Time step MOTA thermostat simulation

International Nuclear Information System (INIS)

Guthrie, G.L.

1978-09-01

The report details the logic, program layout, and operating procedures for the time-step MOTA (Materials Open Test Assembly) thermostat simulation program known as GYRD. It will enable prospective users to understand the operation of the program, run it, and interpret the results. The time-step simulation analysis was the approach chosen to determine the maximum value gain that could be used to minimize steady temperature offset without risking undamped thermal oscillations. The advantage of the GYRD program is that it directly shows hunting, ringing phenomenon, and similar events. Programs BITT and CYLB are faster, but do not directly show ringing time

Real-Time Label-Free Direct Electronic Monitoring of Topoisomerase Enzyme Binding Kinetics on Graphene.

Science.gov (United States)

Zuccaro, Laura; Tesauro, Cinzia; Kurkina, Tetiana; Fiorani, Paola; Yu, Hak Ki; Knudsen, Birgitta R; Kern, Klaus; Desideri, Alessandro; Balasubramanian, Kannan

2015-11-24

Monolayer graphene field-effect sensors operating in liquid have been widely deployed for detecting a range of analyte species often under equilibrium conditions. Here we report on the real-time detection of the binding kinetics of the essential human enzyme, topoisomerase I interacting with substrate molecules (DNA probes) that are immobilized electrochemically on to monolayer graphene strips. By monitoring the field-effect characteristics of the graphene biosensor in real-time during the enzyme-substrate interactions, we are able to decipher the surface binding constant for the cleavage reaction step of topoisomerase I activity in a label-free manner. Moreover, an appropriate design of the capture probes allows us to distinctly follow the cleavage step of topoisomerase I functioning in real-time down to picomolar concentrations. The presented results are promising for future rapid screening of drugs that are being evaluated for regulating enzyme activity.

Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation

Science.gov (United States)

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.

Science.gov (United States)

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.

High-resolution seismic wave propagation using local time stepping

KAUST Repository

Peter, Daniel

2017-03-13

High-resolution seismic wave simulations often require local refinements in numerical meshes to accurately capture e.g. steep topography or complex fault geometry. Together with explicit time schemes, this dramatically reduces the global time step size for ground-motion simulations due to numerical stability conditions. To alleviate this problem, local time stepping (LTS) algorithms allow an explicit time stepping scheme to adapt the time step to the element size, allowing nearoptimal time steps everywhere in the mesh. This can potentially lead to significantly faster simulation runtimes.

Time step size selection for radiation diffusion calculations

International Nuclear Information System (INIS)

Rider, W.J.; Knoll, D.A.

1999-01-01

The purpose of this note is to describe a time step control technique as applied to radiation diffusion. Standard practice only provides a heuristic criteria related to the relative change in the dependent variables. The authors propose an alternative based on relatively simple physical principles. This time step control applies to methods of solution that are unconditionally stable and converges nonlinearities within a time step in the governing equations. Commonly, nonlinearities in the governing equations are evaluated using existing (old time) data. The authors refer to this as the semi-implicit (SI) method. When a method converges nonlinearities within a time step, the entire governing equation including all nonlinearities is self-consistently evaluated using advance time data (with appropriate time centering for accuracy)

Time-step selection considerations in the analysis of reactor transients with DIF3D-K

International Nuclear Information System (INIS)

Taiwo, T.A.; Khalil, H.S.; Cahalan, J.E.; Morris, E.E.

1993-01-01

The DIF3D-K code solves the three-dimensional, time-dependent multigroup neutron diffusion equations by using a nodal approach for spatial discretization and either the theta method or one of three space-time factorization approaches for temporal integration of the nodal equations. The three space-time factorization options (namely, improved quasistatic, adiabatic and conventional point kinetics) were implemented because of their potential efficiency advantage for the analysis of transients in which the flux shape changes more slowly than its amplitude. Here we describe the implementation of DIF3D-K as the neutronics module within the SAS-HWR accident analysis code. We also describe the neutronics-related time step selection algorithms and their influence on the accuracy and efficiency of the various solution options

Time step length versus efficiency of Monte Carlo burnup calculations

International Nuclear Information System (INIS)

Dufek, Jan; Valtavirta, Ville

2014-01-01

Highlights: • Time step length largely affects efficiency of MC burnup calculations. • Efficiency of MC burnup calculations improves with decreasing time step length. • Results were obtained from SIE-based Monte Carlo burnup calculations. - Abstract: We demonstrate that efficiency of Monte Carlo burnup calculations can be largely affected by the selected time step length. This study employs the stochastic implicit Euler based coupling scheme for Monte Carlo burnup calculations that performs a number of inner iteration steps within each time step. In a series of calculations, we vary the time step length and the number of inner iteration steps; the results suggest that Monte Carlo burnup calculations get more efficient as the time step length is reduced. More time steps must be simulated as they get shorter; however, this is more than compensated by the decrease in computing cost per time step needed for achieving a certain accuracy

Time-step selection considerations in the analysis of reactor transients with DIF3D-K

International Nuclear Information System (INIS)

Taiwo, T.A.; Khalil, H.S.; Cahalan, J.E.; Morris, E.E.

1993-01-01

The DIF3D-K code solves the three-dimensional, time-dependent multigroup neutron diffusion equations by using a nodal approach for spatial discretization and either the theta method or one of three space-time factorization approaches for temporal integration of the nodal equations. The three space-time factorization options (namely, improved quasistatic, adiabatic, and conventional point kinetics) were implemented because of their potential efficiency advantage for the analysis of transients in which the flux shape changes more slowly than its amplitude. In this paper, we describe the implementation of DIF3D-K as the neutronics module within the SAS-HWR accident analysis code. We also describe the neuronic-related time-step selection algorithms and their influence on the accuracy and efficiency of the various solution options

Moment analysis of the time-dependent transmission of a step-function input of a radioactive gas through an adsorber bed

International Nuclear Information System (INIS)

Lee, T.V.; Rothstein, D.; Madey, R.

1986-01-01

The time-dependent concentration of a radioactive gas at the outlet of an adsorber bed for a step change in the input concentration is analyzed by the method of moments. This moment analysis yields analytical expressions for calculating the kinetic parameters of a gas adsorbed on a porous solid in terms of observables from a time-dependent transmission curve. Transmission is the ratio of the adsorbate outlet concentration to that at the inlet. The three nonequilibrium parameters are the longitudinal diffusion coefficient, the solid-phase diffusion coefficient, and the interfacial mass-transfer coefficient. Three quantities that can be extracted in principle from an experimental transmission curve are the equilibrium transmission, the average residence (or propagation) time, and the first-moment relative to the propagation time. The propagation time for a radioactive gas is given by the time integral of one minus the transmission (expressed as a fraction of the steady-state transmission). The steady-state transmission, the propagation time, and the first-order moment are functions of the three kinetic parameters and the equilibrium adsorption capacity. The equilibrium adsorption capacity is extracted from an experimental transmission curve for a stable gaseous isotope. The three kinetic parameters can be obtained by solving the three analytical expressions simultaneously. No empirical correlations are required

Diffeomorphic image registration with automatic time-step adjustment

DEFF Research Database (Denmark)

Pai, Akshay Sadananda Uppinakudru; Klein, S.; Sommer, Stefan Horst

2015-01-01

In this paper, we propose an automated Euler's time-step adjustment scheme for diffeomorphic image registration using stationary velocity fields (SVFs). The proposed variational problem aims at bounding the inverse consistency error by adaptively adjusting the number of Euler's step required to r...... accuracy as a fixed time-step scheme however at a much less computational cost....

Stiffness Confinement Method with Pseudo Absorption for Spatial Kinetics

International Nuclear Information System (INIS)

Park, Beom Woo; Joo, Han Gyu; Chao, Yungan

2013-01-01

The primary advantage of the SCM is that it is possible to use larger time step sizes. This advantage comes from the fact because the SCM involves the solution of an eigenvalue problem instead of the ordinary form of a fixed source problem. Since using a large time step size is strongly desired in the direct whole core transport calculation for transient problems, we investigate here the SCM for spatial kinetics first with a simple one-dimensional, one-group diffusion equation and propose an improved formulation. The performance of the improved SCM for spatial kinetics is assessed by comparing the SCM solutions with the standard method solutions employing the Crank-Nicholson method with exponential transform. The stiffness confinement method for spatial kinetics was refined with the pseudo absorption term representing the dynamic frequencies. It was verified that the proposed SCM works much better than the Crank-Nicholson method with exponential transform in that time step sizes larger than 20 msec can be using in a super prompt-critical transient involving 1.5$ reactivity insertion

Stiffness Confinement Method with Pseudo Absorption for Spatial Kinetics

Energy Technology Data Exchange (ETDEWEB)

Park, Beom Woo; Joo, Han Gyu [Seoul National Univ., Seoul (Korea, Republic of); Chao, Yungan [Retired in China, Beijing (China)

2013-05-15

The primary advantage of the SCM is that it is possible to use larger time step sizes. This advantage comes from the fact because the SCM involves the solution of an eigenvalue problem instead of the ordinary form of a fixed source problem. Since using a large time step size is strongly desired in the direct whole core transport calculation for transient problems, we investigate here the SCM for spatial kinetics first with a simple one-dimensional, one-group diffusion equation and propose an improved formulation. The performance of the improved SCM for spatial kinetics is assessed by comparing the SCM solutions with the standard method solutions employing the Crank-Nicholson method with exponential transform. The stiffness confinement method for spatial kinetics was refined with the pseudo absorption term representing the dynamic frequencies. It was verified that the proposed SCM works much better than the Crank-Nicholson method with exponential transform in that time step sizes larger than 20 msec can be using in a super prompt-critical transient involving 1.5$ reactivity insertion.

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

Science.gov (United States)

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.

One-step reduced kinetics for lean hydrogen-air deflagration

Energy Technology Data Exchange (ETDEWEB)

Fernandez-Galisteo, D.; Sanchez, A.L. [Area de Mecanica de Fluidos, Univ. Carlos III de Madrid, Leganes 28911 (Spain); Linan, A. [ETSI Aeronauticos, Pl. Cardenal Cisneros 3, Madrid 28040 (Spain); Williams, F.A. [Dept. of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093-0411 (United States)

2009-05-15

A short mechanism consisting of seven elementary reactions, of which only three are reversible, is shown to provide good predictions of hydrogen-air lean-flame burning velocities. This mechanism is further simplified by noting that over a range of conditions of practical interest, near the lean flammability limit all reaction intermediaries have small concentrations in the important thin reaction zone that controls the hydrogen-air laminar burning velocity and therefore follow a steady state approximation, while the main species react according to the global irreversible reaction 2H{sub 2} + O{sub 2} {yields} 2H{sub 2}O. An explicit expression for the non-Arrhenius rate of this one-step overall reaction for hydrogen oxidation is derived from the seven-step detailed mechanism, for application near the flammability limit. The one-step results are used to calculate flammability limits and burning velocities of planar deflagrations. Furthermore, implications concerning radical profiles in the deflagration and reasons for the success of the approximations are clarified. It is also demonstrated that adding only two irreversible direct recombination steps to the seven-step mechanism accurately reproduces burning velocities of the full detailed mechanism for all equivalence ratios at normal atmospheric conditions and that an eight-step detailed mechanism, constructed from the seven-step mechanism by adding to it the fourth reversible shuffle reaction, improves predictions of O and OH profiles. The new reduced-chemistry descriptions can be useful for both analytical and computational studies of lean hydrogen-air flames, decreasing required computation times. (author)

An explicit multi-time-stepping algorithm for aerodynamic flows

OpenAIRE

Niemann-Tuitman, B.E.; Veldman, A.E.P.

1997-01-01

An explicit multi-time-stepping algorithm with applications to aerodynamic flows is presented. In the algorithm, in different parts of the computational domain different time steps are taken, and the flow is synchronized at the so-called synchronization levels. The algorithm is validated for aerodynamic turbulent flows. For two-dimensional flows speedups in the order of five with respect to single time stepping are obtained.

Newmark local time stepping on high-performance computing architectures

KAUST Repository

Rietmann, Max

2016-11-25

In multi-scale complex media, finite element meshes often require areas of local refinement, creating small elements that can dramatically reduce the global time-step for wave-propagation problems due to the CFL condition. Local time stepping (LTS) algorithms allow an explicit time-stepping scheme to adapt the time-step to the element size, allowing near-optimal time-steps everywhere in the mesh. We develop an efficient multilevel LTS-Newmark scheme and implement it in a widely used continuous finite element seismic wave-propagation package. In particular, we extend the standard LTS formulation with adaptations to continuous finite element methods that can be implemented very efficiently with very strong element-size contrasts (more than 100×). Capable of running on large CPU and GPU clusters, we present both synthetic validation examples and large scale, realistic application examples to demonstrate the performance and applicability of the method and implementation on thousands of CPU cores and hundreds of GPUs.

Newmark local time stepping on high-performance computing architectures

KAUST Repository

Rietmann, Max; Grote, Marcus; Peter, Daniel; Schenk, Olaf

2016-01-01

In multi-scale complex media, finite element meshes often require areas of local refinement, creating small elements that can dramatically reduce the global time-step for wave-propagation problems due to the CFL condition. Local time stepping (LTS) algorithms allow an explicit time-stepping scheme to adapt the time-step to the element size, allowing near-optimal time-steps everywhere in the mesh. We develop an efficient multilevel LTS-Newmark scheme and implement it in a widely used continuous finite element seismic wave-propagation package. In particular, we extend the standard LTS formulation with adaptations to continuous finite element methods that can be implemented very efficiently with very strong element-size contrasts (more than 100×). Capable of running on large CPU and GPU clusters, we present both synthetic validation examples and large scale, realistic application examples to demonstrate the performance and applicability of the method and implementation on thousands of CPU cores and hundreds of GPUs.

Newmark local time stepping on high-performance computing architectures

Energy Technology Data Exchange (ETDEWEB)

Rietmann, Max, E-mail: max.rietmann@erdw.ethz.ch [Institute for Computational Science, Università della Svizzera italiana, Lugano (Switzerland); Institute of Geophysics, ETH Zurich (Switzerland); Grote, Marcus, E-mail: marcus.grote@unibas.ch [Department of Mathematics and Computer Science, University of Basel (Switzerland); Peter, Daniel, E-mail: daniel.peter@kaust.edu.sa [Institute for Computational Science, Università della Svizzera italiana, Lugano (Switzerland); Institute of Geophysics, ETH Zurich (Switzerland); Schenk, Olaf, E-mail: olaf.schenk@usi.ch [Institute for Computational Science, Università della Svizzera italiana, Lugano (Switzerland)

2017-04-01

In multi-scale complex media, finite element meshes often require areas of local refinement, creating small elements that can dramatically reduce the global time-step for wave-propagation problems due to the CFL condition. Local time stepping (LTS) algorithms allow an explicit time-stepping scheme to adapt the time-step to the element size, allowing near-optimal time-steps everywhere in the mesh. We develop an efficient multilevel LTS-Newmark scheme and implement it in a widely used continuous finite element seismic wave-propagation package. In particular, we extend the standard LTS formulation with adaptations to continuous finite element methods that can be implemented very efficiently with very strong element-size contrasts (more than 100x). Capable of running on large CPU and GPU clusters, we present both synthetic validation examples and large scale, realistic application examples to demonstrate the performance and applicability of the method and implementation on thousands of CPU cores and hundreds of GPUs.

Modified mean generation time parameter in the neutron point kinetics equations

Energy Technology Data Exchange (ETDEWEB)

Diniz, Rodrigo C.; Gonçalves, Alessandro C.; Rosa, Felipe S.S., E-mail: alessandro@nuclear.ufrj.br, E-mail: frosa@if.ufrj.br [Coordenacao de Pos-Graduacao e Pesquisa de Engenharia (PEN/COPPE/UFRJ), Rio de Janeiro, RJ (Brazil)

2017-07-01

This paper proposes an approximation for the modified point kinetics equations proposed by NUNES et. al, 2015, through the adjustment of a kinetic parameter. This approximation consists of analyzing the terms of the modified point kinetics equations in order to identify the least important ones for the solution, resulting in a modification of the mean generation time parameter that incorporates all influences of the additional terms of the modified kinetics. This approximation is applied on the inverse kinetics, to compare the results with the inverse kinetics from the modified kinetics in order to validate the proposed model. (author)

Modified mean generation time parameter in the neutron point kinetics equations

International Nuclear Information System (INIS)

Diniz, Rodrigo C.; Gonçalves, Alessandro C.; Rosa, Felipe S.S.

2017-01-01

This paper proposes an approximation for the modified point kinetics equations proposed by NUNES et. al, 2015, through the adjustment of a kinetic parameter. This approximation consists of analyzing the terms of the modified point kinetics equations in order to identify the least important ones for the solution, resulting in a modification of the mean generation time parameter that incorporates all influences of the additional terms of the modified kinetics. This approximation is applied on the inverse kinetics, to compare the results with the inverse kinetics from the modified kinetics in order to validate the proposed model. (author)

Microsecond time-scale kinetics of transient biochemical reactions

NARCIS (Netherlands)

Mitic, S.; Strampraad, M.J.F.; Hagen, W.R.; de Vries, S.

2017-01-01

To afford mechanistic studies in enzyme kinetics and protein folding in the microsecond time domain we have developed a continuous-flow microsecond time-scale mixing instrument with an unprecedented dead-time of 3.8 ± 0.3 μs. The instrument employs a micro-mixer with a mixing time of 2.7 μs

Present status on numerical algorithms and benchmark tests for point kinetics and quasi-static approximate kinetics

International Nuclear Information System (INIS)

Ise, Takeharu

1976-12-01

Review studies have been made on algorithms of numerical analysis and benchmark tests on point kinetics and quasistatic approximate kinetics computer codes to perform efficiently benchmark tests on space-dependent neutron kinetics codes. Point kinetics methods have now been improved since they can be directly applied to the factorization procedures. Methods based on Pade rational function give numerically stable solutions and methods on matrix-splitting are interested in the fact that they are applicable to the direct integration methods. An improved quasistatic (IQ) approximation is the best and the most practical method; it is numerically shown that the IQ method has a high stability and precision and the computation time which is about one tenth of that of the direct method. IQ method is applicable to thermal reactors as well as fast reactors and especially fitted for fast reactors to which many time steps are necessary. Two-dimensional diffusion kinetics codes are most practicable though there exist also three-dimensional diffusion kinetics code as well as two-dimensional transport kinetics code. On developing a space-dependent kinetics code, in any case, it is desirable to improve the method so as to have a high computing speed for solving static diffusion and transport equations. (auth.)

Hydrothermal decomposition of industrial jarosite in alkaline media: The rate determining step of the process kinetics

Directory of Open Access Journals (Sweden)

González-Ibarra A.A.

2016-01-01

Full Text Available This work examines the role of NaOH and Ca(OH2 on the hydrothermal decomposition of industrial jarosite deposited by a Mexican company in a tailings dam. The industrial jarosite is mainly composed by natrojarosite and contains 150 g Ag/t, showing a narrow particle size distribution, as revealed by XRD, fire assay, SEM-EDS and laser-diffraction analysis. The effect of the pH, when using NaOH or Ca(OH2 as alkalinizing agent was studied by carrying out decomposition experiments at different pH values and 60°C in a homogeneous size particle system (pH = 8, 9, 10 and 11 and in a heterogeneous size particle system (pH = 11. Also, the kinetic study of the process and the controlling step of the decomposition reaction when NaOH and Ca(OH2 are used was determined by fitting the data obtained to the shrinking core model for spherical particles of constant size. These results, supported by chemical (EDS, morphological (SEM and mapping of elements (EDS analysis of a partially reacted jarosite particle allowed to conclude that when NaOH is used, the process kinetics is controlled by the chemical reaction and when Ca(OH2 is used, the rate determining step is changed to a diffusion control through a layer of solid products.

Rate-determining Step of Flap Endonuclease 1 (FEN1) Reflects a Kinetic Bias against Long Flaps and Trinucleotide Repeat Sequences.

Science.gov (United States)

Tarantino, Mary E; Bilotti, Katharina; Huang, Ji; Delaney, Sarah

2015-08-21

Flap endonuclease 1 (FEN1) is a structure-specific nuclease responsible for removing 5'-flaps formed during Okazaki fragment maturation and long patch base excision repair. In this work, we use rapid quench flow techniques to examine the rates of 5'-flap removal on DNA substrates of varying length and sequence. Of particular interest are flaps containing trinucleotide repeats (TNR), which have been proposed to affect FEN1 activity and cause genetic instability. We report that FEN1 processes substrates containing flaps of 30 nucleotides or fewer at comparable single-turnover rates. However, for flaps longer than 30 nucleotides, FEN1 kinetically discriminates substrates based on flap length and flap sequence. In particular, FEN1 removes flaps containing TNR sequences at a rate slower than mixed sequence flaps of the same length. Furthermore, multiple-turnover kinetic analysis reveals that the rate-determining step of FEN1 switches as a function of flap length from product release to chemistry (or a step prior to chemistry). These results provide a kinetic perspective on the role of FEN1 in DNA replication and repair and contribute to our understanding of FEN1 in mediating genetic instability of TNR sequences. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Peak Muscle Activation, Joint Kinematics, and Kinetics during Elliptical and Stepping Movement Pattern on a Precor Adaptive Motion Trainer

Science.gov (United States)

Rogatzki, Matthew J.; Kernozek, Thomas W.; Willson, John D.; Greany, John F.; Hong, Di-An; Porcari, John P.

2012-01-01

Kinematic, kinetic, and electromyography data were collected from the biceps femoris, rectus femoris (RF), gluteus maximus, and erector spinae (ES) during a step and elliptical exercise at a standardized workload with no hand use. Findings depicted 95% greater ankle plantar flexion (p = 0.01), 29% more knee extension (p = 0.003), 101% higher peak…

An explicit multi-time-stepping algorithm for aerodynamic flows

NARCIS (Netherlands)

Niemann-Tuitman, B.E.; Veldman, A.E.P.

1997-01-01

An explicit multi-time-stepping algorithm with applications to aerodynamic flows is presented. In the algorithm, in different parts of the computational domain different time steps are taken, and the flow is synchronized at the so-called synchronization levels. The algorithm is validated for

Easy to use program “Simkine3” for simulating kinetic profiles of multi-step chemical Systems and optimisation of predictable rate coefficients therein

Directory of Open Access Journals (Sweden)

S.B. Jonnalagadda

2012-08-01

Full Text Available ‘Simkine3’, a Delphi based software is developed to simulate the kinetic schemes of complex reaction mechanisms involving multiple sequential and competitive elementary steps for homogeneous and heterogeneous chemical reactions. Simkine3 is designed to translate the user specified mechanism into chemical first-order differential equations (ODEs and optimise the estimated rate constants in such a way that simulated curves match the experimental kinetic profiles. TLSoda which uses backward differentiation method is utilised to solve resulting ODEs and Downhill Simplex method is used to optimise the estimated rate constants in a robotic way. An online help file is developed using HelpScrible Demo to guide the users of Simkine3. The versatility of the software is demonstrated by simulating the complex reaction between methylene violet and acidic bromate, a reaction which exhibits complex nonlinear kinetics. The new software is validated after testing it on a 19-step intricate mechanism involving 15 different species. The kinetic profiles of multiple simulated curves, illustrating the effect of initial concentrations of bromate, and bromide were matched with the corresponding experimental curves.DOI: http://dx.doi.org/10.4314/bcse.v26i2.10

Hydrothermal Atomic Force Microscopy Investigation of Barite Growth: Role of Spectator Ions in Elementary Step Edge Growth Kinetics and Hillock Morphology [Supporting Information Only

Energy Technology Data Exchange (ETDEWEB)

Jindra, Sarah A. [Wright State Univ., Dayton, OH (United States); Bertagni, Angela L. [Wright State Univ., Dayton, OH (United States); Bracco, Jacquelyn N. [Wright State Univ., Dayton, OH (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Higgins, Steven R. [Wright State Univ., Dayton, OH (United States)

2017-09-25

Here, to better understand the role of spectator ions in barite growth, the kinetics of step edge growth on barite (001) surfaces were studied under various salt solutions. Hydrothermal atomic force microscopy (HAFM) was used to investigate the effect of background electrolytes (NaCl, NaBr, and NaNO₃) as a function of saturation index and ionic strength (I) on barite growth sourced at dislocations at 108 °C. Results demonstrate that hillock morphology is affected by I, as well as type of anion, where the prevalence of steps aligned on the [010] direction is highest under Cl^–. There is a modest increase in kinetic coefficient of 55–130% with a 10-fold increase in I for each salt. In comparing the kinetic coefficients of the salts at low ionic strength (0.01 M), there is a moderate difference, suggesting that the anion may play a role in barium attachment.

Kinetic mechanism of human DNA ligase I reveals magnesium-dependent changes in the rate-limiting step that compromise ligation efficiency.

Science.gov (United States)

Taylor, Mark R; Conrad, John A; Wahl, Daniel; O'Brien, Patrick J

2011-07-01

DNA ligase I (LIG1) catalyzes the ligation of single-strand breaks to complete DNA replication and repair. The energy of ATP is used to form a new phosphodiester bond in DNA via a reaction mechanism that involves three distinct chemical steps: enzyme adenylylation, adenylyl transfer to DNA, and nick sealing. We used steady state and pre-steady state kinetics to characterize the minimal mechanism for DNA ligation catalyzed by human LIG1. The ATP dependence of the reaction indicates that LIG1 requires multiple Mg(2+) ions for catalysis and that an essential Mg(2+) ion binds more tightly to ATP than to the enzyme. Further dissection of the magnesium ion dependence of individual reaction steps revealed that the affinity for Mg(2+) changes along the reaction coordinate. At saturating concentrations of ATP and Mg(2+) ions, the three chemical steps occur at similar rates, and the efficiency of ligation is high. However, under conditions of limiting Mg(2+), the nick-sealing step becomes rate-limiting, and the adenylylated DNA intermediate is prematurely released into solution. Subsequent adenylylation of enzyme prevents rebinding to the adenylylated DNA intermediate comprising an Achilles' heel of LIG1. These ligase-generated 5'-adenylylated nicks constitute persistent breaks that are a threat to genomic stability if they are not repaired. The kinetic and thermodynamic framework that we have determined for LIG1 provides a starting point for understanding the mechanism and specificity of mammalian DNA ligases.

The Relaxation of Vicinal (001) with ZigZag [110] Steps

Science.gov (United States)

Hawkins, Micah; Hamouda, Ajmi Bh; González-Cabrera, Diego Luis; Einstein, Theodore L.

2012-02-01

This talk presents a kinetic Monte Carlo study of the relaxation dynamics of [110] steps on a vicinal (001) simple cubic surface. This system is interesting because [110] steps have different elementary excitation energetics and favor step diffusion more than close-packed [100] steps. In this talk we show how this leads to relaxation dynamics showing greater fluctuations on a shorter time scale for [110] steps as well as 2-bond breaking processes being rate determining in contrast to 3-bond breaking processes for [100] steps. The existence of a steady state is shown via the convergence of terrace width distributions at times much longer than the relaxation time. In this time regime excellent fits to the modified generalized Wigner distribution (as well as to the Berry-Robnik model when steps can overlap) were obtained. Also, step-position correlation function data show diffusion-limited increase for small distances along the step as well as greater average step displacement for zigzag steps compared to straight steps for somewhat longer distances along the step. Work supported by NSF-MRSEC Grant DMR 05-20471 as well as a DOE-CMCSN Grant.

Aggressive time step selection for the time asymptotic velocity diffusion problem

International Nuclear Information System (INIS)

Hewett, D.W.; Krapchev, V.B.; Hizanidis, K.; Bers, A.

1984-12-01

An aggressive time step selector for an ADI algorithm is preseneted that is applied to the linearized 2-D Fokker-Planck equation including an externally imposed quasilinear diffusion term. This method provides a reduction in CPU requirements by factors of two or three compared to standard ADI. More important, the robustness of the procedure greatly reduces the work load of the user. The procedure selects a nearly optimal Δt with a minimum of intervention by the user thus relieving the need to supervise the algorithm. In effect, the algorithm does its own supervision by discarding time steps made with Δt too large

Deuteration kinetics of the graphene

Energy Technology Data Exchange (ETDEWEB)

Nefedov, Alexei; Woell, Christof [KIT, Leopoldshafen (Germany); Paris, Alessio; Calliari, Lucia [FBK-CMM, Trento (Italy); Verbitskiy, Nikolay [MSU, Moscow (Russian Federation); University of Vienna, Vienna (Austria); Wang, Ying; Irle, Stephan [Nagoya University, Nagoya (Japan); Fedorov, Alexander [IFW Dresden, Dresden (Germany); St. Petersburg University, St. Petersburg (Russian Federation); Haberer, Danny; Knupfer, Martin; Buechner, Bernd [IFW Dresden, Dresden (Germany); Oetzelt, Martin [BESSY II, Berlin (Germany); Petaccia, Luca [Elettra, Trieste (Italy); Usachov, Dmitry [St. Petersburg University, St. Petersburg (Russian Federation); Vyalikh, Denis [St. Petersburg University, St. Petersburg (Russian Federation); TU Dresden, Dresden (Germany); Sagdev, Hermann [MPI fuer Polymerforschung, Mainz (Germany); Yashina, Lada [MSU, Moscow (Russian Federation); Grueneis, Alexander [IFW Dresden, Dresden (Germany); University of Vienna, Vienna (Austria)

2013-07-01

The kinetics of the hydrogenation/deuteration reaction of graphene was studied by time-dependent x-ray photoemission spectroscopy (XPS). The graphene layer was then exposed to hydrogen or deuterium atomic gas beams, obtained by thermal cracking in a tungsten capillary at T=3000 K. After each step XPS of the C1s line was performed in order to measure H/C and D/C ratios. We have observed a strong kinetic isotope effect for the hydrogenation/deuteration reaction leading to substantially faster adsorption and higher maximum D/C ratios as compared to H/C (D/C 35% vs. H/C 25%).

Kinematic and kinetic analysis of the knee joint before and after a PCL retaining total knee replacement during gait and single step ascent.

Science.gov (United States)

Apostolopoulos, Alexandros; Lallos, Stergios; Mastrokalos, Dimitrios; Michos, Ioannis; Darras, Nikolaos; Tzomaki, Magda; Efstathopoulos, Nikolaos

2011-01-01

The objective of this study was to capture and analyze the kinetics and kinematics and determine the functional performance of the osteoarthritic knee after a posterior cruciate ligament (PCL) retaining total knee arthroplasty. Kinematic and kinetic gait analysis of level walking was performed in 20 subjects (12 female and 8 male) with knee ostoarthritis. These patients were free of any neurological diseases that could affect their normal gait. Mean age was 69.6 ± 6.6 years; mean height was 157.6 cm ± 7.6 cm; and mean weight was 77.2 ± 12.1 kg. Full body gait analyses were performed using the BIOKIN 3D motion analysis system before and 9 months after total knee arthroplasty procedures. Single-step ascending kinetic analyses and plantar pressure distribution analyses were also performed for all subjects. International Knee Society Scores (IKSSs) were also assessed pre- and postoperatively. Significant increases were noted postoperatively in average cadence (preoperative mean = 99.26, postoperative mean = 110.5; p knee adduction moment were also reported postoperatively. All patients showed a significant improvement of knee kinetics and kinematics after a PCL retaining total knee arthroplasty. Significant differences were found in the cadence, step length, stride length, and walk velocity postoperatively. IKSSs also significantly improved. Further research is warranted to determine the clinical relevance of these findings.

Real-time hydrogen/deuterium exchange kinetics via supercharged electrospray ionization tandem mass spectrometry.

Science.gov (United States)

Sterling, Harry J; Williams, Evan R

2010-11-01

Amide hydrogen/deuterium exchange (HDX) rate constants of bovine ubiquitin in an ammonium acetate solution containing 1% of the electrospray ionization (ESI) "supercharging" reagent m-nitrobenzyl alcohol (m-NBA) were obtained using top-down, electron transfer dissociation (ETD) tandem mass spectrometry (MS). The supercharging reagent replaces the acid and temperature "quench" step in the conventional MS approach to HDX experiments by causing rapid protein denaturation to occur in the ESI droplet. The higher charge state ions that are produced with m-NBA are more unfolded, as measured by ion mobility, and result in higher fragmentation efficiency and higher sequence coverage with ETD. Single amino acid resolution was obtained for 44 of 72 exchangeable amide sites, and summed kinetic data were obtained for regions of the protein where adjacent fragment ions were not observed, resulting in an overall spatial resolution of 1.3 residues. Comparison of these results with previous values from NMR indicates that the supercharging reagent does not cause significant structural changes to the protein in the initial ESI solution and that scrambling or back-exchange is minimal. This new method for top-down HDX-MS enables real-time kinetic data measurements under physiological conditions, similar to those obtained using NMR, with comparable spatial resolution and significantly better sensitivity.

GOTHIC: Gravitational oct-tree code accelerated by hierarchical time step controlling

Science.gov (United States)

Miki, Yohei; Umemura, Masayuki

2017-04-01

The tree method is a widely implemented algorithm for collisionless N-body simulations in astrophysics well suited for GPU(s). Adopting hierarchical time stepping can accelerate N-body simulations; however, it is infrequently implemented and its potential remains untested in GPU implementations. We have developed a Gravitational Oct-Tree code accelerated by HIerarchical time step Controlling named GOTHIC, which adopts both the tree method and the hierarchical time step. The code adopts some adaptive optimizations by monitoring the execution time of each function on-the-fly and minimizes the time-to-solution by balancing the measured time of multiple functions. Results of performance measurements with realistic particle distribution performed on NVIDIA Tesla M2090, K20X, and GeForce GTX TITAN X, which are representative GPUs of the Fermi, Kepler, and Maxwell generation of GPUs, show that the hierarchical time step achieves a speedup by a factor of around 3-5 times compared to the shared time step. The measured elapsed time per step of GOTHIC is 0.30 s or 0.44 s on GTX TITAN X when the particle distribution represents the Andromeda galaxy or the NFW sphere, respectively, with 224 = 16,777,216 particles. The averaged performance of the code corresponds to 10-30% of the theoretical single precision peak performance of the GPU.

Generalized Runge-Kutta method for two- and three-dimensional space-time diffusion equations with a variable time step

International Nuclear Information System (INIS)

Aboanber, A.E.; Hamada, Y.M.

2008-01-01

An extensive knowledge of the spatial power distribution is required for the design and analysis of different types of current-generation reactors, and that requires the development of more sophisticated theoretical methods. Therefore, the need to develop new methods for multidimensional transient reactor analysis still exists. The objective of this paper is to develop a computationally efficient numerical method for solving the multigroup, multidimensional, static and transient neutron diffusion kinetics equations. A generalized Runge-Kutta method has been developed for the numerical integration of the stiff space-time diffusion equations. The method is fourth-order accurate, using an embedded third-order solution to arrive at an estimate of the truncation error for automatic time step control. In addition, the A(α)-stability properties of the method are investigated. The analyses of two- and three-dimensional benchmark problems as well as static and transient problems, demonstrate that very accurate solutions can be obtained with assembly-sized spatial meshes. Preliminary numerical evaluations using two- and three-dimensional finite difference codes showed that the presented generalized Runge-Kutta method is highly accurate and efficient when compared with other optimized iterative numerical and conventional finite difference methods

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

Science.gov (United States)

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.

Role of step stiffness and kinks in the relaxation of vicinal (001) with zigzag [110] steps

Science.gov (United States)

Mahjoub, B.; Hamouda, Ajmi BH.; Einstein, TL.

2017-08-01

We present a kinetic Monte Carlo study of the relaxation dynamics and steady state configurations of 〈110〉 steps on a vicinal (001) simple cubic surface. This system is interesting because 〈110〉 (fully kinked) steps have different elementary excitation energetics and favor step diffusion more than 〈100〉 (nominally straight) steps. In this study we show how this leads to different relaxation dynamics as well as to different steady state configurations, including that 2-bond breaking processes are rate determining for 〈110〉 steps in contrast to 3-bond breaking processes for 〈100〉-steps found in previous work [Surface Sci. 602, 3569 (2008)]. The analysis of the terrace-width distribution (TWD) shows a significant role of kink-generation-annihilation processes during the relaxation of steps: the kinetic of relaxation, toward the steady state, is much faster in the case of 〈110〉-zigzag steps, with a higher standard deviation of the TWD, in agreement with a decrease of step stiffness due to orientation. We conclude that smaller step stiffness leads inexorably to faster step dynamics towards the steady state. The step-edge anisotropy slows the relaxation of steps and increases the strength of step-step effective interactions.

Flow-Based Systems for Rapid and High-Precision Enzyme Kinetics Studies

Directory of Open Access Journals (Sweden)

Supaporn Kradtap Hartwell

2012-01-01

Full Text Available Enzyme kinetics studies normally focus on the initial rate of enzymatic reaction. However, the manual operation of steps of the conventional enzyme kinetics method has some drawbacks. Errors can result from the imprecise time control and time necessary for manual changing the reaction cuvettes into and out of the detector. By using the automatic flow-based analytical systems, enzyme kinetics studies can be carried out at real-time initial rate avoiding the potential errors inherent in manual operation. Flow-based systems have been developed to provide rapid, low-volume, and high-precision analyses that effectively replace the many tedious and high volume requirements of conventional wet chemistry analyses. This article presents various arrangements of flow-based techniques and their potential use in future enzyme kinetics applications.

An adaptive time-stepping strategy for solving the phase field crystal model

International Nuclear Information System (INIS)

Zhang, Zhengru; Ma, Yuan; Qiao, Zhonghua

2013-01-01

In this work, we will propose an adaptive time step method for simulating the dynamics of the phase field crystal (PFC) model. The numerical simulation of the PFC model needs long time to reach steady state, and then large time-stepping method is necessary. Unconditionally energy stable schemes are used to solve the PFC model. The time steps are adaptively determined based on the time derivative of the corresponding energy. It is found that the use of the proposed time step adaptivity cannot only resolve the steady state solution, but also the dynamical development of the solution efficiently and accurately. The numerical experiments demonstrate that the CPU time is significantly saved for long time simulations

Chemical kinetic modeling of H{sub 2} applications

Energy Technology Data Exchange (ETDEWEB)

Marinov, N.M.; Westbrook, C.K.; Cloutman, L.D. [Lawrence Livermore National Lab., CA (United States)] [and others

1995-09-01

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

A variable-order time-dependent neutron transport method for nuclear reactor kinetics using analytically-integrated space-time characteristics

International Nuclear Information System (INIS)

Hoffman, A. J.; Lee, J. C.

2013-01-01

A new time-dependent neutron transport method based on the method of characteristics (MOC) has been developed. Whereas most spatial kinetics methods treat time dependence through temporal discretization, this new method treats time dependence by defining the characteristics to span space and time. In this implementation regions are defined in space-time where the thickness of the region in time fulfills an analogous role to the time step in discretized methods. The time dependence of the local source is approximated using a truncated Taylor series expansion with high order derivatives approximated using backward differences, permitting the solution of the resulting space-time characteristic equation. To avoid a drastic increase in computational expense and memory requirements due to solving many discrete characteristics in the space-time planes, the temporal variation of the boundary source is similarly approximated. This allows the characteristics in the space-time plane to be represented analytically rather than discretely, resulting in an algorithm comparable in implementation and expense to one that arises from conventional time integration techniques. Furthermore, by defining the boundary flux time derivative in terms of the preceding local source time derivative and boundary flux time derivative, the need to store angularly-dependent data is avoided without approximating the angular dependence of the angular flux time derivative. The accuracy of this method is assessed through implementation in the neutron transport code DeCART. The method is employed with variable-order local source representation to model a TWIGL transient. The results demonstrate that this method is accurate and more efficient than the discretized method. (authors)

A new method to characterize the kinetics of cholinesterases inhibited by carbamates.

Science.gov (United States)

Xiao, Qiaoling; Zhou, Huimin; Wei, Hong; Du, Huaqiao; Tan, Wen; Zhan, Yiyi; Pistolozzi, Marco

2017-09-10

The inhibition of cholinesterases (ChEs) by carbamates includes a carbamylation (inhibition) step, in which the drug transfers its carbamate moiety to the active site of the enzyme and a decarbamylation (activity recovery) step, in which the carbamyl group is hydrolyzed from the enzyme. The carbamylation and decarbamylation kinetics decide the extent and the duration of the inhibition, thus the full characterization of candidate carbamate inhibitors requires the measurement of the kinetic constants describing both steps. Carbamylation and decarbamylation rate constants are traditionally measured by two separate set of experiments, thus making the full characterization of candidate inhibitors time-consuming. In this communication we show that by the analysis of the area under the inhibition-time curve of cholinesterases inhibited by carbamates it is possible to calculate the decarbamylation rate constant from the same data traditionally used to characterize only the carbamylation kinetics, therefore it is possible to obtain a full characterization of the inhibition with a single set of experiments. The characterization of the inhibition kinetics of human and dog plasma butyrylcholinesterase and of human acetylcholinesterase by bambuterol and bambuterol monocarbamate enantiomers was used to demonstrate the validity of the approach. The results showed that the proposed method provides reliable estimations of carbamylation and decarbamylation rate constants thus representing a simple and useful approach to reduce the time required for the characterization of carbamate inhibitors. Copyright © 2017 Elsevier B.V. All rights reserved.

Modeling and Elucidation of the Kinetics of Multiple Consecutive Photoreactions AB4(4Φ) With Φ-order Kinetics. Application to the Photodegradation of Riboflavin.

Science.gov (United States)

Maafi, Mounir; Maafi, Wassila

2016-12-01

New semi-empirical rate-law system of equations is proposed for the first time for consecutive photoreactions that involve up to 4 photoreaction steps, AB 4 (4Φ). The equation system was developed, tested, and validated against synthetic kinetic traces generated by fifth-order Runge-Kutta calculations. The model accurately fitted the kinetic traces of Riboflavin photodegradation in ethanol which decomposes via the AB 2 (2Φ) mechanism involving 2 consecutive photoreaction steps. A kinetic elucidation methodology useful for consecutive photoreactions was also proposed to determine all the kinetic parameters and reaction attributes defining AB 2 (2Φ) reactions. The quantum yields of photodegradation, determined for wavelengths in the visible region 400-480 nm, ranged from 0.005 to 0.00756 and 0.0012 to 8 10 -5 for the first and second photoreaction steps, respectively. They were found to increase with wavelength in defined sigmoid functions. For this monochromatic irradiation range, riboflavin proved to be a useful actinometer. Finally, a photodegradation scale based on pseudo-rate-constant values was also proposed for drugs. This scale (including 4 groups) is thought to contribute to rationalizing photodegradation testing and might prove useful in categorizing drugs' photodegradation reactivity. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

A kinematic analysis of the rapid step test in balance-impaired and unimpaired older women.

Science.gov (United States)

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

2007-04-01

Little is known about the kinematic and kinetic determinants that might explain age and balance-impairment alterations in the results of volitional stepping performance tests. Maximal unipedal stance time (UST) was used to distinguish "balance-impaired" old (BI, UST30s, N=12, mean age=71 years) before they and healthy young females (Y, UST>30s, N=13, mean age=23 years) performed the rapid step test (RST). The RST evaluates the time required to take volitional front, side, and back steps of at least 80% maximum step length in response to verbal commands. Kinematic and kinetic data were recorded during the RST. The results indicate that the initiation phase of the step was the major source of age- and balance impairment-related delays. The delays in BI were primarily caused by increased postural adjustments prior to step initiation, as measured by center-of-pressure (COP) path length (p<0.003). The Step landing phase showed similar, but non-significant, temporal trends. Step length and peak center-of-mass (COM) deceleration during the Step-Out landing decreased in O by 18% (p=0.0002) and 24% (p=0.001), respectively, and a further 12% (p=0.04) and 18% (p=0.08) in BI. We conclude that the delay in BI step initiation was due to the increase in their postural adjustments prior to step initiation.

Coherent states for the time dependent harmonic oscillator: the step function

International Nuclear Information System (INIS)

Moya-Cessa, Hector; Fernandez Guasti, Manuel

2003-01-01

We study the time evolution for the quantum harmonic oscillator subjected to a sudden change of frequency. It is based on an approximate analytic solution to the time dependent Ermakov equation for a step function. This approach allows for a continuous treatment that differs from former studies that involve the matching of two time independent solutions at the time when the step occurs

Butia Yatay coconut oil: Process development for biodiesel production and kinetics of esterification with ethanol

International Nuclear Information System (INIS)

Zanuttini, M.S.; Pisarello, M.L.; Querini, C.A.

2014-01-01

Highlights: • Coconut oil contains high levels of phosphorous and free fatty acids. • Especial degumming process is needed in order to decrease the phosphorous content. • Kinetic constant for esterification reaction decreases as a function of time. • Two-step esterification is more efficient to reduce acidity than one-step. • Approximately 15% of esters are formed by acid-catalyzed transesterification. - Abstract: The aim of this work is to study biodiesel production using Butia Yatay coconut oil. This oil has acid values between 109 and 140 mg KOH/g, and phosphorus content in the order of 600 ppm. A three-step degumming pre-treatment of the raw material was adjusted in order to decrease the phosphorus content to approximately 200 ppm. Afterwards, a two-step esterification followed by transesterification was required in order to obtain a high-quality product. The esterification kinetics was studied including the simultaneous reactions that take place during the esterification of free fatty acids: autocatalysis, triacylglycerides hydrolysis, transesterification, and the reaction of sulphuric acid with the alcohol, being the most important ones. The kinetic parameters for the esterification and autocatalysis reactions were also obtained, being different compared to sunflower oil, due to the presence of short chain fatty acids. The kinetic constant for the esterification reaction rapidly decreases as a function of time, due to the consumption of the catalyst by the alkyl-sulphate formation reaction

Using linear time-invariant system theory to estimate kinetic parameters directly from projection measurements

International Nuclear Information System (INIS)

Zeng, G.L.; Gullberg, G.T.

1995-01-01

It is common practice to estimate kinetic parameters from dynamically acquired tomographic data by first reconstructing a dynamic sequence of three-dimensional reconstructions and then fitting the parameters to time activity curves generated from the time-varying reconstructed images. However, in SPECT, the pharmaceutical distribution can change during the acquisition of a complete tomographic data set, which can bias the estimated kinetic parameters. It is hypothesized that more accurate estimates of the kinetic parameters can be obtained by fitting to the projection measurements instead of the reconstructed time sequence. Estimation from projections requires the knowledge of their relationship between the tissue regions of interest or voxels with particular kinetic parameters and the project measurements, which results in a complicated nonlinear estimation problem with a series of exponential factors with multiplicative coefficients. A technique is presented in this paper where the exponential decay parameters are estimated separately using linear time-invariant system theory. Once the exponential factors are known, the coefficients of the exponentials can be estimated using linear estimation techniques. Computer simulations demonstrate that estimation of the kinetic parameters directly from the projections is more accurate than the estimation from the reconstructed images

Effects of altered sagittal trunk orientation on kinetic pattern in able-bodied walking on uneven ground

Directory of Open Access Journals (Sweden)

Soran Aminiaghdam

2017-07-01

Full Text Available Studies of disturbed human locomotion often focus on the dynamics of the gait when either posture, movement or surface is perturbed. Yet, the interaction effects of variation of trunk posture and ground level on kinetic behaviour of able-bodied gait have not been explored. For 12 participants we investigated the kinetic behaviour, as well as velocity and contact time, across four steps including an unperturbed step on level ground, pre-perturbation, perturbation (10-cm drop and post-perturbation steps while walking with normal speed with four postures: regular erect, with 30°, 50° and maximal sagittal trunk flexion (70°. Two-way repeated measures ANOVAs detected significant interactions of posture×step for the second peak of the vertical ground reaction force (GRF, propulsive impulse, contact time and velocity. An increased trunk flexion was associated with a systematic decrease of the second GRF peak during all steps and with a decreased contact time and an increased velocity across steps, except for the perturbation step. Pre-adaptations were more pronounced in the approach step to the drop in regular erect gait. With increased trunk flexion, walking on uneven ground exhibited reduced changes in GRF kinetic parameters relative to upright walking. It seems that in trunk-flexed gaits the trunk is used in a compensatory way during the step-down to accommodate changes in ground level by adjusting its angle leading to lower variations in centre of mass height. Exploitation of this mechanism resembles the ability of small birds in adjusting their zig-zag-like configured legs to cope with changes in ground level.

Adaptive Time Stepping for Transient Network Flow Simulation in Rocket Propulsion Systems

Science.gov (United States)

Majumdar, Alok K.; Ravindran, S. S.

2017-01-01

Fluid and thermal transients found in rocket propulsion systems such as propellant feedline system is a complex process involving fast phases followed by slow phases. Therefore their time accurate computation requires use of short time step initially followed by the use of much larger time step. Yet there are instances that involve fast-slow-fast phases. In this paper, we present a feedback control based adaptive time stepping algorithm, and discuss its use in network flow simulation of fluid and thermal transients. The time step is automatically controlled during the simulation by monitoring changes in certain key variables and by feedback. In order to demonstrate the viability of time adaptivity for engineering problems, we applied it to simulate water hammer and cryogenic chill down in pipelines. Our comparison and validation demonstrate the accuracy and efficiency of this adaptive strategy.

A novel fractional technique for the modified point kinetics equations

Directory of Open Access Journals (Sweden)

Ahmed E. Aboanber

2016-10-01

Full Text Available A fractional model for the modified point kinetics equations is derived and analyzed. An analytical method is used to solve the fractional model for the modified point kinetics equations. This methodical technique is based on the representation of the neutron density as a power series of the relaxation time as a small parameter. The validity of the fractional model is tested for different cases of step, ramp and sinusoidal reactivity. The results show that the fractional model for the modified point kinetics equations is the best representation of neutron density for subcritical and supercritical reactors.

Evidence for Dynamic Chemical Kinetics at Individual Molecular Ruthenium Catalysts.

Science.gov (United States)

Easter, Quinn T; Blum, Suzanne A

2018-02-05

Catalytic cycles are typically depicted as possessing time-invariant steps with fixed rates. Yet the true behavior of individual catalysts with respect to time is unknown, hidden by the ensemble averaging inherent to bulk measurements. Evidence is presented for variable chemical kinetics at individual catalysts, with a focus on ring-opening metathesis polymerization catalyzed by the second-generation Grubbs' ruthenium catalyst. Fluorescence microscopy is used to probe the chemical kinetics of the reaction because the technique possesses sufficient sensitivity for the detection of single chemical reactions. Insertion reactions in submicron regions likely occur at groups of many (not single) catalysts, yet not so many that their unique kinetic behavior is ensemble averaged. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-resolution seismic wave propagation using local time stepping

KAUST Repository

Peter, Daniel; Rietmann, Max; Galvez, Percy; Ampuero, Jean Paul

2017-01-01

High-resolution seismic wave simulations often require local refinements in numerical meshes to accurately capture e.g. steep topography or complex fault geometry. Together with explicit time schemes, this dramatically reduces the global time step

Molecular dynamics based enhanced sampling of collective variables with very large time steps

Science.gov (United States)

Chen, Pei-Yang; Tuckerman, Mark E.

2018-01-01

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Thermodynamic, kinetic and mechanistic investigations of ...

Indian Academy of Sciences (India)

with respect to the rate determining step and the thermodynamic quantities with respect to the equilibrium steps were evaluated and ... are, (1) to establish a rate law through kinetic measure- ments, (2) to ..... second and third equilibrium steps.

[Collaborative application of BEPS at different time steps.

