Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory

DOE PAGES

Bao, Junwei Lucas; Zheng, Jingjing; Truhlar, Donald G.

2016-02-03

Here, pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry. We employ a new calibration procedure for quantum Rice–Ramsperger–Kassel (QRRK) unimolecular rate theory within a chemical activation mechanism to calculate the pressure-falloff effect of a radical association with an aromatic ring. The new theoretical framework is applied to the reaction of H with toluene, which is a prototypical reaction in the combustion chemistry of aromatic hydrocarbons present in most fuels. Both the hydrogen abstraction reactions and the hydrogen addition reactions are calculated. Our system-specific (SS) QRRK approach is adjusted with SS parameters to agree with multistructural canonical variational transition statemore » theory with multidimensional tunneling (MS-CVT/SCT) at the high-pressure limit. The new method avoids the need for the usual empirical estimations of the QRRK parameters, and it eliminates the need for variational transition state theory calculations as a function of energy, although in this first application we do validate the falloff curves by comparing SS-QRRK results without tunneling to multistructural microcanonical variational transition state theory (MS-μVT) rate constants without tunneling. At low temperatures, the two approaches agree well with each other, but at high temperatures, SS-QRRK tends to overestimate falloff slightly. We also show that the variational effect is important in computing the energy-resolved rate constants. Multiple-structure anharmonicity, torsional–potential anharmonicity, and high-frequency-mode vibrational anharmonicity are all included in the rate computations, and torsional anharmonicity effects on the density of states are investigated. Branching fractions, which are both temperature- and pressure-dependent (and for which only limited data is available from experiment), are predicted as a function of pressure.« less

Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory.

PubMed

Bao, Junwei Lucas; Zheng, Jingjing; Truhlar, Donald G

2016-03-02

Pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry. We employ a new calibration procedure for quantum Rice-Ramsperger-Kassel (QRRK) unimolecular rate theory within a chemical activation mechanism to calculate the pressure-falloff effect of a radical association with an aromatic ring. The new theoretical framework is applied to the reaction of H with toluene, which is a prototypical reaction in the combustion chemistry of aromatic hydrocarbons present in most fuels. Both the hydrogen abstraction reactions and the hydrogen addition reactions are calculated. Our system-specific (SS) QRRK approach is adjusted with SS parameters to agree with multistructural canonical variational transition state theory with multidimensional tunneling (MS-CVT/SCT) at the high-pressure limit. The new method avoids the need for the usual empirical estimations of the QRRK parameters, and it eliminates the need for variational transition state theory calculations as a function of energy, although in this first application we do validate the falloff curves by comparing SS-QRRK results without tunneling to multistructural microcanonical variational transition state theory (MS-μVT) rate constants without tunneling. At low temperatures, the two approaches agree well with each other, but at high temperatures, SS-QRRK tends to overestimate falloff slightly. We also show that the variational effect is important in computing the energy-resolved rate constants. Multiple-structure anharmonicity, torsional-potential anharmonicity, and high-frequency-mode vibrational anharmonicity are all included in the rate computations, and torsional anharmonicity effects on the density of states are investigated. Branching fractions, which are both temperature- and pressure-dependent (and for which only limited data is available from experiment), are predicted as a function of pressure.

Method for detecting and distinguishing between specific types of environmental radiation using a high pressure ionization chamber with pulse-mode readout

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

Degtiarenko, Pavel V.

An environmental radiation detector for detecting and distinguishing between all types of environmental radiation, including photons, charged particles, and neutrons. A large volume high pressure ionization chamber (HPIC) includes BF.sub.3 gas at a specific concentration to render the radiation detector sensitive to the reactions of neutron capture in Boron-10 isotope. A pulse-mode readout is connected to the ionization chamber capable of measuring both the height and the width of the pulse. The heavy charged products of the neutron capture reaction deposit significant characteristic energy of the reaction in the immediate vicinity of the reaction in the gas, producing a signalmore » with a pulse height proportional to the reaction energy, and a narrow pulse width corresponding to the essentially pointlike energy deposition in the gas. Readout of the pulse height and the pulse width parameters of the signals enables distinguishing between the different types of environmental radiation, such as gamma (x-rays), cosmic muons, and neutrons.« less

Energy- and wave-based beam-tracing prediction of room-acoustical parameters using different boundary conditions.

PubMed

Yousefzadeh, Behrooz; Hodgson, Murray

2012-09-01

A beam-tracing model was used to study the acoustical responses of three empty, rectangular rooms with different boundary conditions. The model is wave-based (accounting for sound phase) and can be applied to rooms with extended-reaction surfaces that are made of multiple layers of solid, fluid, or poroelastic materials-the acoustical properties of these surfaces are calculated using Biot theory. Three room-acoustical parameters were studied in various room configurations: sound strength, reverberation time, and RApid Speech Transmission Index. The main objective was to investigate the effects of modeling surfaces as either local or extended reaction on predicted values of these three parameters. Moreover, the significance of modeling interference effects was investigated, including the study of sound phase-change on surface reflection. Modeling surfaces as of local or extended reaction was found to be significant for surfaces consisting of multiple layers, specifically when one of the layers is air. For multilayers of solid materials with an air-cavity, this was most significant around their mass-air-mass resonance frequencies. Accounting for interference effects made significant changes in the predicted values of all parameters. Modeling phase change on reflection, on the other hand, was found to be relatively much less significant.

[Flavonoid oxidation kinetics in aqueous and aqueous organic media in the presence of peroxidase, tyrosynase, and hemoglobin].

PubMed

Barsukova, M E; Tokareva, A I; Buslova, T S; Malinina, L I; Veselova, I A; Shekhovtsova, T N

2017-01-01

The kinetics of oxidation reactions of flavonoids, quercetin, dihydroquercetin, and epicatechin has been studied in the presence of biocatalysts of different natures: horseradish peroxidase, mushroom tyrosinase, and hemoglobin from bull blood. Comparison of the kinetic parameters of the oxidation reaction showed that peroxidase appeared to be the most effective biocatalyst in these processes. The specificity of the enzyme for quercetin increased with increasing the polarity of the solvent in a series of ethanol–acetonitrile–dimethyl sulfoxide.

[Neuropsychological methods of examination of age-specific performance parameters (author's transl)].

PubMed

Quatember, R; Maly, J

1980-11-15

200 test persons were subjected to a double-blind experiment involving a medication of K. H. 3 (Schwarzhaupt). The measurement procedures involved 9 apparatus dealing with psychophysiological measurement level methods and led to the following outcomes: 1) Increase of the psychomotor tempo of the dominant hand after 5 month application of K. H. 3 (motor performance series). -2) Reduction of reaction errors determined by a vigilance measurement instrument after 5 month treatment with K. H. 3 (evidenced by an increase in monotony resistance and continous attention). -3) Improvement of multiple-choice reactions (simultaneous reaction capacity) to optic, acoustic and orientation-linked stimuli (fewer false and delayed reactions). -4) Increase of visual attentiveness and visual short time memory after 5 month medication of K. H. 3 measured by the Cognitron concentration measurement device). No statistically significant differences of the investigated performance parameters were found between K. H. 3 and placebo groups after 3 month application of K. H. 3. The result of the present study involving measurements at the psychophysiological measurement level are compared with data of a previous study.

Vitamin C: Rate of Decay and Stability Characteristics

ERIC Educational Resources Information Center

Kakis, Frederic J.; Rossi, Carl J.

1974-01-01

Describes an experiment designed to provide the opportunity for studying some of the parameters affecting the stability of Vitamin C in various environments, and to acquaint the student with an experimental procedure for studying simple reaction kinetics and the calculations of specific rate constants. (Author/JR)

Combustion performance and heat transfer characterization of LOX/hydrocarbon type propellants

NASA Technical Reports Server (NTRS)

Gross, R. S.

1980-01-01

A sound data base was established by analytically and experimentally generating basic regenerative cooling, combustion performance, combustion stability, and combustion chamber heat transfer parameters for LOX/HC propellants, with specific application to second generation orbit maneuvering and reaction control systems (OMS/RCS) for the Space Shuttle Orbiter.

Spectroscopic detection, characterization and dynamics of free radicals relevant to combustion processes

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

Miller, Terry

2015-06-04

Combustion chemistry is enormously complex. The chemical mechanisms involve a multitude of elementary reaction steps and a comparable number of reactive intermediates, many of which are free radicals. Computer simulations based upon these mechanisms are limited by the validity of the mechanisms and the parameters characterizing the properties of the intermediates and their reactivity. Spectroscopy can provide data for sensitive and selective diagnostics to follow their reactions. Spectroscopic analysis also provides detailed parameters characterizing the properties of these intermediates. These parameters serve as experimental gold standards to benchmark predictions of these properties from large-scale, electronic structure calculations. This work hasmore » demonstrated the unique capabilities of near-infrared cavity ringdown spectroscopy (NIR CRDS) to identify, characterize and monitor intermediates of key importance in complex chemical reactions. Our studies have focussed on the large family of organic peroxy radicals which are arguably themost important intermediates in combustion chemistry and many other reactions involving the oxidation of organic compounds. Our spectroscopic studies have shown that the NIR Ã - ˜X electronic spectra of the peroxy radicals allows one to differentiate among chemical species in the organic peroxy family and also determine their isomeric and conformic structure in many cases. We have clearly demonstrated this capability on saturated and unsaturated peroxy radicals and β-hydroxy peroxy radicals. In addition we have developed a unique dual wavelength CRDS apparatus specifically for the purpose of measuring absolute absorption cross section and following the reaction of chemical intermediates. The utility of the apparatus has been demonstrated by measuring the cross-section and self-reaction rate constant for ethyl peroxy.« less

Kinetic characterisation of primer mismatches in allele-specific PCR: a quantitative assessment.

PubMed

Waterfall, Christy M; Eisenthal, Robert; Cobb, Benjamin D

2002-12-20

A novel method of estimating the kinetic parameters of Taq DNA polymerase during rapid cycle PCR is presented. A model was constructed using a simplified sigmoid function to represent substrate accumulation during PCR in combination with the general equation describing high substrate inhibition for Michaelis-Menten enzymes. The PCR progress curve was viewed as a series of independent reactions where initial rates were accurately measured for each cycle. Kinetic parameters were obtained for allele-specific PCR (AS-PCR) amplification to examine the effect of mismatches on amplification. A high degree of correlation was obtained providing evidence of substrate inhibition as a major cause of the plateau phase that occurs in the later cycles of PCR.

The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology.

PubMed

Blakes, Jonathan; Twycross, Jamie; Romero-Campero, Francisco Jose; Krasnogor, Natalio

2011-12-01

The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology. A modular model specification allows for straightforward creation of large-scale models containing many compartments and reactions. Models are simulated either using stochastic simulation or numerical integration, and visualized in time and space. Model parameters and structure can be optimized with evolutionary algorithms, and model properties calculated using probabilistic model checking. Source code and binaries for Linux, Mac and Windows are available at http://www.infobiotics.org/infobiotics-workbench/; released under the GNU General Public License (GPL) version 3. Natalio.Krasnogor@nottingham.ac.uk.

Study of parameters affecting the conversion in a plug flow reactor for reactions of the type 2A→B

NASA Astrophysics Data System (ADS)

Beltran-Prieto, Juan Carlos; Long, Nguyen Huynh Bach Son

2018-04-01

Modeling of chemical reactors is an important tool to quantify reagent conversion, product yield and selectivity towards a specific compound and to describe the behavior of the system. Proposal of differential equations describing the mass and energy balance are among the most important steps required during the modeling process as they play a special role in the design and operation of the reactor. Parameters governing transfer of heat and mass have a strong relevance in the rate of the reaction. Understanding this information is important for the selection of reactor and operating regime. In this paper we studied the irreversible gas-phase reaction 2A→B. We model the conversion that can be achieved as function of the reactor volume and feeding temperature. Additionally, we discuss the effect of activation energy and the heat of reaction on the conversion achieved in the tubular reactor. Furthermore, we considered that dimerization occurs instantaneously in the catalytic surface to develop equations for the determination of rate of reaction per unit area of three different catalytic surface shapes. This data can be combined with information about the global rate of conversion in the reactor to improve regent conversion and yield of product.

Parametric spatiotemporal oscillation in reaction-diffusion systems.

PubMed

Ghosh, Shyamolina; Ray, Deb Shankar

2016-03-01

We consider a reaction-diffusion system in a homogeneous stable steady state. On perturbation by a time-dependent sinusoidal forcing of a suitable scaling parameter the system exhibits parametric spatiotemporal instability beyond a critical threshold frequency. We have formulated a general scheme to calculate the threshold condition for oscillation and the range of unstable spatial modes lying within a V-shaped region reminiscent of Arnold's tongue. Full numerical simulations show that depending on the specificity of nonlinearity of the models, the instability may result in time-periodic stationary patterns in the form of standing clusters or spatially localized breathing patterns with characteristic wavelengths. Our theoretical analysis of the parametric oscillation in reaction-diffusion system is corroborated by full numerical simulation of two well-known chemical dynamical models: chlorite-iodine-malonic acid and Briggs-Rauscher reactions.

Parametric spatiotemporal oscillation in reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Ghosh, Shyamolina; Ray, Deb Shankar

2016-03-01

We consider a reaction-diffusion system in a homogeneous stable steady state. On perturbation by a time-dependent sinusoidal forcing of a suitable scaling parameter the system exhibits parametric spatiotemporal instability beyond a critical threshold frequency. We have formulated a general scheme to calculate the threshold condition for oscillation and the range of unstable spatial modes lying within a V-shaped region reminiscent of Arnold's tongue. Full numerical simulations show that depending on the specificity of nonlinearity of the models, the instability may result in time-periodic stationary patterns in the form of standing clusters or spatially localized breathing patterns with characteristic wavelengths. Our theoretical analysis of the parametric oscillation in reaction-diffusion system is corroborated by full numerical simulation of two well-known chemical dynamical models: chlorite-iodine-malonic acid and Briggs-Rauscher reactions.

Rapeseed Oil as Renewable Resource for Polyol Synthesis

NASA Astrophysics Data System (ADS)

Stirna, Uldis; Fridrihsone, Anda; Misane, Marija; Vilsone, Dzintra

2011-01-01

Vegetable oils are one of the most important platform chemicals due to their accessibility, specific structure of oils and low price. Rapeseed oil (RO) polyols were prepared by amidization of RO with diethanolamine (DEA). To determine the kinetics of amidization reaction, experiments were carried out. Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), amine (NH) value was determined. Group contribution method by Fedor‵s was used to calculate solubility parameters, van der Waals volume was calculated by Askadskii. Obtained polyol‵s OH and NH value are from 304 up to 415 mg KOH/g. RO polyols synthesis meets the criteria of "green chemistry". In the present study, reaction of RO amidization with DEA was investigated, as well as optimum conditions for polyol synthesis was established to obtain polyols for polyurethane production. Calculations of solubility parameter and cohesion energy density were calculated, as RO polyols will be used as side chains in polymers, and solubility parameter will be used to explain properties of polymers.

Optimization of commercial scale photonuclear production of radioisotopes

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

Bindu, K. C.; Harmon, Frank; Starovoitova, Valeriia N.

2013-04-19

Photonuclear production of radioisotopes driven by bremsstrahlung photons using a linear electron accelerator in the suitable energy range is a promising method for producing radioisotopes. The photonuclear production method is capable of making radioisotopes more conveniently, cheaply and with much less radioactive waste compared to existing methods. Historically, photo-nuclear reactions have not been exploited for isotope production because of the low specific activity that is generally associated with this production process, although the technique is well-known to be capable of producing large quantities of certain radioisotopes. We describe an optimization technique for a set of parameters to maximize specific activitymore » of the final product. This set includes the electron beam energy and current, the end station design (an integrated converter and target as well as cooling system), the purity of materials used, and the activation time. These parameters are mutually dependent and thus their optimization is not trivial. {sup 67}Cu photonuclear production via {sup 68}Zn({gamma}p){sup 67}Cu reaction was used as an example of such an optimization process.« less

Quantum mechanical study of solvent effects in a prototype S{sub N}2 reaction in solution: Cl{sup −} attack on CH{sub 3}Cl

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

Kuechler, Erich R.; Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431; York, Darrin M., E-mail: york@biomaps.rutgers.edu

2014-02-07

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype S{sub N}2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resultingmore » free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.« less

Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.; York, Darrin M.

2014-02-01

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl.

PubMed

Kuechler, Erich R; York, Darrin M

2014-02-07

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

A Luenberger observer for reaction-diffusion models with front position data

NASA Astrophysics Data System (ADS)

Collin, Annabelle; Chapelle, Dominique; Moireau, Philippe

2015-11-01

We propose a Luenberger observer for reaction-diffusion models with propagating front features, and for data associated with the location of the front over time. Such models are considered in various application fields, such as electrophysiology, wild-land fire propagation and tumor growth modeling. Drawing our inspiration from image processing methods, we start by proposing an observer for the eikonal-curvature equation that can be derived from the reaction-diffusion model by an asymptotic expansion. We then carry over this observer to the underlying reaction-diffusion equation by an ;inverse asymptotic analysis;, and we show that the associated correction in the dynamics has a stabilizing effect for the linearized estimation error. We also discuss the extension to joint state-parameter estimation by using the earlier-proposed ROUKF strategy. We then illustrate and assess our proposed observer method with test problems pertaining to electrophysiology modeling, including with a realistic model of cardiac atria. Our numerical trials show that state estimation is directly very effective with the proposed Luenberger observer, while specific strategies are needed to accurately perform parameter estimation - as is usual with Kalman filtering used in a nonlinear setting - and we demonstrate two such successful strategies.

Estimation of parameters in rational reaction rates of molecular biological systems via weighted least squares

NASA Astrophysics Data System (ADS)

Wu, Fang-Xiang; Mu, Lei; Shi, Zhong-Ke

2010-01-01

The models of gene regulatory networks are often derived from statistical thermodynamics principle or Michaelis-Menten kinetics equation. As a result, the models contain rational reaction rates which are nonlinear in both parameters and states. It is challenging to estimate parameters nonlinear in a model although there have been many traditional nonlinear parameter estimation methods such as Gauss-Newton iteration method and its variants. In this article, we develop a two-step method to estimate the parameters in rational reaction rates of gene regulatory networks via weighted linear least squares. This method takes the special structure of rational reaction rates into consideration. That is, in the rational reaction rates, the numerator and the denominator are linear in parameters. By designing a special weight matrix for the linear least squares, parameters in the numerator and the denominator can be estimated by solving two linear least squares problems. The main advantage of the developed method is that it can produce the analytical solutions to the estimation of parameters in rational reaction rates which originally is nonlinear parameter estimation problem. The developed method is applied to a couple of gene regulatory networks. The simulation results show the superior performance over Gauss-Newton method.

Study the effect of chemical reaction and variable viscosity on free convection MHD radiating flow over an inclined plate bounded by porous medium

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

Ali, M., E-mail: ali.mehidi93@gmail.com; Department of Mathematics, Chittagong University of Engineering and Technology, Chittagong-4349; Alim, M. A., E-mail: maalim@math.buet.ac.bd

An analysis is performed to study the free convection heat and mass transfer flow of an electrically conducting incompressible viscous fluid about a semi-infinite inclined porous plate under the action of radiation, chemical reaction in presence of magnetic field with variable viscosity. The dimensionless governing equations are steady, two-dimensional coupled and non-linear ordinary differential equation. Nachtsgeim-Swigert shooting iteration technique along with Runge-Kutta integration scheme is used to solve the non-dimensional governing equations. The effects of magnetic parameter, viscosity parameter and chemical reaction parameter on velocity, temperature and concentration profiles are discussed numerically and shown graphically. Therefore, the results of velocitymore » profile decreases for increasing values of magnetic parameter and viscosity parameter but there is no effect for reaction parameter. The temperature profile decreases in presence of magnetic parameter, viscosity parameter and Prandtl number but increases for radiation parameter. Also, concentration profile decreases for the increasing values of magnetic parameter, viscosity parameter and reaction parameter. All numerical calculations are done with respect to salt water and fixed angle of inclination of the plate.« less

Effects of reaction-kinetic parameters on modeling reaction pathways in GaN MOVPE growth

NASA Astrophysics Data System (ADS)

Zhang, Hong; Zuo, Ran; Zhang, Guoyi

2017-11-01

In the modeling of the reaction-transport process in GaN MOVPE growth, the selections of kinetic parameters (activation energy Ea and pre-exponential factor A) for gas reactions are quite uncertain, which cause uncertainties in both gas reaction path and growth rate. In this study, numerical modeling of the reaction-transport process for GaN MOVPE growth in a vertical rotating disk reactor is conducted with varying kinetic parameters for main reaction paths. By comparisons of the molar concentrations of major Ga-containing species and the growth rates, the effects of kinetic parameters on gas reaction paths are determined. The results show that, depending on the values of the kinetic parameters, the gas reaction path may be dominated either by adduct/amide formation path, or by TMG pyrolysis path, or by both. Although the reaction path varies with different kinetic parameters, the predicted growth rates change only slightly because the total transport rate of Ga-containing species to the substrate changes slightly with reaction paths. This explains why previous authors using different chemical models predicted growth rates close to the experiment values. By varying the pre-exponential factor for the amide trimerization, it is found that the more trimers are formed, the lower the growth rates are than the experimental value, which indicates that trimers are poor growth precursors, because of thermal diffusion effect caused by high temperature gradient. The effective order for the contribution of major species to growth rate is found as: pyrolysis species > amides > trimers. The study also shows that radical reactions have little effect on gas reaction path because of the generation and depletion of H radicals in the chain reactions when NH2 is considered as the end species.

Biological optimization systems for enhancing photosynthetic efficiency and methods of use

DOEpatents

Hunt, Ryan W.; Chinnasamy, Senthil; Das, Keshav C.; de Mattos, Erico Rolim

2012-11-06

Biological optimization systems for enhancing photosynthetic efficiency and methods of use. Specifically, methods for enhancing photosynthetic efficiency including applying pulsed light to a photosynthetic organism, using a chlorophyll fluorescence feedback control system to determine one or more photosynthetic efficiency parameters, and adjusting one or more of the photosynthetic efficiency parameters to drive the photosynthesis by the delivery of an amount of light to optimize light absorption of the photosynthetic organism while providing enough dark time between light pulses to prevent oversaturation of the chlorophyll reaction centers are disclosed.

Kinetics of enzymatic trans-esterification of glycerides for biodiesel production.

PubMed

Calabrò, Vincenza; Ricca, Emanuele; De Paola, Maria Gabriela; Curcio, Stefano; Iorio, Gabriele

2010-08-01

In this paper, the reaction of enzymatic trans-esterification of glycerides with ethanol in a reaction medium containing hexane at a temperature of 37 degrees C has been studied. The enzyme was Lipase from Mucor miehei, immobilized on ionic exchange resin, aimed at achieving high catalytic specific surface and recovering, regenerating and reusing the biocatalyst. A kinetic analysis has been carried out to identify the reaction path; the rate equation and kinetic parameters have been also calculated. The kinetic model has been validated by comparison between predicted and experimental results. Mass transport resistances estimation was undertaken in order to verify that the kinetics found was intrinsic. Model potentialities in terms of reactors design and optimization are also shown.

Critical ignition conditions in exothermically reacting systems: first-order reactions

NASA Astrophysics Data System (ADS)

Filimonov, Valeriy Yu.

2017-10-01

In this paper, the comparative analysis of the thermal explosion (TE) critical conditions on the planes temperature-conversion degree and temperature-time was conducted. It was established that the ignition criteria are almost identical only at relatively small values of Todes parameter. Otherwise, the results of critical conditions analysis on the plane temperature-conversion degree may be wrong. The asymptotic method of critical conditions calculation for the first-order reactions was proposed (taking into account the reactant consumption). The degeneration conditions of TE were determined. The calculation of critical conditions for specific first-order reaction was made. The comparison of the analytical results obtained with the results of numerical calculations and experimental data showed that they are in good agreement.

Critical ignition conditions in exothermically reacting systems: first-order reactions.

PubMed

Filimonov, Valeriy Yu

2017-10-01

In this paper, the comparative analysis of the thermal explosion (TE) critical conditions on the planes temperature-conversion degree and temperature-time was conducted. It was established that the ignition criteria are almost identical only at relatively small values of Todes parameter. Otherwise, the results of critical conditions analysis on the plane temperature-conversion degree may be wrong. The asymptotic method of critical conditions calculation for the first-order reactions was proposed (taking into account the reactant consumption). The degeneration conditions of TE were determined. The calculation of critical conditions for specific first-order reaction was made. The comparison of the analytical results obtained with the results of numerical calculations and experimental data showed that they are in good agreement.

Novel methods to estimate the enantiomeric ratio and the kinetic parameters of enantiospecific enzymatic reactions.

PubMed

Machado, G D.C.; Paiva, L M.C.; Pinto, G F.; Oestreicher, E G.

2001-03-08

1The Enantiomeric Ratio (E) of the enzyme, acting as specific catalysts in resolution of enantiomers, is an important parameter in the quantitative description of these chiral resolution processes. In the present work, two novel methods hereby called Method I and II, for estimating E and the kinetic parameters Km and Vm of enantiomers were developed. These methods are based upon initial rate (v) measurements using different concentrations of enantiomeric mixtures (C) with several molar fractions of the substrate (x). Both methods were tested using simulated "experimental data" and actual experimental data. Method I is easier to use than Method II but requires that one of the enantiomers is available in pure form. Method II, besides not requiring the enantiomers in pure form shown better results, as indicated by the magnitude of the standard errors of estimates. The theoretical predictions were experimentally confirmed by using the oxidation of 2-butanol and 2-pentanol catalyzed by Thermoanaerobium brockii alcohol dehydrogenase as reaction models. The parameters E, Km and Vm were estimated by Methods I and II with precision and were not significantly different from those obtained experimentally by direct estimation of E from the kinetic parameters of each enantiomer available in pure form.

Confocal arthroscopy-based patient-specific constitutive models of cartilaginous tissues - II: prediction of reaction force history of meniscal cartilage specimens.

PubMed

Taylor, Zeike A; Kirk, Thomas B; Miller, Karol

2007-10-01

The theoretical framework developed in a companion paper (Part I) is used to derive estimates of mechanical response of two meniscal cartilage specimens. The previously developed framework consisted of a constitutive model capable of incorporating confocal image-derived tissue microstructural data. In the present paper (Part II) fibre and matrix constitutive parameters are first estimated from mechanical testing of a batch of specimens similar to, but independent from those under consideration. Image analysis techniques which allow estimation of tissue microstructural parameters form confocal images are presented. The constitutive model and image-derived structural parameters are then used to predict the reaction force history of the two meniscal specimens subjected to partially confined compression. The predictions are made on the basis of the specimens' individual structural condition as assessed by confocal microscopy and involve no tuning of material parameters. Although the model does not reproduce all features of the experimental curves, as an unfitted estimate of mechanical response the prediction is quite accurate. In light of the obtained results it is judged that more general non-invasive estimation of tissue mechanical properties is possible using the developed framework.

Studies of the augmentation of reaction rates via laser irradiation in the infrared. Final report, 1 Sep 1973--31 Aug 1976. [H/sub 3/BPF/sub 3/ adduct

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

Bauer, S.H.; Lory, E.R.; Chien, K.

1976-10-15

The objective of this research project, to discover a reaction, involving a sizable substrate (more than three atoms) the rate of which is selectively augmented by infrared laser radiation, has been achieved. A preliminary analysis led to criteria for the selection of an optimum reaction type, and for setting the most suitable experimental parameters. The self-scavenging decomposition was studied for a borane adduct: 2 H/sub 3/BPF/sub 3/ yields B/sub 2/H/sub 6/ + 2PF/sub 3/. The relative photolytic efficiencies of the various lines emitted by a CO2 laser were measured as was also the dependence of the rate on laser power,more » gas pressure and reaction cell temperature. Specificity of vibrational excitation was demonstrated in several ways, most directly by the observed isotope fractionation of H/D and /sup 10/B//sup 11/B ratios. The mechanism of the photoactivation process developed is in quantitative agreement with the observed conversion. A dynamic model (based on a normal mode analysis) was proposed for the selective activation. In a parallel study of borane adducts, we evaluated the thermodynamic and kinetic rate parameters for six exchange and abstraction reactions. Rational structures were proposed for the corresponding transition states. (Author)« less

Solute transport with equilibrium aqueous complexation and either sorption or ion exchange: Simulation methodology and applications

USGS Publications Warehouse

Lewis, F.M.; Voss, C.I.; Rubin, J.

1987-01-01

Methodologies that account for specific types of chemical reactions in the simulation of solute transport can be developed so they are compatible with solution algorithms employed in existing transport codes. This enables the simulation of reactive transport in complex multidimensional flow regimes, and provides a means for existing codes to account for some of the fundamental chemical processes that occur among transported solutes. Two equilibrium-controlled reaction systems demonstrate a methodology for accommodating chemical interaction into models of solute transport. One system involves the sorption of a given chemical species, as well as two aqueous complexations in which the sorbing species is a participant. The other reaction set involves binary ion exchange coupled with aqueous complexation involving one of the exchanging species. The methodology accommodates these reaction systems through the addition of nonlinear terms to the transport equations for the sorbing species. Example simulation results show (1) the effect equilibrium chemical parameters have on the spatial distributions of concentration for complexing solutes; (2) that an interrelationship exists between mechanical dispersion and the various reaction processes; (3) that dispersive parameters of the porous media cannot be determined from reactive concentration distributions unless the reaction is accounted for or the influence of the reaction is negligible; (4) how the concentration of a chemical species may be significantly affected by its participation in an aqueous complex with a second species which also sorbs; and (5) that these coupled chemical processes influencing reactive transport can be demonstrated in two-dimensional flow regimes. ?? 1987.

Gasification Characteristics of Coal/Biomass Mixed Fuels

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

Mitchell, Reginald

2014-09-01

A research project was undertaken that had the overall objective of developing the models needed to accurately predict conversion rates of coal/biomass mixtures to synthesis gas under conditions relevant to a commercially-available coal gasification system configured to co-produce electric power as well as chemicals and liquid fuels. In our efforts to accomplish this goal, experiments were performed in an entrained flow reactor in order to produce coal and biomass chars at high heating rates and temperatures, typical of the heating rates and temperatures fuel particles experience in real systems. Mixed chars derived from coal/biomass mixtures containing up to 50% biomassmore » and the chars of the pure coal and biomass components were subjected to a matrix of reactivity tests in a pressurized thermogravimetric analyzer (TGA) in order to obtain data on mass loss rates as functions of gas temperature, pressure and composition as well as to obtain information on the variations in mass specific surface area during char conversion under kinetically-limited conditions. The experimental data were used as targets when determining the unknown parameters in the chemical reactivity and specific surface area models developed. These parameters included rate coefficients for the reactions in the reaction mechanism, enthalpies of formation and absolute entropies of adsorbed species formed on the carbonaceous surfaces, and pore structure coefficients in the model used to describe how the mass specific surface area of the char varies with conversion. So that the reactivity models can be used at high temperatures when mass transport processes impact char conversion rates, Thiele modulus – effectiveness factor relations were also derived for the reaction mechanisms developed. In addition, the reactivity model and a mode of conversion model were combined in a char-particle gasification model that includes the effects of chemical reaction and diffusion of reactive gases through particle pores and energy exchange between the particle and its environment. This char-particle gasification model is capable of predicting the average mass loss rates, sizes, apparent densities, specific surface areas, and temperatures of the char particles produced when co-firing coal and biomass to the type environments established in entrained flow gasifiers operating at high temperatures and elevated pressures.« less

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method

PubMed Central

Cao, Youfang; Liang, Jie

2013-01-01

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape. PMID:23862966

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method

NASA Astrophysics Data System (ADS)

Cao, Youfang; Liang, Jie

2013-07-01

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape.

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method.

PubMed

Cao, Youfang; Liang, Jie

2013-07-14

Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively by comparing simulation results with true answers. Overall, ABSIS can accurately and efficiently estimate rare event probabilities for all examples, often with smaller variance than other importance sampling algorithms. The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape.

Confining Domains Lead to Reaction Bursts: Reaction Kinetics in the Plasma Membrane

PubMed Central

Kalay, Ziya; Fujiwara, Takahiro K.; Kusumi, Akihiro

2012-01-01

Confinement of molecules in specific small volumes and areas within a cell is likely to be a general strategy that is developed during evolution for regulating the interactions and functions of biomolecules. The cellular plasma membrane, which is the outermost membrane that surrounds the entire cell, was considered to be a continuous two-dimensional liquid, but it is becoming clear that it consists of numerous nano-meso-scale domains with various lifetimes, such as raft domains and cytoskeleton-induced compartments, and membrane molecules are dynamically trapped in these domains. In this article, we give a theoretical account on the effects of molecular confinement on reversible bimolecular reactions in a partitioned surface such as the plasma membrane. By performing simulations based on a lattice-based model of diffusion and reaction, we found that in the presence of membrane partitioning, bimolecular reactions that occur in each compartment proceed in bursts during which the reaction rate is sharply and briefly increased even though the asymptotic reaction rate remains the same. We characterized the time between reaction bursts and the burst amplitude as a function of the model parameters, and discussed the biological significance of the reaction bursts in the presence of strong inhibitor activity. PMID:22479350

Development of MRM-based assays for the absolute quantitation of plasma proteins.

PubMed

Kuzyk, Michael A; Parker, Carol E; Domanski, Dominik; Borchers, Christoph H

2013-01-01

Multiple reaction monitoring (MRM), sometimes called selected reaction monitoring (SRM), is a directed tandem mass spectrometric technique performed on to triple quadrupole mass spectrometers. MRM assays can be used to sensitively and specifically quantify proteins based on peptides that are specific to the target protein. Stable-isotope-labeled standard peptide analogues (SIS peptides) of target peptides are added to enzymatic digests of samples, and quantified along with the native peptides during MRM analysis. Monitoring of the intact peptide and a collision-induced fragment of this peptide (an ion pair) can be used to provide information on the absolute peptide concentration of the peptide in the sample and, by inference, the concentration of the intact protein. This technique provides high specificity by selecting for biophysical parameters that are unique to the target peptides: (1) the molecular weight of the peptide, (2) the generation of a specific fragment from the peptide, and (3) the HPLC retention time during LC/MRM-MS analysis. MRM is a highly sensitive technique that has been shown to be capable of detecting attomole levels of target peptides in complex samples such as tryptic digests of human plasma. This chapter provides a detailed description of how to develop and use an MRM protein assay. It includes sections on the critical "first step" of selecting the target peptides, as well as optimization of MRM acquisition parameters for maximum sensitivity of the ion pairs that will be used in the final method, and characterization of the final MRM assay.

PDF Modeling of Turbulent Combustion

DTIC Science & Technology

2008-11-30

provided on the TNF web site and used in the above investigation includes incorrect specifications of reaction parameters. As a consequence, the above...difference among the different schemes is small. PUBLICATIONS The following papers stemming from the current AFOSR program were written or published...2006. 31st International Symposium on Combustion, Heidelberg, Germany, August 6-11, two contributed papers . 59th Annual Meeting of

Model studies on the release of aroma compounds from structured and nonstructured oil systems using proton-transfer reaction mass spectrometry.

PubMed

Landy, Pascale; Pollien, Philippe; Rytz, Andreas; Leser, Martin E; Sagalowicz, Laurent; Blank, Imre; Spadone, Jean-Claude

2007-03-07

Relative retention, volatility, and temporal release of volatile compounds taken from aldehyde, ester, and alcohol chemical classes were studied at 70 degrees C in model systems using equilibrium static headspace analysis and real time dynamic headspace analysis. These systems were medium-chain triglycerides (MCT), sunflower oil, and two structured systems, i.e., water-in-oil emulsion and L2 phase (water-in-oil microemulsion). Hydrophilic domains of the emulsion type media retained specifically the hydrophilic compounds and alcohols. Four kinetic parameters characterizing the concentration- and time-dependent releases were extracted from the aroma release curves. Most of the kinetic parameter values were higher in structured systems than in oils particularly when using MCT. The oil nature was found to better control the dynamic release profiles than the system structures. The release parameters were well-related (i) to the volatile hydrophobicity as a function of the oil used and (ii) to the retention data in the specific case of the L2 phase due to a specific release behavior of alcohols.

Validation of a thin-layer chromatography/densitometry method for the characterization of invertase activity.

PubMed

Ferey, Justine; Da Silva, David; Bravo-Veyrat, Sophie; Lafite, Pierre; Daniellou, Richard; Maunit, Benoît

2016-12-16

This paper presents a kinetic study of invertase, a specific fructofuranosidase cloned from the Leishmania major genome. The kinetic parameters of the β-d-fructofuranosidase from Leishmania major (BfrA) were determined using Thin-Layer Chromatography (TLC) and UV-densitometry (TLC@UV) specifically developed for the separation and detection of three carbohydrates namely sucrose, glucose and fructose. Separation was performed on TLC silica gel 60 F254 plates impregnated with sodium bisulphate and citrate and heated prior to development. This fast and easy separation was performed with two successive developments using ACN/H 2 O 80/20 (v/v) as mobile phase. Sensitive and repeatable derivatization of sugars was achieved by dipping the plates in a solution of 4-aminobenzoic acid. Quantification was performed by UV-detection. The method was validated according to ICH guidelines Q2(R1) in terms of specificity, limits of detection and quantification, precision and robustness (with n=3 replicates and CV ≤10%). The characterization of BfrA reaction kinetic was performed by monitoring the accumulation of either glucose or fructose detected by TLC@UV. Hydrolysis of sucrose was described by the Michaelis-Menten kinetic parameters (K M ; V max ) respectively equal to 63.09±7.590mM; 0.037±0.00094mM/min using glucose production and 83.01±14.39mM; 0.031±0.0021mM/min monitoring fructose. Hydrolyses of three alternative substrates, raffinose, stachyose and inulin, were also compared and the regiospecificity of the reaction was characterized. This TLC@UV method is shown to be suitable for the refined kinetic analysis of different reactions related to the hydrolysis of sugars. Copyright © 2016. Published by Elsevier B.V.

Specific interface area in a thin layer system of two immiscible liquids with vapour generation at the contact interface

NASA Astrophysics Data System (ADS)

Pimenova, Anastasiya V.; Gazdaliev, Ilias M.; Goldobin, Denis S.

2017-06-01

For well-stirred multiphase fluid systems the mean interface area per unit volume, or “specific interface area” SV, is a significant characteristic of the system state. In particular, it is important for the dynamics of systems of immiscible liquids experiencing interfacial boiling. We estimate the value of parameter SV as a function of the heat influx {\\dot{Q}}V to the system or the average system overheat <Θ> above the interfacial boiling point. The derived results can be reformulated for the case of an endothermic chemical reaction between two liquid reagents with the gaseous form of one of the reaction products. The final results are restricted to the case of thin layers, where the potential gravitational energy of bubbles leaving the contact interface is small compared to their surface tension energy.

Determination of reaction rates and activation energy in aerobic composting processes for yard waste.

PubMed

Uma, R N; Manjula, G; Meenambal, T

2007-04-01

The reaction rates and activation energy in aerobic composting processes for yard waste were determined using specifically designed reactors. Different mixture ratios were fixed before the commencement of the process. The C/N ratio was found to be optimum for a mixture ratio of 1:6 containing one part of coir pith to six parts of other waste which included yard waste, yeast sludge, poultry yard waste and decomposing culture (Pleurotosis). The path of stabilization of the wastes was continuously monitored by observing various parameters such as temperature, pH, Electrical Conductivity, C.O.D, VS at regular time intervals. Kinetic analysis was done to determine the reaction rates and activation energy for the optimum mixture ratio under forced aeration condition. The results of the analysis clearly indicated that the temperature dependence of the reaction rates followed the Arrhenius equation. The temperature coefficients were also determined. The degradation of the organic fraction of the yard waste could be predicted using first order reaction model.

[THE COMPARATIVE ANALYSIS OF EFFECTIVENESS OF QUICK TESTS IN DIAGNOSTIC OF INFLUENZA AND RESPIRATORY SYNCYTIAL VIRAL INFECTION IN CHILDREN].

PubMed

Petrova, E R; Sukhovetskaia, V P; Pisareva, M M; Maiorova, V G; Sverlova, M V; Danilenko, D M; Petrova, P A; Krivitskaia, V Z; Sominina, A A

2015-11-01

The analysis was implemented concerning diagnostic parameters of commercial quick tests (immune chromatographic tests BinaxNOW Influenza A&B and BinaxNow RSV Alere, Scarborough Inc., USA) under detection of antigens of influenza virus A and respiratory syncytial virus in clinical materials. The polymerase chain reaction in real-time and isolation ofviruses in cell cultures. The analysis of naso-pharyngeal smears from 116 children demonstrated that sensitivity and specifcity of detection of influenza virus A using device mariPOC in comparison with polymerase chain reaction made up to 93.8% and 99.0% correspondingly at total concordance of results of both techniques as 98.3%. At diagnosing of respiratory syncytial virus using device mariPOC parameters made up to 77.3%, 98.9% and 862% as compared with polymerase chain reaction. The sensitivity, specificity and total concordance of results of immune chromatographic tests BinaxNOW in comparison ofpolymerase chain reaction made up to 86.7%, 100% and 96.2% correspondingly at detection of influenza virus A and 80.9%, 97.4% and 91.6% correspondingly at detection of respiratory syncytial virus. In comparison with isolation technique in cell cultures sensitivity of system mariPOC and immune chromatographic tests proved to be in 1.3-1.4 times higher at detection of influenza virus A and in 1.7-2 times higher in case of isolation of respiratory syncytial virus. There is no statistically significant differences between diagnostic parameters received for mariPOC and immune chromatographic tests at diagnosing influenza virus A and respiratory syncytial viral infection.

Effect of processing parameters on reaction bonding of silicon nitride

NASA Technical Reports Server (NTRS)

Richman, M. H.; Gregory, O. J.; Magida, M. B.

1980-01-01

Reaction bonded silicon nitride was developed. The relationship between the various processing parameters and the resulting microstructures was to design and synthesize reaction bonded materials with improved room temperature mechanical properties.

Subject-specific finite element modelling of the human foot complex during walking: sensitivity analysis of material properties, boundary and loading conditions.

PubMed

Akrami, Mohammad; Qian, Zhihui; Zou, Zhemin; Howard, David; Nester, Chris J; Ren, Lei

2018-04-01

The objective of this study was to develop and validate a subject-specific framework for modelling the human foot. This was achieved by integrating medical image-based finite element modelling, individualised multi-body musculoskeletal modelling and 3D gait measurements. A 3D ankle-foot finite element model comprising all major foot structures was constructed based on MRI of one individual. A multi-body musculoskeletal model and 3D gait measurements for the same subject were used to define loading and boundary conditions. Sensitivity analyses were used to investigate the effects of key modelling parameters on model predictions. Prediction errors of average and peak plantar pressures were below 10% in all ten plantar regions at five key gait events with only one exception (lateral heel, in early stance, error of 14.44%). The sensitivity analyses results suggest that predictions of peak plantar pressures are moderately sensitive to material properties, ground reaction forces and muscle forces, and significantly sensitive to foot orientation. The maximum region-specific percentage change ratios (peak stress percentage change over parameter percentage change) were 1.935-2.258 for ground reaction forces, 1.528-2.727 for plantar flexor muscles and 4.84-11.37 for foot orientations. This strongly suggests that loading and boundary conditions need to be very carefully defined based on personalised measurement data.

Rapid ELISA Using a Film-Stack Reaction Field with Micropillar Arrays

PubMed Central

Suzuki, Yuma; Morioka, Kazuhiro; Ohata, Soichiro; Nakajima, Hizuru; Uchiyama, Katsumi; Yang, Ming

2017-01-01

A film-stack reaction field with a micropillar array using a motor stirrer was developed for the high sensitivity and rapid enzyme-linked immunosorbent assay (ELISA) reaction. The effects of the incubation time of a protein (30 s, 5 min, and 10 min) on the fluorescence intensity in ELISAs were investigated using a reaction field with different micropillar array dimensions (5-µm, 10-µm and 50-µm gaps between the micropillars). The difference in fluorescence intensity between the well with the reaction field of 50-µm gap for the incubation time of 30 s and the well without the reaction field with for incubation time of 10 min was 6%. The trend of the fluorescence intensity in the gap between the micro pillars in the film-stack reaction field was different between the short incubation time and the long incubation time. The theoretical analysis of the physical parameters related with the biomolecule transport indicated that the reaction efficiency defined in this study was the dominant factor determining the fluorescence intensity for the short incubation time, whereas the volumetric rate of the circulating flow through the space between films and the specific surface area were the dominant factors for the long incubation time. PMID:28696378

Rapid ELISA Using a Film-Stack Reaction Field with Micropillar Arrays.

PubMed

Suzuki, Yuma; Morioka, Kazuhiro; Ohata, Soichiro; Shimizu, Tetsuhide; Nakajima, Hizuru; Uchiyama, Katsumi; Yang, Ming

2017-07-11

A film-stack reaction field with a micropillar array using a motor stirrer was developed for the high sensitivity and rapid enzyme-linked immunosorbent assay (ELISA) reaction. The effects of the incubation time of a protein (30 s, 5 min, and 10 min) on the fluorescence intensity in ELISAs were investigated using a reaction field with different micropillar array dimensions (5-µm, 10-µm and 50-µm gaps between the micropillars). The difference in fluorescence intensity between the well with the reaction field of 50-µm gap for the incubation time of 30 s and the well without the reaction field with for incubation time of 10 min was 6%. The trend of the fluorescence intensity in the gap between the micro pillars in the film-stack reaction field was different between the short incubation time and the long incubation time. The theoretical analysis of the physical parameters related with the biomolecule transport indicated that the reaction efficiency defined in this study was the dominant factor determining the fluorescence intensity for the short incubation time, whereas the volumetric rate of the circulating flow through the space between films and the specific surface area were the dominant factors for the long incubation time.

Quality changes of pasteurised orange juice during storage: A kinetic study of specific parameters and their relation to colour instability.

PubMed

Wibowo, Scheling; Grauwet, Tara; Santiago, Jihan Santanina; Tomic, Jovana; Vervoort, Liesbeth; Hendrickx, Marc; Van Loey, Ann

2015-11-15

In view of understanding colour instability of pasteurised orange juice during storage, to the best of our knowledge, this study reports for the first time in a systematic and quantitative way on a range of changes in specific quality parameters as a function of time and as well as temperature (20-42 °C). A zero-order (°Brix, fructose, glucose), a first-order (vitamin C), a second-order (sucrose) and a fractional conversion model (oxygen) were selected to model the evolution of the parameters between parentheses. Activation energies ranged from 22 to 136 kJ mol(-1), HMF formation being the most temperature sensitive. High correlations were found between sugars, ascorbic acid, their degradation products (furfural and HMF) and total colour difference (ΔE(∗)). Based on PLS regression, the importance of the quality parameters for colour degradation was ranked relatively among each other: the acid-catalysed degradation of sugars and ascorbic acid degradation reactions appeared to be important for browning development in pasteurised orange juice during ambient storage. Copyright © 2015 Elsevier Ltd. All rights reserved.

How computational methods and relativistic effects influence the study of chemical reactions involving Ru-NO complexes?

PubMed

Orenha, Renato Pereira; Santiago, Régis Tadeu; Haiduke, Roberto Luiz Andrade; Galembeck, Sérgio Emanuel

2017-05-05

Two treatments of relativistic effects, namely effective core potentials (ECP) and all-electron scalar relativistic effects (DKH2), are used to obtain geometries and chemical reaction energies for a series of ruthenium complexes in B3LYP/def2-TZVP calculations. Specifically, the reaction energies of reduction (A-F), isomerization (G-I), and Cl - negative trans influence in relation to NH 3 (J-L) are considered. The ECP and DKH2 approaches provided geometric parameters close to experimental data and the same ordering for energy changes of reactions A-L. From geometries optimized with ECP, the electronic energies are also determined by means of the same ECP and basis set combined with the computational methods: MP2, M06, BP86, and its derivatives, so as B2PLYP, LC-wPBE, and CCSD(T) (reference method). For reactions A-I, B2PLYP provides the best agreement with CCSD(T) results. Additionally, B3LYP gave the smallest error for the energies of reactions J-L. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Optimization of random PEGylation reactions by means of high throughput screening.

PubMed

Maiser, Benjamin; Dismer, Florian; Hubbuch, Jürgen

2014-01-01

Since the first FDA approval of a PEGylated product in 1990, so called random PEGylation reactions are still used to increase the efficacy of biopharmaceuticals and represent the major technology of all approved PEG-modified drugs. However, the great influence of process parameters on PEGylation degree and the PEG-binding site results in a lack of reaction specificity which can have severe impact on the product profile. Consequently, reproducible and well characterized processes are essential to meet increasing regulative requirements resulting from the quality-by-design (QbD) initiative, especially for this kind of modification type. In this study we present a general approach which combines the simple chemistry of random PEGylation reactions with high throughput experimentation (HTE) to achieve a well-defined process. Robotic based batch experiments have been established in a 96-well plate format and were analyzed to investigate the influence of different PEGylation conditions for lysozyme as model protein. With common SEC analytics highly reproducible reaction kinetics were measured and a significant influence of PEG-excess, buffer pH, and reaction time could be investigated. Additional mono-PEG-lysozyme analytics showed the impact of varying buffer pH on the isoform distribution, which allowed us to identify optimal process parameters to get a maximum concentration of each isoform. Employing Micrococcus lysodeikticus based activity assays, PEG-lysozyme33 was identified to be the isoform with the highest residual activity, followed by PEG-lysozyme1 . Based on these results, a control space for a PEGylation reaction was defined with respect to an optimal overall volumetric activity of mono-PEG-lysozyme isoform mixtures. © 2013 Wiley Periodicals, Inc.

Decay analysis of compound nuclei with masses A ≈30 - 200 formed in reactions involving loosely bound projectiles

NASA Astrophysics Data System (ADS)

Kaur, Mandeep; Singh, BirBikram; Sharma, Manoj K.; Gupta, Raj K.

2015-08-01

The dynamics of compound nuclei formed in the reactions using loosely bound projectiles are analyzed within the framework of the dynamical cluster-decay model (DCM) of Gupta and Collaborators. We have considered the reactions with neutron-rich and neutron-deficient projectiles, respectively, as 7Li , 9Be , and 7Be , on various targets at three different Elab energies, forming compound nuclei in the mass region A ˜30 - 200. For these reactions, the contributions of light-particle (LP, A ≤4 ) cross sections σLP, energetically favored intermediate-mass-fragment (IMF, 5 ≤A2≤20 ) cross sections σIMF, as well as the fusion-fission ff cross sections σff constitute the σfus(=σLP+σIMF+σff ), i.e., the contributions of the emitted LPs, IMFs, and ff fragments are added for all the angular momenta up to the ℓmax value for the respective reactions. Interestingly, we find that the empirically fitted neck-length parameter Δ Remp , the only parameter of the DCM, is uniquely fixed to address σfus for all the reactions having the same loosely bound projectile at a chosen incident laboratory energy. It may be noted that, in DCM, the dynamical collective mass motion of preformed LPs, IMFs, and ff fragments or clusters, through the modified interaction potential barrier, are treated on parallel footing. The modification of the barrier is due to nonzero Δ Remp , and the values of corresponding modified interaction-barrier heights Δ VBemp for such reactions are almost of the same order, specifically at the respective ℓmax value.

Controlled Synthesis of Polyions of Heavy Main-Group Elements in Ionic Liquids

PubMed Central

Groh, Matthias F.; Wolff, Alexander; Grasser, Matthias A.; Ruck, Michael

2016-01-01

Ionic liquids (ILs) have been proven to be valuable reaction media for the synthesis of inorganic materials among an abundance of other applications in different fields of chemistry. Up to now, the syntheses have remained mostly “black boxes”; and researchers have to resort to trial-and-error in order to establish a new synthetic route to a specific compound. This review comprises decisive reaction parameters and techniques for the directed synthesis of polyions of heavy main-group elements (fourth period and beyond) in ILs. Several families of compounds are presented ranging from polyhalides over carbonyl complexes and selenidostannates to homo and heteropolycations. PMID:27598123

Management of stinging insect hypersensitivity: a 5-year retrospective medical record review.

PubMed

Johnson, Thomas; Dietrich, Jeffrey; Hagan, Larry

2006-08-01

The Joint Task Force on Practice Parameters for Allergy and Immunology recommends that patients with a history of a systemic reaction to an insect sting be educated on ways to avoid insect stings, carry injectable epinephrine for emergency self-treatment, undergo specific IgE testing for stinging insect sensitivity, and be considered for immunotherapy. To review frontline providers' documented care and recommendations for imported fire ant and flying insect hypersensitivity reactions. A retrospective medical record review was performed of emergency department and primary care clinic visits between November 1, 1999, and November 30, 2004. Using International Classification of Diseases, Ninth Revision, codes, medical records were selected for review to identify patients with potential insect hypersensitivity. A total of 769 medical records from patients who experienced an insect sting were reviewed. Of 120 patients with a systemic reaction, 66 (55.0%) received a prescription for injectable epinephrine, and 14 (11.7%) were given information regarding avoidance of the offending insect. Forty-seven patients with systemic reactions (39.2%) were referred to an allergist. Of 28 patients who kept their appointments and underwent skin testing, 3 had negative results and 25 (89%) had positive results and were advised to start immunotherapy. Adherence to the stinging insect hypersensitivity practice parameter recommendations is poor. Many patients who have experienced a systemic reaction after an insect sting and have sought medical care are not afforded an opportunity for potentially lifesaving therapy.

Evaluation and linking of effective parameters in particle-based models and continuum models for mixing-limited bimolecular reactions

NASA Astrophysics Data System (ADS)

Zhang, Yong; Papelis, Charalambos; Sun, Pengtao; Yu, Zhongbo

2013-08-01

Particle-based models and continuum models have been developed to quantify mixing-limited bimolecular reactions for decades. Effective model parameters control reaction kinetics, but the relationship between the particle-based model parameter (such as the interaction radius R) and the continuum model parameter (i.e., the effective rate coefficient Kf) remains obscure. This study attempts to evaluate and link R and Kf for the second-order bimolecular reaction in both the bulk and the sharp-concentration-gradient (SCG) systems. First, in the bulk system, the agent-based method reveals that R remains constant for irreversible reactions and decreases nonlinearly in time for a reversible reaction, while mathematical analysis shows that Kf transitions from an exponential to a power-law function. Qualitative link between R and Kf can then be built for the irreversible reaction with equal initial reactant concentrations. Second, in the SCG system with a reaction interface, numerical experiments show that when R and Kf decline as t-1/2 (for example, to account for the reactant front expansion), the two models capture the transient power-law growth of product mass, and their effective parameters have the same functional form. Finally, revisiting of laboratory experiments further shows that the best fit factor in R and Kf is on the same order, and both models can efficiently describe chemical kinetics observed in the SCG system. Effective model parameters used to describe reaction kinetics therefore may be linked directly, where the exact linkage may depend on the chemical and physical properties of the system.

Use of reduction rate as a quantitative knob for controlling the twin structure and shape of palladium nanocrystals.

PubMed

Wang, Yi; Peng, Hsin-Chieh; Liu, Jingyue; Huang, Cheng Zhi; Xia, Younan

2015-02-11

Kinetic control is a powerful means for maneuvering the twin structure and shape of metal nanocrystals and thus optimizing their performance in a variety of applications. However, there is only a vague understanding of the explicit roles played by reaction kinetics due to the lack of quantitative information about the kinetic parameters. With Pd as an example, here we demonstrate that kinetic parameters, including rate constant and activation energy, can be derived from spectroscopic measurements and then used to calculate the initial reduction rate and further have this parameter quantitatively correlated with the twin structure of a seed and nanocrystal. On a quantitative basis, we were able to determine the ranges of initial reduction rates required for the formation of nanocrystals with a specific twin structure, including single-crystal, multiply twinned, and stacking fault-lined. This work represents a major step forward toward the deterministic syntheses of colloidal noble-metal nanocrystals with specific twin structures and shapes.

CO2 sequestration by mineral carbonation of steel slags under ambient temperature: parameters influence, and optimization.

PubMed

Ghacham, Alia Ben; Pasquier, Louis-César; Cecchi, Emmanuelle; Blais, Jean-François; Mercier, Guy

2016-09-01

This work focuses on the influence of different parameters on the efficiency of steel slag carbonation in slurry phase under ambient temperature. In the first part, a response surface methodology was used to identify the effect and the interactions of the gas pressure, liquid/solid (L/S) ratio, gas/liquid ratio (G/L), and reaction time on the CO2 removed/sample and to optimize the parameters. In the second part, the parameters' effect on the dissolution of CO2 and its conversion into carbonates were studied more in detail. The results show that the pressure and the G/L ratio have a positive effect on both the dissolution and the conversion of CO2. These results have been correlated with the higher CO2 mass introduced in the reactor. On the other hand, an important effect of the L/S ratio on the overall CO2 removal and more specifically on the carbonate precipitation has been identified. The best results were obtained L/S ratios of 4:1 and 10:1 with respectively 0.046 and 0.052 gCO2 carbonated/g sample. These yields were achieved after 10 min reaction, at ambient temperature, and 10.68 bar of total gas pressure following direct gas treatment.

Stable and pH-responsive core-shell nanoparticles based on HEC and PMAA networks via template copolymerization

NASA Astrophysics Data System (ADS)

Zhang, Y.; Jin, Q.; Chen, Y.; Zhao, J.

2011-10-01

Taking advantage of the specific hydrogen bonding interactions, stable and pH-responsive core-shell nanoparticles based on hydroxyethyl cellulose (HEC) and polymethacrylic acid (PMAA) networks, with a < D h > size ranging from 190 to 250 nm, can be efficiently prepared via facile one-step co-polymerization of methacrylic acid (MAA) and N, N'-methylenebisacrylamide (MBA) on HEC template in water. Using dynamic light scattering, electrophoretic light scattering, fluorescence spectrometry, thermo-gravimetric analysis, TEM, and AFM observations, the influence of crosslinker MBA as well as the reaction parameters were studied. The results show that after the introduction of crosslinker MBA, the nanoparticles became less compact; their size exhibited a smaller pH sensitivity, and their stability against pH value was improved greatly. Furthermore, the size, structure, and pH response of the nanoparticles can be adjusted via varying the reaction parameters: nanoparticles of smaller size, more compact structure, and higher swelling capacity were produced as pH value of the reaction medium increased or the HEC/MAA ratio decreased; while nanoparticles of smaller size, less compact structure and smaller swelling capacity were produced as the total feeding concentration increased.

Evaluation of synthesized cross linked polyvinyl alcohol as potential disintegrant.

PubMed

Patel, Ashok R; Vavia, Pradeep R

2010-01-01

The present study deals with evaluation of crosslinked poly vinyl alcohol (PVA) as a potential disintegrant. Crosslinking of PVA was carried out using glutaraldehyde as a crosslinker, in presence of acidic conditions. The crosslinking reaction was optimized for a) polymer: crosslinker ratio; b) temperature requirement and c) reaction duration. Certain physical parameters of the disintegrant (including sedimentation volume, hydration capacity, specific surface area and bulk and tap density) were determined and compared to the known disintegrants. Characterization was carried out using FT-IR, DSC, XRD, SEM and Photo microscopy studies. The developed excipient was also studied for acute toxicity in rats and found to be safe for oral use. Disintegration property of formed product was compared to known disintegrant (Ac-Di-Sol) and it was found to give better results. The disintegration mechanism of developed disintegrant was postulated based on results obtained from various physical evaluations including: Study of effect of disintegrant concentration, fillers, and hardness, mode of incorporation and method of granulation on disintegration activity. By changing the condition parameters of well known crosslinking reaction of PVA, we obtained a crosslinked product which had excellent disintegration activity, good flow and optimal tableting properties.

The Effect of Stiffness Parameter on Mass Distribution in Heavy-Ion Induced Fission

NASA Astrophysics Data System (ADS)

Soheyli, Saeed; Khalil Khalili, Morteza; Ashrafi, Ghazaaleh

2018-06-01

The stiffness parameter of the composite system has been studied for several heavy-ion induced fission reactions without the contribution of non-compound nucleus fission events. In this research, determination of the stiffness parameter is based on the comparison between the experimental data on the mass widths of fission fragments and those predicted by the statistical model treatments at the saddle and scission points. Analysis of the results shows that for the induced fission reactions of different targets by the same projectile, the stiffness parameter of the composite system decreases with increasing the fissility parameter, as well as with increasing the mass number of the compound nucleus. This parameter also exhibits a similar behavior for the reactions of a given target induced by different projectiles. As expected, nearly same stiffness values are obtained for different reactions leading to the same compound nucleus.

Detection of the Haemophilus somnus antibodies in the bulls' reproductive tract fluids using the ELISA. I. Elaboration of the ELISA for the detection of the specific antibodies in the IgG, IgM and IgA classes.

