kJ/mole for charcoal, coke, coal, and preheated coal pellets, respectively.
An enhanced finite volume method to model 2D linear elastic structures
CSIR Research Space (South Africa)
Suliman, Ridhwaan
2014-04-01
Full Text Available . Suliman) Preprint submitted to Applied Mathematical Modelling July 22, 2013 Keywords: finite volume, finite element, locking, error analysis 1. Introduction Since the 1960s, the finite element method has mainly been used for modelling the mechanics... formulation provides higher accuracy 2 for displacement solutions. It is well known that the linear finite element formulation suffers from sensitivity to element aspect ratio or shear locking when subjected to bend- ing [16]. Fallah [8] and Wheel [6] present...
Parameter Identification for a New Circuit Model Aimed to Predict Body Water Volume
Directory of Open Access Journals (Sweden)
GHEORGHE, A.-G.
2012-11-01
Full Text Available Intracellular and extracellular water volumes in the human body have been computed using a sequence of models starting with a linear first order RC circuit (Cole model and finishing with the De Lorenzo model. This last model employs a fractional order impedance whose parameters are identified using the frequency characteristics of the impedance module and phase, the latter being not unique. While the Cole model has a two octaves frequency validity range, the De Lorenzo model can be used for three decades. A new linear RC model, valid for a three decades frequency range, is proposed. This circuit can be viewed as an extension of the Cole model for a larger frequency interval, unlike similar models proposed by the same authors.
Computational Methods for Protein Structure Prediction and Modeling Volume 1: Basic Characterization
Xu, Ying; Liang, Jie
2007-01-01
Volume one of this two volume sequence focuses on the basic characterization of known protein structures as well as structure prediction from protein sequence information. The 11 chapters provide an overview of the field, covering key topics in modeling, force fields, classification, computational methods, and struture prediction. Each chapter is a self contained review designed to cover (1) definition of the problem and an historical perspective, (2) mathematical or computational formulation of the problem, (3) computational methods and algorithms, (4) performance results, (5) existing software packages, and (6) strengths, pitfalls, challenges, and future research directions.
The Three-Dimensional Finite-Volume Non-Hydrostatic Icosahedral Model (NIM)
Lee, J. L.; MacDonald, A. E.
2014-12-01
A multi-scales Non-hydrostatic Icosahedral Model (NIM) has been developed at Earth System Research Laboratory (ESRL) to meet NOAA's future prediction mission ranging from mesoscale short-range, high-impact weather forecasts to longer-term intra-seasonal climate prediction. NIM formulates the latest numerical innovation of the three-dimensional finite-volume control volume on the quasi-uniform icosahedral grid suitable for ultra-high resolution simulations. NIM is designed to utilize the state-of-art computing architecture such as Graphic Processing Units (GPU) processors to run globally at kilometer scale resolution to explicitly resolve convective storms and complex terrains. The novel features of NIM numerical design include: 1.1. A local coordinate system upon which finite-volume integrations are undertaken. The use of a local Cartesian coordinate greatly simplifies the mathematic formulation of the finite-volume operators and leads to the finite-volume integration along straight lines on the plane, rather than along curved lines on the spherical surface. 1.2. A general indirect addressing scheme developed for modeling on irregular grid. It arranges the icosahedral grid with a one-dimensional vector loop structure, table specified memory order, and an indirect addressing scheme that yields very compact code despite the complexities of this grid. 1.3. Use of three-dimensional finite-volume integration over control volumes constructed on the height coordinates. Three-dimensional finite-volume integration accurately represents the Newton Third Law over terrain and improves pressure gradient force over complex terrain. 1.4. Use of the Runge-Kutta 4th order conservative and positive-definite transport scheme 1.5. NIM dynamical solver has been implemented on CPU as well as GPU. As one of the potential candidates for NWS next generation models, NIM dynamical core has been successfully verified with various benchmark test cases including those proposed by DCMIP
DEFF Research Database (Denmark)
Hashemi, Hamid; Christensen, Jakob Munkholt; Glarborg, Peter
of the mixture was varied from oxidizing to reducing conditions. Moreover, a series of experiments in an oxygen atmosphere instead of a nitrogen atmosphere has been done. A reaction mechanism based on a recent work by Burke et al. has been developed. In addition to modeling of the present experiments......, ignition occurs at the temperature of 775–800 K. In general, the present model provides a good agreement with the measurements in the flow reactor and with recent data on laminar burning velocity and ignition delay time....
Atomic-Scale Modeling of Particle Size Effects for the Oxygen Reduction Reaction of Pt
DEFF Research Database (Denmark)
Tritsaris, Georgios; Greeley, Jeffrey Philip; Rossmeisl, Jan
2011-01-01
We estimate the activity of the oxygen reduction reaction on platinum nanoparticles of sizes of practical importance. The proposed model explicitly accounts for surface irregularities and their effect on the activity of neighboring sites. The model reproduces the experimentally observed trends...... in both the specific and mass activities for particle sizes in the range between 2 and 30 nm. The mass activity is calculated to be maximized for particles of a diameter between 2 and 4 nm. Our study demonstrates how an atomic-scale description of the surface microstructure is a key component...
Modeling languages for biochemical network simulation: reaction vs equation based approaches.
Wiechert, Wolfgang; Noack, Stephan; Elsheikh, Atya
2010-01-01
Biochemical network modeling and simulation is an essential task in any systems biology project. The systems biology markup language (SBML) was established as a standardized model exchange language for mechanistic models. A specific strength of SBML is that numerous tools for formulating, processing, simulation and analysis of models are freely available. Interestingly, in the field of multidisciplinary simulation, the problem of model exchange between different simulation tools occurred much earlier. Several general modeling languages like Modelica have been developed in the 1990s. Modelica enables an equation based modular specification of arbitrary hierarchical differential algebraic equation models. Moreover, libraries for special application domains can be rapidly developed. This contribution compares the reaction based approach of SBML with the equation based approach of Modelica and explains the specific strengths of both tools. Several biological examples illustrating essential SBML and Modelica concepts are given. The chosen criteria for tool comparison are flexibility for constraint specification, different modeling flavors, hierarchical, modular and multidisciplinary modeling. Additionally, support for spatially distributed systems, event handling and network analysis features is discussed. As a major result it is shown that the choice of the modeling tool has a strong impact on the expressivity of the specified models but also strongly depends on the requirements of the application context.
Electric field distribution in a finite-volume head model of deep brain stimulation.
Grant, Peadar F; Lowery, Madeleine M
2009-11-01
This study presents a whole-head finite element model of deep brain stimulation to examine the effect of electrical grounding, the finite conducting volume of the head, and scalp, skull and cerebrospinal fluid layers. The impedance between the stimulating and reference electrodes in the whole-head model was found to lie within clinically reported values when the reference electrode was incorporated on a localized surface in the model. Incorporation of the finite volume of the head and inclusion of surrounding outer tissue layers reduced the magnitude of the electric field and activating function by approximately 20% in the region surrounding the electrode. Localized distortions of the electric field were also observed when the electrode was placed close to the skull. Under bipolar conditions the effect of the finite conducting volume was shown to be negligible. The results indicate that, for monopolar stimulation, incorporation of the finite volume and outer tissue layers can alter the magnitude of the electric field and activating function when the electrode is deep within the brain, and may further affect the shape if the electrode is close to the skull.
Alfazazi, Adamu
2016-08-10
The ignition characteristics of isooctane and n-heptane in an ignition quality tester (IQT) were simulated using a two-stage Lagrangian (TSL) model, which is a zero-dimensional (0-D) reactor network method. The TSL model was also used to simulate the ignition delay of n-dodecane and n-heptane in a constant volume combustion chamber (CVCC), which is archived in the engine combustion network (ECN) library (http://www.ca.sandia.gov/ecn). A detailed chemical kinetic model for gasoline surrogates from the Lawrence Livermore National Laboratory (LLNL) was utilized for the simulation of n-heptane and isooctane. Additional simulations were performed using an optimized gasoline surrogate mechanism from RWTH Aachen University. Validations of the simulated data were also performed with experimental results from an IQT at KAUST. For simulation of n-dodecane in the CVCC, two n-dodecane kinetic models from the literature were utilized. The primary aim of this study is to test the ability of TSL to replicate ignition timings in the IQT and the CVCC. The agreement between the model and the experiment is acceptable except for isooctane in the IQT and n-heptane and n-dodecane in the CVCC. The ability of the simulations to replicate observable trends in ignition delay times with regard to changes in ambient temperature and pressure allows the model to provide insights into the reactions contributing towards ignition. Thus, the TSL model was further employed to investigate the physical and chemical processes responsible for controlling the overall ignition under various conditions. The effects of exothermicity, ambient pressure, and ambient oxygen concentration on first stage ignition were also studied. Increasing ambient pressure and oxygen concentration was found to shorten the overall ignition delay time, but does not affect the timing of the first stage ignition. Additionally, the temperature at the end of the first stage ignition was found to increase at higher ambient pressure
Modeling surface tension using a ghost fluid technique within a volume of fluid formulation
Energy Technology Data Exchange (ETDEWEB)
Francois, M. M. (Marianne M.); Kothe, D. B. (Douglas B.); Cummins, S. J. (Sharen J.)
2004-01-01
Ghost fluid methods (GFM) are a viable approach for imposing sharp boundary conditions on interfaces that are arbitrarily embedded within the computational mesh. All GFM to date are formulated with an interface distance function that resides within a level-set (LS) framework. Recently we proposed a technique for reconstructing distance functions from volume fractions. This technique enables the exploitation of GFM within a volume of fluid formulation for modeling an interfacial phenomenon like surface tension. Combining GFM with a volume of fluid (VOF) formulation is attractive because of the VOF method's superior mass conservation and because of the ability of GFM to maintain sharp jump conditions. The continuum surface tension force (CSF) method, however, has the propensity to produce smooth jump. In the following, the combined VOF-GFM and more classical VOF-CSF formulations are compared and contrasted. Static and dynamic numerical results are used to illustrate our findings and support our claims.
Body-Fitted Detonation Shock Dynamics and the Pseudo-Reaction-Zone Energy Release Model
Meyer, Chad; Quirk, James; Short, Mark; Chqiuete, Carlos
2016-11-01
Programmed-burn methods are a class of models used to propagate a detonation wave, without the high resolution cost associated with a direct numerical simulation. They separate the detonation evolution calculation into two components: timing and energy release. The timing component is usually calculated with a Detonation Shock Dynamics model, a surface evolution representation that relates the normal velocity of the surface (Dn) to its local curvature. The energy release component must appropriately capture the degree of energy change associated with chemical reaction while simultaneously remaining synchronized with the timing component. The Pseudo-Reaction-Zone (PRZ) model is a reactive burn like energy release model, converting reactants into products, but with a conversion rate that is a function of the DSD surface Dn field. As such, it requires the DSD calculation produce smooth Dn fields, a challenge in complex geometries. We describe a new body-fitted approach to the Detonation Shock Dynamics calculation which produces the required smooth Dn fields, and a method for calibrating the PRZ model such that the rate of energy release remains as synced as possible with the timing component. We show results for slab, rate-stick and arc geometries.
Short-term Forecast Model of Vehicles Volume Based on ARIMA Seasonal Model and Holt-Winters
Directory of Open Access Journals (Sweden)
Wang Zhi-Hui
2017-01-01
Full Text Available In order to alleviate the urban traffic congestion and ensure traffic safety, we need to do a good job in urban road traffic safety planning, make the real-time analysis and forecast of urban traffic flow to detect changes of current traffic flow in time, make scientific planning of roads and improve the road service ability and the transport efficiency of freight vehicles. The data of short-term vehicles volume is characterized by uncertainty and timing correlation series. Given this, the ARIMA seasonal model and the Holt-Winters model are used to establish a forecasting model for the short-term vehicles volume of the city. Finally, we compare the model with predictions.
Reactions of exotic nuclei with the quark-meson coupling model
McRae, E.; Simenel, C.; Simpson, E. C.; Thomas, A. W.