Science.gov (United States)

Lu, Wei; Fan, Wen Yi; Tian, Tian

2016-09-01

BEPSHourly is committed to simulate the ecological and physiological process of vegetation at hourly time steps, and is often applied to analyze the diurnal change of gross primary productivity (GPP), net primary productivity (NPP) at site scale because of its more complex model structure and time-consuming solving process. However, daily photosynthetic rate calculation in BEPSDaily model is simpler and less time-consuming, not involving many iterative processes. It is suitable for simulating the regional primary productivity and analyzing the spatial distribution of regional carbon sources and sinks. According to the characteristics and applicability of BEPSDaily and BEPSHourly models, this paper proposed a method of collaborative application of BEPS at daily and hourly time steps. Firstly, BEPSHourly was used to optimize the main photosynthetic parameters: the maximum rate of carboxylation (V c max ) and the maximum rate of photosynthetic electron transport (J max ) at site scale, and then the two optimized parameters were introduced into BEPSDaily model to estimate regional NPP at regional scale. The results showed that optimization of the main photosynthesis parameters based on the flux data could improve the simulate ability of the model. The primary productivity of different forest types in descending order was deciduous broad-leaved forest, mixed forest, coniferous forest in 2011. The collaborative application of carbon cycle models at different steps proposed in this study could effectively optimize the main photosynthesis parameters V c max and J max , simulate the monthly averaged diurnal GPP, NPP, calculate the regional NPP, and analyze the spatial distribution of regional carbon sources and sinks.

Extending Newton's law from nonlocal-in-time kinetic energy

International Nuclear Information System (INIS)

Suykens, J.A.K.

2009-01-01

We study a new equation of motion derived from a context of classical Newtonian mechanics by replacing the kinetic energy with a form of nonlocal-in-time kinetic energy. It leads to a hypothetical extension of Newton's second law of motion. In a first stage the obtainable solution form is studied by considering an unknown value for the nonlocality time extent. This is done in relation to higher-order Euler-Lagrange equations and a Hamiltonian framework. In a second stage the free particle case and harmonic oscillator case are studied and compared with quantum mechanical results. For a free particle it is shown that the solution form is a superposition of the classical straight line motion and a Fourier series. We discuss the link with quanta interpretations made in Pais-Uhlenbeck oscillators. The discrete nature emerges from the continuous time setting through application of the least action principle. The harmonic oscillator case leads to energy levels that approximately correspond to the quantum harmonic oscillator levels. The solution to the extended Newton equation also admits a quantization of the nonlocality time extent, which is determined by the classical oscillator frequency. The extended equation suggests a new possible way for understanding the relationship between classical and quantum mechanics

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

Science.gov (United States)

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

Studies on steps affecting tritium residence time in solid blanket

International Nuclear Information System (INIS)

Tanaka, Satoru

1987-01-01

For the self sustaining of CTR fuel cycle, the effective tritium recovery from blankets is essential. This means that not only tritium breeding ratio must be larger than 1.0, but also high recovering speed is required for the short residence time of tritium in blankets. Short residence time means that the tritium inventory in blankets is small. In this paper, the tritium residence time and tritium inventory in a solid blanket are modeled by considering the steps constituting tritium release. Some of these tritium migration processes were experimentally evaluated. The tritium migration steps in a solid blanket using sintered breeding materials consist of diffusion in grains, desorption at grain edges, diffusion and permeation through grain boundaries, desorption at particle edges, diffusion and percolation through interconnected pores to purging stream, and convective mass transfer to stream. Corresponding to these steps, diffusive, soluble, adsorbed and trapped tritium inventories and the tritium in gas phase are conceivable. The code named TTT was made for calculating these tritium inventories and the residence time of tritium. An example of the results of calculation is shown. The blanket is REPUTER-1, which is the conceptual design of a commercial reversed field pinch fusion reactor studied at the University of Tokyo. The experimental studies on the migration steps of tritium are reported. (Kako, I.)

Kinetic analysis of overlapping multistep thermal decomposition comprising exothermic and endothermic processes: thermolysis of ammonium dinitramide.

Science.gov (United States)

Muravyev, Nikita V; Koga, Nobuyoshi; Meerov, Dmitry B; Pivkina, Alla N

2017-01-25

This study focused on kinetic modeling of a specific type of multistep heterogeneous reaction comprising exothermic and endothermic reaction steps, as exemplified by the practical kinetic analysis of the experimental kinetic curves for the thermal decomposition of molten ammonium dinitramide (ADN). It is known that the thermal decomposition of ADN occurs as a consecutive two step mass-loss process comprising the decomposition of ADN and subsequent evaporation/decomposition of in situ generated ammonium nitrate. These reaction steps provide exothermic and endothermic contributions, respectively, to the overall thermal effect. The overall reaction process was deconvoluted into two reaction steps using simultaneously recorded thermogravimetry and differential scanning calorimetry (TG-DSC) curves by considering the different physical meanings of the kinetic data derived from TG and DSC by P value analysis. The kinetic data thus separated into exothermic and endothermic reaction steps were kinetically characterized using kinetic computation methods including isoconversional method, combined kinetic analysis, and master plot method. The overall kinetic behavior was reproduced as the sum of the kinetic equations for each reaction step considering the contributions to the rate data derived from TG and DSC. During reproduction of the kinetic behavior, the kinetic parameters and contributions of each reaction step were optimized using kinetic deconvolution analysis. As a result, the thermal decomposition of ADN was successfully modeled as partially overlapping exothermic and endothermic reaction steps. The logic of the kinetic modeling was critically examined, and the practical usefulness of phenomenological modeling for the thermal decomposition of ADN was illustrated to demonstrate the validity of the methodology and its applicability to similar complex reaction processes.

Optimal order and time-step criterion for Aarseth-type N-body integrators

International Nuclear Information System (INIS)

Makino, Junichiro

1991-01-01

How the selection of the time-step criterion and the order of the integrator change the efficiency of Aarseth-type N-body integrators is discussed. An alternative to Aarseth's scheme based on the direct calculation of the time derivative of the force using the Hermite interpolation is compared to Aarseth's scheme, which uses the Newton interpolation to construct the predictor and corrector. How the number of particles in the system changes the behavior of integrators is examined. The Hermite scheme allows a time step twice as large as that for the standard Aarseth scheme for the same accuracy. The calculation cost of the Hermite scheme per time step is roughly twice as much as that of the standard Aarseth scheme. The optimal order of the integrators depends on both the particle number and the accuracy required. The time-step criterion of the standard Aarseth scheme is found to be inapplicable to higher-order integrators, and a more uniformly reliable criterion is proposed. 18 refs

Empiric model for mean generation time adjustment factor for classic point kinetics equations

Energy Technology Data Exchange (ETDEWEB)

Goes, David A.B.V. de; Martinez, Aquilino S.; Goncalves, Alessandro da C., E-mail: david.goes@poli.ufrj.br, E-mail: aquilino@lmp.ufrj.br, E-mail: alessandro@con.ufrj.br [Coordenacao de Pos-Graduacao e Pesquisa de Engenharia (COPPE/UFRJ), Rio de Janeiro, RJ (Brazil). Departamento de Engenharia Nuclear

2017-11-01

Point reactor kinetics equations are the easiest way to observe the neutron production time behavior in a nuclear reactor. These equations are derived from the neutron transport equation using an approximation called Fick's law leading to a set of first order differential equations. The main objective of this study is to review classic point kinetics equation in order to approximate its results to the case when it is considered the time variation of the neutron currents. The computational modeling used for the calculations is based on the finite difference method. The results obtained with this model are compared with the reference model and then it is determined an empirical adjustment factor that modifies the point reactor kinetics equation to the real scenario. (author)

Empiric model for mean generation time adjustment factor for classic point kinetics equations

International Nuclear Information System (INIS)

Goes, David A.B.V. de; Martinez, Aquilino S.; Goncalves, Alessandro da C.

2017-01-01

Point reactor kinetics equations are the easiest way to observe the neutron production time behavior in a nuclear reactor. These equations are derived from the neutron transport equation using an approximation called Fick's law leading to a set of first order differential equations. The main objective of this study is to review classic point kinetics equation in order to approximate its results to the case when it is considered the time variation of the neutron currents. The computational modeling used for the calculations is based on the finite difference method. The results obtained with this model are compared with the reference model and then it is determined an empirical adjustment factor that modifies the point reactor kinetics equation to the real scenario. (author)

Real-time imaging of vertically aligned carbon nanotube array growth kinetics

International Nuclear Information System (INIS)

Puretzky, A A; Eres, G; Rouleau, C M; Ivanov, I N; Geohegan, D B

2008-01-01

In situ time-lapse photography and laser irradiation are applied to understand unusual coordinated growth kinetics of vertically aligned carbon nanotube arrays including pauses in growth, retraction, and local equilibration in length. A model is presented which explains the measured kinetics and determines the conditions for diffusion-limited growth. Laser irradiation of the growing nanotube arrays is first used to prove that the nanotubes grow from catalyst particles at their bases, and then increase their growth rate and terminal lengths

Three-dimensional space-time kinetic analysis with CORETRAN and RETRAN-3D of the NEACRP PWR rod ejection benchmark

Energy Technology Data Exchange (ETDEWEB)

Ferroukhi, H.; Coddington, P

2001-03-01

One of the activities within the STARS project, in the Laboratory for Reactor Physics and System Behaviour; is the development of a coupling methodology between the three-dimensional, space-time kinetics codes CORETRAN and RETRAN-3D in order to perform core and plant transient analyses of the Swiss LWRs. The CORETRAN code is a 3-D full-core simulator, intended to be used for core-related analyses, while RETRAN-3D is the three-dimensional kinetics version of the plant system code RETRAN, and can therefore be used for best-estimate analyses of a wide range of transients in both PWRs and BWRs. Because the neutronics solver in both codes is based on the same kinetics model, one important advantage is that the codes can be coupled so that the initial conditions for a RETRAN-3D plant analysis are generated by a detailed-core, steady-state calculation using CORETRAN. As a first step towards using CORETRAN and RETRAN-3D for kinetic applications, the NEACRP PWR rod ejection benchmark has been analyzed with both codes, and is presented in this paper. The first objective is to verify the consistency between the static and kinetic solutions of the two codes, and so gain confidence in the coupling methodology. The second objective is to assess the CORETRAN and RETRAN-3D solutions for a well-defined RIA transient, comparing with previously published results. In parallel, several sensitivity studies have been performed in an attempt to identify models and calculational options important for a correct analysis of an RIA event in a LWR using these two codes. (author)

Formulation of an explicit-multiple-time-step time integration method for use in a global primitive equation grid model

Science.gov (United States)

Chao, W. C.

1982-01-01

With appropriate modifications, a recently proposed explicit-multiple-time-step scheme (EMTSS) is incorporated into the UCLA model. In this scheme, the linearized terms in the governing equations that generate the gravity waves are split into different vertical modes. Each mode is integrated with an optimal time step, and at periodic intervals these modes are recombined. The other terms are integrated with a time step dictated by the CFL condition for low-frequency waves. This large time step requires a special modification of the advective terms in the polar region to maintain stability. Test runs for 72 h show that EMTSS is a stable, efficient and accurate scheme.

Time dependent theory of two-step absorption of two pulses

Energy Technology Data Exchange (ETDEWEB)

Rebane, Inna, E-mail: inna.rebane@ut.ee

2015-09-25

The time dependent theory of two step-absorption of two different light pulses with arbitrary duration in the electronic three-level model is proposed. The probability that the third level is excited at the moment t is found in depending on the time delay between pulses, the spectral widths of the pulses and the energy relaxation constants of the excited electronic levels. The time dependent perturbation theory is applied without using “doorway–window” approach. The time and spectral behavior of the spectrum using in calculations as simple as possible model is analyzed. - Highlights: • Time dependent theory of two-step absorption in the three-level model is proposed. • Two different light pulses with arbitrary duration is observed. • The time dependent perturbation theory is applied without “door–window” approach. • The time and spectral behavior of the spectra is analyzed for several cases.

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

Science.gov (United States)

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.

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

International Nuclear Information System (INIS)

Koide, Jun

2002-01-01

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

Multiple time step integrators in ab initio molecular dynamics

International Nuclear Information System (INIS)

Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

2014-01-01

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy

Stability analysis and time-step limits for a Monte Carlo Compton-scattering method

International Nuclear Information System (INIS)

Densmore, Jeffery D.; Warsa, James S.; Lowrie, Robert B.

2010-01-01

A Monte Carlo method for simulating Compton scattering in high energy density applications has been presented that models the photon-electron collision kinematics exactly [E. Canfield, W.M. Howard, E.P. Liang, Inverse Comptonization by one-dimensional relativistic electrons, Astrophys. J. 323 (1987) 565]. However, implementing this technique typically requires an explicit evaluation of the material temperature, which can lead to unstable and oscillatory solutions. In this paper, we perform a stability analysis of this Monte Carlo method and develop two time-step limits that avoid undesirable behavior. The first time-step limit prevents instabilities, while the second, more restrictive time-step limit avoids both instabilities and nonphysical oscillations. With a set of numerical examples, we demonstrate the efficacy of these time-step limits.

Optimization of the Kinetic Activation-Relaxation Technique, an off-lattice and self-learning kinetic Monte-Carlo method

International Nuclear Information System (INIS)

Joly, Jean-François; Béland, Laurent Karim; Brommer, Peter; Mousseau, Normand; El-Mellouhi, Fedwa

2012-01-01

We present two major optimizations for the kinetic Activation-Relaxation Technique (k-ART), an off-lattice self-learning kinetic Monte Carlo (KMC) algorithm with on-the-fly event search THAT has been successfully applied to study a number of semiconducting and metallic systems. K-ART is parallelized in a non-trivial way: A master process uses several worker processes to perform independent event searches for possible events, while all bookkeeping and the actual simulation is performed by the master process. Depending on the complexity of the system studied, the parallelization scales well for tens to more than one hundred processes. For dealing with large systems, we present a near order 1 implementation. Techniques such as Verlet lists, cell decomposition and partial force calculations are implemented, and the CPU time per time step scales sublinearly with the number of particles, providing an efficient use of computational resources.

Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein-Ligand Residence Times.

Science.gov (United States)

Mollica, Luca; Theret, Isabelle; Antoine, Mathias; Perron-Sierra, Françoise; Charton, Yves; Fourquez, Jean-Marie; Wierzbicki, Michel; Boutin, Jean A; Ferry, Gilles; Decherchi, Sergio; Bottegoni, Giovanni; Ducrot, Pierre; Cavalli, Andrea

2016-08-11

Ligand-target residence time is emerging as a key drug discovery parameter because it can reliably predict drug efficacy in vivo. Experimental approaches to binding and unbinding kinetics are nowadays available, but we still lack reliable computational tools for predicting kinetics and residence time. Most attempts have been based on brute-force molecular dynamics (MD) simulations, which are CPU-demanding and not yet particularly accurate. We recently reported a new scaled-MD-based protocol, which showed potential for residence time prediction in drug discovery. Here, we further challenged our procedure's predictive ability by applying our methodology to a series of glucokinase activators that could be useful for treating type 2 diabetes mellitus. We combined scaled MD with experimental kinetics measurements and X-ray crystallography, promptly checking the protocol's reliability by directly comparing computational predictions and experimental measures. The good agreement highlights the potential of our scaled-MD-based approach as an innovative method for computationally estimating and predicting drug residence times.

The instability in the long-time regime of a kinetic model: II

International Nuclear Information System (INIS)

Sanda, F

2003-01-01

The kinetic model of an open system, which embodies an instability in long time regime behaviour, is referred. This result questions some approximations which are standardly used in open system treatments. The deficiency in kinetic treatments was recently referred to as mainly a mathematical curiosity; however, in the present work the application for a physically comprehensive situation is shown. We simplified the previously treated model, which enables us to proceed easily with just pen and paper and to omit numerical modelling whose justification causes difficulties to the reader. We draw some consequences on the found instability, both with respect to the perturbative origin of kinetic equations and also concerning the very philosophy of physical modelling

Analytic solutions of the multigroup space-time reactor kinetics equations

International Nuclear Information System (INIS)

Lee, C.E.; Rottler, S.

1986-01-01

The development of analytical and numerical solutions to the reactor kinetics equations is reviewed. Analytic solutions of the multigroup space-time reactor kinetics equations are developed for bare and reflected slabs and spherical reactors for zero flux, zero current and extrapolated endpoint boundary conditions. The material properties of the reactors are assumed constant in space and time, but spatially-dependent source terms and initial conditions are investigated. The system of partial differential equations is reduced to a set of linear ordinary differential equations by the Laplace transform method. These equations are solved by matrix Green's functions yielding a general matrix solution for the neutron flux and precursor concentration in the Laplace transform space. The detailed pole structure of the Laplace transform matrix solutions is investigated. The temporally- and spatially-dependent solutions are determined from the inverse Laplace transform using the Cauchy residue theorem, the theorem of Frobenius, a knowledge of the detailed pole structure and matrix operators. (author)

A new integral method for solving the point reactor neutron kinetics equations

International Nuclear Information System (INIS)

Li Haofeng; Chen Wenzhen; Luo Lei; Zhu Qian

2009-01-01

A numerical integral method that efficiently provides the solution of the point kinetics equations by using the better basis function (BBF) for the approximation of the neutron density in one time step integrations is described and investigated. The approach is based on an exact analytic integration of the neutron density equation, where the stiffness of the equations is overcome by the fully implicit formulation. The procedure is tested by using a variety of reactivity functions, including step reactivity insertion, ramp input and oscillatory reactivity changes. The solution of the better basis function method is compared to other analytical and numerical solutions of the point reactor kinetics equations. The results show that selecting a better basis function can improve the efficiency and accuracy of this integral method. The better basis function method can be used in real time forecasting for power reactors in order to prevent reactivity accidents.

Kinetic concepts of thermally stimulated reactions in solids

Science.gov (United States)

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.

Recursive solutions for multi-group neutron kinetics diffusion equations in homogeneous three-dimensional rectangular domains with time dependent perturbations

Energy Technology Data Exchange (ETDEWEB)

Petersen, Claudio Z. [Universidade Federal de Pelotas, Capao do Leao (Brazil). Programa de Pos Graduacao em Modelagem Matematica; Bodmann, Bardo E.J.; Vilhena, Marco T. [Universidade Federal do Rio Grande do Sul, Porto Alegre, RS (Brazil). Programa de Pos-graduacao em Engenharia Mecanica; Barros, Ricardo C. [Universidade do Estado do Rio de Janeiro, Nova Friburgo, RJ (Brazil). Inst. Politecnico

2014-12-15

In the present work we solve in analytical representation the three dimensional neutron kinetic diffusion problem in rectangular Cartesian geometry for homogeneous and bounded domains for any number of energy groups and precursor concentrations. The solution in analytical representation is constructed using a hierarchical procedure, i.e. the original problem is reduced to a problem previously solved by the authors making use of a combination of the spectral method and a recursive decomposition approach. Time dependent absorption cross sections of the thermal energy group are considered with step, ramp and Chebyshev polynomial variations. For these three cases, we present numerical results and discuss convergence properties and compare our results to those available in the literature.

Result Variation and Efficiency Kinetics in Real-Time PCR

Directory of Open Access Journals (Sweden)

Reza Shahsiah

2010-10-01

Full Text Available Fluorescent monitoring of DNA amplification is the basis of real-time PCR. Absolute quantification can be achieved using a standard curve method. The standard curve is constructed by amplifying known amounts of standards under identical conditions to that of the samples.The objective of the current study is to propose a mathematical model to assess the acceptability of PCR resulys.Four commercial standards for HCV-RNA (hepatitis C virus RNA along with 6 patient samples were measured by real-time PCR, using two different RT-PCR reagents. The standard deviation of regression (Sy,x was calculated for each group of standard and compared by F-Test. The efficiency kinetics was computed by logistic regression, c2 goodness of fit test was preformed to assess the appropriateness of the efficiency curves.Calculated efficiencies were not significantly different from the value predicted by logistic regression model. Reactions with more variation showed less stable efficiency curves, with wider range of amplification efficiencies.Amplification efficiency kinetics can be computed by fitting a logistic regression curve to the gathered fluorescent data of each reaction. This model can be employed to assess the acceptability of PCR results calculated by standard curve method.

Multi-Time Step Service Restoration for Advanced Distribution Systems and Microgrids

International Nuclear Information System (INIS)

Chen, Bo; Chen, Chen; Wang, Jianhui; Butler-Purry, Karen L.

2017-01-01

Modern power systems are facing increased risk of disasters that can cause extended outages. The presence of remote control switches (RCSs), distributed generators (DGs), and energy storage systems (ESS) provides both challenges and opportunities for developing post-fault service restoration methodologies. Inter-temporal constraints of DGs, ESS, and loads under cold load pickup (CLPU) conditions impose extra complexity on problem formulation and solution. In this paper, a multi-time step service restoration methodology is proposed to optimally generate a sequence of control actions for controllable switches, ESSs, and dispatchable DGs to assist the system operator with decision making. The restoration sequence is determined to minimize the unserved customers by energizing the system step by step without violating operational constraints at each time step. The proposed methodology is formulated as a mixed-integer linear programming (MILP) model and can adapt to various operation conditions. Furthermore, the proposed method is validated through several case studies that are performed on modified IEEE 13-node and IEEE 123-node test feeders.

Nodal approximations in space and time for neutron kinetics

International Nuclear Information System (INIS)

Grossman, L.M.; Hennart, J.P.

2005-01-01

A general formalism is described of the nodal type in time and space for the neutron kinetics equations. In space, several nodal methods are given of the Raviart-Thomas type (RT0 and RT1), of the Brezzi-Douglas-Marini type (BDM0 and BDM1) and of the Brezzi-Douglas-Fortin-Marini type (BDFM 1). In time, polynomial and analytical approximations are derived. In the analytical case, they are based on the inclusion of an exponential term in the basis function. They can be continuous or discontinuous in time, leading in particular to the well-known Crank-Nicolson, Backward Euler and θ schemes

Grief: Difficult Times, Simple Steps.

Science.gov (United States)

Waszak, Emily Lane

This guide presents techniques to assist others in coping with the loss of a loved one. Using the language of 9 layperson, the book contains more than 100 tips for caregivers or loved ones. A simple step is presented on each page, followed by reasons and instructions for each step. Chapters include: "What to Say"; "Helpful Things to Do"; "Dealing…

A Derivation of Source-based Kinetics Equation with Time Dependent Fission Kernel for Reactor Transient Analyses

International Nuclear Information System (INIS)

Kim, Song Hyun; Woo, Myeong Hyun; Shin, Chang Ho; Pyeon, Cheol Ho

2015-01-01

In this study, a new balance equation to overcome the problems generated by the previous methods is proposed using source-based balance equation. And then, a simple problem is analyzed with the proposed method. In this study, a source-based balance equation with the time dependent fission kernel was derived to simplify the kinetics equation. To analyze the partial variations of reactor characteristics, two representative methods were introduced in previous studies; (1) quasi-statics method and (2) multipoint technique. The main idea of quasistatics method is to use a low-order approximation for large integration times. To realize the quasi-statics method, first, time dependent flux is separated into the shape and amplitude functions, and shape function is calculated. It is noted that the method has a good accuracy; however, it can be expensive as a calculation cost aspect because the shape function should be fully recalculated to obtain accurate results. To improve the calculation efficiency, multipoint method was proposed. The multipoint method is based on the classic kinetics equation with using Green's function to analyze the flight probability from region r' to r. Those previous methods have been used to analyze the reactor kinetics analysis; however, the previous methods can have some limitations. First, three group variables (r g , E g , t g ) should be considered to solve the time dependent balance equation. This leads a big limitation to apply large system problem with good accuracy. Second, the energy group neutrons should be used to analyze reactor kinetics problems. In time dependent problem, neutron energy distribution can be changed at different time. It can affect the change of the group cross section; therefore, it can lead the accuracy problem. Third, the neutrons in a space-time region continually affect the other space-time regions; however, it is not properly considered in the previous method. Using birth history of the neutron sources

Adaptive time-stepping Monte Carlo integration of Coulomb collisions

Science.gov (United States)

Särkimäki, K.; Hirvijoki, E.; Terävä, J.

2018-01-01

We report an accessible and robust tool for evaluating the effects of Coulomb collisions on a test particle in a plasma that obeys Maxwell-Jüttner statistics. The implementation is based on the Beliaev-Budker collision integral which allows both the test particle and the background plasma to be relativistic. The integration method supports adaptive time stepping, which is shown to greatly improve the computational efficiency. The Monte Carlo method is implemented for both the three-dimensional particle momentum space and the five-dimensional guiding center phase space. Detailed description is provided for both the physics and implementation of the operator. The focus is in adaptive integration of stochastic differential equations, which is an overlooked aspect among existing Monte Carlo implementations of Coulomb collision operators. We verify that our operator converges to known analytical results and demonstrate that careless implementation of the adaptive time step can lead to severely erroneous results. The operator is provided as a self-contained Fortran 95 module and can be included into existing orbit-following tools that trace either the full Larmor motion or the guiding center dynamics. The adaptive time-stepping algorithm is expected to be useful in situations where the collision frequencies vary greatly over the course of a simulation. Examples include the slowing-down of fusion products or other fast ions, and the Dreicer generation of runaway electrons as well as the generation of fast ions or electrons with ion or electron cyclotron resonance heating.

A parallel nearly implicit time-stepping scheme

OpenAIRE

Botchev, Mike A.; van der Vorst, Henk A.

2001-01-01

Across-the-space parallelism still remains the most mature, convenient and natural way to parallelize large scale problems. One of the major problems here is that implicit time stepping is often difficult to parallelize due to the structure of the system. Approximate implicit schemes have been suggested to circumvent the problem. These schemes have attractive stability properties and they are also very well parallelizable. The purpose of this article is to give an overall assessment of the pa...

Investigation to biodiesel production by the two-step homogeneous base-catalyzed transesterification.

Science.gov (United States)

Ye, Jianchu; Tu, Song; Sha, Yong

2010-10-01

For the two-step transesterification biodiesel production made from the sunflower oil, based on the kinetics model of the homogeneous base-catalyzed transesterification and the liquid-liquid phase equilibrium of the transesterification product, the total methanol/oil mole ratio, the total reaction time, and the split ratios of methanol and reaction time between the two reactors in the stage of the two-step reaction are determined quantitatively. In consideration of the transesterification intermediate product, both the traditional distillation separation process and the improved separation process of the two-step reaction product are investigated in detail by means of the rigorous process simulation. In comparison with the traditional distillation process, the improved separation process of the two-step reaction product has distinct advantage in the energy duty and equipment requirement due to replacement of the costly methanol-biodiesel distillation column. Copyright 2010 Elsevier Ltd. All rights reserved.

Inactivation kinetics of Vibrio vulnificus in phosphate-buffered saline at different freezing and storage temperatures and times.

Science.gov (United States)

Seminario, Diana M; Balaban, Murat O; Rodrick, Gary

2011-03-01

Vibrio vulnificus (Vv) is a pathogen that can be found in raw oysters. Freezing can reduce Vv and increase the shelf life of oysters. The objective of this study was to develop predictive inactivation kinetic models for pure cultures of Vv at different frozen storage temperatures and times. Vv was diluted in phosphate-buffered saline (PBS) to obtain about 10(7) CFU/mL. Samples were frozen at -10, -35, and -80 °C (different freezing rates), and stored at different temperatures. Survival of Vv was followed after freezing and storage at -10 °C (0, 3, 6, and 9 d) and at -35 and -80 °C (every week for 6 wk). For every treatment, time-temperature data was obtained using thermocouples in blank vials. Predictive models were developed using first-order, Weibull and Peleg inactivation kinetics. Different freezing temperatures did not significantly (α = 0.05) affect survival of Vv immediately after freezing. The combined effect of freezing and 1 wk frozen storage resulted in 1.5, 2.6, and 4.9 log10 reductions for samples stored at -80, -35, and -10 °C, respectively. Storage temperature was the critical parameter in survival of Vv. A modified Weibull model successfully predicted Vv survival during frozen storage: log10 Nt = log 10No - 1.22 - ([t/10{-1.163-0.0466T}][0.00025T(2) + 0.049325]). N(o) and N(t) are initial and time t (d) survival counts, T is frozen storage temperature, Celsius degree. Vibrio vulnificus can be inactivated by freezing. Models to predict survival of V. vulnificus at different freezing temperatures and times were developed. This is the first step towards the prediction of V. vulnificus related safety of frozen oysters.

Kinetic and thermodynamic modelling of TBP synthesis processes

International Nuclear Information System (INIS)

Azzouz, A.; Attou, M.

1989-02-01

The present paper deals with kinetic and thermodynamic modellisation of tributylphosphate (TBP) synthesis processes. Its aim consists in a purely comparative study of two different synthesis ways i.e. direct and indirect estirification of butanol. The methodology involves two steps. The first step consists in approximating curves which describe the process evolution and their dependence on the main parameters. The results gave a kinetic model of the process rate yielding in TBP. Further, on the basis of thermodynamic data concerning the various involved compounds a theoretical model was achieved. The calculations were carried out in Basic language and an interpolation mathematical method was applied to approximate the kinetic curves. The thermodynamic calculations were achieved on the basis of GIBBS' free energy using a VAX type computer and a VT240 terminal. The calculations accuracy was reasonable and within the norms. For each process, the confrontation of both models leads to an appreciable accord. In the two processes, the thermodynamic models were similar although the kinetic equations present different reaction orders. Hence the reaction orders were determined by a mathematical method which conists in searching the minimal difference between an empiric relation and a kinetic model with fixed order. This corresponds in fact in testing the model proposed at various reaction order around the suspected value. The main idea which results from such a work is that this kind of processes is well fitting with the model without taking into account the side chain reactions. The process behaviour is like that of a single reaction having a quasi linear dependence of the rate yielding and the reaction time for both processes

Long-time tails of the heat-conductivity time correlation functions for a magnetized plasma - a kinetic theory approach

NARCIS (Netherlands)

Schoolderman, A.J.; Suttorp, L.G.

1989-01-01

The long-time behaviour of the longitudinal and the transverse heat conductivity time correlation functions for a magnetized one-component plasma is studied by means of kinetic theory. To that end these correlation functions, which are defined as the inverse Laplace transforms of the dynamic heat

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

Science.gov (United States)

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.

Reactor kinetics revisited: a coefficient based model (CBM)

International Nuclear Information System (INIS)

Ratemi, W.M.

2011-01-01

In this paper, a nuclear reactor kinetics model based on Guelph expansion coefficients calculation ( Coefficients Based Model, CBM), for n groups of delayed neutrons is developed. The accompanying characteristic equation is a polynomial form of the Inhour equation with the same coefficients of the CBM- kinetics model. Those coefficients depend on Universal abc- values which are dependent on the type of the fuel fueling a nuclear reactor. Furthermore, such coefficients are linearly dependent on the inserted reactivity. In this paper, the Universal abc- values have been presented symbolically, for the first time, as well as with their numerical values for U-235 fueled reactors for one, two, three, and six groups of delayed neutrons. Simulation studies for constant and variable reactivity insertions are made for the CBM kinetics model, and a comparison of results, with numerical solutions of classical kinetics models for one, two, three, and six groups of delayed neutrons are presented. The results show good agreements, especially for single step insertion of reactivity, with the advantage of the CBM- solution of not encountering the stiffness problem accompanying the numerical solutions of the classical kinetics model. (author)

On an efficient multiple time step Monte Carlo simulation of the SABR model

NARCIS (Netherlands)

Leitao Rodriguez, A.; Grzelak, L.A.; Oosterlee, C.W.

2017-01-01

In this paper, we will present a multiple time step Monte Carlo simulation technique for pricing options under the Stochastic Alpha Beta Rho model. The proposed method is an extension of the one time step Monte Carlo method that we proposed in an accompanying paper Leitao et al. [Appl. Math.

Effective computation of stochastic protein kinetic equation by reducing stiffness via variable transformation

Energy Technology Data Exchange (ETDEWEB)

Wang, Lijin, E-mail: ljwang@ucas.ac.cn [School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049 (China)

2016-06-08

The stochastic protein kinetic equations can be stiff for certain parameters, which makes their numerical simulation rely on very small time step sizes, resulting in large computational cost and accumulated round-off errors. For such situation, we provide a method of reducing stiffness of the stochastic protein kinetic equation by means of a kind of variable transformation. Theoretical and numerical analysis show effectiveness of this method. Its generalization to a more general class of stochastic differential equation models is also discussed.

A Derivation of Source-based Kinetics Equation with Time Dependent Fission Kernel for Reactor Transient Analyses

Energy Technology Data Exchange (ETDEWEB)

Kim, Song Hyun; Woo, Myeong Hyun; Shin, Chang Ho [Hanyang University, Seoul (Korea, Republic of); Pyeon, Cheol Ho [Kyoto University, Osaka (Japan)

2015-10-15

In this study, a new balance equation to overcome the problems generated by the previous methods is proposed using source-based balance equation. And then, a simple problem is analyzed with the proposed method. In this study, a source-based balance equation with the time dependent fission kernel was derived to simplify the kinetics equation. To analyze the partial variations of reactor characteristics, two representative methods were introduced in previous studies; (1) quasi-statics method and (2) multipoint technique. The main idea of quasistatics method is to use a low-order approximation for large integration times. To realize the quasi-statics method, first, time dependent flux is separated into the shape and amplitude functions, and shape function is calculated. It is noted that the method has a good accuracy; however, it can be expensive as a calculation cost aspect because the shape function should be fully recalculated to obtain accurate results. To improve the calculation efficiency, multipoint method was proposed. The multipoint method is based on the classic kinetics equation with using Green's function to analyze the flight probability from region r' to r. Those previous methods have been used to analyze the reactor kinetics analysis; however, the previous methods can have some limitations. First, three group variables (r{sub g}, E{sub g}, t{sub g}) should be considered to solve the time dependent balance equation. This leads a big limitation to apply large system problem with good accuracy. Second, the energy group neutrons should be used to analyze reactor kinetics problems. In time dependent problem, neutron energy distribution can be changed at different time. It can affect the change of the group cross section; therefore, it can lead the accuracy problem. Third, the neutrons in a space-time region continually affect the other space-time regions; however, it is not properly considered in the previous method. Using birth history of the

Kinetic models of controllable pore growth of anodic aluminum oxide membrane

Science.gov (United States)

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.

The hyperbolic step potential: Anti-bound states, SUSY partners and Wigner time delays

Energy Technology Data Exchange (ETDEWEB)

Gadella, M. [Departamento de Física Teórica, Atómica y Óptica and IMUVA, Universidad de Valladolid, E-47011 Valladolid (Spain); Kuru, Ş. [Department of Physics, Faculty of Science, Ankara University, 06100 Ankara (Turkey); Negro, J., E-mail: jnegro@fta.uva.es [Departamento de Física Teórica, Atómica y Óptica and IMUVA, Universidad de Valladolid, E-47011 Valladolid (Spain)

2017-04-15

We study the scattering produced by a one dimensional hyperbolic step potential, which is exactly solvable and shows an unusual interest because of its asymmetric character. The analytic continuation of the scattering matrix in the momentum representation has a branch cut and an infinite number of simple poles on the negative imaginary axis which are related with the so called anti-bound states. This model does not show resonances. Using the wave functions of the anti-bound states, we obtain supersymmetric (SUSY) partners which are the series of Rosen–Morse II potentials. We have computed the Wigner reflection and transmission time delays for the hyperbolic step and such SUSY partners. Our results show that the more bound states a partner Hamiltonian has the smaller is the time delay. We also have evaluated time delays for the hyperbolic step potential in the classical case and have obtained striking similitudes with the quantum case. - Highlights: • The scattering matrix of hyperbolic step potential is studied. • The scattering matrix has a branch cut and an infinite number of poles. • The poles are associated to anti-bound states. • Susy partners using antibound states are computed. • Wigner time delays for the hyperbolic step and partner potentials are compared.

Numerical nodal simulation of the axial power distribution within nuclear reactors using a kinetics diffusion model. I

International Nuclear Information System (INIS)

Barros, R.C. de.

1992-05-01

Presented here is a new numerical nodal method for the simulation of the axial power distribution within nuclear reactors using the one-dimensional one speed kinetics diffusion model with one group of delayed neutron precursors. Our method is based on a spectral analysis of the nodal kinetics equations. These equations are obtained by integrating the original kinetics equations separately over a time step and over a spatial node, and then considering flat approximations for the forward difference terms. These flat approximations are the only approximations that are considered in the method. As a result, the spectral nodal method for space - time reactor kinetics generates numerical solutions for space independent problems or for time independent problems that are completely free from truncation errors. We show numerical results to illustrate the method's accuracy for coarse mesh calculations. (author)

Enforcing the Courant-Friedrichs-Lewy condition in explicitly conservative local time stepping schemes

Science.gov (United States)

Gnedin, Nickolay Y.; Semenov, Vadim A.; Kravtsov, Andrey V.

2018-04-01

An optimally efficient explicit numerical scheme for solving fluid dynamics equations, or any other parabolic or hyperbolic system of partial differential equations, should allow local regions to advance in time with their own, locally constrained time steps. However, such a scheme can result in violation of the Courant-Friedrichs-Lewy (CFL) condition, which is manifestly non-local. Although the violations can be considered to be "weak" in a certain sense and the corresponding numerical solution may be stable, such calculation does not guarantee the correct propagation speed for arbitrary waves. We use an experimental fluid dynamics code that allows cubic "patches" of grid cells to step with independent, locally constrained time steps to demonstrate how the CFL condition can be enforced by imposing a constraint on the time steps of neighboring patches. We perform several numerical tests that illustrate errors introduced in the numerical solutions by weak CFL condition violations and show how strict enforcement of the CFL condition eliminates these errors. In all our tests the strict enforcement of the CFL condition does not impose a significant performance penalty.

Errors in Postural Preparation Lead to Increased Choice Reaction Times for Step Initiation in Older Adults

Science.gov (United States)

Nutt, John G.; Horak, Fay B.

2011-01-01

Background. This study asked whether older adults were more likely than younger adults to err in the initial direction of their anticipatory postural adjustment (APA) prior to a step (indicating a motor program error), whether initial motor program errors accounted for reaction time differences for step initiation, and whether initial motor program errors were linked to inhibitory failure. Methods. In a stepping task with choice reaction time and simple reaction time conditions, we measured forces under the feet to quantify APA onset and step latency and we used body kinematics to quantify forward movement of center of mass and length of first step. Results. Trials with APA errors were almost three times as common for older adults as for younger adults, and they were nine times more likely in choice reaction time trials than in simple reaction time trials. In trials with APA errors, step latency was delayed, correlation between APA onset and step latency was diminished, and forward motion of the center of mass prior to the step was increased. Participants with more APA errors tended to have worse Stroop interference scores, regardless of age. Conclusions. The results support the hypothesis that findings of slow choice reaction time step initiation in older adults are attributable to inclusion of trials with incorrect initial motor preparation and that these errors are caused by deficits in response inhibition. By extension, the results also suggest that mixing of trials with correct and incorrect initial motor preparation might explain apparent choice reaction time slowing with age in upper limb tasks. PMID:21498431

Dissolvable fluidic time delays for programming multi-step assays in instrument-free paper diagnostics.

Science.gov (United States)

Lutz, Barry; Liang, Tinny; Fu, Elain; Ramachandran, Sujatha; Kauffman, Peter; Yager, Paul

2013-07-21

Lateral flow tests (LFTs) are an ingenious format for rapid and easy-to-use diagnostics, but they are fundamentally limited to assay chemistries that can be reduced to a single chemical step. In contrast, most laboratory diagnostic assays rely on multiple timed steps carried out by a human or a machine. Here, we use dissolvable sugar applied to paper to create programmable flow delays and present a paper network topology that uses these time delays to program automated multi-step fluidic protocols. Solutions of sucrose at different concentrations (10-70% of saturation) were added to paper strips and dried to create fluidic time delays spanning minutes to nearly an hour. A simple folding card format employing sugar delays was shown to automate a four-step fluidic process initiated by a single user activation step (folding the card); this device was used to perform a signal-amplified sandwich immunoassay for a diagnostic biomarker for malaria. The cards are capable of automating multi-step assay protocols normally used in laboratories, but in a rapid, low-cost, and easy-to-use format.

Glutathione reductase: solvent equilibrium and kinetic isotope effects

International Nuclear Information System (INIS)

Wong, K.K.; Vanoni, M.A.; Blanchard, J.S.

1988-01-01

Glutathione reductase catalyzes the NADPH-dependent reduction of oxidized glutathione (GSSG). The kinetic mechanism is ping-pong, and we have investigated the rate-limiting nature of proton-transfer steps in the reactions catalyzed by the spinach, yeast, and human erythrocyte glutathione reductases using a combination of alternate substrate and solvent kinetic isotope effects. With NADPH or GSSG as the variable substrate, at a fixed, saturating concentration of the other substrate, solvent kinetic isotope effects were observed on V but not V/K. Plots of Vm vs mole fraction of D 2 O (proton inventories) were linear in both cases for the yeast, spinach, and human erythrocyte enzymes. When solvent kinetic isotope effect studies were performed with DTNB instead of GSSG as an alternate substrate, a solvent kinetic isotope effect of 1.0 was observed. Solvent kinetic isotope effect measurements were also performed on the asymmetric disulfides GSSNB and GSSNP by using human erythrocyte glutathione reductase. The Km values for GSSNB and GSSNP were 70 microM and 13 microM, respectively, and V values were 62 and 57% of the one calculated for GSSG, respectively. Both of these substrates yield solvent kinetic isotope effects greater than 1.0 on both V and V/K and linear proton inventories, indicating that a single proton-transfer step is still rate limiting. These data are discussed in relationship to the chemical mechanism of GSSG reduction and the identity of the proton-transfer step whose rate is sensitive to solvent isotopic composition. Finally, the solvent equilibrium isotope effect measured with yeast glutathione reductase is 4.98, which allows us to calculate a fractionation factor for the thiol moiety of GSH of 0.456

On the theory of time dilation in chemical kinetics

Science.gov (United States)

Baig, Mirza Wasif

2017-10-01

The rates of chemical reactions are not absolute but their magnitude depends upon the relative speeds of the moving observers. This has been proved by unifying basic theories of chemical kinetics, which are transition state theory, collision theory, RRKM and Marcus theory, with the special theory of relativity. Boltzmann constant and energy spacing between permitted quantum levels of molecules are quantum mechanically proved to be Lorentz variant. The relativistic statistical thermodynamics has been developed to explain quasi-equilibrium existing between reactants and activated complex. The newly formulated Lorentz transformation of the rate constant from Arrhenius equation, of the collision frequency and of the Eyring and Marcus equations renders the rate of reaction to be Lorentz variant. For a moving observer moving at fractions of the speed of light along the reaction coordinate, the transition state possess less kinetic energy to sweep translation over it. This results in the slower transformation of reactants into products and in a stretched time frame for the chemical reaction to complete. Lorentz transformation of the half-life equation explains time dilation of the half-life period of chemical reactions and proves special theory of relativity and presents theory in accord with each other. To demonstrate the effectiveness of the present theory, the enzymatic reaction of methylamine dehydrogenase and radioactive disintegration of Astatine into Bismuth are considered as numerical examples.

The large discretization step method for time-dependent partial differential equations

Science.gov (United States)

Haras, Zigo; Taasan, Shlomo

1995-01-01

A new method for the acceleration of linear and nonlinear time dependent calculations is presented. It is based on the Large Discretization Step (LDS) approximation, defined in this work, which employs an extended system of low accuracy schemes to approximate a high accuracy discrete approximation to a time dependent differential operator. Error bounds on such approximations are derived. These approximations are efficiently implemented in the LDS methods for linear and nonlinear hyperbolic equations, presented here. In these algorithms the high and low accuracy schemes are interpreted as the same discretization of a time dependent operator on fine and coarse grids, respectively. Thus, a system of correction terms and corresponding equations are derived and solved on the coarse grid to yield the fine grid accuracy. These terms are initialized by visiting the fine grid once in many coarse grid time steps. The resulting methods are very general, simple to implement and may be used to accelerate many existing time marching schemes.

Development of Singlet Oxygen Luminescence Kinetics during the Photodynamic Inactivation of Green Algae

Directory of Open Access Journals (Sweden)

Tobias Bornhütter

2016-04-01

Full Text Available Recent studies show the feasibility of photodynamic inactivation of green algae as a vital step towards an effective photodynamic suppression of biofilms by using functionalized surfaces. The investigation of the intrinsic mechanisms of photodynamic inactivation in green algae represents the next step in order to determine optimization parameters. The observation of singlet oxygen luminescence kinetics proved to be a very effective approach towards understanding mechanisms on a cellular level. In this study, the first two-dimensional measurement of singlet oxygen kinetics in phototrophic microorganisms on surfaces during photodynamic inactivation is presented. We established a system of reproducible algae samples on surfaces, incubated with two different cationic, antimicrobial potent photosensitizers. Fluorescence microscopy images indicate that one photosensitizer localizes inside the green algae while the other accumulates along the outer algae cell wall. A newly developed setup allows for the measurement of singlet oxygen luminescence on the green algae sample surfaces over several days. The kinetics of the singlet oxygen luminescence of both photosensitizers show different developments and a distinct change over time, corresponding with the differences in their localization as well as their photosensitization potential. While the complexity of the signal reveals a challenge for the future, this study incontrovertibly marks a crucial, inevitable step in the investigation of photodynamic inactivation of biofilms: it shows the feasibility of using the singlet oxygen luminescence kinetics to investigate photodynamic effects on surfaces and thus opens a field for numerous investigations.

RNA folding kinetics using Monte Carlo and Gillespie algorithms.

Science.gov (United States)

Clote, Peter; Bayegan, Amir H

2018-04-01

RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny ([Formula: see text]20 nt) RNA sequences, the folding kinetics for larger sequences can only be approximated by binning structures into macrostates in a coarse-grained model, or by repeatedly simulating secondary structure folding with either the Monte Carlo algorithm or the Gillespie algorithm. Here we investigate the relation between the Monte Carlo algorithm and the Gillespie algorithm. We prove that asymptotically, the expected time for a K-step trajectory of the Monte Carlo algorithm is equal to [Formula: see text] times that of the Gillespie algorithm, where [Formula: see text] denotes the Boltzmann expected network degree. If the network is regular (i.e. every node has the same degree), then the mean first passage time (MFPT) computed by the Monte Carlo algorithm is equal to MFPT computed by the Gillespie algorithm multiplied by [Formula: see text]; however, this is not true for non-regular networks. In particular, RNA secondary structure folding kinetics, as computed by the Monte Carlo algorithm, is not equal to the folding kinetics, as computed by the Gillespie algorithm, although the mean first passage times are roughly correlated. Simulation software for RNA secondary structure folding according to the Monte Carlo and Gillespie algorithms is publicly available, as is our software to compute the expected degree of the network of secondary structures of a given RNA sequence-see http://bioinformatics.bc.edu/clote/RNAexpNumNbors .

Fine kinetics of natural physical ageing in glassy As10Se90

International Nuclear Information System (INIS)

Balitska, V.; Golovchak, R.; Kozdras, A.; Shpotyuk, O.

2014-01-01

Sigmoid behavior of natural physical ageing in glassy As 10 Se 90 reveals multi-step-wise growing kinetics of enthalpy losses. Phenomenological description of this kinetics can be adequately developed in terms of first-order relaxation processes, tending atomic structure from initial towards more thermodynamically equilibrium state. This kinetics is shown to obey characteristic stretched exponential behavior originated from a number of growing steps, attributed to the interconnected processes of chalcogen chain alignment and cooperative shrinkage of glass network

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

Science.gov (United States)

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.

Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics.

Science.gov (United States)

Rajabi, Khadijeh

2015-01-01

A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX.

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

Science.gov (United States)

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.

Kinetics of Roasting Decomposition of the Rare Earth Elements by CaO and Coal

Directory of Open Access Journals (Sweden)

Shuai Yuan

2017-06-01

Full Text Available The roasting method of magnetic tailing mixed with CaO and coal was used to recycle the rare earth elements (REE in magnetic tailing. The phase transformation and decomposition process were researched during the roasting processes. The results showed that the decomposition processes of REE in magnetic tailing were divided into two steps. The first step from 380 to 431 °C mainly entailed the decomposition of bastnaesite (REFCO3. The second step from 605 to 716 °C mainly included the decomposition of monazite (REPO4. The decomposition products were primarily RE2O3, Ce0.75Nd0.25O1.875, CeO2, Ca5F(PO43, and CaF2. Adding CaO could reduce the decomposition temperature of REFCO3 and REPO4. Meanwhile, the decomposition effect of CaO on bastnaesite and monazite was significant. Besides, the effects of the roasting time, roasting temperature, and CaO addition level on the decomposition rate were studied. The optimum technological conditions were a roasting time of 60 min; roasting temperature of 750 °C; and CaO addition level of 20% (w/w. The maximum decomposition rate of REFCO3 and REPO4 was 99.87%. The roasting time and temperature were the major factors influencing the decomposition rate. The kinetics process of the decomposition of REFCO3 and REPO4 accorded with the interfacial reaction kinetics model. The reaction rate controlling steps were divided into two steps. The first step (at low temperature was controlled by a chemical reaction with an activation energy of 52.67 kJ/mol. The second step (at high temperature was controlled by diffusion with an activation energy of 8.5 kJ/mol.

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

Science.gov (United States)

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.

Nodal kinetics model upgrade in the Penn State coupled TRAC/NEM codes

International Nuclear Information System (INIS)

Beam, Tara M.; Ivanov, Kostadin N.; Baratta, Anthony J.; Finnemann, Herbert

1999-01-01

The Pennsylvania State University currently maintains and does development and verification work for its own versions of the coupled three-dimensional kinetics/thermal-hydraulics codes TRAC-PF1/NEM and TRAC-BF1/NEM. The subject of this paper is nodal model enhancements in the above mentioned codes. Because of the numerous validation studies that have been performed on almost every aspect of these codes, this upgrade is done without a major code rewrite. The upgrade consists of four steps. The first two steps are designed to improve the accuracy of the kinetics model, based on the nodal expansion method. The polynomial expansion solution of 1D transverse integrated diffusion equation is replaced with a solution, which uses a semi-analytic expansion. Further the standard parabolic polynomial representation of the transverse leakage in the above 1D equations is replaced with an improved approximation. The last two steps of the upgrade address the code efficiency by improving the solution of the time-dependent NEM equations and implementing a multi-grid solver. These four improvements are implemented into the standalone NEM kinetics code. Verification of this code was accomplished based on the original verification studies. The results show that the new methods improve the accuracy and efficiency of the code. The verification of the upgraded NEM model in the TRAC-PF1/NEM and TRAC-BF1/NEM coupled codes is underway

Modified Pressure-Correction Projection Methods: Open Boundary and Variable Time Stepping

KAUST Repository

Bonito, Andrea

2014-10-31

© Springer International Publishing Switzerland 2015. In this paper, we design and study two modifications of the first order standard pressure increment projection scheme for the Stokes system. The first scheme improves the existing schemes in the case of open boundary condition by modifying the pressure increment boundary condition, thereby minimizing the pressure boundary layer and recovering the optimal first order decay. The second scheme allows for variable time stepping. It turns out that the straightforward modification to variable time stepping leads to unstable schemes. The proposed scheme is not only stable but also exhibits the optimal first order decay. Numerical computations illustrating the theoretical estimates are provided for both new schemes.

