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

PubMed Central

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

2014-01-01

The mineralisation kinetics of petroleum refinery effluent (PRE) by Fenton oxidation were evaluated. Within the ambit of the experimental data generated, first-order kinetic model (FKM), generalised lumped kinetic model (GLKM), and generalized kinetic model (GKM) were tested. The obtained apparent kinetic rate constants for the initial oxidation step (k 2′), their final oxidation step (k 1′), and the direct conversion to endproducts step (k 3′) were 10.12, 3.78, and 0.24 min−1 for GKM; 0.98, 0.98, and nil min−1 for GLKM; and nil, nil, and >0.005 min−1 for FKM. The findings showed that GKM is superior in estimating the mineralization kinetics. PMID:24592152

A time to search: finding the meaning of variable activation energy.

PubMed

Vyazovkin, Sergey

2016-07-28

This review deals with the phenomenon of variable activation energy frequently observed when studying the kinetics in the liquid or solid phase. This phenomenon commonly manifests itself through nonlinear Arrhenius plots or dependencies of the activation energy on conversion computed by isoconversional methods. Variable activation energy signifies a multi-step process and has a meaning of a collective parameter linked to the activation energies of individual steps. It is demonstrated that by using appropriate models of the processes, the link can be established in algebraic form. This allows one to analyze experimentally observed dependencies of the activation energy in a quantitative fashion and, as a result, to obtain activation energies of individual steps, to evaluate and predict other important parameters of the process, and generally to gain deeper kinetic and mechanistic insights. This review provides multiple examples of such analysis as applied to the processes of crosslinking polymerization, crystallization and melting of polymers, gelation, and solid-solid morphological and glass transitions. The use of appropriate computational techniques is discussed as well.

Understanding the Elementary Steps in DNA Tile-Based Self-Assembly.

PubMed

Jiang, Shuoxing; Hong, Fan; Hu, Huiyu; Yan, Hao; Liu, Yan

2017-09-26

Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios. With more sticky ends, tile attachment becomes more thermostable with an approximately linear decrease in the free energy change (more negative). The total binding free energy of sticky ends is partially compromised by a sequence-independent energy penalty when tile attachment forms a constrained configuration: "loop". The minimal loop is a 2 × 2 tetramer (Loop4). The energy penalty of loops of 4, 6, and 8 tiles was analyzed with the independent loop model assuming no interloop tension, which is generalizable to arbitrary tile configurations. More sticky ends also contribute to a faster on-rate under isothermal conditions when nucleation is the rate-limiting step. Incorrect sticky end contributes to neither the thermostability nor the kinetics. The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.

Coupling DAEM and CFD for simulating biomass fast pyrolysis in fluidized beds

DOE PAGES

Xiong, Qingang; Zhang, Jingchao; Wiggins, Gavin; ...

2015-12-03

We report results from computational simulations of an experimental, lab-scale bubbling bed biomass pyrolysis reactor that include a distributed activation energy model (DAEM) for the kinetics. In this study, we utilized multiphase computational fluid dynamics (CFD) to account for the turbulent hydrodynamics, and this was combined with the DAEM kinetics in a multi-component, multi-step reaction network. Our results indicate that it is possible to numerically integrate the coupled CFD–DAEM system without significantly increasing computational overhead. It is also clear, however, that reactor operating conditions, reaction kinetics, and multiphase flow dynamics all have major impacts on the pyrolysis products exiting themore » reactor. We find that, with the same pre-exponential factors and mean activation energies, inclusion of distributed activation energies in the kinetics can shift the predicted average value of the exit vapor-phase tar flux and its statistical distribution, compared to single-valued activation-energy kinetics. Perhaps the most interesting observed trend is that increasing the diversity of the DAEM activation energies appears to increase the mean tar yield, all else being equal. As a result, these findings imply that accurate resolution of the reaction activation energy distributions will be important for optimizing biomass pyrolysis processes.« less

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models.

PubMed

Cotten, Cameron; Reed, Jennifer L

2013-01-30

Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

PubMed Central

2013-01-01

Background Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. Results In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. Conclusions This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets. PMID:23360254

Volume Diffusion Growth Kinetics and Step Geometry in Crystal Growth

NASA Technical Reports Server (NTRS)

Mazuruk, Konstantin; Ramachandran, Narayanan

1998-01-01

The role of step geometry in two-dimensional stationary volume diff4sion process used in crystal growth kinetics models is investigated. Three different interface shapes: a) a planar interface, b) an equidistant hemispherical bumps train tAx interface, and c) a train of right angled steps, are used in this comparative study. The ratio of the super-saturation to the diffusive flux at the step position is used as a control parameter. The value of this parameter can vary as much as 50% for different geometries. An approximate analytical formula is derived for the right angled steps geometry. In addition to the kinetic models, this formula can be utilized in macrostep growth models. Finally, numerical modeling of the diffusive and convective transport for equidistant steps is conducted. In particular, the role of fluid flow resulting from the advancement of steps and its contribution to the transport of species to the steps is investigated.

A Multi Water Bag model of drift kinetic electron plasmaa

NASA Astrophysics Data System (ADS)

Morel, Pierre; Ghiro, Florent Dreydemy; Berionni, Vincent; Coulette, David; Besse, Nicolas; Gürcan, Özgür D.

2014-08-01

A Multi Water Bag model is proposed for describing drift kinetic plasmas in a magnetized cylindrical geometry, relevant for various experimental devices, solar wind modeling... The Multi Water Bag (MWB) model is adapted to the description of a plasma with kinetic electrons as well as an arbitrary number of kinetic ions. This allows to describe the kinetic dynamics of the electrons, making possible the study of electron temperature gradient (ETG) modes, in addition to the effects of non adiabatic electrons on the ion temperature gradient (ITG) modes, that are of prime importance in the magnetized plasmas micro-turbulence [X. Garbet, Y. Idomura, L. Villard, T.H. Watanabe, Nucl. Fusion 50, 043002 (2010); J.A. Krommes, Ann. Rev. Fluid Mech. 44, 175 (2012)]. The MWB model is shown to link kinetic and fluid descriptions, depending on the number of bags considered. Linear stability of the ETG modes is presented and compared to the existing results regarding cylindrical ITG modes [P. Morel, E. Gravier, N. Besse, R. Klein, A. Ghizzo, P. Bertrand, W. Garbet, Ph. Ghendrih, V. Grandgirard, Y. Sarazin, Phys. Plasmas 14, 112109 (2007)].

Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data.

PubMed

Kotasidis, F A; Mehranian, A; Zaidi, H

2016-05-07

Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from the measured dynamic data within a unified framework. Such image reconstruction methods have been shown to generate parametric maps of improved precision and accuracy in dynamic PET. However, due to the interleaving between the tomographic and kinetic modelling steps, any tomographic or kinetic modelling errors in certain regions or frames, tend to spatially or temporally propagate. This results in biased kinetic parameters and thus limits the benefits of such direct methods. Kinetic modelling errors originate from the inability to construct a common single kinetic model for the entire field-of-view, and such errors in erroneously modelled regions could spatially propagate. Adaptive models have been used within 4D image reconstruction to mitigate the problem, though they are complex and difficult to optimize. Tomographic errors in dynamic imaging on the other hand, can originate from involuntary patient motion between dynamic frames, as well as from emission/transmission mismatch. Motion correction schemes can be used, however, if residual errors exist or motion correction is not included in the study protocol, errors in the affected dynamic frames could potentially propagate either temporally, to other frames during the kinetic modelling step or spatially, during the tomographic step. In this work, we demonstrate a new strategy to minimize such error propagation in direct 4D image reconstruction, focusing on the tomographic step rather than the kinetic modelling step, by incorporating time-of-flight (TOF) within a direct 4D reconstruction framework. Using ever improving TOF resolutions (580 ps, 440 ps, 300 ps and 160 ps), we demonstrate that direct 4D TOF image reconstruction can substantially prevent kinetic parameter error propagation either from erroneous kinetic modelling, inter-frame motion or emission/transmission mismatch. Furthermore, we demonstrate the benefits of TOF in parameter estimation when conventional post-reconstruction (3D) methods are used and compare the potential improvements to direct 4D methods. Further improvements could possibly be achieved in the future by combining TOF direct 4D image reconstruction with adaptive kinetic models and inter-frame motion correction schemes.

Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data

NASA Astrophysics Data System (ADS)

Kotasidis, F. A.; Mehranian, A.; Zaidi, H.

2016-05-01

Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from the measured dynamic data within a unified framework. Such image reconstruction methods have been shown to generate parametric maps of improved precision and accuracy in dynamic PET. However, due to the interleaving between the tomographic and kinetic modelling steps, any tomographic or kinetic modelling errors in certain regions or frames, tend to spatially or temporally propagate. This results in biased kinetic parameters and thus limits the benefits of such direct methods. Kinetic modelling errors originate from the inability to construct a common single kinetic model for the entire field-of-view, and such errors in erroneously modelled regions could spatially propagate. Adaptive models have been used within 4D image reconstruction to mitigate the problem, though they are complex and difficult to optimize. Tomographic errors in dynamic imaging on the other hand, can originate from involuntary patient motion between dynamic frames, as well as from emission/transmission mismatch. Motion correction schemes can be used, however, if residual errors exist or motion correction is not included in the study protocol, errors in the affected dynamic frames could potentially propagate either temporally, to other frames during the kinetic modelling step or spatially, during the tomographic step. In this work, we demonstrate a new strategy to minimize such error propagation in direct 4D image reconstruction, focusing on the tomographic step rather than the kinetic modelling step, by incorporating time-of-flight (TOF) within a direct 4D reconstruction framework. Using ever improving TOF resolutions (580 ps, 440 ps, 300 ps and 160 ps), we demonstrate that direct 4D TOF image reconstruction can substantially prevent kinetic parameter error propagation either from erroneous kinetic modelling, inter-frame motion or emission/transmission mismatch. Furthermore, we demonstrate the benefits of TOF in parameter estimation when conventional post-reconstruction (3D) methods are used and compare the potential improvements to direct 4D methods. Further improvements could possibly be achieved in the future by combining TOF direct 4D image reconstruction with adaptive kinetic models and inter-frame motion correction schemes.

Modeling 3D-CSIA data: Carbon, chlorine, and hydrogen isotope fractionation during reductive dechlorination of TCE to ethene.

PubMed

Van Breukelen, Boris M; Thouement, Héloïse A A; Stack, Philip E; Vanderford, Mindy; Philp, Paul; Kuder, Tomasz

2017-09-01

Reactive transport modeling of multi-element, compound-specific isotope analysis (CSIA) data has great potential to quantify sequential microbial reductive dechlorination (SRD) and alternative pathways such as oxidation, in support of remediation of chlorinated solvents in groundwater. As a key step towards this goal, a model was developed that simulates simultaneous carbon, chlorine, and hydrogen isotope fractionation during SRD of trichloroethene, via cis-1,2-dichloroethene (and trans-DCE as minor pathway), and vinyl chloride to ethene, following Monod kinetics. A simple correction term for individual isotope/isotopologue rates avoided multi-element isotopologue modeling. The model was successfully validated with data from a mixed culture Dehalococcoides microcosm. Simulation of Cl-CSIA required incorporation of secondary kinetic isotope effects (SKIEs). Assuming a limited degree of intramolecular heterogeneity of δ 37 Cl in TCE decreased the magnitudes of SKIEs required at the non-reacting Cl positions, without compromising the goodness of model fit, whereas a good fit of a model involving intramolecular CCl bond competition required an unlikely degree of intramolecular heterogeneity. Simulation of H-CSIA required SKIEs in H atoms originally present in the reacting compounds, especially for TCE, together with imprints of strongly depleted δ 2 H during protonation in the products. Scenario modeling illustrates the potential of H-CSIA for source apportionment. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Dynamic Model of Basic Oxygen Steelmaking Process Based on Multi-zone Reaction Kinetics: Model Derivation and Validation

NASA Astrophysics Data System (ADS)

Rout, Bapin Kumar; Brooks, Geoff; Rhamdhani, M. Akbar; Li, Zushu; Schrama, Frank N. H.; Sun, Jianjun

2018-04-01

A multi-zone kinetic model coupled with a dynamic slag generation model was developed for the simulation of hot metal and slag composition during the basic oxygen furnace (BOF) operation. The three reaction zones (i) jet impact zone, (ii) slag-bulk metal zone, (iii) slag-metal-gas emulsion zone were considered for the calculation of overall refining kinetics. In the rate equations, the transient rate parameters were mathematically described as a function of process variables. A micro and macroscopic rate calculation methodology (micro-kinetics and macro-kinetics) were developed to estimate the total refining contributed by the recirculating metal droplets through the slag-metal emulsion zone. The micro-kinetics involves developing the rate equation for individual droplets in the emulsion. The mathematical models for the size distribution of initial droplets, kinetics of simultaneous refining of elements, the residence time in the emulsion, and dynamic interfacial area change were established in the micro-kinetic model. In the macro-kinetics calculation, a droplet generation model was employed and the total amount of refining by emulsion was calculated by summing the refining from the entire population of returning droplets. A dynamic FetO generation model based on oxygen mass balance was developed and coupled with the multi-zone kinetic model. The effect of post-combustion on the evolution of slag and metal composition was investigated. The model was applied to a 200-ton top blowing converter and the simulated value of metal and slag was found to be in good agreement with the measured data. The post-combustion ratio was found to be an important factor in controlling FetO content in the slag and the kinetics of Mn and P in a BOF process.

Single-molecule enzymology of steroid transforming enzymes: Transient kinetic studies and what they tell us.

PubMed

Penning, Trevor M

2016-07-01

Structure-function studies on steroid transforming enzymes often use site-directed mutagenesis to inform mechanisms of catalysis and effects on steroid binding, and data are reported in terms of changes in steady state kinetic parameters kcat, Km and kcat/Km. However, this dissection of function is limited since kcat is governed by the rate-determining step and Km is a complex macroscopic kinetic constant. Often site-directed mutagenesis can lead to a change in the rate-determining step which cannot be revealed by just reporting a decrease in kcat alone. These issues are made more complex when it is considered that many steroid transforming enzymes have more than one substrate and product. We present the case for using transient-kinetics performed with stopped-flow spectrometry to assign rate constants to discrete steps in these multi-substrate reactions and their use to interpret enzyme mechanism and the effects of disease and engineered mutations. We demonstrate that fluorescence kinetic transients can be used to measure ligand binding that may be accompanied by isomerization steps, revealing the existence of new enzyme intermediates. We also demonstrate that single-turnover reactions can provide a klim for the chemical step and Ks for steroid-substrate binding and that when coupled with kinetic isotope effect measurements can provide information on transition state intermediates. We also demonstrate how multiple turnover experiments can provide evidence for either "burst-phase" kinetics, which can reveal a slow product release step, or linear-phase kinetics, in which the chemical step can be rate-determining. With these assignments it becomes more straightforward to analyze the effects of mutations. We use examples from the hydroxysteroid dehydrogenases (AKR1Cs) and human steroid 5β-reductase (AKR1D1) to illustrate the utility of the approach, which are members of the aldo-keto reductase (AKR) superfamily. Copyright © 2015 Elsevier Ltd. All rights reserved.

WAKES: Wavelet Adaptive Kinetic Evolution Solvers

NASA Astrophysics Data System (ADS)

Mardirian, Marine; Afeyan, Bedros; Larson, David

2016-10-01

We are developing a general capability to adaptively solve phase space evolution equations mixing particle and continuum techniques in an adaptive manner. The multi-scale approach is achieved using wavelet decompositions which allow phase space density estimation to occur with scale dependent increased accuracy and variable time stepping. Possible improvements on the SFK method of Larson are discussed, including the use of multiresolution analysis based Richardson-Lucy Iteration, adaptive step size control in explicit vs implicit approaches. Examples will be shown with KEEN waves and KEEPN (Kinetic Electrostatic Electron Positron Nonlinear) waves, which are the pair plasma generalization of the former, and have a much richer span of dynamical behavior. WAKES techniques are well suited for the study of driven and released nonlinear, non-stationary, self-organized structures in phase space which have no fluid, limit nor a linear limit, and yet remain undamped and coherent well past the drive period. The work reported here is based on the Vlasov-Poisson model of plasma dynamics. Work supported by a Grant from the AFOSR.

Application of kinetic flux vector splitting scheme for solving multi-dimensional hydrodynamical models of semiconductor devices

NASA Astrophysics Data System (ADS)

Nisar, Ubaid Ahmed; Ashraf, Waqas; Qamar, Shamsul

In this article, one and two-dimensional hydrodynamical models of semiconductor devices are numerically investigated. The models treat the propagation of electrons in a semiconductor device as the flow of a charged compressible fluid. It plays an important role in predicting the behavior of electron flow in semiconductor devices. Mathematically, the governing equations form a convection-diffusion type system with a right hand side describing the relaxation effects and interaction with a self consistent electric field. The proposed numerical scheme is a splitting scheme based on the kinetic flux-vector splitting (KFVS) method for the hyperbolic step, and a semi-implicit Runge-Kutta method for the relaxation step. The KFVS method is based on the direct splitting of macroscopic flux functions of the system on the cell interfaces. The second order accuracy of the scheme is achieved by using MUSCL-type initial reconstruction and Runge-Kutta time stepping method. Several case studies are considered. For validation, the results of current scheme are compared with those obtained from the splitting scheme based on the NT central scheme. The effects of various parameters such as low field mobility, device length, lattice temperature and voltage are analyzed. The accuracy, efficiency and simplicity of the proposed KFVS scheme validates its generic applicability to the given model equations. A two dimensional simulation is also performed by KFVS method for a MESFET device, producing results in good agreement with those obtained by NT-central scheme.

Multi-fluid CFD analysis in Process Engineering

NASA Astrophysics Data System (ADS)

Hjertager, B. H.

2017-12-01

An overview of modelling and simulation of flow processes in gas/particle and gas/liquid systems are presented. Particular emphasis is given to computational fluid dynamics (CFD) models that use the multi-dimensional multi-fluid techniques. Turbulence modelling strategies for gas/particle flows based on the kinetic theory for granular flows are given. Sub models for the interfacial transfer processes and chemical kinetics modelling are presented. Examples are shown for some gas/particle systems including flow and chemical reaction in risers as well as gas/liquid systems including bubble columns and stirred tanks.

Refined BCF-type boundary conditions for mesoscale surface step dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Renjie; Ackerman, David M.; Evans, James W.

Deposition on a vicinal surface with alternating rough and smooth steps is described by a solid-on-solid model with anisotropic interactions. Kinetic Monte Carlo (KMC) simulations of the model reveal step pairing in the absence of any additional step attachment barriers. We explore the description of this behavior within an analytic Burton-Cabrera-Frank (BCF)-type step dynamics treatment. Without attachment barriers, conventional kinetic coefficients for the rough and smooth steps are identical, as are the predicted step velocities for a vicinal surface with equal terrace widths. However, we determine refined kinetic coefficients from a two-dimensional discrete deposition-diffusion equation formalism which accounts for stepmore » structure. These coefficients are generally higher for rough steps than for smooth steps, reflecting a higher propensity for capture of diffusing terrace adatoms due to a higher kink density. Such refined coefficients also depend on the local environment of the step and can even become negative (corresponding to net detachment despite an excess adatom density) for a smooth step in close proximity to a rough step. Incorporation of these refined kinetic coefficients into a BCF-type step dynamics treatment recovers quantitatively the mesoscale step-pairing behavior observed in the KMC simulations.« less

Refined BCF-type boundary conditions for mesoscale surface step dynamics

DOE PAGES

Zhao, Renjie; Ackerman, David M.; Evans, James W.

2015-06-24

Deposition on a vicinal surface with alternating rough and smooth steps is described by a solid-on-solid model with anisotropic interactions. Kinetic Monte Carlo (KMC) simulations of the model reveal step pairing in the absence of any additional step attachment barriers. We explore the description of this behavior within an analytic Burton-Cabrera-Frank (BCF)-type step dynamics treatment. Without attachment barriers, conventional kinetic coefficients for the rough and smooth steps are identical, as are the predicted step velocities for a vicinal surface with equal terrace widths. However, we determine refined kinetic coefficients from a two-dimensional discrete deposition-diffusion equation formalism which accounts for stepmore » structure. These coefficients are generally higher for rough steps than for smooth steps, reflecting a higher propensity for capture of diffusing terrace adatoms due to a higher kink density. Such refined coefficients also depend on the local environment of the step and can even become negative (corresponding to net detachment despite an excess adatom density) for a smooth step in close proximity to a rough step. Incorporation of these refined kinetic coefficients into a BCF-type step dynamics treatment recovers quantitatively the mesoscale step-pairing behavior observed in the KMC simulations.« less

Influence of step length and landing pattern on patellofemoral joint kinetics during running.

PubMed

Willson, J D; Ratcliff, O M; Meardon, S A; Willy, R W

2015-12-01

Elevated patellofemoral joint kinetics during running may contribute to patellofemoral joint symptoms. The purpose of this study was to test for independent effects of foot strike pattern and step length on patellofemoral joint kinetics while running. Effects were tested relative to individual steps and also taking into account the number of steps required to run a kilometer with each step length. Patellofemoral joint reaction force and stress were estimated in 20 participants running at their preferred speed. Participants ran using a forefoot strike and rearfoot strike pattern during three different step length conditions: preferred step length, long (+10%) step length, and short (-10%) step length. Patellofemoral kinetics was estimated using a biomechanical model of the patellofemoral joint that accounted for cocontraction of the knee flexors and extensors. We observed independent effects of foot strike pattern and step length. Patellofemoral joint kinetics per step was 10-13% less during forefoot strike conditions and 15-20% less with a shortened step length. Patellofemoral joint kinetics per kilometer decreased 12-13% using a forefoot strike pattern and 9-12% with a shortened step length. To the extent that patellofemoral joint kinetics contribute to symptoms among runners, these running modifications may be advisable for runners with patellofemoral pain. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Further insights into the kinetics of thermal decomposition during continuous cooling.

PubMed

Liavitskaya, Tatsiana; Guigo, Nathanaël; Sbirrazzuoli, Nicolas; Vyazovkin, Sergey

2017-07-26

Following the previous work (Phys. Chem. Chem. Phys., 2016, 18, 32021), this study continues to investigate the intriguing phenomenon of thermal decomposition during continuous cooling. The phenomenon can be detected and its kinetics can be measured by means of thermogravimetric analysis (TGA). The kinetics of the thermal decomposition of ammonium nitrate (NH 4 NO 3 ), nickel oxalate (NiC 2 O 4 ), and lithium sulfate monohydrate (Li 2 SO 4 ·H 2 O) have been measured upon heating and cooling and analyzed by means of the isoconversional methodology. The results have confirmed the hypothesis that the respective kinetics should be similar for single-step processes (NH 4 NO 3 decomposition) but different for multi-step ones (NiC 2 O 4 decomposition and Li 2 SO 4 ·H 2 O dehydration). It has been discovered that the differences in the kinetics can be either quantitative or qualitative. Physical insights into the nature of the differences have been proposed.

A Method to Predict the Thickness of Poorly-Bonded Material Along Spray and Spray-Layer Boundaries in Cold Spray Deposition

NASA Astrophysics Data System (ADS)

Li, Yangfan; Hamada, Yukitaka; Otobe, Katsunori; Ando, Teiichi

2017-02-01

Multi-traverse CS provides a unique means for the production of thick coatings and bulk materials from powders. However, the material along spray and spray-layer boundaries is often poorly bonded as it is laid by the leading and trailing peripheries of the spray that carry powder particles with insufficient kinetic energy. For the same reason, the splats in the very first layer deposited on the substrate may not be bonded well either. A mathematical spray model was developed based on an axisymmetric Gaussian mass flow rate distribution and a stepped deposition yield to predict the thickness of such poorly-bonded layers in multi-traverse CS deposition. The predicted thickness of poorly-bonded layers in a multi-traverse Cu coating falls in the range of experimental values. The model also predicts that the material that contains poorly bonded splats could exceed 20% of the total volume of the coating.

Multi-temperature model derived from state-to-state kinetics for hypersonic entry in Jupiter atmosphere

NASA Astrophysics Data System (ADS)

Colonna, G.; D'Ambrosio, D.; D'Ammando, G.; Pietanza, L. D.; Capitelli, M.

2014-12-01

A state-to-state model of H2/He plasmas coupling the master equations for internal distributions of heavy species with the transport equation for the free electrons has been used as a basis for implementing a multi-temperature kinetic model. In the multi-temperature model internal distributions of heavy particles are Boltzmann, the electron energy distribution function is Maxwell, and the rate coefficients of the elementary processes become a function of local temperatures associated to the relevant equilibrium distributions. The state-to-state and multi-temperature models have been compared in the case of a homogenous recombining plasma, reproducing the conditions met during supersonic expansion though converging-diverging nozzles.

TG study of the Li0.4Fe2.4Zn0.2O4 ferrite synthesis

NASA Astrophysics Data System (ADS)

Lysenko, E. N.; Nikolaev, E. V.; Surzhikov, A. P.

2016-02-01

In this paper, the kinetic analysis of Li-Zn ferrite synthesis was studied using thermogravimetry (TG) method through the simultaneous application of non-linear regression to several measurements run at different heating rates (multivariate non-linear regression). Using TG-curves obtained for the four heating rates and Netzsch Thermokinetics software package, the kinetic models with minimal adjustable parameters were selected to quantitatively describe the reaction of Li-Zn ferrite synthesis. It was shown that the experimental TG-curves clearly suggest a two-step process for the ferrite synthesis and therefore a model-fitting kinetic analysis based on multivariate non-linear regressions was conducted. The complex reaction was described by a two-step reaction scheme consisting of sequential reaction steps. It is established that the best results were obtained using the Yander three-dimensional diffusion model at the first stage and Ginstling-Bronstein model at the second step. The kinetic parameters for lithium-zinc ferrite synthesis reaction were found and discussed.

Kinetics and thermodynamic analysis in one-pot pyrolysis of rice hull using renewable calcium oxide based catalysts.

PubMed

Gan, Darren Kin Wai; Loy, Adrian Chun Minh; Chin, Bridgid Lai Fui; Yusup, Suzana; Unrean, Pornkamol; Rianawati, Elisabeth; Acda, Menandro N

2018-06-06

Thermodynamic and kinetic parameters of catalytic pyrolysis of rice hull (RH) pyrolysis using two different types of renewable catalysts namely natural limestone (LS) and eggshells (ES) using thermogravimetric analysis (TG) approach at different heating rates of 10-100 K min -1 in temperature range of 323-1173 K are investigated. Catalytic pyrolysis mechanism of both catalysts had shown significant effect on the degradation of RH. Model free kinetic of iso-conversional method (Flynn-Wall-Ozawa) and multi-step reaction model (Distributed Activation Energy Model) were employed into present study. The average activation energy was found in the range of 175.4-177.7 kJ mol -1 (RH), 123.3-132.5 kJ mol -1 (RH-LS), and 96.1-100.4 kJ mol -1 (RH-ES) respectively. The syngas composition had increased from 60.05 wt% to 63.1 wt% (RH-LS) and 63.4 wt% (RH-ES). However, the CO 2 content had decreased from 24.1 wt% (RH) to 20.8 wt% (RH-LS) and 19.9 wt% (RH-ES). Copyright © 2018 Elsevier Ltd. All rights reserved.

Unsteady Crystal Growth Due to Step-Bunch Cascading

NASA Technical Reports Server (NTRS)

Vekilov, Peter G.; Lin, Hong; Rosenberger, Franz

1997-01-01

Based on our experimental findings of growth rate fluctuations during the crystallization of the protein lysozym, we have developed a numerical model that combines diffusion in the bulk of a solution with diffusive transport to microscopic growth steps that propagate on a finite crystal facet. Nonlinearities in layer growth kinetics arising from step interaction by bulk and surface diffusion, and from step generation by surface nucleation, are taken into account. On evaluation of the model with properties characteristic for the solute transport, and the generation and propagation of steps in the lysozyme system, growth rate fluctuations of the same magnitude and characteristic time, as in the experiments, are obtained. The fluctuation time scale is large compared to that of step generation. Variations of the governing parameters of the model reveal that both the nonlinearity in step kinetics and mixed transport-kinetics control of the crystallization process are necessary conditions for the fluctuations. On a microscopic scale, the fluctuations are associated with a morphological instability of the vicinal face, in which a step bunch triggers a cascade of new step bunches through the microscopic interfacial supersaturation distribution.

Update of KDBI: Kinetic Data of Bio-molecular Interaction database

PubMed Central

Kumar, Pankaj; Han, B. C.; Shi, Z.; Jia, J.; Wang, Y. P.; Zhang, Y. T.; Liang, L.; Liu, Q. F.; Ji, Z. L.; Chen, Y. Z.

2009-01-01

Knowledge of the kinetics of biomolecular interactions is important for facilitating the study of cellular processes and underlying molecular events, and is essential for quantitative study and simulation of biological systems. Kinetic Data of Bio-molecular Interaction database (KDBI) has been developed to provide information about experimentally determined kinetic data of protein–protein, protein–nucleic acid, protein–ligand, nucleic acid–ligand binding or reaction events described in the literature. To accommodate increasing demand for studying and simulating biological systems, numerous improvements and updates have been made to KDBI, including new ways to access data by pathway and molecule names, data file in System Biology Markup Language format, more efficient search engine, access to published parameter sets of simulation models of 63 pathways, and 2.3-fold increase of data (19 263 entries of 10 532 distinctive biomolecular binding and 11 954 interaction events, involving 2635 proteins/protein complexes, 847 nucleic acids, 1603 small molecules and 45 multi-step processes). KDBI is publically available at http://bidd.nus.edu.sg/group/kdbi/kdbi.asp. PMID:18971255

A New Insight into the Mechanism of NADH Model Oxidation by Metal Ions in Non-Alkaline Media.

PubMed

Yang, Jin-Dong; Chen, Bao-Long; Zhu, Xiao-Qing

2018-06-11

For a long time, it has been controversial that the three-step (e-H+-e) or two-step (e-H•) mechanism was used for the oxidations of NADH and its models by metal ions in non-alkaline media. The latter mechanism has been accepted by the majority of researchers. In this work, 1-benzyl-1,4-dihydronicotinamide (BNAH) and 1-phenyl-l,4-dihydronicotinamide (PNAH) are used as NADH models, and ferrocenium (Fc+) metal ion as an electron acceptor. The kinetics for oxidations of the NADH models by Fc+ in pure acetonitrile were monitored by using UV-Vis absorption and quadratic relationship between of kobs and the concentrations of NADH models were found for the first time. The rate expression of the reactions developed according to the three-step mechanism is quite consistent with the quadratic curves. The rate constants, thermodynamic driving forces and KIEs of each elementary step for the reactions were estimated. All the results supported the three-step mechanism. The intrinsic kinetic barriers of the proton transfer from BNAH+• to BNAH and the hydrogen atom transfer from BNAH+• to BNAH+• were estimated, the results showed that the former is 11.8 kcal/mol, and the latter is larger than 24.3 kcal/mol. It is the large intrinsic kinetic barrier of the hydrogen atom transfer that makes the reactions choose the three-step rather than two-step mechanism. Further investigation of the factors affecting the intrinsic kinetic barrier of chemical reactions indicated that the large intrinsic kinetic barrier of the hydrogen atom transfer originated from the repulsion of positive charges between BNAH+• and BNAH+•. The greatest contribution of this work is the discovery of the quadratic dependence of kobs on the concentrations of the NADH models, which is inconsistent with the conventional viewpoint of the "two-step mechanism" on the oxidations of NADH and its models by metal ions in the non-alkaline media.

Effects of age and step length on joint kinetics during stepping task.

PubMed

Bieryla, Kathleen A; Buffinton, Christine

2015-07-16

Following a balance perturbation, a stepping response is commonly used to regain support, and the distance of the recovery step can vary. To date, no other studies have examined joint kinetics in young and old adults during increasing step distances, when participants are required to bring their rear foot forward. Therefore, the purpose of this study was to examine age-related differences in joint kinetics with increasing step distance. Twenty young and 20 old adults completed the study. Participants completed a step starting from double support, at an initial distance equal to the individual's average step length. The distance was increased by 10% body height until an unsuccessful attempt. A one-way, repeated measures ANOVA was used to determine the effects of age on joint kinetics during the maximum step distance. A two-way, repeated measures, mixed model ANOVA was used to determine the effects of age, step distance, and their interaction on joint kinetics during the first three step distances for all participants. Young adults completed a significantly longer step than old adults. During the maximum step, in general, kinetic measures were greater in the young than in the old. As step distance increased, all but one kinetic measure increased for both young and old adults. This study has shown the ability to discriminate between young and old adults, and could potentially be used in the future to distinguish between fallers and non-fallers. Copyright © 2015 Elsevier Ltd. All rights reserved.

Theoretical study of gas hydrate decomposition kinetics--model development.

PubMed

Windmeier, Christoph; Oellrich, Lothar R

2013-10-10

In order to provide an estimate of the order of magnitude of intrinsic gas hydrate dissolution and dissociation kinetics, the "Consecutive Desorption and Melting Model" (CDM) is developed by applying only theoretical considerations. The process of gas hydrate decomposition is assumed to comprise two consecutive and repetitive quasi chemical reaction steps. These are desorption of the guest molecule followed by local solid body melting. The individual kinetic steps are modeled according to the "Statistical Rate Theory of Interfacial Transport" and the Wilson-Frenkel approach. All missing required model parameters are directly linked to geometric considerations and a thermodynamic gas hydrate equilibrium model.

CFD-Modeling of the Multistage Gasifier Capacity of 30 KW

NASA Astrophysics Data System (ADS)

Levin, A. A.; Kozlov, A. N.; Svishchev, D. A.; Donskoy, I. G.

2017-11-01

Single-stage fuel gasification processes have been developed and widely studied in Russia and abroad throughout the 20th century. They are fundamental to the creation and design of modern gas generator equipment. Many studies have shown that single-stage gasification process, have already reached the limit of perfection, which was a significant improvement in their performance becomes impossible and unprofitable. The most fully meet modern technical requirements of multistage gasification technology. In the first step of the process, is organized allothermic biomass pyrolysis using heat of exhaust gas and generating power plant. At this stage, the yield of volatile products (gas and tar) of fuel. In the second step, the layer of fuel is, the tar is decomposed by the action of hot air and steam, steam-gas mixture is formed further reacts with the charcoal in the third process stage. The paper presents a model developed by the authors of the multi-stage gasifier for wood chips. The model is made with the use of CFD-modeling software package (COMSOL Multiphisics). To describe the kinetics of wood pyrolysis and gasification of charcoal studies were carried out using a set of simultaneous thermal analysis. For this complex developed original methods of interpretation of measurements, including methods of technical analysis of fuels and determine the parameters of the detailed kinetics and mechanism of pyrolysis.

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

PubMed Central

Farasat, Iman; Kushwaha, Manish; Collens, Jason; Easterbrook, Michael; Guido, Matthew; Salis, Howard M

2014-01-01

Developing predictive models of multi-protein genetic systems to understand and optimize their behavior remains a combinatorial challenge, particularly when measurement throughput is limited. We developed a computational approach to build predictive models and identify optimal sequences and expression levels, while circumventing combinatorial explosion. Maximally informative genetic system variants were first designed by the RBS Library Calculator, an algorithm to design sequences for efficiently searching a multi-protein expression space across a > 10,000-fold range with tailored search parameters and well-predicted translation rates. We validated the algorithm's predictions by characterizing 646 genetic system variants, encoded in plasmids and genomes, expressed in six gram-positive and gram-negative bacterial hosts. We then combined the search algorithm with system-level kinetic modeling, requiring the construction and characterization of 73 variants to build a sequence-expression-activity map (SEAMAP) for a biosynthesis pathway. Using model predictions, we designed and characterized 47 additional pathway variants to navigate its activity space, find optimal expression regions with desired activity response curves, and relieve rate-limiting steps in metabolism. Creating sequence-expression-activity maps accelerates the optimization of many protein systems and allows previous measurements to quantitatively inform future designs. PMID:24952589

Kinetic and theoretical studies of novel biodegradable thermo-sensitive xerogels based on PEG/PVP/silica for sustained release of enrofloxacin

NASA Astrophysics Data System (ADS)

Ebadi, Azra; Rafati, Amir Abbas; Bavafa, Sadeghali; Mohammadi, Masoumah

2017-12-01

This study involves the synthesis of a new silica-based colloidal hybrid system. In this new hybrid system, poly (ethylene glycol) (PEG) and thermo-sensitive amphiphilic biocompatible poly (vinyl pyrrolidone) (PVP) were used to create suitable storage for hydrophobic drugs. The possibility of using variable PVP/PEG molar ratios to modulate drug release rate from silica nanoparticles was a primary goal of the current research. In addition, an investigation of the drug release kinetic was conducted. To achieve this, silica nanoparticles were synthesized in poly (ethylene glycol) (PEG) and poly (vinyl pyrrolidone) (PVP) solution incorporated with enrofloxacin (EFX) (as a model hydrophobic drug), using a simple synthetic strategy of hybrid materials which avoided waste and multi-step processes. The impacts of PVP/PEG molar ratios, temperature, and pH of the release medium on release kinetic were investigated. The physicochemical properties of the drug-loaded composites were studied by Fourier transform infrared (FT-IR) spectra, scanning electron microscopy (SEM), and thermogravimetric analysis (TGA). In vitro drug release studies demonstrated that the drug release rate, which was evaluated by analyzing the experimental data with seven kinetic models in a primarily non-Fickian diffusion-controlled process, aligned well with both Ritger-Peppas and Sahlin-Peppas equations.

Modelling reveals kinetic advantages of co-transcriptional splicing.

PubMed

Aitken, Stuart; Alexander, Ross D; Beggs, Jean D

2011-10-01

Messenger RNA splicing is an essential and complex process for the removal of intron sequences. Whereas the composition of the splicing machinery is mostly known, the kinetics of splicing, the catalytic activity of splicing factors and the interdependency of transcription, splicing and mRNA 3' end formation are less well understood. We propose a stochastic model of splicing kinetics that explains data obtained from high-resolution kinetic analyses of transcription, splicing and 3' end formation during induction of an intron-containing reporter gene in budding yeast. Modelling reveals co-transcriptional splicing to be the most probable and most efficient splicing pathway for the reporter transcripts, due in part to a positive feedback mechanism for co-transcriptional second step splicing. Model comparison is used to assess the alternative representations of reactions. Modelling also indicates the functional coupling of transcription and splicing, because both the rate of initiation of transcription and the probability that step one of splicing occurs co-transcriptionally are reduced, when the second step of splicing is abolished in a mutant reporter.

Permeability and kinetic coefficients for mesoscale BCF surface step dynamics: Discrete two-dimensional deposition-diffusion equation analysis

DOE PAGES

Zhao, Renjie; Evans, James W.; Oliveira, Tiago J.

2016-04-08

Here, a discrete version of deposition-diffusion equations appropriate for description of step flow on a vicinal surface is analyzed for a two-dimensional grid of adsorption sites representing the stepped surface and explicitly incorporating kinks along the step edges. Model energetics and kinetics appropriately account for binding of adatoms at steps and kinks, distinct terrace and edge diffusion rates, and possible additional barriers for attachment to steps. Analysis of adatom attachment fluxes as well as limiting values of adatom densities at step edges for nonuniform deposition scenarios allows determination of both permeability and kinetic coefficients. Behavior of these quantities is assessedmore » as a function of key system parameters including kink density, step attachment barriers, and the step edge diffusion rate.« less

Permeability and kinetic coefficients for mesoscale BCF surface step dynamics: Discrete two-dimensional deposition-diffusion equation analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Renjie; Evans, James W.; Oliveira, Tiago J.

Here, a discrete version of deposition-diffusion equations appropriate for description of step flow on a vicinal surface is analyzed for a two-dimensional grid of adsorption sites representing the stepped surface and explicitly incorporating kinks along the step edges. Model energetics and kinetics appropriately account for binding of adatoms at steps and kinks, distinct terrace and edge diffusion rates, and possible additional barriers for attachment to steps. Analysis of adatom attachment fluxes as well as limiting values of adatom densities at step edges for nonuniform deposition scenarios allows determination of both permeability and kinetic coefficients. Behavior of these quantities is assessedmore » as a function of key system parameters including kink density, step attachment barriers, and the step edge diffusion rate.« less

Direct Parametric Image Reconstruction in Reduced Parameter Space for Rapid Multi-Tracer PET Imaging.

PubMed

Cheng, Xiaoyin; Li, Zhoulei; Liu, Zhen; Navab, Nassir; Huang, Sung-Cheng; Keller, Ulrich; Ziegler, Sibylle; Shi, Kuangyu

2015-02-12

The separation of multiple PET tracers within an overlapping scan based on intrinsic differences of tracer pharmacokinetics is challenging, due to limited signal-to-noise ratio (SNR) of PET measurements and high complexity of fitting models. In this study, we developed a direct parametric image reconstruction (DPIR) method for estimating kinetic parameters and recovering single tracer information from rapid multi-tracer PET measurements. This is achieved by integrating a multi-tracer model in a reduced parameter space (RPS) into dynamic image reconstruction. This new RPS model is reformulated from an existing multi-tracer model and contains fewer parameters for kinetic fitting. Ordered-subsets expectation-maximization (OSEM) was employed to approximate log-likelihood function with respect to kinetic parameters. To incorporate the multi-tracer model, an iterative weighted nonlinear least square (WNLS) method was employed. The proposed multi-tracer DPIR (MTDPIR) algorithm was evaluated on dual-tracer PET simulations ([18F]FDG and [11C]MET) as well as on preclinical PET measurements ([18F]FLT and [18F]FDG). The performance of the proposed algorithm was compared to the indirect parameter estimation method with the original dual-tracer model. The respective contributions of the RPS technique and the DPIR method to the performance of the new algorithm were analyzed in detail. For the preclinical evaluation, the tracer separation results were compared with single [18F]FDG scans of the same subjects measured 2 days before the dual-tracer scan. The results of the simulation and preclinical studies demonstrate that the proposed MT-DPIR method can improve the separation of multiple tracers for PET image quantification and kinetic parameter estimations.

Analysis of a kinetic multi-segment foot model. Part I: Model repeatability and kinematic validity.

PubMed

Bruening, Dustin A; Cooney, Kevin M; Buczek, Frank L

2012-04-01

Kinematic multi-segment foot models are still evolving, but have seen increased use in clinical and research settings. The addition of kinetics may increase knowledge of foot and ankle function as well as influence multi-segment foot model evolution; however, previous kinetic models are too complex for clinical use. In this study we present a three-segment kinetic foot model and thorough evaluation of model performance during normal gait. In this first of two companion papers, model reference frames and joint centers are analyzed for repeatability, joint translations are measured, segment rigidity characterized, and sample joint angles presented. Within-tester and between-tester repeatability were first assessed using 10 healthy pediatric participants, while kinematic parameters were subsequently measured on 17 additional healthy pediatric participants. Repeatability errors were generally low for all sagittal plane measures as well as transverse plane Hindfoot and Forefoot segments (median<3°), while the least repeatable orientations were the Hindfoot coronal plane and Hallux transverse plane. Joint translations were generally less than 2mm in any one direction, while segment rigidity analysis suggested rigid body behavior for the Shank and Hindfoot, with the Forefoot violating the rigid body assumptions in terminal stance/pre-swing. Joint excursions were consistent with previously published studies. Copyright © 2012 Elsevier B.V. All rights reserved.

Hydrodynamic model for expansion and collisional relaxation of x-ray laser-excited multi-component nanoplasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saxena, Vikrant, E-mail: vikrant.saxena@desy.de; Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg; Ziaja, Beata, E-mail: ziaja@mail.desy.de

The irradiation of an atomic cluster with a femtosecond x-ray free-electron laser pulse results in a nanoplasma formation. This typically occurs within a few hundred femtoseconds. By this time the x-ray pulse is over, and the direct photoinduced processes no longer contributing. All created electrons within the nanoplasma are thermalized. The nanoplasma thus formed is a mixture of atoms, electrons, and ions of various charges. While expanding, it is undergoing electron impact ionization and three-body recombination. Below we present a hydrodynamic model to describe the dynamics of such multi-component nanoplasmas. The model equations are derived by taking the moments ofmore » the corresponding Boltzmann kinetic equations. We include the equations obtained, together with the source terms due to electron impact ionization and three-body recombination, in our hydrodynamic solver. Model predictions for a test case, expanding spherical Ar nanoplasma, are obtained. With this model, we complete the two-step approach to simulate x-ray created nanoplasmas, enabling computationally efficient simulations of their picosecond dynamics. Moreover, the hydrodynamic framework including collisional processes can be easily extended for other source terms and then applied to follow relaxation of any finite non-isothermal multi-component nanoplasma with its components relaxed into local thermodynamic equilibrium.« less

Evolution of large amplitude Alfven waves in solar wind plasmas: Kinetic-fluid models

NASA Astrophysics Data System (ADS)

Nariyuki, Y.

2014-12-01

Large amplitude Alfven waves are ubiquitously observed in solar wind plasmas. Mjolhus(JPP, 1976) and Mio et al(JPSJ, 1976) found that nonlinear evolution of the uni-directional, parallel propagating Alfven waves can be described by the derivative nonlinear Schrodinger equation (DNLS). Later, the multi-dimensional extension (Mjolhus and Wyller, JPP, 1988; Passot and Sulem, POP, 1993; Gazol et al, POP, 1999) and ion kinetic modification (Mjolhus and Wyller, JPP, 1988; Spangler, POP, 1989; Medvedev and Diamond, POP, 1996; Nariyuki et al, POP, 2013) of DNLS have been reported. Recently, Nariyuki derived multi-dimensional DNLS from an expanding box model of the Hall-MHD system (Nariyuki, submitted). The set of equations including the nonlinear evolution of compressional wave modes (TDNLS) was derived by Hada(GRL, 1993). DNLS can be derived from TDNLS by rescaling of the variables (Mjolhus, Phys. Scr., 2006). Nariyuki and Hada(JPSJ, 2007) derived a kinetically modified TDNLS by using a simple Landau closure (Hammet and Perkins, PRL, 1990; Medvedev and Diamond, POP, 1996). In the present study, we revisit the ion kinetic modification of multi-dimensional TDNLS through more rigorous derivations, which is consistent with the past kinetic modification of DNLS. Although the original TDNLS was derived in the multi-dimensional form, the evolution of waves with finite propagation angles in TDNLS has not been paid much attention. Applicability of the resultant models to solar wind turbulence is discussed.

Unstable vicinal crystal growth from cellular automata

NASA Astrophysics Data System (ADS)

Krasteva, A.; Popova, H.; KrzyŻewski, F.; Załuska-Kotur, M.; Tonchev, V.

2016-03-01

In order to study the unstable step motion on vicinal crystal surfaces we devise vicinal Cellular Automata. Each cell from the colony has value equal to its height in the vicinal, initially the steps are regularly distributed. Another array keeps the adatoms, initially distributed randomly over the surface. The growth rule defines that each adatom at right nearest neighbor position to a (multi-) step attaches to it. The update of whole colony is performed at once and then time increases. This execution of the growth rule is followed by compensation of the consumed particles and by diffusional update(s) of the adatom population. Two principal sources of instability are employed - biased diffusion and infinite inverse Ehrlich-Schwoebel barrier (iiSE). Since these factors are not opposed by step-step repulsion the formation of multi-steps is observed but in general the step bunches preserve a finite width. We monitor the developing surface patterns and quantify the observations by scaling laws with focus on the eventual transition from diffusion-limited to kinetics-limited phenomenon. The time-scaling exponent of the bunch size N is 1/2 for the case of biased diffusion and 1/3 for the case of iiSE. Additional distinction is possible based on the time-scaling exponents of the sizes of multi-step Nmulti, these are 0.36÷0.4 (for biased diffusion) and 1/4 (iiSE).

Modeling of uncertainties in biochemical reactions.

PubMed

Mišković, Ljubiša; Hatzimanikatis, Vassily

2011-02-01

Mathematical modeling is an indispensable tool for research and development in biotechnology and bioengineering. The formulation of kinetic models of biochemical networks depends on knowledge of the kinetic properties of the enzymes of the individual reactions. However, kinetic data acquired from experimental observations bring along uncertainties due to various experimental conditions and measurement methods. In this contribution, we propose a novel way to model the uncertainty in the enzyme kinetics and to predict quantitatively the responses of metabolic reactions to the changes in enzyme activities under uncertainty. The proposed methodology accounts explicitly for mechanistic properties of enzymes and physico-chemical and thermodynamic constraints, and is based on formalism from systems theory and metabolic control analysis. We achieve this by observing that kinetic responses of metabolic reactions depend: (i) on the distribution of the enzymes among their free form and all reactive states; (ii) on the equilibrium displacements of the overall reaction and that of the individual enzymatic steps; and (iii) on the net fluxes through the enzyme. Relying on this observation, we develop a novel, efficient Monte Carlo sampling procedure to generate all states within a metabolic reaction that satisfy imposed constrains. Thus, we derive the statistics of the expected responses of the metabolic reactions to changes in enzyme levels and activities, in the levels of metabolites, and in the values of the kinetic parameters. We present aspects of the proposed framework through an example of the fundamental three-step reversible enzymatic reaction mechanism. We demonstrate that the equilibrium displacements of the individual enzymatic steps have an important influence on kinetic responses of the enzyme. Furthermore, we derive the conditions that must be satisfied by a reversible three-step enzymatic reaction operating far away from the equilibrium in order to respond to changes in metabolite levels according to the irreversible Michelis-Menten kinetics. The efficient sampling procedure allows easy, scalable, implementation of this methodology to modeling of large-scale biochemical networks. © 2010 Wiley Periodicals, Inc.

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

PubMed Central

2014-01-01

Background The kinetic modeling of biological systems is mainly composed of three steps that proceed iteratively: model building, simulation and analysis. In the first step, it is usually required to set initial metabolite concentrations, and to assign kinetic rate laws, along with estimating parameter values using kinetic data through optimization when these are not known. Although the rapid development of high-throughput methods has generated much omics data, experimentalists present only a summary of obtained results for publication, the experimental data files are not usually submitted to any public repository, or simply not available at all. In order to automatize as much as possible the steps of building kinetic models, there is a growing requirement in the systems biology community for easily exchanging data in combination with models, which represents the main motivation of KiMoSys development. Description KiMoSys is a user-friendly platform that includes a public data repository of published experimental data, containing concentration data of metabolites and enzymes and flux data. It was designed to ensure data management, storage and sharing for a wider systems biology community. This community repository offers a web-based interface and upload facility to turn available data into publicly accessible, centralized and structured-format data files. Moreover, it compiles and integrates available kinetic models associated with the data. KiMoSys also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research. Conclusions KiMoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating data storage and sharing, thus supporting construction of ODE-based kinetic models and collaborative research projects. The web application implemented using Ruby on Rails framework is freely available for web access at http://kimosys.org, along with its full documentation. PMID:25115331

Multi-technique approach for qualitative and quantitative characterization of furazidin degradation kinetics under alkaline conditions.

PubMed

Bērziņš, Kārlis; Kons, Artis; Grante, Ilze; Dzabijeva, Diana; Nakurte, Ilva; Actiņš, Andris

2016-09-10

Degradation of drug furazidin was studied under different conditions of environmental pH (11-13) and temperature (30-60°C). The novel approach of hybrid hard- and soft-multivariate curve resolution-alternating least squares (HS-MCR-ALS) method was applied to UV-vis spectral data to determine a valid kinetic model and kinetic parameters of the degradation process. The system was found to be comprised of three main species and best characterized by two consecutive first-order reactions. Furazidin degradation rate was found to be highly dependent on the applied environmental conditions, showing more prominent differences between both degradation steps towards higher pH and temperature. Complimentary qualitative analysis of the degradation process was carried out using HPLC-DAD-TOF-MS. Based on the obtained chromatographic and mass spectrometric results, as well as additional computational analysis of the species (theoretical UV-vis spectra calculations utilizing TD-DFT methodology), the operating degradation mechanism was proposed to include formation of a 5-hydroxyfuran derivative, followed by complete hydrolysis of furazidin hydantoin ring. Copyright © 2016 Elsevier B.V. All rights reserved.

Signatures of a macroscopic switching transition for a dynamic microtubule

NASA Astrophysics Data System (ADS)

Aparna, J. S.; Padinhateeri, Ranjith; Das, Dibyendu

2017-04-01

Characterising complex kinetics of non-equilibrium self-assembly of bio-filaments is of general interest. Dynamic instability in microtubules, consisting of successive catastrophes and rescues, is observed to occur as a result of the non-equilibrium conversion of GTP-tubulin to GDP-tubulin. We study this phenomenon using a model for microtubule kinetics with GTP/GDP state-dependent polymerisation, depolymerisation and hydrolysis of subunits. Our results reveal a sharp switch-like transition in the mean velocity of the filaments, from a growth phase to a shrinkage phase, with an associated co-existence of the two phases. This transition is reminiscent of the discontinuous phase transition across the liquid-gas boundary. We probe the extent of discontinuity in the transition quantitatively using characteristic signatures such as bimodality in velocity distribution, variance and Binder cumulant, and also hysteresis behaviour of the system. We further investigate ageing behaviour in catastrophes of the filament, and find that the multi-step nature of catastrophes is intensified in the vicinity of the switching transition. This assumes importance in the context of Microtubule Associated Proteins which have the potential of altering kinetic parameter values.

Quantitative Comparisons of a Coarse-Grid LES with Experimental Data for Backward-Facing Step Flow

NASA Astrophysics Data System (ADS)

McDonough, J. M.

1999-11-01

A novel approach to LES employing an additive decomposition of both solutions and governing equations (similar to ``multi-level'' approaches of Dubois et al.,Dynamic Multilevel Methods and the Simulation of Turbulence, Cambridge University Press, 1999) is presented; its main structural features are lack of filtering of governing equations (instead, solutions are filtered to remove aliasing due to under resolution) and direct modeling of subgrid-scale primitive variables (rather than modeling their correlations) in the manner proposed by Hylin and McDonough (Int. J. Fluid Mech. Res. 26, 228-256, 1999). A 2-D implementation of this formalism is applied to the backward-facing step flow studied experimentally by Driver and Seegmiller (AIAA J. 23, 163-171, 1985) and Driver et al. (AIAA J. 25, 914-919, 1987), and run on grids sufficiently coarse to permit easy extension to 3-D, industrially-realistic problems. Comparisons of computed and experimental mean quantities (velocity profiles, turbulence kinetic energy, reattachment lengths, etc.) and effects of grid refinement will be presented.

The Power of Integrating Kinetic Isotope Effects into the Formalism of the Michaelis-Menten Equation

PubMed Central

Klinman, Judith P.

2014-01-01

The final arbiter of enzyme mechanism is the ability to establish and test a kinetic mechanism. Isotope effects play a major role in expanding the scope and insight derived from the Michaelis-Menten equation. The integration of isotope effects into the formalism of the Michaelis-Menten equation began in the 1970s and has continued to this day. This review discusses a family of eukaryotic copper proteins that includes dopamine β-monooxygenase, tyramine β-monooxygenase, and peptidylglycine α-amidating enzyme, responsible for the synthesis of the neuro-active compounds, norepinephrine, octopamine and C-terminally carboxamidated peptides, respectively. Highlighted are results that show how combining kinetic isotope effects with initial rate parameters permits an evaluation of: (i) the order of substrate binding to multi-substrate enzymes; (ii) the magnitude of individual rate constants in complex, multi-step reactions; (iii) the identification of chemical intermediates; and (iv) the role of non-classical (tunneling) behavior in C–H activation. PMID:23937475

Atomic-Scale Design of Iron Fischer-Tropsch Catalysts; A Combined Computational Chemistry, Experimental, and Microkinetic Modeling Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manos Mavrikakis; James Dumesic; Rahul Nabar

2008-09-29

This work focuses on (1) searching/summarizing published Fischer-Tropsch synthesis (FTS) mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) preparation and characterization of unsupported iron catalysts with/without potassium/platinum promoters; (3) measurement of H{sub 2} and CO adsorption/dissociation kinetics on iron catalysts using transient methods; (3) analysis of the transient rate data to calculate kinetic parameters of early elementary steps in FTS; (4) construction of a microkinetic model of FTS on iron, and (5) validation of the model from collection of steady-state rate data for FTS on iron catalysts. Three unsupported iron catalysts and three alumina-supported iron catalysts weremore » prepared by non-aqueous-evaporative deposition (NED) or aqueous impregnation (AI) and characterized by chemisorption, BET, temperature-programmed reduction (TPR), extent-of-reduction, XRD, and TEM methods. These catalysts, covering a wide range of dispersions and metal loadings, are well-reduced and relatively thermally stable up to 500-600 C in H{sub 2} and thus ideal for kinetic and mechanistic studies. Kinetic parameters for CO adsorption, CO dissociation, and surface carbon hydrogenation on these catalysts were determined from temperature-programmed desorption (TPD) of CO and temperature programmed surface hydrogenation (TPSR), temperature-programmed hydrogenation (TPH), and isothermal, transient hydrogenation (ITH). A microkinetic model was constructed for the early steps in FTS on polycrystalline iron from the kinetic parameters of elementary steps determined experimentally in this work and from literature values. Steady-state rate data were collected in a Berty reactor and used for validation of the microkinetic model. These rate data were fitted to 'smart' Langmuir-Hinshelwood rate expressions derived from a sequence of elementary steps and using a combination of fitted steady-state parameters and parameters specified from the transient measurements. The results provide a platform for further development of microkinetic models of FTS on Fe and a basis for more precise modeling of FTS activity of Fe catalysts. Calculations using periodic, self-consistent Density Functional Theory (DFT) methods were performed on various realistic models of industrial, Fe-based FTS catalysts. Close-packed, most stable Fe(110) facet was analyzed and subsequently carbide formation was found to be facile leading to the choice of the FeC(110) model representing a Fe facet with a sub-surface C atom. The Pt adatom (Fe{sup Pt}(110)) was found to be the most stable model for our studies into Pt promotion and finally the role of steps was elucidated by recourse to the defected Fe(211) facet. Binding Energies(BEs), preferred adsorption sites and geometries for all FTS relevant stable species and intermediates were evaluated on each model catalyst facet. A mechanistic model (comprising of 32 elementary steps involving 19 species) was constructed and each elementary step therein was fully characterized with respect to its thermochemistry and kinetics. Kinetic calculations involved evaluation of the Minimum Energy Pathways (MEPs) and activation energies (barriers) for each step. Vibrational frequencies were evaluated for the preferred adsorption configuration of each species with the aim of evaluating entropy-changes, pre exponential factors and serving as a useful connection with experimental surface science techniques. Comparative analysis among these four facets revealed important trends in their relative behavior and roles in FTS catalysis. Overall the First Principles Calculations afforded us a new insight into FTS catalysis on Fe and modified-Fe catalysts.« less

Low Temperature Kinetics of the First Steps of Water Cluster Formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bourgalais, J.; Roussel, V.; Capron, M.

2016-03-01

We present a combined experimental and theoretical low temperature kinetic study of water cluster formation. Water cluster growth takes place in low temperature (23-69 K) supersonic flows. The observed kinetics of formation of water clusters are reproduced with a kinetic model based on theoretical predictions for the first steps of clusterization. The temperature-and pressure-dependent association and dissociation rate coefficients are predicted with an ab initio transition state theory based master equation approach over a wide range of temperatures (20-100 K) and pressures (10(-6) - 10 bar).

Evaluation of a hybrid kinetics/mixing-controlled combustion model for turbulent premixed and diffusion combustion using KIVA-II

NASA Technical Reports Server (NTRS)

Nguyen, H. Lee; Wey, Ming-Jyh

1990-01-01

Two-dimensional calculations were made of spark ignited premixed-charge combustion and direct injection stratified-charge combustion in gasoline fueled piston engines. Results are obtained using kinetic-controlled combustion submodel governed by a four-step global chemical reaction or a hybrid laminar kinetics/mixing-controlled combustion submodel that accounts for laminar kinetics and turbulent mixing effects. The numerical solutions are obtained by using KIVA-2 computer code which uses a kinetic-controlled combustion submodel governed by a four-step global chemical reaction (i.e., it assumes that the mixing time is smaller than the chemistry). A hybrid laminar/mixing-controlled combustion submodel was implemented into KIVA-2. In this model, chemical species approach their thermodynamics equilibrium with a rate that is a combination of the turbulent-mixing time and the chemical-kinetics time. The combination is formed in such a way that the longer of the two times has more influence on the conversion rate and the energy release. An additional element of the model is that the laminar-flame kinetics strongly influence the early flame development following ignition.

Evaluation of a hybrid kinetics/mixing-controlled combustion model for turbulent premixed and diffusion combustion using KIVA-2

NASA Technical Reports Server (NTRS)

Nguyen, H. Lee; Wey, Ming-Jyh

1990-01-01

Two dimensional calculations were made of spark ignited premixed-charge combustion and direct injection stratified-charge combustion in gasoline fueled piston engines. Results are obtained using kinetic-controlled combustion submodel governed by a four-step global chemical reaction or a hybrid laminar kinetics/mixing-controlled combustion submodel that accounts for laminar kinetics and turbulent mixing effects. The numerical solutions are obtained by using KIVA-2 computer code which uses a kinetic-controlled combustion submodel governed by a four-step global chemical reaction (i.e., it assumes that the mixing time is smaller than the chemistry). A hybrid laminar/mixing-controlled combustion submodel was implemented into KIVA-2. In this model, chemical species approach their thermodynamics equilibrium with a rate that is a combination of the turbulent-mixing time and the chemical-kinetics time. The combination is formed in such a way that the longer of the two times has more influence on the conversion rate and the energy release. An additional element of the model is that the laminar-flame kinetics strongly influence the early flame development following ignition.

Analysis of a kinetic multi-segment foot model part II: kinetics and clinical implications.

PubMed

Bruening, Dustin A; Cooney, Kevin M; Buczek, Frank L

2012-04-01

Kinematic multi-segment foot models have seen increased use in clinical and research settings, but the addition of kinetics has been limited and hampered by measurement limitations and modeling assumptions. In this second of two companion papers, we complete the presentation and analysis of a three segment kinetic foot model by incorporating kinetic parameters and calculating joint moments and powers. The model was tested on 17 pediatric subjects (ages 7-18 years) during normal gait. Ground reaction forces were measured using two adjacent force platforms, requiring targeted walking and the creation of two sub-models to analyze ankle, midtarsal, and 1st metatarsophalangeal joints. Targeted walking resulted in only minimal kinematic and kinetic differences compared with walking at self selected speeds. Joint moments and powers were calculated and ensemble averages are presented as a normative database for comparison purposes. Ankle joint powers are shown to be overestimated when using a traditional single-segment foot model, as substantial angular velocities are attributed to the mid-tarsal joint. Power transfer is apparent between the 1st metatarsophalangeal and mid-tarsal joints in terminal stance/pre-swing. While the measurement approach presented here is limited to clinical populations with only minimal impairments, some elements of the model can also be incorporated into routine clinical gait analysis. Copyright © 2011 Elsevier B.V. All rights reserved.

Modeling the impact of bubbling bed hydrodynamics on tar yield and its fluctuations during biomass fast pyrolysis

DOE PAGES

Xiong, Qingang; Ramirez, Emilio; Pannala, Sreekanth; ...

2015-10-09

The impact of bubbling bed hydrodynamics on temporal variations in the exit tar yield for biomass fast pyrolysis was investigated using computational simulations of an experimental laboratory-scale reactor. A multi-fluid computational fluid dynamics model was employed to simulate the differential conservation equations in the reactor, and this was combined with a multi-component, multi-step pyrolysis kinetics scheme for biomass to account for chemical reactions. The predicted mean tar yields at the reactor exit appear to match corresponding experimental observations. Parametric studies predicted that increasing the fluidization velocity should improve the mean tar yield but increase its temporal variations. Increases in themore » mean tar yield coincide with reducing the diameter of sand particles or increasing the initial sand bed height. However, trends in tar yield variability are more complex than the trends in mean yield. The standard deviation in tar yield reaches a maximum with changes in sand particle size. As a result, the standard deviation in tar yield increases with the increases in initial bed height in freely bubbling state, while reaches a maximum in slugging state.« less

Chemistry Resolved Kinetic Flow Modeling of TATB Based Explosives

NASA Astrophysics Data System (ADS)

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

2011-06-01

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

Inhibition of calcium oxalate monohydrate growth by citrate and the effect of the background electrolyte

NASA Astrophysics Data System (ADS)

Weaver, Matthew L.; Qiu, S. Roger; Hoyer, John R.; Casey, William H.; Nancollas, George H.; De Yoreo, James J.

2007-08-01

Pathological mineralization is a common phenomenon in broad range of plants and animals. In humans, kidney stone formation is a well-known example that afflicts approximately 10% of the population. Of the various calcium salt phases that comprise human kidney stones, the primary component is calcium oxalate monohydrate (COM). Citrate, a naturally occurring molecule in the urinary system and a common therapeutic agent for treating stone disease, is a known inhibitor of COM. Understanding the physical mechanisms of citrate inhibition requires quantification of the effects of both background electrolytes and citrate on COM step kinetics. Here we report the results of an in situ AFM study of these effects, in which we measure the effect of the electrolytes LiCl, NaCl, KCl, RbCl, and CsCl, and the dependence of step speed on citrate concentration for a range of COM supersaturations. We find that varying the background electrolyte results in significant differences in the measured step speeds and in step morphology, with KCl clearly producing the smallest impact and NaCl the largest. The kinetic coefficient for the former is nearly three times larger than for the latter, while the steps change from smooth to highly serrated when KCl is changed to NaCl. The results on the dependence of step speed on citrate concentration show that citrate produces a dead zone whose width increases with citrate concentration as well as a continual reduction in kinetic coefficient with increasing citrate level. We relate these results to a molecular-scale view of inhibition that invokes a combination of kink blocking and step pinning. Furthermore, we demonstrate that the classic step-pinning model of Cabrera and Vermilyea (C-V model) does an excellent job of predicting the effect of citrate on COM step kinetics provided the model is reformulated to more realistically account for impurity adsorption, include an expression for the Gibbs-Thomson effect that is correct for all supersaturations, and take into account a reduction in kinetic coefficient through kink blocking. The detailed derivation of this reformulated C-V model is presented and the underlying materials parameters that control its impact are examined. Despite the fact that the basic C-V model was proposed nearly 50 years ago and has seen extensive theoretical treatment, this study represents the first quantitative and molecular scale experimental confirmation for any crystal system.

Multiscale Informatics for Low-Temperature Propane Oxidation: Further Complexities in Studies of Complex Reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burke, Michael P.; Goldsmith, C. Franklin; Klippenstein, Stephen J.

2015-07-16

We have developed a multi-scale approach (Burke, M. P.; Klippenstein, S. J.; Harding, L. B. Proc. Combust. Inst. 2013, 34, 547–555.) to kinetic model formulation that directly incorporates elementary kinetic theories as a means to provide reliable, physics-based extrapolation to unexplored conditions. Here, we extend and generalize the multi-scale modeling strategy to treat systems of considerable complexity – involving multi-well reactions, potentially missing reactions, non-statistical product branching ratios, and non-Boltzmann (i.e. non-thermal) reactant distributions. The methodology is demonstrated here for a subsystem of low-temperature propane oxidation, as a representative system for low-temperature fuel oxidation. A multi-scale model is assembled andmore » informed by a wide variety of targets that include ab initio calculations of molecular properties, rate constant measurements of isolated reactions, and complex systems measurements. Active model parameters are chosen to accommodate both “parametric” and “structural” uncertainties. Theoretical parameters (e.g. barrier heights) are included as active model parameters to account for parametric uncertainties in the theoretical treatment; experimental parameters (e.g. initial temperatures) are included to account for parametric uncertainties in the physical models of the experiments. RMG software is used to assess potential structural uncertainties due to missing reactions. Additionally, branching ratios among product channels are included as active model parameters to account for structural uncertainties related to difficulties in modeling sequences of multiple chemically activated steps. The approach is demonstrated here for interpreting time-resolved measurements of OH, HO2, n-propyl, i-propyl, propene, oxetane, and methyloxirane from photolysis-initiated low-temperature oxidation of propane at pressures from 4 to 60 Torr and temperatures from 300 to 700 K. In particular, the multi-scale informed model provides a consistent quantitative explanation of both ab initio calculations and time-resolved species measurements. The present results show that interpretations of OH measurements are significantly more complicated than previously thought – in addition to barrier heights for key transition states considered previously, OH profiles also depend on additional theoretical parameters for R + O2 reactions, secondary reactions, QOOH + O2 reactions, and treatment of non-Boltzmann reaction sequences. Extraction of physically rigorous information from those measurements may require more sophisticated treatment of all of those model aspects, as well as additional experimental data under more conditions, to discriminate among possible interpretations and ensure model reliability. Keywords: Optimization, Uncertainty quantification, Chemical mechanism, Low-Temperature Oxidation, Non-Boltzmann« less

Application of separable parameter space techniques to multi-tracer PET compartment modeling.

PubMed

Zhang, Jeff L; Michael Morey, A; Kadrmas, Dan J

2016-02-07

Multi-tracer positron emission tomography (PET) can image two or more tracers in a single scan, characterizing multiple aspects of biological functions to provide new insights into many diseases. The technique uses dynamic imaging, resulting in time-activity curves that contain contributions from each tracer present. The process of separating and recovering separate images and/or imaging measures for each tracer requires the application of kinetic constraints, which are most commonly applied by fitting parallel compartment models for all tracers. Such multi-tracer compartment modeling presents challenging nonlinear fits in multiple dimensions. This work extends separable parameter space kinetic modeling techniques, previously developed for fitting single-tracer compartment models, to fitting multi-tracer compartment models. The multi-tracer compartment model solution equations were reformulated to maximally separate the linear and nonlinear aspects of the fitting problem, and separable least-squares techniques were applied to effectively reduce the dimensionality of the nonlinear fit. The benefits of the approach are then explored through a number of illustrative examples, including characterization of separable parameter space multi-tracer objective functions and demonstration of exhaustive search fits which guarantee the true global minimum to within arbitrary search precision. Iterative gradient-descent algorithms using Levenberg-Marquardt were also tested, demonstrating improved fitting speed and robustness as compared to corresponding fits using conventional model formulations. The proposed technique overcomes many of the challenges in fitting simultaneous multi-tracer PET compartment models.

Application of separable parameter space techniques to multi-tracer PET compartment modeling

NASA Astrophysics Data System (ADS)

Zhang, Jeff L.; Morey, A. Michael; Kadrmas, Dan J.

2016-02-01

Multi-tracer positron emission tomography (PET) can image two or more tracers in a single scan, characterizing multiple aspects of biological functions to provide new insights into many diseases. The technique uses dynamic imaging, resulting in time-activity curves that contain contributions from each tracer present. The process of separating and recovering separate images and/or imaging measures for each tracer requires the application of kinetic constraints, which are most commonly applied by fitting parallel compartment models for all tracers. Such multi-tracer compartment modeling presents challenging nonlinear fits in multiple dimensions. This work extends separable parameter space kinetic modeling techniques, previously developed for fitting single-tracer compartment models, to fitting multi-tracer compartment models. The multi-tracer compartment model solution equations were reformulated to maximally separate the linear and nonlinear aspects of the fitting problem, and separable least-squares techniques were applied to effectively reduce the dimensionality of the nonlinear fit. The benefits of the approach are then explored through a number of illustrative examples, including characterization of separable parameter space multi-tracer objective functions and demonstration of exhaustive search fits which guarantee the true global minimum to within arbitrary search precision. Iterative gradient-descent algorithms using Levenberg-Marquardt were also tested, demonstrating improved fitting speed and robustness as compared to corresponding fits using conventional model formulations. The proposed technique overcomes many of the challenges in fitting simultaneous multi-tracer PET compartment models.

Combined TGA-MS kinetic analysis of multistep processes. Thermal decomposition and ceramification of polysilazane and polysiloxane preceramic polymers.

PubMed

García-Garrido, C; Sánchez-Jiménez, P E; Pérez-Maqueda, L A; Perejón, A; Criado, José M

2016-10-26

The polymer-to-ceramic transformation kinetics of two widely employed ceramic precursors, 1,3,5,7-tetramethyl-1,3,5,7-tetravinylcyclotetrasiloxane (TTCS) and polyureamethylvinylsilazane (CERASET), have been investigated using coupled thermogravimetry and mass spectrometry (TG-MS), Raman, XRD and FTIR. The thermally induced decomposition of the pre-ceramic polymer is the critical step in the synthesis of polymer derived ceramics (PDCs) and accurate kinetic modeling is key to attaining a complete understanding of the underlying process and to attempt any behavior predictions. However, obtaining a precise kinetic description of processes of such complexity, consisting of several largely overlapping physico-chemical processes comprising the cleavage of the starting polymeric network and the release of organic moieties, is extremely difficult. Here, by using the evolved gases detected by MS as a guide it has been possible to determine the number of steps that compose the overall process, which was subsequently resolved using a semiempirical deconvolution method based on the Frasier-Suzuki function. Such a function is more appropriate that the more usual Gaussian or Lorentzian functions since it takes into account the intrinsic asymmetry of kinetic curves. Then, the kinetic parameters of each constituent step were independently determined using both model-free and model-fitting procedures, and it was found that the processes obey mostly diffusion models which can be attributed to the diffusion of the released gases through the solid matrix. The validity of the obtained kinetic parameters was tested not only by the successful reconstruction of the original experimental curves, but also by predicting the kinetic curves of the overall processes yielded by different thermal schedules and by a mixed TTCS-CERASET precursor.

HPMA-based block copolymers promote differential drug delivery kinetics for hydrophobic and amphiphilic molecules.