PubMed

Stefaniak, T

1993-01-01

The conditions of the ELISA for detecting the Haemophilus somnus antibodies in IgG, IgM and IgA classes were elaborated. The test was adapted for examining the seminal plasma, preputial washings and blood serum samples of bulls. In order to obtain the more precise evaluation of results, the tests were made for two different dilutions of the examined material. The arising out of this method difficulty in the evaluation of the intensity of reaction was solved by introducing the specific, semi-quantitative method of classification, using the eleven-degree scale. The mean arithmetic classificational values calculated from absorbance readings were called "absorbance index". The introduced parameter proved to be especially useful while comparing the reaction of antibodies in reproductive tract fluids samples.

Correlations of the Specific Rates of Solvolysis of Aromatic Carbamoyl Chlorides, Chloroformates, Chlorothionoformates, and Chlorodithioformates Revisited

PubMed Central

Kevill, Dennis N.; Koyoshi, Fumie; D’Souza, Malcolm J.

2007-01-01

Additional specific rates of solvolysis are determined for phenyl chloroformate. These values are combined with literature values to give a total of 49 data points, which are used within simple and extended Grunwald-Winstein treatments. Literature values are also brought together to allow treatments in more solvents than previously for three N-aryl-N-methylcarbamoyl chlorides, phenyl chlorothionoformate, phenyl chlorodithioformate, and N,N-diphenylcarbamoyl chloride. For the last two listed, moderately strong evidence for a meaningful inclusion of a term governed by the aromatic ring parameter (I) was indicated. No evidence was found requiring inclusion of this parameter for ionization reactions with only one aromatic ring on the nitrogen of carbamoyl chlorides or for the solvolyses of the chloroformate or chlorothionoformate proceeding by an addition-elimination (association-dissociation) mechanism.

Egg shell waste as heterogeneous nanocatalyst for biodiesel production: Optimized by response surface methodology.

PubMed

Pandit, Priti R; Fulekar, M H

2017-08-01

Worldwide consumption of hen eggs results in availability of large amount of discarded egg waste particularly egg shells. In the present study, the waste shells were utilized for the synthesis of highly active heterogeneous calcium oxide (CaO) nanocatalyst to transesterify dry biomass into methyl esters (biodiesel). The CaO nanocatalyst was synthesied by calcination-hydration-dehydration technique and fully characterized by infrared spectroscopy, X-ray powder diffraction (XRD), scanning electron microscope (SEM), transmission electron microscope (TEM), brunauer-emmett-teller (BET) elemental and thermogravimetric analysis. TEM image showed that the nano catalyst had spherical shape with average particle size of 75 nm. BET analysis indicated that the catalyst specific surface area was 16.4 m 2  g -1 with average pore diameter of 5.07 nm. The effect of nano CaO catalyst was investigated by direct transesterification of dry biomass into biodiesel along with other reaction parameters such as catalyst ratio, reaction time and stirring rate. The impact of the transesterification reaction parameters and microalgal biodiesel yield were analyzed by response surface methodology based on a full factorial, central composite design. The significance of the predicted mode was verified and 86.41% microalgal biodiesel yield was reported at optimal parameter conditions 1.7% (w/w), catalyst ratio, 3.6 h reaction time and stirring rate of 140.6 rpm. The biodiesel conversion was determined by 1 H nuclear magnetic resonance spectroscopy (NMR). The fuel properties of prepared biodiesel were found to be highly comply with the biodiesel standard ASTMD6751 and EN14214. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of activation energy in Couette-Poiseuille flow of nanofluid in the presence of chemical reaction and convective boundary conditions

NASA Astrophysics Data System (ADS)

Zeeshan, A.; Shehzad, N.; Ellahi, R.

2018-03-01

The motivation of the current article is to explore the energy activation in MHD radiative Couette-Poiseuille flow nanofluid in horizontal channel with convective boundary conditions. The mathematical model of Buongiorno [1] effectively describes the current flow analysis. Additionally, the impact of chemical reaction is also taken in account. The governing flow equations are simplified with the help of boundary layer approximations. Non-linear coupled equations for momentum, energy and mass transfer are tackled with analytical (HAM) technique. The influence of dimensionless convergence parameter like Brownian motion parameter, radiation parameter, buoyancy ratio parameter, dimensionless activation energy, thermophoresis parameter, temperature difference parameter, dimensionless reaction rate, Schmidt number, Brinkman number, Biot number and convection diffusion parameter on velocity, temperature and concentration profiles are discussed graphically and in tabular form. From the results, it is elaborate that the nanoparticle concentration is directly proportional to the chemical reaction with activation energy and the performance of Brownian motion on nanoparticle concentration gives reverse pattern to that of thermophoresis parameter.

Chapter A6. Section 6.1. Temperature

USGS Publications Warehouse

Revised by Wilde, Franceska D.

2006-01-01

Accurate temperature measurements are required for accurate determinations of important environmental parameters such as pH, specific electrical conductance, and dissolved oxygen, and to the determination of chemical reaction rates and equilibria, biological activity, and physical fluid properties. This section of the National Field Manual (NFM) describes U.S. Geological Survey (USGS) guidance and protocols for measurement of temperature in air, ground water, and surface water and calibration of the equipment used.

Bursting Regimes in a Reaction-Diffusion System with Action Potential-Dependent Equilibrium

PubMed Central

Meier, Stephen R.; Lancaster, Jarrett L.; Starobin, Joseph M.

2015-01-01

The equilibrium Nernst potential plays a critical role in neural cell dynamics. A common approximation used in studying electrical dynamics of excitable cells is that the ionic concentrations inside and outside the cell membranes act as charge reservoirs and remain effectively constant during excitation events. Research into brain electrical activity suggests that relaxing this assumption may provide a better understanding of normal and pathophysiological functioning of the brain. In this paper we explore time-dependent ionic concentrations by allowing the ion-specific Nernst potentials to vary with developing transmembrane potential. As a specific implementation, we incorporate the potential-dependent Nernst shift into a one-dimensional Morris-Lecar reaction-diffusion model. Our main findings result from a region in parameter space where self-sustaining oscillations occur without external forcing. Studying the system close to the bifurcation boundary, we explore the vulnerability of the system with respect to external stimulations which disrupt these oscillations and send the system to a stable equilibrium. We also present results for an extended, one-dimensional cable of excitable tissue tuned to this parameter regime and stimulated, giving rise to complex spatiotemporal pattern formation. Potential applications to the emergence of neuronal bursting in similar two-variable systems and to pathophysiological seizure-like activity are discussed. PMID:25823018

Cellulose extraction from orange peel using sulfite digestion reagents.

PubMed

Bicu, Ioan; Mustata, Fanica

2011-11-01

Orange peel (OP) was used as raw material for cellulose extraction. Two different pulping reagents were used, sodium sulfite and sodium metabisulfite. The effect of the main process parameters, sulfite agent dosage and reaction duration, on cellulose yield was investigated. A central composite rotatable design involving two variables at five levels and response surface methodology were used for the optimization of cellulose recovery. Other two invariable parameters were reaction temperature and hydromodulus. The optimum yields, referred to the weight of double extracted OP, were 40.4% and 45.2% for sodium sulfite and sodium metabisulfite digestions, respectively. The crude celluloses were bleached with hypochlorite and oxygen. The physicochemical characterization data of these cellulose materials indicate good levels of purity, low crystallinities, good whitenesses, good water retention and moderate molecular weights. According to these specific properties the recovered celluloses could be used as fillers, water absorbents, or as raw materials for cellulose derivatives. Copyright © 2011 Elsevier Ltd. All rights reserved.

Inter- and intra-specific variation in drought sensitivity in Abies spec. and its relation to wood density and growth traits

PubMed Central

George, Jan-Peter; Schueler, Silvio; Karanitsch-Ackerl, Sandra; Mayer, Konrad; Klumpp, Raphael T.; Grabner, Michael

2016-01-01

Understanding drought sensitivity of tree species and its intra-specific variation is required to estimate the effects of climate change on forest productivity, carbon sequestration and tree mortality as well as to develop adaptive forest management measures. Here, we studied the variation of drought reaction of six European Abies species and ten provenances of Abies alba planted in the drought prone eastern Austria. Tree-ring and X-ray densitometry data were used to generate early- and latewood measures for ring width and wood density. Moreover, the drought reaction of species and provenances within six distinct drought events between 1970 and 2011, as identified by the standardized precipitation index, was determined by four drought response measures. The mean reaction of species and provenances to drought events was strongly affected by the seasonal occurrence of the drought: a short, strong drought at the beginning of the growing season resulted in growth reductions up to 50%, while droughts at the end of the growing season did not affect annual increment. Wood properties and drought response measures showed significant variation among Abies species as well as among A. alba provenances. Whereas A. alba provenances explained significant parts in the variation of ring width measures, the Abies species explained significant parts in the variation of wood density parameters. A consistent pattern in drought response across the six drought events was observed only at the inter-specific level, where A. nordmanniana showed the highest resistance and A. cephalonica showed the best recovery after drought. In contrast, differences in drought reaction among provenances were only found for the milder drought events in 1986, 1990, 1993 and 2000 and the ranking of provenances varied at each drought event. This indicates that genetic variation in drought response within A. alba is more limited than among Abies species. Low correlations between wood density parameters and drought response measures suggest that wood density is a poor predictor of drought sensitivity in Abies spec. PMID:27713591

Visual but not motor processes predict simple visuomotor reaction time of badminton players.

PubMed

Hülsdünker, Thorben; Strüder, Heiko K; Mierau, Andreas

2018-03-01

The athlete's brain exhibits significant functional adaptations that facilitate visuomotor reaction performance. However, it is currently unclear if the same neurophysiological processes that differentiate athletes from non-athletes also determine performance within a homogeneous group of athletes. This information can provide valuable help for athletes and coaches aiming to optimize existing training regimes. Therefore, this study aimed to identify the neurophysiological correlates of visuomotor reaction performance in a group of skilled athletes. In 36 skilled badminton athletes, electroencephalography (EEG) was used to investigate pattern reversal and motion onset visual-evoked potentials (VEPs) as well as visuomotor reaction time (VMRT) during a simple reaction task. Stimulus-locked and response-locked event-related potentials (ERPs) in visual and motor regions as well as the onset of muscle activation (EMG onset) were determined. Correlation and multiple regression analyses identified the neurophysiological parameters predicting EMG onset and VMRT. For pattern reversal stimuli, the P100 latency and age best predicted EMG onset (r = 0.43; p = .003) and VMRT (r = 0.62; p = .001). In the motion onset experiment, EMG onset (r = 0.80; p < .001) and VMRT (r = 0.78; p < .001) were predicted by N2 latency and age. In both conditions, cortical potentials in motor regions were not correlated with EMG onset or VMRT. It is concluded that previously identified neurophysiological parameters differentiating athletes from non-athletes do not necessarily determine performance within a homogeneous group of athletes. Specifically, the speed of visual perception/processing predicts EMG onset and VMRT in skilled badminton players while motor-related processes, although differentiating athletes from non-athletes, are not associated simple with visuomotor reaction performance.

Contribution to an effective design method for stationary reaction-diffusion patterns.

PubMed

Szalai, István; Horváth, Judit; De Kepper, Patrick

2015-06-01

The British mathematician Alan Turing predicted, in his seminal 1952 publication, that stationary reaction-diffusion patterns could spontaneously develop in reacting chemical or biochemical solutions. The first two clear experimental demonstrations of such a phenomenon were not made before the early 1990s when the design of new chemical oscillatory reactions and appropriate open spatial chemical reactors had been invented. Yet, the number of pattern producing reactions had not grown until 2009 when we developed an operational design method, which takes into account the feeding conditions and other specificities of real open spatial reactors. Since then, on the basis of this method, five additional reactions were shown to produce stationary reaction-diffusion patterns. To gain a clearer view on where our methodical approach on the patterning capacity of a reaction stands, numerical studies in conditions that mimic true open spatial reactors were made. In these numerical experiments, we explored the patterning capacity of Rabai's model for pH driven Landolt type reactions as a function of experimentally attainable parameters that control the main time and length scales. Because of the straightforward reversible binding of protons to carboxylate carrying polymer chains, this class of reaction is at the base of the chemistry leading to most of the stationary reaction-diffusion patterns presently observed. We compare our model predictions with experimental observations and comment on agreements and differences.

Clinical and immunologic follow-up of patients who stop venom immunotherapy.

PubMed

Keating, M U; Kagey-Sobotka, A; Hamilton, R G; Yunginger, J W

1991-09-01

We prospectively studied 51 self-selected Hymenoptera sting-sensitive patients to determine (1) whether a minimal or optimal duration for venom immunotherapy (VIT) exists and (2) whether clinical or immunologic parameters exist that are predictive of clinical immunity after VIT was stopped. After 2 to 10 years of VIT, all patients had deliberate sting challenges (DSCs) from live insects. If DSCs were tolerated, patients voluntarily stopped VIT and returned annually for repeat venom skin tests (VSTs) and DSCs. In most patients, it was possible to monitor VST and venom-specific antibody (Ab) levels before and after VIT was stopped. One-year after VIT, VST and venom-specific IgE and IgG Ab level results were variable; 49 patients tolerated DSC, whereas two patients exhibited generalized reactions. These two patients had pre-VIT histories of grade IV field-sting reactions and had received VIT for 2 years and 4 years, respectively. The short-term (1 year) risk of recurrence of clinical allergy to stings after VIT was higher in patients who had experienced grade IV field-sting reactions before VIT versus patients experiencing grade I to III reactions before VIT (2/15, 13% versus 0/36, 0%) and higher in patients who had received VIT for less than 5 years versus patients who received VIT for 5 or more years (2/20, 10% versus 0/31, 0%). We suggest that VIT should be continued for 5 years in patients with pre-VIT field-sting reactions of grade IV severity. VST and venom-specific Ab results do not reliably predict the outcome of DSC or the subsequent clinical course in individual patients stopping VIT.

Effect of deformation on structure and reaction of Al isotopes using relativistic mean field densities in Glauber model

NASA Astrophysics Data System (ADS)

Panda, R. N.; Sharma, Mahesh K.; Panigrahi, M.; Patra, S. K.

2018-02-01

We have examined the ground state properties of Al isotopes towards the proton rich side from A = 22 to 28 using the well known relativistic mean field (RMF) formalism with NLSH parameter set. The calculated results are compared with the predictions of finite range droplet model and experimental data. The calculation is extended to estimate the reaction cross section for ^{22-28} Al as projectiles with ^{12} C as target. The incident energy of the projectiles are taken as 950 MeV/nucleon, for both spherical and deformed RMF densities as inputs in the Glauber model approximation. Further investigation of enhanced values of total reaction cross section for ^{23} Al and ^{24} Al in comparison to rest of the isotopes indicates the proton skin structure of these isotopes. Specifically, the large value of root mean square radius and total reaction cross section of ^{23} Al could not be ruled out the formation of proton halo.

In-liquid arc plasma jet and its application to phenol degradation

NASA Astrophysics Data System (ADS)

Liu, Jing-Lin; Park, Hyun-Woo; Hamdan, Ahmad; Cha, Min Suk

2018-03-01

We present a new method for achieving chemical reactions induced by plasmas with liquids—an in-liquid arc plasma jet system—designed to have a few advantages over the existing methods. High-speed imaging and optical emission spectroscopy were adopted to highlight the physical aspects of the in-liquid arc plasma jet system, and the feasibility of the system was investigated in a wastewater treatment case with phenol as the model contaminant. We found that the specific energy input is a reasonable parameter by which to characterize the overall process. The phenol removal reaction could be modeled as a pseudo-first-order reaction, and the reaction constant became smaller as the phenol concentration increased. However, complete decomposition of the phenol into water and carbon dioxide required very high energy because the final intermediate, oxalic acid, is relatively stable. Detailed chemical and physical analyses, including byproducts, ions, solution acidity, and conductivity, were conducted to evaluate this new method for use in the appropriate applications.

Effect of deformation on structure and reaction of Al isotopes using relativistic mean field densities in Glauber model

NASA Astrophysics Data System (ADS)

Panda, R. N.; Sharma, Mahesh K.; Panigrahi, M.; Patra, S. K.

2018-06-01

We have examined the ground state properties of Al isotopes towards the proton rich side from A = 22 to 28 using the well known relativistic mean field (RMF) formalism with NLSH parameter set. The calculated results are compared with the predictions of finite range droplet model and experimental data. The calculation is extended to estimate the reaction cross section for ^{22-28}Al as projectiles with ^{12}C as target. The incident energy of the projectiles are taken as 950 MeV/nucleon, for both spherical and deformed RMF densities as inputs in the Glauber model approximation. Further investigation of enhanced values of total reaction cross section for ^{23}Al and ^{24}Al in comparison to rest of the isotopes indicates the proton skin structure of these isotopes. Specifically, the large value of root mean square radius and total reaction cross section of ^{23}Al could not be ruled out the formation of proton halo.

LAMP-based group specific detection of aflatoxin producers within Aspergillus section Flavi in food raw materials, spices, and dried fruit using neutral red for visible-light signal detection.

PubMed

Niessen, Ludwig; Bechtner, Julia; Fodil, Sihem; Taniwaki, Marta H; Vogel, Rudi F

2018-02-02

Aflatoxins can be produced by 21 species within sections Flavi (16 species), Ochraceorosei (2), and Nidulantes (3) of the fungal genus Aspergillus. They pose risks to human and animal health due to high toxicity and carcinogenicity. Detecting aflatoxin producers can help to assess toxicological risks associated with contaminated commodities. Species specific molecular assays (PCR and LAMP) are available for detection of major producers, but fail to detect species of minor importance. To enable rapid and sensitive detection of several aflatoxin producing species in a single analysis, a nor1 gene-specific LAMP assay was developed. Specificity testing showed that among 128 fungal species from 28 genera, 15 aflatoxigenic species in section Flavi were detected, including synonyms of A. flavus and A. parasiticus. No cross reactions were found with other tested species. The detection limit of the assay was 9.03pg of A. parasiticus genomic DNA per reaction. Visual detection of positive LAMP reactions under daylight conditions was facilitated using neutral red to allow unambiguous distinction between positive and negative assay results. Application of the assay to the detection of A. parasiticus conidia revealed a detection limit of 211 conidia per reaction after minimal sample preparation. The usefulness of the assay was demonstrated in the analysis of aflatoxinogenic species in samples of rice, nuts, raisins, dried figs, as well as powdered spices. Comparison of LAMP results with presence/absence of aflatoxins and aflatoxin producing fungi in 50 rice samples showed good correlation between these parameters. Our study suggests that the developed LAMP assay is a rapid, sensitive and user-friendly tool for surveillance and quality control in our food industry. Copyright © 2017 Elsevier B.V. All rights reserved.

Understanding the mechanism of nanotube synthesis for controlled production of specific (n,m) structures

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

Resasco, Daniel E.

2010-02-11

This report shows the extensive research on the mechanism responsible for the formation of single walled carbon nanotubes in order to get control over their structural parameters (diameter and chirality). Catalyst formulations, pre-treatment conditions, and reaction conditions are described in detail as well as mechanisms to produce nanotubes structures of specific arrays (vertical forest, nanotube pillars). Applications of SWNT in different fields are also described in this report. In relation to this project five students have graduated (3 PhD and 2 MS) and 35 papers have been published.

The structure and photochemical transformation of cyclopropylacetylene radical cation as revealed by matrix EPR and quantum chemical study

NASA Astrophysics Data System (ADS)

Shiryaeva, Ekaterina S.; Tyurin, Daniil A.; Feldman, Vladimir I.

2012-05-01

The primary radical cation of cyclopropylacetylene was first characterized by EPR spectroscopy in low-temperature freon matrices. The assignment was confirmed by specific deuteration and quantum-chemical calculations at PBE0 and CCSD(T) levels. Photolysis with visible light led to irreversible transformation of the initial species to a ring-open structure. Detailed computational analysis of energy and magnetic resonance parameters of possible reaction products justified formation of pent-3-en-1-yne radical cation (presumably, a (Z)-isomer). This conclusion was also supported by the effect of specific deuteration.

Magnetohydrodynamic Flow by a Stretching Cylinder with Newtonian Heating and Homogeneous-Heterogeneous Reactions

PubMed Central

Hayat, T.; Hussain, Zakir; Alsaedi, A.; Farooq, M.

2016-01-01

This article examines the effects of homogeneous-heterogeneous reactions and Newtonian heating in magnetohydrodynamic (MHD) flow of Powell-Eyring fluid by a stretching cylinder. The nonlinear partial differential equations of momentum, energy and concentration are reduced to the nonlinear ordinary differential equations. Convergent solutions of momentum, energy and reaction equations are developed by using homotopy analysis method (HAM). This method is very efficient for development of series solutions of highly nonlinear differential equations. It does not depend on any small or large parameter like the other methods i. e., perturbation method, δ—perturbation expansion method etc. We get more accurate result as we increase the order of approximations. Effects of different parameters on the velocity, temperature and concentration distributions are sketched and discussed. Comparison of present study with the previous published work is also made in the limiting sense. Numerical values of skin friction coefficient and Nusselt number are also computed and analyzed. It is noticed that the flow accelerates for large values of Powell-Eyring fluid parameter. Further temperature profile decreases and concentration profile increases when Powell-Eyring fluid parameter enhances. Concentration distribution is decreasing function of homogeneous reaction parameter while opposite influence of heterogeneous reaction parameter appears. PMID:27280883

Magnetohydrodynamic Flow by a Stretching Cylinder with Newtonian Heating and Homogeneous-Heterogeneous Reactions.

PubMed

Hayat, T; Hussain, Zakir; Alsaedi, A; Farooq, M

2016-01-01

This article examines the effects of homogeneous-heterogeneous reactions and Newtonian heating in magnetohydrodynamic (MHD) flow of Powell-Eyring fluid by a stretching cylinder. The nonlinear partial differential equations of momentum, energy and concentration are reduced to the nonlinear ordinary differential equations. Convergent solutions of momentum, energy and reaction equations are developed by using homotopy analysis method (HAM). This method is very efficient for development of series solutions of highly nonlinear differential equations. It does not depend on any small or large parameter like the other methods i. e., perturbation method, δ-perturbation expansion method etc. We get more accurate result as we increase the order of approximations. Effects of different parameters on the velocity, temperature and concentration distributions are sketched and discussed. Comparison of present study with the previous published work is also made in the limiting sense. Numerical values of skin friction coefficient and Nusselt number are also computed and analyzed. It is noticed that the flow accelerates for large values of Powell-Eyring fluid parameter. Further temperature profile decreases and concentration profile increases when Powell-Eyring fluid parameter enhances. Concentration distribution is decreasing function of homogeneous reaction parameter while opposite influence of heterogeneous reaction parameter appears.

Recommendations for terminology and databases for biochemical thermodynamics.

PubMed

Alberty, Robert A; Cornish-Bowden, Athel; Goldberg, Robert N; Hammes, Gordon G; Tipton, Keith; Westerhoff, Hans V

2011-05-01

Chemical equations are normally written in terms of specific ionic and elemental species and balance atoms of elements and electric charge. However, in a biochemical context it is usually better to write them with ionic reactants expressed as totals of species in equilibrium with each other. This implies that atoms of elements assumed to be at fixed concentrations, such as hydrogen at a specified pH, should not be balanced in a biochemical equation used for thermodynamic analysis. However, both kinds of equations are needed in biochemistry. The apparent equilibrium constant K' for a biochemical reaction is written in terms of such sums of species and can be used to calculate standard transformed Gibbs energies of reaction Δ(r)G'°. This property for a biochemical reaction can be calculated from the standard transformed Gibbs energies of formation Δ(f)G(i)'° of reactants, which can be calculated from the standard Gibbs energies of formation of species Δ(f)G(j)° and measured apparent equilibrium constants of enzyme-catalyzed reactions. Tables of Δ(r)G'° of reactions and Δ(f)G(i)'° of reactants as functions of pH and temperature are available on the web, as are functions for calculating these properties. Biochemical thermodynamics is also important in enzyme kinetics because apparent equilibrium constant K' can be calculated from experimentally determined kinetic parameters when initial velocities have been determined for both forward and reverse reactions. Specific recommendations are made for reporting experimental results in the literature. Copyright © 2011 Elsevier B.V. All rights reserved.

Thermodynamically Feasible Kinetic Models of Reaction Networks

PubMed Central

Ederer, Michael; Gilles, Ernst Dieter

2007-01-01

The dynamics of biological reaction networks are strongly constrained by thermodynamics. An holistic understanding of their behavior and regulation requires mathematical models that observe these constraints. However, kinetic models may easily violate the constraints imposed by the principle of detailed balance, if no special care is taken. Detailed balance demands that in thermodynamic equilibrium all fluxes vanish. We introduce a thermodynamic-kinetic modeling (TKM) formalism that adapts the concepts of potentials and forces from irreversible thermodynamics to kinetic modeling. In the proposed formalism, the thermokinetic potential of a compound is proportional to its concentration. The proportionality factor is a compound-specific parameter called capacity. The thermokinetic force of a reaction is a function of the potentials. Every reaction has a resistance that is the ratio of thermokinetic force and reaction rate. For mass-action type kinetics, the resistances are constant. Since it relies on the thermodynamic concept of potentials and forces, the TKM formalism structurally observes detailed balance for all values of capacities and resistances. Thus, it provides an easy way to formulate physically feasible, kinetic models of biological reaction networks. The TKM formalism is useful for modeling large biological networks that are subject to many detailed balance relations. PMID:17208985

Mechanism of C-C and C-H bond cleavage in ethanol oxidation reaction on Cu2O(111): a DFT-D and DFT+U study.

PubMed

Xu, Han; Miao, Bei; Zhang, Minhua; Chen, Yifei; Wang, Lichang

2017-10-04

The performance of transition metal catalysts for ethanol oxidation reaction (EOR) in direct ethanol fuel cells (DEFCs) may be greatly affected by their oxidation. However, the specific effect and catalytic mechanism for EOR of transition metal oxides are still unclear and deserve in-depth exploitation. Copper as a potential anode catalyst can be easily oxidized in air. Thus, in this study, we investigated C-C and C-H bond cleavage reactions of CH x CO (x = 1, 2, 3) species in EOR on Cu 2 O(111) using PBE+U calculations, as well as the specific effect of +U correction on the process of adsorption and reaction on Cu 2 O(111). It was revealed that the catalytic performance of Cu 2 O(111) for EOR was restrained compared with that of Cu(100). Except for the C-H cleavage of CH 2 CO, all the reaction barriers for C-C and C-H cleavage were higher than those on Cu(100). The most probable pathway for CH 3 CO to CHCO on Cu 2 O(111) was the continuous dehydrogenation reaction. Besides, the barrier for C-C bond cleavage increased due to the loss of H atoms in the intermediate. Moreover, by the comparison of the traditional GGA/PBE method and the PBE+U method, it could be concluded that C-C cleavage barriers would be underestimated without +U correction, while C-H cleavage barriers would be overestimated. +U correction was proved to be necessary, and the reaction barriers and the values of the Hubbard U parameter had a proper linear relationship.

The culprit insect but not severity of allergic reactions to bee and wasp venom can be determined by molecular diagnosis.

PubMed

Gattinger, Pia; Lupinek, Christian; Kalogiros, Lampros; Silar, Mira; Zidarn, Mihaela; Korosec, Peter; Koessler, Christine; Novak, Natalija; Valenta, Rudolf; Mittermann, Irene

2018-01-01

Allergy to bee and wasp venom can lead to life-threatening systemic reactions. The identification of the culprit species is important for allergen-specific immunotherapy. To determine a panel of recombinant bee and wasp allergens which is suitable for the identification of bee or wasp as culprit allergen sources and to search for molecular surrogates of clinical severity of sting reactions. Sera from eighty-seven patients with a detailed documentation of their severity of sting reaction (Mueller grade) and who had been subjected to titrated skin testing with bee and wasp venom were analyzed for bee and wasp-specific IgE levels by ImmunoCAPTM. IgE-reactivity testing was performed using a comprehensive panel of recombinant bee and wasp venom allergens (rApi m 1, 2, 3, 4, 5 and 10; rVes v 1 and 5) by ISAC chip technology, ImmunoCAP and ELISA. IgG4 antibodies to rApi m 1 and rVes v 5 were determined by ELISA and IgE/IgG4 ratios were calculated. Results from skin testing, IgE serology and IgE/IgG4 ratios were compared with severity of sting reactions. The panel of rApi m 1, rApi m 10, rVes v 1 and rVes v 5 allowed identification of the culprit venom in all but two of the 87 patients with good agreement to skin testing. Severities of sting reactions were not associated with results obtained by skin testing, venom-specific IgE levels or molecular diagnosis. Severe sting reactions were observed in patients showing < 1 ISU and < 2kUA/L of IgE to Api m 1 and/or Ves v 5. We identified a minimal panel of recombinant bee and wasp allergens for molecular diagnosis which may permit identification of bee and/or wasp as culprit insect in venom-sensitized subjects. The severity of sting reactions was not associated with parameters obtained by molecular diagnosis.

A theoretical model to determine the capacity performance of shape-specific electrodes

NASA Astrophysics Data System (ADS)

Yue, Yuan; Liang, Hong

2018-06-01

A theory is proposed to explain and predict the electrochemical process during reaction between lithium ions and electrode materials. In the model, the process of reaction is proceeded into two steps, surface adsorption and diffusion of lithium ions. The surface adsorption is an instantaneous process for lithium ions to adsorb onto the surface sites of active materials. The diffusion of lithium ions into particles is determined by the charge-discharge condition. A formula to determine the maximum specific capacity of active materials at different charging rates (C-rates) is derived. The maximum specific capacity is correlated to characteristic parameters of materials and cycling - such as size, aspect ratio, surface area, and C-rate. Analysis indicates that larger particle size or greater aspect ratio of active materials and faster C-rates can reduce maximum specific capacity. This suggests that reducing particle size of active materials and slowing the charge-discharge speed can provide enhanced electrochemical performance of a battery cell. Furthermore, the model is validated by published experimental results. This model brings new understanding in quantification of electrochemical kinetics and capacity performance. It enables development of design strategies for novel electrodes and future generation of energy storage devices.

STUDIES ON THE IMMUNE RESPONSE TO A CHARACTERIZED ANTIGENIC DETERMINANT OF THE TOBACCO MOSAIC VIRUS PROTEIN

PubMed Central

Spitler, Lynn; Benjamini, E.; Young, Janis D.; Kaplan, Harvey; Fudenberg, H. H.

1970-01-01

The following peptides have previously been shown to bind specifically with antibodies to TMVP: (a) An eicosapeptide representing residues 93–112 of TMVP and having the sequence Ileu-Ileu-Glu-Val-Glu-AspNH2-GluNH2-Ala-AspNH2-Pro-Thr-Thr-Ala-Glu-Thr-Leu-Asp-Ala-Thr-Arg. (b) Its C-terminal decapeptide. (c) Its C-terminal pentapeptide. (d) N-octanoyl-C-terminal-tripeptide. (e) (Lys)4-C-terminal-pentapeptide. (f) (Lys)7 C-terminal-pentapeptide. The present communication deals with the investigation of several parameters of the immunological activity of the peptides. The results show that none of the peptides tested were immunogenic in guinea pigs, nor did they stimulate the incorporation of 14C-thymidine by spleen cells derived from TMVP-primed animals. Results also showed that all of the peptides tested could elicit specific delayed and immediate skin reactions in TMVP-sensitized guinea pigs, and furthermore, that the peptides could specifically inhibit the migration of peritoneal exudate cells derived from these animals. The elicitation of delayed skin reactions and the ability to inhibit migration of peritoneal exudate cells were independent of carrier specificity. PMID:5409944

Significant consequences of heat generation/absorption and homogeneous-heterogeneous reactions in second grade fluid due to rotating disk

NASA Astrophysics Data System (ADS)

Hayat, Tasawar; Qayyum, Sumaira; Alsaedi, Ahmed; Ahmad, Bashir

2018-03-01

Flow of second grade fluid by a rotating disk with heat and mass transfer is discussed. Additional effects of heat generation/absorption are also analyzed. Flow is also subjected to homogeneous-heterogeneous reactions. The convergence of computed solution is assured through appropriate choices of initial guesses and auxiliary parameters. Investigation is made for the effects of involved parameters on velocities (radial, axial, tangential), temperature and concentration. Skin friction and Nusselt number are also analyzed. Graphical results depict that an increase in viscoelastic parameter enhances the axial, radial and tangential velocities. Opposite behavior of temperature is observed for larger values of viscoelastic and heat generation/absorption parameters. Concentration profile is increasing function of Schmidt number, viscoelastic parameter and heterogeneous reaction parameter. Magnitude of skin friction and Nusselt number are enhanced for larger viscoelastic parameter.

Organic Electrolytes for Sodium Batteries

DTIC Science & Technology

1992-09-01

discussion ................................... 30 3.1 Stability of the organic compounds ...................... 30 3.2 Reactivity with aluminum chloride...Reactions between organic salt/ aluminum chloride. 3.2.1 The MEICI:AICI 3 system. 3.3.1.1 Least-Squares-Fitted Parameters fo, specific conductivitie’s of l...temperature. 3.5.2.3.1 Sodium behavior towards MEICIAICI3 melts. 3.5.2.3.1.1 Standard potential of copper couples in AICt3 :BuPyCI melts versus aluminum

Diskoseismology: Probing accretion disks. II - G-modes, gravitational radiation reaction, and viscosity

NASA Technical Reports Server (NTRS)

Nowak, Michael A.; Wagoner, Robert V.

1992-01-01

A scalar potential is used to derive a single partial differential equation governing the oscillation of a disk. The eigenfunctions and eigenfrequencies of a variety of disk models are found to fall into two main classes which are analogous to the p-modes and g-modes in the sun. Specifically, the eigenfunctions and eigenfrequencies of isothermal disks are computed, and the way in which these results can be generalized to other disk models is indicated. The (assumed) relatively small rates of growth or damping of the modes due to various mechanisms, in particular gravitational radiation reaction and parameterized models of viscosity are also computed. It is found that for certain parameters the p-modes are unstable to gravitational radiation reaction (CFS instability), while both the p-modes and g-modes are unstable to viscosity unless highly anisotropic viscosity models are considered.

Sodium-Hydrogen-Exchanger expression in human sperm and its relationship with semen parameters.

PubMed

Zhang, Zhe; Yang, Yuzhuo; Wu, Han; Zhang, Hongliang; Zhang, Haitao; Mao, Jiaming; Liu, Defeng; Zhao, Lianming; Lin, Haocheng; Tang, Wenhao; Hong, Kai; Jiang, Hui

2017-06-01

Sperm-specific sodium-hydrogen exchanger (sNHE) is essential to maintain sperm normal function in mice; however, its role in human sperm has not been clarified to date. The aim of this study is to investigate the expression pattern of sNHE in human spermatozoa and its relationship with sperm functional parameters. Semen samples from 68 asthenozoospermic and 61 normozoospermic men were analyzed for sperm concentration, motility, and acrosome reaction, and high motile spermatozoa were collected by swim-up method. The expression of sNHE in spermatozoa was detected by Western blot and immunofluorescence staining. The relationship between sNHE expression and sperm parameters was assessed. We identified sNHE is mainly localized to the principal piece of the human sperm tail. The expression of sNHE was positively correlated with sperm concentration, total number, and progressive motility. Moreover, sNHE expression was upregulated in swim-up sperm and associated with most of sperm motility parameters including straight line velocity and curvilinear velocity. Our results also showed that sNHE expression is decreased in sperm from patients with asthenozoospermia compared with that from normal controls. However, no correlation was found between sNHE expression and acrosome reaction in spermatozoa. The expression pattern of sNHE suggested that this protein may be involved in the regulation of sperm motility, and aberration of its expression in sperm may contribute to the pathogenesis of asthenozoospermia.

EVALUATING THE SENSITIVITY OF A SUBSURFACE MULTICOMPONENT REACTIVE TRANSPORT MODEL WITH RESPECT TO TRANSPORT AND REACTION PARAMETERS

EPA Science Inventory

The input variables for a numerical model of reactive solute transport in groundwater include both transport parameters, such as hydraulic conductivity and infiltration, and reaction parameters that describe the important chemical and biological processes in the system. These pa...

Stepped MS(All) Relied Transition (SMART): An approach to rapidly determine optimal multiple reaction monitoring mass spectrometry parameters for small molecules.

PubMed

Ye, Hui; Zhu, Lin; Wang, Lin; Liu, Huiying; Zhang, Jun; Wu, Mengqiu; Wang, Guangji; Hao, Haiping

2016-02-11

Multiple reaction monitoring (MRM) is a universal approach for quantitative analysis because of its high specificity and sensitivity. Nevertheless, optimization of MRM parameters remains as a time and labor-intensive task particularly in multiplexed quantitative analysis of small molecules in complex mixtures. In this study, we have developed an approach named Stepped MS(All) Relied Transition (SMART) to predict the optimal MRM parameters of small molecules. SMART requires firstly a rapid and high-throughput analysis of samples using a Stepped MS(All) technique (sMS(All)) on a Q-TOF, which consists of serial MS(All) events acquired from low CE to gradually stepped-up CE values in a cycle. The optimal CE values can then be determined by comparing the extracted ion chromatograms for the ion pairs of interest among serial scans. The SMART-predicted parameters were found to agree well with the parameters optimized on a triple quadrupole from the same vendor using a mixture of standards. The parameters optimized on a triple quadrupole from a different vendor was also employed for comparison, and found to be linearly correlated with the SMART-predicted parameters, suggesting the potential applications of the SMART approach among different instrumental platforms. This approach was further validated by applying to simultaneous quantification of 31 herbal components in the plasma of rats treated with a herbal prescription. Because the sMS(All) acquisition can be accomplished in a single run for multiple components independent of standards, the SMART approach are expected to find its wide application in the multiplexed quantitative analysis of complex mixtures. Copyright © 2015 Elsevier B.V. All rights reserved.

Herb–drug interaction prediction based on the high specific inhibition of andrographolide derivatives towards UDP-glucuronosyltransferase (UGT) 2B7

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

Ma, Hai-Ying, E-mail: cmu4h-mhy@126.com; Sun, Dong-Xue; Cao, Yun-Feng

2014-05-15

Herb–drug interaction strongly limits the clinical application of herbs and drugs, and the inhibition of herbal components towards important drug-metabolizing enzymes (DMEs) has been regarded as one of the most important reasons. The present study aims to investigate the inhibition potential of andrographolide derivatives towards one of the most important phase II DMEs UDP-glucuronosyltransferases (UGTs). Recombinant UGT isoforms (except UGT1A4)-catalyzed 4-methylumbelliferone (4-MU) glucuronidation reaction and UGT1A4-catalyzed trifluoperazine (TFP) glucuronidation were employed to firstly screen the andrographolide derivatives' inhibition potential. High specific inhibition of andrographolide derivatives towards UGT2B7 was observed. The inhibition type and parameters (K{sub i}) were determined for themore » compounds exhibiting strong inhibition capability towards UGT2B7, and human liver microsome (HLMs)-catalyzed zidovudine (AZT) glucuronidation probe reaction was used to furtherly confirm the inhibition behavior. In combination of inhibition parameters (K{sub i}) and in vivo concentration of andrographolide and dehydroandrographolide, the potential in vivo inhibition magnitude was predicted. Additionally, both the in vitro inhibition data and computational modeling results provide important information for the modification of andrographolide derivatives as selective inhibitors of UGT2B7. Taken together, data obtained from the present study indicated the potential herb–drug interaction between Andrographis paniculata and the drugs mainly undergoing UGT2B7-catalyzed metabolic elimination, and the andrographolide derivatives as potential candidates for the selective inhibitors of UGT2B7. - Highlights: • Specific inhibition of andrographolide derivatives towards UGT2B7. • Herb-drug interaction related withAndrographis paniculata. • Guidance for design of UGT2B7 specific inhibitors.« less

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

PubMed Central

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

2009-01-01

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

Suppression of Antigen-Specific Lymphocyte Activation in Simulated Microgravity

NASA Technical Reports Server (NTRS)

Cooper, David; Pride, Michael W.; Brown, Eric L.; Risin, Diana; Pellis, Neal R.

1999-01-01

Various parameters of immune suppression are observed in astronauts during and after spaceflight, and in isolated immune cells in true and simulated microgravity. Specifically, polyclonal activation of T cells is severely suppressed in true and simulated microgravity. These recent findings with various polyclonal activators suggests a suppression of oligoclonal lymphocyte activation in microgravity. We utilized rotating wall vessel (RWV) bioreactors that simulate aspects of microgravity for cell cultures to analyze three models of antigen-specific activation. A mixed-lymphocyte reaction (MLR), as a model for a primary immune response; a tetanus toxoid (TT) response and a B. burgdorferi (Bb) response, as models of a secondary immune response, were all suppressed in the RWV bioreactor. Our findings confirm that the suppression of activation observed with polyclonal models also encompasses oligoclonal antigen-specific activation.

Red blood cell distribution width and haemoglobin are associated with hospital admission in patients with acute allergic reactions.

PubMed

Lippi, Giuseppe; Buonocore, Ruggero; Picanza, Alessandra; Schirosa, Fabio; Cervellin, Gianfranco

2016-01-01

Red blood cell distribution width (RDW) is significantly associated with a variety of human disorders. This study aimed to investigate whether RDW value at admission may predict the need of hospitalisation in patients presenting to the emergency department (ED) with acute allergic reactions. The study population consisted of adult patients (aged > 17) admitted to the ED for acute allergic reactions. One hundred and thirty-two subjects were included, 12 of whom (9%) required hospital admission for severity of symptoms. Patients who needed hospital admission displayed significantly lower values of haemoglobin and significantly higher values of RDW-coefficient of variation (RDW-CV). In multivariate analysis, haemoglobin and RDW-CV were found to be independent predictors of hospital admission. The area under the curve (AUC), sensitivity and specificity for predicting hospital admission were 0.72, 0.88 and 0.42 for haemoglobin and 0.73, 0.88 and 0.50 for RDW-CV, respectively. The combination of these tests (both positive) was characterised by 0.76 AUC, 0.83 sensitivity, 0.67 specificity, 0.96 negative predictive value and 0.30 positive predictive. The results of this study suggest that two common and inexpensive parameters such as haemoglobin and RDW are independent predictors of hospital admission in patients presenting to the ED with acute allergic reactions.

Nitroxyl (HNO) Reacts with Molecular Oxygen and Forms Peroxynitrite at Physiological pH

PubMed Central

Smulik, Renata; Dębski, Dawid; Zielonka, Jacek; Michałowski, Bartosz; Adamus, Jan; Marcinek, Andrzej; Kalyanaraman, Balaraman; Sikora, Adam

2014-01-01

Nitroxyl (HNO), the protonated one-electron reduction product of NO, remains an enigmatic reactive nitrogen species. Its chemical reactivity and biological activity are still not completely understood. HNO donors show biological effects different from NO donors. Although HNO reactivity with molecular oxygen is described in the literature, the product of this reaction has not yet been unambiguously identified. Here we report that the decomposition of HNO donors under aerobic conditions in aqueous solutions at physiological pH leads to the formation of peroxynitrite (ONOO−) as a major intermediate. We have specifically detected and quantified ONOO− with the aid of boronate probes, e.g. coumarin-7-boronic acid or 4-boronobenzyl derivative of fluorescein methyl ester. In addition to the major phenolic products, peroxynitrite-specific minor products of oxidation of boronate probes were detected under these conditions. Using the competition kinetics method and a set of HNO scavengers, the value of the second order rate constant of the HNO reaction with oxygen (k = 1.8 × 104 m−1 s−1) was determined. The rate constant (k = 2 × 104 m−1 s−1) was also determined using kinetic simulations. The kinetic parameters of the reactions of HNO with selected thiols, including cysteine, dithiothreitol, N-acetylcysteine, captopril, bovine and human serum albumins, and hydrogen sulfide, are reported. Biological and cardiovascular implications of nitroxyl reactions are discussed. PMID:25378389

Development of a Detailed Surface Chemistry Framework in DSMC

NASA Technical Reports Server (NTRS)

Swaminathan-Gopalan, K.; Borner, A.; Stephani, K. A.

2017-01-01

Many of the current direct simulation Monte Carlo (DSMC) codes still employ only simple surface catalysis models. These include only basic mechanisms such as dissociation, recombination, and exchange reactions, without any provision for adsorption and finite rate kinetics. Incorporating finite rate chemistry at the surface is increasingly becoming a necessity for various applications such as high speed re-entry flows over thermal protection systems (TPS), micro-electro-mechanical systems (MEMS), surface catalysis, etc. In the recent years, relatively few works have examined finite-rate surface reaction modeling using the DSMC method.In this work, a generalized finite-rate surface chemistry framework incorporating a comprehensive list of reaction mechanisms is developed and implemented into the DSMC solver SPARTA. The various mechanisms include adsorption, desorption, Langmuir-Hinshelwood (LH), Eley-Rideal (ER), Collision Induced (CI), condensation, sublimation, etc. The approach is to stochastically model the various competing reactions occurring on a set of active sites. Both gas-surface (e.g., ER, CI) and pure-surface (e.g., LH, desorption) reaction mechanisms are incorporated. The reaction mechanisms could also be catalytic or surface altering based on the participation of the bulk-phase species (e.g., bulk carbon atoms). Marschall and MacLean developed a general formulation in which multiple phases and surface sites are used and we adopt a similar convention in the current work. Microscopic parameters of reaction probabilities (for gas-surface reactions) and frequencies (for pure-surface reactions) that are require for DSMC are computed from the surface properties and macroscopic parameters such as rate constants, sticking coefficients, etc. The energy and angular distributions of the products are decided based on the reaction type and input parameters. Thus, the user has the capability to model various surface reactions via user-specified reaction rate constants, surface properties and parameters.

Kinetic Parameters for the Noncatalyzed and Enzyme-Catalyzed Mutarotation of Glucose Using a Blood Glucometer

ERIC Educational Resources Information Center

Hardee, John R.; Delgado, Bryan; Jones, Wray

2011-01-01

The kinetic parameters for the conversion of alpha-D-glucose to beta-D-glucose were measured using a blood glucometer. The reaction order, rate constant, and Arrhenius activation energy are reported for the noncatalyzed reaction and turnover number and Michaelis constant are reported for the reaction catalyzed by porcine kidney mutarotase. The…

Kinetics of heavy metal adsorption and desorption in soil: Developing a unified model based on chemical speciation

NASA Astrophysics Data System (ADS)

Peng, Lanfang; Liu, Paiyu; Feng, Xionghan; Wang, Zimeng; Cheng, Tao; Liang, Yuzhen; Lin, Zhang; Shi, Zhenqing

2018-03-01

Predicting the kinetics of heavy metal adsorption and desorption in soil requires consideration of multiple heterogeneous soil binding sites and variations of reaction chemistry conditions. Although chemical speciation models have been developed for predicting the equilibrium of metal adsorption on soil organic matter (SOM) and important mineral phases (e.g. Fe and Al (hydr)oxides), there is still a lack of modeling tools for predicting the kinetics of metal adsorption and desorption reactions in soil. In this study, we developed a unified model for the kinetics of heavy metal adsorption and desorption in soil based on the equilibrium models WHAM 7 and CD-MUSIC, which specifically consider metal kinetic reactions with multiple binding sites of SOM and soil minerals simultaneously. For each specific binding site, metal adsorption and desorption rate coefficients were constrained by the local equilibrium partition coefficients predicted by WHAM 7 or CD-MUSIC, and, for each metal, the desorption rate coefficients of various binding sites were constrained by their metal binding constants with those sites. The model had only one fitting parameter for each soil binding phase, and all other parameters were derived from WHAM 7 and CD-MUSIC. A stirred-flow method was used to study the kinetics of Cd, Cu, Ni, Pb, and Zn adsorption and desorption in multiple soils under various pH and metal concentrations, and the model successfully reproduced most of the kinetic data. We quantitatively elucidated the significance of different soil components and important soil binding sites during the adsorption and desorption kinetic processes. Our model has provided a theoretical framework to predict metal adsorption and desorption kinetics, which can be further used to predict the dynamic behavior of heavy metals in soil under various natural conditions by coupling other important soil processes.

Accurate prediction of severe allergic reactions by a small set of environmental parameters (NDVI, temperature).

PubMed

Notas, George; Bariotakis, Michail; Kalogrias, Vaios; Andrianaki, Maria; Azariadis, Kalliopi; Kampouri, Errika; Theodoropoulou, Katerina; Lavrentaki, Katerina; Kastrinakis, Stelios; Kampa, Marilena; Agouridakis, Panagiotis; Pirintsos, Stergios; Castanas, Elias

2015-01-01

Severe allergic reactions of unknown etiology,necessitating a hospital visit, have an important impact in the life of affected individuals and impose a major economic burden to societies. The prediction of clinically severe allergic reactions would be of great importance, but current attempts have been limited by the lack of a well-founded applicable methodology and the wide spatiotemporal distribution of allergic reactions. The valid prediction of severe allergies (and especially those needing hospital treatment) in a region, could alert health authorities and implicated individuals to take appropriate preemptive measures. In the present report we have collecterd visits for serious allergic reactions of unknown etiology from two major hospitals in the island of Crete, for two distinct time periods (validation and test sets). We have used the Normalized Difference Vegetation Index (NDVI), a satellite-based, freely available measurement, which is an indicator of live green vegetation at a given geographic area, and a set of meteorological data to develop a model capable of describing and predicting severe allergic reaction frequency. Our analysis has retained NDVI and temperature as accurate identifiers and predictors of increased hospital severe allergic reactions visits. Our approach may contribute towards the development of satellite-based modules, for the prediction of severe allergic reactions in specific, well-defined geographical areas. It could also probably be used for the prediction of other environment related diseases and conditions.

Accurate Prediction of Severe Allergic Reactions by a Small Set of Environmental Parameters (NDVI, Temperature)

PubMed Central

Andrianaki, Maria; Azariadis, Kalliopi; Kampouri, Errika; Theodoropoulou, Katerina; Lavrentaki, Katerina; Kastrinakis, Stelios; Kampa, Marilena; Agouridakis, Panagiotis; Pirintsos, Stergios; Castanas, Elias

2015-01-01

Severe allergic reactions of unknown etiology,necessitating a hospital visit, have an important impact in the life of affected individuals and impose a major economic burden to societies. The prediction of clinically severe allergic reactions would be of great importance, but current attempts have been limited by the lack of a well-founded applicable methodology and the wide spatiotemporal distribution of allergic reactions. The valid prediction of severe allergies (and especially those needing hospital treatment) in a region, could alert health authorities and implicated individuals to take appropriate preemptive measures. In the present report we have collecterd visits for serious allergic reactions of unknown etiology from two major hospitals in the island of Crete, for two distinct time periods (validation and test sets). We have used the Normalized Difference Vegetation Index (NDVI), a satellite-based, freely available measurement, which is an indicator of live green vegetation at a given geographic area, and a set of meteorological data to develop a model capable of describing and predicting severe allergic reaction frequency. Our analysis has retained NDVI and temperature as accurate identifiers and predictors of increased hospital severe allergic reactions visits. Our approach may contribute towards the development of satellite-based modules, for the prediction of severe allergic reactions in specific, well-defined geographical areas. It could also probably be used for the prediction of other environment related diseases and conditions. PMID:25794106

The role of mechanical properties in cavitation erosion resistance. [parameters affecting metal fatigue under cavitation flow conditions

NASA Technical Reports Server (NTRS)

Gould, G. C.

1974-01-01

Methods for determining the correlations of erosion resistance and mechanical properties of materials are discussed. The most common method of testing cavitation erosion resistance of materials is the vibratory cavitation probe. The instrument and its operation are described. The use of the whirling arm device is considered as a second method. Metallographic investigations of the earliest stages of cavitation erosion damage of metallic materials was conducted. The materials show plastic deformation occurring during the incubation period and increasing until cracks form and metal fragments are lost. The parameters of the work done to cause material fractures are identified. The reactions obtained with specific materials are reported.

Upflow fixed bed bioelectrochemical reactor for wastewater treatment applications.

PubMed

González-Gutiérrez, Linda; Frontana, Carlos; Martínez, Eduardo

2015-01-01

A cylindrical Upflow Fixed Bed Reactor (UFB-BER) with granular activated carbon, steel mesh electrodes and anaerobic microorganisms, was constructed for analyzing how hydrodynamic parameters affect the reactions involved during wastewater treatment processes for azo dye degradation. Dye removal percentage was not compromised by decreasing HRTm (99-90% upon changing HRTm from 4 to 1h in single pass mode). Using the residence time distribution method for hydrodynamic characterization, it was found that a higher dispersion in the reactor occurs for HRTm=1h, than for HRTm=4h. A kinetic analysis suggests that this dispersion effect could be associated to a higher specific reaction rate dependent on the azo dye concentration. Copyright © 2014 Elsevier Ltd. All rights reserved.

Beyond Vmax and Km: How details of enzyme function influence geochemical cycles

NASA Astrophysics Data System (ADS)

Steen, A. D.

2015-12-01

Enzymes catalyze the vast majority of chemical reactions relevant to geomicrobiology. Studies of the activities of enzymes in environmental systems often report Vmax (the maximum possible rate of reaction; often proportional to the concentration of enzymes in the system) and sometimes Km (a measure of the affinity between enzymes and their substrates). However, enzyme studies - particularly those related to enzymes involved in organic carbon oxidation - are often limited to only those parameters, and a relatively limited and mixed set of enzymes. Here I will discuss some novel methods to assay and characterize the specific sets of enzymes that may be important to the carbon cycle in aquatic environments. First, kinetic experiments revealed the collective properties of the complex mixtures of extracellular peptidases that occur where microbial communities are diverse. Crystal structures combined with biochemical characterization of specific enzymes can yield more detailed information about key steps in organic carbon transformations. These new techniques have the potential to provide mechanistic grounding to geomicrobiological models.

Bimanual cross-talk during reaching movements is primarily related to response selection, not the specification of motor parameters

NASA Technical Reports Server (NTRS)

Hazeltine, Eliot; Diedrichsen, Joern; Kennerley, Steven W.; Ivry, Richard B.

2003-01-01

Simultaneous reaching movements made with the two hands can show a considerable increase in reaction time (RT) when they differ in terms of direction or extent, compared to when the movements involve the same direction and extent. This cost has been attributed to cross-talk in the specification of the motor parameters for the two hands. However, a recent study [Diedrichsen, Hazeltine, Kennerley, & Ivry, (2001). Psychological Science, 12, 493-498] indicates that when reaching movements are cued by the onset of the target endpoint, no compatibility effects are observed. To determine why directly cued movements are immune from interference, we varied the stimulus onset asynchrony for the two movements and used different combinations of directly cued and symbolically cued movements. In two experiments, compatibility effects were only observed when both movements were symbolically cued. No difference was found between compatible and incompatible movements when both movements were directly cued or when one was directly cued and the other was symbolically cued. These results indicate that interference is not related to the specification of movement parameters but instead emerges from processes associated with response selection. Moreover, the data suggest that cross-talk, when present, primarily shortens the RT of the second movement on compatible trials rather than lengthening this RT on incompatible trials.

Coupled enzyme reactions performed in heterogeneous reaction media: experiments and modeling for glucose oxidase and horseradish peroxidase in a PEG/citrate aqueous two-phase system.

PubMed

Aumiller, William M; Davis, Bradley W; Hashemian, Negar; Maranas, Costas; Armaou, Antonios; Keating, Christine D

2014-03-06

The intracellular environment in which biological reactions occur is crowded with macromolecules and subdivided into microenvironments that differ in both physical properties and chemical composition. The work described here combines experimental and computational model systems to help understand the consequences of this heterogeneous reaction media on the outcome of coupled enzyme reactions. Our experimental model system for solution heterogeneity is a biphasic polyethylene glycol (PEG)/sodium citrate aqueous mixture that provides coexisting PEG-rich and citrate-rich phases. Reaction kinetics for the coupled enzyme reaction between glucose oxidase (GOX) and horseradish peroxidase (HRP) were measured in the PEG/citrate aqueous two-phase system (ATPS). Enzyme kinetics differed between the two phases, particularly for the HRP. Both enzymes, as well as the substrates glucose and H2O2, partitioned to the citrate-rich phase; however, the Amplex Red substrate necessary to complete the sequential reaction partitioned strongly to the PEG-rich phase. Reactions in ATPS were quantitatively described by a mathematical model that incorporated measured partitioning and kinetic parameters. The model was then extended to new reaction conditions, i.e., higher enzyme concentration. Both experimental and computational results suggest mass transfer across the interface is vital to maintain the observed rate of product formation, which may be a means of metabolic regulation in vivo. Although outcomes for a specific system will depend on the particulars of the enzyme reactions and the microenvironments, this work demonstrates how coupled enzymatic reactions in complex, heterogeneous media can be understood in terms of a mathematical model.

Collision Dynamics of O(3P) + DMMP Using a Specific Reaction Parameters Potential Form

DTIC Science & Technology

2012-01-27

CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT Same as Report (SAR) 18 . NUMBER OF PAGES 14 19a. NAME OF RESPONSIBLE PERSON a. REPORT unclassified...b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39- 18 Collision Dynamics of O(3P...SRP POTENTIAL Although there have been great strides in developing accurate, multidimensional, global potential energy surfaces, 18 −24 mole- cules with

Extraction of Polarization Parameters in the p¯p → Ω¯Ω Reaction

NASA Astrophysics Data System (ADS)

Perotti, E.

2018-05-01

A method to extract the polarization of Ω hyperons produced via the strong interaction is presented. Assuming they are spin 3/2 particles, the corresponding spin density matrix can be written in terms of seven non-zero polarization parameters, all retrievable from the angular distribution of the decay products. Moreover by considering the full decay chain Ω → ΛK → pπK the magnitude of the asymmetry parameters β Ω and γ Ω can be obtained. This method, applied here to the specific Ω case, can be generalized to any weakly decaying hyperon and is perfectly suited for the PANDA experiment where hyperon-antihyperon pairs will be copiously produced in proton-antiproton collisions. The aim is to take a step forward towards the understanding of the mechanism that reigns strangeness production in these processes.

Reactivity of fluoroalkanes in reactions of coordinated molecular decomposition

NASA Astrophysics Data System (ADS)

Pokidova, T. S.; Denisov, E. T.

2017-08-01

Experimental results on the coordinated molecular decomposition of RF fluoroalkanes to olefin and HF are analyzed using the model of intersecting parabolas (IPM). The kinetic parameters are calculated to allow estimates of the activation energy ( E) and rate constant ( k) of these reactions, based on enthalpy and IPM algorithms. Parameters E and k are found for the first time for eight RF decomposition reactions. The factors that affect activation energy E of RF decomposition (the enthalpy of the reaction, the electronegativity of the atoms of reaction centers, and the dipole-dipole interaction of polar groups) are determined. The values of E and k for reverse reactions of addition are estimated.

EMPIRE: Nuclear Reaction Model Code System for Data Evaluation

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

Herman, M.; Capote, R.; Carlson, B.V.

EMPIRE is a modular system of nuclear reaction codes, comprising various nuclear models, and designed for calculations over a broad range of energies and incident particles. A projectile can be a neutron, proton, any ion (including heavy-ions) or a photon. The energy range extends from the beginning of the unresolved resonance region for neutron-induced reactions ({approx} keV) and goes up to several hundred MeV for heavy-ion induced reactions. The code accounts for the major nuclear reaction mechanisms, including direct, pre-equilibrium and compound nucleus ones. Direct reactions are described by a generalized optical model (ECIS03) or by the simplified coupled-channels approachmore » (CCFUS). The pre-equilibrium mechanism can be treated by a deformation dependent multi-step direct (ORION + TRISTAN) model, by a NVWY multi-step compound one or by either a pre-equilibrium exciton model with cluster emission (PCROSS) or by another with full angular momentum coupling (DEGAS). Finally, the compound nucleus decay is described by the full featured Hauser-Feshbach model with {gamma}-cascade and width-fluctuations. Advanced treatment of the fission channel takes into account transmission through a multiple-humped fission barrier with absorption in the wells. The fission probability is derived in the WKB approximation within the optical model of fission. Several options for nuclear level densities include the EMPIRE-specific approach, which accounts for the effects of the dynamic deformation of a fast rotating nucleus, the classical Gilbert-Cameron approach and pre-calculated tables obtained with a microscopic model based on HFB single-particle level schemes with collective enhancement. A comprehensive library of input parameters covers nuclear masses, optical model parameters, ground state deformations, discrete levels and decay schemes, level densities, fission barriers, moments of inertia and {gamma}-ray strength functions. The results can be converted into ENDF-6 formatted files using the accompanying code EMPEND and completed with neutron resonances extracted from the existing evaluations. The package contains the full EXFOR (CSISRS) library of experimental reaction data that are automatically retrieved during the calculations. Publication quality graphs can be obtained using the powerful and flexible plotting package ZVView. The graphic user interface, written in Tcl/Tk, provides for easy operation of the system. This paper describes the capabilities of the code, outlines physical models and indicates parameter libraries used by EMPIRE to predict reaction cross sections and spectra, mainly for nucleon-induced reactions. Selected applications of EMPIRE are discussed, the most important being an extensive use of the code in evaluations of neutron reactions for the new US library ENDF/B-VII.0. Future extensions of the system are outlined, including neutron resonance module as well as capabilities of generating covariances, using both KALMAN and Monte-Carlo methods, that are still being advanced and refined.« less

Thermodynamically consistent model calibration in chemical kinetics

PubMed Central

2011-01-01

Background The dynamics of biochemical reaction systems are constrained by the fundamental laws of thermodynamics, which impose well-defined relationships among the reaction rate constants characterizing these systems. Constructing biochemical reaction systems from experimental observations often leads to parameter values that do not satisfy the necessary thermodynamic constraints. This can result in models that are not physically realizable and may lead to inaccurate, or even erroneous, descriptions of cellular function. Results We introduce a thermodynamically consistent model calibration (TCMC) method that can be effectively used to provide thermodynamically feasible values for the parameters of an open biochemical reaction system. The proposed method formulates the model calibration problem as a constrained optimization problem that takes thermodynamic constraints (and, if desired, additional non-thermodynamic constraints) into account. By calculating thermodynamically feasible values for the kinetic parameters of a well-known model of the EGF/ERK signaling cascade, we demonstrate the qualitative and quantitative significance of imposing thermodynamic constraints on these parameters and the effectiveness of our method for accomplishing this important task. MATLAB software, using the Systems Biology Toolbox 2.1, can be accessed from http://www.cis.jhu.edu/~goutsias/CSS lab/software.html. An SBML file containing the thermodynamically feasible EGF/ERK signaling cascade model can be found in the BioModels database. Conclusions TCMC is a simple and flexible method for obtaining physically plausible values for the kinetic parameters of open biochemical reaction systems. It can be effectively used to recalculate a thermodynamically consistent set of parameter values for existing thermodynamically infeasible biochemical reaction models of cellular function as well as to estimate thermodynamically feasible values for the parameters of new models. Furthermore, TCMC can provide dimensionality reduction, better estimation performance, and lower computational complexity, and can help to alleviate the problem of data overfitting. PMID:21548948

Estimating parameters from rotating ring disc electrode measurements

DOE PAGES

Santhanagopalan, Shriram; White, Ralph E.