Modified Pressure-Correction Projection Methods: Open Boundary and Variable Time Stepping

KAUST Repository

Bonito, Andrea; Guermond, Jean-Luc; Lee, Sanghyun

2014-01-01

© Springer International Publishing Switzerland 2015. In this paper, we design and study two modifications of the first order standard pressure increment projection scheme for the Stokes system. The first scheme improves the existing schemes in the case of open boundary condition by modifying the pressure increment boundary condition, thereby minimizing the pressure boundary layer and recovering the optimal first order decay. The second scheme allows for variable time stepping. It turns out that the straightforward modification to variable time stepping leads to unstable schemes. The proposed scheme is not only stable but also exhibits the optimal first order decay. Numerical computations illustrating the theoretical estimates are provided for both new schemes.

Two-Step Time of Arrival Estimation for Pulse-Based Ultra-Wideband Systems

Directory of Open Access Journals (Sweden)

H. Vincent Poor

2008-05-01

Full Text Available In cooperative localization systems, wireless nodes need to exchange accurate position-related information such as time-of-arrival (TOA and angle-of-arrival (AOA, in order to obtain accurate location information. One alternative for providing accurate position-related information is to use ultra-wideband (UWB signals. The high time resolution of UWB signals presents a potential for very accurate positioning based on TOA estimation. However, it is challenging to realize very accurate positioning systems in practical scenarios, due to both complexity/cost constraints and adverse channel conditions such as multipath propagation. In this paper, a two-step TOA estimation algorithm is proposed for UWB systems in order to provide accurate TOA estimation under practical constraints. In order to speed up the estimation process, the first step estimates a coarse TOA of the received signal based on received signal energy. Then, in the second step, the arrival time of the first signal path is estimated by considering a hypothesis testing approach. The proposed scheme uses low-rate correlation outputs and is able to perform accurate TOA estimation in reasonable time intervals. The simulation results are presented to analyze the performance of the estimator.

A combined kinetic and diffusion model for pyrite oxidation in tailings - a change in controls with time

International Nuclear Information System (INIS)

Elberling, B.; Nicholson, R.V.; Scharer, J.M.

1994-01-01

Acidic drainage from the oxidation of mine tailing wastes is an important environmental problem. The purpose of this paper is to develop a model (1) to simulate the rate of oxidation of pyrite over time, (2) to verify the importance of chemical kinetic control and diffusion control on the oxidation rate with time and, (3) to evaluate the sensitivity of the model to critical parameters of the tailings, such as grain size, pyrite content and the effective diffusion coefficient. The source code comprises four main modules including parameter allocation (kinetics, transport), sulphide oxidation (shrinking particle), oxygen transport and pyrite mass balance. The results show that high oxidation rates are observed in the initial time after tailings deposition. During this initial period of high rates, an apparent shift occurs from kinetic to diffusional control over a period of time that depends on the composition and properties of the tailings. Based on the simulation results, it is evident that the overall rate of oxidation after a few years will be controlled dominantly by the diffusion of oxygen rather than by biological or non-biological kinetics in the tailings

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

Science.gov (United States)

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

Implementation of the kinetics in the transport code AZTRAN

International Nuclear Information System (INIS)

Duran G, J. A.; Del Valle G, E.; Gomez T, A. M.

2017-09-01

This paper shows the implementation of the time dependence in the three-dimensional transport code AZTRAN (AZtlan TRANsport), which belongs to the AZTLAN platform, for the analysis of nuclear reactors (currently under development). The AZTRAN code with this implementation is able to numerically solve the time-dependent transport equation in XYZ geometry, for several energy groups, using the discrete ordinate method S n for the discretization of the angular variable, the nodal method RTN-0 for spatial discretization and method 0 for discretization in time. Initially, the code only solved the neutrons transport equation in steady state, so the implementation of the temporal part was made integrating the neutrons transport equation with respect to time and balance equations corresponding to the concentrations of delayed neutron precursors, for which method 0 was applied. After having directly implemented code kinetics, the improved quasi-static method was implemented, which is a tool for reducing computation time, where the angular flow is factored by the product of two functions called shape function and amplitude function, where the first is calculated for long time steps, called macro-steps and the second is resolved for small time steps called micro-steps. In the new version of AZTRAN several Benchmark problems that were taken from the literature were simulated, the problems used are of two and three dimensions which allowed corroborating the accuracy and stability of the code, showing in general in the reference tests a good behavior. (Author)

Transition state kinetics of Hg(II) adsorption at gibbsite-water interface

International Nuclear Information System (INIS)

Weerasooriya, Rohan; Tobschall, Heinz J.; Seneviratne, Wasana; Bandara, Atula

2007-01-01

Kinetics of adsorption plays a pivotal factor in determining the bio-availability and mobility of Hg(II) in the environment. The kinetics of Hg(II) adsorption on gibbsite was examined as a function of pH, temperature and electrolyte type. Adsorption of Hg(II) was highly non-linear where the rate of Hg(II) retention was rapid initially and was followed by gradual or somewhat slow retention behavior with increasing contact time. The respective rate constants designated as k 1 (S-1: fast step) and k 2 (S-2: slow step). Always k 1 follows the order: k 1 ClO 4 >=k 1 (NO 3 ) 4 >>k 1 Cl . Such a relationship was not observed for the S-2 route. A two-step reaction model with pseudo-first order kinetics successfully described the adsorption rates of Hg(II) on gibbsite. Arrhenius and Erying models determined the thermodynamic parameters at activation states, which correspond to S-1 and S-2 routes. In a given system, always the activation energies showed a decrease with the pH. Gibbs free energy (ΔG numbersign ), enthalpy (ΔH numbersign ), and entropy (ΔS numbersign ) values of activation states were almost similar both in NaClO 4 and NaNO 3 which signal a similar Hg(II) adsorptive mechanism on gibbsite. The configurations of different Hg(II)-surface complexes were elucidated by transmission vibration spectroscopy

Radio-Oxidation in Polyolefins: Non-Stationary Kinetic Conditions

International Nuclear Information System (INIS)

Dely, N.

2006-01-01

In the last fifty years, many authors have been interested in the radio-oxidation processes occurring in polymers. The polymer degradation under ionising radiations in presence of dioxygen is well described by a radical chemistry. The radio-oxidation process occurs in three steps: the first one is the production of radicals P degree by interaction between the polymer and the ionising radiations; then radicals P degree react spontaneously with O 2 solved in the polymer giving a peroxy radical POO degree which attacks the polymer forming a hydroperoxide POOH and a new radical P degree (propagation). The third step corresponds to the termination step, that is bimolecular reactions between radicals. It is generally assumed that the stationary state is rapidly reached and consequently that the oxidation induced during the built-up period of the radical concentration can be neglected. However, to our best knowledge, the temporal evolution of radical concentrations before reaching the steady state regime has never been studied in details. We recently performed a complete study of oxygen consumption under electron irradiation for an EPDM elastomer. An analysis, as function of dose rate and oxygen pressure, and assuming steady state conditions, allowed extracting all the kinetic constants. Starting for these experimental data, we calculated the build-up of the radical concentration by solving numerically the differential equations with help of the Minichem code. We conclude that, in fact, the oxidation induced during the built-up period is negligible. In this paper we show that [P degree] could present a quasi-stationary plateau before reaching its stationary level. Consequently, the full radical time evolution is essentially determined by two characteristic times for reaching the quasi and stationary levels and three concentrations: [P degree] and [POO degree] at the stationary level and [P degree] at the quasi-stationary plateau. We show that realistic approximations can

Modelling reveals kinetic advantages of co-transcriptional splicing.

Directory of Open Access Journals (Sweden)

Stuart Aitken

2011-10-01

Full Text Available 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.

Modelling reveals kinetic advantages of co-transcriptional splicing.

Science.gov (United States)

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.

Numerical instability of time-discretized one-point kinetic equations

International Nuclear Information System (INIS)

Hashimoto, Kengo; Ikeda, Hideaki; Takeda, Toshikazu

2000-01-01

The one-point kinetic equations with numerical errors induced by the explicit, implicit and Crank-Nicolson integration methods are derived. The zero-power transfer functions based on the present equations are demonstrated to investigate the numerical stability of the discretized systems. These demonstrations indicate unconditional stability for the implicit and Crank-Nicolson methods but present the possibility of numerical instability for the explicit method. An upper limit of time mesh spacing for the stability is formulated and several numerical calculations are made to confirm the validity of this formula

Some Comments on the Behavior of the RELAP5 Numerical Scheme at Very Small Time Steps

International Nuclear Information System (INIS)

Tiselj, Iztok; Cerne, Gregor

2000-01-01

The behavior of the RELAP5 code at very short time steps is described, i.e., δt [approximately equal to] 0.01 δx/c. First, the property of the RELAP5 code to trace acoustic waves with 'almost' second-order accuracy is demonstrated. Quasi-second-order accuracy is usually achieved for acoustic waves at very short time steps but can never be achieved for the propagation of nonacoustic temperature and void fraction waves. While this feature may be beneficial for the simulations of fast transients describing pressure waves, it also has an adverse effect: The lack of numerical diffusion at very short time steps can cause typical second-order numerical oscillations near steep pressure jumps. This behavior explains why an automatic halving of the time step, which is used in RELAP5 when numerical difficulties are encountered, in some cases leads to the failure of the simulation.Second, the integration of the stiff interphase exchange terms in RELAP5 is studied. For transients with flashing and/or rapid condensation as the main phenomena, results strongly depend on the time step used. Poor accuracy is achieved with 'normal' time steps (δt [approximately equal to] δx/v) because of the very short characteristic timescale of the interphase mass and heat transfer sources. In such cases significantly different results are predicted with very short time steps because of the more accurate integration of the stiff interphase exchange terms

Multi-time-step domain coupling method with energy control

DEFF Research Database (Denmark)

Mahjoubi, N.; Krenk, Steen

2010-01-01

the individual time step. It is demonstrated that displacement continuity between the subdomains leads to cancelation of the interface contributions to the energy balance equation, and thus stability and algorithmic damping properties of the original algorithms are retained. The various subdomains can...... by a numerical example using a refined mesh around concentrated forces. Copyright © 2010 John Wiley & Sons, Ltd....

TUTANK a two-dimensional neutron kinetics code

International Nuclear Information System (INIS)

Watts, M.G.; Halsall, M.J.; Fayers, F.J.

1975-04-01

TUTANK is a two-dimensional neutron kinetics code which treats two neutron energy groups and up to six groups of delayed neutron precursors. A 'theta differencing' method is used to integrate the time dependence of the equations. A position dependent exponential transformation on the time variable is available as an option, which in many circumstances can remove much of the time dependence, and thereby allow longer time steps to be taken. A further manipulation is made to separate the solutions of the neutron fluxes and the precursor concentrations. The spatial equations are based on standard diffusion theory, and their solution is obtained from alternating direction sweeps with a transverse buckling - the so-called ADI-B 2 method. Other features of the code include an elementary temperature feedback and heat removal treatment, automatic time step adjustment, a flexible method of specifying cross-section and heat transfer coefficient variations during a transient, and a restart facility which requires a minimal data specification. Full details of the code input are given. An example of the solution of a NEACRP benchmark for an LWR control rod withdrawal is given. (author)

Transient analysis of carbon monoxide transport phenomena and adsorption kinetics in HT-PEMFC during dynamic current extraction

International Nuclear Information System (INIS)

Raj, Kamal Abdul Rasheedj; Chan, Siew Hwa

2015-01-01

Highlights: • Increasing the fuel cell temperature reduces outlet CO concentration. • Increasing the CO inlet (initial) concentration increases outlet CO concentration. • Increasing current density step and dwell time increases outlet CO concentration. • Increasing in the CL and GDL porosities reduces outlet CO concentration. - Abstract: This paper investigates the transport phenomena of carbon monoxide (CO) and adsorption kinetics, in a high-temperature proton exchange membrane fuel cell (HT-PEMFC) during step-wise current extraction (step-change in current extraction). Step-wise current extraction is a common process done to accommodate a sudden power surge during an operation. Since HT-PEMFCs are capable of handling high impurity of CO, hydrogen fuel that is contaminated with trace amount of CO is usually considered for commercial benefits. Thus, a transient three-dimensional isothermal anodic electro-kinetic numerical model is developed to determine the effect of operating parameters such as fuel cell temperature, CO inlet (initial) concentration, step-change of current density and dwell time on the transport phenomena of CO and adsorption kinetics. In addition, geometrical factors such as the catalyst layer (CL) and gas diffusion layer (GDL) porosity are also varied as well. The results show that the above-mentioned operating parameters can affect the maximum CO concentration at the CL, especially at the outlet of the channel. Specifically, a reduction of fuel cell temperature can significantly increase the CO concentration near the outlet, while increasing CO inlet (initial) concentration, step-change amplitude of current density and current density dwell time can cause an increase in CO concentration at the outlet, albeit to different extent. In addition, the increase in the porosity of CL and GDL, results in the reduction of the maximum CO concentration at the outlet, albeit to different extent. In addition, the CO and hydrogen surface coverage

Cesium removal and kinetics equilibrium: Precipitation kinetics

International Nuclear Information System (INIS)

Barnes, M.J.

1999-01-01

This task consisted of both non-radioactive and radioactive (tracer) tests examining the influence of potentially significant variables on cesium tetraphenylborate precipitation kinetics. The work investigated the time required to reach cesium decontamination and the conditions that affect the cesium precipitation kinetics

Sharing Steps in the Workplace: Changing Privacy Concerns Over Time

DEFF Research Database (Denmark)

Jensen, Nanna Gorm; Shklovski, Irina

2016-01-01

study of a Danish workplace participating in a step counting campaign. We find that concerns of employees who choose to participate and those who choose not to differ. Moreover, privacy concerns of participants develop and change over time. Our findings challenge the assumption that consumers...

Analytical representation for solution of the neutron point kinetics equation with time-dependent reactivity and free of the stiffness character

International Nuclear Information System (INIS)

Silva, Milena Wollmann da

2013-01-01

In this work, we report a genuine analytical representation for the solution of the neutron point kinetics equation free of the stiffness character, assuming that the reactivity is a continuous and sectionally continuous function of time. To this end, we initially cast the point kinetics equation in a first order linear differential equation. Next, we split the corresponding matrix as a sum of a diagonal matrix with a matrix, whose components contain the off-diagonal elements. Next, expanding the neutron density and the delayed neutron precursors concentrations in a truncated series, and replacing these expansions in the matrix equation, we come out with an equation, which allows to construct a recursive system, a first order matrix differential equation with source. The fundamental characteristic of this system relies on the fact that the corresponding matrix is diagonal, meanwhile the source term is written in terms of the matrix with the off-diagonal components. Further, the first equation of the recursive system has no source and satisfies the initial conditions. On the other hand, the remaining equations satisfy the null initial condition. Due to the diagonal feature of the matrix, we attain analytical solutions for these recursive equations. We also mention that we evaluate the results for any time value, without the analytical continuity because the purposed solution is free on the stiffness character. Finally, we present numerical simulations and comparisons against literature results, considering specific the applications for the following reactivity functions: constant, step, ramp, and sine. (author)

Development of a real time activity monitoring Android application utilizing SmartStep.

Science.gov (United States)

Hegde, Nagaraj; Melanson, Edward; Sazonov, Edward

2016-08-01

Footwear based activity monitoring systems are becoming popular in academic research as well as consumer industry segments. In our previous work, we had presented developmental aspects of an insole based activity and gait monitoring system-SmartStep, which is a socially acceptable, fully wireless and versatile insole. The present work describes the development of an Android application that captures the SmartStep data wirelessly over Bluetooth Low energy (BLE), computes features on the received data, runs activity classification algorithms and provides real time feedback. The development of activity classification methods was based on the the data from a human study involving 4 participants. Participants were asked to perform activities of sitting, standing, walking, and cycling while they wore SmartStep insole system. Multinomial Logistic Discrimination (MLD) was utilized in the development of machine learning model for activity prediction. The resulting classification model was implemented in an Android Smartphone. The Android application was benchmarked for power consumption and CPU loading. Leave one out cross validation resulted in average accuracy of 96.9% during model training phase. The Android application for real time activity classification was tested on a human subject wearing SmartStep resulting in testing accuracy of 95.4%.

Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network.

Science.gov (United States)

Culyba, Matthew J; Kubiak, Jeffrey M; Mo, Charlie Y; Goulian, Mark; Kohli, Rahul M

2018-06-01

Biochemical pathways are often genetically encoded as simple transcription regulation networks, where one transcription factor regulates the expression of multiple genes in a pathway. The relative timing of each promoter's activation and shut-off within the network can impact physiology. In the DNA damage repair pathway (known as the SOS response) of Escherichia coli, approximately 40 genes are regulated by the LexA repressor. After a DNA damaging event, LexA degradation triggers SOS gene transcription, which is temporally separated into subsets of 'early', 'middle', and 'late' genes. Although this feature plays an important role in regulating the SOS response, both the range of this separation and its underlying mechanism are not experimentally defined. Here we show that, at low doses of DNA damage, the timing of promoter activities is not separated. Instead, timing differences only emerge at higher levels of DNA damage and increase as a function of DNA damage dose. To understand mechanism, we derived a series of synthetic SOS gene promoters which vary in LexA-operator binding kinetics, but are otherwise identical, and then studied their activity over a large dose-range of DNA damage. In distinction to established models based on rapid equilibrium assumptions, the data best fit a kinetic model of repressor occupancy at promoters, where the drop in cellular LexA levels associated with higher doses of DNA damage leads to non-equilibrium binding kinetics of LexA at operators. Operators with slow LexA binding kinetics achieve their minimal occupancy state at later times than operators with fast binding kinetics, resulting in a time separation of peak promoter activity between genes. These data provide insight into this remarkable feature of the SOS pathway by demonstrating how a single transcription factor can be employed to control the relative timing of each gene's transcription as a function of stimulus dose.

Multi-step cure kinetic model of ultra-thin glass fiber epoxy prepreg exhibiting both autocatalytic and diffusion-controlled regimes under isothermal and dynamic-heating conditions

Science.gov (United States)

Kim, Ye Chan; Min, Hyunsung; Hong, Sungyong; Wang, Mei; Sun, Hanna; Park, In-Kyung; Choi, Hyouk Ryeol; Koo, Ja Choon; Moon, Hyungpil; Kim, Kwang J.; Suhr, Jonghwan; Nam, Jae-Do

2017-08-01

As packaging technologies are demanded that reduce the assembly area of substrate, thin composite laminate substrates require the utmost high performance in such material properties as the coefficient of thermal expansion (CTE), and stiffness. Accordingly, thermosetting resin systems, which consist of multiple fillers, monomers and/or catalysts in thermoset-based glass fiber prepregs, are extremely complicated and closely associated with rheological properties, which depend on the temperature cycles for cure. For the process control of these complex systems, it is usually required to obtain a reliable kinetic model that could be used for the complex thermal cycles, which usually includes both the isothermal and dynamic-heating segments. In this study, an ultra-thin prepreg with highly loaded silica beads and glass fibers in the epoxy/amine resin system was investigated as a model system by isothermal/dynamic heating experiments. The maximum degree of cure was obtained as a function of temperature. The curing kinetics of the model prepreg system exhibited a multi-step reaction and a limited conversion as a function of isothermal curing temperatures, which are often observed in epoxy cure system because of the rate-determining diffusion of polymer chain growth. The modified kinetic equation accurately described the isothermal behavior and the beginning of the dynamic-heating behavior by integrating the obtained maximum degree of cure into the kinetic model development.

Devolatilization kinetics of woody biomass at short residence times and high heating rates and peak temperatures

DEFF Research Database (Denmark)

Johansen, Joakim M.; Gadsbøll, Rasmus; Thomsen, Jesper

2016-01-01

This work combines experimental and computational fluid dynamics (CFD) results to derive global kinetics for biomass (pine wood) devolatilization during heating rates on the order of 105Ks-1, bulk flow peak temperatures between 1405 and 1667K, and particle residence times below 0.1s. Experiments......Jmol-1. The accuracy of the derived global kinetics was supported by comparing predictions to experimental results from a 15kW furnace. The work emphasizes the importance of characterizing the temperature history of the biomass particles when deriving pyrolysis kinetics. The present results indicate...

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

Directory of Open Access Journals (Sweden)

Dalibor Broznić

2016-01-01

Full Text Available 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.

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

Science.gov (United States)

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.

Science.gov (United States)

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.

Analysis of lipid peroxidation kinetics. I

DEFF Research Database (Denmark)

Doktorov, Alexander B.; Lukzen, Nikita N.; Pedersen, Jørgen Boiden

2008-01-01

concentrations of reactants or different ways of initiating the re-  action. Nor has it been possible to predict the time dependence of the  products. The reason for these problems is the complicated structure  of the kinetic scheme, which includes a chain reaction. In this work  we perform an in depth analysis......  The kinetics of the lipid peroxidation reaction is only partly under-  stood. Although the set of reactions constituting the overall reaction  is believed to be known, it has not been possible to predict how the  reaction will respond to a change of one or more of the parameters, e.g.  initial...... of the importance of the individual  reaction steps and we introduce a new quasi-stationary concentration  method based on the assumption that one or more concentrations vary  much slower than the others. We show that it is justified to use a  quasi-stationary concentration approximation for the alkyl radical L...

KINETIC-J: A computational kernel for solving the linearized Vlasov equation applied to calculations of the kinetic, configuration space plasma current for time harmonic wave electric fields

Science.gov (United States)

Green, David L.; Berry, Lee A.; Simpson, Adam B.; Younkin, Timothy R.

2018-04-01

We present the KINETIC-J code, a computational kernel for evaluating the linearized Vlasov equation with application to calculating the kinetic plasma response (current) to an applied time harmonic wave electric field. This code addresses the need for a configuration space evaluation of the plasma current to enable kinetic full-wave solvers for waves in hot plasmas to move beyond the limitations of the traditional Fourier spectral methods. We benchmark the kernel via comparison with the standard k →-space forms of the hot plasma conductivity tensor.

Increasing Running Step Rate Reduces Patellofemoral Joint Forces

Science.gov (United States)

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

Probabilistic parameter estimation in a 2-step chemical kinetics model for n-dodecane jet autoignition

Science.gov (United States)

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.

Measuring border delay and crossing times at the US-Mexico border : part II. Step-by-step guidelines for implementing a radio frequency identification (RFID) system to measure border crossing and wait times.

Science.gov (United States)

2012-06-01

The purpose of these step-by-step guidelines is to assist in planning, designing, and deploying a system that uses radio frequency identification (RFID) technology to measure the time needed for commercial vehicles to complete the northbound border c...

Displacement in the parameter space versus spurious solution of discretization with large time step

International Nuclear Information System (INIS)

Mendes, Eduardo; Letellier, Christophe

2004-01-01

In order to investigate a possible correspondence between differential and difference equations, it is important to possess discretization of ordinary differential equations. It is well known that when differential equations are discretized, the solution thus obtained depends on the time step used. In the majority of cases, such a solution is considered spurious when it does not resemble the expected solution of the differential equation. This often happens when the time step taken into consideration is too large. In this work, we show that, even for quite large time steps, some solutions which do not correspond to the expected ones are still topologically equivalent to solutions of the original continuous system if a displacement in the parameter space is considered. To reduce such a displacement, a judicious choice of the discretization scheme should be made. To this end, a recent discretization scheme, based on the Lie expansion of the original differential equations, proposed by Monaco and Normand-Cyrot will be analysed. Such a scheme will be shown to be sufficient for providing an adequate discretization for quite large time steps compared to the pseudo-period of the underlying dynamics

First off-time treatment prostate-specific antigen kinetics predicts survival in intermittent androgen deprivation for prostate cancer.

Science.gov (United States)

Sanchez-Salas, Rafael; Olivier, Fabien; Prapotnich, Dominique; Dancausa, José; Fhima, Mehdi; David, Stéphane; Secin, Fernando P; Ingels, Alexandre; Barret, Eric; Galiano, Marc; Rozet, François; Cathelineau, Xavier

2016-01-01

Prostate-specific antigen (PSA) doubling time is relying on an exponential kinetic pattern. This pattern has never been validated in the setting of intermittent androgen deprivation (IAD). Objective is to analyze the prognostic significance for PCa of recurrent patterns in PSA kinetics in patients undergoing IAD. A retrospective study was conducted on 377 patients treated with IAD. On-treatment period (ONTP) consisted of gonadotropin-releasing hormone agonist injections combined with oral androgen receptor antagonist. Off-treatment period (OFTP) began when PSA was lower than 4 ng/ml. ONTP resumed when PSA was higher than 20 ng/ml. PSA values of each OFTP were fitted with three basic patterns: exponential (PSA(t) = λ.e(αt)), linear (PSA(t) = a.t), and power law (PSA(t) = a.t(c)). Univariate and multivariate Cox regression model analyzed predictive factors for oncologic outcomes. Only 45% of the analyzed OFTPs were exponential. Linear and power law PSA kinetics represented 7.5% and 7.7%, respectively. Remaining fraction of analyzed OFTPs (40%) exhibited complex kinetics. Exponential PSA kinetics during the first OFTP was significantly associated with worse oncologic outcome. The estimated 10-year cancer-specific survival (CSS) was 46% for exponential versus 80% for nonexponential PSA kinetics patterns. The corresponding 10-year probability of castration-resistant prostate cancer (CRPC) was 69% and 31% for the two patterns, respectively. Limitations include retrospective design and mixed indications for IAD. PSA kinetic fitted with exponential pattern in approximately half of the OFTPs. First OFTP exponential PSA kinetic was associated with a shorter time to CRPC and worse CSS. © 2015 Wiley Periodicals, Inc.

On a closed form solution of the point kinetics equations with reactivity feedback of temperature

International Nuclear Information System (INIS)

Silva, Jeronimo J.A.; Vilhena, Marco T.M.B.; Petersen, Claudio Z.; Bodmann, Bardo E.J.; Alvim, Antonio C.M.

2011-01-01

An analytical solution of the point kinetics equations to calculate reactivity as a function of time by the Decomposition method has recently appeared in the literature. In this paper, we go one step forward, by considering the neutron point kinetics equations together with temperature feedback effects. To accomplish that, we extended the point kinetics by a temperature perturbation, obtaining a second order nonlinear ordinary differential equation. This equation is then solved by the Decomposition Method, that is, by expanding the neutron density in a series and the nonlinear terms into Adomian Polynomials. Substituting these expansions into the nonlinear ordinary equation, we construct a recursive set of linear problems that can be solved by the methodology previously mentioned for the point kinetics equation. We also report on numerical simulations and comparisons against literature results. (author)

Smouldering Combustion of Soil Organic Matter: Inverse Modelling of the Thermal and Oxidative Degradation Kinetics

Science.gov (United States)

Huang, Xinyan; Rein, Guillermo

2013-04-01

Smouldering combustion of soil organic matter (SOM) such as peatlands leads to the largest fires on Earth and posses a possible positive feedback mechanism to climate change. In this work, a kinetic model, including 3-step chemical reactions and 1-step water evaporation is proposed to describe drying, pyrolysis and oxidation behaviour of peat. Peat is chosen as the most important type of SOM susceptible to smoudering, and a Chinese boreal peat sample is selected from the literature. A lumped model of mass loss based on four Arrhenius-type reactions is developed to predict its thermal and oxidative degradation under a range of heating rates. A genetic algorithm is used to solve the inverse problem, and find a group of kinetic and stoichiometric parameters for this peat that provides the best match to the thermogravimetric (TG) data from literature. A multi-objective fitness function is defined using the measurements of both mass loss and mass-loss rate in inert and normal atmospheres under a range of heating rates. Piece-wise optimization is conducted to separate the low temperature drying (450 K). Modelling results shows the proposed 3-step chemistry is the unique simplest scheme to satisfy all given TG data of this particular peat type. Afterward, this kinetic model and its kinetic parameters are incorporated into a simple one-dimensional species model to study the relative position of each reaction inside a smoulder front. Computational results show that the species model agrees with experimental observations. This is the first time that the smouldering kinetics of SOM is explained and predicted, thus helping to understanding this important natural and widespread phenomenon.

Stepping Stones through Time

Directory of Open Access Journals (Sweden)

Emily Lyle

2012-03-01

Full Text Available Indo-European mythology is known only through written records but it needs to be understood in terms of the preliterate oral-cultural context in which it was rooted. It is proposed that this world was conceptually organized through a memory-capsule consisting of the current generation and the three before it, and that there was a system of alternate generations with each generation taking a step into the future under the leadership of a white or red king.

Perturbed Strong Stability Preserving Time-Stepping Methods For Hyperbolic PDEs

KAUST Repository

Hadjimichael, Yiannis

2017-09-30

A plethora of physical phenomena are modelled by hyperbolic partial differential equations, for which the exact solution is usually not known. Numerical methods are employed to approximate the solution to hyperbolic problems; however, in many cases it is difficult to satisfy certain physical properties while maintaining high order of accuracy. In this thesis, we develop high-order time-stepping methods that are capable of maintaining stability constraints of the solution, when coupled with suitable spatial discretizations. Such methods are called strong stability preserving (SSP) time integrators, and we mainly focus on perturbed methods that use both upwind- and downwind-biased spatial discretizations. Firstly, we introduce a new family of third-order implicit Runge–Kuttas methods with arbitrarily large SSP coefficient. We investigate the stability and accuracy of these methods and we show that they perform well on hyperbolic problems with large CFL numbers. Moreover, we extend the analysis of SSP linear multistep methods to semi-discretized problems for which different terms on the right-hand side of the initial value problem satisfy different forward Euler (or circle) conditions. Optimal perturbed and additive monotonicity-preserving linear multistep methods are studied in the context of such problems. Optimal perturbed methods attain augmented monotonicity-preserving step sizes when the different forward Euler conditions are taken into account. On the other hand, we show that optimal SSP additive methods achieve a monotonicity-preserving step-size restriction no better than that of the corresponding non-additive SSP linear multistep methods. Furthermore, we develop the first SSP linear multistep methods of order two and three with variable step size, and study their optimality. We describe an optimal step-size strategy and demonstrate the effectiveness of these methods on various one- and multi-dimensional problems. Finally, we establish necessary conditions

First passage times for multiple particles with reversible target-binding kinetics

Science.gov (United States)

Grebenkov, Denis S.

2017-10-01

We investigate the first passage problem for multiple particles that diffuse towards a target, partially adsorb there, and then desorb after a finite exponentially distributed residence time. We search for the first time when m particles undergoing such reversible target-binding kinetics are found simultaneously on the target that may trigger an irreversible chemical reaction or a biophysical event. Even if the particles are independent, the finite residence time on the target yields an intricate temporal coupling between particles. We compute analytically the mean first passage time (MFPT) for two independent particles by mapping the original problem to higher-dimensional surface-mediated diffusion and solving the coupled partial differential equations. The respective effects of the adsorption and desorption rates on the MFPT are revealed and discussed.

Investigation of 3D spatial effect on point kinetics estimation of the thermal hydraulics code RELAP for the analysis of MSLB accident of KK-NP

International Nuclear Information System (INIS)

Bera, S.; Pradhan, S.K.; Dubey, S.K.; Gupta, S.K.

2011-01-01

In general safety analyses of design basis accident of NPPs are being carried out using system thermal hydraulics code like RELAP. In RELAP, power is calculated based on point kinetics approximation, which virtually ignores the space and energy dependence of neutron flux. To include the space and energy dependence of neutron flux, three-dimensional neutronics code TRIHEXFA has been externally coupled with RELAP through interface program, TRIHEXFA-RELAP Interface Program (TRIP). Calculation methodology of TRIP program is based on adiabatic approximation. In the adiabatic approximation the neutron flux is being factored into spatial and amplitude part. Spatial part of flux is slowly varying with time whereas amplitude part is strongly varying function. The RELAP controls the transient time steps. Transient time is divided into several major and minor time steps. Minor time step is the sub-step of major time step. Thermal hydraulics and neutronics data are exchanged at each major time step. Spatial part of neutron flux has been updated at each major time step using TRIHEXFA code. But amplitude part of the neutron flux is calculated at each minor time step using RELAP code. Convergence of results of the coupled code, TRIP has been checked through coupling time step descritization study. This study determines the minimum coupling time step. Transient concerning VVER-1000 Main Steam Line Break, MSLB has been considered to investigate the space-time effect on point kinetics. MSLB occurs as a consequence of the rupture of one steam line upstream of main steam line isolation valves. Reference design and data from Kudankulam Nuclear Power Plant (KK-NPP) are used for the analysis. From this investigation it is found that TRIP significantly overestimates the maximum reactor power against uncoupled RELAP result. The time of scram also occur six seconds earlier in TRIP calculation compared to the RELAP. This exercise has also shown a proof of principle that coupling 3D

Fine kinetics of natural physical ageing in glassy As{sub 10}Se{sub 90}

Energy Technology Data Exchange (ETDEWEB)

Balitska, V. [Institute of Materials, Scientific Research Company “Carat”, 202 Stryjska Str., 79031 Lviv (Ukraine); Lviv State University of Vital Activity Safety, 35, Kleparivska Str., Lviv 79007 (Ukraine); Golovchak, R. [Department of Physics and Astronomy, Austin Peay State University, Clarksville, TN 37044 (United States); Kozdras, A. [Faculty of Physics of Opole Technical University, 75, Ozimska Str., Opole 45370 (Poland); Shpotyuk, O., E-mail: shpotyuk@novas.lviv.ua [Institute of Materials, Scientific Research Company “Carat”, 202 Stryjska Str., 79031 Lviv (Ukraine); Institute of Physics, Jan Dlugosz University, Al. Armii Krajowej 13/15, Czestochowa 42201 (Poland)

2014-02-01

Sigmoid behavior of natural physical ageing in glassy As{sub 10}Se{sub 90} reveals multi-step-wise growing kinetics of enthalpy losses. Phenomenological description of this kinetics can be adequately developed in terms of first-order relaxation processes, tending atomic structure from initial towards more thermodynamically equilibrium state. This kinetics is shown to obey characteristic stretched exponential behavior originated from a number of growing steps, attributed to the interconnected processes of chalcogen chain alignment and cooperative shrinkage of glass network.

Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles

Directory of Open Access Journals (Sweden)

Gengjie Jia

2012-11-01

Full Text Available Kinetic modeling of metabolic pathways has important applications in metabolic engineering, but significant challenges still remain. The difficulties faced vary from finding best-fit parameters in a highly multidimensional search space to incomplete parameter identifiability. To meet some of these challenges, an ensemble modeling method is developed for characterizing a subset of kinetic parameters that give statistically equivalent goodness-of-fit to time series concentration data. The method is based on the incremental identification approach, where the parameter estimation is done in a step-wise manner. Numerical efficacy is achieved by reducing the dimensionality of parameter space and using efficient random parameter exploration algorithms. The shift toward using model ensembles, instead of the traditional “best-fit” models, is necessary to directly account for model uncertainty during the application of such models. The performance of the ensemble modeling approach has been demonstrated in the modeling of a generic branched pathway and the trehalose pathway in Saccharomyces cerevisiae using generalized mass action (GMA kinetics.

Kinetics of Pressurized Water Reactors with Hot or Cold Moderators

Energy Technology Data Exchange (ETDEWEB)

Norinder, O

1960-11-15

The set of neutron kinetic equations developed in this report permits the use of long integration steps during stepwise integration. Thermal relations which describe the transfer of heat from fuel to coolant are derived. The influence upon the kinetic behavior of the reactor of a number of parameters is studied. A comparison of the kinetic properties of the hot and cold moderators is given.

Modeling the high pressure inactivation kinetics of Listeria monocytogenes on RTE cooked meat products

DEFF Research Database (Denmark)

Hereu, A.; Dalgaard, Paw; Garriga, M.

2012-01-01

High pressure (HP) inactivation curves of Listeria monocytogenes CTC1034 (ca. 107CFU/g) on sliced RTE cooked meat products (ham and mortadella) were obtained at pressures from 300 to 800MPa. A clear tail shape was observed at pressures above 450MPa and the log-linear with tail primary model...... provided the best fit to the HP-inactivation kinetics. The relationships between the primary kinetic parameters (log kmax and log Nres) and pressure treatments were described by a polynomial secondary model. To estimate HP-inactivation of L. monocytogenes in log (N/N0) over time, a one-step global fitting...

Modelling of elementary kinetics of H2 and CO oxidation on ceria pattern cells

International Nuclear Information System (INIS)

Patel, HC; Tabish, AN; Aravind, PV

2015-01-01

Elementary kinetic mechanisms of fuel oxidation on ceria have not been dealt with in detail in literature. An elementary kinetic model is developed considering charge transfer and adsorption steps for electrochemical H 2 and CO oxidation on ceria. The reaction chemistry is solved by fitting previously obtained impedance spectra for H 2 and CO oxidation on ceria. The rate determining step is found to be the charge transfer rather than the adsorption for both H 2 and CO. A method is presented to extend the kinetics obtained from pattern anodes to macroscopic simulations in which the activation overvoltage can be calculated on the basis of elementary kinetics.

Mixtures of rubber tyre and plastic wastes pyrolysis: A kinetic study

International Nuclear Information System (INIS)

Miranda, Miguel; Cabrita, I.; Pinto, Filomena; Gulyurtlu, I.

2013-01-01

The study performed aimed at analysing possible routes for pyrolysis reaction mechanisms of polymeric materials namely RT (rubber tyre) and plastic wastes (PE (polyethylene), PP (polypropylene) and PS (polystyrene)). Consequently, and seeking sustainable transformation of waste streams into valuable chemicals and renewable liquid fuels, mixture of 30% RT, 20% PE, 30% PP and 20% PS was subjected to pyrolysis. Different kinetic models were studied using experimental data. None of the mechanisms found in literature led to a numerical adjustment and different pathways were investigated. Kinetic studies were performed aiming to evaluate direct conversions into new solid, liquid and gaseous products and if parallel reactions and/or reversible elementary steps should be included. Experiments were performed in batch system at different temperatures and reaction times. Kinetic models were evaluated and reaction pathways were proposed. Models reasonably fit experimental data, allow explaining wastes thermal degradation. Kinetic parameters were estimated for all temperatures and dependence of Ea and pre-exponential factor on temperature was evaluated. The rate constant of some reactions exhibited nonlinear temperature dependence on the logarithmic form of Arrhenius law. This fact strongly suggests that temperature has a significant effect on reaction mechanism of pyrolysis of mixtures of rubber tyre and plastic wastes. - Highlights: • Kinetic study of rubber tyre (RT) and different plastic wastes (PE, PP and PS) was performed in batch reactor. • Definition of possible pathways taken into account for the formation of final products. • Kinetic parameters were estimated. • The effect of reaction temperature and reaction time on liquid composition was performed

Faceting of stepped silicon (1 1 3) surfaces: Self assembly of nanoscale gratings

Science.gov (United States)

Mochrie, S. G. J.; Song, S.; Yoon, Mirang; Abernathy, D. L.; Stephenson, G. B.

1996-02-01

Synchrotron X-ray scattering studies of the phase behavior and phase transformations of stepped Si(113) surfaces tilted towards [001] are reviewed for temperatures between 300 and 1500 K. At the highest temperatures, these surfaces are uniformly stepped, and the intensity of near-specularly scattered X-rays increases with decreasing temperature. This is two-dimensional critical opalescence, which foreshadows a faceting transformation. At temperatures below the faceting transformation, (113) facets appear in coexistence with a stepped phase, leading to a mesoscopically grooved morphology. Both the misorientation angle at the phase boundary separating one- and two-phase regions and the intensity of the near-specular diffuse scattering may be described as power laws versus reduced temperature. This can be understood qualitatively on the basis of a mean-field theory, which incorporates an attractive interaction between steps. At lower temperatures, the surfaces are completely faceted, comprising (114) and (113) facets. The kinetics of faceting is also described. Following a quench from a one-phase region of the phase diagram into a two-phase region, the grooved superstructure forms and subsequently coarsens in time. For times between one and several hundred seconds, the surface morphology is self-similar at different times, with a characteristic groove size that evolves as a power law versus time. At later times, the groove size approaches a limiting value, as a result of elastic effects.

Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps

Science.gov (United States)

Tiwary, Pratyush; Limongelli, Vittorio; Salvalaglio, Matteo; Parrinello, Michele

2015-01-01

The ability to predict the mechanisms and the associated rate constants of protein–ligand unbinding is of great practical importance in drug design. In this work we demonstrate how a recently introduced metadynamics-based approach allows exploration of the unbinding pathways, estimation of the rates, and determination of the rate-limiting steps in the paradigmatic case of the trypsin–benzamidine system. Protein, ligand, and solvent are described with full atomic resolution. Using metadynamics, multiple unbinding trajectories that start with the ligand in the crystallographic binding pose and end with the ligand in the fully solvated state are generated. The unbinding rate koff is computed from the mean residence time of the ligand. Using our previously computed binding affinity we also obtain the binding rate kon. Both rates are in agreement with reported experimental values. We uncover the complex pathways of unbinding trajectories and describe the critical rate-limiting steps with unprecedented detail. Our findings illuminate the role played by the coupling between subtle protein backbone fluctuations and the solvation by water molecules that enter the binding pocket and assist in the breaking of the shielded hydrogen bonds. We expect our approach to be useful in calculating rates for general protein–ligand systems and a valid support for drug design. PMID:25605901

Hydrogen electrode reaction: A complete kinetic description

International Nuclear Information System (INIS)

Quaino, P.M.; Gennero de Chialvo, M.R.; Chialvo, A.C.

2007-01-01

The kinetic description of the hydrogen electrode reaction (HER) in the whole range of overpotentials (-0.2 < η (V) < 0.40) is presented. The Volmer-Heyrovsky-Tafel mechanism was solved considering simultaneously the following items: (i) the diffusional contribution of the molecular hydrogen from and towards the electrode surface, (ii) the forward and backward reaction rates of each elementary step and (iii) a Frumkin type adsorption for the reaction intermediate. In order to verify the descriptive capability of the kinetic expressions derived, an experimental study of the HER was carried out on a rotating platinum disc electrode in acid solution. From the correlation of these results the elementary kinetic parameters were evaluated and several aspects related to the kinetic mechanism were discussed. Finally, the use of these kinetic expressions to interpret results obtained on microelectrodes is also analysed

Kinetic study of enzymatic hydrolysis of acid-pretreated coconut coir

Science.gov (United States)

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.

Error Analysis of a Fractional Time-Stepping Technique for Incompressible Flows with Variable Density

KAUST Repository

Guermond, J.-L.; Salgado, Abner J.

2011-01-01

In this paper we analyze the convergence properties of a new fractional time-stepping technique for the solution of the variable density incompressible Navier-Stokes equations. The main feature of this method is that, contrary to other existing algorithms, the pressure is determined by just solving one Poisson equation per time step. First-order error estimates are proved, and stability of a formally second-order variant of the method is established. © 2011 Society for Industrial and Applied Mathematics.

Methane production from cellulosic wastes: kinetic studies

Energy Technology Data Exchange (ETDEWEB)

Goma, G; De La Torre, I; Maugheri, F; Yameogo, T

1979-09-01

The anaerobic fermentation is studied on lignocellulosic materials and sucrose as substrate. With the lignocellulosic material cellulolysis is rate limiting. The reducing sugar concentration in the fermentation broth is less than 15 mgl/sup -1/. With rumen bacteria, 50% of the initial polyoside are used and 12% of the lignin is solubilized. With sucrose studies on the kinetic behaviour of the mixed population responsible of the acidogenesis step permite to find the optimal temperature (40/sup 0/C) feed substrate concentration (50 gl/sup -1/) residence time (60 hours) and pH (5,5 - 6). The better technology is a plug flow fermentor with cell recycling. Modeling of the behaviour of this reactor was performed. The use of this reactor for the selection of acido resistant bacteria is discussed. For methanogenesis, in continuous culture, the ideal technology seems to be an association of two reactors. In the first step, a plug flow reactor must be used for acidogenesis, and in the second step a well mixed reactor permit the conversion of organic acids in methane.

Step width alters iliotibial band strain during running.

Science.gov (United States)

Meardon, Stacey A; Campbell, Samuel; Derrick, Timothy R

2012-11-01

This study assessed the effect of step width during running on factors related to iliotibial band (ITB) syndrome. Three-dimensional (3D) kinematics and kinetics were recorded from 15 healthy recreational runners during overground running under various step width conditions (preferred and at least +/- 5% of their leg length). Strain and strain rate were estimated from a musculoskeletal model of the lower extremity. Greater ITB strain and strain rate were found in the narrower step width condition (p running, especially in persons whose running style is characterized by a narrow step width, may be beneficial in the treatment and prevention of running-related ITB syndrome.

Parallelised Krylov subspace method for reactor kinetics by IQS approach

International Nuclear Information System (INIS)

Gupta, Anurag; Modak, R.S.; Gupta, H.P.; Kumar, Vinod; Bhatt, K.

2005-01-01

Nuclear reactor kinetics involves numerical solution of space-time-dependent multi-group neutron diffusion equation. Two distinct approaches exist for this purpose: the direct (implicit time differencing) approach and the improved quasi-static (IQS) approach. Both the approaches need solution of static space-energy-dependent diffusion equations at successive time-steps; the step being relatively smaller for the direct approach. These solutions are usually obtained by Gauss-Seidel type iterative methods. For a faster solution, the Krylov sub-space methods have been tried and also parallelised by many investigators. However, these studies seem to have been done only for the direct approach. In the present paper, parallelised Krylov methods are applied to the IQS approach in addition to the direct approach. It is shown that the speed-up obtained for IQS is higher than that for the direct approach. The reasons for this are also discussed. Thus, the use of IQS approach along with parallelised Krylov solvers seems to be a promising scheme

Translational step inhibited in vivo by aflatoxin B1 in rat-liver polysomes

International Nuclear Information System (INIS)

Sarasin, A.; Moule, Y.

1975-01-01

Aflatoxin B 1 strongly inhibits protein synthesis in rat liver cells. This paper confirms the foregoing results and represents an attempt to localize the translational step inhibited in vivo by aflatoxin B 1 . We used the simulation study developed by Li, Kisilevsky, Wasan and Hammond, 1972 (Biochim. Biophys. Acta, 272, 451-462) to determine precisely the site inhibited in vivo after drug intoxication. This analysis is based on two parameters: the kinetics of polysome labeling to follow the nascent peptide synthesis, and the kinetics of supernatant labeling to follow the completed protein synthesis. Up to 5 h after dosing, aflatoxin specifically inhibits the elongation and/or termination steps during protein synthesis; after longer periods of time inhibition occurs essentially at the initiation step. When the intracellular concentration of aflatoxin is too high, particularly 2 h after dosing, each step of protein synthesis is blocked. Polypeptide synthesis by the postmitochondrial supernatants isolated from aflatoxin-treated animals is impaired in the same proportion as protein synthesis in vivo. The damage caused by aflatoxin is mostly observed on microsomes. However, purified polysomes isolated from aflatoxin-treated rats synthesize proteins in vitro to the same extent as those from controls. These results suggest that aflatoxin metabolite(s) are bound to polysomes with noncovalent bonds. These active metabolites are probably lost during polysome isolation procedures. Finally, relationships between protein metabolism and aflatoxin carcinogenesis are discussed. (orig./BSC) [de

Simulation of ITG instabilities with fully kinetic ions and drift-kinetic electrons in tokamaks

Science.gov (United States)

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.

An efficient and accurate two-stage fourth-order gas-kinetic scheme for the Euler and Navier-Stokes equations

Science.gov (United States)

Pan, Liang; Xu, Kun; Li, Qibing; Li, Jiequan

2016-12-01

For computational fluid dynamics (CFD), the generalized Riemann problem (GRP) solver and the second-order gas-kinetic scheme (GKS) provide a time-accurate flux function starting from a discontinuous piecewise linear flow distributions around a cell interface. With the adoption of time derivative of the flux function, a two-stage Lax-Wendroff-type (L-W for short) time stepping method has been recently proposed in the design of a fourth-order time accurate method for inviscid flow [21]. In this paper, based on the same time-stepping method and the second-order GKS flux function [42], a fourth-order gas-kinetic scheme is constructed for the Euler and Navier-Stokes (NS) equations. In comparison with the formal one-stage time-stepping third-order gas-kinetic solver [24], the current fourth-order method not only reduces the complexity of the flux function, but also improves the accuracy of the scheme. In terms of the computational cost, a two-dimensional third-order GKS flux function takes about six times of the computational time of a second-order GKS flux function. However, a fifth-order WENO reconstruction may take more than ten times of the computational cost of a second-order GKS flux function. Therefore, it is fully legitimate to develop a two-stage fourth order time accurate method (two reconstruction) instead of standard four stage fourth-order Runge-Kutta method (four reconstruction). Most importantly, the robustness of the fourth-order GKS is as good as the second-order one. In the current computational fluid dynamics (CFD) research, it is still a difficult problem to extend the higher-order Euler solver to the NS one due to the change of governing equations from hyperbolic to parabolic type and the initial interface discontinuity. This problem remains distinctively for the hypersonic viscous and heat conducting flow. The GKS is based on the kinetic equation with the hyperbolic transport and the relaxation source term. The time-dependent GKS flux function

Adjusting kinematics and kinetics in a feedback-controlled toe walking model

Directory of Open Access Journals (Sweden)

Olenšek Andrej

2012-08-01

Full Text Available Abstract Background In clinical gait assessment, the correct interpretation of gait kinematics and kinetics has a decisive impact on the success of the therapeutic programme. Due to the vast amount of information from which primary anomalies should be identified and separated from secondary compensatory changes, as well as the biomechanical complexity and redundancy of the human locomotion system, this task is considerably challenging and requires the attention of an experienced interdisciplinary team of experts. The ongoing research in the field of biomechanics suggests that mathematical modeling may facilitate this task. This paper explores the possibility of generating a family of toe walking gait patterns by systematically changing selected parameters of a feedback-controlled model. Methods From the selected clinical case of toe walking we identified typical toe walking characteristics and encoded them as a set of gait-oriented control objectives to be achieved in a feedback-controlled walking model. They were defined as fourth order polynomials and imposed via feedback control at the within-step control level. At the between-step control level, stance leg lengthening velocity at the end of the single support phase was adaptively adjusted after each step so as to facilitate gait velocity control. Each time the gait velocity settled at the desired value, selected intra-step gait characteristics were modified by adjusting the polynomials so as to mimic the effect of a typical therapeutical intervention - inhibitory casting. Results By systematically adjusting the set of control parameters we were able to generate a family of gait kinematic and kinetic patterns that exhibit similar principal toe walking characteristics, as they were recorded by means of an instrumented gait analysis system in the selected clinical case of toe walking. We further acknowledge that they to some extent follow similar improvement tendencies as those which one can

Performance of neutron kinetics models for ADS transient analyses

International Nuclear Information System (INIS)

Rineiski, A.; Maschek, W.; Rimpault, G.

2002-01-01

can also apply this approach for estimating errors of point-kinetics simulations or for ameliorating the employed point-kinetics models. Though the performance of the point-kinetics model can be insufficient in the subcritical case, the quasi-static approach is still valid if the shape steps are chosen properly. It is worthwhile to mention that in combination with properly computed correction factor tables, one can use the reactivity and power distributions obtained for 'critical' reactor models; this approach can simplify ADS-related application of conventional accident analyses codes (developed in the past for transient analyses of critical reactors). However, for analyzing severe transients in ADSs, which involve gross core material configuration changes, one can hardly avoid using of space-time kinetics methods, this holds similarly for critical reactor systems. (authors)

Rapid expansion method (REM) for time‐stepping in reverse time migration (RTM)

KAUST Repository

Pestana, Reynam C.