PubMed

Tomcin, Stephanie; Kelsch, Annette; Staff, Roland H; Landfester, Katharina; Zentel, Rudolf; Mailänder, Volker

2016-04-15

We describe a method how polymeric nanoparticles stabilized with (2-hydroxypropyl)methacrylamide (HPMA)-based block copolymers are used as drug delivery systems for a fast release of hydrophobic and a controlled release of an amphiphilic molecule. The versatile method of the miniemulsion solvent-evaporation technique was used to prepare polystyrene (PS) as well as poly-d/l-lactide (PDLLA) nanoparticles. Covalently bound or physically adsorbed fluorescent dyes labeled the particles' core and their block copolymer corona. Confocal laser scanning microscopy (CLSM) in combination with flow cytometry measurements were applied to demonstrate the burst release of a fluorescent hydrophobic drug model without the necessity of nanoparticle uptake. In addition, CLSM studies and quantitative calculations using the image processing program Volocity® show the intracellular detachment of the amphiphilic block copolymer from the particles' core after uptake. Our findings offer the possibility to combine the advantages of a fast release for hydrophobic and a controlled release for an amphiphilic molecule therefore pointing to the possibility to a 'multi-step and multi-site' targeting by one nanocarrier. We describe thoroughly how different components of a nanocarrier end up in cells. This enables different cargos of a nanocarrier having a consecutive release and delivery of distinct components. Most interestingly we demonstrate individual kinetics of distinct components of such a system: first the release of a fluorescent hydrophobic drug model at contact with the cell membrane without the necessity of nanoparticle uptake. Secondly, the intracellular detachment of the amphiphilic block copolymer from the particles' core after uptake occurs. This offers the possibility to combine the advantages of a fast release for a hydrophobic substance at the time of interaction of the nanoparticle with the cell surface and a controlled release for an amphiphilic molecule later on therefore pointing to the possibility to a 'multi-step and multisite' targeting by one nanocarrier. We therefore feel that this could be used for many cellular systems where the combined and orchestrated delivery of components is prerequisite in order to obtain the highest efficiency. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Development of a structural concept to resist impacts from multiyear ice floes, ridges, and icebergs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerwick, B.C.; Potter, R.E.; Rojansky, M.

1984-05-01

Large multi-year ice features and icebergs may have masses ranging up to 20 million tons or more and may move in the open water at speeds up to 1 knot, thus developing tremendous kinetic energy. A stepped structure concept has been developed to resist these impacts and to transfer the resultant forces and moments into the foundation thus developing a relatively high concentrated reaction force against the ice tending to spall and split it, thus causing a multi-modal failure of the ice, as well as using up kinetic energy at a relatively controlled rate. Calculated ice forces and ice failuremore » modes will be presented. The stepped structure concept is primarily applicable to production platforms in water depths of 50 to 200 meters, which are subject to impact of large ice features such as multi-year ridges, floes, and icebergs The resulting global ice loads are reduced by 50 percent or more as compared to those developed by a vertical or a steep sided structure. Overturning moments are reduced, thus reducing maxima soil bearing values. The structure itself is efficient in its use of structural materials, and is practicable for construction in prestressed reinforced concrete or steel/ concrete hybrid construction. It has acceptable draft during tow and can carry a fully outfitted deck. It is stable during all stages of installation.« less

Determination of biodegradability kinetics of RCRA compounds using respirometry for structure-activity relationships

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tabak, H.H.; Desai, S.; Govind, R.

1990-01-01

Electrolytic respirometry is attaining prominence in biodegradation studies and is becoming one of the more suitable experimental methods for measuring the biodegradability and the kinetics of biodegradation of toxic organic compounds by the sewage, sludge, and soil microbiota and for determining substrate inhibitory effects to microorganisms in wastewater treatment systems. The purpose of the study was to obtain information on biological treatability of the benzene, phenol, phthalate, ketone organics and of the Superfund CERCLA organics bearing wastes in wastewater treatment systems which will support the development of an EPA technical guidance document on the discharge of the above organics tomore » POTWs. The paper discusses the experimental design and procedural steps for the respirometric biodegradation and toxicity testing approach for individual organics or specific industrial wastes at different concentration levels in a mineral salts medium. A developed multi-level protocol is presented for determination of the biodegradability, microbial acclimation to toxic substrates and first order kinetic parameters of biodegradation for estimation of the Monod kinetic parameter of toxic organic compounds, in order to correlate the extent and rate of biodegradation with a predictive model based on chemical properties and molecular structure of these compounds. Respirometric biodegradation/inhibition and biokinetic data are provided for representative RCRA alkyl benzene and ketone organics.« less

On kinetic modelling for solar redox thermochemical H2O and CO2 splitting over NiFe2O4 for H2, CO and syngas production.

PubMed

Dimitrakis, Dimitrios A; Syrigou, Maria; Lorentzou, Souzana; Kostoglou, Margaritis; Konstandopoulos, Athanasios G

2017-10-11

This study aims at developing a kinetic model that can adequately describe solar thermochemical water and carbon dioxide splitting with nickel ferrite powder as the active redox material. The kinetic parameters of water splitting of a previous study are revised to include transition times and new kinetic parameters for carbon dioxide splitting are developed. The computational results show a satisfactory agreement with experimental data and continuous multicycle operation under varying operating conditions is simulated. Different test cases are explored in order to improve the product yield. At first a parametric analysis is conducted, investigating the appropriate duration of the oxidation and the thermal reduction step that maximizes the hydrogen yield. Subsequently, a non-isothermal oxidation step is simulated and proven as an interesting option for increasing the hydrogen production. The kinetic model is adapted to simulate the production yields in structured solar reactor components, i.e. extruded monolithic structures, as well.

On the biophysics and kinetics of toehold-mediated DNA strand displacement

PubMed Central

Srinivas, Niranjan; Ouldridge, Thomas E.; Šulc, Petr; Schaeffer, Joseph M.; Yurke, Bernard; Louis, Ard A.; Doye, Jonathan P. K.; Winfree, Erik

2013-01-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems. PMID:24019238

On the biophysics and kinetics of toehold-mediated DNA strand displacement.

PubMed

Srinivas, Niranjan; Ouldridge, Thomas E; Sulc, Petr; Schaeffer, Joseph M; Yurke, Bernard; Louis, Ard A; Doye, Jonathan P K; Winfree, Erik

2013-12-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

Ion kinetic effects on the ignition and burn of inertial confinement fusion targets: A multi-scale approach

NASA Astrophysics Data System (ADS)

Peigney, B. E.; Larroche, O.; Tikhonchuk, V.

2014-12-01

In this article, we study the hydrodynamics and burn of the thermonuclear fuel in inertial confinement fusion pellets at the ion kinetic level. The analysis is based on a two-velocity-scale Vlasov-Fokker-Planck kinetic model that is specially tailored to treat fusion products (suprathermal α-particles) in a self-consistent manner with the thermal bulk. The model assumes spherical symmetry in configuration space and axial symmetry in velocity space around the mean flow velocity. A typical hot-spot ignition design is considered. Compared with fluid simulations where a multi-group diffusion scheme is applied to model α transport, the full ion-kinetic approach reveals significant non-local effects on the transport of energetic α-particles. This has a direct impact on hydrodynamic spatial profiles during combustion: the hot spot reactivity is reduced, while the inner dense fuel layers are pre-heated by the escaping α-suprathermal particles, which are transported farther out of the hot spot. We show how the kinetic transport enhancement of fusion products leads to a significant reduction of the fusion yield.

Ion kinetic effects on the ignition and burn of inertial confinement fusion targets: A multi-scale approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peigney, B. E.; Larroche, O.; Tikhonchuk, V.

2014-12-15

In this article, we study the hydrodynamics and burn of the thermonuclear fuel in inertial confinement fusion pellets at the ion kinetic level. The analysis is based on a two-velocity-scale Vlasov-Fokker-Planck kinetic model that is specially tailored to treat fusion products (suprathermal α-particles) in a self-consistent manner with the thermal bulk. The model assumes spherical symmetry in configuration space and axial symmetry in velocity space around the mean flow velocity. A typical hot-spot ignition design is considered. Compared with fluid simulations where a multi-group diffusion scheme is applied to model α transport, the full ion-kinetic approach reveals significant non-local effectsmore » on the transport of energetic α-particles. This has a direct impact on hydrodynamic spatial profiles during combustion: the hot spot reactivity is reduced, while the inner dense fuel layers are pre-heated by the escaping α-suprathermal particles, which are transported farther out of the hot spot. We show how the kinetic transport enhancement of fusion products leads to a significant reduction of the fusion yield.« less

Adsorptive Removal of Cadmium (II) from Aqueous Solution by Multi-Carboxylic-Functionalized Silica Gel: Equilibrium, Kinetics and Thermodynamics

NASA Astrophysics Data System (ADS)

Li, Min; Meng, Xiaojing; Yuan, Jinhai; Deng, Wenwen; Liang, Xiuke

2018-01-01

In the present study, the adsorption behavior of cadmium (II) ion from aqueous solution onto multi-carboxylic-functionalized silica gel (SG-MCF) has been investigated in detail by means of batch and column experiments. Batch experiments were performed to evaluate the effects of various experimental parameters such as pH value, contact time and initial concentration on adsorption capacity of cadmium (II) ion. The kinetic data were analyzed on the basis of the pseudo-first-order kinetic and the pseudo-second-order kinetic models and consequently, the pseudo-second-order kinetic can better describe the adsorption process than the pseudo-first-order kinetic model. Equilibrium isotherms for the adsorption of cadmium (II) ion were analyzed by Freundlich and Langmuir isotherm models, the results indicate that Langmuir isotherm model was found to be credible to express the data for cadmium (II) ion from aqueous solution onto the SG-MCF. Various thermodynamics parameters of the adsorption process, including free energy of adsorption (ΔG0 ), the enthalpy of adsorption (ΔH0 ) and standard entropy changes (ΔS0 ), were calculated to predict the nature of adsorption. The positive value of the enthalpy change and the negative value of free energy change indicate that the process is endothermic and spontaneous process.

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

PubMed Central

Smallbone, Kieran; Messiha, Hanan L.; Carroll, Kathleen M.; Winder, Catherine L.; Malys, Naglis; Dunn, Warwick B.; Murabito, Ettore; Swainston, Neil; Dada, Joseph O.; Khan, Farid; Pir, Pınar; Simeonidis, Evangelos; Spasić, Irena; Wishart, Jill; Weichart, Dieter; Hayes, Neil W.; Jameson, Daniel; Broomhead, David S.; Oliver, Stephen G.; Gaskell, Simon J.; McCarthy, John E.G.; Paton, Norman W.; Westerhoff, Hans V.; Kell, Douglas B.; Mendes, Pedro

2013-01-01

We present an experimental and computational pipeline for the generation of kinetic models of metabolism, and demonstrate its application to glycolysis in Saccharomyces cerevisiae. Starting from an approximate mathematical model, we employ a “cycle of knowledge” strategy, identifying the steps with most control over flux. Kinetic parameters of the individual isoenzymes within these steps are measured experimentally under a standardised set of conditions. Experimental strategies are applied to establish a set of in vivo concentrations for isoenzymes and metabolites. The data are integrated into a mathematical model that is used to predict a new set of metabolite concentrations and reevaluate the control properties of the system. This bottom-up modelling study reveals that control over the metabolic network most directly involved in yeast glycolysis is more widely distributed than previously thought. PMID:23831062

Kinetic and isotherm modeling of Cd (II) adsorption by L-cysteine functionalized multi-walled carbon nanotubes as adsorbent.

PubMed

Taghavi, Mahmoud; Zazouli, Mohammad Ali; Yousefi, Zabihollah; Akbari-adergani, Behrouz

2015-11-01

In this study, multi-walled carbon nanotubes were functionalized by L-cysteine to show the kinetic and isotherm modeling of Cd (II) ions onto L-cysteine functionalized multi-walled carbon nanotubes. The adsorption behavior of Cd (II) ion was studied by varying parameters including dose of L-MWCNTs, contact time, and cadmium concentration. Equilibrium adsorption isotherms and kinetics were also investigated based on Cd (II) adsorption tests. The results showed that an increase in contact time and adsorbent dosage resulted in increase of the adsorption rate. The optimum condition of the Cd (II) removal process was found at pH=7.0, 15 mg/L L-MWCNTs dosage, 6 mg/L cadmium concentration, and contact time of 60 min. The removal percent was equal to 89.56 at optimum condition. Langmuir and Freundlich models were employed to analyze the experimental data. The data showed well fitting with the Langmuir model (R2=0.994) with q max of 43.47 mg/g. Analyzing the kinetic data by the pseudo-first-order and pseudo-second-order equations revealed that the adsorption of cadmium using L-MWSNTs following the pseudo-second-order kinetic model with correlation coefficients (R2) equals to 0.998, 0.992, and 0.998 for 3, 6, and 9 mg/L Cd (II) concentrations, respectively. The experimental data fitted very well with the pseudo-second-order. Overall, treatment of polluted solution to Cd (II) by adsorption process using L-MWCNT can be considered as an effective technology.

IPMP Global Fit - A one-step direct data analysis tool for predictive microbiology.

PubMed

Huang, Lihan

2017-12-04

The objective of this work is to develop and validate a unified optimization algorithm for performing one-step global regression analysis of isothermal growth and survival curves for determination of kinetic parameters in predictive microbiology. The algorithm is incorporated with user-friendly graphical interfaces (GUIs) to develop a data analysis tool, the USDA IPMP-Global Fit. The GUIs are designed to guide the users to easily navigate through the data analysis process and properly select the initial parameters for different combinations of mathematical models. The software is developed for one-step kinetic analysis to directly construct tertiary models by minimizing the global error between the experimental observations and mathematical models. The current version of the software is specifically designed for constructing tertiary models with time and temperature as the independent model parameters in the package. The software is tested with a total of 9 different combinations of primary and secondary models for growth and survival of various microorganisms. The results of data analysis show that this software provides accurate estimates of kinetic parameters. In addition, it can be used to improve the experimental design and data collection for more accurate estimation of kinetic parameters. IPMP-Global Fit can be used in combination with the regular USDA-IPMP for solving the inverse problems and developing tertiary models in predictive microbiology. Published by Elsevier B.V.

Design of a new integrated chitosan-PAMAM dendrimer biosorbent for heavy metals removing and study of its adsorption kinetics and thermodynamics.

PubMed

Zarghami, Zabihullah; Akbari, Ahmad; Latifi, Ali Mohammad; Amani, Mohammad Ali

2016-04-01

In this research, different generations of PAMAM-grafted chitosan as integrated biosorbents were successfully synthesized via step by step divergent growth approach of dendrimer. The synthesized products were utilized as adsorbents for heavy metals (Pb(2+) in this study) removing from aqueous solution and their reactive Pb(2+) removal potential was evaluated. The results showed that as-synthesized products with higher generations of dendrimer, have more adsorption capacity compared to products with lower generations of dendrimer and sole chitosan. Adsorption capacity of as-prepared product with generation 3 of dendrimer is 18times more than sole chitosan. Thermodynamic and kinetic studies were performed for understanding equilibrium data of the uptake capacity and kinetic rate uptake, respectively. Thermodynamic and kinetic studies showed that Langmuir isotherm model and pseudo second order kinetic model are more compatible for describing equilibrium data of the uptake capacity and kinetic rate of the Pb(2+) uptake, respectively. Copyright © 2016 Elsevier Ltd. All rights reserved.

Numerical investigation of spray ignition of a multi-component fuel surrogate

NASA Astrophysics Data System (ADS)

Backer, Lara; Narayanaswamy, Krithika; Pepiot, Perrine

2014-11-01

Simulating turbulent spray ignition, an important process in engine combustion, is challenging, since it combines the complexity of multi-scale, multiphase turbulent flow modeling with the need for an accurate description of chemical kinetics. In this work, we use direct numerical simulation to investigate the role of the evaporation model on the ignition characteristics of a multi-component fuel surrogate, injected as droplets in a turbulent environment. The fuel is represented as a mixture of several components, each one being representative of a different chemical class. A reduced kinetic scheme for the mixture is extracted from a well-validated detailed chemical mechanism, and integrated into the multiphase turbulent reactive flow solver NGA. Comparisons are made between a single-component evaporation model, in which the evaporating gas has the same composition as the liquid droplet, and a multi-component model, where component segregation does occur. In particular, the corresponding production of radical species, which are characteristic of the ignition of individual fuel components, is thoroughly analyzed.

Kinetic evidence for folding and unfolding intermediates in staphylococcal nuclease.

PubMed

Walkenhorst, W F; Green, S M; Roder, H

1997-05-13

The complex kinetic behavior commonly observed in protein folding studies suggests that a heterogeneous population of molecules exists in solution and that a number of discrete steps are involved in the conversion of unfolded molecules to the fully native form. A central issue in protein folding is whether any of these kinetic events represent conformational steps important for efficient folding rather than side reactions caused by slow steps such as proline isomerization or misfolding of the polypeptide chain. In order to address this question, we used stopped-flow fluorescence techniques to characterize the kinetic mechanism of folding and unfolding for a Pro- variant of SNase in which all six proline residues were replaced by glycines or alanines. Compared to the wild-type protein, which exhibits a series of proline-dependent slow folding phases, the folding kinetics of Pro- SNase were much simpler, which made quantitative kinetic analysis possible. Despite the absence of prolines or other complicating factors, the folding kinetics still contain several phases and exhibit a complex denaturant dependence. The GuHCl dependence of the major observable folding phase and a distinct lag in the appearance of the native state provide clear evidence for an early folding intermediate. The fluorescence of Trp140 in the alpha-helical domain is insensitive to the formation of this early intermediate, which is consistent with a partially folded state with a stable beta-domain and a largely disordered alpha-helical region. A second intermediate is required to model the kinetics of unfolding for the Pro- variant, which shows evidence for a denaturant-induced change in the rate-limiting unfolding step. With the inclusion of these two intermediates, we are able to completely model the major phase(s) in both folding and unfolding across a wide range of denaturant concentrations using a sequential four-state folding mechanism. In order to model the minor slow phase observed for the Pro- mutant, a six-state scheme containing a parallel pathway originating from a distinct unfolded state was required. The properties of this alternate unfolded conformation are consistent with those expected due to the presence of a non-prolyl cis peptide bond. To test the kinetic model, we used simulations based on the six-state scheme and were able to completely reproduce the folding kinetics for Pro- SNase across a range of denaturant concentrations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perry, William L; Gunderson, Jake A; Dickson, Peter M

There has been a long history of interest in the decomposition kinetics of HMX and HMX-based formulations due to the widespread use of this explosive in high performance systems. The kinetics allow us to predict, or attempt to predict, the behavior of the explosive when subjected to thermal hazard scenarios that lead to ignition via impact, spark, friction or external heat. The latter, commonly referred to as 'cook off', has been widely studied and contemporary kinetic and transport models accurately predict time and location of ignition for simple geometries. However, there has been relatively little attention given to the problemmore » of localized ignition that results from the first three ignition sources of impact, spark and friction. The use of a zero-order single-rate expression describing the exothermic decomposition of explosives dates to the early work of Frank-Kamanetskii in the late 1930s and continued through the 60's and 70's. This expression provides very general qualitative insight, but cannot provide accurate spatial or timing details of slow cook off ignition. In the 70s, Catalano, et al., noted that single step kinetics would not accurately predict time to ignition in the one-dimensional time to explosion apparatus (ODTX). In the early 80s, Tarver and McGuire published their well-known three step kinetic expression that included an endothermic decomposition step. This scheme significantly improved the accuracy of ignition time prediction for the ODTX. However, the Tarver/McGuire model could not produce the internal temperature profiles observed in the small-scale radial experiments nor could it accurately predict the location of ignition. Those factors are suspected to significantly affect the post-ignition behavior and better models were needed. Brill, et al. noted that the enthalpy change due to the beta-delta crystal phase transition was similar to the assumed endothermic decomposition step in the Tarver/McGuire model. Henson, et al., deduced the kinetics and thermodynamics of the phase transition, providing Dickson, et al. with the information necessary to develop a four-step model that included a two-step nucleation and growth mechanism for the {beta}-{delta} phase transition. Initially, an irreversible scheme was proposed. That model accurately predicted the spatial and temporal cook off behavior of the small-scale radial experiment under slow heating conditions, but did not accurately capture the endothermic phase transition at a faster heating rate. The current version of the four-step model includes reversibility and accurately describes the small-scale radial experiment over a wide range of heating rates. We have observed impact-induced friction ignition of PBX 9501 with grit embedded between the explosive and the lower anvil surface. Observation was done using an infrared camera looking through the sapphire bottom anvil. Time to ignition and temperature-time behavior were recorded. The time to ignition was approximately 500 microseconds and the temperature was approximately 1000 K. The four step reversible kinetic scheme was previously validated for slow cook off scenarios. Our intention was to test the validity for significantly faster hot-spot processes, such as the impact-induced grit friction process studied here. We found the model predicted the ignition time within experimental error. There are caveats to consider when evaluating the agreement. The primary input to the model was friction work over an area computed by a stress analysis. The work rate itself, and the relative velocity of the grit and substrate both have a strong dependence on the initial position of the grit. Any errors in the analysis or the initial grit position would affect the model results. At this time, we do not know the sensitivity to these issues. However, the good agreement does suggest the four step kinetic scheme may have universal applicability for HMX systems.« less

Optimization of propranolol HCl release kinetics from press coated sustained release tablets.

PubMed

Ali, Adel Ahmed; Ali, Ahmed Mahmoud

2013-01-01

Press-coated sustained release tablets offer a valuable, cheap and easy manufacture alternative to the highly expensive, multi-step manufacture and filling of coated beads. In this study, propranolol HCl press-coated tablets were prepared using hydroxylpropylmethylcellulose (HPMC) as tablet coating material together with carbopol 971P and compressol as release modifiers. The prepared formulations were optimized for zero-order release using artificial neural network program (INForm, Intelligensys Ltd, North Yorkshire, UK). Typical zero-order release kinetics with extended release profile for more than 12 h was obtained. The most important variables considered by the program in optimizing formulations were type and proportion of polymer mixture in the coat layer and distribution ratio of drug between core and coat. The key elements found were; incorporation of 31-38 % of the drug in the coat, fixing the amount of polymer in coat to be not less than 50 % of coat layer. Optimum zero-order release kinetics (linear regression r2 = 0.997 and Peppas model n value > 0.80) were obtained when 2.5-10 % carbopol and 25-42.5% compressol were incorporated into the 50 % HPMC coat layer.

Application of separable parameter space techniques to multi-tracer PET compartment modeling

PubMed Central

Zhang, Jeff L; Morey, A Michael; Kadrmas, Dan J

2016-01-01

Multi-tracer positron emission tomography (PET) can image two or more tracers in a single scan, characterizing multiple aspects of biological functions to provide new insights into many diseases. The technique uses dynamic imaging, resulting in time-activity curves that contain contributions from each tracer present. The process of separating and recovering separate images and/or imaging measures for each tracer requires the application of kinetic constraints, which are most commonly applied by fitting parallel compartment models for all tracers. Such multi-tracer compartment modeling presents challenging nonlinear fits in multiple dimensions. This work extends separable parameter space kinetic modeling techniques, previously developed for fitting single-tracer compartment models, to fitting multi-tracer compartment models. The multi-tracer compartment model solution equations were reformulated to maximally separate the linear and nonlinear aspects of the fitting problem, and separable least-squares techniques were applied to effectively reduce the dimensionality of the nonlinear fit. The benefits of the approach are then explored through a number of illustrative examples, including characterization of separable parameter space multi-tracer objective functions and demonstration of exhaustive search fits which guarantee the true global minimum to within arbitrary search precision. Iterative gradient-descent algorithms using Levenberg–Marquardt were also tested, demonstrating improved fitting speed and robustness as compared to corresponding fits using conventional model formulations. The proposed technique overcomes many of the challenges in fitting simultaneous multi-tracer PET compartment models. PMID:26788888

Kinetic exchange models: From molecular physics to social science

NASA Astrophysics Data System (ADS)

Patriarca, Marco; Chakraborti, Anirban

2013-08-01

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

Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies

PubMed Central

Dräger, Andreas; Kronfeld, Marcel; Ziller, Michael J; Supper, Jochen; Planatscher, Hannes; Magnus, Jørgen B; Oldiges, Marco; Kohlbacher, Oliver; Zell, Andreas

2009-01-01

Background To understand the dynamic behavior of cellular systems, mathematical modeling is often necessary and comprises three steps: (1) experimental measurement of participating molecules, (2) assignment of rate laws to each reaction, and (3) parameter calibration with respect to the measurements. In each of these steps the modeler is confronted with a plethora of alternative approaches, e. g., the selection of approximative rate laws in step two as specific equations are often unknown, or the choice of an estimation procedure with its specific settings in step three. This overall process with its numerous choices and the mutual influence between them makes it hard to single out the best modeling approach for a given problem. Results We investigate the modeling process using multiple kinetic equations together with various parameter optimization methods for a well-characterized example network, the biosynthesis of valine and leucine in C. glutamicum. For this purpose, we derive seven dynamic models based on generalized mass action, Michaelis-Menten and convenience kinetics as well as the stochastic Langevin equation. In addition, we introduce two modeling approaches for feedback inhibition to the mass action kinetics. The parameters of each model are estimated using eight optimization strategies. To determine the most promising modeling approaches together with the best optimization algorithms, we carry out a two-step benchmark: (1) coarse-grained comparison of the algorithms on all models and (2) fine-grained tuning of the best optimization algorithms and models. To analyze the space of the best parameters found for each model, we apply clustering, variance, and correlation analysis. Conclusion A mixed model based on the convenience rate law and the Michaelis-Menten equation, in which all reactions are assumed to be reversible, is the most suitable deterministic modeling approach followed by a reversible generalized mass action kinetics model. A Langevin model is advisable to take stochastic effects into account. To estimate the model parameters, three algorithms are particularly useful: For first attempts the settings-free Tribes algorithm yields valuable results. Particle swarm optimization and differential evolution provide significantly better results with appropriate settings. PMID:19144170

Applying the Brakes to Multi-Site SR Protein Phosphorylation: Substrate-Induced Effects on the Splicing Kinase SRPK1†

PubMed Central

Aubol, Brandon E.; Adams, Joseph A.

2011-01-01

To investigate how a protein kinase interacts with its protein substrate during extended, multi-site phosphorylation, the kinetic mechanism of a protein kinase involved in mRNA splicing control was investigated using rapid quench flow techniques. The protein kinase SRPK1 phosphorylates approximately 10 serines in the arginine-serine-rich domain (RS domain) of the SR protein SRSF1 in a C-to-N-terminal direction, a modification that directs this essential splicing factor from the cytoplasm to the nucleus. Transient-state kinetic experiments illustrate that the first phosphate is added rapidly onto the RS domain of SRSF1 (t1/2 = 0.1 sec) followed by slower, multi-site phosphorylation at the remaining serines (t1/2 = 15 sec). Mutagenesis experiments suggest that efficient phosphorylation rates are maintained by an extensive hydrogen bonding and electrostatic network between the RS domain of the SR protein and the active site and docking groove of the kinase. Catalytic trapping and viscosometric experiments demonstrate that while the phosphoryl transfer step is fast, ADP release limits multi-site phosphorylation. By studying phosphate incorporation into selectively pre-phosphorylated forms of the enzyme-substrate complex, the kinetic mechanism for site-specific phosphorylation along the reaction coordinate was assessed. The binding affinity of the SR protein, the phosphoryl transfer rate and ADP exchange rate were found to decline significantly as a function of progressive phosphorylation in the RS domain. These findings indicate that the protein substrate actively modulates initiation, extension and termination events associated with prolonged, multi-site phosphorylation. PMID:21728354

First-Principles Modeling of Hydrogen Storage in Metal Hydride Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

J. Karl Johnson

The objective of this project is to complement experimental efforts of MHoCE partners by using state-of-the-art theory and modeling to study the structure, thermodynamics, and kinetics of hydrogen storage materials. Specific goals include prediction of the heats of formation and other thermodynamic properties of alloys from first principles methods, identification of new alloys that can be tested experimentally, calculation of surface and energetic properties of nanoparticles, and calculation of kinetics involved with hydrogenation and dehydrogenation processes. Discovery of new metal hydrides with enhanced properties compared with existing materials is a critical need for the Metal Hydride Center of Excellence. Newmore » materials discovery can be aided by the use of first principles (ab initio) computational modeling in two ways: (1) The properties, including mechanisms, of existing materials can be better elucidated through a combined modeling/experimental approach. (2) The thermodynamic properties of novel materials that have not been made can, in many cases, be quickly screened with ab initio methods. We have used state-of-the-art computational techniques to explore millions of possible reaction conditions consisting of different element spaces, compositions, and temperatures. We have identified potentially promising single- and multi-step reactions that can be explored experimentally.« less

Kinetically governed polymorphism of d(G₄T₄G₃) quadruplexes in K+ solutions.

PubMed

Prislan, Iztok; Lah, Jurij; Milanic, Matija; Vesnaver, Gorazd

2011-03-01

It has been generally recognized that understanding the molecular basis of some important cellular processes is hampered by the lack of knowledge of forces that drive spontaneous formation/disruption of G-quadruplex structures in guanine-rich DNA sequences. According to numerous biophysical and structural studies G-quadruplexes may occur in the presence of K(+) and Na(+) ions as polymorphic structures formed in kinetically governed processes. The reported kinetic models suggested to describe this polymorphism should be considered inappropriate since, as a rule, they include bimolecular single-step associations characterized by negative activation energies. In contrast, our approach in studying polymorphic behavior of G-quadruplexes is based on model mechanisms that involve only elementary folding/unfolding transitions and structural conversion steps that are characterized by positive activation energies. Here, we are investigating a complex polymorphism of d(G(4)T(4)G(3)) quadruplexes in K(+) solutions. On the basis of DSC, circular dichroism and UV spectroscopy and polyacrylamide gel electrophoresis experiments we propose a kinetic model that successfully describes the observed thermally induced conformational transitions of d(G(4)T(4)G(3)) quadruplexes in terms of single-step reactions that involve besides single strands also one tetramolecular and three bimolecular quadruplex structures.

An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Pathway Optimization.

PubMed

Halper, Sean M; Cetnar, Daniel P; Salis, Howard M

2018-01-01

Engineering many-enzyme metabolic pathways suffers from the design curse of dimensionality. There are an astronomical number of synonymous DNA sequence choices, though relatively few will express an evolutionary robust, maximally productive pathway without metabolic bottlenecks. To solve this challenge, we have developed an integrated, automated computational-experimental pipeline that identifies a pathway's optimal DNA sequence without high-throughput screening or many cycles of design-build-test. The first step applies our Operon Calculator algorithm to design a host-specific evolutionary robust bacterial operon sequence with maximally tunable enzyme expression levels. The second step applies our RBS Library Calculator algorithm to systematically vary enzyme expression levels with the smallest-sized library. After characterizing a small number of constructed pathway variants, measurements are supplied to our Pathway Map Calculator algorithm, which then parameterizes a kinetic metabolic model that ultimately predicts the pathway's optimal enzyme expression levels and DNA sequences. Altogether, our algorithms provide the ability to efficiently map the pathway's sequence-expression-activity space and predict DNA sequences with desired metabolic fluxes. Here, we provide a step-by-step guide to applying the Pathway Optimization Pipeline on a desired multi-enzyme pathway in a bacterial host.

Description of bioremediation of soils using the model of a multistep system of microorganisms

NASA Astrophysics Data System (ADS)

Lubysheva, A. I.; Potashev, K. A.; Sofinskaya, O. A.

2018-01-01

The paper deals with the development of a mathematical model describing the interaction of a multi-step system of microorganisms in soil polluted with oil products. Each step in this system uses products of vital activity of the previous step to feed. Six different models of the multi-step system are considered. The equipping of the models with coefficients was carried out from the condition of minimizing the residual of the calculated and experimental data using an original algorithm based on the Levenberg-Marquardt method in combination with the Monte Carlo method for the initial approximation finding.

Simplification and analysis of models of calcium dynamics based on IP3-sensitive calcium channel kinetics.

PubMed

Tang, Y; Stephenson, J L; Othmer, H G

1996-01-01

We study the models for calcium (Ca) dynamics developed in earlier studies, in each of which the key component is the kinetics of intracellular inositol-1,4,5-trisphosphate-sensitive Ca channels. After rapidly equilibrating steps are eliminated, the channel kinetics in these models are represented by a single differential equation that is linear in the state of the channel. In the reduced kinetic model, the graph of the steady-state fraction of conducting channels as a function of log10(Ca) is a bell-shaped curve. Dynamically, a step increase in inositol-1,4,5-trisphosphate induces an incremental increase in the fraction of conducting channels, whereas a step increase in Ca can either potentiate or inhibit channel activation, depending on the Ca level before and after the increase. The relationships among these models are discussed, and experimental tests to distinguish between them are given. Under certain conditions the models for intracellular calcium dynamics are reduced to the singular perturbed form epsilon dx/d tau = f(x, y, p), dy/d tau = g(x, y, p). Phase-plane analysis is applied to a generic form of these simplified models to show how different types of Ca response, such as excitability, oscillations, and a sustained elevation of Ca, can arise. The generic model can also be used to study frequency encoding of hormonal stimuli, to determine the conditions for stable traveling Ca waves, and to understand the effect of channel properties on the wave speed.

Kinetic modeling of plant metabolism and its predictive power: peppermint essential oil biosynthesis as an example.

PubMed

Lange, Bernd Markus; Rios-Estepa, Rigoberto

2014-01-01

The integration of mathematical modeling with analytical experimentation in an iterative fashion is a powerful approach to advance our understanding of the architecture and regulation of metabolic networks. Ultimately, such knowledge is highly valuable to support efforts aimed at modulating flux through target pathways by molecular breeding and/or metabolic engineering. In this article we describe a kinetic mathematical model of peppermint essential oil biosynthesis, a pathway that has been studied extensively for more than two decades. Modeling assumptions and approximations are described in detail. We provide step-by-step instructions on how to run simulations of dynamic changes in pathway metabolites concentrations.

Electrodiffusion kinetics of ionic transport in a simple membrane channel.

PubMed

Valent, Ivan; Petrovič, Pavol; Neogrády, Pavel; Schreiber, Igor; Marek, Miloš

2013-11-21

We employ numerical techniques for solving time-dependent full Poisson-Nernst-Planck (PNP) equations in 2D to analyze transient behavior of a simple ion channel subject to a sudden electric potential jump across the membrane (voltage clamp). Calculated spatiotemporal profiles of the ionic concentrations and electric potential show that two principal exponential processes can be distinguished in the electrodiffusion kinetics, in agreement with original Planck's predictions. The initial fast process corresponds to the dielectric relaxation, while the steady state is approached in a second slower exponential process attributed to the nonlinear ionic redistribution. Effects of the model parameters such as the channel length, height of the potential step, boundary concentrations, permittivity of the channel interior, and ionic mobilities on electrodiffusion kinetics are studied. Numerical solutions are used to determine spatiotemporal profiles of the electric field, ionic fluxes, and both the conductive and displacement currents. We demonstrate that the displacement current is a significant transient component of the total electric current through the channel. The presented results provide additional information about the classical voltage-clamp problem and offer further physical insights into the mechanism of electrodiffusion. The used numerical approach can be readily extended to multi-ionic models with a more structured domain geometry in 2D or 3D, and it is directly applicable to other systems, such as synthetic nanopores, nanofluidic channels, and nanopipettes.

Multi-Step Time Series Forecasting with an Ensemble of Varied Length Mixture Models.

PubMed

Ouyang, Yicun; Yin, Hujun

2018-05-01

Many real-world problems require modeling and forecasting of time series, such as weather temperature, electricity demand, stock prices and foreign exchange (FX) rates. Often, the tasks involve predicting over a long-term period, e.g. several weeks or months. Most existing time series models are inheritably for one-step prediction, that is, predicting one time point ahead. Multi-step or long-term prediction is difficult and challenging due to the lack of information and uncertainty or error accumulation. The main existing approaches, iterative and independent, either use one-step model recursively or treat the multi-step task as an independent model. They generally perform poorly in practical applications. In this paper, as an extension of the self-organizing mixture autoregressive (AR) model, the varied length mixture (VLM) models are proposed to model and forecast time series over multi-steps. The key idea is to preserve the dependencies between the time points within the prediction horizon. Training data are segmented to various lengths corresponding to various forecasting horizons, and the VLM models are trained in a self-organizing fashion on these segments to capture these dependencies in its component AR models of various predicting horizons. The VLM models form a probabilistic mixture of these varied length models. A combination of short and long VLM models and an ensemble of them are proposed to further enhance the prediction performance. The effectiveness of the proposed methods and their marked improvements over the existing methods are demonstrated through a number of experiments on synthetic data, real-world FX rates and weather temperatures.

Kinetics and mechanism of olefin catalytic hydroalumination by organoaluminum compounds

NASA Astrophysics Data System (ADS)

Koledina, K. F.; Gubaidullin, I. M.

2016-05-01

The complex reaction mechanism of α-olefin catalytic hydroalumination by alkylalanes is investigated via mathematical modeling that involves plotting the kinetic models for the individual reactions that make up a complex system and a separate study of their principles. Kinetic parameters of olefin catalytic hydroalumination are estimated. Activation energies of the possible steps of the schemes of complex reaction mechanisms are compared and possible reaction pathways are determined.

A kinetic study of struvite precipitation recycling technology with NaOH/Mg(OH)2 addition.

PubMed

Yu, Rongtai; Ren, Hongqiang; Wang, Yanru; Ding, Lili; Geng, Jingji; Xu, Ke; Zhang, Yan

2013-09-01

Struvite precipitation recycling technology is received wide attention in removal ammonium and phosphate out of wastewater. While past study focused on process efficiency, and less on kinetics. The kinetic study is essential for the design and optimization in the application of struvite precipitation recycling technology. The kinetics of struvite with NaOH/Mg(OH)2 addition were studied by thermogravimetry analysis with three rates (5, 10, 20 °C/min), using Friedman method and Ozawa-Flynn-Wall method, respectively. Degradation process of struvite with NaOH/Mg(OH)2 addition was three steps. The stripping of ammonia from struvite was mainly occurred at the first step. In the first step, the activation energy was about 70 kJ/mol, which has gradually declined as the reaction progress. By model fitting studies, the proper mechanism function for struvite decomposition process with NaOH/Mg(OH)2 addition was revealed. The mechanism function was f(α)=α(α)-(1-α)(n), a Prout-Tompkins nth order (Bna) model. Copyright © 2013 Elsevier Ltd. All rights reserved.

Step Permeability on the Pt(111) Surface

NASA Astrophysics Data System (ADS)

Altman, Michael

2005-03-01

Surface morphology will be affected, or even dictated, by kinetic limitations that may be present during growth. Asymmetric step attachment is recognized to be an important and possibly common cause of morphological growth instabilities. However, the impact of this kinetic limitation on growth morphology may be hindered by other factors such as the rate limiting step and step permeability. This strongly motivates experimental measurements of these quantities in real systems. Using low energy electron microscopy, we have measured step flow velocities in growth on the Pt(111) surface. The dependence of step velocity upon adjacent terrace width clearly shows evidence of asymmetric step attachment and step permeability. Step velocity is modeled by solving the diffusion equation simultaneously on several adjacent terraces subject to boundary conditions at intervening steps that include asymmetric step attachment and step permeability. This analysis allows a quantitative evaluation of step permeability and the kinetic length, which characterizes the rate limiting step continuously between diffusion and attachment-detachment limited regimes. This work provides information that is greatly needed to set physical bounds on the parameters that are used in theoretical treatments of growth. The observation that steps are permeable even on a simple metal surface should also stimulate more experimental measurements and theoretical treatments of this effect.

Center for Extended Magnetohydrodynamics Modeling - Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parker, Scott

This project funding supported approximately 74 percent of a Ph.D. graduate student, not including costs of travel and supplies. We had a highly successful research project including the development of a second-order implicit electromagnetic kinetic ion hybrid model [Cheng 2013, Sturdevant 2016], direct comparisons with the extended MHD NIMROD code and kinetic simulation [Schnack 2013], modeling of slab tearing modes using the fully kinetic ion hybrid model and finally, modeling global tearing modes in cylindrical geometry using gyrokinetic simulation [Chen 2015, Chen 2016]. We developed an electromagnetic second-order implicit kinetic ion fluid electron hybrid model [Cheng 2013]. As a firstmore » step, we assumed isothermal electrons, but have included drift-kinetic electrons in similar models [Chen 2011]. We used this simulation to study the nonlinear evolution of the tearing mode in slab geometry, including nonlinear evolution and saturation [Cheng 2013]. Later, we compared this model directly to extended MHD calculations using the NIMROD code [Schnack 2013]. In this study, we investigated the ion-temperature-gradient instability with an extended MHD code for the first time and got reasonable agreement with the kinetic calculation in terms of linear frequency, growth rate and mode structure. We then extended this model to include orbit averaging and sub-cycling of the ions and compared directly to gyrokinetic theory [Sturdevant 2016]. This work was highlighted in an Invited Talk at the International Conference on the Numerical Simulation of Plasmas in 2015. The orbit averaging sub-cycling multi-scale algorithm is amenable to hybrid architectures with GPUS or math co-processors. Additionally, our participation in the Center for Extend Magnetohydrodynamics motivated our research on developing the capability for gyrokinetic simulation to model a global tearing mode. We did this in cylindrical geometry where the results could be benchmarked with existing eigenmode calculations. First, we developed a gyrokinetic code capable of simulating long wavelengths using a fluid electron model [Chen 2015]. We benchmarked this code with an eigenmode calculation. Besides having to rewrite the field solver due to the breakdown in the gyrokinetic ordering for long wavelengths, very high radial resolution was required. We developed a technique where we used the solution from the eigenmode solver to specify radial boundary conditions allowing for a very high radial resolution of the inner solution. Using this technique enabled us to use our direct algorithm with gyrokinetic ions and drift kinetic electrons [Chen 2016]. This work was highlighted in an Invited Talk at the American Physical Society - Division of Plasma Physics in 2015.« less

Numerical study of the direct pressure effect of acoustic waves in planar premixed flames

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmidt, H.; Jimenez, C.

Recently the unsteady response of 1-D premixed flames to acoustic pressure waves for the range of frequencies below and above the inverse of the flame transit time was investigated experimentally using OH chemiluminescence Wangher (2008). They compared the frequency dependence of the measured response to the prediction of an analytical model proposed by Clavin et al. (1990), derived from the standard flame model (one-step Arrhenius kinetics) and to a similar model proposed by McIntosh (1991). Discrepancies between the experimental results and the model led to the conclusion that the standard model does not provide an adequate description of the unsteadymore » response of real flames and that it is necessary to investigate more realistic chemical models. Here we follow exactly this suggestion and perform numerical studies of the response of lean methane flames using different reaction mechanisms. We find that the global flame response obtained with both detailed chemistry (GRI3.0) and a reduced multi-step model by Peters (1996) lies slightly above the predictions of the analytical model, but is close to experimental results. We additionally used an irreversible one-step Arrhenius reaction model and show the effect of the pressure dependence of the global reaction rate in the flame response. Our results suggest first that the current models have to be extended to capture the amplitude and phase results of the detailed mechanisms, and second that the correlation between the heat release and the measured OH* chemiluminescence should be studied deeper. (author)« less

Rejoining and misrejoining of radiation-induced chromatin breaks. II. Biophysical Model

NASA Technical Reports Server (NTRS)

Wu, H.; Durante, M.; George, K.; Goodwin, E. H.; Yang, T. C.

1996-01-01

A biophysical model for the kinetics of the formation of radiation-induced chromosome aberrations is developed to account for the recent experimental results obtained with a combination of the premature chromosome condensation (PCC) and fluorescence in situ hybridization (FISH) techniques. In this model, we consider the broken ends of DNA double-strand breaks (DSBs) to be reactant and make use of the interaction distance hypothesis. The repair/misrepair process between broken ends is suggested to consist of two steps; the first step represents the two break ends approaching each other, and the second step represents the enzymatic processes leading to DNA end-to-end rejoining. Only the second step is reflected in the kinetics observed in experiments using PCC. The model appears to be able to fit existing data for human cells. It is shown that the kinetics of the formation of chromosome aberrations can be explained by a single rate that characterizes both rejoining and misrejoining of DSBs, suggesting that repair and misrepair share the same mechanism. Fast repair (completed in minutes) in a subset of DSBs is suggested as an explanation of the complete exchanges observed with PCC in human lymphocytes immediately after irradiation. The fast repair component seems to be absent in human fibroblasts.

Mechanistic Kinetic Modeling of Thiol-Michael Addition Photopolymerizations via Photocaged "Superbase" Generators: An Analytical Approach.

PubMed

Claudino, Mauro; Zhang, Xinpeng; Alim, Marvin D; Podgórski, Maciej; Bowman, Christopher N

2016-11-08

A kinetic mechanism and the accompanying mathematical framework are presented for base-mediated thiol-Michael photopolymerization kinetics involving a photobase generator. Here, model kinetic predictions demonstrate excellent agreement with a representative experimental system composed of 2-(2-nitrophenyl)propyloxycarbonyl-1,1,3,3-tetramethylguanidine (NPPOC-TMG) as a photobase generator that is used to initiate thiol-vinyl sulfone Michael addition reactions and polymerizations. Modeling equations derived from a basic mechanistic scheme indicate overall polymerization rates that follow a pseudo-first-order kinetic process in the base and coreactant concentrations, controlled by the ratio of the propagation to chain-transfer kinetic parameters ( k p / k CT ) which is dictated by the rate-limiting step and controls the time necessary to reach gelation. Gelation occurs earlier as the k p / k CT ratio reaches a critical value, wherefrom gel times become nearly independent of k p / k CT . The theoretical approach allowed determining the effect of induction time on the reaction kinetics due to initial acid-base neutralization for the photogenerated base caused by the presence of protic contaminants. Such inhibition kinetics may be challenging for reaction systems that require high curing rates but are relevant for chemical systems that need to remain kinetically dormant until activated although at the ultimate cost of lower polymerization rates. The pure step-growth character of this living polymerization and the exhibited kinetics provide unique potential for extended dark-cure reactions and uniform material properties. The general kinetic model is applicable to photobase initiators where photolysis follows a unimolecular cleavage process releasing a strong base catalyst without cogeneration of intermediate radical species.

One-dimensional model of interacting-step fluctuations on vicinal surfaces: Analytical formulas and kinetic Monte-Carlo simulations

NASA Astrophysics Data System (ADS)

Patrone, Paul; Einstein, T. L.; Margetis, Dionisios

2011-03-01

We study a 1+1D, stochastic, Burton-Cabrera-Frank (BCF) model of interacting steps fluctuating on a vicinal crystal. The step energy accounts for entropic and nearest-neighbor elastic-dipole interactions. Our goal is to formulate and validate a self-consistent mean-field (MF) formalism to approximately solve the system of coupled, nonlinear stochastic differential equations (SDEs) governing fluctuations in surface motion. We derive formulas for the time-dependent terrace width distribution (TWD) and its steady-state limit. By comparison with kinetic Monte-Carlo simulations, we show that our MF formalism improves upon models in which step interactions are linearized. We also indicate how fitting parameters of our steady state MF TWD may be used to determine the mass transport regime and step interaction energy of certain experimental systems. PP and TLE supported by NSF MRSEC under Grant DMR 05-20471 at U. of Maryland; DM supported by NSF under Grant DMS 08-47587.

Kinetic analysis of non-isothermal solid-state reactions: multi-stage modeling without assumptions in the reaction mechanism.

PubMed

Pomerantsev, Alexey L; Kutsenova, Alla V; Rodionova, Oxana Ye

2017-02-01

A novel non-linear regression method for modeling non-isothermal thermogravimetric data is proposed. Experiments for several heating rates are analyzed simultaneously. The method is applicable to complex multi-stage processes when the number of stages is unknown. Prior knowledge of the type of kinetics is not required. The main idea is a consequent estimation of parameters when the overall model is successively changed from one level of modeling to another. At the first level, the Avrami-Erofeev functions are used. At the second level, the Sestak-Berggren functions are employed with the goal to broaden the overall model. The method is tested using both simulated and real-world data. A comparison of the proposed method with a recently published 'model-free' deconvolution method is presented.

Study on formation of step bunching on 6H-SiC (0001) surface by kinetic Monte Carlo method

NASA Astrophysics Data System (ADS)

Li, Yuan; Chen, Xuejiang; Su, Juan

2016-05-01

The formation and evolution of step bunching during step-flow growth of 6H-SiC (0001) surfaces were studied by three-dimensional kinetic Monte Carlo (KMC) method and compared with the analytic model based on the theory of Burton-Cabera-Frank (BCF). In the KMC model the crystal lattice was represented by a structured mesh which fixed the position of atoms and interatomic bonding. The events considered in the model were adatoms adsorption and diffusion on the terrace, and adatoms attachment, detachment and interlayer transport at the step edges. In addition, effects of Ehrlich-Schwoebel (ES) barriers at downward step edges and incorporation barriers at upwards step edges were also considered. In order to obtain more elaborate information for the behavior of atoms in the crystal surface, silicon and carbon atoms were treated as the minimal diffusing species. KMC simulation results showed that multiple-height steps were formed on the vicinal surface oriented toward [ 1 1 bar 00 ] or [ 11 2 bar 0 ] directions. And then the formation mechanism of the step bunching was analyzed. Finally, to further analyze the formation processes of step bunching, a one-dimensional BCF analytic model with ES and incorporation barriers was used, and then it was solved numerically. In the BCF model, the periodic boundary conditions (PBC) were applied, and the parameters were corresponded to those used in the KMC model. The evolution character of step bunching was consistent with the results obtained by KMC simulation.

Engineering multi-stage nanovectors for controlled degradation and tunable release kinetics

PubMed Central

Martinez, Jonathan O.; Chiappini, Ciro; Ziemys, Arturas; Faust, Ari M.; Kojic, Milos; Liu, Xuewu; Ferrari, Mauro; Tasciotti, Ennio

2013-01-01

Nanovectors hold substantial promise in abating the off-target effects of therapeutics by providing a means to selectively accumulate payloads at the target lesion, resulting in an increase in the therapeutic index. A sophisticated understanding of the factors that govern the degradation and release dynamics of these nanovectors is imperative to achieve these ambitious goals. In this work, we elucidate the relationship that exists between variations in pore size and the impact on the degradation, loading, and release of multistage nanovectors. Larger pored vectors displayed faster degradation and higher loading of nanoparticles, while exhibiting the slowest release rate. The degradation of these particles was characterized to occur in a multi-step progression where they initially decreased in size leaving the porous core isolated, while the pores gradually increased in size. Empirical loading and release studies of nanoparticles along with diffusion modeling revealed that this prolonged release was modulated by the penetration within the porous core of the vectors regulated by their pore size. PMID:23911070

ATOMIC-SCALE DESIGN OF IRON FISCHER-TROPSCH CATALYSTS: A COMBINED COMPUTATIONAL CHEMISTRY, EXPERIMENTAL, AND MICROKINETIC MODELING APPROACH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manos Mavrikakis; James A. Dumesic; Amit A. Gokhale

2005-03-22

Efforts during this first year focused on four areas: (1) searching/summarizing published FTS mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) construction of mass spectrometer-TPD and Berty CSTR reactor systems; (3) preparation and characterization of unsupported iron and alumina-supported iron catalysts at various iron loadings (4) Determination of thermochemical parameters such as binding energies of reactive intermediates, heat of FTS elementary reaction steps, and kinetic parameters such as activation energies, and frequency factors of FTS elementary reaction steps on a number of model surfaces. Literature describing mechanistic and kinetic studies of Fischer-Tropsch synthesis on iron catalysts wasmore » compiled in a draft review. Construction of the mass spectrometer-TPD system is 90% complete and of a Berty CSTR reactor system 98% complete. Three unsupported iron catalysts and three alumina-supported iron catalysts were prepared by nonaqueous-evaporative deposition (NED) or aqueous impregnation (AI) and characterized by chemisorption, BET, extent-of-reduction, XRD, and TEM methods. These catalysts, covering a wide range of dispersions and metal loadings, are well-reduced and relatively thermally stable up to 500-600 C in H{sub 2}, thus ideal for kinetic and mechanistic studies. The alumina-supported iron catalysts will be used for kinetic and mechanistic studies. In the coming year, adsorption/desorption properties, rates of elementary steps, and global reaction rates will be measured for these catalysts, with and without promoters, providing a database for understanding effects of dispersion, metal loading, and support on elementary kinetic parameters and for validation of computational models that incorporate effects of surface structure and promoters. Furthermore, using state-of-the-art self-consistent Density Functional Theory (DFT) methods, we have extensively studied the thermochemistry and kinetics of various elementary steps on three different model surfaces: (1) Fe(110), (2) Fe(110) modified by subsurface C, and (3) Fe surface modified with Pt adatoms. These studies have yielded valuable insights into the reactivity of Fe surfaces for FTS, and provided accurate estimates for the effect of Fe modifiers such as subsurface C and surface Pt.« less

Foot structure is significantly associated to subtalar joint kinetics and mechanical energetics.

PubMed

Maharaj, Jayishni N; Cresswell, Andrew G; Lichtwark, Glen A

2017-10-01

Foot structure has been implicated as a risk factor of numerous overuse injuries, however, the mechanism linking foot structure and the development of soft-tissue overuse injuries are not well understood. The aim of this study was to identify factors that could predict foot function during walking. A total of eleven variables (including measures of foot structure, anthropometry and spatiotemporal gait characteristics) were investigated for their predictive ability on identifying kinematic, kinetic and energetic components of the foot. Three-dimensional motion capture and force data were collected at preferred walking speed on an instrumented treadmill. Mechanical measures were subsequently assessed using a custom multi-segment foot model in Opensim. Factors with significant univariate associations were entered into multiple linear regression models to identify a group of factors independently associated with the mechanical measures. Although no model could be created for any of the kinematic measures analysed, approximately 46% and 37% of the variance in the kinetic and energetic measures were associated with three or two factors respectively. Arch-height ratio, foot length and step width were associated with peak subtalar joint (STJ) moment, while greater STJ negative work was correlated to a low arch-height ratio and greater foot mobility. The models presented in this study suggest that the soft-tissue structures of a flat-arched, mobile foot are at a greater risk of injury as they have greater requirements to absorb energy and generate larger forces. However, as these associations are only moderate, other measures may also have an influence. Copyright © 2017. Published by Elsevier B.V.

A gas-kinetic BGK scheme for the compressible Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Xu, Kun

2000-01-01

This paper presents an improved gas-kinetic scheme based on the Bhatnagar-Gross-Krook (BGK) model for the compressible Navier-Stokes equations. The current method extends the previous gas-kinetic Navier-Stokes solver developed by Xu and Prendergast by implementing a general nonequilibrium state to represent the gas distribution function at the beginning of each time step. As a result, the requirement in the previous scheme, such as the particle collision time being less than the time step for the validity of the BGK Navier-Stokes solution, is removed. Therefore, the applicable regime of the current method is much enlarged and the Navier-Stokes solution can be obtained accurately regardless of the ratio between the collision time and the time step. The gas-kinetic Navier-Stokes solver developed by Chou and Baganoff is the limiting case of the current method, and it is valid only under such a limiting condition. Also, in this paper, the appropriate implementation of boundary condition for the kinetic scheme, different kinetic limiting cases, and the Prandtl number fix are presented. The connection among artificial dissipative central schemes, Godunov-type schemes, and the gas-kinetic BGK method is discussed. Many numerical tests are included to validate the current method.

Adsorptive removal of dissolved organic matter (DOM) in landfill leachate by iron oxide nanoparticles (FeONPs)

NASA Astrophysics Data System (ADS)

Ghani, Zaidi Ab; Yusoff, Mohd Suffian; Zaman, Nastaein Qamaruz; Andas, Jeyashelly; Aziz, Hamidi Abdul

2017-10-01

A study was conducted to investigate the efficiency of iron oxide nanoparticle (FeONPs) adsorption for removing of DOM in landfill leachate. FeONPs was directly prepared via sodium borohydride (KBH4) reduction method. Adsorption kinetics, isotherm and thermodynamic studies were developed to design the model for DOM removal. Pseudo first-order and pseudo second-order model have been studied to fit the experimental data. The regression results showed that the adsorption kinetics were more accurately represented by a pseudo second-order model. The Weber-Morris intraparticle diffusion model was used to analyze the adsorption kinetics data. The plot of qt versus t1/2 represents multi linearity, which showed that the adsorption processes occurred in more than one step. Adsorption isotherms were analyzed by Langmuir, Freundlich, Tempkin and Dubinin-Radushkevich, isotherms model. Equilibrium data were well fitted to the Dubinin- Radushkevich isotherm model. Maximum monolayer adsorption based on Langmuir was calculated to be 21.74 mg/g. Thermodynamic parameters such as free energy changes (ΔG°), enthalpy (ΔH°) and entropy (ΔS°) were evaluated between temperatures of 25 °C and 40 °C. The ΔG° was noticed progressively decrease from -9.620 -9.820 -10.021, and -10.222 kJ/mol as the temperature increase. The ΔH° and ΔS° values were found to be 2.350 kJ/mol and 40.165 J/mol.K respectively. The results showed that the overall adsorption process was endothermic and spontaneous. The results from this study suggested that FeNPs could be a viable adsorbent in managing higher DOM problems associated with landfill leachate.

C. botulinum inactivation kinetics implemented in a computational model of a high-pressure sterilization process.

PubMed

Juliano, Pablo; Knoerzer, Kai; Fryer, Peter J; Versteeg, Cornelis

2009-01-01

High-pressure, high-temperature (HPHT) processing is effective for microbial spore inactivation using mild preheating, followed by rapid volumetric compression heating and cooling on pressure release, enabling much shorter processing times than conventional thermal processing for many food products. A computational thermal fluid dynamic (CTFD) model has been developed to model all processing steps, including the vertical pressure vessel, an internal polymeric carrier, and food packages in an axis-symmetric geometry. Heat transfer and fluid dynamic equations were coupled to four selected kinetic models for the inactivation of C. botulinum; the traditional first-order kinetic model, the Weibull model, an nth-order model, and a combined discrete log-linear nth-order model. The models were solved to compare the resulting microbial inactivation distributions. The initial temperature of the system was set to 90 degrees C and pressure was selected at 600 MPa, holding for 220 s, with a target temperature of 121 degrees C. A representation of the extent of microbial inactivation throughout all processing steps was obtained for each microbial model. Comparison of the models showed that the conventional thermal processing kinetics (not accounting for pressure) required shorter holding times to achieve a 12D reduction of C. botulinum spores than the other models. The temperature distribution inside the vessel resulted in a more uniform inactivation distribution when using a Weibull or an nth-order kinetics model than when using log-linear kinetics. The CTFD platform could illustrate the inactivation extent and uniformity provided by the microbial models. The platform is expected to be useful to evaluate models fitted into new C. botulinum inactivation data at varying conditions of pressure and temperature, as an aid for regulatory filing of the technology as well as in process and equipment design.

Continuous Video Modeling to Assist with Completion of Multi-Step Home Living Tasks by Young Adults with Moderate Intellectual Disability

ERIC Educational Resources Information Center

Mechling, Linda C.; Ayres, Kevin M.; Bryant, Kathryn J.; Foster, Ashley L.

2014-01-01

The current study evaluated a relatively new video-based procedure, continuous video modeling (CVM), to teach multi-step cleaning tasks to high school students with moderate intellectual disability. CVM in contrast to video modeling and video prompting allows repetition of the video model (looping) as many times as needed while the user completes…

Impact of user influence on information multi-step communication in a micro-blog

NASA Astrophysics Data System (ADS)

Wu, Yue; Hu, Yong; He, Xiao-Hai; Deng, Ken

2014-06-01

User influence is generally considered as one of the most critical factors that affect information cascading spreading. Based on this common assumption, this paper proposes a theoretical model to examine user influence on the information multi-step communication in a micro-blog. The multi-steps of information communication are divided into first-step and non-first-step, and user influence is classified into five dimensions. Actual data from the Sina micro-blog is collected to construct the model by means of an approach based on structural equations that uses the Partial Least Squares (PLS) technique. Our experimental results indicate that the dimensions of the number of fans and their authority significantly impact the information of first-step communication. Leader rank has a positive impact on both first-step and non-first-step communication. Moreover, global centrality and weight of friends are positively related to the information non-first-step communication, but authority is found to have much less relation to it.

Stretched-to-compressed-exponential crossover observed in the electrical degradation kinetics of some spinel-metallic screen-printed structures

NASA Astrophysics Data System (ADS)

Balitska, V.; Shpotyuk, O.; Brunner, M.; Hadzaman, I.

2018-02-01

Thermally-induced (170 °C) degradation-relaxation kinetics is examined in screen-printed structures composed of spinel Cu0.1Ni0.1Co1.6Mn1.2O4 ceramics with conductive Ag or Ag-Pd layered electrodes. Structural inhomogeneities due to Ag and Ag-Pd diffusants in spinel phase environment play a decisive role in non-exponential kinetics of negative relative resistance drift. If Ag migration in spinel is inhibited by Pd addition due to Ag-Pd alloy, the kinetics attains stretched exponential behavior with ∼0.58 exponent, typical for one-stage diffusion in structurally-dispersive media. Under deep Ag penetration into spinel ceramics, as for thick films with Ag-layered electrodes, the degradation kinetics drastically changes, attaining features of two-step diffusing process governed by compressed-exponential dependence with power index of ∼1.68. Crossover from stretched- to compressed-exponential kinetics in spinel-metallic structures is mapped on free energy landscape of non-barrier multi-well system under strong perturbation from equilibrium, showing transition with a character downhill scenario resulting in faster than exponential decaying.

Reduced and Validated Kinetic Mechanisms for Hydrogen-CO-sir Combustion in Gas Turbines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yiguang Ju; Frederick Dryer

2009-02-07

Rigorous experimental, theoretical, and numerical investigation of various issues relevant to the development of reduced, validated kinetic mechanisms for synthetic gas combustion in gas turbines was carried out - including the construction of new radiation models for combusting flows, improvement of flame speed measurement techniques, measurements and chemical kinetic analysis of H{sub 2}/CO/CO{sub 2}/O{sub 2}/diluent mixtures, revision of the H{sub 2}/O{sub 2} kinetic model to improve flame speed prediction capabilities, and development of a multi-time scale algorithm to improve computational efficiency in reacting flow simulations.

Direct dynamic kinetic analysis and computer simulation of growth of Clostridium perfringens in cooked turkey during cooling

USDA-ARS?s Scientific Manuscript database

This research applied a new one-step methodology to directly construct a tertiary model for describing the growth of C. perfringens in cooked turkey meat under dynamically cooling conditions. The kinetic parameters of the growth models were determined by numerical analysis and optimization using mu...

Study of Adsorption Mechanism of Congo Red on Graphene Oxide/PAMAM Nanocomposite

PubMed Central

Rafi, Mohammad; Samiey, Babak; Cheng, Chil-Hung

2018-01-01

Graphene oxide/poly(amidoamine) (GO/PAMAM) nanocomposite adsorbed high quantities of congo red (CR) anionic dye in 0.1 M NaCl solution, with the maximum adsorption capacity of 198 mg·g−1. The kinetics and thermodynamics of adsorption were investigated to elucidate the effects of pH, temperature, shaking rate, ionic strength, and contact time. Kinetic data were analyzed by the KASRA model and the KASRA, ISO, and pore-diffusion equations. Adsorption adsorption isotherms were studied by the ARIAN model and the Henry, Langmuir, and Temkin equations. It was shown that adsorption sites of GO/PAMAM at experimental conditions were phenolic hydroxyl groups of GO sheets and terminal amine groups of PAMAM dendrimer. Analysis of kinetic data indicated that amine sites were located on the surface, and that hydroxyl sites were placed in the pores of adsorbent. CR molecules interacted with the adsorption sites via hydrogen bonds. The molecules were adsorbed firstly on the amine sites, and then on the internal hydroxyl sites. Adsorption kinetic parameters indicated that the interaction of CR to the –NH3+ sites was the rate-controlling step of adsorption of CR on this site and adsorption activation energies calculated for different parts of this step. On the other hand, kinetic parameters showed that the intraparticle diffusion was the rate-controlling step during the interaction of CR molecules to –OH sites and activation energy of this step was not calculable. Finally, the used GO/PAMAM was completely regenerated by using ethylenediamine. PMID:29587463

FUEL-FLEXIBLE GASIFICATION-COMBUSTION TECHNOLOGY FOR PRODUCTION OF H2 AND SEQUESTRATION-READY CO2

DOE Office of Scientific and Technical Information (OSTI.GOV)

George Rizeq; Janice West; Arnaldo Frydman

Further development of a combustion Large Eddy Simulation (LES) code for the design of advanced gaseous combustion systems is described in this sixth quarterly report. CFD Research Corporation (CFDRC) is developing the LES module within the parallel, unstructured solver included in the commercial CFD-ACE+ software. In this quarter, in-situ adaptive tabulation (ISAT) for efficient chemical rate storage and retrieval was implemented and tested within the Linear Eddy Model (LEM). ISAT type 3 is being tested so that extrapolation can be performed and further improve the retrieval rate. Further testing of the LEM for subgrid chemistry was performed for parallel applicationsmore » and for multi-step chemistry. Validation of the software on backstep and bluff-body reacting cases were performed. Initial calculations of the SimVal experiment at Georgia Tech using their LES code were performed. Georgia Tech continues the effort to parameterize the LEM over composition space so that a neural net can be used efficiently in the combustion LES code. A new and improved Artificial Neural Network (ANN), with log-transformed output, for the 1-step chemistry was implemented in CFDRC's LES code and gave reasonable results. This quarter, the 2nd consortium meeting was held at CFDRC. Next quarter, LES software development and testing will continue. Alpha testing of the code will continue to be performed on cases of interest to the industrial consortium. Optimization of subgrid models will be pursued, particularly with the ISAT approach. Also next quarter, the demonstration of the neural net approach, for multi-step chemical kinetics speed-up in CFD-ACE+, will be accomplished.« less

Long-term Kinetics of Uranyl Desorption from Sediments Under Advective Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shang, Jianying; Liu, Chongxuan; Wang, Zheming

2014-02-15

Long-term (> 4 months) column experiments were performed to investigate the kinetics of uranyl (U(VI)) desorption in sediments collected from the Integrated Field Research Challenge (IFRC) site at the US Department of Energy (DOE) Hanford 300 Area. The experimental results were used to evaluate alternative multi-rate surface complexation reaction (SCR) approaches to describe the short- and long-term kinetics of U(VI) desorption under flow conditions. The SCR stoichiometry, equilibrium constants, and multi-rate parameters were independently characterized in batch and stirred flow-cell reactors. Multi-rate SCR models that were either additively constructed using the SCRs for individual size fractions (e.g., Shang et al.,more » 2011), or composite in nature could effectively describe short-term U(VI) desorption under flow conditions. The long-term desorption results, however, revealed that using a labile U concentration measured by carbonate extraction under-estimated desorbable U(VI) and the long-term rate of U(VI) desorption. An alternative modeling approach using total U as the desorbable U(VI) concentration was proposed to overcome this difficulty. This study also found that the gravel size fraction (2-8 mm), which is typically treated as non-reactive in modeling U(VI) reactive transport because of low external surface area, can have an important effect on the U(VI) desorption in the sediment. This study demonstrates an approach to effectively extrapolate U(VI) desorption kinetics for field-scale application, and identifies important parameters and uncertainties affecting model predictions.« less

Agent-based modeling of porous scaffold degradation and vascularization: Optimal scaffold design based on architecture and degradation dynamics.

PubMed

Mehdizadeh, Hamidreza; Bayrak, Elif S; Lu, Chenlin; Somo, Sami I; Akar, Banu; Brey, Eric M; Cinar, Ali

2015-11-01

A multi-layer agent-based model (ABM) of biomaterial scaffold vascularization is extended to consider the effects of scaffold degradation kinetics on blood vessel formation. A degradation model describing the bulk disintegration of porous hydrogels is incorporated into the ABM. The combined degradation-angiogenesis model is used to investigate growing blood vessel networks in the presence of a degradable scaffold structure. Simulation results indicate that higher porosity, larger mean pore size, and rapid degradation allow faster vascularization when not considering the structural support of the scaffold. However, premature loss of structural support results in failure for the material. A strategy using multi-layer scaffold with different degradation rates in each layer was investigated as a way to address this issue. Vascularization was improved with the multi-layered scaffold model compared to the single-layer model. The ABM developed provides insight into the characteristics that influence the selection of optimal geometric parameters and degradation behavior of scaffolds, and enables easy refinement of the model as new knowledge about the underlying biological phenomena becomes available. This paper proposes a multi-layer agent-based model (ABM) of biomaterial scaffold vascularization integrated with a structural-kinetic model describing bulk degradation of porous hydrogels to consider the effects of scaffold degradation kinetics on blood vessel formation. This enables the assessment of scaffold characteristics and in particular the disintegration characteristics of the scaffold on angiogenesis. Simulation results indicate that higher porosity, larger mean pore size, and rapid degradation allow faster vascularization when not considering the structural support of the scaffold. However, premature loss of structural support by scaffold disintegration results in failure of the material and disruption of angiogenesis. A strategy using multi-layer scaffold with different degradation rates in each layer was investigated as away to address this issue. Vascularization was improved with the multi-layered scaffold model compared to the single-layer model. The ABM developed provides insight into the characteristics that influence the selection of optimal geometric and degradation characteristics of tissue engineering scaffolds. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Computational model, method, and system for kinetically-tailoring multi-drug chemotherapy for individuals

DOEpatents

Gardner, Shea Nicole

2007-10-23

A method and system for tailoring treatment regimens to individual patients with diseased cells exhibiting evolution of resistance to such treatments. A mathematical model is provided which models rates of population change of proliferating and quiescent diseased cells using cell kinetics and evolution of resistance of the diseased cells, and pharmacokinetic and pharmacodynamic models. Cell kinetic parameters are obtained from an individual patient and applied to the mathematical model to solve for a plurality of treatment regimens, each having a quantitative efficacy value associated therewith. A treatment regimen may then be selected from the plurlaity of treatment options based on the efficacy value.

Kinetic treatment of nonlinear ion-acoustic waves in multi-ion plasma

NASA Astrophysics Data System (ADS)

Ahmad, Zulfiqar; Ahmad, Mushtaq; Qamar, A.

2017-09-01

By applying the kinetic theory of the Valsove-Poisson model and the reductive perturbation technique, a Korteweg-de Vries (KdV) equation is derived for small but finite amplitude ion acoustic waves in multi-ion plasma composed of positive and negative ions along with the fraction of electrons. A correspondent equation is also derived from the basic set of fluid equations of adiabatic ions and isothermal electrons. Both kinetic and fluid KdV equations are stationary solved with different nature of coefficients. Their differences are discussed both analytically and numerically. The criteria of the fluid approach as a limiting case of kinetic theory are also discussed. The presence of negative ion makes some modification in the solitary structure that has also been discussed with its implication at the laboratory level.

Nonlinear Analyte Concentration Gradients for One-Step Kinetic Analysis Employing Optical Microring Resonators

PubMed Central

Marty, Michael T.; Kuhnline Sloan, Courtney D.; Bailey, Ryan C.; Sligar, Stephen G.

2012-01-01

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics. PMID:22686186

Nonlinear analyte concentration gradients for one-step kinetic analysis employing optical microring resonators.

PubMed

Marty, Michael T; Sloan, Courtney D Kuhnline; Bailey, Ryan C; Sligar, Stephen G

2012-07-03

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes, and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics.

Virus Neutralisation: New Insights from Kinetic Neutralisation Curves

PubMed Central

Magnus, Carsten

2013-01-01

Antibodies binding to the surface of virions can lead to virus neutralisation. Different theories have been proposed to determine the number of antibodies that must bind to a virion for neutralisation. Early models are based on chemical binding kinetics. Applying these models lead to very low estimates of the number of antibodies needed for neutralisation. In contrast, according to the more conceptual approach of stoichiometries in virology a much higher number of antibodies is required for virus neutralisation by antibodies. Here, we combine chemical binding kinetics with (virological) stoichiometries to better explain virus neutralisation by antibody binding. This framework is in agreement with published data on the neutralisation of the human immunodeficiency virus. Knowing antibody reaction constants, our model allows us to estimate stoichiometrical parameters from kinetic neutralisation curves. In addition, we can identify important parameters that will make further analysis of kinetic neutralisation curves more valuable in the context of estimating stoichiometries. Our model gives a more subtle explanation of kinetic neutralisation curves in terms of single-hit and multi-hit kinetics. PMID:23468602

Involvement of α-, γ- and δ-Tocopherol Isomers from
Pumpkin (Cucurbita pepo L.) Seed Oil or Oil Mixtures in
the Biphasic DPPH˙ Disappearance Kinetics

PubMed Central

Broznić, Dalibor; Milin, Čedomila

2016-01-01

Summary The antioxidant activity of three types of pumpkin seed oil or oil mixtures (cold- -pressed, produced from roasted seed paste and salad) produced in the northern part of Croatia and the kinetics of their behaviour as free radical scavengers were investigated using DPPH˙. In addition, the involvement of oil tocopherol isomers (α-, γ- and δ-) in different steps of DPPH˙ disappearance and their impact on the rate of reaction were analysed. The kinetics of DPPH˙ disappearance is a two-step process. In the first step, rapid disappearance of DPPH˙ occurs during the first 11 min of the reaction, depending on the oil type, followed by a slower decline in the second step. To describe DPPH˙ disappearance kinetics, six mathematical models (mono- and biphasic) were tested. Our findings showed that γ- and δ-tocopherols affected DPPH˙ disappearance during the first step, and α-tocopherol in the second step of the reaction. Moreover, α-tocopherol demonstrated 30 times higher antioxidant activity than γ- and δ-tocopherols. The results indicated the biphasic double-exponential behaviour of DPPH˙ disappearance in oil samples, due to the complexity of reactions that involve different tocopherol isomers and proceed through different chemical pathways. PMID:27904410

Involvement of α-, γ- and δ-Tocopherol Isomers from
Pumpkin (Cucurbita pepo L.) Seed Oil or Oil Mixtures in
the Biphasic DPPH˙ Disappearance Kinetics.

PubMed

Broznić, Dalibor; Jurešić, Gordana Čanadi; Milin, Čedomila

2016-06-01

The antioxidant activity of three types of pumpkin seed oil or oil mixtures (cold- -pressed, produced from roasted seed paste and salad) produced in the northern part of Croatia and the kinetics of their behaviour as free radical scavengers were investigated using DPPH˙. In addition, the involvement of oil tocopherol isomers (α-, γ- and δ-) in different steps of DPPH˙ disappearance and their impact on the rate of reaction were analysed. The kinetics of DPPH˙ disappearance is a two-step process. In the first step, rapid disappearance of DPPH˙ occurs during the first 11 min of the reaction, depending on the oil type, followed by a slower decline in the second step. To describe DPPH˙ disappearance kinetics, six mathematical models (mono- and biphasic) were tested. Our findings showed that γ- and δ-tocopherols affected DPPH˙ disappearance during the first step, and α-tocopherol in the second step of the reaction. Moreover, α-tocopherol demonstrated 30 times higher antioxidant activity than γ- and δ-tocopherols. The results indicated the biphasic double-exponential behaviour of DPPH˙ disappearance in oil samples, due to the complexity of reactions that involve different tocopherol isomers and proceed through different chemical pathways.