2017-11-01
The nucleon-nucleon interaction is an important requirement for investigations of nuclear structure and reactions, as well as for astrophysical models such as r-process nucleosynthesis and neutron stars. The traditional approach to low-energy nuclear physics is to treat nucleons as immutable objects interacting via phenomenological forces. The use of phenomenological interactions, rather than one derived from a microscopic theory, raises questions as to the reliability of predictions for exotic regions of the nuclear chart. The quark-meson coupling (QMC) model uses a relativistic mean-field approach to provide a microscopically derived nucleon-nucleon interaction, which takes into account the quark structure of the nucleon. The Skyrme energy density functional is a popular phenomenological tool in studies of nuclear structure and reactions. In this work, the QMC density functional was used to produce a set of Skyrme parameterisations, in the hopes that they will give more reliable predictions for exotic nuclei. In conjunction with Hartree-Fock-Bogoliubov (HFB) calculations, the Skyrme-QMC (SQMC) parameterisations have been used to model the ground-state properties of individual nuclei and nucleus-nucleus potentials for Ca + Sn reactions. The SQMC parameterisation performs with an accuracy comparable to modern phenomenological functionals. From this, one can investigate the importance of the isovector terms of the nucleon-nucleon interaction, which are particularly significant for exotic, neutron-rich regions of the nuclear chart. One of the notable successes of the QMC model is its derivation of nuclear spin-orbit coupling. The isovector dependence of the spin-orbit equation of state is remarkably similar to that of the modern UNEDF1 phenomenological density functional. HFB calculations along the Sn isotopic chain reveal that the isovector properties of the spin-orbit term impact binding energies to a level that will be significant for astrophysical r
A reaction-diffusion model of ROS-induced ROS release in a mitochondrial network.
Directory of Open Access Journals (Sweden)
Lufang Zhou
2010-01-01
Full Text Available Loss of mitochondrial function is a fundamental determinant of cell injury and death. In heart cells under metabolic stress, we have previously described how the abrupt collapse or oscillation of the mitochondrial energy state is synchronized across the mitochondrial network by local interactions dependent upon reactive oxygen species (ROS. Here, we develop a mathematical model of ROS-induced ROS release (RIRR based on reaction-diffusion (RD-RIRR in one- and two-dimensional mitochondrial networks. The nodes of the RD-RIRR network are comprised of models of individual mitochondria that include a mechanism of ROS-dependent oscillation based on the interplay between ROS production, transport, and scavenging; and incorporating the tricarboxylic acid (TCA cycle, oxidative phosphorylation, and Ca(2+ handling. Local mitochondrial interaction is mediated by superoxide (O2.- diffusion and the O2.(--dependent activation of an inner membrane anion channel (IMAC. In a 2D network composed of 500 mitochondria, model simulations reveal DeltaPsi(m depolarization waves similar to those observed when isolated guinea pig cardiomyocytes are subjected to a localized laser-flash or antioxidant depletion. The sensitivity of the propagation rate of the depolarization wave to O(2.- diffusion, production, and scavenging in the reaction-diffusion model is similar to that observed experimentally. In addition, we present novel experimental evidence, obtained in permeabilized cardiomyocytes, confirming that DeltaPsi(m depolarization is mediated specifically by O2.-. The present work demonstrates that the observed emergent macroscopic properties of the mitochondrial network can be reproduced in a reaction-diffusion model of RIRR. Moreover, the findings have uncovered a novel aspect of the synchronization mechanism, which is that clusters of mitochondria that are oscillating can entrain mitochondria that would otherwise display stable dynamics. The work identifies the
Reaction selectivity studies on nanolithographically-fabricated platinum model catalyst arrays
Energy Technology Data Exchange (ETDEWEB)
Grunes, Jeffrey Benjamin [Univ. of California, Berkeley, CA (United States)
2004-05-01
In an effort to understand the molecular ingredients of catalytic activity and selectivity toward the end of tuning a catalyst for 100% selectivity, advanced nanolithography techniques were developed and utilized to fabricate well-ordered two-dimensional model catalyst arrays of metal nanostructures on an oxide support for the investigation of reaction selectivity. In-situ and ex-situ surface science techniques were coupled with catalytic reaction data to characterize the molecular structure of the catalyst systems and gain insight into hydrocarbon conversion in heterogeneous catalysis. Through systematic variation of catalyst parameters (size, spacing, structure, and oxide support) and catalytic reaction conditions (hydrocarbon chain length, temperature, pressures, and gas composition), the data presented in this dissertation demonstrate the ability to direct a reaction by rationally adjusting, through precise control, the design of the catalyst system. Electron beam lithography (EBL) was employed to create platinum nanoparticles on an alumina (Al_{2}O_{3}) support. The Pt nanoparticle spacing (100-150-nm interparticle distance) was varied in these samples, and they were characterized using x-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and atomic force microscopy (AFM), both before and after reactions. The TEM studies showed the 28-nm Pt nanoparticles with 100 and 150-nm interparticle spacing on alumina to be polycrystalline in nature, with crystalline sizes of 3-5 nm. The nanoparticle crystallites increased significantly after heat treatment. The nanoparticles were still mostly polycrystalline in nature, with 2-3 domains. The 28-nm Pt nanoparticles deposited on alumina were removed by the AFM tip in contact mode with a normal force of approximately 30 nN. After heat treatment at 500 C in vacuum for 3 hours, the AFM tip, even at 4000 nN, could not remove the platinum
Multivesicular droplets: a cell model system to study compartmentalised biochemical reactions.
Nuti, N; Verboket, P E; Dittrich, P S
2017-09-12
Multivesicular vesicles (MVVs) are artificial liposomal structures widely used as a platform to study the compartmentalisation of cells and as a scaffold for artificial cell/protocell models. Current preparation techniques for MVVs, however, offer poor control on the size, lamellarity, and loading of inner lipid vesicles. Here, we introduce a microfluidic device for the production of multivesicular droplets (MVDs): a novel model system combining the ease of use and control of droplet microfluidics with the biological relevance of MVVs. We use a perfluorinated carrier phase with a biocompatible surfactant to generate monodisperse droplets of an aqueous giant unilamellar lipid vesicle suspension. The successful on-chip formation and stability of MVDs is verified through high-speed microscopy. For bright field or fluorescence microscopy inspection, the MVDs are trapped in an array where the integrity of both lipid vesicles and droplets is preserved for up to 15 minutes. Finally, we show a two-step enzymatic reaction that takes place across the lipid vesicle membranes; the second reaction step occurs in the vesicle's interior, where the enzyme is encapsulated, while both the substrate and fluorescent product permeate across the membrane. Our approach opens the possibility to mimic artificial organelles with optimised reaction parameters (pH, ions, etc.) in each compartment.
Carbon sequestration via reaction with basaltic rocks: geochemical modeling and experimental results
Rosenbauer, Robert J.; Thomas, Burt; Bischoff, James L.; Palandri, James
2012-01-01
Basaltic rocks are potential repositories for sequestering carbon dioxide (CO2) because of their capacity for trapping CO2 in carbonate minerals. We carried out a series of thermodynamic equilibrium models and high pressure experiments, reacting basalt with CO2-charged fluids over a range of conditions from 50 to 200 °C at 300 bar. Results indicate basalt has a high reactivity to CO2 acidified brine. Carbon dioxide is taken up from solution at all temperatures from 50 to 200 °C, 300 bar, but the maximum extent and rate of reaction occurs at 100 °C, 300 bar. Reaction path simulations utilizing the geochemical modeling program CHILLER predicted an equilibrium carbonate alteration assemblage of calcite, magnesite, and siderite, but the only secondary carbonate identified in the experiments was a ferroan magnesite. The amount of uptake at 100 °C, 300 bar ranged from 8% by weight for a typical tholeite to 26% for a picrite. The actual amount of CO2 uptake and extent of rock alteration coincides directly with the magnesium content of the rock suggesting that overall reaction extent is controlled by bulk basalt Mg content. In terms of sequestering CO2, an average basaltic MgO content of 8% is equivalent to 2.6 × 108 metric ton CO2/km3 basalt.
Retrograde reactions in coal processing: The behavior of ether and sulfide model compounds
Energy Technology Data Exchange (ETDEWEB)
Buchanan, A.C. III; Britt, P.F.; Skeen, J.T. [Oak Ridge National Lab., TN (United States). Chemical and Analytical Sciences Div.
1997-04-01
Retrograde reactions that produce more refractory molecular structures are undesirable in coal liquefaction. The authors previously found that restricted mass transport, induced by immobilization on a silica support, promotes retrograde reactions for 1,2-diphenylethane (C{sub 6}H{sub 5}CH{sub 2}CH{sub 2}C{sub 6}H{sub 5}) by both skeletal rearrangement and ring growth (cyclization-dehydrogenation) pathways involving free-radical intermediates. They are now examining the influence of heteroatoms on the retrograde pathways for the corresponding surface-immobilized ether (C{sub 6}H{sub 5}OCH{sub 2}C{sub 6}H{sub 5}) and sulfide (C{sub 6}H{sub 5}SCH{sub 2}C{sub 6}H{sub 5}) model compounds at 275--350 C. Cyclization-dehydrogenation pathways are not detected for either model compound. However, retrograde skeletal rearrangements involving 1,2-phenyl shifts in C{sub 6}H{sub 5}XCH{center_dot}C{sub 6}H{sub 5} (X = O,S) are found to be significant under restricted diffusion, and for X = O, radical coupling at ring carbons to form benzylphenols is also observed as a major pathway. For surface-immobilized benzyl phenyl ether, the two retrograde processes account for ca. 50% of the thermolysis products, and also generate reactive hydroxyl and keto functionalities that can be involved in additional retrograde reactions.
Ogienko, Andrey G; Tkacz, Marek; Manakov, Andrey Yu; Lipkowski, Janusz
2007-11-08
Pressure-temperature (P-T) conditions of the decomposition reaction of the structure H high-pressure methane hydrate to the cubic structure I methane hydrate and fluid methane were studied with a piston-cylinder apparatus at room temperature. For the first time, volume changes accompanying this reaction were determined. With the use of the Clausius-Clapeyron equation the enthalpies of the decomposition reaction of the structure H high-pressure methane hydrate to the cubic structure I methane hydrate and fluid methane have been calculated.
Simulation model for wind energy storage systems. Volume III. Program descriptions. [SIMWEST CODE
Energy Technology Data Exchange (ETDEWEB)
Warren, A.W.; Edsinger, R.W.; Burroughs, J.D.
1977-08-01
The effort developed a comprehensive computer program for the modeling of wind energy/storage systems utilizing any combination of five types of storage (pumped hydro, battery, thermal, flywheel and pneumatic). An acronym for the program is SIMWEST (Simulation Model for Wind Energy Storage). The level of detail of SIMWEST is consistent with a role of evaluating the economic feasibility as well as the general performance of wind energy systems. The software package consists of two basic programs and a library of system, environmental, and load components. Volume III, the SIMWEST program description contains program descriptions, flow charts and program listings for the SIMWEST Model Generation Program, the Simulation program, the File Maintenance program and the Printer Plotter program. Volume III generally would not be required by SIMWEST user.
A Multiorgan Segmentation Model for CT Volumes via Full Convolution-Deconvolution Network
Directory of Open Access Journals (Sweden)
Yangzi Yang
2017-01-01
Full Text Available We propose a model with two-stage process for abdominal segmentation on CT volumes. First, in order to capture the details of organs, a full convolution-deconvolution network (FCN-DecNet is constructed with multiple new unpooling, deconvolutional, and fusion layers. Then, we optimize the coarse segmentation results of FCN-DecNet by multiscale weights probabilistic atlas (MS-PA, which uses spatial and intensity characteristic of atlases. Our coarse-fine model takes advantage of intersubject variability, spatial location, and gray information of CT volumes to minimize the error of segmentation. Finally, using our model, we extract liver, spleen, and kidney with Dice index of 90.1 ± 1%, 89.0 ± 1.6%, and 89.0 ± 1.3%, respectively.
Modeling Accumulated Volume of Landslides Using Remote Sensing and DTM Data
Directory of Open Access Journals (Sweden)
Zhengchao Chen
2014-02-01
Full Text Available Landslides, like other natural hazards, such as avalanches, floods, and debris flows, may result in a lot of property damage and human casualties. The volume of landslide deposits is a key parameter for landslide studies and disaster relief. Using remote sensing and digital terrain model (DTM data, this paper analyzes errors that can occur in calculating landslide volumes using conventional models. To improve existing models, the mechanisms and laws governing the material deposited by landslides are studied and then the mass balance principle and mass balance line are defined. Based on these ideas, a novel and improved model (Mass Balance Model, MBM is proposed. By using a parameter called the “height adaptor”, MBM translates the volume calculation into an automatic search for the mass balance line within the scope of the landslide. Due to the use of mass balance constraints and the height adaptor, MBM is much more effective and reliable. A test of MBM was carried out for the case of a typical landslide, triggered by the Wenchuan Earthquake of 12 May 2008.