2009-01-01

We show that the wave equation solution using a conventional finite‐difference scheme, derived commonly by the Taylor series approach, can be derived directly from the rapid expansion method (REM). After some mathematical manipulation we consider an analytical approximation for the Bessel function where we assume that the time step is sufficiently small. From this derivation we find that if we consider only the first two Chebyshev polynomials terms in the rapid expansion method we can obtain the second order time finite‐difference scheme that is frequently used in more conventional finite‐difference implementations. We then show that if we use more terms from the REM we can obtain a more accurate time integration of the wave field. Consequently, we have demonstrated that the REM is more accurate than the usual finite‐difference schemes and it provides a wave equation solution which allows us to march in large time steps without numerical dispersion and is numerically stable. We illustrate the method with post and pre stack migration results.

The ATP hydrolysis and phosphate release steps control the time course of force development in rabbit skeletal muscle.

Science.gov (United States)

Sleep, John; Irving, Malcolm; Burton, Kevin

2005-03-15

The time course of isometric force development following photolytic release of ATP in the presence of Ca(2+) was characterized in single skinned fibres from rabbit psoas muscle. Pre-photolysis force was minimized using apyrase to remove contaminating ATP and ADP. After the initial force rise induced by ATP release, a rapid shortening ramp terminated by a step stretch to the original length was imposed, and the time course of the subsequent force redevelopment was again characterized. Force development after ATP release was accurately described by a lag phase followed by one or two exponential components. At 20 degrees C, the lag was 5.6 +/- 0.4 ms (s.e.m., n = 11), and the force rise was well fitted by a single exponential with rate constant 71 +/- 4 s(-1). Force redevelopment after shortening-restretch began from about half the plateau force level, and its single-exponential rate constant was 68 +/- 3 s(-1), very similar to that following ATP release. When fibres were activated by the addition of Ca(2+) in ATP-containing solution, force developed more slowly, and the rate constant for force redevelopment following shortening-restretch reached a maximum value of 38 +/- 4 s(-1) (n = 6) after about 6 s of activation. This lower value may be associated with progressive sarcomere disorder at elevated temperature. Force development following ATP release was much slower at 5 degrees C than at 20 degrees C. The rate constant of a single-exponential fit to the force rise was 4.3 +/- 0.4 s(-1) (n = 22), and this was again similar to that after shortening-restretch in the same activation at this temperature, 3.8 +/- 0.2 s(-1). We conclude that force development after ATP release and shortening-restretch are controlled by the same steps in the actin-myosin ATPase cycle. The present results and much previous work on mechanical-chemical coupling in muscle can be explained by a kinetic scheme in which force is generated by a rapid conformational change bracketed by two

A stabilized Runge–Kutta–Legendre method for explicit super-time-stepping of parabolic and mixed equations

International Nuclear Information System (INIS)

Meyer, Chad D.; Balsara, Dinshaw S.; Aslam, Tariq D.

2014-01-01

Parabolic partial differential equations appear in several physical problems, including problems that have a dominant hyperbolic part coupled to a sub-dominant parabolic component. Explicit methods for their solution are easy to implement but have very restrictive time step constraints. Implicit solution methods can be unconditionally stable but have the disadvantage of being computationally costly or difficult to implement. Super-time-stepping methods for treating parabolic terms in mixed type partial differential equations occupy an intermediate position. In such methods each superstep takes “s” explicit Runge–Kutta-like time-steps to advance the parabolic terms by a time-step that is s 2 times larger than a single explicit time-step. The expanded stability is usually obtained by mapping the short recursion relation of the explicit Runge–Kutta scheme to the recursion relation of some well-known, stable polynomial. Prior work has built temporally first- and second-order accurate super-time-stepping methods around the recursion relation associated with Chebyshev polynomials. Since their stability is based on the boundedness of the Chebyshev polynomials, these methods have been called RKC1 and RKC2. In this work we build temporally first- and second-order accurate super-time-stepping methods around the recursion relation associated with Legendre polynomials. We call these methods RKL1 and RKL2. The RKL1 method is first-order accurate in time; the RKL2 method is second-order accurate in time. We verify that the newly-designed RKL1 and RKL2 schemes have a very desirable monotonicity preserving property for one-dimensional problems – a solution that is monotone at the beginning of a time step retains that property at the end of that time step. It is shown that RKL1 and RKL2 methods are stable for all values of the diffusion coefficient up to the maximum value. We call this a convex monotonicity preserving property and show by examples that it is very useful

Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm.

Science.gov (United States)

Chen, Yunjie; Kale, Seyit; Weare, Jonathan; Dinner, Aaron R; Roux, Benoît

2016-04-12

A multiple time-step integrator based on a dual Hamiltonian and a hybrid method combining molecular dynamics (MD) and Monte Carlo (MC) is proposed to sample systems in the canonical ensemble. The Dual Hamiltonian Multiple Time-Step (DHMTS) algorithm is based on two similar Hamiltonians: a computationally expensive one that serves as a reference and a computationally inexpensive one to which the workload is shifted. The central assumption is that the difference between the two Hamiltonians is slowly varying. Earlier work has shown that such dual Hamiltonian multiple time-step schemes effectively precondition nonlinear differential equations for dynamics by reformulating them into a recursive root finding problem that can be solved by propagating a correction term through an internal loop, analogous to RESPA. Of special interest in the present context, a hybrid MD-MC version of the DHMTS algorithm is introduced to enforce detailed balance via a Metropolis acceptance criterion and ensure consistency with the Boltzmann distribution. The Metropolis criterion suppresses the discretization errors normally associated with the propagation according to the computationally inexpensive Hamiltonian, treating the discretization error as an external work. Illustrative tests are carried out to demonstrate the effectiveness of the method.

Positivity-preserving dual time stepping schemes for gas dynamics

Science.gov (United States)

Parent, Bernard

2018-05-01

A new approach at discretizing the temporal derivative of the Euler equations is here presented which can be used with dual time stepping. The temporal discretization stencil is derived along the lines of the Cauchy-Kowalevski procedure resulting in cross differences in spacetime but with some novel modifications which ensure the positivity of the discretization coefficients. It is then shown that the so-obtained spacetime cross differences result in changes to the wave speeds and can thus be incorporated within Roe or Steger-Warming schemes (with and without reconstruction-evolution) simply by altering the eigenvalues. The proposed approach is advantaged over alternatives in that it is positivity-preserving for the Euler equations. Further, it yields monotone solutions near discontinuities while exhibiting a truncation error in smooth regions less than the one of the second- or third-order accurate backward-difference-formula (BDF) for either small or large time steps. The high resolution and positivity preservation of the proposed discretization stencils are independent of the convergence acceleration technique which can be set to multigrid, preconditioning, Jacobian-free Newton-Krylov, block-implicit, etc. Thus, the current paper also offers the first implicit integration of the time-accurate Euler equations that is positivity-preserving in the strict sense (that is, the density and temperature are guaranteed to remain positive). This is in contrast to all previous positivity-preserving implicit methods which only guaranteed the positivity of the density, not of the temperature or pressure. Several stringent reacting and inert test cases confirm the positivity-preserving property of the proposed method as well as its higher resolution and higher computational efficiency over other second-order and third-order implicit temporal discretization strategies.

Coupled kinetic equations for fermions and bosons in the relaxation-time approximation

Science.gov (United States)

Florkowski, Wojciech; Maksymiuk, Ewa; Ryblewski, Radoslaw

2018-02-01

Kinetic equations for fermions and bosons are solved numerically in the relaxation-time approximation for the case of one-dimensional boost-invariant geometry. Fermions are massive and carry baryon number, while bosons are massless. The conservation laws for the baryon number, energy, and momentum lead to two Landau matching conditions, which specify the coupling between the fermionic and bosonic sectors and determine the proper-time dependence of the effective temperature and baryon chemical potential of the system. The numerical results illustrate how a nonequilibrium mixture of fermions and bosons approaches hydrodynamic regime described by the Navier-Stokes equations with appropriate forms of the kinetic coefficients. The shear viscosity of a mixture is the sum of the shear viscosities of fermion and boson components, while the bulk viscosity is given by the formula known for a gas of fermions, however, with the thermodynamic variables characterising the mixture. Thus, we find that massless bosons contribute in a nontrivial way to the bulk viscosity of a mixture, provided fermions are massive. We further observe the hydrodynamization effect, which takes place earlier in the shear sector than in the bulk one. The numerical studies of the ratio of the longitudinal and transverse pressures show, to a good approximation, that it depends on the ratio of the relaxation and proper times only. This behavior is connected with the existence of an attractor solution for conformal systems.

Time Trials Versus Time-to-Exhaustion Tests: Effects on Critical Power, W', and Oxygen-Uptake Kinetics.

Science.gov (United States)

Karsten, Bettina; Baker, Jonathan; Naclerio, Fernando; Klose, Andreas; Bianco, Antonino; Nimmerichter, Alfred

2018-02-01

To investigate single-day time-to-exhaustion (TTE) and time-trial (TT) -based laboratory tests values of critical power (CP), W prime (W'), and respective oxygen-uptake-kinetic responses. Twelve cyclists performed a maximal ramp test followed by 3 TTE and 3 TT efforts interspersed by 60 min recovery between efforts. Oxygen uptake ( V ˙ O 2 ) was measured during all trials. The mean response time was calculated as a description of the overall [Formula: see text]-kinetic response from the onset to 2 min of exercise. TTE-determined CP was 279 ± 52 W, and TT-determined CP was 276 ± 50 W (P = .237). Values of W' were 14.3 ± 3.4 kJ (TTE W') and 16.5 ± 4.2 kJ (TT W') (P = .028). While a high level of agreement (-12 to 17 W) and a low prediction error of 2.7% were established for CP, for W' limits of agreements were markedly lower (-8 to 3.7 kJ), with a prediction error of 18.8%. The mean standard error for TTE CP values was significantly higher than that for TT CP values (2.4% ± 1.9% vs 1.2% ± 0.7% W). The standard errors for TTE W' and TT W' were 11.2% ± 8.1% and 5.6% ± 3.6%, respectively. The [Formula: see text] response was significantly faster during TT (~22 s) than TTE (~28 s). The TT protocol with a 60-min recovery period offers a valid, time-saving, and less error-filled alternative to conventional and more recent testing methods. Results, however, cannot be transferred to W'.

On coupling fluid plasma and kinetic neutral physics models

Directory of Open Access Journals (Sweden)

I. Joseph

2017-08-01

Full Text Available The coupled fluid plasma and kinetic neutral physics equations are analyzed through theory and simulation of benchmark cases. It is shown that coupling methods that do not treat the coupling rates implicitly are restricted to short time steps for stability. Fast charge exchange, ionization and recombination coupling rates exist, even after constraining the solution by requiring that the neutrals are at equilibrium. For explicit coupling, the present implementation of Monte Carlo correlated sampling techniques does not allow for complete convergence in slab geometry. For the benchmark case, residuals decay with particle number and increase with grid size, indicating that they scale in a manner that is similar to the theoretical prediction for nonlinear bias error. Progress is reported on implementation of a fully implicit Jacobian-free Newton–Krylov coupling scheme. The present block Jacobi preconditioning method is still sensitive to time step and methods that better precondition the coupled system are under investigation.

Prediction of Non-Equilibrium Kinetics of Fuel-Rich Kerosene/LOX Combustion in Gas Generator

International Nuclear Information System (INIS)

Yu, Jung Min; Lee, Chang Jin

2007-01-01

Gas generator is the device to produce high enthalpy gases needed to drive turbo-pump system in liquid rocket engine. And, the combustion temperature in gas generator should be controlled below around 1,000K to avoid any possible thermal damages to turbine blade by using either fuel rich combustion or oxidizer rich combustion. Thus, nonequilibrium chemical reaction dominates in fuel-rich combustion of gas generator. Meanwhile, kerosene is a compounded fuel with various types of hydrocarbon elements and difficult to model the chemical kinetics. This study focuses on the prediction of the non-equilibrium reaction of fuel rich kerosene/LOX combustion with detailed kinetics developed by Dagaut using PSR (Perfectly Stirred Reactor) assumption. In Dagaut's surrogate model for kerosene, chemical kinetics of kerosene consists of 1,592 reaction steps with 207 chemical species. Also, droplet evaporation time is taken into account in the PSR calculation by changing the residence time of droplet in the gas generator. Frenklach's soot model was implemented along with detailed kinetics to calculate the gas properties of fuel rich combustion efflux. The results could provide very reliable and accurate numbers in the prediction of combustion gas temperature,species fraction and material properties

One-step electrodeposition process of CuInSe2: Deposition time effect

Indian Academy of Sciences (India)

Administrator

CuInSe2 thin films were prepared by one-step electrodeposition process using a simplified two- electrodes system. ... homojunctions or heterojunctions (Rincon et al 1983). Efficiency of ... deposition times onto indium thin oxide (ITO)-covered.

Preparation of three-dimensional shaped aluminum alloy foam by two-step foaming

International Nuclear Information System (INIS)

Shang, J.T.; Xuming, Chu; Deping, He

2008-01-01

A novel method, named two-step foaming, was investigated to prepare three-dimensional shaped aluminum alloy foam used in car industry, spaceflight, packaging and related areas. Calculations of thermal decomposition kinetics of titanium hydride showed that there is a considerable amount of hydrogen releasing when the titanium hydride is heated at a relatively high temperature after heated at a lower temperature. The hydrogen mass to sustain aluminum alloy foam, having a high porosity, was also estimated by calculations. Calculations indicated that as-received titanium hydride without any pre-treatment can be used as foaming agents in two-step foaming. The processes of two-step foaming, including preparing precursors and baking, were also studied by experiments. Results showed that, low titanium hydride dispersion temperature, long titanium hydride dispersion time and low precursors porosity are beneficial to prepare three-dimensional shaped aluminum alloy foams with uniform pores

Age-related differences in lower-limb force-time relation during the push-off in rapid voluntary stepping.

Science.gov (United States)

Melzer, I; Krasovsky, T; Oddsson, L I E; Liebermann, D G

2010-12-01

This study investigated the force-time relationship during the push-off stage of a rapid voluntary step in young and older healthy adults, to study the assumption that when balance is lost a quick step may preserve stability. The ability to achieve peak propulsive force within a short time is critical for the performance of such a quick powerful step. We hypothesized that older adults would achieve peak force and power in significantly longer times compared to young people, particularly during the push-off preparatory phase. Fifteen young and 15 older volunteers performed rapid forward steps while standing on a force platform. Absolute anteroposterior and body weight normalized vertical forces during the push-off in the preparation and swing phases were used to determine time to peak and peak force, and step power. Two-way analyses of variance ('Group' [young-older] by 'Phase' [preparation-swing]) were used to assess our hypothesis (P ≤ 0.05). Older people exerted lower peak forces (anteroposterior and vertical) than young adults, but not necessarily lower peak power. More significantly, they showed a longer time to peak force, particularly in the vertical direction during the preparation phase. Older adults generate propulsive forces slowly and reach lower magnitudes, mainly during step preparation. The time to achieve a peak force and power, rather than its actual magnitude, may account for failures in quickly performing a preventive action. Such delay may be associated with the inability to react and recruit muscles quickly. Thus, training elderly to step fast in response to relevant cues may be beneficial in the prevention of falls. Copyright © 2010 Elsevier Ltd. All rights reserved.

General Methods for Analysis of Sequential “n-step” Kinetic Mechanisms: Application to Single Turnover Kinetics of Helicase-Catalyzed DNA Unwinding

Science.gov (United States)

Lucius, Aaron L.; Maluf, Nasib K.; Fischer, Christopher J.; Lohman, Timothy M.

2003-01-01

Helicase-catalyzed DNA unwinding is often studied using “all or none” assays that detect only the final product of fully unwound DNA. Even using these assays, quantitative analysis of DNA unwinding time courses for DNA duplexes of different lengths, L, using “n-step” sequential mechanisms, can reveal information about the number of intermediates in the unwinding reaction and the “kinetic step size”, m, defined as the average number of basepairs unwound between two successive rate limiting steps in the unwinding cycle. Simultaneous nonlinear least-squares analysis using “n-step” sequential mechanisms has previously been limited by an inability to float the number of “unwinding steps”, n, and m, in the fitting algorithm. Here we discuss the behavior of single turnover DNA unwinding time courses and describe novel methods for nonlinear least-squares analysis that overcome these problems. Analytic expressions for the time courses, fss(t), when obtainable, can be written using gamma and incomplete gamma functions. When analytic expressions are not obtainable, the numerical solution of the inverse Laplace transform can be used to obtain fss(t). Both methods allow n and m to be continuous fitting parameters. These approaches are generally applicable to enzymes that translocate along a lattice or require repetition of a series of steps before product formation. PMID:14507688

Stability of the high-order finite elements for acoustic or elastic wave propagation with high-order time stepping

KAUST Repository

De Basabe, Jonás D.

2010-04-01

We investigate the stability of some high-order finite element methods, namely the spectral element method and the interior-penalty discontinuous Galerkin method (IP-DGM), for acoustic or elastic wave propagation that have become increasingly popular in the recent past. We consider the Lax-Wendroff method (LWM) for time stepping and show that it allows for a larger time step than the classical leap-frog finite difference method, with higher-order accuracy. In particular the fourth-order LWM allows for a time step 73 per cent larger than that of the leap-frog method; the computational cost is approximately double per time step, but the larger time step partially compensates for this additional cost. Necessary, but not sufficient, stability conditions are given for the mentioned methods for orders up to 10 in space and time. The stability conditions for IP-DGM are approximately 20 and 60 per cent more restrictive than those for SEM in the acoustic and elastic cases, respectively. © 2010 The Authors Journal compilation © 2010 RAS.

A quenched-flow system for measuring heterogeneous enzyme kinetics with sub-second time resolution

DEFF Research Database (Denmark)

Olsen, Johan Pelck; Kari, Jeppe; Borch, Kim

2017-01-01

of insoluble substrate. Perhaps for this reason, transient kinetics has rarely been reported for heterogeneous enzyme reactions. Here, we describe a quenched-flow system using peristaltic pumps and stirred substrate suspensions with a dead time below 100 ms. The general performance was verified by alkali...

Short-time beta grain growth kinetics for a conventional titanium alloy

International Nuclear Information System (INIS)

Semiatin, S.L.; Sukonnik, I.M.

1996-01-01

The kinetics of beta grain growth during short-time, supertransus heat treatment of Ti-5Al-4V were determined using a salt-pot technique. The finite-time, subtransus temperature transient during salt-pot heating was quantified through measurements of the heat transfer coefficient characterizing conduction across the salt-titanium interface and a simple heat conduction analysis which incorporated this heat transfer coefficient. Grain size versus time data adjusted to account for the subtransus temperature transient were successfully fit to the parabolic grain growth law d n - d 0 n = kt exp(-Q/RT) using an exponent n equal to 2.0. Comparison of the present results to rapid, continuous heat treatment data in the literature for a similar titanium alloy revealed a number of semi-quantitative similarities

Solution of the two-dimensional space-time reactor kinetics equation by a locally one-dimensional method

International Nuclear Information System (INIS)

Chen, G.S.; Christenson, J.M.

1985-01-01

In this paper, the authors present some initial results from an investigation of the application of a locally one-dimensional (LOD) finite difference method to the solution of the two-dimensional, two-group reactor kinetics equations. Although the LOD method is relatively well known, it apparently has not been previously applied to the space-time kinetics equations. In this investigation, the LOD results were benchmarked against similar computational results (using the same computing environment, the same programming structure, and the same sample problems) obtained by the TWIGL program. For all of the problems considered, the LOD method provided accurate results in one-half to one-eight of the time required by the TWIGL program

Influence of various irradiation processes on the mechanical properties and polymerisation kinetics of bulk-fill resin based composites.

Science.gov (United States)

Ilie, Nicoleta; Keßler, Andreas; Durner, Jürgen

2013-08-01

To assess the effect of irradiation time and distance of the light tip on the micro-mechanical properties and polymerisation kinetics of two bulk-fill resin-based composites at simulated clinically relevant filling depth. Micro-mechanical properties (Vickers hardness (HV), depth of cure (DOC) and indentation modulus (E)) and polymerisation kinetics (real-time increase of degree of cure (DC)) of two bulk-fill resin-based composites (Tetric EvoCeram(®) Bulk Fill, Ivoclar Vivadent and x-tra base, Voco) were assessed at varying depth (0.1-6mm in 100μm steps for E and HV and 0.1, 2, 4 and 6mm for DC), irradiation time (10, 20 or 40s, Elipar Freelight2) and distances from the light tip (0 and 7mm). Curing unit's irradiance was monitored in 1mm steps at distances up to 10mm away from the light tip on a laboratory-grade spectrometer. Multivariate analysis (α=0.05), Student's t-test and Pearson correlation analysis were considered. The influence of material on the measured mechanical properties was significant (η(2)=0.080 for E and 0.256 for HV), while the parameters irradiation time, distance from the light tip and depth emphasise a stronger influence on Tetric EvoCeram(®) Bulk Fill. The polymerisation kinetics could be described by an exponential sum function, distinguishing between the gel and the glass phase. The above mentioned parameters strongly influenced the start of polymerisation (gel phase), and were of less importance for the glass phase. Both materials enable at least 4mm thick increments to be cured in one step under clinically relevant curing conditions. The susceptibility to variation in irradiance was material dependent, thus properties measured under clinically simulated curing conditions might vary to a different extent from those measured under ideal curing conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

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.

Approach to kinetic energy density functionals: Nonlocal terms with the structure of the von Weizsaecker functional

International Nuclear Information System (INIS)

Garcia-Aldea, David; Alvarellos, J. E.

2008-01-01

We propose a kinetic energy density functional scheme with nonlocal terms based on the von Weizsaecker functional, instead of the more traditional approach where the nonlocal terms have the structure of the Thomas-Fermi functional. The proposed functionals recover the exact kinetic energy and reproduce the linear response function of homogeneous electron systems. In order to assess their quality, we have tested the total kinetic energies as well as the kinetic energy density for atoms. The results show that these nonlocal functionals give as good results as the most sophisticated functionals in the literature. The proposed scheme for constructing the functionals means a step ahead in the field of fully nonlocal kinetic energy functionals, because they are capable of giving better local behavior than the semilocal functionals, yielding at the same time accurate results for total kinetic energies. Moreover, the functionals enjoy the possibility of being evaluated as a single integral in momentum space if an adequate reference density is defined, and then quasilinear scaling for the computational cost can be achieved

Fast Determination of Distribution-Connected PV Impacts Using a Variable Time-Step Quasi-Static Time-Series Approach: Preprint

Energy Technology Data Exchange (ETDEWEB)

Mather, Barry

2017-08-24

The increasing deployment of distribution-connected photovoltaic (DPV) systems requires utilities to complete complex interconnection studies. Relatively simple interconnection study methods worked well for low penetrations of photovoltaic systems, but more complicated quasi-static time-series (QSTS) analysis is required to make better interconnection decisions as DPV penetration levels increase. Tools and methods must be developed to support this. This paper presents a variable-time-step solver for QSTS analysis that significantly shortens the computational time and effort to complete a detailed analysis of the operation of a distribution circuit with many DPV systems. Specifically, it demonstrates that the proposed variable-time-step solver can reduce the required computational time by as much as 84% without introducing any important errors to metrics, such as the highest and lowest voltage occurring on the feeder, number of voltage regulator tap operations, and total amount of losses realized in the distribution circuit during a 1-yr period. Further improvement in computational speed is possible with the introduction of only modest errors in these metrics, such as a 91 percent reduction with less than 5 percent error when predicting voltage regulator operations.

The importance of time-stepping errors in ocean models

Science.gov (United States)

Williams, P. D.

2011-12-01

Many ocean models use leapfrog time stepping. The Robert-Asselin (RA) filter is usually applied after each leapfrog step, to control the computational mode. However, it will be shown in this presentation that the RA filter generates very large amounts of numerical diapycnal mixing. In some ocean models, the numerical diapycnal mixing from the RA filter is as large as the physical diapycnal mixing. This lowers our confidence in the fidelity of the simulations. In addition to the above problem, the RA filter also damps the physical solution and degrades the numerical accuracy. These two concomitant problems occur because the RA filter does not conserve the mean state, averaged over the three time slices on which it operates. The presenter has recently proposed a simple modification to the RA filter, which does conserve the three-time-level mean state. The modified filter has become known as the Robert-Asselin-Williams (RAW) filter. When used in conjunction with the leapfrog scheme, the RAW filter eliminates the numerical damping of the physical solution and increases the amplitude accuracy by two orders, yielding third-order accuracy. The phase accuracy is unaffected and remains second-order. The RAW filter can easily be incorporated into existing models of the ocean, typically via the insertion of just a single line of code. Better simulations are obtained, at almost no additional computational expense. Results will be shown from recent implementations of the RAW filter in various ocean models. For example, in the UK Met Office Hadley Centre ocean model, sea-surface temperature and sea-ice biases in the North Atlantic Ocean are found to be reduced. These improvements are encouraging for the use of the RAW filter in other ocean models.

Generic Schemes for Single-Molecule Kinetics. 2: Information Content of the Poisson Indicator.

Science.gov (United States)

Avila, Thomas R; Piephoff, D Evan; Cao, Jianshu

2017-08-24

Recently, we described a pathway analysis technique (paper 1) for analyzing generic schemes for single-molecule kinetics based upon the first-passage time distribution. Here, we employ this method to derive expressions for the Poisson indicator, a normalized measure of stochastic variation (essentially equivalent to the Fano factor and Mandel's Q parameter), for various renewal (i.e., memoryless) enzymatic reactions. We examine its dependence on substrate concentration, without assuming all steps follow Poissonian kinetics. Based upon fitting to the functional forms of the first two waiting time moments, we show that, to second order, the non-Poissonian kinetics are generally underdetermined but can be specified in certain scenarios. For an enzymatic reaction with an arbitrary intermediate topology, we identify a generic minimum of the Poisson indicator as a function of substrate concentration, which can be used to tune substrate concentration to the stochastic fluctuations and to estimate the largest number of underlying consecutive links in a turnover cycle. We identify a local maximum of the Poisson indicator (with respect to substrate concentration) for a renewal process as a signature of competitive binding, either between a substrate and an inhibitor or between multiple substrates. Our analysis explores the rich connections between Poisson indicator measurements and microscopic kinetic mechanisms.

Elderly fallers enhance dynamic stability through anticipatory postural adjustments during a choice stepping reaction time

Directory of Open Access Journals (Sweden)

Romain Tisserand

2016-11-01

Full Text Available In the case of disequilibrium, the capacity to step quickly is critical to avoid falling for elderly. This capacity can be simply assessed through the choice stepping reaction time test (CSRT, where elderly fallers (F take longer to step than elderly non-fallers (NF. However, reasons why elderly F elongate their stepping time remain unclear. The purpose of this study is to assess the characteristics of anticipated postural adjustments (APA that elderly F develop in a stepping context and their consequences on the dynamic stability. 44 community-dwelling elderly subjects (20 F and 22 NF performed a CSRT where kinematics and ground reaction forces were collected. Variables were analyzed using two-way repeated measures ANOVAs. Results for F compared to NF showed that stepping time is elongated, due to a longer APA phase. During APA, they seem to use two distinct balance strategies, depending on the axis: in the anteroposterior direction, we measured a smaller backward movement and slower peak velocity of the center of pressure (CoP; in the mediolateral direction, the CoP movement was similar in amplitude and peak velocity between groups but lasted longer. The biomechanical consequence of both strategies was an increased margin of stability (MoS at foot-off, in the respective direction. By elongating their APA, elderly F use a safer balance strategy that prioritizes dynamic stability conditions instead of the objective of the task. Such a choice in balance strategy probably comes from muscular limitations and/or a higher fear of falling and paradoxically indicates an increased risk of fall.

Modeling Stepped Leaders Using a Time Dependent Multi-dipole Model and High-speed Video Data

Science.gov (United States)

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.

A kinetic model for the penicillin biosynthetic pathway in

DEFF Research Database (Denmark)

Nielsen, Jens; Jørgensen, Henrik

1996-01-01

A kinetic model for the first two steps in the penicillin biosynthetic pathway, i.e. the ACV synthetase (ACVS) and the isopenicillin N synthetase (IPNS) is proposed. The model is based on Michaelis-Menten type kinetics with non-competitive inhibition of the ACVS by ACV, and competitive inhibition...... of the IPNS by glutathione. The model predicted flux through the pathway corresponds well with the measured rate of penicillin biosynthesis. From the kinetic model the elasticity coefficients and the flux control coefficients are calculated throughout a fed-batch cultivation, and it is found...

Kinetics of spontaneous displacement of RNA from heteroduplexes by DNA.

OpenAIRE

Landgraf, R; Ramamurthi, K S; Sigman, D S

1996-01-01

We have used R-loop formation and direct hybridization techniques to analyze the kinetics by which RNA is displaced from a heteroduplex by DNA of identical sequence. Using random walk simulations we were able to calculate the step times for a single displacement reaction. For RNA with a GC content of 57-60% the data indicate an RNA exchange probability of 50.06%, which is indicative of a modest destabilization of the heteroduplex compared with a DNA duplex in the presence of magnesium. The av...

Kinetic mechanism of DNA polymerase I (Klenow)

International Nuclear Information System (INIS)

Kuchta, R.D.; Mizrahi, V.; Benkovic, P.A.; Johnson, K.A.; Benkovic, S.J.

1987-01-01

The minimal kinetic scheme for DNA polymerization catalyzed by the Klenow fragment of DNA polymerase I (KF) from Escherichia coli has been determined with short DNA oligomers of defined sequence, labeled with [ 32 P]-nucleotides. A key feature of this scheme is a minimal two-step sequence that interconverts the ternary KF-DNA/sub n/-dNTP and KF-DNA/sub n+1/-PP/sub i/ complexes. The rate is not limited by the actual polymerization but by a separate step, possibly important in ensuring fidelity. Evidence for this sequence is supplied by the observation of biphasic kinetics in single-turnover pyrophosphorolysis experiments (the microscopic reverse of polymerization). Data analysis then provides an estimate of the internal equilibrium constant. The dissociations of DNA, dNTP, and PP/sub i/ from the various binary and ternary complexes were measured by partitioning (isotope-trapping) experiments. The rate constant for DNA dissociation from KF is sequence dependent and is rate limiting during nonprocessive DNA synthesis. The combination of single-turnover (both directions) and isotope-trapping experiments provides sufficient information to permit a quantitative evaluation of the kinetic scheme for specific DNA sequences

Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study

International Nuclear Information System (INIS)

Das, Biswajit; Gangopadhyay, Gautam

2012-01-01

Graphical abstract: Stochastic theory of interfacial enzyme kinetics is formulated. Numerical results of macroscopic phenomenon of lag-burst kinetics is obtained by using a kinetic Monte Carlo approach to single enzyme activity. Highlights: ► An enzyme is attached with the fluid state phospholipid molecules on the Langmuir monolayer. ► Through the diffusion, the enzyme molecule reaches the gel–fluid interface. ► After hydrolysing a phospholipid molecule it predominantly leaves the surface in the lag phase. ► The enzyme is strictly attached to the surface with scooting mode of motion and the burst phase appears. - Abstract: In the spirit of Gillespie’s stochastic approach we have formulated a theory to explore the advancement of the interfacial enzyme kinetics at the single enzyme level which is ultimately utilized to obtain the ensemble average macroscopic feature, lag-burst kinetics. We have provided a theory of the transition from the lag phase to the burst phase kinetics by considering the gradual development of electrostatic interaction among the positively charged enzyme and negatively charged product molecules deposited on the phospholipid surface. It is shown that the different diffusion time scales of the enzyme over the fluid and product regions are responsible for the memory effect in the correlation of successive turnover events of the hopping mode in the single trajectory analysis which again is reflected on the non-Gaussian distribution of turnover times on the macroscopic kinetics in the lag phase unlike the burst phase kinetics.

Implementation of Real-Time Machining Process Control Based on Fuzzy Logic in a New STEP-NC Compatible System

Directory of Open Access Journals (Sweden)

Po Hu

2016-01-01

Full Text Available Implementing real-time machining process control at shop floor has great significance on raising the efficiency and quality of product manufacturing. A framework and implementation methods of real-time machining process control based on STEP-NC are presented in this paper. Data model compatible with ISO 14649 standard is built to transfer high-level real-time machining process control information between CAPP systems and CNC systems, in which EXPRESS language is used to define new STEP-NC entities. Methods for implementing real-time machining process control at shop floor are studied and realized on an open STEP-NC controller, which is developed using object-oriented, multithread, and shared memory technologies conjunctively. Cutting force at specific direction of machining feature in side mill is chosen to be controlled object, and a fuzzy control algorithm with self-adjusting factor is designed and embedded in the software CNC kernel of STEP-NC controller. Experiments are carried out to verify the proposed framework, STEP-NC data model, and implementation methods for real-time machining process control. The results of experiments prove that real-time machining process control tasks can be interpreted and executed correctly by the STEP-NC controller at shop floor, in which actual cutting force is kept around ideal value, whether axial cutting depth changes suddenly or continuously.

Mesoscopic dynamics of diffusion-influenced enzyme kinetics.

Science.gov (United States)

Chen, Jiang-Xing; Kapral, Raymond

2011-01-28

A particle-based mesoscopic model for enzyme kinetics is constructed and used to investigate the influence of diffusion on the reactive dynamics. Enzymes and enzyme-substrate complexes are modeled as finite-size soft spherical particles, while substrate, product, and solvent molecules are point particles. The system is evolved using a hybrid molecular dynamics-multiparticle collision dynamics scheme. Both the nonreactive and reactive dynamics are constructed to satisfy mass, momentum, and energy conservation laws, and reversible reaction steps satisfy detailed balance. Hydrodynamic interactions among the enzymes and complexes are automatically accounted for in the dynamics. Diffusion manifests itself in various ways, notably in power-law behavior in the evolution of the species concentrations. In accord with earlier investigations, regimes where the product production rate exhibits either monotonic or nonmonotonic behavior as a function of time are found. In addition, the species concentrations display both t(-1/2) and t(-3/2) power-law behavior, depending on the dynamical regime under investigation. For high enzyme volume fractions, cooperative effects influence the enzyme kinetics. The time dependent rate coefficient determined from the mass action rate law is computed and shown to depend on the enzyme concentration. Lifetime distributions of substrate molecules newly released in complex dissociation events are determined and shown to have either a power-law form for rebinding to the same enzyme from which they were released or an exponential form for rebinding to different enzymes. The model can be used and extended to explore a variety of issues related concentration effects and diffusion on enzyme kinetics.

Mesoscopic dynamics of diffusion-influenced enzyme kinetics

Science.gov (United States)

Chen, Jiang-Xing; Kapral, Raymond

2011-01-01

A particle-based mesoscopic model for enzyme kinetics is constructed and used to investigate the influence of diffusion on the reactive dynamics. Enzymes and enzyme-substrate complexes are modeled as finite-size soft spherical particles, while substrate, product, and solvent molecules are point particles. The system is evolved using a hybrid molecular dynamics-multiparticle collision dynamics scheme. Both the nonreactive and reactive dynamics are constructed to satisfy mass, momentum, and energy conservation laws, and reversible reaction steps satisfy detailed balance. Hydrodynamic interactions among the enzymes and complexes are automatically accounted for in the dynamics. Diffusion manifests itself in various ways, notably in power-law behavior in the evolution of the species concentrations. In accord with earlier investigations, regimes where the product production rate exhibits either monotonic or nonmonotonic behavior as a function of time are found. In addition, the species concentrations display both t^{-1/2} and t^{-3/2} power-law behavior, depending on the dynamical regime under investigation. For high enzyme volume fractions, cooperative effects influence the enzyme kinetics. The time dependent rate coefficient determined from the mass action rate law is computed and shown to depend on the enzyme concentration. Lifetime distributions of substrate molecules newly released in complex dissociation events are determined and shown to have either a power-law form for rebinding to the same enzyme from which they were released or an exponential form for rebinding to different enzymes. The model can be used and extended to explore a variety of issues related concentration effects and diffusion on enzyme kinetics.

Rapid expansion method (REM) for time‐stepping in reverse time migration (RTM)

KAUST Repository

Pestana, Reynam C.; Stoffa, Paul L.

2009-01-01

an analytical approximation for the Bessel function where we assume that the time step is sufficiently small. From this derivation we find that if we consider only the first two Chebyshev polynomials terms in the rapid expansion method we can obtain the second

a Time-Resolved X-Ray Scattering Study of the Ordering Kinetics in COPPER(3)-GOLD

Science.gov (United States)

Shannon, Robert Francis, Jr.

Time-resolved x-ray scattering has been used to study ordering kinetics in single crystal bulk Cu _3Au, as well as in sputtered and molecular beam epitaxy grown films. After annealing at high temperatures the sample is rapidly quenched to fixed temperatures below the order-disorder transition temperature. The development of order is monitored in real time using scattering techniques. The bulk sample clearly showed three regimes: nucleation, ordering, and coarsening. The anisotropic superlattice peaks that reflect the domains structure are investigated in connection with the ordering kinetics. The line shape of the scattering function exhibits a crossover from gaussian to lorentzian-squared as the system goes from the ordering regime to the coarsening regime. Coarsening in Cu_3Au is consistent with curvature driven growth. Domain coarsening in stoichiometric sputtered films is also consistent with curvature driven growth. However, coarsening in copper rich films proceeds much more slowly. The results suggest the extra copper affects the ordering kinetics in the same way diffusive impurities would, resulting in a logarithmic like time dependence. The M.B.E. films show a slowing of the growth at late times. The 4500A film starts out with curvature driven growth but then continuously slows down as the domains grow. The 710A film shows an interesting temperature dependence for the growth, in such a way that at temperatures close to the transition, the domain growth almost freezes at late times. The dominate factor is probably strain, all of the trends for slower growth are consistent with greater strain. The dimensionality in the M.B.E. film systems is considered. The scaling in the 4500A and 710A films is clearly three dimensional. However, the dimension of the scaling in the 260A film is unclear.

Multi-step-prediction of chaotic time series based on co-evolutionary recurrent neural network

International Nuclear Information System (INIS)

Ma Qianli; Zheng Qilun; Peng Hong; Qin Jiangwei; Zhong Tanwei

2008-01-01

This paper proposes a co-evolutionary recurrent neural network (CERNN) for the multi-step-prediction of chaotic time series, it estimates the proper parameters of phase space reconstruction and optimizes the structure of recurrent neural networks by co-evolutionary strategy. The searching space was separated into two subspaces and the individuals are trained in a parallel computational procedure. It can dynamically combine the embedding method with the capability of recurrent neural network to incorporate past experience due to internal recurrence. The effectiveness of CERNN is evaluated by using three benchmark chaotic time series data sets: the Lorenz series, Mackey-Glass series and real-world sun spot series. The simulation results show that CERNN improves the performances of multi-step-prediction of chaotic time series

Symmetry Relations in Chemical Kinetics Arising from Microscopic Reversibility

Science.gov (United States)

Adib, Artur B.

2006-01-01

It is shown that the kinetics of time-reversible chemical reactions having the same equilibrium constant but different initial conditions are closely related to one another by a directly measurable symmetry relation analogous to chemical detailed balance. In contrast to detailed balance, however, this relation does not require knowledge of the elementary steps that underlie the reaction, and remains valid in regimes where the concept of rate constants is ill defined, such as at very short times and in the presence of low activation barriers. Numerical simulations of a model of isomerization in solution are provided to illustrate the symmetry under such conditions, and potential applications in protein folding or unfolding are pointed out.

Kinetics of the nitridation of dysprosium during mechanochemical processing

Energy Technology Data Exchange (ETDEWEB)

Alanko, Gordon A.; Osterberg, Daniel D.; Jaques, Brian J. [Department of Materials Science and Engineering, College of Engineering, Boise State University, 1910 University Drive, Boise, ID 83725 (United States); Hurley, Michael F. [Department of Materials Science and Engineering, College of Engineering, Boise State University, 1910 University Drive, Boise, ID 83725 (United States); Center for Advanced Energy Studies, 995 University Boulevard, Idaho Falls, ID 83401 (United States); Butt, Darryl P., E-mail: darrylbutt@boisestate.edu [Department of Materials Science and Engineering, College of Engineering, Boise State University, 1910 University Drive, Boise, ID 83725 (United States); Center for Advanced Energy Studies, 995 University Boulevard, Idaho Falls, ID 83401 (United States)

2015-01-25

Highlights: • DyN was mechanochemically synthesized by milling pure metal under nitrogen. • Temperature and pressure were monitored to investigate reaction progress. • The effects of metal adhered to media on the impact energetics was measured. • The reactive milling kinetics are described in terms of reactive surface formation. - Abstract: Dysprosium nitride was synthesized by the reactive milling of the rare earth metal under 400 kPa nitrogen gas in a planetary ball mill. The nitrogen consumption rate was calculated from in situ temperature and pressure measurements to find the reaction extent as a function of milling time at milling speeds from 350 to 650 rpm. The results are analyzed in terms of a fundamental milling dynamics model in which the input milling energy is the primary driving force for reaction and the rate limiting step of the nitridation kinetics is the formation of chemically active surfaces. The model differs from traditional gas–solid reactions which are often limited by diffusion of a species through a surface layer or by dissociation of the gas molecule. These results give fresh insight into reactive gas–solid milling kinetics.

Origin of two time-scale regimes in potentiometric titration of metal oxides. A replica kinetic Monte Carlo study

International Nuclear Information System (INIS)

Zarzycki, Piotr P.; Rosso, Kevin M.

2009-01-01

Replica Kinetic Monte Carlo simulations were used to study the characteristic time scales of potentiometric titration of the metal oxides and (oxy)hydroxides. The effect of surface heterogeneity and surface transformation on the titration kinetics were also examined. Two characteristic relaxation times are often observed experimentally, with the trailing slower part attributed to surface non-uniformity, porosity, polymerization, amorphization, and other dynamic surface processes induced by unbalanced surface charge. However, our simulations show that these two characteristic relaxation times are intrinsic to the proton binding reaction for energetically homogeneous surfaces, and therefore surface heterogeneity or transformation do not necessarily need to be invoked. However, all such second-order surface processes are found to intensify the separation and distinction of the two kinetic regimes. The effect of surface energetic-topographic non-uniformity, as well dynamic surface transformation, interface roughening/smoothing were described in a statistical fashion. Furthermore, our simulations show that a shift in the point-of-zero charge is expected from increased titration speed and the pH-dependence of the titration measurement error is in excellent agreement with experimental studies.

Origin of two time-scale regimes in potentiometric titration of metal oxides. A replica kinetic Monte Carlo study.

Science.gov (United States)

Zarzycki, Piotr; Rosso, Kevin M

2009-06-16

Replica kinetic Monte Carlo simulations were used to study the characteristic time scales of potentiometric titration of the metal oxides and (oxy)hydroxides. The effect of surface heterogeneity and surface transformation on the titration kinetics were also examined. Two characteristic relaxation times are often observed experimentally, with the trailing slower part attributed to surface nonuniformity, porosity, polymerization, amorphization, and other dynamic surface processes induced by unbalanced surface charge. However, our simulations show that these two characteristic relaxation times are intrinsic to the proton-binding reaction for energetically homogeneous surfaces, and therefore surface heterogeneity or transformation does not necessarily need to be invoked. However, all such second-order surface processes are found to intensify the separation and distinction of the two kinetic regimes. The effect of surface energetic-topographic nonuniformity, as well dynamic surface transformation, interface roughening/smoothing were described in a statistical fashion. Furthermore, our simulations show that a shift in the point-of-zero charge is expected from increased titration speed, and the pH-dependence of the titration measurement error is in excellent agreement with experimental studies.

Receptor binding kinetics equations: Derivation using the Laplace transform method.

Science.gov (United States)

Hoare, Sam R J

Measuring unlabeled ligand receptor binding kinetics is valuable in optimizing and understanding drug action. Unfortunately, deriving equations for estimating kinetic parameters is challenging because it involves calculus; integration can be a frustrating barrier to the pharmacologist seeking to measure simple rate parameters. Here, a well-known tool for simplifying the derivation, the Laplace transform, is applied to models of receptor-ligand interaction. The method transforms differential equations to a form in which simple algebra can be applied to solve for the variable of interest, for example the concentration of ligand-bound receptor. The goal is to provide instruction using familiar examples, to enable investigators familiar with handling equilibrium binding equations to derive kinetic equations for receptor-ligand interaction. First, the Laplace transform is used to derive the equations for association and dissociation of labeled ligand binding. Next, its use for unlabeled ligand kinetic equations is exemplified by a full derivation of the kinetics of competitive binding equation. Finally, new unlabeled ligand equations are derived using the Laplace transform. These equations incorporate a pre-incubation step with unlabeled or labeled ligand. Four equations for measuring unlabeled ligand kinetics were compared and the two new equations verified by comparison with numerical solution. Importantly, the equations have not been verified with experimental data because no such experiments are evident in the literature. Equations were formatted for use in the curve-fitting program GraphPad Prism 6.0 and fitted to simulated data. This description of the Laplace transform method will enable pharmacologists to derive kinetic equations for their model or experimental paradigm under study. Application of the transform will expand the set of equations available for the pharmacologist to measure unlabeled ligand binding kinetics, and for other time

Thermal and kinetic behaviors of biomass and plastic wastes in co-pyrolysis

International Nuclear Information System (INIS)

Çepelioğullar, Özge; Pütün, Ayşe E.

2013-01-01

Graphical abstract: - Highlights: • Co-pyrolysis of biomass together with the plastic wastes in thermogravimetric analyzer. • Investigations into thermal and kinetic behaviors at high temperature regions. • Determination of the kinetic parameters. - Abstract: In this study, co-pyrolysis characteristics and kinetics of biomass-plastic blends were investigated. Cotton stalk, hazelnut shell, sunflower residue, and arid land plant Euphorbia rigida, were blended in definite ratio (1:1, w/w) with polyvinyl chloride (PVC) and polyethylene terephthalate (PET). Experiments were conducted with a heating rate of 10 °C min −1 from room temperature to 800 °C in the presence of N 2 atmosphere with a flow rate of 100 cm 3 min −1 . After thermal decomposition in TGA, a kinetic analysis was performed to fit thermogravimetric data and a detailed discussion of co-pyrolysis mechanism was achieved. Experimental results demonstrated that the structural differences between biomass and plastics directly affect their thermal decomposition behaviors. Biomass pyrolysis generally based on three main steps while plastic material’s pyrolysis mechanism resulted in two steps for PET and three steps for PVC. Also, the required activation energies needed to achieve the thermal degradation for plastic were found higher than the biomass materials. In addition, it can be concluded that the evaluation of plastic materials together with biomass created significant changes not only for the thermal behaviors but also for the kinetic behaviors

Analysis of reaction schemes using maximum rates of constituent steps

Science.gov (United States)

Motagamwala, Ali Hussain; Dumesic, James A.

2016-01-01

We show that the steady-state kinetics of a chemical reaction can be analyzed analytically in terms of proposed reaction schemes composed of series of steps with stoichiometric numbers equal to unity by calculating the maximum rates of the constituent steps, rmax,i, assuming that all of the remaining steps are quasi-equilibrated. Analytical expressions can be derived in terms of rmax,i to calculate degrees of rate control for each step to determine the extent to which each step controls the rate of the overall stoichiometric reaction. The values of rmax,i can be used to predict the rate of the overall stoichiometric reaction, making it possible to estimate the observed reaction kinetics. This approach can be used for catalytic reactions to identify transition states and adsorbed species that are important in controlling catalyst performance, such that detailed calculations using electronic structure calculations (e.g., density functional theory) can be carried out for these species, whereas more approximate methods (e.g., scaling relations) are used for the remaining species. This approach to assess the feasibility of proposed reaction schemes is exact for reaction schemes where the stoichiometric coefficients of the constituent steps are equal to unity and the most abundant adsorbed species are in quasi-equilibrium with the gas phase and can be used in an approximate manner to probe the performance of more general reaction schemes, followed by more detailed analyses using full microkinetic models to determine the surface coverages by adsorbed species and the degrees of rate control of the elementary steps. PMID:27162366

Kinetics of waterborne fluoropolymers prepared by one-step semi-continuous emulsion polymerization of chlorotrifluoroethylene, vinyl acetate, butyl acrylate and Veova 10

Science.gov (United States)

Liu, H. Z.; Wang, M. H.; Wang, Z. F.; Bian, J. M.

2018-01-01

Due to using gaseous fluorine monomer with toxicity, waterborne fluoropolymers are synthesized by semi-continuous high-pressure emulsion polymerization method which differs from free-pressure emulsion polymerization. To dates, the research on preparing process and kinetics for high-pressure emulsion polymerization is reported relatively less, which hinders researchers from understanding of mechanisms for monomer-fluorinated emulsion polymerization. The paper also provides a new method by element auxiliary analysis to calculate kinetics parameters of high-pressure emulsion polymerization. Based on aforementioned consideration, waterborne fluoropolymers were prepared by copolymerization of chlorotrifluoroethylene (CTFE), vinyl acetate (VAc), butyl acrylate (BA) and vinyl ester of versatic acid (Veova 10) using potassium persulfate as initiator and mixed surfactants. The kinetics of emulsion polymerization of waterborne fluoropolymers was then investigated. Effects of emulsifier concentration, initiator concentration, and polymerization temperature on polymerization rate (Rp) were evaluated, and relationship was described as Rp∝[I]0.10 and Rp∝[E]0.12. The apparent activation energy was determined to be 33.61 kJ·mol-1. Moreover, the relative conversion rate of CTFE with the other monomers was observed, and results indicated that CTFE monomer more uniformly copolymerized with the other monomers. The resulting emulsion properties and pressure change in an autoclave were evaluated at different stirring rates. The initial reaction time, defined as the beginning time of dropwise addition, was determined by the change in solid content and particle size of emulsion.

Comparing an Annual and a Daily Time-Step Model for Predicting Field-Scale Phosphorus Loss.

Science.gov (United States)

Bolster, Carl H; Forsberg, Adam; Mittelstet, Aaron; Radcliffe, David E; Storm, Daniel; Ramirez-Avila, John; Sharpley, Andrew N; Osmond, Deanna

2017-11-01

A wide range of mathematical models are available for predicting phosphorus (P) losses from agricultural fields, ranging from simple, empirically based annual time-step models to more complex, process-based daily time-step models. In this study, we compare field-scale P-loss predictions between the Annual P Loss Estimator (APLE), an empirically based annual time-step model, and the Texas Best Management Practice Evaluation Tool (TBET), a process-based daily time-step model based on the Soil and Water Assessment Tool. We first compared predictions of field-scale P loss from both models using field and land management data collected from 11 research sites throughout the southern United States. We then compared predictions of P loss from both models with measured P-loss data from these sites. We observed a strong and statistically significant ( loss between the two models; however, APLE predicted, on average, 44% greater dissolved P loss, whereas TBET predicted, on average, 105% greater particulate P loss for the conditions simulated in our study. When we compared model predictions with measured P-loss data, neither model consistently outperformed the other, indicating that more complex models do not necessarily produce better predictions of field-scale P loss. Our results also highlight limitations with both models and the need for continued efforts to improve their accuracy. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Development of a generalized stochastic model for the analysis of monoenergetic space-time nuclear factor Kinetics

International Nuclear Information System (INIS)

Pham, Nhu Viet Ha

2011-02-01

To predict the space-time dependent behavior of a nuclear reactor, the conventional space-dependent kinetics equations are widely used for treating the spatial variables. However, the solutions of such deterministic space-dependent kinetics equations, which give only the mean values of the neutron population and the delayed neutron precursor concentrations, do not offer sufficient insight into the actual dynamic processes within a reactor, where the interacting populations vary randomly with space and time. It is also noted that at high power levels, the random behavior of a reactor is negligible but at low power levels, such as at start-up, random fluctuations in population dynamics can be significant. To mathematically describe the evolution of the state of a nuclear reactor using a set of stochastic kinetics equations, the forward stochastic model (FSM) in stochastic kinetics theory is devised through the concept of reactor transition probability and its probability generating function as the spatial domain of a reactor is partitioned into a number of space cells. Nevertheless, the FSM equations for the mean value of neutron and precursor distribution are deterministic-like. Furthermore, the numerical treatment of the FSM equations for the means, variances, and covariances is quite complicated and time-consuming. In the present study, a generalized stochastic model (called the stochastic space-dependent kinetics model or SSKM) based on the FSM and the Its stochastic differential equations was newly developed for the analysis of monoenergetic spacetime nuclear reactor kinetics in one dimension. First, the FSM equations for determining the mean values of neutron and delayed-neutron precursor populations were considered as the deterministic ones without taking into account their variances and covariances. Second, the system of interest was randomized again in the light of the Its stochastic differential equations in order to derive the SSKM. The proposed model

Kinetics of thermal decomposition of aluminium hydride: I-non-isothermal decomposition under vacuum and in inert atmosphere (argon)

International Nuclear Information System (INIS)

Ismail, I.M.K.; Hawkins, T.