The tRNA-modifying function of MnmE is controlled by post-hydrolysis steps of its GTPase cycle

PubMed Central

Prado, Silvia; Villarroya, Magda; Medina, Milagros; Armengod, M.-Eugenia

2013-01-01

MnmE is a homodimeric multi-domain GTPase involved in tRNA modification. This protein differs from Ras-like GTPases in its low affinity for guanine nucleotides and mechanism of activation, which occurs by a cis, nucleotide- and potassium-dependent dimerization of its G-domains. Moreover, MnmE requires GTP hydrolysis to be functionally active. However, how GTP hydrolysis drives tRNA modification and how the MnmE GTPase cycle is regulated remains unresolved. Here, the kinetics of the MnmE GTPase cycle was studied under single-turnover conditions using stopped- and quench-flow techniques. We found that the G-domain dissociation is the rate-limiting step of the overall reaction. Mutational analysis and fast kinetics assays revealed that GTP hydrolysis, G-domain dissociation and Pi release can be uncoupled and that G-domain dissociation is directly responsible for the ‘ON’ state of MnmE. Thus, MnmE provides a new paradigm of how the ON/OFF cycling of GTPases may regulate a cellular process. We also demonstrate that the MnmE GTPase cycle is negatively controlled by the reaction products GDP and Pi. This feedback mechanism may prevent inefficacious GTP hydrolysis in vivo. We propose a biological model whereby a conformational change triggered by tRNA binding is required to remove product inhibition and initiate a new GTPase/tRNA-modification cycle. PMID:23630314

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

Work being carried out at LLNL has concentrated on studies of the role of chemical kinetics in a variety of problems related to hydrogen combustion in practical combustion systems, with an emphasis on vehicle propulsion. Use of hydrogen offers significant advantages over fossil fuels, and computer modeling provides advantages when used in concert with experimental studies. Many numerical {open_quotes}experiments{close_quotes} can be carried out quickly and efficiently, reducing the cost and time of system development, and many new and speculative concepts can be screened to identify those with sufficient promise to pursue experimentally. This project uses chemical kinetic and fluid dynamicmore » computational modeling to examine the combustion characteristics of systems burning hydrogen, either as the only fuel or mixed with natural gas. Oxidation kinetics are combined with pollutant formation kinetics, including formation of oxides of nitrogen but also including air toxics in natural gas combustion. We have refined many of the elementary kinetic reaction steps in the detailed reaction mechanism for hydrogen oxidation. To extend the model to pressures characteristic of internal combustion engines, it was necessary to apply theoretical pressure falloff formalisms for several key steps in the reaction mechanism. We have continued development of simplified reaction mechanisms for hydrogen oxidation, we have implemented those mechanisms into multidimensional computational fluid dynamics models, and we have used models of chemistry and fluid dynamics to address selected application problems. At the present time, we are using computed high pressure flame, and auto-ignition data to further refine the simplified kinetics models that are then to be used in multidimensional fluid mechanics models. Detailed kinetics studies have investigated hydrogen flames and ignition of hydrogen behind shock waves, intended to refine the detailed reactions mechanisms.« less

A multi-dimensional high-order DG-ALE method based on gas-kinetic theory with application to oscillating bodies

NASA Astrophysics Data System (ADS)

Ren, Xiaodong; Xu, Kun; Shyy, Wei

2016-07-01

This paper presents a multi-dimensional high-order discontinuous Galerkin (DG) method in an arbitrary Lagrangian-Eulerian (ALE) formulation to simulate flows over variable domains with moving and deforming meshes. It is an extension of the gas-kinetic DG method proposed by the authors for static domains (X. Ren et al., 2015 [22]). A moving mesh gas kinetic DG method is proposed for both inviscid and viscous flow computations. A flux integration method across a translating and deforming cell interface has been constructed. Differently from the previous ALE-type gas kinetic method with piecewise constant mesh velocity at each cell interface within each time step, the mesh velocity variation inside a cell and the mesh moving and rotating at a cell interface have been accounted for in the finite element framework. As a result, the current scheme is applicable for any kind of mesh movement, such as translation, rotation, and deformation. The accuracy and robustness of the scheme have been improved significantly in the oscillating airfoil calculations. All computations are conducted in a physical domain rather than in a reference domain, and the basis functions move with the grid movement. Therefore, the numerical scheme can preserve the uniform flow automatically, and satisfy the geometric conservation law (GCL). The numerical accuracy can be maintained even for a largely moving and deforming mesh. Several test cases are presented to demonstrate the performance of the gas-kinetic DG-ALE method.

Impact of multi-resolution analysis of artificial intelligence models inputs on multi-step ahead river flow forecasting

NASA Astrophysics Data System (ADS)

Badrzadeh, Honey; Sarukkalige, Ranjan; Jayawardena, A. W.

2013-12-01

Discrete wavelet transform was applied to decomposed ANN and ANFIS inputs.Novel approach of WNF with subtractive clustering applied for flow forecasting.Forecasting was performed in 1-5 step ahead, using multi-variate inputs.Forecasting accuracy of peak values and longer lead-time significantly improved.

Effects of Step Length, Age, and Fall History on Hip and Knee Kinetics and Knee Co-contraction during the Maximum Step Length Test

PubMed Central

Schulz, Brian W.; Jongprasithporn, Manutchanok; Hart-Hughes, Stephanie J.; Bulat, Tatjana

2017-01-01

Background Maximum step length is a brief clinical test involving stepping out and back as far as possible with the arms folded across the chest. This test has been shown to predict fall risk, but the biomechanics of this test are not fully understood. Knee and hip kinetics (moments and powers) are greater for longer steps and for younger subjects, but younger subjects also step farther. Methods To separate effects of step length, age, and fall history on joint kinetics; 14 healthy younger, 14 older non-fallers, and 11 older fallers (27(5), 72(5), 75(6) years respectively) all stepped to the same relative target distances of 20-80% of their height. Knee and hip kinetics and knee co-contraction were calculated. Findings Hip and knee kinetics and knee co-contraction all increased with step length, but older non-fallers and fallers utilized greater stepping hip and less stepping knee extensor kinetics. Fallers had greater stepping knee co-contraction than non-fallers. Stance knee co-contraction of non-fallers was similar to young for shorter steps and similar to fallers for longer steps. Interpretation Age had minimal effects and fall history had no effects on joint kinetics of steps to similar distances. Effects of age and fall history on knee co-contraction may contribute to age-related kinetic differences and shorter maximal step lengths of older non-fallers and fallers, but step length correlated with every variable tested. Thus, declines in maximum step length could indicate declines in hip and knee extensor kinetics and impaired performance on similar tasks like recovering from a trip. PMID:23978310

Implicit gas-kinetic unified algorithm based on multi-block docking grid for multi-body reentry flows covering all flow regimes

NASA Astrophysics Data System (ADS)

Peng, Ao-Ping; Li, Zhi-Hui; Wu, Jun-Lin; Jiang, Xin-Yu

2016-12-01

Based on the previous researches of the Gas-Kinetic Unified Algorithm (GKUA) for flows from highly rarefied free-molecule transition to continuum, a new implicit scheme of cell-centered finite volume method is presented for directly solving the unified Boltzmann model equation covering various flow regimes. In view of the difficulty in generating the single-block grid system with high quality for complex irregular bodies, a multi-block docking grid generation method is designed on the basis of data transmission between blocks, and the data structure is constructed for processing arbitrary connection relations between blocks with high efficiency and reliability. As a result, the gas-kinetic unified algorithm with the implicit scheme and multi-block docking grid has been firstly established and used to solve the reentry flow problems around the multi-bodies covering all flow regimes with the whole range of Knudsen numbers from 10 to 3.7E-6. The implicit and explicit schemes are applied to computing and analyzing the supersonic flows in near-continuum and continuum regimes around a circular cylinder with careful comparison each other. It is shown that the present algorithm and modelling possess much higher computational efficiency and faster converging properties. The flow problems including two and three side-by-side cylinders are simulated from highly rarefied to near-continuum flow regimes, and the present computed results are found in good agreement with the related DSMC simulation and theoretical analysis solutions, which verify the good accuracy and reliability of the present method. It is observed that the spacing of the multi-body is smaller, the cylindrical throat obstruction is greater with the flow field of single-body asymmetrical more obviously and the normal force coefficient bigger. While in the near-continuum transitional flow regime of near-space flying surroundings, the spacing of the multi-body increases to six times of the diameter of the single-body, the interference effects of the multi-bodies tend to be negligible. The computing practice has confirmed that it is feasible for the present method to compute the aerodynamics and reveal flow mechanism around complex multi-body vehicles covering all flow regimes from the gas-kinetic point of view of solving the unified Boltzmann model velocity distribution function equation.

Persistent Step-Flow Growth of Strained Films on Vicinal Substrates

NASA Astrophysics Data System (ADS)

Hong, Wei; Lee, Ho Nyung; Yoon, Mina; Christen, Hans M.; Lowndes, Douglas H.; Suo, Zhigang; Zhang, Zhenyu

2005-08-01

We propose a model of persistent step flow, emphasizing dominant kinetic processes and strain effects. Within this model, we construct a morphological phase diagram, delineating a regime of step flow from regimes of step bunching and island formation. In particular, we predict the existence of concurrent step bunching and island formation, a new growth mode that competes with step flow for phase space, and show that the deposition flux and temperature must be chosen within a window in order to achieve persistent step flow. The model rationalizes the diverse growth modes observed in pulsed laser deposition of SrRuO3 on SrTiO3.

Thermal denaturation of β-glucosidase B from Paenibacillus polymyxa proceeds through a Lumry-Eyring mechanism.

PubMed

Camarillo-Cadena, Menandro; Garza-Ramos, Georgina; Peimbert, Mariana; Pérez-Hernández, Gerardo; Zubillaga, Rafael A

2011-06-01

β-glucosidase B (BglB), 1,4-β-D: -glucanohydrolase, is an enzyme with various technological applications for which some thermostable mutants have been obtained. Because BglB denatures irreversibly with heating, the stabilities of these mutants are assessed kinetically. It, therefore, becomes relevant to determine whether the measured rate constants reflect one or several elementary kinetic steps. We have analyzed the kinetics of heat denaturation of BglB from Paenibacillus polymyxa under various conditions by following the loss of secondary structure and enzymatic activity. The denaturation is accompanied by aggregation and an initial reversible step at low temperatures. At T ≥ T ( m ), the process follows a two-state irreversible mechanism for which the kinetics does not depend on the enzyme concentration. This behavior can be explained by a Lumry-Eyring model in which the difference between the rates of the irreversible and the renaturation steps increases with temperature. Accordingly, at high scan rates (≥1 °C min(-1)) or temperatures (T ≥ T ( m )), the measurable activation energy involves only the elementary step of denaturation.

Molecular salt effects in the gas phase: tuning the kinetic basicity of [HCCLiCl]⁻ and [HCCMgCl₂]⁻ by LiCl and MgCl₂.

PubMed

Khairallah, George N; da Silva, Gabriel; O'Hair, Richard A J

2014-10-06

A combination of gas-phase ion-molecule reaction experiments and theoretical kinetic modeling is used to examine how a salt can influence the kinetic basicity of organometallates reacting with water. [HC≡CLiCl](-) reacts with water more rapidly than [HC≡CMgCl2](-), consistent with the higher reactivity of organolithium versus organomagnesium reagents. Addition of LiCl to [HC≡CLiCl](-) or [HC≡CMgCl2](-) enhances their reactivity towards water by a factor of about 2, while addition of MgCl2 to [HC≡CMgCl2](-) enhances its reactivity by a factor of about 4. Ab initio calculations coupled with master equation/RRKM theory kinetic modeling show that these reactions proceed via a mechanism involving formation of a water adduct followed by rearrangement, proton transfer, and acetylene elimination as either discrete or concerted steps. Both the energy and entropy requirements for these elementary steps need to be considered in order to explain the observed kinetics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multi-target QSPR modeling for simultaneous prediction of multiple gas-phase kinetic rate constants of diverse chemicals

NASA Astrophysics Data System (ADS)

Basant, Nikita; Gupta, Shikha

2018-03-01

The reactions of molecular ozone (O3), hydroxyl (•OH) and nitrate (NO3) radicals are among the major pathways of removal of volatile organic compounds (VOCs) in the atmospheric environment. The gas-phase kinetic rate constants (kO3, kOH, kNO3) are thus, important in assessing the ultimate fate and exposure risk of atmospheric VOCs. Experimental data for rate constants are not available for many emerging VOCs and the computational methods reported so far address a single target modeling only. In this study, we have developed a multi-target (mt) QSPR model for simultaneous prediction of multiple kinetic rate constants (kO3, kOH, kNO3) of diverse organic chemicals considering an experimental data set of VOCs for which values of all the three rate constants are available. The mt-QSPR model identified and used five descriptors related to the molecular size, degree of saturation and electron density in a molecule, which were mechanistically interpretable. These descriptors successfully predicted three rate constants simultaneously. The model yielded high correlations (R2 = 0.874-0.924) between the experimental and simultaneously predicted endpoint rate constant (kO3, kOH, kNO3) values in test arrays for all the three systems. The model also passed all the stringent statistical validation tests for external predictivity. The proposed multi-target QSPR model can be successfully used for predicting reactivity of new VOCs simultaneously for their exposure risk assessment.

Adsorption kinetic and desorption studies of Cd2+ on Multi-Carboxylic-Functionalized Silica Gel

NASA Astrophysics Data System (ADS)

Li, Min; Wei, Jian; Meng, Xiaojing; Wu, Zhuqiang; Liang, Xiuke

2018-01-01

In the present study, the adsorption behavior of cadmium (II) ion from aqueous solution onto multi-carboxylic-functionalized silica gel (SG-MCF) has been investigated in detail by means of batch and column experiments. Batch experiments were performed to evaluate the effects of contact time on adsorption capacity of cadmium (II) ion. The kinetic data were analyzed on the basis of the pseudo-first-order kinetic and the pseudo-second-order kinetic models and consequently, the pseudo-second-order kinetic can better describe the adsorption process than the pseudo-first-order kinetic model. And the adsorption mechanism of the process was studied by intra-particle and film diffusion, it was found out that the adsorption rate was governed primarily by film diffusion to the adsorption onto the SG-MCF. In addition, column experiments were conducted to assess the effects initial inlet concentration and the flow rate on breakthrough time and adsorption capacity ascertaining the practical applicability of the adsorbent. The results suggest that the total amount of adsorbed cadmium (II) ion increased with declined flow rate and increased the inlet concentration. The adsorption-desorption experiment confirmed that adsorption capacity of cadmium (II) ion didn’t present an obvious decrease after five cycles.

Adsorption kinetic and desorption studies of Cu2+ on Multi-Carboxylic-Functionalized Silica Gel

NASA Astrophysics Data System (ADS)

Li, Min; Meng, Xiaojing; Liu, Yushuang; Hu, Xinju; Liang, Xiuke

2018-01-01

In the present study, the adsorption behavior of copper (II) ion from aqueous solution onto multi-carboxylic-functionalized silica gel (SG-MCF) has been investigated in detail by means of batch and column experiments. Batch experiments were performed to evaluate the effects of contact time on adsorption capacity of copper (II) ion. The kinetic data were analyzed on the basis of the pseudo-first-order kinetic and the pseudo-second-order kinetic models and consequently, the pseudo-second-order kinetic can better describe the adsorption process than the pseudo-first-order kinetic model. And the adsorption mechanism of the process was studied by intra-particle and film diffusion, it was found out that the adsorption rate was governed primarily by film diffusion to the adsorption onto the SG-MCF. In addition, column experiments were conducted to assess the effects initial inlet concentration and the flow rate on breakthrough time and adsorption capacity ascertaining the practical applicability of the adsorbent. The results suggest that the total amount of adsorbed copper (II) ion increased with declined flow rate and increased the inlet concentration. The adsorption-desorption experiment confirmed that adsorption capacity of copper (II) ion didn’t present an obvious decrease after five cycles.

Anomalous diffusion with linear reaction dynamics: from continuous time random walks to fractional reaction-diffusion equations.

PubMed

Henry, B I; Langlands, T A M; Wearne, S L

2006-09-01

We have revisited the problem of anomalously diffusing species, modeled at the mesoscopic level using continuous time random walks, to include linear reaction dynamics. If a constant proportion of walkers are added or removed instantaneously at the start of each step then the long time asymptotic limit yields a fractional reaction-diffusion equation with a fractional order temporal derivative operating on both the standard diffusion term and a linear reaction kinetics term. If the walkers are added or removed at a constant per capita rate during the waiting time between steps then the long time asymptotic limit has a standard linear reaction kinetics term but a fractional order temporal derivative operating on a nonstandard diffusion term. Results from the above two models are compared with a phenomenological model with standard linear reaction kinetics and a fractional order temporal derivative operating on a standard diffusion term. We have also developed further extensions of the CTRW model to include more general reaction dynamics.

Integration of topological modification within the modeling of multi-physics systems: Application to a Pogo-stick

NASA Astrophysics Data System (ADS)

Abdeljabbar Kharrat, Nourhene; Plateaux, Régis; Miladi Chaabane, Mariem; Choley, Jean-Yves; Karra, Chafik; Haddar, Mohamed

2018-05-01

The present work tackles the modeling of multi-physics systems applying a topological approach while proceeding with a new methodology using a topological modification to the structure of systems. Then the comparison with the Magos' methodology is made. Their common ground is the use of connectivity within systems. The comparison and analysis of the different types of modeling show the importance of the topological methodology through the integration of the topological modification to the topological structure of a multi-physics system. In order to validate this methodology, the case of Pogo-stick is studied. The first step consists in generating a topological graph of the system. Then the connectivity step takes into account the contact with the ground. During the last step of this research; the MGS language (Modeling of General System) is used to model the system through equations. Finally, the results are compared to those obtained by MODELICA. Therefore, this proposed methodology may be generalized to model multi-physics systems that can be considered as a set of local elements.

Load and Pi control flux through the branched kinetic cycle of myosin V.

PubMed

Kad, Neil M; Trybus, Kathleen M; Warshaw, David M

2008-06-20

Myosin V is a processive actin-based motor protein that takes multiple 36-nm steps to deliver intracellular cargo to its destination. In the laser trap, applied load slows myosin V heavy meromyosin stepping and increases the probability of backsteps. In the presence of 40 mm phosphate (P(i)), both forward and backward steps become less load-dependent. From these data, we infer that P(i) release commits myosin V to undergo a highly load-dependent transition from a state in which ADP is bound to both heads and its lead head trapped in a pre-powerstroke conformation. Increasing the residence time in this state by applying load increases the probability of backstepping or detachment. The kinetics of detachment indicate that myosin V can detach from actin at two distinct points in the cycle, one of which is turned off by the presence of P(i). We propose a branched kinetic model to explain these data. Our model includes P(i) release prior to the most load-dependent step in the cycle, implying that P(i) release and load both act as checkpoints that control the flux through two parallel pathways.

Kinetically Defined Mechanisms and Positions of Action of Two New Modulators of Glucocorticoid Receptor-regulated Gene Induction*

PubMed Central

Pradhan, Madhumita A.; Blackford, John A.; Devaiah, Ballachanda N.; Thompson, Petria S.; Chow, Carson C.; Singer, Dinah S.; Simons, S. Stoney

2016-01-01

Most of the steps in, and many of the factors contributing to, glucocorticoid receptor (GR)-regulated gene induction are currently unknown. A competition assay, based on a validated chemical kinetic model of steroid hormone action, is now used to identify two new factors (BRD4 and negative elongation factor (NELF)-E) and to define their sites and mechanisms of action. BRD4 is a kinase involved in numerous initial steps of gene induction. Consistent with its complicated biochemistry, BRD4 is shown to alter both the maximal activity (Amax) and the steroid concentration required for half-maximal induction (EC50) of GR-mediated gene expression by acting at a minimum of three different kinetically defined steps. The action at two of these steps is dependent on BRD4 concentration, whereas the third step requires the association of BRD4 with P-TEFb. BRD4 is also found to bind to NELF-E, a component of the NELF complex. Unexpectedly, NELF-E modifies GR induction in a manner that is independent of the NELF complex. Several of the kinetically defined steps of BRD4 in this study are proposed to be related to its known biochemical actions. However, novel actions of BRD4 and of NELF-E in GR-controlled gene induction have been uncovered. The model-based competition assay is also unique in being able to order, for the first time, the sites of action of the various reaction components: GR < Cdk9 < BRD4 ≤ induced gene < NELF-E. This ability to order factor actions will assist efforts to reduce the side effects of steroid treatments. PMID:26504077

Evaluation and optimisation of phenomenological multi-step soot model for spray combustion under diesel engine-like operating conditions

NASA Astrophysics Data System (ADS)

Pang, Kar Mun; Jangi, Mehdi; Bai, Xue-Song; Schramm, Jesper

2015-05-01

In this work, a two-dimensional computational fluid dynamics study is reported of an n-heptane combustion event and the associated soot formation process in a constant volume combustion chamber. The key interest here is to evaluate the sensitivity of the chemical kinetics and submodels of a semi-empirical soot model in predicting the associated events. Numerical computation is performed using an open-source code and a chemistry coordinate mapping approach is used to expedite the calculation. A library consisting of various phenomenological multi-step soot models is constructed and integrated with the spray combustion solver. Prior to the soot modelling, combustion simulations are carried out. Numerical results show that the ignition delay times and lift-off lengths exhibit good agreement with the experimental measurements across a wide range of operating conditions, apart from those in the cases with ambient temperature lower than 850 K. The variation of the soot precursor production with respect to the change of ambient oxygen levels qualitatively agrees with that of the conceptual models when the skeletal n-heptane mechanism is integrated with a reduced pyrene chemistry. Subsequently, a comprehensive sensitivity analysis is carried out to appraise the existing soot formation and oxidation submodels. It is revealed that the soot formation is captured when the surface growth rate is calculated using a square root function of the soot specific surface area and when a pressure-dependent model constant is considered. An optimised soot model is then proposed based on the knowledge gained through this exercise. With the implementation of optimised model, the simulated soot onset and transport phenomena before reaching quasi-steady state agree reasonably well with the experimental observation. Also, variation of spatial soot distribution and soot mass produced at oxygen molar fractions ranging from 10.0 to 21.0% for both low and high density conditions are reproduced.

Kinetic modelling of a diesel-polluted clayey soil bioremediation process.

PubMed

Fernández, Engracia Lacasa; Merlo, Elena Moliterni; Mayor, Lourdes Rodríguez; Camacho, José Villaseñor

2016-07-01

A mathematical model is proposed to describe a diesel-polluted clayey soil bioremediation process. The reaction system under study was considered a completely mixed closed batch reactor, which initially contacted a soil matrix polluted with diesel hydrocarbons, an aqueous liquid-specific culture medium and a microbial inoculation. The model coupled the mass transfer phenomena and the distribution of hydrocarbons among four phases (solid, S; water, A; non-aqueous liquid, NAPL; and air, V) with Monod kinetics. In the first step, the model simulating abiotic conditions was used to estimate only the mass transfer coefficients. In the second step, the model including both mass transfer and biodegradation phenomena was used to estimate the biological kinetic and stoichiometric parameters. In both situations, the model predictions were validated with experimental data that corresponded to previous research by the same authors. A correct fit between the model predictions and the experimental data was observed because the modelling curves captured the major trends for the diesel distribution in each phase. The model parameters were compared to different previously reported values found in the literature. Pearson correlation coefficients were used to show the reproducibility level of the model. Copyright © 2016. Published by Elsevier B.V.

Mathematical Methods for Studying DNA and Protein Interactions

NASA Astrophysics Data System (ADS)

LeGresley, Sarah

Deoxyribnucleic Acid (DNA) damage can lead to health related issues such as developmental disorders, aging, and cancer. It has been estimated that damage rates may be as high as 100,000 per cell per day. Because of the devastating effects that DNA damage can have, DNA repair mechanisms are of great interest yet are not completely understood. To gain a better understanding of possible DNA repair mechanisms, my dissertation focused on mathematical methods for understanding the interactions between DNA and proteins. I developed a damaged DNA model to estimate the probabilities of damaged DNA being located at specific positions. Experiments were then performed that suggested that the damaged DNA may be repositioned. These experimental results were consistent with the model's prediction that damaged DNA has preferred locations. To study how proteins might be moving along the DNA, I studied the use of the uniform motion "n-step" model. The n-step model has been used to determine the kinetics parameters (e.g. rates at which a protein moves along the DNA, how much energy is required to move a protein along a specified amount of DNA, etc.) of proteins moving along the DNA. Monte Carlo methods were used to simulate proteins moving with different types of non-uniform motion (e.g. backward, jumping, etc.) along the DNA. Estimates for the kinetics parameters in the n-step model were found by fitting of the Monte Carlo simulation data. Analysis indicated that non-uniform motion of the protein may lead to over or underestimation of the kinetic parameters of this n-step model.

Nonlinear Response of Layer Growth Dynamics in the Mixed Kinetics-Bulk-Transport Regime

NASA Technical Reports Server (NTRS)

Vekilov, Peter G.; Alexander, J. Iwan D.; Rosenberger, Franz

1996-01-01

In situ high-resolution interferometry on horizontal facets of the protein lysozyme reveal that the local growth rate R, vicinal slope p, and tangential (step) velocity v fluctuate by up to 80% of their average values. The time scale of these fluctuations, which occur under steady bulk transport conditions through the formation and decay of step bunches (macrosteps), is of the order of 10 min. The fluctuation amplitude of R increases with growth rate (supersaturation) and crystal size, while the amplitude of the v and p fluctuations changes relatively little. Based on a stability analysis for equidistant step trains in the mixed transport-interface-kinetics regime, we argue that the fluctuations originate from the coupling of bulk transport with nonlinear interface kinetics. Furthermore, step bunches moving across the interface in the direction of or opposite to the buoyancy-driven convective flow increase or decrease in height, respectively. This is in agreement with analytical treatments of the interaction of moving steps with solution flow. Major excursions in growth rate are associated with the formation of lattice defects (striations). We show that, in general, the system-dependent kinetic Peclet number, Pe(sub k) , i.e., the relative weight of bulk transport and interface kinetics in the control of the growth process, governs the step bunching dynamics. Since Pe(sub k) can be modified by either forced solution flow or suppression of buoyancy-driven convection under reduced gravity, this model provides a rationale for the choice of specific transport conditions to minimize the formation of compositional inhomogeneities under steady bulk nutrient crystallization conditions.

GPU-accelerated computational tool for studying the effectiveness of asteroid disruption techniques

NASA Astrophysics Data System (ADS)

Zimmerman, Ben J.; Wie, Bong

2016-10-01

This paper presents the development of a new Graphics Processing Unit (GPU) accelerated computational tool for asteroid disruption techniques. Numerical simulations are completed using the high-order spectral difference (SD) method. Due to the compact nature of the SD method, it is well suited for implementation with the GPU architecture, hence solutions are generated at orders of magnitude faster than the Central Processing Unit (CPU) counterpart. A multiphase model integrated with the SD method is introduced, and several asteroid disruption simulations are conducted, including kinetic-energy impactors, multi-kinetic energy impactor systems, and nuclear options. Results illustrate the benefits of using multi-kinetic energy impactor systems when compared to a single impactor system. In addition, the effectiveness of nuclear options is observed.

One-dimensional model of interacting-step fluctuations on vicinal surfaces: Analytical formulas and kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Patrone, Paul N.; Einstein, T. L.; Margetis, Dionisios

2010-12-01

We study analytically and numerically a one-dimensional model of interacting line defects (steps) fluctuating on a vicinal crystal. Our goal is to formulate and validate analytical techniques for approximately solving systems of coupled nonlinear stochastic differential equations (SDEs) governing fluctuations in surface motion. In our analytical approach, the starting point is the Burton-Cabrera-Frank (BCF) model by which step motion is driven by diffusion of adsorbed atoms on terraces and atom attachment-detachment at steps. The step energy accounts for entropic and nearest-neighbor elastic-dipole interactions. By including Gaussian white noise to the equations of motion for terrace widths, we formulate large systems of SDEs under different choices of diffusion coefficients for the noise. We simplify this description via (i) perturbation theory and linearization of the step interactions and, alternatively, (ii) a mean-field (MF) approximation whereby widths of adjacent terraces are replaced by a self-consistent field but nonlinearities in step interactions are retained. We derive simplified formulas for the time-dependent terrace-width distribution (TWD) and its steady-state limit. Our MF analytical predictions for the TWD compare favorably with kinetic Monte Carlo simulations under the addition of a suitably conservative white noise in the BCF equations.

Multi-step prediction for influenza outbreak by an adjusted long short-term memory.

PubMed

Zhang, J; Nawata, K

2018-05-01

Influenza results in approximately 3-5 million annual cases of severe illness and 250 000-500 000 deaths. We urgently need an accurate multi-step-ahead time-series forecasting model to help hospitals to perform dynamical assignments of beds to influenza patients for the annually varied influenza season, and aid pharmaceutical companies to formulate a flexible plan of manufacturing vaccine for the yearly different influenza vaccine. In this study, we utilised four different multi-step prediction algorithms in the long short-term memory (LSTM). The result showed that implementing multiple single-output prediction in a six-layer LSTM structure achieved the best accuracy. The mean absolute percentage errors from two- to 13-step-ahead prediction for the US influenza-like illness rates were all <15%, averagely 12.930%. To the best of our knowledge, it is the first time that LSTM has been applied and refined to perform multi-step-ahead prediction for influenza outbreaks. Hopefully, this modelling methodology can be applied in other countries and therefore help prevent and control influenza worldwide.

Kinetics of piroxicam release from low-methylated pectin/zein hydrogel microspheres

USDA-ARS?s Scientific Manuscript database

The kinetics of a model drug (piroxicam) release from pectin/zein hydrogel microspheres was studied under conditions simulating the gastrointestinal tract. It is established that the rate-limiting step in the release mechanism is drug diffusion out of the microspheres rather than its dissolution. ...

An adaptive multi-level simulation algorithm for stochastic biological systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lester, C., E-mail: lesterc@maths.ox.ac.uk; Giles, M. B.; Baker, R. E.

2015-01-14

Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, “Multi-level Montemore » Carlo for continuous time Markov chains, with applications in biochemical kinetics,” SIAM Multiscale Model. Simul. 10(1), 146–179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ. This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the efficiency of our method using a number of examples.« less

Effect of Humic Acid on As Redox Transformation and Kinetic Adsorption onto Iron Oxide Based Adsorbent (IBA)

PubMed Central

Fakour, Hoda; Lin, Tsair-Fuh

2014-01-01

Due to the importance of adsorption kinetics and redox transformation of arsenic (As) during the adsorption process, the present study elucidated natural organic matter (NOM) effects on As adsorption-desorption kinetics and speciation transformation. The experimental procedures were conducted by examining interactions of arsenate and arsenite with different concentrations of humic acid (HA) as a model representative of NOM, in the presence of iron oxide based adsorbent (IBA), as a model solid surface in three environmentally relevant conditions, including the simultaneous adsorption of both As and HA onto IBA, HA adsorption onto As-presorbed IBA, and As adsorption onto HA-presorbed IBA. Experimental adsorption-desorption data were all fitted by original and modified Lagergren pseudo-first and -second order adsorption kinetic models, respectively. Weber’s intraparticle diffusion was also used to gain insight into the mechanisms and rate controlling steps, which the results suggested that intraparticle diffusion of As species onto IBA is the main rate-controlling step. Different concentrations of HA mediated the redox transformation of As species, with a higher oxidation ability than reduction. The overall results indicated the significant effect of organic matter on the adsorption kinetics and redox transformation of As species, and consequently, the fate, transport and mobility of As in different environmentally relevant conditions. PMID:25325357

Spectral optimization and uncertainty quantification in combustion modeling

NASA Astrophysics Data System (ADS)

Sheen, David Allan

Reliable simulations of reacting flow systems require a well-characterized, detailed chemical model as a foundation. Accuracy of such a model can be assured, in principle, by a multi-parameter optimization against a set of experimental data. However, the inherent uncertainties in the rate evaluations and experimental data leave a model still characterized by some finite kinetic rate parameter space. Without a careful analysis of how this uncertainty space propagates into the model's predictions, those predictions can at best be trusted only qualitatively. In this work, the Method of Uncertainty Minimization using Polynomial Chaos Expansions is proposed to quantify these uncertainties. In this method, the uncertainty in the rate parameters of the as-compiled model is quantified. Then, the model is subjected to a rigorous multi-parameter optimization, as well as a consistency-screening process. Lastly, the uncertainty of the optimized model is calculated using an inverse spectral optimization technique, and then propagated into a range of simulation conditions. An as-compiled, detailed H2/CO/C1-C4 kinetic model is combined with a set of ethylene combustion data to serve as an example. The idea that the hydrocarbon oxidation model should be understood and developed in a hierarchical fashion has been a major driving force in kinetics research for decades. How this hierarchical strategy works at a quantitative level, however, has never been addressed. In this work, we use ethylene and propane combustion as examples and explore the question of hierarchical model development quantitatively. The Method of Uncertainty Minimization using Polynomial Chaos Expansions is utilized to quantify the amount of information that a particular combustion experiment, and thereby each data set, contributes to the model. This knowledge is applied to explore the relationships among the combustion chemistry of hydrogen/carbon monoxide, ethylene, and larger alkanes. Frequently, new data will become available, and it will be desirable to know the effect that inclusion of these data has on the optimized model. Two cases are considered here. In the first, a study of H2/CO mass burning rates has recently been published, wherein the experimentally-obtained results could not be reconciled with any extant H2/CO oxidation model. It is shown in that an optimized H2/CO model can be developed that will reproduce the results of the new experimental measurements. In addition, the high precision of the new experiments provide a strong constraint on the reaction rate parameters of the chemistry model, manifested in a significant improvement in the precision of simulations. In the second case, species time histories were measured during n-heptane oxidation behind reflected shock waves. The highly precise nature of these measurements is expected to impose critical constraints on chemical kinetic models of hydrocarbon combustion. The results show that while an as-compiled, prior reaction model of n-alkane combustion can be accurate in its prediction of the detailed species profiles, the kinetic parameter uncertainty in the model remains to be too large to obtain a precise prediction of the data. Constraining the prior model against the species time histories within the measurement uncertainties led to notable improvements in the precision of model predictions against the species data as well as the global combustion properties considered. Lastly, we show that while the capability of the multispecies measurement presents a step-change in our precise knowledge of the chemical processes in hydrocarbon combustion, accurate data of global combustion properties are still necessary to predict fuel combustion.

In vitro evaluation of flow patterns and turbulent kinetic energy in trans-catheter aortic valve prostheses.

PubMed

Giese, Daniel; Weiss, Kilian; Baeßler, Bettina; Madershahian, Navid; Choi, Yeong-Hoon; Maintz, David; Bunck, Alexander C

2018-02-01

The objective of the current work was to evaluate flow and turbulent kinetic energy in different transcatheter aortic valve implants using highly undersampled time-resolved multi-point 3-directional phase-contrast measurements (4D Flow MRI) in an in vitro setup. A pulsatile flow setup was used with a compliant tubing mimicking a stiff left ventricular outflow tract and ascending aorta. Five different implants were measured using a highly undersampled multi-point 4D Flow MRI sequence. Velocities and turbulent kinetic energy values were analysed and compared. Strong variations of turbulent kinetic energy distributions between the valves were observed. Maximum turbulent kinetic energy values ranged from 100 to over 500 J/m 3 while through-plane velocities were similar between all valves. Highly accelerated 4D Flow MRI for the measurement of velocities and turbulent kinetic energy values allowed for the assessment of hemodynamic parameters in five different implant models. The presented setup, measurement protocol and analysis methods provides an efficient approach to compare different valve implants and could aid future novel valve designs.

Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arampatzis, Giorgos, E-mail: garab@math.uoc.gr; Katsoulakis, Markos A., E-mail: markos@math.umass.edu; Plechac, Petr, E-mail: plechac@math.udel.edu

2012-10-01

We present a mathematical framework for constructing and analyzing parallel algorithms for lattice kinetic Monte Carlo (KMC) simulations. The resulting algorithms have the capacity to simulate a wide range of spatio-temporal scales in spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms. Rather than focusing on constructing exactly the stochastic trajectories, our approach relies on approximating the evolution of observables, such as density, coverage, correlations and so on. More specifically, we develop a spatial domain decomposition of the Markov operator (generator) that describes the evolution of all observables according to the kinetic Monte Carlo algorithm. This domain decompositionmore » corresponds to a decomposition of the Markov generator into a hierarchy of operators and can be tailored to specific hierarchical parallel architectures such as multi-core processors or clusters of Graphical Processing Units (GPUs). Based on this operator decomposition, we formulate parallel Fractional step kinetic Monte Carlo algorithms by employing the Trotter Theorem and its randomized variants; these schemes, (a) are partially asynchronous on each fractional step time-window, and (b) are characterized by their communication schedule between processors. The proposed mathematical framework allows us to rigorously justify the numerical and statistical consistency of the proposed algorithms, showing the convergence of our approximating schemes to the original serial KMC. The approach also provides a systematic evaluation of different processor communicating schedules. We carry out a detailed benchmarking of the parallel KMC schemes using available exact solutions, for example, in Ising-type systems and we demonstrate the capabilities of the method to simulate complex spatially distributed reactions at very large scales on GPUs. Finally, we discuss work load balancing between processors and propose a re-balancing scheme based on probabilistic mass transport methods.« less

Microsecond kinetics in model single- and double-stranded amylose polymers.

PubMed

Sattelle, Benedict M; Almond, Andrew

2014-05-07

Amylose, a component of starch with increasing biotechnological significance, is a linear glucose polysaccharide that self-organizes into single- and double-helical assemblies. Starch granule packing, gelation and inclusion-complex formation result from finely balanced macromolecular kinetics that have eluded precise experimental quantification. Here, graphics processing unit (GPU) accelerated multi-microsecond aqueous simulations are employed to explore conformational kinetics in model single- and double-stranded amylose. The all-atom dynamics concur with prior X-ray and NMR data while surprising and previously overlooked microsecond helix-coil, glycosidic linkage and pyranose ring exchange are hypothesized. In a dodecasaccharide, single-helical collapse was correlated with linkages and rings transitioning from their expected syn and (4)C1 chair conformers. The associated microsecond exchange rates were dependent on proximity to the termini and chain length (comparing hexa- and trisaccharides), while kinetic features of dodecasaccharide linkage and ring flexing are proposed to be a good model for polymers. Similar length double-helices were stable on microsecond timescales but the parallel configuration was sturdier than the antiparallel equivalent. In both, tertiary organization restricted local chain dynamics, implying that simulations of single amylose strands cannot be extrapolated to dimers. Unbiased multi-microsecond simulations of amylose are proposed as a valuable route to probing macromolecular kinetics in water, assessing the impact of chemical modifications on helical stability and accelerating the development of new biotechnologies.

The Roles of Biofilm Conductivity and Donor Substrate Kinetics in a Mixed-Culture Biofilm Anod

EPA Science Inventory

We experimentally assessed kinetics and thermodynamics of electron transfer (ET) from the donor substrate (acetate) to the anode for a mixed-culture biofilm anode. We interpreted the results with a modified biofilm-conduction model consisting of three ET steps: (1) intracellular...

Change of wandering pattern with anisotropy in step kinetics

NASA Astrophysics Data System (ADS)

Sato, Masahide; Uwaha, Makio

1999-03-01

We study the effect of anisotropy in step kinetics on the wandering instability of an isolated step. With the asymmetry of the step kinetics, a straight step becomes unstable for long wavelength fluctuations and wanders when the step velocity exceeds a critical value. Near the threshold of the instability, an isotropic step obeys the Kuramoto-Sivashinsky equation, HT=- HXX- HXXXX+( H2X/2), and shows a chaotic pattern. A step with anisotropic kinetics obeys the Benney equation, HT=- HXX- δHXXX- HXXXX+( H2X/2), and the wandering pattern changes: when the anisotropy is strong, δ≫1, the step shows a regular pattern. Near the threshold of the instability, the anisotropy effect becomes strong while that of the step stiffness becomes weak.

Continuum kinetic and multi-fluid simulations of classical sheaths

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cagas, P.; Hakim, A.; Juno, J.

The kinetic study of plasma sheaths is critical, among other things, to understand the deposition of heat on walls, the effect of sputtering, and contamination of the plasma with detrimental impurities. The plasma sheath also provides a boundary condition and can often have a significant global impact on the bulk plasma. In this paper, kinetic studies of classical sheaths are performed with the continuum kinetic code, Gkeyll, which directly solves the Vlasov-Maxwell equations. The code uses a novel version of the finite-element discontinuous Galerkin scheme that conserves energy in the continuous-time limit. The fields are computed using Maxwell equations. Ionizationmore » and scattering collisions are included; however, surface effects are neglected. The aim of this work is to introduce the continuum kinetic method and compare its results with those obtained from an already established finite-volume multi-fluid model also implemented in Gkeyll. Novel boundary conditions on the fluids allow the sheath to form without specifying wall fluxes, so the fluids and fields adjust self-consistently at the wall. Our work demonstrates that the kinetic and fluid results are in agreement for the momentum flux, showing that in certain regimes, a multifluid model can be a useful approximation for simulating the plasma boundary. There are differences in the electrostatic potential between the fluid and kinetic results. Further, the direct solutions of the distribution function presented here highlight the non-Maxwellian distribution of electrons in the sheath, emphasizing the need for a kinetic model. The densities, velocities, and the potential show a good agreement between the kinetic and fluid results. But, kinetic physics is highlighted through higher moments such as parallel and perpendicular temperatures which provide significant differences from the fluid results in which the temperature is assumed to be isotropic. Besides decompression cooling, the heat flux is shown to play a role in the temperature differences that are observed, especially inside the collisionless sheath. Published by AIP Publishing.« less

Continuum kinetic and multi-fluid simulations of classical sheaths

DOE PAGES

Cagas, P.; Hakim, A.; Juno, J.; ...

2017-02-21

The kinetic study of plasma sheaths is critical, among other things, to understand the deposition of heat on walls, the effect of sputtering, and contamination of the plasma with detrimental impurities. The plasma sheath also provides a boundary condition and can often have a significant global impact on the bulk plasma. In this paper, kinetic studies of classical sheaths are performed with the continuum kinetic code, Gkeyll, which directly solves the Vlasov-Maxwell equations. The code uses a novel version of the finite-element discontinuous Galerkin scheme that conserves energy in the continuous-time limit. The fields are computed using Maxwell equations. Ionizationmore » and scattering collisions are included; however, surface effects are neglected. The aim of this work is to introduce the continuum kinetic method and compare its results with those obtained from an already established finite-volume multi-fluid model also implemented in Gkeyll. Novel boundary conditions on the fluids allow the sheath to form without specifying wall fluxes, so the fluids and fields adjust self-consistently at the wall. Our work demonstrates that the kinetic and fluid results are in agreement for the momentum flux, showing that in certain regimes, a multifluid model can be a useful approximation for simulating the plasma boundary. There are differences in the electrostatic potential between the fluid and kinetic results. Further, the direct solutions of the distribution function presented here highlight the non-Maxwellian distribution of electrons in the sheath, emphasizing the need for a kinetic model. The densities, velocities, and the potential show a good agreement between the kinetic and fluid results. But, kinetic physics is highlighted through higher moments such as parallel and perpendicular temperatures which provide significant differences from the fluid results in which the temperature is assumed to be isotropic. Besides decompression cooling, the heat flux is shown to play a role in the temperature differences that are observed, especially inside the collisionless sheath. Published by AIP Publishing.« less

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly.

PubMed

Fonseca, Pedro; Romano, Flavio; Schreck, John S; Ouldridge, Thomas E; Doye, Jonathan P K; Louis, Ard A

2018-04-07

Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.

MESOSCALE MODELING OF DEFLAGRATION-INDUCED DECONSOLIDATION IN POLYMER-BONDED EXPLOSIVES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Springer, H K; Glascoe, E A; Reaugh, J E

Initially undamaged polymer-bonded explosives can transition from conductive burning to more violent convective burning via rapid deconsolidation at higher pressures. The pressure-dependent infiltration of cracks and pores, i.e., damage, by product gases at the burn-front is a key step in the transition to convective burning. However, the relative influence of pre-existing damage and the evolution of deflagration-induced damage during the transition to convective burning is not well understood. The objective of this study is to investigate the role of microstructure and initial pressurization on deconsolidation. We performed simulations using the multi-physics hydrocode, ALE3D. HMX-Viton A served as our model explosive.more » A Prout-Tompkins chemical kinetic model, Vielle's Law pressure-dependent burning, Gruneisen equation-of-state, and simplified strength model were used for the HMX. The propensity for deconsolidation increased with increasing defect size and decreasing initial pressurization, as measured by the increase in burning surface area. These studies are important because they enable the development of continuum-scale damage models and the design of inherently safer explosives.« less

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

NASA Astrophysics Data System (ADS)

Fonseca, Pedro; Romano, Flavio; Schreck, John S.; Ouldridge, Thomas E.; Doye, Jonathan P. K.; Louis, Ard A.

2018-04-01

Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.

Foundations of modelling of nonequilibrium low-temperature plasmas

NASA Astrophysics Data System (ADS)

Alves, L. L.; Bogaerts, A.; Guerra, V.; Turner, M. M.

2018-02-01

This work explains the need for plasma models, introduces arguments for choosing the type of model that better fits the purpose of each study, and presents the basics of the most common nonequilibrium low-temperature plasma models and the information available from each one, along with an extensive list of references for complementary in-depth reading. The paper presents the following models, organised according to the level of multi-dimensional description of the plasma: kinetic models, based on either a statistical particle-in-cell/Monte-Carlo approach or the solution to the Boltzmann equation (in the latter case, special focus is given to the description of the electron kinetics); multi-fluid models, based on the solution to the hydrodynamic equations; global (spatially-average) models, based on the solution to the particle and energy rate-balance equations for the main plasma species, usually including a very complete reaction chemistry; mesoscopic models for plasma-surface interaction, adopting either a deterministic approach or a stochastic dynamical Monte-Carlo approach. For each plasma model, the paper puts forward the physics context, introduces the fundamental equations, presents advantages and limitations, also from a numerical perspective, and illustrates its application with some examples. Whenever pertinent, the interconnection between models is also discussed, in view of multi-scale hybrid approaches.

Computational Models for Understanding of Structure, Function and Pharmacology of the Cardiac Potassium Channel Kv11.1 (hERG).

PubMed

Wacker, Soren; Noskov, Sergei Yu; Perissinotti, Laura L

2017-01-01

The rapid delayed rectifier current IKr is one of the major K+ currents involved in repolarization of the human cardiac action potential. Various inherited or drug-induced forms of the long QT syndrome (LQTS) in humans are linked to functional and structural modifications in the IKr conducting channels. IKr is carried by the potassium channel Kv11.1 encoded by the gene KCNH2 (commonly referred to as human ether-a-go-go-related gene or hERG) [1, 2]. The first necessary step for predicting emergent drug effects on the heart is determining and modeling the binding thermodynamics and kinetics of primary and major off-target drug interactions with subcellular targets. The bulk of drugs that target hERG channels are known to have complex interactions at the atomic scale. Accordingly, one of the goals for this review is to provide comprehensive guide in the universe of computational models aiming to refine our understanding of structure-function relations in Kv11.1 and its isoforms. The special emphasis is placed on the mapping of drug binding sites and tentative mechanisms of channel inhibition and activation by drugs. An overview over recent structural models and mapping of binding sites for blockers and activators of IKr current along with the discussion on agreements and discrepancies among different models is presented. There is an apparent reciprocity or feedback loop between drug binding and action potential of the cardiac myocytes. Thus one has to connect drug binding to a particular receptor so that its functional consequences impact on the action potential duration. The natural pathway is to develop multi-scale models that connect between receptor and cellular scales. The potential for such multi-scale model development is discussed through the lens of common gating models. Accordingly, the second part of this review covers an ongoing development of the kinetic models of gating transitions and cardiac ion currents carried by hERG channels with and without drug bound. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Development of a Multi-Centre Clinical Trial Data Archiving and Analysis Platform for Functional Imaging

NASA Astrophysics Data System (ADS)

Driscoll, Brandon; Jaffray, David; Coolens, Catherine

2014-03-01

Purpose: To provide clinicians & researchers participating in multi-centre clinical trials with a central repository for large volume dynamic imaging data as well as a set of tools for providing end-to-end testing and image analysis standards of practice. Methods: There are three main pieces to the data archiving and analysis system; the PACS server, the data analysis computer(s) and the high-speed networks that connect them. Each clinical trial is anonymized using a customizable anonymizer and is stored on a PACS only accessible by AE title access control. The remote analysis station consists of a single virtual machine per trial running on a powerful PC supporting multiple simultaneous instances. Imaging data management and analysis is performed within ClearCanvas Workstation® using custom designed plug-ins for kinetic modelling (The DCE-Tool®), quality assurance (The DCE-QA Tool) and RECIST. Results: A framework has been set up currently serving seven clinical trials spanning five hospitals with three more trials to be added over the next six months. After initial rapid image transfer (+ 2 MB/s), all data analysis is done server side making it robust and rapid. This has provided the ability to perform computationally expensive operations such as voxel-wise kinetic modelling on very large data archives (+20 GB/50k images/patient) remotely with minimal end-user hardware. Conclusions: This system is currently in its proof of concept stage but has been used successfully to send and analyze data from remote hospitals. Next steps will involve scaling up the system with a more powerful PACS and multiple high powered analysis machines as well as adding real-time review capabilities.

Analysis of the phosphorescent dye concentration dependence of triplet-triplet annihilation in organic host-guest systems

NASA Astrophysics Data System (ADS)

Zhang, L.; van Eersel, H.; Bobbert, P. A.; Coehoorn, R.

2016-10-01

Using a novel method for analyzing transient photoluminescence (PL) experiments, a microscopic description is obtained for the dye concentration dependence of triplet-triplet annihilation (TTA) in phosphorescent host-guest systems. It is demonstrated that the TTA-mechanism, which could be a single-step dominated process or a diffusion-mediated multi-step process, can be deduced for any given dye concentration from a recently proposed PL intensity analysis. A comparison with the results of kinetic Monte Carlo simulations provides the TTA-Förster radius and shows that the TTA enhancement due to triplet diffusion can be well described in a microscopic manner assuming Förster- or Dexter-type energy transfer.

Distributed activation energy model parameters of some Turkish coals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunes, M.; Gunes, S.K.

2008-07-01

A multi-reaction model based on distributed activation energy has been applied to some Turkish coals. The kinetic parameters of distributed activation energy model were calculated via computer program developed for this purpose. It was observed that the values of mean of activation energy distribution vary between 218 and 248 kJ/mol, and the values of standard deviation of activation energy distribution vary between 32 and 70 kJ/mol. The correlations between kinetic parameters of the distributed activation energy model and certain properties of coal have been investigated.

Prospects of in vivo singlet oxygen luminescence monitoring: Kinetics at different locations on living mice.

PubMed

Pfitzner, Michael; Schlothauer, Jan C; Bastien, Estelle; Hackbarth, Steffen; Bezdetnaya, Lina; Lassalle, Henri-Pierre; Röder, Beate

2016-06-01

Singlet oxygen observation is considered a valuable tool to assess and optimize PDT treatment. In complex systems, such as tumors in vivo, only the direct, time-resolved singlet oxygen luminescence detection can give reliable information about generation and interaction of singlet oxygen. Up to now, evaluation of kinetics was not possible due to insufficient signal-to-noise ratio. Here we present high signal-to-noise ratio singlet oxygen luminescence kinetics obtained in mouse tumor model under PDT relevant conditions. A highly optimized system based on a custom made laser diode excitation source and a high aperture multi-furcated fiber, utilizing a photomultiplier tube with a multi photon counting device was used. Luminescence kinetics with unsurpassed signal-to-noise ratio were gained from tumor bearing nude mice in vivo upon topic application, subcutaneous injection as well as intravenous injection of different photosensitizers (chlorin e6 and dendrimer formulations of chlorin e6). Singlet oxygen kinetics in appropriate model systems are discussed to facilitate the interpretation of complex kinetics obtained from in vivo tumor tissue. This is the first study addressing the complexity of singlet oxygen luminescence kinetics in tumor tissue. At present, further investigations are needed to fully explain the processes involved. Nevertheless, the high signal-to-noise ratio proves the applicability of direct time-resolved singlet oxygen luminescence detection as a prospective tool for monitoring photodynamic therapy. Copyright © 2016 Elsevier B.V. All rights reserved.

Dynamic Neuromuscular Control of the Lower Limbs in Response to Unexpected Single-Planar versus Multi-Planar Support Perturbations in Young, Active Adults.

PubMed

Malfait, Bart; Staes, Filip; de Vries, Aijse; Smeets, Annemie; Hawken, Malcolm; Robinson, Mark A; Vanrenterghem, Jos; Verschueren, Sabine

2015-01-01

An anterior cruciate ligament (ACL) injury involves a multi-planar injury mechanism. Nevertheless, unexpected multi-planar perturbations have not been used to screen athletes in the context of ACL injury prevention yet could reveal those more at risk. The objective of this study was to compare neuromuscular responses to multi-planar (MPP) and single-planar perturbations (SPP) during a stepping-down task. These results might serve as a basis for future implementation of external perturbations in ACL injury screening programs. Thirteen young adults performed a single leg stepping-down task in eight conditions (four MPP and four SPP with a specified amplitude and velocity). The amplitudes of vastus lateralis (VL), vastus medialis (VM), hamstrings lateralis (HL), hamstrings medialis (HM) EMG activity, medio-lateral and anterior-posterior centre of mass (COM) displacements, the peak knee flexion and abduction angles were compared between conditions using an one-way ANOVA. Number of stepping responses were monitored during all conditions. Significantly greater muscle activity levels were found in response to the more challenging MPP and SPP compared to the less challenging conditions (p < 0.05). No differences in neuromuscular activity were found between the MPP conditions and their equivalents in the SPP. Eighteen stepping responses were monitored in the SPP versus nine in the MPP indicating that the overall neuromuscular control was even more challenged during the SPP which was supported by greater COM displacements in the SPP. The more intense MPP and SPP evoked different neuromuscular responses resulting in greater muscle activity levels compared to small perturbations. Based on the results of COM displacements and based on the amount of stepping responses, dynamic neuromuscular control of the knee joint appeared less challenged during the MPP. Therefore, future work should investigate extensively if other neuromuscular differences (i.e. co-activation patterns and kinetics) exist between MPP and SPP. In addition, future work should examine the influence on the neuromuscular control of the magnitude of the perturbations and the magnitude of stepping height and stepping distance.

VAMPnets for deep learning of molecular kinetics.

PubMed

Mardt, Andreas; Pasquali, Luca; Wu, Hao; Noé, Frank

2018-01-02

There is an increasing demand for computing the relevant structures, equilibria, and long-timescale kinetics of biomolecular processes, such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transformation of simulated coordinates into structural features, dimension reduction, clustering the dimension-reduced data, and estimation of a Markov state model or related model of the interconversion rates between molecular structures. This handcrafted approach demands a substantial amount of modeling expertise, as poor decisions at any step will lead to large modeling errors. Here we employ the variational approach for Markov processes (VAMP) to develop a deep learning framework for molecular kinetics using neural networks, dubbed VAMPnets. A VAMPnet encodes the entire mapping from molecular coordinates to Markov states, thus combining the whole data processing pipeline in a single end-to-end framework. Our method performs equally or better than state-of-the-art Markov modeling methods and provides easily interpretable few-state kinetic models.

Quantifying Fenton reaction pathways driven by self-generated H2O2 on pyrite surfaces

NASA Astrophysics Data System (ADS)

Gil-Lozano, C.; Davila, A. F.; Losa-Adams, E.; Fairén, A. G.; Gago-Duport, L.

2017-03-01

Oxidation of pyrite (FeS2) plays a significant role in the redox cycling of iron and sulfur on Earth and is the primary cause of acid mine drainage (AMD). It has been established that this process involves multi-step electron-transfer reactions between surface defects and adsorbed O2 and H2O, releasing sulfoxy species (e.g., S2O32-, SO42-) and ferrous iron (Fe2+) to the solution and also producing intermediate by-products, such as hydrogen peroxide (H2O2) and other reactive oxygen species (ROS), however, our understanding of the kinetics of these transient species is still limited. We investigated the kinetics of H2O2 formation in aqueous suspensions of FeS2 microparticles by monitoring, in real time, the H2O2 and dissolved O2 concentration under oxic and anoxic conditions using amperometric microsensors. Additional spectroscopic and structural analyses were done to track the dependencies between the process of FeS2 dissolution and the degradation of H2O2 through the Fenton reaction. Based on our experimental results, we built a kinetic model which explains the observed trend of H2O2, showing that FeS2 dissolution can act as a natural Fenton reagent, influencing the oxidation of third-party species during the long term evolution of geochemical systems, even in oxygen-limited environments.

Biosorption kinetics of heavy metals by leaf biomass of Jatropha curcas in single and multi-metal system.

PubMed

Rawat, Anand Prabha; Giri, Krishna; Rai, J P N

2014-03-01

Biosorption of Cu(2+), Zn(2+), and Cr(6+) from aqueous solutions by leaf biomass of Jatropha curcas was investigated as a function of biomass concentration, initial metal ion concentration, contact time, and pH of the solution systematically. The aim of this study was to optimize biosorption process and find out a suitable kinetic model for the metal removal in single and multi-metal system. The experimental data were analyzed using two sorption kinetic models, viz., pseudo-first- and pseudo-second-order equations, to determine the best fit equation for the biosorption of metal ions Cu(2+), Zn(2+), and Cr(6+) onto the leaf biomass of J. curcas in different metal systems. The experimental data fitted well the pseudo-second-order equation and provided the best correlation for the biosorption process. The findings of the present investigation revealed that J. curcas leaf biomass was an eco-friendly and cost-effective biosorbent for the removal of heavy metal ions from wastewater.

Asynchronous adaptive time step in quantitative cellular automata modeling

PubMed Central

Zhu, Hao; Pang, Peter YH; Sun, Yan; Dhar, Pawan

2004-01-01

Background The behaviors of cells in metazoans are context dependent, thus large-scale multi-cellular modeling is often necessary, for which cellular automata are natural candidates. Two related issues are involved in cellular automata based multi-cellular modeling: how to introduce differential equation based quantitative computing to precisely describe cellular activity, and upon it, how to solve the heavy time consumption issue in simulation. Results Based on a modified, language based cellular automata system we extended that allows ordinary differential equations in models, we introduce a method implementing asynchronous adaptive time step in simulation that can considerably improve efficiency yet without a significant sacrifice of accuracy. An average speedup rate of 4–5 is achieved in the given example. Conclusions Strategies for reducing time consumption in simulation are indispensable for large-scale, quantitative multi-cellular models, because even a small 100 × 100 × 100 tissue slab contains one million cells. Distributed and adaptive time step is a practical solution in cellular automata environment. PMID:15222901

Predicting the F(ab)-mediated effect of monoclonal antibodies in vivo by combining cell-level kinetic and pharmacokinetic modelling.

PubMed

Krippendorff, Ben-Fillippo; Oyarzún, Diego A; Huisinga, Wilhelm

2012-04-01

Cell-level kinetic models for therapeutically relevant processes increasingly benefit the early stages of drug development. Later stages of the drug development processes, however, rely on pharmacokinetic compartment models while cell-level dynamics are typically neglected. We here present a systematic approach to integrate cell-level kinetic models and pharmacokinetic compartment models. Incorporating target dynamics into pharmacokinetic models is especially useful for the development of therapeutic antibodies because their effect and pharmacokinetics are inherently interdependent. The approach is illustrated by analysing the F(ab)-mediated inhibitory effect of therapeutic antibodies targeting the epidermal growth factor receptor. We build a multi-level model for anti-EGFR antibodies by combining a systems biology model with in vitro determined parameters and a pharmacokinetic model based on in vivo pharmacokinetic data. Using this model, we investigated in silico the impact of biochemical properties of anti-EGFR antibodies on their F(ab)-mediated inhibitory effect. The multi-level model suggests that the F(ab)-mediated inhibitory effect saturates with increasing drug-receptor affinity, thereby limiting the impact of increasing antibody affinity on improving the effect. This indicates that observed differences in the therapeutic effects of high affinity antibodies in the market and in clinical development may result mainly from Fc-mediated indirect mechanisms such as antibody-dependent cell cytotoxicity.

The kinetics of thermal generation of flavour.

PubMed

Parker, Jane K

2013-01-01

Control and optimisation of flavour is the ultimate challenge for the food and flavour industry. The major route to flavour formation during thermal processing is the Maillard reaction, which is a complex cascade of interdependent reactions initiated by the reaction between a reducing sugar and an amino compound. The complexity of the reaction means that researchers turn to kinetic modelling in order to understand the control points of the reaction and to manipulate the flavour profile. Studies of the kinetics of flavour formation have developed over the past 30 years from single- response empirical models of binary aqueous systems to sophisticated multi-response models in food matrices, based on the underlying chemistry, with the power to predict the formation of some key aroma compounds. This paper discusses in detail the development of kinetic models of thermal generation of flavour and looks at the challenges involved in predicting flavour. Copyright © 2012 Society of Chemical Industry.

How to use multi-criteria decision analysis methods for reimbursement decision-making in healthcare: a step-by-step guide.

PubMed

Diaby, Vakaramoko; Goeree, Ron

2014-02-01

In recent years, the quest for more comprehensiveness, structure and transparency in reimbursement decision-making in healthcare has prompted the research into alternative decision-making frameworks. In this environment, multi-criteria decision analysis (MCDA) is arising as a valuable tool to support healthcare decision-making. In this paper, we present the main MCDA decision support methods (elementary methods, value-based measurement models, goal programming models and outranking models) using a case study approach. For each family of methods, an example of how an MCDA model would operate in a real decision-making context is presented from a critical perspective, highlighting the parameters setting, the selection of the appropriate evaluation model as well as the role of sensitivity and robustness analyses. This study aims to provide a step-by-step guide on how to use MCDA methods for reimbursement decision-making in healthcare.

Radical Cations and Acid Protection during Radiolysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mincher, Bruce J.; Zarzana, Christopher A.; Mezyk, Stephen P.

2016-09-09

Ligand molecules for used nuclear fuel separation schemes are exposed to high radiation fields and high concentrations of acid. Thus, an understanding of the complex interactions between extraction ligands, diluent, and acid is critical to understanding the performance of a separation process. The diglycolamides are ligands with important structural similarities to CMPO; however, previous work has shown that their radiolytic degradation has important mechanistic differences from CMPO. The DGAs do not enjoy radioprotection by HNO3 and the kinetics of DGA radiolytic degradation are different. CMPO degrades with pseudo-zero-order kinetics in linear fashion with absorbed dose while the DGAs degrade inmore » pseudo-first-order, exponential fashion. This suggests that the DGAs degrade by simple reaction with some product of direct diluent radiolysis, while CMPO degradation is probably multi-step, with a slow step that is not dependent on the CMPO concentration, and mitigated by HNO 3. It is thus believed that radio-protection and the zero-order radiolytic degradation kinetics are related, and that these phenomena are a function of either the formation of strong acid complexes with CMPO and/or to the presence of the CMPO phenyl ring. Experiments to test both these hypotheses have been designed and partially conducted. This report summarizes findings related to these phenomena for FY16, in satisfaction of milestone M3FT-16IN030104053. It also reports continued kinetic measurements for the reactions of the dodecane radical cation with solvent extraction ligands.« less

Combining experimental techniques with non-linear numerical models to assess the sorption of pesticides on soils

NASA Astrophysics Data System (ADS)

Magga, Zoi; Tzovolou, Dimitra N.; Theodoropoulou, Maria A.; Tsakiroglou, Christos D.

2012-03-01

The risk assessment of groundwater pollution by pesticides may be based on pesticide sorption and biodegradation kinetic parameters estimated with inverse modeling of datasets from either batch or continuous flow soil column experiments. In the present work, a chemical non-equilibrium and non-linear 2-site sorption model is incorporated into solute transport models to invert the datasets of batch and soil column experiments, and estimate the kinetic sorption parameters for two pesticides: N-phosphonomethyl glycine (glyphosate) and 2,4-dichlorophenoxy-acetic acid (2,4-D). When coupling the 2-site sorption model with the 2-region transport model, except of the kinetic sorption parameters, the soil column datasets enable us to estimate the mass-transfer coefficients associated with solute diffusion between mobile and immobile regions. In order to improve the reliability of models and kinetic parameter values, a stepwise strategy that combines batch and continuous flow tests with adequate true-to-the mechanism analytical of numerical models, and decouples the kinetics of purely reactive steps of sorption from physical mass-transfer processes is required.

On the driving force of PAH production

NASA Technical Reports Server (NTRS)

Frenklach, Michael

1989-01-01

The kinetic factors affecting the production of polycyclic aromatic hydrocarbons (PAH) in high-temperature pyrolysis and combustion environments are analyzed. A lumped kinetic model representing polymerization-type growth by one irreversible step and two reversible steps is considered. It is shown that at high temperatures, PAH growth is controlled by the superequilibrium of hydrogen atoms; at low temperatures and low H2 concentrations, the PAH growth rate is proportional to the rate of the H-abstraction of a hydrogen atom from aromatic molecules; while at low temperatures and high H2 concentrations, it is controlled by the thermodynamics of the H-abstraction and the kinetics of acetylene addition to aromatic radicals. The presence of oxygen mainly affects the small-molecule reactions during the induction period.

A multi-time-step noise reduction method for measuring velocity statistics from particle tracking velocimetry

NASA Astrophysics Data System (ADS)

Machicoane, Nathanaël; López-Caballero, Miguel; Bourgoin, Mickael; Aliseda, Alberto; Volk, Romain

2017-10-01

We present a method to improve the accuracy of velocity measurements for fluid flow or particles immersed in it, based on a multi-time-step approach that allows for cancellation of noise in the velocity measurements. Improved velocity statistics, a critical element in turbulent flow measurements, can be computed from the combination of the velocity moments computed using standard particle tracking velocimetry (PTV) or particle image velocimetry (PIV) techniques for data sets that have been collected over different values of time intervals between images. This method produces Eulerian velocity fields and Lagrangian velocity statistics with much lower noise levels compared to standard PIV or PTV measurements, without the need of filtering and/or windowing. Particle displacement between two frames is computed for multiple different time-step values between frames in a canonical experiment of homogeneous isotropic turbulence. The second order velocity structure function of the flow is computed with the new method and compared to results from traditional measurement techniques in the literature. Increased accuracy is also demonstrated by comparing the dissipation rate of turbulent kinetic energy measured from this function against previously validated measurements.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamireddy, Srinivas Reddy; Kozliak, Evguenii I.; Tucker, Melvin

A kinetic study of acid pretreatment was conducted for sorghum non-brown mid rib (SNBMR) ( Sorghum bicolor L Moench), sorghum-brown mid rib (SBMR), sunn hemp ( Crotalaria juncea L) and kenaf ( Gossypiumhirsutum L), focusing on rates of xylose monomer and furfural formation. The kinetics was investigated using two independent variables, reaction temperature (150 and 160°C) and acid concentration (1 and 2 wt%), with a constant dry biomass loading of 10 wt% and a treatment time up to 20 min while sampling the mixture every 2 min. The experimental data were fitted using a two-step kinetic model based on irreversiblemore » pseudo first order kinetics at each step. Varied kinetic orders on the acid concentration, ranging from 0.2 to >3, were observed for both xylose and furfural formation, the values depending on the feedstock. The crystallinity index of raw biomass was shown to be a major factor influencing the rate of both xylose and furfural formation. As a result, a positive correlation was observed between the activation energy and biomass crystallinity index for xylose formation.« less

Technical note: Equivalent genomic models with a residual polygenic effect.

PubMed

Liu, Z; Goddard, M E; Hayes, B J; Reinhardt, F; Reents, R

2016-03-01

Routine genomic evaluations in animal breeding are usually based on either a BLUP with genomic relationship matrix (GBLUP) or single nucleotide polymorphism (SNP) BLUP model. For a multi-step genomic evaluation, these 2 alternative genomic models were proven to give equivalent predictions for genomic reference animals. The model equivalence was verified also for young genotyped animals without phenotypes. Due to incomplete linkage disequilibrium of SNP markers to genes or causal mutations responsible for genetic inheritance of quantitative traits, SNP markers cannot explain all the genetic variance. A residual polygenic effect is normally fitted in the genomic model to account for the incomplete linkage disequilibrium. In this study, we start by showing the proof that the multi-step GBLUP and SNP BLUP models are equivalent for the reference animals, when they have a residual polygenic effect included. Second, the equivalence of both multi-step genomic models with a residual polygenic effect was also verified for young genotyped animals without phenotypes. Additionally, we derived formulas to convert genomic estimated breeding values of the GBLUP model to its components, direct genomic values and residual polygenic effect. Third, we made a proof that the equivalence of these 2 genomic models with a residual polygenic effect holds also for single-step genomic evaluation. Both the single-step GBLUP and SNP BLUP models lead to equal prediction for genotyped animals with phenotypes (e.g., reference animals), as well as for (young) genotyped animals without phenotypes. Finally, these 2 single-step genomic models with a residual polygenic effect were proven to be equivalent for estimation of SNP effects, too. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A prospectus on kinetic heliophysics

NASA Astrophysics Data System (ADS)

Howes, Gregory G.

2017-05-01

Under the low density and high temperature conditions typical of heliospheric plasmas, the macroscopic evolution of the heliosphere is strongly affected by the kinetic plasma physics governing fundamental microphysical mechanisms. Kinetic turbulence, collisionless magnetic reconnection, particle acceleration, and kinetic instabilities are four poorly understood, grand-challenge problems that lie at the new frontier of kinetic heliophysics. The increasing availability of high cadence and high phase-space resolution measurements of particle velocity distributions by current and upcoming spacecraft missions and of massively parallel nonlinear kinetic simulations of weakly collisional heliospheric plasmas provides the opportunity to transform our understanding of these kinetic mechanisms through the full utilization of the information contained in the particle velocity distributions. Several major considerations for future investigations of kinetic heliophysics are examined. Turbulent dissipation followed by particle heating is highlighted as an inherently two-step process in weakly collisional plasmas, distinct from the more familiar case in fluid theory. Concerted efforts must be made to tackle the big-data challenge of visualizing the high-dimensional (3D-3V) phase space of kinetic plasma theory through physics-based reductions. Furthermore, the development of innovative analysis methods that utilize full velocity-space measurements, such as the field-particle correlation technique, will enable us to gain deeper insight into these four grand-challenge problems of kinetic heliophysics. A systems approach to tackle the multi-scale problem of heliophysics through a rigorous connection between the kinetic physics at microscales and the self-consistent evolution of the heliosphere at macroscales will propel the field of kinetic heliophysics into the future.

A prospectus on kinetic heliophysics

PubMed Central

2017-01-01

Under the low density and high temperature conditions typical of heliospheric plasmas, the macroscopic evolution of the heliosphere is strongly affected by the kinetic plasma physics governing fundamental microphysical mechanisms. Kinetic turbulence, collisionless magnetic reconnection, particle acceleration, and kinetic instabilities are four poorly understood, grand-challenge problems that lie at the new frontier of kinetic heliophysics. The increasing availability of high cadence and high phase-space resolution measurements of particle velocity distributions by current and upcoming spacecraft missions and of massively parallel nonlinear kinetic simulations of weakly collisional heliospheric plasmas provides the opportunity to transform our understanding of these kinetic mechanisms through the full utilization of the information contained in the particle velocity distributions. Several major considerations for future investigations of kinetic heliophysics are examined. Turbulent dissipation followed by particle heating is highlighted as an inherently two-step process in weakly collisional plasmas, distinct from the more familiar case in fluid theory. Concerted efforts must be made to tackle the big-data challenge of visualizing the high-dimensional (3D-3V) phase space of kinetic plasma theory through physics-based reductions. Furthermore, the development of innovative analysis methods that utilize full velocity-space measurements, such as the field-particle correlation technique, will enable us to gain deeper insight into these four grand-challenge problems of kinetic heliophysics. A systems approach to tackle the multi-scale problem of heliophysics through a rigorous connection between the kinetic physics at microscales and the self-consistent evolution of the heliosphere at macroscales will propel the field of kinetic heliophysics into the future. PMID:29104421

Tungsten oxide--fly ash oxide composites in adsorption and photocatalysis.

PubMed

Visa, Maria; Bogatu, Cristina; Duta, Anca

2015-05-30

A novel composite based on tungsten oxide and fly ash was hydrothermally synthetized to be used as substrate in the advanced treatment of wastewaters with complex load resulted from the textile industry. The proposed treatment consists of one single step process combining photocatalysis and adsorption. The composite's crystalline structure was investigated by X-ray diffraction and FTIR, while atomic force microscopy (AFM) and scanning electron microscopy (SEM) were used to analyze the morphology. The adsorption capacity and photocatalytic properties of the material were tested on mono- and multi-pollutants systems containing two dyes (Bemacid Blau - BB and Bemacid Rot - BR) and one heavy metal ion-Cu(2+), and the optimized process conditions were identified. The results indicate better removal efficiencies using the novel composite material in the combined adsorption and photocatalysis, as compared to the separated processes. Dyes removal was significantly enhanced in the photocatalytic process by adding hydrogen peroxide and the mechanism was presented and discussed. The pseudo second order kinetics model best fitted the experimental data, both in the adsorption and in the combined processes. The kinetic parameters were calculated and correlated with the properties of the composite substrate. Copyright © 2015 Elsevier B.V. All rights reserved.

Harvesting multiple electron-hole pairs generated through plasmonic excitation of Au nanoparticles.