2017-10-21

Rotating ring disc electrode (RRDE) experiments are a classic tool for investigating kinetics of electrochemical reactions. Several standardized methods exist for extracting transport parameters and reaction rate constants using RRDE measurements. Here in this work, we compare some approximate solutions to the convective diffusion used popularly in the literature to a rigorous numerical solution of the Nernst-Planck equations coupled to the three dimensional flow problem. In light of these computational advancements, we explore design aspects of the RRDE that will help improve sensitivity of our parameter estimation procedure to experimental data. We use the oxygen reduction in acidic media involvingmore » three charge transfer reactions and a chemical reaction as an example, and identify ways to isolate reaction currents for the individual processes in order to accurately estimate the exchange current densities.« less

The HNC/HCN ratio in star-forming regions

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

Graninger, Dawn M.; Öberg, Karin I.; Herbst, Eric

2014-05-20

HNC and HCN, typically used as dense gas tracers in molecular clouds, are a pair of isomers that have great potential as a temperature probe because of temperature dependent, isomer-specific formation and destruction pathways. Previous observations of the HNC/HCN abundance ratio show that the ratio decreases with increasing temperature, something that standard astrochemical models cannot reproduce. We have undertaken a detailed parameter study on which environmental characteristics and chemical reactions affect the HNC/HCN ratio and can thus contribute to the observed dependence. Using existing gas and gas-grain models updated with new reactions and reaction barriers, we find that in staticmore » models the H + HNC gas-phase reaction regulates the HNC/HCN ratio under all conditions, except for very early times. We quantitatively constrain the combinations of H abundance and H + HNC reaction barrier that can explain the observed HNC/HCN temperature dependence and discuss the implications in light of new quantum chemical calculations. In warm-up models, gas-grain chemistry contributes significantly to the predicted HNC/HCN ratio and understanding the dynamics of star formation is therefore key to model the HNC/HCN system.« less

Model-based analysis of coupled equilibrium-kinetic processes: indirect kinetic studies of thermodynamic parameters using the dynamic data.

PubMed

Emami, Fereshteh; Maeder, Marcel; Abdollahi, Hamid

2015-05-07

Thermodynamic studies of equilibrium chemical reactions linked with kinetic procedures are mostly impossible by traditional approaches. In this work, the new concept of generalized kinetic study of thermodynamic parameters is introduced for dynamic data. The examples of equilibria intertwined with kinetic chemical mechanisms include molecular charge transfer complex formation reactions, pH-dependent degradation of chemical compounds and tautomerization kinetics in micellar solutions. Model-based global analysis with the possibility of calculating and embedding the equilibrium and kinetic parameters into the fitting algorithm has allowed the complete analysis of the complex reaction mechanisms. After the fitting process, the optimal equilibrium and kinetic parameters together with an estimate of their standard deviations have been obtained. This work opens up a promising new avenue for obtaining equilibrium constants through the kinetic data analysis for the kinetic reactions that involve equilibrium processes.

A qualitative quantum rate model for hydrogen transfer in soybean lipoxygenase

NASA Astrophysics Data System (ADS)

Jevtic, S.; Anders, J.

2017-09-01

The hydrogen transfer reaction catalysed by soybean lipoxygenase (SLO) has been the focus of intense study following observations of a high kinetic isotope effect (KIE). Today high KIEs are generally thought to indicate departure from classical rate theory and are seen as a strong signature of tunnelling of the transferring particle, hydrogen or one of its isotopes, through the reaction energy barrier. In this paper, we build a qualitative quantum rate model with few free parameters that describes the dynamics of the transferring particle when it is exposed to energetic potentials exerted by the donor and the acceptor. The enzyme's impact on the dynamics is modelled by an additional energetic term, an oscillatory contribution known as "gating." By varying two key parameters, the gating frequency and the mean donor-acceptor separation, the model is able to reproduce well the KIE data for SLO wild-type and a variety of SLO mutants over the experimentally accessible temperature range. While SLO-specific constants have been considered here, it is possible to adapt these for other enzymes.

In situ precipitation of nano-hydroxyapatite in gelatin polymatrix towards specific fluoride sorption.

PubMed

Pandi, Kalimuthu; Viswanathan, Natrayasamy

2015-03-01

This study investigates the synthesis of nano-hydroxyapatite (n-HAp) incorporated gelatin (Gel) biocomposite namely n-HAp@Gel composite for efficient removal of fluoride from aqueous solution. The results demonstrated that, the developed n-HAp@Gel biocomposite possess an enhanced defluoridation capacity (DC) of 4157 mgF-/kg. The batch experiments were optimized as a function of various influencing parameters like contact time, pH, co-ions, temperature and initial fluoride concentration. The physicochemical characteristics of n-HAp@Gel composite was examined by using different instrumental techniques like FTIR, XRD, TGA-DSC and SEM with EDAX analysis. The sorption data were fitted with various isotherm models. The acquired thermodynamic parameters showed that the sorption of fluoride onto the sorbent was endothermic and spontaneous in nature. The reaction-based and diffusion-based models were used to identify the kinetics of the reaction. At field conditions, n-HAp@Gel composite reduce the fluoride concentration below the tolerance limit. A regeneration technique was proposed in order to reuse the sorbent. Copyright © 2014 Elsevier B.V. All rights reserved.

Kinetic study of an enzymic cycling system coupled to an enzymic step: determination of alkaline phosphatase activity.

PubMed Central

Valero, E; Varón, R; García-Carmona, F

1995-01-01

A kinetic study is made of a system consisting of a specific enzymic cycling assay coupled to an enzymic reaction. A kinetic analysis of this system is presented, and the accumulation of chromophore involved in the cycle is seen to be parabolic, i.e. the rate of the reaction increases continuously with constant acceleration. The system is illustrated by the measurement of alkaline phosphatase activity using beta-NADP+ as substrate. The enzymes alcohol dehydrogenase and diaphorase are used to cycle beta-NAD+ in the presence of ethanol and p-Iodonitrotetrazolium Violet. During each turn of the cycle, one molecule of the tetrazolium salt is reduced to an intensely coloured formazan. A simple procedure for evaluating the kinetic parameters involved in the system and for optimizing this cycling assay is described. The method is applicable to the measurement of any enzyme, and its amplification capacity as well as the simplicity of determining kinetic parameters enable it to be employed in enzyme immunoassays to increase the magnitude of the measured response. PMID:7619054

Consistent Estimation of Gibbs Energy Using Component Contributions

PubMed Central

Milo, Ron; Fleming, Ronan M. T.

2013-01-01

Standard Gibbs energies of reactions are increasingly being used in metabolic modeling for applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic parameters. The increasing scope and diversity of metabolic models has led scientists to look for genome-scale solutions that can estimate the standard Gibbs energy of all the reactions in metabolism. Group contribution methods greatly increase coverage, albeit at the price of decreased precision. We present here a way to combine the estimations of group contribution with the more accurate reactant contributions by decomposing each reaction into two parts and applying one of the methods on each of them. This method gives priority to the reactant contributions over group contributions while guaranteeing that all estimations will be consistent, i.e. will not violate the first law of thermodynamics. We show that there is a significant increase in the accuracy of our estimations compared to standard group contribution. Specifically, our cross-validation results show an 80% reduction in the median absolute residual for reactions that can be derived by reactant contributions only. We provide the full framework and source code for deriving estimates of standard reaction Gibbs energy, as well as confidence intervals, and believe this will facilitate the wide use of thermodynamic data for a better understanding of metabolism. PMID:23874165

Moderate anxiety modifies the electromyographic activity of a forearm muscle during a time-reaction task in women.

PubMed

Langlet, C; Hainaut, J P; Bolmont, B

2017-03-16

Arousal anxiety has a great impact on reaction time, physiological parameters and motor performance. Numerous studies have focused on the influence of anxiety on muscular activity during simple non ecologic task. We investigate the impact of a moderate state-anxiety (arousal stressor) on the specific component of a complex multi-joint ecologic movement during a reaction time task of auditory stimulus-response. Our objective is to know if central and peripheral voluntary motor processes were modulated in the same way by an arousal stressor. Eighteen women volunteers performed simple reaction time tasks of auditory stimulus-response. Video-recorded Stroop test with interferences was used to induced moderate state-anxiety. Electromyographic activity of the wrist extensor was recorded in order to analyse the two components of the reaction time: the premotor and motor time. In anxiogenic condition, an acceleration and an increase of muscular activity of the reaction time was obtained. This increase was due to a stronger muscle activity during the premotor time in the anxiogenic condition. Arousal anxiety has a different impact on central and peripheral voluntary motor processes. The modifications observed could be related to an increase in arousal related to a higher anxiety in order to prepare the body to act. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of D-allose sensor on the basis of three strategic enzyme reactions.

PubMed

Miyanishi, Nobumitsu; Nakakita, Shin-Ichi; Sumiyoshi, Wataru; Okuma, Hirokazu; Izumori, Ken; Hirabayashi, Jun

2010-09-15

Rare sugars are defined as monosaccharides and their derivatives that rarely exist in nature, according to the International Society of Rare Sugars. D-Allose (3-epi d-glucose) is one of the rare sugars, for which various physiological activities have recently been found, with increasing attention to its applications to bio-industry. Until now, however, there is no convenient method of measuring these sugars in a specific manner. For detecting D-allose, three consecutive enzyme reactions were devised by fabricating of a reaction batch chamber packed with L-rhamnose isomerase (LRI), D-tagatose 3-epimerase (DTE) and a screen-printed electrode, on which D-fructose dehydrogenase (DFDH) was immobilized. To obtain a substantial sensing system, extensive experimental parameters were optimized. These included the concentration of photo-crosslinkable poly (vinyl alcohol) bearing stilbazolium groups (PVA-SbQ), reaction ratios, and temperature of the batch chamber. By adopting the three consecutive enzyme reactions, an undesirable reverse reaction was minimized. As a result, the developed sensor system exhibited a good linear response on D-allose in the range from 0.1 to 50 mM (r(2)=0.998). The system has an apparent advantage over the previous chromatography approach in terms of simplicity and inexpensiveness. Copyright 2010 Elsevier B.V. All rights reserved.

Nonequilibrium Self-Assembly of π-Conjugated Oligopeptides in Solution.

PubMed

Li, Bo; Li, Songsong; Zhou, Yuecheng; Ardoña, Herdeline Ann M; Valverde, Lawrence R; Wilson, William L; Tovar, John D; Schroeder, Charles M

2017-02-01

Supramolecular assembly is a powerful method that can be used to generate materials with well-defined structures across multiple length scales. Supramolecular assemblies consisting of biopolymer-synthetic polymer subunits are specifically known to exhibit exceptional structural and functional diversity as well as programmable control of noncovalent interactions through hydrogen bonding in biopolymer subunits. Despite recent progress, there is a need to control and quantitatively understand assembly under nonequilibrium conditions. In this work, we study the nonequilibrium self-assembly of π-conjugated synthetic oligopeptides using a combination of experiments and analytical modeling. By isolating an aqueous peptide solution droplet within an immiscible organic layer, the rate of peptide assembly in the aqueous solution can be controlled by tuning the transport rate of acid that is used to trigger assembly. Using this approach, peptides are guided to assemble under reaction-dominated and diffusion-dominated conditions, with results showing a transition from a diffusion-limited reaction front to spatially homogeneous assembly as the transport rate of acid decreases. Interestingly, our results show that the morphology of self-assembled peptide fibers is controlled by the assembly kinetics such that increasingly homogeneous structures of self-assembled synthetic oligopeptides were generally obtained using slower rates of assembly. We further developed an analytical reaction-diffusion model to describe oligopeptide assembly, and experimental results are compared to the reaction-diffusion model across a range of parameters. Overall, this work highlights the importance of molecular self-assembly under nonequilibrium conditions, specifically showing that oligopeptide assembly is governed by a delicate balance between reaction kinetics and transport processes.

A COMPUTATIONAL ANALYSIS OF BONE FORMATION IN THE CRANIAL VAULT USING A COUPLED REACTION-DIFFUSION-STRAIN MODEL

PubMed Central

LEE, CHANYOUNG; RICHTSMEIER, JOAN T.; KRAFT, REUBEN H.

2017-01-01

Bones of the murine cranial vault are formed by differentiation of mesenchymal cells into osteoblasts, a process that is primarily understood to be controlled by a cascade of reactions between extracellular molecules and cells. We assume that the process can be modeled using Turing’s reaction-diffusion equations, a mathematical model describing the pattern formation controlled by two interacting molecules (activator and inhibitor). In addition to the processes modeled by reaction-diffusion equations, we hypothesize that mechanical stimuli of the cells due to growth of the underlying brain contribute significantly to the process of cell differentiation in cranial vault development. Structural analysis of the surface of the brain was conducted to explore the effects of the mechanical strain on bone formation. We propose a mechanobiological model for the formation of cranial vault bones by coupling the reaction-diffusion model with structural mechanics. The mathematical formulation was solved using the finite volume method. The computational domain and model parameters are determined using a large collection of experimental data that provide precise three dimensional (3D) measures of murine cranial geometry and cranial vault bone formation for specific embryonic time points. The results of this study suggest that mechanical strain contributes information to specific aspects of bone formation. Our mechanobiological model predicts some key features of cranial vault bone formation that were verified by experimental observations including the relative location of ossification centers of individual vault bones, the pattern of cranial vault bone growth over time, and the position of cranial vault sutures. PMID:29225392

Improvements in Obstacle Clearance Parameters and Reaction Time Over a Series of Obstacles Revealed After Five Repeated Testing Sessions in Older Adults.

PubMed

Jehu, Deborah A; Lajoie, Yves; Paquet, Nicole

2017-12-21

The purpose of this study was to investigate obstacle clearance and reaction time parameters when crossing a series of six obstacles in older adults. A second aim was to examine the repeated exposure of this testing protocol once per week for 5 weeks. In total, 10 older adults (five females; age: 67.0 ± 6.9 years) walked onto and over six obstacles of varying heights (range: 100-200 mm) while completing no reaction time, simple reaction time, and choice reaction time tasks once per week for 5 weeks. The highest obstacles elicited the lowest toe clearance, and the first three obstacles revealed smaller heel clearance compared with the last three obstacles. Dual tasking negatively impacted obstacle clearance parameters when information processing demands were high. Longer and less consistent time to completion was observed in Session 1 compared with Sessions 2-5. Finally, improvements in simple reaction time were displayed after Session 2, but choice reaction time gradually improved and did not reach a plateau after repeated testing.

Dynamic Parameters Variability: Time Interval Interference on Ground Reaction Force During Running.

PubMed

Pennone, Juliana; Mezêncio, Bruno; Amadio, Alberto C; Serrão, Júlio C

2016-04-01

The aim of this study was to determine the effect of the time between measures on ground reaction force running variability; 15 healthy men (age = 23.8 ± 3.7 years; weight = 72.8 ± 7.7 kg; height 174.3 ± 8.4 cm) performed two trials of running 45 minutes at 9 km/hr at intervals of seven days. The ground reaction forces were recorded every 5 minutes. The coefficients of variation of indicative parameters of the ground reaction forces for each condition were compared. The coefficients of variations of the ground reaction forces curve analyzed between intervals and sessions were 21.9% and 21.48%, respectively. There was no significant difference for the ground reaction forces parameters Fy1, tFy1, TC1, Imp50, Fy2, and tFy2 between intervals and sessions. Although the ground reaction forces variables present a natural variability, this variability in intervals and in sessions remained consistent, ensuring a high reliability in repeated measures designs. © The Author(s) 2016.

Time-ordered product expansions for computational stochastic system biology.

PubMed

Mjolsness, Eric

2013-06-01

The time-ordered product framework of quantum field theory can also be used to understand salient phenomena in stochastic biochemical networks. It is used here to derive Gillespie's stochastic simulation algorithm (SSA) for chemical reaction networks; consequently, the SSA can be interpreted in terms of Feynman diagrams. It is also used here to derive other, more general simulation and parameter-learning algorithms including simulation algorithms for networks of stochastic reaction-like processes operating on parameterized objects, and also hybrid stochastic reaction/differential equation models in which systems of ordinary differential equations evolve the parameters of objects that can also undergo stochastic reactions. Thus, the time-ordered product expansion can be used systematically to derive simulation and parameter-fitting algorithms for stochastic systems.

Uncertainty evaluation of nuclear reaction model parameters using integral and microscopic measurements. Covariances evaluation with CONRAD code

NASA Astrophysics Data System (ADS)

de Saint Jean, C.; Habert, B.; Archier, P.; Noguere, G.; Bernard, D.; Tommasi, J.; Blaise, P.

2010-10-01

In the [eV;MeV] energy range, modelling of the neutron induced reactions are based on nuclear reaction models having parameters. Estimation of co-variances on cross sections or on nuclear reaction model parameters is a recurrent puzzle in nuclear data evaluation. Major breakthroughs were asked by nuclear reactor physicists to assess proper uncertainties to be used in applications. In this paper, mathematical methods developped in the CONRAD code[2] will be presented to explain the treatment of all type of uncertainties, including experimental ones (statistical and systematic) and propagate them to nuclear reaction model parameters or cross sections. Marginalization procedure will thus be exposed using analytical or Monte-Carlo solutions. Furthermore, one major drawback found by reactor physicist is the fact that integral or analytical experiments (reactor mock-up or simple integral experiment, e.g. ICSBEP, …) were not taken into account sufficiently soon in the evaluation process to remove discrepancies. In this paper, we will describe a mathematical framework to take into account properly this kind of information.

Theoretical and experimental study on the effects of particle size and temperature on the reaction kinetics of cubic nano-Cu2O

NASA Astrophysics Data System (ADS)

Tang, Huanfeng; Huang, Zaiyin; Xiao, Ming; Liang, Min; Chen, Liying; Tan, XueCai

2017-09-01

The activities, selectivities, and stabilities of nanoparticles in heterogeneous reactions are size-dependent. In order to investigate the influencing laws of particle size and temperature on kinetic parameters in heterogeneous reactions, cubic nano-Cu2O particles of four different sizes in the range of 40-120 nm have been controllably synthesized. In situ microcalorimetry has been used to attain thermodynamic data on the reaction of Cu2O with aqueous HNO3 and, combined with thermodynamic principles and kinetic transition-state theory, the relevant reaction kinetic parameters have been evaluated. The size dependences of the kinetic parameters are discussed in terms of the established kinetic model and the experimental results. It was found that the reaction rate constants increased with decreasing particle size. Accordingly, the apparent activation energy, pre-exponential factor, activation enthalpy, activation entropy, and activation Gibbs energy decreased with decreasing particle size. The reaction rate constants and activation Gibbs energies increased with increasing temperature. Moreover, the logarithms of the apparent activation energies, pre-exponential factors, and rate constants were found to be linearly related to the reciprocal of particle size, consistent with the kinetic models. The influence of particle size on these reaction kinetic parameters may be explained as follows: the apparent activation energy is affected by the partial molar enthalpy, the pre-exponential factor is affected by the partial molar entropy, and the reaction rate constant is affected by the partial molar Gibbs energy. [Figure not available: see fulltext.

Intrinsic Thermodynamics and Structure Correlation of Benzenesulfonamides with a Pyrimidine Moiety Binding to Carbonic Anhydrases I, II, VII, XII, and XIII

PubMed Central

Kišonaitė, Miglė; Zubrienė, Asta; Čapkauskaitė, Edita; Smirnov, Alexey; Smirnovienė, Joana; Kairys, Visvaldas; Michailovienė, Vilma; Manakova, Elena; Gražulis, Saulius; Matulis, Daumantas

2014-01-01

The early stage of drug discovery is often based on selecting the highest affinity lead compound. To this end the structural and energetic characterization of the binding reaction is important. The binding energetics can be resolved into enthalpic and entropic contributions to the binding Gibbs free energy. Most compound binding reactions are coupled to the absorption or release of protons by the protein or the compound. A distinction between the observed and intrinsic parameters of the binding energetics requires the dissection of the protonation/deprotonation processes. Since only the intrinsic parameters can be correlated with molecular structural perturbations associated with complex formation, it is these parameters that are required for rational drug design. Carbonic anhydrase (CA) isoforms are important therapeutic targets to treat a range of disorders including glaucoma, obesity, epilepsy, and cancer. For effective treatment isoform-specific inhibitors are needed. In this work we investigated the binding and protonation energetics of sixteen [(2-pyrimidinylthio)acetyl]benzenesulfonamide CA inhibitors using isothermal titration calorimetry and fluorescent thermal shift assay. The compounds were built by combining four sulfonamide headgroups with four tailgroups yielding 16 compounds. Their intrinsic binding thermodynamics showed the limitations of the functional group energetic additivity approach used in fragment-based drug design, especially at the level of enthalpies and entropies of binding. Combined with high resolution crystal structural data correlations were drawn between the chemical functional groups on selected inhibitors and intrinsic thermodynamic parameters of CA-inhibitor complex formation. PMID:25493428

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Acute Normal Tissue Reactions in Head-and-Neck Cancer Patients Treated With IMRT: Influence of Dose and Association With Genetic Polymorphisms in DNA DSB Repair Genes

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

Werbrouck, Joke; Ruyck, Kim de; Duprez, Frederic

2009-03-15

Purpose: To investigate the association between dose-related parameters and polymorphisms in DNA DSB repair genes XRCC3 (c.-1843A>G, c.562-14A>G, c.722C>T), Rad51 (c.-3429G>C, c.-3392G>T), Lig4 (c.26C>T, c.1704T>C), Ku70 (c.-1310C>G), and Ku80 (c.2110-2408G>A) and the occurrence of acute reactions after radiotherapy. Materials and Methods: The study population consisted of 88 intensity-modulated radiation therapy (IMRT)-treated head-and-neck cancer patients. Mucositis, dermatitis, and dysphagia were scored using the Common Terminology Criteria (CTC) for Adverse Events v.3.0 scale. The population was divided into a CTC0-2 and CTC3+ group for the analysis of each acute effect. The influence of the dose on critical structures was analyzed using dose-volumemore » histograms. Genotypes were determined by polymerase chain reaction (PCR) combined with restriction fragment length polymorphism or PCR-single base extension assays. Results: The mean dose (D{sub mean}) to the oral cavity and constrictor pharyngeus (PC) muscles was significantly associated with the development of mucositis and dysphagia, respectively. These parameters were considered confounding factors in the radiogenomics analyses. The XRCC3c.722CT/TT and Ku70c.-1310CG/GG genotypes were significantly associated with the development of severe dysphagia (CTC3+). No association was found between the investigated polymorphisms and the development of mucositis or dermatitis. A risk analysis model for severe dysphagia, which was developed based on the XRCC3c.722CT/TT and Ku70c.-1310CG/GG genotypes and the PC dose, showed a sensitivity of 78.6% and a specificity of 77.6%. Conclusions: The XRCC3c.722C>T and Ku70c.-1310C>G polymorphisms as well as the D{sub mean} to the PC muscles were highly associated with the development of severe dysphagia after IMRT. The prediction model developed using these parameters showed a high sensitivity and specificity.« less

Presenting a new kinetic model for methanol to light olefins reactions over a hierarchical SAPO-34 catalyst using the Langmuir-Hinshelwood-Hougen-Watson mechanism

NASA Astrophysics Data System (ADS)

Javad Azarhoosh, Mohammad; Halladj, Rouein; Askari, Sima

2017-10-01

In this study, a new kinetic model for methanol to light olefins (MTO) reactions over a hierarchical SAPO-34 catalyst using the Langmuir-Hinshelwood-Hougen-Watson (LHHW) mechanism was presented and the kinetic parameters was obtained using a genetic algorithm (GA) and genetic programming (GP). Several kinetic models for the MTO reactions have been presented. However, due to the complexity of the reactions, most reactions are considered lumped and elementary, which cannot be deemed a completely accurate kinetic model of the process. Therefore, in this study, the LHHW mechanism is presented as kinetic models of MTO reactions. Because of the non-linearity of the kinetic models and existence of many local optimal points, evolutionary algorithms (GA and GP) are used in this study to estimate the kinetic parameters in the rate equations. Via the simultaneous connection of the code related to modelling the reactor and the GA and GP codes in the MATLAB R2013a software, optimization of the kinetic models parameters was performed such that the least difference between the results from the kinetic models and experiential results was obtained and the best kinetic parameters of MTO process reactions were achieved. A comparison of the results from the model with experiential results showed that the present model possesses good accuracy.

Modeling the formation of N-nitrosodimethylamine (NDMA) from the reaction of natural organic matter (NOM) with monochloramine.

PubMed

Chen, Zhuo; Valentine, Richard L

2006-12-01

This paper presents mechanistic studies on the formation of NDMA, a newly identified chloramination disinfection byproduct, from reactions of monochloramine with natural organic matter. A kinetic model was developed to validate proposed reactions and to predict NDMA formation in chloraminated water during the time frame of 1-5 days. This involved incorporating NDMA formation reactions into an established comprehensive model describing the oxidation of humic-type natural organic matter by monochloramine. A rate-limiting step involving the oxidation of NOM is theorized to control the rate of NDMA formation which is assumed to be proportional to the rate of NOM oxidized by monochloramine. The applicability of the model to describe NDMA formation in the presence of three NOM sources over a wide range in water quality (i.e., pH, DOC, and ammonia concentrations) was evaluated. Results show that with accurate measurement of monochloramine demand for a specific supply, NDMA formation could be modeled over an extended range of experimental conditions by considering a single NOM source-specific value of thetaNDMA, a stoichiometric coefficient relating the amount of NDMA produced to the amount of NOM oxidized, and several kinetic parameters describing NOM oxidation. Furthermore, the oxidation of NOM is the rate-limiting step governing NDMA formation. This suggests that NDMA formation over a 1-5 day time frame may be estimated from information on the chloramine or free chlorine demand of the NOM and the source-specific linear relationship between this demand and NDMA formation. Although the proposed model has not yet been validated for shorter time periods that may better characterize the residence time in some distribution systems, the improved understanding of the important reactions governing NDMA formation and the resulting model should benefit the water treatment industry as a tool in developing strategies that minimize NDMA formation.

Impact of a Pharmacy-Cardiology Collaborative Practice on Dofetilide Safety Monitoring.

PubMed

Quffa, Lieth H; Panna, Mark; Kaufmann, Michael R; McKillop, Matthew; Dietrich, Nicole Maltese; Franck, Andrew J

2017-01-01

Limited studies have been published examining dofetilide's postmarketing use and its recommended monitoring. To evaluate the impact of a collaborative pharmacy-cardiology antiarrhythmic drug (AAD) monitoring program on dofetilide monitoring. This retrospective cohort study was performed to assess if a novel monitoring program improved compliance with dofetilide-specific monitoring parameters based on the Food and Drug Administration's Risk Evaluation and Mitigation Strategy. A total of 30 patients were included in the analysis. The monitoring parameters evaluated included electrocardiogram, serum potassium, serum magnesium, and kidney function. The primary outcome evaluated was the composite of these dofetilide monitoring parameters obtained in each cohort. In the standard cohort, 245 of 352 (69.6%) monitoring parameters were completed versus 134 of 136 (98.5%) in the intervention group ( P < 0.05). A collaborative pharmacy-cardiology AAD monitoring program was associated with a significant improvement in dofetilide monitoring. This improvement could potentially translate into enhanced patient safety outcomes, such as prevention of adverse drug reactions and decreased hospitalizations.

Crystal Growth Simulations To Establish Physically Relevant Kinetic Parameters from the Empirical Kolmogorov-Johnson-Mehl-Avrami Model

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

Dill, Eric D.; Folmer, Jacob C.W.; Martin, James D.

A series of simulations was performed to enable interpretation of the material and physical significance of the parameters defined in the Kolmogorov, Johnson and Mehl, and Avrami (KJMA) rate expression commonly used to describe phase boundary controlled reactions of condensed matter. The parameters k, n, and t 0 are shown to be highly correlated, which if unaccounted for seriously challenge mechanistic interpretation. It is demonstrated that rate measurements exhibit an intrinsic uncertainty without precise knowledge of the location and orientation of nucleation with respect to the free volume into which it grows. More significantly, it is demonstrated that the KJMAmore » rate constant k is highly dependent on sample size. However, under the simulated conditions of slow nucleation relative to crystal growth, sample volume and sample anisotropy correction affords a means to eliminate the experimental condition dependence of the KJMA rate constant, k, producing the material-specific parameter, the velocity of the phase boundary, v pb.« less

A generalized methodology to characterize composite materials for pyrolysis models

NASA Astrophysics Data System (ADS)

McKinnon, Mark B.

The predictive capabilities of computational fire models have improved in recent years such that models have become an integral part of many research efforts. Models improve the understanding of the fire risk of materials and may decrease the number of expensive experiments required to assess the fire hazard of a specific material or designed space. A critical component of a predictive fire model is the pyrolysis sub-model that provides a mathematical representation of the rate of gaseous fuel production from condensed phase fuels given a heat flux incident to the material surface. The modern, comprehensive pyrolysis sub-models that are common today require the definition of many model parameters to accurately represent the physical description of materials that are ubiquitous in the built environment. Coupled with the increase in the number of parameters required to accurately represent the pyrolysis of materials is the increasing prevalence in the built environment of engineered composite materials that have never been measured or modeled. The motivation behind this project is to develop a systematic, generalized methodology to determine the requisite parameters to generate pyrolysis models with predictive capabilities for layered composite materials that are common in industrial and commercial applications. This methodology has been applied to four common composites in this work that exhibit a range of material structures and component materials. The methodology utilizes a multi-scale experimental approach in which each test is designed to isolate and determine a specific subset of the parameters required to define a material in the model. Data collected in simultaneous thermogravimetry and differential scanning calorimetry experiments were analyzed to determine the reaction kinetics, thermodynamic properties, and energetics of decomposition for each component of the composite. Data collected in microscale combustion calorimetry experiments were analyzed to determine the heats of complete combustion of the volatiles produced in each reaction. Inverse analyses were conducted on sample temperature data collected in bench-scale tests to determine the thermal transport parameters of each component through degradation. Simulations of quasi-one-dimensional bench-scale gasification tests generated from the resultant models using the ThermaKin modeling environment were compared to experimental data to independently validate the models.

Inference of reaction rate parameters based on summary statistics from experiments

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

Khalil, Mohammad; Chowdhary, Kamaljit Singh; Safta, Cosmin

Here, we present the results of an application of Bayesian inference and maximum entropy methods for the estimation of the joint probability density for the Arrhenius rate para meters of the rate coefficient of the H 2/O 2-mechanism chain branching reaction H + O 2 → OH + O. Available published data is in the form of summary statistics in terms of nominal values and error bars of the rate coefficient of this reaction at a number of temperature values obtained from shock-tube experiments. Our approach relies on generating data, in this case OH concentration profiles, consistent with the givenmore » summary statistics, using Approximate Bayesian Computation methods and a Markov Chain Monte Carlo procedure. The approach permits the forward propagation of parametric uncertainty through the computational model in a manner that is consistent with the published statistics. A consensus joint posterior on the parameters is obtained by pooling the posterior parameter densities given each consistent data set. To expedite this process, we construct efficient surrogates for the OH concentration using a combination of Pad'e and polynomial approximants. These surrogate models adequately represent forward model observables and their dependence on input parameters and are computationally efficient to allow their use in the Bayesian inference procedure. We also utilize Gauss-Hermite quadrature with Gaussian proposal probability density functions for moment computation resulting in orders of magnitude speedup in data likelihood evaluation. Despite the strong non-linearity in the model, the consistent data sets all res ult in nearly Gaussian conditional parameter probability density functions. The technique also accounts for nuisance parameters in the form of Arrhenius parameters of other rate coefficients with prescribed uncertainty. The resulting pooled parameter probability density function is propagated through stoichiometric hydrogen-air auto-ignition computations to illustrate the need to account for correlation among the Arrhenius rate parameters of one reaction and across rate parameters of different reactions.« less

Inference of reaction rate parameters based on summary statistics from experiments

DOE PAGES

Khalil, Mohammad; Chowdhary, Kamaljit Singh; Safta, Cosmin; ...

2016-10-15

Here, we present the results of an application of Bayesian inference and maximum entropy methods for the estimation of the joint probability density for the Arrhenius rate para meters of the rate coefficient of the H 2/O 2-mechanism chain branching reaction H + O 2 → OH + O. Available published data is in the form of summary statistics in terms of nominal values and error bars of the rate coefficient of this reaction at a number of temperature values obtained from shock-tube experiments. Our approach relies on generating data, in this case OH concentration profiles, consistent with the givenmore » summary statistics, using Approximate Bayesian Computation methods and a Markov Chain Monte Carlo procedure. The approach permits the forward propagation of parametric uncertainty through the computational model in a manner that is consistent with the published statistics. A consensus joint posterior on the parameters is obtained by pooling the posterior parameter densities given each consistent data set. To expedite this process, we construct efficient surrogates for the OH concentration using a combination of Pad'e and polynomial approximants. These surrogate models adequately represent forward model observables and their dependence on input parameters and are computationally efficient to allow their use in the Bayesian inference procedure. We also utilize Gauss-Hermite quadrature with Gaussian proposal probability density functions for moment computation resulting in orders of magnitude speedup in data likelihood evaluation. Despite the strong non-linearity in the model, the consistent data sets all res ult in nearly Gaussian conditional parameter probability density functions. The technique also accounts for nuisance parameters in the form of Arrhenius parameters of other rate coefficients with prescribed uncertainty. The resulting pooled parameter probability density function is propagated through stoichiometric hydrogen-air auto-ignition computations to illustrate the need to account for correlation among the Arrhenius rate parameters of one reaction and across rate parameters of different reactions.« less

[Individual typological peculiarities of system blood flow, physical capacity for work and cardiac activity regulation in patients with different resistance to periodontal diseases].

PubMed

Bragin, A V

2008-01-01

From position of typological variability of physiological individuality concept-functional constitution types - the principle of organism integrity was substantiated for stomatological pathology. There were isolated typical and specific reactions of cardiac-vessel system in patients with different resistance to periodontal diseases. Each functional type - patients with different levels of usual motion activity - had their own physiological peculiarities of parameters of system blood flow, physical capacity for work and cardiac activity regulation, that determined individual typological organism reaction in cases of maxillo-facial system pathology. The received data gives the objective base for physiological approach to single out the extreme variants of norm for forming risk contingent and groups of resistant people to periodontal diseases.

Ab initio state-specific N2 + O dissociation and exchange modeling for molecular simulations

NASA Astrophysics Data System (ADS)

Luo, Han; Kulakhmetov, Marat; Alexeenko, Alina

2017-02-01

Quasi-classical trajectory (QCT) calculations are used in this work to calculate state-specific N2(X1Σ ) +O(3P ) →2 N(4S ) +O(3P ) dissociation and N2(X1Σ ) +O(3P ) →NO(X2Π ) +N(4S ) exchange cross sections and rates based on the 13A″ and 13A' ab initio potential energy surface by Gamallo et al. [J. Chem. Phys. 119, 2545-2556 (2003)]. The calculations consider translational energies up to 23 eV and temperatures between 1000 K and 20 000 K. Vibrational favoring is observed for dissociation reaction at the whole range of collision energies and for exchange reaction around the dissociation limit. For the same collision energy, cross sections for v = 30 are 4 to 6 times larger than those for the ground state. The exchange reaction has an effective activation energy that is dependent on the initial rovibrational level, which is different from dissociation reaction. In addition, the exchange cross sections have a maximum when the total collision energy (TCE) approaches dissociation energy. The calculations are used to generate compact QCT-derived state-specific dissociation (QCT-SSD) and QCT-derived state-specific exchange (QCT-SSE) models, which describe over 1 × 106 cross sections with about 150 model parameters. The models can be used directly within direct simulation Monte Carlo and computational fluid dynamics simulations. Rate constants predicted by the new models are compared to the experimental measurements, direct QCT calculations and predictions by other models that include: TCE model, Bose-Candler QCT-based exchange model, Macheret-Fridman dissociation model, Macheret's exchange model, and Park's two-temperature model. The new models match QCT-calculated and experimental rates within 30% under nonequilibrium conditions while other models under predict by over an order of magnitude under vibrationally-cold conditions.

Global sensitivity analysis of groundwater transport

NASA Astrophysics Data System (ADS)

Cvetkovic, V.; Soltani, S.; Vigouroux, G.

2015-12-01

In this work we address the model and parametric sensitivity of groundwater transport using the Lagrangian-Stochastic Advection-Reaction (LaSAR) methodology. The 'attenuation index' is used as a relevant and convenient measure of the coupled transport mechanisms. The coefficients of variation (CV) for seven uncertain parameters are assumed to be between 0.25 and 3.5, the highest value being for the lower bound of the mass transfer coefficient k0 . In almost all cases, the uncertainties in the macro-dispersion (CV = 0.35) and in the mass transfer rate k0 (CV = 3.5) are most significant. The global sensitivity analysis using Sobol and derivative-based indices yield consistent rankings on the significance of different models and/or parameter ranges. The results presented here are generic however the proposed methodology can be easily adapted to specific conditions where uncertainty ranges in models and/or parameters can be estimated from field and/or laboratory measurements.

Thermodynamic analysis of Bacillus subtilis endospore protonation using isothermal titration calorimetry

NASA Astrophysics Data System (ADS)

Harrold, Zoë R.; Gorman-Lewis, Drew

2013-05-01

Bacterial proton and metal adsorption reactions have the capacity to affect metal speciation and transport in aqueous environments. We coupled potentiometric titration and isothermal titration calorimetry (ITC) analyses to study Bacillus subtilis spore-proton adsorption. We modeled the potentiometric data using a four and five-site non-electrostatic surface complexation model (NE-SCM). Heats of spore surface protonation from coupled ITC analyses were used to determine site specific enthalpies of protonation based on NE-SCMs. The five-site model resulted in a substantially better model fit for the heats of protonation but did not significantly improve the potentiometric titration model fit. The improvement observed in the five-site protonation heat model suggests the presence of a highly exothermic protonation reaction circa pH 7 that cannot be resolved in the less sensitive potentiometric data. From the log Ks and enthalpies we calculated corresponding site specific entropies. Log Ks and site concentrations describing spore surface protonation are statistically equivalent to B. subtilis cell surface protonation constants. Spore surface protonation enthalpies, however, are more exothermic relative to cell based adsorption suggesting a different bonding environment. The thermodynamic parameters defined in this study provide insight on molecular scale spore-surface protonation reactions. Coupled ITC and potentiometric titrations can reveal highly exothermic, and possibly endothermic, adsorption reactions that are overshadowed in potentiometric models alone. Spore-proton adsorption NE-SCMs derived in this study provide a framework for future metal adsorption studies.

Spectrofluorimetric assay method for glutathione and glutathione transferase using monobromobimane.

PubMed

Yakubu, S I; Yakasai, I A; Musa, A

2011-06-01

The primary role of glutathione transferase is to defend an organism from toxicities through catalyzing the reaction of glutathione (GSH) with potentially toxic compounds or metabolites to their chemically and biologically inert conjugates. The objective of the study was to develop a simple and sensitive spectrofluorimetric assay method for glutathione transferase using monobromobimane (MBB), a non fluorescent compound with electrophilic site. MBB slowly reacted with glutathione to form fluorescent glutathione conjugate and that the reaction was catalysed by glutathione transferase. Both non-enzymatic and enzymatic reaction products of MBB, in presence of GSH in phosphate buffer (pH 6.5), were measured by following increase of fluorescence at wavelength of 475nm. For validation of the assay method, the kinetic parameters such as the apparent Michaelis-Mente constants and maximum rates of conjugate formation as well as the specific activity of rat hepatic glutathione transferase were determined. The method was found to be sensitive, thus, applied to measure glutathione contents of crude preparation of rat hepatic cytosol fraction.

Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points

PubMed Central

Barenholz, Uri; Davidi, Dan; Reznik, Ed; Bar-On, Yinon; Antonovsky, Niv; Noor, Elad; Milo, Ron

2017-01-01

A set of chemical reactions that require a metabolite to synthesize more of that metabolite is an autocatalytic cycle. Here, we show that most of the reactions in the core of central carbon metabolism are part of compact autocatalytic cycles. Such metabolic designs must meet specific conditions to support stable fluxes, hence avoiding depletion of intermediate metabolites. As such, they are subjected to constraints that may seem counter-intuitive: the enzymes of branch reactions out of the cycle must be overexpressed and the affinity of these enzymes to their substrates must be relatively weak. We use recent quantitative proteomics and fluxomics measurements to show that the above conditions hold for functioning cycles in central carbon metabolism of E. coli. This work demonstrates that the topology of a metabolic network can shape kinetic parameters of enzymes and lead to seemingly wasteful enzyme usage. DOI: http://dx.doi.org/10.7554/eLife.20667.001 PMID:28169831

Synthesis and evaluation of fluorogenic triglycerides as lipase assay substrates.

PubMed

Andersen, Rokhsana J; Brask, Jesper

2016-06-01

Three racemic fluorogenic triglycerides are synthesized and evaluated as lipase assay substrates. The presented synthesis route goes through a key triglyceride intermediate which can be chemoselectively functionalized with a wide range of different probes. Hence the substrate can be tailor-made for a specific assay, or focus can be on low cost in larger scale for applications in high-throughput screening (HTS) assays. In the specific examples, TG-ED, TG-FD and TG-F2 are assembled with the Edans-Dabcyl or the fluorescein-Dabcyl FRET pair, or relying on fluorescein self-quenching, respectively. Proof-of-concept assays allowed determination of 1st order kinetic parameters (kcat/KM) of 460s(-1)M(-1), 59s(-1)M(-1) and 346s(-1)M(-1), respectively, for the three substrates. Commercially available EnzChek lipase substrate provided 204s(-1)M(-1). Substrate concentration was identified as a critical parameter, with measured reaction rates decreasing at higher concentrations when intermolecular quenching becomes significant. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A systematic investigation of the (α, 2nγ) reaction on medium-heavy nuclei

NASA Astrophysics Data System (ADS)

Fields, C. A.; De Boer, F. W. N.; Ristinen, R. A.; Smith, P. A.; Sugarbaker, E.

1982-03-01

Exclusive neutron spectra and angular distributions have been measured for 28-35 MeV (α, 2nγ) reactions on various nuclei in the 80 ≦ A ≦ 210 region. Pre-equilibrium processes dominate the 35 MeV (α, 2nγ) reaction mechanism in much of this region. Analysis of systematic variation in the neutron spectrum parameters shows that the reaction mechanism is strongly correlated with the target neutron excess parameter ( N- Z/ A. Analysis of the γ-decay of the entry states shows that well-defined incident angular momentum windows exist for the pre-etjuilibrium (α, 2nγ) reaction. These features are discussed in terms of various models for the reaction mechanism.

Impact of texting on young drivers' behavior and safety on urban and rural roads through a simulation experiment.

PubMed

Yannis, George; Laiou, Alexandra; Papantoniou, Panagiotis; Christoforou, Charalambos

2014-06-01

This research aims to investigate the impact of texting on the behavior and safety of young drivers on urban and rural roads. A driving simulator experiment was carried out in which 34 young participants drove in different driving scenarios; specifically, driving in good weather, in raining conditions, in daylight and in night were examined. Lognormal regression methods were used to investigate the influence of texting as well as various other parameters on the mean speed and mean reaction time. Binary logistic methods were used to investigate the influence of texting use as well as various other parameters in the probability of an accident. It appears that texting leads to statistically significant decrease of the mean speed and increase of the mean reaction time in urban and rural road environment. Simultaneously, it leads to an increased accident probability due to driver distraction and delayed reaction at the moment of the incident. It appeared that drivers using mobile phones with a touch screen present different driving behavior with respect to their speed, however, they had an even higher probability of being involved in an accident. The analysis of the distracted driving performance of drivers who are texting while driving may allow for the identification of measures for the improvement of driving performance (e.g., restrictive measures, training and licensing, information campaigns). The identification of some of the parameters that have an impact on the behavior and safety of young drivers concerning texting and the consequent results can be exploited by policy decision makers in future efforts for the improvement of road safety. Copyright © 2014 Elsevier Ltd. All rights reserved.

ENHANCING THE STABILITY OF POROUS CATALYSTS WITH SUPERCRITICAL REACTION MEDIA. (R826034)

EPA Science Inventory

Adsorption/desorption and pore-transport are key parameters influencing the activity and product selectivity in porous catalysts. With conventional reaction media (gas or liquid phase), one of these parameters is generally favorable while the other is not. For instance, while ...

Chemical reaction and radiation effects on MHD flow past an exponentially stretching sheet with heat sink

NASA Astrophysics Data System (ADS)

Nur Wahida Khalili, Noran; Aziz Samson, Abdul; Aziz, Ahmad Sukri Abdul; Ali, Zaileha Md

2017-09-01

In this study, the problem of MHD boundary layer flow past an exponentially stretching sheet with chemical reaction and radiation effects with heat sink is studied. The governing system of PDEs is transformed into a system of ODEs. Then, the system is solved numerically by using Runge-Kutta-Fehlberg fourth fifth order (RKF45) method available in MAPLE 15 software. The numerical results obtained are presented graphically for the velocity, temperature and concentration. The effects of various parameters are studied and analyzed. The numerical values for local Nusselt number, skin friction coefficient and local Sherwood number are tabulated and discussed. The study shows that various parameters give significant effect on the profiles of the fluid flow. It is observed that the reaction rate parameter affected the concentration profiles significantly and the concentration thickness of boundary layer decreases when reaction rate parameter increases. The analysis found is validated by comparing with the results previous work done and it is found to be in good agreement.

Psychological differences between influence of temperament with the hemishere asymmetry of a brain on size of sensorymotor reactions of male and female cosmonauts

NASA Astrophysics Data System (ADS)

Prisniakova, Lyudmila; Prisniakov, Volodymyr; Volkov, D. S.

The purpose of research was definition and comparison of relative parameters of sensorimotor reactions with a choice depending on a level of lateral asymmetry of hemispheres of a brain at representatives of various types of temperament OF male and female cosmonauts . These parameters were by the bases for verification of theoretical dependence for the latent period of reaction in conditions of weightlessness and overloads. The hypothesis about influence of functional asymmetry on parameters of psychomotor in sensory-motor reactions was laid in a basis of experiment. Techniques of definition of individual characters of the sensori-motor asymmetries were used, and G. Ajzenk's questionnaire EPQ adapted by Prisniakova L. Time of sensorimotor reaction has significant distinctions between representatives of different types of temperament with a various level interchemishere asymmetry OF male and female cosmonauts. With increase in expressiveness of the right hemisphere time of reaction tends to reduction at representatives of all types of temperament, the number of erroneous reactions as a whole increases also a level of achievement tends to reduction. Results of time of sensorimotor reaction correspond with parameter L. Prisniakova which characterizes individual - psychological features. .Earlier the received experimental data of constant time of processing of the information in memory at a period of a sensorimotor reactions of the man and new results for women were used for calculation of these time constants for overloads distinct from terrestrial. These data enable to predict dynamics of behavior of cosmonauts with differing sex in conditions of flight in view of their individual characteristics connected with the hemisphere asymmetry of a brain and with by a various degree of lateralization.

Impact of Auditory Context on Executed Motor Actions

PubMed Central

Yoles-Frenkel, Michal; Avron, Maayan; Prut, Yifat

2016-01-01

The auditory and motor systems are strongly coupled, as is evident in the specifically tight motor synchronization that occurs in response to regularly occurring auditory cues compared with cues of other modalities. Timing of rhythmic action is known to rely on multiple neural centers including the cerebellum and the basal-ganglia which have access to both motor cortical and spinal circuitries. To date, however, there is little information on the motor mechanisms that operate during preparation and execution of rhythmic vs. non-rhythmic movements. We measured acceleration profile and muscle activity while subjects performed tapping movements in response to auditory cues. We found that when tapping at random intervals there was a higher variability of both acceleration profile and muscle activity during motor preparation compared to rhythmic tapping. However, the specific rhythmic context (cued, self-paced, or syncopation) did not affect the motor parameters of the executed taps. Finally, during entrainment we found a gradual as opposed to episodic change in low-level motor parameters (i.e., preparatory muscle activity) that was strongly correlated with changes in high-level parameters (i.e., shift in the reaction time to negative asynchrony). These findings suggest that motor entrainment involves not only adjusting the timing of movement but also modifying parameters that are related to its production. These changes in motor output were insensitive to the specifics of the rhythmic cue: although it took subjects different times to become entrained to different types of rhythmic cues, the motor actions produced once entrainment was obtained were indistinguishable. These findings suggest that motor entrainment involves not only adjusting the timing of movement but also modifying parameters related to its production. The reduced variability of muscle activity during the preparatory period could be one mechanism used by the motor system to enhance the accuracy of motor timing. PMID:26834584

Computational manipulation of a radiative MHD flow with Hall current and chemical reaction in the presence of rotating fluid

NASA Astrophysics Data System (ADS)

Alias Suba, Subbu; Muthucumaraswamy, R.

2018-04-01

A numerical analysis of transient radiative MHD(MagnetoHydroDynamic) natural convective flow of a viscous, incompressible, electrically conducting and rotating fluid along a semi-infinite isothermal vertical plate is carried out taking into consideration Hall current, rotation and first order chemical reaction.The coupled non-linear partial differential equations are expressed in difference form using implicit finite difference scheme. The difference equations are then reduced to a system of linear algebraic equations with a tri-diagonal structure which is solved by Thomas Algorithm. The primary and secondary velocity profiles, temperature profile, concentration profile, skin friction, Nusselt number and Sherwood Number are depicted graphically for a range of values of rotation parameter, Hall parameter,magnetic parameter, chemical reaction parameter, radiation parameter, Prandtl number and Schmidt number.It is recognized that rate of heat transfer and rate of mass transfer decrease with increase in time but they increase with increasing values of radiation parameter and Schmidt number respectively.

Novel duplex vapor-electrochemical method for silicon solar cells

NASA Technical Reports Server (NTRS)

Nanis, L.; Sanjurjo, A.; Westphal, S.

1979-01-01

Optimization studies were carried out for the SiF4-Na reaction with solid Na feed. The goals of the study were the consistent production of high purity reaction products and the gathering of relevant information needed to scale-up the reactor. Parameters studied include: (1) effect of surface to volume ratio of Na slices on the extent of reaction; (2) effect of Na surface oxidation on the extent of reaction; (3) effect of external heating on the extent of SiF4-Na reaction; (4) effect of Na slice addition rate on extent of the reaction; and (5) SiF4-Na reaction - high pressure experiments. An investigation was also made of the possible role played by NaF as a fluxing agent during the separation of silicon by melting of the reaction product (Si + NaF) mixture. Since silicon can be produced by the thermite reaction between Na2SiF6 and Na, studies were initiated to gather information on parameters which control the efficiency of the thermite reaction.

Monitoring of performance and training in rowing.

PubMed

Mäestu, Jarek; Jürimäe, Jaak; Jürimäe, Toivo

2005-01-01

Rowing is a strength-endurance type of sport and competition performance depends on factors such as aerobic and anaerobic power, physical power, rowing technique and tactics. Therefore, a rower has to develop several capacities in order to be successful and a valid testing battery of a rower has to include parameters that are highly related to rowing performance. Endurance training is the mainstay in rowing. For the 2000 m race, power training at high velocities should be preferred to resistance training at low velocities in order to train more specifically during the off-season. The specific training of the international rower has to be approximately 70% of the whole training time. Several studies have reported different biochemical parameters for monitoring the training of rowers. There is some evidence that plasma leptin is more sensitive to training volume changes than specific stress hormones (e.g. cortisol, testosterone, growth hormone). In rowing, the stress hormone reactions to training volume and/or intensity changes are controversial. The Recovery-Stress Questionnaire for Athletes measures both stress and recovery, and may therefore be more effective than the previously used Borg ratio scale or the Profile of Mood States, which both focus mainly on the stress component. In the future, probably the most effective way to evaluate the training of rowers is to monitor both stress and recovery components at the same time, using both psychometric data together with the biochemical and performance parameters.

Code C# for chaos analysis of relativistic many-body systems with reactions

NASA Astrophysics Data System (ADS)

Grossu, I. V.; Besliu, C.; Jipa, Al.; Stan, E.; Esanu, T.; Felea, D.; Bordeianu, C. C.

2012-04-01

In this work we present a reaction module for “Chaos Many-Body Engine” (Grossu et al., 2010 [1]). Following our goal of creating a customizable, object oriented code library, the list of all possible reactions, including the corresponding properties (particle types, probability, cross section, particle lifetime, etc.), could be supplied as parameter, using a specific XML input file. Inspired by the Poincaré section, we propose also the “Clusterization Map”, as a new intuitive analysis method of many-body systems. For exemplification, we implemented a numerical toy-model for nuclear relativistic collisions at 4.5 A GeV/c (the SKM200 Collaboration). An encouraging agreement with experimental data was obtained for momentum, energy, rapidity, and angular π distributions. Catalogue identifier: AEGH_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGH_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 184 628 No. of bytes in distributed program, including test data, etc.: 7 905 425 Distribution format: tar.gz Programming language: Visual C#.NET 2005 Computer: PC Operating system: Net Framework 2.0 running on MS Windows Has the code been vectorized or parallelized?: Each many-body system is simulated on a separate execution thread. One processor used for each many-body system. RAM: 128 Megabytes Classification: 6.2, 6.5 Catalogue identifier of previous version: AEGH_v1_0 Journal reference of previous version: Comput. Phys. Comm. 181 (2010) 1464 External routines: Net Framework 2.0 Library Does the new version supersede the previous version?: Yes Nature of problem: Chaos analysis of three-dimensional, relativistic many-body systems with reactions. Solution method: Second order Runge-Kutta algorithm for simulating relativistic many-body systems with reactions. Object oriented solution, easy to reuse, extend and customize, in any development environment which accepts .Net assemblies or COM components. Treatment of two particles reactions and decays. For each particle, calculation of the time measured in the particle reference frame, according to the instantaneous velocity. Possibility to dynamically add particle properties (spin, isospin, etc.), and reactions/decays, using a specific XML input file. Basic support for Monte Carlo simulations. Implementation of: Lyapunov exponent, “fragmentation level”, “average system radius”, “virial coefficient”, “clusterization map”, and energy conservation precision test. As an example of use, we implemented a toy-model for nuclear relativistic collisions at 4.5 A GeV/c. Reasons for new version: Following our goal of applying chaos theory to nuclear relativistic collisions at 4.5 A GeV/c, we developed a reaction module integrated with the Chaos Many-Body Engine. In the previous version, inheriting the Particle class was the only possibility of implementing more particle properties (spin, isospin, and so on). In the new version, particle properties can be dynamically added using a dictionary object. The application was improved in order to calculate the time measured in the own reference frame of each particle. two particles reactions: a+b→c+d, decays: a→c+d, stimulated decays, more complicated schemas, implemented as various combinations of previous reactions. Following our goal of creating a flexible application, the reactions list, including the corresponding properties (cross sections, particles lifetime, etc.), could be supplied as parameter, using a specific XML configuration file. The simulation output files were modified for systems with reactions, assuring also the backward compatibility. We propose the “Clusterization Map” as a new investigation method of many-body systems. The multi-dimensional Lyapunov Exponent was adapted in order to be used for systems with variable structure. Basic support for Monte Carlo simulations was also added. Additional comments: Windows forms application for testing the engine. Easy copy/paste based deployment method. Running time: Quadratic complexity.

A free, easy-to-use, computer-based simple and four-choice reaction time programme: the Deary-Liewald reaction time task.

PubMed

Deary, Ian J; Liewald, David; Nissan, Jack

2011-03-01

Reaction time tasks are used widely in basic and applied psychology. There is a need for an easy-to-use, freely available programme that can run simple and choice reaction time tasks with no special software. We report the development of, and make available, the Deary-Liewald reaction time task. It is initially tested here on 150 participants, aged from 18 to 80, alongside another widely used reaction time device and tests of fluid and crystallised intelligence and processing speed. The new task's parameters perform as expected with respect to age and intelligence differences. The new task's parameters are reliable, and have very high correlations with the existing task. We also provide instructions for downloading and using the new reaction time programme, and we encourage other researchers to use it.

Inverse Modeling of Water-Rock-CO2 Batch Experiments: Potential Impacts on Groundwater Resources at Carbon Sequestration Sites.

PubMed

Yang, Changbing; Dai, Zhenxue; Romanak, Katherine D; Hovorka, Susan D; Treviño, Ramón H

2014-01-01

This study developed a multicomponent geochemical model to interpret responses of water chemistry to introduction of CO2 into six water-rock batches with sedimentary samples collected from representative potable aquifers in the Gulf Coast area. The model simulated CO2 dissolution in groundwater, aqueous complexation, mineral reactions (dissolution/precipitation), and surface complexation on clay mineral surfaces. An inverse method was used to estimate mineral surface area, the key parameter for describing kinetic mineral reactions. Modeling results suggested that reductions in groundwater pH were more significant in the carbonate-poor aquifers than in the carbonate-rich aquifers, resulting in potential groundwater acidification. Modeled concentrations of major ions showed overall increasing trends, depending on mineralogy of the sediments, especially carbonate content. The geochemical model confirmed that mobilization of trace metals was caused likely by mineral dissolution and surface complexation on clay mineral surfaces. Although dissolved inorganic carbon and pH may be used as indicative parameters in potable aquifers, selection of geochemical parameters for CO2 leakage detection is site-specific and a stepwise procedure may be followed. A combined study of the geochemical models with the laboratory batch experiments improves our understanding of the mechanisms that dominate responses of water chemistry to CO2 leakage and also provides a frame of reference for designing monitoring strategy in potable aquifers.

Efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems

PubMed Central

Yang, Jin; Hlavacek, William S.

2011-01-01

Rule-based models, which are typically formulated to represent cell signaling systems, can now be simulated via various network-free simulation methods. In a network-free method, reaction rates are calculated for rules that characterize molecular interactions, and these rule rates, which each correspond to the cumulative rate of all reactions implied by a rule, are used to perform a stochastic simulation of reaction kinetics. Network-free methods, which can be viewed as generalizations of Gillespie’s method, are so named because these methods do not require that a list of individual reactions implied by a set of rules be explicitly generated, which is a requirement of other methods for simulating rule-based models. This requirement is impractical for rule sets that imply large reaction networks (i.e., long lists of individual reactions), as reaction network generation is expensive. Here, we compare the network-free simulation methods implemented in RuleMonkey and NFsim, general-purpose software tools for simulating rule-based models encoded in the BioNetGen language. The method implemented in NFsim uses rejection sampling to correct overestimates of rule rates, which introduces null events (i.e., time steps that do not change the state of the system being simulated). The method implemented in RuleMonkey uses iterative updates to track rule rates exactly, which avoids null events. To ensure a fair comparison of the two methods, we developed implementations of the rejection and rejection-free methods specific to a particular class of kinetic models for multivalent ligand-receptor interactions. These implementations were written with the intention of making them as much alike as possible, minimizing the contribution of irrelevant coding differences to efficiency differences. Simulation results show that performance of the rejection method is equal to or better than that of the rejection-free method over wide parameter ranges. However, when parameter values are such that ligand-induced aggregation of receptors yields a large connected receptor cluster, the rejection-free method is more efficient. PMID:21832806

Mixing effects on apparent reaction rates and isotope fractionation during denitrification in a heterogeneous aquifer

USGS Publications Warehouse

Green, Christopher T.; Böhlke, John Karl; Bekins, Barbara A.; Phillips, Steven P.