Azaroual, M. M.; Parmentier, M.; Andre, L.; Croiset, N.; Pettenati, M.; Kremer, S.
2010-12-01
Microbial processes interact closely with abiotic geochemical reactions and mineralogical transformations in several hydrogeochemical systems. Reactive transport models are aimed to analyze these complex mechanisms integrating as well as the degradation of organic matter as the redox reactions involving successive terminal electron acceptors (TEAPs) mediated by microbes through the continuum of unsaturated zone (soil) - saturated zone (aquifer). The involvement of microbial processes in reactive transport in soil and subsurface geologic greatly complicates the mastery of the major mechanisms and the numerical modelling of these systems. The introduction of kinetic constraints of redox reactions in aqueous phase requires the decoupling of equilibrium reactions and the redefinition of mass balance of chemical elements including the concept of basis species and secondary species of thermodynamic databases used in geochemical modelling tools. An integrated methodology for modelling the reactive transport has been developed and implemented to simulate the transfer of arsenic, denitrification processes and the role of metastable aqueous sulfur species with pyrite and organic matter as electron donors entities. A mechanistic rate law of microbial respiration in various geochemical environments was used to simulate reactive transport of arsenic, nitrate and organic matter combined to the generalized rate law of mineral dissolution - precipitation reactions derived from the transition state theory was used for dissolution - precipitation of silica, aluminosilicate, carbonate, oxyhydroxide, and sulphide minerals. The kinetic parameters are compiled from the literature measurements based on laboratory constrained experiments and field observations. Numerical simulations, using the geochemical software PHREEQC, were performed aiming to identify the key reactions mediated by microbes in the framework of in the first hand the concept of the unsaturated - saturated zones of an
Poux, T; Bonnefont, A; Ryabova, A; Kéranguéven, G; Tsirlina, G A; Savinova, E R
2014-07-21
Hydrogen peroxide has been identified as a stable intermediate of the electrochemical oxygen reduction reaction on various electrodes including metal, metal oxide and carbon materials. In this article we study the hydrogen peroxide oxidation and reduction reactions in alkaline medium using a rotating disc electrode (RDE) method on oxides of the perovskite family (LaCoO3, LaMnO3 and La0.8Sr0.2MnO3) which are considered as promising electrocatalytic materials for the cathode of liquid and solid alkaline fuel cells. The experimental findings, such as the higher activity of Mn-compared to that of Co-perovskites, the shape of RDE curves, and the influence of the H2O2 concentration, are rationalized with the help of a microkinetic model.
Reaction pathways of model compounds of biomass-derived oxygenates on Fe/Ni bimetallic surfaces
Yu, Weiting; Chen, Jingguang G.
2015-10-01
Controlling the activity and selectivity of converting biomass-derivatives to fuels and valuable chemicals is critical for the utilization of biomass feedstocks. There are primarily three classes of non-food competing biomass, cellulose, hemicellulose and lignin. In the current work, glycolaldehyde, furfural and acetaldehyde are studied as model compounds of the three classes of biomass-derivatives. Monometallic Ni(111) and monolayer (ML) Fe/Ni(111) bimetallic surfaces are studied for the reaction pathways of the three biomass surrogates. The ML Fe/Ni(111) surface is identified as an efficient surface for the conversion of biomass-derivatives from the combined results of density functional theory (DFT) calculations and temperature programmed desorption (TPD) experiments. A correlation is also established between the optimized adsorption geometry and experimental reaction pathways. These results should provide helpful insights in catalyst design for the upgrading and conversion of biomass.
Experimental study and nuclear model calculations of {sup 3}He-induced nuclear reactions on zinc
Energy Technology Data Exchange (ETDEWEB)
Al-Abyad, M.; Mohamed, Gehan Y. [Nuclear Research Centre, Atomic Energy Authority, Physics Department (Cyclotron Facility), Cairo (Egypt); Ditroi, F.; Takacs, S.; Tarkanyi, F. [Hungarian Academy of Sciences (ATOMKI), Institute for Nuclear Research, Debrecen (Hungary)
2017-05-15
Excitation functions of {sup 3}He-induced nuclear reactions on natural zinc were measured using the standard stacked-foil technique and high-resolution gamma-ray spectrometry. From their threshold energies up to 27 MeV, the cross-sections for {sup nat}Zn ({sup 3}He,xn) {sup 69}Ge, {sup nat}Zn({sup 3}He,xnp) {sup 66,67,68}Ga, and {sup nat}Zn({sup 3}He,x){sup 62,65}Zn reactions were measured. The nuclear model codes TALYS-1.6, EMPIRE-3.2 and ALICE-IPPE were used to describe the formation of these products. The present data were compared with the theoretical results and with the available experimental data. Integral yields for some important radioisotopes were determined. (orig.)
Experimental study and nuclear model calculations of 3He-induced nuclear reactions on zinc
Al-Abyad, M.; Mohamed, Gehan Y.; Ditrói, F.; Takács, S.; Tárkányi, F.
2017-05-01
Excitation functions of 3He -induced nuclear reactions on natural zinc were measured using the standard stacked-foil technique and high-resolution gamma-ray spectrometry. From their threshold energies up to 27MeV, the cross-sections for natZn (3He, xn) 69Ge, natZn(3He, xnp) 66,67,68Ga, and natZn(3He, x)62,65Zn reactions were measured. The nuclear model codes TALYS-1.6, EMPIRE-3.2 and ALICE-IPPE were used to describe the formation of these products. The present data were compared with the theoretical results and with the available experimental data. Integral yields for some important radioisotopes were determined.
Modeling-gas phase reactions in indoor environments using computational fluid dynamics
DEFF Research Database (Denmark)
Sørensen, Dan Nørtoft; Weschler, Charles J.
2002-01-01
This CFD modeling study examines the concentrations of two gaseous compounds that react in an indoor setting to produce a hypothetical product. The reactants are ozone and either d-limonene or alpha-terpinene (which reacts with ozone about 40 times faster than d-limonene). In addition to two...... surfaces while the terpenes do not. The results show that for all four scenarios, under steady-state conditions, there are large concentration gradients within the room for both reactants and product. To some extent this is due to imperfect mixing. However. it also reflects that reactions occur...... at different rates across the room (because of varying reactant concentrations) and that the time available for reactions to occur varies with the room location (because the "age of the air" varies from point to point). Locally, within the room, the concentrations calculated by the CFID method differ...
DEFF Research Database (Denmark)
Jin, Biao; Rolle, Massimo
2016-01-01
to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic......The degradation of organic micropollutants occurs via different reaction pathways. Compound specific isotope analysis is a valuable tool to identify such degradation pathways in different environmental systems. We propose a mechanism-based modeling approach that provides a quantitative framework...... description of isotope fractionation occurring at different molecular positions. To demonstrate specific features of the modeling approach, we simulated the degradation of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model accurately reproduces...
Acid-base chemical reaction model for nucleation rates in the polluted atmospheric boundary layer.
Chen, Modi; Titcombe, Mari; Jiang, Jingkun; Jen, Coty; Kuang, Chongai; Fischer, Marc L; Eisele, Fred L; Siepmann, J Ilja; Hanson, David R; Zhao, Jun; McMurry, Peter H
2012-11-13
Climate models show that particles formed by nucleation can affect cloud cover and, therefore, the earth's radiation budget. Measurements worldwide show that nucleation rates in the atmospheric boundary layer are positively correlated with concentrations of sulfuric acid vapor. However, current nucleation theories do not correctly predict either the observed nucleation rates or their functional dependence on sulfuric acid concentrations. This paper develops an alternative approach for modeling nucleation rates, based on a sequence of acid-base reactions. The model uses empirical estimates of sulfuric acid evaporation rates obtained from new measurements of neutral molecular clusters. The model predicts that nucleation rates equal the sulfuric acid vapor collision rate times a prefactor that is less than unity and that depends on the concentrations of basic gaseous compounds and preexisting particles. Predicted nucleation rates and their dependence on sulfuric acid vapor concentrations are in reasonable agreement with measurements from Mexico City and Atlanta.
Hot-gas cleanup system model development. Volume I. Final report
Energy Technology Data Exchange (ETDEWEB)
Ushimaru, K.; Bennett, A.; Bekowies, P.J.
1982-11-01
This two-volume report summarizes the state of the art in performance modeling of advanced high-temperature, high-pressure (HTHP) gas cleanup devices. Volume I contains the culmination of the research effort carried over the past 12 months and is a summary of research achievements. Volume II is the user's manual for the computer programs developed under the present research project. In this volume, Section 2 presents background information on pressurized, fluidized-bed combustion concepts, a description of the role of the advanced gas cleanup systems, and a list of advanced gas cleanup systems that are currently in development under DOE sponsorship. Section 3 describes the methodology for the software architecture that forms the basis of the well-disciplined and structured computer programs developed under the present project. Section 4 reviews the fundamental theories that are important in analyzing the cleanup performance of HTHP gas filters. Section 5 discusses the effect of alkali agents in HTHP gas cleanup. Section 6 evaluates the advanced HTHP gas cleanup models based on their mathematical integrity, availability of supporting data, and the likelihood of commercialization. As a result of the evaluation procedure detailed in Section 6, five performance models were chosen to be incorporated into the overall system simulation code, ASPEN. These five models (the electrocyclone, ceramic bag filter, moving granular bed filter, electrostatic granular bed filter, and electrostatic precipitator) are described in Section 7. The method of cost projection for these five models is discussed in Section 8. The supporting data and validation of the computer codes are presented in Section 9, and finally the conclusions and recommendations for the HTHP gas cleanup system model development are given in Section 10. 72 references, 19 figures, 25 tables.
Energy Technology Data Exchange (ETDEWEB)
Solomon, P.R.; Serio, M.A.; Hamblen, D.G. [and others
1995-09-01
This report describes work pertaining to the development of models for coal gasification and combustion processes. This volume, volume 1, part 2, contains research progress in the areas of large particle oxidation at high temperatures, large particle, thick-bed submodels, sulfur oxide/nitrogen oxides submodels, and comprehensive model development and evaluation.