2005-01-01

Recently, interest in aluminium hydride (alane) as a rocket propulsion ingredient has been renewed due to improvements in its manufacturing process and an increase in thermal stability. When alane is added to solid propellant formulations, rocket performance is enhanced and the specific impulse increases. Preliminary work was performed at AFRL on the characterization and evaluation of two alane samples. Decomposition kinetics were determined from gravimetric TGA data and volumetric vacuum thermal stability (VTS) results. Chemical analysis showed the samples had 88.30% (by weight) aluminium and 9.96% hydrogen. The average density, as measured by helium pycnometery, was 1.486 g/cc. Scanning electron microscopy showed that the particles were mostly composed of sharp edged crystallographic polyhedral such as simple cubes, cubic octahedrons and hexagonal prisms. Thermogravimetric analysis was utilized to investigate the decomposition kinetics of alane in argon atmosphere and to shed light on the mechanism of alane decomposition. Two kinetic models were successfully developed and used to propose a mechanism for the complete decomposition of alane and to predict its shelf-life during storage. Alane decomposes in two steps. The slowest (rate-determining) step is solely controlled by solid state nucleation of aluminium crystals; the fastest step is due to growth of the crystals. Thus, during decomposition, hydrogen gas is liberated and the initial polyhedral AlH 3 crystals yield a final mix of amorphous aluminium and aluminium crystals. After establishing the kinetic model, prediction calculations indicated that alane can be stored in inert atmosphere at temperatures below 10 deg. C for long periods of time (e.g., 15 years) without significant decomposition. After 15 years of storage, the kinetic model predicts ∼0.1% decomposition, but storage at higher temperatures (e.g. 30 deg. C) is not recommended

Ultrasound assisted two-stage biodiesel synthesis from non-edible Schleichera triguga oil using heterogeneous catalyst: Kinetics and thermodynamic analysis.

Science.gov (United States)

Sarve, Antaram N; Varma, Mahesh N; Sonawane, Shriram S

2016-03-01

Present work deals with the ultrasound-assisted biodiesel production from low cost, substantial acid value kusum (Schleichera triguga) oil using a two-step method of esterification in presence of acid (H2SO4) catalyst followed by transesterification using a basic heterogeneous barium hydroxide (Ba(OH)2) catalyst. The initial acid value of kusum oil was reduced from 21.65 to 0.84 mg of KOH/g of oil, by acid catalyzed esterification with 4:1 methanol to oil molar ratio, catalyst concentration 1% (v/v), ultrasonic irradiation time 20 min at 40 °C. Then, Ba(OH)2 concentration of 3% (w/w), methanol to oil molar ratio of 9:1, ultrasonic irradiation time of 80 min, and temperature of 50 °C was found to be the optimum conditions for transesterification step and triglyceride conversion of 96.8% (wt) was achieved. This paper also examined the kinetics as well as the evaluation of thermodynamic parameters for both esterification and transesterification reactions. The lower value of activation energy and higher values of kinetic constants indicated a fast rate of reaction, which could be attributed to the physical effect of emulsification, in which the microturbulence generated due to radial motion of bubbles, creates an intimate mixing of the immiscible reactants causing the increase in the interfacial area, giving faster reaction kinetics. The positive values of Gibbs-free energy (ΔG), enthalpy (ΔH) and negative value of entropy (ΔS) revealed that both the esterification and transesterification were non-spontaneous, endothermic and endergonic reactions. Therefore, the present work has not only established the escalation obtained due to ultrasonication but also exemplified the two-step approach for synthesis of biodiesel from non-edible kusum oil based on the use of heterogeneous catalyst for the transesterification step. Copyright © 2015 Elsevier B.V. All rights reserved.

Stability of the high-order finite elements for acoustic or elastic wave propagation with high-order time stepping

KAUST Repository

De Basabe, Joná s D.; Sen, Mrinal K.

2010-01-01

popular in the recent past. We consider the Lax-Wendroff method (LWM) for time stepping and show that it allows for a larger time step than the classical leap-frog finite difference method, with higher-order accuracy. In particular the fourth-order LWM

Sharp Penalty Term and Time Step Bounds for the Interior Penalty Discontinuous Galerkin Method for Linear Hyperbolic Problems

NARCIS (Netherlands)

Geevers, Sjoerd; van der Vegt, J.J.W.

2017-01-01

We present sharp and sucient bounds for the interior penalty term and time step size to ensure stability of the symmetric interior penalty discontinuous Galerkin (SIPDG) method combined with an explicit time-stepping scheme. These conditions hold for generic meshes, including unstructured

A coupled weather generator - rainfall-runoff approach on hourly time steps for flood risk analysis

Science.gov (United States)

Winter, Benjamin; Schneeberger, Klaus; Dung Nguyen, Viet; Vorogushyn, Sergiy; Huttenlau, Matthias; Merz, Bruno; Stötter, Johann

2017-04-01

The evaluation of potential monetary damage of flooding is an essential part of flood risk management. One possibility to estimate the monetary risk is to analyze long time series of observed flood events and their corresponding damages. In reality, however, only few flood events are documented. This limitation can be overcome by the generation of a set of synthetic, physically and spatial plausible flood events and subsequently the estimation of the resulting monetary damages. In the present work, a set of synthetic flood events is generated by a continuous rainfall-runoff simulation in combination with a coupled weather generator and temporal disaggregation procedure for the study area of Vorarlberg (Austria). Most flood risk studies focus on daily time steps, however, the mesoscale alpine study area is characterized by short concentration times, leading to large differences between daily mean and daily maximum discharge. Accordingly, an hourly time step is needed for the simulations. The hourly metrological input for the rainfall-runoff model is generated in a two-step approach. A synthetic daily dataset is generated by a multivariate and multisite weather generator and subsequently disaggregated to hourly time steps with a k-Nearest-Neighbor model. Following the event generation procedure, the negative consequences of flooding are analyzed. The corresponding flood damage for each synthetic event is estimated by combining the synthetic discharge at representative points of the river network with a loss probability relation for each community in the study area. The loss probability relation is based on exposure and susceptibility analyses on a single object basis (residential buildings) for certain return periods. For these impact analyses official inundation maps of the study area are used. Finally, by analyzing the total event time series of damages, the expected annual damage or losses associated with a certain probability of occurrence can be estimated for

Kinetics of the Br2-CH3CHO Photochemical Chain Reaction

Science.gov (United States)

Nicovich, J. M.; Shackelford, C. J.; Wine, P. H.

1997-01-01

Time-resolved resonance fluorescence spectroscopy was employed in conjunction with laser flash photolysis of Br2 to study the kinetics of the two elementary steps in the photochemical chain reaction nBr2 + nCH3CHO + hv yields nCH3CBrO + nHBr. In the temperature range 255-400 K, the rate coefficient for the reaction Br((sup 2)P(sub 3/2)) + CH3CHO yields CH3CO + HBr is given by the Arrhenius expression k(sub 6)(T) = (1.51 +/- 0.20) x 10(exp -11) exp(-(364 +/- 41)/T)cu cm/(molecule.s). At 298 K, the reaction CH3CO + Br2 yields CH3CBrO + Br proceeds at a near gas kinetic rate, k(sub 7)(298 K) = (1.08 +/- 0.38) x 10(exp -10)cu cm/(molecule.s).

Thermodynamics of accuracy in kinetic proofreading: dissipation and efficiency trade-offs

International Nuclear Information System (INIS)

Rao, Riccardo; Peliti, Luca

2015-01-01

The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e. by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide a consistent thermodynamic description of enzyme-assisted assembly processes involving competing substrates, in a master equation framework. We introduce and evaluate a measure of the efficiency based on rigorous non-equilibrium inequalities. The performance of several proofreading models are thus analyzed and the related time, dissipation and efficiency versus error trade-offs exhibited for different discrimination regimes. We finally introduce and analyze in the same framework a simple model which takes into account correlations between consecutive enzyme-assisted assembly steps. This work highlights the relevance of the distinction between energetic and kinetic discrimination regimes in enzyme-substrate interactions. (paper)

Different seeds to solve the equations of stochastic point kinetics using the Euler-Maruyama method

International Nuclear Information System (INIS)

Suescun D, D.; Oviedo T, M.

2017-09-01

In this paper, a numerical study of stochastic differential equations that describe the kinetics in a nuclear reactor is presented. These equations, known as the stochastic equations of punctual kinetics they model temporal variations in neutron population density and concentrations of deferred neutron precursors. Because these equations are probabilistic in nature (since random oscillations in the neutrons and population of precursors were considered to be approximately normally distributed, and these equations also possess strong coupling and stiffness properties) the proposed method for the numerical simulations is the Euler-Maruyama scheme that provides very good approximations for calculating the neutron population and concentrations of deferred neutron precursors. The method proposed for this work was computationally tested for different seeds, initial conditions, experimental data and forms of reactivity for a group of precursors and then for six groups of deferred neutron precursors at each time step with 5000 Brownian movements per seed. In a paper reported in the literature, the Euler-Maruyama method was proposed, but there are many doubts about the reported values, in addition to not reporting the seed used, so in this work is expected to rectify the reported values. After taking the average of the different seeds used to generate the pseudo-random numbers the results provided by the Euler-Maruyama scheme will be compared in mean and standard deviation with other methods reported in the literature and results of the deterministic model of the equations of the punctual kinetics. This comparison confirms in particular that the Euler-Maruyama scheme is an efficient method to solve the equations of stochastic point kinetics but different from the values found and reported by another author. The Euler-Maruyama method is simple and easy to implement, provides acceptable results for neutron population density and concentration of deferred neutron precursors and

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

Science.gov (United States)

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.

Kinetic equation solution by inverse kinetic method

International Nuclear Information System (INIS)

Salas, G.

1983-01-01

We propose a computer program (CAMU) which permits to solve the inverse kinetic equation. The CAMU code is written in HPL language for a HP 982 A microcomputer with a peripheral interface HP 9876 A ''thermal graphic printer''. The CAMU code solves the inverse kinetic equation by taking as data entry the output of the ionization chambers and integrating the equation with the help of the Simpson method. With this program we calculate the evolution of the reactivity in time for a given disturbance

Modified Gompertz equation for electrotherapy murine tumor growth kinetics: predictions and new hypotheses

International Nuclear Information System (INIS)

Cabrales, Luis E Bergues; Mateus, Miguel A O'Farril; Brooks, Soraida C Acosta; Palencia, Fabiola Suárez; Zamora, Lisset Ortiz; Quevedo, María C Céspedes; Seringe, Sarah Edward; Cuitié, Vladimir Crombet; Cabrales, Idelisa Bergues; González, Gustavo Sierra; Nava, Juan J Godina; Aguilera, Andrés Ramírez; Joa, Javier A González; Ciria, Héctor M Camué; González, Maraelys Morales; Salas, Miriam Fariñas; Jarque, Manuel Verdecia; González, Tamara Rubio

2010-01-01

Electrotherapy effectiveness at different doses has been demonstrated in preclinical and clinical studies; however, several aspects that occur in the tumor growth kinetics before and after treatment have not yet been revealed. Mathematical modeling is a useful instrument that can reveal some of these aspects. The aim of this paper is to describe the complete growth kinetics of unperturbed and perturbed tumors through use of the modified Gompertz equation in order to generate useful insight into the mechanisms that underpin this devastating disease. The complete tumor growth kinetics for control and treated groups are obtained by interpolation and extrapolation methods with different time steps, using experimental data of fibrosarcoma Sa-37. In the modified Gompertz equation, a delay time is introduced to describe the tumor's natural history before treatment. Different graphical strategies are used in order to reveal new information in the complete kinetics of this tumor type. The first stage of complete tumor growth kinetics is highly non linear. The model, at this stage, shows different aspects that agree with those reported theoretically and experimentally. Tumor reversibility and the proportionality between regions before and after electrotherapy are demonstrated. In tumors that reach partial remission, two antagonistic post-treatment processes are induced, whereas in complete remission, two unknown antitumor mechanisms are induced. The modified Gompertz equation is likely to lead to insights within cancer research. Such insights hold promise for increasing our understanding of tumors as self-organizing systems and, the possible existence of phase transitions in tumor growth kinetics, which, in turn, may have significant impacts both on cancer research and on clinical practice

Shoe collar height effect on athletic performance, ankle joint kinematics and kinetics during unanticipated maximum-effort side-cutting performance.

Science.gov (United States)

Lam, Gilbert Wing Kai; Park, Eun Jung; Lee, Ki-Kwang; Cheung, Jason Tak-Man

2015-01-01

Side-step cutting manoeuvres comprise the coordination between planting and non-planting legs. Increased shoe collar height is expected to influence ankle biomechanics of both legs and possibly respective cutting performance. This study examined the shoe collar height effect on kinematics and kinetics of planting and non-planting legs during an unanticipated side-step cutting. Fifteen university basketball players performed maximum-effort side-step cutting to the left 45° direction or a straight ahead run in response to a random light signal. Seven successful cutting trials were collected for each condition. Athletic performance, ground reaction force, ankle kinematics and kinetics of both legs were analysed using paired t-tests. Results indicated that high-collar shoes resulted in less ankle inversion and external rotation during initial contact for the planting leg. The high-collar shoes also exhibited a smaller ankle range of motion in the sagittal and transverse planes for both legs, respectively. However, no collar effect was found for ankle moments and performance indicators including cutting performance time, ground contact time, propulsion ground reaction forces and impulses. These findings indicated that high-collar shoes altered ankle positioning and restricted ankle joint freedom movements in both legs, while no negative effect was found for athletic cutting performance.

Combined Effects of Numerical Method Type and Time Step on Water Stressed Actual Crop ET

Directory of Open Access Journals (Sweden)

B. Ghahraman

2016-02-01

Full Text Available Introduction: Actual crop evapotranspiration (Eta is important in hydrologic modeling and irrigation water management issues. Actual ET depends on an estimation of a water stress index and average soil water at crop root zone, and so depends on a chosen numerical method and adapted time step. During periods with no rainfall and/or irrigation, actual ET can be computed analytically or by using different numerical methods. Overal, there are many factors that influence actual evapotranspiration. These factors are crop potential evapotranspiration, available root zone water content, time step, crop sensitivity, and soil. In this paper different numerical methods are compared for different soil textures and different crops sensitivities. Materials and Methods: During a specific time step with no rainfall or irrigation, change in soil water content would be equal to evapotranspiration, ET. In this approach, however, deep percolation is generally ignored due to deep water table and negligible unsaturated hydraulic conductivity below rooting depth. This differential equation may be solved analytically or numerically considering different algorithms. We adapted four different numerical methods, as explicit, implicit, and modified Euler, midpoint method, and 3-rd order Heun method to approximate the differential equation. Three general soil types of sand, silt, and clay, and three different crop types of sensitive, moderate, and resistant under Nishaboor plain were used. Standard soil fraction depletion (corresponding to ETc=5 mm.d-1, pstd, below which crop faces water stress is adopted for crop sensitivity. Three values for pstd were considered in this study to cover the common crops in the area, including winter wheat and barley, cotton, alfalfa, sugar beet, saffron, among the others. Based on this parameter, three classes for crop sensitivity was considered, sensitive crops with pstd=0.2, moderate crops with pstd=0.5, and resistive crops with pstd=0

ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

Science.gov (United States)

Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

2006-12-15

We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

Kinetics of enzymatic high-solid hydrolysis of lignocellulosic biomass studied by calorimetry.

Science.gov (United States)

Olsen, Søren N; Lumby, Erik; McFarland, Kc; Borch, Kim; Westh, Peter

2011-03-01

Enzymatic hydrolysis of high-solid biomass (>10% w/w dry mass) has become increasingly important as a key step in the production of second-generation bioethanol. To this end, development of quantitative real-time assays is desirable both for empirical optimization and for detailed kinetic analysis. In the current work, we have investigated the application of isothermal calorimetry to study the kinetics of enzymatic hydrolysis of two substrates (pretreated corn stover and Avicel) at high-solid contents (up to 29% w/w). It was found that the calorimetric heat flow provided a true measure of the hydrolysis rate with a detection limit of about 500 pmol glucose s(-1). Hence, calorimetry is shown to be a highly sensitive real-time method, applicable for high solids, and independent on the complexity of the substrate. Dose-response experiments with a typical cellulase cocktail enabled a multidimensional analysis of the interrelationships of enzyme load and the rate, time, and extent of the reaction. The results suggest that the hydrolysis rate of pretreated corn stover is limited initially by available attack points on the substrate surface (conversion) but becomes proportional to enzyme dosage (excess of attack points) at later stages (>10% conversion). This kinetic profile is interpreted as an increase in polymer end concentration (substrate for CBH) as the hydrolysis progresses, probably due to EG activity in the enzyme cocktail. Finally, irreversible enzyme inactivation did not appear to be the source of reduced hydrolysis rate over time.

Understanding Yield Anomalies in ICF Implosions via Fully Kinetic Simulations

Science.gov (United States)

Taitano, William

2017-10-01

In the quest towards ICF ignition, plasma kinetic effects are among prime candidates for explaining some significant discrepancies between experimental observations and rad-hydro simulations. To assess their importance, high-fidelity fully kinetic simulations of ICF capsule implosions are needed. Owing to the extremely multi-scale nature of the problem, kinetic codes have to overcome nontrivial numerical and algorithmic challenges, and very few options are currently available. Here, we present resolutions of some long-standing yield discrepancy conundrums using a novel, LANL-developed, 1D-2V Vlasov-Fokker-Planck code iFP. iFP possesses an unprecedented fidelity and features fully implicit time-stepping, exact mass, momentum, and energy conservation, and optimal grid adaptation in phase space, all of which are critically important for ensuring long-time numerical accuracy of the implosion simulations. Specifically, we concentrate on several anomalous yield degradation instances observed in Omega campaigns, with the so-called ``Rygg effect'', or an anomalous yield scaling with the fuel composition, being a prime example. Understanding the physical mechanisms responsible for such degradations in non-ignition-grade Omega experiments is of great interest, as such experiments are often used for platform and diagnostic development, which are then used in ignition-grade experiments on NIF. In the case of Rygg's experiments, effects of a kinetic stratification of fuel ions on the yield have been previously proposed as the anomaly explanation, studied with a kinetic code FPION, and found unimportant. We have revisited this issue with iFP and obtained excellent yield-over-clean agreement with the original Rygg results, and several subsequent experiments. This validates iFP and confirms that the kinetic fuel stratification is indeed at the root of the observed yield degradation. This work was sponsored by the Metropolis Postdoctoral Fellowship, LDRD office, Thermonuclear Burn

Testing the behaviour of different kinetic models for uptake/release of radionuclides between water and sediments when implemented in a marine dispersion model

International Nuclear Information System (INIS)

Perianez, R.

2004-01-01

Three kinetic models for adsorption/release of 137 Cs between water and sediments have been tested when they are included in a previously validated dispersion model of the English Channel. Radionuclides are released to the Channel from La Hague nuclear fuel reprocessing plant (France). The kinetic models are a 1-step model consisting of a single reversible reaction, a 2-step model consisting of two consecutive reversible reactions and an irreversible model consisting of three parallel reactions: two reversible and one irreversible. The models have been tested under three typical situations that correspond to the source terms that can generally be found: instantaneous release, continuous release and redissolution of radionuclides from contaminated sediments. Differences between the models become more evident when contact times between water and sediments are larger (continuous release) and in the case of redissolution from sediments. Time scales for the redissolution process are rather different between the three models. The 1-step model produces a redissolution that is too fast when compared with experimental evidence. The irreversible model requires that saturation effects of the irreversible phase are included. Probably, the 2-step model represents the best compromise between ease and level of detail of the description of sorption/release processes

Modeling Taylor series approximations for prompt neutron kinetics with lab view simulations

International Nuclear Information System (INIS)

Adzri, E. P.

2012-09-01

The reactor point kinetics equations have been subjected to intense research in an effort to find simple yet accurate numerical solutions methods. The equations are very stiff numerically, meaning that there is a wide variation in the decay constants, so that using a particular time step in the numerical solution may provide sufficient accuracy for the group, but not for another. Several solutions techniques have been presented on the point kinetics equations with varying degrees of complexity. These include Power Series Solutions, CORE, PCA, Genapol and Taylor series methods. In this research, algorithms were developed based on the first and second order Taylor series expansion and simulated in LabVIEW to solve the Reactor Point Kinetics equations using block diagram nodes implemented within stacked sequences. The algorithms developed were fast,accurate and simple to code. Several reactivity insertions were used to simulate the change in neutron population with time. The LabVIEW- Taylor series solutions were compared with other solution techniques such as Power Series Solutions, CORE, PCA, Genapol and McMahon and Pierson's Taylor series approximation. The results of LabVIEW-Taylor series technique used by McMahon and Pearson The LabVIEW-implemented techniques were found to agree very well with these other methods. At 1x10 -8 s the neutron population was 1.000220 neutrons / cm 3 , at 1 x 10 -2 s it was 2.007681 neutrons / cm 3 and at 1x10 -1 s it was 2.075317 neutrons / cm 3 ; same results reported by Genapol for a fast reactor, it produced good and accurate results and compared very favorably with other methods found in the literature. Using much smaller time steps to the order or 10 -8 s commensurate with fast reactor parameters also produced very satisfactory results, indicating that the LabVIEW-based Taylor series technique is suitable for simulating the kinetics of fast reactors as well as thermal reactors. Algorithms developed that included second order terms

Drug kinetics release from Eudragit – Tenofovir@SiOC tablets

Energy Technology Data Exchange (ETDEWEB)

Tamayo, A., E-mail: aitanath@icv.csic.es [Ceramics and Glass Institute, CSIC, Madrid (Spain); Mazo, M.A. [Ceramics and Glass Institute, CSIC, Madrid (Spain); Veiga, M.D.; Ruiz-Caro, R.; Notario-Pérez, F. [Dpt. Pharmaceutical Technology, Faculty of Pharmacy, Complutense University of Madrid, Madrid (Spain); Rubio, J. [Ceramics and Glass Institute, CSIC, Madrid (Spain)

2017-06-01

A novel drug release system has been obtained in form of tablets from Eudragit® RS and tenofovir loaded on porous silicon oxycarbide glasses (SiOC). Active carbon (AC) and mesoporous silica (MCM-41) have also been used for comparative purposes. The porous silicon oxycarbide presents a bimodal mesopore size distribution that is maintained after functionalization with amino groups. We have studied the adsorption kinetics and adsorption equilibrium when the materials are loaded with tenofovir and, in all cases, pseudo-second order kinetics and Langmuir isotherm have been revealed as the most representative models describing the kinetic and thermodynamic parameters. Besides, the tenofovir adsorption on these materials turns out to be a favorable process. In vitro release of tenofovir has been studied in simulated vaginal medium by applying different release models. Continuous tenofovir release for > 20 days has been obtained for the SiOC material functionalized with amine groups. We concluded that the drug release occurs in two steps that involve a drug diffusion step through the material pores and diffusion through the swollen polymer. The interactions between the tenofovir drug and de amine groups of the functionalized silicon oxycarbide also play an important role in the release process. - Highlights: • Kinetic and thermodinamic parameters of the adsorption of tenofovir on porous substrates have been obtained. • Sustained release of TFV for > 20 days in SVF when it is supported on SiOC and manufactured as Eudragit®RS-containing tablets. • Release described by a two-step process involving diffusion through SiOC matrix and subsequent diffusion through the polymer.

From atoms to steps: The microscopic origins of crystal evolution

Science.gov (United States)

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

2014-07-01

The Burton-Cabrera-Frank (BCF) theory of crystal growth has been successful in describing a wide range of phenomena in surface physics. Typical crystal surfaces are slightly misoriented with respect to a facet plane; thus, the BCF theory views such systems as composed of staircase-like structures of steps separating terraces. Adsorbed atoms (adatoms), which are represented by a continuous density, diffuse on terraces, and steps move by absorbing or emitting these adatoms. Here we shed light on the microscopic origins of the BCF theory by deriving a simple, one-dimensional (1D) version of the theory from an atomistic, kinetic restricted solid-on-solid (KRSOS) model without external material deposition. We define the time-dependent adatom density and step position as appropriate ensemble averages in the KRSOS model, thereby exposing the non-equilibrium statistical mechanics origins of the BCF theory. Our analysis reveals that the BCF theory is valid in a low adatom-density regime, much in the same way that an ideal gas approximation applies to dilute gasses. We find conditions under which the surface remains in a low-density regime and discuss the microscopic origin of corrections to the BCF model.

Modeling of subtle kinetic processes in plasma simulation

International Nuclear Information System (INIS)

Sydora, R.D.; Decyk, V.K.; Dawson, J.M.

1988-01-01

A new diagnostic method for plasma simulation models is presented which enables one to probe the subtle dielectric properties of the plasma medium. The procedure involves the removal of the background plasma response in order to isolate the effects of small perturbing influences which are externally added. We have found the technique accurately describes fundamental kinetic plasma behavior such as the shielding of individual test charges and currents. Wave emission studies and drag of test particles has been carried out in explicit particle algorithms as well as large time step implicit and gyrokinetic models. Accurate plasma behavior is produced and it is possible to investigate in detail, processes which can be compared with plasma kinetic theory. The technique of subtraction is not only limited to particle simulation models but also can be used in MHD or fluid models where resolution is difficult due to the intensity of the background response relative to the phenomena one is interested in measuring, such as a weakly grouwing instability or nonlinear mode coupling effect. (author)

On mathematical modeling and numerical simulation of chemical kinetics in turbulent lean premixed combustion

Energy Technology Data Exchange (ETDEWEB)

Lilleberg, Bjorn

2011-07-01

This thesis investigates turbulent reacting lean premixed flows with detailed treatment of the chemistry. First, the fundamental equations which govern laminar and turbulent reacting flows are presented. A perfectly stirred reactor numerical code is developed to investigate the role of unmixedness and chemical kinetics in driving combustion instabilities. This includes both global single-step and detailed chemical kinetic mechanisms. The single-step mechanisms predict to some degree a similar behavior as the detailed mechanisms. However, it is shown that simple mechanisms can by themselves introduce instabilities. Magnussens Eddy Dissipation Concept (EDC) for turbulent combustion is implemented in the open source CFD toolbox OpenFOAM R for treatment of both fast and detailed chemistry. RANS turbulence models account for the turbulent compressible flow. A database of pre-calculated chemical time scales, which contains the influence of chemical kinetics, is coupled to EDC with fast chemistry to account for local extinction in both diffusion and premixed flames. Results are compared to fast and detailed chemistry calculations. The inclusion of the database shows significantly better results than the fast chemistry calculations while having a comparably small computational cost. Numerical simulations of four piloted lean premixed jet flames falling into the 'well stirred reactor/broken reaction zones' regime, with strong finite-rate chemistry effects, are performed. Measured and predicted scalars compare well for the two jets with the lowest velocities. The two jets with the highest velocities experience extinction and reignition, and the simulations are able to capture the decrease and increase of the OH mass fractions, but the peak values are higher than in the experiments. Also numerical simulations of a lean premixed lifted jet flame with high sensitivity to turbulence modeling and chemical kinetics are performed. Limitations of the applied turbulence and

Time step size limitation introduced by the BSSN Gamma Driver

Energy Technology Data Exchange (ETDEWEB)

Schnetter, Erik, E-mail: schnetter@cct.lsu.ed [Department of Physics and Astronomy, Louisiana State University, LA (United States)

2010-08-21

Many mesh refinement simulations currently performed in numerical relativity counteract instabilities near the outer boundary of the simulation domain either by changes to the mesh refinement scheme or by changes to the gauge condition. We point out that the BSSN Gamma Driver gauge condition introduces a time step size limitation in a similar manner as a Courant-Friedrichs-Lewy condition, but which is independent of the spatial resolution. We give a didactic explanation of this issue, show why, especially, mesh refinement simulations suffer from it, and point to a simple remedy. (note)

Reduced detonation kinetics and detonation structure in one- and multi-fuel gaseous mixtures

Science.gov (United States)

Fomin, P. A.; Trotsyuk, A. V.; Vasil'ev, A. A.

2017-10-01

Two-step approximate models of chemical kinetics of detonation combustion of (i) one-fuel (CH4/air) and (ii) multi-fuel gaseous mixtures (CH4/H2/air and CH4/CO/air) are developed for the first time. The models for multi-fuel mixtures are proposed for the first time. Owing to the simplicity and high accuracy, the models can be used in multi-dimensional numerical calculations of detonation waves in corresponding gaseous mixtures. The models are in consistent with the second law of thermodynamics and Le Chatelier’s principle. Constants of the models have a clear physical meaning. Advantages of the kinetic model for detonation combustion of methane has been demonstrated via numerical calculations of a two-dimensional structure of the detonation wave in a stoichiometric and fuel-rich methane-air mixtures and stoichiometric methane-oxygen mixture. The dominant size of the detonation cell, determines in calculations, is in good agreement with all known experimental data.

Ordering kinetics in quasi-one-dimensional Ising-like systems

International Nuclear Information System (INIS)

Mueller, M.; Paul, W.

1993-01-01

Results are presented of a Monte Carlo simulation of the kinetics of ordering in the two-dimensional nearest-neighbor Ising model in an L x M geometry with two free boundaries of length M much-gt L. This model can be viewed as representing an adsorbant on a stepped surface with mean terrace width L. The authors follow the ordering kinetics after quenches to temperatures 0.25 ≤T/T c ≤1 starting from a random initial configuration at a coverage of Θ=0.5 in the corresponding lattice gas picture. The systems evolve in time according to a Glauber kinetics with nonconserved order parameter. The equilibrium structure is given by a one-dimensional sequence of ordered domains. The ordering process evolves from a short initial two-dimensional ordering process through a crossover region to a quasi-one-dimensional behavior. The whole process is diffusive (inverse half-width of the structure factor peak 1/Δq parallel ∝ √t), in contrast to a model proposed by Kawasaki et al., where an intermediate logarithmic growth law is expected. All results are completely describable in the picture of an annihilating random walk (ARW) of domain walls. 36 refs., 16 figs

Kinetic partitioning mechanism of HDV ribozyme folding

Energy Technology Data Exchange (ETDEWEB)

Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing, E-mail: wbzhang@whu.edu.cn [Department of Physics, Wuhan University, Wuhan, Hubei 430072 (China)

2014-01-14

RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

Evolution of inhibitor-resistant natural mutant forms of HIV-1 protease probed by pre-steady state kinetic analysis.

Science.gov (United States)

Zakharova, Maria Yu; Kuznetsova, Alexandra A; Kaliberda, Elena N; Dronina, Maria A; Kolesnikov, Alexander V; Kozyr, Arina V; Smirnov, Ivan V; Rumsh, Lev D; Fedorova, Olga S; Knorre, Dmitry G; Gabibov, Alexander G; Kuznetsov, Nikita A

2017-11-01

Pre-steady state kinetic analysis of mechanistic features of substrate binding and processing is crucial for insight into the evolution of inhibitor-resistant forms of HIV-1 protease. These data may provide a correct vector for rational drug design assuming possible intrinsic dynamic effects. These data should also give some clues to the molecular mechanism of protease action and resistance to inhibitors. Here we report pre-steady state kinetics of the interaction of wild type or mutant forms of HIV-1 protease with a FRET-labeled peptide. The three-stage "minimal" kinetic scheme with first and second reversible steps of substrate binding and with following irreversible peptide cleavage step adequately described experimental data. For the first time, a set of "elementary" kinetic parameters of wild type HIV-1 protease and its natural mutant inhibitor-resistant forms MDR-HM, ANAM-11 and prDRV4 were compared. Inhibitors of the first and second generation were used to estimate the inhibitory effects on HIV-1 protease activity. The resulting set of kinetic data supported that the mutant forms are kinetically unaffected by inhibitors of the first generation, proving their functional resistance to these compounds. The second generation inhibitor darunavir inhibited mutant forms MDR-HM and ANAM-11, but was ineffective against prDRV4. Our kinetic data revealed that these inhibitors induced different conformational changes in the enzyme and, thereby they have different mode of binding in the enzyme active site. These data confirmed hypothesis that the driving force of the inhibitor-resistance evolution is disruption of enzyme-inhibitor complex by changing of the contact network in the inhibitor binding site. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Effects of the lateral amplitude and regularity of upper body fluctuation on step time variability evaluated using return map analysis.

Science.gov (United States)

Chidori, Kazuhiro; Yamamoto, Yuji

2017-01-01

The aim of this study was to evaluate the effects of the lateral amplitude and regularity of upper body fluctuation on step time variability. Return map analysis was used to clarify the relationship between step time variability and a history of falling. Eleven healthy, community-dwelling older adults and twelve younger adults participated in the study. All of the subjects walked 25 m at a comfortable speed. Trunk acceleration was measured using triaxial accelerometers attached to the third lumbar vertebrae (L3) and the seventh cervical vertebrae (C7). The normalized average magnitude of acceleration, the coefficient of determination ($R^2$) of the return map, and the step time variabilities, were calculated. Cluster analysis using the average fluctuation and the regularity of C7 fluctuation identified four walking patterns in the mediolateral (ML) direction. The participants with higher fluctuation and lower regularity showed significantly greater step time variability compared with the others. Additionally, elderly participants who had fallen in the past year had higher amplitude and a lower regularity of fluctuation during walking. In conclusion, by focusing on the time evolution of each step, it is possible to understand the cause of stride and/or step time variability that is associated with a risk of falls.

Antimicrobial Activities and Time-Kill Kinetics of Extracts of Selected Ghanaian Mushrooms

Directory of Open Access Journals (Sweden)

Theresa Appiah

2017-01-01

Full Text Available The rapid rise of antimicrobial resistance is a worldwide problem. This has necessitated the need to search for new antimicrobial agents. Mushrooms are rich sources of potential antimicrobial agents. This study investigated the antimicrobial properties of methanol extracts of Trametes gibbosa, Trametes elegans, Schizophyllum commune, and Volvariella volvacea. Agar well diffusion, broth microdilution, and time-kill kinetic assays were used to determine the antimicrobial activity of the extracts against selected test organisms. Preliminary mycochemical screening revealed the presence of tannins, flavonoids, triterpenoids, anthraquinones, and alkaloids in the extracts. Methanol extracts of T. gibbosa, T. elegans, S. commune, and V. volvacea showed mean zone of growth inhibition of 10.00±0.0 to 21.50±0.84, 10.00±0.0 to 22.00±1.10, 9.00±0.63 to 21.83±1.17, and 12.00±0.0 to 21.17±1.00 mm, respectively. The minimum inhibitory concentration of methanol extracts of T. gibbosa, T. elegans, S. commune, and V. volvacea ranged from 4.0 to 20, 6.0 to 30.0, 8.0 to 10.0, and 6.0 to 20.0 mg/mL, respectively. Time-kill kinetics studies showed that the extracts possess bacteriostatic action. Methanol extracts of T. gibbosa, T. elegans, S. commune, and V. volvacea exhibited antimicrobial activity and may contain bioactive compounds which may serve as potential antibacterial and antifungal agents.

An accurate solution of point reactor neutron kinetics equations of multi-group of delayed neutrons

International Nuclear Information System (INIS)

Yamoah, S.; Akaho, E.H.K.; Nyarko, B.J.B.

2013-01-01

Highlights: ► Analytical solution is proposed to solve the point reactor kinetics equations (PRKE). ► The method is based on formulating a coefficient matrix of the PRKE. ► The method was applied to solve the PRKE for six groups of delayed neutrons. ► Results shows good agreement with other traditional methods in literature. ► The method is accurate and efficient for solving the point reactor kinetics equations. - Abstract: The understanding of the time-dependent behaviour of the neutron population in a nuclear reactor in response to either a planned or unplanned change in the reactor conditions is of great importance to the safe and reliable operation of the reactor. In this study, an accurate analytical solution of point reactor kinetics equations with multi-group of delayed neutrons for specified reactivity changes is proposed to calculate the change in neutron density. The method is based on formulating a coefficient matrix of the homogenous differential equations of the point reactor kinetics equations and calculating the eigenvalues and the corresponding eigenvectors of the coefficient matrix. A small time interval is chosen within which reactivity relatively stays constant. The analytical method was applied to solve the point reactor kinetics equations with six-groups delayed neutrons for a representative thermal reactor. The problems of step, ramp and temperature feedback reactivities are computed and the results compared with other traditional methods. The comparison shows that the method presented in this study is accurate and efficient for solving the point reactor kinetics equations of multi-group of delayed neutrons

NO kinetics in pulsed low-pressure nitrogen plasmas studied by time resolved quantum cascade laser absorption spectroscopy

NARCIS (Netherlands)

Welzel, S.; Guaitella, O.; Lazzaroni, C.; Pintassilgo, C.; Rousseau, A.; Röpcke, J.

2011-01-01

Time-resolved quantum cascade laser absorption spectroscopy at 1897 cm-1 (5.27 µm) has been applied to study the NO(X) kinetics on the micro- and millisecond time scale in pulsed low-pressure N2/NO dc discharges. Experiments have been performed under flowing and static gas conditions to infer the

Desorption Kinetics and Mechanisms of CO2 on Amine-Based Mesoporous Silica Materials

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Yang Teng

2017-01-01

Full Text Available Tetraethylenepentamine (TEPA-based mesoporous MCM-41 is used as the adsorbent to determine the CO2 desorption kinetics of amine-modified materials after adsorption. The experimental data of CO2 desorption as a function of time are derived by zero-length column at different temperatures (35, 50, and 70 °C and analyzed by Avrami’s fractional-order kinetic model. A new method is used to distinguish the physical desorption and chemical desorption performance of surface-modified mesoporous MCM-41. The activation energy Ea of CO2 physical desorption and chemical desorption calculated from Arrhenius equation are 15.86 kJ/mol and 57.15 kJ/mol, respectively. Furthermore, intraparticle diffusion and Boyd’s film models are selected to investigate the mechanism of CO2 desorption from MCM-41 and surface-modified MCM-41. For MCM-41, there are three rate-limiting steps during the desorption process. Film diffusion is more prominent for the CO2 desorption rates at low temperatures, and pore diffusion mainly governs the rate-limiting process under higher temperatures. Besides the surface reaction, the desorption process contains four rate-limiting steps on surface-modified MCM-41.

Simulation methods with extended stability for stiff biochemical Kinetics

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Rué Pau

2010-08-01

Full Text Available Abstract Background With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (biochemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA. The key quantity is the step size, or waiting time, τ, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where τ can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called τ-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as τ grows. Results In this paper we extend Poisson τ-leap methods to a general class of Runge-Kutta (RK τ-leap methods. We show that with the proper selection of the coefficients, the variance of the extended τ-leap can be well-behaved, leading to significantly larger step sizes. Conclusions The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original τ-leap method. The approach paves the way to explore new multiscale methods to simulate (biochemical systems.

Development and evaluation of a real-time one step Reverse-Transcriptase PCR for quantitation of Chandipura Virus

Directory of Open Access Journals (Sweden)

Tandale Babasaheb V

2008-12-01

Full Text Available Abstract Background Chandipura virus (CHPV, a member of family Rhabdoviridae was attributed to an explosive outbreak of acute encephalitis in children in Andhra Pradesh, India in 2003 and a small outbreak among tribal children from Gujarat, Western India in 2004. The case-fatality rate ranged from 55–75%. Considering the rapid progression of the disease and high mortality, a highly sensitive method for quantifying CHPV RNA by real-time one step reverse transcriptase PCR (real-time one step RT-PCR using TaqMan technology was developed for rapid diagnosis. Methods Primers and probe for P gene were designed and used to standardize real-time one step RT-PCR assay for CHPV RNA quantitation. Standard RNA was prepared by PCR amplification, TA cloning and run off transcription. The optimized real-time one step RT-PCR assay was compared with the diagnostic nested RT-PCR and different virus isolation systems [in vivo (mice in ovo (eggs, in vitro (Vero E6, PS, RD and Sand fly cell line] for the detection of CHPV. Sensitivity and specificity of real-time one step RT-PCR assay was evaluated with diagnostic nested RT-PCR, which is considered as a gold standard. Results Real-time one step RT-PCR was optimized using in vitro transcribed (IVT RNA. Standard curve showed linear relationship for wide range of 102-1010 (r2 = 0.99 with maximum Coefficient of variation (CV = 5.91% for IVT RNA. The newly developed real-time RT-PCR was at par with nested RT-PCR in sensitivity and superior to cell lines and other living systems (embryonated eggs and infant mice used for the isolation of the virus. Detection limit of real-time one step RT-PCR and nested RT-PCR was found to be 1.2 × 100 PFU/ml. RD cells, sand fly cells, infant mice, and embryonated eggs showed almost equal sensitivity (1.2 × 102 PFU/ml. Vero and PS cell-lines (1.2 × 103 PFU/ml were least sensitive to CHPV infection. Specificity of the assay was found to be 100% when RNA from other viruses or healthy

CRYSTALLIZATION KINETICS OF AMMONIUM PERCHLORATE IN AN AGITATED VESSEL

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Nahidh Kaseer

2013-05-01

Full Text Available 31Overall crystal growth kinetics for ammonium perchlorate in laboratory scale batch  agitated vessel crystallizer have been determined from batch experiments performed in an integral mode. The effects of temperature between 30-60ºC, seed size 0.07, 0.120 and 0.275 mm and stirrer speed 160, 340, and 480 rpm, on the kinetics of crystal growth were investigated. Two different methods, viz. polynomial fitting and initial derivative were used to predict the kinetics expression. In general both methods gave comparable results for growth kinetics estimation. The order of growth process is not more than two. The activation energy for crystal growth of ammonium perchlorate was determined and found  to be equal to 5.8 kJ/ mole.            Finally, the influence of the affecting parameters on the crystal growth rate gives general expression that had an obvious dependence of the growth rate on each variables of concern (temperature, seed size, and stirrer speed .The general overall growth rate expression had shown that super saturation is the most significant variable. While the positive dependence of the stirrer speed demonstrates the importance of the diffusional step in the growth rate model. Moreover, the positive dependence of the seed size demonstrate the importance of the surface integration  step in the growth rate model. All the studied variables tend to suggest that the growth rate characteristics  of ammonium perchlorate from aqueous solution commenced in a batch crystallizer are diffusion kinetic controlled process.

Kinetics of alpha-amylase secretion in Aspergillus oryzae

DEFF Research Database (Denmark)

Henriksen, Anne Laurence Santerre; Carlsen, Morten; Bang de, H.

1999-01-01

-chase experiments were carried out to investigate the alpha-amylase secretion kinetics in A. oryzae. No unglycosylated alpha-amylase was detected neither intracellularly nor extracellularly demonstrating that glycosylation was not the rate controlling step in the secretory pathway. The pulse chase experiments...... indicated that there are two pools of intracellular alpha-amylase: a fast secreted and a slow secreted. The secretion of those two pools were described with a kinetic model, which was fitted to the pulse chase experiments. (C) 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 65: 76-82, 1999....

Kinetic parameters from thermogravimetric analysis

Science.gov (United States)

Kiefer, Richard L.

1993-01-01

High performance polymeric materials are finding increased use in aerospace applications. Proposed high speed aircraft will require materials to withstand high temperatures in an oxidative atmosphere for long periods of time. It is essential that accurate estimates be made of the performance of these materials at the given conditions of temperature and time. Temperatures of 350 F (177 C) and times of 60,000 to 100,000 hours are anticipated. In order to survey a large number of high performance polymeric materials on a reasonable time scale, some form of accelerated testing must be performed. A knowledge of the rate of a process can be used to predict the lifetime of that process. Thermogravimetric analysis (TGA) has frequently been used to determine kinetic information for degradation reactions in polymeric materials. Flynn and Wall studied a number of methods for using TGA experiments to determine kinetic information in polymer reactions. Kinetic parameters, such as the apparent activation energy and the frequency factor, can be determined in such experiments. Recently, researchers at the McDonnell Douglas Research Laboratory suggested that a graph of the logarithm of the frequency factor against the apparent activation energy can be used to predict long-term thermo-oxidative stability for polymeric materials. Such a graph has been called a kinetic map. In this study, thermogravimetric analyses were performed in air to study the thermo-oxidative degradation of several high performance polymers and to plot their kinetic parameters on a kinetic map.

Real-time, single-step bioassay using nanoplasmonic resonator with ultra-high sensitivity

Energy Technology Data Exchange (ETDEWEB)

Zhang, Xiang; Ellman, Jonathan A; Chen, Fanqing Frank; Su, Kai-Hang; Wei, Qi-Huo; Sun, Cheng

2014-04-01

A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

Implicit unified gas-kinetic scheme for steady state solutions in all flow regimes

Science.gov (United States)

Zhu, Yajun; Zhong, Chengwen; Xu, Kun

2016-06-01

This paper presents an implicit unified gas-kinetic scheme (UGKS) for non-equilibrium steady state flow computation. The UGKS is a direct modeling method for flow simulation in all regimes with the updates of both macroscopic flow variables and microscopic gas distribution function. By solving the macroscopic equations implicitly, a predicted equilibrium state can be obtained first through iterations. With the newly predicted equilibrium state, the evolution equation of the gas distribution function and the corresponding collision term can be discretized in a fully implicit way for fast convergence through iterations as well. The lower-upper symmetric Gauss-Seidel (LU-SGS) factorization method is implemented to solve both macroscopic and microscopic equations, which improves the efficiency of the scheme. Since the UGKS is a direct modeling method and its physical solution depends on the mesh resolution and the local time step, a physical time step needs to be fixed before using an implicit iterative technique with a pseudo-time marching step. Therefore, the physical time step in the current implicit scheme is determined by the same way as that in the explicit UGKS for capturing the physical solution in all flow regimes, but the convergence to a steady state speeds up through the adoption of a numerical time step with large CFL number. Many numerical test cases in different flow regimes from low speed to hypersonic ones, such as the Couette flow, cavity flow, and the flow passing over a cylinder, are computed to validate the current implicit method. The overall efficiency of the implicit UGKS can be improved by one or two orders of magnitude in comparison with the explicit one.

Taylor's series method for solving the nonlinear point kinetics equations

International Nuclear Information System (INIS)

Nahla, Abdallah A.

2011-01-01

Highlights: → Taylor's series method for nonlinear point kinetics equations is applied. → The general order of derivatives are derived for this system. → Stability of Taylor's series method is studied. → Taylor's series method is A-stable for negative reactivity. → Taylor's series method is an accurate computational technique. - Abstract: Taylor's series method for solving the point reactor kinetics equations with multi-group of delayed neutrons in the presence of Newtonian temperature feedback reactivity is applied and programmed by FORTRAN. This system is the couples of the stiff nonlinear ordinary differential equations. This numerical method is based on the different order derivatives of the neutron density, the precursor concentrations of i-group of delayed neutrons and the reactivity. The r th order of derivatives are derived. The stability of Taylor's series method is discussed. Three sets of applications: step, ramp and temperature feedback reactivities are computed. Taylor's series method is an accurate computational technique and stable for negative step, negative ramp and temperature feedback reactivities. This method is useful than the traditional methods for solving the nonlinear point kinetics equations.

Shape based kinetic outlier detection in real-time PCR

Directory of Open Access Journals (Sweden)

D'Atri Mario

2010-04-01

Full Text Available Abstract Background Real-time PCR has recently become the technique of choice for absolute and relative nucleic acid quantification. The gold standard quantification method in real-time PCR assumes that the compared samples have similar PCR efficiency. However, many factors present in biological samples affect PCR kinetic, confounding quantification analysis. In this work we propose a new strategy to detect outlier samples, called SOD. Results Richards function was fitted on fluorescence readings to parameterize the amplification curves. There was not a significant correlation between calculated amplification parameters (plateau, slope and y-coordinate of the inflection point and the Log of input DNA demonstrating that this approach can be used to achieve a "fingerprint" for each amplification curve. To identify the outlier runs, the calculated parameters of each unknown sample were compared to those of the standard samples. When a significant underestimation of starting DNA molecules was found, due to the presence of biological inhibitors such as tannic acid, IgG or quercitin, SOD efficiently marked these amplification profiles as outliers. SOD was subsequently compared with KOD, the current approach based on PCR efficiency estimation. The data obtained showed that SOD was more sensitive than KOD, whereas SOD and KOD were equally specific. Conclusion Our results demonstrated, for the first time, that outlier detection can be based on amplification shape instead of PCR efficiency. SOD represents an improvement in real-time PCR analysis because it decreases the variance of data thus increasing the reliability of quantification.

Stepping reaction time and gait adaptability are significantly impaired in people with Parkinson's disease: Implications for fall risk.

Science.gov (United States)

Caetano, Maria Joana D; Lord, Stephen R; Allen, Natalie E; Brodie, Matthew A; Song, Jooeun; Paul, Serene S; Canning, Colleen G; Menant, Jasmine C

2018-02-01

Decline in the ability to take effective steps and to adapt gait, particularly under challenging conditions, may be important reasons why people with Parkinson's disease (PD) have an increased risk of falling. This study aimed to determine the extent of stepping and gait adaptability impairments in PD individuals as well as their associations with PD symptoms, cognitive function and previous falls. Thirty-three older people with PD and 33 controls were assessed in choice stepping reaction time, Stroop stepping and gait adaptability tests; measurements identified as fall risk factors in older adults. People with PD had similar mean choice stepping reaction times to healthy controls, but had significantly greater intra-individual variability. In the Stroop stepping test, the PD participants were more likely to make an error (48 vs 18%), took 715 ms longer to react (2312 vs 1517 ms) and had significantly greater response variability (536 vs 329 ms) than the healthy controls. People with PD also had more difficulties adapting their gait in response to targets (poorer stepping accuracy) and obstacles (increased number of steps) appearing at short notice on a walkway. Within the PD group, higher disease severity, reduced cognition and previous falls were associated with poorer stepping and gait adaptability performances. People with PD have reduced ability to adapt gait to unexpected targets and obstacles and exhibit poorer stepping responses, particularly in a test condition involving conflict resolution. Such impaired stepping responses in Parkinson's disease are associated with disease severity, cognitive impairment and falls. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bile salt-induced cholesterol crystal formation from model bile vesicles: a time course study

NARCIS (Netherlands)

van de Heijning, B. J.; Stolk, M. F.; van Erpecum, K. J.; Renooij, W.; Groen, A. K.; vanBerge-Henegouwen, G. P.