PubMed

Kim, Youngsoo; Smith, Jeremy G; Jain, Prashant K

2018-05-07

Multi-electron redox reactions, although central to artificial photosynthesis, are kinetically sluggish. Amidst the search for synthetic catalysts for such processes, plasmonic nanoparticles have been found to catalyse multi-electron reduction of CO 2 under visible light. This example motivates the need for a general, insight-driven framework for plasmonic catalysis of such multi-electron chemistry. Here, we elucidate the principles underlying the extraction of multiple redox equivalents from a plasmonic photocatalyst. We measure the kinetics of electron harvesting from a gold nanoparticle photocatalyst as a function of photon flux. Our measurements, supported by theoretical modelling, reveal a regime where two-electron transfer from the excited gold nanoparticle becomes prevalent. Multiple electron harvesting becomes possible under continuous-wave, visible-light excitation of moderate intensity due to strong interband transitions in gold and electron-hole separation accomplished using a hole scavenger. These insights will help expand the utility of plasmonic photocatalysis beyond CO 2 reduction to other challenging multi-electron, multi-proton transformations such as N 2 fixation.

Temperature-Dependent Kinetic Prediction for Reactions Described by Isothermal Mathematics

DOE PAGES

Dinh, L. N.; Sun, T. C.; McLean, W.

2016-09-12

Most kinetic models are expressed in isothermal mathematics. In addition, this may lead unaware scientists either to the misconception that classical isothermal kinetic models cannot be used for any chemical process in an environment with a time-dependent temperature profile or, even worse, to a misuse of them. In reality, classical isothermal models can be employed to make kinetic predictions for reactions in environments with time-dependent temperature profiles, provided that there is a continuity/conservation in the reaction extent at every temperature–time step. In this article, fundamental analyses, illustrations, guiding tables, and examples are given to help the interested readers using eithermore » conventional isothermal reacted fraction curves or rate equations to make proper kinetic predictions for chemical reactions in environments with temperature profiles that vary, even arbitrarily, with time simply by the requirement of continuity/conservation of reaction extent whenever there is an external temperature change.« less

A self-consistent first-principle based approach to model carrier mobility in organic materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meded, Velimir; Friederich, Pascal; Symalla, Franz

2015-12-31

Transport through thin organic amorphous films, utilized in OLEDs and OPVs, has been a challenge to model by using ab-initio methods. Charge carrier mobility depends strongly on the disorder strength and reorganization energy, both of which are significantly affected by the details in environment of each molecule. Here we present a multi-scale approach to describe carrier mobility in which the materials morphology is generated using DEPOSIT, a Monte Carlo based atomistic simulation approach, or, alternatively by molecular dynamics calculations performed with GROMACS. From this morphology we extract the material specific hopping rates, as well as the on-site energies using amore » fully self-consistent embedding approach to compute the electronic structure parameters, which are then used in an analytic expression for the carrier mobility. We apply this strategy to compute the carrier mobility for a set of widely studied molecules and obtain good agreement between experiment and theory varying over several orders of magnitude in the mobility without any freely adjustable parameters. The work focuses on the quantum mechanical step of the multi-scale workflow, explains the concept along with the recently published workflow optimization, which combines density functional with semi-empirical tight binding approaches. This is followed by discussion on the analytic formula and its agreement with established percolation fits as well as kinetic Monte Carlo numerical approaches. Finally, we skatch an unified multi-disciplinary approach that integrates materials science simulation and high performance computing, developed within EU project MMM@HPC.« less

Three-dimensional multi-scale model of deformable platelets adhesion to vessel wall in blood flow

PubMed Central

Wu, Ziheng; Xu, Zhiliang; Kim, Oleg; Alber, Mark

2014-01-01

When a blood vessel ruptures or gets inflamed, the human body responds by rapidly forming a clot to restrict the loss of blood. Platelets aggregation at the injury site of the blood vessel occurring via platelet–platelet adhesion, tethering and rolling on the injured endothelium is a critical initial step in blood clot formation. A novel three-dimensional multi-scale model is introduced and used in this paper to simulate receptor-mediated adhesion of deformable platelets at the site of vascular injury under different shear rates of blood flow. The novelty of the model is based on a new approach of coupling submodels at three biological scales crucial for the early clot formation: novel hybrid cell membrane submodel to represent physiological elastic properties of a platelet, stochastic receptor–ligand binding submodel to describe cell adhesion kinetics and lattice Boltzmann submodel for simulating blood flow. The model implementation on the GPU cluster significantly improved simulation performance. Predictive model simulations revealed that platelet deformation, interactions between platelets in the vicinity of the vessel wall as well as the number of functional GPIbα platelet receptors played significant roles in platelet adhesion to the injury site. Variation of the number of functional GPIbα platelet receptors as well as changes of platelet stiffness can represent effects of specific drugs reducing or enhancing platelet activity. Therefore, predictive simulations can improve the search for new drug targets and help to make treatment of thrombosis patient-specific. PMID:24982253

Oxidation kinetics for conversion of U 3O 8 to ε-UO 3 with NO 2

DOE PAGES

Johnson, J. A.; Rawn, C. J.; Spencer, B. B.; ...

2017-04-04

The oxidation kinetics of U 3O 8 powder to ε-UO 3 in an NO 2 environment was measured by in situ x-ray diffraction (XRD). Experiments were performed at temperatures of 195, 210, 235, and 250°C using a custom designed and fabricated sample isolation stage. Data were refined to quantify phase fractions using a newly proposed structure for the ε-UO 3 polymorph. The kinetics data were modeled using a shrinking core approach. A proposed two-step reaction process is presented based on the developed models.

A Model for Dissolution of Lime in Steelmaking Slags

NASA Astrophysics Data System (ADS)

Sarkar, Rahul; Roy, Ushasi; Ghosh, Dinabandhu

2016-08-01

In a previous study by Sarkar et al. (Metall. Mater. Trans. B 46B:961 2015), a dynamic model of the LD steelmaking was developed. The prediction of the previous model (Sarkar et al. in Metall. Mater. Trans. B 46B:961 2015) for the bath (metal) composition matched well with the plant data (Cicutti et al. in Proceedings of 6th International Conference on Molten Slags, Fluxes and Salts, Stockholm City, 2000). However, with respect to the slag composition, the prediction was not satisfactory. The current study aims to improve upon the previous model Sarkar et al. (Metall. Mater. Trans. B 46B:961 2015) by incorporating a lime dissolution submodel into the earlier one. From the industrial point of view, the understanding of the lime dissolution kinetics is important to meet the ever-increasing demand of producing low-P steel at a low basicity. In the current study, three-step kinetics for the lime dissolution is hypothesized on the assumption that a solid layer of 2CaO·SiO2 should form around the unreacted core of the lime. From the available experimental data, it seems improbable that the observed kinetics should be controlled singly by any one kinetic step. Accordingly, a general, mixed control model has been proposed to calculate the dissolution rate of the lime under varying slag compositions and temperatures. First, the rate equation for each of the three rate-controlling steps has been derived, for three different lime geometries. Next, the rate equation for the mixed control kinetics has been derived and solved to find the dissolution rate. The model predictions have been validated by means of the experimental data available in the literature. In addition, the effects of the process conditions on the dissolution rate have been studied, and compared with the experimental results wherever possible. Incorporation of this submodel into the earlier global model (Sarkar et al. in Metall. Mater. Trans. B 46B:961 2015) enables the prediction of the lime dissolution rate in the dynamic system of LD steelmaking. In addition, with the inclusion of this submodel, significant improvement in the prediction of the slag composition during the main blow period has been observed.

Kinetics of the pyrolysis of arundo, sawdust, corn stover and switch grass biomass by thermogravimetric analysis using a multi-stage model.

PubMed

Biney, Paul O; Gyamerah, Michael; Shen, Jiacheng; Menezes, Bruna

2015-03-01

A new multi-stage kinetic model has been developed for TGA pyrolysis of arundo, corn stover, sawdust and switch grass that accounts for the initial biomass weight (W0). The biomass were decomposed in a nitrogen atmosphere from 23°C to 900°C in a TGA at a single 20°C/min ramp rate in contrast with the isoconversion technique. The decomposition was divided into multiple stages based on the absolute local minimum values of conversion derivative, (dx/dT), obtained from DTG curves. This resulted in three decomposition stages for arundo, corn stover and sawdust and four stages for switch grass. A linearized multi-stage model was applied to the TGA data for each stage to determine the pre-exponential factor, activation energy, and reaction order. The activation energies ranged from 54.7 to 60.9 kJ/mol, 62.9 to 108.7 kJ/mol, and 18.4 to 257.9 kJ/mol for the first, second and the third decomposition stages respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

A new predictive multi-zone model for HCCI engine combustion

DOE PAGES

Bissoli, Mattia; Frassoldati, Alessio; Cuoci, Alberto; ...

2016-06-30

Here, this work introduces a new predictive multi-zone model for the description of combustion in Homogeneous Charge Compression Ignition (HCCI) engines. The model exploits the existing OpenSMOKE++ computational suite to handle detailed kinetic mechanisms, providing reliable predictions of the in-cylinder auto-ignition processes. All the elements with a significant impact on the combustion performances and emissions, like turbulence, heat and mass exchanges, crevices, residual burned gases, thermal and feed stratification are taken into account. Compared to other computational approaches, this model improves the description of mixture stratification phenomena by coupling a wall heat transfer model derived from CFD application with amore » proper turbulence model. Furthermore, the calibration of this multi-zone model requires only three parameters, which can be derived from a non-reactive CFD simulation: these adaptive variables depend only on the engine geometry and remain fixed across a wide range of operating conditions, allowing the prediction of auto-ignition, pressure traces and pollutants. This computational framework enables the use of detail kinetic mechanisms, as well as Rate of Production Analysis (RoPA) and Sensitivity Analysis (SA) to investigate the complex chemistry involved in the auto-ignition and the pollutants formation processes. In the final sections of the paper, these capabilities are demonstrated through the comparison with experimental data.« less

Parameter Balancing in Kinetic Models of Cell Metabolism†

PubMed Central

2010-01-01

Kinetic modeling of metabolic pathways has become a major field of systems biology. It combines structural information about metabolic pathways with quantitative enzymatic rate laws. Some of the kinetic constants needed for a model could be collected from ever-growing literature and public web resources, but they are often incomplete, incompatible, or simply not available. We address this lack of information by parameter balancing, a method to complete given sets of kinetic constants. Based on Bayesian parameter estimation, it exploits the thermodynamic dependencies among different biochemical quantities to guess realistic model parameters from available kinetic data. Our algorithm accounts for varying measurement conditions in the input data (pH value and temperature). It can process kinetic constants and state-dependent quantities such as metabolite concentrations or chemical potentials, and uses prior distributions and data augmentation to keep the estimated quantities within plausible ranges. An online service and free software for parameter balancing with models provided in SBML format (Systems Biology Markup Language) is accessible at www.semanticsbml.org. We demonstrate its practical use with a small model of the phosphofructokinase reaction and discuss its possible applications and limitations. In the future, parameter balancing could become an important routine step in the kinetic modeling of large metabolic networks. PMID:21038890

Thermodynamics and Kinetics of Prenucleation Clusters, Classical and Non-Classical Nucleation

PubMed Central

Zahn, Dirk

2015-01-01

Recent observations of prenucleation species and multi-stage crystal nucleation processes challenge the long-established view on the thermodynamics of crystal formation. Here, we review and generalize extensions to classical nucleation theory. Going beyond the conventional implementation as has been used for more than a century now, nucleation inhibitors, precursor clusters and non-classical nucleation processes are rationalized as well by analogous concepts based on competing interface and bulk energy terms. This is illustrated by recent examples of species formed prior to/instead of crystal nucleation and multi-step nucleation processes. Much of the discussed insights were obtained from molecular simulation using advanced sampling techniques, briefly summarized herein for both nucleation-controlled and diffusion-controlled aggregate formation. PMID:25914369

How Different kinds of Communication and the Mass Media Affect Tourism.

DTIC Science & Technology

1984-12-01

C. Criticism of the Two-Step Flow Model------------------------------ 38 3. The Multi-Step Flow Model or Theory------- 39 4. One-Step Flow Model or... Criticism of the Two-Step Flow Model Researchers have identified deficiencies in the r,,c-w:er :low-model. McNelly, for instance, se,7s mass...evidence of the relative importance of cc munication on the diffusion flow. 38 Rogers ’as criticized ] the theor-y on the grounds that: neither its

A CFD model for biomass fast pyrolysis in fluidized-bed reactors

NASA Astrophysics Data System (ADS)

Xue, Qingluan; Heindel, T. J.; Fox, R. O.

2010-11-01

A numerical study is conducted to evaluate the performance and optimal operating conditions of fluidized-bed reactors for fast pyrolysis of biomass to bio-oil. A comprehensive CFD model, coupling a pyrolysis kinetic model with a detailed hydrodynamics model, is developed. A lumped kinetic model is applied to describe the pyrolysis of biomass particles. Variable particle porosity is used to account for the evolution of particle physical properties. The kinetic scheme includes primary decomposition and secondary cracking of tar. Biomass is composed of reference components: cellulose, hemicellulose, and lignin. Products are categorized into groups: gaseous, tar vapor, and solid char. The particle kinetic processes and their interaction with the reactive gas phase are modeled with a multi-fluid model derived from the kinetic theory of granular flow. The gas, sand and biomass constitute three continuum phases coupled by the interphase source terms. The model is applied to investigate the effect of operating conditions on the tar yield in a fluidized-bed reactor. The influence of various parameters on tar yield, including operating temperature and others are investigated. Predicted optimal conditions for tar yield and scale-up of the reactor are discussed.

Analytical modelling of temperature effects on an AMPA-type synapse.

PubMed

Kufel, Dominik S; Wojcik, Grzegorz M

2018-05-11

It was previously reported, that temperature may significantly influence neural dynamics on the different levels of brain function. Thus, in computational neuroscience, it would be useful to make models scalable for a wide range of various brain temperatures. However, lack of experimental data and an absence of temperature-dependent analytical models of synaptic conductance does not allow to include temperature effects at the multi-neuron modeling level. In this paper, we propose a first step to deal with this problem: A new analytical model of AMPA-type synaptic conductance, which is able to incorporate temperature effects in low-frequency stimulations. It was constructed based on Markov model description of AMPA receptor kinetics using the set of coupled ODEs. The closed-form solution for the set of differential equations was found using uncoupling assumption (introduced in the paper) with few simplifications motivated both from experimental data and from Monte Carlo simulation of synaptic transmission. The model may be used for computationally efficient and biologically accurate implementation of temperature effects on AMPA receptor conductance in large-scale neural network simulations. As a result, it may open a wide range of new possibilities for researching the influence of temperature on certain aspects of brain functioning.

Multi-scale modeling of irradiation effects in spallation neutron source materials

NASA Astrophysics Data System (ADS)

Yoshiie, T.; Ito, T.; Iwase, H.; Kaneko, Y.; Kawai, M.; Kishida, I.; Kunieda, S.; Sato, K.; Shimakawa, S.; Shimizu, F.; Hashimoto, S.; Hashimoto, N.; Fukahori, T.; Watanabe, Y.; Xu, Q.; Ishino, S.

2011-07-01

Changes in mechanical property of Ni under irradiation by 3 GeV protons were estimated by multi-scale modeling. The code consisted of four parts. The first part was based on the Particle and Heavy-Ion Transport code System (PHITS) code for nuclear reactions, and modeled the interactions between high energy protons and nuclei in the target. The second part covered atomic collisions by particles without nuclear reactions. Because the energy of the particles was high, subcascade analysis was employed. The direct formation of clusters and the number of mobile defects were estimated using molecular dynamics (MD) and kinetic Monte-Carlo (kMC) methods in each subcascade. The third part considered damage structural evolutions estimated by reaction kinetic analysis. The fourth part involved the estimation of mechanical property change using three-dimensional discrete dislocation dynamics (DDD). Using the above four part code, stress-strain curves for high energy proton irradiated Ni were obtained.

Thermogravimetric kinetic study of agricultural residue biomass pyrolysis based on combined kinetics.

PubMed

Wang, Xun; Hu, Mian; Hu, Wanyong; Chen, Zhihua; Liu, Shiming; Hu, Zhiquan; Xiao, Bo

2016-11-01

Pyrolytic kinetic of an agricultural residue (AR) feedstock, a mixture of plants (cotton, wheat, rich, corn) stems, was investigated based on combined kinetics. The most suitable mechanism for AR one-step pyrolysis was f(α)=(1-α)(1.1816)α(-1.8428) with kinetic parameters of: apparent activation energy 221.7kJ/mol, pre-exponential factor 4.17E16s(-1). Pyrolysis of AR feedstock could not be described by one-step reaction attributes to heterogeneous features of pyrolysis processes. Combined kinetics three-parallel-reaction (CK-TPR) model fitted the pyrolysis experimental data very well. Reaction mechanisms for pseudo hemicelluloses, cellulose, lignin in CK-TPR model was f(α)=(1-α)(1.6244)α(-0.3371)[-ln(1-α)](-0.0515), f(α)=(1-α)(1.0597)α(-0.6909)[-ln(1-α)](0.9026) and f(α)=(1-α)(2.9577)α(-4.7719), respectively. Apparent activation energy of three pseudo components followed the order of Elignin(197.3kJ/mol)>Ecellulose(176.3kJ/mol)>Ehemicelluloses (151.1kJ/mol). Mechanism of hemicelluloses pyrolysis could be further expressed as f(α)=(1-α)(1.4). The pyrolytic mechanism of cellulose met the Nucleation well. However, mechanism of lignin pyrolysis was complex, which possibly was the combined effects of Nucleation, Diffusion, Geometrical contraction, and Power law. Copyright © 2016 Elsevier Ltd. All rights reserved.

Discrete dynamic modeling of cellular signaling networks.

PubMed

Albert, Réka; Wang, Rui-Sheng

2009-01-01

Understanding signal transduction in cellular systems is a central issue in systems biology. Numerous experiments from different laboratories generate an abundance of individual components and causal interactions mediating environmental and developmental signals. However, for many signal transduction systems there is insufficient information on the overall structure and the molecular mechanisms involved in the signaling network. Moreover, lack of kinetic and temporal information makes it difficult to construct quantitative models of signal transduction pathways. Discrete dynamic modeling, combined with network analysis, provides an effective way to integrate fragmentary knowledge of regulatory interactions into a predictive mathematical model which is able to describe the time evolution of the system without the requirement for kinetic parameters. This chapter introduces the fundamental concepts of discrete dynamic modeling, particularly focusing on Boolean dynamic models. We describe this method step-by-step in the context of cellular signaling networks. Several variants of Boolean dynamic models including threshold Boolean networks and piecewise linear systems are also covered, followed by two examples of successful application of discrete dynamic modeling in cell biology.

Atmospheric flow over two-dimensional bluff surface obstructions

NASA Technical Reports Server (NTRS)

Bitte, J.; Frost, W.

1976-01-01

The phenomenon of atmospheric flow over a two-dimensional surface obstruction, such as a building (modeled as a rectangular block, a fence or a forward-facing step), is analyzed by three methods: (1) an inviscid free streamline approach, (2) a turbulent boundary layer approach using an eddy viscosity turbulence model and a horizontal pressure gradient determined by the inviscid model, and (3) an approach using the full Navier-Stokes equations with three turbulence models; i.e., an eddy viscosity model, a turbulence kinetic-energy model and a two-equation model with an additional transport equation for the turbulence length scale. A comparison of the performance of the different turbulence models is given, indicating that only the two-equation model adequately accounts for the convective character of turbulence. Turbulence flow property predictions obtained from the turbulence kinetic-energy model with prescribed length scale are only insignificantly better than those obtained from the eddy viscosity model. A parametric study includes the effects of the variation of the characteristics parameters of the assumed logarithmic approach velocity profile. For the case of the forward-facing step, it is shown that in the downstream flow region an increase of the surface roughness gives rise to higher turbulence levels in the shear layer originating from the step corner.

Unraveling reaction pathways and specifying reaction kinetics for complex systems.

PubMed

Vinu, R; Broadbelt, Linda J

2012-01-01

Many natural and industrial processes involve a complex set of competing reactions that include several different species. Detailed kinetic modeling of such systems can shed light on the important pathways involved in various transformations and therefore can be used to optimize the process conditions for the desired product composition and properties. This review focuses on elucidating the various components involved in modeling the kinetics of pyrolysis and oxidation of polymers. The elementary free radical steps that constitute the chain reaction mechanism of gas-phase/nonpolar liquid-phase processes are outlined. Specification of the rate coefficients of the various reaction families, which is central to the theme of kinetics, is described. Construction of the reaction network on the basis of the types of end groups and reactive moieties in a polymer chain is discussed. Modeling frameworks based on the method of moments and kinetic Monte Carlo are evaluated using illustrations. Finally, the prospects and challenges in modeling biomass conversion are addressed.

Uncovering Oscillations, Complexity, and Chaos in Chemical Kinetics Using Mathematica

NASA Astrophysics Data System (ADS)

Ferreira, M. M. C.; Ferreira, W. C., Jr.; Lino, A. C. S.; Porto, M. E. G.

1999-06-01

Unlike reactions with no peculiar temporal behavior, in oscillatory reactions concentrations can rise and fall spontaneously in a cyclic or disorganized fashion. In this article, the software Mathematica is used for a theoretical study of kinetic mechanisms of oscillating and chaotic reactions. A first simple example is introduced through a three-step reaction, called the Lotka model, which exhibits a temporal behavior characterized by damped oscillations. The phase plane method of dynamic systems theory is introduced for a geometric interpretation of the reaction kinetics without solving the differential rate equations. The equations are later numerically solved using the built-in routine NDSolve and the results are plotted. The next example, still with a very simple mechanism, is the Lotka-Volterra model reaction, which oscillates indefinitely. The kinetic process and rate equations are also represented by a three-step reaction mechanism. The most important difference between this and the former reaction is that the undamped oscillation has two autocatalytic steps instead of one. The periods of oscillations are obtained by using the discrete Fourier transform (DFT)-a well-known tool in spectroscopy, although not so common in this context. In the last section, it is shown how a simple model of biochemical interactions can be useful to understand the complex behavior of important biological systems. The model consists of two allosteric enzymes coupled in series and activated by its own products. This reaction scheme is important for explaining many metabolic mechanisms, such as the glycolytic oscillations in muscles, yeast glycolysis, and the periodic synthesis of cyclic AMP. A few of many possible dynamic behaviors are exemplified through a prototype glycolytic enzymatic reaction proposed by Decroly and Goldbeter. By simply modifying the initial concentrations, limit cycles, chaos, and birhythmicity are computationally obtained and visualized.

Linear stability analysis of detonations via numerical computation and dynamic mode decomposition

NASA Astrophysics Data System (ADS)

Kabanov, Dmitry I.; Kasimov, Aslan R.

2018-03-01

We introduce a new method to investigate linear stability of gaseous detonations that is based on an accurate shock-fitting numerical integration of the linearized reactive Euler equations with a subsequent analysis of the computed solution via the dynamic mode decomposition. The method is applied to the detonation models based on both the standard one-step Arrhenius kinetics and two-step exothermic-endothermic reaction kinetics. Stability spectra for all cases are computed and analyzed. The new approach is shown to be a viable alternative to the traditional normal-mode analysis used in detonation theory.

A kinetic model of the formation of organic monolayers on hydrogen-terminated silicon by hydrosilation of alkenes.

PubMed

Woods, M; Carlsson, S; Hong, Q; Patole, S N; Lie, L H; Houlton, A; Horrocks, B R

2005-12-22

We have analyzed a kinetic model for the formation of organic monolayers based on a previously suggested free radical chain mechanism for the reaction of unsaturated molecules with hydrogen-terminated silicon surfaces (Linford, M. R.; Fenter, P. M.; Chidsey, C. E. D. J. Am. Chem. Soc 1995, 117, 3145). A direct consequence of this mechanism is the nonexponential growth of the monolayer, and this has been observed spectroscopically. In the model, the initiation of silyl radicals on the surface is pseudo first order with rate constant, ki, and the rate of propagation is determined by the concentration of radicals and unreacted Si-H nearest neighbor sites with a rate constant, kp. This propagation step determines the rate at which the monolayer forms by addition of alkene molecules to form a track of molecules that constitute a self-avoiding random walk on the surface. The initiation step describes how frequently new random walks commence. A termination step by which the radicals are destroyed is also included. The solution of the kinetic equations yields the fraction of alkylated surface sites and the mean length of the random walks as a function of time. In mean-field approximation we show that (1) the average length of the random walk is proportional to (kp/ki)1/2, (2) the monolayer surface coverage grows exponentially only after an induction period, (3) the effective first-order rate constant describing the growth of the monolayer and the induction period (kt) is k = (2ki kp)1/2, (4) at long times the effective first-order rate constant drops to ki, and (5) the overall activation energy for the growth kinetics is the mean of the activation energies for the initiation and propagation steps. Monte Carlo simulations of the mechanism produce qualitatively similar kinetic plots, but the mean random walk length (and effective rate constant) is overestimated by the mean field approximation and when kp > ki, we find k approximately ki0.7kp0.3 and Ea = (0.7Ei+ 0.3Ep). However the most striking prediction of the Monte Carlo simulations is that at long times, t > 1/k, the effective first-order rate constant decreases to ki even in the absence of a chemical termination step. Experimental kinetic data for the reaction of undec-1-ene with hydrogen-terminated porous silicon under thermal reflux in toluene and ethylbenzene gave a value of k = 0.06 min(-1) and an activation energy of 107 kJ mol(-1). The activation energy is in reasonable agreement with density functional calculations of the transition state energies for the initiation and propagation steps.

Removal of humic acid from aqueous solution using dual PMMA/PVDF composite nanofiber: kinetics study

NASA Astrophysics Data System (ADS)

Zulfikar, M. A.; Afrianingsih, I.; Bahri, A.; Nasir, M.; Alni, A.; Setiyanto, H.

2018-05-01

The removal of humic acid from aqueous solution using dual poly(methyl methacrylate)/polyvinyl difluoride composite nanofiber under the influence of concentration has been studied. The experiments were performed using humic acid (HA) as an adsorbate at concentration in the range of 50-200 mg/L. Pseudo-first-order, pseudo-second-order, and intra-particle diffusion models were used to describe the kinetic data and the rate constants were evaluated. It was observed that the amount of humic acid removed decrease with increasing concentration. The kinetic study revealed that pseudo-second order model fitted well the kinetic data, while the external diffusion or boundary layer diffusion was the main rate determining step in the removal process.

Toward a Model Framework of Generalized Parallel Componential Processing of Multi-Symbol Numbers

ERIC Educational Resources Information Center

Huber, Stefan; Cornelsen, Sonja; Moeller, Korbinian; Nuerk, Hans-Christoph

2015-01-01

In this article, we propose and evaluate a new model framework of parallel componential multi-symbol number processing, generalizing the idea of parallel componential processing of multi-digit numbers to the case of negative numbers by considering the polarity signs similar to single digits. In a first step, we evaluated this account by defining…

BEARKIMPE-2: A VBA Excel program for characterizing granular iron in treatability studies

NASA Astrophysics Data System (ADS)

Firdous, R.; Devlin, J. F.

2014-02-01

The selection of a suitable kinetic model to investigate the reaction rate of a contaminant with granular iron (GI) is essential to optimize the permeable reactive barrier (PRB) performance in terms of its reactivity. The newly developed Kinetic Iron Model (KIM) determines the surface rate constant (k) and sorption parameters (Cmax &J) which were not possible to uniquely identify previously. The code was written in Visual Basic (VBA), within Microsoft Excel, was adapted from earlier command line FORTRAN codes, BEARPE and KIMPE. The program is organized with several user interface screens (UserForms) that guide the user step by step through the analysis. BEARKIMPE-2 uses a non-linear optimization algorithm to calculate transport and chemical kinetic parameters. Both reactive and non-reactive sites are considered. A demonstration of the functionality of BEARKIMPE-2, with three nitroaromatic compounds showed that the differences in reaction rates for these compounds could be attributed to differences in their sorption behavior rather than their propensities to accept electrons in the reduction process.

Estimation of kinetics parameters for the adsorption of human serum albumin onto hydroxyapatite-modified silver electrodes by piezoelectric quartz crystal impedance analysis.

PubMed

Tian, Lu; Wei, Wan-Zhi; Mao, You-An

2004-04-01

The adsorption of human serum albumin onto hydroxyapatite-modified silver electrodes has been in situ investigated by utilizing the piezoelectric quartz crystal impedance technique. The changes of equivalent circuit parameters were used to interpret the adsorption process. A kinetic model of two consecutive steps was derived to describe the process and compared with a first-order kinetic model by using residual analysis. The experimental data of frequency shift fitted to the model and kinetics parameters, k1, k2, psi1, psi2 and qr, were obtained. All fitted results were in reasonable agreement with the corresponding experimental results. Two adsorption constants (7.19 kJ mol(-1) and 22.89 kJ mol(-1)) were calculated according to the Arrhenius formula.

Multi-Model Combination techniques for Hydrological Forecasting: Application to Distributed Model Intercomparison Project Results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ajami, N K; Duan, Q; Gao, X

2005-04-11

This paper examines several multi-model combination techniques: the Simple Multi-model Average (SMA), the Multi-Model Super Ensemble (MMSE), Modified Multi-Model Super Ensemble (M3SE) and the Weighted Average Method (WAM). These model combination techniques were evaluated using the results from the Distributed Model Intercomparison Project (DMIP), an international project sponsored by the National Weather Service (NWS) Office of Hydrologic Development (OHD). All of the multi-model combination results were obtained using uncalibrated DMIP model outputs and were compared against the best uncalibrated as well as the best calibrated individual model results. The purpose of this study is to understand how different combination techniquesmore » affect the skill levels of the multi-model predictions. This study revealed that the multi-model predictions obtained from uncalibrated single model predictions are generally better than any single member model predictions, even the best calibrated single model predictions. Furthermore, more sophisticated multi-model combination techniques that incorporated bias correction steps work better than simple multi-model average predictions or multi-model predictions without bias correction.« less

Multi-water-bag models of ion temperature gradient instability in cylindrical geometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coulette, David; Besse, Nicolas

2013-05-15

Ion temperature gradient instabilities play a major role in the understanding of anomalous transport in core fusion plasmas. In the considered cylindrical geometry, ion dynamics is described using a drift-kinetic multi-water-bag model for the parallel velocity dependency of the ion distribution function. In a first stage, global linear stability analysis is performed. From the obtained normal modes, parametric dependencies of the main spectral characteristics of the instability are then examined. Comparison of the multi-water-bag results with a reference continuous Maxwellian case allows us to evaluate the effects of discrete parallel velocity sampling induced by the Multi-Water-Bag model. Differences between themore » global model and local models considered in previous works are discussed. Using results from linear, quasilinear, and nonlinear numerical simulations, an analysis of the first stage saturation dynamics of the instability is proposed, where the divergence between the three models is examined.« less

Biochemical Kinetics Model of DSB Repair and GammaH2AX FOCI by Non-homologous End Joining

NASA Technical Reports Server (NTRS)

Cucinotta, Francis, A.; Pluth, Janice M.; Anderson, Jennifer A.; Harper, Jane V.; O'Neill, Peter

2007-01-01

We developed a biochemical kinetics approach to describe the repair of double strand breaks (DSB) produced by low LET radiation by modeling molecular events associated with the mechanisms of non-homologous end-joining (NHEJ). A system of coupled non-linear ordinary differential equations describes the induction of DSB and activation pathways for major NHEJ components including Ku(sub 70/80), DNA-PK(sub cs), and the Ligase IV-XRCC4 hetero-dimer. The autophosphorylation of DNA-PK(sub cs and subsequent induction of gamma-H2AX foci observed after ionizing radiation exposure were modeled. A two-step model of DNA-PK(sub cs) regulation of repair was developed with the initial step allowing access of other NHEJ components to breaks, and a second step limiting access to Ligase IV-XRCC4. Our model assumes that the transition from the first to second-step depends on DSB complexity, with a much slower-rate for complex DSB. The model faithfully reproduced several experimental data sets, including DSB rejoining as measured by pulsed-field electrophoresis (PFGE), quantification of the induction of gamma-H2AX foci, and live cell imaging of the induction of Ku(sub 70/80). Predictions are made for the behaviors of NHEJ components at low doses and dose-rates, where a steady-state is found at dose-rates of 0.1 Gy/hr or lower.

Kinetic coupling of phosphate release, force generation and rate-limiting steps in the cross-bridge cycle.

PubMed

Stehle, Robert; Tesi, Chiara

2017-08-01

A basic goal in muscle research is to understand how the cyclic ATPase activity of cross-bridges is converted into mechanical force. A direct approach to study the chemo-mechanical coupling between P i release and the force-generating step is provided by the kinetics of force response induced by a rapid change in [P i ]. Classical studies on fibres using caged-P i discovered that rapid increases in [P i ] induce fast force decays dependent on final [P i ] whose kinetics were interpreted to probe a fast force-generating step prior to P i release. However, this hypothesis was called into question by studies on skeletal and cardiac myofibrils subjected to P i jumps in both directions (increases and decreases in [P i ]) which revealed that rapid decreases in [P i ] trigger force rises with slow kinetics, similar to those of calcium-induced force development and mechanically-induced force redevelopment at the same [P i ]. A possible explanation for this discrepancy came from imaging of individual sarcomeres in cardiac myofibrils, showing that the fast force decay upon increase in [P i ] results from so-called sarcomere 'give'. The slow force rise upon decrease in [P i ] was found to better reflect overall sarcomeres cross-bridge kinetics and its [P i ] dependence, suggesting that the force generation coupled to P i release cannot be separated from the rate-limiting transition. The reasons for the different conclusions achieved in fibre and myofibril studies are re-examined as the recent findings on cardiac myofibrils have fundamental consequences for the coupling between P i release, rate-limiting steps and force generation. The implications from P i -induced force kinetics of myofibrils are discussed in combination with historical and recent models of the cross-bridge cycle.

Ultra-fast consensus of discrete-time multi-agent systems with multi-step predictive output feedback

NASA Astrophysics Data System (ADS)

Zhang, Wenle; Liu, Jianchang

2016-04-01

This article addresses the ultra-fast consensus problem of high-order discrete-time multi-agent systems based on a unified consensus framework. A novel multi-step predictive output mechanism is proposed under a directed communication topology containing a spanning tree. By predicting the outputs of a network several steps ahead and adding this information into the consensus protocol, it is shown that the asymptotic convergence factor is improved by a power of q + 1 compared to the routine consensus. The difficult problem of selecting the optimal control gain is solved well by introducing a variable called convergence step. In addition, the ultra-fast formation achievement is studied on the basis of this new consensus protocol. Finally, the ultra-fast consensus with respect to a reference model and robust consensus is discussed. Some simulations are performed to illustrate the effectiveness of the theoretical results.

Model predictive control design for polytopic uncertain systems by synthesising multi-step prediction scenarios

NASA Astrophysics Data System (ADS)

Lu, Jianbo; Xi, Yugeng; Li, Dewei; Xu, Yuli; Gan, Zhongxue

2018-01-01

A common objective of model predictive control (MPC) design is the large initial feasible region, low online computational burden as well as satisfactory control performance of the resulting algorithm. It is well known that interpolation-based MPC can achieve a favourable trade-off among these different aspects. However, the existing results are usually based on fixed prediction scenarios, which inevitably limits the performance of the obtained algorithms. So by replacing the fixed prediction scenarios with the time-varying multi-step prediction scenarios, this paper provides a new insight into improvement of the existing MPC designs. The adopted control law is a combination of predetermined multi-step feedback control laws, based on which two MPC algorithms with guaranteed recursive feasibility and asymptotic stability are presented. The efficacy of the proposed algorithms is illustrated by a numerical example.

The effects of chemical kinetics and wall temperature on performance of porous media burners

NASA Astrophysics Data System (ADS)

mohammadi, Iman; Hossainpour, Siamak

2013-06-01

This paper reports a two-dimensional numerical prediction of premixed methane-air combustion in inert porous media burner by using of four multi-step mechanisms: GRI-3.0 mechanism, GRI-2.11 mechanism and the skeletal and 17 Species mechanisms. The effects of these models on temperature, chemical species and pollutant emissions are studied. A two-dimensional axisymmetric model for premixed methane-air combustion in porous media burner has developed. The finite volume method has used to solve the governing equations of methane-air combustion in inert porous media burner. The results indicate that the present four models have the same accuracy in predicting temperature profiles and the difference between these profiles is not more than 2 %. In addition, the Gri-3.0 mechanism shows the best prediction of NO emission in comparison with experimental data. The 17 Species mechanism shows good agreement in prediction of temperature and pollutant emissions with GRI-3.0, GRI-2.11 and the skeletal mechanisms. Also the effects of wall temperature on the gas temperature and mass fraction of species such as NO and CH4 are studied.

Kinematic predictors of loading during running differ by demographic group.

PubMed

Harrison, Kathryn; Thakkar, Bhushan; Kwon, Yong Ung; Crosswell, Gregory; Morgan, Jacqueline; Williams, D S Blaise

2018-05-24

To investigate whether previously-determined kinematic predictors of kinetics during running differ between demographic groups. Young male (n = 13, age = 22 (2) yrs), young female (n = 13, age = 25 (4) yrs), older male (n = 13, age = 50 (4) yrs) and older female (n = 13, age = 52 (3) yrs) runners. Sagittal plane kinematics and kinetics were assessed while participants ran at their preferred pace. Linear regression models were developed to predict kinetics in each group using kinematics as independent variables. Step length was positively associated with magnitude of at least one kinetic variable in all groups. Step position was inversely associated with vertical ground reaction force variables in all groups. Step frequency and CoM excursion were also important to all groups, however direction of the associations varied. Foot angle at initial contact was important to all groups except older females. Peak knee flexion was most important to older females, but was not important to any other groups. Optimal parameters for gait analysis of runners may depend on demographics of the individual. This provides insight for clinicians into the most effective evaluation and interventions strategies for different types of runners. Copyright © 2018. Published by Elsevier Ltd.

Modified kinetic theory applied to the shear flows of granular materials

DOE PAGES

Duan, Yifei; Feng, Zhi -Gang; Michaelides, Efstathios E.; ...

2017-04-11

Here, granular materials are characterized by large collections of discrete particles, where the particle-particle interactions are significantly more important than the particle-fluid interactions. The current kinetic theory captures fairly accurately the granular flow behavior in the dilute case, when only binary interactions are significant, but is not accurate at all in the dense flow regime, where multi-particle interactions and contacts must be modeled. To improve the kinetic theory results for granular flows in the dense flow regime, we propose a Modified Kinetic Theory (MKT) model that utilizes the contact duration or cut-off time to account for the complex particle-particle interactionsmore » in the dense regime. The contact duration model, also called TC model, is originally proposed by Luding and McNamara to solve the inelastic collapse issue existing in the Inelastic Hard Sphere (IHS) model. This model defines a cut-off time t c such that dissipation is not counted if the time between two consecutive contacts is less than t c. As shown in their study, the use of a cut-off time t c can also reduce the dissipation during multi-particle contacts. In this paper we relate the TC model with the Discrete Element Method (DEM) by choosing the cut-off time t c to be the duration of contact calculated from the linear-spring-dashpot soft-sphere model of the DEM. We examine two types of granular flows: simple shear flow and the plane shear flow, and compare the results of the classical Kinetic Theory (KT) model, the present MKT model, and the DEM model. Here, we show that the MKT model entails a significant improvement over the KT model for simple shear flows at inertial regimes. With the MKT model the calculations are close to the DEM results at solid fractions as high as 0.57. Even for the plane shear flows, where shear rate and solid fraction are inhomogeneous, the results of the MKT model agree very well with the DEM results.« less

Modified kinetic theory applied to the shear flows of granular materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duan, Yifei; Feng, Zhi -Gang; Michaelides, Efstathios E.

Here, granular materials are characterized by large collections of discrete particles, where the particle-particle interactions are significantly more important than the particle-fluid interactions. The current kinetic theory captures fairly accurately the granular flow behavior in the dilute case, when only binary interactions are significant, but is not accurate at all in the dense flow regime, where multi-particle interactions and contacts must be modeled. To improve the kinetic theory results for granular flows in the dense flow regime, we propose a Modified Kinetic Theory (MKT) model that utilizes the contact duration or cut-off time to account for the complex particle-particle interactionsmore » in the dense regime. The contact duration model, also called TC model, is originally proposed by Luding and McNamara to solve the inelastic collapse issue existing in the Inelastic Hard Sphere (IHS) model. This model defines a cut-off time t c such that dissipation is not counted if the time between two consecutive contacts is less than t c. As shown in their study, the use of a cut-off time t c can also reduce the dissipation during multi-particle contacts. In this paper we relate the TC model with the Discrete Element Method (DEM) by choosing the cut-off time t c to be the duration of contact calculated from the linear-spring-dashpot soft-sphere model of the DEM. We examine two types of granular flows: simple shear flow and the plane shear flow, and compare the results of the classical Kinetic Theory (KT) model, the present MKT model, and the DEM model. Here, we show that the MKT model entails a significant improvement over the KT model for simple shear flows at inertial regimes. With the MKT model the calculations are close to the DEM results at solid fractions as high as 0.57. Even for the plane shear flows, where shear rate and solid fraction are inhomogeneous, the results of the MKT model agree very well with the DEM results.« less

Multiscale Models for the Two-Stream Instability

NASA Astrophysics Data System (ADS)

Joseph, Ilon; Dimits, Andris; Banks, Jeffrey; Berger, Richard; Brunner, Stephan; Chapman, Thomas

2017-10-01

Interpenetrating streams of plasma found in many important scenarios in nature and in the laboratory can develop kinetic two-stream instabilities that exchange momentum and energy between the streams. A quasilinear model for the electrostatic two-stream instability is under development as a component of a multiscale model that couples fluid simulations to kinetic theory. Parameters of the model will be validated with comparison to full kinetic simulations using LOKI and efficient strategies for numerical solution of the quasilinear model and for coupling to the fluid model will be discussed. Extending the kinetic models into the collisional regime requires an efficient treatment of the collision operator. Useful reductions of the collision operator relative to the full multi-species Landau-Fokker-Plank operator are being explored. These are further motivated both by careful consideration of the parameter orderings relevant to two-stream scenarios and by the particular 2D+2V phase space used in the LOKI code. Prepared for US DOE by LLNL under Contract DE-AC52-07NA27344 and LDRD project 17- ERD-081.

Pre-Steady State Kinetic Analysis of cis-3-Chloroacrylic Acid Dehalogenase: Analysis and Implications†

PubMed Central

Robertson, Brooklyn A.; Schroeder, Gottfried K.; Jin, Zhinan; Johnson, Kenneth A.; Whitman, Christian P.

2009-01-01

Isomer-specific 3-chloroacrylic acid dehalogenases catalyze the hydrolytic dehalogenation of the cis- and trans-isomers of 3-chloroacrylate to yield malonate semialdehyde. These reactions represent key steps in the degradation of the nematocide, 1,3-dichloropropene. The kinetic mechanism of cis-3-chloroacrylic acid dehalogenase (cis-CaaD) has now been examined using stopped-flow and chemical-quench techniques. Stopped-flow analysis of the reaction, following the fluorescence of an active site tryptophan, is consistent with a minimal three-step model involving substrate binding, chemistry, and product release. Chemical quench experiments show burst kinetics, indicating that product release is at least partially rate limiting. Global fitting of all of the kinetic results by simulation is best accommodated by a four-step mechanism. In the final kinetic model, the enzyme binds substrate and isomerizes to an alternate fluorescent form, chemistry occurs, and is followed by the ordered release of two products, with the release of the first product as the rate-limiting step. Bromide ion is a competitive inhibitor of the reaction indicating that it binds to the free enzyme rather than to the enzyme with one product still bound. This observation suggests that malonate semialdehyde is the first product released by the enzyme (rate limiting), followed by halide. A comparison of the unliganded cis-CaaD crystal structure with that of an inactivated cis-CaaD where the prolyl nitrogen of Pro-1 is covalently attached to (R)-2-hydroxypropanoate provides a possible explanation for the isomerization step. The structure of the covalently modified enzyme shows that a 7-residue loop comprised of residues 32-38 is closed down on the active site cavity where the backbone amides of two residues (Phe-37 and Leu-38) interact with the carboxylate group of the adduct. In the unliganded form, the same loop points away from the active site cavity. Similarly, substrate binding may cause this loop to close down on the active site and sequester the reaction from the external environment. PMID:19856961

Model calibration and validation for OFMSW and sewage sludge co-digestion reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Esposito, G., E-mail: giovanni.esposito@unicas.it; Frunzo, L., E-mail: luigi.frunzo@unina.it; Panico, A., E-mail: anpanico@unina.it

2011-12-15

Highlights: > Disintegration is the limiting step of the anaerobic co-digestion process. > Disintegration kinetic constant does not depend on the waste particle size. > Disintegration kinetic constant depends only on the waste nature and composition. > The model calibration can be performed on organic waste of any particle size. - Abstract: A mathematical model has recently been proposed by the authors to simulate the biochemical processes that prevail in a co-digestion reactor fed with sewage sludge and the organic fraction of municipal solid waste. This model is based on the Anaerobic Digestion Model no. 1 of the International Watermore » Association, which has been extended to include the co-digestion processes, using surface-based kinetics to model the organic waste disintegration and conversion to carbohydrates, proteins and lipids. When organic waste solids are present in the reactor influent, the disintegration process is the rate-limiting step of the overall co-digestion process. The main advantage of the proposed modeling approach is that the kinetic constant of such a process does not depend on the waste particle size distribution (PSD) and rather depends only on the nature and composition of the waste particles. The model calibration aimed to assess the kinetic constant of the disintegration process can therefore be conducted using organic waste samples of any PSD, and the resulting value will be suitable for all the organic wastes of the same nature as the investigated samples, independently of their PSD. This assumption was proven in this study by biomethane potential experiments that were conducted on organic waste samples with different particle sizes. The results of these experiments were used to calibrate and validate the mathematical model, resulting in a good agreement between the simulated and observed data for any investigated particle size of the solid waste. This study confirms the strength of the proposed model and calibration procedure, which can thus be used to assess the treatment efficiency and predict the methane production of full-scale digesters.« less

Physiological Response of Plants Grown on Porous Ceramic Tubes

NASA Technical Reports Server (NTRS)

Tsao, David; Okos, Martin

1997-01-01

This research involves the manipulation of the root-zone water potential for the purposes of discriminating the rate limiting step in the inorganic nutrient uptake mechanism utilized by higher plants. This reaction sequence includes the pathways controlled by the root-zone conditions such as water tension and gradient concentrations. Furthermore, plant based control mechanisms dictated by various protein productions are differentiated as well. For the nutrients limited by the environmental availability, the kinetics were modeled using convection and diffusion equations. Alternatively, for the nutrients dependent upon enzyme manipulations, the uptakes are modeled using Michaelis-Menten kinetics. In order to differentiate between these various mechanistic steps, an experimental apparatus known as the Porous Ceramic Tube - Nutrient Delivery System (PCT-NDS) was used. Manipulation of the applied suction pressure circulating a nutrient solution through this system imposes a change in the matric component of the water potential. This compensates for the different osmotic components of water potential dictated by nutrient concentration. By maintaining this control over the root-zone conditions, the rate limiting steps in the uptake of the essential nutrients into tomato plants (Lycopersicon esculentum cv. Cherry Elite) were differentiated. Results showed that the uptake of some nutrients were mass transfer limited while others were limited by the enzyme kinetics. Each of these were adequately modeled with calculations and discussions of the parameter estimations provided.

Kinetic modeling of non-ideal explosives with CHEETAH

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

1998-08-06

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

Self-Regulated Strategy Development Instruction for Teaching Multi-Step Equations to Middle School Students Struggling in Math

ERIC Educational Resources Information Center

Cuenca-Carlino, Yojanna; Freeman-Green, Shaqwana; Stephenson, Grant W.; Hauth, Clara

2016-01-01

Six middle school students identified as having a specific learning disability or at risk for mathematical difficulties were taught how to solve multi-step equations by using the self-regulated strategy development (SRSD) model of instruction. A multiple-probe-across-pairs design was used to evaluate instructional effects. Instruction was provided…

Evaluation of BTEX and phenol removal from aqueous solution by multi-solute adsorption onto smectite organoclay.

PubMed

Carvalho, M N; da Motta, M; Benachour, M; Sales, D C S; Abreu, C A M

2012-11-15

The removal process of BTEX and phenol was evaluated. The smectite organoclay for single-solute system reached removal was evaluated by adsorption on smectite organoclay adsorbent by kinetic and equilibrium efficiencies between 55 and 90% while was reached between 30 and 90% for multi-solute system at 297 K and pH 9. The Langmuir-Freundlich model was used to fit the experimental data with correlation coefficient between 0.98 and 0.99 providing kinetic and equilibrium parameter values. Phenol and ethylbenzene presented high maximum adsorbed amount, 8.28 and 6.67 mg/g, respectively, compared to the other compounds for single-solute. Toluene and p-xylene presented high values of adsorption constant which indicates a high adsorption affinity of compounds to organoclay surface and high binding energy of adsorption. Phenol presented low kinetic adsorption constant value indicating slow rate of adsorption. Copyright © 2012 Elsevier B.V. All rights reserved.

Transient Simulation of the Multi-SERTTA Experiment with MAMMOTH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ortensi, Javier; Baker, Benjamin; Wang, Yaqi

This work details the MAMMOTH reactor physics simulations of the Static Environment Rodlet Transient Test Apparatus (SERTTA) conducted at Idaho National Laboratory in FY-2017. TREAT static-environment experiment vehicles are being developed to enable transient testing of Pressurized Water Reactor (PWR) type fuel specimens, including fuel concepts with enhanced accident tolerance (Accident Tolerant Fuels, ATF). The MAMMOTH simulations include point reactor kinetics as well as spatial dynamics for a temperature-limited transient. The strongly coupled multi-physics solutions of the neutron flux and temperature fields are second order accurate both in the spatial and temporal domains. MAMMOTH produces pellet stack powers that are within 1.5% of the Monte Carlo reference solutions. Some discrepancies between the MCNP model used in the design of the flux collars and the Serpent/MAMMOTH models lead to higher power and energy deposition values in Multi-SERTTA unit 1. The TREAT core results compare well with the safety case computed with point reactor kinetics in RELAP5-3D. The reactor period is 44 msec, which corresponds to a reactivity insertion of 2.685% delta k/kmore » $. The peak core power in the spatial dynamics simulation is 431 MW, which the point kinetics model over-predicts by 12%. The pulse width at half the maximum power is 0.177 sec. Subtle transient effects are apparent at the beginning insertion in the experimental samples due to the control rod removal. Additional difference due to transient effects are observed in the sample powers and enthalpy. The time dependence of the power coupling factor (PCF) is calculated for the various fuel stacks of the Multi-SERTTA vehicle. Sample temperatures in excess of 3100 K, the melting point UO$$_2$$, are computed with the adiabatic heat transfer model. The planned shaped-transient might introduce additional effects that cannot be predicted with PRK models. Future modeling will be focused on the shaped-transient by improving the control rod models in MAMMOTH and adding the BISON thermo-elastic models and thermal-fluids heat transfer.« less

Kinetic Modelling and Experimental Studies for the Effects of Fe 2+ Ions on Xylan Hydrolysis with Dilute-Acid Pretreatment and Subsequent Enzymatic Hydrolysis

DOE PAGES

Wei, Hui; Chen, Xiaowen; Shekiro, Joseph; ...

2018-01-20

High-temperature (150-170 degrees C) pretreatment of lignocellulosic biomass with mineral acids is well established for xylan breakdown. Fe 2+ is known to be a cocatalyst of this process although kinetics of its action remains unknown. The present work addresses the effect of ferrous ion concentration on sugar yield and degradation product formation from corn stover for the entire two-step treatment, including the subsequent enzymatic cellulose hydrolysis. The feedstock was impregnated with 0.5% acid and 0.75 mM iron cocatalyst, which was found to be optimal in preliminary experiments. The detailed kinetic data of acid pretreatment, with and without iron, was satisfactorilymore » modelled with a four-step linear sequence of first-order irreversible reactions accounting for the formation of xylooligomers, xylose and furfural as intermediates to provide the values of Arrhenius activation energy. Based on this kinetic modelling, Fe 2+ turned out to accelerate all four reactions, with a significant alteration of the last two steps, that is, xylose degradation. Consistent with this model, the greatest xylan conversion occurred at the highest severity tested under 170 ⁰C/30 min with 0.75 mM Fe 2+, with a total of 8% xylan remaining in the pretreated solids, whereas the operational conditions leading to the highest xylose monomer yield, 63%, were milder, 150 degrees C with 0.75 mM Fe 2+ for 20 min. Furthermore, the subsequent enzymatic hydrolysis with the prior addition of 0.75 mM of iron(II) increased the glucose production to 56.3% from 46.3% in the control (iron-free acid). The detailed analysis indicated that conducting the process at lower temperatures yet long residence times benefits the yield of sugars. The above kinetic modelling results of Fe 2+ accelerating all four reactions are in line with our previous mechanistic research showing that the pretreatment likely targets multiple chemistries in plant cell wall polymer networks, including those represented by the C-O-C and C-H bonds in cellulose, resulting in enhanced sugar solubilization and digestibility.« less

Kinetic Modelling and Experimental Studies for the Effects of Fe 2+ Ions on Xylan Hydrolysis with Dilute-Acid Pretreatment and Subsequent Enzymatic Hydrolysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei, Hui; Chen, Xiaowen; Shekiro, Joseph

High-temperature (150-170 degrees C) pretreatment of lignocellulosic biomass with mineral acids is well established for xylan breakdown. Fe 2+ is known to be a cocatalyst of this process although kinetics of its action remains unknown. The present work addresses the effect of ferrous ion concentration on sugar yield and degradation product formation from corn stover for the entire two-step treatment, including the subsequent enzymatic cellulose hydrolysis. The feedstock was impregnated with 0.5% acid and 0.75 mM iron cocatalyst, which was found to be optimal in preliminary experiments. The detailed kinetic data of acid pretreatment, with and without iron, was satisfactorilymore » modelled with a four-step linear sequence of first-order irreversible reactions accounting for the formation of xylooligomers, xylose and furfural as intermediates to provide the values of Arrhenius activation energy. Based on this kinetic modelling, Fe 2+ turned out to accelerate all four reactions, with a significant alteration of the last two steps, that is, xylose degradation. Consistent with this model, the greatest xylan conversion occurred at the highest severity tested under 170 ⁰C/30 min with 0.75 mM Fe 2+, with a total of 8% xylan remaining in the pretreated solids, whereas the operational conditions leading to the highest xylose monomer yield, 63%, were milder, 150 degrees C with 0.75 mM Fe 2+ for 20 min. Furthermore, the subsequent enzymatic hydrolysis with the prior addition of 0.75 mM of iron(II) increased the glucose production to 56.3% from 46.3% in the control (iron-free acid). The detailed analysis indicated that conducting the process at lower temperatures yet long residence times benefits the yield of sugars. The above kinetic modelling results of Fe 2+ accelerating all four reactions are in line with our previous mechanistic research showing that the pretreatment likely targets multiple chemistries in plant cell wall polymer networks, including those represented by the C-O-C and C-H bonds in cellulose, resulting in enhanced sugar solubilization and digestibility.« less

Rapid Multi-Tracer PET Tumor Imaging With F-FDG and Secondary Shorter-Lived Tracers.

PubMed

Black, Noel F; McJames, Scott; Kadrmas, Dan J

2009-10-01

Rapid multi-tracer PET, where two to three PET tracers are rapidly scanned with staggered injections, can recover certain imaging measures for each tracer based on differences in tracer kinetics and decay. We previously showed that single-tracer imaging measures can be recovered to a certain extent from rapid dual-tracer (62)Cu - PTSM (blood flow) + (62)Cu - ATSM (hypoxia) tumor imaging. In this work, the feasibility of rapidly imaging (18)F-FDG plus one or two of these shorter-lived secondary tracers was evaluated in the same tumor model. Dynamic PET imaging was performed in four dogs with pre-existing tumors, and the raw scan data was combined to emulate 60 minute long dual- and triple-tracer scans, using the single-tracer scans as gold standards. The multi-tracer data were processed for static (SUV) and kinetic (K(1), K(net)) endpoints for each tracer, followed by linear regression analysis of multi-tracer versus single-tracer results. Static and quantitative dynamic imaging measures of FDG were both accurately recovered from the multi-tracer scans, closely matching the single-tracer FDG standards (R > 0.99). Quantitative blood flow information, as measured by PTSM K(1) and SUV, was also accurately recovered from the multi-tracer scans (R = 0.97). Recovery of ATSM kinetic parameters proved more difficult, though the ATSM SUV was reasonably well recovered (R = 0.92). We conclude that certain additional information from one to two shorter-lived PET tracers may be measured in a rapid multi-tracer scan alongside FDG without compromising the assessment of glucose metabolism. Such additional and complementary information has the potential to improve tumor characterization in vivo, warranting further investigation of rapid multi-tracer techniques.

Rapid Multi-Tracer PET Tumor Imaging With 18F-FDG and Secondary Shorter-Lived Tracers

PubMed Central

Black, Noel F.; McJames, Scott; Kadrmas, Dan J.

2009-01-01

Rapid multi-tracer PET, where two to three PET tracers are rapidly scanned with staggered injections, can recover certain imaging measures for each tracer based on differences in tracer kinetics and decay. We previously showed that single-tracer imaging measures can be recovered to a certain extent from rapid dual-tracer 62Cu – PTSM (blood flow) + 62Cu — ATSM (hypoxia) tumor imaging. In this work, the feasibility of rapidly imaging 18F-FDG plus one or two of these shorter-lived secondary tracers was evaluated in the same tumor model. Dynamic PET imaging was performed in four dogs with pre-existing tumors, and the raw scan data was combined to emulate 60 minute long dual- and triple-tracer scans, using the single-tracer scans as gold standards. The multi-tracer data were processed for static (SUV) and kinetic (K1, Knet) endpoints for each tracer, followed by linear regression analysis of multi-tracer versus single-tracer results. Static and quantitative dynamic imaging measures of FDG were both accurately recovered from the multi-tracer scans, closely matching the single-tracer FDG standards (R > 0.99). Quantitative blood flow information, as measured by PTSM K1 and SUV, was also accurately recovered from the multi-tracer scans (R = 0.97). Recovery of ATSM kinetic parameters proved more difficult, though the ATSM SUV was reasonably well recovered (R = 0.92). We conclude that certain additional information from one to two shorter-lived PET tracers may be measured in a rapid multi-tracer scan alongside FDG without compromising the assessment of glucose metabolism. Such additional and complementary information has the potential to improve tumor characterization in vivo, warranting further investigation of rapid multi-tracer techniques. PMID:20046800

Understanding the barriers to crystal growth: dynamical simulation of the dissolution and growth of urea from aqueous solution.

PubMed

Piana, Stefano; Gale, Julian D

2005-02-16

Both the dissolution and growth of a molecular crystalline material, urea, has been studied using dynamical atomistic simulation. The kinetic steps of dissolution and growth are clearly identified, and the activation energies for each possible step are calculated. Our molecular dynamics simulations indicate that crystal growth on the [001] face is characterized by a nucleation and growth mechanism. Nucleation on the [001] urea crystal face is predicted to occur at a very high rate, followed by rapid propagation of the steps. The rate-limiting step for crystallization is actually found to be the removal of surface defects, rather than the initial formation of the next surface layer. Through kinetic Monte Carlo modeling of the surface growth, it is found that this crystal face evolves via a rough surface topography, rather than a clean layer-by-layer mechanism.

Kinetic features of xylan de-polymerization in production of xylose monomer and furfural during acid pretreatment for kenaf, forage sorghums and sunn hemp feedstocks

DOE PAGES

Kamireddy, Srinivas Reddy; Kozliak, Evguenii I.; Tucker, Melvin; ...

2014-08-01

A kinetic study of acid pretreatment was conducted for sorghum non-brown mid rib (SNBMR) ( Sorghum bicolor L Moench), sorghum-brown mid rib (SBMR), sunn hemp ( Crotalaria juncea L) and kenaf ( Gossypiumhirsutum L), focusing on rates of xylose monomer and furfural formation. The kinetics was investigated using two independent variables, reaction temperature (150 and 160°C) and acid concentration (1 and 2 wt%), with a constant dry biomass loading of 10 wt% and a treatment time up to 20 min while sampling the mixture every 2 min. The experimental data were fitted using a two-step kinetic model based on irreversiblemore » pseudo first order kinetics at each step. Varied kinetic orders on the acid concentration, ranging from 0.2 to >3, were observed for both xylose and furfural formation, the values depending on the feedstock. The crystallinity index of raw biomass was shown to be a major factor influencing the rate of both xylose and furfural formation. As a result, a positive correlation was observed between the activation energy and biomass crystallinity index for xylose formation.« less

An investigation on the modelling of kinetics of thermal decomposition of hazardous mercury wastes.

PubMed

Busto, Yailen; M G Tack, Filip; Peralta, Luis M; Cabrera, Xiomara; Arteaga-Pérez, Luis E

2013-09-15

The kinetics of mercury removal from solid wastes generated by chlor-alkali plants were studied. The reaction order and model-free method with an isoconversional approach were used to estimate the kinetic parameters and reaction mechanism that apply to the thermal decomposition of hazardous mercury wastes. As a first approach to the understanding of thermal decomposition for this type of systems (poly-disperse and multi-component), a novel scheme of six reactions was proposed to represent the behaviour of mercury compounds in the solid matrix during the treatment. An integration-optimization algorithm was used in the screening of nine mechanistic models to develop kinetic expressions that best describe the process. The kinetic parameters were calculated by fitting each of these models to the experimental data. It was demonstrated that the D₁-diffusion mechanism appeared to govern the process at 250°C and high residence times, whereas at 450°C a combination of the diffusion mechanism (D₁) and the third order reaction mechanism (F3) fitted the kinetics of the conversions. The developed models can be applied in engineering calculations to dimension the installations and determine the optimal conditions to treat a mercury containing sludge. Copyright © 2013 Elsevier B.V. All rights reserved.

Phosphoryl transfer is not rate-limiting for the ROCK I-catalyzed kinase reaction.

PubMed

Futer, Olga; Saadat, Ahmad R; Doran, John D; Raybuck, Scott A; Pazhanisamy, S

2006-06-27

Rho-associated coiled-coil kinase, ROCK, is implicated in Rho-mediated cell adhesion and smooth muscle contraction. Animal models suggest that the inhibition of ROCK can ameliorate conditions, such as vasospasm, hypertension, and inflammation. As part of our effort to design novel inhibitors of ROCK, we investigated the kinetic mechanism of ROCK I. Steady-state bisubstrate kinetics, inhibition kinetics, isotope partition analysis, viscosity effects, and presteady-state kinetics were used to explore the kinetic mechanism. Plots of reciprocals of initial rates obtained in the presence of nonhydrolyzable ATP analogues and the small molecule inhibitor of ROCK, Y-27632, against the reciprocals of the peptide concentrations yielded parallel lines (uncompetitive pattern). This pattern is indicative of an ordered binding mechanism, with the peptide adding first. The staurosporine analogue K252a, however, gave a noncompetitive pattern. When a pulse of (33)P-gamma-ATP mixed with ROCK was chased with excess unlabeled ATP and peptide, 0.66 enzyme equivalent of (33)P-phosphate was incorporated into the product in the first turnover. The presence of ATPase activity coupled with the isotope partition data is a clear evidence for the existence of a viable [E-ATP] complex in the kinase reaction and implicates a random binding mechanism. The k(cat)/K(m) parameters were fully sensitive to viscosity (viscosity effects of 1.4 +/- 0.2 and 0.9 +/- 0.3 for ATP and peptide 5, respectively), and therefore, the barriers to dissociation of either substrate are higher than the barrier for the phosphoryl transfer step. As a consequence, not all the binding steps are at fast equilibrium. The observation of a burst in presteady-state kinetics (k(b) = 10.2 +/- 2.1 s(-)(1)) and the viscosity effect on k(cat) of 1.3 +/- 0.2 characterize the phosphoryl transfer step to be fast and the release of product and/or the enzyme isomerization step accompanying it as rate-limiting at V(max) conditions. From the multiple kinetic studies, most of the rate constants for the individual steps were either evaluated or estimated.

Mechanisms and kinetics models for ultrasonic waste activated sludge disintegration.

PubMed

Wang, Fen; Wang, Yong; Ji, Min

2005-08-31

Ultrasonic energy can be applied as pre-treatment to disintegrate sludge flocs and disrupt bacterial cells' walls, and the hydrolysis can be improved, so that the rate of sludge digestion and methane production is improved. In this paper, by adding NaHCO3 to mask the oxidizing effect of OH, the mechanisms of disintegration are investigated. In addition, kinetics models for ultrasonic sludge disintegration are established by applying multi-variable linear regression method. It has been found that hydro-mechanical shear forces predominantly responsible for the disintegration, and the contribution of oxidizing effect of OH increases with the amount of the ultrasonic density and ultrasonic intensity. It has also been inferred from the kinetics model which dependent variable is SCOD+ that both sludge pH and sludge concentration significantly affect the disintegration.

Quantifying Fenton reaction pathways driven by self-generated H2O2 on pyrite surfaces.

PubMed

Gil-Lozano, C; Davila, A F; Losa-Adams, E; Fairén, A G; Gago-Duport, L

2017-03-06

Oxidation of pyrite (FeS 2 ) plays a significant role in the redox cycling of iron and sulfur on Earth and is the primary cause of acid mine drainage (AMD). It has been established that this process involves multi-step electron-transfer reactions between surface defects and adsorbed O 2 and H 2 O, releasing sulfoxy species (e.g., S 2 O 3 2- , SO 4 2- ) and ferrous iron (Fe 2+ ) to the solution and also producing intermediate by-products, such as hydrogen peroxide (H 2 O 2 ) and other reactive oxygen species (ROS), however, our understanding of the kinetics of these transient species is still limited. We investigated the kinetics of H 2 O 2 formation in aqueous suspensions of FeS 2 microparticles by monitoring, in real time, the H 2 O 2 and dissolved O 2 concentration under oxic and anoxic conditions using amperometric microsensors. Additional spectroscopic and structural analyses were done to track the dependencies between the process of FeS 2 dissolution and the degradation of H 2 O 2 through the Fenton reaction. Based on our experimental results, we built a kinetic model which explains the observed trend of H 2 O 2 , showing that FeS 2 dissolution can act as a natural Fenton reagent, influencing the oxidation of third-party species during the long term evolution of geochemical systems, even in oxygen-limited environments.

A family of high-order gas-kinetic schemes and its comparison with Riemann solver based high-order methods

NASA Astrophysics Data System (ADS)

Ji, Xing; Zhao, Fengxiang; Shyy, Wei; Xu, Kun

2018-03-01

Most high order computational fluid dynamics (CFD) methods for compressible flows are based on Riemann solver for the flux evaluation and Runge-Kutta (RK) time stepping technique for temporal accuracy. The advantage of this kind of space-time separation approach is the easy implementation and stability enhancement by introducing more middle stages. However, the nth-order time accuracy needs no less than n stages for the RK method, which can be very time and memory consuming due to the reconstruction at each stage for a high order method. On the other hand, the multi-stage multi-derivative (MSMD) method can be used to achieve the same order of time accuracy using less middle stages with the use of the time derivatives of the flux function. For traditional Riemann solver based CFD methods, the lack of time derivatives in the flux function prevents its direct implementation of the MSMD method. However, the gas kinetic scheme (GKS) provides such a time accurate evolution model. By combining the second-order or third-order GKS flux functions with the MSMD technique, a family of high order gas kinetic methods can be constructed. As an extension of the previous 2-stage 4th-order GKS, the 5th-order schemes with 2 and 3 stages will be developed in this paper. Based on the same 5th-order WENO reconstruction, the performance of gas kinetic schemes from the 2nd- to the 5th-order time accurate methods will be evaluated. The results show that the 5th-order scheme can achieve the theoretical order of accuracy for the Euler equations, and present accurate Navier-Stokes solutions as well due to the coupling of inviscid and viscous terms in the GKS formulation. In comparison with Riemann solver based 5th-order RK method, the high order GKS has advantages in terms of efficiency, accuracy, and robustness, for all test cases. The 4th- and 5th-order GKS have the same robustness as the 2nd-order scheme for the capturing of discontinuous solutions. The current high order MSMD GKS is a multi-dimensional scheme with incorporation of both normal and tangential spatial derivatives of flow variables at a cell interface in the flux evaluation. The scheme can be extended straightforwardly to viscous flow computation in unstructured mesh. It provides a promising direction for the development of high-order CFD methods for the computation of complex flows, such as turbulence and acoustics with shock interactions.

Phase-field modeling of two-dimensional crystal growth with anisotropic diffusion.

PubMed

Meca, Esteban; Shenoy, Vivek B; Lowengrub, John

2013-11-01

In the present article, we introduce a phase-field model for thin-film growth with anisotropic step energy, attachment kinetics, and diffusion, with second-order (thin-interface) corrections. We are mainly interested in the limit in which kinetic anisotropy dominates, and hence we study how the expected shape of a crystallite, which in the long-time limit is the kinetic Wulff shape, is modified by anisotropic diffusion. We present results that prove that anisotropic diffusion plays an important, counterintuitive role in the evolving crystal shape, and we add second-order corrections to the model that provide a significant increase in accuracy for small supersaturations. We also study the effect of different crystal symmetries and discuss the influence of the deposition rate.

Electron correlations and pre-collision in the re-collision picture of high harmonic generation

NASA Astrophysics Data System (ADS)

Mašín, Zdeněk; Harvey, Alex G.; Spanner, Michael; Patchkovskii, Serguei; Ivanov, Misha; Smirnova, Olga

2018-07-01

We discuss the seminal three-step model and the re-collision picture in the context of high harmonic generation in molecules. In particular, we stress the importance of multi-electron correlation during the first and the third of the three steps of the process: (1) the strong-field ionization and (3) the recombination. We point out how an accurate account of multi-electron correlations during the third recombination step allows one to gauge the importance of pre-collision: the term coined by Eberly (n.d. private communication) to describe unusual pathways during the first, ionization, step.

Chemistry Resolved Kinetic Flow Modeling of TATB Based Explosives

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vitello, P A; Fried, L E; Howard, W M

2011-07-21

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

Biophysical synaptic dynamics in an analog VLSI network of Hodgkin-Huxley neurons.

PubMed

Yu, Theodore; Cauwenberghs, Gert

2009-01-01

We study synaptic dynamics in a biophysical network of four coupled spiking neurons implemented in an analog VLSI silicon microchip. The four neurons implement a generalized Hodgkin-Huxley model with individually configurable rate-based kinetics of opening and closing of Na+ and K+ ion channels. The twelve synapses implement a rate-based first-order kinetic model of neurotransmitter and receptor dynamics, accounting for NMDA and non-NMDA type chemical synapses. The implemented models on the chip are fully configurable by 384 parameters accounting for conductances, reversal potentials, and pre/post-synaptic voltage-dependence of the channel kinetics. We describe the models and present experimental results from the chip characterizing single neuron dynamics, single synapse dynamics, and multi-neuron network dynamics showing phase-locking behavior as a function of synaptic coupling strength. The 3mm x 3mm microchip consumes 1.29 mW power making it promising for applications including neuromorphic modeling and neural prostheses.

Thermodynamics, kinetics, and catalytic effect of dehydrogenation from MgH2 stepped surfaces and nanocluster: a DFT study

NASA Astrophysics Data System (ADS)

Reich, Jason; Wang, Linlin; Johnson, Duane

2013-03-01

We detail the results of a Density Functional Theory (DFT) based study of hydrogen desorption, including thermodynamics and kinetics with(out) catalytic dopants, on stepped (110) rutile and nanocluster MgH2. We investigate competing configurations (optimal surface and nanoparticle configurations) using simulated annealing with additional converged results at 0 K, necessary for finding the low-energy, doped MgH2 nanostructures. Thermodynamics of hydrogen desorption from unique dopant sites will be shown, as well as activation energies using the Nudged Elastic Band algorithm. To compare to experiment, both stepped structures and nanoclusters are required to understanding and predict the effects of ball milling. We demonstrate how these model systems relate to the intermediary sized structures typically seen in ball milling experiments.

A New Folding Kinetic Mechanism for Human Transthyretin and the Influence of the Amyloidogenic V30M Mutation.

PubMed

Jesus, Catarina S H; Almeida, Zaida L; Vaz, Daniela C; Faria, Tiago Q; Brito, Rui M M

2016-08-31

Protein aggregation into insoluble amyloid fibrils is the hallmark of several neurodegenerative diseases, chief among them Alzheimer's and Parkinson's. Although caused by different proteins, these pathologies share some basic molecular mechanisms with familial amyloidotic polyneuropathy (FAP), a rare hereditary neuropathy caused by amyloid formation and deposition by transthyretin (TTR) in the peripheral and autonomic nervous systems. Among the amyloidogenic TTR mutations known, V30M-TTR is the most common in FAP. TTR amyloidogenesis (ATTR) is triggered by tetramer dissociation, followed by partial unfolding and aggregation of the low conformational stability monomers formed. Thus, tetramer dissociation kinetics, monomer conformational stability and competition between refolding and aggregation pathways do play a critical role in ATTR. Here, we propose a new model to analyze the refolding kinetics of WT-TTR and V30M-TTR, showing that at pH and protein concentrations close to physiological, a two-step mechanism with a unimolecular first step followed by a second-order second step adjusts well to the experimental data. Interestingly, although sharing the same kinetic mechanism, V30M-TTR refolds at a much slower rate than WT-TTR, a feature that may favor the formation of transient species leading to kinetic partition into amyloidogenic pathways and, thus, significantly increasing the probability of amyloid formation in vivo.

A New Folding Kinetic Mechanism for Human Transthyretin and the Influence of the Amyloidogenic V30M Mutation

PubMed Central

Jesus, Catarina S. H.; Almeida, Zaida L.; Vaz, Daniela C.; Faria, Tiago Q.; Brito, Rui M. M.