Moraes, Alvaro
2015-01-01
Epidemics have shaped, sometimes more than wars and natural disasters, demo- graphic aspects of human populations around the world, their health habits and their economies. Ebola and the Middle East Respiratory Syndrome (MERS) are clear and current examples of potential hazards at planetary scale. During the spread of an epidemic disease, there are phenomena, like the sudden extinction of the epidemic, that can not be captured by deterministic models. As a consequence, stochastic models have been proposed during the last decades. A typical forward problem in the stochastic setting could be the approximation of the expected number of infected individuals found in one month from now. On the other hand, a typical inverse problem could be, given a discretely observed set of epidemiological data, infer the transmission rate of the epidemic or its basic reproduction number. Markovian epidemic models are stochastic models belonging to a wide class of pure jump processes known as Stochastic Reaction Networks (SRNs), that are intended to describe the time evolution of interacting particle systems where one particle interacts with the others through a finite set of reaction channels. SRNs have been mainly developed to model biochemical reactions but they also have applications in neural networks, virus kinetics, and dynamics of social networks, among others. 4 This PhD thesis is focused on novel fast simulation algorithms and statistical inference methods for SRNs. Our novel Multi-level Monte Carlo (MLMC) hybrid simulation algorithms provide accurate estimates of expected values of a given observable of SRNs at a prescribed final time. They are designed to control the global approximation error up to a user-selected accuracy and up to a certain confidence level, and with near optimal computational work. We also present novel dual-weighted residual expansions for fast estimation of weak and strong errors arising from the MLMC methodology. Regarding the statistical inference
Energy Technology Data Exchange (ETDEWEB)
Krupka, Kenneth M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Cantrell, Kirk J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); McGrail, B. Peter [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
2010-09-01
Permanent storage of anthropogenic CO2 in deep geologic formations is being considered as a means to reduce the concentration of atmospheric CO2 and thus its contribution to global climate change. To ensure safe and effective geologic sequestration, numerous studies have been completed of the extent to which the CO2 migrates within geologic formations and what physical and geochemical changes occur in these formations when CO2 is injected. Sophisticated, computerized reservoir simulations are used as part of field site and laboratory CO2 sequestration studies. These simulations use coupled multiphase flow-reactive chemical transport models and/or standalone (i.e., no coupled fluid transport) geochemical models to calculate gas solubility, aqueous complexation, reduction/oxidation (redox), and/or mineral solubility reactions related to CO2 injection and sequestration. Thermodynamic data are critical inputs to modeling geochemical processes. The adequacy of thermodynamic data for carbonate compounds has been identified as an important data requirement for the successful application of these geochemical reaction models to CO2 sequestration. A review of thermodynamic data for CO2 gas and carbonate aqueous species and minerals present in published data compilations and databases used in geochemical reaction models was therefore completed. Published studies that describe mineralogical analyses from CO2 sequestration field and natural analogue sites and laboratory studies were also reviewed to identify specific carbonate minerals that are important to CO2 sequestration reactions and therefore require thermodynamic data. The results of the literature review indicated that an extensive thermodynamic database exists for CO2 and CH4 gases, carbonate aqueous species, and carbonate minerals. Values of ΔfG298° and/or log Kr,298° are available for essentially all of these compounds. However, log Kr,T° or heat capacity values at temperatures above 298 K exist for less than
Richter, Otto; Moenickes, Sylvia; Suhling, Frank
2012-02-01
The spatial dynamics of range expansion is studied in dependence of temperature. The main elements population dynamics, competition and dispersal are combined in a coherent approach based on a system of coupled partial differential equations of the reaction-diffusion type. The nonlinear reaction terms comprise population dynamic models with temperature dependent reproduction rates subject to an Allee effect and mutual competition. The effect of temperature on travelling wave solutions is investigated for a one dimensional model version. One main result is the importance of the Allee effect for the crossing of regions with unsuitable habitats. The nonlinearities of the interaction terms give rise to a richness of spatio-temporal dynamic patterns. In two dimensions, the resulting non-linear initial boundary value problems are solved over geometries of heterogeneous landscapes. Geo referenced model parameters such as mean temperature and elevation are imported into the finite element tool COMSOL Multiphysics from a geographical information system. The model is applied to the range expansion of species at the scale of middle Europe. Copyright © 2011 Elsevier Inc. All rights reserved.
Impact of organic-mineral matter interactions on thermal reaction pathways for coal model compounds
Energy Technology Data Exchange (ETDEWEB)
Buchanan, A.C. III; Britt, P.F.; Struss, J.A. [Oak Ridge National Lab., TN (United States). Chemical and Analytical Sciences Div.
1995-07-01
Coal is a complex, heterogeneous solid that includes interdispersed mineral matter. However, knowledge of organic-mineral matter interactions is embryonic, and the impact of these interactions on coal pyrolysis and liquefaction is incomplete. Clay minerals, for example, are known to be effective catalysts for organic reactions. Furthermore, clays such as montmorillonite have been proposed to be key catalysts in the thermal alteration of lignin into vitrinite during the coalification process. Recent studies by Hatcher and coworkers on the evolution of coalified woods using microscopy and NMR have led them to propose selective, acid-catalyzed, solid state reaction chemistry to account for retained structural integrity in the wood. However, the chemical feasibility of such reactions in relevant solids is difficult to demonstrate. The authors have begun a model compound study to gain a better molecular level understanding of the effects in the solid state of organic-mineral matter interactions relevant to both coal formation and processing. To satisfy the need for model compounds that remain nonvolatile solids at temperatures ranging to 450 C, model compounds are employed that are chemically bound to the surface of a fumed silica (Si-O-C{sub aryl}linkage). The organic structures currently under investigation are phenethyl phenyl ether (C{sub 6}H{sub 5}CH{sub 2}CH{sub 2}OC{sub 6}H{sub 5}) derivatives, which serve as models for {beta}-alkyl aryl ether units that are present in lignin and lignitic coals. The solid-state chemistry of these materials at 200--450 C in the presence of interdispersed acid catalysts such as small particle size silica-aluminas and montmorillonite clay will be reported. Initial focus will be on defining the potential impact of these interactions on coal pyrolysis and liquefaction.
Reaction modeling of drainage quality in the Duluth Complex, northern Minnesota, USA
Seal, Robert; Lapakko, Kim; Piatak, Nadine; Woodruff, Laurel G.
2015-01-01
Reaction modeling can be a valuable tool in predicting the long-term behavior of waste material if representative rate constants can be derived from long-term leaching tests or other approaches. Reaction modeling using the REACT program of the Geochemist’s Workbench was conducted to evaluate long-term drainage quality affected by disseminated Cu-Ni-(Co-)-PGM sulfide mineralization in the basal zone of the Duluth Complex where significant resources have been identified. Disseminated sulfide minerals, mostly pyrrhotite and Cu-Fe sulfides, are hosted by clinopyroxene-bearing troctolites. Carbonate minerals are scarce to non-existent. Long-term simulations of up to 20 years of weathering of tailings used two different sets of rate constants: one based on published laboratory single-mineral dissolution experiments, and one based on leaching experiments using bulk material from the Duluth Complex conducted by the Minnesota Department of Natural Resources (MNDNR). The simulations included only plagioclase, olivine, clinopyroxene, pyrrhotite, and water as starting phases. Dissolved oxygen concentrations were assumed to be in equilibrium with atmospheric oxygen. The simulations based on the published single-mineral rate constants predicted that pyrrhotite would be effectively exhausted in less than two years and pH would rise accordingly. In contrast, only 20 percent of the pyrrhotite was depleted after two years using the MNDNR rate constants. Predicted pyrrhotite depletion by the simulation based on the MNDNR rate constant matched well with published results of laboratory tests on tailings. Modeling long-term weathering of mine wastes also can provide important insights into secondary reactions that may influence the permeability of tailings and thereby affect weathering behavior. Both models predicted the precipitation of a variety of secondary phases including goethite, gibbsite, and clay (nontronite).
Rugor, Agnieszka; Wójcik-Augustyn, Anna; Niedzialkowska, Ewa; Mordalski, Stefan; Staroń, Jakub; Bojarski, Andrzej; Szaleniec, Maciej
2017-08-01
Steroid C25 dehydrogenase (S25DH) is a molybdenum-containing oxidoreductase isolated from the anaerobic Sterolibacterium denitrificans Chol-1S. S25DH is classified as 'EBDH-like' enzyme (EBDH, ethylbenzene dehydrogenase) and catalyzes the introduction of an OH group to the C25 atom of a sterol aliphatic side-chain. Due to its regioselectivity, S25DH is proposed as a catalyst in production of pharmaceuticals: calcifediol or 25-hydroxycholesterol. The aim of presented research was to obtain structural model of catalytic subunit α and investigate the reaction mechanism of the O2-independent tertiary carbon atom activation. Based on homology modeling and theoretical calculations, a S25DH α subunit model was for the first time characterized and compared to other S25DH-like isoforms. The molecular dynamics simulations of the enzyme-substrate complexes revealed two stable binding modes of a substrate, which are stabilized predominantly by van der Waals forces in the hydrophobic substrate channel. However, H-bond interactions involving polar residues with C3=O/C3-OH in the steroid ring appear to be responsible for positioning the substrate. These results may explain the experimental kinetic results which showed that 3-ketosterols are hydroxylated 5-10-fold faster than 3-hydroxysterols. The reaction mechanism was studied using QM:MM and QM-only cluster models. The postulated mechanism involves homolytic CH cleavage by the MoO ligand, giving rise to a radical intermediate with product obtained in an OH rebound process. The hypothesis was supported by kinetic isotopic effect (KIE) experiments involving 25,26,26,26-[2H]-cholesterol (4.5) and the theoretically predicted intrinsic KIE (7.0-7.2). Finally, we have demonstrated that the recombinant S25DH-like isoform catalyzes the same reaction as S25DH. Copyright © 2017 Elsevier Inc. All rights reserved.
Strychalski, Wanda; Adalsteinsson, David; Elston, Timothy C
2010-01-01
Cells use signaling networks consisting of multiple interacting proteins to respond to changes in their environment. In many situations, such as chemotaxis, spatial and temporal information must be transmitted through the network. Recent computational studies have emphasized the importance of cellular geometry in signal transduction, but have been limited in their ability to accurately represent complex cell morphologies. We present a finite volume method that addresses this problem. Our method uses Cartesian cut cells and is second order in space and time. We use our method to simulate several models of signaling systems in realistic cell morphologies obtained from live cell images and examine the effects of geometry on signal transduction.
Directory of Open Access Journals (Sweden)
Gmel Gerrit
2010-03-01
Full Text Available Abstract Background Alcohol consumption is a major risk factor in the global burden of disease, with overall volume of exposure as the principal underlying dimension. Two main sources of data on volume of alcohol exposure are available: surveys and per capita consumption derived from routine statistics such as taxation. As both sources have significant problems, this paper presents an approach that triangulates information from both sources into disaggregated estimates in line with the overall level of per capita consumption. Methods A modeling approach was applied to the US using data from a large and representative survey, the National Epidemiologic Survey on Alcohol and Related Conditions. Different distributions (log-normal, gamma, Weibull were used to model consumption among drinkers in subgroups defined by sex, age, and ethnicity. The gamma distribution was used to shift the fitted distributions in line with the overall volume as derived from per capita estimates. Implications for alcohol-attributable fractions were presented, using liver cirrhosis as an example. Results The triangulation of survey data with aggregated per capita consumption data proved feasible and allowed for modeling of alcohol exposure disaggregated by sex, age, and ethnicity. These models can be used in combination with risk relations for burden of disease calculations. Sensitivity analyses showed that the gamma distribution chosen yielded very similar results in terms of fit and alcohol-attributable mortality as the other tested distributions. Conclusions Modeling alcohol consumption via the gamma distribution was feasible. To further refine this approach, research should focus on the main assumptions underlying the approach to explore differences between volume estimates derived from surveys and per capita consumption figures.
Foy, E.; Ronan, G.; Chinitz, W.
1982-01-01
A principal element to be derived from modeling turbulent reacting flows is an expression for the reaction rates of the various species involved in any particular combustion process under consideration. A temperature-derived most-likely probability density function (pdf) was used to describe the effects of temperature fluctuations on the Arrhenius reaction rate constant. A most-likely bivariate pdf described the effects of temperature and species concentrations fluctuations on the reaction rate. A criterion is developed for the use of an "appropriate" temperature pdf. The formulation of models to calculate the mean turbulent Arrhenius reaction rate constant and the mean turbulent reaction rate is considered and the results of calculations using these models are presented.
Modeling of stimulated hydrogel volume changes in photonic crystal Pb2+ sensing materials.
Goponenko, Alexander V; Asher, Sanford A
2005-08-03
We modeled the stimulated hydrogel volume transitions of a material which binds Pb2+ and is used as a photonic crystal chemical sensing material. This material consists of a polymerized crystalline colloidal array (PCCA) hydrogel which contains a crown ether molecular recognition group. The PCCA is a polyacrylamide hydrogel which embeds a crystalline colloidal array (CCA) of monodisperse polystyrene spheres of approximately 100 nm. The array spacing is set to diffract light in the visible spectral region. Changes in the hydrogel volume induced by Pb2+ binding alter the array spacing and shift the diffracted wavelength. This system allows us to sensitively follow the hydrogel swelling behavior which results from the immobilization of the Pb2+ by the crown ether chelating groups. Binding of the Pb2+ immobilizes its counterions. This results in a Donnan potential, which results in an osmotic pressure which swells the hydrogel. We continue here our development of a predictive model for hydrogel swelling based on Flory's theory of gel swelling. We are qualitatively able to model the PCCA swelling but cannot correctly model the large responsivity observed at the lowest Pb2+ concentrations which give rise to the experimentally observed low detection limits for Pb2+. These PCCA materials enable stimulated hydrogel volume transitions to be studied.
Verification of Conjugate Heat Transfer Models in a Closed Volume with Radiative Heat Source
Directory of Open Access Journals (Sweden)
Maksimov Vyacheslav I.