2010-01-01

Gradients in contaminant concentrations and isotopic compositions commonly are used to derive reaction parameters for natural attenuation in aquifers. Differences between field‐scale (apparent) estimated reaction rates and isotopic fractionations and local‐scale (intrinsic) effects are poorly understood for complex natural systems. For a heterogeneous alluvial fan aquifer, numerical models and field observations were used to study the effects of physical heterogeneity on reaction parameter estimates. Field measurements included major ions, age tracers, stable isotopes, and dissolved gases. Parameters were estimated for the O2 reduction rate, denitrification rate, O2 threshold for denitrification, and stable N isotope fractionation during denitrification. For multiple geostatistical realizations of the aquifer, inverse modeling was used to establish reactive transport simulations that were consistent with field observations and served as a basis for numerical experiments to compare sample‐based estimates of “apparent” parameters with “true“ (intrinsic) values. For this aquifer, non‐Gaussian dispersion reduced the magnitudes of apparent reaction rates and isotope fractionations to a greater extent than Gaussian mixing alone. Apparent and true rate constants and fractionation parameters can differ by an order of magnitude or more, especially for samples subject to slow transport, long travel times, or rapid reactions. The effect of mixing on apparent N isotope fractionation potentially explains differences between previous laboratory and field estimates. Similarly, predicted effects on apparent O2threshold values for denitrification are consistent with previous reports of higher values in aquifers than in the laboratory. These results show that hydrogeological complexity substantially influences the interpretation and prediction of reactive transport.

Modelling the fate of six common pharmaceuticals in a small stream: quantification of attenuation and retention in different stream-specific environments

NASA Astrophysics Data System (ADS)

Riml, Joakim; Wörman, Anders; Kunkel, Uwe; Radke, Michael

2013-04-01

Detection of pharmaceutical residues in streaming waters is common in urbanized areas. Although the occurrence and source of these micropollutants is known, their behavior in these aquatic ecosystems is still only partly understood. Specifically, quantitative information of biogeochemical processes in stream-specific environments where predominant reactions occur is often missing. In an attempt to address this knowledge gap, we performed simultaneous tracer tests in Säva Brook, Sweden, with bezafibrate, clofibric acid, diclofenac, ibuprofen, metoprolol and naproxen, as well as with the more inert solutes uranine and Rhodamine WT. The breakthrough curves at five successive sampling stations along a 16 km long stream reach were evaluated using a coupled physical-biogeochemical model framework containing surface water transport together with a representation of transient storage in slow/immobile zones of the stream. The multi-tracer experiment opens for decoupling of hydrological and biogeochemical contribution to the fate, and by linking impact and sensitivity analyses to relative significance of model parameters the most important processes for each contaminant were elucidated. Specifically for Säva Brook, the proposed methodology revealed that the pharmaceutical-contaminated stream water remained in the storage zones for times corresponding to 5-25% of the flow time of the stream. Furthermore, the results indicate a great variability in terms of predominant biogeochemical processes between the different contaminants. Rapid reactions occurring in the transient storage zone attenuated both ibuprofen and clofibric acid, and we conclude that a major degradation pathway for these contaminants was biodegradation in the hyporheic zone. In contrast, bezafibrate, metoprolol, and naproxen were mainly affected by sorption both in the storage zone and the main channel, while diclofenac displayed negligible effects of biogeochemical reactions.

Caffeine Reduces Reaction Time and Improves Performance in Simulated-Contest of Taekwondo

PubMed Central

Santos, Victor G. F.; Santos, Vander R. F.; Felippe, Leandro J. C.; Almeida, Jose W.; Bertuzzi, Rômulo; Kiss, Maria A. P. D. M.; Lima-Silva, Adriano E.

2014-01-01

The aim of this study was to investigate the effects of caffeine on reaction time during a specific taekwondo task and athletic performance during a simulated taekwondo contest. Ten taekwondo athletes ingested either 5 mg·kg−1 body mass caffeine or placebo and performed two combats (spaced apart by 20 min). The reaction-time test (five kicks “Bandal Tchagui”) was performed immediately prior to the first combat and immediately after the first and second combats. Caffeine improved reaction time (from 0.42 ± 0.05 to 0.37 ± 0.07 s) only prior to the first combat (P = 0.004). During the first combat, break times during the first two rounds were shorter in caffeine ingestion, followed by higher plasma lactate concentrations compared with placebo (P = 0.029 and 0.014, respectively). During the second combat, skipping-time was reduced, and relative attack times and attack/skipping ratio was increased following ingestion of caffeine during the first two rounds (all P < 0.05). Caffeine resulted in no change in combat intensity parameters between the first and second combat (all P > 0.05), but combat intensity was decreased following placebo (all P < 0.05). In conclusion, caffeine reduced reaction time in non-fatigued conditions and delayed fatigue during successive taekwondo combats. PMID:24518826

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

PubMed Central

Kaltenbacher, Barbara; Hasenauer, Jan

2017-01-01

Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small- and medium-scale biological processes. While the same should in principle hold for large- and genome-scale processes, the computational methods for the analysis of ODE models which describe hundreds or thousands of biochemical species and reactions are missing so far. While individual simulations are feasible, the inference of the model parameters from experimental data is computationally too intensive. In this manuscript, we evaluate adjoint sensitivity analysis for parameter estimation in large scale biochemical reaction networks. We present the approach for time-discrete measurement and compare it to state-of-the-art methods used in systems and computational biology. Our comparison reveals a significantly improved computational efficiency and a superior scalability of adjoint sensitivity analysis. The computational complexity is effectively independent of the number of parameters, enabling the analysis of large- and genome-scale models. Our study of a comprehensive kinetic model of ErbB signaling shows that parameter estimation using adjoint sensitivity analysis requires a fraction of the computation time of established methods. The proposed method will facilitate mechanistic modeling of genome-scale cellular processes, as required in the age of omics. PMID:28114351

Nitrate formation during ozonation as a surrogate parameter for abatement of micropollutants and the N-nitrosodimethylamine (NDMA) formation potential.

PubMed

Song, Yang; Breider, Florian; Ma, Jun; von Gunten, Urs

2017-10-01

In this study, nitrate formation from ammonium and/or dissolved organic nitrogen (DON) was investigated as a novel surrogate parameter to evaluate the abatement of micropollutants during ozonation of synthetic waters containing natural organic matter (NOM) isolates, a natural water and secondary wastewater effluents. Nitrate formation during ozonation was compared to the changes in UV absorbance at 254 nm (UVA 254 ) including the effect of pH. For low specific ozone doses UVA 254 was abated more efficiently than nitrate was formed. This is due to a relatively slow rate-limiting step for nitrate formation from the reaction between ozone and a proposed nitrogen-containing intermediate. This reaction cannot compete with the fast reactions between ozone and UV-absorbing moieties (e.g., activated aromatic compounds). To further test the kinetics of nitrate formation, two possible intermediates formed during ozonation of DON were tested. At pH 7, nitrate was formed during ozonation of acetone oxime and methyl nitroacetate with second-order rate constants of 256.7 ± 4.7 M -1  s -1 and 149.5 ± 5.8 M -1  s -1 , respectively. The abatement of the selected micropollutants (i.e., 17α-ethinylestradiol (EE2), carbamazepine (CBZ), bezafibrate (BZF), ibuprofen (IBU), and p-chlorobenzoic acid (pCBA)) was investigated for specific ozone doses ≤1.53 mgO 3 /mgDOC and its efficiency depended strongly on the reactivity of the selected compounds with ozone. The relative abatement of micropollutants (i.e., EE2 and CBZ) with high ozone reactivity showed linear relationships with nitrate formation. The abatement of micropollutants with intermediate-low ozone reactivity (BZF, IBU, and pCBA) followed one- and two-phase behaviors relative to nitrate formation during ozonation of water samples containing high and low concentrations of nitrate-forming DON, respectively. During ozonation of a wastewater sample, the N-nitrosodimethylamine formation potential (NDMA-FP) during chloramination decreased with increasing specific ozone doses. A good correlation was obtained between NDMA-FP abatement and nitrate formation. Therefore, nitrate formation after pre-ozonation may be a useful parameter to estimate the reduction of the NDMA-FP during post-chloramination. Overall, the results of this study suggest that nitrate formation (possibly in combination with UVA 254 abatement) during ozonation of DON-containing waters may be a good surrogate for assessing the abatement of micropollutants and the NDMA-FP. Copyright © 2017 Elsevier Ltd. All rights reserved.

Production and characterization of hydrophobic zinc borate by using palm oil

NASA Astrophysics Data System (ADS)

Acarali, Nil Baran; Tugrul, Nurcan; Derun, Emek Moroydor; Piskin, Sabriye

2013-11-01

Zinc borate (ZB) was synthesized using zinc oxide, boric acid synthesized from colemanite, and reference ZB as seed. The effects of reaction parameters such as reaction time, reactant ratio, and seed ratio on its yield were examined. Then, the effects of palm oil with solvents (isopropyl alcohol (IPA), ethanol, and methanol) added to the reaction on its hydrophobicity were explored. Reactions were carried out under determined reaction conditions with magnetically and mechanically stirred systems. The produced ZB was characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), and measurements of contact angle identified hydrophobicity. The results showed that hydrophobic ZB was successfully produced under determined reaction conditions. The change of process parameters influenced its yield and the usage of palm oil provided hydrophobicity.

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

Mondy, Lisa Ann; Rao, Rekha Ranjana; Shelden, Bion

We are developing computational models to elucidate the expansion and dynamic filling process of a polyurethane foam, PMDI. The polyurethane of interest is chemically blown, where carbon dioxide is produced via the reaction of water, the blowing agent, and isocyanate. The isocyanate also reacts with polyol in a competing reaction, which produces the polymer. Here we detail the experiments needed to populate a processing model and provide parameters for the model based on these experiments. The model entails solving the conservation equations, including the equations of motion, an energy balance, and two rate equations for the polymerization and foaming reactions,more » following a simplified mathematical formalism that decouples these two reactions. Parameters for the polymerization kinetics model are reported based on infrared spectrophotometry. Parameters describing the gas generating reaction are reported based on measurements of volume, temperature and pressure evolution with time. A foam rheology model is proposed and parameters determined through steady-shear and oscillatory tests. Heat of reaction and heat capacity are determined through differential scanning calorimetry. Thermal conductivity of the foam as a function of density is measured using a transient method based on the theory of the transient plane source technique. Finally, density variations of the resulting solid foam in several simple geometries are directly measured by sectioning and sampling mass, as well as through x-ray computed tomography. These density measurements will be useful for model validation once the complete model is implemented in an engineering code.« less

Direct asymmetric N-specific reaction of nitrosobenzene with aldehydes catalyzed by a chiral primary amine-based organocatalyst.

PubMed

Qin, Long; Li, Lei; Yi, Lei; Da, Chao-Shan; Zhou, Yi-Feng

2011-08-01

Nitroso compounds have two reactive nitrogen and oxygen atoms. It is interesting and important to perform a nitrogen or oxygen selective reaction with interesting substrates. These atom specific reactions are crucial to specifically synthesis of specific compounds. An enantioselective N-specific reaction of nitrosobenzene with unmodified aldehydes was successfully achieved catalyzed first by a variety of primary amine-based organocatalysts with higher yield and enantioselectivity. The bulkier substituted groups of the organocatalyst and two hydrogen bonds from the organocatalyst and the oxygen atom of nitrosobenzene make the reaction preferentially N-specific and predominantly afford R products. Copyright © 2011 Wiley-Liss, Inc.

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

PubMed

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.

Transport of reacting solutes subject to a moving dissolution boundary: Numerical methods and solutions

USGS Publications Warehouse

Willis, Catherine; Rubin, Jacob

1987-01-01

A moving boundary problem which arises during transport with precipitation-dissolution reactions is solved by three different numerical methods. Two of these methods (one explicit and one implicit) are based on an integral formulation of mass balance and lead to an approximation of a weak solution. These methods are compared to a front-tracking scheme. Although the two approaches are conceptually different, the numerical solutions showed good agreement. As the ratio of dispersion to convection decreases, the methods based on the integral formulation become computationally more efficient. Specific reactions were modeled to examine the dependence of the system on the physical and chemical parameters. Although the water flow rate does not explicitly appear in the equation for the velocity of the moving boundary, the speed of the boundary depends more on the flux rate than on the dispersion coefficient. The discontinuity in the gradient of the solute concentration profile at the boundary increases with convection and with the initial concentration of the mineral. Our implicit method is extended to allow participation of the solutes in complexation reactions as well as the precipitation-dissolution reaction. This extension is easily made and does not change the basic method.

Overview of Development and Formulation of ¹⁷⁷Lu-DOTA-TATE for PRRT.

PubMed

Breeman, Wouter A P; Chan, Ho Sze; de Zanger, Rory M S; Konijnenberg, Mark K; de Blois, Erik

2016-01-01

Peptide receptor radionuclide therapy (PRRT) using radiolabeled somatostatin analogs has become an established procedure for the treatment of patients suffering from inoperable neuroendocrine cancers over-expressing somatostatin receptors. Success of PRRT depends on the availability of the radiolabeled peptide with adequately high specific activity, so that required therapeutic efficacy can be achieved without saturating the limited number of receptors available on the target lesions. Specific activity of the radionuclide and the radiolabeled somatostatin analog are therefore an important parameters. Although these analogs have been investigated and improved, and successfully applied for PRRT for more than 15 years, there are still many possibilities for further improvements that fully exploit PRRT with 177Lu-DOTA-TATE. The here summarized data presented herein on increased knowledge of the components of 177Lu-DOTA-TATE (especially the purity of 177Lu and specific activity of 177Lu) and the reaction kinetics during labeling 177Lu-DOTA-TATE clearly show that the peptide dose and dose in GBq can be varied. Here we present an overview of the development, formulation and optimisation of 177Lu-DOTA-TATE, mainly addressing radiochemical parameters.

New functionalities of Maillard reaction products as emulsifiers and encapsulating agents, and the processing parameters: a brief review.

PubMed

Lee, Yee-Ying; Tang, Teck-Kim; Phuah, Eng-Tong; Alitheen, Noorjahan Banu Mohamed; Tan, Chin-Ping; Lai, Oi-Ming

2017-03-01

Non-enzymatic browning has been a wide and interesting research area in the food industry, ranging from the complexity of the reaction to its applications in the food industry as well as its ever-debatable health effects. This review provides a new perspective to the Maillard reaction apart from its ubiquitous function in enhancing food flavour, taste and appearance. It focuses on the recent application of Maillard reaction products as an inexpensive and excellent source of emulsifiers as well as superior encapsulating matrices for the entrapment of bioactive compounds. Additionally, it will also discuss the latest approaches employed to perform the Maillard reaction as well as several important reaction parameters that need to be taken into consideration when conducting the Maillard reaction. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Statistical methods for thermonuclear reaction rates and nucleosynthesis simulations

NASA Astrophysics Data System (ADS)

Iliadis, Christian; Longland, Richard; Coc, Alain; Timmes, F. X.; Champagne, Art E.

2015-03-01

Rigorous statistical methods for estimating thermonuclear reaction rates and nucleosynthesis are becoming increasingly established in nuclear astrophysics. The main challenge being faced is that experimental reaction rates are highly complex quantities derived from a multitude of different measured nuclear parameters (e.g., astrophysical S-factors, resonance energies and strengths, particle and γ-ray partial widths). We discuss the application of the Monte Carlo method to two distinct, but related, questions. First, given a set of measured nuclear parameters, how can one best estimate the resulting thermonuclear reaction rates and associated uncertainties? Second, given a set of appropriate reaction rates, how can one best estimate the abundances from nucleosynthesis (i.e., reaction network) calculations? The techniques described here provide probability density functions that can be used to derive statistically meaningful reaction rates and final abundances for any desired coverage probability. Examples are given for applications to s-process neutron sources, core-collapse supernovae, classical novae, and Big Bang nucleosynthesis.

Raman spectroscopic analysis of gunshot residue offering great potential for caliber differentiation.

PubMed

Bueno, Justin; Sikirzhytski, Vitali; Lednev, Igor K

2012-05-15

Near-infrared (NIR) Raman microspectroscopy combined with advanced statistics was used to differentiate gunshot residue (GSR) particles originating from different caliber ammunition. The firearm discharge process is analogous to a complex chemical reaction. The reagents of this process are represented by the chemical composition of the ammunition, firearm, and cartridge case. The specific firearm parameters determine the conditions of the reaction and thus the subsequent product, GSR. We found that Raman spectra collected from these products are characteristic for different caliber ammunition. GSR particles from 9 mm and 0.38 caliber ammunition, collected under identical discharge conditions, were used to demonstrate the capability of confocal Raman microspectroscopy for the discrimination and identification of GSR particles. The caliber differentiation algorithm is based on support vector machines (SVM) and partial least squares (PLS) discriminant analyses, validated by a leave-one-out cross-validation method. This study demonstrates for the first time that NIR Raman microspectroscopy has the potential for the reagentless differentiation of GSR based upon forensically relevant parameters, such as caliber size. When fully developed, this method should have a significant impact on the efficiency of crime scene investigations.

Solutal and thermal buoyancy effects in self-powered phosphatase micropumps.

PubMed

Valdez, Lyanne; Shum, Henry; Ortiz-Rivera, Isamar; Balazs, Anna C; Sen, Ayusman

2017-04-12

Immobilized enzymes generate net fluid flow when exposed to specific reagents in solution. Thus, they function as self-powered platforms that combine sensing and on-demand fluid pumping. To uncover the mechanism of pumping, we examine the effects of solutal and thermal buoyancy on the behavior of phosphatase-based micropumps, using a series of reactants with known thermodynamic and kinetic parameters. By combining modeling and experiments, we perform the first quantitative comparison of thermal and solutal effects in an enzyme micropump system. Despite the significant exothermicity of the catalyzed reactions, we find that thermal effects play a minimal role in the observed fluid flow. Instead, fluid transport in phosphatase micropumps is governed by the density difference between the reactants and the products of the reaction. This surprising conclusion suggests new design principles for catalytic pumps.

Predicting CYP2C19 Catalytic Parameters for Enantioselective Oxidations Using Artificial Neural Networks and a Chirality Code

PubMed Central

Hartman, Jessica H.; Cothren, Steven D.; Park, Sun-Ha; Yun, Chul-Ho; Darsey, Jerry A.; Miller, Grover P.

2013-01-01

Cytochromes P450 (CYP for isoforms) play a central role in biological processes especially metabolism of chiral molecules; thus, development of computational methods to predict parameters for chiral reactions is important for advancing this field. In this study, we identified the most optimal artificial neural networks using conformation-independent chirality codes to predict CYP2C19 catalytic parameters for enantioselective reactions. Optimization of the neural networks required identifying the most suitable representation of structure among a diverse array of training substrates, normalizing distribution of the corresponding catalytic parameters (kcat, Km, and kcat/Km), and determining the best topology for networks to make predictions. Among different structural descriptors, the use of partial atomic charges according to the CHelpG scheme and inclusion of hydrogens yielded the most optimal artificial neural networks. Their training also required resolution of poorly distributed output catalytic parameters using a Box-Cox transformation. End point leave-one-out cross correlations of the best neural networks revealed that predictions for individual catalytic parameters (kcat and Km) were more consistent with experimental values than those for catalytic efficiency (kcat/Km). Lastly, neural networks predicted correctly enantioselectivity and comparable catalytic parameters measured in this study for previously uncharacterized CYP2C19 substrates, R- and S-propranolol. Taken together, these seminal computational studies for CYP2C19 are the first to predict all catalytic parameters for enantioselective reactions using artificial neural networks and thus provide a foundation for expanding the prediction of cytochrome P450 reactions to chiral drugs, pollutants, and other biologically active compounds. PMID:23673224

Calculation of (n,α) reaction cross sections by using some Skyrme force parameters for Potassium (41K) target nuclei

NASA Astrophysics Data System (ADS)

Tel, Eyyup; Sahan, Muhittin; Alkanli, Hasancan; Sahan, Halide; Yigit, Mustafa

2017-09-01

In this study, the (n,α) nuclear reaction cross section was calculated for 41K target nuclei for neutron and proton density parameters using SKa, SKb, SLy5, and SLy6 Skyrme force. Theoretical cross section for the (n,α) nuclear reaction was obtained using a formula constituted by Tel et al. (2008). Results are compared with experimental data from EXFOR. The calculated results from formula was found in a close agreement with experimental data.

Low gravity synthesis of polymers with controlled molecular configuration

NASA Technical Reports Server (NTRS)

Heimbuch, A. H.; Parker, J. A.; Schindler, A.; Olf, H. G.

1975-01-01

Heterogeneous chemical systems have been studied for the synthesis of isotactic polypropylene in order to establish baseline parameters for the reaction process and to develop sensitive and accurate methods of analysis. These parameters and analytical methods may be used to make a comparison between the polypropylene obtained at one g with that of zero g (gravity). Baseline reaction parameters have been established for the slurry (liquid monomer in heptane/solid catalyst) polymerization of propylene to yield high purity, 98% isotactic polypropylene. Kinetic data for the slurry reaction showed that a sufficient quantity of polymer for complete characterization can be produced in a reaction time of 5 min; this time is compatible with that available on a sounding rocket for a zero-g simulation experiment. The preformed (activated) catalyst was found to be more reproducible in its activity than the in situ formed catalyst.

Synthesis of Cesium Lead Halide Perovskite Nanocrystals in a Droplet-Based Microfluidic Platform: Fast Parametric Space Mapping.

PubMed

Lignos, Ioannis; Stavrakis, Stavros; Nedelcu, Georgian; Protesescu, Loredana; deMello, Andrew J; Kovalenko, Maksym V

2016-03-09

Prior to this work, fully inorganic nanocrystals of cesium lead halide perovskite (CsPbX3, X = Br, I, Cl and Cl/Br and Br/I mixed halide systems), exhibiting bright and tunable photoluminescence, have been synthesized using conventional batch (flask-based) reactions. Unfortunately, our understanding of the parameters governing the formation of these nanocrystals is still very limited due to extremely fast reaction kinetics and multiple variables involved in ion-metathesis-based synthesis of such multinary halide systems. Herein, we report the use of a droplet-based microfluidic platform for the synthesis of CsPbX3 nanocrystals. The combination of online photoluminescence and absorption measurements and the fast mixing of reagents within such a platform allows the rigorous and rapid mapping of the reaction parameters, including molar ratios of Cs, Pb, and halide precursors, reaction temperatures, and reaction times. This translates into enormous savings in reagent usage and screening times when compared to analogous batch synthetic approaches. The early-stage insight into the mechanism of nucleation of metal halide nanocrystals suggests similarities with multinary metal chalcogenide systems, albeit with much faster reaction kinetics in the case of halides. Furthermore, we show that microfluidics-optimized synthesis parameters are also directly transferrable to the conventional flask-based reaction.

Evaluating Warning Sound Urgency with Reaction Times

ERIC Educational Resources Information Center

Suied, Clara; Susini, Patrick; McAdams, Stephen

2008-01-01

It is well-established that subjective judgments of perceived urgency of alarm sounds can be affected by acoustic parameters. In this study, the authors investigated an objective measurement, the reaction time (RT), to test the effectiveness of temporal parameters of sounds in the context of warning sounds. Three experiments were performed using a…

[Differentiation of nonspecific serological reactions in brucellosis].

PubMed

Khristoforov, L

1979-01-01

Differentiation of non-specific agglutination was performed by the complement binding reaction, Coombs' reaction, Hajdu reaction, the surface fixation and agglutination reaction and the reaction of complement binding with heterologic antigens. For that purpose the following were used: 1) Serums--antiglobulin against cattle globulin, 5720 serum of various animals which had manifested non-specific agglutination with brucella antigen and brucella serums of experimentally infected sheep, of naturally infected swine and of cattle--received from abroad. 2) Antigens--of Br. abortus 99, of bacteria heterologic to brucellae: Proteus vulgaris, Listeria monocytogenes, Staphylococcus albus, Escherichia coli, Streptococcus pyogenes, S. abortus ovis, for O and OH agglutination, water extraction antigens--for complement binding and concentrated suspensions of all bacteria used in brucellose and non-brucellose serum absorption. Highest number of non-specific reactions were observed in cattle serums and lowest--in goat serums. Titers with heterologic antigens were higher than these with brucella antigens. Often the serum having non-specific agglutiantion reacted not only with one, but with more heterologic antigens. Non-specific complement binding reactions were not produced in complete antibodies with the brucella antigen. Heterologic brucella antigens were exhausted more fully than heterologic complement binding antibodies. In their effectiveness (differentiation of non-specific agglutination with brucella antigen in cattle serum) the serological reactions studied rank as follows: complement binding reaction, slow agglutination with serums absorbed by heterologic antigens, surface fixation reaction, Coombs' reaction, and Hadju agglutination.

Thermodynamic criteria for estimating the kinetic parameters of catalytic reactions

NASA Astrophysics Data System (ADS)

Mitrichev, I. I.; Zhensa, A. V.; Kol'tsova, E. M.

2017-01-01

Kinetic parameters are estimated using two criteria in addition to the traditional criterion that considers the consistency between experimental and modeled conversion data: thermodynamic consistency and the consistency with entropy production (i.e., the absolute rate of the change in entropy due to exchange with the environment is consistent with the rate of entropy production in the steady state). A special procedure is developed and executed on a computer to achieve the thermodynamic consistency of a set of kinetic parameters with respect to both the standard entropy of a reaction and the standard enthalpy of a reaction. A problem of multi-criterion optimization, reduced to a single-criterion problem by summing weighted values of the three criteria listed above, is solved. Using the reaction of NO reduction with CO on a platinum catalyst as an example, it is shown that the set of parameters proposed by D.B. Mantri and P. Aghalayam gives much worse agreement with experimental values than the set obtained on the basis of three criteria: the sum of the squares of deviations for conversion, the thermodynamic consistency, and the consistency with entropy production.

Anisotropy of the angular distribution of fission fragments in heavy-ion fusion-fission reactions: The influence of the level-density parameter and the neck thickness

NASA Astrophysics Data System (ADS)

Naderi, D.; Pahlavani, M. R.; Alavi, S. A.

2013-05-01

Using the Langevin dynamical approach, the neutron multiplicity and the anisotropy of angular distribution of fission fragments in heavy ion fusion-fission reactions were calculated. We applied one- and two-dimensional Langevin equations to study the decay of a hot excited compound nucleus. The influence of the level-density parameter on neutron multiplicity and anisotropy of angular distribution of fission fragments was investigated. We used the level-density parameter based on the liquid drop model with two different values of the Bartel approach and Pomorska approach. Our calculations show that the anisotropy and neutron multiplicity are affected by level-density parameter and neck thickness. The calculations were performed on the 16O+208Pb and 20Ne+209Bi reactions. Obtained results in the case of the two-dimensional Langevin with a level-density parameter based on Bartel and co-workers approach are in better agreement with experimental data.

Optimisation of the zinc sulphate turbidity test for the determination of immune status.

PubMed

Hogan, I; Doherty, M; Fagan, J; Kennedy, E; Conneely, M; Crowe, B; Lorenz, I

2016-02-13

Failure of passive transfer of maternal immunity occurs in calves that fail to absorb sufficient immunoglobulins from ingested colostrum. The zinc sulphate turbidity test has been developed to test bovine neonates for this failure. The specificity of this test has been shown to be less than ideal. The objective was to examine how parameters of the zinc sulphate turbidity test may be manipulated in order to improve its diagnostic accuracy. One hundred and five blood samples were taken from calves of dairy cows receiving various rates of colostrum feeding. The zinc sulphate turbidity test was carried out multiple times on each sample, varying the solution strength, time of reaction and wavelength of light used and the results compared with those of a radial immunodiffusion test, which is the reference method for measuring immunoglobulin concentration in serum. Reducing the time over which the reaction occurs, or increasing the wavelength of light used to read the turbidity, resulted in decreased specificity without improving sensitivity. Increasing the concentration of the zinc sulphate solution used in the test was shown to improve the specificity without decreasing sensitivity. Examination of the cut-off points suggested that a lower cut-off point would improve the performance. British Veterinary Association.

A variational approach to parameter estimation in ordinary differential equations.

PubMed

Kaschek, Daniel; Timmer, Jens

2012-08-14

Ordinary differential equations are widely-used in the field of systems biology and chemical engineering to model chemical reaction networks. Numerous techniques have been developed to estimate parameters like rate constants, initial conditions or steady state concentrations from time-resolved data. In contrast to this countable set of parameters, the estimation of entire courses of network components corresponds to an innumerable set of parameters. The approach presented in this work is able to deal with course estimation for extrinsic system inputs or intrinsic reactants, both not being constrained by the reaction network itself. Our method is based on variational calculus which is carried out analytically to derive an augmented system of differential equations including the unconstrained components as ordinary state variables. Finally, conventional parameter estimation is applied to the augmented system resulting in a combined estimation of courses and parameters. The combined estimation approach takes the uncertainty in input courses correctly into account. This leads to precise parameter estimates and correct confidence intervals. In particular this implies that small motifs of large reaction networks can be analysed independently of the rest. By the use of variational methods, elements from control theory and statistics are combined allowing for future transfer of methods between the two fields.

Improvement of the efficiency of a space oxygen-hydrogen electrochemical generator

NASA Astrophysics Data System (ADS)

Glukhikh, I. N.; Shcherbakov, A. N.; Chelyaev, V. F.

2014-12-01

This paper describes the method used for cooling of an on-board oxygen-hydrogen electrochemical generator (ECG). Apart from electric power, such a unit produces water of reaction and heat; the latter is an additional load on the thermal control system of a space vehicle. This load is undesirable in long-duration space flights, when specific energy characteristics of on-board systems are the determining factors. It is suggested to partially compensate the energy consumption by the thermal control system of a space vehicle required for cooling of the electrochemical generator through evaporation of water of reaction from the generator into a vacuum (or through ice sublimation if the pressure in the ambient space is lower than that in the triple point of water.) Such method of cooling of an electrochemical generator improves specific energy parameters of an on-board electric power supply system, and, due to the presence of the negative feedback, it makes the operation of this system more stable. Estimates suggest that it is possible to compensate approximately one half of heat released from the generator through evaporation of its water of reaction at the electrical efficiency of the electrochemical generator equal to 60%. In this case, even minor increase in the efficiency of the generator would result in a considerable increase in the efficiency of the evaporative system intended for its cooling.

Design requirements for ERD in diffusion-dominated media: how do injection interval, bioactive zones and reaction kinetics affect remediation performance?

NASA Astrophysics Data System (ADS)

Chambon, J.; Lemming, G.; Manoli, G.; Broholm, M. M.; Bjerg, P.; Binning, P. J.

2011-12-01

Enhanced Reductive Dechlorination (ERD) has been successfully used in high permeability media, such as sand aquifers, and is considered to be a promising technology for low permeability settings. Pilot and full-scale applications of ERD at several sites in Denmark have shown that the main challenge is to get contact between the injected bacteria and electron donor and the contaminants trapped in the low-permeability matrix. Sampling of intact cores from the low-permeability matrix has shown that the bioactive zones (where degradation occurs) are limited in the matrix, due to the slow diffusion transport processes, and this affects the timeframes for the remediation. Due to the limited ERD applications and the complex transport and reactive processes occurring in low-permeability media, design guidelines are currently not available for ERD in such settings, and remediation performance assessments are limited. The objective of this study is to combine existing knowledge from several sites with numerical modeling to assess the effect of the injection interval, development of bioactive zones and reaction kinetics on the remediation efficiency for ERD in diffusion-dominated media. A numerical model is developed to simulate ERD at a contaminated site, where the source area (mainly TCE) is located in a clayey till with fractures and interbedded sand lenses. Such contaminated sites are common in North America and Europe. Hydro-geological characterization provided information on geological heterogeneities and hydraulic parameters, which are relevant for clay till sites in general. The numerical model couples flow and transport in the fracture network and low-permeability matrix. Sequential degradation of TCE to ethene is modeled using Monod kinetics, and the kinetic parameters are obtained from laboratory experiments. The influence of the reaction kinetics on remediation efficiency is assessed by varying the biomass concentration of the specific degraders. The injected reactants (donor and bacteria) are assumed to spread in horizontal injection zones of various widths, depending on the development of bioactive zones. These injection zones are spaced at various intervals over depth, corresponding to the injection interval chosen. The results from the numerical model show that remediation timeframes can be reduced significantly by using closely spaced injection intervals and by ensuring the efficient spreading of the reactants into the clay till matrix. In contrast the reaction kinetics affect mass removal only up to a point where diffusive transport becomes limiting. Based on these results, guidelines on when ERD can be an effective remediation strategy in practice are provided. These take the form of dimensionless groupings (such as the Damkohler number), which combine site specific (physical and biogeochemical) and design parameters, and graphs showing how the main parameters affect remediation timeframes. Finally it is shown how model results can be used as input to other decision making tools such as life cycle assessment to guide remedial choices.

Scale-up of organic reactions in ball mills: process intensification with regard to energy efficiency and economy of scale.

PubMed

Stolle, Achim; Schmidt, Robert; Jacob, Katharina

2014-01-01

The scale-up of the Knoevenagel-condensation between vanillin and barbituric acid carried out in planetary ball mills is investigated from an engineering perspective. Generally, the reaction proceeded in the solid state without intermediate melting and afforded selectively only one product. The reaction has been used as a model to analyze the influence and relationship of different parameters related to operation in planetary ball mills. From the viewpoint of technological parameters the milling ball diameter, dMB, the filling degree with respect to the milling balls' packing, ΦMB,packing, and the filling degree of the substrates with respect to the void volume of the milling balls' packing, ΦGS, have been investigated at different reaction scales. It was found that milling balls with small dMB lead to higher yields within shorter reaction time, treaction, or lower rotation frequency, rpm. Thus, the lower limit is set considering the technology which is available for the separation of the milling balls from the product after the reaction. Regarding ΦMB,packing, results indicate that the optimal value is roughly 50% of the total milling beakers' volume, VB,total, independent of the reaction scale or reaction conditions. Thus, 30% of VB,total are taken by the milling balls. Increase of the initial batch sizes changes ΦGS significantly. However, within the investigated parameter range no negative influence on the yield was observed. Up to 50% of VB,total can be taken over by the substrates in addition to 30% for the total milling ball volume. Scale-up factors of 15 and 11 were realized considering the amount of substrates and the reactor volume, respectively. Beside technological parameters, variables which influence the process itself, treaction and rpm, were investigated also. Variation of those allowed to fine-tune the reaction conditions in order to maximize the yield and minimize the energy intensity.

Prediction of human gait parameters from temporal measures of foot-ground contact

NASA Technical Reports Server (NTRS)

Breit, G. A.; Whalen, R. T.

1997-01-01

Investigation of the influence of human physical activity on bone functional adaptation requires long-term histories of gait-related ground reaction force (GRF). Towards a simpler portable GRF measurement, we hypothesized that: 1) the reciprocal of foot-ground contact time (1/tc); or 2) the reciprocal of stride-period-normalized contact time (T/tc) predict peak vertical and horizontal GRF, loading rates, and horizontal speed during gait. GRF data were collected from 24 subjects while they walked and ran at a variety of speeds. Linear regression and ANCOVA determined the dependence of gait parameters on 1/tc and T/tc, and prediction SE. All parameters were significantly correlated to 1/tc and T/tc. The closest pooled relationship existed between peak running vertical GRF and T/tc (r2 = 0.896; SE = 3.6%) and improved with subject-specific regression (r2 = 0.970; SE = 2.2%). We conclude that temporal measures can predict force parameters of gait and may represent an alternative to direct GRF measurements for determining daily histories of habitual lower limb loading quantities necessary to quantify a bone remodeling stimulus.

Effect of homogenous-heterogeneous reactions on MHD Prandtl fluid flow over a stretching sheet

NASA Astrophysics Data System (ADS)

Khan, Imad; Malik, M. Y.; Hussain, Arif; Salahuddin, T.

An analysis is performed to explore the effects of homogenous-heterogeneous reactions on two-dimensional flow of Prandtl fluid over a stretching sheet. In present analysis, we used the developed model of homogeneous-heterogeneous reactions in boundary layer flow. The mathematical configuration of presented flow phenomenon yields the nonlinear partial differential equations. Using scaling transformations, the governing partial differential equations (momentum equation and homogenous-heterogeneous reactions equations) are transformed into non-linear ordinary differential equations (ODE's). Then, resulting non-linear ODE's are solved by computational scheme known as shooting method. The quantitative and qualitative manners of concerned physical quantities (velocity, concentration and drag force coefficient) are examined under prescribed physical constrained through figures and tables. It is observed that velocity profile enhances verses fluid parameters α and β while Hartmann number reduced it. The homogeneous and heterogeneous reactions parameters have reverse effects on concentration profile. Concentration profile shows retarding behavior for large values of Schmidt number. Skin fraction coefficient enhances with increment in Hartmann number H and fluid parameter α .

Simple real-time computerized tasks for detection of malingering among murderers with schizophrenia.

PubMed

Kertzman, Semion; Grinspan, Haim; Birger, Moshe; Shliapnikov, Nina; Alish, Yakov; Ben Nahum, Zeev; Mester, Roberto; Kotler, Moshe

2006-01-01

It is our contention that computer-based two-alternative forced choice techniques can be useful tools for the detection of patients with schizophrenia who feign acute psychotic symptoms and cognitive impairment as opposed to patients with schizophrenia with a true active psychosis. In our experiment, Visual Simple and Choice Reaction Time tasks were used. Reaction time in milliseconds was recorded and accuracy rate was obtained for all subjects' responses. Both types of task were administered to 27 patients with schizophrenia suspected of having committed murder. Patients with schizophrenia who were clinically assessed as malingerers achieved significantly fewer correct results, were significantly slower and less consistent in their reaction time. Congruence of performance between the Simple and Choice tasks was an additional parameter for the accurate diagnosis of malingering. The four parameters of both tests (accuracy of response, reaction time, standard deviation of reaction time and task congruency) are simple and constitute a user-friendly means for the detection of malingering in forensic practice. Another advantage of this procedure is that the software automatically measures and evaluates all the parameters.

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

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

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

2015-07-16

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

Effects of Variable Thermal Conductivity and Non-linear Thermal Radiation Past an Eyring Powell Nanofluid Flow with Chemical Reaction

NASA Astrophysics Data System (ADS)

Ramzan, M.; Bilal, M.; Kanwal, Shamsa; Chung, Jae Dong

2017-06-01

Present analysis discusses the boundary layer flow of Eyring Powell nanofluid past a constantly moving surface under the influence of nonlinear thermal radiation. Heat and mass transfer mechanisms are examined under the physically suitable convective boundary condition. Effects of variable thermal conductivity and chemical reaction are also considered. Series solutions of all involved distributions using Homotopy Analysis method (HAM) are obtained. Impacts of dominating embedded flow parameters are discussed through graphical illustrations. It is observed that thermal radiation parameter shows increasing tendency in relation to temperature profile. However, chemical reaction parameter exhibits decreasing behavior versus concentration distribution. Supported by the World Class 300 Project (No. S2367878) of the SMBA (Korea)

Cognitive-motivational deficits in ADHD: development of a classification system.

PubMed

Gupta, Rashmi; Kar, Bhoomika R; Srinivasan, Narayanan

2011-01-01

The classification systems developed so far to detect attention deficit/hyperactivity disorder (ADHD) do not have high sensitivity and specificity. We have developed a classification system based on several neuropsychological tests that measure cognitive-motivational functions that are specifically impaired in ADHD children. A total of 240 (120 ADHD children and 120 healthy controls) children in the age range of 6-9 years and 32 Oppositional Defiant Disorder (ODD) children (aged 9 years) participated in the study. Stop-Signal, Task-Switching, Attentional Network, and Choice Delay tests were administered to all the participants. Receiver operating characteristic (ROC) analysis indicated that percentage choice of long-delay reward best classified the ADHD children from healthy controls. Single parameters were not helpful in making a differential classification of ADHD with ODD. Multinominal logistic regression (MLR) was performed with multiple parameters (data fusion) that produced improved overall classification accuracy. A combination of stop-signal reaction time, posterror-slowing, mean delay, switch cost, and percentage choice of long-delay reward produced an overall classification accuracy of 97.8%; with internal validation, the overall accuracy was 92.2%. Combining parameters from different tests of control functions not only enabled us to accurately classify ADHD children from healthy controls but also in making a differential classification with ODD. These results have implications for the theories of ADHD.

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

Santhanagopalan, Shriram; White, Ralph E.

Rotating ring disc electrode (RRDE) experiments are a classic tool for investigating kinetics of electrochemical reactions. Several standardized methods exist for extracting transport parameters and reaction rate constants using RRDE measurements. Here in this work, we compare some approximate solutions to the convective diffusion used popularly in the literature to a rigorous numerical solution of the Nernst-Planck equations coupled to the three dimensional flow problem. In light of these computational advancements, we explore design aspects of the RRDE that will help improve sensitivity of our parameter estimation procedure to experimental data. We use the oxygen reduction in acidic media involvingmore » three charge transfer reactions and a chemical reaction as an example, and identify ways to isolate reaction currents for the individual processes in order to accurately estimate the exchange current densities.« less

Assessing Cognitive Performance in Badminton Players: A Reproducibility and Validity Study

PubMed Central

van de Water, Tanja; Faber, Irene; Elferink-Gemser, Marije

2017-01-01

Abstract Fast reaction and good inhibitory control are associated with elite sports performance. To evaluate the reproducibility and validity of a newly developed Badminton Reaction Inhibition Test (BRIT), fifteen elite (25 ± 4 years) and nine non-elite (24 ± 4 years) Dutch male badminton players participated in the study. The BRIT measured four components: domain-general reaction time, badminton-specific reaction time, domain-general inhibitory control and badminton-specific inhibitory control. Five participants were retested within three weeks on the badminton-specific components. Reproducibility was acceptable for badminton-specific reaction time (ICC = 0.626, CV = 6%) and for badminton-specific inhibitory control (ICC = 0.317, CV = 13%). Good construct validity was shown for badminton-specific reaction time discriminating between elite and non-elite players (F = 6.650, p < 0.05). Elite players did not outscore non-elite players on domain-general reaction time nor on both components of inhibitory control (p > 0.05). Concurrent validity for domain-general reaction time was good, as it was associated with a national ranking for elite (p = 0.70, p < 0.01) and non-elite (p = 0.70, p < 0.05) players. No relationship was found between the national ranking and badminton-specific reaction time, nor both components of inhibitory control (p > 0.05). In conclusion, reproducibility and validity of inhibitory control assessment was not confirmed, however, the BRIT appears a reproducible and valid measure of reaction time in badminton players. Reaction time measured with the BRIT may provide input for training programs aiming to improve badminton players’ performance. PMID:28210347

Assessing Cognitive Performance in Badminton Players: A Reproducibility and Validity Study.

PubMed

van de Water, Tanja; Huijgen, Barbara; Faber, Irene; Elferink-Gemser, Marije

2017-01-01

Fast reaction and good inhibitory control are associated with elite sports performance. To evaluate the reproducibility and validity of a newly developed Badminton Reaction Inhibition Test (BRIT), fifteen elite (25 ± 4 years) and nine non-elite (24 ± 4 years) Dutch male badminton players participated in the study. The BRIT measured four components: domain-general reaction time, badminton-specific reaction time, domain-general inhibitory control and badminton-specific inhibitory control. Five participants were retested within three weeks on the badminton-specific components. Reproducibility was acceptable for badminton-specific reaction time (ICC = 0.626, CV = 6%) and for badminton-specific inhibitory control (ICC = 0.317, CV = 13%). Good construct validity was shown for badminton-specific reaction time discriminating between elite and non-elite players (F = 6.650, p < 0.05). Elite players did not outscore non-elite players on domain-general reaction time nor on both components of inhibitory control (p > 0.05). Concurrent validity for domain-general reaction time was good, as it was associated with a national ranking for elite (p = 0.70, p < 0.01) and non-elite (p = 0.70, p < 0.05) players. No relationship was found between the national ranking and badminton-specific reaction time, nor both components of inhibitory control (p > 0.05). In conclusion, reproducibility and validity of inhibitory control assessment was not confirmed, however, the BRIT appears a reproducible and valid measure of reaction time in badminton players. Reaction time measured with the BRIT may provide input for training programs aiming to improve badminton players' performance.

Centrifugal Microfluidic System for Nucleic Acid Amplification and Detection.

PubMed

Miao, Baogang; Peng, Niancai; Li, Lei; Li, Zheng; Hu, Fei; Zhang, Zengming; Wang, Chaohui

2015-11-04

We report here the development of a rapid PCR microfluidic system comprising a double-shaft turntable and centrifugal-based disc that rapidly drives the PCR mixture between chambers set at different temperatures, and the bidirectional flow improved the space utilization of the disc. Three heating resistors and thermistors maintained uniform, specific temperatures for the denaturation, annealing, and extension steps of the PCR. Infrared imaging showed that there was little thermal interference between reaction chambers; the system enabled the cycle number and reaction time of each step to be independently adjusted. To validate the function and efficiency of the centrifugal microfluidic system, a 350-base pair target gene from the hepatitis B virus was amplified and quantitated by fluorescence detection. By optimizing the cycling parameters, the reaction time was reduced to 32 min as compared to 120 min for a commercial PCR machine. DNA samples with concentrations ranging from 10 to 10⁶ copies/mL could be quantitatively analyzed using this system. This centrifugal-based microfluidic platform is a useful system and possesses industrialization potential that can be used for portable diagnostics.

Modeling of the oxidation of methyl esters—Validation for methyl hexanoate, methyl heptanoate, and methyl decanoate in a jet-stirred reactor

PubMed Central

Glaude, Pierre Alexandre; Herbinet, Olivier; Bax, Sarah; Biet, Joffrey; Warth, Valérie; Battin-Leclerc, Frédérique

2013-01-01

The modeling of the oxidation of methyl esters was investigated and the specific chemistry, which is due to the presence of the ester group in this class of molecules, is described. New reactions and rate parameters were defined and included in the software EXGAS for the automatic generation of kinetic mechanisms. Models generated with EXGAS were successfully validated against data from the literature (oxidation of methyl hexanoate and methyl heptanoate in a jet-stirred reactor) and a new set of experimental results for methyl decanoate. The oxidation of this last species was investigated in a jet-stirred reactor at temperatures from 500 to 1100 K, including the negative temperature coefficient region, under stoichiometric conditions, at a pressure of 1.06 bar and for a residence time of 1.5 s: more than 30 reaction products, including olefins, unsaturated esters, and cyclic ethers, were quantified and successfully simulated. Flow rate analysis showed that reactions pathways for the oxidation of methyl esters in the low-temperature range are similar to that of alkanes. PMID:23710076

Centrifugal Microfluidic System for Nucleic Acid Amplification and Detection

PubMed Central

Miao, Baogang; Peng, Niancai; Li, Lei; Li, Zheng; Hu, Fei; Zhang, Zengming; Wang, Chaohui

2015-01-01

We report here the development of a rapid PCR microfluidic system comprising a double-shaft turntable and centrifugal-based disc that rapidly drives the PCR mixture between chambers set at different temperatures, and the bidirectional flow improved the space utilization of the disc. Three heating resistors and thermistors maintained uniform, specific temperatures for the denaturation, annealing, and extension steps of the PCR. Infrared imaging showed that there was little thermal interference between reaction chambers; the system enabled the cycle number and reaction time of each step to be independently adjusted. To validate the function and efficiency of the centrifugal microfluidic system, a 350-base pair target gene from the hepatitis B virus was amplified and quantitated by fluorescence detection. By optimizing the cycling parameters, the reaction time was reduced to 32 min as compared to 120 min for a commercial PCR machine. DNA samples with concentrations ranging from 10 to 106 copies/mL could be quantitatively analyzed using this system. This centrifugal-based microfluidic platform is a useful system and possesses industrialization potential that can be used for portable diagnostics. PMID:26556354

Monitoring biodiesel reactions of soybean oil and sunflower oil using ultrasonic parameters

NASA Astrophysics Data System (ADS)

Figueiredo, M. K. K.; Silva, C. E. R.; Alvarenga, A. V.; Costa-Félix, R. P. B.

2015-01-01

Biodiesel is an innovation that attempts to substitute diesel oil with biomass. The aim of this paper is to show the development of a real-time method to monitor transesterification reactions by using low-power ultrasound and pulse/echo techniques. The results showed that it is possible to identify different events during the transesterification process by using the proposed parameters, showing that the proposed method is a feasible way to monitor the reactions of biodiesel during its fabrication, in real time, and with relatively low- cost equipment.

Level density inputs in nuclear reaction codes and the role of the spin cutoff parameter

DOE PAGES

Voinov, A. V.; Grimes, S. M.; Brune, C. R.; ...

2014-09-03

Here, the proton spectrum from the 57Fe(α,p) reaction has been measured and analyzed with the Hauser-Feshbach model of nuclear reactions. Different input level density models have been tested. It was found that the best description is achieved with either Fermi-gas or constant temperature model functions obtained by fitting them to neutron resonance spacing and to discrete levels and using the spin cutoff parameter with much weaker excitation energy dependence than it is predicted by the Fermi-gas model.

Application of ADM1 for modeling of biogas production from anaerobic digestion of Hydrilla verticillata.

PubMed

Chen, Xiaojuan; Chen, Zhihua; Wang, Xun; Huo, Chan; Hu, Zhiquan; Xiao, Bo; Hu, Mian

2016-07-01

The present study focused on the application of anaerobic digestion model no. 1 (ADM1) to simulate biogas production from Hydrilla verticillata. Model simulation was carried out by implementing ADM1 in AQUASIM 2.0 software. Sensitivity analysis was used to select the most sensitive parameters for estimation using the absolute-relative sensitivity function. Among all the kinetic parameters, disintegration constant (kdis), hydrolysis constant of protein (khyd_pr), Monod maximum specific substrate uptake rate (km_aa, km_ac, km_h2) and half-saturation constants (Ks_aa, Ks_ac) affect biogas production significantly, which were optimized by fitting of the model equations to the data obtained from batch experiments. The ADM1 model after parameter estimation was able to well predict the experimental results of daily biogas production and biogas composition. The simulation results of evolution of organic acids, bacteria concentrations and inhibition effects also helped to get insight into the reaction mechanisms. Copyright © 2016. Published by Elsevier Ltd.

An experimental and modeling study of isothermal charge/discharge behavior of commercial Ni-MH cells

NASA Astrophysics Data System (ADS)

Pan, Y. H.; Srinivasan, V.; Wang, C. Y.

In this study, a previously developed nickel-metal hydride (Ni-MH) battery model is applied in conjunction with experimental characterization. Important geometric parameters, including the active surface area and micro-diffusion length for both electrodes, are measured and incorporated in the model. The kinetic parameters of the oxygen evolution reaction are also characterized using constant potential experiments. Two separate equilibrium equations for the Ni electrode, one for charge and the other for discharge, are determined to provide a better description of the electrode hysteresis effect, and their use results in better agreement of simulation results with experimental data on both charge and discharge. The Ni electrode kinetic parameters are re-calibrated for the battery studied. The Ni-MH cell model coupled with the updated electrochemical properties is then used to simulate a wide range of experimental discharge and charge curves with satisfactory agreement. The experimentally validated model is used to predict and compare various charge algorithms so as to provide guidelines for application-specific optimization.

Adenine specific DNA chemical sequencing reaction.

PubMed Central

Iverson, B L; Dervan, P B

1987-01-01

Reaction of DNA with K2PdCl4 at pH 2.0 followed by a piperidine workup produces specific cleavage at adenine (A) residues. Product analysis revealed the K2PdCl4 reaction involves selective depurination at adenine, affording an excision reaction analogous to the other chemical DNA sequencing reactions. Adenine residues methylated at the exocyclic amine (N6) react with lower efficiency than unmethylated adenine in an identical sequence. This simple protocol specific for A may be a useful addition to current chemical sequencing reactions. Images PMID:3671067

Novozyme 435-catalyzed asymmetric acylation of (R, S)-3-n- butylphthalide in hexane.

PubMed

He, Laping; Li, Cuiqin; Gao, Bing

2009-01-01

The asymmetric acylation of (R, S)-3-n-butylphthalide could be efficiently catalyzed by Novozyme 435. The effect of various reaction parameters such as water activity, temperature, molar ratio of acetic anhydride to (R, S)-3-n-butylphthalide, and reaction time on the asymmetric acylation were studied. The optimums of the reaction parameters were water activity 0.62, temperature 30 degrees C, molar ratio of acetic anhydride to (R, S)-3-n-butylphthalide 8:1, and reaction time 48 h, respectively. Under the optimum conditions, enantiopure 3-n-butylphthalide with an optical purity of 95.7% enantiomeric excess and 49.1% yield could be obtained. Furthermore, the enantiomeric excess of product was over 98%.

Direct conversion from Jerusalem artichoke to hydroxymethylfurfural (HMF) using the Fenton reaction.

PubMed

Seo, Yeong Hwan; Han, Jong-In

2014-05-15

A simple method for hydroxymethylfurfural (HMF) production from non-crop biomass of the Jerusalem artichoke was developed using the Fenton reaction, in a mixture of 2-butanol and water. Four parameters (temperature, reaction time, Fe(2+) concentration, and H2O2 concentration) were identified as experimental factors, and HMF yield was selected as the response parameter. The experimental factors were optimised by employing Response Surface Methodology (RSM). The maximum HMF yield, of 46%, was obtained with a reaction time of 90 min, Fe(2+) concentration of 1.3 mM, and 0.47 M of H2O2 at 180 °C. Copyright © 2014. Published by Elsevier Ltd.

Correlation Analysis of Reactivity in the Photo- and Electro-Reduction of Cobalt(III) Complexes in Binary Organic Solvent/Water Mixtures

NASA Astrophysics Data System (ADS)

Sivaraj, Kumarasamy; Elango, Kuppanagounder P.

2008-08-01

The photo- and electro-reduction of a series of cobalt(III) complexes of the type cis-β - [Co(trien)(RC6H4NH2)Cl]Cl2 with R = H, p-OMe, p-OEt, p-Me, p-Et, p-F, and m-Me has been studied in binary propan-2-ol/water mixtures. The redox potential (E1/2) and photo-reduction quantum yield (ΦCo(II)) data were correlated with solvent and structural parameters with the aim to shed some light on the mechanism of these reactions. The correlation of E1/2 and ΦCo(II) with macroscopic solvent parameters, viz. relative permittivity, indicated that the reactivity is influenced by both specific and non-specific solute-solvent interactions. The Kamlet-Taft solvatochromic comparison method was used to separate and quantify these effects: An increase in the percentage of organic cosolvent in the medium enhances both reduction processes, and there exists a good linear correlation between E1/2 and ΦCo(II), suggesting a similar solvation of the participants in these redox processes.

(Bio)Sensing Using Nanoparticle Arrays: On the Effect of Analyte Transport on Sensitivity.

PubMed

Lynn, N Scott; Homola, Jiří

2016-12-20

There has recently been an extensive amount of work regarding the development of optical, electrical, and mechanical (bio)sensors employing planar arrays of surface-bound nanoparticles. The sensor output for these systems is dependent on the rate at which analyte is transported to, and interacts with, each nanoparticle in the array. There has so far been little discussion on the relationship between the design parameters of an array and the interplay of convection, diffusion, and reaction. Moreover, current methods providing such information require extensive computational simulation. Here we demonstrate that the rate of analyte transport to a nanoparticle array can be quantified analytically. We show that such rates are bound by both the rate to a single NP and that to a planar surface (having equivalent size as the array), with the specific rate determined by the fill fraction: the ratio between the total surface area used for biomolecular capture with respect to the entire sensing area. We characterize analyte transport to arrays with respect to changes in numerous parameters relevant to experiment, including variation of the nanoparticle shape and size, packing density, flow conditions, and analyte diffusivity. We also explore how analyte capture is dependent on the kinetic parameters related to an affinity-based biosensor, and furthermore, we classify the conditions under which the array might be diffusion- or reaction-limited. The results obtained herein are applicable toward the design and optimization of all (bio)sensors based on nanoparticle arrays.

Driving Ability of HMX based Aluminized Explosive Affected by the Reaction Degree of Aluminum Powder

NASA Astrophysics Data System (ADS)

Duan, Yingliang

2017-06-01

Due to the time scale of aluminum reaction, the detonation process of the aluminized explosive becomes very complex, and there is less agreement on the reaction mechanism of aluminum powder. If the reaction of aluminum occurs in the reaction zone, the energy released will further strengthen the work ability of detonation wave. So it is very important for characterizing the detonation parameters and detonation driving ability to accurately understand the role of aluminum powder in the reaction zone. In this paper, detonation driving process of HMX based aluminized explosive was studied by cylinder test, obtaining the expansion track of cylinder wall. In order to further research the reaction degree (λ) of aluminum in the reaction zone, the thermodynamic program VHL was used to calculate the detonation process at different reaction degrees, obtaining the parameters of detonation products thermodynamic state. Using the dynamic software LS-DYNA and the JWL equation of state by fitting the pressure and relative volume relationship, the cylinder test was simulated. Compared with the experimental results, when the reaction degree is 20%, the driving ability is found to be in agreement with measured ones. It is concluded that the driving ability of HMX based aluminized explosive can be more accurately characterized by considering the reaction degree of aluminum powder in the reaction zone.

Dry mechanochemical synthesis of hydroxyapatites from DCPD and CaO: influence of instrumental parameters on the reaction kinetics.

PubMed

Mochales, Carolina; El Briak-BenAbdeslam, Hassane; Ginebra, Maria Pau; Terol, Alain; Planell, Josep A; Boudeville, Philippe

2004-01-01

Mechanochemistry is a possible route to synthesize calcium deficient hydroxyapatite (CDHA) with an expected molar calcium-to-phosphate (Ca/P) ratio +/-0.01. To optimize the experimental conditions of CDHA preparation from dicalcium phosphate dihydrate (DCPD) and calcium oxide by dry mechanosynthesis reaction, we performed the kinetic study varying some experimental parameters. This kinetic study was carried out with two different planetary ball mills (Retsch or Fritsch Instuments). Results obtained with the two mills led to the same conclusions although the values of the rate constants of DCPD disappearance and times for complete reaction were very different. Certainly, the origin of these differences was from the mills used, thus we investigated the influence of instrumental parameters such as the mass and the surface area of the balls or the rotation velocity on the mechanochemical reaction kinetics of DCPD with CaO. Results show that the DCPD reaction rate constant and the inverse of the time for complete disappearance of CaO both vary linearly with (i) the square of the rotation velocity, (ii) the square of eccentricity of the vial on the rotating disc and (iii) the product of the mass by the surface area of the balls. These observations comply with theoretical models developed for mechanical alloying. The consideration of these four parameters allows the transposition of experimental conditions from one mill to another or the comparison between results obtained with different planetary ball mills. These instrumental parameters have to be well described in papers concerning mechanochemistry or when grinding is an important stage in a process.

Effect of electric signal frequency and form on physical-chemical oxidation of organic wastes

NASA Astrophysics Data System (ADS)

Morozov, Yegor; Tikhomirov, Alexander A.; Trifonov, Sergey V.; Kudenko, D.. Yurii A.

The behavior conditions of physical-chemical reactions securing organic wastes’ oxidation in H _{2}O _{2} aqueous medium aimed at an increase of mass exchange processes in a life support system (LSS) for a space purpose have been under study. The character of dependence of organic wastes oxidation rate in H _{2}O _{2} aqueous medium, activated with alternating current of different frequency and form have been considered. Ways of those parameters optimization for the purpose to efficiently increase the physical-chemical decomposition of organic wastes in LSS have been proposed. Specifically, power consumption and reaction time of wastes mineralization have been determined to reduce more than twice. Involvement ways of mineralized organic wastes received in intrasystem mass exchange have been shown. Application feasibility of the obtained results both for space and terrestrial purpose has been discussed. Key words: life support sustem, mineralization, turnover, frequency, organic wastes

Use of Antibody to Membrane Adenosine Triphosphatase in the Study of Bacterial Relationships1

PubMed Central

Whiteside, Theresa L.; De Siervo, August J.; Salton, Milton R. J.

1971-01-01

An antiserum to Ca2+-activated adenosine triphosphatase from membranes of Micrococcus lysodeikticus cross-reacted in agar gels with membrane adenosine triphosphatases from other pigmented micrococci and related species. Species of Micrococcus and Sarcina showed different levels of inhibition of adenosine triphosphatase activities in heterologous reactions with antiserum. Inter- and intraspecific relationships based on the inhibition reaction were compared with an independent parameter, namely the quantitative and qualitative composition of the bacterial membrane phospholipids and fatty acids. The guanine plus cytosine contents in the deoxyribonucleic acid of the species studied correlated well with the serological cross-reactivity of adenosine triphosphatases from their membranes. The types of cross-bridges found in the peptidoglycans of these cocci were also compared with the other properties. The results suggest that an antiserum specific for a major membrane protein may be a reliable and most useful adjunct in studying bacterial serotaxonomy. Images PMID:4323299

Use of antibody to membrane adenosine triphosphatase in the study of bacterial relatioships.