2016-01-01

Protein aggregation into insoluble amyloid fibrils is the hallmark of several neurodegenerative diseases, chief among them Alzheimer’s and Parkinson’s. Although caused by different proteins, these pathologies share some basic molecular mechanisms with familial amyloidotic polyneuropathy (FAP), a rare hereditary neuropathy caused by amyloid formation and deposition by transthyretin (TTR) in the peripheral and autonomic nervous systems. Among the amyloidogenic TTR mutations known, V30M-TTR is the most common in FAP. TTR amyloidogenesis (ATTR) is triggered by tetramer dissociation, followed by partial unfolding and aggregation of the low conformational stability monomers formed. Thus, tetramer dissociation kinetics, monomer conformational stability and competition between refolding and aggregation pathways do play a critical role in ATTR. Here, we propose a new model to analyze the refolding kinetics of WT-TTR and V30M-TTR, showing that at pH and protein concentrations close to physiological, a two-step mechanism with a unimolecular first step followed by a second-order second step adjusts well to the experimental data. Interestingly, although sharing the same kinetic mechanism, V30M-TTR refolds at a much slower rate than WT-TTR, a feature that may favor the formation of transient species leading to kinetic partition into amyloidogenic pathways and, thus, significantly increasing the probability of amyloid formation in vivo. PMID:27589730

Control of DNA strand displacement kinetics using toehold exchange.

PubMed

Zhang, David Yu; Winfree, Erik

2009-12-02

DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Many of these enzyme-free constructions function by DNA strand displacement reactions. The kinetics of strand displacement can be modulated by toeholds, short single-stranded segments of DNA that colocalize reactant DNA molecules. Recently, the toehold exchange process was introduced as a method for designing fast and reversible strand displacement reactions. Here, we characterize the kinetics of DNA toehold exchange and model it as a three-step process. This model is simple and quantitatively predicts the kinetics of 85 different strand displacement reactions from the DNA sequences. Furthermore, we use toehold exchange to construct a simple catalytic reaction. This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices.

ssDNA aptamer-based column for simultaneous removal of nanogram per liter level of illicit and analgesic pharmaceuticals in drinking water.

PubMed

Hu, Xiangang; Mu, Li; Zhou, Qixing; Wen, Jianping; Pawliszyn, Janusz

2011-06-01

Aptamers are a new class of single-stranded DNA/RNA molecules selected from synthetic nucleic acid libraries for molecular recognition. Our group reports a novel aptamer column for the removal of trace (ng/L) pharmaceuticals in drinking water. In this study, cocaine and diclofenac were chosen as model molecules to test the aptamer column which presented high removal capacity, selectivity, and stability. The removal of pharmaceuticals was as high as 88-95%. The data of adsorption were fitted with Langmuir isotherm and a pseudo-second-order kinetic model. A thermodynamic experiment proved the adsorption processes were exothermic in spontaneity. The kinetics of aptamer was composed of three steps: activation, binding, and hybridization. The first step was the rate-controlling step. The adsorption system was divided into three parts: kinetic, mixed, and thermodynamic zones from 0% to 100% binding fraction of aptamer. Furthermore, the aptamer column was reusable and achieved strong removal efficiency from 4 to 30 °C at normal cation ion concentration (5-100 mg/L) for multipollutants without cross effects and secondary pollution. This work indicates that aptamer, as a new sorbent, can be used in the removal of persistent organic pollutants, biological toxins, and pathogenic bacteria from surface, drinking, and ground water.

Development of interactive graphic user interfaces for modeling reaction-based biogeochemical processes in batch systems with BIOGEOCHEM

NASA Astrophysics Data System (ADS)

Chang, C.; Li, M.; Yeh, G.

2010-12-01

The BIOGEOCHEM numerical model (Yeh and Fang, 2002; Fang et al., 2003) was developed with FORTRAN for simulating reaction-based geochemical and biochemical processes with mixed equilibrium and kinetic reactions in batch systems. A complete suite of reactions including aqueous complexation, adsorption/desorption, ion-exchange, redox, precipitation/dissolution, acid-base reactions, and microbial mediated reactions were embodied in this unique modeling tool. Any reaction can be treated as fast/equilibrium or slow/kinetic reaction. An equilibrium reaction is modeled with an implicit finite rate governed by a mass action equilibrium equation or by a user-specified algebraic equation. A kinetic reaction is modeled with an explicit finite rate with an elementary rate, microbial mediated enzymatic kinetics, or a user-specified rate equation. None of the existing models has encompassed this wide array of scopes. To ease the input/output learning curve using the unique feature of BIOGEOCHEM, an interactive graphic user interface was developed with the Microsoft Visual Studio and .Net tools. Several user-friendly features, such as pop-up help windows, typo warning messages, and on-screen input hints, were implemented, which are robust. All input data can be real-time viewed and automated to conform with the input file format of BIOGEOCHEM. A post-processor for graphic visualizations of simulated results was also embedded for immediate demonstrations. By following data input windows step by step, errorless BIOGEOCHEM input files can be created even if users have little prior experiences in FORTRAN. With this user-friendly interface, the time effort to conduct simulations with BIOGEOCHEM can be greatly reduced.

A multi-species reactive transport model to estimate biogeochemical rates based on single-well push-pull test data

NASA Astrophysics Data System (ADS)

Phanikumar, Mantha S.; McGuire, Jennifer T.

2010-08-01

Push-pull tests are a popular technique to investigate various aquifer properties and microbial reaction kinetics in situ. Most previous studies have interpreted push-pull test data using approximate analytical solutions to estimate (generally first-order) reaction rate coefficients. Though useful, these analytical solutions may not be able to describe important complexities in rate data. This paper reports the development of a multi-species, radial coordinate numerical model (PPTEST) that includes the effects of sorption, reaction lag time and arbitrary reaction order kinetics to estimate rates in the presence of mixing interfaces such as those created between injected "push" water and native aquifer water. The model has the ability to describe an arbitrary number of species and user-defined reaction rate expressions including Monod/Michelis-Menten kinetics. The FORTRAN code uses a finite-difference numerical model based on the advection-dispersion-reaction equation and was developed to describe the radial flow and transport during a push-pull test. The accuracy of the numerical solutions was assessed by comparing numerical results with analytical solutions and field data available in the literature. The model described the observed breakthrough data for tracers (chloride and iodide-131) and reactive components (sulfate and strontium-85) well and was found to be useful for testing hypotheses related to the complex set of processes operating near mixing interfaces.

On the Development of Multi-Step Inverse FEM with Shell Model

NASA Astrophysics Data System (ADS)

Huang, Y.; Du, R.

2005-08-01

The inverse or one-step finite element approach is increasingly used in the sheet metal stamping industry to predict strain distribution and the initial blank shape in the preliminary design stage. Based on the existing theory, there are two types of method: one is based on the principle of virtual work and the other is based on the principle of extreme work. Much research has been conducted to improve the accuracy of simulation results. For example, based on the virtual work principle, Batoz et al. developed a new method using triangular DKT shell elements. In this new method, the bending and unbending effects are considered. Based on the principle of extreme work, Majlessi and et al. proposed the multi-step inverse approach with membrane elements and applied it to an axis-symmetric part. Lee and et al. presented an axis-symmetric shell element model to solve the similar problem. In this paper, a new multi-step inverse method is introduced with no limitation on the workpiece shape. It is a shell element model based on the virtual work principle. The new method is validated by means of comparing to the commercial software system (PAMSTAMP®). The comparison results indicate that the accuracy is good.

Growth of non-toxigenic Clostridium botulinum mutant LNT01 in cooked beef: One-step kinetic analysis and comparison with C. sporogenes and C. perfringens.

PubMed

Huang, Lihan

2018-05-01

The objective of this study was to investigate the growth kinetics of Clostridium botulinum LNT01, a non-toxigenic mutant of C. botulinum 62A, in cooked ground beef. The spores of C. botulinum LNT01 were inoculated to ground beef and incubated anaerobically under different temperature conditions to observe growth and develop growth curves. A one-step kinetic analysis method was used to analyze the growth curves simultaneously to minimize the global residual error. The data analysis was performed using the USDA IPMP-Global Fit, with the Huang model as the primary model and the cardinal parameters model as the secondary model. The results of data analysis showed that the minimum, optimum, and maximum growth temperatures of this mutant are 11.5, 36.4, and 44.3 °C, and the estimated optimum specific growth rate is 0.633 ln CFU/g per h, or 0.275 log CFU/g per h. The maximum cell density is 7.84 log CFU/g. The models and kinetic parameters were validated using additional isothermal and dynamic growth curves. The resulting residual errors of validation followed a Laplace distribution, with about 60% of the residual errors within ±0.5 log CFU/g of experimental observations, suggesting that the models could predict the growth of C. botulinum LNT01 in ground beef with reasonable accuracy. Comparing with C. perfringens, C. botulinum LNT01 grows at much slower rates and with much longer lag times. Its growth kinetics is also very similar to C. sporogenes in ground beef. The results of computer simulation using kinetic models showed that, while prolific growth of C. perfringens may occur in ground beef during cooling, no growth of C. botulinum LNT01 or C. sporogenes would occur under the same cooling conditions. The models developed in this study may be used for prediction of the growth and risk assessments of proteolytic C. botulinum in cooked meats. Published by Elsevier Ltd.

Kinetics of liquid-solid reactions in naphthenic acid conversion and Kraft pulping

NASA Astrophysics Data System (ADS)

Yang, Ling

Two liquid-solid reactions, in which the morphology of the solid changes as the reactions proceeds, were examined. One is the NA conversion in oil by decarboxylation on metal oxides and carbonates, and the other is the Kraft pulping in which lignin removal by delignification reaction. In the study of the NA conversion, CaO was chosen as the catalyst for the kinetic study from the tested catalysts based on NA conversion. Two reaction mixtures, carrier oil plus commercial naphthenic acids and heavy vacuum gas oil (HVGO) from Athabasca bitumen, were applied in the kinetic study. The influence of TAN, temperature, and catalyst loading on the NA conversion and decarboxylation were studied systematically. The results showed that the removal rate of TAN and the decarboxylation of NA were both independent of the concentration of NA over the range studied, and significantly dependent on reaction temperature. The data from analyzing the spent catalyst demonstrated that calcium naphthenate was an intermediate of the decarboxylation reaction of NA, and the decomposition of calcium naphthenate was a rate-determining step. In the study on the delignification of the Kraft pulping, a new mechanism was proposed for the heterogeneous delignification reaction during the Kraft pulping process. In particular, the chemical reaction mechanism took into account the heterogeneous nature of Kraft pulping. Lignin reacted in parallel with sodium hydroxide and sodium sulfide. The mechanism consists of three key kinetic steps: (1) adsorption of hydroxide and hydrosulfide ions on lignin; (2) surface reaction on the solid surface to produce degraded lignin products; and (3) desorption of degradation products from the solid surface. The most important step for the delignification process is the surface reaction, rather than the reactions occurring in the liquid phase. A kinetic model has, thus, been developed based on the proposed mechanism. The derived kinetic model showed that the mechanism could be employed to predict the pulping behavior under a variety of conditions with good accuracy.

The effects of age and step length on joint kinematics and kinetics of large out-and-back steps.

PubMed

Schulz, Brian W; Ashton-Miller, James A; Alexander, Neil B

2008-06-01

Maximum step length (MSL) is a clinical test that has been shown to correlate with age, various measures of fall risk, and knee and hip joint extension speed, strength, and power capacities, but little is known about the kinematics and kinetics of the large out-and-back step utilized. Body motions and ground reaction forces were recorded for 11 unimpaired younger and 10 older women while attaining maximum step length. Joint kinematics and kinetics were calculated using inverse dynamics. The effects of age group and step length on the biomechanics of these large out-and-back steps were determined. Maximum step length was 40% greater in the younger than in the older women (P<0.0001). Peak knee and hip, but not ankle, angle, velocity, moment, and power were generally greater for younger women and longer steps. After controlling for age group, step length generally explained significant additional variance in hip and torso kinematics and kinetics (incremental R2=0.09-0.37). The young reached their peak knee extension moment immediately after landing of the step out, while the old reached their peak knee extension moment just before the return step liftoff (P=0.03). Maximum step length is strongly associated with hip kinematics and kinetics. Delays in peak knee extension moment that appear to be unrelated to step length, may indicate a reduced ability of older women to rapidly apply force to the ground with the stepping leg and thus arrest the momentum of a fall.

The effects of age and step length on joint kinematics and kinetics of large out-and-back steps

PubMed Central

Schulz, Brian W.; Ashton-Miller, James A.; Alexander, Neil B.

2008-01-01

Background Maximum Step Length is a clinical test that has been shown to correlate with age, various measures of fall risk, and knee and hip joint extension speed, strength, and power capacities, but little is known about the kinematics and kinetics of the large out-and-back step utilized. Methods Body motions and ground reaction forces were recorded for 11 unimpaired younger and 10 older women while attaining Maximum Step Length. Joint kinematics and kinetics were calculated using inverse dynamics. The effects of age group and step length on the biomechanics of these large out-and-back steps were determined. Findings Maximum Step Length was 40% greater in the younger than in the older women (p<0.0001). Peak knee and hip, but not ankle, angle, velocity, moment, and power were generally greater for younger women and longer steps. After controlling for age group, step length generally explained significant additional variance in hip and torso kinematics and kinetics (incremental R2=0.09–0.37). The young reached their peak knee extension moment immediately after landing of the step out, while the old reached their peak knee extension moment just before the return step lift off (p=0.03). Interpretation Maximum Step Length is strongly associated with hip kinematics and kinetics. Delays in peak knee extension moment that appear to be unrelated to step length, may indicate a reduced ability of older women to rapidly apply force to the ground with the stepping leg and thus arrest the momentum of a fall. PMID:18308435

Multi-component sorption of Pb(II), Cu(II) and Zn(II) onto low-cost mineral adsorbent.

PubMed

Prasad, Murari; Xu, Huan-yan; Saxena, Sona

2008-06-15

Multi-component sorption studies were carried out for attenuation of divalent heavy metal cations (Pb2+, Cu2+ and Zn2+) by a low-cost mineral adsorbent from the aqueous solution. Kinetic and equilibrium batch-type sorption experiments were conducted under variable conditions for multi-component using low-grade (<12%P2O5) phosphate rock. Percentage of multiple heavy metal species removal increases with decreasing initial metals concentration and particle size. The equilibrium data were well described to a lesser extent by Freundlich model but Langmuir model seemed to be more appropriate with the fixation capacity obtained at room temperature for Pb2+, Cu2+ and Zn2+ was 227.2, 769.2 and 666.6 micromol g(-1), respectively. Two simple kinetic models were tested to investigate the adsorption mechanism. Rate constants have been found nearly constant at all metal concentrations for first order. The comparison of adsorption capacity of low-grade phosphate rock decreases in multi-component system as compared to single component due to ionic interactions. X-ray powder diffraction (XRPD) technique was used to ascertain the formation of new metal phases followed by surface complexation. Used adsorbents have been converted into a value added product by utilizing innovative Zero-waste concept to solve the used adsorbents disposal problem and thus protecting the environment.

Atomic-Scale Design of Iron Fischer-Tropsch Catalysts: A Combined Computational Chemistry, Experimental, and Microkinetic Modeling Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manos Mavrikakis; James A. Dumesic; Amit A. Gokhale

2006-03-03

Efforts during this second year focused on four areas: (1) continued searching and summarizing of published Fischer-Tropsch synthesis (FTS) mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) investigation of CO adsorption/desorption and temperature programmed hydrogenation (TPH) of carbonaceous species after FTS on unsupported iron and alumina-supported iron catalysts; (3) activity tests of alumina-supported iron catalysts in a fixed bed reactor; (4) sequential design of experiments, for the collection of rate data in a Berty CSTR reactor, and nonlinear-regression analysis to obtain kinetic parameters. Literature sources describing mechanistic and kinetic studies of Fischer-Tropsch synthesis on iron catalysts weremore » compiled in a review. Temperature-programmed desorption/reaction methods (the latter using mass-spectrometry detection and also thermogravimetric analyzer (TGA)) were utilized to study CO adsorption/-desorption on supported and unsupported iron catalysts. Molecular and dissociative adsorptions of CO occur on iron catalysts at 25-150 C. The amounts adsorbed and bond strengths of adsorption are influenced by supports and promoters. That CO adsorbs dissociatively on polycrystalline Fe at temperatures well below those of FT reaction indicates that CO dissociation is facile and unlikely to be the rate-limiting step during FTS. Carbonaceous species formed after FT reaction for only 5 minutes at 200 C were initially hydrogenated under mild, isothermal condition (200 C and 1 atm), followed by TPH to 800 C. During the mild, isothermal hydrogenation, only about 0.1-0.2 mL of atomic carbon is apparently removed, while during TPH to 800 C multilayer equivalents of atomic, polymeric, carbidic, and graphitic carbons are removed. Rates of CO conversion on alumina-supported iron catalysts at 220-260 C and 20 atm are correlated well by a Langmuir-Hinshelwood expression, derived assuming carbon hydrogenation to CH and OH recombination to water to be rate-determining steps. In the coming year, studies will focus on quantitative determination of the rates of kinetically-relevant elementary steps on Fe catalysts with/without K and Pt promoters and at various levels of Al{sub 2}O{sub 3} support, providing a database for understanding (1) effects of promoter and support on elementary kinetic parameters and (2) for validation of computational models that incorporate effects of surface structure and promoters. Kinetic parameters will be incorporated into a microkinetics model, enabling prediction of rate without invoking assumptions, e.g. of a rate-determining step or a most-abundant surface intermediate. Calculations using periodic, self-consistent Density Functional Theory (DFT) methods were performed on two model surfaces: (1) Fe(110) with 1/4 ML subsurface carbon, and (2) Fe(110) with 1/4 ML Pt adatoms. Reaction networks for FTS on these systems were characterized in full detail by evaluating the thermodynamics and kinetics of each elementary step. We discovered that subsurface C stabilizes all the reactive intermediates, in contrast to Pt, which destabilizes most of them. A comparative study of the reactivities of the modified-Fe surfaces against pure Fe is expected to yield a more comprehensive understanding of promotion mechanisms for FTS on Fe.« less

Adsorption of methylene blue onto activated carbon produced from tea (Camellia sinensis L.) seed shells: kinetics, equilibrium, and thermodynamics studies.

PubMed

Gao, Jun-Jie; Qin, Ye-Bo; Zhou, Tao; Cao, Dong-Dong; Xu, Ping; Hochstetter, Danielle; Wang, Yue-Fei

2013-07-01

Tea (Camellia sinensis L.) seed shells, the main byproduct of the manufacture of tea seed oil, were used as precursors for the preparation of tea activated carbon (TAC) in the present study. A high yield (44.1%) of TAC was obtained from tea seed shells via a one-step chemical method using ZnCl2 as an agent. The Brunauer-Emmett-Teller (BET) surface area and the total pore volumes of the obtained TAC were found to be 1530.67 mg(2)/g and 0.7826 cm(3)/g, respectively. The equilibrium adsorption results were complied with Langmuir isotherm model and its maximum monolayer adsorption capacity was 324.7 mg/g for methylene blue. Adsorption kinetics studies indicated that the pseudo-second-order model yielded the best fit for the kinetic data. An intraparticle diffusion model suggested that the intraparticle diffusion was not the only rate-controlling step. Thermodynamics studies revealed the spontaneous and exothermic nature of the sorption process. These results indicate that tea seed shells could be utilized as a renewable resource to develop activated carbon which is a potential adsorbent for methylene blue.

Adsorption of methylene blue onto activated carbon produced from tea (Camellia sinensis L.) seed shells: kinetics, equilibrium, and thermodynamics studies*

PubMed Central

Gao, Jun-jie; Qin, Ye-bo; Zhou, Tao; Cao, Dong-dong; Xu, Ping; Hochstetter, Danielle; Wang, Yue-fei

2013-01-01

Tea (Camellia sinensis L.) seed shells, the main byproduct of the manufacture of tea seed oil, were used as precursors for the preparation of tea activated carbon (TAC) in the present study. A high yield (44.1%) of TAC was obtained from tea seed shells via a one-step chemical method using ZnCl2 as an agent. The Brunauer-Emmett-Teller (BET) surface area and the total pore volumes of the obtained TAC were found to be 1 530.67 mg2/g and 0.782 6 cm3/g, respectively. The equilibrium adsorption results were complied with Langmuir isotherm model and its maximum monolayer adsorption capacity was 324.7 mg/g for methylene blue. Adsorption kinetics studies indicated that the pseudo-second-order model yielded the best fit for the kinetic data. An intraparticle diffusion model suggested that the intraparticle diffusion was not the only rate-controlling step. Thermodynamics studies revealed the spontaneous and exothermic nature of the sorption process. These results indicate that tea seed shells could be utilized as a renewable resource to develop activated carbon which is a potential adsorbent for methylene blue. PMID:23825151

Cost-effectiveness Analysis in R Using a Multi-state Modeling Survival Analysis Framework: A Tutorial.

PubMed

Williams, Claire; Lewsey, James D; Briggs, Andrew H; Mackay, Daniel F

2017-05-01

This tutorial provides a step-by-step guide to performing cost-effectiveness analysis using a multi-state modeling approach. Alongside the tutorial, we provide easy-to-use functions in the statistics package R. We argue that this multi-state modeling approach using a package such as R has advantages over approaches where models are built in a spreadsheet package. In particular, using a syntax-based approach means there is a written record of what was done and the calculations are transparent. Reproducing the analysis is straightforward as the syntax just needs to be run again. The approach can be thought of as an alternative way to build a Markov decision-analytic model, which also has the option to use a state-arrival extended approach. In the state-arrival extended multi-state model, a covariate that represents patients' history is included, allowing the Markov property to be tested. We illustrate the building of multi-state survival models, making predictions from the models and assessing fits. We then proceed to perform a cost-effectiveness analysis, including deterministic and probabilistic sensitivity analyses. Finally, we show how to create 2 common methods of visualizing the results-namely, cost-effectiveness planes and cost-effectiveness acceptability curves. The analysis is implemented entirely within R. It is based on adaptions to functions in the existing R package mstate to accommodate parametric multi-state modeling that facilitates extrapolation of survival curves.

Pyrolytic Characteristics and Kinetics of Phragmites australis

PubMed Central

Zhao, Hui; Yan, Huaxiao; Zhang, Congwang; Liu, Xiaodong; Xue, Yanhui; Qiao, Yingyun; Tian, Yuanyu; Qin, Song

2011-01-01

The pyrolytic kinetics of Phragmites australis was investigated using thermogravimetric analysis (TGA) method with linear temperature programming process under an inert atmosphere. Kinetic expressions for the degradation rate in devolatilization and combustion steps have been obtained for P. australis with Dollimore method. The values of apparent activation energy, the most probable mechanism functions, and the corresponding preexponential factor were determined. The results show that the model agrees well with the experimental data and provide useful information for the design of pyrolytic processing system using P. australis as feedstock to produce biofuel. PMID:22007256

Numerical modeling of the solar wind flow with observational boundary conditions

DOE PAGES

Pogorelov, N. V.; Borovikov, S. N.; Burlaga, L. F.; ...

2012-11-20

In this paper we describe our group efforts to develop a self-consistent, data-driven model of the solar wind (SW) interaction with the local interstellar medium. The motion of plasma in this model is described with the MHD approach, while the transport of neutral atoms is addressed by either kinetic or multi-fluid equations. The model and its implementation in the Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS) are continuously tested and validated by comparing our results with other models and spacecraft measurements. In particular, it was successfully applied to explain an unusual SW behavior discovered by the Voyager 1 spacecraft, i.e., the developmentmore » of a substantial negative radial velocity component, flow turning in the transverse direction, while the latitudinal velocity component goes to very small values. We explain recent SW velocity measurements at Voyager 1 in the context of our 3-D, MHD modeling. We also present a comparison of different turbulence models in their ability to reproduce the SW temperature profile from Voyager 2 measurements. Lastly, the boundary conditions obtained at 50 solar radii from data-driven numerical simulations are used to model a CME event throughout the heliosphere.« less

Simplified Two-Time Step Method for Calculating Combustion and Emission Rates of Jet-A and Methane Fuel With and Without Water Injection

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2005-01-01

A simplified kinetic scheme for Jet-A, and methane fuels with water injection was developed to be used in numerical combustion codes, such as the National Combustor Code (NCC) or even simple FORTRAN codes. The two time step method is either an initial time averaged value (step one) or an instantaneous value (step two). The switch is based on the water concentration in moles/cc of 1x10(exp -20). The results presented here results in a correlation that gives the chemical kinetic time as two separate functions. This two time step method is used as opposed to a one step time averaged method previously developed to determine the chemical kinetic time with increased accuracy. The first time averaged step is used at the initial times for smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, initial water to fuel mass ratio, temperature, and pressure. The second instantaneous step, to be used with higher water concentrations, gives the chemical kinetic time as a function of instantaneous fuel and water mole concentration, pressure and temperature (T4). The simple correlations would then be compared to the turbulent mixing times to determine the limiting rates of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates are used to calculate the necessary chemical kinetic times. Chemical kinetic time equations for fuel, carbon monoxide and NOx are obtained for Jet-A fuel and methane with and without water injection to water mass loadings of 2/1 water to fuel. A similar correlation was also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium concentrations of carbon monoxide and nitrogen oxide as functions of overall equivalence ratio, water to fuel mass ratio, pressure and temperature (T3). The temperature of the gas entering the turbine (T4) was also correlated as a function of the initial combustor temperature (T3), equivalence ratio, water to fuel mass ratio, and pressure.

Simplified jet-A kinetic mechanism for combustor application

NASA Technical Reports Server (NTRS)

Lee, Chi-Ming; Kundu, Krishna; Ghorashi, Bahman

1993-01-01

Successful modeling of combustion and emissions in gas turbine engine combustors requires an adequate description of the reaction mechanism. For hydrocarbon oxidation, detailed mechanisms are only available for the simplest types of hydrocarbons such as methane, ethane, acetylene, and propane. These detailed mechanisms contain a large number of chemical species participating simultaneously in many elementary kinetic steps. Current computational fluid dynamic (CFD) models must include fuel vaporization, fuel-air mixing, chemical reactions, and complicated boundary geometries. To simulate these conditions a very sophisticated computer model is required, which requires large computer memory capacity and long run times. Therefore, gas turbine combustion modeling has frequently been simplified by using global reaction mechanisms, which can predict only the quantities of interest: heat release rates, flame temperature, and emissions. Jet fuels are wide-boiling-range hydrocarbons with ranges extending through those of gasoline and kerosene. These fuels are chemically complex, often containing more than 300 components. Jet fuel typically can be characterized as containing 70 vol pct paraffin compounds and 25 vol pct aromatic compounds. A five-step Jet-A fuel mechanism which involves pyrolysis and subsequent oxidation of paraffin and aromatic compounds is presented here. This mechanism is verified by comparing with Jet-A fuel ignition delay time experimental data, and species concentrations obtained from flametube experiments. This five-step mechanism appears to be better than the current one- and two-step mechanisms.

A new methodology to determine kinetic parameters for one- and two-step chemical models

NASA Technical Reports Server (NTRS)

Mantel, T.; Egolfopoulos, F. N.; Bowman, C. T.

1996-01-01

In this paper, a new methodology to determine kinetic parameters for simple chemical models and simple transport properties classically used in DNS of premixed combustion is presented. First, a one-dimensional code is utilized to performed steady unstrained laminar methane-air flame in order to verify intrinsic features of laminar flames such as burning velocity and temperature and concentration profiles. Second, the flame response to steady and unsteady strain in the opposed jet configuration is numerically investigated. It appears that for a well determined set of parameters, one- and two-step mechanisms reproduce the extinction limit of a laminar flame submitted to a steady strain. Computations with the GRI-mech mechanism (177 reactions, 39 species) and multicomponent transport properties are used to validate these simplified models. A sensitivity analysis of the preferential diffusion of heat and reactants when the Lewis number is close to unity indicates that the response of the flame to an oscillating strain is very sensitive to this number. As an application of this methodology, the interaction between a two-dimensional vortex pair and a premixed laminar flame is performed by Direct Numerical Simulation (DNS) using the one- and two-step mechanisms. Comparison with the experimental results of Samaniego et al. (1994) shows a significant improvement in the description of the interaction when the two-step model is used.

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

PubMed Central

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

2015-01-01

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

A comparison of simple global kinetic models for coal devolatilization with the CPD model

DOE PAGES

Richards, Andrew P.; Fletcher, Thomas H.

2016-08-01

Simulations of coal combustors and gasifiers generally cannot incorporate the complexities of advanced pyrolysis models, and hence there is interest in evaluating simpler models over ranges of temperature and heating rate that are applicable to the furnace of interest. In this paper, six different simple model forms are compared to predictions made by the Chemical Percolation Devolatilization (CPD) model. The model forms included three modified one-step models, a simple two-step model, and two new modified two-step models. These simple model forms were compared over a wide range of heating rates (5 × 10 3 to 10 6 K/s) at finalmore » temperatures up to 1600 K. Comparisons were made of total volatiles yield as a function of temperature, as well as the ultimate volatiles yield. Advantages and disadvantages for each simple model form are discussed. In conclusion, a modified two-step model with distributed activation energies seems to give the best agreement with CPD model predictions (with the fewest tunable parameters).« less

Inorganic and Protein Crystal Assembly in Solutions

NASA Technical Reports Server (NTRS)

Chernov, A. A.

2005-01-01

The basic kinetic and thermodynamic concepts of crystal growth will be revisited in view of recent AFM and interferometric findings. These concepts are as follows: 1) The Kossel crystal model that allows only one kink type on the crystal surface. The modern theory is developed overwhelmingly for the Kessel model; 2) Presumption that intensive step fluctuations maintain kink density sufficiently high to allow applicability of Gibbs-Thomson law; 3) Common experience that unlimited step bunching (morphological instability) during layer growth from solutions and supercooled melts always takes place if the step flow direction coincides with that of the fluid.

Comparison of analytical models for zonal flow generation in ion-temperature-gradient mode turbulence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, J.; Miki, K.; Uzawa, K.

2006-11-30

During the past years the understanding of the multi scale interaction problems have increased significantly. However, at present there exists a flora of different analytical models for investigating multi scale interactions and hardly any specific comparisons have been performed among these models. In this work two different models for the generation of zonal flows from ion-temperature-gradient (ITG) background turbulence are discussed and compared. The methods used are the coherent mode coupling model and the wave kinetic equation model (WKE). It is shown that the two models give qualitatively the same results even though the assumption on the spectral difference ismore » used in the (WKE) approach.« less

Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective

NASA Astrophysics Data System (ADS)

Chowdhury, Debashish

2013-08-01

A molecular motor is made of either a single macromolecule or a macromolecular complex. Just like their macroscopic counterparts, molecular motors “transduce” input energy into mechanical work. All the nano-motors considered here operate under isothermal conditions far from equilibrium. Moreover, one of the possible mechanisms of energy transduction, called Brownian ratchet, does not even have any macroscopic counterpart. But, molecular motor is not synonymous with Brownian ratchet; a large number of molecular motors execute a noisy power stroke, rather than operating as Brownian ratchet. We review not only the structural design and stochastic kinetics of individual single motors, but also their coordination, cooperation and competition as well as the assembly of multi-module motors in various intracellular kinetic processes. Although all the motors considered here execute mechanical movements, efficiency and power output are not necessarily good measures of performance of some motors. Among the intracellular nano-motors, we consider the porters, sliders and rowers, pistons and hooks, exporters, importers, packers and movers as well as those that also synthesize, manipulate and degrade “macromolecules of life”. We review mostly the quantitative models for the kinetics of these motors. We also describe several of those motor-driven intracellular stochastic processes for which quantitative models are yet to be developed. In part I, we discuss mainly the methodology and the generic models of various important classes of molecular motors. In part II, we review many specific examples emphasizing the unity of the basic mechanisms as well as diversity of operations arising from the differences in their detailed structure and kinetics. Multi-disciplinary research is presented here from the perspective of physicists.

Study on Synthesis of Thoreau-modified 3, 5-Dimethyl-Thioltoluenediamine Used as Epoxy Resin Curing Agent and Its Performance

NASA Astrophysics Data System (ADS)

Peng, Yongli; Xiao, Wenzheng

2017-06-01

A novel curing agent Thoreau modified 3, 5-Dimethyl-thioltoluenediamine was synthesized and its molecular structure was characterized by FTIR and DSC. The curing kinetics of a high toughness and low volume shrinkage ratio epoxy system (modified DMTDA/DGEBA) was studied by differential scanning calorimetry (DSC) under noni so thermal conditions. The data were fitted to an order model and autocatalytic model respectively. The results indicate that in order model deviates significantly from experimental data. Malik’s method was used to prove that the curing kinetics of the system concerned follow single-step autocatalytic model, and a “single-point model-free” approach was employed to calculate meaningful kinetic parameters. The DSC curves derived from autocatalytic model gave satisfactory agreement with that of experiment in the range 5K/min∼25K/min. As the heating rate increased, the predicted DSC curves deviated from experimental curves, and the total exothermic enthalpy declined owing to the transition of competition relationship between kinetics control and diffusion control.

Kinetic Effects in Parametric Instabilities of Finite Amplitude Alfven Waves in a Drifting Multi-Species Plasma

NASA Astrophysics Data System (ADS)

Maneva, Y. G.; Araneda, J. A.; Poedts, S.

2014-12-01

We consider parametric instabilities of finite-amplitude large-scale Alfven waves in a low-beta collisionless multi-species plasma, consisting of fluid electrons, kinetic protons and a drifting population of minor ions. Complementary to many theoretical studies, relying on fluid or multi-fluid approach, in this work we present the solutions of the parametric instability dispersion relation, including kinetic effects in the parallel direction, along the ambient magnetic field. This provides us with the opportunity to predict the importance of some wave-particle interactions like Landau damping of the daughter ion-acoustic waves for the given pump wave and plasma conditions. We apply the dispersion relation to plasma parameters, typical for low-beta collisionless solar wind close to the Sun. We compare the analytical solutions to the linear stage of hybrid numerical simulations and discuss the application of the model to the problems of preferential heating and differential acceleration of minor ions in the solar corona and the fast solar wind. The results of this study provide tools for prediction and interpretation of the magnetic field and particles data as expected from the future Solar Orbiter and Solar Probe Plus missions.

Mechanism and microstructures in Ga2O3 pseudomartensitic solid phase transition.

PubMed

Zhu, Sheng-Cai; Guan, Shu-Hui; Liu, Zhi-Pan

2016-07-21

Solid-to-solid phase transition, although widely exploited in making new materials, challenges persistently our current theory for predicting its complex kinetics and rich microstructures in transition. The Ga2O3α-β phase transformation represents such a common but complex reaction with marked change in cation coordination and crystal density, which was known to yield either amorphous or crystalline products under different synthetic conditions. Here we, via recently developed stochastic surface walking (SSW) method, resolve for the first time the atomistic mechanism of Ga2O3α-β phase transformation, the pathway of which turns out to be the first reaction pathway ever determined for a new type of diffusionless solid phase transition, namely, pseudomartensitic phase transition. We demonstrate that the sensitivity of product crystallinity is caused by its multi-step, multi-type reaction pathway, which bypasses seven intermediate phases and involves all types of elementary solid phase transition steps, i.e. the shearing of O layers (martensitic type), the local diffusion of Ga atoms (reconstructive type) and the significant lattice dilation (dilation type). While the migration of Ga atoms across the close-packed O layers is the rate-determining step and yields "amorphous-like" high energy intermediates, the shearing of O layers contributes to the formation of coherent biphase junctions and the presence of a crystallographic orientation relation, (001)α//(201[combining macron])β + [120]α//[13[combining macron]2]β. Our experiment using high-resolution transmission electron microscopy further confirms the theoretical predictions on the atomic structure of biphase junction and the formation of (201[combining macron])β twin, and also discovers the late occurrence of lattice expansion in the nascent β phase that grows out from the parent α phase. By distinguishing pseudomartensitic transition from other types of mechanisms, we propose general rules to predict the product crystallinity of solid phase transition. The new knowledge on the kinetics of pseudomartensitic transition complements the theory of diffusionless solid phase transition.

Purification of monoclonal antibodies from clarified cell culture fluid using Protein A capture continuous countercurrent tangential chromatography

PubMed Central

Dutta, Amit K.; Tran, Travis; Napadensky, Boris; Teella, Achyuta; Brookhart, Gary; Ropp, Philip A.; Zhang, Ada W.; Tustian, Andrew D.; Zydney, Andrew L.; Shinkazh, Oleg

2015-01-01

Recent studies using simple model systems have demonstrated that Continuous Countercurrent Tangential Chromatography (CCTC) has the potential to overcome many of the limitations of conventional Protein A chromatography using packed columns. The objective of this work was to optimize and implement a CCTC system for monoclonal antibody purification from clarified Chinese Hamster Ovary (CHO) cell culture fluid using a commercial Protein A resin. Several improvements were introduced to the previous CCTC system including the use of retentate pumps to maintain stable resin concentrations in the flowing slurry, the elimination of a slurry holding tank to improve productivity, and the introduction of an “after binder” to the binding step to increase antibody recovery. A kinetic binding model was developed to estimate the required residence times in the multi-stage binding step to optimize yield and productivity. Data were obtained by purifying two commercial antibodies from two different manufactures, one with low titer (~0.67 g/L) and one with high titer (~6.9 g/L), demonstrating the versatility of the CCTC system. Host cell protein removal, antibody yields and purities were similar to that obtained with conventional column chromatography; however, the CCTC system showed much higher productivity. These results clearly demonstrate the capabilities of continuous countercurrent tangential chromatography for the commercial purification of monoclonal antibody products. PMID:25747172

Purification of monoclonal antibodies from clarified cell culture fluid using Protein A capture continuous countercurrent tangential chromatography.

PubMed

Dutta, Amit K; Tran, Travis; Napadensky, Boris; Teella, Achyuta; Brookhart, Gary; Ropp, Philip A; Zhang, Ada W; Tustian, Andrew D; Zydney, Andrew L; Shinkazh, Oleg

2015-11-10

Recent studies using simple model systems have demonstrated that continuous countercurrent tangential chromatography (CCTC) has the potential to overcome many of the limitations of conventional Protein A chromatography using packed columns. The objective of this work was to optimize and implement a CCTC system for monoclonal antibody purification from clarified Chinese Hamster Ovary (CHO) cell culture fluid using a commercial Protein A resin. Several improvements were introduced to the previous CCTC system including the use of retentate pumps to maintain stable resin concentrations in the flowing slurry, the elimination of a slurry holding tank to improve productivity, and the introduction of an "after binder" to the binding step to increase antibody recovery. A kinetic binding model was developed to estimate the required residence times in the multi-stage binding step to optimize yield and productivity. Data were obtained by purifying two commercial antibodies from two different manufactures, one with low titer (∼ 0.67 g/L) and one with high titer (∼ 6.9 g/L), demonstrating the versatility of the CCTC system. Host cell protein removal, antibody yields and purities were similar to those obtained with conventional column chromatography; however, the CCTC system showed much higher productivity. These results clearly demonstrate the capabilities of continuous countercurrent tangential chromatography for the commercial purification of monoclonal antibody products. Copyright © 2015 Elsevier B.V. All rights reserved.

Evolution of atomic structure during nanoparticle formation

DOE PAGES

Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M. Ø.; ...

2014-04-14

Understanding the mechanism of nanoparticle formation during synthesis is a key prerequisite for the rational design and engineering of desirable materials properties, yet remains elusive due to the difficulty of studying structures at the nanoscale under real conditions. Here, the first comprehensive structural description of the formation of a nanoparticle, yttria-stabilized zirconia (YSZ), all the way from its ionic constituents in solution to the final crystal, is presented. The transformation is a complicated multi-step sequence of atomic reorganizations as the material follows the reaction pathway towards the equilibrium product. Prior to nanoparticle nucleation, reagents reorganize into polymeric species whose structuremore » is incompatible with the final product. Instead of direct nucleation of clusters into the final product lattice, a highly disordered intermediate precipitate forms with a local bonding environment similar to the product yet lacking the correct topology. During maturation, bond reforming occurs by nucleation and growth of distinct domains within the amorphous intermediary. The present study moves beyond kinetic modeling by providing detailed real-time structural insight, and it is demonstrated that YSZ nanoparticle formation and growth is a more complex chemical process than accounted for in conventional models. This level of mechanistic understanding of the nanoparticle formation is the first step towards more rational control over nanoparticle synthesis through control of both solution precursors and reaction intermediaries.« less

Atomic-Scale Design of Iron Fischer-Tropsch Catalysts: A Combined Computational Chemistry, Experimental, and Microkinetic Modeling Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manos Mavrikakis; James A. Dumesic; Rahul P. Nabar

2006-09-29

Work continued on the development of a microkinetic model of Fischer-Tropsch synthesis (FTS) on supported and unsupported Fe catalysts. The following aspects of the FT mechanism on unsupported iron catalysts were investigated on during this third year: (1) the collection of rate data in a Berty CSTR reactor based on sequential design of experiments; (2) CO adsorption and CO-TPD for obtaining the heat of adsorption of CO on polycrystalline iron; and (3) isothermal hydrogenation (IH) after Fischer Tropsch reaction to identify and quantify surface carbonaceous species. Rates of C{sub 2+} formation on unsupported iron catalysts at 220 C and 20more » atm correlated well to a Langmuir-Hinshelwood type expression, derived assuming carbon hydrogenation to CH and OH recombination to water to be rate-determining steps. From desorption of molecularly adsorbed CO at different temperatures the heat of adsorption of CO on polycrystalline iron was determined to be 100 kJ/mol. Amounts and types of carbonaceous species formed after FT reaction for 5-10 minutes at 150, 175, 200 and 285 C vary significantly with temperature. Mr. Brian Critchfield completed his M.S. thesis work on a statistically designed study of the kinetics of FTS on 20% Fe/alumina. Preparation of a paper describing this work is in progress. Results of these studies were reported at the Annual Meeting of the Western States Catalysis and at the San Francisco AIChE meeting. In the coming period, studies will focus on quantitative determination of the rates of kinetically-relevant elementary steps on unsupported Fe catalysts with/without K and Pt promoters by SSITKA method. This study will help us to (1) understand effects of promoter and support on elementary kinetic parameters and (2) build a microkinetics model for FTS on iron. Calculations using periodic, self-consistent Density Functional Theory (DFT) methods were performed on models of defected Fe surfaces, most significantly the stepped Fe(211) surface. Binding Energies (BE's), preferred adsorption sites and geometries of all the FTS relevant stable species and intermediates were evaluated. Each elementary step of our reaction model was fully characterized with respect to its thermochemistry and comparisons between the stepped Fe(211) facet and the most-stable Fe(110) facet were established. In most cases the BE's on Fe(211) reflected the trends observed earlier on Fe(110), yet there were significant variations imposed on the underlying trends. Vibrational frequencies were evaluated for the preferred adsorption configurations of each species with the aim of evaluating the entropy-changes and preexponential factors for each elementary step. Kinetic studies were performed for the early steps of FTS (up to CH{sub 4} formation) and CO dissociation. This involved evaluation of the Minimum Energy Pathway (MEP) and activation energy barrier for the steps involved. We concluded that Fe(211) would allow for far more facile CO dissociation in comparison to other Fe catalysts studied so far, but the other FTS steps studied remained mostly unchanged.« less

Non-thermal plasma destruction of allyl alcohol in waste gas: kinetics and modelling

NASA Astrophysics Data System (ADS)

DeVisscher, A.; Dewulf, J.; Van Durme, J.; Leys, C.; Morent, R.; Van Langenhove, H.

2008-02-01

Non-thermal plasma treatment is a promising technique for the destruction of volatile organic compounds in waste gas. A relatively unexplored technique is the atmospheric negative dc multi-pin-to-plate glow discharge. This paper reports experimental results of allyl alcohol degradation and ozone production in this type of plasma. A new model was developed to describe these processes quantitatively. The model contains a detailed chemical degradation scheme, and describes the physics of the plasma by assuming that the fraction of electrons that takes part in chemical reactions is an exponential function of the reduced field. The model captured the experimental kinetic data to less than 2 ppm standard deviation.

Effects of correlated parameters and uncertainty in electronic-structure-based chemical kinetic modelling

NASA Astrophysics Data System (ADS)

Sutton, Jonathan E.; Guo, Wei; Katsoulakis, Markos A.; Vlachos, Dionisios G.

2016-04-01

Kinetic models based on first principles are becoming common place in heterogeneous catalysis because of their ability to interpret experimental data, identify the rate-controlling step, guide experiments and predict novel materials. To overcome the tremendous computational cost of estimating parameters of complex networks on metal catalysts, approximate quantum mechanical calculations are employed that render models potentially inaccurate. Here, by introducing correlative global sensitivity analysis and uncertainty quantification, we show that neglecting correlations in the energies of species and reactions can lead to an incorrect identification of influential parameters and key reaction intermediates and reactions. We rationalize why models often underpredict reaction rates and show that, despite the uncertainty being large, the method can, in conjunction with experimental data, identify influential missing reaction pathways and provide insights into the catalyst active site and the kinetic reliability of a model. The method is demonstrated in ethanol steam reforming for hydrogen production for fuel cells.

Assessment of mean-field microkinetic models for CO methanation on stepped metal surfaces using accelerated kinetic Monte Carlo

NASA Astrophysics Data System (ADS)

Andersen, Mie; Plaisance, Craig P.; Reuter, Karsten

2017-10-01

First-principles screening studies aimed at predicting the catalytic activity of transition metal (TM) catalysts have traditionally been based on mean-field (MF) microkinetic models, which neglect the effect of spatial correlations in the adsorbate layer. Here we critically assess the accuracy of such models for the specific case of CO methanation over stepped metals by comparing to spatially resolved kinetic Monte Carlo (kMC) simulations. We find that the typical low diffusion barriers offered by metal surfaces can be significantly increased at step sites, which results in persisting correlations in the adsorbate layer. As a consequence, MF models may overestimate the catalytic activity of TM catalysts by several orders of magnitude. The potential higher accuracy of kMC models comes at a higher computational cost, which can be especially challenging for surface reactions on metals due to a large disparity in the time scales of different processes. In order to overcome this issue, we implement and test a recently developed algorithm for achieving temporal acceleration of kMC simulations. While the algorithm overall performs quite well, we identify some challenging cases which may lead to a breakdown of acceleration algorithms and discuss possible directions for future algorithm development.

A Fuzzy Goal Programming for a Multi-Depot Distribution Problem

NASA Astrophysics Data System (ADS)

Nunkaew, Wuttinan; Phruksaphanrat, Busaba

2010-10-01

A fuzzy goal programming model for solving a Multi-Depot Distribution Problem (MDDP) is proposed in this research. This effective proposed model is applied for solving in the first step of Assignment First-Routing Second (AFRS) approach. Practically, a basic transportation model is firstly chosen to solve this kind of problem in the assignment step. After that the Vehicle Routing Problem (VRP) model is used to compute the delivery cost in the routing step. However, in the basic transportation model, only depot to customer relationship is concerned. In addition, the consideration of customer to customer relationship should also be considered since this relationship exists in the routing step. Both considerations of relationships are solved using Preemptive Fuzzy Goal Programming (P-FGP). The first fuzzy goal is set by a total transportation cost and the second fuzzy goal is set by a satisfactory level of the overall independence value. A case study is used for describing the effectiveness of the proposed model. Results from the proposed model are compared with the basic transportation model that has previously been used in this company. The proposed model can reduce the actual delivery cost in the routing step owing to the better result in the assignment step. Defining fuzzy goals by membership functions are more realistic than crisps. Furthermore, flexibility to adjust goals and an acceptable satisfactory level for decision maker can also be increased and the optimal solution can be obtained.

Sulfur Tolerant Solid Oxide Fuel Cell for Coal Syngas Application: Experimental Study on Diverse Impurity Effects and Fundamental Modeling of Electrode Kinetics

NASA Astrophysics Data System (ADS)

Gong, Mingyang

With demand over green energy economy, fuel cells have been developed as a promising energy conversion technology with higher efficiency and less emission. Solid oxide fuel cells (SOFC) can utilize various fuels in addition to hydrogen including coal derived sygas, and thus are favored for future power generation due to dependence on coal in electrical industry. However impurities such as sulfur and phosphorous present in coal syngas in parts per million (p.p.m.) levels can severely poison SOFC anode typically made of Ni/yttria-stabilized-zirconia (Ni-YSZ) and limit SOFC applicability in economically derivable fuels. The focus of the research is to develop strategy for application of high performance SOFC in coal syngas with tolerance against trace impurities such as H2S and PH3. To realize the research goal, the experimental study on sulfur tolerant anode materials and examination of various fuel impurity effects on SOFC anode are combined with electrochemical modeling of SOFC cathode kinetics in order to benefit design of direct-coal-syngas SOFC. Tolerant strategy for SOFC anode against sulfur is studied by using alternative materials which can both mitigate sulfur poisoning and function as active anode components. The Ni-YSZ anode was modified by incorporation of lanthanum doped ceria (LDC) nano-coatings via impregnation. Cell test in coal syngas containing 20 ppm H2S indicated the impregnated LDC coatings inhibited on-set of sulfur poisoning by over 10hrs. Cell analysis via X-ray photon spectroscopy (XPS), X-ray diffraction (XRD) and electrochemistry revealed LDC coatings reacted with H2S via chemisorptions, resulting in less sulfur blocking triple--phase-boundary and minimized performance loss. Meanwhile the effects of PH3 impurity on SOFC anode is examined by using Ni-YSZ anode supported SOFC. Degradation of cell is found to be irreversible due to adsorption of PH3 on TPB and further reaction with Ni to form secondary phases with low melting point. The feasibility of mixed ionic and electronic conductive (MIEC) metal oxides with perovskite structure (ABO3) as alternative ceramic SOFC anodes in coal syngas has been examined by PH3 exposure test. The study found although perovskite anodes can be generally more tolerant against H2S, further examination on PH3 tolerance is indispensable before their extensive application in coal syngas. On the theoretical end it is this research's initiative that oxygen reduction reaction at mixed ionic and electronic conductive (MIEC) cathode is a key factor controlling SOFC performance at intermediate temperature (700˜850°C). It is generally recognized that the overall charge-transfer process could occur through both surface pathway at triple-phase boundary (3PB) and bulk pathway at electrolyte/cathode interface (2PB). A modified one-dimensional model is thus developed to predict defect evolution of MIEC cathode under overpotential by incorporating multi-step charge-transfer into the bi-pathway continuum model. Finite volume control method is applied to obtain solutions for the model. The simulation predicted kinetics transition from 3PB control to 2PB control as cathodic overpotential stepping from -0.2V to -0.4V, depending on the material properties parameters. Meanwhile significant activation behavior of the MIEC electrode was also observed as indicated by extension of reaction region towards gas-exposed oxide surface. This model addressed contribution from electrochemical-controlled rate-limiting steps (RLSs) on the reduction kinetics, and identified the role played by multiple material property parameters such as surface oxygen ion concentration and bulk vacancy concentration on the kinetics transition. Combined academic knowledge gained through experimental investigation and theoretical simulation in this research would benefit the future design, development and application strategy of high-performance SOFC in coal syngas fuels.

Simplified jet fuel reaction mechanism for lean burn combustion application

NASA Technical Reports Server (NTRS)

Lee, Chi-Ming; Kundu, Krishna; Ghorashi, Bahman

1993-01-01

Successful modeling of combustion and emissions in gas turbine engine combustors requires an adequate description of the reaction mechanism. Detailed mechanisms contain a large number of chemical species participating simultaneously in many elementary kinetic steps. Current computational fluid dynamic models must include fuel vaporization, fuel-air mixing, chemical reactions, and complicated boundary geometries. A five-step Jet-A fuel mechanism which involves pyrolysis and subsequent oxidation of paraffin and aromatic compounds is presented. This mechanism is verified by comparing with Jet-A fuel ignition delay time experimental data, and species concentrations obtained from flametube experiments. This five-step mechanism appears to be better than the current one- and two-step mechanisms.

Kinetic modeling of low density lipoprotein oxidation in arterial wall and its application in atherosclerotic lesions prediction.

PubMed

Karimi, Safoora; Dadvar, Mitra; Modarress, Hamid; Dabir, Bahram

2013-01-01

Oxidation of low-density lipoprotein (LDL) is one of the major factors in atherogenic process. Trapped oxidized LDL (Ox-LDL) in the subendothelial matrix is taken up by macrophage and leads to foam cell generation creating the first step in atherosclerosis development. Many researchers have studied LDL oxidation using in vitro cell-induced LDL oxidation model. The present study provides a kinetic model for LDL oxidation in intima layer that can be used in modeling of atherosclerotic lesions development. This is accomplished by considering lipid peroxidation kinetic in LDL through a system of elementary reactions. In comparison, characteristics of our proposed kinetic model are consistent with the results of previous experimental models from other researches. Furthermore, our proposed LDL oxidation model is added to the mass transfer equation in order to predict the LDL concentration distribution in intima layer which is usually difficult to measure experimentally. According to the results, LDL oxidation kinetic constant is an important parameter that affects LDL concentration in intima layer so that existence of antioxidants that is responsible for the reduction of initiating rates and prevention of radical formations, have increased the concentration of LDL in intima by reducing the LDL oxidation rate. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Examination of Wildland Fire Spread at Small Scales Using Direct Numerical Simulations and High-Speed Laser Diagnostics

NASA Astrophysics Data System (ADS)

Wimer, N. T.; Mackoweicki, A. S.; Poludnenko, A. Y.; Hoffman, C.; Daily, J. W.; Rieker, G. B.; Hamlington, P.

2017-12-01

Results are presented from a joint computational and experimental research effort focused on understanding and characterizing wildland fire spread at small scales (roughly 1m-1mm) using direct numerical simulations (DNS) with chemical kinetics mechanisms that have been calibrated using data from high-speed laser diagnostics. The simulations are intended to directly resolve, with high physical accuracy, all small-scale fluid dynamic and chemical processes relevant to wildland fire spread. The high fidelity of the simulations is enabled by the calibration and validation of DNS sub-models using data from high-speed laser diagnostics. These diagnostics have the capability to measure temperature and chemical species concentrations, and are used here to characterize evaporation and pyrolysis processes in wildland fuels subjected to an external radiation source. The chemical kinetics code CHEMKIN-PRO is used to study and reduce complex reaction mechanisms for water removal, pyrolysis, and gas phase combustion during solid biomass burning. Simulations are then presented for a gaseous pool fire coupled with the resulting multi-step chemical reaction mechanisms, and the results are connected to the fundamental structure and spread of wildland fires. It is anticipated that the combined computational and experimental approach of this research effort will provide unprecedented access to information about chemical species, temperature, and turbulence during the entire pyrolysis, evaporation, ignition, and combustion process, thereby permitting more complete understanding of the physics that must be represented by coarse-scale numerical models of wildland fire spread.

Development of Multi-Route Physiologically-based Pharmacokinetic Models for Ethanol in the Adult, Pregnant, and Neonatal Rat

EPA Science Inventory

Biofuel blends of 10% ethanol (EtOH) and gasoline are common in the United States, and higher EtOH concentrations are being considered (15-85%). Currently, no physiologically-based pharmacokinetic (PBPK) models are available to describe the kinetics of EtOH-based biofuels. PBPK...

[Research progress of multi-model medical image fusion and recognition].

PubMed

Zhou, Tao; Lu, Huiling; Chen, Zhiqiang; Ma, Jingxian

2013-10-01

Medical image fusion and recognition has a wide range of applications, such as focal location, cancer staging and treatment effect assessment. Multi-model medical image fusion and recognition are analyzed and summarized in this paper. Firstly, the question of multi-model medical image fusion and recognition is discussed, and its advantage and key steps are discussed. Secondly, three fusion strategies are reviewed from the point of algorithm, and four fusion recognition structures are discussed. Thirdly, difficulties, challenges and possible future research direction are discussed.

Kinetic dissection of individual steps in the poly(C)-directed oligoguanylate synthesis from guanosine 5'-monophosphate 2-methylimidazolide

NASA Technical Reports Server (NTRS)

Kanavarioti, A.; Bernasconi, C. F.; Alberas, D. J.; Baird, E. E.

1993-01-01

A kinetic study of oligoguanylate synthesis on a polycytidylate template, poly(C), as a function of the concentration of the activated monomer, guanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpG, is reported. Reactions were run with 0.005-0.045 M 2-MeImpG in the presence of 0.05 M poly(C) at 23 degrees C. The kinetic results are consistent with a reaction scheme (eq 1) that consists of a series of consecutive steps, each step representing the addition of one molecule of 2-MeImpG to the growing oligomer. This scheme allows the calculation of second-order rate constants for every step by analyzing the time-dependent growth of each oligomer. Computer simulations of the course of reaction based on the determined rate constants and eq 1 are in excellent agreement with the product distributions seen in the HPLC profiles. In accord with an earlier study (Fakhrai, H.; Inoue, T.; Orgel, L. E. Tetrahedron 1984, 40, 39), rate constants, ki, for the formation of the tetramer and longer oligomers up to the 16-mer were found to be independent of length and somewhat higher than k3 (formation of trimer), which in turn is much higher than k2 (formation of dimer). The ki (i > or = 4), k3, and k2 values are not true second-order rate constants but vary with monomer concentration. Mechanistic models for the dimerization (Scheme I) and elongation reactions (Scheme II) are proposed that are consistent with our results. These models take into account that the monomer associates with the template in a cooperative manner. Our kinetic analysis allowed the determination of rate constants for the elementary processes of covalent bond formation between two monomers (dimerization) and between an oligomer and a monomer (elongation) on the template. A major conclusion from our study is that bond formation between two monomer units or between a primer and a monomer is assisted by the presence of additional next-neighbor monomer units. This is consistent with recent findings with hairpin oligonucleotides (Wu, T.; Orgel, L. E. J. Am. Chem. Soc. 1992, 114, 317). Our study is the first of its kind that shows the feasibility of a thorough kinetic analysis of a template-directed oligomerization and provides a detailed mechanistic model of these reactions.

Hybrid Parallelization of Adaptive MHD-Kinetic Module in Multi-Scale Fluid-Kinetic Simulation Suite

DOE PAGES

Borovikov, Sergey; Heerikhuisen, Jacob; Pogorelov, Nikolai

2013-04-01

The Multi-Scale Fluid-Kinetic Simulation Suite has a computational tool set for solving partially ionized flows. In this paper we focus on recent developments of the kinetic module which solves the Boltzmann equation using the Monte-Carlo method. The module has been recently redesigned to utilize intra-node hybrid parallelization. We describe in detail the redesign process, implementation issues, and modifications made to the code. Finally, we conduct a performance analysis.

Examinations of the Chemical Step in Enzyme Catalysis.

PubMed

Singh, P; Islam, Z; Kohen, A

2016-01-01

Advances in computational and experimental methods in enzymology have aided comprehension of enzyme-catalyzed chemical reactions. The main difficulty in comparing computational findings to rate measurements is that the first examines a single energy barrier, while the second frequently reflects a combination of many microscopic barriers. We present here intrinsic kinetic isotope effects and their temperature dependence as a useful experimental probe of a single chemical step in a complex kinetic cascade. Computational predictions are tested by this method for two model enzymes: dihydrofolate reductase and thymidylate synthase. The description highlights the significance of collaboration between experimentalists and theoreticians to develop a better understanding of enzyme-catalyzed chemical conversions. © 2016 Elsevier Inc. All rights reserved.

Measuring the Acoustic Release of a Chemotherapeutic Agent from Folate-Targeted Polymeric Micelles.

PubMed

Abusara, Ayah; Abdel-Hafez, Mamoun; Husseini, Ghaleb

2018-08-01

In this paper, we compare the use of Bayesian filters for the estimation of release and re-encapsulation rates of a chemotherapeutic agent (namely Doxorubicin) from nanocarriers in an acoustically activated drug release system. The study is implemented using an advanced kinetic model that takes into account cavitation events causing the antineoplastic agent's release from polymeric micelles upon exposure to ultrasound. This model is an improvement over the previous representations of acoustic release that used simple zero-, first- and second-order release and re-encapsulation kinetics to study acoustically triggered drug release from polymeric micelles. The new model incorporates drug release and micellar reassembly events caused by cavitation allowing for the controlled release of chemotherapeutics specially and temporally. Different Bayesian estimators are tested for this purpose including Kalman filters (KF), Extended Kalman filters (EKF), Particle filters (PF), and multi-model KF and EKF. Simulated and experimental results are used to verify the performance of the above-mentioned estimators. The proposed methods demonstrate the utility and high-accuracy of using estimation methods in modeling this drug delivery technique. The results show that, in both cases (linear and non-linear dynamics), the modeling errors are expensive but can be minimized using a multi-model approach. In addition, particle filters are more flexible filters that perform reasonably well compared to the other two filters. The study improved the accuracy of the kinetic models used to capture acoustically activated drug release from polymeric micelles, which may in turn help in designing hardware and software capable of precisely controlling the delivered amount of chemotherapeutics to cancerous tissue.

Synthesis, kinetics and characterizations of polyimide based semi-IPN systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tai, H.J.

1992-01-01

The PMR-15 polyimide is the leading matrix resin for high performance composites for use in high temperature and thermo-oxidative environments. This resin has superior mechanical properties, good processability and a high working temperature at around 300[degrees]C. It has the disadvantages of being brittle and high susceptibility to microcracking from thermal cycling that limit its widespread application. To improve the fracture toughness, a thermoplastic polyimide, LARC-TPI, and a thermoplastic poly (amide imide), Amoco AI-10, were added individually to PMR-15 resin to form sequential semi-interpenetrating polymer networks (semi-2-IPNs). the kinetics of imidization of LARC-TPI were studied using TGA technique. Both the solventmore » and the glass transition temperature were found to greatly affect the imidization kinetics. The kinetics could be well modeled by a two-step reaction: the first step being a second order reaction followed by a first order diffusion controlled reaction as the second step. The curing of PMR-15 and PMR-15/LARC-TPI semi-IPN was investigated by DSC. A first order reaction kinetics could describe the curing process adequately, implying that the reverse Diels-Alder reaction of the Norbornene end group was the rate controlling step. The glass transition temperature played an important role. The higher the fraction LARC-TPI, the higher the glass transition temperature of the semi-IPN prepolymer, and the slower the cure reaction. From a knowledge of kinetics, the molding cycle of PMR-15 and PMR-15/LARC-TPI semi-IPNs were determined. Both PMR-15/LARC-TPI and PMR-15/AI-10 semi-IPN systems exhibited much higher fracture toughness than PMR-15, but at the compromise of a reduction in the glass transition temperature. A single glass transition temperature for each semi-IPN was observed but there was presence of special intermolecular interaction. Tg measurements and IR spectroscopy indicated that both semi-IPN systems were compatible polymer pairs.« less

Computer-Aided Construction of Chemical Kinetic Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Green, William H.

2014-12-31

The combustion chemistry of even simple fuels can be extremely complex, involving hundreds or thousands of kinetically significant species. The most reasonable way to deal with this complexity is to use a computer not only to numerically solve the kinetic model, but also to construct the kinetic model in the first place. Because these large models contain so many numerical parameters (e.g. rate coefficients, thermochemistry) one never has sufficient data to uniquely determine them all experimentally. Instead one must work in “predictive” mode, using theoretical rather than experimental values for many of the numbers in the model, and as appropriatemore » refining the most sensitive numbers through experiments. Predictive chemical kinetics is exactly what is needed for computer-aided design of combustion systems based on proposed alternative fuels, particularly for early assessment of the value and viability of proposed new fuels before those fuels are commercially available. This project was aimed at making accurate predictive chemical kinetics practical; this is a challenging goal which requires a range of science advances. The project spanned a wide range from quantum chemical calculations on individual molecules and elementary-step reactions, through the development of improved rate/thermo calculation procedures, the creation of algorithms and software for constructing and solving kinetic simulations, the invention of methods for model-reduction while maintaining error control, and finally comparisons with experiment. Many of the parameters in the models were derived from quantum chemistry calculations, and the models were compared with experimental data measured in our lab or in collaboration with others.« less

Toward a Multi-scale Phase Transition Kinetics Methodology: From Non-Equilibrium Statistical Mechanics to Hydrodynamics

NASA Astrophysics Data System (ADS)

Belof, Jonathan; Orlikowski, Daniel; Wu, Christine; McLaughlin, Keith

2013-06-01

Shock and ramp compression experiments are allowing us to probe condensed matter under extreme conditions where phase transitions and other non-equilibrium aspects can now be directly observed, but first principles simulation of kinetics remains a challenge. A multi-scale approach is presented here, with non-equilibrium statistical mechanical quantities calculated by molecular dynamics (MD) and then leveraged to inform a classical nucleation and growth kinetics model at the hydrodynamic scale. Of central interest is the free energy barrier for the formation of a critical nucleus, with direct NEMD presenting the challenge of relatively long timescales necessary to resolve nucleation. Rather than attempt to resolve the time-dependent nucleation sequence directly, the methodology derived here is built upon the non-equilibrium work theorem in order to bias the formation of a critical nucleus and thus construct the nucleation and growth rates. Having determined these kinetic terms from MD, a hydrodynamics implementation of Kolmogorov-Johnson-Mehl-Avrami (KJMA) kinetics and metastabilty is applied to the dynamic compressive freezing of water and compared with recent ramp compression experiments [Dolan et al., Nature (2007)] Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344.

Comparison of kinetic model for biogas production from corn cob

NASA Astrophysics Data System (ADS)

Shitophyta, L. M.; Maryudi

2018-04-01

Energy demand increases every day, while the energy source especially fossil energy depletes increasingly. One of the solutions to overcome the energy depletion is to provide renewable energies such as biogas. Biogas can be generated by corn cob and food waste. In this study, biogas production was carried out by solid-state anaerobic digestion. The steps of biogas production were the preparation of feedstock, the solid-state anaerobic digestion, and the measurement of biogas volume. This study was conducted on TS content of 20%, 22%, and 24%. The aim of this research was to compare kinetic models of biogas production from corn cob and food waste as a co-digestion using the linear, exponential equation, and first-kinetic models. The result showed that the exponential equation had a better correlation than the linear equation on the ascending graph of biogas production. On the contrary, the linear equation had a better correlation than the exponential equation on the descending graph of biogas production. The correlation values on the first-kinetic model had the smallest value compared to the linear and exponential models.

Kinetic models of controllable pore growth of anodic aluminum oxide membrane

NASA Astrophysics Data System (ADS)

Huang, Yan; Zeng, Hong-yan; Zhao, Ce; Qu, Ye-qing; Zhang, Pin

2012-06-01

An anodized Al2O3 (AAO) membrane with apertures about 72 nm in diameter was prepared by two-step anodic oxidation. The appearance and pore arrangement of the AAO membrane were characterized by energy dispersive x-ray spectroscopy and scanning electron microscopy. It was confirmed that the pores with high pore aspect ratio were parallel, well-ordered, and uniform. The kinetics of pores growth in the AAO membrane was derived, and the kinetic models showed that pores stopped developing when the pressure ( σ) trended to equal the surface tension at the end of anodic oxidation. During pore expansion, the effects of the oxalic acid concentration and expansion time on the pore size were investigated, and the kinetic behaviors were explained with two kinetic models derived in this study. They showed that the pore size increased with extended time ( r= G· t+ G'), but decreased with increased concentration ( r = - K·ln c- K') through the derived mathematic formula. Also, the values of G, G', K, and K' were derived from our experimental data.

Integrated Modeling of Time Evolving 3D Kinetic MHD Equilibria and NTV Torque

NASA Astrophysics Data System (ADS)

Logan, N. C.; Park, J.-K.; Grierson, B. A.; Haskey, S. R.; Nazikian, R.; Cui, L.; Smith, S. P.; Meneghini, O.

2016-10-01

New analysis tools and integrated modeling of plasma dynamics developed in the OMFIT framework are used to study kinetic MHD equilibria evolution on the transport time scale. The experimentally observed profile dynamics following the application of 3D error fields are described using a new OMFITprofiles workflow that directly addresses the need for rapid and comprehensive analysis of dynamic equilibria for next-step theory validation. The workflow treats all diagnostic data as fundamentally time dependent, provides physics-based manipulations such as ELM phase data selection, and is consistent across multiple machines - including DIII-D and NSTX-U. The seamless integration of tokamak data and simulation is demonstrated by using the self-consistent kinetic EFIT equilibria and profiles as input into 2D particle, momentum and energy transport calculations using TRANSP as well as 3D kinetic MHD equilibrium stability and neoclassical transport modeling using General Perturbed Equilibrium Code (GPEC). The result is a smooth kinetic stability and NTV torque evolution over transport time scales. Work supported by DE-AC02-09CH11466.

Evolution of optimal Hill coefficients in nonlinear public goods games.

PubMed

Archetti, Marco; Scheuring, István

2016-10-07

In evolutionary game theory, the effect of public goods like diffusible molecules has been modelled using linear, concave, sigmoid and step functions. The observation that biological systems are often sigmoid input-output functions, as described by the Hill equation, suggests that a sigmoid function is more realistic. The Michaelis-Menten model of enzyme kinetics, however, predicts a concave function, and while mechanistic explanations of sigmoid kinetics exist, we lack an adaptive explanation: what is the evolutionary advantage of a sigmoid benefit function? We analyse public goods games in which the shape of the benefit function can evolve, in order to determine the optimal and evolutionarily stable Hill coefficients. We find that, while the dynamics depends on whether output is controlled at the level of the individual or the population, intermediate or high Hill coefficients often evolve, leading to sigmoid input-output functions that for some parameters are so steep to resemble a step function (an on-off switch). Our results suggest that, even when the shape of the benefit function is unknown, biological public goods should be modelled using a sigmoid or step function rather than a linear or concave function. Copyright © 2016 Elsevier Ltd. All rights reserved.

Interactive lesion segmentation on dynamic contrast enhanced breast MRI using a Markov model

NASA Astrophysics Data System (ADS)

Wu, Qiu; Salganicoff, Marcos; Krishnan, Arun; Fussell, Donald S.; Markey, Mia K.

2006-03-01

The purpose of this study is to develop a method for segmenting lesions on Dynamic Contrast-Enhanced (DCE) breast MRI. DCE breast MRI, in which the breast is imaged before, during, and after the administration of a contrast agent, enables a truly 3D examination of breast tissues. This functional angiogenic imaging technique provides noninvasive assessment of microcirculatory characteristics of tissues in addition to traditional anatomical structure information. Since morphological features and kinetic curves from segmented lesions are to be used for diagnosis and treatment decisions, lesion segmentation is a key pre-processing step for classification. In our study, the ROI is defined by a bounding box containing the enhancement region in the subtraction image, which is generated by subtracting the pre-contrast image from 1st post-contrast image. A maximum a posteriori (MAP) estimate of the class membership (lesion vs. non-lesion) for each voxel is obtained using the Iterative Conditional Mode (ICM) method. The prior distribution of the class membership is modeled as a multi-level logistic model, a Markov Random Field model in which the class membership of each voxel is assumed to depend upon its nearest neighbors only. The likelihood distribution is assumed to be Gaussian. The parameters of each Gaussian distribution are estimated from a dozen voxels manually selected as representative of the class. The experimental segmentation results demonstrate anatomically plausible breast tissue segmentation and the predicted class membership of voxels from the interactive segmentation algorithm agrees with the manual classifications made by inspection of the kinetic enhancement curves. The proposed method is advantageous in that it is efficient, flexible, and robust.

The synthesis and dynamics research of new curing agent for epoxy resin

NASA Astrophysics Data System (ADS)

Peng, Yongli; Huang, Hengyu; Sun, Yong

2017-05-01

Two-step synthesis of trimellitic anhydride trimellitic anhydride n - butyl ester (TMNB) was introduced which could be used as an epoxy resin curing agent. The kinetics of the curing reaction was analyzed by N-order model and autocatalytic model. The curing kinetics parameters, the results show that the curing activation energy (Ea) of this system was 35.79kJ / mol. The kinetic equation of curing was d/a d t =2.1061 ×104e x p (-35.79/R T ) α0.5163(l-α ) 0.366 . Combined with β-1 / T extrapolation and experimental adjustment to obtain the resin system curing process: 75°C for 1h, 140°C for 3h, 160°C for 2h.

Chemical kinetic modeling of propane oxidation behind shock waves

NASA Technical Reports Server (NTRS)

Mclain, A. G.; Jachimowski, C. J.

1977-01-01

The stoichiometric combustion of propane behind incident shock waves was studied experimentally and analytically over a temperature range from 1700 K to 2600 K and a pressure range from 1.2 to 1.9 atm. Measurements of the concentrations of carbon monoxide (CO) and carbon dioxide (CO2) and the product of the oxygen atom and carbon dioxide concentrations (O)(CO) were made after passage of the incident shock wave. A kinetic mechanism was developed which, when used in a computer program for a flowing, reacting gas behind an incident shock wave predicted experimentally measured results quite well. Ignition delay times from the literature were also predicted quite well. The kinetic mechanism consisted of 59 individual kinetic steps.

Implementing the Indiana Model. Indiana Leadership Consortium: Equity through Change.

ERIC Educational Resources Information Center

Indiana Leadership Consortium.

This guide, which was developed as a part of a multi-year, statewide effort to institutionalize gender equity in various educational settings throughout Indiana, presents a step-by-step process model for achieving gender equity in the state's secondary- and postsecondary-level vocational programs through coalition building and implementation of a…

Precise non-steady-state characterization of solid active materials with no preliminary mechanistic assumptions

DOE PAGES

Constales, Denis; Yablonsky, Gregory S.; Wang, Lucun; ...

2017-04-25

This paper presents a straightforward and user-friendly procedure for extracting a reactivity characterization of catalytic reactions on solid materials under non-steady-state conditions, particularly in temporal analysis of products (TAP) experiments. The kinetic parameters derived by this procedure can help with the development of detailed mechanistic understanding. The procedure consists of the following two major steps: 1) Three “Laplace reactivities” are first determined based on the moments of the exit flow pulse response data; 2) Depending on a select kinetic model, kinetic constants of elementary reaction steps can then be expressed as a function of reactivities and determined accordingly. In particular,more » we distinguish two calculation methods based on the availability and reliability of reactant and product data. The theoretical results are illustrated using a reverse example with given parameters as well as an experimental example of CO oxidation over a supported Au/SiO 2 catalyst. The procedure presented here provides an efficient tool for kinetic characterization of many complex chemical reactions.« less

Modified ADM1 disintegration/hydrolysis structures for modeling batch thermophilic anaerobic digestion of thermally pretreated waste activated sludge.