2016-01-01
Full Text Available The results of verification of mathematical model of convective-conductive heat transfer in a closed volume with a thermally conductive enclosing structures are presented. Experiments were carried out to determine the temperature of floor premises in the working conditions of radiant heating systems. Comparison of mathematical modelling of temperature fields and experiments showed their good agreement. It is concluded that the mathematical model of conjugate heat transfers in the air cavity with a heat-conducting and heat-retaining walls correspond to the real process of formation of temperature fields in premises with gas infrared heaters system.
Hybrid approaches for multiple-species stochastic reaction-diffusion models
Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen
2015-10-01
Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.
Hybrid approaches for multiple-species stochastic reaction-diffusion models.
Spill, Fabian
2015-10-01
Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.
Directory of Open Access Journals (Sweden)
Sarmad ISTEPHAN
2015-06-01
Full Text Available Volumetric medical image datasets contain vital information for noninvasive diagnosis, treatment planning and prognosis. However, direct and unlimited query of such datasets is hindered due to the unstructured nature of the imaging data. This study is a step towards the unlimited query of medical image datasets by focusing on specific Structures of Interest (SOI. A requirement in achieving this objective is having both the surface and volume models of the SOI. However, typically, only the surface model is available. Therefore, this study focuses on creating a fast method to convert a surface model to a volume model. Three methods (1D, 2D and 3D are proposed and evaluated using simulated and real data of Deep Perisylvian Area (DPSA within the human brain. The 1D method takes 80 msec for DPSA model; about 4 times faster than 2D method and 7.4 fold faster than 3D method, with over 97% accuracy. The proposed 1D method is feasible for surface to volume conversion in computer aided diagnosis, treatment planning and prognosis systems containing large amounts of unstructured medical images.
Kuechler, Erich R.
Molecular modeling and computer simulation techniques can provide detailed insight into biochemical phenomena. This dissertation describes the development, implementation and parameterization of two methods for the accurate modeling of chemical reactions in aqueous environments, with a concerted scientific effort towards the inclusion of charge-dependent non-bonded non-electrostatic interactions into currently used computational frameworks. The first of these models, QXD, modifies interactions in a hybrid quantum mechanical/molecular (QM/MM) mechanical framework to overcome the current limitations of 'atom typing' QM atoms; an inaccurate and non-intuitive practice for chemically active species as these static atom types are dictated by the local bonding and electrostatic environment of the atoms they represent, which will change over the course of the simulation. The efficacy QXD model is demonstrated using a specific reaction parameterization (SRP) of the Austin Model 1 (AM1) Hamiltonian by simultaneously capturing the reaction barrier for chloride ion attack on methylchloride in solution and the solvation free energies of a series of compounds including the reagents of the reaction. The second, VRSCOSMO, is an implicit solvation model for use with the DFTB3/3OB Hamiltonian for biochemical reactions; allowing for accurate modeling of ionic compound solvation properties while overcoming the discontinuous nature of conventional PCM models when chemical reaction coordinates. The VRSCOSMO model is shown to accurately model the solvation properties of over 200 chemical compounds while also providing smooth, continuous reaction surfaces for a series of biologically motivated phosphoryl transesterification reactions. Both of these methods incorporate charge-dependent behavior into the non-bonded interactions variationally, allowing the 'size' of atoms to change in meaningful ways with respect to changes in local charge state, as to provide an accurate, predictive and
Methionine and Choline Deficient (MCD) Model in Predicting Adverse Drug Reactions in Human NASH.
Li, Hui; Toth, Erica; Cherrington, Nathan J
2017-11-14
In the past few decades, great conceptual and technological advances have been made in the field of toxicology, but animal model-based research still remains one of the most widely-used and readily available tools for furthering our current knowledge. However, animal models are not perfect in predicting all systemic toxicity in humans. Extrapolating animal data to accurately predict human toxicities remains a challenge, and researchers are obligated to question the appropriateness of their chosen animal model. This paper provides an assessment of the utility of the methionine choline deficient (MCD) diet fed animal model in reflecting human nonalcoholic steatohepatitis (NASH) and the potential risks of adverse drug reactions (ADRs) and toxicities that are associated with the disease. As a commonly used NASH model, the MCD model fails to exhibit most metabolic abnormalities in a similar manner to the human disease. The MCD model, on the other hand, closely resembles human NASH histology, and reflects signatures of drug transporter alterations in humans. Due to the nature of the MCD model, it should be avoided in studies of NASH pathogenesis, metabolic parameter evaluation and biomarker identification. but it can be used to accurately predict altered drug disposition due to NASH-associated transporter alterations. © The Author 2017. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For permissions, please email: journals.permissions@oup.com.
Molga, E.J.; van Woezik, B.A.A.; Westerterp, K.R.
2000-01-01
Application of neural networks to model the conversion rates of a heterogeneous oxidation reaction has been investigated — oxidation of 2-octanol with nitric acid has been considered as a case study. Due to a more complex and unknown kinetics of the investigated reaction the proposed approach based
Chinitz, W.
1986-01-01
A computationally-viable model describing the interaction between fluid-mechanical turbulence and finite-rate combustion reactions, principally in high-speed flows was developed. Chemical kinetic mechanisms, complete and global, were developed describing the finite rate reaction of fuels of interest to NASA. These fuels included principally hydrogen and silane, although a limited amount of work involved hydrocarbon fuels as well.
Ganesh, Karthik
Owing to the perceived decline of the fossil fuel reserves in the world and environmental issues like pollution, conventional fuels may be replaced by cleaner alternative fuels. The potential of hydrogen as a fuel in vehicular applications is being explored. Hydrogen as an energy carrier potentially finds applications in internal combustion engines and fuel cells because it is considered a clean fuel and has high specific energy. However, at 6 to 8 per kilogram, not only is hydrogen produced from conventional methods like steam reforming expensive, but also there are storage and handling issues, safety concerns and lack of hydrogen refilling stations across the country. The purpose of this research is to suggest a cheap and viable system that generates hydrogen on demand through a chemical reaction between an aluminum-water slurry and an aqueous sodium hydroxide solution to power a 2 kW fuel cell on a fuel cell hybrid motorcycle. This reaction is essentially an aluminum-water reaction where sodium hydroxide acts as a reaction promoter or catalyst. The Horizon 2000 fuel cell used for this purpose has a maximum hydrogen intake rate of 28 lpm. The study focuses on studying the exothermic reaction between the reactants and proposes a rate law that best describes the rate of generation of hydrogen in connection to the surface area of aluminum available for the certain reaction and the concentration of the sodium hydroxide solution. Further, the proposed rate law is used in the simulation model of the chemical reactor onboard the hybrid motorcycle to determine the hydrogen flow rate to the fuel cell with time. Based on the simulated rate of production of hydrogen from the chemical system, its feasibility of use on different drive cycles is analyzed. The rate of production of hydrogen with a higher concentration of sodium hydroxide and smaller aluminum powder size was found to enable the installation of the chemical reactor on urban cycles with frequent stops and starts
Garzón-Alvarado, Diego A; Velasco, Marco A; Narváez-Tovar, Carlos A
2012-02-01
One of the most important areas of Tissue Engineering is the research about bone regeneration and the replacement of its function. To meet this requirement, scaffolds have been developed to allow the cell migration, the growth of bone tissue, the transport of growth factors and nutrients and the renovation of the mechanical properties of bone. Scaffolds are made of different biomaterials and manufactured using various techniques that, in some cases, do not allow full control over the size and orientation of the pores that characterize the scaffold microstructure. From this perspective, we propose a novel hypothesis that a reaction-diffusion system can be used to design the geometrical specifications of the bone matrix. The validation of this hypothesis is performed by simulations of the reaction-diffusion system in a representative tridimensional unit cell, coupled with a model of scaffold degradation by hydrolysis. The results show the possibility that a Reaction-Diffusion system can control features such as the percentage of porosity, trabecular size, orientation, and interconnectivity of pores. Copyright © 2011 Elsevier Ltd. All rights reserved.
Evolution of the Maillard Reaction in Glutamine or Arginine-Dextrinomaltose Model Systems
Directory of Open Access Journals (Sweden)
Silvia Pastoriza
2016-12-01
Full Text Available Enteral formulas are foods designed for medical uses to feed patients who are unable to eat normally. They are prepared by mixing proteins, amino acids, carbohydrates and fats and submitted to sterilization. During thermal treatment, the Maillard reaction takes place through the reaction of animo acids with reducing sugars. Thus, although glutamine and arginine are usually added to improve the nutritional value of enteral formulas, their final concentration may vary. Thus, in the present paper the early, intermediate, and advanced states of the Maillard reaction were studied in model systems by measuring loss of free amino acids through the decrease of fluorescence intensity with o-phtaldialdehyde (OPA, 5-Hydroximethylfurfural (HMF, furfural, glucosylisomaltol, fluorescence, and absorbance at 420 nm. The systems were prepared by mixing glutamine or arginine with dextrinomaltose (similar ingredients to those used in special enteral formula, and heated at 100 °C, 120 °C and 140 °C for 0 to 30 min. The recorded changes in the concentration of furanic compounds was only useful for longer heating times of high temperatures, while absorbance and fluorescence measurements were useful in all the assayed conditions. In addition, easiness and sensitivity of absorbance and fluorescence make them useful techniques that could be implemented as indicators for monitoring the manufacture of special enteral formulas. Glucosylisomaltol is a useful indicator to monitor the manufacture of glutamine-enriched enteral formulas.
Convective instability and boundary driven oscillations in a reaction-diffusion-advection model
Vidal-Henriquez, Estefania; Zykov, Vladimir; Bodenschatz, Eberhard; Gholami, Azam
2017-10-01
In a reaction-diffusion-advection system, with a convectively unstable regime, a perturbation creates a wave train that is advected downstream and eventually leaves the system. We show that the convective instability coexists with a local absolute instability when a fixed boundary condition upstream is imposed. This boundary induced instability acts as a continuous wave source, creating a local periodic excitation near the boundary, which initiates waves travelling both up and downstream. To confirm this, we performed analytical analysis and numerical simulations of a modified Martiel-Goldbeter reaction-diffusion model with the addition of an advection term. We provide a quantitative description of the wave packet appearing in the convectively unstable regime, which we found to be in excellent agreement with the numerical simulations. We characterize this new instability and show that in the limit of high advection speed, it is suppressed. This type of instability can be expected for reaction-diffusion systems that present both a convective instability and an excitable regime. In particular, it can be relevant to understand the signaling mechanism of the social amoeba Dictyostelium discoideum that may experience fluid flows in its natural habitat.
Use of model peptide reactions for the characterization of kinetically controlled ligation.
Lee, Joongoo; Kwon, Yoonjin; Pentelute, Brad L; Bang, Duhee
2011-08-17
Since the introduction of kinetically controlled ligation (KCL), a chemoselective reaction between a peptide-(α)thioarylester and a Cys-peptide-(α)thioalkylester, KCL has been utilized for the total chemical synthesis of large proteins (i.e., lysozyme and HIV-protease) by providing fully convergent synthetic routes. Although KCL has the potential to become an important chemistry for protein synthesis, the principle of KCL is not fully characterized. In particular, prior work on KCL has focused on the reactivity difference of the two different -(α)thioester forms-alkyl vs aryl. Another equally important feature of KCL, Xaa-Cys ligation sites, has not been investigated. The work reported here describes combinatorial KCL reactions using model peptides to dissect the interplay of the Xaa(1), Xaa(2), -(α)thioarylester, and -(α)thioalkylester. Results from these studies provide fundamental insights into the KCL reaction, and will lead to the optimal synthetic route for the routine chemical synthesis of large target protein molecules.
Energy Technology Data Exchange (ETDEWEB)
Bonnardot, J.