1994-01-01

Precipitation of cholesterol crystals from vesicles is an important step in the pathogenesis of cholesterol gallstones. Little is known, however, about the kinetics and the mechanisms involved in cholesterol crystallization. Therefore, the time course of cholesterol crystal precipitation and lipid

Numerical simulation of stochastic point kinetic equation in the dynamical system of nuclear reactor

International Nuclear Information System (INIS)

Saha Ray, S.

2012-01-01

Highlights: ► In this paper stochastic neutron point kinetic equations have been analyzed. ► Euler–Maruyama method and Strong Taylor 1.5 order method have been discussed. ► These methods are applied for the solution of stochastic point kinetic equations. ► Comparison between the results of these methods and others are presented in tables. ► Graphs for neutron and precursor sample paths are also presented. -- Abstract: In the present paper, the numerical approximation methods, applied to efficiently calculate the solution for stochastic point kinetic equations () in nuclear reactor dynamics, are investigated. A system of Itô stochastic differential equations has been analyzed to model the neutron density and the delayed neutron precursors in a point nuclear reactor. The resulting system of Itô stochastic differential equations are solved over each time-step size. The methods are verified by considering different initial conditions, experimental data and over constant reactivities. The computational results indicate that the methods are simple and suitable for solving stochastic point kinetic equations. In this article, a numerical investigation is made in order to observe the random oscillations in neutron and precursor population dynamics in subcritical and critical reactors.

Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models

Directory of Open Access Journals (Sweden)

Joseph A. Wayman

2015-03-01

Full Text Available Cell-free systems offer many advantages for the study, manipulation and modeling of metabolism compared to in vivo processes. Many of the challenges confronting genome-scale kinetic modeling can potentially be overcome in a cell-free system. For example, there is no complex transcriptional regulation to consider, transient metabolic measurements are easier to obtain, and we no longer have to consider cell growth. Thus, cell-free operation holds several significant advantages for model development, identification and validation. Theoretically, genome-scale cell-free kinetic models may be possible for industrially important organisms, such as E. coli, if a simple, tractable framework for integrating allosteric regulation with enzyme kinetics can be formulated. Toward this unmet need, we present an effective biochemical network modeling framework for building dynamic cell-free metabolic models. The key innovation of our approach is the integration of simple effective rules encoding complex allosteric regulation with traditional kinetic pathway modeling. We tested our approach by modeling the time evolution of several hypothetical cell-free metabolic networks. We found that simple effective rules, when integrated with traditional enzyme kinetic expressions, captured complex allosteric patterns such as ultrasensitivity or non-competitive inhibition in the absence of mechanistic information. Second, when integrated into network models, these rules captured classic regulatory patterns such as product-induced feedback inhibition. Lastly, we showed, at least for the network architectures considered here, that we could simultaneously estimate kinetic parameters and allosteric connectivity from synthetic data starting from an unbiased collection of possible allosteric structures using particle swarm optimization. However, when starting with an initial population that was heavily enriched with incorrect structures, our particle swarm approach could converge

AIREK-PUL, Periodic Kinetics Problems of Pulsed Reactors

International Nuclear Information System (INIS)

Inzaghi, A.; Misenta, R.

1984-01-01

1 - Nature of physical problem solved: Solves periodic problems about the kinetics of pulsed reactors or problems where the reactivity has rapid variations. The program uses two constant steps for the integration of the system of differential equations, the first step during the first half-period and the second step during the second half-period. Available for either single or double precision. 2 - Method of solution: The differential equations are integrated using the fourth-order Runge-Kutta method as modified by E.R. Cohen (Geneva Conference, 1958). 3 - Restrictions on the complexity of the problem: The maximum number of differential equations that can be solved simultaneously is 50

Friction analysis of kinetic schemes : the friction coefficient

NARCIS (Netherlands)

Lolkema, Juke S.

1995-01-01

Friction analysis is proposed as the application of general control analysis to single enzymes to describe the control of elementary kinetic steps on the overall catalytic rate. For each transition, a friction coefficient is defined that measures the sensitivity of the turnover rate to the free

Kinetic interaction in hydrogenitrogenation of quinoline and acridine

International Nuclear Information System (INIS)

El-Bishtawi, R.F.; Seapan, M.

1988-01-01

Liquid fossil fuels contain numerous nitrogen compounds. During hydrodenitrogenation processes, these compounds for the active catalytic sites, with each compound affecting the kinetics of the other compounds. An understanding of the kinetic interaction is essential in using the results of model compound kinetics to predict the behavior of complex mixtures. In this work, the authors study the hydrodenitrogenation of quinoline and acridine in n-hexadecane over a commercial nickel-molybdenum catalyst in a batch autoclave reactor at 8.3 MPa (1200 psig) and 357-390 0 C. The reaction networks and kinetics of individual compounds were developed. These results confirm the existing knowledge of reaction networks for quinoline and acridine. Furthermore, their experiments show that formation for o-ethylaniline, o-toluidine and aniline are also important steps in quinoline denitrogenation. For total nitrogen removal, a dual site Langmuir-Hinshelwood type model considering separate sites for adsorption of hydrogen and nitrogen compounds give the best fit

Collective behaviours: from biochemical kinetics to electronic circuits

Science.gov (United States)

Agliari, Elena; Barra, Adriano; Burioni, Raffaella; di Biasio, Aldo; Uguzzoni, Guido

2013-12-01

In this work we aim to highlight a close analogy between cooperative behaviors in chemical kinetics and cybernetics; this is realized by using a common language for their description, that is mean-field statistical mechanics. First, we perform a one-to-one mapping between paradigmatic behaviors in chemical kinetics (i.e., non-cooperative, cooperative, ultra-sensitive, anti-cooperative) and in mean-field statistical mechanics (i.e., paramagnetic, high and low temperature ferromagnetic, anti-ferromagnetic). Interestingly, the statistical mechanics approach allows a unified, broad theory for all scenarios and, in particular, Michaelis-Menten, Hill and Adair equations are consistently recovered. This framework is then tested against experimental biological data with an overall excellent agreement. One step forward, we consistently read the whole mapping from a cybernetic perspective, highlighting deep structural analogies between the above-mentioned kinetics and fundamental bricks in electronics (i.e. operational amplifiers, flashes, flip-flops), so to build a clear bridge linking biochemical kinetics and cybernetics.

Kinetic investigation of uranyl-uranophile complexation. 1. Macrocyclic kinetic effect and macrocyclic protection effect

International Nuclear Information System (INIS)

Tabushi, I.; Yoshizawa, A.

1986-01-01

Equilibria and rates of ligand-exchange reactions between uranyl tricarbonate and dithiocarbamates and between uranyl tris-(dithiocarbamates) and carbonate were studied under a variety of conditions. The dithiocarbamates used were acyclic diethyl-dithiocarbamate and macrocyclic tris(dithiocarbamate). The acyclic ligand showed a triphasic (successive three-step) equilibrium with three different equilibrium constants while the macrocyclic ligand showed a clear monophasic (one-step) equilibrium with a much larger stability constant for the dithiocarbamate-uranyl complex. The macrocyclic ligand showed the S/sub N/2-type ligand-exchange rate in the forward as well as reverse process, while the first step of the acyclic ligand-exchange reaction proceeded via the S/sub N/1-type mechanism. This kinetic macrocyclic effect on molecularity is interpreted as the result of a unique topological requirement of uranyl complexation. The macrocyclic ligand also exhibited a clear protection effect, leading to the large stability constant. 19 references, 10 figures, 2 tables

Dsc cure kinetics of an unsaturated polyester resin using empirical kinetic model

International Nuclear Information System (INIS)

Abdullah, I.

2015-01-01

In this paper, the kinetics of curing of unsaturated polyester resin initiated with benzoyl peroxide was studied. In case of unsaturated polyester (UP) resin, isothermal test alone could not predict correctly the curing time of UP resin. Therefore, isothermal kinetic analysis through isoconventional adjustment was used to correctly predict the curing time and temperature of UP resin. Isothermal kinetic analysis through isoconversional adjustment indicated that 97% of UP resin cures in 33 min at 120 degree C. Curing of UP resin through microwaves was also studied and found that 67% of UP resin cures in 1 min at 120 degree C. The crosslinking reaction of UP resin is so fast at 120 degree C that it becomes impossible to predict correctly the curing time of UP resin using isothermal test and the burial of C=C bonds in microgels makes it impossible to be fully cured by microwaves at 120 degree C. The rheological behaviour of unsaturated polyester resin was also studied to observe the change in viscosity with respect to time and temperature. (author)

Experimental study of the kinetics of dry, forward combustion. Final report

Energy Technology Data Exchange (ETDEWEB)

Thomas, G.W.; Buthod, A.P.; Allag, O.

1979-02-01

Results are presented of an experimental investigation of dry, forward combustion with two main objectives, viz, (1) to develop a method for determining the kinetic perameters of fuel laydown and burnoff from combustion tube data, and (2) to evaluate them for a particular crude-sand mixture. In the light of past experimental work, a two-step chain reaction model is postulated in which fuel laydown and burnoff are considered as competitive kinetic reactions. Laboratory equipment consisting of a combustion tube assembly and sampling probe, a flow control system, an electronic control assembly, and a fluid analysis system are described in detail. The sampling probe provides a novel method for taking fluid samples at selected interior points within the combustion cell. Six experimental runs were performed using a 27/sup 0/ API Prudhoe Bay crude. Analyses of the data indicte that, in addition to the coke residue, some light ends of the crude enter into the total fuel consumed by the burning zone. The use of the moveable sampling probe permitted the reconstruction of CO + CO/sub 2/ production rate curves as functions of time and distance. A technique is presented for solving the integral equation and estimating the activation energies, pre-exponential factors, and some associated constants for fuel deposition and combustion. It was found that operating pressure has essentially no effect on the exponential energy, but it does affect the preexponential (or frequency) factor. It is concluded that the essential phenomena of forward combustion can be adequately depicted by the two-step chain reaction concept, and that kinetic data,or their bounds, can be determined from combustion tube data.

Multiple-time-stepping generalized hybrid Monte Carlo methods

Energy Technology Data Exchange (ETDEWEB)

Escribano, Bruno, E-mail: bescribano@bcamath.org [BCAM—Basque Center for Applied Mathematics, E-48009 Bilbao (Spain); Akhmatskaya, Elena [BCAM—Basque Center for Applied Mathematics, E-48009 Bilbao (Spain); IKERBASQUE, Basque Foundation for Science, E-48013 Bilbao (Spain); Reich, Sebastian [Universität Potsdam, Institut für Mathematik, D-14469 Potsdam (Germany); Azpiroz, Jon M. [Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P.K. 1072, Donostia (Spain)

2015-01-01

Performance of the generalized shadow hybrid Monte Carlo (GSHMC) method [1], which proved to be superior in sampling efficiency over its predecessors [2–4], molecular dynamics and hybrid Monte Carlo, can be further improved by combining it with multi-time-stepping (MTS) and mollification of slow forces. We demonstrate that the comparatively simple modifications of the method not only lead to better performance of GSHMC itself but also allow for beating the best performed methods, which use the similar force splitting schemes. In addition we show that the same ideas can be successfully applied to the conventional generalized hybrid Monte Carlo method (GHMC). The resulting methods, MTS-GHMC and MTS-GSHMC, provide accurate reproduction of thermodynamic and dynamical properties, exact temperature control during simulation and computational robustness and efficiency. MTS-GHMC uses a generalized momentum update to achieve weak stochastic stabilization to the molecular dynamics (MD) integrator. MTS-GSHMC adds the use of a shadow (modified) Hamiltonian to filter the MD trajectories in the HMC scheme. We introduce a new shadow Hamiltonian formulation adapted to force-splitting methods. The use of such Hamiltonians improves the acceptance rate of trajectories and has a strong impact on the sampling efficiency of the method. Both methods were implemented in the open-source MD package ProtoMol and were tested on a water and a protein systems. Results were compared to those obtained using a Langevin Molly (LM) method [5] on the same systems. The test results demonstrate the superiority of the new methods over LM in terms of stability, accuracy and sampling efficiency. This suggests that putting the MTS approach in the framework of hybrid Monte Carlo and using the natural stochasticity offered by the generalized hybrid Monte Carlo lead to improving stability of MTS and allow for achieving larger step sizes in the simulation of complex systems.

Study of N-13 decay on time using continuous kinetic function method

International Nuclear Information System (INIS)

Tran Dai Nghiep; Vu Hoang Lam; Nguyen Ngoc Son; Nguyen Duc Thanh

1993-01-01

The decay function from radioisotope 13 N formed in the reaction 14 N(γ,n) 13 N was registered by high resolution gamma spectrometer in multiscanning mode with gamma energy 511 keV. The experimental data was processed by common and kinetic function method. The continuous comparison of the decay function on time permits to determinate possible deviation from purely exponential decay curve. The results were described by several decay theories. The degrees of corresponding between theories and experiment were evaluated by goodness factor. A complex type of decay was considered. (author). 9 refs, 2 tabs, 6 figs

Study on coupling of three-dimension space time neutron kinetics model and RELAP5 and improvement of RELAP5

International Nuclear Information System (INIS)

Gui Xuewen; Cai Qi; Luo Bangqi

2007-01-01

A two-group three-dimension space-time neutron kinetics model is applied to the RELAP5 code, which replaces the point reactor kinetics model. A visual operation interface is designed to convenience interactive operation between operator and computer. The calculation results and practical applications indicate that the functions and precision of improved RELAP5 are enhanced and can be easily used. The improved RELAP5 has a good application perspective in nuclear power plant simulation. (authors)

Non-Linear Response to Periodic Forcing of Methane-Air Global and Detailed Kinetics in Continuous Stirred Tank Reactors Close to Extinction Conditions

Directory of Open Access Journals (Sweden)

Francesco Saverio Marra

2015-09-01

Full Text Available This paper focus on the behavior of a continuous stirred tank reactor (CSTR subject to perturbations of finite amplitude and frequency. Two main objectives are pursued: to determine the extinction line in the equivalence ratio (φ - residence time (τ plane, fixed the thermodynamic state conditions; and to characterize the response of the chemical system to periodic forcing of the residence time. Transient simulations of combustion of methane with air, using both global single-step and detailed chemical kinetic mechanisms, have been conducted and the corresponding asymptotic solutions analyzed. Results indicate very different dynamical behaviors, posing the issue of a proper choice of the kinetic scheme for the numerical study of combustion oscillations.

Kinetics of transient electroluminescence in organic light emitting diodes

Science.gov (United States)

Shukla, Manju; Kumar, Pankaj; Chand, Suresh; Brahme, Nameeta; Kher, R. S.; Khokhar, M. S. K.

2008-08-01

Mathematical simulation on the rise and decay kinetics of transient electroluminescence (EL) in organic light emitting diodes (OLEDs) is presented. The transient EL is studied with respect to a step voltage pulse. While rising, for lower values of time, the EL intensity shows a quadratic dependence on (t - tdel), where tdel is the time delay observed in the onset of EL, and finally attains saturation at a sufficiently large time. When the applied voltage is switched off, the initial EL decay shows an exponential dependence on (t - tdec), where tdec is the time when the voltage is switched off. The simulated results are compared with the transient EL performance of a bilayer OLED based on small molecular bis(2-methyl 8-hydroxyquinoline)(triphenyl siloxy) aluminium (SAlq). Transient EL studies have been carried out at different voltage pulse amplitudes. The simulated results show good agreement with experimental data. Using these simulated results the lifetime of the excitons in SAlq has also been calculated.

Kinetics of transient electroluminescence in organic light emitting diodes

International Nuclear Information System (INIS)

Shukla, Manju; Brahme, Nameeta; Kumar, Pankaj; Chand, Suresh; Kher, R S; Khokhar, M S K

2008-01-01

Mathematical simulation on the rise and decay kinetics of transient electroluminescence (EL) in organic light emitting diodes (OLEDs) is presented. The transient EL is studied with respect to a step voltage pulse. While rising, for lower values of time, the EL intensity shows a quadratic dependence on (t - t del ), where t del is the time delay observed in the onset of EL, and finally attains saturation at a sufficiently large time. When the applied voltage is switched off, the initial EL decay shows an exponential dependence on (t - t dec ), where t dec is the time when the voltage is switched off. The simulated results are compared with the transient EL performance of a bilayer OLED based on small molecular bis(2-methyl 8-hydroxyquinoline)(triphenyl siloxy) aluminium (SAlq). Transient EL studies have been carried out at different voltage pulse amplitudes. The simulated results show good agreement with experimental data. Using these simulated results the lifetime of the excitons in SAlq has also been calculated

Scalable explicit implementation of anisotropic diffusion with Runge-Kutta-Legendre super-time stepping

Science.gov (United States)

Vaidya, Bhargav; Prasad, Deovrat; Mignone, Andrea; Sharma, Prateek; Rickler, Luca

2017-12-01

An important ingredient in numerical modelling of high temperature magnetized astrophysical plasmas is the anisotropic transport of heat along magnetic field lines from higher to lower temperatures. Magnetohydrodynamics typically involves solving the hyperbolic set of conservation equations along with the induction equation. Incorporating anisotropic thermal conduction requires to also treat parabolic terms arising from the diffusion operator. An explicit treatment of parabolic terms will considerably reduce the simulation time step due to its dependence on the square of the grid resolution (Δx) for stability. Although an implicit scheme relaxes the constraint on stability, it is difficult to distribute efficiently on a parallel architecture. Treating parabolic terms with accelerated super-time-stepping (STS) methods has been discussed in literature, but these methods suffer from poor accuracy (first order in time) and also have difficult-to-choose tuneable stability parameters. In this work, we highlight a second-order (in time) Runge-Kutta-Legendre (RKL) scheme (first described by Meyer, Balsara & Aslam 2012) that is robust, fast and accurate in treating parabolic terms alongside the hyperbolic conversation laws. We demonstrate its superiority over the first-order STS schemes with standard tests and astrophysical applications. We also show that explicit conduction is particularly robust in handling saturated thermal conduction. Parallel scaling of explicit conduction using RKL scheme is demonstrated up to more than 104 processors.

A 3D nodal mixed dual method for nuclear reactor kinetics with improved quasistatic model and a semi-implicit scheme to solve the precursor equations

International Nuclear Information System (INIS)

Dahmani, M.; Baudron, A.M.; Lautard, J.J.; Erradi, L.

2001-01-01

The mixed dual nodal method MINOS is used to solve the reactor kinetics equations with improved quasistatic IQS model and the θ method is used to solve the precursor equations. The speed of calculation which is the main advantage of the MINOS method and the possibility to use the large time step for shape flux calculation permitted by the IQS method, allow us to reduce considerably the computing time. The IQS/MINOS method is implemented in CRONOS 3D reactor code. Numerical tests on different transient benchmarks show that the results obtained with the IQS/MINOS method and the direct numerical method used to solve the kinetics equations, are very close and the total computing time is largely reduced

Binary nucleation kinetics. III. Transient behavior and time lags

International Nuclear Information System (INIS)

Wyslouzil, B.E.; Wilemski, G.

1996-01-01

Transient binary nucleation is more complex than unary because of the bidimensionality of the cluster formation kinetics. To investigate this problem qualitatively and quantitatively, we numerically solved the birth-death equations for vapor-to-liquid phase transitions. Our previous work showed that the customary saddle point and growth path approximations are almost always valid in steady state gas phase nucleation and only fail if the nucleated solution phase is significantly nonideal. Now, we demonstrate that in its early transient stages, binary nucleation rarely, if ever, occurs via the saddle point. This affects not only the number of particles forming but their composition and may be important for nucleation in glasses and other condensed mixtures for which time scales are very long. Before reaching the state of saddle point nucleation, most binary systems pass through a temporary stage in which the region of maximum flux extends over a ridge on the free energy surface. When ridge crossing nucleation is the steady state solution, it thus arises quite naturally as an arrested intermediate state that normally occurs in the development of saddle point nucleation. While the time dependent and steady state distributions of the fluxes and concentrations for each binary system are strongly influenced by the gas composition and species impingement rates, the ratio of nonequilibrium to equilibrium concentrations has a quasiuniversal behavior that is determined primarily by the thermodynamic properties of the liquid mixture. To test our quantitive results of the transient behavior, we directly calculated the time lag for the saddle point flux and compared it with the available analytical predictions. Although the analytical results overestimate the time lag by factors of 1.2-5, they should be adequate for purposes of planning experiments. We also found that the behavior of the saddle point time lag can indicate when steady state ridge crossing nucleation will occur

Microsoft Office professional 2010 step by step

CERN Document Server

Cox, Joyce; Frye, Curtis

2011-01-01

Teach yourself exactly what you need to know about using Office Professional 2010-one step at a time! With STEP BY STEP, you build and practice new skills hands-on, at your own pace. Covering Microsoft Word, PowerPoint, Outlook, Excel, Access, Publisher, and OneNote, this book will help you learn the core features and capabilities needed to: Create attractive documents, publications, and spreadsheetsManage your e-mail, calendar, meetings, and communicationsPut your business data to workDevelop and deliver great presentationsOrganize your ideas and notes in one placeConnect, share, and accom

The enhancement of time-stepping procedures in SYVAC A/C

International Nuclear Information System (INIS)

Broyd, T.W.

1986-01-01

This report summarises the work carried out an SYVAC A/C between February and May 1985 aimed at improving the way in which time-stepping procedures are handled. The majority of the work was concerned with three types of problem, viz: i) Long vault release, short geosphere response ii) Short vault release, long geosphere response iii) Short vault release, short geosphere response The report contains details of changes to the logic and structure of SYVAC A/C, as well as the results of code implementation tests. It has been written primarily for members of the UK SYVAC development team, and should not be used or referred to in isolation. (author)

Performance of an attention-demanding task during treadmill walking shifts the noise qualities of step-to-step variation in step width.

Science.gov (United States)

Grabiner, Mark D; Marone, Jane R; Wyatt, Marilynn; Sessoms, Pinata; Kaufman, Kenton R

2018-06-01

The fractal scaling evident in the step-to-step fluctuations of stepping-related time series reflects, to some degree, neuromotor noise. The primary purpose of this study was to determine the extent to which the fractal scaling of step width, step width and step width variability are affected by performance of an attention-demanding task. We hypothesized that the attention-demanding task would shift the structure of the step width time series toward white, uncorrelated noise. Subjects performed two 10-min treadmill walking trials, a control trial of undisturbed walking and a trial during which they performed a mental arithmetic/texting task. Motion capture data was converted to step width time series, the fractal scaling of which were determined from their power spectra. Fractal scaling decreased by 22% during the texting condition (p Step width and step width variability increased 19% and five percent, respectively (p step width fractal scaling. The change of the fractal scaling of step width is consistent with increased cognitive demand and suggests a transition in the characteristics of the signal noise. This may reflect an important advance toward the understanding of the manner in which neuromotor noise contributes to some types of falls. However, further investigation of the repeatability of the results, the sensitivity of the results to progressive increases in cognitive load imposed by attention-demanding tasks, and the extent to which the results can be generalized to the gait of older adults seems warranted. Copyright © 2018 Elsevier B.V. All rights reserved.

Discrete maximal regularity of time-stepping schemes for fractional evolution equations.

Science.gov (United States)

Jin, Bangti; Li, Buyang; Zhou, Zhi

2018-01-01

In this work, we establish the maximal [Formula: see text]-regularity for several time stepping schemes for a fractional evolution model, which involves a fractional derivative of order [Formula: see text], [Formula: see text], in time. These schemes include convolution quadratures generated by backward Euler method and second-order backward difference formula, the L1 scheme, explicit Euler method and a fractional variant of the Crank-Nicolson method. The main tools for the analysis include operator-valued Fourier multiplier theorem due to Weis (Math Ann 319:735-758, 2001. doi:10.1007/PL00004457) and its discrete analogue due to Blunck (Stud Math 146:157-176, 2001. doi:10.4064/sm146-2-3). These results generalize the corresponding results for parabolic problems.

Comparison of step-by-step kinematics of resisted, assisted and unloaded 20-m sprint runs.

Science.gov (United States)

van den Tillaar, Roland; Gamble, Paul

2018-03-26

This investigation examined step-by-step kinematics of sprint running acceleration. Using a randomised counterbalanced approach, 37 female team handball players (age 17.8 ± 1.6 years, body mass 69.6 ± 9.1 kg, height 1.74 ± 0.06 m) performed resisted, assisted and unloaded 20-m sprints within a single session. 20-m sprint times and step velocity, as well as step length, step frequency, contact and flight times of each step were evaluated for each condition with a laser gun and an infrared mat. Almost all measured parameters were altered for each step under the resisted and assisted sprint conditions (η 2  ≥ 0.28). The exception was step frequency, which did not differ between assisted and normal sprints. Contact time, flight time and step frequency at almost each step were different between 'fast' vs. 'slow' sub-groups (η 2  ≥ 0.22). Nevertheless overall both groups responded similarly to the respective sprint conditions. No significant differences in step length were observed between groups for the respective condition. It is possible that continued exposure to assisted sprinting might allow the female team-sports players studied to adapt their coordination to the 'over-speed' condition and increase step frequency. It is notable that step-by-step kinematics in these sprints were easy to obtain using relatively inexpensive equipment with possibilities of direct feedback.

Aspartate beta-decarboxylase from Alcaligenes faecalis: carbon-13 kinetic isotope effect and deuterium exchange experiments

International Nuclear Information System (INIS)

Rosenberg, R.M.; O'Leary, M.H.

1985-01-01

The authors have measured the 13 C kinetic isotope effect at pH 4.0, 5.0, 6.0, and 6.5 and in D 2 O at pH 5.0 and the rate of D-H exchange of the alpha and beta protons of aspartic acid in D 2 O at pH 5.0 for the reaction catalyzed by the enzyme aspartate beta-decarboxylase from Alcaligenes faecalis. The 13 C kinetic isotope effect, with a value of 1.0099 +/- 0.0002 at pH 5.0, is less than the intrinsic isotope effect for the decarboxylation step, indicating that the decarboxylation step is not entirely rate limiting. The authors have been able to estimate probable values of the relative free energies of the transition states of the enzymatic reaction up to and including the decarboxylation step from the 13 C kinetic isotope effect and the rate of D-H exchange of alpha-H. The pH dependence of the kinetic isotope effect reflects the pKa of the pyridine nitrogen of the coenzyme pyridoxal 5'-phosphate but not that of the imine nitrogen. A mechanism is proposed for the exchange of aspartate beta-H that is consistent with the stereochemistry suggested earlier

Control of DNA strand displacement kinetics using toehold exchange.

Science.gov (United States)

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.

Sinusoidal voltage protocols for rapid characterisation of ion channel kinetics.

Science.gov (United States)

Beattie, Kylie A; Hill, Adam P; Bardenet, Rémi; Cui, Yi; Vandenberg, Jamie I; Gavaghan, David J; de Boer, Teun P; Mirams, Gary R

2018-03-24

Ion current kinetics are commonly represented by current-voltage relationships, time constant-voltage relationships and subsequently mathematical models fitted to these. These experiments take substantial time, which means they are rarely performed in the same cell. Rather than traditional square-wave voltage clamps, we fitted a model to the current evoked by a novel sum-of-sinusoids voltage clamp that was only 8 s long. Short protocols that can be performed multiple times within a single cell will offer many new opportunities to measure how ion current kinetics are affected by changing conditions. The new model predicts the current under traditional square-wave protocols well, with better predictions of underlying currents than literature models. The current under a novel physiologically relevant series of action potential clamps is predicted extremely well. The short sinusoidal protocols allow a model to be fully fitted to individual cells, allowing us to examine cell-cell variability in current kinetics for the first time. Understanding the roles of ion currents is crucial to predict the action of pharmaceuticals and mutations in different scenarios, and thereby to guide clinical interventions in the heart, brain and other electrophysiological systems. Our ability to predict how ion currents contribute to cellular electrophysiology is in turn critically dependent on our characterisation of ion channel kinetics - the voltage-dependent rates of transition between open, closed and inactivated channel states. We present a new method for rapidly exploring and characterising ion channel kinetics, applying it to the hERG potassium channel as an example, with the aim of generating a quantitatively predictive representation of the ion current. We fitted a mathematical model to currents evoked by a novel 8 second sinusoidal voltage clamp in CHO cells overexpressing hERG1a. The model was then used to predict over 5 minutes of recordings in the same cell in response to

A one-step, real-time PCR assay for rapid detection of rhinovirus.

Science.gov (United States)

Do, Duc H; Laus, Stella; Leber, Amy; Marcon, Mario J; Jordan, Jeanne A; Martin, Judith M; Wadowsky, Robert M

2010-01-01

One-step, real-time PCR assays for rhinovirus have been developed for a limited number of PCR amplification platforms and chemistries, and some exhibit cross-reactivity with genetically similar enteroviruses. We developed a one-step, real-time PCR assay for rhinovirus by using a sequence detection system (Applied Biosystems; Foster City, CA). The primers were designed to amplify a 120-base target in the noncoding region of picornavirus RNA, and a TaqMan (Applied Biosystems) degenerate probe was designed for the specific detection of rhinovirus amplicons. The PCR assay had no cross-reactivity with a panel of 76 nontarget nucleic acids, which included RNAs from 43 enterovirus strains. Excellent lower limits of detection relative to viral culture were observed for the PCR assay by using 38 of 40 rhinovirus reference strains representing different serotypes, which could reproducibly detect rhinovirus serotype 2 in viral transport medium containing 10 to 10,000 TCID(50) (50% tissue culture infectious dose endpoint) units/ml of the virus. However, for rhinovirus serotypes 59 and 69, the PCR assay was less sensitive than culture. Testing of 48 clinical specimens from children with cold-like illnesses for rhinovirus by the PCR and culture assays yielded detection rates of 16.7% and 6.3%, respectively. For a batch of 10 specimens, the entire assay was completed in 4.5 hours. This real-time PCR assay enables detection of many rhinovirus serotypes with the Applied Biosystems reagent-instrument platform.

A third-order gas-kinetic CPR method for the Euler and Navier-Stokes equations on triangular meshes

Science.gov (United States)

Zhang, Chao; Li, Qibing; Fu, Song; Wang, Z. J.

2018-06-01

A third-order accurate gas-kinetic scheme based on the correction procedure via reconstruction (CPR) framework is developed for the Euler and Navier-Stokes equations on triangular meshes. The scheme combines the accuracy and efficiency of the CPR formulation with the multidimensional characteristics and robustness of the gas-kinetic flux solver. Comparing with high-order finite volume gas-kinetic methods, the current scheme is more compact and efficient by avoiding wide stencils on unstructured meshes. Unlike the traditional CPR method where the inviscid and viscous terms are treated differently, the inviscid and viscous fluxes in the current scheme are coupled and computed uniformly through the kinetic evolution model. In addition, the present scheme adopts a fully coupled spatial and temporal gas distribution function for the flux evaluation, achieving high-order accuracy in both space and time within a single step. Numerical tests with a wide range of flow problems, from nearly incompressible to supersonic flows with strong shocks, for both inviscid and viscous problems, demonstrate the high accuracy and efficiency of the present scheme.

Issues in measure-preserving three dimensional flow integrators: Self-adjointness, reversibility, and non-uniform time stepping

International Nuclear Information System (INIS)

Finn, John M.

2015-01-01

Properties of integration schemes for solenoidal fields in three dimensions are studied, with a focus on integrating magnetic field lines in a plasma using adaptive time stepping. It is shown that implicit midpoint (IM) and a scheme we call three-dimensional leapfrog (LF) can do a good job (in the sense of preserving KAM tori) of integrating fields that are reversible, or (for LF) have a “special divergence-free” (SDF) property. We review the notion of a self-adjoint scheme, showing that such schemes are at least second order accurate and can always be formed by composing an arbitrary scheme with its adjoint. We also review the concept of reversibility, showing that a reversible but not exactly volume-preserving scheme can lead to a fractal invariant measure in a chaotic region, although this property may not often be observable. We also show numerical results indicating that the IM and LF schemes can fail to preserve KAM tori when the reversibility property (and the SDF property for LF) of the field is broken. We discuss extensions to measure preserving flows, the integration of magnetic field lines in a plasma and the integration of rays for several plasma waves. The main new result of this paper relates to non-uniform time stepping for volume-preserving flows. We investigate two potential schemes, both based on the general method of Feng and Shang [Numer. Math. 71, 451 (1995)], in which the flow is integrated in split time steps, each Hamiltonian in two dimensions. The first scheme is an extension of the method of extended phase space, a well-proven method of symplectic integration with non-uniform time steps. This method is found not to work, and an explanation is given. The second method investigated is a method based on transformation to canonical variables for the two split-step Hamiltonian systems. This method, which is related to the method of non-canonical generating functions of Richardson and Finn [Plasma Phys. Controlled Fusion 54, 014004 (2012

Drug-Target Kinetics in Drug Discovery.

Science.gov (United States)

Tonge, Peter J

2018-01-17

The development of therapies for the treatment of neurological cancer faces a number of major challenges including the synthesis of small molecule agents that can penetrate the blood-brain barrier (BBB). Given the likelihood that in many cases drug exposure will be lower in the CNS than in systemic circulation, it follows that strategies should be employed that can sustain target engagement at low drug concentration. Time dependent target occupancy is a function of both the drug and target concentration as well as the thermodynamic and kinetic parameters that describe the binding reaction coordinate, and sustained target occupancy can be achieved through structural modifications that increase target (re)binding and/or that decrease the rate of drug dissociation. The discovery and deployment of compounds with optimized kinetic effects requires information on the structure-kinetic relationships that modulate the kinetics of binding, and the molecular factors that control the translation of drug-target kinetics to time-dependent drug activity in the disease state. This Review first introduces the potential benefits of drug-target kinetics, such as the ability to delineate both thermodynamic and kinetic selectivity, and then describes factors, such as target vulnerability, that impact the utility of kinetic selectivity. The Review concludes with a description of a mechanistic PK/PD model that integrates drug-target kinetics into predictions of drug activity.

Stopped-flow kinetic studies of poly(amidoamine) dendrimer-calf thymus DNA to form dendriplexes.

Science.gov (United States)

Dey, Debabrata; Kumar, Santosh; Maiti, Souvik; Dhara, Dibakar

2013-11-07

Poly(amidoamine) (PAMAM) dendrimers are known to be highly efficient nonviral carriers in gene delivery. Dendrimer-mediated transfection is known to be a function of the dendrimer to DNA charge ratio as well as the size of the dendrimer. In the present study, the binding kinetics of four PAMAM dendrimers (G1, G2, G3, and G4) with calf thymus DNA (CT-DNA) has been studied using stopped-flow fluorescence spectroscopy. The effect of dendrimer-to-DNA charge ratio and dendrimer generation on the binding kinetics was investigated. In most cases, the results of dendrimer-CT-DNA binding can be explained by a two-step reaction mechanism: a rapid electrostatic binding between the dendrimer and DNA, followed by a conformational change of the dendrimer-DNA complex that ultimately leads to DNA condensation. It was observed that the charge ratio on the dendrimer and the DNA phosphate groups, as well as the dendrimer generation (size), has a marked effect on the kinetics of binding between the DNA and the dendrimers. The rate constant (k'1) of the first step was much higher compared to that of the second step (k'2), and both were found to increase with an increase in dendrimer concentration. Among the four generations of dendrimers, G4 exhibited significantly faster binding kinetics compared to the three smaller generation dendrimers.

Kinetics of oxygen adsorption on ZnS nanoparticles synthesized by precipitation process

Directory of Open Access Journals (Sweden)

Ahmadi Reza

2016-06-01

Full Text Available ZnS nanoparticles were synthesized through a one-step precipitation process. Effect of time and temperature on the formation reaction was investigated. The synthesized samples were characterized by X-ray diffraction (XRD, ultraviolet (UV visible absorption and photoluminescence (PL spectrophotometry. Based on XRD and UV-Vis data, the particles produced at 70 °C had a mean particle size of about 5 nm. Increasing time and temperature of the synthesis reaction resulted in photoluminescence intensification. PL spectroscopy helped understanding the adsorption kinetics of oxygen on ZnS nanoparticles during the precipitation synthesis process. Fabrication of ZnS structures with appropriate oxygen adsorption capacity was suggested as a means of PL emission intensity control.

A step-defined sedentary lifestyle index: <5000 steps/day.

Science.gov (United States)

Tudor-Locke, Catrine; Craig, Cora L; Thyfault, John P; Spence, John C

2013-02-01

Step counting (using pedometers or accelerometers) is widely accepted by researchers, practitioners, and the general public. Given the mounting evidence of the link between low steps/day and time spent in sedentary behaviours, how few steps/day some populations actually perform, and the growing interest in the potentially deleterious effects of excessive sedentary behaviours on health, an emerging question is "How many steps/day are too few?" This review examines the utility, appropriateness, and limitations of using a reoccurring candidate for a step-defined sedentary lifestyle index: 10 000) to lower (sedentary lifestyle index for adults is appropriate for researchers and practitioners and for communicating with the general public. There is little evidence to advocate any specific value indicative of a step-defined sedentary lifestyle index in children and adolescents.

Time-dependent cell disintegration kinetics in lung tumors after irradiation

International Nuclear Information System (INIS)

Chvetsov, Alexei V; Palta, Jatinder J; Nagata, Yasushi

2008-01-01

We study the time-dependent disintegration kinetics of tumor cells that did not survive radiotherapy treatment. To evaluate the cell disintegration rate after irradiation, we studied the volume changes of solitary lung tumors after stereotactic radiotherapy. The analysis is performed using two approximations: (1) tumor volume is a linear function of the total cell number in the tumor and (2) the cell disintegration rate is governed by the exponential decay with constant risk, which is defined by the initial cell number and a half-life T 1/2 . The half-life T 1/2 is determined using the least-squares fit to the clinical data on lung tumor size variation with time after stereotactic radiotherapy. We show that the tumor volume variation after stereotactic radiotherapy of solitary lung tumors can be approximated by an exponential function. A small constant component in the volume variation does not change with time; however, this component may be the residual irregular density due to radiation fibrosis and was, therefore, subtracted from the total volume variation in our computations. Using computerized fitting of the exponent function to the clinical data for selected patients, we have determined that the average half-life T 1/2 of cell disintegration is 28.2 days for squamous cell carcinoma and 72.4 days for adenocarcinoma. This model is needed for simulating the tumor volume variation during radiotherapy, which may be important for time-dependent treatment planning of proton therapy that is sensitive to density variations

Visualization and quantification of four steps in magnetic field induced two-dimensional ordering of superparamagnetic submicron particles

DEFF Research Database (Denmark)

Gajula, Gnana Prakash; Neves Petersen, Teresa; Petersen, Steffen B.

2010-01-01

, resolved growth steps (condensation, polarization, co-linearity and concatenation), the average chain growth rate, and inter-particle interaction length were calculated in the presence of a 120 G external magnetic field using optical microscopy and ‘in-house' developed image analysis software......We hereby report a methodology that permits a quantitative investigation of the temporal self-organization of superparamagnetic nanoparticles in the presence of an external magnetic field. The kinetics of field-induced self-organization into linear chains, time-dependent chain-size distribution...

Kinetics with deactivation of methylcyclohexane dehydrogenation for hydrogen energy storage

Energy Technology Data Exchange (ETDEWEB)

Maria, G; Marin, A; Wyss, C; Mueller, S; Newson, E [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

1997-06-01

The methylcyclohexane dehydrogenation step to recycle toluene and release hydrogen is being studied as part of a hydrogen energy storage project. The reaction is performed catalytically in a fixed bed reactor, and the efficiency of this step significantly determines overall system economics. The fresh catalyst kinetics and the deactivation of the catalyst by coke play an important role in the process analysis. The main reaction kinetics were determined from isothermal experiments using a parameter sensitivity analysis for model discrimination. An activation energy for the main reaction of 220{+-}11 kJ/mol was obtained from a two-parameter model. From non-isothermal deactivation in PC-controlled integral reactors, an activation energy for deactivation of 160 kJ/mol was estimated. A model for catalyst coke content of 3-17 weight% was compared with experimental data. (author) 3 figs., 6 refs.

Understanding the Broad Substrate Repertoire of Nitroreductase Based on Its Kinetic Mechanism*

Science.gov (United States)

Pitsawong, Warintra; Hoben, John P.; Miller, Anne-Frances

2014-01-01

The oxygen-insensitive nitroreductase from Enterobacter cloacae (NR) catalyzes two-electron reduction of nitroaromatics to the corresponding nitroso compounds and, subsequently, to hydroxylamine products. NR has an unusually broad substrate repertoire, which may be related to protein dynamics (flexibility) and/or a simple non-selective kinetic mechanism. To investigate the possible role of mechanism in the broad substrate repertoire of NR, the kinetics of oxidation of NR by para-nitrobenzoic acid (p-NBA) were investigated using stopped-flow techniques at 4 °C. The results revealed a hyperbolic dependence on the p-NBA concentration with a limiting rate of 1.90 ± 0.09 s−1, indicating one-step binding before the flavin oxidation step. There is no evidence for a distinct binding step in which specificity might be enforced. The reduction of p-NBA is rate-limiting in steady-state turnover (1.7 ± 0.3 s−1). The pre-steady-state reduction kinetics of NR by NADH indicate that NADH reduces the enzyme with a rate constant of 700 ± 20 s−1 and a dissociation constant of 0.51 ± 0.04 mm. Thus, we demonstrate simple transient kinetics in both the reductive and oxidative half-reactions that help to explain the broad substrate repertoire of NR. Finally, we tested the ability of NR to reduce para-hydroxylaminobenzoic acid, demonstrating that the corresponding amine does not accumulate to significant levels even under anaerobic conditions. Thus E. cloacae NR is not a good candidate for enzymatic production of aromatic amines. PMID:24706760

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

Science.gov (United States)

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.

Kinetic studies of uranyl ion adsorption on acrylonitrile (AN)/polyethylene glycol (PEG) interpenetrating networks (IPN)

International Nuclear Information System (INIS)

Aycik, G.A.; Gurellier, R.

2004-01-01

Full text: The kinetics of the adsorption of uranyl ions on amidoximated acrylonitrile (AN)/ polyethylene glycol (PEG) interpenetrating network (IPNs) from aqueous solutions was studied as a function of time and temperature. The IPNs were prepared by irradiation initiated gamma polymerisation using Co-60 gamma source. Adsorption capacities were performed for definite uranyl ion concentrations of 1x10 -2 M and at four different temperatures as 290K, 298K, 308K and 318K by gamma spectrometer. Adsorption time was increased from zero to 48 hours. The results indicate that adsorption capacity increases linearly with increasing temperature. Temperature and agitation hardly influence equilibrium and kinetics and decreasing of temperature results in a slightly greater time to reach equilibrium. The adsorption of uranyl ions has been studied in a multi step mechanism processes thus comparing chemical sorption and diffusion sorption processes. The experimental data was analysed using various kinetic models to determine the best-fit equation for the adsorption mechanisms. However, it was shown that all models, in general according to the reaction time and uranyl ion concentration in the solution, could describe the adsorption of uranyl ion onto amidoximated IPN, the adsorption kinetics was best described by zeroth order and intraparticle diffusion model whereas that of in increasing time by pseudo first and pseudo second order response respectively. External-intraparticle diffusion and zeroth order process in the IPN structure is proposed as a mass transfer mechanism and the results indicate a diffusion-controlled process. The Mean Activation Energy Of Uranyl Ions Adsorption Was Found As 4,1 Kj/Mole By Using Arrhenius Equation. The Rate Constant, The Equilibrium Adsorption Capacity And The Initial Adsorption Rate Were Calculated For All Models At Each Temperature. Kinetic Parameters Of All Models And The Normalized Standard Deviations Between The Measured And Predicted

Time-Dependent Effect of Refrigeration on Viscosity and Conversion Kinetics of Dental Adhesive Resins

Science.gov (United States)

Faria-e-Silva, André L; Piva, Evandro; Moraes, Rafael R

2010-01-01

Objectives: This study evaluated the effect of refrigeration at 4°C and post-refrigeration times (immediate, 5, 10, 15, or 20 min) on the viscosity and conversion kinetics of adhesive bonding resins. Methods: Scotchbond Dual-Cure (3M ESPE) and Clearfil SE Bond (Kuraray) were tested. Control samples were kept at 25°C for 24 h. At each post-refrigeration time, the temperature was checked with a K-type thermocouple. Viscosity measurements as a function of temperature were performed using a cone-plate viscometer. Real-time polymerization was monitored by infrared spectroscopy. Degree of conversion (DC) was calculated for each second during polymerization, and the rate of polymerization analyzed. Data were separately submitted to two-way ANOVA and Tukey’s test (P<.05). Results: Clearfil presented faster increase in temperature after exposure to room temperature than Scotchbond. A continuous decrease in viscosity (Pa.s) was observed for both Scotchbond (0.49, 0.34, 0.30, 0.26, 0.23, 0.23) and Clearfil (0.38, 0.37, 0.34, 0.25, 0.24, 0.22). For Scotchbond, higher final DC was detected for the control (62.7%) compared with the immediate (53.3%) and 5 min (54.7%) groups. For Clearfil, the control sample (81.4%) showed higher DC than all refrigerated groups (68.8–69.5%). Clearfil always showed significantly higher DC than Scotchbond. Conclusions: Refrigeration presented a significant time- and material-dependent effect on the viscosity and polymerization kinetics of the bonding resins. Under clinical conditions, adhesive agents should be removed from the refrigerator at least 20 min before being used. PMID:20396445

Comparison of step-by-step kinematics in repeated 30m sprints in female soccer players.

Science.gov (United States)

van den Tillaar, Roland

2018-01-04

The aim of this study was to compare kinematics in repeated 30m sprints in female soccer players. Seventeen subjects performed seven 30m sprints every 30s in one session. Kinematics were measured with an infrared contact mat and laser gun, and running times with an electronic timing device. The main findings were that sprint times increased in the repeated sprint ability test. The main changes in kinematics during the repeated sprint ability test were increased contact time and decreased step frequency, while no change in step length was observed. The step velocity increased in almost each step until the 14, which occurred around 22m. After this, the velocity was stable until the last step, when it decreased. This increase in step velocity was mainly caused by the increased step length and decreased contact times. It was concluded that the fatigue induced in repeated 30m sprints in female soccer players resulted in decreased step frequency and increased contact time. Employing this approach in combination with a laser gun and infrared mat for 30m makes it very easy to analyse running kinematics in repeated sprints in training. This extra information gives the athlete, coach and sports scientist the opportunity to give more detailed feedback and help to target these changes in kinematics better to enhance repeated sprint performance.

Deviation from the kinetic law of mass action for reactions induced by binary encounters in liquid solutions

International Nuclear Information System (INIS)

Doktorov, Alexander B; Kipriyanov, Alexey A

2007-01-01

In considering the irreversible chemical reaction A+B→ C+B in liquid solutions two many-particle approaches to the derivation of binary non-Markovian kinetic equations are compared: simple superposition decoupling and a method of extracting 'pair' channels from three-particle correlation evolution. It is shown that both methods provide an almost identical description of this reaction. However, in studies of reversible reactions in liquid solutions only the channel extraction method gives a correct physically clear description of the reaction though it consists of a sequence of steps: the development of integral encounter theory (IET), effective pairs approximation (EPA), modified encounter theory (MET), and the final regular form (RF) of kinetic equations. It is shown that the rate equations often encountered in the literature correspond to the independence of transient channels of 'scattering' in the bimolecular reversible reaction (A+B -B), while the independent transient channel of 'decay' in the reversible reactionA+B -C is defined solely by time integral convolution. In the general case transient channels in non-Markovian theory are not independent, and their interference manifests itself as a non-Markovian inhomogeneous source in binary non-Markovian kinetic equations in regular form. Based on the derived equations new universal kinetics (independent of models) of chemical equilibrium attainment have been obtained. It is shown that these kinetics can differ essentially from the kinetics corresponding to the kinetic law of mass action of formal chemical kinetics

Traffic safety and step-by-step driving licence for young people

DEFF Research Database (Denmark)

Tønning, Charlotte; Agerholm, Niels

2017-01-01

presents a review of safety effects from step-by-step driving licence schemes. Most of the investigated schemes consist of a step-by-step driving licence with Step 1) various tests and education, Step 2) a period where driving is only allowed together with an experienced driver and Step 3) driving without...... companion is allowed but with various restrictions and, in some cases, additional driving education and tests. In general, a step-by-step driving licence improves traffic safety even though the young people are permitted to drive a car earlier on. The effects from driving with an experienced driver vary......Young novice car drivers are much more accident-prone than other drivers - up to 10 times that of their parents' generation. A central solution to improve the traffic safety for this group is implementation of a step-by-step driving licence. A number of countries have introduced a step...

Application of Detailed Chemical Kinetics to Combustion Instability Modeling

Science.gov (United States)

2016-01-04

Clearance Number 15692 Clearance Date 12/3/2015 14. ABSTRACT A comparison of a single step global reaction and the detailed GRI -Mech 1.2 for combustion...comparison of a single step global reaction and the detailed GRI -Mech 1.2 for com- bustion instability modeling in a methane-fueled longitudinal-mode...methane as the fuel. We use the GRI -Mech 1.2 kinetics mechanism for methane oxidation.11 The GRI -Mech 1.2 was chosen over 2.11 because the only

Fast and calibration free determination of first order reaction kinetics in API synthesis using in-situ ATR-FTIR.

Science.gov (United States)

Rehbein, Moritz C; Husmann, Sascha; Lechner, Christian; Kunick, Conrad; Scholl, Stephan

2018-05-01

In early stages of drug development only sparse amounts of the key substances are available, which is problematic for the determination of important process data like reaction kinetics. Therefore, it is important to perform experiments as economically as possible, especially in regards to limiting compounds. Here we demonstrate the use of a temperature step experiment enabling the determination of complete reaction kinetics in a single non-isothermal experiment. In contrast to the traditionally used HPLC, the method takes advantage of the high measuring rate and the low amount of labor involved in using in-situ ATR-FTIR to determine time-dependent concentration-equivalent data. Copyright © 2017 Elsevier B.V. All rights reserved.

New approaches for the reliable in vitro assessment of binding affinity based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics.

Science.gov (United States)

Zeilinger, Markus; Pichler, Florian; Nics, Lukas; Wadsak, Wolfgang; Spreitzer, Helmut; Hacker, Marcus; Mitterhauser, Markus

2017-12-01

Resolving the kinetic mechanisms of biomolecular interactions have become increasingly important in early-phase drug development. Since traditional in vitro methods belong to dose-dependent assessments, binding kinetics is usually overlooked. The present study aimed at the establishment of two novel experimental approaches for the assessment of binding affinity of both, radiolabelled and non-labelled compounds targeting the A 3 R, based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics. A novel time-resolved competition assay was developed and applied to determine the K i of eight different A 3 R antagonists, using CHO-K1 cells stably expressing the hA 3 R. In addition, a new kinetic real-time cell-binding approach was established to quantify the rate constants k on and k off , as well as the dedicated K d of the A 3 R agonist [ 125 I]-AB-MECA. Furthermore, lipophilicity measurements were conducted to control influences due to physicochemical properties of the used compounds. Two novel real-time cell-binding approaches were successfully developed and established. Both experimental procedures were found to visualize the kinetic binding characteristics with high spatial and temporal resolution, resulting in reliable affinity values, which are in good agreement with values previously reported with traditional methods. Taking into account the lipophilicity of the A 3 R antagonists, no influences on the experimental performance and the resulting affinity were investigated. Both kinetic binding approaches comprise tracer administration and subsequent binding to living cells, expressing the dedicated target protein. Therefore, the experiments resemble better the true in vivo physiological conditions and provide important markers of cellular feedback and biological response.