PubMed

Whiteside, T L; De Siervo, A J; Salton, M R

1971-03-01

An antiserum to Ca(2+)-activated adenosine triphosphatase from membranes of Micrococcus lysodeikticus cross-reacted in agar gels with membrane adenosine triphosphatases from other pigmented micrococci and related species. Species of Micrococcus and Sarcina showed different levels of inhibition of adenosine triphosphatase activities in heterologous reactions with antiserum. Inter- and intraspecific relationships based on the inhibition reaction were compared with an independent parameter, namely the quantitative and qualitative composition of the bacterial membrane phospholipids and fatty acids. The guanine plus cytosine contents in the deoxyribonucleic acid of the species studied correlated well with the serological cross-reactivity of adenosine triphosphatases from their membranes. The types of cross-bridges found in the peptidoglycans of these cocci were also compared with the other properties. The results suggest that an antiserum specific for a major membrane protein may be a reliable and most useful adjunct in studying bacterial serotaxonomy.

Pattern formation in three-dimensional reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Callahan, T. K.; Knobloch, E.

1999-08-01

Existing group theoretic analysis of pattern formation in three dimensions [T.K. Callahan, E. Knobloch, Symmetry-breaking bifurcations on cubic lattices, Nonlinearity 10 (1997) 1179-1216] is used to make specific predictions about the formation of three-dimensional patterns in two models of the Turing instability, the Brusselator model and the Lengyel-Epstein model. Spatially periodic patterns having the periodicity of the simple cubic (SC), face-centered cubic (FCC) or body-centered cubic (BCC) lattices are considered. An efficient center manifold reduction is described and used to identify parameter regimes permitting stable lamellæ, SC, FCC, double-diamond, hexagonal prism, BCC and BCCI states. Both models possess a special wavenumber k* at which the normal form coefficients take on fixed model-independent ratios and both are described by identical bifurcation diagrams. This property is generic for two-species chemical reaction-diffusion models with a single activator and inhibitor.

Temporal cross-correlation asymmetry and departure from equilibrium in a bistable chemical system.

PubMed

Bianca, C; Lemarchand, A

2014-06-14

This paper aims at determining sustained reaction fluxes in a nonlinear chemical system driven in a nonequilibrium steady state. The method relies on the computation of cross-correlation functions for the internal fluctuations of chemical species concentrations. By employing Langevin-type equations, we derive approximate analytical formulas for the cross-correlation functions associated with nonlinear dynamics. Kinetic Monte Carlo simulations of the chemical master equation are performed in order to check the validity of the Langevin equations for a bistable chemical system. The two approaches are found in excellent agreement, except for critical parameter values where the bifurcation between monostability and bistability occurs. From the theoretical point of view, the results imply that the behavior of cross-correlation functions cannot be exploited to measure sustained reaction fluxes in a specific nonlinear system without the prior knowledge of the associated chemical mechanism and the rate constants.

[How aliphatic alcohols and ph affect reactional capability of the horse blood serum cholinesterase at its interaction with organophosphorus inhibitors].

PubMed

Basova, N E; Kormilitsin, B N; Perchenok, A Iu; Rozengart, E V; Saakov, V S; Suvorov, A A

2013-01-01

There was studied action of aliphatic alcohols (ethanol, propanol, isopropanol, n-butanol, isobutanol, secbutanol, tretbetanol) and pH on various kinds of reactional capability the serum cholinesterase. At the alcohols-affected inhibition of the cholinesterase hydrolytic activity, the determining role was played not the total number carbon atoms in the alcohol molecule, but by the "effective length" of the carbohydrate chain. The fact that the presence of alcohols did not affect parameters of the reverse cholinesterase inhibition with onium ions tetramethylammonium and choline allows suggesting the absence of effect solvents on specific acetylcholine sorption in the enzyme active center. With aid of two rows of hydrophobic organophosphorus inhibitors (OPI), we have managed to estimate both the degree and the character itself of the modifying action of alcohols and pH on the process of irreversible inhibition of serum cholinesterase.

Kinetics and mechanism of degradation of some 2-sulfanilamidopyrimidine derivatives. Part VI. The use of Hammett equation for kinetic investigation of 2-sulfanilamidopyrimidine derivatives hydrolysis.

PubMed

Zajac, M

1977-01-01

General, k, and specific, k1 and k2, first-order rate constants for the parallel reaction of hydrolysis catalized by H+ ions were estimated for sulfadiazine (I), sulfamerazine (II), sulfadimidine (III), sulfaperine (IV) and sulfamethoxydiazine (V), hydrolyzed in 1 mole/dm3 HCl at 333, 343, 355 and 363 K. General first-order rate constants for the spontaneous hydrolysis of I--V in borate buffer pH 9.20 at 403, 411 and 418 K were also determined. Thermodynamic parameters of the reaction (delta Ha, deltaH not equal to, deltaS not equal to, deltaG not equal to and log A) were calculated. The effect of substituents in positions 4, 5 and 6 of the pyrimidine ring on the rate of hydrolysis was interpreted in terms of Hammett equation.

Investigations on the Maillard reaction of dextrins during aging of Pilsner type beer.

PubMed

Rakete, Stefan; Klaus, Alexander; Glomb, Marcus A

2014-10-08

Although Maillard reaction plays a pivotal role during preparation of food, only few investigations concerning the role of carbohydrate degradation in beer aging have been carried out. The formation of Maillard specific precursor structures and their follow-up products during degradation of low molecular carbohydrate dextrins in the presence of proline and lysine was studied in model incubations and in beer. Twenty-one α-dicarbonyl compounds were identified and quantitated as reactive intermediates. The oxidative formation of 3-deoxypentosone as the precursor of furfural from oligosaccharides was verified. N-Carboxymethylproline and N-formylproline were established as novel proline derived Maillard advanced glycation end products. Formation of N-carboxymethylproline and furfural responded considerably to the presence of oxygen and was positively correlated to aging of Pilsner type beer. The present study delivers an in-depth view on the mechanisms behind the formation of beer relevant aging parameters.

The stability of N-[2-(4-o-fluorophenylpiperazin-1-yl)ethyl]-2,5-dimethyl-1 -phenylpyrrole-3,4-dicarboximide in aqueous-organic solutions.

PubMed

Zajac, Marianna; Sobczak, Agnieszka; Malinka, Wiesław; Redzicka, Aleksandra

2010-01-01

The first-order reaction of solvolysis of N-[2-(4-o-fluorophenylpiperazin-1-yl)ethyl]-2,5-dimethyl-1-phenylpyrrole-3,4-dicarboximide (PDI) was investigated as a function of pH at 333, 328, 323, 318 and 308 K in the pH range 1.11 - 12.78. The decomposition of PDI was followed by the HPLC method (Nucleosil 10-C8 column (250 x 4 mm I.D., dp = 10 microm), mobile phase: 0.018 mol/L ammonia acetate - acetonitrile (40: 60 v/v), UV detector: 240 nm, flow rate: 1 mL/min. Specific acid-base catalysis involves solvolysis of the undissociated molecules of PDI catalyzed by hydroxide ions and spontaneous solvolysis of the undissociated and monoprotonated forms of PDI under the influence of solvents. The thermodynamic parameters of the reactions--activation energy (E(a)), enthalpy (DH(#)), entropy (DS(#))--were calculated.

OSP Parameters and the Cognitive Component of Reaction Time to a Missing Stimulus: Linking Brain and Behavior

ERIC Educational Resources Information Center

Hernandez, Oscar H.; Vogel-Sprott, Muriel

2009-01-01

This within-subjects experiment tested the relationship between the premotor (cognitive) component of reaction time (RT) to a missing stimulus and parameters of the omitted stimulus potential (OSP) brain wave. Healthy young men (N = 28) completed trials with an auditory stimulus that recurred at 2 s intervals and ceased unpredictably. Premotor RT…

A novel high-throughput format assay for HIV-1 integrase strand transfer reaction using magnetic beads.

PubMed

He, Hong-qiu; Ma, Xiao-hui; Liu, Bin; Chen, Wei-zu; Wang, Cun-xin; Cheng, Shao-hui

2008-03-01

To develop a novel high-throughput format assay to monitor the integrase (IN) strand transfer (ST) reaction in vitro and apply it to a reaction character study and the identification of antiviral drugs. The donor DNA duplex, with a sequence identical to the U5 end of HIV-1 long terminal repeats, is labeled at its 5' end with biotin (BIO). The target DNA duplex is labeled at its 3' end with digoxin (DIG). IN mediates the integration of donor DNA into target DNA and results in a 5' BIO and 3' DIG-labeled duplex DNA product. Streptavidin-coated magnetic beads were used to capture the product, and the amount of DIG was measured as the ST reaction product. The assay was optimized in 96-well microplate format for high-throughput screening purpose. Moreover, the assay was applied in a ST reaction character study, and the efficiency of the assay in the identification of antiviral compounds was tested. The end-point values, measured as absorbance at 405 nm was approximately 1.5 for the IN-mediated ST reaction as compared with no more than 0.05 of background readings. The ST reaction character and the half maximal inhibitory concentration (IC50) values of 2 known IN inhibitors obtained in our assay were similar to previously reported results using other assays. The evaluation parameter Z' factor for this assay ranged from 0.6 to 0.9. The assay presented here has been proven to be rapid, sensitive, and specific for the detection of IN ST activity, the reaction character study, as well as for the identification of antiviral drugs targeting IN.

Intrinsic thermodynamics of ethoxzolamide inhibitor binding to human carbonic anhydrase XIII

PubMed Central

2012-01-01

Background Human carbonic anhydrases (CAs) play crucial role in various physiological processes including carbon dioxide and hydrocarbon transport, acid homeostasis, biosynthetic reactions, and various pathological processes, especially tumor progression. Therefore, CAs are interesting targets for pharmaceutical research. The structure-activity relationships (SAR) of designed inhibitors require detailed thermodynamic and structural characterization of the binding reaction. Unfortunately, most publications list only the observed thermodynamic parameters that are significantly different from the intrinsic parameters. However, only intrinsic parameters could be used in the rational design and SAR of the novel compounds. Results Intrinsic binding parameters for several inhibitors, including ethoxzolamide, trifluoromethanesulfonamide, and acetazolamide, binding to recombinant human CA XIII isozyme were determined. The parameters were the intrinsic Gibbs free energy, enthalpy, entropy, and the heat capacity. They were determined by titration calorimetry and thermal shift assay in a wide pH and temperature range to dissect all linked protonation reaction contributions. Conclusions Precise determination of the inhibitor binding thermodynamics enabled correct intrinsic affinity and enthalpy ranking of the compounds and provided the means for SAR analysis of other rationally designed CA inhibitors. PMID:22676044

A kinetic and thermochemical database for organic sulfur and oxygen compounds.

PubMed

Class, Caleb A; Aguilera-Iparraguirre, Jorge; Green, William H

2015-05-28

Potential energy surfaces and reaction kinetics were calculated for 40 reactions involving sulfur and oxygen. This includes 11 H2O addition, 8 H2S addition, 11 hydrogen abstraction, 7 beta scission, and 3 elementary tautomerization reactions, which are potentially relevant in the combustion and desulfurization of sulfur compounds found in various fuel sources. Geometry optimizations and frequencies were calculated for reactants and transition states using B3LYP/CBSB7, and potential energies were calculated using CBS-QB3 and CCSD(T)-F12a/VTZ-F12. Rate coefficients were calculated using conventional transition state theory, with corrections for internal rotations and tunneling. Additionally, thermochemical parameters were calculated for each of the compounds involved in these reactions. With few exceptions, rate parameters calculated using the two potential energy methods agreed reasonably, with calculated activation energies differing by less than 5 kJ mol(-1). The computed rate coefficients and thermochemical parameters are expected to be useful for kinetic modeling.

Use of Specific IgE and Skin Prick Test to Determine Clinical Reaction Severity

PubMed Central

Ta, Von; Weldon, Brittany; Yu, Grace; Humblet, Olivier; Neale-May, Susan; Nadeau, Kari

2012-01-01

Aims To determine whether specific IgE and skin prick test correlate better in predicting reaction severity during a double-blinded placebo controlled food challenge (DBPCFC) for egg, milk, and multiple tree nut allergens. Study design Prospective study. Place and Duration of Study Department of Pediatrics, Stanford University School of Medicine, August 2009 and ongoing. Methodology We examined the reaction severity of twenty-four subjects to nine possible food allergens: milk, egg, almond, cashew, hazelnut, peanut, sesame, pecan and walnut. Specific IgE and SPT were performed before each DBPCFC. DBPCFC results were classified into mild (1), moderate (2), or severe (3) reactions using a modified Bock’s criteria. Results Twenty four subjects underwent a total of 80 DBPCFC. Eighty percent of all DBPCFCs resulted in a positive reaction. A majority, 71%, were classified as mild. No reactions occurred with a SPT of zero mm while three reactions occurred with a negative specific IgE. All reactions were reversible with medication. Conclusion These data suggest that SPT and specific IgE levels are not associated with reaction severity (p<0.64 and 0.27, respectively). We also found that combining specific IgE and SPT improved specificity but did not help to achieve clinically useful sensitivity. For instance, an SPT > 5mm had a sensitivity of 91% and specificity of 50%. Combining SPT > 5mm and IgE > 7 resulted in a reduced sensitivity of 64%. Unexpectedly, a history of anaphylaxis 70% (n=17) was not predictive of anaphylaxis on challenge 4% (n=2). PMID:22993721

Synthesis and radiolabeling of chelator-RNA aptamer bioconjugates with copper-64 for targeted molecular imaging

PubMed Central

Rockey, William M.; Huang, Ling; Kloepping, Kyle C.; Baumhover, Nicholas J.; Giangrande, Paloma H.; Schultz, Michael K.

2014-01-01

Ribonucleic acid (RNA) aptamers with high affinity and specificity for cancer-specific cell-surface antigens are promising reagents for targeted molecular imaging of cancer using positron emission tomography (PET). For this application, aptamers must be conjugated to chelators capable of coordinating PET-radionuclides (e.g. copper-64, 64Cu) to enable radiolabeling for in vivo imaging of tumors. This study investigates the choice of chelator and radiolabeling parameters such as pH and temperature for the development of 64Cu-labeled RNA-based targeted agents for PET imaging. The characterization and optimization of labeling conditions are described for four chelator-aptamer complexes. Three commercially available bifunctional macrocyclic chelators (1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid mono N-hydroxysuccinimide [DOTA-NHS]; S-2-(4-isothiocyanatobenzyl)-1,4,7-triazacyclononane-1,4,7-triacetic acid [p-SCN-Bn-NOTA]; and p-SCN-Bn-3,6,9,15-tetraazabicyclo [9.3.1]pentadeca-1(15),11,13-triene-3,6,9-triacetic acid [p-SCN-Bn-PCTA]), as well as the polyamino-macrocyclic diAmSar (3,6,10,13,16,19-hexaazabicyclo[6.6.6] icosane-1,8-diamine) were conjugated to A10–3.2, a RNA aptamer which has been shown to bind specifically to a prostate cancer-specific cell-surface antigen (PSMA). Although a commercial bifunctional version of diAmSar was not available, RNA conjugation with this chelator was achieved in a two-step reaction by the addition of a disuccinimidyl suberate linker. Radiolabeling parameters (e.g. pH, temperature, and time) for each chelator-RNA conjugate were assessed in order to optimize specific activity and RNA stability. Furthermore, the radiolabeled chelator-coupled RNA aptamers were evaluated for binding specificity to their target antigen. In summary, key parameters were established for optimal radiolabeling of RNA aptamers for eventual PET imaging with 64Cu. PMID:21658962

Hydrothermal Synthesis of Analcime from Kutingkeng Formation Mudstone

NASA Astrophysics Data System (ADS)

Hsiao, Yin-Hsiu; Chen, Kuan-Ting; Ray, Dah-Tong

2015-04-01

In southwest of Taiwan, the foothill located in Tainan-Kaohsiung city is the exposed area of Pliocene strata to early Pleistocene strata. The strata are about a depth of five thousand, named as Kutigkeng Formation. The outcrop of Kutigkeng Formation is typical badlands, specifically called 'Moon World.' It is commonly known as no important economic applications of agricultural land. The mineral compositions of Kutingkeng Formation are quartz, clay minerals and feldspar. The clay minerals consist of illite, clinochlore and swelling clays. To study how the phase and morphology of analcime formed by hydrothermal synthesis were affected, analcime was synthesized from the mudstone of Kutinkeng Formation with microwave hydrothermal reaction was investigated. The parameters of the experiment were the reaction temperature, the concentration of mineralizer, solids/liquid ratio and time. The sodium silicate (Na2SiO3) were used as mineralizer. The results showed that the analcime could be synthesized by hydrothermal reaction above 180° from Kutinkeng Formation mudstone samples. At the highest temperature (240°) of this study, the high purity analcime could be produced. When the concentration of Na2SiO3=3~6M, analcime could be synthesized at 240°. The best solids/liquid ratio was approximate 1 to 5. The hydrothermal reaction almost was completed after 4 hours.

Biogeochemical metabolic modeling of methanogenesis by Methanosarcina barkeri

NASA Astrophysics Data System (ADS)

Jensvold, Z. D.; Jin, Q.

2015-12-01

Methanogenesis, the biological process of methane production, is the final step of natural organic matter degradation. In studying natural methanogenesis, important questions include how fast methanogenesis proceeds and how methanogens adapt to the environment. To address these questions, we propose a new approach - biogeochemical reaction modeling - by simulating the metabolic networks of methanogens. Biogeochemical reaction modeling combines geochemical reaction modeling and genome-scale metabolic modeling. Geochemical reaction modeling focuses on the speciation of electron donors and acceptors in the environment, and therefore the energy available to methanogens. Genome-scale metabolic modeling predicts microbial rates and metabolic strategies. Specifically, this approach describes methanogenesis using an enzyme network model, and computes enzyme rates by accounting for both the kinetics and thermodynamics. The network model is simulated numerically to predict enzyme abundances and rates of methanogen metabolism. We applied this new approach to Methanosarcina barkeri strain fusaro, a model methanogen that makes methane by reducing carbon dioxide and oxidizing dihydrogen. The simulation results match well with the results of previous laboratory experiments, including the magnitude of proton motive force and the kinetic parameters of Methanosarcina barkeri. The results also predict that in natural environments, the configuration of methanogenesis network, including the concentrations of enzymes and metabolites, differs significantly from that under laboratory settings.

A novel simulation theory and model system for multi-field coupling pipe-flow system

NASA Astrophysics Data System (ADS)

Chen, Yang; Jiang, Fan; Cai, Guobiao; Xu, Xu

2017-09-01

Due to the lack of a theoretical basis for multi-field coupling in many system-level models, a novel set of system-level basic equations for flow/heat transfer/combustion coupling is put forward. Then a finite volume model of quasi-1D transient flow field for multi-species compressible variable-cross-section pipe flow is established by discretising the basic equations on spatially staggered grids. Combining with the 2D axisymmetric model for pipe-wall temperature field and specific chemical reaction mechanisms, a finite volume model system is established; a set of specific calculation methods suitable for multi-field coupling system-level research is structured for various parameters in this model; specific modularisation simulation models can be further derived in accordance with specific structures of various typical components in a liquid propulsion system. This novel system can also be used to derive two sub-systems: a flow/heat transfer two-field coupling pipe-flow model system without chemical reaction and species diffusion; and a chemical equilibrium thermodynamic calculation-based multi-field coupling system. The applicability and accuracy of two sub-systems have been verified through a series of dynamic modelling and simulations in earlier studies. The validity of this system is verified in an air-hydrogen combustion sample system. The basic equations and the model system provide a unified universal theory and numerical system for modelling and simulation and even virtual testing of various pipeline systems.

Computational intelligence-based polymerase chain reaction primer selection based on a novel teaching-learning-based optimisation.

PubMed

Cheng, Yu-Huei

2014-12-01

Specific primers play an important role in polymerase chain reaction (PCR) experiments, and therefore it is essential to find specific primers of outstanding quality. Unfortunately, many PCR constraints must be simultaneously inspected which makes specific primer selection difficult and time-consuming. This paper introduces a novel computational intelligence-based method, Teaching-Learning-Based Optimisation, to select the specific and feasible primers. The specified PCR product lengths of 150-300 bp and 500-800 bp with three melting temperature formulae of Wallace's formula, Bolton and McCarthy's formula and SantaLucia's formula were performed. The authors calculate optimal frequency to estimate the quality of primer selection based on a total of 500 runs for 50 random nucleotide sequences of 'Homo species' retrieved from the National Center for Biotechnology Information. The method was then fairly compared with the genetic algorithm (GA) and memetic algorithm (MA) for primer selection in the literature. The results show that the method easily found suitable primers corresponding with the setting primer constraints and had preferable performance than the GA and the MA. Furthermore, the method was also compared with the common method Primer3 according to their method type, primers presentation, parameters setting, speed and memory usage. In conclusion, it is an interesting primer selection method and a valuable tool for automatic high-throughput analysis. In the future, the usage of the primers in the wet lab needs to be validated carefully to increase the reliability of the method.

Steady state and transient simulation of anion exchange membrane fuel cells

NASA Astrophysics Data System (ADS)

Dekel, Dario R.; Rasin, Igal G.; Page, Miles; Brandon, Simon

2018-01-01

We present a new model for anion exchange membrane fuel cells. Validation against experimental polarization curve data is obtained for current densities ranging from zero to above 2 A cm-2. Experimental transient data is also successfully reproduced. The model is very flexible and can be used to explore the system's sensitivity to a wide range of material properties, cell design specifications, and operating parameters. We demonstrate the impact of gas inlet relative humidity (RH), operating current density, ionomer loading and ionomer ion exchange capacity (IEC) values on cell performance. In agreement with the literature, high air RH levels are shown to improve cell performance. At high current densities (>1 A cm-2) this effect is observed to be especially significant. Simulated hydration number distributions across the cell reveal the related critical dependence of cathode hydration on air RH and current density values. When exploring catalyst layer design, optimal intermediate ionomer loading values are demonstrated. The benefits of asymmetric (cathode versus anode) electrode design are revealed, showing enhanced performance using higher cathode IEC levels. Finally, electrochemical reaction profiles across the electrodes uncover inhomogeneous catalyst utilization. Specifically, at high current densities the cathodic reaction is confined to a narrow region near the membrane.

Strategic enzyme patterning for microfluidic biofuel cells

NASA Astrophysics Data System (ADS)

Kjeang, E.; Sinton, D.; Harrington, D. A.

The specific character of biological enzyme catalysts enables combined fuel and oxidant channels and simplified non-compartmentalized fuel cell assemblies. In this work, a microstructured enzymatic biofuel cell architecture is proposed, and species transport phenomena combined with consecutive chemical reactions are studied computationally in order to provide guidelines for optimization. This is the first computational study of this technology, and a 2D CFD model for species transport coupled with laminar fluid flow and Michaelis-Menten enzyme kinetics is established. It is shown that the system is reaction rate limited, indicating that enzyme specific turnover numbers are key parameters for biofuel cell performance. Separated and mixed enzyme patterns in different proportions are analyzed for various Peclet numbers. High fuel utilization is achieved in the diffusion dominated and mixed species transport regimes with separated enzymes arranged in relation to individual turnover rates. However, the Peclet number has to be above a certain threshold value to obtain satisfying current densities. The mixed transport regime is particularly attractive while current densities are maintained close to maximum levels. Optimum performance is achieved by mixed enzyme patterning tailored with respect to individual turnover rates, enabling high current densities combined with nearly complete fuel utilization.

Evolution of a chemically reacting plume in a ventilated room

NASA Astrophysics Data System (ADS)

Conroy, D. T.; Smith, Stefan G. Llewellyn; Caulfield, C. P.

2005-08-01

The dynamics of a second-order chemical reaction in an enclosed space driven by the mixing produced by a turbulent buoyant plume are studied theoretically, numerically and experimentally. An isolated turbulent buoyant plume source is located in an enclosure with a single external opening. Both the source and the opening are located at the bottom of the enclosure. The enclosure is filled with a fluid of a given density with a fixed initial concentration of a chemical. The source supplies a constant volume flux of fluid of different density containing a different chemical of known and constant concentration. These two chemicals undergo a second-order non-reversible reaction, leading to the creation of a third product chemical. For simplicity, we restrict attention to the situation where the reaction process does not affect the density of the fluids involved. Because of the natural constraint of volume conservation, fluid from the enclosure is continually vented. We study the evolution of the various chemical species as they are advected by the developing ventilated filling box process within the room that is driven by the plume dynamics. In particular, we study both the mean and vertical distributions of the chemical species as a function of time within the room. We compare the results of analogue laboratory experiments with theoretical predictions derived from reduced numerical models, and find excellent agreement. Important parameters for the behaviour of the system are associated with the source volume flux and specific momentum flux relative to the source specific buoyancy flux, the ratio of the initial concentrations of the reacting chemical input in the plume and the reacting chemical in the enclosed space, the reaction rate of the chemicals and the aspect ratio of the room. Although the behaviour of the system depends on all these parameters in a non-trivial way, in general the concentration within the room of the chemical input at the isolated source passes through three distinct phases. Initially, as the source fluid flows into the room, the mean concentration of the input chemical increases due to the inflow, with some loss due to the reaction with the chemical initially within the room. After a finite time, the layer of fluid contaminated by the inflow reaches the opening to the exterior at the base of the room. During an ensuing intermediate phase, the rate of increase in the concentration of the input chemical then drops non-trivially, due to the extra sink for the input chemical of the outflow through the opening. During this intermediate stage, the concentration of the input chemical continues to rise, but at a rate that is reduced due to the reaction with the fluid in the room. Ultimately, all the fluid (and hence the chemical) that was originally within the room is lost, both through reaction and outflow through the opening, and the room approaches its final steady state, being filled completely with source fluid.

Gelatin-specific humoral and cellular immune responses in children with immediate- and nonimmediate-type reactions to live measles, mumps, rubella, and varicella vaccines.

PubMed

Kumagai, T; Yamanaka, T; Wataya, Y; Umetsu, A; Kawamura, N; Ikeda, K; Furukawa, H; Kimura, K; Chiba, S; Saito, S; Sugawara, N; Kurimoto, F; Sakaguchi, M; Inouye, S

1997-07-01

This study was designed to investigate the development of both cellular and humoral immune responses to gelatin in patients with vaccine-related immediate and nonimmediate reactions. Our purpose was to define the nature of the responses in the different clinical states. Six patients with immediate reactions and 21 patients with nonimmediate reactions after inoculation of various live vaccines were studied. Measurement of gelatin-specific IgE was performed in all subjects. Gelatin-specific T-cell responses detected by an in vitro lymphocyte proliferation assay and by an assay for IL-2 responsiveness were investigated to compare the immune response in patients with the two types of reaction. All six patients with immediate reactions had IgE responses to gelatin, whereas none of the 21 patients with nonimmediate reactions had any anti-gelatin IgE. All of the six patients with immediate reactions and 17 of the 21 patients with nonimmediate reactions exhibited positive T-lymphocyte responses specific to gelatin. Immediate and nonimmediate reactions are caused by different types of allergy to gelatin, and cell-mediated immunity to gelatin may play an important role in the pathogenesis of nonimmediate reactions.

Testing and evaluation of the LES-6 pulsed plasma thruster by means of a torsion pendulum system

NASA Technical Reports Server (NTRS)

Hamidian, J. P.; Dahlgren, J. B.

1973-01-01

Performance characteristics of the LES-6 pulsed plasma thruster over a range of input conditions were investigated by means of a torsion pendulum system. Parameters of particular interest included the impulse bit and time average thrust (and their repeatability), specific impulse, mass ablated per discharge, specific thrust, energy per unit area, efficiency, and variation of performance with ignition command rate. Intermittency of the thruster as affected by input energy and igniter resistance were also investigated. Comparative experimental data correlation with the data presented. The results of these tests indicate that the LES-6 thruster, with some identifiable design improvements, represents an attractive reaction control thruster for attitude contol applications on long-life spacecraft requiring small metered impulse bits for precise pointing control of science instruments.

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

PubMed

Cotten, Cameron; Reed, Jennifer L

2013-01-30

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

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

PubMed Central

2013-01-01

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

Biconvection flow of Carreau fluid over an upper paraboloid surface: A computational study

NASA Astrophysics Data System (ADS)

Khan, Mair; Hussain, Arif; Malik, M. Y.; Salahuddin, T.

Present article explored the physical characteristics of biconvection effects on the MHD flow of Carreau nanofluid over upper horizontal surface of paraboloid revolution along with chemical reaction. The concept of the Carreau nanofluid was introduced the new parameterization achieve the momentum governing equation. Using similarity transformed, the governing partial differential equations are converted into the ordinary differential equations. The obtained governing equations are solved computationally by using implicit finite difference method known as the Keller box technique. The numerical solutions are obtained for the velocity, temperature, concentration, friction factor, local heat and mass transfer coefficients by varying controlling parameters i.e. Biconvection parameter, fluid parameter, Weissenberg number, Hartmann number, Prandtl number, Brownian motion parameter, thermophoresis parameter, Lewis number and chemical reaction parameter. The obtained results are discussed via graphs and tables.

Numerical Problem Solving Using Mathcad in Undergraduate Reaction Engineering

ERIC Educational Resources Information Center

Parulekar, Satish J.

2006-01-01

Experience in using a user-friendly software, Mathcad, in the undergraduate chemical reaction engineering course is discussed. Example problems considered for illustration deal with simultaneous solution of linear algebraic equations (kinetic parameter estimation), nonlinear algebraic equations (equilibrium calculations for multiple reactions and…

40 CFR 264.98 - Detection monitoring program.

Code of Federal Regulations, 2010 CFR

2010-07-01

... conductance, total organic carbon, or total organic halogen), waste constituents, or reaction products that... reaction products in the unsaturated zone beneath the waste management area; (3) The detectability of indicator parameters, waste constituents, and reaction products in ground water; and (4) The concentrations...

Substrate specificity and subcellular localization of the aldehyde-alcohol redox-coupling reaction in carp cones.

PubMed

Sato, Shinya; Fukagawa, Takashi; Tachibanaki, Shuji; Yamano, Yumiko; Wada, Akimori; Kawamura, Satoru

2013-12-20

Our previous study suggested the presence of a novel cone-specific redox reaction that generates 11-cis-retinal from 11-cis-retinol in the carp retina. This reaction is unique in that 1) both 11-cis-retinol and all-trans-retinal were required to produce 11-cis-retinal; 2) together with 11-cis-retinal, all-trans-retinol was produced at a 1:1 ratio; and 3) the addition of enzyme cofactors such as NADP(H) was not necessary. This reaction is probably part of the reactions in a cone-specific retinoid cycle required for cone visual pigment regeneration with the use of 11-cis-retinol supplied from Müller cells. In this study, using purified carp cone membrane preparations, we first confirmed that the reaction is a redox-coupling reaction between retinals and retinols. We further examined the substrate specificity, reaction mechanism, and subcellular localization of this reaction. Oxidation was specific for 11-cis-retinol and 9-cis-retinol. In contrast, reduction showed low specificity: many aldehydes, including all-trans-, 9-cis-, 11-cis-, and 13-cis-retinals and even benzaldehyde, supported the reaction. On the basis of kinetic studies of this reaction (aldehyde-alcohol redox-coupling reaction), we found that formation of a ternary complex of a retinol, an aldehyde, and a postulated enzyme seemed to be necessary, which suggested the presence of both the retinol- and aldehyde-binding sites in this enzyme. A subcellular fractionation study showed that the activity is present almost exclusively in the cone inner segment. These results suggest the presence of an effective production mechanism of 11-cis-retinal in the cone inner segment to regenerate visual pigment.

A novel and well tolerated mite allergoid subcutaneous immunotherapy: evidence of clinical and immunologic efficacy

PubMed Central

Roger, Albert; Depreux, Nathalie; Jurgens, Yani; Heath, Matthew D; Garcia, Gloria; Skinner, Murray A

2014-01-01

Allergy to house dust mite is one of the most common causes of allergic rhinitis. A novel tyrosine-adsorbed, modified allergen product, Acarovac Plus, developed for the treatment of perennial mite allergy seeks to address the underlying cause of allergic rhinitis in this instance. One of two dosing regimens may be used, either the Conventional Regimen or the Cluster Regimen. We sought to compare the efficacy and safety of a specific immunotherapy, developed for the treatment of perennial mite allergy, administered under a Conventional and Clustered dosing schedule in patients with persistent allergic rhinitis. Thirty adult patients, between 18 and 65 years old, with allergic rhinitis and/or asthma secondary to hypersensitivity to Dermatophagoides pteronyssinus were administered with either conventional or cluster initial regime, with a final visit one week after the last dose administration. The efficacy to the Conventional and Cluster regimens was measured using a Nasal Challenge Test monitoring clinical symptoms and peak nasal inspiratory flow. Total IgE, serum-specific inmunoglobulins (IgE and IgG4) to Dermatophagoides pteronyssinus and relevant cytokines (IFN-γ, IL-4, IL-5, IL-10 and IL-13) were assessed. A Satisfaction Questionnaire (TSQM) was completed after each patient's final visit. The tolerability of the vaccine was assessed monitoring adverse reactions. No adverse events were recorded in either conventional or cluster regime. The specific Nasal Challenge Test led to a decrease in symptom scores and a significant decrease in mean nasal peak inspiratory flow drop was recorded in both dosing regimen groups. A significant increase in IgG4-specific antibody titres was assessed. No significant changes were observed in concentrations of total IgE, specific IgE or cytokines (IFN-γ, IL-4, IL-5, IL-10 and IL-13). Patients declared themselves most satisfied in relation to “Secondary effects”, with high overall satisfaction in both groups. Cluster and conventional specific immunotherapy resulted in no adverse reaction(s) and led to similar improvements in immunological parameters, clinical efficacy (Nasal Challenge Test) and high overall satisfaction. PMID:25400929

Multiscale stochastic simulations of chemical reactions with regulated scale separation

NASA Astrophysics Data System (ADS)

Koumoutsakos, Petros; Feigelman, Justin

2013-07-01

We present a coupling of multiscale frameworks with accelerated stochastic simulation algorithms for systems of chemical reactions with disparate propensities. The algorithms regulate the propensities of the fast and slow reactions of the system, using alternating micro and macro sub-steps simulated with accelerated algorithms such as τ and R-leaping. The proposed algorithms are shown to provide significant speedups in simulations of stiff systems of chemical reactions with a trade-off in accuracy as controlled by a regulating parameter. More importantly, the error of the methods exhibits a cutoff phenomenon that allows for optimal parameter choices. Numerical experiments demonstrate that hybrid algorithms involving accelerated stochastic simulations can be, in certain cases, more accurate while faster, than their corresponding stochastic simulation algorithm counterparts.

Homogeneous-heterogeneous reactions in curved channel with porous medium

NASA Astrophysics Data System (ADS)

Hayat, T.; Ayub, Sadia; Alsaedi, A.

2018-06-01

Purpose of the present investigation is to examine the peristaltic flow through porous medium in a curved conduit. Problem is modeled for incompressible electrically conducting Ellis fluid. Influence of porous medium is tackled via modified Darcy's law. The considered model utilizes homogeneous-heterogeneous reactions with equal diffusivities for reactant and autocatalysis. Constitutive equations are formulated in the presence of viscous dissipation. Channel walls are compliant in nature. Governing equations are modeled and simplified under the assumptions of small Reynolds number and large wavelength. Graphical results for velocity, temperature, heat transfer coefficient and homogeneous-heterogeneous reaction parameters are examined for the emerging parameters entering into the problem. Results reveal an activation in both homogenous-heterogenous reaction effect and heat transfer rate with increasing curvature of the channel.

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

Bandyopadhyay, S.; Chowdhury, R.; Biswas, G.K.

A mathematical model based on the mechanistic approach to the reaction kinetics of pyrolysis reactions and the realistic analysis of the interaction between simultaneous heat and mass transfer along with the chemical reaction has been developed for the design of smoothly running pyrolyzers. The model of a fixed-bed pyrolysis reactor has been proposed on the basis of the dimensionless parameters with respect to time and radial position. The variation of physical parameters like bed voidage, heat capacity, diffusivity, density, thermal conductivity, etc., on temperature and conversion has been taken into account. A deactivation model has also been incorporated to explainmore » the behavior of pyrolysis reactions at temperatures above 673 K. The simulated results of the model have been explained by comparing them with the experimental results.« less

A multiphysics microstructure-resolved model for silicon anode lithium-ion batteries

NASA Astrophysics Data System (ADS)

Wang, Miao; Xiao, Xinran; Huang, Xiaosong

2017-04-01

Silicon (Si) is one of the most promising next generation anode materials for lithium-ion batteries (LIBs), but the use of Si in LIBs has been rather limited. The main challenge is its large volume change (up to 300%) during battery cycling. This can lead to the fracture of Si, failure at the interfaces between electrode components, and large dimensional change on the cell level. To optimize the Si electrode/battery design, a model that considers the interactions of different cell components is needed. This paper presents the development of a multiphysics microstructure-resolved model (MRM) for LIB cells with a-Si anode. The model considered the electrochemical reactions, Li transports in electrolyte and electrodes, dimensional changes and stresses, property evolution with the structure, and the coupling relationships. Important model parameters, such as the diffusivity, reaction rate constant, and apparent transfer coefficient, were determined by correlating the simulation results to experiments. The model was validated with experimental results in the literature. The use of this model was demonstrated in a parameter study of Si nanowall|Li cells. The specific and volumetric capacities of the cell as a function of the size, length/size ratio, spacing of the nanostructure, and Li+ concentration in electrolyte were investigated.

Preparation and reactions of an iodinated imidoester reagent with actin and alpha-actinin.

PubMed

Bright, G R; Spooner, B S

1983-06-01

The chemical iodination of an imidoester (methyl-p-hydroxybenzimidate, Wood et al. (1975) Anal. Biochem. 68, 339) and subsequent coupling of iodinated imidoester (IIE) to protein is an indirect method of iodinating proteins that is specific for the epsilon amino group of lysine residues and maintains the positive charge on the amino group at physiological pH. Purification of the IIE from chloramine-T and free iodine by benzene extraction eliminates the need for isoelectric precipitation and produces a more time- and cost-efficient IIE preparation and purification protocol. The separation of free from protein-bound label by chromatography, using centrifugal elution, provides a separation method that is rapid and efficient, without the generation of large volumes of radioactive wastes characteristic of conventional chromatographic and dialysis methods. To optimize the parameters of labeling protein with IIE, a systematic assessment of the effects of pH, reactant concentrations, and reaction time was made using purified cardiac actin and gizzard alpha-actinin. The parameters were defined to achieve an average labeling ratio of one IIE per protein polypeptide. The data demonstrate that both proteins appear to be labeled at the same rate and define several determining factors that limit the rate and extent of IIE incorporation into protein.

Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin

PubMed Central

Isaksen, Geir Villy; Åqvist, Johan; Brandsdal, Bjørn Olav

2014-01-01

Life has effectively colonized most of our planet and extremophilic organisms require specialized enzymes to survive under harsh conditions. Cold-loving organisms (psychrophiles) express heat-labile enzymes that possess a high specific activity and catalytic efficiency at low temperatures. A remarkable universal characteristic of cold-active enzymes is that they show a reduction both in activation enthalpy and entropy, compared to mesophilic orthologs, which makes their reaction rates less sensitive to falling temperature. Despite significant efforts since the early 1970s, the important question of the origin of this effect still largely remains unanswered. Here we use cold- and warm-active trypsins as model systems to investigate the temperature dependence of the reaction rates with extensive molecular dynamics free energy simulations. The calculations quantitatively reproduce the catalytic rates of the two enzymes and further yield high-precision Arrhenius plots, which show the characteristic trends in activation enthalpy and entropy. Detailed structural analysis indicates that the relationship between these parameters and the 3D structure is reflected by significantly different internal protein energy changes during the reaction. The origin of this effect is not localized to the active site, but is found in the outer regions of the protein, where the cold-active enzyme has a higher degree of softness. Several structural mechanisms for softening the protein surface are identified, together with key mutations responsible for this effect. Our simulations further show that single point-mutations can significantly affect the thermodynamic activation parameters, indicating how these can be optimized by evolution. PMID:25165981

An introduction to the 'Psycho-Physiological-Stress-Test' (PPST)-A standardized instrument for evaluating stress reactions.

PubMed

Neureiter, Elisabeth; Hajfani, Loreen; Ahnis, Anne; Mierke, Annett; Rose, Matthias; Danzer, Gerhard; Klapp, Burghard F

2017-01-01

Using a standardized instrument to evaluate patients' stress reactions has become more important in daily clinical routines. Different signs or symptoms of stress are often unilaterally explored: the physiological, psychological or social aspects of stress disorders are each viewed on a single dimension. However, all dimensions afflict patients who have persistent health problems due to chronic stress. Therefore, it is important to use a multidimensional approach to acquire data. The 'Psycho-Physiological-Stress-Test' (PPST) was established to achieve a comprehensive understanding of stress and was further developed at the Charité-Universitätsmedizin Berlin in collaboration with the Psychological Department of Freie Universität Berlin. The PPST includes a series of varying stress phases, embedded in two periods of rest. Physiological and psychological parameters are simultaneously measured throughout the test session. Specifically, the PPST activates the sympathetic stress axis, which is measured by heart rate, blood pressure, respiration depth and rate, electro dermal activation and muscle tension (frontalis, masseter, trapezius). Psychological data are simultaneously collected, and include performance, motivation, emotion and behavior. After conducting this diagnostic test, it is possible to identify individual stress patterns that can be discussed with the individual patient to develop and recommend (outpatient) treatment strategies. This paper introduces the PPST as a standardized way to evaluate stress reactions by presenting the results from a sample of psychosomatic inpatients (n = 139) who were treated in Charité-Universitätsmedizin Berlin, Germany. We observed that the varying testing conditions provoked adjusted changes in the different physiological parameters and psychological levels.

Response preparation and intra-individual reaction time variability in schizophrenia.

PubMed

Dankinas, Denisas; Mėlynytė, Sigita; Šiurkutė, Aldona; Dapšys, Kastytis

2016-01-01

Background. It is important to prepare response in advance to increase the efficiency of its execution. The process of response preparation is usually studied using the precueing paradigm. In this paradigm subjects have to employ the preceding information about further imperative stimulus to perform proper response preparation, which shortens the reaction time of subsequent response execution. Previous studies detected the impairment of response preparation in schizophrenia only with the help of electroencephalographic parameters, but not with the assessing of reaction time. Therefore, in this study we attempted to find a behavioural parameter that could detect impairment in response preparation of schizophrenia patients. It was recently found that appropriate response preparation not only shortens the reaction time but also increases its stability, which is measured with the intra-individual reaction time variability. It was also revealed that response stability could better find cognitive dysfunction in some studies of schizophrenia disorder than classical behavioural parameters. Hence, the main goal of this study was to verify if intra-individual reaction time variability could detect the impairment of response preparation in schizophrenia patients. Materials and methods. In order to achieve the main purpose, we carried out a study with 14 schizophrenia patients and 14 control group subjects. We used precueing paradigm in our research, in which participants had to employ information about stimulus probability for the proper response preparation. Results. Our main result showed that despite the responses of schizophrenia patients were faster to the high-probability stimulus than to the low-probability one ( F (1, 13) = 30.9, p < 0.001), intra-individual reaction time variability did not differ in this group between the responses to more and less probable stimuli ( F (1, 13) = 0.64, p = 0.44). Conclusions. Results of the study suggest that people with schizophrenia were able to use precueing probabilistic information only to shorten their reaction time, but not to increase response stability. Therefore, it was found that intra-individual reaction time variability parameter could detect response preparation impairment in schizophrenia, and could be used in clinical purposes.

Kinetics and mechanisms of thiol-disulfide exchange covering direct substitution and thiol oxidation-mediated pathways.

PubMed

Nagy, Péter

2013-05-01

Disulfides are important building blocks in the secondary and tertiary structures of proteins, serving as inter- and intra-subunit cross links. Disulfides are also the major products of thiol oxidation, a process that has primary roles in defense mechanisms against oxidative stress and in redox regulation of cell signaling. Although disulfides are relatively stable, their reduction, isomerisation, and interconversion as well as their production reactions are catalyzed by delicate enzyme machineries, providing a dynamic system in biology. Redox homeostasis, a thermodynamic parameter that determines which reactions can occur in cellular compartments, is also balanced by the thiol-disulfide pool. However, it is the kinetic properties of the reactions that best represent cell dynamics, because the partitioning of the possible reactions depends on kinetic parameters. This review is focused on the kinetics and mechanisms of thiol-disulfide substitution and redox reactions. It summarizes the challenges and advances that are associated with kinetic investigations in small molecular and enzymatic systems from a rigorous chemical perspective using biological examples. The most important parameters that influence reaction rates are discussed in detail. Kinetic studies of proteins are more challenging than small molecules, and quite often investigators are forced to sacrifice the rigor of the experimental approach to obtain the important kinetic and mechanistic information. However, recent technological advances allow a more comprehensive analysis of enzymatic systems via using the systematic kinetics apparatus that was developed for small molecule reactions, which is expected to provide further insight into the cell's machinery.

Predictive beyond-mean-field rate equations for multisite lattice–gas models of catalytic surface reactions: CO oxidation on Pd(100)

DOE PAGES

Liu, Da -Jiang; Zahariev, Federico; Gordon, Mark S.; ...

2016-11-29

Tailored multisite lattice–gas (msLG) models are developed for CO oxidation on Pd(100) at low-pressures. These models include multiple adsorption site types and superlattice adlayer ordering due to short-range exclusion for highly mobile reactant adspecies. However, they are simplified to neglect longer-range weaker adspecies interactions, so that the key energetic parameters are the CO desorption barrier and the reaction barrier. We discuss existing density functional theory results for these energies and present additional analysis for CO adsorption. After also including an appropriate nontrivial specification of the dynamics of adsorption onto mixed reactant adlayers, we develop rate equations for the reaction kinetics.more » Our formulation goes beyond traditional mean-field (MF) Langmuirian treatments by accounting for multiple adsorption sites and for the strong spatial correlations associated with superlattice ordering. Specifically, we utilize factorization approximations based on appropriate site motifs, and also Padé resummation of exact low-coverage expansions for sticking coefficients. Our beyond-MF rate equations are successful in accurately predicting key aspects of reactive steady-state behavior, and thus expand the utility of rate equation formulations in surface chemistry. This is confirmed by comparison with precise kinetic Monte Carlo simulation results. Furthermore, we not only assess bistability and criticality observed for CO oxidation but also find more complex multistability associated with symmetry-breaking transitions in high-coverage CO adlayers.« less

Influence of surface features of hydroxyapatite on the adsorption of proteins relevant to bone regeneration.

PubMed

Fernández-Montes Moraleda, Belén; San Román, Julio; Rodríguez-Lorenzo, Luís M

2013-08-01

Protein-surface interaction may determine the success or failure of an implanted device. Not much attention have been paid to the specific surface parametes of hydroxyapatite (OHAp) that modulates and determines the formation and potential activity of the layer of proteins that is first formed when the material get in contact with the host tissue. the influence of specific surface area (SSA), crystallite size (CS) and particle size (PS) of OHAp on the adsorption of proteins relevant for bone regeneration is evaluated in this article. OHAp have been prepared by a wet chemical reaction of Ca(OH)2 with H3PO4. One set of reactions included poly acrylic acid in the reactant solution to modify the properties of the powder. Fibrinogen (Fg) Fraction I, type I: from Human plasma, (67% Protein), and Fibronectin (Fn) from Human plasma were selected to perform the adsorption experiments. The analysis of protein adsorption was carried out by UV/Vis spectrometry. A lower SSA and a different aspect ratio are obtained when the acrylic acid is included in the reaction badge. The deconvolution of the amide I band on the Raman spectra of free and adsorbed proteins reveals that the interaction apatite-protein happens through the carboxylate groups of the proteins. The combined analysis of CS, SSA and PS should be considered on the design of OHAp materials intended to interact with proteins. Copyright © 2013 Wiley Periodicals, Inc.

Optimization of digital droplet polymerase chain reaction for quantification of genetically modified organisms

PubMed Central

Gerdes, Lars; Iwobi, Azuka; Busch, Ulrich; Pecoraro, Sven

2016-01-01

Digital PCR in droplets (ddPCR) is an emerging method for more and more applications in DNA (and RNA) analysis. Special requirements when establishing ddPCR for analysis of genetically modified organisms (GMO) in a laboratory include the choice between validated official qPCR methods and the optimization of these assays for a ddPCR format. Differentiation between droplets with positive reaction and negative droplets, that is setting of an appropriate threshold, can be crucial for a correct measurement. This holds true in particular when independent transgene and plant-specific reference gene copy numbers have to be combined to determine the content of GM material in a sample. Droplets which show fluorescent units ranging between those of explicit positive and negative droplets are called ‘rain’. Signals of such droplets can hinder analysis and the correct setting of a threshold. In this manuscript, a computer-based algorithm has been carefully designed to evaluate assay performance and facilitate objective criteria for assay optimization. Optimized assays in return minimize the impact of rain on ddPCR analysis. We developed an Excel based ‘experience matrix’ that reflects the assay parameters of GMO ddPCR tests performed in our laboratory. Parameters considered include singleplex/duplex ddPCR, assay volume, thermal cycler, probe manufacturer, oligonucleotide concentration, annealing/elongation temperature, and a droplet separation evaluation. We additionally propose an objective droplet separation value which is based on both absolute fluorescence signal distance of positive and negative droplet populations and the variation within these droplet populations. The proposed performance classification in the experience matrix can be used for a rating of different assays for the same GMO target, thus enabling employment of the best suited assay parameters. Main optimization parameters include annealing/extension temperature and oligonucleotide concentrations. The droplet separation value allows for easy and reproducible assay performance evaluation. The combination of separation value with the experience matrix simplifies the choice of adequate assay parameters for a given GMO event. PMID:27077048

Optimization of digital droplet polymerase chain reaction for quantification of genetically modified organisms.

PubMed

Gerdes, Lars; Iwobi, Azuka; Busch, Ulrich; Pecoraro, Sven

2016-03-01

Digital PCR in droplets (ddPCR) is an emerging method for more and more applications in DNA (and RNA) analysis. Special requirements when establishing ddPCR for analysis of genetically modified organisms (GMO) in a laboratory include the choice between validated official qPCR methods and the optimization of these assays for a ddPCR format. Differentiation between droplets with positive reaction and negative droplets, that is setting of an appropriate threshold, can be crucial for a correct measurement. This holds true in particular when independent transgene and plant-specific reference gene copy numbers have to be combined to determine the content of GM material in a sample. Droplets which show fluorescent units ranging between those of explicit positive and negative droplets are called 'rain'. Signals of such droplets can hinder analysis and the correct setting of a threshold. In this manuscript, a computer-based algorithm has been carefully designed to evaluate assay performance and facilitate objective criteria for assay optimization. Optimized assays in return minimize the impact of rain on ddPCR analysis. We developed an Excel based 'experience matrix' that reflects the assay parameters of GMO ddPCR tests performed in our laboratory. Parameters considered include singleplex/duplex ddPCR, assay volume, thermal cycler, probe manufacturer, oligonucleotide concentration, annealing/elongation temperature, and a droplet separation evaluation. We additionally propose an objective droplet separation value which is based on both absolute fluorescence signal distance of positive and negative droplet populations and the variation within these droplet populations. The proposed performance classification in the experience matrix can be used for a rating of different assays for the same GMO target, thus enabling employment of the best suited assay parameters. Main optimization parameters include annealing/extension temperature and oligonucleotide concentrations. The droplet separation value allows for easy and reproducible assay performance evaluation. The combination of separation value with the experience matrix simplifies the choice of adequate assay parameters for a given GMO event.

Development of a Subject-Specific Foot-Ground Contact Model for Walking.

PubMed

Jackson, Jennifer N; Hass, Chris J; Fregly, Benjamin J

2016-09-01

Computational walking simulations could facilitate the development of improved treatments for clinical conditions affecting walking ability. Since an effective treatment is likely to change a patient's foot-ground contact pattern and timing, such simulations should ideally utilize deformable foot-ground contact models tailored to the patient's foot anatomy and footwear. However, no study has reported a deformable modeling approach that can reproduce all six ground reaction quantities (expressed as three reaction force components, two center of pressure (CoP) coordinates, and a free reaction moment) for an individual subject during walking. This study proposes such an approach for use in predictive optimizations of walking. To minimize complexity, we modeled each foot as two rigid segments-a hindfoot (HF) segment and a forefoot (FF) segment-connected by a pin joint representing the toes flexion-extension axis. Ground reaction forces (GRFs) and moments acting on each segment were generated by a grid of linear springs with nonlinear damping and Coulomb friction spread across the bottom of each segment. The stiffness and damping of each spring and common friction parameter values for all springs were calibrated for both feet simultaneously via a novel three-stage optimization process that used motion capture and ground reaction data collected from a single walking trial. The sequential three-stage process involved matching (1) the vertical force component, (2) all three force components, and finally (3) all six ground reaction quantities. The calibrated model was tested using four additional walking trials excluded from calibration. With only small changes in input kinematics, the calibrated model reproduced all six ground reaction quantities closely (root mean square (RMS) errors less than 13 N for all three forces, 25 mm for anterior-posterior (AP) CoP, 8 mm for medial-lateral (ML) CoP, and 2 N·m for the free moment) for both feet in all walking trials. The largest errors in AP CoP occurred at the beginning and end of stance phase when the vertical ground reaction force (vGRF) was small. Subject-specific deformable foot-ground contact models created using this approach should enable changes in foot-ground contact pattern to be predicted accurately by gait optimization studies, which may lead to improvements in personalized rehabilitation medicine.

Development of a Subject-Specific Foot-Ground Contact Model for Walking

PubMed Central

Jackson, Jennifer N.; Hass, Chris J.; Fregly, Benjamin J.

2016-01-01

Computational walking simulations could facilitate the development of improved treatments for clinical conditions affecting walking ability. Since an effective treatment is likely to change a patient's foot-ground contact pattern and timing, such simulations should ideally utilize deformable foot-ground contact models tailored to the patient's foot anatomy and footwear. However, no study has reported a deformable modeling approach that can reproduce all six ground reaction quantities (expressed as three reaction force components, two center of pressure (CoP) coordinates, and a free reaction moment) for an individual subject during walking. This study proposes such an approach for use in predictive optimizations of walking. To minimize complexity, we modeled each foot as two rigid segments—a hindfoot (HF) segment and a forefoot (FF) segment—connected by a pin joint representing the toes flexion–extension axis. Ground reaction forces (GRFs) and moments acting on each segment were generated by a grid of linear springs with nonlinear damping and Coulomb friction spread across the bottom of each segment. The stiffness and damping of each spring and common friction parameter values for all springs were calibrated for both feet simultaneously via a novel three-stage optimization process that used motion capture and ground reaction data collected from a single walking trial. The sequential three-stage process involved matching (1) the vertical force component, (2) all three force components, and finally (3) all six ground reaction quantities. The calibrated model was tested using four additional walking trials excluded from calibration. With only small changes in input kinematics, the calibrated model reproduced all six ground reaction quantities closely (root mean square (RMS) errors less than 13 N for all three forces, 25 mm for anterior–posterior (AP) CoP, 8 mm for medial–lateral (ML) CoP, and 2 N·m for the free moment) for both feet in all walking trials. The largest errors in AP CoP occurred at the beginning and end of stance phase when the vertical ground reaction force (vGRF) was small. Subject-specific deformable foot-ground contact models created using this approach should enable changes in foot-ground contact pattern to be predicted accurately by gait optimization studies, which may lead to improvements in personalized rehabilitation medicine. PMID:27379886

Parameters governing ruthenium sawhorse-based decarboxylation of oleic acid

USDA-ARS?s Scientific Manuscript database

Ruthenium-catalyzed decarboxylation of 9-cisoctadecenoic is a path to produce biobased olefins. Here, a mechanistic study of this reaction was undertaken utilizing a closed reaction system and a pressure reactor. The proposed mechanism of an isomerization followed by a decarboxylation reaction was c...

Design of experiments for zeroth and first-order reaction rates.

PubMed

Amo-Salas, Mariano; Martín-Martín, Raúl; Rodríguez-Aragón, Licesio J

2014-09-01

This work presents optimum designs for reaction rates experiments. In these experiments, time at which observations are to be made and temperatures at which reactions are to be run need to be designed. Observations are performed along time under isothermal conditions. Each experiment needs a fixed temperature and so the reaction can be measured at the designed times. For these observations under isothermal conditions over the same reaction a correlation structure has been considered. D-optimum designs are the aim of our work for zeroth and first-order reaction rates. Temperatures for the isothermal experiments and observation times, to obtain the most accurate estimates of the unknown parameters, are provided in these designs. D-optimum designs for a single observation in each isothermal experiment or for several correlated observations have been obtained. Robustness of the optimum designs for ranges of the correlation parameter and comparisons of the information gathered by different designs are also shown. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advanced materials for 193-nm resists

NASA Astrophysics Data System (ADS)

Ushirogouchi, Tohru; Asakawa, Koji; Shida, Naomi; Okino, Takeshi; Saito, Satoshi; Funaki, Yoshinori; Takaragi, Akira; Tsutsumi, Kentaro; Nakano, Tatsuya

2000-06-01

Acrylate monomers containing alicyclic side chains featuring a series of polar substituent groups were assumed to be model compounds. Solubility parameters were calculated for the corresponding acrylate polymers. These acrylate monomers were synthesized using a novel aerobic oxidation reaction employing N-hydroxyphtalimide (NHPI) as a catalyst, and then polymerized. These reactions were confirmed to be applicable for the mass-production of those compounds. The calculation results agreed with the hydrophilic parameters measured experimentally. Moreover, the relationship between the resist performance and the above-mentioned solubility parameter has been studied. As a result, a correlation between the resist performance and the calculated solubility parameter was observed. Finally, resolution of 0.13-micron patterns, based on the 1G DRAM design rule, could be successfully fabricated by optimizing the solubility parameter and the resist composition.

PDF investigations of turbulent non-premixed jet flames with thin reaction zones

NASA Astrophysics Data System (ADS)

Wang, Haifeng; Pope, Stephen

2012-11-01

PDF (probability density function) modeling studies are carried out for the Sydney piloted jet flames. These Sydney flames feature much thinner reaction zones in the mixture fraction space compared to those in the well-studied Sandia piloted jet flames. The performance of the different turbulent combustion models in the Sydney flames with thin reaction zones has not been examined extensively before, and this work aims at evaluating the capability of the PDF method to represent the thin turbulent flame structures in the Sydney piloted flames. Parametric and sensitivity PDF studies are performed with respect to the different models and model parameters. A global error parameter is defined to quantify the departure of the simulation results from the experimental data, and is used to assess the performance of the different set of models and model parameters.

Catalytic effects of inorganic acids on the decomposition of ammonium nitrate.

PubMed

Sun, Jinhua; Sun, Zhanhui; Wang, Qingsong; Ding, Hui; Wang, Tong; Jiang, Chuansheng

2005-12-09

In order to evaluate the catalytic effects of inorganic acids on the decomposition of ammonium nitrate (AN), the heat releases of decomposition or reaction of pure AN and its mixtures with inorganic acids were analyzed by a heat flux calorimeter C80. Through the experiments, the different reaction mechanisms of AN and its mixtures were analyzed. The chemical reaction kinetic parameters such as reaction order, activation energy and frequency factor were calculated with the C80 experimental results for different samples. Based on these parameters and the thermal runaway models (Semenov and Frank-Kamenestkii model), the self-accelerating decomposition temperatures (SADTs) of AN and its mixtures were calculated and compared. The results show that the mixtures of AN with acid are more unsteady than pure AN. The AN decomposition reaction is catalyzed by acid. The calculated SADTs of AN mixtures with acid are much lower than that of pure AN.

Effects of Nordic walking and walking on spatiotemporal gait parameters and ground reaction force.

PubMed

Park, Seung Kyu; Yang, Dae Jung; Kang, Yang Hun; Kim, Je Ho; Uhm, Yo Han; Lee, Yong Seon

2015-09-01

[Purpose] The purpose of this study was to investigate the effects of Nordic walking and walking on spatiotemporal gait parameters and ground reaction force. [Subjects] The subjects of this study were 30 young adult males, who were divided into a Nordic walking group of 15 subjects and a walking group of 15 subjects. [Methods] To analyze the spatiotemporal parameters and ground reaction force during walking in the two groups, the six-camera Vicon MX motion analysis system was used. The subjects were asked to walk 12 meters using the more comfortable walking method for them between Nordic walking and walking. After they walked 12 meters more than 10 times, their most natural walking patterns were chosen three times and analyzed. To determine the pole for Nordic walking, each subject's height was multiplied by 0.68. We then measured the spatiotemporal gait parameters and ground reaction force. [Results] Compared with the walking group, the Nordic walking group showed an increase in cadence, stride length, and step length, and a decrease in stride time, step time, and vertical ground reaction force. [Conclusion] The results of this study indicate that Nordic walking increases the stride and can be considered as helping patients with diseases affecting their gait. This demonstrates that Nordic walking is more effective in improving functional capabilities by promoting effective energy use and reducing the lower limb load, because the weight of the upper and lower limbs is dispersed during Nordic walking.