1998-11-19
Hydro-treatment of petroleum shortcuts permits elimination of unwanted components in order to increase combustion in engine and to decrease atmospheric pollution. Hydro-desulfurization (HDS), Hydro-denitrogenation (HDN) and Hydrogenation of aromatics (HDA) of a LCO (Light Cycle Oil)-Type gas oil have been studied using a new pilot at a fixed temperature with a NiMo/Al{sub 2}O{sub 3} catalyst. A hydrodynamic study showed that reactions occurring in the up-flow fixed bed reactor that has been used during the experiments, were governed exclusively by chemical reaction rates and not by diffusion. Through detailed chemical analysis, height chemical groups have been considered: three aromatics groups, one sulfided group, one nitrogenized and NH{sub 3}, H{sub 2}S, H{sub 2}. Two Langmuir-Hinshelwood-type kinetic models with either one or two types of sites have been established. The model with two types of site - one site of hydrogenation and one site of hydrogenolysis - showed a better fit in the modeling of the experimental results. This model enables to forecast the influence of partial pressure of H{sub 2}S and partial pressure of H{sub 2} on hydro-treatment reactions of a LCO-type gas oil. (author) 119 refs.
STEPS: modeling and simulating complex reaction-diffusion systems with Python
Directory of Open Access Journals (Sweden)
Stefan Wils
2009-06-01
Full Text Available We describe how the use of the Python language improved the user interface of the program STEPS. STEPS is a simulation platform for modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional boundary conditions. Setting up such models is a complicated process that consists of many phases. Initial versions of STEPS relied on a static input format that did not cleanly separate these phases, limiting modelers in how they could control the simulation and becoming increasingly complex as new features and new simulation algorithms were added. We solved all of these problems by tightly integrating STEPS with Python, using SWIG to expose our existing simulation code.
Local tetrahedron modeling of microelectronics using the finite-volume hybrid-grid technique
Energy Technology Data Exchange (ETDEWEB)
Riley, D.J.; Turner, C.D.
1995-12-01
The finite-volume hybrid-grid (FVHG) technique uses both structured and unstructured grid regions in obtaining a solution to the time-domain Maxwell`s equations. The method is based on explicit time differencing and utilizes rectilinear finite-difference time-domain (FDTD) and nonorthogonal finite-volume time-domain (FVTD). The technique directly couples structured FDTD grids with unstructured FVTD grids without the need for spatial interpolation across grid interfaces. In this paper, the FVHG method is applied to simple planar microelectronic devices. Local tetrahedron grids are used to model portions of the device under study, with the remainder of the problem space being modeled with cubical hexahedral cells. The accuracy of propagating microstrip-guided waves from a low-density hexahedron region through a high-density tetrahedron grid is investigated.
Monte Carlo method for critical systems in infinite volume: The planar Ising model.
Herdeiro, Victor; Doyon, Benjamin
2016-10-01
In this paper we propose a Monte Carlo method for generating finite-domain marginals of critical distributions of statistical models in infinite volume. The algorithm corrects the problem of the long-range effects of boundaries associated to generating critical distributions on finite lattices. It uses the advantage of scale invariance combined with ideas of the renormalization group in order to construct a type of "holographic" boundary condition that encodes the presence of an infinite volume beyond it. We check the quality of the distribution obtained in the case of the planar Ising model by comparing various observables with their infinite-plane prediction. We accurately reproduce planar two-, three-, and four-point of spin and energy operators. We also define a lattice stress-energy tensor, and numerically obtain the associated conformal Ward identities and the Ising central charge.
The Meshfree Finite Volume Method with application to multi-phase porous media models
Foy, Brody H.; Perré, Patrick; Turner, Ian
2017-03-01
Numerical methods form a cornerstone of the analysis and investigation of mathematical models for physical processes. Many classical numerical schemes rely on the application of strict meshing structures to generate accurate solutions, which in some applications are an infeasible constraint. Within this paper we outline a new meshfree numerical scheme, which we call the Meshfree Finite Volume Method (MFVM). The MFVM uses interpolants to approximate fluxes in a disjoint finite volume scheme, allowing for the accurate solution of strong-form PDEs. We present a derivation of the MFVM, and give error bounds on the spatial and temporal approximations used within the scheme. We present a wide variety of applications of the method, showing key features, and advantages over traditional meshed techniques. We close with an application of the method to a non-linear multi-phase wood drying model, showing the potential for solving numerically challenging problems.
Simulation model for wind energy storage systems. Volume II. Operation manual. [SIMWEST code
Energy Technology Data Exchange (ETDEWEB)
Warren, A.W.; Edsinger, R.W.; Burroughs, J.D.
1977-08-01
The effort developed a comprehensive computer program for the modeling of wind energy/storage systems utilizing any combination of five types of storage (pumped hydro, battery, thermal, flywheel and pneumatic). An acronym for the program is SIMWEST (Simulation Model for Wind Energy Storage). The level of detail of SIMWEST is consistent with a role of evaluating the economic feasibility as well as the general performance of wind energy systems. The software package consists of two basic programs and a library of system, environmental, and load components. Volume II, the SIMWEST operation manual, describes the usage of the SIMWEST program, the design of the library components, and a number of simple example simulations intended to familiarize the user with the program's operation. Volume II also contains a listing of each SIMWEST library subroutine.
Directory of Open Access Journals (Sweden)
Stuart Bartlett
2017-08-01
Full Text Available The lattice Boltzmann method is an efficient computational fluid dynamics technique that can accurately model a broad range of complex systems. As well as single-phase fluids, it can simulate thermohydrodynamic systems and passive scalar advection. In recent years, it also gained attention as a means of simulating chemical phenomena, as interest in self-organization processes increased. This paper will present a widely-used and versatile lattice Boltzmann model that can simultaneously incorporate fluid dynamics, heat transfer, buoyancy-driven convection, passive scalar advection, chemical reactions and enthalpy changes. All of these effects interact in a physically accurate framework that is simple to code and readily parallelizable. As well as a complete description of the model equations, several example systems will be presented in order to demonstrate the accuracy and versatility of the method. New simulations, which analyzed the effect of a reversible reaction on the transport properties of a convecting fluid, will also be described in detail. This extra chemical degree of freedom was utilized by the system to augment its net heat flux. The numerical method outlined in this paper can be readily deployed for a vast range of complex flow problems, spanning a variety of scientific disciplines.
A novel approach to modeling the reaction kinetics of tetracycline antibiotics with aqueous ozone.
Hopkins, Zachary R; Blaney, Lee
2014-01-15
Tetracycline antibiotics represent one of the most successful classes of pharmaceuticals and are extensively used around the world for human and veterinary health. Ozone-based processes have emerged as a selective water treatment process for many pharmaceuticals. The primary objective of this study was to determine the reaction kinetics for transformation of five tetracycline antibiotics (i.e., chlortetracycline, doxycycline, oxytetracycline, rolitetracycline, and tetracycline) by ozone across the pH2 to 9 range. The apparent second-order rate constant for tetracycline was on the order of 1-6 × 10(4) M(-1) s(-1) at low pH, and 0.6-2.0 × 10(6) M(-1) s(-1) at near neutral pH. The apparent second-order rate constants did not fit a conventional pKa-based model, presumably due to the complex acid/base speciation of tetracycline antibiotics. A model that considers the net charge on tetracycline molecules in solution provided a nice fit to experimental data for all five tetracyclines. The five tetracycline antibiotics demonstrated similar reaction kinetics with ozone, and a cumulative analysis of all kinetics data provides a baseline model for other tetracycline compounds. The ozone exposure required for complete transformation of tetracycline antibiotics (10(-5) M-s) is well below that achieved during ozone disinfection processes (10(-3) M-s), indicating that ozone is an effective treatment for tetracycline antibiotics. © 2013 Elsevier B.V. All rights reserved.
Williams, Jonathan H.
2010-01-01
The Upper Stage Reaction Control System provides three-axis attitude control for the Ares I launch vehicle during active Upper Stage flight. The system design must accommodate rapid thruster firing to maintain the proper launch trajectory and thus allow for the possibility to pulse multiple thrusters simultaneously. Rapid thruster valve closure creates an increase in static pressure, known as waterhammer, which propagates throughout the propellant system at pressures exceeding nominal design values. A series of development tests conducted in the fall of 2009 at Marshall Space Flight Center were performed using a water-flow test article to better understand fluid performance characteristics of the Upper Stage Reaction Control System. A subset of the tests examined waterhammer along with the subsequent pressure and frequency response in the flight-representative system and provided data to anchor numerical models. This thesis presents a comparison of waterhammer test results with numerical model and analytical results. An overview of the flight system, test article, modeling and analysis are also provided.
Pietak, Alexis; Levin, Michael
2017-09-01
Gene regulatory networks (GRNs) describe interactions between gene products and transcription factors that control gene expression. In combination with reaction-diffusion models, GRNs have enhanced comprehension of biological pattern formation. However, although it is well known that biological systems exploit an interplay of genetic and physical mechanisms, instructive factors such as transmembrane potential (Vmem) have not been integrated into full GRN models. Here we extend regulatory networks to include bioelectric signalling, developing a novel synthesis: the bioelectricity-integrated gene and reaction (BIGR) network. Using in silico simulations, we highlight the capacity for Vmem to alter steady-state concentrations of key signalling molecules inside and out of cells. We characterize fundamental feedbacks where Vmem both controls, and is in turn regulated by, biochemical signals and thereby demonstrate Vmem homeostatic control, Vmem memory and Vmem controlled state switching. BIGR networks demonstrating hysteresis are identified as a mechanisms through which more complex patterns of stable Vmem spots and stripes, along with correlated concentration patterns, can spontaneously emerge. As further proof of principle, we present and analyse a BIGR network model that mechanistically explains key aspects of the remarkable regenerative powers of creatures such as planarian flatworms. The functional properties of BIGR networks generate the first testable, quantitative hypotheses for biophysical mechanisms underlying the stability and adaptive regulation of anatomical bioelectric pattern. © 2017 The Author(s).
Monitoring, Modeling, and Diagnosis of Alkali-Silica Reaction in Small Concrete Samples
Energy Technology Data Exchange (ETDEWEB)
Agarwal, Vivek [Idaho National Lab. (INL), Idaho Falls, ID (United States); Cai, Guowei [Idaho National Lab. (INL), Idaho Falls, ID (United States); Gribok, Andrei V. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Mahadevan, Sankaran [Idaho National Lab. (INL), Idaho Falls, ID (United States)
2015-09-01
Assessment and management of aging concrete structures in nuclear power plants require a more systematic approach than simple reliance on existing code margins of safety. Structural health monitoring of concrete structures aims to understand the current health condition of a structure based on heterogeneous measurements to produce high-confidence actionable information regarding structural integrity that supports operational and maintenance decisions. This report describes alkali-silica reaction (ASR) degradation mechanisms and factors influencing the ASR. A fully coupled thermo-hydro-mechanical-chemical model developed by Saouma and Perotti by taking into consideration the effects of stress on the reaction kinetics and anisotropic volumetric expansion is presented in this report. This model is implemented in the GRIZZLY code based on the Multiphysics Object Oriented Simulation Environment. The implemented model in the GRIZZLY code is randomly used to initiate ASR in a 2D and 3D lattice to study the percolation aspects of concrete. The percolation aspects help determine the transport properties of the material and therefore the durability and service life of concrete. This report summarizes the effort to develop small-size concrete samples with embedded glass to mimic ASR. The concrete samples were treated in water and sodium hydroxide solution at elevated temperature to study how ingress of sodium ions and hydroxide ions at elevated temperature impacts concrete samples embedded with glass. Thermal camera was used to monitor the changes in the concrete sample and results are summarized.
Extended sudden approximation model for high-energy nucleon removal reactions
Energy Technology Data Exchange (ETDEWEB)
Carstoiu, F.; Sauvan, E.; Orr, N.A. [Caen Univ., Lab. de Physique Corpusculaire, Institut des Sciences de la Matiere et du Rayonnement, IN2P3-CNRS ISMRA, 14 (France); Carstoiu, F. [IFIN-HH, Bucharest-Magurele (Romania); Bonaccorso, A. [Istituto Nazionale di Fisica Nucleare, Pisa (Italy)
2004-04-01
A model based on the sudden approximation has been developed to describe high energy single nucleon removal reactions. Within this approach, which takes as its starting point the formalism of Hansen, the nucleon-removal cross section and the full 3-dimensional momentum distributions of the core fragments including absorption, diffraction, Coulomb and nuclear-Coulomb interference amplitudes, have been calculated. The Coulomb breakup has been treated to all orders for the dipole interaction. The model has been compared to experimental data for a range of light, neutron-rich psd-shell nuclei. Good agreement was found for both the inclusive cross sections and momentum distributions. In the case of {sup 17}C, comparison is also made with the results of calculations using the transfer-to-the-continuum model. The calculated 3-dimensional momentum distributions exhibit longitudinal and transverse momentum components that are strongly coupled by the reaction for s-wave states, whilst no such effect is apparent for d-waves. Incomplete detection of transverse momenta arising from limited experimental acceptances thus leads to a narrowing of the longitudinal distributions for nuclei with significant s-wave valence neutron configurations, as confirmed by the data. Asymmetries in the longitudinal momentum distributions attributed to diffractive dissociation are also explored. (authors)
Guzmán, H. A.; Lárraga, M. E.; Alvarez-Icaza, L.; Carvajal, J.