PubMed

Ramirez, Ivan; Mottet, Alexis; Carrère, Hélène; Déléris, Stéphane; Vedrenne, Fabien; Steyer, Jean-Philippe

2009-08-01

Anaerobic digestion disintegration and hydrolysis have been traditionally modeled according to first-order kinetics assuming that their rates do not depend on disintegration/hydrolytic biomass concentrations. However, the typical sigmoid-shape increase in time of the disintegration/hydrolysis rates cannot be described with first-order models. For complex substrates, first-order kinetics should thus be modified to account for slowly degradable material. In this study, a slightly modified IWA ADM1 model is presented to simulate thermophilic anaerobic digestion of thermally pretreated waste activated sludge. Contois model is first included for disintegration and hydrolysis steps instead of first-order kinetics and Hill function is then used to model ammonia inhibition of aceticlastic methanogens instead of a non-competitive function. One batch experimental data set of anaerobic degradation of a raw waste activated sludge is used to calibrate the proposed model and three additional data sets from similar sludge thermally pretreated at three different temperatures are used to validate the parameters values.

Multi-Sided Markets for Transforming Healthcare Service Delivery.

PubMed

Kuziemsky, Craig; Vimarlund, Vivian

2018-01-01

Changes in healthcare delivery needs have necessitated the design of new models for connecting providers and consumers of services. While healthcare delivery has traditionally been a push market, multi-sided markets offer the potential for transitioning to a pull market for service delivery. However, there is a need to better understand the business model for multi-sided markets as a first step to using them in healthcare. This paper addressed that need and describes a multi-sided market evaluation framework. Our framework identifies patient, governance and service delivery as three levels of brokerage consideration for evaluating multi-sided markets in healthcare.

Modelling and kinetics studies of a corn-rape blend combustion in an oxy-fuel atmosphere.

PubMed

López, R; Fernández, C; Martínez, O; Sánchez, M E

2015-05-01

A kinetic oxy-combustion study of a previously optimized lignocellulose blend is proposed. Kinetic and diffusion control mechanism are considered. The proposed correlations fit properly with the experimental results and diffusion effects are identified as be important enough to be taken into account. Afterwards, with the results obtained in the kinetic study, a detailed consecutive and parallel kinetic scheme is proposed for modelling the oxy-combustion of the blend. A discussion of the temperature and concentration profiles are included. Variation of products final distribution is considered. Smaller particles than 0.001 m are proposed for reducing temperature and concentration profiles and obtaining a good final product distribution. CO2-char reaction is identified as one of the most important step to be optimized for obtaining the lowest final residue. In this study, char is mainly oxidised at 950 K and this situation is attributed to an optimized blending of the bioresidues. Copyright © 2015 Elsevier Ltd. All rights reserved.

New Reduced Two-Time Step Method for Calculating Combustion and Emission Rates of Jet-A and Methane Fuel With and Without Water Injection

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2004-01-01

A simplified kinetic scheme for Jet-A, and methane fuels with water injection was developed to be used in numerical combustion codes, such as the National Combustor Code (NCC) or even simple FORTRAN codes that are being developed at Glenn. The two time step method is either an initial time averaged value (step one) or an instantaneous value (step two). The switch is based on the water concentration in moles/cc of 1x10(exp -20). The results presented here results in a correlation that gives the chemical kinetic time as two separate functions. This two step method is used as opposed to a one step time averaged method previously developed to determine the chemical kinetic time with increased accuracy. The first time averaged step is used at the initial times for smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, initial water to fuel mass ratio, temperature, and pressure. The second instantaneous step, to be used with higher water concentrations, gives the chemical kinetic time as a function of instantaneous fuel and water mole concentration, pressure and temperature (T4). The simple correlations would then be compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates were then used to calculate the necessary chemical kinetic times. Chemical kinetic time equations for fuel, carbon monoxide and NOx were obtained for Jet-A fuel and methane with and without water injection to water mass loadings of 2/1 water to fuel. A similar correlation was also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium concentrations of carbon monoxide and nitrogen oxide as functions of overall equivalence ratio, water to fuel mass ratio, pressure and temperature (T3). The temperature of the gas entering the turbine (T4) was also correlated as a function of the initial combustor temperature (T3), equivalence ratio, water to fuel mass ratio, and pressure.

Development of Turbulence Models for Shear Flows by a Double Expansion technique.

DTIC Science & Technology

1991-07-01

Let us introduce the dimensionless variables 7 = -; I -_o E ~ Ko where S = (2Sij Sij)112 and K0 is the initial turbulent kinetic energy. In...simulation of Bardina eta 1 4 for co/ SKo = 0.296 Figure 2 19 IlI H- L -1 y x Turbulent flow over a backward facing step Figure 3 20 BACKWARD-FACING STEP

Motion of kinesin in a viscoelastic medium

NASA Astrophysics Data System (ADS)

Knoops, Gert; Vanderzande, Carlo

2018-05-01

Kinesin is a molecular motor that transports cargo along microtubules. The results of many in vitro experiments on kinesin-1 are described by kinetic models in which one transition corresponds to the forward motion and subsequent binding of the tethered motor head. We argue that in a viscoelastic medium like the cytosol of a cell this step is not Markov and has to be described by a nonexponential waiting time distribution. We introduce a semi-Markov kinetic model for kinesin that takes this effect into account. We calculate, for arbitrary waiting time distributions, the moment generating function of the number of steps made, and determine from this the average velocity and the diffusion constant of the motor. We illustrate our results for the case of a waiting time distribution that is Weibull. We find that for realistic parameter values, viscoelasticity decreases the velocity and the diffusion constant, but increases the randomness (or Fano factor).

Kinetic model for astaxanthin aggregation in water-methanol mixtures

NASA Astrophysics Data System (ADS)

Giovannetti, Rita; Alibabaei, Leila; Pucciarelli, Filippo

2009-07-01

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

Protocols for Copying and Proofreading in Template-Assisted Polymerization

NASA Astrophysics Data System (ADS)

Pigolotti, Simone; Sartori, Pablo

2016-03-01

We discuss how information encoded in a template polymer can be stochastically copied into a copy polymer. We consider four different stochastic copy protocols of increasing complexity, inspired by building blocks of the mRNA translation pathway. In the first protocol, monomer incorporation occurs in a single stochastic transition. We then move to a more elaborate protocol in which an intermediate step can be used for error correction. Finally, we discuss the operating regimes of two kinetic proofreading protocols: one in which proofreading acts from the final copying step, and one in which it acts from an intermediate step. We review known results for these models and, in some cases, extend them to analyze all possible combinations of energetic and kinetic discrimination. We show that, in each of these protocols, only a limited number of these combinations leads to an improvement of the overall copying accuracy.

Kinetics of alkali-based photocathode degradation

DOE PAGES

Pavlenko, Vitaly; Liu, Fangze; Hoffbauer, Mark A.; ...

2016-11-02

Here, we report on a kinetic model that describes the degradation of the quantum efficiency (QE) of Cs 3Sb and negative electron affinity (NEA) GaAs photocathodes under UHV conditions. Additionally, the generally accepted irreversible chemical change of a photocathode’s surface due to reactions with residual gases, such as O 2, CO 2, and H 2O, the model incorporates an intermediate reversible physisorption step, similar to Langmuir adsorption. Moreover, this intermediate step is needed to satisfactorily describe the strongly non-exponential QE degradation curves for two distinctly different classes of photocathodes –surface-activated and “bulk,” indicating that in both systems the QE degradationmore » results from surface damage. The recovery of the QE upon improvement of vacuum conditions is also accurately predicted by this model with three parameters (rates of gas adsorption, desorption, and irreversible chemical reaction with the surface) comprising metrics to better characterize the lifetime of the cathodes, instead of time-pressure exposure expressed in Langmuir units.« less

Path lumping: An efficient algorithm to identify metastable path channels for conformational dynamics of multi-body systems

NASA Astrophysics Data System (ADS)

Meng, Luming; Sheong, Fu Kit; Zeng, Xiangze; Zhu, Lizhe; Huang, Xuhui

2017-07-01

Constructing Markov state models from large-scale molecular dynamics simulation trajectories is a promising approach to dissect the kinetic mechanisms of complex chemical and biological processes. Combined with transition path theory, Markov state models can be applied to identify all pathways connecting any conformational states of interest. However, the identified pathways can be too complex to comprehend, especially for multi-body processes where numerous parallel pathways with comparable flux probability often coexist. Here, we have developed a path lumping method to group these parallel pathways into metastable path channels for analysis. We define the similarity between two pathways as the intercrossing flux between them and then apply the spectral clustering algorithm to lump these pathways into groups. We demonstrate the power of our method by applying it to two systems: a 2D-potential consisting of four metastable energy channels and the hydrophobic collapse process of two hydrophobic molecules. In both cases, our algorithm successfully reveals the metastable path channels. We expect this path lumping algorithm to be a promising tool for revealing unprecedented insights into the kinetic mechanisms of complex multi-body processes.

Pyrolysis characteristics and kinetics of acid tar waste from crude benzol refining: A thermogravimetry-mass spectrometry analysis.

PubMed

Chihobo, Chido H; Chowdhury, Arindrajit; Kuipa, Pardon K; Simbi, David J

2016-12-01

Pyrolysis is an attractive thermochemical conversion technology that may be utilised as a safe disposal option for acid tar waste. The kinetics of acid tar pyrolysis were investigated using thermogravimetry coupled with mass spectrometry under a nitrogen atmosphere at different heating rates of 10, 15 and 20 K min -1 The thermogravimetric analysis shows three major reaction peaks centred around 178 °C, 258 °C, and 336 °C corresponding to the successive degradation of water soluble lower molecular mass sulphonic acids, sulphonated high molecular mass hydrocarbons, and high molecular mass hydrocarbons. The kinetic parameters were evaluated using the iso-conversional Kissinger-Akahira-Sunose method. A variation in the activation energy with conversion revealed that the pyrolysis of the acid tar waste progresses through complex multi-step kinetics. Mass spectrometry results revealed a predominance of gases such as hydrogen, methane and carbon monoxide, implying that the pyrolysis of acid tar waste is potentially an energy source. Thus the pyrolysis of acid tar waste may present a viable option for its environmental treatment. There are however, some limitations imposed by the co-evolution of corrosive gaseous components for which appropriate considerations must be provided in both pyrolysis reactor design and selection of construction materials. © The Author(s) 2016.

Ascending Stairway Modeling: A First Step Toward Autonomous Multi-Floor Exploration

DTIC Science & Technology

2012-10-01

Many robotics platforms are capable of ascending stairways, but all existing approaches for autonomous stair climbing use stairway detection as a...the rich potential of an autonomous ground robot that can climb stairs while exploring a multi-floor building. Our proposed solution to this problem is...over several steps. However, many ground robots are not capable of traversing tight spiral stairs , and so we do not focus on these types. The stairway is

Whole-body PET parametric imaging employing direct 4D nested reconstruction and a generalized non-linear Patlak model

NASA Astrophysics Data System (ADS)

Karakatsanis, Nicolas A.; Rahmim, Arman

2014-03-01

Graphical analysis is employed in the research setting to provide quantitative estimation of PET tracer kinetics from dynamic images at a single bed. Recently, we proposed a multi-bed dynamic acquisition framework enabling clinically feasible whole-body parametric PET imaging by employing post-reconstruction parameter estimation. In addition, by incorporating linear Patlak modeling within the system matrix, we enabled direct 4D reconstruction in order to effectively circumvent noise amplification in dynamic whole-body imaging. However, direct 4D Patlak reconstruction exhibits a relatively slow convergence due to the presence of non-sparse spatial correlations in temporal kinetic analysis. In addition, the standard Patlak model does not account for reversible uptake, thus underestimating the influx rate Ki. We have developed a novel whole-body PET parametric reconstruction framework in the STIR platform, a widely employed open-source reconstruction toolkit, a) enabling accelerated convergence of direct 4D multi-bed reconstruction, by employing a nested algorithm to decouple the temporal parameter estimation from the spatial image update process, and b) enhancing the quantitative performance particularly in regions with reversible uptake, by pursuing a non-linear generalized Patlak 4D nested reconstruction algorithm. A set of published kinetic parameters and the XCAT phantom were employed for the simulation of dynamic multi-bed acquisitions. Quantitative analysis on the Ki images demonstrated considerable acceleration in the convergence of the nested 4D whole-body Patlak algorithm. In addition, our simulated and patient whole-body data in the postreconstruction domain indicated the quantitative benefits of our extended generalized Patlak 4D nested reconstruction for tumor diagnosis and treatment response monitoring.

Transmission of a detonation across a density interface

NASA Astrophysics Data System (ADS)

Tang Yuk, K. C.; Mi, X. C.; Lee, J. H. S.; Ng, H. D.

2018-05-01

The present study investigates the transmission of a detonation wave across a density interface. The problem is first studied theoretically considering an incident Chapman-Jouguet (CJ) detonation wave, neglecting its detailed reaction-zone structure. It is found that, if there is a density decrease at the interface, a transmitted strong detonation wave and a reflected expansion wave would be formed; if there is a density increase, one would obtain a transmitted CJ detonation wave followed by an expansion wave and a reflected shock wave. Numerical simulations are then performed considering that the incident detonation has the Zel'dovich-von Neumann-Döring reaction-zone structure. The transient process that occurs subsequently to the detonation-interface interaction has been captured by the simulations. The effects of the magnitude of density change across the interface and different reaction kinetics (i.e., single-step Arrhenius kinetics vs. two-step induction-reaction kinetics) on the dynamics of the transmission process are explored. After the transient relaxation process, the transmitted wave reaches the final state in the new medium. For the cases with two-step induction-reaction kinetics, the transmitted wave fails to evolve to a steady detonation wave if the magnitude of density increase is greater than a critical value. For the cases wherein the transmitted wave can evolve to a steady detonation, the numerical results for both reaction models give final propagation states that agree with the theoretical solutions.

Warming rate drives microbial limitation and enzyme expression during peat decomposition

NASA Astrophysics Data System (ADS)

Inglett, P.; Sihi, D.; Inglett, K. S.

2015-12-01

Recent developments of enzyme-based decomposition models highlight the importance of enzyme kinetics with warming, but most modeling exercises are based on studies with a step-wise warming. This approach may mask the effect of temperature in controlling in-situ activities as in most ecosystems soil temperature change more gradually than air temperature. We conducted an experiment to test the effects of contrasting warming rates on the kinetics of C, N, and P degradation enzymes in subtropical peat soils. We also wanted to evaluate if the stoichiometry of enzyme kinetics shifts under contrasting warming rates and if so, how does it relate to the stoichiometry in microbial biomass. Contrasting warming rates altered microbial biomass stoichiometry leading to differing patterns of enzyme expression and microbial nutrient limitation. Activity (higher Vmax) and efficiency (lower Km) of C acquisition enzymes were greater in the step treatment; however, expressions of nutrient (N and P) acquiring enzymes were enhanced in the ramp treatment at the end of the experiment. In the step treatment, there was a typical pattern of an initial peak in the Vmax and drop in the Km for all enzyme groups followed by later adjustments. On the other hand, a consistent increase in Vmax and decline in Km of all enzyme groups were observed in the slow warming treatment. These changes were sufficient to alter microbial identity (as indicated by enzyme Km and biomass stoichiometry) with two apparently stable endpoints under contrasting warming rates. This observation resembles the concept of alternate stable states and highlights a need for improved representation of warming in models.

Identifying functional zones of denitrification in heterogeneous aquifer systems by numerical simulations - a case study

NASA Astrophysics Data System (ADS)

Jang, E.; Kalbacher, T.; He, W.; Shao, H.; Schueth, C.; Kolditz, O.

2014-12-01

Nitrate contamination in shallow groundwater is still one of the common problems in many countries. Because of its high solubility and anionic nature, nitrate can easily leach through soil and persist in groundwater for decades. High nitrate concentration has been suggested as a major cause of accelerated eutrophication, methemoglobinemia and gastric cancer. There are several factors influencing the fate of nitrate in groundwater system, which is e.g. distribution of N- sources to soil and groundwater, distribution and amount of reactive substances maintaining denitrification, rate of nitrate degradation and its kinetics, and geological characteristics of the aquifer. Nitrate transport and redox transformation processes are closely linked to complex and spatially distributed physical and chemical interaction, therefore it is difficult to predict and quantify in the field and laboratory experiment. Models can play a key role in elucidation of nitrate reduction pathway in groundwater system and in the design and evaluation of field tests to investigate in situ remediation technologies as well. The goal of the current study is to predict groundwater vulnerability to nitrate, to identify functional zones of denitrification in heterogeneous aquifer systems and to describe the uncertainty of the predictions due to scale effects. For this aim, we developed a kinetic model using multi-component mass transport code OpenGeoSys coupling with IPhreeqc module of the geochemical solver PHREEQC. The developed model included sequential aerobic and nitrate-based respiration, multi-Monod kinetics, multi-species biogeochemical reactions, and geological characteristics of the groundwater aquifer. Moreover water-rock interaction such as secondary mineral precipitation was also included in this model. In this presentation, we focused on the general modelling approach and present the simulation results of nitrate transport simulation in a hypothetical aquifer systems based on data from Hessian Ried, an important groundwater resource for the densely populated Rhine-Main region in Germany.

Genomic Insights into Geothermal Spring Community Members using a 16S Agnostic Single-Cell Approach

NASA Astrophysics Data System (ADS)

Bowers, R. M.

2016-12-01

INSTUTIONS (ALL): DOE Joint Genome Institute, Walnut Creek, CA USA. Bigelow Laboratory for Ocean Sciences, East Boothbay, ME USA. Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada. ABSTRACT BODY: With recent advances in DNA sequencing, rapid and affordable screening of single-cell genomes has become a reality. Single-cell sequencing is a multi-step process that takes advantage of any number of single-cell sorting techniques, whole genome amplification (WGA), and 16S rRNA gene based PCR screening to identify the microbes of interest prior to shotgun sequencing. However, the 16S PCR based screening step is costly and may lead to unanticipated losses of microbial diversity, as cells that do not produce a clean 16S amplicon are typically omitted from downstream shotgun sequencing. While many of the sorted cells that fail the 16S PCR step likely originate from poor quality amplified DNA, some of the cells with good WGA kinetics may instead represent bacteria or archaea with 16S genes that fail to amplify due to primer mis-matches or the presence of intervening sequences. Using cell material from Dewar Creek, a hot spring in British Columbia, we sequenced all sorted cells with good WGA kinetics irrespective of their 16S amplification success. We show that this high-throughput approach to single-cell sequencing (i) can reduce the overall cost of single-cell genome production, and (ii). may lead to the discovery of previously unknown branches on the microbial tree of life.

Multi-scale simulation of quantum dot formation in Al/Al (110) homoepitaxy

NASA Astrophysics Data System (ADS)

Tiwary, Yogesh; Fichthorn, Kristen

2007-03-01

In experimental studies of Al(110) homoepitaxy, it is observed that over a certain temperature window (330-500K), 3D huts, up to 50 nm high with well defined and smooth (111) and (100) facets, form and self-organize over the micron scale [1]. The factors leading to this kinetic self-organization are currently unclear. To understand how these structures form and evolve, we simulated multi-layer, homoepitaxial growth on Al(110) using ab initio kinetic Monte Carlo (KMC). At the high temperatures, where nano-huts form, the KMC simulations are slow. To tackle this problem, we use a technique developed by Devita & Sander [2], in which isolated adatoms make multiple moves in one step. We achieve high efficiency with this algorithm and we explore very high temperatures on large simulation lattices. We uncover a variety of interesting morphologies (Ripples, mounds, smooth surface, huts) that depend on the growth temperature. By varying the barriers for various rate processes, we discern the factors that determine hut sizes, aspect ratios, and self-organization. [1] F. Buatier de Mongeot, W. Zhu, A. Molle, R. Buzio, C. Boragno, U. Valbusa, E. Wang, and Z. Zhang, Phys. Rev. Lett. 91, 016102 (2003). [2] J.P. Devita & L.M. Sander, Phys. Rev. B 72, 205421 (2005).

Influence of Natural Convection and Thermal Radiation Multi-Component Transport in MOCVD Reactors

NASA Technical Reports Server (NTRS)

Lowry, S.; Krishnan, A.; Clark, I.

1999-01-01

The influence of Grashof and Reynolds number in Metal Organic Chemical Vapor (MOCVD) reactors is being investigated under a combined empirical/numerical study. As part of that research, the deposition of Indium Phosphide in an MOCVD reactor is modeled using the computational code CFD-ACE. The model includes the effects of convection, conduction, and radiation as well as multi-component diffusion and multi-step surface/gas phase chemistry. The results of the prediction are compared with experimental data for a commercial reactor and analyzed with respect to the model accuracy.

On the Voyager 1 Zero Radial Velocity Measurements in the Inner Heliosheath

NASA Astrophysics Data System (ADS)

Pogorelov, N. V.; Borovikov, S. N.; Kryukov, I.; Zank, G. P.

2011-12-01

Theoretical analysis of the Voyager 1 data revealed a very small, or even negative, value of the solar wind (SW) radial velocity component. This should not be surprising if we take into account time-dependent processes that take place in the inner heliosheath (IHS). We analyze solar cycle modeling of the SW interaction with the local interstellar medium (LISM) and demonstrate the existence of small and negative values of the SW radial velocity. It shown that, in reality, a similar picture can be observed in the outer heliosheath (OHS), where on the contrary, extended regions of the positive radial velocity are observed. Another scenario discussed in this talk is related to effects of transients, such as global merged interaction regions and corotating interacting regions. Numerical results are obtained with the SW-LISM interaction model developed in the UAHuntsville and implemented in the Multi-Scale Fluid-Kinetic Simulation Suite. This model treats ions magnetohydrodynamically while the transport of neutral atoms is performed kinetically by solving the Boltzmann equation with a Monte Carlo approach or using a multi-fluid approach developed in mid-90's by G. P. Zank. Pickup ions (PUIs) can be treated as a separate fluid. The evolution of the PUI-generated turbulence is addressed on the differential level by adding three additional equations, which are solved self-consistently with the MHD-kinetic system of equations.

The single-process biochemical reaction of Rubisco: a unified theory and model with the effects of irradiance, CO₂ and rate-limiting step on the kinetics of C₃ and C₄ photosynthesis from gas exchange.

PubMed

Farazdaghi, Hadi

2011-02-01

Photosynthesis is the origin of oxygenic life on the planet, and its models are the core of all models of plant biology, agriculture, environmental quality and global climate change. A theory is presented here, based on single process biochemical reactions of Rubisco, recognizing that: In the light, Rubisco activase helps separate Rubisco from the stored ribulose-1,5-bisphosphate (RuBP), activates Rubisco with carbamylation and addition of Mg²(+), and then produces two products, in two steps: (Step 1) Reaction of Rubisco with RuBP produces a Rubisco-enediol complex, which is the carboxylase-oxygenase enzyme (Enco) and (Step 2) Enco captures CO₂ and/or O₂ and produces intermediate products leading to production and release of 3-phosphoglycerate (PGA) and Rubisco. PGA interactively controls (1) the carboxylation-oxygenation, (2) electron transport, and (3) triosephosphate pathway of the Calvin-Benson cycle that leads to the release of glucose and regeneration of RuBP. Initially, the total enzyme participates in the two steps of the reaction transitionally and its rate follows Michaelis-Menten kinetics. But, for a continuous steady state, Rubisco must be divided into two concurrently active segments for the two steps. This causes a deviation of the steady state from the transitional rate. Kinetic models are developed that integrate the transitional and the steady state reactions. They are tested and successfully validated with verifiable experimental data. The single-process theory is compared to the widely used two-process theory of Farquhar et al. (1980. Planta 149, 78-90), which assumes that the carboxylation rate is either Rubisco-limited at low CO₂ levels such as CO₂ compensation point, or RuBP regeneration-limited at high CO₂. Since the photosynthesis rate cannot increase beyond the two-process theory's Rubisco limit at the CO₂ compensation point, net photosynthesis cannot increase above zero in daylight, and since there is always respiration at night, it leads to progressively negative daily CO₂ fixation with no possibility of oxygenic life on the planet. The Rubisco-limited theory at low CO₂ also contradicts all experimental evidence for low substrate reactions, and for all known enzymes, Rubisco included. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis

DOEpatents

Vandersall, Jennifer A.; Gardner, Shea N.; Clague, David S.

2010-05-04

A computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method and system include modules that address the bioinformatics, kinetics, and thermodynamics of DNA amplification and synthesis. Specifically, the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, are addressed, which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature and concentration of species.

Adsorption of Reactive Red M-2BE dye from water solutions by multi-walled carbon nanotubes and activated carbon.

PubMed

Machado, Fernando M; Bergmann, Carlos P; Fernandes, Thais H M; Lima, Eder C; Royer, Betina; Calvete, Tatiana; Fagan, Solange B

2011-09-15

Multi-walled carbon nanotubes and powdered activated carbon were used as adsorbents for the successful removal of Reactive Red M-2BE textile dye from aqueous solutions. The adsorbents were characterised by infrared spectroscopy, N(2) adsorption/desorption isotherms and scanning electron microscopy. The effects of pH, shaking time and temperature on adsorption capacity were studied. In the acidic pH region (pH 2.0), the adsorption of the dye was favourable using both adsorbents. The contact time to obtain equilibrium at 298K was fixed at 1h for both adsorbents. The activation energy of the adsorption process was evaluated from 298 to 323K for both adsorbents. The Avrami fractional-order kinetic model provided the best fit to the experimental data compared with pseudo-first-order or pseudo-second-order kinetic adsorption models. For Reactive Red M-2BE dye, the equilibrium data were best fitted to the Liu isotherm model. Simulated dyehouse effluents were used to check the applicability of the proposed adsorbents for effluent treatment. Copyright © 2011 Elsevier B.V. All rights reserved.

Correlation between lifetime heterogeneity and kinetics heterogeneity during chlorophyll fluorescence induction in leaves: 2. Multi-frequency phase and modulation analysis evidences a loosely connected PSII pigment-protein complex.

PubMed

Moise, Nicolae; Moya, Ismaël

2004-06-28

We report the first direct decomposition of the fluorescence lifetime heterogeneity during multiphasic fluorescence induction in dark-adapted leaves by multi-frequency phase and modulation fluorometry (PMF). A very fast component, assigned to photosystem I (PSI), was found to be constant in lifetime and yield, whereas the two slow components, which are strongly affected by the closure of the reaction centers by light, were assigned to PSII. Based on a modified "reversible radical pair" kinetic model with three compartments, we showed that a loosely connected pigment complex, which is assumed to be the CP47 complex, plays a specific role with respect to the structure and function of the PSII: (i) it explains the heterogeneity of PSII fluorescence lifetime as a compartmentation of excitation energy in the antenna, (ii) it is the site of a conformational change in the first second of illumination, and (iii) it is involved in the mechanisms of nonphotochemical quenching (NPQ). On the basis of the multi-frequency PMF analysis, we reconciled two apparently antagonistic aspects of chlorophyll a fluorescence in vivo: it is heterogeneous with respect to the kinetic structure (several lifetime components) and homogeneous with respect to average quantities (quasi-linear mean tau-Phi relationship).

Photodarkening kinetics in a high-power YDFA versus CW or short-pulse seed conditions

NASA Astrophysics Data System (ADS)

Jolly, Alain; Vinçont, Cyril; Boullet, Johan

2017-02-01

We propose an innovating model to describe the kinetics of competing photo-darkening and photo-bleaching phenomena in high-power, Ytterbium-Doped-Fibre-Amplifiers. This model makes use of aggregated species of trivalent Ytterbium and divalent ions, which operate as primarily efficient color-centers. This ensures multi-photon excitation, partly from the pump and partly from the signal. The fit of numerical computations with dedicated experiments help to validate our theoretical assumptions, in the definition of the involved physics. Potential applications of this study include further discussions for the selection of processing options with fibre-manufacturers and the optimization of operating conditions.

Kinetics Modeling of Hypergolic Propellants

DTIC Science & Technology

2013-07-01

comprehensive preconditioning and employs the line Gauss Seidel algorithm for the solution of the linear system. A multi-block unstructured mesh is...Explosives, Pyrotechnics, 33(3):209–212, 2008. 24Wei-Guang Liu, Shiqing Wang, Siddharth Dasgupta, Stefan T Thynell, William A Goddard III, Sergey Zybin

Noninvasive in situ observation of the crystallization kinetics of biological macromolecules by confocal laser scanning microscopy.

PubMed

Mühlig, P; Klupsch, Th; Kaulmann, U; Hilgenfeld, R

2003-04-01

High-resolution confocal laser scanning microscopy (CLSM) is a powerful tool for in situ observation and analysis of protein crystal growth kinetics. Because the resolution of CLSM is not diffraction-limited by the object, it is possible to visualize, under certain conditions, objects in molecular dimensions. A modified batch technique is applied which allows the growth kinetics of sufficiently small crystallites fixed at the lower side of a cover glass, within a hanging drop, to be studied in reflected light near the total reflection angle. A gap, or cavity, filled with solution is formed between the cover glass and the upper crystal face, which acts to fix small crystallites by hydrodynamic friction forces. The cavity height enables the propagation of molecular steps across the upper crystal face without constraint, so that the propagation velocity and geometrical parameters can be measured by CLSM. The layer growth kinetics of monoclinic crystallites of a long-acting insulin derivative (Insulin Glargine) is investigated. For a twofold supersaturation of the solution, the growth is governed by 2D nucleation at the edges of the crystallites followed by a spreading of molecular steps. The layer growth kinetics are well fitted by the simple cubic kinetic lattice model. We find that only about one of a thousand solute (protein) molecules which push a kink place due to their Brownian motion becomes really incorporated into the growing crystal.

Novel kinetic model of the removal of divalent heavy metal ions from aqueous solutions by natural clinoptilolite.

PubMed

Jovanovic, Mina; Rajic, Nevenka; Obradovic, Bojana

2012-09-30

Removal of heavy metal ions from aqueous solutions using zeolites is widely described by pseudo-second order kinetics although this model may not be valid under all conditions. In this work, we have extended approaches used for derivation of this model in order to develop a novel kinetic model that is related to the ion exchange mechanism underlying sorption of metal ions in zeolites. The novel model assumed two reversible steps, i.e. release of sodium ions from the zeolite lattice followed by bonding of the metal ion. The model was applied to experimental results of Cu(II) sorption by natural clinoptilolite-rich zeolitic tuff at different initial concentrations and temperatures and then validated by predictions of ion exchange kinetics of other divalent heavy metal ions (i.e. Mn(II), Zn(II) and Pb(II)). Model predictions were in excellent agreements with experimental data for all investigated systems. In regard to the proposed mechanism, modeling results implied that the sodium ion release rate was constant for all investigated metals while the overall rate was mainly determined by the rate of heavy metal ion bonding to the lattice. In addition, prediction capabilities of the novel model were demonstrated requiring one experimentally determined parameter, only. Copyright © 2012 Elsevier B.V. All rights reserved.

3D Hall MHD-EPIC Simulations of Ganymede's Magnetosphere

NASA Astrophysics Data System (ADS)

Zhou, H.; Toth, G.; Jia, X.

2017-12-01

Fully kinetic modeling of a complete 3D magnetosphere is still computationally expensive and not feasible on current computers. While magnetohydrodynamic (MHD) models have been successfully applied to a wide range of plasma simulation, they cannot capture some important kinetic effects. We have recently developed a new modeling tool to embed the implicit particle-in-cell (PIC) model iPIC3D into the Block-Adaptive-Tree-Solarwind-Roe-Upwind-Scheme (BATS-R-US) magnetohydrodynamic model. This results in a kinetic model of the regions where kinetic effects are important. In addition to the MHD-EPIC modeling of the magnetosphere, the improved model presented here is now able to represent the moon as a resistive body. We use a stretched spherical grid with adaptive mesh refinement (AMR) to capture the resistive body and its boundary. A semi-implicit scheme is employed for solving the magnetic induction equation to allow time steps that are not limited by the resistivity. We have applied the model to Ganymede, the only moon in the solar system known to possess a strong intrinsic magnetic field, and included finite resistivity beneath the moon`s surface to model the electrical properties of the interior in a self-consistent manner. The kinetic effects of electrons and ions on the dayside magnetopause and tail current sheet are captured with iPIC3D. Magnetic reconnections under different upstream background conditions of several Galileo flybys are simulated to study the global reconnection rate and the magnetospheric dynamics

Correlation between Gas Bubble Formation and Hydrogen Evolution Reaction Kinetics at Nanoelectrodes.

PubMed

Chen, Qianjin; Luo, Long

2018-04-17

We report the correlation between H 2 gas bubble formation potential and hydrogen evolution reaction (HER) activity for Au and Pt nanodisk electrodes (NEs). Microkinetic models were formulated to obtain the HER kinetic information for individual Au and Pt NEs. We found that the rate-determining steps for the HER at Au and Pt NEs were the Volmer step and the Heyrovsky step, respectively. More interestingly, the standard rate constant ( k 0 ) of the rate-determining step was found to vary over 2 orders of magnitude for the same type of NEs. The observed variations indicate the HER activity heterogeneity at the nanoscale. Furthermore, we discovered a linear relationship between bubble formation potential ( E bubble ) and log( k 0 ) with a slope of 125 mV/decade for both Au and Pt NEs. As log ( k 0 ) increases, E bubble shifts linearly to more positive potentials, meaning NEs with higher HER activities form H 2 bubbles at less negative potentials. Our theoretical model suggests that such linear relationship is caused by the similar critical bubble formation condition for Au and Pt NEs with varied sizes. Our results have potential implications for using gas bubble formation to evaluate the HER activity distribution of nanoparticles in an ensemble.

Phosphate uptake studies of cross-linked chitosan bead materials.

PubMed

Mahaninia, Mohammad H; Wilson, Lee D

2017-01-01

A systematic experimental study is reported that provides a molecular based understanding of cross-linked chitosan beads and their adsorption properties in aqueous solution containing phosphate dianion (HPO 4 2- ) species. Synthetically modified chitosan using epichlorohydrin and glutaraldehyde cross-linkers result in surface modified beads with variable hydrophile-lipophile character and tunable HPO 4 2- uptake properties. The kinetic and thermodynamic adsorption properties of cross-linked chitosan beads with HPO 4 2- species were studied in aqueous solution. Complementary structure and physicochemical characterization of chitosan beads via potentiometry, Raman spectroscopy, DSC, and dye adsorption measurements was carried out to establish structure-property relationships. The maximum uptake (Q m ) of bead systems with HPO 4 2- at equilibrium was 52.1mgg -1 ; whereas, kinetic uptake results for chitosan bead/phosphate systems are relatively rapid (0.111-0.113min -1 ) with an intraparticle diffusion rate-limiting step. The adsorption process follows a multi-step pathway involving inner- and outer-sphere complexes with significant changes in hydration. Phosphate uptake strongly depends on the composition and type of cross-linker used for preparation of chitosan beads. The adsorption isotherms and structural characterization of bead systems illustrate the role of surface charge, hydrophile-lipophile balance, adsorption site accessibility, and hydration properties of the chitosan bead surface. Copyright © 2016 Elsevier Inc. All rights reserved.

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks.

PubMed

Chen, Yuan-Jyue; Rao, Sundipta D; Seelig, Georg

2015-11-25

DNA nanotechnology requires large amounts of highly pure DNA as an engineering material. Plasmid DNA could meet this need since it is replicated with high fidelity, is readily amplified through bacterial culture and can be stored indefinitely in the form of bacterial glycerol stocks. However, the double-stranded nature of plasmid DNA has so far hindered its efficient use for construction of DNA nanostructures or devices that typically contain single-stranded or branched domains. In recent work, it was found that nicked double stranded DNA (ndsDNA) strand displacement gates could be sourced from plasmid DNA. The following is a protocol that details how these ndsDNA gates can be efficiently encoded in plasmids and can be derived from the plasmids through a small number of enzymatic processing steps. Also given is a protocol for testing ndsDNA gates using fluorescence kinetics measurements. NdsDNA gates can be used to implement arbitrary chemical reaction networks (CRNs) and thus provide a pathway towards the use of the CRN formalism as a prescriptive molecular programming language. To demonstrate this technology, a multi-step reaction cascade with catalytic kinetics is constructed. Further it is shown that plasmid-derived components perform better than identical components assembled from synthetic DNA.

Montmorillonite nanodevices for the colon metronidazole delivery.

PubMed

Calabrese, Ilaria; Cavallaro, Gennara; Scialabba, Cinzia; Licciardi, Mariano; Merli, Marcello; Sciascia, Luciana; Turco Liveri, Maria Liria

2013-11-30

The adsorption profiles of the antibiotic metronidazole (MNE) into the K10-montmorillonite (MMT-K10) clay and the subsequent release have been investigated as a function of pH and MNE/MMT-K10 ratio, in order to evaluate the potential of the MNE/MMT-K10 hybrids as controlled drug delivery system. The adsorption mechanism has been first elucidated by performing complementary equilibrium and kinetic studies and through the X-ray diffractometry (XRD) characterization of the obtained composite materials. The gathered results allowed us to propose a mechanism consisting of a multi-step pathway involving the neutral and the cationic form of the drug, which interact with different sites of the clay surfaces, i.e. the interlayer region and the faces of the lamella. In a second step the drug release kinetics has been studied under physiological pH mimicking conditions simulating the oral drug administration and delivery. For the sake of comparison the commercial formulation has also been employed for the release studies. The investigation of the release profiles and the comparison with the commercial formulation of the drug reveal that the new-tailor made formulation could be fruitful exploited for successfully prolonged the action of drug in the desired site. Copyright © 2013 Elsevier B.V. All rights reserved.

Optimization of PET-MR Registrations for Nonhuman Primates Using Mutual Information Measures: A Multi-Transform Method (MTM)

PubMed Central

Sandiego, Christine M.; Weinzimmer, David; Carson, Richard E.

2012-01-01

An important step in PET brain kinetic analysis is the registration of functional data to an anatomical MR image. Typically, PET-MR registrations in nonhuman primate neuroreceptor studies used PET images acquired early post-injection, (e.g., 0–10 min) to closely resemble the subject’s MR image. However, a substantial fraction of these registrations (~25%) fail due to the differences in kinetics and distribution for various radiotracer studies and conditions (e.g., blocking studies). The Multi-Transform Method (MTM) was developed to improve the success of registrations between PET and MR images. Two algorithms were evaluated, MTM-I and MTM-II. The approach involves creating multiple transformations by registering PET images of different time intervals, from a dynamic study, to a single reference (i.e., MR image) (MTM-I) or to multiple reference images (i.e., MR and PET images pre-registered to the MR) (MTM-II). Normalized mutual information was used to compute similarity between the transformed PET images and the reference image(s) to choose the optimal transformation. This final transformation is used to map the dynamic dataset into the animal’s anatomical MR space, required for kinetic analysis. The chosen transformed from MTM-I and MTM-II were evaluated using visual rating scores to assess the quality of spatial alignment between the resliced PET and reference. One hundred twenty PET datasets involving eleven different tracers from 3 different scanners were used to evaluate the MTM algorithms. Studies were performed with baboons and rhesus monkeys on the HR+, HRRT, and Focus-220. Successful transformations increased from 77.5%, 85.8%, to 96.7% using the 0–10 min method, MTM-I, and MTM-II, respectively, based on visual rating scores. The Multi-Transform Methods proved to be a robust technique for PET-MR registrations for a wide range of PET studies. PMID:22926293

A New 3D Multi-fluid Model: A Study of Kinetic Effects and Variations of Physical Conditions in the Cometary Coma

NASA Astrophysics Data System (ADS)

Shou, Y.; Combi, M.; Toth, G.; Tenishev, V.; Fougere, N.; Jia, X.; Rubin, M.; Huang, Z.; Hansen, K.; Gombosi, T.; Bieler, A.

2016-12-01

Physics-based numerical coma models are desirable whether to interpret the spacecraft observations of the inner coma or to compare with the ground-based observations of the outer coma. In this work, we develop a multi-neutral-fluid model based on the BATS-R-US code of the University of Michigan, which is capable of computing both the inner and outer coma and simulating time-variable phenomena. It treats H2O, OH, H2, O, and H as separate fluids and each fluid has its own velocity and temperature, with collisions coupling all fluids together. The self-consistent collisional interactions decrease the velocity differences, re-distribute the excess energy deposited by chemical reactions among all species, and account for the varying heating efficiency under various physical conditions. Recognizing that the fluid approach has limitations in capturing all of the correct physics for certain applications, especially for very low density environment, we applied our multi-fluid coma model to comet 67P/Churyumov-Gerasimenko at various heliocentric distances and demonstrated that it yields comparable results to the Direct Simulation Monte Carlo (DSMC) model, which is based on a kinetic approach that is valid under these conditions. Therefore, our model may be a powerful alternative to the particle-based model, especially for some computationally intensive simulations. In addition, by running the model with several combinations of production rates and heliocentric distances, we characterize the cometary H2O expansion speeds and demonstrate the nonlinear dependencies of production rate and heliocentric distance. Our results are also compared to previous modeling work and remote observations, which serve as further validation of our model.

Mathematical modeling and validation of growth of Salmonella Enteritidis and background microorganisms in potato salad – one-step kinetic analysis and model development

USDA-ARS?s Scientific Manuscript database

This study was conducted to examine the growth of Salmonella Enteritidis (SE) in potato salad caused by cross-contamination and temperature abuse, and develop mathematical models to predict its growth. The growth of SE was investigated under constant temperature conditions (8, 10, 15, 20, 25, 30, a...

The Relay/Converter Interface Influences Hydrolysis of ATP by Skeletal Muscle Myosin II*

PubMed Central

Bloemink, Marieke J.; Melkani, Girish C.; Bernstein, Sanford I.; Geeves, Michael A.

2016-01-01

The interface between relay and converter domain of muscle myosin is critical for optimal myosin performance. Using Drosophila melanogaster indirect flight muscle S1, we performed a kinetic analysis of the effect of mutations in the converter and relay domain. Introduction of a mutation (R759E) in the converter domain inhibits the steady-state ATPase of myosin S1, whereas an additional mutation in the relay domain (N509K) is able to restore the ATPase toward wild-type values. The R759E S1 construct showed little effect on most steps of the actomyosin ATPase cycle. The exception was a 25–30% reduction in the rate constant of the hydrolysis step, the step coupled to the cross-bridge recovery stroke that involves a change in conformation at the relay/converter domain interface. Significantly, the double mutant restored the hydrolysis step to values similar to the wild-type myosin. Modeling the relay/converter interface suggests a possible interaction between converter residue 759 and relay residue 509 in the actin-detached conformation, which is lost in R759E but is restored in N509K/R759E. This detailed kinetic analysis of Drosophila myosin carrying the R759E mutation shows that the interface between the relay loop and converter domain is important for fine-tuning myosin kinetics, in particular ATP binding and hydrolysis. PMID:26586917

Thermogravimetric study on pyrolysis kinetics of Chlorella pyrenoidosa and bloom-forming cyanobacteria.

PubMed

Hu, Mian; Chen, Zhihua; Guo, Dabin; Liu, Cuixia; Xiao, Bo; Hu, Zhiquan; Liu, Shiming

2015-02-01

The pyrolysis process of two microalgae, Chlorella pyrenoidosa (CP) and bloom-forming cyanobacteria (CB) was examined by thermo-gravimetry to investigate their thermal decomposition behavior under non-isothermal conditions. It has found that the pyrolysis of both microalgae consists of three stages and stage II is the major mass reduction stage with mass loss of 70.69% for CP and 64.43% for CB, respectively. The pyrolysis kinetics of both microalgae was further studied using single-step global model (SSGM) and distributed activation energy model (DAEM). The mean apparent activation energy of CP and CB in SSGM was calculated as 143.71 and 173.46 kJ/mol, respectively. However, SSGM was not suitable for modeling pyrolysis kinetic of both microalgae due to the mechanism change during conversion. The DAEM with 200 first-order reactions showed an excellent fit between simulated data and experimental results. Copyright © 2014 Elsevier Ltd. All rights reserved.

Some aspects of modeling hydrocarbon oxidation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gal, D.; Botar, L.; Danoczy, E.

1981-01-01

A modeling procedure for the study of hydrocarbon oxidation is suggested, and its effectiveness for the oxidation of ethylbenzene is demonstrated. As a first step in modeling, systematization involves compilation of possible mechanisms. Then, by introduction of the concept of kinetic communication, the chaotic set of possible mechanisms is systematized into a network. Experimentation serves both as feedback to the systematic arrangement of information and source of new information. Kinetic treatment of the possible mechanism has been accomplished by two different approaches: by classical inductive calculations starting with a small mechanism and using kinetic approximations, and by computer simulation. Themore » authors have compiled a so-called Main Contributory Mechanism, involving processes - within the possible mechanism - which contribute basically to the formation and consumption of the intermediates, to the consumption of the starting compounds and to the formation of the end products. 24 refs.« less

On direct internal methane steam reforming kinetics in operating solid oxide fuel cells with nickel-ceria anodes

NASA Astrophysics Data System (ADS)

Thallam Thattai, A.; van Biert, L.; Aravind, P. V.

2017-12-01

Major operating challenges remain to safely operate methane fuelled solid oxide fuel cells due to undesirable temperature gradients across the porous anode and carbon deposition. This article presents an experimental study on methane steam reforming (MSR) global kinetics for single operating SOFCs with Ni-GDC (gadolinium doped ceria) anodes for low steam to carbon (S/C) ratios and moderate current densities. The study points out the hitherto insufficient research on MSR global and intrinsic kinetics for operating SOFCs with complete Ni-ceria anodes. Further, it emphasizes the need to develop readily applicable global kinetic models as a subsequent step from previously reported state-of-art and complex intrinsic models. Two rate expressions of the Power law (PL) and Langmuir-Hinshelwood (LH) type have been compared and based on the analysis, limitations of using previously proposed rate expressions for Ni catalytic beds to study MSR kinetics for complete cermet anodes have been identified. Firstly, it has been shown that methane reforming on metallic (Ni) current collectors may not be always negligible, contrary to literature reports. Both PL and LH kinetic models predict significantly different local MSR reaction rate and species partial pressure distributions along the normalized reactor length, indicating a strong need for further experimental verifications.

Kinetics and Mechanisms of Phosphorus Adsorption in Soils from Diverse Ecological Zones in the Source Area of a Drinking-Water Reservoir

PubMed Central

Zhang, Liang; Loáiciga, Hugo A.; Xu, Meng; Du, Chao; Du, Yun

2015-01-01

On-site soils are increasingly used in the treatment and restoration of ecosystems to harmonize with the local landscape and minimize costs. Eight natural soils from diverse ecological zones in the source area of a drinking-water reservoir in central China are used as adsorbents for the uptake of phosphorus from aqueous solutions. The X-ray fluorescence (XRF) spectrometric and BET (Brunauer-Emmett-Teller) tests and the Scanning Electron Microscopy (SEM) and Fourier Transform Infrared (FTIR) spectral analyses are carried out to investigate the soils’ chemical properties and their potential changes with adsorbed phosphorous from aqueous solutions. The intra-particle diffusion, pseudo-first-order, and pseudo-second-order kinetic models describe the adsorption kinetic processes. Our results indicate that the adsorption processes of phosphorus in soils occurred in three stages and that the rate-controlling steps are not solely dependent on intra-particle diffusion. A quantitative comparison of two kinetics models based on their linear and non-linear representations, and using the chi-square (χ2) test and the coefficient of determination (r2), indicates that the adsorptive properties of the soils are best described by the non-linear pseudo-second-order kinetic model. The adsorption characteristics of aqueous phosphorous are determined along with the essential kinetic parameters. PMID:26569278

Combined Economic and Hydrologic Modeling to Support Collaborative Decision Making Processes

NASA Astrophysics Data System (ADS)

Sheer, D. P.

2008-12-01

For more than a decade, the core concept of the author's efforts in support of collaborative decision making has been a combination of hydrologic simulation and multi-objective optimization. The modeling has generally been used to support collaborative decision making processes. The OASIS model developed by HydroLogics Inc. solves a multi-objective optimization at each time step using a mixed integer linear program (MILP). The MILP can be configured to include any user defined objective, including but not limited too economic objectives. For example, an estimated marginal value for water for crops and M&I use were included in the objective function to drive trades in a model of the lower Rio Grande. The formulation of the MILP, constraints and objectives, in any time step is conditional: it changes based on the value of state variables and dynamic external forcing functions, such as rainfall, hydrology, market prices, arrival of migratory fish, water temperature, etc. It therefore acts as a dynamic short term multi-objective economic optimization for each time step. MILP is capable of solving a general problem that includes a very realistic representation of the physical system characteristics in addition to the normal multi-objective optimization objectives and constraints included in economic models. In all of these models, the short term objective function is a surrogate for achieving long term multi-objective results. The long term performance for any alternative (especially including operating strategies) is evaluated by simulation. An operating rule is the combination of conditions, parameters, constraints and objectives used to determine the formulation of the short term optimization in each time step. Heuristic wrappers for the simulation program have been developed improve the parameters of an operating rule, and are initiating research on a wrapper that will allow us to employ a genetic algorithm to improve the form of the rule (conditions, constraints, and short term objectives) as well. In the models operating rules represent different models of human behavior, and the objective of the modeling is to find rules for human behavior that perform well in terms of long term human objectives. The conceptual model used to represent human behavior incorporates economic multi-objective optimization for surrogate objectives, and rules that set those objectives based on current conditions and accounting for uncertainty, at least implicitly. The author asserts that real world operating rules follow this form and have evolved because they have been perceived as successful in the past. Thus, the modeling efforts focus on human behavior in much the same way that economic models focus on human behavior. This paper illustrates the above concepts with real world examples.

Effect of nucleation on instability of step meandering during step-flow growth on vicinal 3C-SiC (0001) surfaces

NASA Astrophysics Data System (ADS)

Li, Yuan; Chen, Xuejiang; Su, Juan

2017-06-01

A three-dimensional kinetic Monte Carlo (KMC) model has been developed to study the step instability caused by nucleation during the step-flow growth of 3C-SiC. In the model, a lattice mesh was established to fix the position of atoms and bond partners based on the crystal lattice of 3C-SiC. The events considered in the model were adsorption and diffusion of adatoms on the terraces, attachment, detachment and interlayer transport of adatoms at the step edges, and nucleation of adatoms. Then the effects of nucleation on the instability of step meandering and the coalescence of both islands and steps were simulated by the model. The results showed that the instability of step meandering caused by nucleation was affected by the growth temperature. And the effects of nucleation on the instability was also analyzed. Moreover, the surface roughness as a function of time for different temperatures was discussed. Finally, a phase diagram was presented to predict in which conditions the effects of nucleation on step meandering become significant and the three different regimes, the step-flow (SF), 2D nucleation (2DN), and 3D layer by layer (3DLBL) were determined.

Application of granular activated carbon/MnFe2O4 composite immobilized on C. glutamicum MTCC 2745 to remove As(III) and As(V): Kinetic, mechanistic and thermodynamic studies

NASA Astrophysics Data System (ADS)

Podder, M. S.; Majumder, C. B.

2016-01-01

The main objective of the present study was to investigate the efficiency of Corynebacterium glutamicum MTCC 2745 immobilized on granular activated carbon/MnFe2O4 (GAC/MnFe2O4) composite to treat high concentration of arsenic bearing wastewater. Non-linear regression analysis was done for determining the best-fit kinetic model on the basis of three correlation coefficients and three error functions and also for predicting the parameters involved in kinetic models. The results showed that Fractal-like mixed 1,2 order model for As(III) and Brouser-Weron-Sototlongo as well as Fractal-like pseudo second order models for As(V) were proficient to provide realistic description of biosorption/bioaccumulation kinetic. Applicability of mechanistic models in the current study exhibited that the rate governing step in biosorption/bioaccumulation of both As(III) and As(V) was film diffusion rather than intraparticle diffusion. The evaluated thermodynamic parameters ΔG0, ΔH0 and ΔS0 revealed that biosorption/bioaccumulation of both As(III) and As(V) was feasible, spontaneous and exothermic under studied conditions.

Separation of time scales in one-dimensional directed nucleation-growth processes

NASA Astrophysics Data System (ADS)

Pierobon, Paolo; Miné-Hattab, Judith; Cappello, Giovanni; Viovy, Jean-Louis; Lagomarsino, Marco Cosentino

2010-12-01

Proteins involved in homologous recombination such as RecA and hRad51 polymerize on single- and double-stranded DNA according to a nucleation-growth kinetics, which can be monitored by single-molecule in vitro assays. The basic models currently used to extract biochemical rates rely on ensemble averages and are typically based on an underlying process of bidirectional polymerization, in contrast with the often observed anisotropic polymerization of similar proteins. For these reasons, if one considers single-molecule experiments, the available models are useful to understand observations only in some regimes. In particular, recent experiments have highlighted a steplike polymerization kinetics. The classical model of one-dimensional nucleation growth, the Kolmogorov-Avrami-Mehl-Johnson (KAMJ) model, predicts the correct polymerization kinetics only in some regimes and fails to predict the steplike behavior. This work illustrates by simulations and analytical arguments the limitation of applicability of the KAMJ description and proposes a minimal model for the statistics of the steps based on the so-called stick-breaking stochastic process. We argue that this insight might be useful to extract information on the time and length scales involved in the polymerization kinetics.

A model-based understanding of solid-oxide electrolysis cells (SOECs) for syngas production by H2O/CO2 co-electrolysis

NASA Astrophysics Data System (ADS)

Menon, Vikram; Fu, Qingxi; Janardhanan, Vinod M.; Deutschmann, Olaf

2015-01-01

High temperature co-electrolysis of H2O and CO2 offers a promising route for syngas (H2, CO) production via efficient use of heat and electricity. The performance of a SOEC during co-electrolysis is investigated by focusing on the interactions between transport processes and electrochemical parameters. Electrochemistry at the three-phase boundary is modeled by a modified Butler-Volmer approach that considers H2O electrolysis and CO2 electrolysis, individually, as electrochemically active charge transfer pathways. The model is independent of the geometrical structure. A 42-step elementary heterogeneous reaction mechanism for the thermo-catalytic chemistry in the fuel electrode, the dusty gas model (DGM) to account for multi-component diffusion through porous media, and a plug flow model for flow through the channels are used in the model. Two sets of experimental data are reproduced by the simulations, in order to deduce parameters of the electrochemical model. The influence of micro-structural properties, inlet cathode gas velocity, and temperature are discussed. Reaction flow analysis is performed, at OCV, to study methane production characteristics and kinetics during co-electrolysis. Simulations are carried out for configurations ranging from simple one-dimensional electrochemical button cells to quasi-two-dimensional co-flow planar cells, to demonstrate the effectiveness of the computational tool for performance and design optimization.

Nanosecond Plasma Enhanced H2/O2/N2 Premixed Flat Flames

DTIC Science & Technology

2014-01-01

Simulations are conducted with a one-dimensional, multi-scale, pulsed -discharge model with detailed plasma-combustion kinetics to develop additional insight... model framework. The reduced electric field, E/N, during each pulse varies inversely with number density. A significant portion of the input energy is...dimensional numerical model [4, 12] capable of resolving electric field transients over nanosecond timescales (during each discharge pulse ) and radical

Challenges and Development of a Multi-Scale Computational Model for Photosystem I Decoupled Energy Conversion

DTIC Science & Technology

2013-06-01

Applications of Molecular Modeling to Challenges in Clean Energy; Fitzgerald, G., et al .; ACS Symposium Series; American Chemical Society: Washington, DC...to 178 In Applications of Molecular Modeling to Challenges in Clean Energy; Fitzgerald, G., et al .; ACS Symposium Series; American Chemical Society...Washington, DC, 2013. developmodels of spectral properties and energy transfer kinetics (20–22). Ivashin et al . optimized select ligands (α

Coupling of exothermic and endothermic hydrogen storage materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brooks, Kriston P.; Bowden, Mark E.; Karkamkar, Abhijeet J.

2016-08-01

Chemical hydrogen storage (CHS) materials are a high-storage-density alternative to the gaseous compressed hydrogen currently used to provide hydrogen for fuel cell vehicles. One of the challenges of CHS materials is addressing the thermodynamic and kinetic barriers required to break the chemical bonds and release the hydrogen. Coupling CHS reactions that are endothermic and exothermic during the dehydrogenation can improve the system on-board energy efficiency and thermal control, making such materials viable. Acceptable coupling between reactions requires both thermodynamic and kinetics considerations. Models were developed to predict the reaction enthalpy and rate required to achieve high conversions for both reactionsmore » based on experimental measurements. These modeling results show that the efficiency of coupling of an exothermic and endothermic reaction is more sensitive the magnitude of the ratio of the exothermic and endothermic enthalpies than the ratio of the rates of the two steps. The modeling shows further that a slower rate of the endothermic step is desirable to permit sufficient heating of the reactor by the exothermic step. We look at two examples of a sequential and parallel reaction scheme and provide some of the first insight into the required temperature range to maximize the H2 release from 1,2-BN cyclohexane and indoline.« less

48 CFR 15.202 - Advisory multi-step process.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Advisory multi-step... Information 15.202 Advisory multi-step process. (a) The agency may publish a presolicitation notice (see 5.204... participate in the acquisition. This process should not be used for multi-step acquisitions where it would...

Evaluation of accuracy in implant site preparation performed in single- or multi-step drilling procedures.

PubMed

Marheineke, Nadine; Scherer, Uta; Rücker, Martin; von See, Constantin; Rahlf, Björn; Gellrich, Nils-Claudius; Stoetzer, Marcus

2018-06-01

Dental implant failure and insufficient osseointegration are proven results of mechanical and thermal damage during the surgery process. We herein performed a comparative study of a less invasive single-step drilling preparation protocol and a conventional multiple drilling sequence. Accuracy of drilling holes was precisely analyzed and the influence of different levels of expertise of the handlers and additional use of drill template guidance was evaluated. Six experimental groups, deployed in an osseous study model, were representing template-guided and freehanded drilling actions in a stepwise drilling procedure in comparison to a single-drill protocol. Each experimental condition was studied by the drilling actions of respectively three persons without surgical knowledge as well as three highly experienced oral surgeons. Drilling actions were performed and diameters were recorded with a precision measuring instrument. Less experienced operators were able to significantly increase the drilling accuracy using a guiding template, especially when multi-step preparations are performed. Improved accuracy without template guidance was observed when experienced operators were executing single-step versus multi-step technique. Single-step drilling protocols have shown to produce more accurate results than multi-step procedures. The outcome of any protocol can be further improved by use of guiding templates. Operator experience can be a contributing factor. Single-step preparations are less invasive and are promoting osseointegration. Even highly experienced surgeons are achieving higher levels of accuracy by combining this technique with template guidance. Hereby template guidance enables a reduction of hands-on time and side effects during surgery and lead to a more predictable clinical diameter.

A synergic simulation-optimization approach for analyzing biomolecular dynamics in living organisms.

PubMed

Sadegh Zadeh, Kouroush

2011-01-01

A synergic duo simulation-optimization approach was developed and implemented to study protein-substrate dynamics and binding kinetics in living organisms. The forward problem is a system of several coupled nonlinear partial differential equations which, with a given set of kinetics and diffusion parameters, can provide not only the commonly used bleached area-averaged time series in fluorescence microscopy experiments but more informative full biomolecular/drug space-time series and can be successfully used to study dynamics of both Dirac and Gaussian fluorescence-labeled biomacromolecules in vivo. The incomplete Cholesky preconditioner was coupled with the finite difference discretization scheme and an adaptive time-stepping strategy to solve the forward problem. The proposed approach was validated with analytical as well as reference solutions and used to simulate dynamics of GFP-tagged glucocorticoid receptor (GFP-GR) in mouse cancer cell during a fluorescence recovery after photobleaching experiment. Model analysis indicates that the commonly practiced bleach spot-averaged time series is not an efficient approach to extract physiological information from the fluorescence microscopy protocols. It was recommended that experimental biophysicists should use full space-time series, resulting from experimental protocols, to study dynamics of biomacromolecules and drugs in living organisms. It was also concluded that in parameterization of biological mass transfer processes, setting the norm of the gradient of the penalty function at the solution to zero is not an efficient stopping rule to end the inverse algorithm. Theoreticians should use multi-criteria stopping rules to quantify model parameters by optimization. Copyright © 2010 Elsevier Ltd. All rights reserved.

Application of the Multi-Doorway Continuum Shell Model to the Magnetic Dipole Strength Distribution in 58Ni

NASA Astrophysics Data System (ADS)

Spangenberger, H.; Beck, F.; Richter, A.

The usual continuum shell model is extended so as to include a statistical treatment of multi-doorway processes. The total configuration space of the nuclear reaction problem is subdivided into the primary doorway states which are coupled by the initial excitation to the nuclear ground state and the secondary doorway states which represent the complicated nature of multi-step reactions. The latter are evaluated within the exciton model which gives the coupling widths between the various finestructure subspaces. This coupling is determined by a statistical factor related to the exciton model and a dynamical factor given by the interaction matrix elements of the interacting excitons. The whole structure defines the multi-doorway continuum shell model. In this work it is applied to the highly fragmented magnetic dipole strength in 58Ni observed in high resolution electron scattering.Translated AbstractAnwendung des Multi-Doorway-Kontinuum-Schalenmodells auf die Verteilung der magnetischen Dipolstärke von 58NiDas Kontinuum-Schalenmodell wurde so erweitert, daß auch statistische Multi-Doorway-Prozesse berücksichtigt werden können. Hierzu wird der Konfigurationsraum unterteilt in den Raum der primären Doorway-Zustände, die direkt aus dem Grundzustand angeregt werden, und den der sekundären Doorway-Zustände, die die komplizierte Struktur der Multi-Step-Reaktionen repräsentieren. Während die primären Doorway-Zustände inclusive ihrer Anregungen mittels üblicher Schalenmodellmethoden beschrieben werden können, werden die sekundären Doorway-Zustände sowie ihre verschiedenen Kopplungen im Rahmen des Exciton-Modells behandelt. Diese Kopplungen sind durch einen aus dem Exciton-Modell resultierenden Faktor sowie durch einen dynamischen Faktor bestimmt, der sich aus dem Matrixelement der wechselwirkenden Excitonen berechnet. Die Struktur der Kopplungen definiert das Multi-Doorway-Kontinuum-Schalenmodell, das hier auf die Beschreibung der stark fragmentierten magnetischen Dipolstärke in 58Ni angewendet wird.

Multi-Paradigm Multi-Scale Simulations for Fuel Cell Catalysts and Membranes

DTIC Science & Technology

2006-01-01

transfer studies on model systems. . Applying newly developed density functionals QM ( X3LYP ) for estimating the thermodynamics and kinetic energy...Density functional theory methods We have used many QM methods to probe chemical reaction mechanisms and find that the B3LYP and X3LYP [6] flavors of DFT...carried out QM calculations on the surface reactivity of the Pt and PtRu anode catalysts. This QM uses a new ab initio DFT-GGA method ( X3LYP ) [6

Chemical reactions at aqueous interfaces

NASA Astrophysics Data System (ADS)

Vecitis, Chad David

2009-12-01

Interfaces or phase boundaries are a unique chemical environment relative to individual gas, liquid, or solid phases. Interfacial reaction mechanisms and kinetics are often at variance with homogeneous chemistry due to mass transfer, molecular orientation, and catalytic effects. Aqueous interfaces are a common subject of environmental science and engineering research, and three environmentally relevant aqueous interfaces are investigated in this thesis: 1) fluorochemical sonochemistry (bubble-water), 2) aqueous aerosol ozonation (gas-water droplet), and 3) electrolytic hydrogen production and simultaneous organic oxidation (water-metal/semiconductor). Direct interfacial analysis under environmentally relevant conditions is difficult, since most surface-specific techniques require relatively `extreme' conditions. Thus, the experimental investigations here focus on the development of chemical reactors and analytical techniques for the completion of time/concentration-dependent measurements of reactants and their products. Kinetic modeling, estimations, and/or correlations were used to extract information on interfacially relevant processes. We found that interfacial chemistry was determined to be the rate-limiting step to a subsequent series of relatively fast homogeneous reactions, for example: 1) Pyrolytic cleavage of the ionic headgroup of perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) adsorbed to cavitating bubble-water interfaces during sonolysis was the rate-determining step in transformation to their inorganic constituents carbon monoxide, carbon dioxide, and fluoride; 2) ozone oxidation of aqueous iodide to hypoiodous acid at the aerosol-gas interface is the rate-determining step in the oxidation of bromide and chloride to dihalogens; 3) Electrolytic oxidation of anodic titanol surface groups is rate-limiting for the overall oxidation of organics by the dichloride radical. We also found chemistry unique to the interface, for example: 1) Adsorption of dilute PFOS(aq) and PFOA(aq) to acoustically cavitating bubble interfaces was greater than equilibrium expectations due to high-velocity bubble radial oscillations; 2) Relative ozone oxidation kinetics of aqueous iodide, sulfite, and thiosulfate were at variance with previously reported bulk aqueous kinetics; 3) Organics that directly chelated with the anode surface were oxidized by direct electron transfer, resulting in immediate carbon dioxide production but slower overall oxidation kinetics. Chemical reactions at aqueous interfaces can be the rate-limiting step of a reaction network and often display novel mechanisms and kinetics as compared to homogeneous chemistry.

Effect of high energy electrons on H⁻ production and destruction in a high current DC negative ion source for cyclotron.

PubMed

Onai, M; Etoh, H; Aoki, Y; Shibata, T; Mattei, S; Fujita, S; Hatayama, A; Lettry, J

2016-02-01

Recently, a filament driven multi-cusp negative ion source has been developed for proton cyclotrons in medical applications. In this study, numerical modeling of the filament arc-discharge source plasma has been done with kinetic modeling of electrons in the ion source plasmas by the multi-cusp arc-discharge code and zero dimensional rate equations for hydrogen molecules and negative ions. In this paper, main focus is placed on the effects of the arc-discharge power on the electron energy distribution function and the resultant H(-) production. The modelling results reasonably explains the dependence of the H(-) extraction current on the arc-discharge power in the experiments.

Results from the OH-PT model: a Kinetic-MHD Model of the Outer Heliosphere within SWMF

NASA Astrophysics Data System (ADS)

Michael, A.; Opher, M.; Tenishev, V.; Borovikov, D.; Toth, G.

2017-12-01

We present an update of the OH-PT model, a kinetic-MHD model of the outer heliosphere. The OH-PT model couples the Outer Heliosphere (OH) and Particle Tracker (PT) components within the Space Weather Modeling Framework (SWMF). The OH component utilizes the Block-Adaptive Tree Solarwind Roe-type Upwind Scheme (BATS-R-US) MHD code, a highly parallel, 3D, and block-adaptive solver. As a stand-alone model, the OH component solves the ideal MHD equations for the plasma and a separate set of Euler's equations for the different populations of neutral atoms. The neutrals and plasma in the outer heliosphere are coupled through charge-exchange. While this provides an accurate solution for the plasma, it is an inaccurate description of the neutrals. The charge-exchange mean free path is on the order of the size of the heliosphere; therefore the neutrals cannot be described as a fluid. The PT component is based on the Adaptive Mesh Particle Simulator (AMPS) model, a 3D, direct simulation Monte Carlo model that solves the Boltzmann equation for the motion and interaction of multi-species plasma and is used to model the neutral distribution functions throughout the domain. The charge-exchange process occurs within AMPS, which handles each event on a particle-by-particle basis and calculates the resulting source terms to the MHD equations. The OH-PT model combines the MHD solution for the plasma with the kinetic solution for the neutrals to form a self-consistent model of the heliosphere. In this work, we present verification and validation of the model as well as demonstrate the codes capabilities. Furthermore we provide a comparison of the OH-PT model to our multi-fluid approximation and detail the differences between the models in both the plasma solution and neutral distribution functions.

Effects of Convective Solute and Impurity Transport in Protein Crystal Growth

NASA Technical Reports Server (NTRS)

Vekilov, Peter G.; Thomas, Bill R.; Rosenberger, Franz

1998-01-01

High-resolution optical interferometry was used to investigate the effects of forced solution convection on the crystal growth kinetics of the model protein lysozyme. Most experiments were conducted with 99.99% pure protein solutions. To study impurity effects, approx. 1% of lysozyme dimer (covalently bound) was added in some cases. We show that the unsteady kinetics, corresponding to bunching of growth steps, can be characterized by the Fourier components of time traces of the growth rate. Specific Fourier spectra are uniquely determined by the solution conditions (composition, temperature, and flow rate) and the growth layer source activity. We found that the average step velocity and growth rate increase by approx. I0% with increasing flow rate, as a result of the enhanced solute supply to the interface. More importantly, faster convective transport results in lower fluctuation amplitudes. This observation supports our rationale for system-dependent effects of transport on the structural perfection of protein crystals. We also found that solution flow rates greater than 500 microns/s result in stronger fluctuations while the average growth rate is decreased. This can lead to growth cessation at low supersaturations. With the intentionally contaminated solutions, these undesirable phenomena occurred at about half the flow rates required in pure solutions. Thus, we conclude that they are due to enhanced convective supply of impurities that are incorporated into the crystal during growth. Furthermore, we found that the impurity effects are reduced at higher crystal growth rates. Since the exposure time of terraces is inversely proportional to the growth rate, this observation suggests that the increased kinetics instability results from impurity adsorption on the interface. Finally, we provide evidence relating earlier observations of "slow protein crystal growth kinetics" to step bunch formation in response to nonsteady step generation.

Unified gas-kinetic scheme with multigrid convergence for rarefied flow study

NASA Astrophysics Data System (ADS)

Zhu, Yajun; Zhong, Chengwen; Xu, Kun

2017-09-01

The unified gas kinetic scheme (UGKS) is based on direct modeling of gas dynamics on the mesh size and time step scales. With the modeling of particle transport and collision in a time-dependent flux function in a finite volume framework, the UGKS can connect the flow physics smoothly from the kinetic particle transport to the hydrodynamic wave propagation. In comparison with the direct simulation Monte Carlo (DSMC) method, the current equation-based UGKS can implement implicit techniques in the updates of macroscopic conservative variables and microscopic distribution functions. The implicit UGKS significantly increases the convergence speed for steady flow computations, especially in the highly rarefied and near continuum regimes. In order to further improve the computational efficiency, for the first time, a geometric multigrid technique is introduced into the implicit UGKS, where the prediction step for the equilibrium state and the evolution step for the distribution function are both treated with multigrid acceleration. More specifically, a full approximate nonlinear system is employed in the prediction step for fast evaluation of the equilibrium state, and a correction linear equation is solved in the evolution step for the update of the gas distribution function. As a result, convergent speed has been greatly improved in all flow regimes from rarefied to the continuum ones. The multigrid implicit UGKS (MIUGKS) is used in the non-equilibrium flow study, which includes microflow, such as lid-driven cavity flow and the flow passing through a finite-length flat plate, and high speed one, such as supersonic flow over a square cylinder. The MIUGKS shows 5-9 times efficiency increase over the previous implicit scheme. For the low speed microflow, the efficiency of MIUGKS is several orders of magnitude higher than the DSMC. Even for the hypersonic flow at Mach number 5 and Knudsen number 0.1, the MIUGKS is still more than 100 times faster than the DSMC method for obtaining a convergent steady state solution.

Multiplexed immunosensing and kinetics monitoring in nanofluidic devices with highly enhanced target capture efficiency

PubMed Central

Lin, Yii-Lih; Huang, Yen-Jun; Teerapanich, Pattamon; Leïchlé, Thierry

2016-01-01

Nanofluidic devices promise high reaction efficiency and fast kinetic responses due to the spatial constriction of transported biomolecules with confined molecular diffusion. However, parallel detection of multiple biomolecules, particularly proteins, in highly confined space remains challenging. This study integrates extended nanofluidics with embedded protein microarray to achieve multiplexed real-time biosensing and kinetics monitoring. Implementation of embedded standard-sized antibody microarray is attained by epoxy-silane surface modification and a room-temperature low-aspect-ratio bonding technique. An effective sample transport is achieved by electrokinetic pumping via electroosmotic flow. Through the nanoslit-based spatial confinement, the antigen-antibody binding reaction is enhanced with ∼100% efficiency and may be directly observed with fluorescence microscopy without the requirement of intermediate washing steps. The image-based data provide numerous spatially distributed reaction kinetic curves and are collectively modeled using a simple one-dimensional convection-reaction model. This study represents an integrated nanofluidic solution for real-time multiplexed immunosensing and kinetics monitoring, starting from device fabrication, protein immobilization, device bonding, sample transport, to data analysis at Péclet number less than 1. PMID:27375819

The study of zinc ions binding to casein.

PubMed

Pomastowski, P; Sprynskyy, M; Buszewski, B

2014-08-01

The presented research was focused on physicochemical study of casein properties and the kinetics of zinc ions binding to the protein. Moreover, a fast and simple method of casein extraction from cow's milk has been proposed. Casein isoforms, zeta potential (ζ) and particle size of the separated caseins were characterized with the use of capillary electrophoresis, zeta potential analysis and field flow fractionation (FFF) technique, respectively. The kinetics of the metal-binding process was investigated in batch adsorption experiments. Intraparticle diffusion model, first-order and zero-order kinetic models were applied to test the kinetic experimental data. Analysis of changes in infrared bands registered for casein before and after zinc binding was also performed. The obtained results showed that the kinetic process of zinc binding to casein is not homogeneous but is expressed with an initial rapid stage with about 70% of zinc ions immobilized by casein and with a much slower second step. Maximum amount of bound zinc in the experimental conditions was 30.04mgZn/g casein. Copyright © 2014 Elsevier B.V. All rights reserved.

Coupling of TRAC-PF1/MOD2, Version 5.4.25, with NESTLE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knepper, P.L.; Hochreiter, L.E.; Ivanov, K.N.