Computations and estimates of rate coefficients for hydrocarbon reactions of interest to the atmospheres of outer solar system

NASA Technical Reports Server (NTRS)

Laufer, A. H.; Gardner, E. P.; Kwok, T. L.; Yung, Y. L.

1983-01-01

The rate coefficients, including Arrhenius parameters, have been computed for a number of chemical reactions involving hydrocarbon species for which experimental data are not available and which are important in planetary atmospheric models. The techniques used to calculate the kinetic parameters include the Troe and semiempirical bond energy-bond order (BEBO) or bond strength-bond length (BSBL) methods.

Unsteady MHD Mixed Convection Slip Flow of Casson Fluid over Nonlinearly Stretching Sheet Embedded in a Porous Medium with Chemical Reaction, Thermal Radiation, Heat Generation/Absorption and Convective Boundary Conditions

PubMed Central

Ullah, Imran; Bhattacharyya, Krishnendu; Shafie, Sharidan; Khan, Ilyas

2016-01-01

Numerical results are presented for the effect of first order chemical reaction and thermal radiation on mixed convection flow of Casson fluid in the presence of magnetic field. The flow is generated due to unsteady nonlinearly stretching sheet placed inside a porous medium. Convective conditions on wall temperature and wall concentration are also employed in the investigation. The governing partial differential equations are converted to ordinary differential equations using suitable transformations and then solved numerically via Keller-box method. It is noticed that fluid velocity rises with increase in radiation parameter in the case of assisting flow and is opposite in the case of opposing fluid while radiation parameter has no effect on fluid velocity in the forced convection. It is also seen that fluid velocity and concentration enhances in the case of generative chemical reaction whereas both profiles reduces in the case of destructive chemical reaction. Further, increase in local unsteadiness parameter reduces fluid velocity, temperature and concentration. Over all the effects of physical parameters on fluid velocity, temperature and concentration distribution as well as on the wall shear stress, heat and mass transfer rates are discussed in detail. PMID:27776174

Theoretical derivation for reaction rate constants of H abstraction from thiophenol by the H/O radical pool

PubMed Central

Batiha, Marwan; Altarawneh, Mohammednoor; Al-Harahsheh, Mohammad; Altarawneh, Ibrahem; Rawadieh, Saleh

2011-01-01

Reaction and activation energy barriers are calculated for the H abstraction reactions (C6H5SH + X• → C6H5S + XH, X = H, OH and HO2) at the BB1K/GTLarge level of theory. The corresponding reactions with H2S and CH3SH are also investigated using the G3B3 and CBS-QB3 methods in order to demonstrate the accuracy of BB1K functional in finding activation barriers for hydrogen atom transfer reactions. Arrhenius parameters for the title reactions are fitted in the temperature range of 300 K–2000 K. The calculated reaction enthalpies are in good agreement with their corresponding experimental reaction enthalpies. It is found that H abstraction by OH radicals from the thiophenol molecule proceed in a much slower rate in reference to the analogous phenol molecule. ΔfH298o of thiophenoxy radical is calculated to be 63.3 kcal/mol. Kinetic parameters presented herein should be useful in describing the decomposition rate of thiophenol; i.e., one of the major aromatic sulfur carriers, at high temperatures. PMID:22485200

Topological and kinetic determinants of the modal matrices of dynamic models of metabolism

PubMed Central

2017-01-01

Large-scale kinetic models of metabolism are becoming increasingly comprehensive and accurate. A key challenge is to understand the biochemical basis of the dynamic properties of these models. Linear analysis methods are well-established as useful tools for characterizing the dynamic response of metabolic networks. Central to linear analysis methods are two key matrices: the Jacobian matrix (J) and the modal matrix (M-1) arising from its eigendecomposition. The modal matrix M-1 contains dynamically independent motions of the kinetic model near a reference state, and it is sparse in practice for metabolic networks. However, connecting the structure of M-1 to the kinetic properties of the underlying reactions is non-trivial. In this study, we analyze the relationship between J, M-1, and the kinetic properties of the underlying network for kinetic models of metabolism. Specifically, we describe the origin of mode sparsity structure based on features of the network stoichiometric matrix S and the reaction kinetic gradient matrix G. First, we show that due to the scaling of kinetic parameters in real networks, diagonal dominance occurs in a substantial fraction of the rows of J, resulting in simple modal structures with clear biological interpretations. Then, we show that more complicated modes originate from topologically-connected reactions that have similar reaction elasticities in G. These elasticities represent dynamic equilibrium balances within reactions and are key determinants of modal structure. The work presented should prove useful towards obtaining an understanding of the dynamics of kinetic models of metabolism, which are rooted in the network structure and the kinetic properties of reactions. PMID:29267329

Electrode performance parameters for a radioisotope-powered AMTEC for space power applications

NASA Technical Reports Server (NTRS)

Underwood, M. L.; O'Connor, D.; Williams, R. M.; Jeffries-Nakamura, B.; Ryan, M. A.; Bankston, C. P.

1992-01-01

The alkali metal thermoelastic converter (AMTEC) is a device for the direct conversion of heat to electricity. Recently a design of an AMTEC using a radioisotope heat source was described, but the optimum condenser temperature was hotter than the temperatures used in the laboratory to develop the electrode performance model. Now laboratory experiments have confirmed the dependence of two model parameters over a broader range of condenser and electrode temperatures for two candidate electrode compositions. One parameter, the electrochemical exchange current density at the reaction interface, is independent of the condenser temperature, and depends only upon the collision rate of sodium at the reaction zone. The second parameter, a morphological parameter, which measures the mass transport resistance through the electrode, is independent of condenser and electrode temperatures for molybdenum electrodes. For rhodium-tungsten electrodes, however, this parameter increases for decreasing electrode temperature, indicating an activated mass transport mechanism such as surface diffusion.

New Developments in the Field of Reaction Technology: The Multiparallel Reactor HPMR 50-96

PubMed Central

Allwardt, Arne; Wendler, Christian; Thurow, Kerstin

2005-01-01

Catalytic high-pressure reactions play an important role in classic bulk chemistry. The optimization of common reactions, the search for new and more effective catalysts, and the increasing use of catalytic pressure reactions in the field of drug development call for high-parallel reaction systems. A crucial task of current developments, apart from the parameters of pressure, temperature, and number of reaction chambers, is, in this respect, the systems' integration into complex laboratory automation environments. PMID:18924722

Experimental test of the mechanism of reaction for (e,e'p) coincidence experiment. [/sup 12/C(e,e'p): DWIA

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

Bernheim, M.; Bussiere, A.; Frullani, S.

1977-06-27

In order to test the validity of the distorted wave impulse approximation to describe (e,e'p) reactions and/or the suitability of the available optical potential parameters to calculate the distortion, the spectral function was measured for /sub 12/C(e,e'p)/sub 11/B in different kinematical configurations. Experimental results are shown together with the distributions computed with several values of the optical potential parameters. Data seem to indicate the necessity of using different parameters for p hole states and s hole states.

Sensitivity analysis of conservative and reactive stream transient storage models applied to field data from multiple-reach experiments

USGS Publications Warehouse

Gooseff, M.N.; Bencala, K.E.; Scott, D.T.; Runkel, R.L.; McKnight, Diane M.

2005-01-01

The transient storage model (TSM) has been widely used in studies of stream solute transport and fate, with an increasing emphasis on reactive solute transport. In this study we perform sensitivity analyses of a conservative TSM and two different reactive solute transport models (RSTM), one that includes first-order decay in the stream and the storage zone, and a second that considers sorption of a reactive solute on streambed sediments. Two previously analyzed data sets are examined with a focus on the reliability of these RSTMs in characterizing stream and storage zone solute reactions. Sensitivities of simulations to parameters within and among reaches, parameter coefficients of variation, and correlation coefficients are computed and analyzed. Our results indicate that (1) simulated values have the greatest sensitivity to parameters within the same reach, (2) simulated values are also sensitive to parameters in reaches immediately upstream and downstream (inter-reach sensitivity), (3) simulated values have decreasing sensitivity to parameters in reaches farther downstream, and (4) in-stream reactive solute data provide adequate data to resolve effective storage zone reaction parameters, given the model formulations. Simulations of reactive solutes are shown to be equally sensitive to transport parameters and effective reaction parameters of the model, evidence of the control of physical transport on reactive solute dynamics. Similar to conservative transport analysis, reactive solute simulations appear to be most sensitive to data collected during the rising and falling limb of the concentration breakthrough curve. ?? 2005 Elsevier Ltd. All rights reserved.

Suppression of antigen-specific lymphocyte activation in modeled microgravity

NASA Technical Reports Server (NTRS)

Cooper, D.; Pride, M. W.; Brown, E. L.; Risin, D.; Pellis, N. R.; McIntire, L. V. (Principal Investigator)

2001-01-01

Various parameters of immune suppression are observed in lymphocytes from astronauts during and after a space flight. It is difficult to ascribe this suppression to microgravity effects on immune cells in crew specimens, due to the complex physiological response to space flight and the resultant effect on in vitro immune performance. Use of isolated immune cells in true and modeled microgravity in immune performance tests, suggests a direct effect of microgravity on in vitro cellular function. Specifically, polyclonal activation of T-cells is severely suppressed in true and modeled microgravity. These recent findings suggest a potential suppression of oligoclonal antigen-specific lymphocyte activation in microgravity. We utilized rotating wall vessel (RWV) bioreactors as an analog of microgravity for cell cultures to analyze three models of antigen-specific activation. A mixed-lymphocyte reaction, as a model for a primary immune response, a tetanus toxoid response and a Borrelia burgdorferi response, as models of a secondary immune response, were all suppressed in the RWV bioreactor. Our findings confirm that the suppression of activation observed with polyclonal models also encompasses oligoclonal antigen-specific activation.

Curcumin and kaempferol prevent lysozyme fibril formation by modulating aggregation kinetic parameters.

PubMed

Borana, Mohanish S; Mishra, Pushpa; Pissurlenkar, Raghuvir R S; Hosur, Ramakrishna V; Ahmad, Basir

2014-03-01

Interaction of small molecule inhibitors with protein aggregates has been studied extensively, but how these inhibitors modulate aggregation kinetic parameters is little understood. In this work, we investigated the ability of two potential aggregation inhibiting drugs, curcumin and kaempferol, to control the kinetic parameters of aggregation reaction. Using thioflavin T fluorescence and static light scattering, the kinetic parameters such as amplitude, elongation rate constant and lag time of guanidine hydrochloride-induced aggregation reactions of hen egg white lysozyme were studied. We observed a contrasting effect of inhibitors on the kinetic parameters when aggregation reactions were measured by these two probes. The interactions of these inhibitors with hen egg white lysozyme were investigated using fluorescence quench titration method and molecular dynamics simulations coupled with binding free energy calculations. We conclude that both the inhibitors prolong nucleation of amyloid aggregation through binding to region of the protein which is known to form the core of the protein fibril, but once the nucleus is formed the rate of elongation is not affected by the inhibitors. This work would provide insight into the mechanism of aggregation inhibition by these potential drug molecules. Copyright © 2014 Elsevier B.V. All rights reserved.

Immunotoxicological Evaluation of Corn Genetically Modified with Bacillus thuringiensis Cry1Ah Gene by a 30-Day Feeding Study in BALB/c Mice

PubMed Central

Song, Yan; Liang, Chunlai; Wang, Wei; Fang, Jin; Sun, Nana; Jia, Xudong; Li, Ning

2014-01-01

This study was to investigate the immunotoxicological potential of corn genetically modified (GM) with Bacillus thuringiensis (Bt) Cry1Ah gene in BALB/c mice. Female BALB/c mice were randomly assigned to one of the four groups: the negative control group, the parental corn group, the GM corn group and the positive control group with 10 mice per group. Mice in the GM corn group and the parental corn group were fed with diets containing 70% corresponding corn for 30 days. Mice in the negative control group and the positive control group were fed with AIN93G diet, administered with saline or 200 mg/kg of cyclophosphamide (CY) via intraperitoneal injection 24 h before the termination of the study, respectively. At the end of the study, the immunotoxicological effects of the GM corn were evaluated through immunopathology parameters including body and organ weights, hematology and clinical chemistry parameters, histological examination, peripheral blood lymphocytes phenotype; humoral immunity including antibody plaque-forming cell, serum immunoglobulin, cytokine and half hemolysis value; cellular immunity such as mitogen-induced splenocyte proliferation, cytotoxic T-lymphocyte reaction, delayed-type hypersensitivity reaction; non-specific immunity including phagocytic activities of phagocytes, natural killer cell activity. A single dose of cyclophosphamide (200 mg/kg bw) was found to have significant adverse effects on immunopathology, cellular immunity, and humoral immunity in mice. The corn genetically modified with Bt Cry1Ah gene is considered consistent with the parental corn in terms of immunopathology, humoral immunity, cellular immunity and non-specific immunity. No adverse immunotoxicological effects of GM corn with Bt Cry1Ah gene were found when feeding mice for 30 days. PMID:24520311

[Response of sensorimotor cortex neurons to weak disturbances of the magnetic field in Wistar rats. Cytochemical study].

PubMed

Shpin'kova, V N; Nikol'skaia, K A; Gershteĭn, L M

2000-01-01

The influence of weak disturbances (up to 300 microT) of natural magnetic field on the protein metabolism in neurons of sensomotor cortex (layers III and V) in Wistar rats upon learning in a complex maze was studied. It was found that sensomotor neurons were very sensitive to weak disturbances of magnetic field. The protein content increased, while the nucleus-cytoplasm ratio and osmotic state of neurons remained unchanged. The specificity of neuron's reaction manifested itself in a sharp increase of nucleus and cytoplasm dimensions. In associative neurons (layer III), both the nucleus and cytoplasm were involved in the response; in efferent neurons (layer V), only nuclear parameters changed. The variance coefficients of all parameters of protein metabolism in sensomotor neurons, independently of their functional properties, were much higher than in control, which resulted in a wide diversity of cytochemical response.

Development of high strength, high temperature ceramics

NASA Technical Reports Server (NTRS)

Hall, W. B.

1982-01-01

Improvement in the high-pressure turbopumps, both fuel and oxidizer, in the Space Shuttle main engine were considered. The operation of these pumps is limited by temperature restrictions of the metallic components used in these pumps. Ceramic materials that retain strength at high temperatures and appear to be promising candidates for use as turbine blades and impellers are discussed. These high strength materials are sensitive to many related processing parameters such as impurities, sintering aids, reaction aids, particle size, processing temperature, and post thermal treatment. The specific objectives of the study were to: (1) identify and define the processing parameters that affect the properties of Si3N4 ceramic materials, (2) design and assembly equipment required for processing high strength ceramics, (3) design and assemble test apparatus for evaluating the high temperature properties of Si3N4, and (4) conduct a research program of manufacturing and evaluating Si3N4 materials as applicable to rocket engine applications.

Reaction of bromine and chlorine with phenolic compounds and natural organic matter extracts--Electrophilic aromatic substitution and oxidation.

PubMed

Criquet, Justine; Rodriguez, Eva M; Allard, Sebastien; Wellauer, Sven; Salhi, Elisabeth; Joll, Cynthia A; von Gunten, Urs

2015-11-15

Phenolic compounds are known structural moieties of natural organic matter (NOM), and their reactivity is a key parameter for understanding the reactivity of NOM and the disinfection by-product formation during oxidative water treatment. In this study, species-specific and/or apparent second order rate constants and mechanisms for the reactions of bromine and chlorine have been determined for various phenolic compounds (phenol, resorcinol, catechol, hydroquinone, phloroglucinol, bisphenol A, p-hydroxybenzoic acid, gallic acid, hesperetin and tannic acid) and flavone. The reactivity of bromine with phenolic compounds is very high, with apparent second order rate constants at pH 7 in the range of 10(4) to 10(7) M(-1) s(-1). The highest value was recorded for the reaction between HOBr and the fully deprotonated resorcinol (k = 2.1 × 10(9) M(-1) s(-1)). The reactivity of phenolic compounds is enhanced by the activating character of the phenolic substituents, e.g. further hydroxyl groups. With the data set from this study, the ratio between the species-specific rate constants for the reactions of chlorine versus bromine with phenolic compounds was confirmed to be about 3000. Phenolic compounds react with bromine or chlorine either by oxidation (electron transfer, ET) or electrophilic aromatic substitution (EAS) processes. The dominant process mainly depends on the relative position of the hydroxyl substituents and the possibility of quinone formation. While phenol, p-hydroxybenzoic acid and bisphenol A undergo EAS, hydroquinone, catechol, gallic acid and tannic acid, with hydroxyl substituents in ortho or para positions, react with bromine by ET leading to quantitative formation of the corresponding quinones. Some compounds (e.g. phloroglucinol) show both partial oxidation and partial electrophilic aromatic substitution and the ratio observed for the pathways depends on the pH. For the reaction of six NOM extracts with bromine, electrophilic aromatic substitution accounted for only 20% of the reaction, and for one NOM extract (Pony Lake fulvic acid) it accounted for <10%. This shows that for natural organic matter samples, oxidation (ET) is far more important than bromine incorporation (EAS). Copyright © 2015 Elsevier Ltd. All rights reserved.

Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water

PubMed Central

Juraszek, Jarek; Bolhuis, Peter G.

2008-01-01

We report rate constant calculations and a reaction coordinate analysis of the rate-limiting folding and unfolding process of the Trp-cage mini-protein in explicit solvent using transition interface sampling. Previous transition path sampling simulations revealed that in this (un)folding process the protein maintains its compact configuration, while a (de)increase of secondary structure is observed. The calculated folding rate agrees reasonably with experiment, while the unfolding rate is 10 times higher. We discuss possible origins for this mismatch. We recomputed the rates with the forward flux sampling method, and found a discrepancy of four orders of magnitude, probably caused by the method's higher sensitivity to the choice of order parameter with respect to transition interface sampling. Finally, we used the previously computed transition path-sampling ensemble to screen combinations of many order parameters for the best model of the reaction coordinate by employing likelihood maximization. We found that a combination of the root mean-square deviation of the helix and of the entire protein was, of the set of tried order parameters, the one that best describes the reaction coordination. PMID:18676648

Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path–Force Matching QM/MM Method

PubMed Central

Zhou, Y.; Ojeda-May, P.; Nagaraju, M.; Pu, J.

2016-01-01

Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are ubiquitous ATP-dependent membrane proteins involved in translocations of a wide variety of substrates across cellular membranes. To understand the chemomechanical coupling mechanism as well as functional asymmetry in these systems, a quantitative description of how ABC transporters hydrolyze ATP is needed. Complementary to experimental approaches, computer simulations based on combined quantum mechanical and molecular mechanical (QM/MM) potentials have provided new insights into the catalytic mechanism in ABC transporters. Quantitatively reliable determination of the free energy requirement for enzymatic ATP hydrolysis, however, requires substantial statistical sampling on QM/MM potential. A case study shows that brute force sampling of ab initio QM/MM (AI/MM) potential energy surfaces is computationally impractical for enzyme simulations of ABC transporters. On the other hand, existing semiempirical QM/MM (SE/MM) methods, although affordable for free energy sampling, are unreliable for studying ATP hydrolysis. To close this gap, a multiscale QM/MM approach named reaction path–force matching (RP–FM) has been developed. In RP–FM, specific reaction parameters for a selected SE method are optimized against AI reference data along reaction paths by employing the force matching technique. The feasibility of the method is demonstrated for a proton transfer reaction in the gas phase and in solution. The RP–FM method may offer a general tool for simulating complex enzyme systems such as ABC transporters. PMID:27498639

Relationships between the structure of natural organic matter and its reactivity towards molecular ozone and hydroxyl radicals

USGS Publications Warehouse

Westerhoff, P.; Aiken, G.; Amy, G.; Debroux, J.

1999-01-01

Oxidation reaction rate parameters for molecular ozone (O3) and hydroxyl (HO) radicals with a variety of hydrophobic organic acids (HOAs) isolated from different geographic locations were determined from batch ozonation studies. Rate parameter values, obtained under equivalent dissolved organic carbon concentrations in both the presence and absence of non-NOM HO radical scavengers, varied as a function of NOM structure. First-order rate constants for O3 consumption (k(O3)) averaged 8.8 x 10-3 s-1, ranging from 3.9 x 10-3 s-1 for a groundwater HOA to > 16 x 10-3 s-1 for river HOAs with large terrestrial carbon inputs. The average second-order rate constant (k(HO,DOC) between HO radicals and NOM was 3.6 x 108 l (mol C)-1 s-1; a mass of 12 g C per mole C was used in all calculations. Specific ultraviolet absorbance (SUVA) at 254 or 280 nm of the HOAs correlated well (r > 0.9) with O3 consumption rate parameters, implying that organic ??-electrons strongly and selectively influence oxidative reactivity. HO radical reactions with NOM were less selective, although correlation between k(HO,DOC) and SUVA existed. Other physical-chemical properties of NOM, such as aromatic and aliphatic carbon content from 13C-NMR spectroscopy, proved less sensitive for predicting oxidation reactivity than SUVA. The implication of this study is that the structural nature of NOM varies temporally and spatially in a water source, and both the nature and amount of NOM will influence oxidation rates.

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

Stein, R.L.

A procedure for the analysis of observed isotope effects on rates of complex reactions is outlined which can be applied to kinetic isotope effect data for any reaction having a virtual transition state whose structure can be varied by adjusting a reaction parameter. This procedure is applied to the basic hydrolysis of p-nitroacetanilide. 3 tables. (DLC)

Effects of mass transfer on MHD three dimensional flow of a Prandtl liquid over a flat plate in the presence of chemical reaction

NASA Astrophysics Data System (ADS)

Ganesh Kumar, K.; Rizwan-ul-Haq; Rudraswamy, N. G.; Gireesha, B. J.

The present study addresses the three-dimensional flow of a Prandtl fluid over a Riga plate in the presence of chemical reaction and convective condition. The converted set of boundary layer equations are solved numerically by RKF four-fifth method. Obtained numerical results for flow and mass transfer characteristics are discussed for various physical parameters. Additionally, the skin friction coefficient and Sherwood number are also presented. It is found that, the momentum boundary layer thickness is dominant for higher values of α and solutal boundary layer is low for higher Schmidt number and chemical reaction parameter.

Fundamental study on photodynamic therapy for atrial fibrillation: effect of photosensitization reaction parameters on myocardial necrosis in vitro

NASA Astrophysics Data System (ADS)

Ogawa, Emiyu; Ito, Arisa; Arai, Tsunenori

2012-03-01

We studied necrotic cell death effect on myocardial cells with photosensitizer existed outside the cells varying photosensitization reaction parameters widely in vitro. We have developed non-thermal ablator with the application of photosensitization reaction for atrial fibrillation. Since laser irradiation is applied shortly after photosensitizer injection, the photosensitization reaction is induced outside the cells. The interaction for the myocardial cells by the photosensitization reaction is not well understood yet on various photosensitization reaction parameters. Rat myocardial cells were cultured in 96 well plates for 7 days. The photosensitization reaction was applied with talaporfin sodium (NPe6) and the semiconductor laser of 663nm wavelength. The average drug light interval was set 8 mins. The photosensitizer concentration and radiant exposure were varied from 5 to 40 μg/ml and 1.2 to 60 J/cm2, respectively. The well bottom was irradiated by the red laser with irradiance of 293 mW/cm2. The photosensitizer fluorescence was monitored during the photosensitization reaction. Alive cell rate was measured by WST assay after 2 hours from the irradiation. In the case of the photosensitizer concentration of 10 μg/ml, the myocardial cells were almost alive even thought 60 J/cm2 in the radiant exposure was applied. In the 15 μg/ml case, the alive cell rate was almost linear relation to the photosensitizer concentration and radiant exposure. We obtained that the threshold for myocardial cell necrosis on the photosensitizer concentration was around 15 μg/ml with 20 J/cm2 in the radiant exposure. This threshold on the photosensitizer concentration was similar to the reported threshold for cancer therapy.

TMEM16A inhibition impedes capacitation and acquisition of hyperactivated motility in guinea pig sperm.

PubMed

Cordero-Martínez, Joaquín; Reyes-Miguel, Tania; Rodríguez-Páez, Lorena; Garduño-Siciliano, Leticia; Maldonado-García, Deneb; Roa-Espitia, Ana L; Hernández-González, Enrique O

2018-07-01

Ca 2+ -activated Cl - channels (CaCCs) are anionic channels that regulate many important physiological functions associated with chloride and calcium flux in some somatic cells. The molecular identity of CaCCs was revealed to be TMEM16A and TMEM16B (also known as Anoctamin or ANO1 and ANO2, respectively) in all eukaryotes. A recent study suggests the presence of TMEM16A in human sperm and a relationship with the rhZP-induced acrosome reaction. However, to the best of our knowledge, little is known about the role of TMEM16A in other spermatic processes such as capacitation or motility. In this study, we evaluated the effects of two TMEM16A antagonists on capacitation, acrosome reaction, and motility in guinea pig sperm; these antagonists were T16Ainh-A01, belonging to a second generation of potent antagonists of TMEM16A, and niflumic acid (NFA), a well-known antagonist of TMEM16A (CaCCs). First of all, we confirmed that the absence of Cl - in the capacitation medium changes motility parameters, capacitation, and the progesterone-induced acrosome reaction. Using a specific antibody, TMEM16A was found as a protein band of ∼120 kDa, which localization was in the apical crest of the acrosome and the middle piece of the flagellum. Inhibition of TMEM16A by T16Ainh-A01 affected sperm physiology by reducing capacitation, blocking the progesterone-induced acrosome reaction under optimal capacitation conditions, inhibiting progressive motility, and the acquisition of hyperactivated motility, diminishing [Ca 2+ ]i, and increasing [Cl - ]i. These changes in sperm kinematic parameters provide new evidence of the important role played by TMEM16A in the production of sperm capable of fertilizing oocytes. © 2018 Wiley Periodicals, Inc.

Trainable Nonlinear Reaction Diffusion: A Flexible Framework for Fast and Effective Image Restoration.

PubMed

Chen, Yunjin; Pock, Thomas

2017-06-01

Image restoration is a long-standing problem in low-level computer vision with many interesting applications. We describe a flexible learning framework based on the concept of nonlinear reaction diffusion models for various image restoration problems. By embodying recent improvements in nonlinear diffusion models, we propose a dynamic nonlinear reaction diffusion model with time-dependent parameters (i.e., linear filters and influence functions). In contrast to previous nonlinear diffusion models, all the parameters, including the filters and the influence functions, are simultaneously learned from training data through a loss based approach. We call this approach TNRD-Trainable Nonlinear Reaction Diffusion. The TNRD approach is applicable for a variety of image restoration tasks by incorporating appropriate reaction force. We demonstrate its capabilities with three representative applications, Gaussian image denoising, single image super resolution and JPEG deblocking. Experiments show that our trained nonlinear diffusion models largely benefit from the training of the parameters and finally lead to the best reported performance on common test datasets for the tested applications. Our trained models preserve the structural simplicity of diffusion models and take only a small number of diffusion steps, thus are highly efficient. Moreover, they are also well-suited for parallel computation on GPUs, which makes the inference procedure extremely fast.

Uncertainty quantification of reaction mechanisms accounting for correlations introduced by rate rules and fitted Arrhenius parameters

DOE PAGES

Prager, Jens; Najm, Habib N.; Sargsyan, Khachik; ...

2013-02-23

We study correlations among uncertain Arrhenius rate parameters in a chemical model for hydrocarbon fuel-air combustion. We consider correlations induced by the use of rate rules for modeling reaction rate constants, as well as those resulting from fitting rate expressions to empirical measurements arriving at a joint probability density for all Arrhenius parameters. We focus on homogeneous ignition in a fuel-air mixture at constant-pressure. We also outline a general methodology for this analysis using polynomial chaos and Bayesian inference methods. Finally, we examine the uncertainties in both the Arrhenius parameters and in predicted ignition time, outlining the role of correlations,more » and considering both accuracy and computational efficiency.« less

Parameter Selection Methods in Inverse Problem Formulation

DTIC Science & Technology

2010-11-03

clinical data and used for prediction and a model for the reaction of the cardiovascular system to an ergometric workload. Key Words: Parameter selection...model for HIV dynamics which has been successfully validated with clinical data and used for prediction and a model for the reaction of the...recently developed in-host model for HIV dynamics which has been successfully validated with clinical data and used for prediction [4, 8]; b) a global

Modification on liquid retention property of cassava starch by radiation grafting with acrylonitrile. I. Effect of γ-irradiation on grafting parameters

NASA Astrophysics Data System (ADS)

Kiatkamjornwong, S.; Chvajarernpun, J.; Nakason, C.

1993-07-01

Radiation modification on liquid retention properties of native cassava starch, gelatinized at 85°C, by graft copolymerization with acrylonitrile was carried out by mutual irradiation to gamma-rays. A thin aluminum foil was used to cover the inner wall of the reaction vessel, so that the homopolymer concentration was reduced to be less than 1.0% with a distilled water retention value of 665 g/g of the dry weight of the saponified grafted product. Confirmation of graft copolymerization and saponification reactions was made by the infrared spectrophotometric technique. The combined effect of radiation parameters in terms of an irradiation time and a dose rate to the total dose on the extent of the grafting reaction expressed in terms of grafting parameters which directly influenced liquid retention values was evaluated in conjunction with statistical analysis.

Determination of detonation parameters for liquid High Explosives

NASA Astrophysics Data System (ADS)

Mochalova, Valentina; Utkin, Alexander

2011-06-01

The experimental investigation of detonation parameters and reaction zone structure in liquid HE (bis-(2-fluoro-2,2-dinitroethyl)formal (FEFO), tetranitromethane (TNM), nitromethane (NM)) was conducted. Detonation front in TNM and NM was stable while the instability of detonation in FEFO was observed. Von Neumann spike was recorded for these HE and its parameters were determined. The different methods for C-J point determination were used for each HE. For FEFO reaction time τ was found from experiments with different charge diameters (τ is approximately equal to 300 ns); for TNM - at fixed diameter and different lengths of charges (τ ~ 200 ns); for NM - at fixed diameter and length of charges, but detonation initiation was carried out by different explosive charges (τ ~ 50 ns). It was found that in TNM the detonation velocity depends on charge diameter. Maximum value of reaction rate in investigated liquid HE was observed after shock jump and induction time was not recorded.

Determination of detonation parameters for liquid high explosives

NASA Astrophysics Data System (ADS)

Mochalova, Valentina; Utkin, Alexander

2012-03-01

The experimental investigation of detonation parameters and reaction zone structure in liquid HE (bis-(2-fluoro-2,2-dinitroethyl)formal (FEFO), tetranitromethane (TNM), nitromethane (NM)) was conducted by means of laser interferometer VISAR. Detonation front in TNM and NM was stable while the instability of detonation in FEFO was observed. The parameters of Von Neumann spike were determined for these HE. The different methods for C-J point determination were used for each HE. For FEFO reaction time t was found from experiments with different charge diameters (τ is approximately equal to 300 ns); for TNM - at fixed diameter and different lengths of charges (τ ≈ 200 ns); for NM - at fixed diameter and length of charges, but detonation initiation was carried out by different explosive charges (τ ≈ 50 ns). It was found that in TNM the detonation velocity depends on charge diameter. Maximum value of reaction rate in investigated liquid HE was observed after shock jump.

Velocity locking and pulsed invasions of fragmented habitats with seasonal growth

NASA Astrophysics Data System (ADS)

Korolev, Kirill; Wang, Ching-Hao

From crystal growth to epidemics, spatial spreading is a common mechanism of change in nature. Typically, spreading results from two processes: growth and dispersal in ecology or chemical reactions and diffusion in physics. These two processes combine to produce a reaction-diffusion wave, an invasion front advancing at a constant velocity. We show that the properties of these waves are remarkably different depending whether space and time are continuous, as they are for a chemical reaction, or discrete, as they are for a pest invading a patchy habitat in seasonal climates. For discrete space and time, we report a new type of expansions with velocities that can lock into specific values and become insensitive to changes in dispersal and growth, i.e. the dependence of the velocity on model parameters exhibits plateaus or pauses. As a result, the evolution and response to perturbations in locked expansions can be markedly different compared to the expectations based on continuous models. The phenomenon of velocity locking requires cooperative growth and does not occur when per capita growth rate decline monotonically with population density. We obtain both numerical and analytical results describing highly non-analytic properties of locked expansions.

Selective chemical detection by energy modulation of sensors

DOEpatents

Stetter, J.R.; Otagawa, T.

1991-09-10

A portable instrument for use in the field in detecting, identifying, and quantifying a component of a sampled fluid includes a sensor which chemically reacts with the component of interest or a derivative thereof, an electrical heating filament for heating the sample before it is applied to the sensor, and modulator for continuously varying the temperature of the filament (and hence the reaction rate) between two values sufficient to produce the chemical reaction. In response to this thermal modulation, the sensor produces a modulated output signal, the modulation of which is a function of the activation energy of the chemical reaction, which activation energy is specific to the particular component of interest and its concentration. Microprocessor which compares the modulated output signal with standard responses for a plurality of components to identify and quantify the particular component of interest. In particular, the concentration of the component of interest is proportional to the amplitude of the modulated output signal, while the identifying activation output energy of the chemical interaction indicative of that component is proportional to a normalized parameter equal to the peak-to-peak amplitude divided by the height of the upper peaks above a base line signal level. 5 figures.

Selective chemical detection by energy modulation of sensors

DOEpatents

Stetter, Joseph R.; Otagawa, Takaaki

1991-01-01

A portable instrument for use in the field in detecting, identifying, and quantifying a component of a sampled fluid includes a sensor which chemically reacts with the component of interest or a derivative thereof, an electrical heating filament for heating the sample before it is applied to the sensor, and modulator for continuously varying the temperature of the filament (and hence the reaction rate) between two values sufficient to produce the chemical reaction. In response to this thermal modulation, the sensor produces a modulated output signal, the modulation of which is a function of the activation energy of the chemical reaction, which activation energy is specific to the particular component of interest and its concentration. Microprocessor which compares the modulated output signal with standard responses for a plurality of components to identify and quantify the particular component of interest. In particular, the concentration of the component of interest is proportional to the amplitude of the modulated output signal, while the identifying activation output energy of the chemical interaction indicative of that component is proportional to a normalized parameter equal to the peak-to-peak amplitude divided by the height of the upper peaks above a base line signal level.

Kinetics of reactions of aquacobalamin with aspartic and glutamic acids and their amides in water solutions

NASA Astrophysics Data System (ADS)

Bui, T. T. T.; Sal'nikov, D. S.; Dereven'kov, I. A.; Makarov, S. V.

2017-04-01

The kinetics of aquacobalamin reaction with aspartic and glutamic acids, and with their amides in water solutions, is studied via spectrophotometry. The kinetic and activation parameters of the process are determined. It is shown that the reaction product is cobalamin-amino acid complex. The data are compared to results on the reaction between aquacobalamin and primary amines.

Kinetics and Mechanisms of Thiol–Disulfide Exchange Covering Direct Substitution and Thiol Oxidation-Mediated Pathways

PubMed Central

2013-01-01

Abstract Significance: Disulfides are important building blocks in the secondary and tertiary structures of proteins, serving as inter- and intra-subunit cross links. Disulfides are also the major products of thiol oxidation, a process that has primary roles in defense mechanisms against oxidative stress and in redox regulation of cell signaling. Although disulfides are relatively stable, their reduction, isomerisation, and interconversion as well as their production reactions are catalyzed by delicate enzyme machineries, providing a dynamic system in biology. Redox homeostasis, a thermodynamic parameter that determines which reactions can occur in cellular compartments, is also balanced by the thiol–disulfide pool. However, it is the kinetic properties of the reactions that best represent cell dynamics, because the partitioning of the possible reactions depends on kinetic parameters. Critical Issues: This review is focused on the kinetics and mechanisms of thiol–disulfide substitution and redox reactions. It summarizes the challenges and advances that are associated with kinetic investigations in small molecular and enzymatic systems from a rigorous chemical perspective using biological examples. The most important parameters that influence reaction rates are discussed in detail. Recent Advances and Future Directions: Kinetic studies of proteins are more challenging than small molecules, and quite often investigators are forced to sacrifice the rigor of the experimental approach to obtain the important kinetic and mechanistic information. However, recent technological advances allow a more comprehensive analysis of enzymatic systems via using the systematic kinetics apparatus that was developed for small molecule reactions, which is expected to provide further insight into the cell's machinery. Antioxid. Redox Signal. 18, 1623–1641. PMID:23075118

Chapter Eight - Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases

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

King, Paul W; Mulder, David W; Artz, Jacob H.

The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas-treatments. Other themesmore » presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.« less

Clinical and pathological tools for identifying microsatellite instability in colorectal cancer

PubMed Central

Krivokapić, Zoran; Marković, Srdjan; Antić, Jadranka; Dimitrijević, Ivan; Bojić, Daniela; Svorcan, Petar; Jojić, Njegica; Damjanović, Svetozar

2012-01-01

Aim To assess practical accuracy of revised Bethesda criteria (BGrev), pathological predictive model (MsPath), and histopathological parameters for detection of high-frequency of microsatellite instability (MSI-H) phenotype in patients with colorectal carcinoma (CRC). Method Tumors from 150 patients with CRC were analyzed for MSI using a fluorescence-based pentaplex polymerase chain reaction technique. For all patients, we evaluated age, sex, family history of cancer, localization, tumor differentiation, mucin production, lymphocytic infiltration (TIL), and Union for International Cancer Control stage. Patients were classified according to the BGrev, and the groups were compared. The utility of the BGrev, MsPath, and clinical and histopathological parameters for predicting microsatellite tumor status were assessed by univariate logistic regression analysis and by calculating the sensitivity, specificity, and positive (PPV) and negative (NPV) predictive values. Results Fifteen out of 45 patients who met and 4 of 105 patients who did not meet the BGrev criteria had MSI-H CRC. Sensitivity, specificity, PPV, and NPV for BGrev were 78.9%, 77%, 30%, and 70%, respectively. MSI histology (the third BGrev criterion without age limit) was as sensitive as BGrev, but more specific. MsPath model was more sensitive than BGrev (86%), with similar specificity. Any BGrev criterion fulfillment, mucinous differentiation, and right-sided CRC were singled out as independent factors to identify MSI-H colorectal cancer. Conclusion The BGrev, MsPath model, and MSI histology are useful tools for selecting patients for MSI testing. PMID:22911525

Heat exchanger selection and design analyses for metal hydride heat pump systems

DOE PAGES

Mazzucco, Andrea; Voskuilen, Tyler G.; Waters, Essene L.; ...

2016-01-01

This paper presents a design analysis for the development of highly efficient heat exchangers within stationary metal hydride heat pumps. The design constraints and selected performance criteria are applied to three representative heat exchangers. The proposed thermal model can be applied to select the most efficient heat exchanger design and provides outcomes generally valid in a pre-design stage. Heat transfer effectiveness is the principal performance parameter guiding the selection analysis, the results of which appear to be mildly (up to 13%) affected by the specific Nusselt correlation used. The thermo-physical properties of the heat transfer medium and geometrical parameters aremore » varied in the sensitivity analysis, suggesting that the length of independent tubes is the physical parameter that influences the performance of the heat exchangers the most. The practical operative regions for each heat exchanger are identified by finding the conditions over which the heat removal from the solid bed enables a complete and continuous hydriding reaction. The most efficient solution is a design example that achieves the target effectiveness of 95%.« less

Influence of fusion dynamics on fission observables: A multidimensional analysis

NASA Astrophysics Data System (ADS)

Schmitt, C.; Mazurek, K.; Nadtochy, P. N.

2018-01-01

An attempt to unfold the respective influence of the fusion and fission stages on typical fission observables, and namely the neutron prescission multiplicity, is proposed. A four-dimensional dynamical stochastic Langevin model is used to calculate the decay by fission of excited compound nuclei produced in a wide set of heavy-ion collisions. The comparison of the results from such a calculation and experimental data is discussed, guided by predictions of the dynamical deterministic HICOL code for the compound-nucleus formation time. While the dependence of the latter on the entrance-channel properties can straigthforwardly explain some observations, a complex interplay between the various parameters of the reaction is found to occur in other cases. A multidimensional analysis of the respective role of these parameters, including entrance-channel asymmetry, bombarding energy, compound-nucleus fissility, angular momentum, and excitation energy, is proposed. It is shown that, depending on the size of the system, apparent inconsistencies may be deduced when projecting onto specific ordering parameters. The work suggests the possibility of delicate compensation effects in governing the measured fission observables, thereby highlighting the necessity of a multidimensional discussion.

Self-organization and information in biosystems: a case study.

PubMed

Haken, Hermann

2018-05-01

Eigen's original molecular evolution equations are extended in two ways. (1) By an additional nonlinear autocatalytic term leading to new stability features, their dependence on the relative size of fitness parameters and on initial conditions is discussed in detail. (2) By adding noise terms that represent the spontaneous generation of molecules by mutations of substrate molecules, these terms are taken care of by both Langevin and Fokker-Planck equations. The steady-state solution of the latter provides us with a potential landscape giving a bird's eye view on all stable states (attractors). Two different types of evolutionary processes are suggested: (a) in a fixed attractor landscape and (b) caused by a changed landscape caused by changed fitness parameters. This may be related to Gould's concept of punctuated equilibria. External signals in the form of additional molecules may generate a new initial state within a specific basin of attraction. The corresponding attractor is then reached by self-organization. This approach allows me to define pragmatic information as signals causing a specific reaction of the receiver and to use equations equivalent to (1) as model of (human) pattern recognition as substantiated by the synergetic computer.

Controlling Complex Systems and Developing Dynamic Technology

NASA Astrophysics Data System (ADS)

Avizienis, Audrius Victor

In complex systems, control and understanding become intertwined. Following Ilya Prigogine, we define complex systems as having control parameters which mediate transitions between distinct modes of dynamical behavior. From this perspective, determining the nature of control parameters and demonstrating the associated dynamical phase transitions are practically equivalent and fundamental to engaging with complexity. In the first part of this work, a control parameter is determined for a non-equilibrium electrochemical system by studying a transition in the morphology of structures produced by an electroless deposition reaction. Specifically, changing the size of copper posts used as the substrate for growing metallic silver structures by the reduction of Ag+ from solution under diffusion-limited reaction conditions causes a dynamical phase transition in the crystal growth process. For Cu posts with edge lengths on the order of one micron, local forces promoting anisotropic growth predominate, and the reaction produces interconnected networks of Ag nanowires. As the post size is increased above 10 microns, the local interfacial growth reaction dynamics couple with the macroscopic diffusion field, leading to spatially propagating instabilities in the electrochemical potential which induce periodic branching during crystal growth, producing dendritic deposits. This result is interesting both as an example of control and understanding in a complex system, and as a useful combination of top-down lithography with bottom-up electrochemical self-assembly. The second part of this work focuses on the technological development of devices fabricated using this non-equilibrium electrochemical process, towards a goal of integrating a complex network as a dynamic functional component in a neuromorphic computing device. Self-assembled networks of silver nanowires were reacted with sulfur to produce interfacial "atomic switches": silver-silver sulfide junctions, which exhibit complex dynamics (e.g. both short- and long-term changes in conductivity) in response to applied voltage signals. Characterization of these atomic switch networks (ASNs) brought out interesting parallels to biological neural networks, including power-law scaling in the statistics of electrical signal propagation and dynamic self-organization of differentiated subnetworks. A reservoir computing (RC) strategy was employed to utilize measurements of electrical signals dynamically generated in ASNs to perform time-series memory and manipulation tasks including a parity test and arbitrary waveform generation. These results represent the useful integration of a complex network into a dynamic physical RC device.

Soccer athletes are superior to non-athletes at perceiving soccer-specific and non-sport specific human biological motion

PubMed Central

Romeas, Thomas; Faubert, Jocelyn

2015-01-01

Recent studies have shown that athletes’ domain specific perceptual-cognitive expertise can transfer to everyday tasks. Here we assessed the perceptual-cognitive expertise of athletes and non-athletes using sport specific and non-sport specific biological motion perception (BMP) tasks. Using a virtual environment, university-level soccer players and university students’ non-athletes were asked to perceive the direction of a point-light walker and to predict the trajectory of a masked-ball during a point-light soccer kick. Angles of presentation were varied for orientation (upright, inverted) and distance (2 m, 4 m, 16 m). Accuracy and reaction time were measured to assess observers’ performance. The results highlighted athletes’ superior ability compared to non-athletes to accurately predict the trajectory of a masked soccer ball presented at 2 m (reaction time), 4 m (accuracy and reaction time), and 16 m (accuracy) of distance. More interestingly, experts also displayed greater performance compared to non-athletes throughout the more fundamental and general point-light walker direction task presented at 2 m (reaction time), 4 m (accuracy and reaction time), and 16 m (reaction time) of distance. In addition, athletes showed a better performance throughout inverted conditions in the walker (reaction time) and soccer kick (accuracy and reaction time) tasks. This implies that during human BMP, athletes demonstrate an advantage for recognizing body kinematics that goes beyond sport specific actions. PMID:26388828

Specific attentional dysfunction in adults following early start of cannabis use.

PubMed

Ehrenreich, H; Rinn, T; Kunert, H J; Moeller, M R; Poser, W; Schilling, L; Gigerenzer, G; Hoehe, M R

1999-03-01

The present study tested the hypothesis that chronic interference by cannabis with endogenous cannabinoid systems during peripubertal development causes specific and persistent brain alterations in humans. As an index of cannabinoid action, visual scanning, along with other attentional functions, was chosen. Visual scanning undergoes a major maturation process around age 12-15 years and, in addition, the visual system is known to react specifically and sensitively to cannabinoids. From 250 individuals consuming cannabis regularly, 99 healthy pure cannabis users were selected. They were free of any other past or present drug abuse, or history of neuropsychiatric disease. After an interview, physical examination, analysis of routine laboratory parameters, plasma/urine analyses for drugs, and MMPI testing, users and respective controls were subjected to a computer-assisted attention test battery comprising visual scanning, alertness, divided attention, flexibility, and working memory. Of the potential predictors of test performance within the user group, including present age, age of onset of cannabis use, degree of acute intoxication (THC+THCOH plasma levels), and cumulative toxicity (estimated total life dose), an early age of onset turned out to be the only predictor, predicting impaired reaction times exclusively in visual scanning. Early-onset users (onset before age 16; n = 48) showed a significant impairment in reaction times in this function, whereas late-onset users (onset after age 16; n = 51) did not differ from controls (n = 49). These data suggest that beginning cannabis use during early adolescence may lead to enduring effects on specific attentional functions in adulthood. Apparently, vulnerable periods during brain development exist that are subject to persistent alterations by interfering exogenous cannabinoids.

The role of gas phase reactions in the deflagration-to-detonation transition of high energy propellants

NASA Technical Reports Server (NTRS)

Boggs, T. L.; Price, C. F.; Atwood, A. I.; Zurn, D. E.; Eisel, J. L.; Derr, R. L.

1980-01-01

The inadequacies of the two commonly used assumptions are shown, along with the need for considering gas phase reactions. Kinetic parameters that describe the gas phase reactions for several ingredients are provided, and the first steps in convective combustion leading to deflagration to detonation transition are described.

Catalytic wet-oxidation of a mixed liquid waste: COD and AOX abatement.

PubMed

Goi, D; de Leitenburg, C; Trovarelli, A; Dolcetti, G

2004-12-01

A series of catalytic wet oxidation (CWO) reactions, at temperatures of 430-500 K and in a batch bench-top pressure vessel were carried out utilizing a strong wastewater composed of landfill leachate and heavily organic halogen polluted industrial wastewater. A CeO2-SiO2 mixed oxide catalyst with large surface area to assure optimal oxidation performance was prepared. The catalytic process was examined during batch reactions controlling Chemical Oxygen Demand (COD) and Adsorbable Organic Halogen (AOX) parameters, resulting AOX abatement to achieve better effect. Color and pH were also controlled during batch tests. A simple first order-two stage reaction behavior was supposed and verified with the considered parameters. Finally an OUR test was carried out to evaluate biodegradability changes of wastewater as a result of the catalytic reaction.

Graphical user interface for yield and dose estimations for cyclotron-produced technetium

NASA Astrophysics Data System (ADS)

Hou, X.; Vuckovic, M.; Buckley, K.; Bénard, F.; Schaffer, P.; Ruth, T.; Celler, A.

2014-07-01

The cyclotron-based 100Mo(p,2n)99mTc reaction has been proposed as an alternative method for solving the shortage of 99mTc. With this production method, however, even if highly enriched molybdenum is used, various radioactive and stable isotopes will be produced simultaneously with 99mTc. In order to optimize reaction parameters and estimate potential patient doses from radiotracers labeled with cyclotron produced 99mTc, the yields for all reaction products must be estimated. Such calculations, however, are extremely complex and time consuming. Therefore, the objective of this study was to design a graphical user interface (GUI) that would automate these calculations, facilitate analysis of the experimental data, and predict dosimetry. The resulting GUI, named Cyclotron production Yields and Dosimetry (CYD), is based on Matlab®. It has three parts providing (a) reaction yield calculations, (b) predictions of gamma emissions and (c) dosimetry estimations. The paper presents the outline of the GUI, lists the parameters that must be provided by the user, discusses the details of calculations and provides examples of the results. Our initial experience shows that the proposed GUI allows the user to very efficiently calculate the yields of reaction products and analyze gamma spectroscopy data. However, it is expected that the main advantage of this GUI will be at the later clinical stage when entering reaction parameters will allow the user to predict production yields and estimate radiation doses to patients for each particular cyclotron run.

Graphical user interface for yield and dose estimations for cyclotron-produced technetium.

PubMed

Hou, X; Vuckovic, M; Buckley, K; Bénard, F; Schaffer, P; Ruth, T; Celler, A

2014-07-07

The cyclotron-based (100)Mo(p,2n)(99m)Tc reaction has been proposed as an alternative method for solving the shortage of (99m)Tc. With this production method, however, even if highly enriched molybdenum is used, various radioactive and stable isotopes will be produced simultaneously with (99m)Tc. In order to optimize reaction parameters and estimate potential patient doses from radiotracers labeled with cyclotron produced (99m)Tc, the yields for all reaction products must be estimated. Such calculations, however, are extremely complex and time consuming. Therefore, the objective of this study was to design a graphical user interface (GUI) that would automate these calculations, facilitate analysis of the experimental data, and predict dosimetry. The resulting GUI, named Cyclotron production Yields and Dosimetry (CYD), is based on Matlab®. It has three parts providing (a) reaction yield calculations, (b) predictions of gamma emissions and (c) dosimetry estimations. The paper presents the outline of the GUI, lists the parameters that must be provided by the user, discusses the details of calculations and provides examples of the results. Our initial experience shows that the proposed GUI allows the user to very efficiently calculate the yields of reaction products and analyze gamma spectroscopy data. However, it is expected that the main advantage of this GUI will be at the later clinical stage when entering reaction parameters will allow the user to predict production yields and estimate radiation doses to patients for each particular cyclotron run.

Influence of Polarity and Activation Energy in Microwave–Assisted Organic Synthesis (MAOS)

PubMed Central

Rodríguez, Antonio M; Prieto, Pilar; de la Hoz, Antonio; Díaz-Ortiz, Ángel; Martín, D Raúl; García, José I

2015-01-01

The aim of this work was to determine the parameters that have decisive roles in microwave-assisted reactions and to develop a model, using computational chemistry, to predict a priori the type of reactions that can be improved under microwaves. For this purpose, a computational study was carried out on a variety of reactions, which have been reported to be improved under microwave irradiation. This comprises six types of reactions. The outcomes obtained in this study indicate that the most influential parameters are activation energy, enthalpy, and the polarity of all the species that participate. In addition to this, in most cases, slower reacting systems observe a much greater improvement under microwave irradiation. Furthermore, for these reactions, the presence of a polar component in the reaction (solvent, reagent, susceptor, etc.) is necessary for strong coupling with the electromagnetic radiation. We also quantified that an activation energy of 20–30 kcal mol−1 and a polarity (μ) between 7–20 D of the species involved in the process is required to obtain significant improvements under microwave irradiation. PMID:26246993

Investigation of 14-15 MeV ( n, t) Reaction Cross-sections by Using New Evaluated Empirical and Semi-empirical Systematic Formulas

NASA Astrophysics Data System (ADS)

Tel, E.; Aydın, A.; Kaplan, A.; Şarer, B.

2008-09-01

In the hybrid reactor, tritium self-sufficiency must be maintained for a commercial power plant. For self-sustaining (D-T) fusion driver tritium breeding ratio should be greater than 1.05. Working out the systematics of ( n, t) reaction cross-sections are of great importance for the definition of the excitation function character for the given reaction taking place on various nuclei at energies up to 20 MeV. In this study we have investigated asymmetry term effect for the ( n, t) reaction cross-sections at 14-15 neutron incident energy. It has been discussed the odd-even effect and the pairing effect considering binding energy systematic of the nuclear shell model for the new experimental data and new cross-sections formulas ( n, t) reactions developed by Tel et al. We have determined a different parameter groups by the classification of nuclei into even-even, even-odd and odd-even for ( n, t) reactions cross-sections. The obtained empirical and semi-empirical formulas by fitting two parameter for ( n, t) reactions were given. All calculated results have been compared with the experimental data and the other semi-empirical formulas.

Diagnostic Criteria for the Characterization of Electrode Reactions with Chemically Coupled Reactions Preceding the Electron Transfer by Cyclic Square Wave Voltammetry.

PubMed

Helfrick, John C; Mann, Megan A; Bottomley, Lawrence A

2016-08-18

Theory for cyclic square wave voltammetry of electrode reactions with chemical reactions preceding the electron transfer is presented. Theoretical voltammograms were calculated following systematic variation of empirical parameters to assess their impact on the shape of the voltammogram. From the trends obtained, diagnostic criteria for this mechanism were deduced. When properly applied, these criteria will enable non-experts in voltammetry to assign the electrode reaction mechanism and accurately measure reaction kinetics. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ozonation of the oxybenzone, octinoxate, and octocrylene UV-filters: Reaction kinetics, absorbance characteristics, and transformation products.

PubMed

Hopkins, Zachary R; Snowberger, Sebastian; Blaney, Lee

2017-09-15

UV-filters (UVFs) are active ingredients in personal care products that protect skin from exposure to UV light. Environmentally-relevant concentrations of UVFs have recently been linked to toxicity in aquatic organisms, necessitating research into improved UVF removal in water/wastewater treatment. Here, we investigated ozonation of the three most commonly employed UVFs: octinoxate (OMC), octocrylene (OC), and oxybenzone (OXY). Specific second-order rate constants for UVF reaction with ozone were identified as follows: OMC, 5.25×10 4 M -1 s -1 ; OC, 1.58M -1 s -1 ; OXY (neutral), 3.80×10 2 M -1 s -1 ; and, OXY (anion), 1.51×10 6 M -1 s -1 . These kinetic parameters indicated that OMC and OXY undergo significant (2-log or greater) transformation for typical ozone exposures in disinfection processes; however, minimal oxidation is expected for OC. UV absorbance mapping was employed to characterize the loss of UVF activity (i.e., absorbance across the UV-A, UV-B, and UV-C ranges) during ozonation. These 4-dimensional maps also confirmed ozone attack mechanisms, namely reaction at phenolate (OXY) and olefin (OMC, OC) groups. Primary transformation products from these reactions were identified for all three UVFs of concern. For OC and OXY, the benzophenone structure is conserved, suggesting that transformation products retain toxicity concerns. Copyright © 2017 Elsevier B.V. All rights reserved.

Mechanism of catalytic gasification of coal char. Quarterly technical report No. 5, October 1 to December 31, 1981

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

Wood, B. J.; Sancier, K. M.; Sheridan, D. R.

1982-02-26

The purpose of this study is to determine the mechanisms involved in the catalytic reactions of coal char and to identify the specific reaction steps and the parameters that control the catalytic process. The mode of action of the catalyst can be viewed in two ways. In one view, the catalyst participates in a reduction/oxidation cycle. The initial reaction between the carbon and the catalyst reduces the KOH to potassium accompanied by the gaseous reactant (H/sub 2/O or CO/sub 2/), producing further gaseous products (CO and H/sub 2/) and regenerating the initial state of the catalyst. In an alternative view,more » the catalyst initially forms an alkali metal addition compound with the carbon network of the char. The carbon-carbon bonds are altered by the formation of the metal-carbon linkage, possibly by electron transfer from the alkali metal atom to the carbon structure. As a result, the carbon structure is more readily attacked by the gaseous reactant (CO or H/sub 2/O) to produce the products of gasification. The following areas were investigated to provide experimental evidence for these catalytic modes of action: chemical kinetic measurements; thermodynamic measurements; free radicals in reacting carbon; electrical conductivity measurements. A detailed discussion on the catalyst-carbon interaction and on the reaction intermediate is provided.« less

A Mechanism-Based Model for the Prediction of the Metabolic Sites of Steroids Mediated by Cytochrome P450 3A4.

PubMed

Dai, Zi-Ru; Ai, Chun-Zhi; Ge, Guang-Bo; He, Yu-Qi; Wu, Jing-Jing; Wang, Jia-Yue; Man, Hui-Zi; Jia, Yan; Yang, Ling

2015-06-30

Early prediction of xenobiotic metabolism is essential for drug discovery and development. As the most important human drug-metabolizing enzyme, cytochrome P450 3A4 has a large active cavity and metabolizes a broad spectrum of substrates. The poor substrate specificity of CYP3A4 makes it a huge challenge to predict the metabolic site(s) on its substrates. This study aimed to develop a mechanism-based prediction model based on two key parameters, including the binding conformation and the reaction activity of ligands, which could reveal the process of real metabolic reaction(s) and the site(s) of modification. The newly established model was applied to predict the metabolic site(s) of steroids; a class of CYP3A4-preferred substrates. 38 steroids and 12 non-steroids were randomly divided into training and test sets. Two major metabolic reactions, including aliphatic hydroxylation and N-dealkylation, were involved in this study. At least one of the top three predicted metabolic sites was validated by the experimental data. The overall accuracy for the training and test were 82.14% and 86.36%, respectively. In summary, a mechanism-based prediction model was established for the first time, which could be used to predict the metabolic site(s) of CYP3A4 on steroids with high predictive accuracy.

Tandem mass spectrometry: analysis of complex mixtures

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

Singleton, K.E.

1985-01-01

Applications of tandem mass spectrometry (MS/MS) for the analysis of complex mixtures results in increased specificity and selectivity by using a variety of reagent gases in both negative and positive ion modes. Natural isotopic abundance ratios were examined in both simple and complex mixtures using parent, daughter and neutral loss scans. MS/MS was also used to discover new compounds. Daughter scans were used to identify seven new alkaloids in a cactus species. Three of these alkaloids were novel compounds, and included the first simple, fully aromatic isoquinoline alkaloids reported in Cactaceae. MS/MS was used to characterize the chemical reaction productsmore » of coal in studies designed to probe its macromolecular structure. Negative ion chemical ionization was utilized to study reaction products resulting from the oxidation of coal. Possible structural units in the precursor coal were predicted based on the reaction products identified, aliphatic and aromatic acids and their anhydrides. The MS/MS method was also used to characterize reaction products resulting from coal liquefaction and/or extraction. These studies illustrate the types of problems for which MS/MS is useful. Emphasis has been placed on characterization of complex mixtures by selecting experimental parameters which enhance the information obtained. The value of using MS/MS in conjunction with other analytical techniques as well as the chemical pretreatment is demonstrated.« less

Drosophila segmentation: supercomputer simulation of prepattern hierarchy.

PubMed

Hunding, A; Kauffman, S A; Goodwin, B C

1990-08-09

Spontaneous prepattern formation in a two level hierarchy of reaction-diffusion systems is simulated in three space co-ordinates and time, mimicking gap gene and primary pair-rule gene expression. The model rests on the idea of Turing systems of the second kind, in which one prepattern generates position dependent rate constants for a subsequent reaction-diffusion system. Maternal genes are assumed responsible for setting up gradients from the anterior and posterior ends, one of which is needed to stabilize a double period prepattern suggested to underly the read out of the gap genes. The resulting double period pattern in turn stabilizes the next prepattern in the hierarchy, which has a short wavelength with many characteristics of the stripes seen in actual primary pair-rule gene expression. Without such hierarchical stabilization, reaction-diffusion mechanisms yield highly patchy short wave length patterns, and thus unreliable stripes. The model yields seven stable stripes located in the middle of the embryo, with the potential for additional expression near the poles, as observed experimentally. The model does not rely on specific chemical reaction kinetics, rather the effect is general to many such kinetic schemes. This makes it robust to parameter changes, and it has good potential for adapting to size and shape changes as well. The study thus suggests that the crucial organizing principle in early Drosophila embryogenesis is based on global field mechanisms, not on particular local interactions.