The oxidation kinetics and the structure of the oxide film on Zircaloy before and after the kinetic transition

International Nuclear Information System (INIS)

Arima, T.; Masuzumi, T.; Furuya, H.; Idemitsu, K.; Inagaki, Y.

2001-01-01

Oxidation kinetics of Zircaloy-4 have been measured using a micro-balance technique in CO-CO 2 gas mixtures between 450 deg. C and 600 deg. C. Oxidation kinetics of Zircaloy-4 obeyed a cubic rate law with time at 450-600 deg. C up to 24 h. At 600 deg. C, the kinetic transition occurred after about 36 h. After the transition, oxidation kinetics obeyed a linear rate law. X-ray diffraction patterns for the samples oxidized at 600 deg. C showed that the volume fraction of tetragonal phase of zirconia decreased with time until the kinetic transition occurred and was almost constant after that. In addition, stresses in the oxide films were found to be larger for the pre-transition samples than for the post-transition ones. (authors)

Kinetics Study of Silver Electrocrystallization on (3-mercaptopropyl)trimethoxysilane-grafted Indium Tin Oxide Plastic Substrate

International Nuclear Information System (INIS)

Hau, Nga Yu; Chang, Ya-Huei; Feng, Shien-Ping

2015-01-01

Highlights: • The larger charge transfer coefficient supports that MPS promotes electrodeposition. • ACV shows that electron-transfer rate enhanced by 2.5 times after MPS treatment. • The fitting of CA defined the Ag nucleation mode on blank and MPS-grafted ITO-PEN. • MPS treatment changed the nucleation mode from 2-step to a single step one. - Abstract: 3-mercaptopropyl-trimethoxysilane (MPS) self-assembled monolayer (SAM) has been demonstrated as effective promoters to enable direct electroplated metallization on indium tin oxide (ITO) plastic substrate. In this paper, the detail kinetics in Ag electrocrystallization on MPS-grafted ITO-PEN is reported. Contact angle measurement provides evidence of bridging-link effect between the sulfur head groups of MPS and the Ag + ions in the electrolyte. Electrochemical techniques including cyclic voltammetry and Tafel plot were used to investigate the redox kinetics. Quantitative evaluation was conducted by alternating current voltammetry to determine the rate constant of electron transfer. The chronoamperograms and their fitting results suggest a combined model with two-dimensional/three-dimensional nucleation transition and Shariker-Hills model for electroplated Ag on blank ITO-PEN and MPS-grafted ITO-PEN respectively

Formalization of the kinetics for autocatalytic dissolutions. Focus on the dissolution of uranium dioxide in nitric medium

International Nuclear Information System (INIS)

Charlier, F.; Canion, D.; Gravinese, A.; Magnaldo, A.; Lalleman, S.; Borda, G.; Schaer, E.

2017-01-01

Uranium dioxide dissolution in nitric acid is a complex reaction. On the one hand, the dissolution produces nitrous oxides (NOX), which makes it a triphasic reaction. On the other hand, one of the products accelerates the kinetic rate; the reaction is hence called autocatalytic.The kinetics for these kinds of reactions need to be formalized in order to optimize and design innovative dissolution reactors. In this work, the kinetics rates have been measured by optical microscopy using a single particle approach. The advantages of this analytical technique are an easier management of species transport in solution and a precise following of the dissolution rate. The global rate is well described by a mechanism considering two steps: a non-catalyzed reaction, where the catalyst concentration has no influence on the dissolution rate, and a catalyzed reaction. The mass transfer rate of the catalyst was quantified in order to discriminate when the reaction was influenced by catalyst accumulated in the boundary layer or uncatalyzed. This first approximation described well the sigmoid dissolution curve profile. Moreover, experiments showed that solutions filled with catalyst proved to lose reactivity over time. Results pointed out that the higher the liquid-gas exchanges, the faster the kinetic rate decreases with time. Thus, it was demonstrated, for the first time, that there is a link between catalyst and nitrous oxides. The outcome of this study leads to new ways for improving the design of dissolvers. Gas-liquid exchanges are indeed a lever to impact dissolution rates. Temperature and catalyst concentration can be optimized to reduce residence times in dissolvers. (authors)

kinetic studies of colour and phenol removal from wastewater using

African Journals Online (AJOL)

user

Kinetic studies by batch technique were carried out using activated carbon prepared from mango seed ... and the rate controlling steps of sorption which ... as follows (Lagergren, 1898): … ... plot of t /qt against t of Equation (6) should give a.

Extended Kalman filter (EKF) application in vitamin C two-step fermentation process.

Science.gov (United States)

Wei, D; Yuan, W; Yuan, Z; Yin, G; Chen, M

1993-01-01

Based on kinetic model study of vitamin C two-step fermentation, the extended Kalman filter (EKF) theory is conducted for studying the process which is disturbed by white noise to some extent caused by the model, the fermentation system and operation fluctuation. EKF shows that calculated results from estimated process parameters agree with the experimental results considerably better than model prediction without using estimated parameters. Parameter analysis gives a better understanding of the kinetics and provides a basis for state estimation and state prediction.

Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems.

Science.gov (United States)

Sivak, David A; Chodera, John D; Crooks, Gavin E

2014-06-19

When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic equations of motion (e.g., Langevin dynamics), there is still broad disagreement over which integration algorithms are most appropriate. While multiple desiderata have been proposed throughout the literature, consensus on which criteria are important is absent, and no published integration scheme satisfies all desiderata simultaneously. Additional nontrivial complications stem from simulating systems driven out of equilibrium using existing stochastic integration schemes in conjunction with recently developed nonequilibrium fluctuation theorems. Here, we examine a family of discrete time integration schemes for Langevin dynamics, assessing how each member satisfies a variety of desiderata that have been enumerated in prior efforts to construct suitable Langevin integrators. We show that the incorporation of a novel time step rescaling in the deterministic updates of position and velocity can correct a number of dynamical defects in these integrators. Finally, we identify a particular splitting (related to the velocity Verlet discretization) that has essentially universally appropriate properties for the simulation of Langevin dynamics for molecular systems in equilibrium, nonequilibrium, and path sampling contexts.

Tracer kinetic model-driven registration for dynamic contrast-enhanced MRI time-series data.

Science.gov (United States)

Buonaccorsi, Giovanni A; O'Connor, James P B; Caunce, Angela; Roberts, Caleb; Cheung, Sue; Watson, Yvonne; Davies, Karen; Hope, Lynn; Jackson, Alan; Jayson, Gordon C; Parker, Geoffrey J M

2007-11-01

Dynamic contrast-enhanced MRI (DCE-MRI) time series data are subject to unavoidable physiological motion during acquisition (e.g., due to breathing) and this motion causes significant errors when fitting tracer kinetic models to the data, particularly with voxel-by-voxel fitting approaches. Motion correction is problematic, as contrast enhancement introduces new features into postcontrast images and conventional registration similarity measures cannot fully account for the increased image information content. A methodology is presented for tracer kinetic model-driven registration that addresses these problems by explicitly including a model of contrast enhancement in the registration process. The iterative registration procedure is focused on a tumor volume of interest (VOI), employing a three-dimensional (3D) translational transformation that follows only tumor motion. The implementation accurately removes motion corruption in a DCE-MRI software phantom and it is able to reduce model fitting errors and improve localization in 3D parameter maps in patient data sets that were selected for significant motion problems. Sufficient improvement was observed in the modeling results to salvage clinical trial DCE-MRI data sets that would otherwise have to be rejected due to motion corruption. Copyright 2007 Wiley-Liss, Inc.

Modelling of Sub-daily Hydrological Processes Using Daily Time-Step Models: A Distribution Function Approach to Temporal Scaling

Science.gov (United States)

Kandel, D. D.; Western, A. W.; Grayson, R. B.

2004-12-01

Mismatches in scale between the fundamental processes, the model and supporting data are a major limitation in hydrologic modelling. Surface runoff generation via infiltration excess and the process of soil erosion are fundamentally short time-scale phenomena and their average behaviour is mostly determined by the short time-scale peak intensities of rainfall. Ideally, these processes should be simulated using time-steps of the order of minutes to appropriately resolve the effect of rainfall intensity variations. However, sub-daily data support is often inadequate and the processes are usually simulated by calibrating daily (or even coarser) time-step models. Generally process descriptions are not modified but rather effective parameter values are used to account for the effect of temporal lumping, assuming that the effect of the scale mismatch can be counterbalanced by tuning the parameter values at the model time-step of interest. Often this results in parameter values that are difficult to interpret physically. A similar approach is often taken spatially. This is problematic as these processes generally operate or interact non-linearly. This indicates a need for better techniques to simulate sub-daily processes using daily time-step models while still using widely available daily information. A new method applicable to many rainfall-runoff-erosion models is presented. The method is based on temporal scaling using statistical distributions of rainfall intensity to represent sub-daily intensity variations in a daily time-step model. This allows the effect of short time-scale nonlinear processes to be captured while modelling at a daily time-step, which is often attractive due to the wide availability of daily forcing data. The approach relies on characterising the rainfall intensity variation within a day using a cumulative distribution function (cdf). This cdf is then modified by various linear and nonlinear processes typically represented in hydrological and

Early Events, Kinetic Intermediates and the Mechanism of Protein Folding in Cytochrome c

Directory of Open Access Journals (Sweden)

David S. Kliger

2009-04-01

Full Text Available Kinetic studies of the early events in cytochrome c folding are reviewed with a focus on the evidence for folding intermediates on the submillisecond timescale. Evidence from time-resolved absorption, circular dichroism, magnetic circular dichroism, fluorescence energy and electron transfer, small-angle X-ray scattering and amide hydrogen exchange studies on the t £ 1 ms timescale reveals a picture of cytochrome c folding that starts with the ~ 1-ms conformational diffusion dynamics of the unfolded chains. A fractional population of the unfolded chains collapses on the 1 – 100 ms timescale to a compact intermediate IC containing some native-like secondary structure. Although the existence and nature of IC as a discrete folding intermediate remains controversial, there is extensive high time-resolution kinetic evidence for the rapid formation of IC as a true intermediate, i.e., a metastable state separated from the unfolded state by a discrete free energy barrier. Final folding to the native state takes place on millisecond and longer timescales, depending on the presence of kinetic traps such as heme misligation and proline mis-isomerization. The high folding rates observed in equilibrium molten globule models suggest that IC may be a productive folding intermediate. Whether it is an obligatory step on the pathway to the high free energy barrier associated with millisecond timescale folding to the native state, however, remains to be determined.

Supercritical kinetic analysis in simplified system of fuel debris using integral kinetic model

International Nuclear Information System (INIS)

Tuya, Delgersaikhan; Obara, Toru

2016-01-01

Highlights: • Kinetic analysis in simplified weakly coupled fuel debris system was performed. • The integral kinetic model was used to simulate criticality accidents. • The fission power and released energy during simulated accident were obtained. • Coupling between debris regions and its effect on the fission power was obtained. - Abstract: Preliminary prompt supercritical kinetic analyses in a simplified coupled system of fuel debris designed to roughly resemble a melted core of a nuclear reactor were performed using an integral kinetic model. The integral kinetic model, which can describe region- and time-dependent fission rate in a coupled system of arbitrary geometry, was used because the fuel debris system is weakly coupled in terms of neutronics. The results revealed some important characteristics of coupled systems, such as the coupling between debris regions and the effect of the coupling on the fission rate and released energy in each debris region during the simulated criticality accident. In brief, this study showed that the integral kinetic model can be applied to supercritical kinetic analysis in fuel debris systems and also that it can be a useful tool for investigating the effect of the coupling on consequences of a supercritical accident.

Kinetic comparison of older men and women during walk-to-stair descent transition.

Science.gov (United States)

Singhal, Kunal; Kim, Jemin; Casebolt, Jeffrey; Lee, Sangwoo; Han, Ki Hoon; Kwon, Young-Hoo

2014-09-01

Stair walking is one of the most challenging tasks for older adults, with women reporting higher incidence of falls. The purpose of this study was to investigate the gender differences in kinetics during stair descent transition. Twenty-eight participants (12 male and 16 female; 68.5 and 69.0 years of mean age, respectively) performed stair descent from level walking in a step-over-step manner at a self-selected speed over a custom-made three-step staircase with embedded force plates. Kinematic and force data were combined using inverse dynamics to generate kinetic data for gender comparison. The top and the first step on the staircase were chosen for analysis. Women showed a higher trail leg peak hip abductor moment (-1.0 Nm/kg), lower trail leg peak knee extensor moment and eccentric power (0.74 Nm/kg and 3.15 W/kg), and lower peak concentric power at trail leg ankle joint (1.29 W/kg) as compared to men (ppredispose women to a higher risk of fall. Copyright © 2014 Elsevier B.V. All rights reserved.

Kinetics of thermal decomposition of γ-irradiated and unirradiated complexes of mandelhydroxamic acid

International Nuclear Information System (INIS)

Hassan, R.M.; Farid, T.; El-Bellihi, A.A.

1992-01-01

The thermal decomposition of γ-irradiated and unirradiated complexes of mandelhydroxamic acid (HMA), Co (HMA) 2 .1/2H 2 O, Mn (HMA) 2 .2H 2 O, Ba (HMA) 2 .2H 2 O and Cd (HMA) 2 .2H 2 O have been studied thermogravimetrically (under isothermal conditions). The thermal dehydration of each complex occured in one step, while the decomposition of dehydrated complexes occured in two steps. The kinetic parameters for dehydration were computed by different models. The thermal dehydration is regulated by random nucleation A 3 for Co-, Mn-, and Cd-complexes and by phase-boundary (R 3 ) for Ba-complex. The effect of γ-irradiation on the kinetic parameters of thermal decomposition is discussed. Radiation did not modify the mechanism of the reaction but accelarated the dehydration steps in the case of Mn- and Co-complexes. (author) 7 refs.; 1 fig.; 4 tabs

Coupling Chemical Kinetics and Flashes in Reactive, Thermal and Compositional Reservoir Simulation

DEFF Research Database (Denmark)

Kristensen, Morten Rode; Gerritsen, Margot G.; Thomsen, Per Grove

2007-01-01

of convergence and error test failures by more than 50% compared to direct integration without the new algorithm. To facilitate the algorithmic development we construct a virtual kinetic cell model. We use implicit one-step ESDIRK (Explicit Singly Diagonal Implicit Runge-Kutta) methods for integration...... of the kinetics. The kinetic cell model serves both as a tool for the development and testing of tailored solvers as well as a testbed for studying the interactions between chemical kinetics and phase behavior. A comparison between a Kvalue correlation based approach and a more rigorous equation of state based......Phase changes are known to cause convergence problems for integration of stiff kinetics in thermal and compositional reservoir simulations. We propose an algorithm for detection and location of phase changes based on discrete event system theory. The algorithm provides a robust way for handling...

EFFECT OF DIATOMEAOUS EARTH TREATMENT USING HYDROGEN CHLORIDE AND SULFURIC ACID ON KINETICS OF CADMIUM(II ADSORPTION

Directory of Open Access Journals (Sweden)

Nuryono Nuryono

2010-06-01

Full Text Available In this research, treatment of diatomaceous earth, Sangiran, Central Java using hydrogen chloride (HCl and sulfuric acid (H2SO4 on kinetics of Cd(II adsorption in aqueous solution has been carried out. The work was conducted by mixing an amount of grounded diatomaceous earth (200 mesh in size with HCl or H2SO4 solution in various concentrations for two hours at temperature range of 100 - 150oC. The mixture was then filtered and washed with water until the filtrate pH is approximately 7 and then the residue was dried for four hours at a temperature of 70oC. The product was used as an adsorbent to adsorb Cd(II in aqueous solution with various concentrations. The Cd(II adsorbed was determined by analyzing the rest of Cd(II in the solution using atomic absorption spectrophotometry. The effect of treatment was evaluated from kinetic parameter of adsorption rate constant calculated based on the simple kinetic model. Results showed  that before equilibrium condition reached, adsorpstion of Cd(II occurred through two steps, i.e. a step tends to follow a reaction of irreversible first order  (step I followed by reaction of reversible first order (step II. Treatment with acids, either hydrogen chloride or sulfuric acid, decreased adsorption rate constant for the step I from 15.2/min to a range of 6.4 - 9.4/min.  However, increasing concentration of acid (in a range of concentration investigated did not give significant and constant change of adsorption rate constant. For step II process,  adsorption involved physical interaction with the sufficient low adsorption energy (in a range of 311.3 - 1001 J/mol.     Keywords: adsorption, cdmium, diatomaceous earth, kinetics.

In-situ study of hydriding kinetics in Pd-based thin film systems

Energy Technology Data Exchange (ETDEWEB)

Delmelle, Renaud; Proost, Joris [Univ. Catholique de Louvain, Louvain-la-Neuve (Belgium). Div. of Materials and Process Engineering

2010-07-01

The hydriding kinetics of Pd thin films has been investigated in detail. The key experimental technique used in this work consists of a high resolution curvature measurement setup, which continuously monitors the reflections of multiple laser beams coming off a cantilevered sample. After mounting the sample inside a vacuum chamber, a H-containing gas mixture is introduced to instantaneously generate a given hydrogen partial pressure (p{sub H2}) inside the chamber. The resulting interaction of H with the Pd layer then leads to a volume expansion of the thin film system. This induces in turn changes in the sample curvature as a result of internal stresses developing in the Pd film during a hydriding cycle. Based on such curvature date obtained in-situ at different p{sub H2}, a two-step model for the kinetics of Pd-hydride formation has been proposed and expressions for the hydrogen adsorption and absorption velocities have been derived. The rate-limiting steps have been identified by studying the p{sub H2}-dependence of these velocities. Furthermore, from our in-situ experimental data, relevant kinetic parameters have been calculated. The effect of dry air exposure of the Pd films on the hydriding kinetics has been considered as well. (orig.)

A positive and multi-element conserving time stepping scheme for biogeochemical processes in marine ecosystem models

Science.gov (United States)

Radtke, H.; Burchard, H.

2015-01-01

In this paper, an unconditionally positive and multi-element conserving time stepping scheme for systems of non-linearly coupled ODE's is presented. These systems of ODE's are used to describe biogeochemical transformation processes in marine ecosystem models. The numerical scheme is a positive-definite modification of the Runge-Kutta method, it can have arbitrarily high order of accuracy and does not require time step adaption. If the scheme is combined with a modified Patankar-Runge-Kutta method from Burchard et al. (2003), it also gets the ability to solve a certain class of stiff numerical problems, but the accuracy is restricted to second-order then. The performance of the new scheme on two test case problems is shown.

Dual kinetic curves in reversible electrochemical systems.

Directory of Open Access Journals (Sweden)

Michael J Hankins

Full Text Available We introduce dual kinetic chronoamperometry, in which reciprocal relations are established between the kinetic curves of electrochemical reactions that start from symmetrical initial conditions. We have performed numerical and experimental studies in which the kinetic curves of the electron-transfer processes are analyzed for a reversible first order reaction. Experimental tests were done with the ferrocyanide/ferricyanide system in which the concentrations of each component could be measured separately using the platinum disk/gold ring electrode. It is shown that the proper ratio of the transient kinetic curves obtained from cathodic and anodic mass transfer limited regions give thermodynamic time invariances related to the reaction quotient of the bulk concentrations. Therefore, thermodynamic time invariances can be observed at any time using the dual kinetic curves for reversible reactions. The technique provides a unique possibility to extract the non-steady state trajectory starting from one initial condition based only on the equilibrium constant and the trajectory which starts from the symmetrical initial condition. The results could impact battery technology by predicting the concentrations and currents of the underlying non-steady state processes in a wide domain from thermodynamic principles and limited kinetic information.

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

Science.gov (United States)

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

Relaxation and kinetics in scalar field theories

International Nuclear Information System (INIS)

Boyanovsky, D.; Lawrie, I.D.; Lee, D.

1996-01-01

A new approach to the dynamics of relaxation and kinetics of thermalization in a scalar field theory is presented that incorporates the relevant time scales through the resummation of hard thermal loops. An alternative derivation of the kinetic equations for the open-quote open-quote quasiparticle close-quote close-quote distribution functions is obtained that allows a clear understanding of the different open-quote open-quote coarse-graining close-quote close-quote approximations usually involved in a kinetic description. This method leads to a systematic perturbative expansion to obtain the kinetic equations including hard thermal loop resummation and to an improvement including renormalization, off-shell effects, and contributions that change chemical equilibrium on short time scales. As a by-product of these methods we establish the equivalence between the relaxation time scale in the linearized equation of motion of the quasiparticles and the thermalization time scale of the quasiparticle distribution function in the open-quote open-quote relaxation time approximation close-quote close-quote including hard thermal loop effects. Hard thermal loop resummation dramatically modifies the scattering rate for long wavelength modes as compared to the usual (semi)classical estimate. Relaxation and kinetics are studied both in the unbroken and broken symmetry phases of the theory. The broken symmetry phase also provides the setting to obtain the contribution to the kinetic equations from processes that involve decay of a heavy scalar into light scalar particles in the medium. copyright 1996 The American Physical Society

Time to pause before the next step

International Nuclear Information System (INIS)

Siemon, R.E.

1998-01-01

Many scientists, who have staunchly supported ITER for years, are coming to realize it is time to further rethink fusion energy's development strategy. Specifically, as was suggested by Grant Logan and Dale Meade, and in keeping with the restructuring of 1996, a theme of better, cheaper, faster fusion would serve the program more effectively than ''demonstrating controlled ignition...and integrated testing of the high-heat-flux and nuclear components required to utilize fusion energy...'' which are the important ingredients of ITER's objectives. The author has personally shifted his view for a mixture of technical and political reasons. On the technical side, he senses that through advanced tokamak research, spherical tokamak research, and advanced stellarator work, scientists are coming to a new understanding that might make a burning-plasma device significantly smaller and less expensive. Thus waiting for a few years, even ten years, seems prudent. Scientifically, there is fascinating physics to be learned through studies of burning plasma on a tokamak. And clearly if one wishes to study burning plasma physics in a sustained plasma, there is no other configuration with an adequate database on which to proceed. But what is the urgency of moving towards an ITER-like step focused on burning plasma? Some of the arguments put forward and the counter arguments are discussed here

Combined angle-resolved X-ray photoelectron spectroscopy, density functional theory and kinetic study of nitridation of gallium arsenide

Science.gov (United States)

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.

An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates

International Nuclear Information System (INIS)

Gal, Maayan; Kern, Thomas; Schanda, Paul; Frydman, Lucio; Brutscher, Bernhard

2009-01-01

Multidimensional NMR spectroscopy is a well-established technique for the characterization of structure and fast-time-scale dynamics of highly populated ground states of biological macromolecules. The investigation of short-lived excited states that are important for molecular folding, misfolding and function, however, remains a challenge for modern biomolecular NMR techniques. Off-equilibrium real-time kinetic NMR methods allow direct observation of conformational or chemical changes by following peak positions and intensities in a series of spectra recorded during a kinetic event. Because standard multidimensional NMR methods required to yield sufficient atom-resolution are intrinsically time-consuming, many interesting phenomena are excluded from real-time NMR analysis. Recently, spatially encoded ultrafast 2D NMR techniques have been proposed that allow one to acquire a 2D NMR experiment within a single transient. In addition, when combined with the SOFAST technique, such ultrafast experiments can be repeated at high rates. One of the problems detected for such ultrafast protein NMR experiments is related to the heteronuclear decoupling during detection with interferences between the pulses and the oscillatory magnetic field gradients arising in this scheme. Here we present a method for improved ultrafast data acquisition yielding higher signal to noise and sharper lines in single-scan 2D NMR spectra. In combination with a fast-mixing device, the recording of 1 H- 15 N correlation spectra with repetition rates of up to a few Hertz becomes feasible, enabling real-time studies of protein kinetics occurring on time scales down to a few seconds

Stepping out: dare to step forward, step back, or just stand still and breathe.

Science.gov (United States)

Waisman, Mary Sue

2012-01-01

It is important to step out and make a difference. We have one of the most unique and diverse professions that allows for diversity in thought and practice, permitting each of us to grow in our unique niches and make significant contributions. I was frightened to 'step out' to go to culinary school at the age of 46, but it changed forever the way I look at my profession and I have since experienced the most enjoyable and innovative career. There are also times when it is important to 'step back' to relish the roots of our profession; to help bring food back into nutrition; to translate all of our wonderful science into a language of food that Canadians understand. We all need to take time to 'just stand still and breathe': to celebrate our accomplishments, reflect on our actions, ensure we are heading toward our vision, keep the profession vibrant and relevant, and cherish one another.

Kinetics and mechanism of sphalerite leaching by sodium nitrate in sulphuric acid solution

Directory of Open Access Journals (Sweden)

Sokić M.

2012-01-01

Full Text Available Interest for application of hydrometallurgical processes in a processing of complex sulphide ores and concentrates has increased in recent years. Their application provides better metal recoveries and reduced emission of gaseous and toxic ageneses in the environment. The kinetics and mechanism of sphalerite leaching from complex sulphide concentrate with sulphuric acid and sodium nitrate solution at standard conditions was presented in this paper. The influences of temperature and time on the leaching degree of zinc were investigated and kinetic analysis of the process was accomplished. With temperature increasing from 60 to 90°C, the zinc leaching increased from 25.23% to 71.66% after 2 hours, i.e. from 59.40% to 99.83% after 4 hours. The selected kinetic model indicated that the diffusion through the product layer was the rate-controlling step during the sphalerite leaching. The activation energy was determined to be 55 kJ/mol in the temperature range 60-90°C. XRD, light microscopy and SEM/EDX analyses of the complex concentrate and leach residue confirmed formation of elemental sulphur and diffusion-controlled leaching mechanism.

Time-dependent cell disintegration kinetics in lung tumors after irradiation

Energy Technology Data Exchange (ETDEWEB)

Chvetsov, Alexei V; Palta, Jatinder J [Department of Radiation Oncology, University of Florida, Gainesville, FL (United States); Nagata, Yasushi [Department of Therapeutic Radiology and Oncology, Kyoto University, Kyoto (Japan)], E-mail: chvetsov@ufl.edu

2008-05-07

We study the time-dependent disintegration kinetics of tumor cells that did not survive radiotherapy treatment. To evaluate the cell disintegration rate after irradiation, we studied the volume changes of solitary lung tumors after stereotactic radiotherapy. The analysis is performed using two approximations: (1) tumor volume is a linear function of the total cell number in the tumor and (2) the cell disintegration rate is governed by the exponential decay with constant risk, which is defined by the initial cell number and a half-life T{sub 1/2}. The half-life T{sub 1/2} is determined using the least-squares fit to the clinical data on lung tumor size variation with time after stereotactic radiotherapy. We show that the tumor volume variation after stereotactic radiotherapy of solitary lung tumors can be approximated by an exponential function. A small constant component in the volume variation does not change with time; however, this component may be the residual irregular density due to radiation fibrosis and was, therefore, subtracted from the total volume variation in our computations. Using computerized fitting of the exponent function to the clinical data for selected patients, we have determined that the average half-life T{sub 1/2} of cell disintegration is 28.2 days for squamous cell carcinoma and 72.4 days for adenocarcinoma. This model is needed for simulating the tumor volume variation during radiotherapy, which may be important for time-dependent treatment planning of proton therapy that is sensitive to density variations.

Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study

Science.gov (United States)

Kouza, Maksim; Co, Nguyen Truong; Li, Mai Suan; Kmiecik, Sebastian; Kolinski, Andrzej; Kloczkowski, Andrzej; Buhimschi, Irina Alexandra

2018-06-01

Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite much progress in the understanding of the protein aggregation process, the factors governing fibril formation rates and fibril stability have not been fully understood. Using lattice models, we have shown that the fibril formation time is controlled by the kinetic stability of the fibril state but not by its energy. Having performed all-atom explicit solvent molecular dynamics simulations with the GROMOS43a1 force field for full-length amyloid beta peptides Aβ40 and Aβ42 and truncated peptides, we demonstrated that kinetic stability can be accessed via mechanical stability in such a way that the higher the mechanical stability or the kinetic stability, the faster the fibril formation. This result opens up a new way for predicting fibril formation rates based on mechanical stability that may be easily estimated by steered molecular dynamics.

Implosion anisotropy of neutron kinetic energy distributions as measured with the neutron time-of-flight diagnostics at the National Ignition Facility

Science.gov (United States)

Hartouni, Edward; Eckart, Mark; Field, John; Grim, Gary; Hatarik, Robert; Moore, Alastair; Munro, David; Sayer, Daniel; Schlossberg, David

2017-10-01

Neutron kinetic energy distributions from fusion reactions are characterized predominantly by the excess energy, Q, of the fusion reaction and the variance of kinetic energy which is related to the thermal temperature of the plasma as shown by e.g. Brysk. High statistics, high quality neutron time-of-flight spectra obtained at the National Ignition Facility provide a means of measuring small changes to the neutron kinetic energy due to the spatial and temporal distribution of plasma temperature, density and velocity. The modifications to the neutron kinetic energy distribution as described by Munro include plasma velocity terms with spatial orientation, suggesting that the neutron kinetic energy distributions could be anisotropic when viewed by multiple lines-of-sight. These anisotropies provide a diagnostic of burn averaged plasma velocity distributions. We present the results of measurements made for a variety of DT implosions and discuss their possible physical interpretations. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344. Lawrence Livermore National Security, LLC.

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.

Science.gov (United States)

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

Time of erythema onset after application of methyl nicotinate ointments as response parameter: influence of penetration kinetics and enhancing agents.

Science.gov (United States)

Remane, Y; Leopold, C S

2006-01-01

The time of erythema onset may be used as a response parameter for quantification of the cutaneous erythema response induced by methyl nicotinate. The vehicles light mineral oil (LMO; test) and medium chain triglycerides (MCT; standard) were compared with regard to the pharmacodynamic response. Moreover, the influence of penetration enhancers on the time of erythema onset was investigated under zero order penetration kinetics. The enhancers dimethyl sulfoxide, diethylene glycol monoethyl ether and three different glycerides in different concentrations were added to MCT as a standard vehicle. All preparations were applied to the forearms of volunteers under infinite dose conditions at different thermodynamic drug activity levels (0.2-3.2% of the saturation level) and different drug concentrations (0.051-0.816%), respectively. Different penetration kinetics do not influence data of erythema onset, as these data are comparable to those obtained under finite dose conditions (first order penetration kinetics). With regard to the penetration enhancers, a significantly enhanced penetration of methyl nicotinate could be observed only for diethylene glycol monoethyl ether and dimethyl sulfoxide. However, no significant difference between light mineral oil and MCT could be found with regard to penetration enhancement. The time of erythema onset is an easy and efficient parameter for quantification of the pharmacodynamic response caused by nicotinates.

Time constants and feedback transfer functions of EBR-II subassembly types

International Nuclear Information System (INIS)

Grimm, K.N.; Meneghetti, D.

1986-01-01

Time constants, feedback reactivity transfer functions and power coefficients are calculated for stereotypical subassemblies in the EBR-II reactor. These quantities are calculated from nodal reactivities obtained from a reactor kinetic code analysis for a step change in power. Due to the multiplicity of eigenvalues, there are several time constants for each nodal position in a subassembly. Compared with these calculated values are analytically derived values for the initial node of a given channel

Time constants and feedback transfer functions of EBR-II subassembly types

International Nuclear Information System (INIS)

Grimm, K.N.; Meneghetti, D.

1987-01-01

Time constants, feedback reactivity transfer functions and power coefficients are calculated for stereotypical subassemblies in the EBR-II reactor. These quantities are calculated from nodal reactivities obtained from a reactor kinetic code analysis for a step change in power. Due to the multiplicity of eigenvalues, there are several time constants for each nodal position in a subassembly. Compared with these calculated values are analytically derived values for the initial node of a given channel. (author)

Coupled electron and atomic kinetics through the solution of the Boltzmann equation for generating time-dependent X-ray spectra

International Nuclear Information System (INIS)

Sherrill, M.E.; Abdallah, J. Jr.; Csanak, G.; Kilcrease, D.P.; Dodd, E.S.; Fukuda, Y.; Akahane, Y.; Aoyama, M.; Inoue, N.; Ueda, H.; Yamakawa, K.; Faenov, A.Ya.; Magunov, A.I.; Pikuz, T.A.; Skobelev, I.Yu.

2006-01-01

In this work, we present a model that solves self-consistently the electron and atomic kinetics to characterize highly non-equilibrium plasmas, in particular for those systems where both the electron distribution function is far from Maxwellian and the evolution of the ion level populations are dominated by time-dependent atomic kinetics. In this model, level populations are obtained from a detailed collisional-radiative model where collision rates are computed from a time varying electron distribution function obtained from the solution of the zero-dimensional Boltzmann equation. The Boltzmann collision term includes the effects of electron-electron collisions, electron collisional ionization, excitation and de-excitation. An application for He α spectra from a short pulse laser irradiated argon cluster target will be shown to illustrate the results of our model

Coupled electron and atomic kinetics through the solution of the Boltzmann equation for generating time-dependent X-ray spectra

Energy Technology Data Exchange (ETDEWEB)

Sherrill, M.E. [Los Alamos National Laboratory, T-4, Los Alamos, NM 87545 (United States)]. E-mail: manolo@t4.lanl.gov; Abdallah, J. Jr. [Los Alamos National Laboratory, T-4, Los Alamos, NM 87545 (United States); Csanak, G. [Los Alamos National Laboratory, T-4, Los Alamos, NM 87545 (United States); Kilcrease, D.P. [Los Alamos National Laboratory, T-4, Los Alamos, NM 87545 (United States); Dodd, E.S. [Los Alamos National Laboratory, X-1, Los Alamos, NM 87545 (United States); Fukuda, Y. [Advanced Photon Research Center, JAERI, Kyoto 619-0215 (Japan); Akahane, Y. [Advanced Photon Research Center, JAERI, Kyoto 619-0215 (Japan); Aoyama, M. [Advanced Photon Research Center, JAERI, Kyoto 619-0215 (Japan); Inoue, N. [Advanced Photon Research Center, JAERI, Kyoto 619-0215 (Japan); Ueda, H. [Advanced Photon Research Center, JAERI, Kyoto 619-0215 (Japan); Yamakawa, K. [Advanced Photon Research Center, JAERI, Kyoto 619-0215 (Japan); Faenov, A.Ya. [Multicharged Ions Spectra Data Center of VNIIFTRI, Mendeleevo, Moscow Region 141570 (Russian Federation); Magunov, A.I. [Multicharged Ions Spectra Data Center of VNIIFTRI, Mendeleevo, Moscow Region 141570 (Russian Federation); Pikuz, T.A. [Multicharged Ions Spectra Data Center of VNIIFTRI, Mendeleevo, Moscow Region 141570 (Russian Federation); Skobelev, I.Yu. [Multicharged Ions Spectra Data Center of VNIIFTRI, Mendeleevo, Moscow Region 141570 (Russian Federation)

2006-05-15

In this work, we present a model that solves self-consistently the electron and atomic kinetics to characterize highly non-equilibrium plasmas, in particular for those systems where both the electron distribution function is far from Maxwellian and the evolution of the ion level populations are dominated by time-dependent atomic kinetics. In this model, level populations are obtained from a detailed collisional-radiative model where collision rates are computed from a time varying electron distribution function obtained from the solution of the zero-dimensional Boltzmann equation. The Boltzmann collision term includes the effects of electron-electron collisions, electron collisional ionization, excitation and de-excitation. An application for He{sub {alpha}} spectra from a short pulse laser irradiated argon cluster target will be shown to illustrate the results of our model.

Effects of step rate manipulation on joint mechanics during running.

Science.gov (United States)

Heiderscheit, Bryan C; Chumanov, Elizabeth S; Michalski, Max P; Wille, Christa M; Ryan, Michael B

2011-02-01

the objective of this study was to characterize the biomechanical effects of step rate modification during running on the hip, knee, and ankle joints so as to evaluate a potential strategy to reduce lower extremity loading and risk for injury. three-dimensional kinematics and kinetics were recorded from 45 healthy recreational runners during treadmill running at constant speed under various step rate conditions (preferred, ± 5%, and ± 10%). We tested our primary hypothesis that a reduction in energy absorption by the lower extremity joints during the loading response would occur, primarily at the knee, when step rate was increased. less mechanical energy was absorbed at the knee (P running and may prove beneficial in the prevention and treatment of common running-related injuries.

Effects of fatigue on kinematics and kinetics during overground running: a systematic review.

Science.gov (United States)

Winter, Sara; Gordon, Susan; Watt, Kerrianne

2017-06-01

Understanding kinematic and kinetic changes with fatigue during running is important to assess changes that may influence performance and injury. The aim of this systematic review was to identify, critique and summarize literature about the effects of fatigue on kinematics and kinetics during a fatiguing overground run and present the reported influence on performance and injury. An electronic search was conducted of MEDLINE, SPORTDiscus, CINAHL and PubMed databases. Two reviewers assessed articles for inclusion, and evaluated the quality of articles included using a modified version of the Downs and Black Quality Index. A total of twelve articles were identified for review. The mean quality assessment score was seven out of a possible 12. Kinematic and kinetic changes reported to affect performance included decreased speed, step or stride frequency and length, increased trunk flexion, lower leg position at heel strike, mediolateral acceleration, changes in hip and knee ranges, and decreased stride regularity, heel lift, maximum knee rotation and backward ankle velocity. Alterations reported to increase risk of injury included decreased step frequency, increased upper body rotation and lower leg position at heel strike, and decreased knee flexion during stance. Reduced risk of injury has been linked to decreased step length and hip ranges, and increased trunk flexion. This review found limited evidence regarding changes in kinematic and kinetic during a fatiguing run in relation to performance and injury. Higher quality studies are warranted, with a larger sample of homogenous runners, and type of run carefully selected to provide quality information for runners, coaches and clinicians.

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

Science.gov (United States)

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.

Schwinger pair production in space- and time-dependent electric fields: Relating the Wigner formalism to quantum kinetic theory

International Nuclear Information System (INIS)

Hebenstreit, F.; Alkofer, R.; Gies, H.

2010-01-01

The nonperturbative electron-positron pair production (Schwinger effect) is considered for space- and time-dependent electric fields E-vector(x-vector,t). Based on the Dirac-Heisenberg-Wigner formalism, we derive a system of partial differential equations of infinite order for the 16 irreducible components of the Wigner function. In the limit of spatially homogeneous fields the Vlasov equation of quantum kinetic theory is rediscovered. It is shown that the quantum kinetic formalism can be exactly solved in the case of a constant electric field E(t)=E 0 and the Sauter-type electric field E(t)=E 0 sech 2 (t/τ). These analytic solutions translate into corresponding expressions within the Dirac-Heisenberg-Wigner formalism and allow to discuss the effect of higher derivatives. We observe that spatial field variations typically exert a strong influence on the components of the Wigner function for large momenta or for late times.

High Time-Resolved Kinetic Temperatures of Solar Wind Minor Ions Measured with SOHO/CELIAS/CTOF

Science.gov (United States)

Janitzek, N. P.; Berger, L.; Drews, C.; Wimmer-Schweingruber, R. F.

2017-12-01

Solar wind heavy ions with an atomic number Z > 2 are referred to as minor ions since they represent a fraction of less than one percent of all solar wind ions. They can be therefore regarded as test particles, only reacting to but not driving the dynamics of the solar wind plasma, which makes them a unique diagnostic tool for plasma wave phenomena both in the solar atmosphere and the extended heliosphere. In the past, several studies have investigated the kinetic temperatures of minor ions, but due to low counting statistics these studies are based on ion velocity distribution functions (VDFs) recorded over time periods of several hours. The Charge Time-Of-Flight (CTOF) mass spectrometer as part of the Charge, ELement and Isotope Analysis System (CELIAS) onboard the SOlar and Heliospheric Observatory (SOHO) provides solar wind heavy ion 1D radial VDFs with excellent charge state separation, an unprecedented cadence of 5 minutes and very high counting statistics, exceeding similar state-of-the-art instruments by a factor of ten. In our study, based on CTOF measurements at Langrangian point L1 between DOY 150 and DOY 220 in 1996, we investigate systematically the influence of the VDF time resolution on the derived kinetic temperatures for solar wind silicon and iron ions. The selected ion set spans a wide range of mass-per-charge from 3 amu/e heavy ions with ion-cyclotron waves.

SENSITIVITY ANALYSIS OF KINETIC CONSTANTS AS A TOOL FOR ELUCIDATING THE POLYMERIZATION MECHANISM OF ACRYL-FURANIC COMPOUNDS

Directory of Open Access Journals (Sweden)

Jurgen Lange

2013-12-01

Full Text Available By means of the sensitivity analysis of kinetics constants in a proposed mechanism for radical polymerization of acrylfuranic compounds [Furfuryl Acrylate (FA and Methacrylate (FM],it is elucidated which elementary steps are relevant in the phenomenology. In this analysis, the application of Come's methodology allows to classify the elementary steps of a mechanism in three categories: Non-sensible, Non-determinant, Sensible. The results obtained with this tool in modeling of experimental data in free radical polymerization of FA and FM suggest that kinetic mechanism consists mainly on five elementary steps: 1 Primary initiation, 2 propagation, 3 degradative transfers (which include intermolecular and primary, 4 re-initiation and 5 cross-termination. Thus, taking into account these elementary steps in mathematical modeling, the polymerization of FA and FM in different experimental conditions was successfully simulated.

Step training improves reaction time, gait and balance and reduces falls in older people: a systematic review and meta-analysis.

Science.gov (United States)

Okubo, Yoshiro; Schoene, Daniel; Lord, Stephen R

2017-04-01

To examine the effects of stepping interventions on fall risk factors and fall incidence in older people. Electronic databases (PubMed, EMBASE, CINAHL, Cochrane, CENTRAL) and reference lists of included articles from inception to March 2015. Randomised (RCT) or clinical controlled trials (CCT) of volitional and reactive stepping interventions that included older (minimum age 60) people providing data on falls or fall risk factors. Meta-analyses of seven RCTs (n=660) showed that the stepping interventions significantly reduced the rate of falls (rate ratio=0.48, 95% CI 0.36 to 0.65, prisk ratio=0.51, 95% CI 0.38 to 0.68, pfalls and proportion of fallers. A meta-analysis of two RCTs (n=62) showed that stepping interventions significantly reduced laboratory-induced falls, and meta-analysis findings of up to five RCTs and CCTs (n=36-416) revealed that stepping interventions significantly improved simple and choice stepping reaction time, single leg stance, timed up and go performance (pfalls among older adults by approximately 50%. This clinically significant reduction may be due to improvements in reaction time, gait, balance and balance recovery but not in strength. Further high-quality studies aimed at maximising the effectiveness and feasibility of stepping interventions are required. CRD42015017357. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Time ordering of two-step processes in energetic ion-atom collisions: Basic formalism

International Nuclear Information System (INIS)

Stolterfoht, N.

1993-01-01

The semiclassical approximation is applied in second order to describe time ordering of two-step processes in energetic ion-atom collisions. Emphasis is given to the conditions for interferences between first- and second-order terms. In systems with two active electrons, time ordering gives rise to a pair of associated paths involving a second-order process and its time-inverted process. Combining these paths within the independent-particle frozen orbital model, time ordering is lost. It is shown that the loss of time ordering modifies the second-order amplitude so that its ability to interfere with the first-order amplitude is essentially reduced. Time ordering and the capability for interference is regained, as one path is blocked by means of the Pauli exclusion principle. The time-ordering formalism is prepared for papers dealing with collision experiments of single excitation [Stolterfoht et al., following paper, Phys. Rev. A 48, 2986 (1993)] and double excitation [Stolterfoht et al. (unpublished)

Determination of kinetic parameters of heterogeneous isotopic exchange reaction

International Nuclear Information System (INIS)

Huang, Ting-Chia; Tsai, Fuan-Nan

1977-01-01

A mathematical model has been proposed for a heterogeneous isotopic exchange reaction which involves film diffusion, surface chemical reaction and intraparticle diffusion. The exchange equation to predict the exchange fraction as a function of time for the spherical particles immersed in a solution of finite volume has been derived. The relations between the exchange fraction and dimensionless time are plotted with xi(=ak sub(f)/KD sub(e)), xi 1 (=K 1 a 2 /D sub(e)) and final fractional uptake as parameters. From the values of the kinetic parameters xi and xi 1 , the relative importance of each limiting step is discussed. Experimental results of the isotopic exchange reaction of calcium ion in both system CaCO 3 (s)/Ca 2+ (aq) and system calcium type resin Dowex 50W-X8/Ca 2+ (aq) are coincident with the theoretical equation proposed in this study. (auth.)

Computer-Aided Construction of Chemical Kinetic Models

Energy Technology Data Exchange (ETDEWEB)

Green, William H. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

2014-12-31

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

Kinetics and mechanism of oxidation of tellurium (IV) by periodate in alkaline medium

International Nuclear Information System (INIS)

Srinivas, K.; Vani, P.; Dikshitulu, L.S.A.

1995-01-01

Detailed kinetic study of the oxidation of tellurium (IV) by periodate in alkaline medium has been carried out to compare the mechanisms of oxidation in the acid and alkaline media. It is interesting to note that the rate step involves a two-electron transfer from tellurium (IV) to periodate in alkaline medium although the kinetic pattern is somewhat different from that in the acid medium. 7 refs., 1 tab

SQERTSS: Dynamic rank based throttling of transition probabilities in kinetic Monte Carlo simulations

International Nuclear Information System (INIS)

Danielson, Thomas; Sutton, Jonathan E.; Hin, Céline; Virginia Polytechnic Institute and State University; Savara, Aditya

2017-01-01

Lattice based Kinetic Monte Carlo (KMC) simulations offer a powerful simulation technique for investigating large reaction networks while retaining spatial configuration information, unlike ordinary differential equations. However, large chemical reaction networks can contain reaction processes with rates spanning multiple orders of magnitude. This can lead to the problem of “KMC stiffness” (similar to stiffness in differential equations), where the computational expense has the potential to be overwhelmed by very short time-steps during KMC simulations, with the simulation spending an inordinate amount of KMC steps / cpu-time simulating fast frivolous processes (FFPs) without progressing the system (reaction network). In order to achieve simulation times that are experimentally relevant or desired for predictions, a dynamic throttling algorithm involving separation of the processes into speed-ranks based on event frequencies has been designed and implemented with the intent of decreasing the probability of FFP events, and increasing the probability of slow process events -- allowing rate limiting events to become more likely to be observed in KMC simulations. This Staggered Quasi-Equilibrium Rank-based Throttling for Steady-state (SQERTSS) algorithm designed for use in achieving and simulating steady-state conditions in KMC simulations. Lastly, as shown in this work, the SQERTSS algorithm also works for transient conditions: the correct configuration space and final state will still be achieved if the required assumptions are not violated, with the caveat that the sizes of the time-steps may be distorted during the transient period.

Time-dependent photoluminescence spectroscopy as a tool to measure the ligand exchange kinetics on a quantum dot surface

NARCIS (Netherlands)

Koole, R.; Schapotschnikow, P.Z.; de Mello Donega, C.; Vlugt, T.J.H.; Meijerink, A.

2008-01-01

The exchange kinetics of native ligands that passivate CdSe quantum dots (hexadecylamine (HDA), trioctylphosphine oxide (TOPO), and trioctylphosphine (TOP)) by thiols is followed in situ. This is realized by measuring, in real-time, the decrease in emission intensity of the QDs upon addition of

Kinetic study of time-dependent fixation of U{sup VI} on biochar

Energy Technology Data Exchange (ETDEWEB)

Ashry, A. [Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD (United Kingdom); Radiation Protection Department, Nuclear Research Centre, Egyptian Atomic Energy Authority, Cairo (Egypt); Bailey, E.H., E-mail: liz.bailey@nottingham.ac.uk [Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD (United Kingdom); Chenery, S.R.N. [British Geological Survey, Nicker Hill, Keyworth, Nottingham NG12 5GG (United Kingdom); Young, S.D. [Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD (United Kingdom)

2016-12-15

Biochar, a by-product from the production of biofuel and syngas by gasification, was tested as a material for adsorption and fixation of U{sup VI} from aqueous solutions. A batch experiment was conducted to study the factors that influence the adsorption and time-dependent fixation on biochar at 20 °C, including pH, initial concentration of U{sup VI} and contact time. Uranium (U{sup VI}) adsorption was highly dependent on pH but adsorption on biochar was high over a wide range of pH values, from 4.5 to 9.0, and adsorption strength was time-dependent over several days. The experimental data for pH > 7 were most effectively modelled using a Freundlich adsorption isotherm coupled to a reversible first order kinetic equation to describe the time-dependent fixation of U{sup VI} within the biochar structure. Desorption experiments showed that U{sup VI} was only sparingly desorbable from the biochar with time and isotopic dilution with {sup 233}U{sup VI} confirmed the low, or time-dependent, lability of adsorbed {sup 238}U{sup VI}. Below pH 7 the adsorption isotherm trend suggested precipitation, rather than true adsorption, may occur. However, across all pH values (4.5-9) measured saturation indices suggested precipitation was possible: autunite below pH 6.5 and either swartzite, liebigite or bayleyite above pH 6.5.

Kinetic analysis of enzyme systems with suicide substrate in the presence of a reversible competitive inhibitor, tested by simulated progress curves.

Science.gov (United States)

Moruno-Dávila, M A; Garrido-del Solo, C; García-Moreno, M; Havsteen, B H; Garcia-Sevilla, F; Garcia-Cánovas, F; Varón, R

2001-02-01

The use of suicide substrates remains a very important and useful method in enzymology for studying enzyme mechanisms and designing potential drugs. Suicide substrates act as modified substrates for the target enzymes and bind to the active site. Therefore the presence of a competitive reversible inhibitor decreases the rate of substrate-induced inactivation and protects the enzyme from this inactivation. This lowering on the inactivation rate has evident physiological advantages, since it allows the easy acquisition of experimental data and facilitates kinetic data analysis by providing another variable (inhibitor concentration). However despite the importance of the simultaneous action of a suicide substrate and a competitive reversible inhibition, to date no corresponding kinetic analysis has been carried out. Therefore we present a general kinetic analysis of a Michaelis-Menten reaction mechanism with double inhibition caused by both, a suicide substrate and a competitive reversible inhibitor. We assume rapid equilibrium of the reversible reaction steps involved, while the time course equations for the reaction product have been derived with the assumption of a limiting enzyme. The goodness of the analytical solutions has been tested by comparison with the simulated curves obtained by numerical integration. A kinetic data analysis to determine the corresponding kinetic parameters from the time progress curve of the product is suggested. In conclusion, we present a complete kinetic analysis of an enzyme reaction mechanism as described above in an attempt to fill a gap in the theoretical treatment of this type of system.

Ground reaction forces and knee kinetics during single and repeated badminton lunges.