2018-02-01
In this paper, a reliable cellular automata model oriented to faithfully reproduce deceleration and acceleration according to realistic reactions of drivers, when vehicles with different deceleration capabilities are considered is presented. The model focuses on describing complex traffic phenomena by coding in its rules the basic mechanisms of drivers behavior, vehicles capabilities and kinetics, while preserving simplicity. In particular, vehiclés kinetics is based on uniform accelerated motion, rather than in impulsive accelerated motion as in most existing CA models. Thus, the proposed model calculates in an analytic way three safe preserving distances to determine the best action a follower vehicle can take under a worst case scenario. Besides, the prediction analysis guarantees that under the proper assumptions, collision between vehicles may not happen at any future time. Simulations results indicate that all interactions of heterogeneous vehicles (i.e., car-truck, truck-car, car-car and truck-truck) are properly reproduced by the model. In addition, the model overcomes one of the major limitations of CA models for traffic modeling: the inability to perform smooth approach to slower or stopped vehicles. Moreover, the model is also capable of reproducing most empirical findings including the backward speed of the downstream front of the traffic jam, and different congested traffic patterns induced by a system with open boundary conditions with an on-ramp. Like most CA models, integer values are used to make the model run faster, which makes the proposed model suitable for real time traffic simulation of large networks.
Hot-gas cleanup system model development. Volume II. Final report
Energy Technology Data Exchange (ETDEWEB)
Ushimaru, K.; Bennett, A.; Bekowies, P.J.
1982-11-01
Under Contract to the Department of Energy (DOE) through the Morgantown Energy Technology Center (METC), Flow Industries, Inc., has developed computer models to simulate the physical performance of five hot-gas cleanup devices for pressurized, fluidized-bed combustion (PFBC), combined-cycle power plants. Separate cost models have also been developed to estimate the cost of each device. The work leading to the development of these models is described in Volume I of this report. This volume contains the user's manuals for both the physical and cost models. The manuals for the physical models are given first followed by those for the cost models. Each manual is a complete and separate document. The model names and devices and their respective subroutine names are: (1) Moving Granular Bed Filter by Combustion Power Company, USRCGB, QFCOST; (2) Ceramic Bag Filter by Acurex, USRACB, QDCOST; (3) Electrostatic Granular Bed Filter by General Electric, USRGGB, QACOST; (4) Electrostatic Precipitator by Research Cottrell, USRCEP, QECOST; and (5) Electrocyclone by General Electric, USRGCY, QBCOST.
DEFF Research Database (Denmark)
Skulason, Egill; Tripkovic, Vladimir; Björketun, Mårten
2010-01-01
, W, Mo, and Nb, different facets, and step of surfaces. We compare the results for different facets of the Pt electrode to experimental data. Our results suggest that the most important parameter for describing the HOR or the HER activity of an electrode is its binding free energy of H. We present...... a detailed kinetic model based entirely on the DFT reactions and show that the exchange current follows a volcano curve when plotted against the H adsorption free energy in excellent agreement with experimental data....
On one model problem for the reaction-diffusion-advection equation
Davydova, M. A.; Zakharova, S. A.; Levashova, N. T.
2017-09-01
The asymptotic behavior of the solution with boundary layers in the time-independent mathematical model of reaction-diffusion-advection arising when describing the distribution of greenhouse gases in the surface atmospheric layer is studied. On the basis of the asymptotic method of differential inequalities, the existence of a boundary-layer solution and its asymptotic Lyapunov stability as a steady-state solution of the corresponding parabolic problem is proven. One of the results of this work is the determination of the local domain of the attraction of a boundary-layer solution.
Design and analysis of ADER-type schemes for model advection-diffusion-reaction equations
Busto, S.; Toro, E. F.; Vázquez-Cendón, M. E.
2016-12-01
We construct, analyze and assess various schemes of second order of accuracy in space and time for model advection-diffusion-reaction differential equations. The constructed schemes are meant to be of practical use in solving industrial problems and are derived following two related approaches, namely ADER and MUSCL-Hancock. Detailed analysis of linear stability and local truncation error are carried out. In addition, the schemes are implemented and assessed for various test problems. Empirical convergence rate studies confirm the theoretically expected accuracy in both space and time.
Onsager reaction-field theory for magnetic models on diamond and hcp lattices
Wysin, G. M.
2000-08-01
The Onsager reaction-field (ORF) theory is extended to apply to three-dimensional Bravais lattices with a basis. The ORF calculation is used to predict the critical temperature for classical Ising, XY, and Heisenberg magnetic models, in particular, on diamond and hexagonal close-packed lattices. Results are compared with series extrapolations and other theoretical approaches where available. For the hcp lattice the ORF calculation is seen to be equivalent to a Green's-function approach by Adler [Physica B&C 107B, 207 (1981)].
Al-Abyad, M; Abdel-Hamid, A S; Tárkányi, F; Ditrói, F; Takács, S; Seddik, U; Bashter, I I
2012-01-01
Proton induced nuclear reactions were measured with stacked-foil technique on natural zirconium targets up to 16.7MeV. Excitation functions were measured for the production of (90,92m,95m,95g,96)Nb and (88)Y. Cumulative cross-section, thick target yields and activation functions were deduced and compared with the available experimental data, as well as with the nuclear models codes; ALICE-IPPE, EMPIRE and TALYS. The integral yields for thick targets were deduced from the measured excitation function of the produced radionuclides. Copyright © 2011 Elsevier Ltd. All rights reserved.
Directory of Open Access Journals (Sweden)
Luisa Malaguti
2011-01-01
Full Text Available The paper deals with a degenerate reaction-diffusion equation, including aggregative movements and convective terms. The model also incorporates a real parameter causing the change from a purely diffusive to a diffusive-aggregative and to a purely aggregative regime. Existence and qualitative properties of traveling wave solutions are investigated, and estimates of their threshold speeds are furnished. Further, the continuous dependence of the threshold wave speed and of the wave profiles on a real parameter is studied, both when the process maintains its diffusion-aggregation nature and when it switches from it to another regime.
Demand modelling of passenger air travel: An analysis and extension, volume 2
Jacobson, I. D.
1978-01-01
Previous intercity travel demand models in terms of their ability to predict air travel in a useful way and the need for disaggregation in the approach to demand modelling are evaluated. The viability of incorporating non-conventional factors (i.e. non-econometric, such as time and cost) in travel demand forecasting models are determined. The investigation of existing models is carried out in order to provide insight into their strong points and shortcomings. The model is characterized as a market segmentation model. This is a consequence of the strengths of disaggregation and its natural evolution to a usable aggregate formulation. The need for this approach both pedagogically and mathematically is discussed. In addition this volume contains two appendices which should prove useful to the non-specialist in the area.
Time, Dose, and Volume Responses in a Mouse Pulmonary Injury Model Following Ablative Irradiation.
Hong, Zhen-Yu; Lee, Chang Geol; Shim, Hyo Sup; Lee, Eun Jung; Song, Kwang Hyun; Choi, Byoung Wook; Cho, Jaeho; Story, Michael D
2016-02-01
We aimed to determine the time, dose, and volume responses in a mouse pulmonary injury model following ablative dose focal irradiation (ADFIR) in order to better understand normal lung injury. ADFIR was administered to the left lung of mice using a small animal micro-irradiator. Histopathological evaluation and micro-computed tomography (micro-CT) analyses were performed at 1, 2, 6, and 12 weeks after irradiation. Dose responses were tested at doses of 0-90 Gy in C57BL/6 and C3H/HeJCr mice at 6 weeks after irradiation. The volume effect was evaluated with 1-, 3-, and 5-mm diameter collimators at 1-4 weeks after 90-Gy irradiation. ADFIR caused gross local lung injury of the inflated lung in just 1 week, with extensive hyaline material visible in the irradiated area. The fibrosing process was initiated as early as 2 weeks after irradiation. C3H and C57 mice did not show significant differences in dose response. Six weeks after irradiation, the radiation dose-response curve had a sigmoidal shape, where the lag, log, and stationary phases occurred at 80 Gy, respectively. ADFIR induced substantial volume-dependent structural and functional damage to the lungs, and the volume changes of lung consolidation on micro-CT correlated inversely with lung fibrosis over time. We determined the time, dose, and volume responses in our established small animal model, and found that lung injury was substantially accelerated and phenotypically different from that of prior studies using non-ablative hemi-thorax and complete thorax irradiation schemes.
Directory of Open Access Journals (Sweden)
Ya-Fei Tan
2008-09-01
Full Text Available A natural product, stilbene glycoside (2,3,5,4Ã¢Â€Â™-tetrahydroxydiphenylethylene-2-O-glucoside, TBG, has been evaluated for the first time as a potential substrate for horseradish peroxidase (HRP-catalyzed fluorogenic reactions. The properties of TBG as a fluorogenic substrate for HRP and its application in a fluorometric enzyme-linked immunosensing system were compared with commercially available substrates such as p-hydroxyphenylpropionic acid (pHPPA, chavicol and Amplex red using Brucella melitensis antibody (BrAb as a model analyte. The immunosensing body based on HRP-BrAb was constructed by dispersing graphite, BrAg and paraffin wax at room temperature. In a competitive immunoassay procedure, the BrAb competed with HRP-BrAb to react with the immobilized BrAg. In the enzymatic reaction, the binding HRP-BrAb on the sensing body surface can catalyze the polymerization reaction of TBG by H2O2 forming fluorescent dimers and causing an increase in fluorescence intensity. TBG showed comparable ability for HRP detection and its enzyme-linked immunosensing reaction system, in a linear detection ranging of 3.5Ã‚Â´10-8~7.6Ã‚Â´10-6g/L and with a detection limit of 1.7Ã‚Â´10-9 g/L. The immobilized biocomposite surface could be regenerated with excellent reproducibility (RSD=3.8% by simply polishing with an alumina paper. The proposed immunosensing system has been used to determine the BrAb in rabbit serum samples with satisfactory results.
Dynamical Cluster-decay Model (DCM) applied to 9Li+208Pb reaction
Kaur, Arshdeep; Hemdeep; Kaushal, Pooja; Behera, Bivash R.; Gupta, Raj K.
2017-10-01
The decay mechanism of 217At* formed in 9Li+208Pb reaction is studied within the dynamical cluster-decay model (DCM) at various center-of-mass energies. The aim is to see the behavior of a light neutron-rich radioactive beam on a doubly-magic target nucleus for the (total) fusion cross section σfus and the individual decay channel cross sections. Experimentally, only the isotopic yield of heavy mass residues 211-214At * [equivalently, the light-particles (LPs) evaporation residue cross sections σxn for x = 3- 6 neutrons emission] are measured, with the fusion-fission (ff) component σff taken zero. For a fixed neck-length parameter ΔR, the only parameter in the DCM, we are able to fit σfus =∑x=16σxn almost exactly for 9Li on 208Pb at all E c . m .'s. However, the observed individual decay channels (3n-6n) are very poorly fitted, with unobserved channels (1n, 2n) and σff strongly over-estimated. Different ΔR values, meaning thereby different reaction time scales, are required to fit individually both the observed and unobserved evaporation residue channels (1n-6n) and σff, but then the compound nucleus (CN) contribution σCN is very small (< 1%), and the non-compound nucleus (nCN) decay cross section σnCN contributes the most towards total σfus (=σCN +σnCN). Thus, the 9Li induced reaction on doubly-magic 208Pb is more of a quasi-fission-like nCN decay, which is further analyzed in terms of the statistical CN formation probability PCN and CN survival probability Psurv. For the reaction under study, PCN < < 1 and Psurv → 1, in particular at above barrier energies.