Changes in H(+)-ATP Synthase Activity, Proton Electrochemical Gradient, and pH in Pea Chloroplast Can Be Connected with Variation Potential.

PubMed

Sukhov, Vladimir; Surova, Lyubov; Morozova, Ekaterina; Sherstneva, Oksana; Vodeneev, Vladimir

2016-01-01

Local stimulation induces generation and propagation of electrical signals, including the variation potential (VP) and action potential, in plants. Burning-induced VP changes the physiological state of plants; specifically, it inactivates photosynthesis. However, the mechanisms that decrease photosynthesis are poorly understood. We investigated these mechanisms by measuring VP-connected systemic changes in CO2 assimilation, parameters of light reactions of photosynthesis, electrochromic pigment absorbance shifts, and light scattering. We reveal that inactivation of photosynthesis in the pea, including inactivation of dark and light reactions, was connected with the VP. Inactivation of dark reactions decreased the rate constant of the fast relaxation of the electrochromic pigment absorbance shift, which reflected a decrease in the H(+)-ATP synthase activity. This decrease likely contributed to the acidification of the chloroplast lumen, which developed after VP induction. However, VP-connected decrease of the proton motive force across the thylakoid membrane, possibly, reflected a decreased pH in the stroma. This decrease may be another mechanism of chloroplast lumen acidification. Overall, stroma acidification can decrease electron flow through photosystem I, and lumen acidification induces growth of fluorescence non-photochemical quenching and decreases electron flow through photosystem II, i.e., pH decreases in the stroma and lumen, possibly, contribute to the VP-induced inactivation of light reactions of photosynthesis.

The instant blood-mediated inflammatory reaction characterized in hepatocyte transplantation.

PubMed

Gustafson, Elisabet K; Elgue, Graciela; Hughes, Robin D; Mitry, Ragai R; Sanchez, Javier; Haglund, Ulf; Meurling, Staffan; Dhawan, Anil; Korsgren, Olle; Nilsson, Bo

2011-03-27

Hepatocyte transplantation (HcTx) has proven to be a safe procedure, although the functional results have been unsatisfactory, probably due to insufficient engraftment or a loss of transplanted mass or function. In this study, we investigate whether hepatocytes in contact with blood induce an inflammatory reaction leading to, similar to what happens in clinical islet transplantation, an instant blood-mediated inflammatory reaction (IBMIR) resulting in an early loss of transplanted cells. By using an experimental model that mimics the portal vein blood flow, we could study different parameters reflecting the effects on the innate immunity elicited by hepatocytes in contact with ABO-matched human blood. We report that all aspects of the IBMIR such as platelet and granulocyte consumption, coagulation, and complement activation were demonstrated. Addition of various specific inhibitors of coagulation allowed us to clearly delineate the various stages of the hepatocyte-triggered IBMIR and show that the reaction was triggered by tissue factor. Analysis of a case of clinical HcTx showed that hepatocyte-induced IBMIR also occurs in vivo. Both the inflammatory and the coagulation aspects were controlled by low-molecular-weight dextran sulfate. Isolated hepatocytes in contact with blood induce the IBMIR in vitro, and there are indications that these events are also relevant in vivo. According to these findings, HcTx would benefit from controlling a wider range of signals from the innate immune system.

Optimization of reaction parameters of radiation induced grafting of 1-vinylimidazole onto poly(ethylene-co-tetraflouroethene) using response surface method

NASA Astrophysics Data System (ADS)

Nasef, Mohamed Mahmoud; Aly, Amgad Ahmed; Saidi, Hamdani; Ahmad, Arshad

2011-11-01

Radiation induced grafting of 1-vinylimidazole (1-VIm) onto poly(ethylene-co-tetraflouroethene) (ETFE) was investigated. The grafting parameters such as absorbed dose, monomer concentration, grafting time and temperature were optimized using response surface method (RSM). The Box-Behnken module available in the design expert software was used to investigate the effect of reaction conditions (independent parameters) varied in four levels on the degree of grafting ( G%) (response parameter). The model yielded a polynomial equation that relates the linear, quadratic and interaction effects of the independent parameters to the response parameter. The analysis of variance (ANOVA) was used to evaluate the results of the model and detect the significant values for the independent parameters. The optimum parameters to achieve a maximum G% were found to be monomer concentration of 55 vol%, absorbed dose of 100 kGy, time in the range of 14-20 h and a temperature of 61 °C. Fourier transform infrared (FTIR), thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) were used to investigate the properties of the obtained films and provide evidence for grafting.

Maxillary reaction patterns identified by three-dimensional analysis of casts from infants with unilateral cleft lip and palate.

PubMed

Neuschulz, J; Schaefer, I; Scheer, M; Christ, H; Braumann, B

2013-07-01

In order to visualize and quantify the direction and extent of morphological upper-jaw changes in infants with unilateral cleft lip and palate (UCLP) during early orthodontic treatment, a three-dimensional method of cast analysis for routine application was developed. In the present investigation, this method was used to identify reaction patterns associated with specific cleft forms. The study included a cast series reflecting the upper-jaw situations of 46 infants with complete (n=27) or incomplete (n=19) UCLP during week 1 and months 3, 6, and 12 of life. Three-dimensional datasets were acquired and visualized with scanning software (DigiModel®; OrthoProof, The Netherlands). Following interactive identification of landmarks on the digitized surface relief, a defined set of representative linear parameters were three-dimensionally measured. At the same time, the three-dimensional surfaces of one patient series were superimposed based on a defined reference plane. Morphometric differences were statistically analyzed. Thanks to the user-friendly software, all landmarks could be identified quickly and reproducibly, thus, allowing for simultaneous three-dimensional measurement of all defined parameters. The measured values revealed that significant morphometric differences were present in all three planes of space between the two patient groups. Patients with complete UCLP underwent significantly larger reductions in cleft width (p<0.001), and sagittal growth in the complete UCLP group exceeded sagittal growth in the incomplete UCLP group by almost 50% within the first year of life. Based on patients with incomplete versus complete UCLP, different reaction patterns were identified that depended not on apparent severities of malformation but on cleft forms.

d-3-Hydroxybutyrate dehydrogenase from Rhodopseudomonas spheroides. Kinetic mechanism from steady-state kinetics of the reaction catalysed by the enzyme in solution and covalently attached to diethylaminoethylcellulose

PubMed Central

Preuveneers, M. J.; Peacock, D.; Crook, E. M.; Clark, J. B.; Brocklehurst, K.

1973-01-01

1. The reversible NAD+-linked oxidation of d-3-hydroxybutyrate to acetoacetate in 0.1m-sodium pyrophosphate buffer, pH8.5, at 25.0°C, catalysed by d-3-hydroxybutyrate dehydrogenase (d-3-hydroxybutyrate–NAD+ oxidoreductase, EC 1.1.1.30), was studied by initial-velocity, dead-end inhibition and product-inhibition analysis. 2. The reactions were carried out on (a) the soluble enzyme from Rhodopseudomonas spheroides and (b) an insoluble derivative of this enzyme prepared by its covalent attachment to DEAE-cellulose by using 2-amino-4,6-dichloro-s-triazine as coupling agent. 3. The insolubilized enzyme preparation contained 5mg of protein/g wet wt. of total material, and when freshly prepared its specific activity was 1.2μmol/min per mg of protein, which is 67% of that of the soluble dialysed enzyme. 4. The reactions catalysed by both the enzyme in solution and the insolubilized enzyme were shown to follow sequential pathways in which the nicotinamide nucleotides bind obligatorily first to the enzyme. Evidence is presented for kinetically significant ternary complexes and that the rate-limiting step(s) of both catalyses probably involves isomerization of the enzyme–nicotinamide nucleotide complexes and/or dissociation of the nicotinamide nucleotides from the enzyme. Both catalyses therefore are probably best described as ordered Bi Bi mechanisms, possibly with multiple enzyme–nicotinamide nucleotide complexes. 5. The kinetic parameters and the calculable rate constants for the catalysis by the soluble enzyme are similar to the corresponding parameters and rate constants for the catalysis by the insolubilized enzyme. PMID:4352835

Tidal Disruption of a White Dwarf by a Black Hole: The Diversity of Nucleosynthesis, Explosion Energy, and the Fate of Debris Streams

NASA Astrophysics Data System (ADS)

Kawana, Kojiro; Tanikawa, Ataru; Yoshida, Naoki

2018-03-01

We run a suite of hydrodynamics simulations of tidal disruption events (TDEs) of a white dwarf (WD) by a black hole (BH) with a wide range of WD/BH masses and orbital parameters. We implement nuclear reactions to study nucleosynthesis and its dynamical effect through release of nuclear energy. The released nuclear energy effectively increases the fraction of unbound ejecta. This effect is weaker for a heavy WD with 1.2 M⊙, because the specific orbital energy distribution of the debris is predominantly determined by the tidal force, rather than by the explosive reactions. The elemental yield of a TDE depends critically on the initial composition of a WD, while the BH mass and the orbital parameters also affect the total amount of synthesized elements. Tanikawa et al. (2017) find that simulations of WD-BH TDEs with low resolution suffer from spurious heating and inaccurate nuclear reaction results. In order to examine the validity of our calculations, we compare the amounts of the synthesized elements with the upper limits of them derived in a way where we can avoid uncertainties due to low resolution. The results are largely consistent, and thus support our findings. We find particular TDEs where early self-intersection of a WD occurs during the first pericenter passage, promoting formation of an accretion disk. We expect that relativistic jets and/or winds would form in these cases because accretion rates would be super-Eddington. The WD-BH TDEs result in a variety of events depending on the WD/BH mass and pericenter radius of the orbit.

Synthesis of phase-pure and monodisperse iron oxide nanoparticles by thermal decomposition

NASA Astrophysics Data System (ADS)

Hufschmid, Ryan; Arami, Hamed; Ferguson, R. Matthew; Gonzales, Marcela; Teeman, Eric; Brush, Lucien N.; Browning, Nigel D.; Krishnan, Kannan M.

2015-06-01

Superparamagnetic iron oxide nanoparticles (SPIONs) are used for a wide range of biomedical applications requiring precise control over their physical and magnetic properties, which are dependent on their size and crystallographic phase. Here we present a comprehensive template for the design and synthesis of iron oxide nanoparticles with control over size, size distribution, phase, and resulting magnetic properties. We investigate critical parameters for synthesis of monodisperse SPIONs by organic thermal decomposition. Three different, commonly used, iron containing precursors (iron oleate, iron pentacarbonyl, and iron oxyhydroxide) are evaluated under a variety of synthetic conditions. We compare the suitability of these three kinetically controlled synthesis protocols, which have in common the use of iron oleate as a starting precursor or reaction intermediate, for producing nanoparticles with specific size and magnetic properties. Monodisperse particles were produced over a tunable range of sizes from approximately 2-30 nm. Reaction parameters such as precursor concentration, addition of surfactant, temperature, ramp rate, and time were adjusted to kinetically control size and size-distribution, phase, and magnetic properties. In particular, large quantities of excess surfactant (up to 25 : 1 molar ratio) alter reaction kinetics and result in larger particles with uniform size; however, there is often a trade-off between large particles and a narrow size distribution. Iron oxide phase, in addition to nanoparticle size and shape, is critical for establishing magnetic properties such as differential susceptibility (dm/dH) and anisotropy. As an example, we show the importance of obtaining the required size and iron oxide phase for application to Magnetic Particle Imaging (MPI), and describe how phase purity can be controlled. These results provide much of the information necessary to determine which iron oxide synthesis protocol is best suited to a particular application.

Substrate and inhibitor studies of thermolysin-like neutral metalloendopeptidase from kidney membrane fractions. Comparison with bacterial thermolysin.

PubMed

Pozsgay, M; Michaud, C; Liebman, M; Orlowski, M

1986-03-25

The inhibitory constants of a series of synthetic N-carboxymethyl peptide inhibitors and the kinetic parameters (Km, kcat, and kcat/Km) of a series of model synthetic substrates were determined for the membrane-bound kidney metalloendopeptidase isolated from rabbit kidney and compared with those of bacterial thermolysin. The two enzymes show striking similarities with respect to structural requirements for substrate binding to the hydrophobic pocket at the S1' subsite of the active site. Both enzymes showed the highest reaction rates with substrates having leucine residues in this position while phenylalanine residues gave the lowest Km. The two enzymes were also inhibited by the same N-carboxymethyl peptide inhibitors. Although the mammalian enzyme was more susceptible to inhibition than its bacterial counterpart, structural variations in the inhibitor molecules affected the inhibitory constants for both enzymes in a similar manner. The two enzymes differed significantly, however, with respect to the effect of structural changes in the P1 and P2' positions of the substrate on the kinetic parameters of the reaction. The mammalian enzyme showed the highest reaction rates and specificity constants with substrates having the sequence -Phe-Gly-Phe- or -Phe-Ala-Phe- in positions P2, P1, and P1', respectively, while the sequence -Ala-Phe-Phe- was the most favored by the bacterial enzyme. The sequence -Gly-Gly-Phe- as found in enkephalins was not favored by either of the enzymes. Of the substrates having an aminobenzoate group in the P2' position, the mammalian enzyme favored those with the carboxyl group in the meta position while the bacterial enzyme favored those with the carboxyl group in the para position.(ABSTRACT TRUNCATED AT 250 WORDS)

Tidal disruption of a white dwarf by a black hole: the diversity of nucleosynthesis, explosion energy, and the fate of debris streams

NASA Astrophysics Data System (ADS)

Kawana, Kojiro; Tanikawa, Ataru; Yoshida, Naoki

2018-07-01

We run a suite of hydrodynamic simulations of tidal disruption events (TDEs) of a white dwarf (WD) by a black hole (BH) with a wide range of WD/BH masses and orbital parameters. We implement nuclear reactions to study nucleosynthesis and its dynamical effect through release of nuclear energy. The released nuclear energy effectively increases the fraction of unbound ejecta. This effect is weaker for a heavy WD with 1.2 M⊙, because the specific orbital energy distribution of the debris is predominantly determined by the tidal force, rather than by the explosive reactions. The elemental yield of a TDE depends critically on the initial composition of a WD, while the BH mass and the orbital parameters also affect the total amount of synthesized elements. Tanikawa et al. (2017) find that simulations of WD-BH TDEs with low resolution suffer from spurious heating and inaccurate nuclear reaction results. In order to examine the validity of our calculations, we compare the amounts of the synthesized elements with the upper limits of them derived in a way where we can avoid uncertainties due to low resolution. The results are largely consistent, and thus support our findings. We find particular TDEs where early self-intersection of a WD occurs during the first pericentre passage, promoting formation of an accretion disc. We expect that relativistic jets and/or winds would form in these cases because accretion rates would be super-Eddington. The WD-BH TDEs result in a variety of events depending on the WD/BH mass and pericentre radius of the orbit.

URPD: a specific product primer design tool

PubMed Central

2012-01-01

Background Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users. Findings URPD (yoUR Primer Design), a web-based specific product primer design tool, combines the NCBI Reference Sequences (RefSeq), UCSC In-Silico PCR, memetic algorithm (MA) and genetic algorithm (GA) primer design methods to obtain specific primer sets. A friendly user interface is accomplished by built-in parameter settings. The incorporated smooth pipeline operations effectively guide both occasional and advanced users. URPD contains an automated process, which produces feasible primer pairs that satisfy the specific needs of the experimental design with practical PCR amplifications. Visual virtual gel electrophoresis and in silico PCR provide a simulated PCR environment. The comparison of Practical gel electrophoresis comparison to virtual gel electrophoresis facilitates and verifies the PCR experiment. Wet-laboratory validation proved that the system provides feasible primers. Conclusions URPD is a user-friendly tool that provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter settings assist sophisticated researchers in performing experiential PCR. Several novel functions, such as a nucleotide accession number template sequence input, local and global specificity estimation, primer pair redesign, user-interactive sequence scale selection, and virtual and practical PCR gel electrophoresis discrepancies have been developed and integrated into URPD. The URPD program is implemented in JAVA and freely available at http://bio.kuas.edu.tw/urpd/. PMID:22713312

URPD: a specific product primer design tool.

PubMed

Chuang, Li-Yeh; Cheng, Yu-Huei; Yang, Cheng-Hong

2012-06-19

Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users. URPD (yoUR Primer Design), a web-based specific product primer design tool, combines the NCBI Reference Sequences (RefSeq), UCSC In-Silico PCR, memetic algorithm (MA) and genetic algorithm (GA) primer design methods to obtain specific primer sets. A friendly user interface is accomplished by built-in parameter settings. The incorporated smooth pipeline operations effectively guide both occasional and advanced users. URPD contains an automated process, which produces feasible primer pairs that satisfy the specific needs of the experimental design with practical PCR amplifications. Visual virtual gel electrophoresis and in silico PCR provide a simulated PCR environment. The comparison of Practical gel electrophoresis comparison to virtual gel electrophoresis facilitates and verifies the PCR experiment. Wet-laboratory validation proved that the system provides feasible primers. URPD is a user-friendly tool that provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter settings assist sophisticated researchers in performing experiential PCR. Several novel functions, such as a nucleotide accession number template sequence input, local and global specificity estimation, primer pair redesign, user-interactive sequence scale selection, and virtual and practical PCR gel electrophoresis discrepancies have been developed and integrated into URPD. The URPD program is implemented in JAVA and freely available at http://bio.kuas.edu.tw/urpd/.

Bee sting allergy in beekeepers.

PubMed

Eich-Wanger, C; Müller, U R

1998-10-01

Beekeepers are strongly exposed to honey bee stings and therefore at an increased risk to develop IgE-mediated allergy to bee venom. We wondered whether bee venom-allergic beekeepers were different from normally exposed bee venom-allergic patients with regard to clinical and immunological parameters as well as their response to venom immunotherapy. Among the 459 bee venom-allergic patients seen over the 5 year period 1987-91, 62 (14%) were beekeepers and 44 (10%) family members of beekeepers. These two groups were compared with 101 normally exposed bee venom-allergic patients matched with the allergic beekeepers for age and sex, regarding clinical parameters, skin sensitivity, specific IgE and IgG antibodies to bee venom as well as safety and efficacy of venom immunotherapy. As expected, allergic beekeepers had been stung most frequently before the first allergic reaction. The three groups showed a similar severity of allergic symptoms following bee stings and had an equal incidence of atopic diseases. Allergic beekeepers showed higher levels of bee venom-specific serum IgG, lower skin sensitivity and lower levels of bee venom specific serum IgE than bee venom-allergic control patients. A negative correlation between number of stings and skin sensitivity as well as specific IgE was found in allergic beekeepers and their family members, while the number of stings was positively correlated with specific IgG in these two groups. Venom immunotherapy was equally effective in the three groups, but better tolerated by allergic beekeepers than the two other groups. The majority of allergic beekeepers continued bee-keeping successfully under the protection of venom immunotherapy. The lower level of sensitivity in diagnostic tests and the better tolerance of immunotherapy in allergic beekeepers is most likely related to the high level of specific IgG in this group.

Kinetics and mechanism of olefin catalytic hydroalumination by organoaluminum compounds

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

The role of electrostatic interactions in protease surface diffusion and the consequence for interfacial biocatalysis.

PubMed

Feller, Bob E; Kellis, James T; Cascão-Pereira, Luis G; Robertson, Channing R; Frank, Curtis W

2010-12-21

This study examines the influence of electrostatic interactions on enzyme surface diffusion and the contribution of diffusion to interfacial biocatalysis. Surface diffusion, adsorption, and reaction were investigated on an immobilized bovine serum albumin (BSA) multilayer substrate over a range of solution ionic strength values. Interfacial charge of the enzyme and substrate surface was maintained by performing the measurements at a fixed pH; therefore, electrostatic interactions were manipulated by changing the ionic strength. The interfacial processes were investigated using a combination of techniques: fluorescence recovery after photobleaching, surface plasmon resonance, and surface plasmon fluorescence spectroscopy. We used an enzyme charge ladder with a net charge ranging from -2 to +4 with respect to the parent to systematically probe the contribution of electrostatics in interfacial enzyme biocatalysis on a charged substrate. The correlation between reaction rate and adsorption was determined for each charge variant within the ladder, each of which displayed a maximum rate at an intermediate surface concentration. Both the maximum reaction rate and adsorption value at which this maximum rate occurs increased in magnitude for the more positive variants. In addition, the specific enzyme activity increased as the level of adsorption decreased, and for the lowest adsorption values, the specific enzyme activity was enhanced compared to the trend at higher surface concentrations. At a fixed level of adsorption, the specific enzyme activity increased with positive enzyme charge; however, this effect offers diminishing returns as the enzyme becomes more highly charged. We examined the effect of electrostatic interactions on surface diffusion. As the binding affinity was reduced by increasing the solution ionic strength, thus weakening electrostatic interaction, the rate of surface diffusion increased considerably. The enhancement in specific activity achieved at the lowest adsorption values is explained by the substantial rise in surface diffusion at high ionic strength due to decreased interactions with the surface. Overall, knowledge of the electrostatic interactions can be used to control surface parameters such as surface concentration and surface diffusion, which intimately correlate with surface biocatalysis. We propose that the maximum reaction rate results from a balance between adsorption and surface diffusion. The above finding suggests enzyme engineering and process design strategies for improving interfacial biocatalysis in industrial, pharmaceutical, and food applications.

The role of surface nonuniformity in controlling the initiation of a galvanic replacement reaction.

PubMed

Cobley, Claire M; Zhang, Qiang; Song, Wilbur; Xia, Younan

2011-06-06

The use of silver nanocrystals--asymmetrically truncated octahedrons and nanobars--characterized by a nonuniform surface as substrates for a galvanic replacement reaction was investigated. As the surfaces of these nanocrystals contain facets with a variety of different areas, shapes, and atomic arrangements, we were able to examine the roles of these parameters in different stages of the galvanic replacement reaction with HAuCl(4) (e.g., pitting, hollowing, pit closing, and pore formation), and thus obtain a deeper understanding of the reaction mechanism than is possible with silver nanocubes. We found that the most important of these parameters was the atomic arrangement, that is, whether the surface was capped by a {100} or {111} facet, and that the area and shape of the facet had essentially no effect on the initiation of the reaction. Interestingly, through the reaction with asymmetrically truncated octahedrons, we were also able to demonstrate that even when pitting occurred over a large area, this region would be sealed through a combination of atomic diffusion and deposition during the intermediate stages of the reaction. Consequently, even if pitting occurred across a large percentage of the nanocrystal surface, it was still possible to maintain the morphology of the template throughout the reaction. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experimental Studies of Nuclear Physics Input for γ -Process Nucleosynthesis

NASA Astrophysics Data System (ADS)

Scholz, Philipp; Heim, Felix; Mayer, Jan; Netterdon, Lars; Zilges, Andreas

The predictions of reaction rates for the γ process in the scope of the Hauser-Feshbach statistical model crucially depend on nuclear physics input-parameters as optical-model potentials (OMP) or γ -ray strength functions. Precise cross-section measurements at astrophysically relevant energies help to constrain adopted models and, therefore, to reduce the uncertainties in the theoretically predicted reaction rates. During the last years, several cross-sections of charged-particle induced reactions on heavy nuclei have been measured at the University of Cologne. Either by means of the in-beam method at the HORUS γ -ray spectrometer or the activation technique using the Cologne Clover Counting Setup, total and partial cross-sections could be used to further constrain different models for nuclear physics input-parameters. It could be shown that modifications on the α -OMP in the case of the 112Sn(α , γ ) reaction also improve the description of the recently measured cross sections of the 108Cd(α , γ ) and 108Cd(α , n) reaction and other reactions as well. Partial cross-sections of the 92Mo(p, γ ) reaction were used to improve the γ -strength function model in 93Tc in the same way as it was done for the 89Y(p, γ ) reaction.

Heavy metal recovery from electric arc furnace steel slag by using hydrochloric acid leaching

NASA Astrophysics Data System (ADS)

Wei, Lim Jin; Haan, Ong Teng; Shean Yaw, Thomas Choong; Chuah Abdullah, Luqman; Razak, Mus'ab Abdul; Cionita, Tezara; Toudehdehghan, Abdolreza

2018-03-01

Electric Arc Furnace steel slag (EAFS) is the waste produced in steelmaking industry. Environmental problem such as pollution will occur when dumping the steel slag waste into the landfill. These steel slags have properties that are suitable for various applications such as water treatment and wastewater. The objective of this study is to develop efficient and economical chlorination route for EAFS extraction by using leaching process. Various parameters such as concentration of hydrochloric acid, particle size of steel slag, reaction time and reaction temperature are investigated to determine the optimum conditions. As a result, the dissolution rate can be determined by changing the parameters, such as concentration of hydrochloric acid, particle size of steel slag, reaction time and reaction temperature. The optimum conditions for dissolution rates for the leaching process is at 3.0 M hydrochloric acid, particle size of 1.18 mm, reaction time of 2.5 hour and the temperature of 90°C.

Influences of growth parameters on the reaction pathway during GaN synthesis

NASA Astrophysics Data System (ADS)

Zhang, Zhi; Liu, Zhongyi; Fang, Haisheng

2018-01-01

Gallium nitride (GaN) film growth is a complicated physical and chemical process including fluid flow, heat transfer, species transport and chemical reaction. Study of the reaction mechanism, i.e., the reaction pathway, is important for optimizing the growth process in the actual manufacture. In the paper, the growth pathway of GaN in a closed-coupled showerhead metal-organic chemical vapor deposition (CCS-MOCVD) reactor is investigated in detail using computational fluid dynamics (CFD). Influences of the process parameters, such as the chamber pressure, the inlet temperature, the susceptor temperature and the pre-exponential factor, on the reaction pathway are examined. The results show that increases of the chamber pressure or the inlet temperature, as well as reductions of the susceptor temperature or the pre-exponential factor lead to the adduct route dominating the growth. The deposition rate contributed by the decomposition route, however, can be enhanced dramatically by increasing the inlet temperature, the susceptor temperature and the pre-exponential factor.

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

Radiation reaction in fusion plasmas.

PubMed

Hazeltine, R D; Mahajan, S M

2004-10-01

The effects of a radiation reaction on thermal electrons in a magnetically confined plasma, with parameters typical of planned burning plasma experiments, are studied. A fully relativistic kinetic equation that includes the radiation reaction is derived. The associated rate of phase-space contraction is computed and the relative importance of the radiation reaction in phase space is estimated. A consideration of the moments of the radiation reaction force show that its effects are typically small in reactor-grade confined plasmas, but not necessarily insignificant.

[Study of Reaction Dynamics between Bovine Serum Albumin and Folic Acid by Stopped-Flow/Fluorescence].

PubMed

Ye, San-xian; Luo, Yun-jing; Qiao, Shu-liang; Li, Li; Liu, Cai-hong; Shi, Jian-long; An, Xue-jing

2016-01-01

As a kind of coenzyme of one-carbon enzymes in vivo, folic acid belongs to B vitamins, which can interact with other vitamins and has great significance for converting among amino acids, dividing growth of cells and protein synthesis reactions. Half-life, concentration and reaction rate constant of drugs are important parameters in pharmacokinetic study. In this paper, by utilizing fluorescence spectrophotometer and stopped-flow spectrum analyzer, reaction kinetic parameters between bovine serum albumin(BSA) and folic acid in a bionic system have been investigated, which provide references for parameters of drug metabolism related to folic acid. By using Stern-Volmer equation dealing with fluorescence quenching experiments data, we concluded that under 25, 30, and 37 degrees C, the static quenching constants of folic acid to intrinsic fluorescence from bovine serum albumin were 2.455 x 10(10), 4.900 x 10(10) and 6.427 x 10(10) L x mol(-1) x s(-1) respectively; The results of kinetic reaction rate have shown that the reaction rate of BSA and folic acid are greater than 100 mol x L(-1) x s(-1) at different temperatures, pH and buffering media, illustrating that the quenching mechanism between BSA and folic acid is to form composite static quenching process. Reaction concentration of bovine serum albumin and its initial concentration were equal to the secondary reaction formula, and the correlation coefficient was 0.998 7, while the half-life (t1/2) was 0.059 s at physiological temperature. With the increase of folic acid concentration, the apparent rate constant of this reaction had a linear increasing trend, the BSA fluorescence quenching rate constant catalyzed by folic acid was 3.174 x 10(5) mol x L(-1) x s(-1). Furthermore, with different buffer, the apparent rate constant and reaction rate constant of BSA interacting with folic acid were detected to explore the influence on the reaction under physiological medium, which is of great significance to determine the clinical regimen, forecast the efficacy and toxicity of drugs and rational drug.

Task inhibition, conflict, and the n-2 repetition cost: A combined computational and empirical approach.

PubMed

Sexton, Nicholas J; Cooper, Richard P

2017-05-01

Task inhibition (also known as backward inhibition) is an hypothesised form of cognitive inhibition evident in multi-task situations, with the role of facilitating switching between multiple, competing tasks. This article presents a novel cognitive computational model of a backward inhibition mechanism. By combining aspects of previous cognitive models in task switching and conflict monitoring, the model instantiates the theoretical proposal that backward inhibition is the direct result of conflict between multiple task representations. In a first simulation, we demonstrate that the model produces two effects widely observed in the empirical literature, specifically, reaction time costs for both (n-1) task switches and n-2 task repeats. Through a systematic search of parameter space, we demonstrate that these effects are a general property of the model's theoretical content, and not specific parameter settings. We further demonstrate that the model captures previously reported empirical effects of inter-trial interval on n-2 switch costs. A final simulation extends the paradigm of switching between tasks of asymmetric difficulty to three tasks, and generates novel predictions for n-2 repetition costs. Specifically, the model predicts that n-2 repetition costs associated with hard-easy-hard alternations are greater than for easy-hard-easy alternations. Finally, we report two behavioural experiments testing this hypothesis, with results consistent with the model predictions. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

eFurniture for home-based frailty detection using artificial neural networks and wireless sensors.

PubMed

Chang, Yu-Chuan; Lin, Chung-Chih; Lin, Pei-Hsin; Chen, Chun-Chang; Lee, Ren-Guey; Huang, Jing-Siang; Tsai, Tsai-Hsuan

2013-02-01

The purpose of this study is to integrate wireless sensor technologies and artificial neural networks to develop a system to manage personal frailty information automatically. The system consists of five parts: (1) an eScale to measure the subject's reaction time; (2) an eChair to detect slowness in movement, weakness and weight loss; (3) an ePad to measure the subject's balancing ability; (4) an eReach to measure body extension; and (5) a Home-based Information Gateway, which collects all the data and predicts the subject's frailty. Using a furniture-based measuring device to provide home-based measurement means that health checks are not confined to health institutions. We designed two experiments to obtain optimum frailty prediction model and test overall system performance: (1) We developed a three-step process to adjust different parameters to obtain an optimized neural identification network whose parameters include initialization, L.R. dec and L.R. inc. The post-process identification rate increased from 77.85% to 83.22%. (2) We used 149 cases to evaluate the sensitivity and specificity of our frailty prediction algorithm. The sensitivity and specificity of this system are 79.71% and 86.25% respectively. These results show that our system is a high specificity prediction tool that can be used to assess frailty. Copyright © 2011 IPEM. Published by Elsevier Ltd. All rights reserved.

Systems analysis of the CO2 concentrating mechanism in cyanobacteria

PubMed Central

Mangan, Niall M; Brenner, Michael P

2014-01-01

Cyanobacteria are photosynthetic bacteria with a unique CO2 concentrating mechanism (CCM), enhancing carbon fixation. Understanding the CCM requires a systems level perspective of how molecular components work together to enhance CO2 fixation. We present a mathematical model of the cyanobacterial CCM, giving the parameter regime (expression levels, catalytic rates, permeability of carboxysome shell) for efficient carbon fixation. Efficiency requires saturating the RuBisCO reaction, staying below saturation for carbonic anhydrase, and avoiding wasteful oxygenation reactions. We find selectivity at the carboxysome shell is not necessary; there is an optimal non-specific carboxysome shell permeability. We compare the efficacy of facilitated CO2 uptake, CO2 scavenging, and HCO3− transport with varying external pH. At the optimal carboxysome permeability, contributions from CO2 scavenging at the cell membrane are small. We examine the cumulative benefits of CCM spatial organization strategies: enzyme co-localization and compartmentalization. DOI: http://dx.doi.org/10.7554/eLife.02043.001 PMID:24842993

Investigation of activation cross sections of deuteron induced reactions on indium up to 40 MeV for production of a 113 Sn/113m In generator.

PubMed

Tárkányi, F; Hermanne, A; Király, B; Takács, S; Ditrói, F; Baba, M; Ignatyuk, A V

2011-01-01

(113)Sn (115.09 d) is the parent nuclide of the (113)Sn/(113m)In generator system. (113m)In (99.476 min) is used in diagnostic nuclear medicine and as an Auger-electron emitter is a candidate for internal radiotherapy. Excitation functions of the (nat)In(d,x) (113 mg)Sn, (116 m)In, (ind115m)In, (114m)In, (ind113m)In, (cum111)In, (115g)Cd,(111m)Cd reactions were measured up to 40 MeV for the first time. The experimental results were compared with the curves calculated with the ALICE-D and EMPIRE-D theoretical model codes and curves given in the EAF-2007 and TENDL-2009 databases. Thick target yields, impurity levels and specific activities for the optimal energy range were deduced and compared with the same parameters of other charged particle production routes of (113)Sn. Copyright © 2010 Elsevier Ltd. All rights reserved.

Core-Shell Structuring of Pure Metallic Aerogels towards Highly Efficient Platinum Utilization for the Oxygen Reduction Reaction

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

Cai, Bin; Hübner, René; Sasaki, Kotaro

The development of core–shell structures remains a fundamental challenge for pure metallic aerogels. Here we report the synthesis of Pd xAu-Pt core–shell aerogels composed of an ultrathin Pt shell and a composition-tunable Pd xAu alloy core. The universality of this strategy ensures the extension of core compositions to Pd transition-metal alloys. The core–shell aerogels exhibited largely improved Pt utilization efficiencies for the oxygen reduction reaction and their activities show a volcano-type relationship as a function of the lattice parameter of the core substrate. The maximum mass and specific activities are 5.25 A mg Pt -1 and 2.53 mA cm -2,more » which are 18.7 and 4.1 times higher than those of Pt/C, respectively, demonstrating the superiority of the core–shell metallic aerogels. The proposed core-based activity descriptor provides a new possible strategy for the design of future core–shell electrocatalysts.« less

Microwave-Assisted Superheating and/or Microwave-Specific Superboiling (Nucleation-Limited Boiling) of Liquids Occurs under Certain Conditions but is Mitigated by Stirring.

PubMed

Ferrari, Anthony; Hunt, Jacob; Stiegman, Albert; Dudley, Gregory B

2015-12-04

Temporary superheating and sustained nucleation-limited "superboiling" of unstirred liquids above the normal atmospheric boiling point have been documented during microwave heating. These phenomena are reliably observed under prescribed conditions, although the duration (of superheating) and magnitude (of superheating and superboiling) vary according to system parameters such as volume of the liquid and the size and shape of the vessel. Both phenomena are mitigated by rapid stirring with an appropriate stir bar and/or with the addition of boiling chips, which provide nucleation sites to support the phase-change from liquid to gas. With proper experimental design and especially proper stirring, the measured temperature of typical organic reaction mixtures heated at reflux will be close to the normal boiling point temperature of the solvent, whether heated using microwave radiation or conventional convective heat transfer. These observations are important to take into consideration when comparing reaction rates under conventional and microwave heating.

Cold work study on a 316LN modified alloy for the ITER TF coil conduit

DOE PAGES

Walsh, Robert; Toplosky, V. J.; McRae, D. M.; ...

2012-06-01

The primary structural component of the cable-in-conduit conductor (CICC) magnets, such as the ITER TF coils is the conduit. This function creates requirements for 4 K strength, toughness, fatigue crack resistance, and ductility after exposure to the superconductor's reaction heat treatment. The tensile ductility of a steel is a quality factor related to fatigue and fracture resistance that can be evaluated more economically with tensile tests rather than fatigue and fracture tests. We subject 316LN modified base metal and welds to a range of cold work from 0% to 20% and a subsequent Nb 3Sn reaction heat treatment to evaluatemore » the effects on the tensile properties. With the addition of cold work, the 4 K yield strength increases while tensile elongation decreases in both the base metal and weld. Our results are compared to previously published data on the same alloy to evaluate the use of tensile ductility parameters as a materials qualification specification in magnet design.« less

Competition between Hydrogen Bonding and Proton Transfer during Specific Anion Recognition by Dihomooxacalix[4]arene Bidentate Ureas.

PubMed

Martínez-González, Eduardo; González, Felipe J; Ascenso, José R; Marcos, Paula M; Frontana, Carlos

2016-08-05

Competition between hydrogen bonding and proton transfer reactions was studied for systems composed of electrogenerated dianionic species from dinitrobenzene isomers and substituted dihomooxacalix[4]arene bidentate urea derivatives. To analyze this competition, a second-order ErCrCi mechanism was considered where the binding process is succeeded by proton transfer and the voltammetric responses depend on two dimensionless parameters: the first related to hydrogen bonding reactions, and the second one to proton transfer processes. Experimental results indicated that, upon an increase in the concentration of phenyl-substituted dihomooxacalix[4]arene bidentate urea, voltammetric responses evolve from diffusion-controlled waves (where the binding process is at chemical equilibrium) into irreversible kinetic responses associated with proton transfer. In particular, the 1,3-dinitrobenzene isomer showed a higher proton transfer rate constant (∼25 M(-1) s(-1)) compared to that of the 1,2-dinitrobenzene (∼5 M(-1) s(-1)), whereas the 1,4-dinitrobenzene did not show any proton transfer effect in the experimental conditions employed.

What dictates which ion, I- or Br-, mediates the growth of cubic Pd nanocrystals?

PubMed

Wang, Ze-Hong; Wu, Ya-Jiao; Xue, Huan-Huan; Zhou, Lin-Nan; Geng, Wen-Chao; Yi, Hai-Bo; Li, Yong-Jun

2018-04-25

Cubic Pd nanocrystals (CPNCs) as one of typical nanostructures are generally fabricated using I- or Br- as capping ions. However, which ion, I- or Br-, exclusively mediates the growth of CPNCs in a given reaction system is not well understood. Herein, regardless of I- or Br- as the capping ion, we successfully achieved CPNCs in the same reaction system simply by adjusting the pH. Based on the Finke-Watzky kinetic model, an increase in pH accelerates the overall reduction rate of Pd2+, and the formation of CPNCs only occurs over the range of specific solution reduction rate constants (k1). This kinetically illuminates that the reduction rate of Pd2+ is the physicochemical parameter that determines which ion, I- or Br-, dictates the growth of CPNCs. Also, density functional theory (DFT) calculations further elucidate the dependence of the reduction rate of Pd2+ on pH and the configuration of the activated Pd2+ complex.

Study of the prevalence of chronic, non-specific lung disease and related health problems in the grain-handling industry. Technical report

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

Rankin, J.; Bates, J.; Claremont, A.

1986-10-01

A total of 310 grain handlers was studied, with attention to prevalence and characteristics of clinical, psychological, immunological, radiological, serological blood and urine parameters to determine any apparent effects from grain-dust exposure. Grain handlers had a higher prevalence of respiratory symptoms and signs than did the city workers who comprised the comparison group. Evidence of accumulative respiratory effect due to recurring exposures to grain dust was found. Acute and chronic airway reactions were induced by exposure to grain dust. Wheezing and dyspnea on exposure were related to length of employment. Grain fever syndrome was prevalent. Cases of acute recurrent conjunctivitismore » and rhinitis were found along with skin pruritus, mainly on exposure to barley dust. Pesticide exposure caused temporary disabling symptoms. Lung function was adversely affected by grain-dust exposure. Exposure to grain mites and insects in contaminated cereal grain caused a reaction among grain workers.« less

Properties of targeted preamplification in DNA and cDNA quantification.

PubMed

Andersson, Daniel; Akrap, Nina; Svec, David; Godfrey, Tony E; Kubista, Mikael; Landberg, Göran; Ståhlberg, Anders

2015-01-01

Quantification of small molecule numbers often requires preamplification to generate enough copies for accurate downstream enumerations. Here, we studied experimental parameters in targeted preamplification and their effects on downstream quantitative real-time PCR (qPCR). To evaluate different strategies, we monitored the preamplification reaction in real-time using SYBR Green detection chemistry followed by melting curve analysis. Furthermore, individual targets were evaluated by qPCR. The preamplification reaction performed best when a large number of primer pairs was included in the primer pool. In addition, preamplification efficiency, reproducibility and specificity were found to depend on the number of template molecules present, primer concentration, annealing time and annealing temperature. The amount of nonspecific PCR products could also be reduced about 1000-fold using bovine serum albumin, glycerol and formamide in the preamplification. On the basis of our findings, we provide recommendations how to perform robust and highly accurate targeted preamplification in combination with qPCR or next-generation sequencing.

Core-Shell Structuring of Pure Metallic Aerogels towards Highly Efficient Platinum Utilization for the Oxygen Reduction Reaction

DOE PAGES

Cai, Bin; Hübner, René; Sasaki, Kotaro; ...

2018-02-08

The development of core–shell structures remains a fundamental challenge for pure metallic aerogels. Here we report the synthesis of Pd xAu-Pt core–shell aerogels composed of an ultrathin Pt shell and a composition-tunable Pd xAu alloy core. The universality of this strategy ensures the extension of core compositions to Pd transition-metal alloys. The core–shell aerogels exhibited largely improved Pt utilization efficiencies for the oxygen reduction reaction and their activities show a volcano-type relationship as a function of the lattice parameter of the core substrate. The maximum mass and specific activities are 5.25 A mg Pt -1 and 2.53 mA cm -2,more » which are 18.7 and 4.1 times higher than those of Pt/C, respectively, demonstrating the superiority of the core–shell metallic aerogels. The proposed core-based activity descriptor provides a new possible strategy for the design of future core–shell electrocatalysts.« less

Parameterization of phosphine ligands demonstrates enhancement of nickel catalysis via remote steric effects.

PubMed

Wu, Kevin; Doyle, Abigail G

2017-08-01

The field of Ni-catalysed cross-coupling has seen rapid recent growth because of the low cost of Ni, its earth abundance, and its ability to promote unique cross-coupling reactions. Whereas advances in the related field of Pd-catalysed cross-coupling have been driven by ligand design, the development of ligands specifically for Ni has received minimal attention. Here, we disclose a class of phosphines that enable the Ni-catalysed Csp 3 Suzuki coupling of acetals with boronic acids to generate benzylic ethers, a reaction that failed with known ligands for Ni and designer phosphines for Pd. Using parameters to quantify phosphine steric and electronic properties together with regression statistical analysis, we identify a model for ligand success. The study suggests that effective phosphines feature remote steric hindrance, a concept that could guide future ligand design tailored to Ni. Our analysis also reveals that two classic descriptors for ligand steric environment-cone angle and % buried volume-are not equivalent, despite their treatment in the literature.

Polynucleotide: adenosine glycosidase activity of saporin-L1: effect on DNA, RNA and poly(A).

PubMed Central

Barbieri, L; Valbonesi, P; Gorini, P; Pession, A; Stirpe, F

1996-01-01

The ribosome-inactivating proteins (RIPs) are a family of plant enzymes for which a unique activity has been determined: rRNA N-glycosidase, which removes adenine at a specific universally conserved position (A4324 in the case of rat ribosomes). Here we report that saporin-L1, a RIP from the leaves of Saponaria officinalis, recognizes other substrates, including RNAs from different sources, DNA and poly(A). Saporin-L1 depurinated DNA extensively and released adenine from all adenine-containing polynucleotides tested. Adenine was the only base released from DNA or artificial polynucleotides. The characteristics of the reactions catalysed by saporin-L1 have been determined: optimal pH and temperature, ionic requirements, and the kinetic parameters Km and kcat. The reaction proceeded without cofactors, at low ionic strength, in the absence of Mg2+ and K+. Saporin-L1 had no activity towards various adenine-containing non-polynucleotide compounds (cytokinins, cofactors, nucleotides). This plant protein may now be classified as a polynucleotide: adenosine glycosidase. PMID:8912688

Substrate milling pretreatment as a key parameter for Solid-State Anaerobic Digestion optimization.

PubMed

Motte, J-C; Escudié, R; Hamelin, J; Steyer, J-P; Bernet, N; Delgenes, J-P; Dumas, C

2014-12-01

The effect of milling pretreatment on performances of Solid-State Anaerobic Digestion (SS-AD) of raw lignocellulosic residue is still controverted. Three batch reactors treating different straw particle sizes (milled 0.25 mm, 1 mm and 10 mm) were followed during 62 days (6 sampling dates). Although a fine milling improves substrate accessibility and conversion rate (up to 30% compared to coarse milling), it also increases the risk of media acidification because of rapid and high acids production during fermentation of the substrate soluble fraction. Meanwhile, a gradual adaptation of microbial communities, were observed according to both reaction progress and methanogenic performances. The study concluded that particle size reduction affected strongly the performances of the reaction due to an increase of substrate bioaccessibility. An optimization of SS-AD processes thanks to particle size reduction could therefore be applied at farm or industrial scale only if a specific management of the soluble compounds is established. Copyright © 2014 Elsevier Ltd. All rights reserved.

The impact of physical activity and sex differences on intraindividual variability in inhibitory performance in older adults.

PubMed

Fagot, Delphine; Chicherio, Christian; Albinet, Cédric T; André, Nathalie; Audiffren, Michel

2017-09-04

It is well-known that processing speed and executive functions decline with advancing age. However, physical activity (PA) has a positive impact on cognitive performances in aging, specifically for inhibition. Less is known concerning intraindividual variability (iiV) in reaction times. This study aims to investigate the influence of PA and sex differences on iiV in inhibitory performance during aging. Healthy adults were divided into active and sedentary groups according to PA level. To analyse iiV in reaction times, individual mean, standard deviation and the ex-Gaussian parameters were considered. An interaction between activity level and sex was revealed, sedentary females being slower and more variable than sedentary men. No sex differences were found in the active groups. These results indicate that the negative impact of sedentariness on cognitive performance in older age is stronger for females. The present findings underline the need to consider sex differences in active aging approaches.

Green synthesis of isopropyl myristate in novel single phase medium Part I: Batch optimization studies.

PubMed

Vadgama, Rajeshkumar N; Odaneth, Annamma A; Lali, Arvind M

2015-12-01

Isopropyl myristate finds many applications in food, cosmetic and pharmaceutical industries as an emollient, thickening agent, or lubricant. Using a homogeneous reaction phase, non-specific lipase derived from Candida antartica, marketed as Novozym 435, was determined to be most suitable for the enzymatic synthesis of isopropyl myristate. The high molar ratio of alcohol to acid creates novel single phase medium which overcomes mass transfer effects and facilitates downstream processing. The effect of various reaction parameters was optimized to obtain a high yield of isopropyl myristate. Effect of temperature, agitation speed, organic solvent, biocatalyst loading and batch operational stability of the enzyme was systematically studied. The conversion of 87.65% was obtained when the molar ratio of isopropyl alcohol to myristic acid (15:1) was used with 4% (w/w) catalyst loading and agitation speed of 150 rpm at 60 °C. The enzyme has also shown good batch operational stability under optimized conditions.

Parameterization of phosphine ligands demonstrates enhancement of nickel catalysis via remote steric effects

NASA Astrophysics Data System (ADS)

Wu, Kevin; Doyle, Abigail G.

2017-08-01

The field of Ni-catalysed cross-coupling has seen rapid recent growth because of the low cost of Ni, its earth abundance, and its ability to promote unique cross-coupling reactions. Whereas advances in the related field of Pd-catalysed cross-coupling have been driven by ligand design, the development of ligands specifically for Ni has received minimal attention. Here, we disclose a class of phosphines that enable the Ni-catalysed Csp3 Suzuki coupling of acetals with boronic acids to generate benzylic ethers, a reaction that failed with known ligands for Ni and designer phosphines for Pd. Using parameters to quantify phosphine steric and electronic properties together with regression statistical analysis, we identify a model for ligand success. The study suggests that effective phosphines feature remote steric hindrance, a concept that could guide future ligand design tailored to Ni. Our analysis also reveals that two classic descriptors for ligand steric environment—cone angle and % buried volume—are not equivalent, despite their treatment in the literature.

Dichotomous-noise-induced pattern formation in a reaction-diffusion system

NASA Astrophysics Data System (ADS)

Das, Debojyoti; Ray, Deb Shankar

2013-06-01

We consider a generic reaction-diffusion system in which one of the parameters is subjected to dichotomous noise by controlling the flow of one of the reacting species in a continuous-flow-stirred-tank reactor (CSTR) -membrane reactor. The linear stability analysis in an extended phase space is carried out by invoking Furutzu-Novikov procedure for exponentially correlated multiplicative noise to derive the instability condition in the plane of the noise parameters (correlation time and strength of the noise). We demonstrate that depending on the correlation time an optimal strength of noise governs the self-organization. Our theoretical analysis is corroborated by numerical simulations on pattern formation in a chlorine-dioxide-iodine-malonic acid reaction-diffusion system.

Residual thermal stresses in a solid sphere cast from a thermosetting material

NASA Technical Reports Server (NTRS)

Levitsky, M.; Shaffer, B. W.

1975-01-01

Expressions are developed for the residual thermal stresses in a solid sphere cast from a chemically hardening thermosetting material in a rigid spherical mold. The description of the heat generation rate and temperature variation is derived from a first-order chemical reaction. Solidification is described by the continuous transformation of the material from an inviscid liquidlike state into an elastic solid, with intermediate properties determined by the degree of chemical reaction. Residual stress components are obtained as functions of the parameters of the hardening process and the properties of the hardening material. Variation of the residual stresses with a nondimensionalized reaction rate parameter and the relative compressibility of the hardened material is discussed in detail.

Accuracy of Reaction Cross Section for Exotic Nuclei in Glauber Model Based on MCMC Diagnostics

NASA Astrophysics Data System (ADS)

Rueter, Keiti; Novikov, Ivan

2017-01-01

Parameters of a nuclear density distribution for an exotic nuclei with halo or skin structures can be determined from the experimentally measured reaction cross-section. In the presented work, to extract parameters such as nuclear size information for a halo and core, we compare experimental data on reaction cross-sections with values obtained using expressions of the Glauber Model. These calculations are performed using a Markov Chain Monte Carlo algorithm. We discuss the accuracy of the Monte Carlo approach and its dependence on k*, the power law turnover point in the discreet power spectrum of the random number sequence and on the lag-1 autocorrelation time of the random number sequence.

A preliminary study of head-up display assessment techniques. 2: HUD symbology and panel information search time

NASA Technical Reports Server (NTRS)

Guercio, J. G.; Haines, R. F.

1978-01-01

Twelve commercial pilots were shown 50 high-fidelity slides of a standard aircraft instrument panel with the airspeed, altitude, ADI, VSI, and RMI needles in various realistic orientations. Fifty slides showing an integrated head-up display (HUD) symbology containing an equivalent number of flight parameters as above (with flight path replacing VSI) were also shown. Each subject was told what flight parameter to search for just before each slide was exposed and was given as long as needed (12 sec maximum) to respond by verbalizing the parameter's displayed value. The results for the 100-percent correct data indicated that: there was no significant difference in mean reaction time (averaged across all five flight parameters) between the instrument panel and HUD slides; and a statistically significant difference in mean reaction time was found in responding to different flight parameters.

Burst nucleation by hot injection for size controlled synthesis of ε-cobalt nanoparticles.

PubMed

Zacharaki, Eirini; Kalyva, Maria; Fjellvåg, Helmer; Sjåstad, Anja Olafsen

2016-01-01

Reproducible growth of narrow size distributed ε-Co nanoparticles with a specific size requires full understanding and identification of the role of essential synthesis parameters for the applied synthesis method. For the hot injection methodology, a significant discrepancy with respect to obtained sizes and applied reaction conditions is reported. Currently, a systematic investigation controlling key synthesis parameters as injection-temperature and time, metal to surfactant ratio and reaction holding time in terms of their impact on mean ([Formula: see text]mean) and median ([Formula: see text]median) particle diameter using dichlorobenzene (DCB), Co2(CO)8 and oleic acid (OA) as the reactant matrix is lacking. A series of solution-based ε-Co nanoparticles were synthesized using the hot injection method. Suspensions and obtained particles were analyzed by DLS, ICP-OES, (synchrotron)XRD and TEM. Rietveld refinements were used for structural analysis. Mean ([Formula: see text]mean) and median ([Formula: see text]median) particle diameters were calculated with basis in measurements of 250-500 particles for each synthesis. 95 % bias corrected confidence intervals using bootstrapping were calculated for syntheses with three or four replicas. ε-Co NPs in the size range ~4-10 nm with a narrow size distribution are obtained via the hot injection method, using OA as the sole surfactant. Typically the synthesis yield is ~75 %, and the particles form stable colloidal solutions when redispersed in hexane. Reproducibility of the adopted synthesis procedure on replicate syntheses was confirmed. We describe in detail the effects of essential synthesis parameters, such as injection-temperature and time, metal to surfactant ratio and reaction holding time in terms of their impact on mean ([Formula: see text]mean) and median ([Formula: see text]median) particle diameter. The described synthesis procedure towards ε-Co nanoparticles (NPs) is concluded to be robust when controlling key synthesis parameters, giving targeted particle diameters with a narrow size distribution. We have identified two major synthesis parameters which control particle size, i.e., the metal to surfactant molar ratio and the injection temperature of the hot OA-DCB solution into which the cobalt precursor is injected. By increasing the metal to surfactant molar ratio, the mean particle diameter of the ε-Co NPs has been found to increase. Furthermore, an increase in the injection temperature of the hot OA-DCB solution into which the cobalt precursor is injected, results in a decrease in the mean particle diameter of the ε-Co NPs, when the metal to surfactant molar ratio [Formula: see text] is fixed at ~12.9.

Mechanism of protein precipitation and stabilization by co-solvents

NASA Astrophysics Data System (ADS)

Timasheff, Serge N.; Arakawa, Tsutomu

1988-07-01

The interactions between proteins and a number of substances which, when present at high concentration, stabilize or precipitate proteins, have been analyzed in terms of the preferential interactions of these co-solvents with proteins. In all cases, stabilization or precipitation was accompanied by preferential exclusion of the co-solvent from the immediate domain of the protein, i.e., preferential hydration of the protein. This means that addition of the co-solvent to the aqueous protein solution increased the chemical potentials of both components. The thermodynamic interaction parameters derived from such data make it possible to calculate the salting out constant, Ks, as well as to construct a phase isotherm for any given solvent mixture which indicates the limiting protein solubility. The salting-out effect can be decomposed into contributions from non-specific preferential exclusion and specific binding of the ligand to the protein, the balance leading to solubilization or precipitation. In reactions, such as denaturation, the effect of co-solvent on the reaction depends on the difference in the preferential interactions of the two end states of the protein. Principal sources of preferential exclusion have been identified as steric exclusion, increase of the surface tension of water by the co-solvent, repulsion by charged loci on the protein and solvophobicity.

Late-time emission of prompt fission γ rays

DOE PAGES

Talou, Patrick; Kawano, Toshihiko; Stetcu, Ionel; ...

2016-12-22

The emission of prompt fission γ rays within a few nanoseconds to a few microseconds following the scission point is studied in the Hauser-Feshbach formalism applied to the deexcitation of primary excited fission fragments. Neutron and γ-ray evaporations from fully accelerated fission fragments are calculated in competition at each stage of the decay, and the role of isomers in the fission products, before β decay, is analyzed. The time evolution of the average total γ-ray energy, the average total γ-ray multiplicity, and the fragment-specific γ-ray spectra is presented in the case of neutron-induced fission reactions of 235U and 239Pu, asmore » well as spontaneous fission of 252Cf. The production of specific isomeric states is calculated and compared to available experimental data. About 7% of all prompt fission γ rays are predicted to be emitted between 10 ns and 5 μs following fission, in the case of 235U and 239Pu( nth,f) reactions, and up to 3% in the case of 252Cf spontaneous fission. The cumulative average total γ-ray energy increases by 2% to 5% in the same time interval. Lastly, those results are shown to be robust against significant changes in the model input parameters.« less

Aspergillus Polymerase Chain Reaction: Systematic Review of Evidence for Clinical Use in Comparison With Antigen Testing

PubMed Central

White, P. Lewis; Wingard, John R.; Bretagne, Stéphane; Löffler, Jürgen; Patterson, Thomas F.; Slavin, Monica A.; Barnes, Rosemary A.; Pappas, Peter G.; Donnelly, J. Peter

2015-01-01

Background. Aspergillus polymerase chain reaction (PCR) was excluded from the European Organisation for the Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG) definitions of invasive fungal disease because of limited standardization and validation. The definitions are being revised. Methods. A systematic literature review was performed to identify analytical and clinical information available on inclusion of galactomannan enzyme immunoassay (GM-EIA) (2002) and β-d-glucan (2008), providing a minimal threshold when considering PCR. Categorical parameters and statistical performance were compared. Results. When incorporated, GM-EIA and β-d-glucan sensitivities and specificities for diagnosing invasive aspergillosis were 81.6% and 91.6%, and 76.9% and 89.4%, respectively. Aspergillus PCR has similar sensitivity and specificity (76.8%–88.0% and 75.0%–94.5%, respectively) and comparable utility. Methodological recommendations and commercial PCR assays assist standardization. Although all tests have limitations, currently, PCR is the only test with independent quality control. Conclusions. We propose that there is sufficient evidence that is at least equivalent to that used to include GM-EIA and β-d-glucan testing, and that PCR is now mature enough for inclusion in the EORTC/MSG definitions. PMID:26113653

Aspergillus Polymerase Chain Reaction: Systematic Review of Evidence for Clinical Use in Comparison With Antigen Testing.

PubMed

White, P Lewis; Wingard, John R; Bretagne, Stéphane; Löffler, Jürgen; Patterson, Thomas F; Slavin, Monica A; Barnes, Rosemary A; Pappas, Peter G; Donnelly, J Peter

2015-10-15

Aspergillus polymerase chain reaction (PCR) was excluded from the European Organisation for the Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG) definitions of invasive fungal disease because of limited standardization and validation. The definitions are being revised. A systematic literature review was performed to identify analytical and clinical information available on inclusion of galactomannan enzyme immunoassay (GM-EIA) (2002) and β-d-glucan (2008), providing a minimal threshold when considering PCR. Categorical parameters and statistical performance were compared. When incorporated, GM-EIA and β-d-glucan sensitivities and specificities for diagnosing invasive aspergillosis were 81.6% and 91.6%, and 76.9% and 89.4%, respectively. Aspergillus PCR has similar sensitivity and specificity (76.8%-88.0% and 75.0%-94.5%, respectively) and comparable utility. Methodological recommendations and commercial PCR assays assist standardization. Although all tests have limitations, currently, PCR is the only test with independent quality control. We propose that there is sufficient evidence that is at least equivalent to that used to include GM-EIA and β-d-glucan testing, and that PCR is now mature enough for inclusion in the EORTC/MSG definitions. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America.

Identification and genotyping of molluscum contagiosum virus from genital swab samples by real-time PCR and Pyrosequencing.

PubMed

Trama, Jason P; Adelson, Martin E; Mordechai, Eli

2007-12-01

Laboratory diagnosis of molluscum contagiosum virus (MCV) is important as lesions can be confused with those caused by Cryptococcus neoformans, herpes simplex virus, human papillomavirus, and varicella-zoster virus. To develop a rapid method for identifying patients infected with MCV via swab sampling. Two dual-labeled probe real-time PCR assays, one homologous to the p43K gene and one to the MC080R gene, were designed. The p43K PCR was designed to be used in conjunction with Pyrosequencing for confirmation of PCR products and discrimination between MCV1 and MCV2. Both PCR assays were optimized with respect to reaction components, thermocycling parameters, and primer and probe concentrations. The specificities of both PCR assays were confirmed by non-amplification of 38 known human pathogens. Sensitivity assays demonstrated detection of as few as 10 copies per reaction. Testing 703 swabs, concordance between the two real-time PCR assays was 99.9%. Under the developed conditions, Pyrosequencing of the p43K PCR product was capable of providing enough nucleotide sequence to definitively differentiate MCV1 and MCV2. These real-time PCR assays can be used for the rapid, sensitive, and specific detection of MCV and, when combined with Pyrosequencing, can further discriminate between MCV1 and MCV2.

Predicting and detecting adverse drug reactions in old age: challenges and opportunities.

PubMed

Mangoni, Arduino A

2012-05-01

Increased, often inappropriate, drug exposure, pharmacokinetic and pharmacodynamic changes, reduced homeostatic reserve and frailty increase the risk of adverse drug reactions (ADRs) in the older population, thereby imposing a significant public health burden. Predicting and diagnosing ADRs in old age presents significant challenges for the clinician, even when specific risk scoring systems are available. The picture is further compounded by the potential adverse impact of several drugs on more 'global' health indicators, for example, physical function and independence, and the fragmentation of care (e.g., increased number of treating doctors and care transitions) experienced by older patients during their clinical journey. The current knowledge of drug safety in old age is also curtailed by the lack of efficacy and safety data from pre-marketing studies. Moreover, little consideration is given to individual patients' experiences and reporting of specific ADRs, particularly in the presence of cognitive impairment. Pending additional data on these issues, the close review and monitoring of individual patients' drug prescribing, clinical status and biochemical parameters remain essential to predict and detect ADRs in old age. Recently developed strategies, for example, medication reconciliation and trigger tool methodology, have the potential for ADRs risk mitigation in this population. However, more information is required on their efficacy and applicability in different healthcare settings.