1999-09-01

A three-dimensional (3-D) spatial kinetics capability within a thermal-hydraulics system code provides a more correct description of the core physics during reactor transients that involve significant variations in the neutron flux distribution. Coupled codes provide the ability to forecast safety margins in a best-estimate manner. The behavior of a reactor core and the feedback to the plant dynamics can be accurately simulated. For each time step, coupled codes are capable of resolving system interaction effects on neutronics feedback and are capable of describing local neutronics effects caused by the thermal hydraulics and neutronics coupling. With the improvements in computational technology,more » modeling complex reactor behaviors with coupled thermal hydraulics and spatial kinetics is feasible. Previously, reactor analysis codes were limited to either a detailed thermal-hydraulics model with simplified kinetics or multidimensional neutron kinetics with a simplified thermal-hydraulics model. The authors discuss the coupling of the Transient Reactor Analysis Code (TRAC)-PF1/MOD2, Version 5.4.25, with the NESTLE code.« less

Experimental and Computational Interrogation of Fast SCR Mechanism and Active Sites on H-Form SSZ-13

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Sichi; Zheng, Yang; Gao, Feng

Experiment and density functional theory (DFT) models are combined to develop a unified, quantitative model of the mechanism and kinetics of fast selective catalytic reduction (SCR) of NO/NO2 mixtures over H-SSZ-13 zeolite. Rates, rate orders, and apparent activation energies collected under differential conditions reveal two distinct kinetic regimes. First-principles thermodynamics simulations are used to determine the relative coverages of free Brønsted sites, chemisorbed NH4+ and physisorbed NH3 as a function of reaction conditions. First-principles metadynamics calculations show that all three sites can contribute to the rate-limiting N-N bond forming step in fast SCR. The results are used to parameterize amore » kinetic model that encompasses the full range of reaction conditions and recovers observed rate orders and apparent activation energies. Observed kinetic regimes are related to changes in most-abundant surface intermediates. Financial support was provided by the National Science Foundation GAOLI program under award number 1258690-CBET. We thank the Center for Research Computing at Notre« less

Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell

EPA Science Inventory

Multi-anode microbial electrochemical cells (MXCs) are considered as one of the most promising configurations for scale-up of MXCs, but fundamental understanding of anode kinetics governing current density is limited in the MXCs. In this study we first assessed microbial communi...

Kinetics of hydrophobic organic contaminant extraction from sediment by granular activated carbon.

PubMed

Rakowska, M I; Kupryianchyk, D; Smit, M P J; Koelmans, A A; Grotenhuis, J T C; Rijnaarts, H H M

2014-03-15

Ex situ solid phase extraction with granular activated carbon (GAC) is a promising technique to remediate contaminated sediments. The methods' efficiency depends on the rate by which contaminants are transferred from the sediment to the surface of GAC. Here, we derive kinetic parameters for extraction of polycyclic aromatic hydrocarbons (PAH) from sediment by GAC, using a first-order multi-compartment kinetic model. The parameters were obtained by modeling sediment-GAC exchange kinetic data following a tiered model calibration approach. First, parameters for PAH desorption from sediment were calibrated using data from systems with 50% (by weight) GAC acting as an infinite sink. Second, the estimated parameters were used as fixed input to obtain GAC uptake kinetic parameters in sediment slurries with 4% GAC, representing the ex situ remediation scenario. PAH uptake rate constants (kGAC) by GAC ranged from 0.44 to 0.0005 d(-1), whereas GAC sorption coefficients (KGAC) ranged from 10(5.57) to 10(8.57) L kg(-1). These values are the first provided for GAC in the presence of sediment and show that ex situ extraction with GAC is sufficiently fast and effective to reduce the risks of the most available PAHs among those studied, such as fluorene, phenanthrene and anthracene. Copyright © 2013 Elsevier Ltd. All rights reserved.

Growth of vertically aligned nanowires in metal-oxide nanocomposites: kinetic Monte-Carlo modeling versus experiments.

PubMed

Hennes, M; Schuler, V; Weng, X; Buchwald, J; Demaille, D; Zheng, Y; Vidal, F

2018-04-26

We employ kinetic Monte-Carlo simulations to study the growth process of metal-oxide nanocomposites obtained via sequential pulsed laser deposition. Using Ni-SrTiO3 (Ni-STO) as a model system, we reduce the complexity of the computational problem by choosing a coarse-grained approach mapping Sr, Ti and O atoms onto a single effective STO pseudo-atom species. With this ansatz, we scrutinize the kinetics of the sequential synthesis process, governed by alternating deposition and relaxation steps, and analyze the self-organization propensity of Ni atoms into straight vertically aligned nanowires embedded in the surrounding STO matrix. We finally compare the predictions of our binary toy model with experiments and demonstrate that our computational approach captures fundamental aspects of self-assembled nanowire synthesis. Despite its simplicity, our modeling strategy successfully describes the impact of relevant parameters like the concentration or laser frequency on the final nanoarchitecture of metal-oxide thin films grown via pulsed laser deposition.

A globally applicable location-specific screening model for assessing the relative risk of pesticide leaching.

PubMed

Whelan, M J; Davenport, E J; Smith, B G

2007-05-15

A screening model of pesticide leaching loss is described which forms part of a multi-criteria risk-based indicator system called PRoMPT (Pesticide Risk Management and Profiling Tool). The leaching model evaluates pesticide fate in soil for any application rate and time of application (including multiple applications), for any land-based location in the world. It considers a generic evaluative environment with fixed dimensions and soil properties. The soil profile is conceptualised as a number of discrete layers. Equilibrium partitioning between adsorbed and dissolved chemical (based on the organic carbon-water partition coefficient [K(OC)]) is assumed in each time step, in each layer. Non-leaching losses are described using first order kinetics. Drainage is assumed to be uniform throughout the soil profile but varies temporally. The drainage rate, which can be augmented by evapotranspiration-adjusted irrigation, is derived from long-term mean monthly water balance model calculations performed for 30 arc-minute grid cells across the entire ice-free land surface of the earth. Although, such predictions are approximate, they do capture the seasonality and relative magnitude of drainage and allow the model to be applied anywhere, without the need for extensive data compilation. PRoMPT predictions are shown to be consistent with those made by more sophisticated models (PRZM, PELMO and PEARL) for the FOCUS groundwater scenarios.

A critical comparison of several low Reynolds number k-epsilon turbulence models for flow over a backward facing step

NASA Technical Reports Server (NTRS)

Steffen, C. J., Jr.

1993-01-01

Turbulent backward-facing step flow was examined using four low turbulent Reynolds number k-epsilon models and one standard high Reynolds number technique. A tunnel configuration of 1:9 (step height: exit tunnel height) was used. The models tested include: the original Jones and Launder; Chien; Launder and Sharma; and the recent Shih and Lumley formulation. The experimental reference of Driver and Seegmiller was used to make detailed comparisons between reattachment length, velocity, pressure, turbulent kinetic energy, Reynolds shear stress, and skin friction predictions. The results indicated that the use of a wall function for the standard k-epsilon technique did not reduce the calculation accuracy for this separated flow when compared to the low turbulent Reynolds number techniques.

Kinetic characterization of thermophilic and mesophilic anaerobic digestion for coffee grounds and waste activated sludge.

PubMed

Li, Qian; Qiao, Wei; Wang, Xiaochang; Takayanagi, Kazuyuki; Shofie, Mohammad; Li, Yu-You

2015-02-01

This study was conducted to characterize the kinetics of an anaerobic process (hydrolysis, acetogenesis, acidogenesis and methanogenesis) under thermophilic (55 °C) and mesophilic (35 °C) conditions with coffee grounds and waste activated sludge (WAS) as the substrates. Special focus was given to the kinetics of propionic acid degradation to elucidate the accumulation of VFAs. Under the thermophilic condition, the methane production rate of all substrates (WAS, ground coffee and raw coffee) was about 1.5 times higher than that under the mesophilic condition. However, the effects on methane production of each substrate under the thermophilic condition differed: WAS increased by 35.8-48.2%, raw coffee decreased by 76.3-64.5% and ground coffee decreased by 74.0-57.9%. Based on the maximum reaction rate (Rmax) of each anaerobic stage obtained from the modified Gompertz model, acetogenesis was found to be the rate-limiting step for coffee grounds and WAS. This can be explained by the kinetics of propionate degradation under thermophilic condition in which a long lag-phase (more than 18 days) was observed, although the propionate concentration was only 500 mg/L. Under the mesophilic condition, acidogenesis and hydrolysis were found to be the rate-limiting step for coffee grounds and WAS, respectively. Even though reducing the particle size accelerated the methane production rate of coffee grounds, but did not change the rate-limiting step: acetogenesis in thermophilic and acidogenesis in mesophilic. Copyright © 2014 Elsevier Ltd. All rights reserved.

A kinetic model for the synthesis of high-molecular-weight alcohols over a sulfided Co-K-Mo/C catalyst

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunturu, A.K.; Kugler, E.L.; Cropley, J.B.

A statistically designed set of experiments was run in a recycle reactor to evaluate the kinetics of the formation of higher-molecular-weight alcohols (higher alcohols) and total hydrocarbon byproducts from synthesis gas (hydrogen and carbon monoxide) in a range of experimental conditions that mirrors the limits of commercial production. The alkali-promoted, C-supported Co-Mo sulfide catalyst that was employed in this study is well known for its sulfur resistance. The reaction was carried out in a gradientless Berty-type recycle reactor. A two-level fractional-factorial set consisting of 16 experiments was performed. Five independent variables were selected for this study, namely, temperature, partial pressuremore » of carbon monoxide, partial pressure of hydrogen, partial pressure of inerts, and methanol concentration in the feed. The major oxygenated products were linear alcohols up to n-butanol, but alcohols of higher carbon number were also detected, and analysis of the liquid product revealed the presence of trace amounts of ethers also. Yields of hydrocarbons were non-negligible. The alcohol product followed an Anderson-Schultz-Flory distribution. From the results of the factorial experiments, a preliminary power-law model was developed, and the statistically significant variables in the rate expression for the production of each alcohol were found. Based on the results of the power-law models, rate expressions of the Langmuir-Hinshelwood type were fitted. The observed kinetics are consistent with the rate-limiting step for the production of each higher alcohol being a surface reaction of the alcohol of next-lower carbon number. All other steps, including CO-insertion, H{sub 2}-cleavage, and hydrogenation steps, do not appear to affect the rate correlations.« less

Simulation of ITG instabilities with fully kinetic ions and drift-kinetic electrons in tokamaks

NASA Astrophysics Data System (ADS)

Hu, Youjun; Chen, Yang; Parker, Scott

2017-10-01

A turbulence simulation model with fully kinetic ions and drift-kinetic electrons is being developed in the toroidal electromagnetic turbulence code GEM. This is motivated by the observation that gyrokinetic ions are not well justified in simulating turbulence in tokamak edges with steep density profile, where ρi / L is not small enough to be used a small parameter needed by the gyrokinetic ordering (here ρi is the gyro-radius of ions and L is the scale length of density profile). In this case, the fully kinetic ion model may be useful. Our model uses an implicit scheme to suppress high-frequency compressional Alfven waves and waves associated with the gyro-motion of ions. The ion orbits are advanced by using the well-known Boris scheme, which reproduces correct drift-motion even with large time-step comparable to the ion gyro-period. The field equation in this model is Ampere's law with the magnetic field eliminated by using an implicit scheme of Faraday's law. The current contributed by ions are computed by using an implicit δf method. A flux tube approximation is adopted, which makes the field equation much easier to solve. Numerical results of electromagnetic ITG obtained from this model will be presented and compared with the gyrokinetic results. This work is supported by U.S. Department of Energy, Office of Fusion Energy Sciences under Award No. DE-SC0008801.

Optimization of time-course experiments for kinetic model discrimination.

PubMed

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

2012-01-01

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

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data

NASA Astrophysics Data System (ADS)

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-01

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data.

PubMed

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-07

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

Hydrodynamic effects on β-amyloid (16-22) peptide aggregation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chiricotto, Mara; Sterpone, Fabio, E-mail: fabio.sterpone@ibpc.fr; Melchionna, Simone

Computer simulations based on simplified representations are routinely used to explore the early steps of amyloid aggregation. However, when protein models with implicit solvent are employed, these simulations miss the effect of solvent induced correlations on the aggregation kinetics and lifetimes of metastable states. In this work, we apply the multi-scale Lattice Boltzmann Molecular Dynamics technique (LBMD) to investigate the initial aggregation phases of the amyloid Aβ{sub 16−22} peptide. LBMD includes naturally hydrodynamic interactions (HIs) via a kinetic on-lattice representation of the fluid kinetics. The peptides are represented by the flexible OPEP coarse-grained force field. First, we have tuned themore » essential parameters that control the coupling between the molecular and fluid evolutions in order to reproduce the experimental diffusivity of elementary species. The method is then deployed to investigate the effect of HIs on the aggregation of 100 and 1000 Aβ{sub 16−22} peptides. We show that HIs clearly impact the aggregation process and the fluctuations of the oligomer sizes by favouring the fusion and exchange dynamics of oligomers between aggregates. HIs also guide the growth of the leading largest cluster. For the 100 Aβ{sub 16−22} peptide system, the simulation of ∼300 ns allowed us to observe the transition from ellipsoidal assemblies to an elongated and slightly twisted aggregate involving almost the totality of the peptides. For the 1000 Aβ{sub 16−22} peptides, a system of unprecedented size at quasi-atomistic resolution, we were able to explore a branched disordered fibril-like structure that has never been described by other computer simulations, but has been observed experimentally.« less

Kinetic Analysis of DNA Strand Joining by Chlorella Virus DNA Ligase and the Role of Nucleotidyltransferase Motif VI in Ligase Adenylylation*

PubMed Central

Samai, Poulami; Shuman, Stewart

2012-01-01

Chlorella virus DNA ligase (ChVLig) is an instructive model for mechanistic studies of the ATP-dependent DNA ligase family. ChVLig seals 3′-OH and 5′-PO4 termini via three chemical steps: 1) ligase attacks the ATP α phosphorus to release PPi and form a covalent ligase-adenylate intermediate; 2) AMP is transferred to the nick 5′-phosphate to form DNA-adenylate; 3) the 3′-OH of the nick attacks DNA-adenylate to join the polynucleotides and release AMP. Each chemical step requires Mg2+. Kinetic analysis of nick sealing by ChVLig-AMP revealed that the rate constant for phosphodiester synthesis (kstep3 = 25 s−1) exceeds that for DNA adenylylation (kstep2 = 2.4 s−1) and that Mg2+ binds with similar affinity during step 2 (Kd = 0.77 mm) and step 3 (Kd = 0.87 mm). The rates of DNA adenylylation and phosphodiester synthesis respond differently to pH, such that step 3 becomes rate-limiting at pH ≤ 6.5. The pH profiles suggest involvement of one and two protonation-sensitive functional groups in catalysis of steps 2 and 3, respectively. We suggest that the 5′-phosphate of the nick is the relevant protonation-sensitive moiety and that a dianionic 5′-phosphate is necessary for productive step 2 catalysis. Motif VI, located at the C terminus of the OB-fold domain of ChVLig, is a conserved feature of ATP-dependent DNA ligases and GTP-dependent mRNA capping enzymes. Presteady state and burst kinetic analysis of the effects of deletion and missense mutations highlight the catalytic contributions of ChVLig motif VI, especially the Asp-297 carboxylate, exclusively during the ligase adenylylation step. PMID:22745124

Calculation of Rate Spectra from Noisy Time Series Data

PubMed Central

Voelz, Vincent A.; Pande, Vijay S.

2011-01-01

As the resolution of experiments to measure folding kinetics continues to improve, it has become imperative to avoid bias that may come with fitting data to a predetermined mechanistic model. Towards this end, we present a rate spectrum approach to analyze timescales present in kinetic data. Computing rate spectra of noisy time series data via numerical discrete inverse Laplace transform is an ill-conditioned inverse problem, so a regularization procedure must be used to perform the calculation. Here, we show the results of different regularization procedures applied to noisy multi-exponential and stretched exponential time series, as well as data from time-resolved folding kinetics experiments. In each case, the rate spectrum method recapitulates the relevant distribution of timescales present in the data, with different priors on the rate amplitudes naturally corresponding to common biases toward simple phenomenological models. These results suggest an attractive alternative to the “Occam’s razor” philosophy of simply choosing models with the fewest number of relaxation rates. PMID:22095854

Theoretical analysis of the effects of light intensity on the photocorrosion of semiconductor electrodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benito, R.M.; Nozik, A.J.

1985-07-18

A kinetic model was developed to describe the effects of light intensity on the photocorrosion of n-type semiconductor electrodes. The model is an extension of previous work by Gomes and co-workers that includes the possibility of multiple steps for the oxidation reaction of the reducing agent in the electrolyte. Six cases are considered where the semiconductor decomposition reaction is multistep (each step involves a hole); the oxidation reaction of the reducing agent is multistep (each step after the first involves a hole or a chemical intermediate), and the first steps of the competing oxidation reactions are reversible or irreversible. Itmore » was found, contrary to previous results, that the photostability of semiconductor electrodes could increase with increased light intensity if the desired oxidation reaction of the reducing agent in the electrolyte was multistep with the first step being reversible. 14 references, 5 figures, 1 table.« less

Local operators in kinetic wealth distribution

NASA Astrophysics Data System (ADS)

Andrecut, M.

2016-05-01

The statistical mechanics approach to wealth distribution is based on the conservative kinetic multi-agent model for money exchange, where the local interaction rule between the agents is analogous to the elastic particle scattering process. Here, we discuss the role of a class of conservative local operators, and we show that, depending on the values of their parameters, they can be used to generate all the relevant distributions. We also show numerically that in order to generate the power-law tail, an heterogeneous risk aversion model is required. By changing the parameters of these operators, one can also fine tune the resulting distributions in order to provide support for the emergence of a more egalitarian wealth distribution.

Simplified Two-Time Step Method for Calculating Combustion Rates and Nitrogen Oxide Emissions for Hydrogen/Air and Hydorgen/Oxygen

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2005-01-01

A simplified single rate expression for hydrogen combustion and nitrogen oxide production was developed. Detailed kinetics are predicted for the chemical kinetic times using the complete chemical mechanism over the entire operating space. These times are then correlated to the reactor conditions using an exponential fit. Simple first order reaction expressions are then used to find the conversion in the reactor. The method uses a two-time step kinetic scheme. The first time averaged step is used at the initial times with smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, temperature, and pressure. The second instantaneous step is used at higher water concentrations (> 1 x 10(exp -20) moles/cc) in the mixture which gives the chemical kinetic time as a function of the instantaneous fuel and water mole concentrations, pressure and temperature (T4). The simple correlations are then compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates are used to calculate the necessary chemical kinetic times. This time is regressed over the complete initial conditions using the Excel regression routine. Chemical kinetic time equations for H2 and NOx are obtained for H2/air fuel and for the H2/O2. A similar correlation is also developed using data from NASA s Chemical Equilibrium Applications (CEA) code to determine the equilibrium temperature (T4) as a function of overall fuel/air ratio, pressure and initial temperature (T3). High values of the regression coefficient R2 are obtained.

Summary of Simplified Two Time Step Method for Calculating Combustion Rates and Nitrogen Oxide Emissions for Hydrogen/Air and Hydrogen/Oxygen

NASA Technical Reports Server (NTRS)

Marek, C. John; Molnar, Melissa

2005-01-01

A simplified single rate expression for hydrogen combustion and nitrogen oxide production was developed. Detailed kinetics are predicted for the chemical kinetic times using the complete chemical mechanism over the entire operating space. These times are then correlated to the reactor conditions using an exponential fit. Simple first order reaction expressions are then used to find the conversion in the reactor. The method uses a two time step kinetic scheme. The first time averaged step is used at the initial times with smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, temperature, and pressure. The second instantaneous step is used at higher water concentrations (greater than l x 10(exp -20)) moles per cc) in the mixture which gives the chemical kinetic time as a function of the instantaneous fuel and water mole concentrations, pressure and temperature (T(sub 4)). The simple correlations are then compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates are used to calculate the necessary chemical kinetic times. This time is regressed over the complete initial conditions using the Excel regression routine. Chemical kinetic time equations for H2 and NOx are obtained for H2/Air fuel and for H2/O2. A similar correlation is also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium temperature (T(sub 4)) as a function of overall fuel/air ratio, pressure and initial temperature (T(sub 3)). High values of the regression coefficient R squared are obtained.

Fast pyrolysis kinetics of alkali lignin: Evaluation of apparent rate parameters and product time evolution.

PubMed

Ojha, Deepak Kumar; Viju, Daniel; Vinu, R

2017-10-01

In this study, the apparent kinetics of fast pyrolysis of alkali lignin was evaluated by obtaining isothermal mass loss data in the timescale of 2-30s at 400-700°C in an analytical pyrolyzer. The data were analyzed using different reaction models to determine the rate constants and apparent rate parameters. First order and one dimensional diffusion models resulted in good fits with experimental data with apparent activation energy of 23kJmol -1 . Kinetic compensation effect was established using a large number of kinetic parameters reported in the literature for pyrolysis of different lignins. The time evolution of the major functional groups in the pyrolysate was analyzed using in situ Fourier transform infrared spectroscopy. Maximum production of the volatiles occurred around 10-12s. A clear transformation of guaiacols to phenol, catechol and their derivatives, and aromatic hydrocarbons was observed with increasing temperature. The plausible reaction steps involved in various transformations are discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Kinetics for the distribution of acrylamide in French fries, fried oil and vapour during frying of potatoes.

PubMed

Hsu, Hui-Tsung; Chen, Ming-Jen; Tseng, Tzu-Ping; Cheng, Li-Hsin; Huang, Li-Jen; Yeh, Tai-Sheng

2016-11-15

Kinetic analysis for the formation of acrylamide in heated foods has been typically performed using only measured data of acrylamide in foods; however, its possible loss caused by release from heated foods into fried oil and air has seldom been considered. The results obtained from the monitoring of acrylamide by frying French fries indicated that acrylamide is distributed in three phases: French fries, frying oil, and air. From the evolved gas analysis of acrylamide and the measured concentration profile of the total acrylamide amount present in these phases, the kinetic behaviour for acrylamide formation does not obey the commonly used model of two-step consecutive reactions during frying, while a lumped kinetic model was proposed for the total acrylamide amount. Moreover, a high acrylamide level in air was observed, implying that, apart from consumers of French fries, fast-food restaurant workers are potentially subject to occupational hazards from acrylamide inhalation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Equilibrium and Kinetic Studies of Cd2+ Biosorption by the Brown Algae Sargassum fusiforme

PubMed Central

Zou, Hui-Xi; Li, Nan; Wang, Li-Hua; Yu, Ping; Yan, Xiu-Feng

2014-01-01

A fundamental investigation of the biosorption of Cd2+ from aqueous solution by the edible seaweed Sargassum fusiforme was performed under batch conditions. The influences of experimental parameters, such as the initial pH, sorption time, temperature, and initial Cd2+ concentration, on Cd2+ uptake by S. fusiforme were evaluated. The results indicated that the biosorption of Cd2+ depended on the initial Cd2+ concentration, as well as the pH. The uptake of Cd2+ could be described by the Langmuir isotherm model, and both the Langmuir biosorption equilibrium constant and the maximum biosorption capacity of the monolayer decreased with increasing temperature, thereby confirming the exothermic character of the sorption process. The biosorption kinetics follows the pseudo-second-order kinetic model, and intraparticle diffusion is the sole rate-limiting step for the entire biosorption period. These fundamental equilibrium and kinetic results can support further studies to the removal of cadmium from S. fusiforme harvested from cadmium-polluted waters. PMID:24736449

Adaptive multi-step Full Waveform Inversion based on Waveform Mode Decomposition

NASA Astrophysics Data System (ADS)

Hu, Yong; Han, Liguo; Xu, Zhuo; Zhang, Fengjiao; Zeng, Jingwen

2017-04-01

Full Waveform Inversion (FWI) can be used to build high resolution velocity models, but there are still many challenges in seismic field data processing. The most difficult problem is about how to recover long-wavelength components of subsurface velocity models when seismic data is lacking of low frequency information and without long-offsets. To solve this problem, we propose to use Waveform Mode Decomposition (WMD) method to reconstruct low frequency information for FWI to obtain a smooth model, so that the initial model dependence of FWI can be reduced. In this paper, we use adjoint-state method to calculate the gradient for Waveform Mode Decomposition Full Waveform Inversion (WMDFWI). Through the illustrative numerical examples, we proved that the low frequency which is reconstructed by WMD method is very reliable. WMDFWI in combination with the adaptive multi-step inversion strategy can obtain more faithful and accurate final inversion results. Numerical examples show that even if the initial velocity model is far from the true model and lacking of low frequency information, we still can obtain good inversion results with WMD method. From numerical examples of anti-noise test, we see that the adaptive multi-step inversion strategy for WMDFWI has strong ability to resist Gaussian noise. WMD method is promising to be able to implement for the land seismic FWI, because it can reconstruct the low frequency information, lower the dominant frequency in the adjoint source, and has a strong ability to resist noise.

CME Simulations with Boundary Conditions Derived from Multiple Viewpoints of STEREO

NASA Astrophysics Data System (ADS)

Singh, T.; Yalim, M. S.; Pogorelov, N. V.

2017-12-01

Coronal Mass Ejections (CMEs) are major drivers of extreme space weather conditions, which is a matter of huge concern for our modern technologically dependent society. Development of numerical approaches that would reproduce CME propagation through the interplanetary space is an important step towards our capability to predict CME arrival time at Earth and their geo-effectiveness. It is also important that CMEs are propagating through a realistic, data-driven background solar wind (SW). In this study, we use a version of the flux-rope-driven Gibson-Low (GL) model to simulate CMEs. We derive inner boundary conditions for the GL flux rope model using the Graduate Cylindrical Shell (GCS) method. This method uses viewpoints from STEREO A and B, and SOHO/LASCO coronagraphs to determine the size and orientation of a CME flux rope as it starts to erupt from Sun. A flux rope created this way is inserted into an SDO/HMI vector magnetogram driven SW background obtained with the Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS). Numerical results are compared with STEREO, SDO/AIA and SOHO/LASCO observations in particular in terms of the CME speed, acceleration and magnetic field structure.

Computational modeling of transport and electrochemical reactions in proton-exchange membrane fuel cells

NASA Astrophysics Data System (ADS)

Um, Sukkee

A comprehensive, multi-physics computational fuel cell dynamics (CFCD) model integrating electrochemical kinetics, charge transport, mass transport (particularly water transport), and flow dynamics is developed in this thesis. The numerical model is validated against published experimental data and utilized to generate results that reveal the internal operation of a PEM fuel cell. A number of model applications are demonstrated in the present work. First, the CFCD model is applied to explore hydrogen dilution effects in the anode feed. Detailed two-dimensional electrochemical and flow/transport simulations are provided to examine substantial anode concentration polarization due to hydrogen depletion at the reaction sites. A transient simulation of the cell current response to a step change in cell voltage is also attempted to elucidate characteristics of the dynamic response of a fuel cell for the first time. After the two-dimensional computational study, the CFCD model is applied to illustrate three-dimensional interactions between mass transfer and electrochemical kinetics. Emphasis is placed on obtaining a fundamental understanding of fully three-dimensional flow in the air cathode with interdigitated flowfield design and how it impacts the transport and electrochemical reaction processes. The innovative design concept for enhanced oxygen transport to, and effective water removal from the cathode, is explored numerically. Next, an analytical study of water transport is performed to investigate various water transport regimes of practical interest. The axial locations characteristic of anode water loss and cathode flooding are predicted theoretically and compared with numerical results. A continuous stirred fuel cell reactor (CSFCR) model is also proposed for the limiting situation where the anode and cathode sides reach equilibrium in water concentration with a thin ionomer membrane in between. In addition to the analytical solutions, a detailed water transport model extending the CFCD framework is developed in which a unified water equation is arrived at using the equilibrium water uptake curve between the gas and membrane phases. Various modes of water transport, i.e. diffusion, convection, and electro-osmotic drag, are incorporated in the unified water transport equation. This water transport model is then applied to elucidate water management in three-dimensional fuel cells with dry to low humidified inlet gases after its validation against available experimental data with dry oxidant and fuel streams. An internal circulation of water with the aid of counter-flow design is found to be essential for low-humidity operation, for example, in portable application of a PEM fuel cell without external humidifier. Finally, to handle the most important issue associated with PEM fuel cells using reformate gas, namely the CO poisoning anode Pt catalysts, a major modification of the present CFCD model is made to include CO oxidation processes. A four-step CO poisoning mechanism is implemented here and anode species equation for CO is added to model the electro- and chemical-oxidation processes on the anode. Numerical results of CO poisoning effects using a commercial package, STAR-CD, are presented. Basic features of CO poisoning are delineated and discussed. Future research areas of the fuel cell modeling are also indicated. As an example, preliminary results of extending the CFCD model to include heat transfer using a commercial package, FLUENTRTM, are given to demonstrate the need for careful thermal management in a multi-cell stack design.

One-step synthesized calcium phosphate-based material for the removal of alizarin S dye from aqueous solutions: isothermal, kinetics, and thermodynamics studies

NASA Astrophysics Data System (ADS)

Adeogun, Abideen Idowu; Babu, Ramesh Balakrishnan

2015-07-01

Calcium phosphate hydroxyapatite (Ca-Hap) synthesized from CaCO3 and H3PO5, it was characterized by scanning electron microscopy, Fourier transform infrared, and X-ray diffraction. The Ca-Hap was used for the removal of Alizarin Red S dye from its aqueous solution. The kinetics, equilibrium, and thermodynamic of the adsorption of the dye onto the Ca-Hap were investigated. The effects of contact time, initial dye concentration, pH as well as temperature on adsorption capacity of Ca-Hap were studied. Experimental data were analyzed using six model equations: Langmuir, Freudlinch, Redlich-Peterson, Temkin, Dubinin-Radushkevich, and Sips isotherms and it was found that the data fitted well with Sips and Dubinin-Radushkevich isotherm models. Pseudo-first-order, pseudo-second-order, Elovic, and Avrami kinetic models were used to test the experimental data in order to elucidate the kinetic adsorption process and it was found that pseudo-second-order model best fit the data. The calculated thermodynamics parameters (∆G°, ∆H° and ∆S°) indicated that the process is spontaneous and endothermic in nature.

Experimental and modeling study on decomposition kinetics of methane hydrates in different media.

PubMed

Liang, Minyan; Chen, Guangjin; Sun, Changyu; Yan, Lijun; Liu, Jiang; Ma, Qinglan

2005-10-13

The decomposition kinetic behaviors of methane hydrates formed in 5 cm3 porous wet activated carbon were studied experimentally in a closed system in the temperature range of 275.8-264.4 K. The decomposition rates of methane hydrates formed from 5 cm3 of pure free water and an aqueous solution of 650 g x m(-3) sodium dodecyl sulfate (SDS) were also measured for comparison. The decomposition rates of methane hydrates in seven different cases were compared. The results showed that the methane hydrates dissociate more rapidly in porous activated carbon than in free systems. A mathematical model was developed for describing the decomposition kinetic behavior of methane hydrates below ice point based on an ice-shielding mechanism in which a porous ice layer was assumed to be formed during the decomposition of hydrate, and the diffusion of methane molecules through it was assumed to be one of the control steps. The parameters of the model were determined by correlating the decomposition rate data, and the activation energies were further determined with respect to three different media. The model was found to well describe the decomposition kinetic behavior of methane hydrate in different media.

Online kinetic studies on intermediates of laccase-catalyzed reaction in reversed micelle.

PubMed

Liu, Zhi-Hong; Shao, Mei; Cai, Ru-Xiu; Shen, Ping

2006-02-01

Using water/AOT/n-octane reversed micelle as the medium, the optical signal of the reactive intermediate of laccase-catalyzed oxidation of o-phenylenediamine, which was indetectable in aqueous solutions, was successfully captured. Thus online kinetic studies of the intermediate were accomplished. Two-way kinetic spectral data were acquired with stopped-flow technique. By resolving the data with global analysis software, both the kinetic curves and the absorption spectra of the components involved in the reaction process were simultaneously obtained. The whole reaction in the reversed micelle was proved to be composed of two successive steps, an enzymatic generation of the intermediate and a following nonenzymatic decay of the intermediate. A consecutive first-order kinetic model of the whole reaction was confirmed. The influences of microenvironmental factors of the medium (such as the pH value of the water pool and the water/AOT ratio) on the detection of the intermediate were also investigated.

Individualized Inservice Teacher Education (Project In-Step). Evaluation Report. Phase III.

ERIC Educational Resources Information Center

Thurber, John C.

This is a report on the third phase of Project IN-STEP, which was intended to develop a viable model for individualized, multi-media in-service teacher education programs. (Phase I and II are reported in ED 033 905, and ED 042 709). The rationale for Phase III was to see if the model could be successfully transferred to an area other than teaching…

A model for the kinetics of homotypic cellular aggregation under static conditions

NASA Technical Reports Server (NTRS)

Neelamegham, S.; Munn, L. L.; Zygourakis, K.; McIntire, L. V. (Principal Investigator)

1997-01-01

We present the formulation and testing of a mathematical model for the kinetics of homotypic cellular aggregation. The model considers cellular aggregation under no-flow conditions as a two-step process. Individual cells and cell aggregates 1) move on the tissue culture surface and 2) collide with other cells (or aggregates). These collisions lead to the formation of intercellular bonds. The aggregation kinetics are described by a system of coupled, nonlinear ordinary differential equations, and the collision frequency kernel is derived by extending Smoluchowski's colloidal flocculation theory to cell migration and aggregation on a two-dimensional surface. Our results indicate that aggregation rates strongly depend upon the motility of cells and cell aggregates, the frequency of cell-cell collisions, and the strength of intercellular bonds. Model predictions agree well with data from homotypic lymphocyte aggregation experiments using Jurkat cells activated by 33B6, an antibody to the beta 1 integrin. Since cell migration speeds and all the other model parameters can be independently measured, the aggregation model provides a quantitative methodology by which we can accurately evaluate the adhesivity and aggregation behavior of cells.

Helicase Stepping Investigated with One-Nucleotide Resolution Fluorescence Resonance Energy Transfer

NASA Astrophysics Data System (ADS)

Lin, Wenxia; Ma, Jianbing; Nong, Daguan; Xu, Chunhua; Zhang, Bo; Li, Jinghua; Jia, Qi; Dou, Shuoxing; Ye, Fangfu; Xi, Xuguang; Lu, Ying; Li, Ming

2017-09-01

Single-molecule Förster resonance energy transfer is widely applied to study helicases by detecting distance changes between a pair of dyes anchored to overhangs of a forked DNA. However, it has been lacking single-base pair (1-bp) resolution required for revealing stepping kinetics of helicases. We designed a nanotensioner in which a short DNA is bent to exert force on the overhangs, just as in optical or magnetic tweezers. The strategy improved the resolution of Förster resonance energy transfer to 0.5 bp, high enough to uncover differences in DNA unwinding by yeast Pif1 and E. coli RecQ whose unwinding behaviors cannot be differentiated by currently practiced methods. We found that Pif1 exhibits 1-bp-stepping kinetics, while RecQ breaks 1 bp at a time but sequesters the nascent nucleotides and releases them randomly. The high-resolution data allowed us to propose a three-parameter model to quantitatively interpret the apparently different unwinding behaviors of the two helicases which belong to two superfamilies.

Transient performance analysis of the master cylinder hydraulic system of a 6.3 MN fineblanking press

NASA Astrophysics Data System (ADS)

Yi, Guodong; Li, Jin

2018-03-01

The master cylinder hydraulic system is the core component of the fineblanking press that seriously affects the machine performance. A key issue in the design of the master cylinder hydraulic system is dealing with the heavy shock loads in the fineblanking process. In this paper, an equivalent model of the master cylinder hydraulic system is established based on typical process parameters for practical fineblanking; then, the response characteristics of the master cylinder slider to the step changes in the load and control current are analyzed, and lastly, control strategies for the proportional valve are studied based on the impact of the control parameters on the kinetic stability of the slider. The results show that the kinetic stability of the slider is significantly affected by the step change of the control current, while it is slightly affected by the step change of the system load, which can be improved by adjusting the flow rate and opening time of the proportional valve.

Composite PET and MRI for accurate localization and metabolic modeling: a very useful tool for research and clinic

NASA Astrophysics Data System (ADS)

Bidaut, Luc M.

1991-06-01

In order to help in analyzing PET data and really take advantage of their metabolic content, a system was designed and implemented to align and process data from various medical imaging modalities, particularly (but not only) for brain studies. Although this system is for now mostly used for anatomical localization, multi-modality ROIs and pharmaco-kinetic modeling, more multi-modality protocols will be implemented in the future, not only to help in PET reconstruction data correction and semi-automated ROI definition, but also for helping in improving diagnostic accuracy along with surgery and therapy planning.

Two-step infiltration of aluminum melts into Al-Ti-B4C-CuO powder mixture pellets

NASA Astrophysics Data System (ADS)

Zhang, Jingjing; Lee, Jung-Moo; Cho, Young-Hee; Kim, Su-Hyeon; Yu, Huashun

2016-03-01

Aluminum matrix composites with a high volume fraction of B4C and TiB2 were fabricated by a novel processing technique - a quick spontaneous infiltration process. The process combines a pressureless infiltration with the combustion reaction of Al-Ti-B4C-CuO in molten aluminum. The process is realized in a simple and economical way in which the whole process is performed in air in a few minutes. To verify the rapidity of the process, the infiltration kinetics was calculated based on the Washburn equation in which melt flows into a porous skeleton. However, there was a noticeable deviation from the calculated results with the experimental results. Considering the cross-sections of the samples at different processing times, a new infiltration model (two step infiltration) consisting of macro-infiltration and micro-infiltration is suggested. The calculated kinetics results in light of the proposed model agree well with the experimental results.

On the Connection between Kinetic Monte Carlo and the Burton-Cabrera-Frank Theory

NASA Astrophysics Data System (ADS)

Patrone, Paul; Margetis, Dionisios; Einstein, T. L.

2013-03-01

In the many years since it was first proposed, the Burton- Cabrera-Frank (BCF) model of step-flow has been experimentally established as one of the cornerstones of surface physics. However, many questions remain regarding the underlying physical processes and theoretical assumptions that give rise to the BCF theory. In this work, we formally derive the BCF theory from an atomistic, kinetic Monte Carlo model of the surface in 1 +1 dimensions with one step. Our analysis (i) shows how the BCF theory describes a surface with a low density of adsorbed atoms, and (ii) establishes a set of near-equilibrium conditions ensuring that the theory remains valid for all times. Support for PP was provided by the NIST-ARRA Fellowship Award No. 70NANB10H026 through UMD. Support for TLE and PP was also provided by the CMTC at UMD, with ancillary support from the UMD MRSEC. Support for DM was provided by NSF DMS0847587 at UMD.

New insight into the ZnO sulfidation reaction: mechanism and kinetics modeling of the ZnS outward growth.

PubMed

Neveux, Laure; Chiche, David; Pérez-Pellitero, Javier; Favergeon, Loïc; Gay, Anne-Sophie; Pijolat, Michèle

2013-02-07

Zinc oxide based materials are commonly used for the final desulfurization of synthesis gas in Fischer-Tropsch based XTL processes. Although the ZnO sulfidation reaction has been widely studied, little is known about the transformation at the crystal scale, its detailed mechanism and kinetics. A model ZnO material with well-determined characteristics (particle size and shape) has been synthesized to perform this study. Characterizations of sulfided samples (using XRD, TEM and electron diffraction) have shown the formation of oriented polycrystalline ZnS nanoparticles with a predominant hexagonal form (wurtzite phase). TEM observations also have evidenced an outward development of the ZnS phase, showing zinc and oxygen diffusion from the ZnO-ZnS internal interface to the surface of the ZnS particle. The kinetics of ZnO sulfidation by H(2)S has been investigated using isothermal and isobaric thermogravimetry. Kinetic tests have been performed that show that nucleation of ZnS is instantaneous compared to the growth process. A reaction mechanism composed of eight elementary steps has been proposed to account for these results, and various possible rate laws have been determined upon approximation of the rate-determining step. Thermogravimetry experiments performed in a wide range of H(2)S and H(2)O partial pressures have shown that the ZnO sulfidation reaction rate has a nonlinear variation with H(2)S partial pressure at the same time no significant influence of water vapor on reaction kinetics has been observed. From these observations, a mixed kinetics of external interface reaction with water desorption and oxygen diffusion has been determined to control the reaction kinetics and the proposed mechanism has been validated. However, the formation of voids at the ZnO-ZnS internal interface, characterized by TEM and electron tomography, strongly slows down the reaction rate. Therefore, the impact of the decreasing ZnO-ZnS internal interface on reaction kinetics has been taken into account in the reaction rate expression. In this way the void formation at the interface has been modeled considering a random nucleation followed by an isotropic growth of cavities. Very good agreement has been observed between both experimental and calculated rates after taking into account the decrease in the ZnO-ZnS internal interface.

Increasing Running Step Rate Reduces Patellofemoral Joint Forces

PubMed Central

Lenhart, Rachel L.; Thelen, Darryl G.; Wille, Christa M.; Chumanov, Elizabeth S.; Heiderscheit, Bryan C.

2013-01-01

Purpose Increasing step rate has been shown to elicit changes in joint kinematics and kinetics during running, and has been suggested as a possible rehabilitation strategy for runners with patellofemoral pain. The purpose of this study was to determine how altering step rate affects internal muscle forces and patellofemoral joint loads, and then to determine what kinematic and kinetic factors best predict changes in joint loading. Methods We recorded whole body kinematics of 30 healthy adults running on an instrumented treadmill at three step rate conditions (90%, 100%, and 110% of preferred step rate). We then used a 3D lower extremity musculoskeletal model to estimate muscle, patellar tendon, and patellofemoral joint forces throughout the running gait cycles. Additionally, linear regression analysis allowed us to ascertain the relative influence of limb posture and external loads on patellofemoral joint force. Results Increasing step rate to 110% of preferred reduced peak patellofemoral joint force by 14%. Peak muscle forces were also altered as a result of the increased step rate with hip, knee and ankle extensor forces, and hip abductor forces all reduced in mid-stance. Compared to the 90% step rate condition, there was a concomitant increase in peak rectus femoris and hamstring loads during early and late swing, respectively, at higher step rates. Peak stance phase knee flexion decreased with increasing step rate, and was found to be the most important predictor of the reduction in patellofemoral joint loading. Conclusion Increasing step rate is an effective strategy to reduce patellofemoral joint forces and could be effective in modulating biomechanical factors that can contribute to patellofemoral pain. PMID:23917470

Adsorption of crystal violet onto functionalised multi-walled carbon nanotubes: Equilibrium and kinetic studies.

PubMed

Sabna, V; Thampi, Santosh G; Chandrakaran, S

2016-12-01

Synthetic dyes present in effluent from textile, paper and paint industries contain crystal violet (CV), a known carcinogenic agent. This study investigates the modification of multiwalled carbon nanotubes by acid reflux method and equilibrium and kinetic behaviour of adsorption of CV onto functionalized multi-walled carbon nanotubes (fMWNTs) in batch system. High stability of the fMWNTs suspension in water indicates the hydrophilicity of fMWNTs induced due to the formation of functional groups that make hydrogen bonds with water molecules. fMWNTs were characterized by Fourier Transform Infra Red (FTIR) spectroscopy and the functional groups present on the fMWNTs were confirmed. Characteristic variation was observed in the FTIR spectra of fMWNTs after adsorption of crystal violet onto it. Adsorption characteristics were evaluated as a function of system variables such as contact time, dosage of fMWNTs and initial concentration and pH of the crystal violet solution. Adsorption capacity of fMWNTs and percentage removal of the dye increased with increase in contact time, adsorbent dosage and pH but declined with increase in initial concentration of the dye. fMWNTs showed higher adsorption capacity compared to that of pristine MWNTs. Data showed good fit with the Langmuir and Freundlich isotherm models and the pseudo-second order kinetic model; the maximum adsorption capacity was 90.52mg/g. Kinetic parameters such as rate constants, equilibrium adsorption capacities and regression coefficients were estimated. Results indicate that fMWNTs are an effective adsorbent for the removal of crystal violet from aqueous solution. Copyright © 2015 Elsevier Inc. All rights reserved.

A systematic study of multiple minerals precipitation modelling in wastewater treatment.

PubMed

Kazadi Mbamba, Christian; Tait, Stephan; Flores-Alsina, Xavier; Batstone, Damien J

2015-11-15

Mineral solids precipitation is important in wastewater treatment. However approaches to minerals precipitation modelling are varied, often empirical, and mostly focused on single precipitate classes. A common approach, applicable to multi-species precipitates, is needed to integrate into existing wastewater treatment models. The present study systematically tested a semi-mechanistic modelling approach, using various experimental platforms with multiple minerals precipitation. Experiments included dynamic titration with addition of sodium hydroxide to synthetic wastewater, and aeration to progressively increase pH and induce precipitation in real piggery digestate and sewage sludge digestate. The model approach consisted of an equilibrium part for aqueous phase reactions and a kinetic part for minerals precipitation. The model was fitted to dissolved calcium, magnesium, total inorganic carbon and phosphate. Results indicated that precipitation was dominated by the mineral struvite, forming together with varied and minor amounts of calcium phosphate and calcium carbonate. The model approach was noted to have the advantage of requiring a minimal number of fitted parameters, so the model was readily identifiable. Kinetic rate coefficients, which were statistically fitted, were generally in the range 0.35-11.6 h(-1) with confidence intervals of 10-80% relative. Confidence regions for the kinetic rate coefficients were often asymmetric with model-data residuals increasing more gradually with larger coefficient values. This suggests that a large kinetic coefficient could be used when actual measured data is lacking for a particular precipitate-matrix combination. Correlation between the kinetic rate coefficients of different minerals was low, indicating that parameter values for individual minerals could be independently fitted (keeping all other model parameters constant). Implementation was therefore relatively flexible, and would be readily expandable to include other minerals. Copyright © 2015 Elsevier Ltd. All rights reserved.

Full particle-in-cell simulations of kinetic equilibria and the role of the initial current sheet on steady asymmetric magnetic reconnection

NASA Astrophysics Data System (ADS)

Dargent, J.; Aunai, N.; Belmont, G.; Dorville, N.; Lavraud, B.; Hesse, M.

2016-06-01

> Tangential current sheets are ubiquitous in space plasmas and yet hard to describe with a kinetic equilibrium. In this paper, we use a semi-analytical model, the BAS model, which provides a steady ion distribution function for a tangential asymmetric current sheet and we prove that an ion kinetic equilibrium produced by this model remains steady in a fully kinetic particle-in-cell simulation even if the electron distribution function does not satisfy the time independent Vlasov equation. We then apply this equilibrium to look at the dependence of magnetic reconnection simulations on their initial conditions. We show that, as the current sheet evolves from a symmetric to an asymmetric upstream plasma, the reconnection rate is impacted and the X line and the electron flow stagnation point separate from one another and start to drift. For the simulated systems, we investigate the overall evolution of the reconnection process via the classical signatures discussed in the literature and searched in the Magnetospheric MultiScale data. We show that they seem robust and do not depend on the specific details of the internal structure of the initial current sheet.

The Control Based on Internal Average Kinetic Energy in Complex Environment for Multi-robot System

NASA Astrophysics Data System (ADS)

Yang, Mao; Tian, Yantao; Yin, Xianghua

In this paper, reference trajectory is designed according to minimum energy consumed for multi-robot system, which nonlinear programming and cubic spline interpolation are adopted. The control strategy is composed of two levels, which lower-level is simple PD control and the upper-level is based on the internal average kinetic energy for multi-robot system in the complex environment with velocity damping. Simulation tests verify the effectiveness of this control strategy.

Modeling Stepped Leaders Using a Time Dependent Multi-dipole Model and High-speed Video Data

NASA Astrophysics Data System (ADS)

Karunarathne, S.; Marshall, T.; Stolzenburg, M.; Warner, T. A.; Orville, R. E.

2012-12-01

In summer of 2011, we collected lightning data with 10 stations of electric field change meters (bandwidth of 0.16 Hz - 2.6 MHz) on and around NASA/Kennedy Space Center (KSC) covering nearly 70 km × 100 km area. We also had a high-speed video (HSV) camera recording 50,000 images per second collocated with one of the electric field change meters. In this presentation we describe our use of these data to model the electric field change caused by stepped leaders. Stepped leaders of a cloud to ground lightning flash typically create the initial path for the first return stroke (RS). Most of the time, stepped leaders have multiple complex branches, and one of these branches will create the ground connection for the RS to start. HSV data acquired with a short focal length lens at ranges of 5-25 km from the flash are useful for obtaining the 2-D location of these multiple branches developing at the same time. Using HSV data along with data from the KSC Lightning Detection and Ranging (LDAR2) system and the Cloud to Ground Lightning Surveillance System (CGLSS), the 3D path of a leader may be estimated. Once the path of a stepped leader is obtained, the time dependent multi-dipole model [ Lu, Winn,and Sonnenfeld, JGR 2011] can be used to match the electric field change at various sensor locations. Based on this model, we will present the time-dependent charge distribution along a leader channel and the total charge transfer during the stepped leader phase.

Migration of antioxidants from polylactic acid films, a parameter estimation approach: Part I - A model including convective mass transfer coefficient.

PubMed

Samsudin, Hayati; Auras, Rafael; Burgess, Gary; Dolan, Kirk; Soto-Valdez, Herlinda

2018-03-01

A two-step solution based on the boundary conditions of Crank's equations for mass transfer in a film was developed. Three driving factors, the diffusion (D), partition (K p,f ) and convective mass transfer coefficients (h), govern the sorption and/or desorption kinetics of migrants from polymer films. These three parameters were simultaneously estimated. They provide in-depth insight into the physics of a migration process. The first step was used to find the combination of D, K p,f and h that minimized the sums of squared errors (SSE) between the predicted and actual results. In step 2, an ordinary least square (OLS) estimation was performed by using the proposed analytical solution containing D, K p,f and h. Three selected migration studies of PLA/antioxidant-based films were used to demonstrate the use of this two-step solution. Additional parameter estimation approaches such as sequential and bootstrap were also performed to acquire a better knowledge about the kinetics of migration. The proposed model successfully provided the initial guesses for D, K p,f and h. The h value was determined without performing a specific experiment for it. By determining h together with D, under or overestimation issues pertaining to a migration process can be avoided since these two parameters are correlated. Copyright © 2017 Elsevier Ltd. All rights reserved.

Role of spatial inhomogenity in GPCR dimerisation predicted by receptor association-diffusion models

NASA Astrophysics Data System (ADS)

Deshpande, Sneha A.; Pawar, Aiswarya B.; Dighe, Anish; Athale, Chaitanya A.; Sengupta, Durba

2017-06-01

G protein-coupled receptor (GPCR) association is an emerging paradigm with far reaching implications in the regulation of signalling pathways and therapeutic interventions. Recent super resolution microscopy studies have revealed that receptor dimer steady state exhibits sub-second dynamics. In particular the GPCRs, muscarinic acetylcholine receptor M1 (M1MR) and formyl peptide receptor (FPR), have been demonstrated to exhibit a fast association/dissociation kinetics, independent of ligand binding. In this work, we have developed a spatial kinetic Monte Carlo model to investigate receptor homo-dimerisation at a single receptor resolution. Experimentally measured association/dissociation kinetic parameters and diffusion coefficients were used as inputs to the model. To test the effect of membrane spatial heterogeneity on the simulated steady state, simulations were compared to experimental statistics of dimerisation. In the simplest case the receptors are assumed to be diffusing in a spatially homogeneous environment, while spatial heterogeneity is modelled to result from crowding, membrane micro-domains and cytoskeletal compartmentalisation or ‘corrals’. We show that a simple association-diffusion model is sufficient to reproduce M1MR association statistics, but fails to reproduce FPR statistics despite comparable kinetic constants. A parameter sensitivity analysis is required to reproduce the association statistics of FPR. The model reveals the complex interplay between cytoskeletal components and their influence on receptor association kinetics within the features of the membrane landscape. These results constitute an important step towards understanding the factors modulating GPCR organisation.

Combined angle-resolved X-ray photoelectron spectroscopy, density functional theory and kinetic study of nitridation of gallium arsenide

NASA Astrophysics Data System (ADS)

Mehdi, H.; Monier, G.; Hoggan, P. E.; Bideux, L.; Robert-Goumet, C.; Dubrovskii, V. G.

2018-01-01

The high density of interface and surface states that cause the strong Fermi pinning observed on GaAs surfaces can be reduced by depositing GaN ultra-thin films on GaAs. To further improve this passivation, it is necessary to investigate the nitridation phenomena by identifying the distinct steps occurring during the process and to understand and quantify the growth kinetics of GaAs nitridation under different conditions. Nitridation of the cleaned GaAs substrate was performed using N2 plasma source. Two approaches have been combined. Firstly, an AR-XPS (Angle Resolved X-ray Photoelectron Spectroscopy) study is carried out to determine the chemical environments of the Ga, As and N atoms and the composition depth profile of the GaN thin film which allow us to summarize the nitridation process in three steps. Moreover, the temperature and time treatment have been investigated and show a significant impact on the formation of the GaN layer. The second approach is a refined growth kinetic model which better describes the GaN growth as a function of the nitridation time. This model clarifies the exchange mechanism of arsenic with nitrogen atoms at the GaN/GaAs interface and the phenomenon of quasi-saturation of the process observed experimentally.

Image-based modeling of tumor shrinkage in head and neck radiation therapy1

PubMed Central

Chao, Ming; Xie, Yaoqin; Moros, Eduardo G.; Le, Quynh-Thu; Xing, Lei

2010-01-01

Purpose: Understanding the kinetics of tumor growth∕shrinkage represents a critical step in quantitative assessment of therapeutics and realization of adaptive radiation therapy. This article presents a novel framework for image-based modeling of tumor change and demonstrates its performance with synthetic images and clinical cases. Methods: Due to significant tumor tissue content changes, similarity-based models are not suitable for describing the process of tumor volume changes. Under the hypothesis that tissue features in a tumor volume or at the boundary region are partially preserved, the kinetic change was modeled in two steps: (1) Autodetection of homologous tissue features shared by two input images using the scale invariance feature transformation (SIFT) method; and (2) establishment of a voxel-to-voxel correspondence between the images for the remaining spatial points by interpolation. The correctness of the tissue feature correspondence was assured by a bidirectional association procedure, where SIFT features were mapped from template to target images and reversely. A series of digital phantom experiments and five head and neck clinical cases were used to assess the performance of the proposed technique. Results: The proposed technique can faithfully identify the known changes introduced when constructing the digital phantoms. The subsequent feature-guided thin plate spline calculation reproduced the “ground truth” with accuracy better than 1.5 mm. For the clinical cases, the new algorithm worked reliably for a volume change as large as 30%. Conclusions: An image-based tumor kinetic algorithm was developed to model the tumor response to radiation therapy. The technique provides a practical framework for future application in adaptive radiation therapy. PMID:20527569

Microbial community composition of a multi-stage moving bed biofilm reactor and its interaction with kinetic model parameters estimation.

PubMed

Wang, Xiaodong; Bi, Xuejun; Hem, Lars John; Ratnaweera, Harsha

2018-07-15

Microbial community diversity determines the function of each chamber of multi-stage moving bed biofilm reactor (MBBR) systems. How the microbial community data can be further used to serve wastewater treatment process modelling and optimization has been rarely studied. In this study, a MBBR system was set up to investigate the microbial community diversity of biofilm in each functional chamber. The compositions of microbial community of biofilm from different chambers of MBBR were quantified by high-throughput sequencing. Significantly higher proportion of autotrophs were found in the second aerobic chamber (15.4%), while 4.3% autotrophs were found in the first aerobic chamber. Autotrophs in anoxic chamber were negligible. Moreover, ratios of active heterotrophic biomass and autotrophic biomass (X H /X A ) were obtained by performing respiration tests. By setting heterotroph/autotroph ratios obtained from sequencing analysis equal to X H /X A , a novel approach for kinetic model parameters estimation was developed. This work not only investigated microbial community of MBBR system, but also it provided an approach to make further use of molecular microbiology analysis results. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Relay/Converter Interface Influences Hydrolysis of ATP by Skeletal Muscle Myosin II.

PubMed

Bloemink, Marieke J; Melkani, Girish C; Bernstein, Sanford I; Geeves, Michael A

2016-01-22

The interface between relay and converter domain of muscle myosin is critical for optimal myosin performance. Using Drosophila melanogaster indirect flight muscle S1, we performed a kinetic analysis of the effect of mutations in the converter and relay domain. Introduction of a mutation (R759E) in the converter domain inhibits the steady-state ATPase of myosin S1, whereas an additional mutation in the relay domain (N509K) is able to restore the ATPase toward wild-type values. The R759E S1 construct showed little effect on most steps of the actomyosin ATPase cycle. The exception was a 25-30% reduction in the rate constant of the hydrolysis step, the step coupled to the cross-bridge recovery stroke that involves a change in conformation at the relay/converter domain interface. Significantly, the double mutant restored the hydrolysis step to values similar to the wild-type myosin. Modeling the relay/converter interface suggests a possible interaction between converter residue 759 and relay residue 509 in the actin-detached conformation, which is lost in R759E but is restored in N509K/R759E. This detailed kinetic analysis of Drosophila myosin carrying the R759E mutation shows that the interface between the relay loop and converter domain is important for fine-tuning myosin kinetics, in particular ATP binding and hydrolysis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Global minimum profile error (GMPE) - a least-squares-based approach for extracting macroscopic rate coefficients for complex gas-phase chemical reactions.

PubMed

Duong, Minh V; Nguyen, Hieu T; Mai, Tam V-T; Huynh, Lam K

2018-01-03

Master equation/Rice-Ramsperger-Kassel-Marcus (ME/RRKM) has shown to be a powerful framework for modeling kinetic and dynamic behaviors of a complex gas-phase chemical system on a complicated multiple-species and multiple-channel potential energy surface (PES) for a wide range of temperatures and pressures. Derived from the ME time-resolved species profiles, the macroscopic or phenomenological rate coefficients are essential for many reaction engineering applications including those in combustion and atmospheric chemistry. Therefore, in this study, a least-squares-based approach named Global Minimum Profile Error (GMPE) was proposed and implemented in the MultiSpecies-MultiChannel (MSMC) code (Int. J. Chem. Kinet., 2015, 47, 564) to extract macroscopic rate coefficients for such a complicated system. The capability and limitations of the new approach were discussed in several well-defined test cases.

Aromatic sulfonation with sulfur trioxide: mechanism and kinetic model.

PubMed

Moors, Samuel L C; Deraet, Xavier; Van Assche, Guy; Geerlings, Paul; De Proft, Frank

2017-01-01

Electrophilic aromatic sulfonation of benzene with sulfur trioxide is studied with ab initio molecular dynamics simulations in gas phase, and in explicit noncomplexing (CCl 3 F) and complexing (CH 3 NO 2 ) solvent models. We investigate different possible reaction pathways, the number of SO 3 molecules participating in the reaction, and the influence of the solvent. Our simulations confirm the existence of a low-energy concerted pathway with formation of a cyclic transition state with two SO 3 molecules. Based on the simulation results, we propose a sequence of elementary reaction steps and a kinetic model compatible with experimental data. Furthermore, a new alternative reaction pathway is proposed in complexing solvent, involving two SO 3 and one CH 3 NO 2 .

Simple model of inhibition of chain-branching combustion processes

NASA Astrophysics Data System (ADS)

Babushok, Valeri I.; Gubernov, Vladimir V.; Minaev, Sergei S.; Miroshnichenko, Taisia P.

2017-11-01

A simple kinetic model has been suggested to describe the inhibition and extinction of flame propagation in reaction systems with chain-branching reactions typical for hydrocarbon systems. The model is based on the generalised model of the combustion process with chain-branching reaction combined with the one-stage reaction describing the thermal mode of flame propagation with the addition of inhibition reaction steps. Inhibitor addition suppresses the radical overshoot in flame and leads to the change of reaction mode from the chain-branching reaction to a thermal mode of flame propagation. With the increase of inhibitor the transition of chain-branching mode of reaction to the reaction with straight-chains (non-branching chain reaction) is observed. The inhibition part of the model includes a block of three reactions to describe the influence of the inhibitor. The heat losses are incorporated into the model via Newton cooling. The flame extinction is the result of the decreased heat release of inhibited reaction processes and the suppression of radical overshoot with the further decrease of the reaction rate due to the temperature decrease and mixture dilution. A comparison of the results of modelling laminar premixed methane/air flames inhibited by potassium bicarbonate (gas phase model, detailed kinetic model) with the results obtained using the suggested simple model is presented. The calculations with the detailed kinetic model demonstrate the following modes of combustion process: (1) flame propagation with chain-branching reaction (with radical overshoot, inhibitor addition decreases the radical overshoot down to the equilibrium level); (2) saturation of chemical influence of inhibitor, and (3) transition to thermal mode of flame propagation (non-branching chain mode of reaction). The suggested simple kinetic model qualitatively reproduces the modes of flame propagation with the addition of the inhibitor observed using detailed kinetic models.

Short hold times in dynamic vapor sorption measurements mischaracterize the equilibrium moisture content of wood

Treesearch

Samuel V. Glass; Charles R. Boardman; Samuel L. Zelinka

2017-01-01

Recently, the dynamic vapor sorption (DVS) technique has been used to measure sorption isotherms and develop moisture-mechanics models for wood and cellulosic materials. This method typically involves measuring the time-dependent mass response of a sample following step changes in relative humidity (RH), fitting a kinetic model to the data, and extrapolating the...

Simulations of Flame Acceleration and Deflagration-to-Detonation Transitions in Methane-Air Systems

DTIC Science & Technology

2010-03-17

are neglected. 3. Model parameter calibration The one-step Arrhenius kinetics used in this model cannot ex- actly reproduce all properties of laminar...with obstacles are compared to previ- ously reported experimental data. The results obtained using the simple reaction model qualitatively, and in...have taken in developing a multidimensional numerical model to study explosions in large-scale systems containing mixtures of nat- ural gas and air

Gamma prime precipitation modeling and strength responses in powder metallurgy superalloys

NASA Astrophysics Data System (ADS)

Mao, Jian

Precipitation-hardened nickel-based superalloys have been widely used as high temperature structural materials in gas turbine engine applications for more than 50 years. Powder metallurgy (P/M) technology was introduced as an innovative manufacturing process to overcome severe segregation and poor workability of alloys with high alloying contents. The excellent mechanical properties of P/M superalloys also depend upon the characteristic microstructures, including grain size and size distribution of gamma' precipitates. Heat treatment is the most critical processing step that has ultimate influences on the microstructure, and hence, on the mechanical properties of the materials. The main objective of this research was to study the gamma ' precipitation kinetics in various cooling circumstances and also study the strength response to the cooling history in two model alloys, Rne88DT and U720LI. The research is summarized below: (1) An experimental method was developed to allow accurate simulation and control of any desired cooling profile. Two novel cooling methods were introduced: continuous cooling and interrupt cooling. Isothermal aging was also carried out. (2) The growth and coarsening kinetics of the cooling gamma' precipitates were experimentally studied under different cooling and aging conditions, and the empirical equations were established. It was found that the cooling gamma' precipitate versus the cooling rate follows a power law. The gamma' precipitate size versus aging time obeys the LSW cube law for coarsening. (3) The strengthening of the material responses to the cooling rate and the decreasing temperature during cooling was investigated in both alloys. The tensile strength increases with the cooling rate. In addition, the non-monotonic response of strength versus interrupt temperature is of great interest. (4) An energy-driven model integrated with the classic growth and coarsen theories was successfully embedded in a computer program developed to simulate the cooling gamma ' precipitation based on the first principle of thermodynamics. The combination of the thermodynamic and the kinetic approaches provided a more practical method to determine the critical nucleation energy. (5) The simulation results proved the gamma' burst theory and the existence of the multi-stage burst of gamma' precipitates, which shows good agreement with the experimental data in a variety of aspects.

Governance for public health and health equity: The Tröndelag model for public health work.

PubMed

Lillefjell, Monica; Magnus, Eva; Knudtsen, Margunn SkJei; Wist, Guri; Horghagen, Sissel; Espnes, Geir Arild; Maass, Ruca; Anthun, Kirsti Sarheim

2018-06-01

Multi-sectoral governance of population health is linked to the realization that health is the property of many societal systems. This study aims to contribute knowledge and methods that can strengthen the capacities of municipalities regarding how to work more systematically, knowledge-based and multi-sectoral in promoting health and health equity in the population. Process evaluation was conducted, applying a mixed-methods research design, combining qualitative and quantitative data collection methods. Processes strengthening systematic and multi-sectoral development, implementation and evaluation of research-based measures to promote health, quality of life, and health equity in, for and with municipalities were revealed. A step-by-step model, that emphasizes the promotion of knowledge-based, systematic, multi-sectoral public health work, as well as joint ownership of local resources, initiatives and policies has been developed. Implementation of systematic, knowledge-based and multi-sectoral governance of public health measures in municipalities demand shared understanding of the challenges, updated overview of the population health and impact factors, anchoring in plans, new skills and methods for selection and implementation of measures, as well as development of trust, ownership, shared ethics and goals among those involved.

Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions.

PubMed

Götz, Markus; Wortmann, Philipp; Schmid, Sonja; Hugel, Thorsten

2018-01-30

Single-molecule Förster resonance energy transfer (smFRET) has become a widely used biophysical technique to study the dynamics of biomolecules. For many molecular machines in a cell proteins have to act together with interaction partners in a functional cycle to fulfill their task. The extension of two-color to multi-color smFRET makes it possible to simultaneously probe more than one interaction or conformational change. This not only adds a new dimension to smFRET experiments but it also offers the unique possibility to directly study the sequence of events and to detect correlated interactions when using an immobilized sample and a total internal reflection fluorescence microscope (TIRFM). Therefore, multi-color smFRET is a versatile tool for studying biomolecular complexes in a quantitative manner and in a previously unachievable detail. Here, we demonstrate how to overcome the special challenges of multi-color smFRET experiments on proteins. We present detailed protocols for obtaining the data and for extracting kinetic information. This includes trace selection criteria, state separation, and the recovery of state trajectories from the noisy data using a 3D ensemble Hidden Markov Model (HMM). Compared to other methods, the kinetic information is not recovered from dwell time histograms but directly from the HMM. The maximum likelihood framework allows us to critically evaluate the kinetic model and to provide meaningful uncertainties for the rates. By applying our method to the heat shock protein 90 (Hsp90), we are able to disentangle the nucleotide binding and the global conformational changes of the protein. This allows us to directly observe the cooperativity between the two nucleotide binding pockets of the Hsp90 dimer.

Kinetic sorption of contaminants of emerging concern by a palygorskite-montmorillonite filter medium.

PubMed

Berhane, Tedros M; Levy, Jonathan; Krekeler, Mark P S; Danielson, Neil D

2017-06-01

Kinetic sorption of bisphenol A (BPA), carbamazepine (CMZ) and ciprofloxacin (CIP) by three palygorskite-montmorillonite (Pal-Mt) granule sizes was studied. For BPA, CMZ and CIP, apparent sorption equilibrium was reached within about 3, 5 and 16 h, respectively. The highest and the lowest sorption capacities were by the small and the large granule sizes, respectively. Experimental results were compared to various sorption kinetics models to gain insights regarding the sorption processes and achieve a predictive capacity. The pseudo-second order (PSO) and the Elovich models performed the best while the pseudo-first order (PFO) model was only adequate for CMZ. The intraparticle-diffusion (IPD) model showed a two-step linear plot of BPA, CMZ and CIP sorption versus square root of time that was indicative of surface-sorption followed by IPD as a rate-limiting process before equilibrium was reached. Using the pseudo-first order (PFO) and the pseudo-second order (PSO) rate constants combined with previously-established Langmuir equilibrium sorption models, the kinetic sorption (k a ) and desorption (k d ) Langmuir kinetic rate constants were theoretically calculated for BPA and CIP. Kinetic sorption was then simulated using these theoretically calculated k a and k d values, and the simulations were compared to the observed behavior. The simulations fit the observed sorbed concentrations better during the early part of the experiments; the observed sorption during later times occurred more slowly than expected, supporting the hypothesis that IPD becomes a rate-limiting process during the course of the experiment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Kinetic concepts of thermally stimulated reactions in solids

NASA Astrophysics Data System (ADS)

Vyazovkin, Sergey

Historical analysis suggests that the basic kinetic concepts of reactions in solids were inherited from homogeneous kinetics. These concepts rest upon the assumption of a single-step reaction that disagrees with the multiple-step nature of solid-state processes. The inadequate concepts inspire such unjustified anticipations of kinetic analysis as evaluating constant activation energy and/or deriving a single-step reaction mechanism for the overall process. A more adequate concept is that of the effective activation energy, which may vary with temperature and extent of conversion. The adequacy of this concept is illustrated by literature data as well as by experimental data on the thermal dehydration of calcium oxalate monohydrate and thermal decomposition of calcium carbonate, ammonium nitrate and 1,3,5,7- tetranitro-1,3,5,7-tetrazocine.

Kinetics modelling of Cu(II) biosorption on to coconut shell and Moringa oleifera seeds from tropical regions.

PubMed

Acheampong, Mike A; Pereira, Joana P C; Meulepas, Roel J W; Lens, Piet N L

2012-01-01

Adsorption kinetic studies are of great significance in evaluating the performance of a given adsorbent and gaining insight into the underlying mechanism. This work investigated the sorption kinetics of Cu(II) on to coconut shell and Moringa oleifera seeds using batch techniques. To understand the mechanisms of the biosorption process and the potential rate-controlling steps, kinetic models were used to fit the experimental data. The results indicate that kinetic data were best described by the pseudo-second-order model with correlation coefficients (R2) of 0.9974 and 0.9958 for the coconut shell and Moringa oleifera seeds, respectively. The initial sorption rates obtained for coconut shell and Moringa oleifera seeds were 9.6395 x 10(-3) and 8.3292 x 10(-2) mg g(-1) min(-1), respectively. The values of the mass transfer coefficients obtained for coconut shell (1.2106 x 10(-3) cm s(-1)) and Moringa oleifera seeds (8.965 x 10(-4) cm s(-1)) indicate that the transport of Cu(II) from the bulk liquid to the solid phase was quite fast for both materials investigated. The results indicate that intraparticle diffusion controls the rate of sorption in this study; however, film diffusion cannot be neglected, especially at the initial stage of sorption.

Identification of the most sensitive parameters in the activated sludge model implemented in BioWin software.

PubMed

Liwarska-Bizukojc, Ewa; Biernacki, Rafal

2010-10-01

In order to simulate biological wastewater treatment processes, data concerning wastewater and sludge composition, process kinetics and stoichiometry are required. Selection of the most sensitive parameters is an important step of model calibration. The aim of this work is to verify the predictability of the activated sludge model, which is implemented in BioWin software, and select its most influential kinetic and stoichiometric parameters with the help of sensitivity analysis approach. Two different measures of sensitivity are applied: the normalised sensitivity coefficient (S(i,j)) and the mean square sensitivity measure (delta(j)(msqr)). It occurs that 17 kinetic and stoichiometric parameters of the BioWin activated sludge (AS) model can be regarded as influential on the basis of S(i,j) calculations. Half of the influential parameters are associated with growth and decay of phosphorus accumulating organisms (PAOs). The identification of the set of the most sensitive parameters should support the users of this model and initiate the elaboration of determination procedures for the parameters, for which it has not been done yet. Copyright 2010 Elsevier Ltd. All rights reserved.

Ground Based Program for the Physical Analysis of Macromolecular Crystal Growth

NASA Technical Reports Server (NTRS)

Malkin, Alexander J.

1998-01-01

During the past year we have focused on application of in situ Atomic Force Microscopy (AFM) for studies of the growth mechanisms and kinetics of crystallization for different macromolecular systems. Mechanisms of macrostep formation and their decay, which are important in understanding of defect formation, were studied on the surfaces of thaumatin, catalase, canavalin and lysozyme crystals. Experiments revealed that step bunching on crystalline surfaces occurred either due to two- or three-dimensional nucleation on the terraces of vicinal slopes or as a result of uneven step generation by complex dislocation sources. No step bunching arising from interaction of individual steps in the course of the experiment was observed. The molecular structure of the growth steps for thaumatin and lipase crystals were deduced. It was further shown that growth step advance occurs by incorporation of single protein molecules. In singular directions growth steps move by one-dimensional nucleation on step edges followed by lateral growth. One-dimensional nuclei have different sizes, less then a single unit cell, varying for different directions of step movement. There is no roughness due to thermal fluctuations, and each protein molecule which incorporated into the step remained. Growth kinetics for catalase crystals was investigated over wide supersaturation ranges. Strong directional kinetic anisotropy in the tangential step growth rates in different directions was seen. The influence of impurities on growth kinetics and cessation of macromolecular crystals was studied. Thus, for catalase, in addition to pronounced impurity effects on the kinetics of crystallization, we were also able to directly observe adsorption of some impurities. At low supersaturation we repeatedly observed filaments which formed from impurity molecules sedimenting on the surfaces. Similar filaments were observed on the surfaces of thaumatin, canavalin and STMV crystals as well, but the frequency was low compared with catalase crystallization. Cessation of growth of xylanase and lysozyme crystals was also observed and appeared to be a consequence of the formation of dense impurity adsorption layers. Attachment: "An in situ AFM investigation of catalase crystallization", "Atomic force microscopy studies of living cells: visualization of motility, division, aggregation, transformation, and apoptosis", AFM studies on mechanisms of nucleation and growth of macromolecular crystals", and "In situ atomic force microscopy studies of surface morphology, growth kinetics, defect structure and dissolution in macromolecular crystallization".

Development of multi-metal interaction model for Daphnia magna: Significance of metallothionein in cellular redistribution.

PubMed

Wang, Xiangrui; Liu, Jianyu; Tan, Qiaoguo; Ren, Jinqian; Liang, Dingyuan; Fan, Wenhong

2018-04-30

Despite the great progress made in metal-induced toxicity mechanisms, a critical knowledge gap still exists in predicting adverse effects of heavy metals on living organisms in the natural environment, particularly during exposure to multi-metals. In this study, a multi-metal interaction model of Daphnia manga was developed in an effort to provide reasonable explanations regarding the joint effects resulting from exposure to multi-metals. Metallothionein (MT), a widely used biomarker, was selected. In this model, MT was supposed to play the role of a crucial transfer protein rather than detoxifying protein. Therefore, competitive complexation of metals to MT could highly affect the cellular metal redistribution. Thus, competitive complexation of MT in D. magna with metals like Pb 2+ , Cd 2+ and Cu 2+ was qualitatively studied. The results suggested that Cd 2+ had the highest affinity towards MT, followed by Pb 2+ and Cu 2+ . On the other hand, the combination of MT with Cu 2+ appeared to alter its structure which resulted in higher affinity towards Pb 2+ . Overall, the predicted bioaccumulation of metals under multi-metal exposure was consisted with earlier reported studies. This model provided an alternative angle for joint effect through a combination of kinetic process and internal interactions, which could help to develop future models predicting toxicity to multi-metal exposure. Copyright © 2017 Elsevier Inc. All rights reserved.