Science.gov (United States)

Lam, Wing Kai; Ding, Rui; Qu, Yi

2017-03-01

Repeated movement (RM) lunge that frequently executed in badminton might be used for footwear evaluation. This study examined the influence of single movement (SM) and RM lunges on the ground reaction forces (GRFs) and knee kinetics during the braking phase of a badminton lunge step. Thirteen male university badminton players performed left-forward lunges in both SM and RM sessions. Force platform and motion capturing system were used to measure GRFs and knee kinetics variables. Paired t-test was performed to determine any significant differences between SM and RM lunges regarding mean and coefficient of variation (CV) in each variable. The kinetics results indicated that compared to SM lunges, the RM lunges had shorter contact time and generated smaller maximum loading rate of impact force, peak knee anterior-posterior force, and peak knee sagittal moment but generated larger peak horizontal resultant forces (Ps < 0.05). Additionally, the RM lunges had lower CV for peak knee medial-lateral and vertical forces (Ps < 0.05). These results suggested that the RM testing protocols had a distinct loading response and adaptation pattern during lunge and that the RM protocol showed higher within-trial reliability, which may be beneficial for the knee joint loading evaluation under different interventions.

Kinetics of tritium isotope exchange between liquid pyrrole and gaseous hydrogen

International Nuclear Information System (INIS)

Stolarz, A.

1994-01-01

The kinetics of tritium isotope exchange between liquid pyrrole and gaseous hydrogen has been studied over the temperature range of 290-303 K. The reaction was carried out in the presence of platinum black but in spite of that, it appeared to be relatively slow. The kinetics of the exchange reaction studied could be described by the simple McKay equation. The results obtained suggest that diffusion is the rate-determining step. A mechanism of exchange is proposed. (author) 10 refs.; 2 figs.; 1 tab

On the Convexity of Step out - Step in Sequencing Games

NARCIS (Netherlands)

Musegaas, Marieke; Borm, Peter; Quant, Marieke

2016-01-01

The main result of this paper is the convexity of Step out - Step in (SoSi) sequencing games, a class of relaxed sequencing games first analyzed by Musegaas, Borm, and Quant (2015). The proof makes use of a polynomial time algorithm determining the value and an optimal processing order for an

Using Equation-Free Computation to Accelerate Network-Free Stochastic Simulation of Chemical Kinetics.

Science.gov (United States)

Lin, Yen Ting; Chylek, Lily A; Lemons, Nathan W; Hlavacek, William S

2018-06-21

The chemical kinetics of many complex systems can be concisely represented by reaction rules, which can be used to generate reaction events via a kinetic Monte Carlo method that has been termed network-free simulation. Here, we demonstrate accelerated network-free simulation through a novel approach to equation-free computation. In this process, variables are introduced that approximately capture system state. Derivatives of these variables are estimated using short bursts of exact stochastic simulation and finite differencing. The variables are then projected forward in time via a numerical integration scheme, after which a new exact stochastic simulation is initialized and the whole process repeats. The projection step increases efficiency by bypassing the firing of numerous individual reaction events. As we show, the projected variables may be defined as populations of building blocks of chemical species. The maximal number of connected molecules included in these building blocks determines the degree of approximation. Equation-free acceleration of network-free simulation is found to be both accurate and efficient.

Kinetic Behaviour of Nanoparticles Across the Biological Physiology

Energy Technology Data Exchange (ETDEWEB)

Emond, Claude, E-mail: claude.emond@biosmc.com [BioSimulation Consulting Inc., 220E. Delaware Avenue 1182, Newark, DE, 19711 (United States)

2011-07-06

Nanotoxicokinetics is a subsection of the toxicology field that involves the study of kinetic displacement of nanoparticles (NPs) in an organism. Four different steps, namely absorption, distribution, metabolism and elimination (ADME), are involved in nanotoxicokinetics. However, only ADE will be covert in this mini review. Because of their size, NPs react differently than particulate matter larger than the nanometre unit in diameter. In the organism, a closer interaction between NPs and biological matrices, called nanotoxicodynamics, might increase the health effects. (Animals are usually in studies to evaluate the global interaction of NPs and biological matrices and to control and reduce the bias.) Understanding the different steps of kinetics is very important to increase the confidence of the amount of NP delivery in the target organ and to assess the level of risk. The objective of this work was to review the behaviour of the NPs interacting with the biological kinetic steps of the ADME and their limitations and constraints. Specifically, it was reviewed the impact of each of the four steps of nanotoxicokinetics, from exposure to elimination in the organism. Recent publications have provided some information on this issue, allowing for a better understanding on how the NPs behave across physiology; however, information is still lacking. We also systematically reviewed the ADME process, and supported our review with examples from the literature. We reviewed the two major factors that influence the absorption of NPs: enumerated biotransformation and elimination limitations. One of the focuses of this study was the interaction between NPs and biological matrices because the morphology and chemical properties may drive the potential for exposure. This paper present different examples of interactions find from literature. To study these interactions, we used a classical pharmacokinetic approach employed in the pharmaceutical industry and compared it to a dynamic

Pulmonary O2 uptake on-kinetics in endurance- and sprint-trained master athletes.

Science.gov (United States)

Berger, N J A; Rittweger, J; Kwiet, A; Michaelis, I; Williams, A G; Tolfrey, K; Jones, A M

2006-12-01

The purpose of this study was to characterise the VO2 kinetic response to moderate intensity cycle exercise in endurance-trained (END) and sprint or power-trained (SPR) track and field master athletes ranging in age from 45 to 85 years. We hypothesised that the time constant (tau) describing the Phase II VO2 on-response would be smaller in the END compared to the SPR athletes, and that the tau would become greater with increasing age in both groups. Eighty-four master athletes who were competing at either the British or European Veteran Athletics Championships acted as subjects, and were classified as either END (800 m - marathon; n = 41), or SPR (100 - 400 m and field events; n = 43) specialists. Subjects completed two 6 minute "step" transitions to a work rate of moderate intensity on a cycle ergometer and pulmonary gas exchange was measured breath-by-breath. Analysis of variance revealed that SPR athletes had slower VO2 on-kinetics (i.e., greater tau) compared to END athletes at each of the age groups studied: 46 - 55 yrs (END: 25 +/- 6 vs. SPR: 36 +/- 9 s; p kinetics became slower with advancing age in the SPR athletes (p kinetics in SPR compared to END master athletes is consistent both with differences in physiology (e.g., muscle fibre type, oxidative/glycolytic capacity) and training between these specialist athletes. Master END athletes have similar tau values to their younger counterparts (approximately 25 s) suggesting that participation in endurance exercise training limits the slowing of VO2 on-kinetics with age in this population.

Analyses of intricate kinetics of the serum proteome during and after colon surgery by protein expression time series

NARCIS (Netherlands)

Roelofsen, Johan; Alvarez Llamas, Gloria; Dijkstra, Martijn; Breitling, Rainer; Havenga, Klaas; Bijzet, Johannes; Zandbergen, Wouter; de Vries, Marcel; Ploeg, Rutger J.; Vonk, Roel J.

Analyses of intricate kinetics of the serum proteome during and after colon surgery by protein expression time series.Roelofsen H, Alvarez-Llamas G, Dijkstra M, Breitling R, Havenga K, Bijzet J, Zandbergen W, de Vries MP, Ploeg RJ, Vonk RJ. Centre for Medical Biomics, University Medical Centre

Study on the numerical analysis of nuclear reactor kinetics equations

International Nuclear Information System (INIS)

Yang, J.C.

1980-01-01

A two-step alternating direction explict method is proposed for the solution of the space-and time-dependent diffusion theory reactor kinetics equations in two space dimensions as a special case of the general class of alternating direction implicit method and the truncation error of this method is estimated. To test the validity of this method it is applied to the Pressurized Water Reactor and CANDU-PHW reactor which have been operating and underconstructing in Korea. The time dependent neutron flux of the PWR reactor during control rod insertion and time dependent neutronic power of CANDU-PHW reactor in the case of postulated loss of coolant accident are obtained from the numerical calculation results. The results of the PWR reactor problem are shown the close agreement between implicit-difference method used in the TWIGL program and this method, and the results of the CANDU-PHW reactor are compared with the results of improved quasistic method and modal method. (Author)

Implementation of the kinetics in the transport code AZTRAN; Implementacion de la cinetica en el codigo de transporte AZTRAN

Energy Technology Data Exchange (ETDEWEB)

Duran G, J. A.; Del Valle G, E. [IPN, Escuela Superior de Fisica y Matematicas, Av. IPN s/n, San Pedro Zacatenco, 07738 Ciudad de Mexico (Mexico); Gomez T, A. M., E-mail: redfield1290@gmail.com [ININ, Carretera Mexico-Toluca s/n, 52750 Ocoyoacac, Estado de Mexico (Mexico)

2017-09-15

This paper shows the implementation of the time dependence in the three-dimensional transport code AZTRAN (AZtlan TRANsport), which belongs to the AZTLAN platform, for the analysis of nuclear reactors (currently under development). The AZTRAN code with this implementation is able to numerically solve the time-dependent transport equation in XYZ geometry, for several energy groups, using the discrete ordinate method S{sub n} for the discretization of the angular variable, the nodal method RTN-0 for spatial discretization and method 0 for discretization in time. Initially, the code only solved the neutrons transport equation in steady state, so the implementation of the temporal part was made integrating the neutrons transport equation with respect to time and balance equations corresponding to the concentrations of delayed neutron precursors, for which method 0 was applied. After having directly implemented code kinetics, the improved quasi-static method was implemented, which is a tool for reducing computation time, where the angular flow is factored by the product of two functions called shape function and amplitude function, where the first is calculated for long time steps, called macro-steps and the second is resolved for small time steps called micro-steps. In the new version of AZTRAN several Benchmark problems that were taken from the literature were simulated, the problems used are of two and three dimensions which allowed corroborating the accuracy and stability of the code, showing in general in the reference tests a good behavior. (Author)

Kinetics of Enzymatic High-Solid Hydrolysis of Lignocellulosic Biomass Studied by Calorimetry

DEFF Research Database (Denmark)

Olsen, Søren Nymand; Rasmussen, Erik Lumby; McFarland, K.C.

2011-01-01

analysis of the interrelationships of enzyme load and the rate, time, and extent of the reaction. The results suggest that the hydrolysis rate of pretreated corn stover is limited initially by available attack points on the substrate surface (conversion) but becomes proportional to enzyme dosage......Enzymatic hydrolysis of high-solid biomass (>10% w/w dry mass) has become increasingly important as a key step in the production of second-generation bioethanol. To this end, development of quantitative real-time assays is desirable both for empirical optimization and for detailed kinetic analysis...... rate with a detection limit of about 500 pmol glucose s−1. Hence, calorimetry is shown to be a highly sensitive real-time method, applicable for high solids, and independent on the complexity of the substrate. Dose–response experiments with a typical cellulase cocktail enabled a multidimensional...

The kinetics of formation and transformation of silver atoms on solid surfaces subjected to ionizing irradiation

International Nuclear Information System (INIS)

Popovich, G.M.

1988-01-01

The paper discusses the results obtained in ESR-assisted studies of the kinetics of formation and transformation of silver atoms generated by γ-irradiation of silver-containing carriers. Three types of dependences have been established: (1) extreme; (2) saturation curves and (3) step-like. All the kinetic curves display, after a definite period of time, stable concentrations of adsorbed silver atoms per unit of the surface at a given temperature. Depending on the temperature of the experiment, the composition and nature of the carrier, the number of adsorbed silver ions, the irradiation dose and conditions of the experiment, a stable concentration of silver atoms at a given temperature may be equal to, higher or lower than the number of silver atoms measured immediately after γ-irradiation at a temperature of liquid nitrogen. A kinetic scheme is proposed to explain the obtained curves. The model suggests that the silver atoms adsorbed on the surface, as well as those formed after γ-irradiation, are bonded to the surface by various energies, which are related to heterogeneity of the carrier surface. (author)

Timing of the steps in transformation of C3H 10T1/2 cells by X-irradiation

International Nuclear Information System (INIS)

Kennedy, A.R.; Cairns, J.; Little, J.B.

1984-01-01

Transformation of cells in culture by chemical carcinogens or X-rays seems to require at least two steps. The initial step is a frequent event; for example, after transient exposure to either methylcholanthrene or X-rays. It has been hypothesized that the second step behaves like a spontaneous mutation in having a constant but small probability of occurring each time an initiated cell divides. We show here that the clone size distribution of transformed cells in growing cultures initiated by X-rays, is, indeed, exactly what would be expected on that hypothesis. (author)

Time-resolved small angle neutron scattering measurements of asphaltene nanoparticle aggregation kinetics in incompatible crude oil mixtures

International Nuclear Information System (INIS)

Mason, Thomas G.; Lin, Min Y.

2003-01-01

We use time-resolved-small angle neutron scattering to study the kinetics of asphaltene nanoparticle aggregation in incompatible crude oil mixtures. We induce asphaltene aggregation by mixing asphaltene-rich Syrian crude oil (SACO) with a paraffinic British crude oil and observe the scattered neutron intensity, I, as a function of wave number, q, over times, t, ranging from twenty minutes to about a week. We observe a growth in I at low q as the nanoscale asphaltenes agglomerate into microscale aggregates and interpret this growth as an increase in surface scattering from the aggregates. We fit I(q,t) to an empirical model and measure the growth in the power-law exponent, α, associated with the low-q logarithmic slope of I(q). We define a time, τ α , associated with the first appearance of the aggregates when α>3; τ α increases as a function of the volume fraction, φ m , of SACO in the mixture. The surface scattering intensity initially increases and then saturates at long times when the aggregate structures no longer evolve at the length scales we probe. Based on this saturation, we define a time scale, τ I , which is larger than τ α but has essentially the same dependence on φ m . We interpret τ α (φ m ) and τ I (φ m ) in terms of a simple aggregation model based on diffusion-limited kinetics and a repulsive potential barrier that models the effective solvent quality

Imaginary Time Step Method to Solve the Dirac Equation with Nonlocal Potential

International Nuclear Information System (INIS)

Zhang Ying; Liang Haozhao; Meng Jie

2009-01-01

The imaginary time step (ITS) method is applied to solve the Dirac equation with nonlocal potentials in coordinate space. Taking the nucleus 12 C as an example, even with nonlocal potentials, the direct ITS evolution for the Dirac equation still meets the disaster of the Dirac sea. However, following the recipe in our former investigation, the disaster can be avoided by the ITS evolution for the corresponding Schroedinger-like equation without localization, which gives the convergent results exactly the same with those obtained iteratively by the shooting method with localized effective potentials.

Microsoft® Visual Basic® 2010 Step by Step

CERN Document Server

Halvorson, Michael

2010-01-01

Your hands-on, step-by-step guide to learning Visual Basic® 2010. Teach yourself the essential tools and techniques for Visual Basic® 2010-one step at a time. No matter what your skill level, you'll find the practical guidance and examples you need to start building professional applications for Windows® and the Web. Discover how to: Work in the Microsoft® Visual Studio® 2010 Integrated Development Environment (IDE)Master essential techniques-from managing data and variables to using inheritance and dialog boxesCreate professional-looking UIs; add visual effects and print supportBuild com

Real-time relaxation and kinetics in hot scalar QED: Landau damping

International Nuclear Information System (INIS)

Boyanovsky, D.; Vega, H.J. de; Holman, R.; Kumar, S.P.; Pisarski, R.D.

1998-01-01

The real time evolution of non-equilibrium expectation values with soft length scales ∼k -1 >(eT) -1 is solved in hot scalar electrodynamics, with a view towards understanding relaxational phenomena in the QGP and the electroweak plasma. We find that the gauge invariant non-equilibrium expectation values relax via power laws to asymptotic amplitudes that are determined by the quasiparticle poles. The long time relaxational dynamics and relevant time scales are determined by the behavior of the retarded self-energy not at the small frequencies, but at the Landau damping thresholds. This explains the presence of power laws and not of exponential decay. In the process we rederive the HTL effective action using non-equilibrium field theory. Furthermore we obtain the influence functional, the Langevin equation and the fluctuation-dissipation theorem for the soft modes, identifying the correlators that emerge in the classical limit. We show that a Markovian approximation fails to describe the dynamics both at short and long times. We find that the distribution function for soft quasiparticles relaxes with a power law through Landau damping. We also introduce a novel kinetic approach that goes beyond the standard Boltzmann equation by incorporating off-shell processes and find that the distribution function for soft quasiparticles relaxes with a power law through Landau damping. We find an unusual dressing dynamics of bare particles and anomalous (logarithmic) relaxation of hard quasiparticles. copyright 1998 The American Physical Society

Biochemistry of methyl-coenzyme M reductase: the nickel metalloenzyme that catalyzes the final step in synthesis and the first step in anaerobic oxidation of the greenhouse gas methane.

Science.gov (United States)

Ragsdale, Stephen W

2014-01-01

Methane, the major component of natural gas, has been in use in human civilization since ancient times as a source of fuel and light. Methanogens are responsible for synthesis of most of the methane found on Earth. The enzyme responsible for catalyzing the chemical step of methanogenesis is methyl-coenzyme M reductase (MCR), a nickel enzyme that contains a tetrapyrrole cofactor called coenzyme F430, which can traverse the Ni(I), (II), and (III) oxidation states. MCR and methanogens are also involved in anaerobic methane oxidation. This review describes structural, kinetic, and computational studies aimed at elucidating the mechanism of MCR. Such studies are expected to impact the many ramifications of methane in our society and environment, including energy production and greenhouse gas warming.

Canadian children's and youth's pedometer-determined steps/day, parent-reported TV watching time, and overweight/obesity: The CANPLAY Surveillance Study

Directory of Open Access Journals (Sweden)

Craig Cora L

2011-06-01

Full Text Available Abstract Background This study examines associations between pedometer-determined steps/day and parent-reported child's Body Mass Index (BMI and time typically spent watching television between school and dinner. Methods Young people (aged 5-19 years were recruited through their parents by random digit dialling and mailed a data collection package. Information on height and weight and time spent watching television between school and dinner on a typical school day was collected from parents. In total, 5949 boys and 5709 girls reported daily steps. BMI was categorized as overweight or obese using Cole's cut points. Participants wore pedometers for 7 days and logged daily steps. The odds of being overweight and obese by steps/day and parent-reported time spent television watching were estimated using logistic regression for complex samples. Results Girls had a lower median steps/day (10682 versus 11059 for boys and also a narrower variation in steps/day (interquartile range, 4410 versus 5309 for boys. 11% of children aged 5-19 years were classified as obese; 17% of boys and girls were overweight. Both boys and girls watched, on average, Discussion Television viewing is the more prominent factor in terms of predicting overweight, and it contributes to obesity, but steps/day attenuates the association between television viewing and obesity, and therefore can be considered protective against obesity. In addition to replacing opportunities for active alternative behaviours, exposure to television might also impact body weight by promoting excess energy intake. Conclusions In this large nationally representative sample, pedometer-determined steps/day was associated with reduced odds of being obese (but not overweight whereas each parent-reported hour spent watching television between school and dinner increased the odds of both overweight and obesity.

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

Science.gov (United States)

Costa, Rafael S; Veríssimo, André; Vinga, Susana

2014-08-13

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. 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. 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

Step by step parallel programming method for molecular dynamics code

International Nuclear Information System (INIS)

Orii, Shigeo; Ohta, Toshio

1996-07-01

Parallel programming for a numerical simulation program of molecular dynamics is carried out with a step-by-step programming technique using the two phase method. As a result, within the range of a certain computing parameters, it is found to obtain parallel performance by using the level of parallel programming which decomposes the calculation according to indices of do-loops into each processor on the vector parallel computer VPP500 and the scalar parallel computer Paragon. It is also found that VPP500 shows parallel performance in wider range computing parameters. The reason is that the time cost of the program parts, which can not be reduced by the do-loop level of the parallel programming, can be reduced to the negligible level by the vectorization. After that, the time consuming parts of the program are concentrated on less parts that can be accelerated by the do-loop level of the parallel programming. This report shows the step-by-step parallel programming method and the parallel performance of the molecular dynamics code on VPP500 and Paragon. (author)

PHISICS/RELAP5-3D Adaptive Time-Step Method Demonstrated for the HTTR LOFC#1 Simulation

Energy Technology Data Exchange (ETDEWEB)

Baker, Robin Ivey [Idaho National Lab. (INL), Idaho Falls, ID (United States); Balestra, Paolo [Univ. of Rome (Italy); Strydom, Gerhard [Idaho National Lab. (INL), Idaho Falls, ID (United States)

2017-05-01

A collaborative effort between Japan Atomic Energy Agency (JAEA) and Idaho National Laboratory (INL) as part of the Civil Nuclear Energy Working Group is underway to model the high temperature engineering test reactor (HTTR) loss of forced cooling (LOFC) transient that was performed in December 2010. The coupled version of RELAP5-3D, a thermal fluids code, and PHISICS, a neutronics code, were used to model the transient. The focus of this report is to summarize the changes made to the PHISICS-RELAP5-3D code for implementing an adaptive time step methodology into the code for the first time, and to test it using the full HTTR PHISICS/RELAP5-3D model developed by JAEA and INL and the LOFC simulation. Various adaptive schemes are available based on flux or power convergence criteria that allow significantly larger time steps to be taken by the neutronics module. The report includes a description of the HTTR and the associated PHISICS/RELAP5-3D model test results as well as the University of Rome sub-contractor report documenting the adaptive time step theory and methodology implemented in PHISICS/RELAP5-3D. Two versions of the HTTR model were tested using 8 and 26 energy groups. It was found that most of the new adaptive methods lead to significant improvements in the LOFC simulation time required without significant accuracy penalties in the prediction of the fission power and the fuel temperature. In the best performing 8 group model scenarios, a LOFC simulation of 20 hours could be completed in real-time, or even less than real-time, compared with the previous version of the code that completed the same transient 3-8 times slower than real-time. A few of the user choice combinations between the methodologies available and the tolerance settings did however result in unacceptably high errors or insignificant gains in simulation time. The study is concluded with recommendations on which methods to use for this HTTR model. An important caveat is that these findings

Kinetic modeling of the effect of solids retention time on methanethiol dynamics in anaerobic digestion.

Science.gov (United States)

Zhang, Dian; Strawn, Mary; Novak, John T; Wang, Zhi-Wu

2018-07-01

The highly volatile methanethiol (MT) with an extremely low odor threshold and distinctive putrid smell is often identified as a major odorous compound generated under anaerobic conditions. As an intermediate compound in the course of anaerobic digestion, the extent of MT emission is closely related to the time of anaerobic reaction. In this study, lab-scale anaerobic digesters were operated at solids retention time (SRTs) of 15, 20, 25, 30, 40 and 50 days to investigate the effect of SRT on MT emission. The experimental results demonstrated a bell-shaped curve of MT emission versus SRT with a peak around 20 days SRT. In order to understand this SRT effect, a kinetic model was developed to describe MT production and utilization dynamics in the course of anaerobic digestion and calibrated with the experimental results collected from this study. The model outcome revealed that the high protein content in the feed sludge together with the large maintenance coefficient of MT fermenters are responsible for the peak MT emission emergence in the range of typical SRT used for anaerobic digestion. A further analysis of the kinetic model shows that it can be extensively simplified with reasonable approximation to a form that anaerobic digestion practitioners could easily use to predict the MT and SRT relationship. Copyright © 2018 Elsevier Ltd. All rights reserved.

Kinetics and Mechanism of Paracetamol Oxidation by Chromium(VI in Absence and Presence of Manganese(II and Sodiumdodecyl Sulphate

Directory of Open Access Journals (Sweden)

Maqsood Ahmad Malik

2007-11-01

Full Text Available The kinetics of paracetamol oxidation are first order each in [paracetamol] and [HClO4]. The kinetic study shows that the oxidation proceeds in two steps. The effects of anionic micelles of sodiumdodecyl sulphate (SDS and complexing agents (ethylenediammine tetraacetic acid (EDTA and 2,2′-bipyridyl (bpy were also studied. Fast kinetic spectrophotometric method has been described for the determination of paracetamol. The method is based on the catalytic effect of manganese(II on the oxidation of paracetamol by chromium(VI in the presence of HClO4 (= 0.23 mol dm−3. Optimum reaction time is 4 to 6 minutes at a temperature of 30∘C. The addition of manganese(II ions largely decreased the absorbance of chromium(VI at 350 nm. This reaction can be utilized for the determination of paracetamol in drugs.

Development, validation and application of multi-point kinetics model in RELAP5 for analysis of asymmetric nuclear transients

Energy Technology Data Exchange (ETDEWEB)

Pradhan, Santosh K., E-mail: santosh@aerb.gov.in [Nuclear Safety Analysis Division, Atomic Energy Regulatory Board, Mumbai 400094 (India); Obaidurrahman, K. [Nuclear Safety Analysis Division, Atomic Energy Regulatory Board, Mumbai 400094 (India); Iyer, Kannan N. [Department of Mechanical Engineering, IIT Bombay, Mumbai 400076 (India); Gaikwad, Avinash J. [Nuclear Safety Analysis Division, Atomic Energy Regulatory Board, Mumbai 400094 (India)

2016-04-15

Highlights: • A multi-point kinetics model is developed for RELAP5 system thermal hydraulics code. • Model is validated against extensive 3D kinetics code. • RELAP5 multi-point kinetics formulation is used to investigate critical break for LOCA in PHWR. - Abstract: Point kinetics approach in system code RELAP5 limits its use for many of the reactivity induced transients, which involve asymmetric core behaviour. Development of fully coupled 3D core kinetics code with system thermal-hydraulics is the ultimate requirement in this regard; however coupling and validation of 3D kinetics module with system code is cumbersome and it also requires access to source code. An intermediate approach with multi-point kinetics is appropriate and relatively easy to implement for analysis of several asymmetric transients for large cores. Multi-point kinetics formulation is based on dividing the entire core into several regions and solving ODEs describing kinetics in each region. These regions are interconnected by spatial coupling coefficients which are estimated from diffusion theory approximation. This model offers an advantage that associated ordinary differential equations (ODEs) governing multi-point kinetics formulation can be solved using numerical methods to the desired level of accuracy and thus allows formulation based on user defined control variables, i.e., without disturbing the source code and hence also avoiding associated coupling issues. Euler's method has been used in the present formulation to solve several coupled ODEs internally at each time step. The results have been verified against inbuilt point-kinetics models of RELAP5 and validated against 3D kinetics code TRIKIN. The model was used to identify the critical break in RIH of a typical large PHWR core. The neutronic asymmetry produced in the core due to the system induced transient was effectively handled by the multi-point kinetics model overcoming the limitation of in-built point kinetics model

On-rate based optimization of structure-kinetic relationship--surfing the kinetic map.

Science.gov (United States)

Schoop, Andreas; Dey, Fabian

2015-10-01

In the lead discovery process residence time has become an important parameter for the identification and characterization of the most efficacious compounds in vivo. To enable the success of compound optimization by medicinal chemistry toward a desired residence time the understanding of structure-kinetic relationship (SKR) is essential. This article reviews various approaches to monitor SKR and suggests using the on-rate as the key monitoring parameter. The literature is reviewed and examples of compound series with low variability as well as with significant changes in on-rates are highlighted. Furthermore, findings of kinetic on-rate changes are presented and potential underlying rationales are discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Kinetic Mechanism of OMP Synthase:  A Slow Physical Step Following

DEFF Research Database (Denmark)

Wang, G.P.; Lundegaard, Claus; Jensen, Kaj Frank

1999-01-01

medium was increased with sucrose, the forward kcat decreased in proportion to ¿rel with a slope of 0.8. In the reverse reaction a more limited dependence of kcat (slope = 0.3) was observed. On the basis of the known structures of OPRTase, we propose that a highly conserved, catalytically important......, solvent-exposed loop descends during catalysis to shield the active site. In the accompanying paper, the slow product release step is shown to relate to movement of the solvent-exposed loop....

Kinetic study of time-dependent fixation of U"V"I on biochar

International Nuclear Information System (INIS)

Ashry, A.; Bailey, E.H.; Chenery, S.R.N.; Young, S.D.

2016-01-01

Biochar, a by-product from the production of biofuel and syngas by gasification, was tested as a material for adsorption and fixation of U"V"I from aqueous solutions. A batch experiment was conducted to study the factors that influence the adsorption and time-dependent fixation on biochar at 20 °C, including pH, initial concentration of U"V"I and contact time. Uranium (U"V"I) adsorption was highly dependent on pH but adsorption on biochar was high over a wide range of pH values, from 4.5 to 9.0, and adsorption strength was time-dependent over several days. The experimental data for pH > 7 were most effectively modelled using a Freundlich adsorption isotherm coupled to a reversible first order kinetic equation to describe the time-dependent fixation of U"V"I within the biochar structure. Desorption experiments showed that U"V"I was only sparingly desorbable from the biochar with time and isotopic dilution with "2"3"3U"V"I confirmed the low, or time-dependent, lability of adsorbed "2"3"8U"V"I. Below pH 7 the adsorption isotherm trend suggested precipitation, rather than true adsorption, may occur. However, across all pH values (4.5-9) measured saturation indices suggested precipitation was possible: autunite below pH 6.5 and either swartzite, liebigite or bayleyite above pH 6.5.

Recovery Estimation of Dried Foodborne Pathogens Is Directly Related to Rehydration Kinetics

Science.gov (United States)

Lang, Emilie; Zoz, Fiona; Iaconelli, Cyril; Guyot, Stéphane; Alvarez-Martin, Pablo; Beney, Laurent; Perrier-Cornet, Jean-Marie; Gervais, Patrick

2016-01-01

Drying is a common process which is used to preserve food products and technological microorganisms, but which is deleterious for the cells. The aim of this study is to differentiate the effects of drying alone from the effects of the successive and necessary rehydration. Rehydration of dried bacteria is a critical step already studied in starter culture but not for different kinetics and not for pathogens. In the present study, the influence of rehydration kinetics was investigated for three foodborne pathogens involved in neonatal diseases caused by the consumption of rehydrated milk powder: Salmonella enterica subsp. enterica serovar Typhimurium, Salmonella enterica subsp. enterica serovar Senftenberg and Cronobacter sakazakii. Bacteria were dried in controlled relative humidity atmospheres and then rehydrated using different methods. Our results showed that the survival of the three pathogens was strongly related to rehydration kinetics. Consequently, rehydration is an important step to consider during food safety assessment or during studies of dried foodborne pathogens. Also, it has to be considered with more attention in consumers’ homes during the preparation of food, like powdered infant formula, to avoid pathogens recovery. PMID:27494169

Recovery Estimation of Dried Foodborne Pathogens Is Directly Related to Rehydration Kinetics.

Directory of Open Access Journals (Sweden)

Emilie Lang

Full Text Available Drying is a common process which is used to preserve food products and technological microorganisms, but which is deleterious for the cells. The aim of this study is to differentiate the effects of drying alone from the effects of the successive and necessary rehydration. Rehydration of dried bacteria is a critical step already studied in starter culture but not for different kinetics and not for pathogens. In the present study, the influence of rehydration kinetics was investigated for three foodborne pathogens involved in neonatal diseases caused by the consumption of rehydrated milk powder: Salmonella enterica subsp. enterica serovar Typhimurium, Salmonella enterica subsp. enterica serovar Senftenberg and Cronobacter sakazakii. Bacteria were dried in controlled relative humidity atmospheres and then rehydrated using different methods. Our results showed that the survival of the three pathogens was strongly related to rehydration kinetics. Consequently, rehydration is an important step to consider during food safety assessment or during studies of dried foodborne pathogens. Also, it has to be considered with more attention in consumers' homes during the preparation of food, like powdered infant formula, to avoid pathogens recovery.

Kinetics of the epoxy–thiol click reaction initiated by a tertiary amine: Calorimetric study using monofunctional components

International Nuclear Information System (INIS)

Loureiro, Roi Meizoso; Amarelo, Tánia Carballeira; Abuin, Senen Paz; Soulé, Ezequiel R.; Williams, Roberto J.J.

2015-01-01

Graphical abstract: - Highlights: • Reaction kinetics of a monoepoxy and a monothiol was studied by DSC. • Benzyldimethylamine (BDMA) was used as initiator. • Reaction exhibited a long induction period followed by a fast autocatalytic rate. • A mechanistic kinetic model provided a reasonable fitting of the kinetic behavior. • The formulation simulates the behavior of room-temperature-cure commercial epoxies. - Abstract: An analysis of the kinetics of the epoxy–thiol reaction in a model stoichiometric system of monofunctional reagents, 3-mercaptopropionate (BMP) and phenylglycidylether (PGE) is reported. Benzyldimethylamine (BDMA) was employed as initiator in amounts ranging from 0.5 to 2 wt%. These formulations showed a kinetic behavior qualitatively similar to that of commercial adhesives and coatings formulated for a room-temperature cure. Isothermal DSC scans revealed the existence of a relatively long induction period preceding a fast autocatalytic reaction step. Dynamic DSC scans showed that the reaction was shifted to a lower temperature range by increasing the storage period of the initial formulation at 20 °C. This unusual kinetic behavior could be modeled assuming that thiolate anions, slowly generated during the induction period, initiated a fast autocatalytic propagation/proton transfer reaction. The kinetic model included a pseudo-steady state for the initiator concentration and an equilibrium reaction between epoxy and OH groups generated by reaction. A reasonable fitting of isothermal and dynamic DSC runs was achieved in a broad range of temperatures and amine concentrations. In particular, both the length of the induction time and the effect of the storage period were correctly predicted

Kinetics of the epoxy–thiol click reaction initiated by a tertiary amine: Calorimetric study using monofunctional components

Energy Technology Data Exchange (ETDEWEB)

Loureiro, Roi Meizoso; Amarelo, Tánia Carballeira [Gairesa, Outeiro 1, Lago (Valdoviño), 15551 A Coruña (Spain); Abuin, Senen Paz, E-mail: senen@gairesa.com [Gairesa, Outeiro 1, Lago (Valdoviño), 15551 A Coruña (Spain); Soulé, Ezequiel R. [Institute of Materials Science and Technology (INTEMA), University of Mar del Plata and National Research Council (CONICET), J. B. Justo 4302, 7600 Mar del Plata (Argentina); Williams, Roberto J.J., E-mail: williams@fi.mdp.edu.ar [Institute of Materials Science and Technology (INTEMA), University of Mar del Plata and National Research Council (CONICET), J. B. Justo 4302, 7600 Mar del Plata (Argentina)

2015-09-20

Graphical abstract: - Highlights: • Reaction kinetics of a monoepoxy and a monothiol was studied by DSC. • Benzyldimethylamine (BDMA) was used as initiator. • Reaction exhibited a long induction period followed by a fast autocatalytic rate. • A mechanistic kinetic model provided a reasonable fitting of the kinetic behavior. • The formulation simulates the behavior of room-temperature-cure commercial epoxies. - Abstract: An analysis of the kinetics of the epoxy–thiol reaction in a model stoichiometric system of monofunctional reagents, 3-mercaptopropionate (BMP) and phenylglycidylether (PGE) is reported. Benzyldimethylamine (BDMA) was employed as initiator in amounts ranging from 0.5 to 2 wt%. These formulations showed a kinetic behavior qualitatively similar to that of commercial adhesives and coatings formulated for a room-temperature cure. Isothermal DSC scans revealed the existence of a relatively long induction period preceding a fast autocatalytic reaction step. Dynamic DSC scans showed that the reaction was shifted to a lower temperature range by increasing the storage period of the initial formulation at 20 °C. This unusual kinetic behavior could be modeled assuming that thiolate anions, slowly generated during the induction period, initiated a fast autocatalytic propagation/proton transfer reaction. The kinetic model included a pseudo-steady state for the initiator concentration and an equilibrium reaction between epoxy and OH groups generated by reaction. A reasonable fitting of isothermal and dynamic DSC runs was achieved in a broad range of temperatures and amine concentrations. In particular, both the length of the induction time and the effect of the storage period were correctly predicted.

Multiresponse kinetic modelling of Maillard reaction and caramelisation in a heated glucose/wheat flour system.

Science.gov (United States)

Kocadağlı, Tolgahan; Gökmen, Vural

2016-11-15

The study describes the kinetics of the formation and degradation of α-dicarbonyl compounds in glucose/wheat flour system heated under low moisture conditions. Changes in the concentrations of glucose, fructose, individual free amino acids, lysine and arginine residues, glucosone, 1-deoxyglucosone, 3-deoxyglucosone, 3,4-dideoxyglucosone, 5-hydroxymethyl-2-furfural, glyoxal, methylglyoxal and diacetyl concentrations were determined to form a multiresponse kinetic model for isomerisation and degradation reactions of glucose. Degradation of Amadori product mainly produced 1-deoxyglucosone. Formation of 3-deoxyglucosone proceeded directly from glucose and also Amadori product degradation. Glyoxal formation was predominant from glucosone while methylglyoxal and diacetyl originated from 1-deoxyglucosone. Formation of 5-hydroxymethyl-2-furfural from fructose was found to be a key step. Multi-response kinetic modelling of Maillard reaction and caramelisation simultaneously indicated quantitatively predominant parallel and consecutive pathways and rate limiting steps by estimating the reaction rate constants. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparison of two forms of Vlasov-type relativistic kinetic equations in hadrodynamics

International Nuclear Information System (INIS)

Mashnik, S.G.; Maino, G.

1996-01-01

A comparison of two methods in the relativistic kinetic theory of the Fermi systems is carried out assuming, as an example, the simplest σω-version of quantum hadrodynamics with allowance for strong mean meson fields. It is shown that the Vlasov-type relativistic kinetic equation (VRKE) obtained by means of the procedure of squaring at an intermediate step is responsible for unphysical features. A direct method of derivation of kinetic equations is proposed. This method does not contain such drawback and gives rise to VRKE in hydrodynamics of a non-contradictory form in which both spin degrees of freedom and states with positive and negative energies are taken into account. 17 refs

Kinetics of apoptotic markers in exogeneously induced apoptosis of EL4 cells.

Science.gov (United States)

Jessel, Robert; Haertel, Steffen; Socaciu, Carmen; Tykhonova, Svetlana; Diehl, Horst A

2002-01-01

We investigated the time-dependence of apoptotic events in EL4 cells by monitoring plasma membrane changes in correlation to DNA fragmentation and cell shrinkage. We applied three apoptosis inducers (staurosporine, tubericidine and X-rays) and we looked at various markers to follow the early-to-late apoptotic events: phospholipid translocation (identified through annexin V-fluorescein assay and propidium iodide), lipid package (via merocyanine assay), membrane fluidity and anisotropy (via fluorescent measurements), DNA fragmentation by the fluorescence-labeling test and cell size measurements. The different apoptotic inducers caused different reactions of the cells: staurosporine induced apoptosis most rapidly in a high number of cells, tubercidine triggered apoptosis only in the S phase cells, while X-rays caused a G2/M arrest and subsequently apoptosis. Loss of lipid asymmetry is promptly detectable after one hour of incubation time. The phosphatidylserine translocation, decrease of lipid package and anisotropy, and the increase of membrane fluidity appeared to be based on the same process of lipid asymmetry loss. Therefore, the DNA fragmentation and the cell shrinkage appear to be parallel and independent processes running on different time scales but which are kinetically inter-related. The results indicate different signal steps to apoptosis dependent on inducer characteristics but the kinetics of "early-to-late" apoptosis appears to be a fixed program.

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

Science.gov (United States)

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. ...

Plasmon-induced photoelectrochemical biosensor for in situ real-time measurement of biotin-streptavidin binding kinetics under visible light irradiation

International Nuclear Information System (INIS)

Guo, Jingchun; Oshikiri, Tomoya; Ueno, Kosei; Shi, Xu; Misawa, Hiroaki

2017-01-01

We developed a localized surface plasmon-induced visible light-responsive photoelectrochemical (PEC) biosensor using a titanium dioxide (TiO_2) photoelectrode loaded with gold nanoislands (AuNIs) for in situ real-time measurement of biotin-streptavidin association. As a proof of concept, self-assembled thiol-terminated biotin molecules bound on a AuNIs/TiO_2 photoelectrode were successfully utilized to explore the photocurrent response to streptavidin-modified gold nanoparticle (STA-AuNP) solutions. This plasmon-induced PEC biosensor is simple and easy to miniaturize. Additionally, the PEC biosensor achieves highly sensitive measurements under only visible light irradiation and prevents the UV-induced damage of samples. Furthermore, a novel approach has been proposed to realize the real-time monitoring of biotin-STA binding affinities and kinetics by analyzing the PEC sensing characteristics. This PEC biosensor and novel analysis method could provide a new approach for the specific electrical detection and real-time kinetic measurements for clinical diagnostics and drug development. - Highlights: • A plasmon-induced visible light-responsive photoelectrochemical biosensor is developed and the system can be miniaturized.

Plasmon-induced photoelectrochemical biosensor for in situ real-time measurement of biotin-streptavidin binding kinetics under visible light irradiation

Energy Technology Data Exchange (ETDEWEB)

Guo, Jingchun; Oshikiri, Tomoya; Ueno, Kosei; Shi, Xu [Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0021 (Japan); Misawa, Hiroaki, E-mail: misawa@es.hokudai.ac.jp [Research Institute for Electronic Science, Hokkaido University, Sapporo 001-0021 (Japan); Department of Applied Chemistry & Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan (China)

2017-03-08

We developed a localized surface plasmon-induced visible light-responsive photoelectrochemical (PEC) biosensor using a titanium dioxide (TiO{sub 2}) photoelectrode loaded with gold nanoislands (AuNIs) for in situ real-time measurement of biotin-streptavidin association. As a proof of concept, self-assembled thiol-terminated biotin molecules bound on a AuNIs/TiO{sub 2} photoelectrode were successfully utilized to explore the photocurrent response to streptavidin-modified gold nanoparticle (STA-AuNP) solutions. This plasmon-induced PEC biosensor is simple and easy to miniaturize. Additionally, the PEC biosensor achieves highly sensitive measurements under only visible light irradiation and prevents the UV-induced damage of samples. Furthermore, a novel approach has been proposed to realize the real-time monitoring of biotin-STA binding affinities and kinetics by analyzing the PEC sensing characteristics. This PEC biosensor and novel analysis method could provide a new approach for the specific electrical detection and real-time kinetic measurements for clinical diagnostics and drug development. - Highlights: • A plasmon-induced visible light-responsive photoelectrochemical biosensor is developed and the system can be miniaturized.

Comparison of different chemical kinetic mechanisms of methane combustion in an internal combustion engine configuration

OpenAIRE

Ennetta Ridha; Hamdi Mohamed; Said Rachid

2008-01-01

Three chemical kinetic mechanisms of methane combustion were tested and compared using the internal combustion engine model of Chemkin 4.02 [1]: one-step global reaction mechanism, four-step mechanism, and the standard detailed scheme GRIMECH 3.0. This study shows good concordances, especially between the four-step and the detailed mechanisms in the prediction of temperature and main species profiles. But reduced schemes were incapables to predict pollutant emissions in an internal combustion...

Kinetic and Mechanism Study of Vanadium Acid Leaching from Black Shale Using Microwave Heating Method

Science.gov (United States)

Wang, Jing-peng; Zhang, Yi-min; Huang, Jing; Liu, Tao

2018-04-01

The leaching kinetics of the vanadium leaching process were investigated by the comparison of microwave heating and conventional heating methods. Microwave heating with CaF2 had a synergistic effect and improved the vanadium leaching efficiency. In contrast to conventional heating leaching, microwave heating accelerated the vanadium leaching rate by approximately 1-3% and by approximately 15% when CaF2 was also used. The kinetics analysis showed that the calculated activation energy decreased in the microwave heating method in the presence and absence of CaF2. The control procedure of leaching also changed from a chemical reaction control step to a mixed chemical diffusion control step upon the addition of CaF2. Microwave heating was shown to be suitable for leaching systems with diffusion or mixed chemical diffusion control steps when the target mineral does not have a microwave absorbing ability.

Kinetic and Mechanism Study of Vanadium Acid Leaching from Black Shale Using Microwave Heating Method

Science.gov (United States)

Wang, Jing-peng; Zhang, Yi-min; Huang, Jing; Liu, Tao

2018-06-01

The leaching kinetics of the vanadium leaching process were investigated by the comparison of microwave heating and conventional heating methods. Microwave heating with CaF2 had a synergistic effect and improved the vanadium leaching efficiency. In contrast to conventional heating leaching, microwave heating accelerated the vanadium leaching rate by approximately 1-3% and by approximately 15% when CaF2 was also used. The kinetics analysis showed that the calculated activation energy decreased in the microwave heating method in the presence and absence of CaF2. The control procedure of leaching also changed from a chemical reaction control step to a mixed chemical diffusion control step upon the addition of CaF2. Microwave heating was shown to be suitable for leaching systems with diffusion or mixed chemical diffusion control steps when the target mineral does not have a microwave absorbing ability.

Time scale of random sequential adsorption.

Science.gov (United States)

Erban, Radek; Chapman, S Jonathan

2007-04-01

A simple multiscale approach to the diffusion-driven adsorption from a solution to a solid surface is presented. The model combines two important features of the adsorption process: (i) The kinetics of the chemical reaction between adsorbing molecules and the surface and (ii) geometrical constraints on the surface made by molecules which are already adsorbed. The process (i) is modeled in a diffusion-driven context, i.e., the conditional probability of adsorbing a molecule provided that the molecule hits the surface is related to the macroscopic surface reaction rate. The geometrical constraint (ii) is modeled using random sequential adsorption (RSA), which is the sequential addition of molecules at random positions on a surface; one attempt to attach a molecule is made per one RSA simulation time step. By coupling RSA with the diffusion of molecules in the solution above the surface the RSA simulation time step is related to the real physical time. The method is illustrated on a model of chemisorption of reactive polymers to a virus surface.

Bainitic transformation during the two-step quenching and partitioning process in a medium carbon steel containing silicon

Energy Technology Data Exchange (ETDEWEB)

Li, H.Y.; Lu, X.W. [School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240 (China); Wu, X.C.; Min, Y.A. [School of Materials Science and Engineering, Shanghai University, Shanghai 200240 (China); Jin, X.J., E-mail: jin@sjtu.edu.cn [School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240 (China)

2010-09-15

Research highlights: In this paper, SEM and TEM were used to characterize microstructure of Q and P steels with different partitioning time at 300 deg. C. The interesting phenomena were discovered and discussed: 1.Lower bainite (bainitic ferrite plus {epsilon}-carbide) rather than carbide-free bainite was observed during partitioning process. 2.The mechanical properties of Q and P steels can be tailored and adjusted through balance volume fraction of retained austenite and lower bainite during partitioning process. 3.The final amount of austenite was influenced by the transformation kinetics of lower bainite during partitioning process. According to the analysis, it can be concluded that associated with carbon partitioning from martensite to austenite, lower bainite transformation inevitably occurred. More importantly, lower bainite transformation seriously affected the mechanical properties of Q and P steels and final amount of austenite. - Abstract: A study of 40SiMnNiCr steel subjected to a two-step quenching and partitioning process (Q and P) is presented. The result suggests that strength variation of Q and P steels during the two-step Q and P process was a cumulative effect of increase of retained austenite fraction, decrease of carbon supersaturation of virgin martensite, and particularly much of lower bainite formation. A trade-off between high strength and good ductility of two-step Q and P steels can be tailored and adjusted by controlling lower bainite fraction. The final amount of austenite was influenced by the transformation kinetics of lower bainite during the partitioning process.

Bainitic transformation during the two-step quenching and partitioning process in a medium carbon steel containing silicon

International Nuclear Information System (INIS)

Li, H.Y.; Lu, X.W.; Wu, X.C.; Min, Y.A.; Jin, X.J.

2010-01-01

Research highlights: In this paper, SEM and TEM were used to characterize microstructure of Q and P steels with different partitioning time at 300 deg. C. The interesting phenomena were discovered and discussed: 1.Lower bainite (bainitic ferrite plus ε-carbide) rather than carbide-free bainite was observed during partitioning process. 2.The mechanical properties of Q and P steels can be tailored and adjusted through balance volume fraction of retained austenite and lower bainite during partitioning process. 3.The final amount of austenite was influenced by the transformation kinetics of lower bainite during partitioning process. According to the analysis, it can be concluded that associated with carbon partitioning from martensite to austenite, lower bainite transformation inevitably occurred. More importantly, lower bainite transformation seriously affected the mechanical properties of Q and P steels and final amount of austenite. - Abstract: A study of 40SiMnNiCr steel subjected to a two-step quenching and partitioning process (Q and P) is presented. The result suggests that strength variation of Q and P steels during the two-step Q and P process was a cumulative effect of increase of retained austenite fraction, decrease of carbon supersaturation of virgin martensite, and particularly much of lower bainite formation. A trade-off between high strength and good ductility of two-step Q and P steels can be tailored and adjusted by controlling lower bainite fraction. The final amount of austenite was influenced by the transformation kinetics of lower bainite during the partitioning process.

AIREK-MOD, Time Dependent Reactor Kinetics with Feedback Differential Equation

International Nuclear Information System (INIS)

Tamagnini, C.

1984-01-01

1 - Nature of physical problem solved: Solves the reactor kinetic equations with respect to time. A standard form for the reactivity behaviour has been introduced in which the reactivity is given by the sum of a polynomial, sine, cosine and exponential expansion. Tabular form is also included. The presence of feedback differential equations in which the dependence on variables different from the considered one is considered enables many heat-exchange problems to be dealt with. 2 - Method of solution: The method employed for the solution of the differential equations is the one developed by E.R. Cohen (Geneva Conference, 1958). 3 - Restrictions on the complexity of the problem: The maximum number of differential equations that can be solved simultaneously is 50. Within this limitation there may be n delayed neutron groups (n less than or equal to 25), on m other linear feedback equations (n+m less than or equal to 49). CDC 1604 version was offered by EIR (Institut Federal de Recherches en matiere de reacteurs, Switzerland)

Approximate method for stochastic chemical kinetics with two-time scales by chemical Langevin equations

International Nuclear Information System (INIS)

Wu, Fuke; Tian, Tianhai; Rawlings, James B.; Yin, George

2016-01-01

The frequently used reduction technique is based on the chemical master equation for stochastic chemical kinetics with two-time scales, which yields the modified stochastic simulation algorithm (SSA). For the chemical reaction processes involving a large number of molecular species and reactions, the collection of slow reactions may still include a large number of molecular species and reactions. Consequently, the SSA is still computationally expensive. Because the chemical Langevin equations (CLEs) can effectively work for a large number of molecular species and reactions, this paper develops a reduction method based on the CLE by the stochastic averaging principle developed in the work of Khasminskii and Yin [SIAM J. Appl. Math. 56, 1766–1793 (1996); ibid. 56, 1794–1819 (1996)] to average out the fast-reacting variables. This reduction method leads to a limit averaging system, which is an approximation of the slow reactions. Because in the stochastic chemical kinetics, the CLE is seen as the approximation of the SSA, the limit averaging system can be treated as the approximation of the slow reactions. As an application, we examine the reduction of computation complexity for the gene regulatory networks with two-time scales driven by intrinsic noise. For linear and nonlinear protein production functions, the simulations show that the sample average (expectation) of the limit averaging system is close to that of the slow-reaction process based on the SSA. It demonstrates that the limit averaging system is an efficient approximation of the slow-reaction process in the sense of the weak convergence.

Smart Wireless Power Transfer Operated by Time-Modulated Arrays via a Two-Step Procedure

Directory of Open Access Journals (Sweden)

Diego Masotti

2015-01-01

Full Text Available The paper introduces a novel method for agile and precise wireless power transmission operated by a time-modulated array. The unique, almost real-time reconfiguration capability of these arrays is fully exploited by a two-step procedure: first, a two-element time-modulated subarray is used for localization of tagged sensors to be energized; the entire 16-element TMA then provides the power to the detected tags, by exploiting the fundamental and first-sideband harmonic radiation. An investigation on the best array architecture is carried out, showing the importance of the adopted nonlinear/full-wave computer-aided-design platform. Very promising simulated energy transfer performance of the entire nonlinear radiating system is demonstrated.