1994-05-01
associated with the Educational Technology Assessment Model ( ETAM ). It contains relevant background information and results of prior studies leading to...the finalized ETAM procedures and computerized routines. A comparison of the manual and automated approach is included, and data base structures and... ETAM program flow are described. The second volume (see PA, Vol 59:11358) contains the 344-page appendix. 039Duffy, L.R., Miller, R.B., & Staley, J.D
Volume ignition for inertial confinement fusion tested by different stopping power models
Energy Technology Data Exchange (ETDEWEB)
Hora, H.; Eliezer, S.; Honrubia, J.J.; Hoepfl, R.; Martinez-Val, J.M.; Peria, M.; Velarde, G. [European Network High Energy Density Matter-Polytechnic University of Madrid (Spain)
1996-05-01
Within the low cost energy alternatives to carbon burning, nuclear fusion based on inertial confinement offers the earliest solution. The existing difficulties with spark (hot spot) ignition are reduced by volume ignition. Two basically different computations with different stopping power models are compared and only minor differences in the fusion gains established. An effective density-radius criterion results in comparably very high values if the strong effect of self-heat is included. {copyright} {ital 1996 American Institute of Physics.}
Lütkenhöner, Bernd; Menninghaus, Elisabeth; Steinsträter, Olaf; Wienbruch, Christian; Gißler, Hans Martin; Elbert, Thomas
1995-01-01
Sources of the somatosensory evoked fields (SEF) for one subject were estimated using constraints from the magnetic resonance images (MRI) of the same subject. A realistic volume conductor model was shaped corresponding to the inside of the skull. Sources were restricted to a dipole patch riding on the surface of the cortex, reconstructed from the individual MRI. Such a patch can be considered as a uniformly activated cortical area giving rise to distributed currents which flow perpendicular ...
AN AUTOMATIC FEATURE BASED MODEL FOR CELL SEGMENTATION FROM CONFOCAL MICROSCOPY VOLUMES
Delibaltov, Diana; Ghosh, Pratim; Veeman, Michael; Smith, William; Manjunath, B.S.
2011-01-01
We present a model for the automated segmentation of cells from confocal microscopy volumes of biological samples. The segmentation task for these images is exceptionally challenging due to weak boundaries and varying intensity during the imaging process. To tackle this, a two step pruning process based on the Fast Marching Method is first applied to obtain an over-segmented image. This is followed by a merging step based on an effective feature representation. The algorithm is applied on two...
Ripka, Wagner L; Ulbricht, Leandra; Gewehr, Pedro M
2014-01-01
Background There are several ways to measure the respiratory system, among them inductance plethysmography and three-dimensional kinematic analysis, methods of high cost and difficult transportability. The objective of this study was to correlate respiratory volumes obtained by spirometry standard equipment with a biomechanical model photogrammetric analysis of adolescents. Methods We evaluated 50 subjects of both genders, aged between 14 and 17 years old, excluding those with respiratory obs...
Nishibori, S; Berhnard, R A; Osawa, T; Kawakishi, S
1998-01-01
Volatile components formed from the reaction of monosaccharides or disaccharides with beta-alanine were investigated in a dry condition as a model system of cookie processing. Maltol is a common compound formed in the Maillard reaction, but it was very difficult to detect it in previous experiments using actual cookie materials. In this work, we investigated the principal compounds and maltol formation from the reaction of monosaccharides or disaccharides with beta-alanine at 150 degrees C for 10 min. Neither the reaction of monosaccharides nor the disaccharides with beta-alanine resulted in the formation of maltol. 2,3-Dihydro-3,5-dihydroxy-6-methyl-4(H)-pyran-4-one (DDMP) was detected as a principal product from the reaction of monosaccharides with beta-alanine. 5-Hydroxymethyl-2-furfural was also confirmed as being a major product in both reactions.
Ye, Yuan; Liao, Yunjun; Lu, Feng; Gao, Jianhua
2017-02-01
Fat grafting has variable and sometimes poor outcomes, and therefore new methods are needed. Multiple studies have demonstrated the excellent performance of external volume expansion and focused only on preexpansion with emphasis on the recipient. Two mouse models (a suction model and a fat-exchange transplantation model) were established to investigate changes in the origins and biological behaviors of regeneration-related cells in grafted fat under daily suction provided by external volume expansion. Blood supply increased from new host-derived capillaries or macrophage infiltration under suction. CD34-positive cells showed increased migration from the host into the grafts under suction. At week 12, nearly half of the mature adipocytes regenerated in the grafts in the suction group were derived from the host. Peroxisome proliferator-activated receptor γ expression of the suction group was significantly higher than that of controls at weeks 2 and 4 during adipogenesis. The normalized sample weight of the grafted fat was significantly greater than that of controls at 1 (0.081 ± 0.001 versus 0.072 ± 0.005; p suction provided by external volume expansion favors the regeneration of grafted fat and improves retention by promoting the migration of regeneration-related cells and the differentiation of adipocytes. Thus, more mature fat tissue with a well-organized structure was formed under suction.
An improved thermodiffusion model for ternary mixtures using Fujita's free volume theory
Abbasi, Alireza; Saghir, M. Ziad; Kawaji, Masahiro
2011-09-01
Thermodiffusion along molecular diffusion is one of the major mechanisms of transport phenomena. They have an important role in displacement of hydrocarbon fluid components in an oil reservoir. Free volume controls the diffusivity of the molecule in diffusion-limited systems. It states that the transfer kinetics of molecules depends greatly on molecular size and shape as well as the concentration. A new proposed model based on Fujita-type model is used to predict the thermodiffusion coefficients in ternary mixtures such as n-dodecane (nC12), n-butane (nC4), methane (C1), n-dodecane (nC12), isobutylbenzene (IBB), tetrahydronaphtalene (THN) and n-octane (C8), n-decane (nC10), 1-methylnaphtalene (MN). The ratio of evaporation energy to activation energy required for estimating the thermodiffusion coefficients is calculated by the available free volume theory. In particular, the combination of available free volume theory and Shukla and Firoozabadi's model is applied to predict the thermodiffusion coefficient. The results show a good performance of the new approach in estimating the thermodiffusion coefficients.
Productivity Analysis of Volume Fractured Vertical Well Model in Tight Oil Reservoirs
Directory of Open Access Journals (Sweden)
Jiahang Wang
2017-01-01
Full Text Available This paper presents a semianalytical model to simulate the productivity of a volume fractured vertical well in tight oil reservoirs. In the proposed model, the reservoir is a composite system which contains two regions. The inner region is described as formation with finite conductivity hydraulic fracture network and the flow in fracture is assumed to be linear, while the outer region is simulated by the classical Warren-Root model where radial flow is applied. The transient rate is calculated, and flow patterns and characteristic flowing periods caused by volume fractured vertical well are analyzed. Combining the calculated results with actual production data at the decline stage shows a good fitting performance. Finally, the effects of some sensitive parameters on the type curves are also analyzed extensively. The results demonstrate that the effect of fracture length is more obvious than that of fracture conductivity on improving production in tight oil reservoirs. When the length and conductivity of main fracture are constant, the contribution of stimulated reservoir volume (SRV to the cumulative oil production is not obvious. When the SRV is constant, the length of fracture should also be increased so as to improve the fracture penetration and well production.
A Multiscale, Mortar-Coupled Advection-Diffusion-Reaction Model for Biofilm Growth in Porous Media
Valocchi, A. J.; Laleian, A.; Werth, C. J.
2016-12-01
Multiscale models of reactive transport and biofilm growth in porous media are capable of capturing complex pore-scale processes while leveraging the efficiency of continuum-scale models. In particular, porosity and permeability changes caused by biofilm development result in complex feedbacks between transport and reaction that are difficult to quantify at the continuum scale. Pore-scale models are needed to accurately resolve these dynamics but are often impractical for applications due to their high computational cost. To address this challenge, we develop a multiscale model of biofilm growth in which non-overlapping regions at pore and continuum spatial scales are coupled with a mortar method that ensures continuity of flux across the interface. Thus, regions of high reactivity are resolved at the pore scale for accuracy while regions of low reactivity are resolved at the continuum scale for efficiency. By benchmarking the multiscale model against a fully pore-scale model, we find the multiscale model has a reduced run time while producing a consistent result in terms of biofilm growth, distribution, and solute utilization. We effectively extend a previous model by incorporating a multiscale flow solver and parallelizing solution of the computationally-intensive pore-scale component for increased scalability. We find that mortar coupling is a flexible and effective technique able to join differing computational grids and differing physics in adjacent regions for both fluid flow and solute transport. These results demonstrate the practicality of multiscale mortar-coupled models in studying the complexity of subsurface systems while considering computational limitations in their numerical solution. While recent work has demonstrated growing interest in the development of general multiscale models, more work is needed for their use in real-world applications. Our contribution is a step on the path toward accurate, efficient, and practical reactive transport
Bornadel, Amin; Akerman, Cecilia Orellana; Adlercreutz, Patrick; Hatti-Kaul, Rajni; Borg, Niklas
2013-01-01
Kinetic models are among the tools that can be used for optimization of biocatalytic reactions as well as for facilitating process design and upscaling in order to improve productivity and economy of these processes. Mechanism pathways for multi-substrate multi-product enzyme-catalyzed reactions can become very complex and lead to kinetic models comprising several tens of terms. Hence the models comprise too many parameters, which are in general highly correlated and their estimations are often prone to huge errors. In this study, Novozym(®) 435 catalyzed esterification reaction between oleic acid (OA) and trimethylolpropane (TMP) with continuous removal of side-product (water) was carried out as an example for reactions that follow multi-substrate multi-product ping-pong mechanisms. A kinetic model was developed based on a simplified ping-pong mechanism proposed for the reaction. The model considered both enzymatic and spontaneous reactions involved and also the effect of product removal during the reaction. The kinetic model parameters were estimated using nonlinear curve fitting through unconstrained optimization methodology and the model was verified by using empirical data from different experiments and showed good predictability of the reaction under different conditions. This approach can be applied to similar biocatalytic processes to facilitate their optimization and design. © 2013 American Institute of Chemical Engineers.
Modelling The Effects of Aggregate Size on Alkali Aggregate Reaction Expansion
Directory of Open Access Journals (Sweden)
N. Z. Sekrane
2014-06-01
Full Text Available This work aims at developing models to predict the potential expansion of concrete containing alkali-reactive aggregates. The paper gives measurements in order to provide experimental data concerning the effect of particle size of an alkali-reactive siliceous limestone on mortar expansion. Results show that no expansion was measured on the mortars using small particles (0.5-1.0 mm while the particles (1.0–2.0 mm gave the largest expansions (0.217%. Two models are proposed, the first one studies the correlations between the measured expansions and the size of aggregates, the second one calculates the thickness of the porous zone necessary to take again all the volume of the gel created.
Energy Technology Data Exchange (ETDEWEB)
Berlowitz, D.R.
1996-11-01
In the last few decades the negative impact by humans on the thin atmospheric layer enveloping the earth, the basis for life on this planet, has increased steadily. In order to halt, or at least slow down this development, the knowledge and study of these anthropogenic influence has to be increased and possible remedies have to be suggested. An important tool for these studies are computer models. With their help the atmospheric system can be approximated and the various processes, which have led to the current situation can be quantified. They also serve as an instrument to assess short or medium term strategies to reduce this human impact. However, to assure efficiency as well as accuracy, a careful analysis of the numerous processes involved in the dispersion of pollutants in the atmosphere is called for. This should help to concentrate on the essentials and also prevent excessive usage of sometimes scarce computing resources. The basis of the presented work is the EUMAC Zooming Model (ETM), and particularly the component calculating the dispersion of pollutants in the atmosphere, the model MARS. The model has two main parts: an explicit solver, where the advection and the horizontal diffusion of pollutants are calculated, and an implicit solution mechanism, allowing the joint computation of the change of concentration due to chemical reactions, coupled with the respective influence of the vertical diffusion of the species. The aim of this thesis is to determine particularly the influence of the horizontal components of the turbulent diffusion on the existing implicit solver of the model. Suggestions for a more comprehensive inclusion of the full three dimensional diffusion operator in the implicit solver are made. This is achieved by an appropriate operator splitting. A selection of numerical approaches to tighten the coupling of the diffusion processes with the calculation of the applied chemical reaction mechanisms are examined. (author) figs., tabs., refs.