Uncertainty analysis of multi-rate kinetics of uranium desorption from sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xiaoying; Liu, Chongxuan; Hu, Bill X.

2014-01-01

A multi-rate expression for uranyl [U(VI)] surface complexation reactions has been proposed to describe diffusion-limited U(VI) sorption/desorption in heterogeneous subsurface sediments. An important assumption in the rate expression is that its rate constants follow a certain type probability distribution. In this paper, a Bayes-based, Differential Evolution Markov Chain method was used to assess the distribution assumption and to analyze parameter and model structure uncertainties. U(VI) desorption from a contaminated sediment at the US Hanford 300 Area, Washington was used as an example for detail analysis. The results indicated that: 1) the rate constants in the multi-rate expression contain uneven uncertaintiesmore » with slower rate constants having relative larger uncertainties; 2) the lognormal distribution is an effective assumption for the rate constants in the multi-rate model to simualte U(VI) desorption; 3) however, long-term prediction and its uncertainty may be significantly biased by the lognormal assumption for the smaller rate constants; and 4) both parameter and model structure uncertainties can affect the extrapolation of the multi-rate model with a larger uncertainty from the model structure. The results provide important insights into the factors contributing to the uncertainties of the multi-rate expression commonly used to describe the diffusion or mixing-limited sorption/desorption of both organic and inorganic contaminants in subsurface sediments.« less

Process optimization and kinetics of biodiesel production from neem oil using copper doped zinc oxide heterogeneous nanocatalyst.

PubMed

Gurunathan, Baskar; Ravi, Aiswarya

2015-08-01

Heterogeneous nanocatalyst has become the choice of researchers for better transesterification of vegetable oils to biodiesel. In the present study, transesterification reaction was optimized and kinetics was studied for biodiesel production from neem oil using CZO nanocatalyst. The highly porous and non-uniform surface of the CZO nanocatalyst was confirmed by AFM analysis, which leads to the aggregation of CZO nanoparticles in the form of multi layered nanostructures. The 97.18% biodiesel yield was obtained in 60min reaction time at 55°C using 10% (w/w) CZO nanocatalyst and 1:10 (v:v) oil:methanol ratio. Biodiesel yield of 73.95% was obtained using recycled nanocatalyst in sixth cycle. The obtained biodiesel was confirmed using GC-MS and (1)H NMR analysis. Reaction kinetic models were tested on biodiesel production, first order kinetic model was found fit with experimental data (R(2)=0.9452). The activation energy of 233.88kJ/mol was required for transesterification of neem oil into biodiesel using CZO nanocatalyst. Copyright © 2015 Elsevier Ltd. All rights reserved.

An analysis of artificial viscosity effects on reacting flows using a spectral multi-domain technique

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.; Streett, C. L.; Hussaini, M. Y.

1987-01-01

Standard techniques used to model chemically-reacting flows require an artificial viscosity for stability in the presence of strong shocks. The resulting shock is smeared over at least three computational cells, so that the thickness of the shock is dictated by the structure of the overall mesh and not the shock physics. A gas passing through a strong shock is thrown into a nonequilibrium state and subsequently relaxes down over some finite distance to an equilibrium end state. The artificial smearing of the shock envelops this relaxation zone which causes the chemical kinetics of the flow to be altered. A method is presented which can investigate these issues by following the chemical kinetics and flow kinetics of a gas passing through a fully resolved shock wave at hypersonic Mach numbers. A nonequilibrium chemistry model for air is incorporated into a spectral multidomain Navier-Stokes solution method. Since no artificial viscosity is needed for stability of the multidomain technique, the precise effect of this artifice on the chemical kinetics and relevant flow features can be determined.

Methodology for extracting local constants from petroleum cracking flows

DOEpatents

Chang, Shen-Lin; Lottes, Steven A.; Zhou, Chenn Q.

2000-01-01

A methodology provides for the extraction of local chemical kinetic model constants for use in a reacting flow computational fluid dynamics (CFD) computer code with chemical kinetic computations to optimize the operating conditions or design of the system, including retrofit design improvements to existing systems. The coupled CFD and kinetic computer code are used in combination with data obtained from a matrix of experimental tests to extract the kinetic constants. Local fluid dynamic effects are implicitly included in the extracted local kinetic constants for each particular application system to which the methodology is applied. The extracted local kinetic model constants work well over a fairly broad range of operating conditions for specific and complex reaction sets in specific and complex reactor systems. While disclosed in terms of use in a Fluid Catalytic Cracking (FCC) riser, the inventive methodology has application in virtually any reaction set to extract constants for any particular application and reaction set formulation. The methodology includes the step of: (1) selecting the test data sets for various conditions; (2) establishing the general trend of the parametric effect on the measured product yields; (3) calculating product yields for the selected test conditions using coupled computational fluid dynamics and chemical kinetics; (4) adjusting the local kinetic constants to match calculated product yields with experimental data; and (5) validating the determined set of local kinetic constants by comparing the calculated results with experimental data from additional test runs at different operating conditions.

A two-column formalism for time-dependent modelling of stellar convection. I. Description of the method

NASA Astrophysics Data System (ADS)

Stökl, A.

2008-11-01

Context: In spite of all the advances in multi-dimensional hydrodynamics, investigations of stellar evolution and stellar pulsations still depend on one-dimensional computations. This paper devises an alternative to the mixing-length theory or turbulence models usually adopted in modelling convective transport in such studies. Aims: The present work attempts to develop a time-dependent description of convection, which reflects the essential physics of convection and that is only moderately dependent on numerical parameters and far less time consuming than existing multi-dimensional hydrodynamics computations. Methods: Assuming that the most extensive convective patterns generate the majority of convective transport, the convective velocity field is described using two parallel, radial columns to represent up- and downstream flows. Horizontal exchange, in the form of fluid flow and radiation, over their connecting interface couples the two columns and allows a simple circulating motion. The main parameters of this convective description have straightforward geometrical meanings, namely the diameter of the columns (corresponding to the size of the convective cells) and the ratio of the cross-section between up- and downdrafts. For this geometrical setup, the time-dependent solution of the equations of radiation hydrodynamics is computed from an implicit scheme that has the advantage of being unaffected by the Courant-Friedrichs-Lewy time-step limit. This implementation is part of the TAPIR-Code (short for The adaptive, implicit RHD-Code). Results: To demonstrate the approach, results for convection zones in Cepheids are presented. The convective energy transport and convective velocities agree with expectations for Cepheids and the scheme reproduces both the kinetic energy flux and convective overshoot. A study of the parameter influence shows that the type of solution derived for these stars is in fact fairly robust with respect to the constitutive numerical parameters.

Accurate prediction of vaccine stability under real storage conditions and during temperature excursions.

PubMed

Clénet, Didier

2018-04-01

Due to their thermosensitivity, most vaccines must be kept refrigerated from production to use. To successfully carry out global immunization programs, ensuring the stability of vaccines is crucial. In this context, two important issues are critical, namely: (i) predicting vaccine stability and (ii) preventing product damage due to excessive temperature excursions outside of the recommended storage conditions (cold chain break). We applied a combination of advanced kinetics and statistical analyses on vaccine forced degradation data to accurately describe the loss of antigenicity for a multivalent freeze-dried inactivated virus vaccine containing three variants. The screening of large amounts of kinetic models combined with a statistical model selection approach resulted in the identification of two-step kinetic models. Predictions based on kinetic analysis and experimental stability data were in agreement, with approximately five percentage points difference from real values for long-term stability storage conditions, after excursions of temperature and during experimental shipments of freeze-dried products. Results showed that modeling a few months of forced degradation can be used to predict various time and temperature profiles endured by vaccines, i.e. long-term stability, short time excursions outside the labeled storage conditions or shipments at ambient temperature, with high accuracy. Pharmaceutical applications of the presented kinetics-based approach are discussed. Copyright © 2018 The Author. Published by Elsevier B.V. All rights reserved.

Look and Feel: Haptic Interaction for Biomedicine

DTIC Science & Technology

1995-10-01

algorithm that is evaluated within the topology of the model. During each time step, forces are summed for each mobile atom based on external forces...volumetric properties; (b) conserving computation power by rendering media local to the interaction point; and (c) evaluating the simulation within...alteration of the model topology. Simulation of the DSM state is accomplished by a multi-step algorithm that is evaluated within the topology of the

Degree of time dependency of kinetic coefficient as a function of adsorbate concentration; new insights from adsorption of tetracycline onto monodispersed starch-stabilized magnetic nanocomposite.

PubMed

Okoli, Chukwunonso P; Ofomaja, Augustine E

2018-07-15

The realization that the observed kinetic coefficient (k obs ) varies with time in most real-time adsorption system, as against the constant value conceived in the most widely-applied adsorption kinetic models, have attracted much attention in recent time. Understanding the factors that control the extent/degree of time dependency (otherwise known as fractal-like kinetics), is therefore central in taking manipulative advantage of this phenomenon in critical adsorption applications. This study therefore deployed non-fractal-like and fractal-like kinetic approach to study the adsorption of tetracycline on monodispersed starch-stabilized magnetite nanocomposite (MSM). MSM was synthesized by in-situ coprecipitation of magnetite in the presence of starch, and successfully characterized with classical solid-state techniques. Isotherm studies indicated that MSM has heterogenous surface adsorption sites. Equilibrium and kinetic data indicated the existence of π-cation interaction as the underlying mechanism, while pH study revealed that tetracycline was adsorbed in its zwitterion form. Though the non-fractal kinetic models exhibited some level of relevance in explaining the tetracycline adsorption interactions, the best fitting of the fractal-like pseudo second order model to the adsorption kinetic data, indicated that the real-time adsorption kinetics occurred in fractal-like manner. The study also revealed that the degree of time dependency of k obs had negative correlation with the initial tetracycline concentration. Apart from developing a low-cost strategy for addressing tetracycline water pollution, the result of this study serves a positive step towards gaining manipulative control of adsorption mechanism in potential application of MSM for targeted drug delivery and controlled release of tetracycline antibiotics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation

NASA Astrophysics Data System (ADS)

Jung, Jaewoon; Kobayashi, Chigusa; Sugita, Yuji

2018-04-01

In molecular dynamics (MD) simulations, a proper definition of kinetic energy is essential for controlling pressure as well as temperature in the isothermal-isobaric condition. The virial theorem provides an equation that connects the average kinetic energy with the product of particle coordinate and force. In this paper, we show that the theorem is satisfied in MD simulations with a larger time step and holonomic constraints of bonds, only when a proper definition of kinetic energy is used. We provide a novel definition of kinetic energy, which is calculated from velocities at the half-time steps (t - Δt/2 and t + Δt/2) in the velocity Verlet integration method. MD simulations of a 1,2-dispalmitoyl-sn-phosphatidylcholine (DPPC) lipid bilayer and a water box using the kinetic energy definition could reproduce the physical properties in the isothermal-isobaric condition properly. We also develop a multiple time step (MTS) integration scheme with the kinetic energy definition. MD simulations with the MTS integration for the DPPC and water box systems provided the same quantities as the velocity Verlet integration method, even when the thermostat and barostat are updated less frequently.

Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation.

PubMed

Jung, Jaewoon; Kobayashi, Chigusa; Sugita, Yuji

2018-04-28

In molecular dynamics (MD) simulations, a proper definition of kinetic energy is essential for controlling pressure as well as temperature in the isothermal-isobaric condition. The virial theorem provides an equation that connects the average kinetic energy with the product of particle coordinate and force. In this paper, we show that the theorem is satisfied in MD simulations with a larger time step and holonomic constraints of bonds, only when a proper definition of kinetic energy is used. We provide a novel definition of kinetic energy, which is calculated from velocities at the half-time steps (t - Δt/2 and t + Δt/2) in the velocity Verlet integration method. MD simulations of a 1,2-dispalmitoyl-sn-phosphatidylcholine (DPPC) lipid bilayer and a water box using the kinetic energy definition could reproduce the physical properties in the isothermal-isobaric condition properly. We also develop a multiple time step (MTS) integration scheme with the kinetic energy definition. MD simulations with the MTS integration for the DPPC and water box systems provided the same quantities as the velocity Verlet integration method, even when the thermostat and barostat are updated less frequently.

Probabilistic parameter estimation in a 2-step chemical kinetics model for n-dodecane jet autoignition

NASA Astrophysics Data System (ADS)

Hakim, Layal; Lacaze, Guilhem; Khalil, Mohammad; Sargsyan, Khachik; Najm, Habib; Oefelein, Joseph

2018-05-01

This paper demonstrates the development of a simple chemical kinetics model designed for autoignition of n-dodecane in air using Bayesian inference with a model-error representation. The model error, i.e. intrinsic discrepancy from a high-fidelity benchmark model, is represented by allowing additional variability in selected parameters. Subsequently, we quantify predictive uncertainties in the results of autoignition simulations of homogeneous reactors at realistic diesel engine conditions. We demonstrate that these predictive error bars capture model error as well. The uncertainty propagation is performed using non-intrusive spectral projection that can also be used in principle with larger scale computations, such as large eddy simulation. While the present calibration is performed to match a skeletal mechanism, it can be done with equal success using experimental data only (e.g. shock-tube measurements). Since our method captures the error associated with structural model simplifications, we believe that the optimised model could then lead to better qualified predictions of autoignition delay time in high-fidelity large eddy simulations than the existing detailed mechanisms. This methodology provides a way to reduce the cost of reaction kinetics in simulations systematically, while quantifying the accuracy of predictions of important target quantities.

Molecular details of dimerization kinetics reveal negligible populations of transient µ-opioid receptor homodimers at physiological concentrations.

PubMed

Meral, Derya; Provasi, Davide; Prada-Gracia, Diego; Möller, Jan; Marino, Kristen; Lohse, Martin J; Filizola, Marta

2018-05-16

Various experimental and computational techniques have been employed over the past decade to provide structural and thermodynamic insights into G Protein-Coupled Receptor (GPCR) dimerization. Here, we use multiple microsecond-long, coarse-grained, biased and unbiased molecular dynamics simulations (a total of ~4 milliseconds) combined with multi-ensemble Markov state models to elucidate the kinetics of homodimerization of a prototypic GPCR, the µ-opioid receptor (MOR), embedded in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/cholesterol lipid bilayer. Analysis of these computations identifies kinetically distinct macrostates comprising several different short-lived dimeric configurations of either inactive or activated MOR. Calculated kinetic rates and fractions of dimers at different MOR concentrations suggest a negligible population of MOR homodimers at physiological concentrations, which is supported by acceptor photobleaching fluorescence resonance energy transfer (FRET) experiments. This study provides a rigorous, quantitative explanation for some conflicting experimental data on GPCR oligomerization.

A multidimensional unified gas-kinetic scheme for radiative transfer equations on unstructured mesh

NASA Astrophysics Data System (ADS)

Sun, Wenjun; Jiang, Song; Xu, Kun

2017-12-01

In order to extend the unified gas kinetic scheme (UGKS) to solve radiative transfer equations in a complex geometry, a multidimensional asymptotic preserving implicit method on unstructured mesh is constructed in this paper. With an implicit formulation, the CFL condition for the determination of the time step in UGKS can be much relaxed, and a large time step is used in simulations. Differently from previous direction-by-direction UGKS on orthogonal structured mesh, on unstructured mesh the interface flux transport takes into account multi-dimensional effect, where gradients of radiation intensity and material temperature in both normal and tangential directions of a cell interface are included in the flux evaluation. The multiple scale nature makes the UGKS be able to capture the solutions in both optically thin and thick regions seamlessly. In the optically thick region the condition of cell size being less than photon's mean free path is fully removed, and the UGKS recovers a solver for diffusion equation in such a limit on unstructured mesh. For a distorted quadrilateral mesh, the UGKS goes to a nine-point scheme for the diffusion equation, and it naturally reduces to the standard five-point scheme for a orthogonal quadrilateral mesh. Numerical computations covering a wide range of transport regimes on unstructured and distorted quadrilateral meshes will be presented to validate the current approach.

Theoretical Basis for Estimated Test Times and Conditions for Drop Tower and Space-Based Droplet Burning Experiments With Methanol and N-Heptane

NASA Technical Reports Server (NTRS)

Marchese, Anthony J.; Dryer, Fredrick L.; Choi, Mun Y.

1994-01-01

In order to develop an extensive envelope of test conditions for NASA's space-based Droplet Combustion Experiment (DCE) as well those droplet experiments which can be performed using a drop tower, the transient vaporization and combustion of methanol and n-heptane droplets were simulated using a recently developed fully time-dependent, spherically symmetric droplet combustion model. The transient vaporization of methanol and n-heptane was modeled to characterize the instantaneous gas phase composition surrounding the droplet prior to the introduction of an ignition source. The results for methanol/air showed that the entire gas phase surrounding a 2 mm methanol droplet deployed in zero-g .quickly falls outside the lean flammability limit. The gas phase surrounding an identically-sized n-heptane droplet, on the other hand, remains flammable. The combustion of methanol was then modeled considering a detailed gas phase chemical kinetic mechanism (168 steps, 26 species) and the effect of the dissolution of flame-generated water into the liquid droplet. These results were used to determine the critical ignition diameter required to achieve quasi-steady droplet combustion in a given oxidizing environment. For droplet diameters greater than the critical ignition diameter, the model predicted a finite diameter at which the flame would extinguish. These extinction diameters were found to vary significantly with initial droplet diameter. This phenomenon appears to be unique to the transient heat transfer, mass transfer and chemical kinetics of the system and thus has not been reported elsewhere to date. The extinction diameter was also shown to vary significantly with the liquid phase Lewis number since the amount of water present in the droplet at extinction is largely governed by the rate at which water is transported into the droplet via mass diffusion. Finally, the numerical results for n-heptane combustion were obtained using both 2 step and 96 step semi-emperical chemical kinetic mechanisms. Neither mechanism exhibited the variation of extinction diameter with initial diameter.

A hybrid constructed wetland for organic-material and nutrient removal from sewage: Process performance and multi-kinetic models.

PubMed

Nguyen, X Cuong; Chang, S Woong; Nguyen, Thi Loan; Ngo, H Hao; Kumar, Gopalakrishnan; Banu, J Rajesh; Vu, M Cuong; Le, H Sinh; Nguyen, D Duc

2018-09-15

A pilot-scale hybrid constructed wetland with vertical flow and horizontal flow in series was constructed and used to investigate organic material and nutrient removal rate constants for wastewater treatment and establish a practical predictive model for use. For this purpose, the performance of multiple parameters was statistically evaluated during the process and predictive models were suggested. The measurement of the kinetic rate constant was based on the use of the first-order derivation and Monod kinetic derivation (Monod) paired with a plug flow reactor (PFR) and a continuously stirred tank reactor (CSTR). Both the Lindeman, Merenda, and Gold (LMG) analysis and Bayesian model averaging (BMA) method were employed for identifying the relative importance of variables and their optimal multiple regression (MR). The results showed that the first-order-PFR (M 2 ) model did not fit the data (P > 0.05, and R 2  < 0.5), whereas the first-order-CSTR (M 1 ) model for the chemical oxygen demand (COD Cr ) and Monod-CSTR (M 3 ) model for the COD Cr and ammonium nitrogen (NH 4 -N) showed a high correlation with the experimental data (R 2  > 0.5). The pollutant removal rates in the case of M 1 were 0.19 m/d (COD Cr ) and those for M 3 were 25.2 g/m 2 ∙d for COD Cr and 2.63 g/m 2 ∙d for NH 4 -N. By applying a multi-variable linear regression method, the optimal empirical models were established for predicting the final effluent concentration of five days' biochemical oxygen demand (BOD 5 ) and NH 4 -N. In general, the hydraulic loading rate was considered an important variable having a high value of relative importance, which appeared in all the optimal predictive models. Copyright © 2018 Elsevier Ltd. All rights reserved.

Simulating the Response of a Composite Honeycomb Energy Absorber. Part 1; Dynamic Crushing of Components and Multi-Terrain Impacts

NASA Technical Reports Server (NTRS)

Jackson, Karen E.; Fasanella, Edwin L.; Polanco, Michael A.

2012-01-01

This paper describes the experimental and analytical evaluation of an externally deployable composite honeycomb structure that is designed to attenuate impact energy during helicopter crashes. The concept, designated the Deployable Energy Absorber (DEA), utilizes an expandable Kevlar (Registered Trademark) honeycomb to dissipate kinetic energy through crushing. The DEA incorporates a unique flexible hinge design that allows the honeycomb to be packaged and stowed until needed for deployment. Experimental evaluation of the DEA included dynamic crush tests of multi-cell components and vertical drop tests of a composite fuselage section, retrofitted with DEA blocks, onto multi-terrain. Finite element models of the test articles were developed and simulations were performed using the transient dynamic code, LSDYNA (Registered Trademark). In each simulation, the DEA was represented using shell elements assigned two different material properties: Mat 24, an isotropic piecewise linear plasticity model, and Mat 58, a continuum damage mechanics model used to represent laminated composite fabrics. DEA model development and test-analysis comparisons are presented.

Kinetic Model of the Initial Stage of the Nanowire Growth

NASA Astrophysics Data System (ADS)

Filimonov, S. N.; Hervieu, Yu. Yu.

2018-03-01

A kinetic model of the formation of pyramid-like bulges (pedestals) at the bases of vertical nanowires is proposed. The formation of the pedestals at the early stage of the nanowire growth is assumed to be induced by a higher nucleation rate of two-dimensional islands under the catalyst droplet, as compared to the nucleation rate at the non-activated surface areas. Kinetics of the nucleation and propagation of the steps in the pyramid is described with a model of the multilayer growth, taking into account that the catalyst droplet at the nanowire top is a strong sink for adatoms. It is shown that the transition from the growth of the pyramid to the axial growth of the nanowire is possible if the appearance of a nucleus of the new layer under the catalyst droplet results in a partial dissolution of the underlying layer. In this case a segment of the nanowire sidewall is formed, preventing the lateral growth of the layers generated by the droplet.

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

NASA Astrophysics Data System (ADS)

Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.

2016-06-01

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

The comparative kinetic analysis of Acetocell and Lignoboost® lignin pyrolysis: the estimation of the distributed reactivity models.

PubMed

Janković, Bojan

2011-10-01

The non-isothermal pyrolysis kinetics of Acetocell (the organosolv) and Lignoboost® (kraft) lignins, in an inert atmosphere, have been studied by thermogravimetric analysis. Using isoconversional analysis, it was concluded that the apparent activation energy for all lignins strongly depends on conversion, showing that the pyrolysis of lignins is not a single chemical process. It was identified that the pyrolysis process of Acetocell and Lignoboost® lignin takes place over three reaction steps, which was confirmed by appearance of the corresponding isokinetic relationships (IKR). It was found that major pyrolysis stage of both lignins is characterized by stilbene pyrolysis reactions, which were subsequently followed by decomposition reactions of products derived from the stilbene pyrolytic process. It was concluded that non-isothermal pyrolysis of Acetocell and Lignoboost® lignins can be best described by n-th (n>1) reaction order kinetics, using the Weibull mixture model (as distributed reactivity model) with alternating shape parameters. Copyright © 2011 Elsevier Ltd. All rights reserved.

A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics.

PubMed

Chapman, Brian

2017-06-01

This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis-Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis- substrate binding, cis → trans bound enzyme shuttling, trans -substrate dissociation and trans → cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive 'tuning' of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force-flux relations, with only a minority of cases having their quasi -linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically 'tuned' to its particular task, dependent on the cis- and trans- substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport.

A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics

PubMed Central

2017-01-01

This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis–Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis-substrate binding, cis→trans bound enzyme shuttling, trans-substrate dissociation and trans→cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive ‘tuning’ of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force–flux relations, with only a minority of cases having their quasi-linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically ‘tuned’ to its particular task, dependent on the cis- and trans-substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport. PMID:28680687

Multi-equilibrium property of metabolic networks: SSI module.

PubMed

Lei, Hong-Bo; Zhang, Ji-Feng; Chen, Luonan

2011-06-20

Revealing the multi-equilibrium property of a metabolic network is a fundamental and important topic in systems biology. Due to the complexity of the metabolic network, it is generally a difficult task to study the problem as a whole from both analytical and numerical viewpoint. On the other hand, the structure-oriented modularization idea is a good choice to overcome such a difficulty, i.e. decomposing the network into several basic building blocks and then studying the whole network through investigating the dynamical characteristics of the basic building blocks and their interactions. Single substrate and single product with inhibition (SSI) metabolic module is one type of the basic building blocks of metabolic networks, and its multi-equilibrium property has important influence on that of the whole metabolic networks. In this paper, we describe what the SSI metabolic module is, characterize the rates of the metabolic reactions by Hill kinetics and give a unified model for SSI modules by using a set of nonlinear ordinary differential equations with multi-variables. Specifically, a sufficient and necessary condition is first given to describe the injectivity of a class of nonlinear systems, and then, the sufficient condition is used to study the multi-equilibrium property of SSI modules. As a main theoretical result, for the SSI modules in which each reaction has no more than one inhibitor, a sufficient condition is derived to rule out multiple equilibria, i.e. the Jacobian matrix of its rate function is nonsingular everywhere. In summary, we describe SSI modules and give a general modeling framework based on Hill kinetics, and provide a sufficient condition for ruling out multiple equilibria of a key type of SSI module.

Multi-equilibrium property of metabolic networks: SSI module

PubMed Central

2011-01-01

Background Revealing the multi-equilibrium property of a metabolic network is a fundamental and important topic in systems biology. Due to the complexity of the metabolic network, it is generally a difficult task to study the problem as a whole from both analytical and numerical viewpoint. On the other hand, the structure-oriented modularization idea is a good choice to overcome such a difficulty, i.e. decomposing the network into several basic building blocks and then studying the whole network through investigating the dynamical characteristics of the basic building blocks and their interactions. Single substrate and single product with inhibition (SSI) metabolic module is one type of the basic building blocks of metabolic networks, and its multi-equilibrium property has important influence on that of the whole metabolic networks. Results In this paper, we describe what the SSI metabolic module is, characterize the rates of the metabolic reactions by Hill kinetics and give a unified model for SSI modules by using a set of nonlinear ordinary differential equations with multi-variables. Specifically, a sufficient and necessary condition is first given to describe the injectivity of a class of nonlinear systems, and then, the sufficient condition is used to study the multi-equilibrium property of SSI modules. As a main theoretical result, for the SSI modules in which each reaction has no more than one inhibitor, a sufficient condition is derived to rule out multiple equilibria, i.e. the Jacobian matrix of its rate function is nonsingular everywhere. Conclusions In summary, we describe SSI modules and give a general modeling framework based on Hill kinetics, and provide a sufficient condition for ruling out multiple equilibria of a key type of SSI module. PMID:21689474

Multi-step-ahead crude oil price forecasting using a hybrid grey wave model

NASA Astrophysics Data System (ADS)

Chen, Yanhui; Zhang, Chuan; He, Kaijian; Zheng, Aibing

2018-07-01

Crude oil is crucial to the operation and economic well-being of the modern society. Huge changes of crude oil price always cause panics to the global economy. There are many factors influencing crude oil price. Crude oil price prediction is still a difficult research problem widely discussed among researchers. Based on the researches on Heterogeneous Market Hypothesis and the relationship between crude oil price and macroeconomic factors, exchange market, stock market, this paper proposes a hybrid grey wave forecasting model, which combines Random Walk (RW)/ARMA to forecast multi-step-ahead crude oil price. More specifically, we use grey wave forecasting model to model the periodical characteristics of crude oil price and ARMA/RW to simulate the daily random movements. The innovation also comes from using the information of the time series graph to forecast crude oil price, since grey wave forecasting is a graphical prediction method. The empirical results demonstrate that based on the daily data of crude oil price, the hybrid grey wave forecasting model performs well in 15- to 20-step-ahead prediction and it always dominates ARMA and Random Walk in correct direction prediction.

SPECIFYING PHYSIOLOGICAL PARAMETERS FOR THE KINETICS OF INHALED TOLUENE IN RATS PERFORMING THE VISUAL SIGNAL DETECTION TASK (SDT).

EPA Science Inventory

A physiologically-based pharmacokinetic (PBPK) model is being developed to estimate the dosimetry of toluene in rats inhaling the VOC under various experimental conditions. The effects of physical activity are currently being estimated utilizing a three-step process. First, we d...

Pressure Modeling of Char-Forming and Laminated Materials.

DTIC Science & Technology

1983-06-01

flame spread rates for various types of materials. For instance, the PMMA fuel used for the laminated wall fires in the present study has a pyroly - sis...thermal conduction and pyroly - sis with one-step Arrhenius kinetics. This numerical procedure is documented in detail in Appendix A, which is taken from

Isoconversional approach for non-isothermal decomposition of un-irradiated and photon-irradiated 5-fluorouracil.

PubMed

Mohamed, Hala Sh; Dahy, AbdelRahman A; Mahfouz, Refaat M

2017-10-25

Kinetic analysis for the non-isothermal decomposition of un-irradiated and photon-beam-irradiated 5-fluorouracil (5-FU) as anti-cancer drug, was carried out in static air. Thermal decomposition of 5-FU proceeds in two steps. One minor step in the temperature range of (270-283°C) followed by the major step in the temperature range of (285-360°C). The non-isothermal data for un-irradiated and photon-irradiated 5-FU were analyzed using linear (Tang) and non-linear (Vyazovkin) isoconversional methods. The results of the application of these free models on the present kinetic data showed quite a dependence of the activation energy on the extent of conversion. For un-irradiated 5-FU, the non-isothermal data analysis indicates that the decomposition is generally described by A3 and A4 modeles for the minor and major decomposition steps, respectively. For a photon-irradiated sample of 5-FU with total absorbed dose of 10Gy, the decomposition is controlled by A2 model throughout the coversion range. The activation energies calculated in case of photon-irradiated 5-FU were found to be lower compared to the values obtained from the thermal decomposition of the un-irradiated sample probably due to the formation of additional nucleation sites created by a photon-irradiation. The decomposition path was investigated by intrinsic reaction coordinate (IRC) at the B3LYP/6-311++G(d,p) level of DFT. Two transition states were involved in the process by homolytic rupture of NH bond and ring secession, respectively. Published by Elsevier B.V.

Particle-In-Cell Modeling For MJ Dense Plasma Focus with Varied Anode Shape

NASA Astrophysics Data System (ADS)

Link, A.; Halvorson, C.; Schmidt, A.; Hagen, E. C.; Rose, D.; Welch, D.

2014-10-01

Megajoule scale dense plasma focus (DPF) Z-pinches with deuterium gas fill are compact devices capable of producing 1012 neutrons per shot but past predictive models of large-scale DPF have not included kinetic effects such as ion beam formation or anomalous resistivity. We report on progress of developing a predictive DPF model by extending our 2D axisymmetric collisional kinetic particle-in-cell (PIC) simulations to the 1 MJ, 2 MA Gemini DPF using the PIC code LSP. These new simulations incorporate electrodes, an external pulsed-power driver circuit, and model the plasma from insulator lift-off through the pinch phase. The simulations were performed using a new hybrid fluid-to-kinetic model transitioning from a fluid description to a fully kinetic PIC description during the run-in phase. Simulations are advanced through the final pinch phase using an adaptive variable time-step to capture the fs and sub-mm scales of the kinetic instabilities involved in the ion beam formation and neutron production. Results will be present on the predicted effects of different anode configurations. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory (LLNL) under Contract DE-AC52-07NA27344 and supported by the Laboratory Directed Research and Development Program (11-ERD-063) and the Computing Grand Challenge program at LLNL. This work supported by Office of Defense Nuclear Nonproliferation Research and Development within U.S. Department of Energy's National Nuclear Security Administration.

Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range

PubMed Central

Ventura, Alejandra C.; Bush, Alan; Vasen, Gustavo; Goldín, Matías A.; Burkinshaw, Brianne; Bhattacharjee, Nirveek; Folch, Albert; Brent, Roger; Chernomoretz, Ariel; Colman-Lerner, Alejandro

2014-01-01

Cell signaling systems sense and respond to ligands that bind cell surface receptors. These systems often respond to changes in the concentration of extracellular ligand more rapidly than the ligand equilibrates with its receptor. We demonstrate, by modeling and experiment, a general “systems level” mechanism cells use to take advantage of the information present in the early signal, before receptor binding reaches a new steady state. This mechanism, pre-equilibrium sensing and signaling (PRESS), operates in signaling systems in which the kinetics of ligand-receptor binding are slower than the downstream signaling steps, and it typically involves transient activation of a downstream step. In the systems where it operates, PRESS expands and shifts the input dynamic range, allowing cells to make different responses to ligand concentrations so high as to be otherwise indistinguishable. Specifically, we show that PRESS applies to the yeast directional polarization in response to pheromone gradients. Consideration of preexisting kinetic data for ligand-receptor interactions suggests that PRESS operates in many cell signaling systems throughout biology. The same mechanism may also operate at other levels in signaling systems in which a slow activation step couples to a faster downstream step. PMID:25172920

A solvable model of Vlasov-kinetic plasma turbulence in Fourier-Hermite phase space

NASA Astrophysics Data System (ADS)

Adkins, T.; Schekochihin, A. A.

2018-02-01

A class of simple kinetic systems is considered, described by the one-dimensional Vlasov-Landau equation with Poisson or Boltzmann electrostatic response and an energy source. Assuming a stochastic electric field, a solvable model is constructed for the phase-space turbulence of the particle distribution. The model is a kinetic analogue of the Kraichnan-Batchelor model of chaotic advection. The solution of the model is found in Fourier-Hermite space and shows that the free-energy flux from low to high Hermite moments is suppressed, with phase mixing cancelled on average by anti-phase-mixing (stochastic plasma echo). This implies that Landau damping is an ineffective route to dissipation (i.e. to thermalisation of electric energy via velocity space). The full Fourier-Hermite spectrum is derived. Its asymptotics are -3/2$ at low wavenumbers and high Hermite moments ( ) and -1/2k-2$ at low Hermite moments and high wavenumbers ( ). These conclusions hold at wavenumbers below a certain cutoff (analogue of Kolmogorov scale), which increases with the amplitude of the stochastic electric field and scales as inverse square of the collision rate. The energy distribution and flows in phase space are a simple and, therefore, useful example of competition between phase mixing and nonlinear dynamics in kinetic turbulence, reminiscent of more realistic but more complicated multi-dimensional systems that have not so far been amenable to complete analytical solution.

A new 3D multi-fluid model: a study of kinetic effects and variations of physical conditions in the cometary coma

NASA Astrophysics Data System (ADS)

Shou, Yinsi; Combi, Michael R.; Toth, Gabor; Huang, Zhenguang; Jia, Xianzhe; Fougere, Nicolas; Tenishev, Valeriy; Gombosi, T. I.; Hansen, Kenneth C.; Bieler, Andre

2016-10-01

Physics-based numerical coma models are desirable whether to interpret the spacecraft observations of the inner coma or to compare with the ground-based observations of the outer coma. In this work, we develop a multi-neutral-fluid model based on BATS-R-US in the University of Michigan's SWMF (Space Weather Modeling Framework), which is capable of computing both the inner and the outer coma and simulating time-variable phenomena. It treats H2O, OH, H2, O, and H as separate fluids and each fluid has its own velocity and temperature, with collisions coupling all fluids together. The self-consistent collisional interactions decrease the velocity differences, re-distribute the excess energy deposited by chemical reactions among all species, and account for the varying heating efficiency under various physical conditions. Recognizing that the fluid approach has limitations in capturing all of the correct physics for certain applications, especially for very low density environment, we applied our multi-fluid coma model to comet 67P/Churyumov-Gerasimenko (CG) at various heliocentric distances and demonstrated that it is able to yield comparable results as the Direct Simulation Monte Carlo (DSMC) model, which is based on a kinetic approach that is valid under these conditions. Therefore, our model may be a powerful alternative to the particle-based model, especially for some computationally intensive simulations. In addition, by running the model with several combinations of production rates and heliocentric distances, we can characterize the cometary H2O expansion speeds and demonstrate the nonlinear effect of production rates or photochemical heating. Our results are also compared to previous modeling work (e.g., Bockelee-Morvan & Crovisier 1987) and remote observations (e.g., Tseng et al. 2007), which serve as further validation of our model. This work has been partially supported by grant NNX14AG84G from the NASA Planetary Atmospheres Program, and US Rosetta contracts JPL #1266313, JPL #1266314 and JPL #1286489.

Hot kinetic model as a guide to improve organic photovoltaic materials.

PubMed

Sosorev, Andrey Yu; Godovsky, Dmitry Yu; Paraschuk, Dmitry Yu

2018-01-31

The modeling of organic solar cells (OSCs) can provide a roadmap for their further improvement. Many OSC models have been proposed in recent years; however, the impact of the key intermediates from photons to electricity-hot charge-transfer (CT) states-on the OSC efficiency is highly ambiguous. In this study, we suggest an analytical kinetic model for OSC that considers a two-step charge generation via hot CT states. This hot kinetic model allowed us to evaluate the impact of different material parameters on the OSC performance: the driving force for charge separation, optical bandgap, charge mobility, geminate recombination rate, thermalization rate, average electron-hole separation distance in the CT state, dielectric permittivity, reorganization energy and charge delocalization. In contrast to a widespread trend of lowering the material bandgap, the model predicts that this approach is only efficient along with improvement of the other material properties. The most promising ways to increase the OSC performance are decreasing the reorganization energy, i.e., an energy change accompanying CT from the donor molecule to the acceptor, increasing the dielectric permittivity and charge delocalization. The model suggests that there are no fundamental limitations that can prevent achieving the OSC efficiency above 20%.

Comprehensive investigations of kinetics of alkaline hydrolysis of TNT (2,4,6-trinitrotoluene), DNT (2,4-dinitrotoluene), and DNAN (2,4-dinitroanisole).

PubMed

Sviatenko, Liudmyla; Kinney, Chad; Gorb, Leonid; Hill, Frances C; Bednar, Anthony J; Okovytyy, Sergiy; Leszczynski, Jerzy

2014-09-02

Combined experimental and computational techniques were used to analyze multistep chemical reactions in the alkaline hydrolysis of three nitroaromatic compounds: 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), and 2,4-dinitroanisole (DNAN). The study reveals common features and differences in the kinetic behavior of these compounds. The analysis of the predicted pathways includes modeling of the reactions, along with simulation of UV-vis spectra, experimental monitoring of reactions using LC/MS techniques, development of the kinetic model by designing and solving the system of differential equations, and obtaining computationally predicted kinetics for decay and accumulation of reactants and products. Obtained results suggest that DNT and DNAN are more resistant to alkaline hydrolysis than TNT. The direct substitution of a nitro group by a hydroxide represents the most favorable pathway for all considered compounds. The formation of Meisenheimer complexes leads to the kinetic first-step intermediates in the hydrolysis of TNT. Janovsky complexes can also be formed during hydrolysis of TNT and DNT but in small quantities. Methyl group abstraction is one of the suggested pathways of DNAN transformation during alkaline hydrolysis.

Separation of aflatoxin B1 from synthetic physiological fluids using talc and diatomite: Kinetic and isotherm aspects.

PubMed

Sprynskyy, Myroslav; Krzemień-Konieczka, Iwona; Gadzała-Kopciuch, Renata; Buszewski, Bogusław

2018-01-01

The objective of the study was to examine adsorption of the aflatoxin B1 from synthetic gastric fluid and synthetic intestinal fluid by talc, raw and calcined diatomite. The kinetic and equilibrium adsorption processes were studied in the batch adsorption experiments applying high performance liquid chromatography for the aflatoxin B1 determination. The kinetic study showed a very fast adsorption of the aflatoxin B1 onto the selected adsorbents from the both physiological fluids with reaching equilibrium within 1-15min. The aflatoxin B1 was almost completely adsorbed in initial linear step of the kinetic process that can be described well by the zero-order kinetics model. The experimental data of the equilibrium adsorption were characterized using the Langmuir and Freundlich isotherm models. The high adsorption effectiveness was found in a range of 90%-100% and 60%-100% for the diatomite samples and the talc respectively at the initial concentrations of the aflatoxin B1 as 31-300ng/mL. The possible mechanisms of the aflatoxin adsorption onto the used mineral adsorbents are also discussed in the work. Copyright © 2017 Elsevier B.V. All rights reserved.

4-Chlorophenol biodegradation facilitator composed of recombinant multi-biocatalysts immobilized onto montmorillonite.

PubMed

Kwean, Oh Sung; Cho, Su Yeon; Yang, Jun Won; Cho, Wooyoun; Park, Sungyoon; Lim, Yejee; Shin, Min Chul; Kim, Han-Suk; Park, Joonhong; Kim, Han S

2018-07-01

A biodegradation facilitator which catalyzes the initial steps of 4-chlorophenol (4-CP) oxidation was prepared by immobilizing multiple enzymes (monooxygenase, CphC-I and dioxygenase, CphA-I) onto a natural inorganic support. The enzymes were obtained via overexpression and purification after cloning the corresponding genes (cphC-I and cphA-I) from Arthrobacter chlorophenolicus A6. Then, the recombinant CphC-I was immobilized onto fulvic acid-activated montmorillonite. The immobilization yield was 60%, and the high enzyme activity (82.6%) was retained after immobilization. Kinetic analysis indicated that the Michaelis-Menten model parameters for the immobilized CphC-I were similar to those for the free enzyme. The enzyme stability was markedly enhanced after immobilization. The immobilized enzyme exhibited a high level of activity even after repetitive use (84.7%) and powdering (65.8%). 4-CP was sequentially oxidized by a multiple enzyme complex, comprising the immobilized CphC-I and CphA-I, via the hydroquinone pathway: oxidative transformation of 4-CP to hydroxyquinol followed by ring fission of hydroxyquinol. Copyright © 2018 Elsevier Ltd. All rights reserved.

A unified inversion scheme to process multifrequency measurements of various dispersive electromagnetic properties

NASA Astrophysics Data System (ADS)

Han, Y.; Misra, S.

2018-04-01

Multi-frequency measurement of a dispersive electromagnetic (EM) property, such as electrical conductivity, dielectric permittivity, or magnetic permeability, is commonly analyzed for purposes of material characterization. Such an analysis requires inversion of the multi-frequency measurement based on a specific relaxation model, such as Cole-Cole model or Pelton's model. We develop a unified inversion scheme that can be coupled to various type of relaxation models to independently process multi-frequency measurement of varied EM properties for purposes of improved EM-based geomaterial characterization. The proposed inversion scheme is firstly tested in few synthetic cases in which different relaxation models are coupled into the inversion scheme and then applied to multi-frequency complex conductivity, complex resistivity, complex permittivity, and complex impedance measurements. The method estimates up to seven relaxation-model parameters exhibiting convergence and accuracy for random initializations of the relaxation-model parameters within up to 3-orders of magnitude variation around the true parameter values. The proposed inversion method implements a bounded Levenberg algorithm with tuning initial values of damping parameter and its iterative adjustment factor, which are fixed in all the cases shown in this paper and irrespective of the type of measured EM property and the type of relaxation model. Notably, jump-out step and jump-back-in step are implemented as automated methods in the inversion scheme to prevent the inversion from getting trapped around local minima and to honor physical bounds of model parameters. The proposed inversion scheme can be easily used to process various types of EM measurements without major changes to the inversion scheme.

Kinetic Landscape of a Peptide Bond-Forming Prolyl Oligopeptidase

PubMed Central

2017-01-01

Prolyl oligopeptidase B from Galerina marginata (GmPOPB) has recently been discovered as a peptidase capable of breaking and forming peptide bonds to yield a cyclic peptide. Despite the relevance of prolyl oligopeptidases in human biology and disease, a kinetic analysis pinpointing rate-limiting steps for a member of this enzyme family is not available. Macrocyclase enzymes are currently exploited to produce cyclic peptides with potential therapeutic applications. Cyclic peptides are promising druglike molecules because of their stability and conformational rigidity. Here we describe an in-depth kinetic characterization of a prolyl oligopeptidase acting as a macrocyclase enzyme. By combining steady-state and pre-steady-state kinetics, we propose a kinetic sequence in which a step after macrocyclization limits steady-state turnover. Additionally, product release is ordered, where the cyclic peptide departs first followed by the peptide tail. Dissociation of the peptide tail is slow and significantly contributes to the turnover rate. Furthermore, trapping of the enzyme by the peptide tail becomes significant beyond initial rate conditions. The presence of a burst of product formation and a large viscosity effect further support the rate-limiting nature of a physical step occurring after macrocyclization. This is the first detailed description of the kinetic sequence of a macrocyclase enzyme from this class. GmPOPB is among the fastest macrocyclases described to date, and this work is a necessary step toward designing broad-specificity efficient macrocyclases. PMID:28332820

Kinetic study of enzymatic hydrolysis of acid-pretreated coconut coir

NASA Astrophysics Data System (ADS)

Fatmawati, Akbarningrum; Agustriyanto, Rudy

2015-12-01

Biomass waste utilization for biofuel production such as bioethanol, has become more prominent currently. Coconut coir is one of lignocellulosic food wastes, which is abundant in Indonesia. Bioethanol production from such materials consists of more than one step. Pretreatment and enzymatic hydrolysis is crucial steps to produce sugar which can then be fermented into bioethanol. In this research, ground coconut coir was pretreated using dilute sulfuric acid at 121°C. This pretreatment had increased the cellulose content and decreased the lignin content of coconut coir. The pretreated coconut coir was hydrolyzed using a mix of two commercial cellulase enzymes at pH of 4.8 and temperature of 50°C. The enzymatic hydrolysis was conducted at several initial coconut coir slurry concentrations (0.1-2 g/100 mL) and reaction times (2-72 hours). The reducing sugar concentration profiles had been produced and can be used to obtain reaction rates. The highest reducing sugar concentration obtained was 1,152.567 mg/L, which was produced at initial slurry concentration of 2 g/100 mL and 72 hours reaction time. In this paper, the reducing sugar concentrations were empirically modeled as a function of reaction time using power equations. Michaelis-Menten kinetic model for enzymatic hydrolysis reaction is adopted. The kinetic parameters of that model for sulfuric acid-pretreated coconut coir enzymatic hydrolysis had been obtained which are Vm of 3.587×104 mg/L.h, and KM of 130.6 mg/L.

Using the Binary Phase-Field Crystal Model to Describe Non-Classical Nucleation Pathways in Gold Nanoparticles

NASA Astrophysics Data System (ADS)

Smith, Nathan; Provatas, Nikolas

Recent experimental work has shown that gold nanoparticles can precipitate from an aqueous solution through a non-classical, multi-step nucleation process. This multi-step process begins with spinodal decomposition into solute-rich and solute-poor liquid domains followed by nucleation from within the solute-rich domains. We present a binary phase-field crystal theory that shows the same phenomology and examine various cross-over regimes in the growth and coarsening of liquid and solid domains. We'd like to the thank Canada Research Chairs (CRC) program for funding this work.

ICCK Conference Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Green, William H.

2013-05-28

The 7th International Conference on Chemical Kinetics (ICCK) was held July 10-14, 2011, at Massachusetts Institute of Technology (MIT), in Cambridge, MA, hosted by Prof. William H. Green of MIT's Chemical Engineering department. This cross-disciplinary meeting highlighted the importance of fundamental understanding of elementary reactions to the full range of chemical investigations. The specific conference focus was on elementary-step kinetics in both the gas phase and in condensed phase. The meeting provided a unique opportunity to discuss how the same reactive species and reaction motifs manifest under very different reaction conditions (e.g. atmospheric, aqueous, combustion, plasma, in nonaqueous solvents, onmore » surfaces.). The conference featured special sessions on new/improved experimental techniques, improved models and data analysis for interpreting complicated kinetics, computational kinetics (especially rate estimates for large kinetic models), and a panel discussion on how the community should document/archive kinetic data. In the past, this conference had been limited to homogeneous gas-phase and liquid-phase systems. This conference included studies of heterogeneous kinetics which provide rate constants for, or insight into, elementary reaction steps. This Grant from DOE BES covered about half of the subsidies we provided to students and postdocs who attended the conference, by charging them reduced-rate registration fees. The complete list of subsidies provided are listed in Table 1 below. This DOE funding was essential to making the conference affordable to graduate students, and indeed the attendance at this conference was higher than at previous conferences in this series. Donations made by companies provided additional subsidies, leveraging the DOE funding. The conference was very effective in educating graduate students and important in fostering scientific interactions, particularly between scientists studying gas phase and liquid phase kinetics, since those two communities do not meet very often (it had been 6 years since the last time this conference had been held). The conference at MIT was so successful that European scientists decided to organize a similar conference (it will be held in Seville, Spain in July 2013). Almost 200 scientists participated, with more than 100 oral presentations and many poster presentations. A complete list of the presentations and their abstracts are given in the attachment. The conference led to many peer-reviewed papers published in several Special Issues of the International Journal of Chemical Kinetics in early 2012.« less

The effects of surface chemistry of mesoporous silica materials and solution pH on kinetics of molsidomine adsorption

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dolinina, E.S.; Parfenyuk, E.V., E-mail: terrakott37@mail.ru

2014-01-15

Adsorption kinetics of molsidomine on mesoporous silica material (UMS), the phenyl- (PhMS) and mercaptopropyl-functionalized (MMS) derivatives from solution with different pH and 298 K was studied. The adsorption kinetics was found to follow the pseudo-second-order kinetic model for all studied silica materials and pH. Effects of surface functional groups and pH on adsorption efficiency and kinetic adsorption parameters were investigated. At all studied pH, the highest molsidomine amount is adsorbed on PhMS due to π–π interactions and hydrogen bonding between surface groups of PhMS and molsidomine molecules. An increase of pH results in a decrease of the amounts of adsorbedmore » molsidomine onto the silica materials. Furthermore, the highest adsorption rate kinetically evaluated using a pseudo-second-order model, is observed onto UMS and it strongly depends on pH. The mechanism of the adsorption process was determined from the intraparticle diffusion and Boyd kinetic film–diffusion models. The results showed that the molsidomine adsorption on the silica materials is controlled by film diffusion. Effect of pH on the diffusion parameters is discussed. - Graphical abstract: The kinetic study showed that the k{sub 2} value, the rate constant of pseudo-second order kinetic model, is the highest for molsidomine adsorption on UMS and strongly depends on pH because it is determined by availability and accessibility of the reaction sites of the adsorbents molsidomine binding. Display Omitted - Highlights: • The adsorption capacities of UMS, PhMS and MMS were dependent on the pH. • At all studied pH, the highest molsidomine amount is adsorbed on PhMS. • The highest adsorption rate, k{sub 2}, is observed onto UMS and strongly depends on pH. • Film diffusion was the likely rate-limiting step in the adsorption process.« less

A non-oscillatory energy-splitting method for the computation of compressible multi-fluid flows

NASA Astrophysics Data System (ADS)

Lei, Xin; Li, Jiequan

2018-04-01

This paper proposes a new non-oscillatory energy-splitting conservative algorithm for computing multi-fluid flows in the Eulerian framework. In comparison with existing multi-fluid algorithms in the literature, it is shown that the mass fraction model with isobaric hypothesis is a plausible choice for designing numerical methods for multi-fluid flows. Then we construct a conservative Godunov-based scheme with the high order accurate extension by using the generalized Riemann problem solver, through the detailed analysis of kinetic energy exchange when fluids are mixed under the hypothesis of isobaric equilibrium. Numerical experiments are carried out for the shock-interface interaction and shock-bubble interaction problems, which display the excellent performance of this type of schemes and demonstrate that nonphysical oscillations are suppressed around material interfaces substantially.

Kinetic mechanism of the dimeric ATP sulfurylase from plants

PubMed Central

Ravilious, Geoffrey E.; Herrmann, Jonathan; Goo Lee, Soon; Westfall, Corey S.; Jez, Joseph M.

2013-01-01

In plants, sulfur must be obtained from the environment and assimilated into usable forms for metabolism. ATP sulfurylase catalyses the thermodynamically unfavourable formation of a mixed phosphosulfate anhydride in APS (adenosine 5′-phosphosulfate) from ATP and sulfate as the first committed step of sulfur assimilation in plants. In contrast to the multi-functional, allosterically regulated ATP sulfurylases from bacteria, fungi and mammals, the plant enzyme functions as a mono-functional, non-allosteric homodimer. Owing to these differences, here we examine the kinetic mechanism of soybean ATP sulfurylase [GmATPS1 (Glycine max (soybean) ATP sulfurylase isoform 1)]. For the forward reaction (APS synthesis), initial velocity methods indicate a single-displacement mechanism. Dead-end inhibition studies with chlorate showed competitive inhibition versus sulfate and non-competitive inhibition versus APS. Initial velocity studies of the reverse reaction (ATP synthesis) demonstrate a sequential mechanism with global fitting analysis suggesting an ordered binding of substrates. ITC (isothermal titration calorimetry) showed tight binding of APS to GmATPS1. In contrast, binding of PPi (pyrophosphate) to GmATPS1 was not detected, although titration of the E•APS complex with PPi in the absence of magnesium displayed ternary complex formation. These results suggest a kinetic mechanism in which ATP and APS are the first substrates bound in the forward and reverse reactions, respectively. PMID:23789618

Dye adsorption mechanisms in TiO2 films, and their effects on the photodynamic and photovoltaic properties in dye-sensitized solar cells.

PubMed

Hwang, Kyung-Jun; Shim, Wang-Geun; Kim, Youngjin; Kim, Gunwoo; Choi, Chulmin; Kang, Sang Ook; Cho, Dae Won

2015-09-14

The adsorption mechanism for the N719 dye on a TiO2 electrode was examined by the kinetic and diffusion models (pseudo-first order, pseudo-second order, and intra-particle diffusion models). Among these methods, the observed adsorption kinetics are well-described using the pseudo-second order model. Moreover, the film diffusion process was the main controlling step of adsorption, which was analysed using a diffusion-based model. The photodynamic properties in dye-sensitized solar cells (DSSCs) were investigated using time-resolved transient absorption techniques. The photodynamics of the oxidized N719 species were shown to be dependent on the adsorption time, and also the adsorbed concentration of N719. The photovoltaic parameters (Jsc, Voc, FF and η) of this DSSC were determined in terms of the dye adsorption amounts. The solar cell performance correlates significantly with charge recombination and dye regeneration dynamics, which are also affected by the dye adsorption amounts. Therefore, the photovoltaic performance of this DSSC can be interpreted in terms of the adsorption kinetics and the photodynamics of oxidized N719.

Kinetic analysis of the effects of target structure on siRNA efficiency

NASA Astrophysics Data System (ADS)

Chen, Jiawen; Zhang, Wenbing

2012-12-01

RNAi efficiency for target cleavage and protein expression is related to the target structure. Considering the RNA-induced silencing complex (RISC) as a multiple turnover enzyme, we investigated the effect of target mRNA structure on siRNA efficiency with kinetic analysis. The 4-step model was used to study the target cleavage kinetic process: hybridization nucleation at an accessible target site, RISC-mRNA hybrid elongation along with mRNA target structure melting, target cleavage, and enzyme reactivation. At this model, the terms accounting for the target accessibility, stability, and the seed and the nucleation site effects are all included. The results are in good agreement with that of experiments which show different arguments about the structure effects on siRNA efficiency. It shows that the siRNA efficiency is influenced by the integrated factors of target's accessibility, stability, and the seed effects. To study the off-target effects, a simple model of one siRNA binding to two mRNA targets was designed. By using this model, the possibility for diminishing the off-target effects by the concentration of siRNA was discussed.

Mathematical model for Trametes versicolor growth in submerged cultivation.

PubMed

Tisma, Marina; Sudar, Martina; Vasić-Racki, Durda; Zelić, Bruno

2010-08-01

Trametes versicolor is a white-rot fungus known as a producer of extracellular enzymes such as laccase, manganese-peroxidase, and lignin-peroxidase. The production of these enzymes requires detailed knowledge of the growth characteristics and physiology of the fungus. Submerged cultivations of T. versicolor on glucose, fructose, and sucrose as sole carbon sources were performed in shake flasks. Sucrose hydrolysis catalyzed by the whole cells of T. versicolor was considered as one-step enzymatic reaction described with Michaelis-Menten kinetics. Kinetic parameters of invertase-catalyzed sucrose hydrolysis were estimated (K (m) = 7.99 g dm(-3) and V (m) = 0.304 h(-1)). Monod model was used for description of kinetics of T. versicolor growth on glucose and fructose as sole carbon sources. Growth associated model parameters were estimated from the experimental results obtained by independent experiments (mu(G)(max) = 0.14 h(-1), K(G)(S) = 8.06 g dm(-3), mu(F)(max) = 0.37 h(-1) and K(F)(S) = 54.8 g dm(-3)). Developed mathematical model is in good agreement with the experimental results.

Design Principles of DNA Enzyme-Based Walkers: Translocation Kinetics and Photoregulation.

PubMed

Cha, Tae-Gon; Pan, Jing; Chen, Haorong; Robinson, Heather N; Li, Xiang; Mao, Chengde; Choi, Jong Hyun

2015-07-29

Dynamic DNA enzyme-based walkers complete their stepwise movements along the prescribed track through a series of reactions, including hybridization, enzymatic cleavage, and strand displacement; however, their overall translocation kinetics is not well understood. Here, we perform mechanistic studies to elucidate several key parameters that govern the kinetics and processivity of DNA enzyme-based walkers. These parameters include DNA enzyme core type and structure, upper and lower recognition arm lengths, and divalent metal cation species and concentration. A theoretical model is developed within the framework of single-molecule kinetics to describe overall translocation kinetics as well as each reaction step. A better understanding of kinetics and design parameters enables us to demonstrate a walker movement near 5 μm at an average speed of ∼1 nm s(-1). We also show that the translocation kinetics of DNA walkers can be effectively controlled by external light stimuli using photoisomerizable azobenzene moieties. A 2-fold increase in the cleavage reaction is observed when the hairpin stems of enzyme catalytic cores are open under UV irradiation. This study provides general design guidelines to construct highly processive, autonomous DNA walker systems and to regulate their translocation kinetics, which would facilitate the development of functional DNA walkers.

Robust model predictive control for multi-step short range spacecraft rendezvous

NASA Astrophysics Data System (ADS)

Zhu, Shuyi; Sun, Ran; Wang, Jiaolong; Wang, Jihe; Shao, Xiaowei

2018-07-01

This work presents a robust model predictive control (MPC) approach for the multi-step short range spacecraft rendezvous problem. During the specific short range phase concerned, the chaser is supposed to be initially outside the line-of-sight (LOS) cone. Therefore, the rendezvous process naturally includes two steps: the first step is to transfer the chaser into the LOS cone and the second step is to transfer the chaser into the aimed region with its motion confined within the LOS cone. A novel MPC framework named after Mixed MPC (M-MPC) is proposed, which is the combination of the Variable-Horizon MPC (VH-MPC) framework and the Fixed-Instant MPC (FI-MPC) framework. The M-MPC framework enables the optimization for the two steps to be implemented jointly rather than to be separated factitiously, and its computation workload is acceptable for the usually low-power processors onboard spacecraft. Then considering that disturbances including modeling error, sensor noise and thrust uncertainty may induce undesired constraint violations, a robust technique is developed and it is attached to the above M-MPC framework to form a robust M-MPC approach. The robust technique is based on the chance-constrained idea, which ensures that constraints can be satisfied with a prescribed probability. It improves the robust technique proposed by Gavilan et al., because it eliminates the unnecessary conservativeness by explicitly incorporating known statistical properties of the navigation uncertainty. The efficacy of the robust M-MPC approach is shown in a simulation study.

Computation Molecular Kinetics Model of HZE Induced Cell Cycle Arrest

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Ren, Lei

2004-01-01

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

Reactive Fluid Flow and Applications to Diagenesis, Mineral Deposits, and Crustal Rocks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rye, Danny M.; Bolton, Edward W.

2002-11-04

The objective is to initiate new: modeling of coupled fluid flow and chemical reactions of geologic environments; experimental and theoretical studies of water-rock reactions; collection and interpretation of stable isotopic and geochemical field data at many spatial scales of systems involving fluid flow and reaction in environments ranging from soils to metamorphic rocks. Theoretical modeling of coupled fluid flow and chemical reactions, involving kinetics, has been employed to understand the differences between equilibrium, steady-state, and non-steady-state behavior of the chemical evolution of open fluid-rock systems. The numerical codes developed in this project treat multi-component, finite-rate reactions combined with advective andmore » dispersive transport in multi-dimensions. The codes incorporate heat, mass, and isotopic transfer in both porous and fractured media. Experimental work has obtained the kinetic rate laws of pertinent silicate-water reactions and the rates of Sr release during chemical weathering. Ab-initio quantum mechanical techniques have been applied to obtain the kinetics and mechanisms of silicate surface reactions and isotopic exchange between water and dissolved species. Geochemical field-based studies were carried out on the Wepawaug metamorphic schist, on the Irish base-metal sediment-hosted ore system, in the Dalradian metamorphic complex in Scotland, and on weathering in the Columbia River flood basalts. The geochemical and isotopic field data, and the experimental and theoretical rate data, were used as constraints on the numerical models and to determine the length and time scales relevant to each of the field areas.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, XF; Zhao, X; Huang, K

A high-fidelity two-dimensional axial symmetrical multi-physics model is described in this paper as an effort to simulate the cycle performance of a recently discovered solid oxide metal-air redox battery (SOMARB). The model collectively considers mass transport, charge transfer and chemical redox cycle kinetics occurring across the components of the battery, and is validated by experimental data obtained from independent research. In particular, the redox kinetics at the energy storage unit is well represented by Johnson-Mehl-Avrami-Kolmogorov (JIVIAK) and Shrinking Core models. The results explicitly show that the reduction of Fe3O4 during the charging cycle limits the overall performance. Distributions of electrodemore » potential, overpotential, Nernst potential, and H-2/H2O-concentration across various components of the battery are also systematically investigated. (C) 2015 Elsevier B.V. All rights reserved.« less

Kinetic simulations and reduced modeling of longitudinal sideband instabilities in non-linear electron plasma waves

DOE PAGES

Brunner, S.; Berger, R. L.; Cohen, B. I.; ...

2014-10-01

Kinetic Vlasov simulations of one-dimensional finite amplitude Electron Plasma Waves are performed in a multi-wavelength long system. A systematic study of the most unstable linear sideband mode, in particular its growth rate γ and quasi- wavenumber δk, is carried out by scanning the amplitude and wavenumber of the initial wave. Simulation results are successfully compared against numerical and analytical solutions to the reduced model by Kruer et al. [Phys. Rev. Lett. 23, 838 (1969)] for the Trapped Particle Instability (TPI). A model recently suggested by Dodin et al. [Phys. Rev. Lett. 110, 215006 (2013)], which in addition to the TPImore » accounts for the so-called Negative Mass Instability because of a more detailed representation of the trapped particle dynamics, is also studied and compared with simulations.« less

3-D Wave-Structure Interaction with Coastal Sediments - A Multi-Physics/Multi-Solution Techniques Approach

DTIC Science & Technology

2007-01-01

Stokes (RANS) and the particle finite element method ( PFEM ) will be used in the water/mine/sand domain. Sand and the geomaterials around the sand will...wave propagation over a bottom mine at various time steps (Soil and Foam model) 8 SOLID/FEM SAND/SPH GEOMATERIALS FNPF/BEM FNPF/BEM RANS/ PFEM

Theoretical analysis of factors controlling the nonalternating CO/C(2)H(4) copolymerization.

PubMed

Haras, Alicja; Michalak, Artur; Rieger, Bernhard; Ziegler, Tom

2005-06-22

A [P-O]Pd catalyst based on o-alkoxy derivatives of diphenylphosphinobenzene sulfonic acid (I) has recently been shown by Drent et al. to perform nonalternating CO/C(2)H(4) copolymerization with subsequent incorporation of ethylene units into the polyketone chain. The origin of the nonalternation is investigated in a theoretical study of I, where calculated activation barriers and reaction heats of all involved elementary steps are used to generate a complete kinetic model. The kinetic model is able to account for the observed productivity and degree of nonalternation as a function of temperature. Consistent with the energy changes obtained for the real catalyst model, the selectivity toward a nonalternating distribution of both comonomers appears to be mainly a result of a strong destabilization of the Pd-acyl complex.

Microkinetic modeling of the autoxidative curing of an alkyd and oil-based paint model system

NASA Astrophysics Data System (ADS)

Oakley, Lindsay H.; Casadio, Francesca; Shull, Kenneth R.; Broadbelt, Linda J.

2015-11-01

Elucidating the curing and aging mechanisms of alkyd and other oil-based paints is valuable for the fields of conservation and bio-based coatings. Recent research has demonstrated the limitations of artificial aging in predicting the actual properties of paints that are hundreds of years old. Kinetic modeling offers pathways to develop a realistic and dynamic description of the composition of these oil-based paint coatings and facilitates the exploration of the effects of various environmental conditions on their long-term chemical stability. This work presents the construction of a kinetic Monte Carlo framework from elementary steps for the cobalt-catalyzed autoxidative curing of an ethyl linoleate model system up to the formation of single cross-links. Kinetic correlations for reaction families of similar chemistry are employed to reduce the number of parameters required to calculate rate constants in Arrhenius form. The model, developed from mechanisms proposed in the literature, shows good agreement with experiment for the formation of primary products in the early stages of curing. The model has also revealed that the mechanisms proposed in the literature for the formation of secondary products, such as volatile aldehydes, are still not well established, and alternative routes are under evaluation.

Microstructure design of low alloy transformation-induced plasticity assisted steels

NASA Astrophysics Data System (ADS)

Zhu, Ruixian

The microstructure of low alloy Transformation Induced Plasticity (TRIP) assisted steels has been systematically varied through the combination of computational and experimental methodologies in order to enhance the mechanical performance and to fulfill the requirement of the next generation Advanced High Strength Steels (AHSS). The roles of microstructural parameters, such as phase constitutions, phase stability, and volume fractions on the strength-ductility combination have been revealed. Two model alloy compositions (i.e. Fe-1.5Mn-1.5Si-0.3C, and Fe-3Mn-1Si-0.3C in wt%, nominal composition) were studied. Multiphase microstructures including ferrite, bainite, retained austenite and martensite were obtained through conventional two step heat treatment (i.e. intercritical annealing-IA, and bainitic isothermal transformation-BIT). The effect of phase constitution on the mechanical properties was first characterized experimentally via systematically varying the volume fractions of these phases through computational thermodynamics. It was found that martensite was the main phase to deteriorate ductility, meanwhile the C/VA ratio (i.e. carbon content over the volume fraction of austenite) could be another indicator for the ductility of the multiphase microstructure. Following the microstructural characterization of the multiphase alloys, two microstructural design criteria (i.e. maximizing ferrite and austenite, suppressing athermal martensite) were proposed in order to optimize the corresponding mechanical performance. The volume fraction of ferrite was maximized during the IA with the help of computational thermodyanmics. On the other hand, it turned out theoretically that the martensite suppression could not be avoided on the low Mn contained alloy (i.e. Fe- 1.5Mn-1.5Si-0.3C). Nevertheless, the achieved combination of strength (~1300MPa true strength) and ductility (˜23% uniform elongation) on the low Mn alloy following the proposed design criteria fulfilled the requirement of the next generation AHSS. To further optimize the microstructure such that the designed criteria can be fully satisfied, further efforts have been made on two aspects: heat treatment and alloy addition. A multi-step BIT treatment was designed and successfully reduced the martensite content on the Fe-1.5Mn-1.5Si-0.3C alloy. Microstructure analysis showed a significant reduction on the volume fraction of martensite after the multi-step BIT as compared to the single BIT step. It was also found that, a slow cooling rate between the two BIT treatments resulted in a better combination of strength and ductility than rapid cooling or conventional one step BIT. Moreover, the athermal martensite formation can be fully suppressed by increasing the Mn content (Fe-3Mn-1Si-0.3C) and through carefully designed heat treatments. The athermal martensite-free alloy provided consistently better ductility than the martensite containing alloy. Finally, a microstructure based semi-empirical constitutive model has been developed to predict the monotonic tensile behavior of the multiphase TRIP assisted steels. The stress rule of mixture and isowork assumption for individual phases was presumed. Mecking-Kocks model was utilized to simulate the flow behavior of ferrite, bainitic ferrite and untransformed retained austenite. The kinetics of strain induced martensitic transformation was modeled following the Olson-Cohen method. The developed model has results in good agreements with the experimental results for both TRIP steels studied with same model parameters.

Assessment of ion kinetic effects in shock-driven inertial confinement fusion implosions using fusion burn imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosenberg, M. J., E-mail: mros@lle.rochester.edu; Séguin, F. H.; Rinderknecht, H. G.

The significance and nature of ion kinetic effects in D{sup 3}He-filled, shock-driven inertial confinement fusion implosions are assessed through measurements of fusion burn profiles. Over this series of experiments, the ratio of ion-ion mean free path to minimum shell radius (the Knudsen number, N{sub K}) was varied from 0.3 to 9 in order to probe hydrodynamic-like to strongly kinetic plasma conditions; as the Knudsen number increased, hydrodynamic models increasingly failed to match measured yields, while an empirically-tuned, first-step model of ion kinetic effects better captured the observed yield trends [Rosenberg et al., Phys. Rev. Lett. 112, 185001 (2014)]. Here, spatiallymore » resolved measurements of the fusion burn are used to examine kinetic ion transport effects in greater detail, adding an additional dimension of understanding that goes beyond zero-dimensional integrated quantities to one-dimensional profiles. In agreement with the previous findings, a comparison of measured and simulated burn profiles shows that models including ion transport effects are able to better match the experimental results. In implosions characterized by large Knudsen numbers (N{sub K} ∼ 3), the fusion burn profiles predicted by hydrodynamics simulations that exclude ion mean free path effects are peaked far from the origin, in stark disagreement with the experimentally observed profiles, which are centrally peaked. In contrast, a hydrodynamics simulation that includes a model of ion diffusion is able to qualitatively match the measured profile shapes. Therefore, ion diffusion or diffusion-like processes are identified as a plausible explanation of the observed trends, though further refinement of the models is needed for a more complete and quantitative understanding of ion kinetic effects.« less

Assessment of ion kinetic effects in shock-driven inertial confinement fusion (ICF) implosions using fusion burn imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosenberg, M. J.; Séguin, F. H.; Amendt, P. A.

The significance and nature of ion kinetic effects in D³He-filled, shock-driven inertial confinement fusion implosions are assessed through measurements of fusion burn profiles. Over this series of experiments, the ratio of ion-ion mean free path to minimum shell radius (the Knudsen number, N K) was varied from 0.3 to 9 in order to probe hydrodynamic-like to strongly kinetic plasma conditions; as the Knudsen number increased, hydrodynamic models increasingly failed to match measured yields, while an empirically-tuned, first-step model of ion kinetic effects better captured the observed yield trends [Rosenberg et al., Phys. Rev. Lett. 112, 185001 (2014)]. Here, spatially resolvedmore » measurements of the fusion burn are used to examine kinetic ion transport effects in greater detail, adding an additional dimension of understanding that goes beyond zero-dimensional integrated quantities to one-dimensional profiles. In agreement with the previous findings, a comparison of measured and simulated burn profiles shows that models including ion transport effects are able to better match the experimental results. In implosions characterized by large Knudsen numbers (N K ~ 3), the fusion burn profiles predicted by hydrodynamics simulations that exclude ion mean free path effects are peaked far from the origin, in stark disagreement with the experimentally observed profiles, which are centrally peaked. In contrast, a hydrodynamics simulation that includes a model of ion diffusion is able to qualitatively match the measured profile shapes. Therefore, ion diffusion or diffusion-like processes are identified as a plausible explanation of the observed trends, though further refinement of the models is needed for a more complete and quantitative understanding of ion kinetic effects.« less

Assessment of ion kinetic effects in shock-driven inertial confinement fusion implosions using fusion burn imaging

NASA Astrophysics Data System (ADS)

Rosenberg, M. J.; Séguin, F. H.; Amendt, P. A.; Atzeni, S.; Rinderknecht, H. G.; Hoffman, N. M.; Zylstra, A. B.; Li, C. K.; Sio, H.; Gatu Johnson, M.; Frenje, J. A.; Petrasso, R. D.; Glebov, V. Yu.; Stoeckl, C.; Seka, W.; Marshall, F. J.; Delettrez, J. A.; Sangster, T. C.; Betti, R.; Wilks, S. C.; Pino, J.; Kagan, G.; Molvig, K.; Nikroo, A.

2015-06-01

The significance and nature of ion kinetic effects in D3He-filled, shock-driven inertial confinement fusion implosions are assessed through measurements of fusion burn profiles. Over this series of experiments, the ratio of ion-ion mean free path to minimum shell radius (the Knudsen number, NK) was varied from 0.3 to 9 in order to probe hydrodynamic-like to strongly kinetic plasma conditions; as the Knudsen number increased, hydrodynamic models increasingly failed to match measured yields, while an empirically-tuned, first-step model of ion kinetic effects better captured the observed yield trends [Rosenberg et al., Phys. Rev. Lett. 112, 185001 (2014)]. Here, spatially resolved measurements of the fusion burn are used to examine kinetic ion transport effects in greater detail, adding an additional dimension of understanding that goes beyond zero-dimensional integrated quantities to one-dimensional profiles. In agreement with the previous findings, a comparison of measured and simulated burn profiles shows that models including ion transport effects are able to better match the experimental results. In implosions characterized by large Knudsen numbers (NK ˜ 3), the fusion burn profiles predicted by hydrodynamics simulations that exclude ion mean free path effects are peaked far from the origin, in stark disagreement with the experimentally observed profiles, which are centrally peaked. In contrast, a hydrodynamics simulation that includes a model of ion diffusion is able to qualitatively match the measured profile shapes. Therefore, ion diffusion or diffusion-like processes are identified as a plausible explanation of the observed trends, though further refinement of the models is needed for a more complete and quantitative understanding of ion kinetic effects.