Relation of thromboelastography parameters to conventional coagulation tests used to evaluate the hypercoagulable state of aged fracture patients

PubMed Central

Liu, Chen; Guan, Zhao; Xu, Qinzhu; Zhao, Lei; Song, Ying; Wang, Hui

2016-01-01

Abstract Fractures are common among aged people, and rapid assessment of the coagulation status is important. The thromboelastography (TEG) test can give a series of coagulation parameters and has been widely used in clinics. In this research, we looked at fracture patients over 60 and compared their TEG results with those of healthy controls. Since there is a paucity of studies comparing TEG assessments with conventional coagulation tests, we aim to clarify the relationship between TEG values and the values given by conventional coagulation tests. Forty fracture patients (27 femur and 13 humerus) over 60 years old were included in the study. The change in their coagulation status was evaluated by TEG before surgery within 4 hours after the fracture. Changes in TEG parameters were analyzed compared with controls. Conventional coagulation test results for the patients, including activated partial thromboplastin time (APTT), international normalized ratio (INR), fibrinogen, and platelets, were also acquired, and correlation analysis was done with TEG parameters, measuring similar aspects of the coagulation cascade. In addition, the sensitivity and specificity of TEG parameters for detecting raised fibrinogen levels were also analyzed. The K (time to 20 mm clot amplitude) and R (reaction time) values of aged fracture patients were lower than controls. The values for angle, maximal amplitude (MA), and coagulation index (CI) were raised compared with controls, indicating a hypercoagulable state. Correlation analysis showed that there were significant positive correlations between fibrinogen and MA/angle, between platelets and MA, and between APTT and R as well. There was significant negative correlation between fibrinogen and K. In addition, K values have better sensitivity and specificity for detecting elevated fibrinogen concentration than angle and MA values. Aged fracture patients tend to be in a hypercoagulable state, and this could be effectively reflected by a TEG test. There were correlations between TEG parameters and corresponding conventional tests. K values can better predict elevated fibrinogen levels in aged fracture patients. PMID:27311005

Relation of thromboelastography parameters to conventional coagulation tests used to evaluate the hypercoagulable state of aged fracture patients.

PubMed

Liu, Chen; Guan, Zhao; Xu, Qinzhu; Zhao, Lei; Song, Ying; Wang, Hui

2016-06-01

Fractures are common among aged people, and rapid assessment of the coagulation status is important. The thromboelastography (TEG) test can give a series of coagulation parameters and has been widely used in clinics. In this research, we looked at fracture patients over 60 and compared their TEG results with those of healthy controls. Since there is a paucity of studies comparing TEG assessments with conventional coagulation tests, we aim to clarify the relationship between TEG values and the values given by conventional coagulation tests.Forty fracture patients (27 femur and 13 humerus) over 60 years old were included in the study. The change in their coagulation status was evaluated by TEG before surgery within 4 hours after the fracture. Changes in TEG parameters were analyzed compared with controls. Conventional coagulation test results for the patients, including activated partial thromboplastin time (APTT), international normalized ratio (INR), fibrinogen, and platelets, were also acquired, and correlation analysis was done with TEG parameters, measuring similar aspects of the coagulation cascade. In addition, the sensitivity and specificity of TEG parameters for detecting raised fibrinogen levels were also analyzed.The K (time to 20 mm clot amplitude) and R (reaction time) values of aged fracture patients were lower than controls. The values for angle, maximal amplitude (MA), and coagulation index (CI) were raised compared with controls, indicating a hypercoagulable state. Correlation analysis showed that there were significant positive correlations between fibrinogen and MA/angle, between platelets and MA, and between APTT and R as well. There was significant negative correlation between fibrinogen and K. In addition, K values have better sensitivity and specificity for detecting elevated fibrinogen concentration than angle and MA values.Aged fracture patients tend to be in a hypercoagulable state, and this could be effectively reflected by a TEG test. There were correlations between TEG parameters and corresponding conventional tests. K values can better predict elevated fibrinogen levels in aged fracture patients.

A sensitivity analysis method for the body segment inertial parameters based on ground reaction and joint moment regressor matrices.

PubMed

Futamure, Sumire; Bonnet, Vincent; Dumas, Raphael; Venture, Gentiane

2017-11-07

This paper presents a method allowing a simple and efficient sensitivity analysis of dynamics parameters of complex whole-body human model. The proposed method is based on the ground reaction and joint moment regressor matrices, developed initially in robotics system identification theory, and involved in the equations of motion of the human body. The regressor matrices are linear relatively to the segment inertial parameters allowing us to use simple sensitivity analysis methods. The sensitivity analysis method was applied over gait dynamics and kinematics data of nine subjects and with a 15 segments 3D model of the locomotor apparatus. According to the proposed sensitivity indices, 76 segments inertial parameters out the 150 of the mechanical model were considered as not influent for gait. The main findings were that the segment masses were influent and that, at the exception of the trunk, moment of inertia were not influent for the computation of the ground reaction forces and moments and the joint moments. The same method also shows numerically that at least 90% of the lower-limb joint moments during the stance phase can be estimated only from a force-plate and kinematics data without knowing any of the segment inertial parameters. Copyright © 2017 Elsevier Ltd. All rights reserved.

Plackett-Burman experimental design for bacterial cellulose-silica composites synthesis.

PubMed

Guzun, Anicuta Stoica; Stroescu, Marta; Jinga, Sorin Ion; Voicu, Georgeta; Grumezescu, Alexandru Mihai; Holban, Alina Maria

2014-09-01

Bacterial cellulose-silica hybrid composites were prepared starting from wet bacterial cellulose (BC) membranes using Stöber reaction. The structure and surface morphology of hybrid composites were examined by FTIR and SEM. The SEM pictures revealed that the silica particles are attached to BC fibrils and are well dispersed in the BC matrix. The influence of silica particles upon BC crystallinity was studied using XRD analysis. Thermogravimetric (TG) analysis showed that the composites are stable up to 300°C. A Plackett-Burman design was applied in order to investigate the influence of process parameters upon silica particle sizes and silica content of BC-silica composites. The statistical model predicted that it is possible for silica particles size to vary the synthesis parameters in order to obtain silica particles deposed on BC membranes in the range from 34.5 to 500 nm, the significant parameters being ammonia concentration, reaction time and temperature. The silica content also varies depending on process parameters, the statistical model predicting that the most influential parameters are water-tetraethoxysilane (TEOS) ratio and reaction temperature. The antimicrobial behavior on Staphylococcus aureus of BC-silica composites functionalized with usnic acid (UA) was also studied, in order to create improved surfaces with antiadherence and anti-biofilm properties. Copyright © 2014 Elsevier B.V. All rights reserved.

Bio indices for 2,4-D sensitivity between two plant species: Azolla pinnata R.Br. and Vernonia cinerea L. with their cellular responses.

PubMed

De, Arnab Kumar; Dey, Narottam; Adak, Malay Kumar

2016-07-01

In the present experiment a pteridophytic species Azolla and an angiospermic species Vernonia were evaluated on the basis of cellular reactivity for herbicidal action through ongoing concentrations. Initially, both the species recorded a significant activity of IAA-oxidase as mark of IAA metabolism with herbicidal sensitivity. Still, Vernonia species were more affected on 2,4-D mediated auxin catabolism. The loss of auxin concentrations on the tissues by 2,4-D reaction was also reflected on growth parameters including relative growth rate and chlorophyll biosynthesis. In a dose dependent manner Vernonia plants were more affected with loss of chlorophyll content and decline in relative growth rate. On the other hand, both those parameters were adjusted significantly with 2,4-D accumulation in Azolla . The stability of cellular metabolism was documented by significant down regulation of protein and lipid peroxidation with concomitant moderation to superoxide and hydrogen peroxide accumulation. The later two were more vulnerable to damage in the Vernonia plant with profuse accumulation of protein and lipid peroxidation products. Similarly, tissue specific reaction to superoxide and hydrogen peroxide accumulation were distinctly demarcated in two species significantly. As a whole, the cellular responses and metabolite distribution to 2,4-D sensitization are the features to describe bio-indices for aquatic fern species Azolla with comparison to angiospermic species Vernonia .

New approaches for the standardization and validation of a real-time qPCR assay using TaqMan probes for quantification of yellow fever virus on clinical samples with high quality parameters

PubMed Central

Fernandes-Monteiro, Alice G; Trindade, Gisela F; Yamamura, Anna MY; Moreira, Otacilio C; de Paula, Vanessa S; Duarte, Ana Cláudia M; Britto, Constança; Lima, Sheila Maria B

2015-01-01

The development and production of viral vaccines, in general, involve several steps that need the monitoring of viral load throughout the entire process. Applying a 2-step quantitative reverse transcription real time PCR assay (RT-qPCR), viral load can be measured and monitored in a few hours. In this context, the development, standardization and validation of a RT-qPCR test to quickly and efficiently quantify yellow fever virus (YFV) in all stages of vaccine production are extremely important. To serve this purpose we used a plasmid construction containing the NS5 region from 17DD YFV to generate the standard curve and to evaluate parameters such as linearity, precision and specificity against other flavivirus. Furthermore, we defined the limits of detection as 25 copies/reaction, and quantification as 100 copies/reaction for the test. To ensure the quality of the method, reference controls were established in order to avoid false negative results. The qRT-PCR technique based on the use of TaqMan probes herein standardized proved to be effective for determining yellow fever viral load both in vivo and in vitro, thus becoming a very important tool to assure the quality control for vaccine production and evaluation of viremia after vaccination or YF disease. PMID:26011746

New approaches for the standardization and validation of a real-time qPCR assay using TaqMan probes for quantification of yellow fever virus on clinical samples with high quality parameters.

PubMed

Fernandes-Monteiro, Alice G; Trindade, Gisela F; Yamamura, Anna M Y; Moreira, Otacilio C; de Paula, Vanessa S; Duarte, Ana Cláudia M; Britto, Constança; Lima, Sheila Maria B

2015-01-01

The development and production of viral vaccines, in general, involve several steps that need the monitoring of viral load throughout the entire process. Applying a 2-step quantitative reverse transcription real time PCR assay (RT-qPCR), viral load can be measured and monitored in a few hours. In this context, the development, standardization and validation of a RT-qPCR test to quickly and efficiently quantify yellow fever virus (YFV) in all stages of vaccine production are extremely important. To serve this purpose we used a plasmid construction containing the NS5 region from 17DD YFV to generate the standard curve and to evaluate parameters such as linearity, precision and specificity against other flavivirus. Furthermore, we defined the limits of detection as 25 copies/reaction, and quantification as 100 copies/reaction for the test. To ensure the quality of the method, reference controls were established in order to avoid false negative results. The qRT-PCR technique based on the use of TaqMan probes herein standardized proved to be effective for determining yellow fever viral load both in vivo and in vitro, thus becoming a very important tool to assure the quality control for vaccine production and evaluation of viremia after vaccination or YF disease.

Electrode performance parameters for a radioisotope-powered AMTEC for space power applications

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

Underwood, M.L.; O'Connor, D.; Williams, R.M.

1992-08-01

The alkali metal thermoelastic converter (AMTEC) is a device for the direct conversion of heat to electricity. Recently a design of an AMTEC using a radioisotope heat source was described, but the optimum condenser temperature was hotter than the temperatures used in the laboratory to develop the electrode performance model. Now laboratory experiments have confirmed the dependence of two model parameters over a broader range of condenser and electrode temperatures for two candidate electrode compositions. One parameter, the electrochemical exchange current density at the reaction interface, is independent of the condenser temperature, and depends only upon the collision rate ofmore » sodium at the reaction zone. The second parameter, a morphological parameter, which measures the mass transport resistance through the electrode, is independent of condenser and electrode temperatures for molybdenum electrodes. For rhodium-tungsten electrodes, however, this parameter increases for decreasing electrode temperature, indicating an activated mass transport mechanism such as surface diffusion. 21 refs.« less

Magnetic transition in Y-site doped multiferroic YMnO3

NASA Astrophysics Data System (ADS)

Thakur, Rajesh K.; Thakur, Rasna; Gaur, N. K.

2016-05-01

We have synthesized polycrystalline hexagonal Y1-xSrxMnO3 (x=0.02, 0.1) compounds by using conventional solid state reaction method. The detailed structural investigations are carried out by using XRD studies which reveals the single phase formation of the reported compounds with hexagonal structure and space group P63cm (JCPDS: 25-1079). Further the XRD data of reported compounds were analyzed by RIETVELD (FULLPROFF) method which shows the decrease in the lattice parameter with increasing concentration of divalent strontium to Y-site. The observed pointed kinks in the specific heat study are indicative of the probable coupling in between the electric and magnetic orders in this class of materials. The reported systematic specific heat studies shows that the antiferromagnetic (AFM) transition temperature (TN) shifts to higher value with increasing concentration of Sr2+ ion in the YMnO3 compound which is attributed to the enhanced lattice contribution to the specific heat in the this compound. The present compound shows the independence of specific heat and magnetic transition temperature with applied magnetic field of 8T and 12T.

Clinical and immunological surveys in bee keepers.

PubMed

Bousquet, J; Coulomb, Y; Robinet-Levy, M; Michel, F B

1982-07-01

Two hundred and fifty bee keepers in the South of France, working seasonally, were clinically investigated by means of a questionnaire. Forty-three per cent had presented anaphylactic symptoms and 7.0% toxic reactions when stung by bees. The personal atopic history was found to be significantly (P less than 0.01) elevated in bee keepers who experienced anaphylaxis. Total serum IgE and been venom-specific IgE were titrated in 100 subjects. Total serum IgE was significantly elevated in allergic bee keepers (P = 0.02). Although bee venom-specific IgE were significantly (P less than 0.01) higher in allergic bee keepers this parameter cannot discriminate between allergic and non-allergic bee keepers owing to a considerable overlap. Bee venom-specific IgG was assayed in seventy subjects. Their level was significantly (P less than 0.001) higher in allergic and non-allergic bee keepers as compared with non-allergic blood donors and non-bee-keeping allergic patients. In both bee keeper groups there was no difference in bee venom-specific IgG titres.

Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models

PubMed Central

Rosenblatt, Marcus; Timmer, Jens; Kaschek, Daniel

2016-01-01

Ordinary differential equation models have become a wide-spread approach to analyze dynamical systems and understand underlying mechanisms. Model parameters are often unknown and have to be estimated from experimental data, e.g., by maximum-likelihood estimation. In particular, models of biological systems contain a large number of parameters. To reduce the dimensionality of the parameter space, steady-state information is incorporated in the parameter estimation process. For non-linear models, analytical steady-state calculation typically leads to higher-order polynomial equations for which no closed-form solutions can be obtained. This can be circumvented by solving the steady-state equations for kinetic parameters, which results in a linear equation system with comparatively simple solutions. At the same time multiplicity of steady-state solutions is avoided, which otherwise is problematic for optimization. When solved for kinetic parameters, however, steady-state constraints tend to become negative for particular model specifications, thus, generating new types of optimization problems. Here, we present an algorithm based on graph theory that derives non-negative, analytical steady-state expressions by stepwise removal of cyclic dependencies between dynamical variables. The algorithm avoids multiple steady-state solutions by construction. We show that our method is applicable to most common classes of biochemical reaction networks containing inhibition terms, mass-action and Hill-type kinetic equations. Comparing the performance of parameter estimation for different analytical and numerical methods of incorporating steady-state information, we show that our approach is especially well-tailored to guarantee a high success rate of optimization. PMID:27243005

Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models.

PubMed

Rosenblatt, Marcus; Timmer, Jens; Kaschek, Daniel

2016-01-01

Ordinary differential equation models have become a wide-spread approach to analyze dynamical systems and understand underlying mechanisms. Model parameters are often unknown and have to be estimated from experimental data, e.g., by maximum-likelihood estimation. In particular, models of biological systems contain a large number of parameters. To reduce the dimensionality of the parameter space, steady-state information is incorporated in the parameter estimation process. For non-linear models, analytical steady-state calculation typically leads to higher-order polynomial equations for which no closed-form solutions can be obtained. This can be circumvented by solving the steady-state equations for kinetic parameters, which results in a linear equation system with comparatively simple solutions. At the same time multiplicity of steady-state solutions is avoided, which otherwise is problematic for optimization. When solved for kinetic parameters, however, steady-state constraints tend to become negative for particular model specifications, thus, generating new types of optimization problems. Here, we present an algorithm based on graph theory that derives non-negative, analytical steady-state expressions by stepwise removal of cyclic dependencies between dynamical variables. The algorithm avoids multiple steady-state solutions by construction. We show that our method is applicable to most common classes of biochemical reaction networks containing inhibition terms, mass-action and Hill-type kinetic equations. Comparing the performance of parameter estimation for different analytical and numerical methods of incorporating steady-state information, we show that our approach is especially well-tailored to guarantee a high success rate of optimization.

Overall kinetics of heterogeneous elemental mercury reactions on TiO2 sorbent particles with UV radiation

EPA Science Inventory

A system consisting of a photochemical reaction was used to evaluate the kinetic parameters, such as reaction order and rate constant for the elemental mercury uptake by TiO2 in the presence of uv irradiation. TiO2 particles generated by an aerosol route were used in a fixed bed...

Use of Moessbauer spectroscopy to study reaction products of polyphenols and iron compounds

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

Gust, J.; Suwalski, J.

1994-05-01

Moessbauer spectroscopy was used to study parameters of the reaction products of iron compounds (Fe[sup III]) and polyphenols with hydroxyl (OH) groups in ortho positions. Polyphenols used in the reaction were catechol, pyrogallol, gallic acid, and oak tannin. The Fe-containing compounds were hydrated ferric sulfate (Fe[sub 2][SO[sub 4

A review of engineering aspects of intensification of chemical synthesis using ultrasound.

PubMed

Sancheti, Sonam V; Gogate, Parag R

2017-05-01

Cavitation generated using ultrasound can enhance the rates of several chemical reactions giving better selectivity based on the physical and chemical effects. The present review focuses on overview of the different reactions that can be intensified using ultrasound followed by the discussion on the chemical kinetics for ultrasound assisted reactions, engineering aspects related to reactor designs and effect of operating parameters on the degree of intensification obtained for chemical synthesis. The cavitational effects in terms of magnitudes of collapse temperatures and collapse pressure, number of free radicals generated and extent of turbulence are strongly dependent on the operating parameters such as ultrasonic power, frequency, duty cycle, temperature as well as physicochemical parameters of liquid medium which controls the inception of cavitation. Guidelines have been presented for the optimum selection based on the critical analysis of the existing literature so that maximum process intensification benefits can be obtained. Different reactor designs have also been analyzed with guidelines for efficient scale up of the sonochemical reactor, which would be dependent on the type of reaction, controlling mechanism of reaction, catalyst and activation energy requirements. Overall, it has been established that sonochemistry offers considerable potential for green and sustainable processing and efficient scale up procedures are required so as to harness the effects at actual commercial level. Copyright © 2016 Elsevier B.V. All rights reserved.

Substrate mass transfer: analytical approach for immobilized enzyme reactions

NASA Astrophysics Data System (ADS)

Senthamarai, R.; Saibavani, T. N.

2018-04-01

In this paper, the boundary value problem in immobilized enzyme reactions is formulated and approximate expression for substrate concentration without external mass transfer resistance is presented. He’s variational iteration method is used to give approximate and analytical solutions of non-linear differential equation containing a non linear term related to enzymatic reaction. The relevant analytical solution for the dimensionless substrate concentration profile is discussed in terms of dimensionless reaction parameters α and β.

A quantitative approach to nucleophilic organocatalysis

PubMed Central

Lakhdar, Sami; Maji, Biplab; Ofial, Armin R

2012-01-01

Summary The key steps in most organocatalytic cyclizations are the reactions of electrophiles with nucleophiles. Their rates can be calculated by the linear free-energy relationship log k(20 °C) = s N(E + N), where electrophiles are characterized by one parameter (E) and nucleophiles are characterized by the solvent-dependent nucleophilicity (N) and sensitivity (s N) parameters. Electrophilicity parameters in the range –10 < E < –5 were determined for iminium ions derived from cinnamaldehyde and common organocatalysts, such as pyrrolidines and imidazolidinones, by studying the rates of their reactions with reference nucleophiles. Iminium activated reactions of α,β-unsaturated aldehydes can, therefore, be expected to proceed with nucleophiles of 2 < N < 14, because such nucleophiles are strong enough to react with iminium ions but weak enough not to react with their precursor aldehydes. With the N parameters of enamines derived from phenylacetaldehyde and MacMillan’s imidazolidinones one can rationalize why only strong electrophiles, such as stabilized carbenium ions (–8 < E < –2) or hexachlorocyclohexadienone (E = –6.75), are suitable electrophiles for enamine activated reactions with imidazolidinones. Several mechanistic controversies concerning iminium and enamine activated reactions could thus be settled by studying the reactivities of independently synthesized intermediates. Kinetic investigations of the reactions of N-heterocyclic carbenes (NHCs) with benzhydrylium ions showed that they have similar nucleophilicities to common organocatalysts (e.g., PPh3, DMAP, DABCO) but are much stronger (100–200 kJ mol–1) Lewis bases. While structurally analogous imidazolylidenes and imidazolidinylidenes have comparable nucleophilicities and Lewis basicities, the corresponding deoxy Breslow intermediates differ dramatically in reactivity. The thousand-fold higher nucleophilicity of 2-benzylidene-imidazoline relative to 2-benzylidene-imidazolidine is explained by the gain of aromaticity during electrophilic additions to the imidazoline derivatives. O-Methylated Breslow intermediates are a hundred-fold less nucleophilic than deoxy Breslow intermediates. PMID:23019481

Diabatic models with transferrable parameters for generalized chemical reactions

NASA Astrophysics Data System (ADS)

Reimers, Jeffrey R.; McKemmish, Laura K.; McKenzie, Ross H.; Hush, Noel S.

2017-05-01

Diabatic models applied to adiabatic electron-transfer theory yield many equations involving just a few parameters that connect ground-state geometries and vibration frequencies to excited-state transition energies and vibration frequencies to the rate constants for electron-transfer reactions, utilizing properties of the conical-intersection seam linking the ground and excited states through the Pseudo Jahn-Teller effect. We review how such simplicity in basic understanding can also be obtained for general chemical reactions. The key feature that must be recognized is that electron-transfer (or hole transfer) processes typically involve one electron (hole) moving between two orbitals, whereas general reactions typically involve two electrons or even four electrons for processes in aromatic molecules. Each additional moving electron leads to new high-energy but interrelated conical-intersection seams that distort the shape of the critical lowest-energy seam. Recognizing this feature shows how conical-intersection descriptors can be transferred between systems, and how general chemical reactions can be compared using the same set of simple parameters. Mathematical relationships are presented depicting how different conical-intersection seams relate to each other, showing that complex problems can be reduced into an effective interaction between the ground-state and a critical excited state to provide the first semi-quantitative implementation of Shaik’s “twin state” concept. Applications are made (i) demonstrating why the chemistry of the first-row elements is qualitatively so different to that of the second and later rows, (ii) deducing the bond-length alternation in hypothetical cyclohexatriene from the observed UV spectroscopy of benzene, (iii) demonstrating that commonly used procedures for modelling surface hopping based on inclusion of only the first-derivative correction to the Born-Oppenheimer approximation are valid in no region of the chemical parameter space, and (iv), demonstrating the types of chemical reactions that may be suitable for exploitation as a chemical qubit in some quantum information processor.

Calibration of Complex Subsurface Reaction Models Using a Surrogate-Model Approach

EPA Science Inventory

Application of model assessment techniques to complex subsurface reaction models involves numerous difficulties, including non-trivial model selection, parameter non-uniqueness, and excessive computational burden. To overcome these difficulties, this study introduces SAMM (Simult...

Origins of the temperature dependence of hammerhead ribozyme catalysis.

PubMed Central

Peracchi, A

1999-01-01

The difficulties in interpreting the temperature dependence of protein enzyme reactions are well recognized. Here, the hammerhead ribozyme cleavage was investigated under single-turnover conditions between 0 and 60 degrees C as a model for RNA-catalyzed reactions. Under the adopted conditions, the chemical step appears to be rate-limiting. However, the observed rate of cleavage is affected by pre-catalytic equilibria involving deprotonation of an essential group and binding of at least one low-affinity Mg2+ion. Thus, the apparent entropy and enthalpy of activation include contributions from the temperature dependence of these equilibria, precluding a simple physical interpretation of the observed activation parameters. Similar pre-catalytic equilibria likely contribute to the observed activation parameters for ribozyme reactions in general. The Arrhenius plot for the hammerhead reaction is substantially curved over the temperature range considered, which suggests the occurrence of a conformational change of the ribozyme ground state around physiological temperatures. PMID:10390528

Correlating defect density with growth time in continuous graphene films.

PubMed

Kang, Cheong; Jung, Da Hee; Nam, Ji Eun; Lee, Jin Seok

2014-12-01

We report that graphene flakes and films which were synthesized by copper-catalyzed atmospheric pressure chemical vapor deposition (APCVD) method using a mixture of Ar, H2, and CH4 gases. It was found that variations in the reaction parameters, such as reaction temperature, annealing time, and growth time, influenced the domain size of as-grown graphene. Besides, the reaction parameters influenced the number of layers, degree of defects and uniformity of the graphene films. The increase in growth temperature and annealing time tends to accelerate the graphene growth rate and increase the diffusion length, respectively, thereby increasing the average size of graphene domains. In addition, we confirmed that the number of pinholes reduced with increase in the growth time. Micro-Raman analysis of the as-grown graphene films confirmed that the continuous graphene monolayer film with low defects and high uniformity could be obtained with prolonged reaction time, under the appropriate annealing time and growth temperature.

Calculation and analysis of cross-sections for p+184W reactions up to 200 MeV

NASA Astrophysics Data System (ADS)

Sun, Jian-Ping; Zhang, Zheng-Jun; Han, Yin-Lu

2015-08-01

A set of optimal proton optical potential parameters for p+ 184W reactions are obtained at incident proton energy up to 250 MeV. Based on these parameters, the reaction cross-sections, elastic scattering angular distributions, energy spectra and double differential cross sections of proton-induced reactions on 184W are calculated and analyzed by using theoretical models which integrate the optical model, distorted Born wave approximation theory, intra-nuclear cascade model, exciton model, Hauser-Feshbach theory and evaporation model. The calculated results are compared with existing experimental data and good agreement is achieved. Supported by National Basic Research Program of China, Technology Research of Accelerator Driven Sub-critical System for Nuclear Waste Transmutation (2007CB209903) and Strategic Priority Research Program of Chinese Academy of Sciences, Thorium Molten Salt Reactor Nuclear Energy System (XDA02010100)

Microwave-assisted chemistry: synthetic applications for rapid assembly of nanomaterials and organics.

PubMed

Gawande, Manoj B; Shelke, Sharad N; Zboril, Radek; Varma, Rajender S

2014-04-15

The magic of microwave (MW) heating technique, termed the Bunsen burner of the 21st century, has emerged as a valuable alternative in the synthesis of organic compounds, polymers, inorganic materials, and nanomaterials. Important innovations in MW-assisted chemistry now enable chemists to prepare catalytic materials or nanomaterials and desired organic molecules, selectively, in almost quantitative yields and with greater precision than using conventional heating. By controlling the specific MW parameters (temperature, pressure, and ramping of temperature) and choice of solvents, researchers can now move into the next generation of advanced nanomaterial design and development. Microwave-assisted chemical reactions are now well-established practices in the laboratory setting although some controversy lingers as to how MW irradiation is able to enhance or influence the outcome of chemical reactions. Much of the discussion has focused on whether the observed effects can, in all instances, be rationalized by purely thermal Arrhenius-based phenomena (thermal microwave effects), that is, the importance of the rapid heating and high bulk reaction temperatures that are achievable using MW dielectric heating in sealed reaction vessels, or whether these observations can be explained by so-called "nonthermal" or "specific microwave" effects. In recent years, innovative and significant advances have occurred in MW hardware development to help delineate MW effects, especially the use of silicon carbide (SiC) reaction vessels and the accurate measurement of temperature using fiber optic (FO) temperature probes. SiC reactors appear to be good alternatives to MW transparent borosilicate glass, because of their high microwave absorptivity, and as such they serve as valuable tools to demystify the claimed magical MW effects. This enables one to evaluate the influence of the electromagnetic field on the specific chemical reactions, under truly identical conventional heating conditions, wherein temperature is measured accurately by fiber optic (FO) probe. This Account describes the current status of MW-assisted synthesis highlighting the introduction of various prototypes of equipment, classes of organic reactions pursued using nanomaterials, and the synthesis of unique and multifunctional nanomaterials; the ensuing nanomaterials possess zero-dimensional to three-dimensional shapes, such as spherical, hexagonal, nanoprisms, star shapes, and nanorods. The synthesis of well-defined nanomaterials and nanocatalysts is an integral part of nanotechnology and catalysis science, because it is imperative to control their size, shape, and compositional engineering for unique deployment in the field of nanocatalysis and organic synthesis. MW-assisted methods have been employed for the convenient and reproducible synthesis of well-defined noble and transition core-shell metallic nanoparticles with tunable shell thicknesses. Some of the distinctive attributes of MW-selective heating in the synthesis and applications of magnetic nanocatalysts in organic synthesis under benign reaction conditions are highlighted. Sustainable nanomaterials and their applications in benign media are an ideal blend for the development of greener methodologies in organic synthesis; MW heating provides superb value to the overall sustainable process development via process intensification including the flow systems.

Elastic, inelastic, and 1-nucleon transfer channels in the 7Li+120Sn system

NASA Astrophysics Data System (ADS)

Kundu, A.; Santra, S.; Pal, A.; Chattopadhyay, D.; Tripathi, R.; Roy, B. J.; Nag, T. N.; Nayak, B. K.; Saxena, A.; Kailas, S.

2017-03-01

Background: Simultaneous description of major outgoing channels for a nuclear reaction by coupled-channels calculations using the same set of potential and coupling parameters is one of the difficult tasks to accomplish in nuclear reaction studies. Purpose: To measure the elastic, inelastic, and transfer cross sections for as many channels as possible in 7Li+120Sn system at different beam energies and simultaneously describe them by a single set of model calculations using fresco. Methods: Projectile-like fragments were detected using six sets of Si-detector telescopes to measure the cross sections for elastic, inelastic, and 1-nucleon transfer channels at two beam energies of 28 and 30 MeV. Optical model analysis of elastic data and coupled-reaction-channels (CRC) calculations that include around 30 reaction channels coupled directly to the entrance channel, with respective structural parameters, were performed to understand the measured cross sections. Results: Structure information available in the literature for some of the identified states did not reproduce the present data. Cross sections obtained from CRC calculations using a modified but single set of potential and coupling parameters were able to describe simultaneously the measured data for all the channels at both the measured energies as well as the existing data for elastic and inelastic cross sections at 44 MeV. Conclusions: Non-reproduction of some of the cross sections using the structure information available in the literature which are extracted from reactions involving different projectiles indicates that such measurements are probe dependent. New structural parameters were assigned for such states as well as for several new transfer states whose spectroscopic factors were not known.

TECHNICAL NOTE: System for monitoring the evolution of the thermal expansion coefficient and autogenous deformation of hardening materials

NASA Astrophysics Data System (ADS)

Viviani, M.; Glisic, B.; Smith, I. F. C.

2006-12-01

This article presents an experimental system developed to determine the kinetic parameters of hardening materials. Kinetic parameters allow computation of the degree of reaction indices (DRIs). DRIs are used in predictive formulae for strength and are used to decouple the autogenous deformation (AD) and thermal deformation (TD). Although there are several methods to determine values for kinetic reaction parameters, most require extensive testing and large databases. A measurement system has been developed in order to determine kinetic parameters. The measurement system consists of optical fiber sensors embedded in specimens that are cured at varying temperatures and conditions. Sensors are used in pairs inside each specimen, and each pair has two deformation sensors that, aside from their axial stiffness, have the same characteristics. The study of the interaction between sensors and hardening material leads to establishment of a link between the deformations measured and the degree of reaction, by means of the newly developed concept of the equivalency point. The equivalency point is assumed to be an indicator of the degree of reaction and it allows the determination of the apparent activation energy (Ea) which defines the equivalent time. Equivalent time is a degree of reaction index (DRI) and it accounts for the combined effect of time and temperature in concrete. This new methodology has been used to predict the compressive strength and separate the AD and thermal expansion coefficient (TEC) in seven types of concrete. The measurement system allows gathering of data necessary for fast and efficient predictions. Due to its robustness and reduced dimensions it also has potential for in situ application.

Reliability of spatiotemporal and kinetic gait parameters determined by a new instrumented treadmill system.

PubMed

Reed, Lloyd F; Urry, Stephen R; Wearing, Scott C

2013-08-21

Despite the emerging use of treadmills integrated with pressure platforms as outcome tools in both clinical and research settings, published evidence regarding the measurement properties of these new systems is limited. This study evaluated the within- and between-day repeatability of spatial, temporal and vertical ground reaction force parameters measured by a treadmill system instrumented with a capacitance-based pressure platform. Thirty three healthy adults (mean age, 21.5 ± 2.8 years; height, 168.4 ± 9.9 cm; and mass, 67.8 ± 18.6 kg), walked barefoot on a treadmill system (FDM-THM-S, Zebris Medical GmbH) on three separate occasions. For each testing session, participants set their preferred pace but were blinded to treadmill speed. Spatial (foot rotation, step width, stride and step length), temporal (stride and step times, duration of stance, swing and single and double support) and peak vertical ground reaction force variables were collected over a 30-second capture period, equating to an average of 52 ± 5 steps of steady-state walking. Testing was repeated one week following the initial trial and again, for a third time, 20 minutes later. Repeated measures ANOVAs within a generalized linear modelling framework were used to assess between-session differences in gait parameters. Agreement between gait parameters measured within the same day (session 2 and 3) and between days (session 1 and 2; 1 and 3) were evaluated using the 95% repeatability coefficient. There were statistically significant differences in the majority (14/16) of temporal, spatial and kinetic gait parameters over the three test sessions (P < .01). The minimum change that could be detected with 95% confidence ranged between 3% and 17% for temporal parameters, 14% and 33% for spatial parameters, and 4% and 20% for kinetic parameters between days. Within-day repeatability was similar to that observed between days. Temporal and kinetic gait parameters were typically more consistent than spatial parameters. The 95% repeatability coefficient for vertical force peaks ranged between ± 53 and ± 63 N. The limits of agreement in spatial parameters and ground reaction forces for the treadmill system encompass previously reported changes with neuromuscular pathology and footwear interventions. These findings provide clinicians and researchers with an indication of the repeatability and sensitivity of the Zebris treadmill system to detect changes in common spatiotemporal gait parameters and vertical ground reaction forces.

Chemical reaction for Carreau-Yasuda nanofluid flow past a nonlinear stretching sheet considering Joule heating

NASA Astrophysics Data System (ADS)

Khan, Mair; Shahid, Amna; Malik, M. Y.; Salahuddin, T.

2018-03-01

Current analysis has been made to scrutinize the consequences of chemical response against magneto-hydrodynamic Carreau-Yasuda nanofluid flow induced by a non-linear stretching surface considering zero normal flux, slip and convective boundary conditions. Joule heating effect is also considered. Appropriate similarity approach is used to convert leading system of PDE's for Carreau-Yasuda nanofluid into nonlinear ODE's. Well known mathematical scheme namely shooting method is utilized to solve the system numerically. Physical parameters, namely Weissenberg number We , thermal slip parameter δ , thermophoresis number NT, non-linear stretching parameter n, magnetic field parameter M, velocity slip parameter k , Lewis number Le, Brownian motion parameter NB, Prandtl number Pr, Eckert number Ec and chemical reaction parameter γ upon temperature, velocity and concentration profiles are visualized through graphs and tables. Numerical influence of mass and heat transfer rates and friction factor are also represented in tabular as well as graphical form respectively. Skin friction coefficient reduces when Weissenberg number We is incremented. Rate of heat transfer enhances for large values of Brownian motion constraint NB. By increasing Lewis quantity Le rate of mass transfer declines.

Optimization of Maillard Reaction in Model System of Glucosamine and Cysteine Using Response Surface Methodology

PubMed Central

Arachchi, Shanika Jeewantha Thewarapperuma; Kim, Ye-Joo; Kim, Dae-Wook; Oh, Sang-Chul; Lee, Yang-Bong

2017-01-01

Sulfur-containing amino acids play important roles in good flavor generation in Maillard reaction of non-enzymatic browning, so aqueous model systems of glucosamine and cysteine were studied to investigate the effects of reaction temperature, initial pH, reaction time, and concentration ratio of glucosamine and cysteine. Response surface methodology was applied to optimize the independent reaction parameters of cysteine and glucosamine in Maillard reaction. Box-Behnken factorial design was used with 30 runs of 16 factorial levels, 8 axial levels and 6 central levels. The degree of Maillard reaction was determined by reading absorption at 425 nm in a spectrophotometer and Hunter’s L, a, and b values. ΔE was consequently set as the fifth response factor. In the statistical analyses, determination coefficients (R2) for their absorbance, Hunter’s L, a, b values, and ΔE were 0.94, 0.79, 0.73, 0.96, and 0.79, respectively, showing that the absorbance and Hunter’s b value were good dependent variables for this model system. The optimum processing parameters were determined to yield glucosamine-cysteine Maillard reaction product with higher absorbance and higher colour change. The optimum estimated absorbance was achieved at the condition of initial pH 8.0, 111°C reaction temperature, 2.47 h reaction time, and 1.30 concentration ratio. The optimum condition for colour change measured by Hunter’s b value was 2.41 h reaction time, 114°C reaction temperature, initial pH 8.3, and 1.26 concentration ratio. These results can provide the basic information for Maillard reaction of aqueous model system between glucosamine and cysteine. PMID:28401086

Optimization of Maillard Reaction in Model System of Glucosamine and Cysteine Using Response Surface Methodology.

PubMed

Arachchi, Shanika Jeewantha Thewarapperuma; Kim, Ye-Joo; Kim, Dae-Wook; Oh, Sang-Chul; Lee, Yang-Bong

2017-03-01

Sulfur-containing amino acids play important roles in good flavor generation in Maillard reaction of non-enzymatic browning, so aqueous model systems of glucosamine and cysteine were studied to investigate the effects of reaction temperature, initial pH, reaction time, and concentration ratio of glucosamine and cysteine. Response surface methodology was applied to optimize the independent reaction parameters of cysteine and glucosamine in Maillard reaction. Box-Behnken factorial design was used with 30 runs of 16 factorial levels, 8 axial levels and 6 central levels. The degree of Maillard reaction was determined by reading absorption at 425 nm in a spectrophotometer and Hunter's L, a, and b values. ΔE was consequently set as the fifth response factor. In the statistical analyses, determination coefficients (R 2 ) for their absorbance, Hunter's L, a, b values, and ΔE were 0.94, 0.79, 0.73, 0.96, and 0.79, respectively, showing that the absorbance and Hunter's b value were good dependent variables for this model system. The optimum processing parameters were determined to yield glucosamine-cysteine Maillard reaction product with higher absorbance and higher colour change. The optimum estimated absorbance was achieved at the condition of initial pH 8.0, 111°C reaction temperature, 2.47 h reaction time, and 1.30 concentration ratio. The optimum condition for colour change measured by Hunter's b value was 2.41 h reaction time, 114°C reaction temperature, initial pH 8.3, and 1.26 concentration ratio. These results can provide the basic information for Maillard reaction of aqueous model system between glucosamine and cysteine.

Wave-front propagation in a discrete model of excitable media

NASA Astrophysics Data System (ADS)

Feldman, A. B.; Chernyak, Y. B.; Cohen, R. J.

1998-06-01

We generalize our recent discrete cellular automata (CA) model of excitable media [Y. B. Chernyak, A. B. Feldman, and R. J. Cohen, Phys. Rev. E 55, 3215 (1997)] to incorporate the effects of inhibitory processes on the propagation of the excitation wave front. In the common two variable reaction-diffusion (RD) models of excitable media, the inhibitory process is described by the v ``controller'' variable responsible for the restoration of the equilibrium state following excitation. In myocardial tissue, the inhibitory effects are mainly due to the inactivation of the fast sodium current. We represent inhibition using a physical model in which the ``source'' contribution of excited elements to the excitation of their neighbors decreases with time as a simple function with a single adjustable parameter (a rate constant). We sought specific solutions of the CA state transition equations and obtained (both analytically and numerically) the dependence of the wave-front speed c on the four model parameters and the wave-front curvature κ. By requiring that the major characteristics of c(κ) in our CA model coincide with those obtained from solutions of a specific RD model, we find a unique set of CA parameter values for a given excitable medium. The basic structure of our CA solutions is remarkably similar to that found in typical RD systems (similar behavior is observed when the analogous model parameters are varied). Most notably, the ``turn-on'' of the inhibitory process is accompanied by the appearance of a solution branch of slow speed, unstable waves. Additionally, when κ is small, we obtain a family of ``eikonal'' relations c(κ) that are suitable for the kinematic analysis of traveling waves in the CA medium. We compared the solutions of the CA equations to CA simulations for the case of plane waves and circular (target) waves and found excellent agreement. We then studied a spiral wave using the CA model adjusted to a specific RD system and found good correspondence between the shapes of the RD and CA spiral arms in the region away from the tip where kinematic theory applies. Our analysis suggests that only four physical parameters control the behavior of wave fronts in excitable media.

On the Origin of the Catalytic power of Caboxypetidase A and Other Metalloenzymes

PubMed Central

Kilshtain, Alexandra Vardi; Warshel, Arieh

2009-01-01

Zinc metalloenzymes play a major role in key biological processes and Carboxypeptidase-A (CPA) is a major prototype of such enzymes. The present work quantifies the energetics of the catalytic reaction of CPA and its mutants using the EVB approach. The simulations allow us to quantify the origin of the catalytic power of this enzyme and to examine different mechanistic alternatives. The first step of the analysis used experimental information to determine the activation energy of each assumed mechanism of the reference reaction without the enzyme. The next step of the analysis involved EVB simulations of the reference reaction and then a calibration of the simulations by forcing them to reproduce the energetics of the reference reaction, in each assumed mechanism. The calibrated EVB was then used in systematic simulations of the catalytic reaction in the protein environment, without changing any parameter. The simulations reproduced the observed rate enhancement in two feasible general acid-general base mechanisms (GAGB-1 and GAGB-2), although the calculations with the GAGB-2 mechanism underestimated the catalytic effect in some treatments. We also reproduced the catalytic effect in the R127A mutant. The mutation calculations indicate that the GAGB-2 mechanism is significantly less likely than the GAGB-1 mechanism. It is also found, that the enzyme loses all its catalytic effect without the metal. This and earlier studies show that the catalytic effect of the metal is not some constant electrostatic effect, that can be assessed from gas phase studies, but a reflection of the dielectric effect of the specific environment. PMID:19480013

Annual Research Review: Reaction time variability in ADHD and autism spectrum disorders: measurement and mechanisms of a proposed trans-diagnostic phenotype

PubMed Central

Karalunas, Sarah L.; Geurts, Hilde M.; Konrad, Kerstin; Bender, Stephan; Nigg, Joel T.

2014-01-01

Background Intraindividual variability in reaction time (RT) has received extensive discussion as an indicator of cognitive performance, a putative intermediate phenotype of many clinical disorders, and a possible trans-diagnostic phenotype that may elucidate shared risk factors for mechanisms of psychiatric illnesses. Scope and Methodology Using the examples of attention deficit hyperactivity disorder (ADHD) and autism spectrum disorders (ASD), we discuss RT variability. We first present a new meta-analysis of RT variability in ASD with and without comorbid ADHD. We then discuss potential mechanisms that may account for RT variability and statistical models that disentangle the cognitive processes affecting RTs. We then report a second meta-analysis comparing ADHD and non-ADHD children on diffusion model parameters. We consider how findings inform the search for neural correlates of RT variability. Findings Results suggest that RT variability is increased in ASD only when children with comorbid ADHD are included in the sample. Furthermore, RT variability in ADHD is explained by moderate to large increases (d = 0.63–0.99) in the ex-Gaussian parameter τ and the diffusion parameter drift rate, as well as by smaller differences (d = 0.32) in the diffusion parameter of nondecision time. The former may suggest problems in state regulation or arousal and difficulty detecting signal from noise, whereas the latter may reflect contributions from deficits in motor organization or output. The neuroimaging literature converges with this multicomponent interpretation and also highlights the role of top-down control circuits. Conclusion We underscore the importance of considering the interactions between top-down control, state regulation (e.g. arousal), and motor preparation when interpreting RT variability and conclude that decomposition of the RT signal provides superior interpretive power and suggests mechanisms convergent with those implicated using other cognitive paradigms. We conclude with specific recommendations for the field for next steps in the study of RT variability in neurodevelopmental disorders. PMID:24628425

A review of parameters and heuristics for guiding metabolic pathfinding.

PubMed

Kim, Sarah M; Peña, Matthew I; Moll, Mark; Bennett, George N; Kavraki, Lydia E

2017-09-15

Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, thebaine. Synthesizing these traditionally plant-derived compounds in genetically modified yeast cells introduces the possibility of significantly reducing the total time and resources required for their production, and in turn, allows these valuable compounds to become cheaper and more readily available. Most biosynthesis pathways used in metabolic engineering applications have been discovered manually, requiring a tedious search of existing literature and metabolic databases. However, the recent rapid development of available metabolic information has enabled the development of automated approaches for identifying novel pathways. Computer-assisted pathfinding has the potential to save biochemists time in the initial discovery steps of metabolic engineering. In this paper, we review the parameters and heuristics used to guide the search in recent pathfinding algorithms. These parameters and heuristics capture information on the metabolic network structure, compound structures, reaction features, and organism-specificity of pathways. No one metabolic pathfinding algorithm or search parameter stands out as the best to use broadly for solving the pathfinding problem, as each method and parameter has its own strengths and shortcomings. As assisted pathfinding approaches continue to become more sophisticated, the development of better methods for visualizing pathway results and integrating these results into existing metabolic engineering practices is also important for encouraging wider use of these pathfinding methods.

Toward simulating complex systems with quantum effects

NASA Astrophysics Data System (ADS)

Kenion-Hanrath, Rachel Lynn

Quantum effects like tunneling, coherence, and zero point energy often play a significant role in phenomena on the scales of atoms and molecules. However, the exact quantum treatment of a system scales exponentially with dimensionality, making it impractical for characterizing reaction rates and mechanisms in complex systems. An ongoing effort in the field of theoretical chemistry and physics is extending scalable, classical trajectory-based simulation methods capable of capturing quantum effects to describe dynamic processes in many-body systems; in the work presented here we explore two such techniques. First, we detail an explicit electron, path integral (PI)-based simulation protocol for predicting the rate of electron transfer in condensed-phase transition metal complex systems. Using a PI representation of the transferring electron and a classical representation of the transition metal complex and solvent atoms, we compute the outer sphere free energy barrier and dynamical recrossing factor of the electron transfer rate while accounting for quantum tunneling and zero point energy effects. We are able to achieve this employing only a single set of force field parameters to describe the system rather than parameterizing along the reaction coordinate. Following our success in describing a simple model system, we discuss our next steps in extending our protocol to technologically relevant materials systems. The latter half focuses on the Mixed Quantum-Classical Initial Value Representation (MQC-IVR) of real-time correlation functions, a semiclassical method which has demonstrated its ability to "tune'' between quantum- and classical-limit correlation functions while maintaining dynamic consistency. Specifically, this is achieved through a parameter that determines the quantumness of individual degrees of freedom. Here, we derive a semiclassical correction term for the MQC-IVR to systematically characterize the error introduced by different choices of simulation parameters, and demonstrate the ability of this approach to optimize MQC-IVR simulations.

A chlorhexidine-loaded biodegradable cellulosic device for periodontal pockets treatment.

PubMed

Tabary, Nicolas; Chai, Feng; Blanchemain, Nicolas; Neut, Christel; Pauchet, Lucile; Bertini, Sabrina; Delcourt-Debruyne, Elisabeth; Hildebrand, Hartmut Frederic; Martel, Bernard

2014-01-01

Absorbent points widely used in endodontic therapy were transformed into bioresorbable chlorhexidine delivery systems for the treatment of the periodontal pocket by preventing its recolonization by the subgingival microflora. These paper points (PPs) were first oxidized to promote their resorption, then grafted with β-cyclodextrin (CD) or maltodextrin (MD) in order to achieve sustained delivery of chlorhexidine. We investigated the oxidation step parameters through the time of reaction and the nitric and phosphoric acid ratios in the oxidizing mixture, and then the dextrin grafting step parameters through the time and temperature of reaction. A first selection of the appropriate functionalization parameters was undertaken in relation to the degradation profile kinetics of the oxidized (PPO) and oxidized-grafted samples (PPO-CD and PPO-MD). Samples were then loaded with chlorhexidine digluconate (digCHX), a widely used antiseptic agent in periodontal therapy. The release kinetics of digCHX from PPO-CD and PPO-MD samples were compared to PP, PPO and to PerioChip(®) (a commercial digCHX containing gelatine chip) in phosphate buffered saline (pH 7.4) by ultraviolet spectrophotometry. The cytocompatibility of the oxidized-grafted PP was demonstrated by cell proliferation assays. Finally, the disc diffusion test from digCHX loaded PPO-MD samples immersed in human plasma was developed on pre-inoculated agar plates with four common periodontal pathogenic strains: Fusobacterium nucleatum, Prevotella melaninogenica, Aggregatibacter actinomycetem comitans and Porphyromonas gingivalis. To conclude, the optimized oxidized-dextrin-grafted PPs responded to our initial specifications in terms of resorption and digCHX release rates and therefore could be adopted as a reliable complementary periodontal therapy. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Very Tiny Rocks: Site-Specific, Size-Dependent Reaction Kinetics at Nanoparticle-Water Interfaces

NASA Astrophysics Data System (ADS)

Rustad, J. R.

2008-12-01

One of the most fundamental challenges in geochemistry is to be able to understand the rates and mechanisms of elementary reactions that describe chemical processes occurring at mineral-water interfaces. One of the reasons for the primitive conceptual state of reaction kinetics in solid earth geochemistry is that it is very difficult to identify defensible elementary reactions where theoretical predictions can be made and the results can tested experimentally at the same length and time scale of the prediction. For example, the most fundamental predictor of complexation kinetics in aqueous solution is the characteristic water exchange rate, which are well known for the aquo ions and vary by 20 orders of magnitude even for simple trivalent ions. In contrast, for interfacial reactions, it was not even known whether water exchange rates were faster or slower than equivalent metal sites in solution, prohibiting any quantitive understanding of mineral reaction kinetics at the molecular level. Recent advances in synthesis and characterization of materials at nanometer length scales has been able to bridge the gap in scale, and nanometer-sized minerals have given us our first quantitative understanding of elementary reaction rates for fundamental processes involving water and hydroxide exchange reactions. I describe the results of molecular dynamics calculation and experimental measurement of the rates of water, hydroxide, and proton exchange reactions on nanoparticle surfaces. The calculations already show that transition state theory is completely inadequate to understand the rates of even the simplest elementary reactions. Furthermore, the mechanistic implications of rate parameters such as activation volume and activation enthalpy may be different in moving from aquo ions to interfaces. Is a molecular understanding of geochemical processes really needed? One might have asked a biologist at the turn of the century whether studying the structure of proteins would ever be useful for curing disease. True molecular level understanding of interfacial interactions has the potential to revolutionize geology, allowing unprecedented detail and accuracy in such important contexts as climate reconstruction and tectonic history. Geology has an inevitable molecular future.

Associations among immunological, parasitological and clinical parameters in canine visceral leishmaniasis: Emaciation, spleen parasitism, specific antibodies and leishmanin skin test reaction.

PubMed

Dos-Santos, W L C; Jesus, E E; Paranhos-Silva, M; Pereira, A M; Santos, J C; Baleeiro, C O; Nascimento, E G; Moreira, E D; Oliveira, G G S; Pontes-de-Carvalho, L C

2008-06-15

Associations among parameters commonly used as markers of infection by Leishmania sp., or of susceptibility to visceral leishmaniasis, were investigated in 325 stray dogs from an area where this disease is endemic. Evidence of infection (presence of Leishmania in splenic cultures, positive leishmanin skin test (LST) or detection of anti-Leishmania antibody activity in the serum) was found in 57% of the animals. Both evidence of weight loss (chi(2)-test, P=0.0005) and presence of specific antibody activity in the serum (chi(2)-test, P<0.0001) were directly associated with positive splenic culture. The frequencies of animals with positive splenic culture were directly correlated with the intensities of antibody activity in the serum as measured by ELISA (relative risk of 3.4 for animals with moderate antibody levels and relative risk of 8.43 for animals with high-antibody levels). A negative association was observed between positive leishmanin skin test results and emaciation (chi(2), P=0.0089). Furthermore, animals with positive splenic cultures and negative leishmanin skin test results had higher levels of total serum IgG (Kruskal-Wallis test, P=0.001) and IgG2 (Kruskal-Wallis test, P=0.05) than animals with negative splenic cultures, and were more emaciated than animals with negative LST results and positive splenic cultures. The data presented herein suggest that associating these common parameters may improve their performance in predicting susceptibility to canine visceral leishmaniasis.

Evaluation of an S-system root-finding method for estimating parameters in a metabolic reaction model.

PubMed

Iwata, Michio; Miyawaki-Kuwakado, Atsuko; Yoshida, Erika; Komori, Soichiro; Shiraishi, Fumihide

2018-02-02

In a mathematical model, estimation of parameters from time-series data of metabolic concentrations in cells is a challenging task. However, it seems that a promising approach for such estimation has not yet been established. Biochemical Systems Theory (BST) is a powerful methodology to construct a power-law type model for a given metabolic reaction system and to then characterize it efficiently. In this paper, we discuss the use of an S-system root-finding method (S-system method) to estimate parameters from time-series data of metabolite concentrations. We demonstrate that the S-system method is superior to the Newton-Raphson method in terms of the convergence region and iteration number. We also investigate the usefulness of a translocation technique and a complex-step differentiation method toward the practical application of the S-system method. The results indicate that the S-system method is useful to construct mathematical models for a variety of metabolic reaction networks. Copyright © 2018 Elsevier Inc. All rights reserved.

Velocity and thermal slip effects on MHD third order blood flow in an irregular channel though a porous medium with homogeneous/ heterogeneous reactions

NASA Astrophysics Data System (ADS)

Gnaneswara Reddy, M.

2017-09-01

This communication presents the transportation of third order hydromagnetic fluid with thermal radiation by peristalsis through an irregular channel configuration filled a porous medium under the low Reynolds number and large wavelength approximations. Joule heating, Hall current and homogeneous-heterogeneous reactions effects are considered in the energy and species equations. The Second-order velocity and energy slip restrictions are invoked. Final dimensionless governing transport equations along the boundary restrictions are resolved numerically with the help of NDsolve in Mathematica package. Impact of involved sundry parameters on the non-dimensional axial velocity, fluid temperature and concentration characteristics have been analyzed via plots and tables. It is manifest that an increasing porosity parameter leads to maximum velocity in the core part of the channel. Fluid velocity boosts near the walls of the channel where as the reverse effect in the central part of the channel for higher values of first order slip. Larger values of thermal radiation parameter R reduce the fluid temperature field. Also, an increase in heterogeneous reaction parameter Ks magnifies the concentration profile. The present study has the crucial application of thermal therapy in biomedical engineering.

Buoyancy effects on the radiative magneto Micropolar nanofluid flow with double stratification, activation energy and binary chemical reaction.

PubMed

Ramzan, M; Ullah, Naeem; Chung, Jae Dong; Lu, Dianchen; Farooq, Umer

2017-10-10

A mathematical model has been developed to examine the magneto hydrodynamic micropolar nanofluid flow with buoyancy effects. Flow analysis is carried out in the presence of nonlinear thermal radiation and dual stratification. The impact of binary chemical reaction with Arrhenius activation energy is also considered. Apposite transformations are engaged to transform nonlinear partial differential equations to differential equations with high nonlinearity. Resulting nonlinear system of differential equations is solved by differential solver method in Maple software which uses Runge-Kutta fourth and fifth order technique (RK45). To authenticate the obtained results, a comparison with the preceding article is also made. The evaluations are executed graphically for numerous prominent parameters versus velocity, micro rotation component, temperature, and concentration distributions. Tabulated numerical calculations of Nusselt and Sherwood numbers with respective well-argued discussions are also presented. Our findings illustrate that the angular velocity component declines for opposing buoyancy forces and enhances for aiding buoyancy forces by changing the micropolar parameter. It is also found that concentration profile increases for higher values of chemical reaction parameter, whereas it diminishes for growing values of solutal stratification parameter.

The Effect of MHD on Free Convection with Periodic Temperature and Concentration in the Presence of Thermal Radiation and Chemical Reaction

NASA Astrophysics Data System (ADS)

Zigta, B.; Koya, P. R.

2017-12-01

This paper studies the effect of magneto hydrodynamics on unsteady free convection between a pair of infinite vertical Couette plates. The temperature of the plates and concentration between the plates vary with time. Convection between the plates is considered in the presence of thermal radiation and chemical reaction. The solution is obtained using perturbation techniques. These techniques are used to transform nonlinear coupled partial differential equations to a system of ordinary differential equations. The resulting equations are solved analytically. The solution is expressed in terms of power series with some small parameter. The effect of various parameters, viz., velocity, temperature and concentration, has been discussed. Mat lab code simulation study is carried out to support the theoretical results. The result shows that as the thermal radiation parameter R increases, the temperature decreases near the moving porous plate while it approaches to a zero in the region close to the boundary layer of the stationary plate. Moreover, as the modified Grashof number, i.e., based on concentration difference, increases, the velocity of the fluid flow increases hence the concentration decreases. An increase in both the chemical reaction parameter and Schmidt number results in decreased concentration.

Determination of the Nucleon-Nucleon Interaction in the ImQMD Model by Nuclear Reactions at Fermi Energy

NASA Astrophysics Data System (ADS)

Li, Cheng; Tian, Jun-Long; Wang, Ning

2013-11-01

The nucleon-nucleon interaction is investigated by using the ImQMD model with the three sets of parameters IQ1, IQ2 and IQ3 in which the corresponding incompressibility coefficients of nuclear matter are different. Fusion excitation function and the charge distribution of fragments are calculated for reaction systems 40Ca+40Ca at different incident energies. It is found that obvious differences in the charge distribution were observed at the energy region 10-25A MeV by adopting the three sets of parameters, while the results were close to each other at energy region of 30-45A MeV for the reaction system. It indicates that the Fermi energy region is a sensitive energy region to explore the N-N interaction. The fragment multiplicity spectrum for 238U+197Au at 15A MeV are reproduced by the ImQMD model with the set of parameter IQ3. It is concluded that charge distribution of the fragments and the fragment multiplicity spectrum are good observables for studying N-N interaction, and IQ3 is a suitable set of parameters for the ImQMD model.

Assessment of dynamic closure for premixed combustion large eddy simulation

NASA Astrophysics Data System (ADS)

Langella, Ivan; Swaminathan, Nedunchezhian; Gao, Yuan; Chakraborty, Nilanjan

2015-09-01

Turbulent piloted Bunsen flames of stoichiometric methane-air mixtures are computed using the large eddy simulation (LES) paradigm involving an algebraic closure for the filtered reaction rate. This closure involves the filtered scalar dissipation rate of a reaction progress variable. The model for this dissipation rate involves a parameter βc representing the flame front curvature effects induced by turbulence, chemical reactions, molecular dissipation, and their interactions at the sub-grid level, suggesting that this parameter may vary with filter width or be a scale-dependent. Thus, it would be ideal to evaluate this parameter dynamically by LES. A procedure for this evaluation is discussed and assessed using direct numerical simulation (DNS) data and LES calculations. The probability density functions of βc obtained from the DNS and LES calculations are very similar when the turbulent Reynolds number is sufficiently large and when the filter width normalised by the laminar flame thermal thickness is larger than unity. Results obtained using a constant (static) value for this parameter are also used for comparative evaluation. Detailed discussion presented in this paper suggests that the dynamic procedure works well and physical insights and reasonings are provided to explain the observed behaviour.

Evaluation of diaphragmatic mobility following intra-abdominal sub-diaphragmatic fixation of a double-layered mesh in rats.

PubMed

Ioannis, Tzanoglou; George, Sakorafas; Nikolaos, Kostomitsopoulos; George, Mantziaras; Charalampos, Patraleksis; Nikolaos, Danias; Spyridon, Stergiopoulos; Michael, Safioleas

2016-04-01

To evaluate the tissue integration of a double-sided mesh after fixation in diaphragm and to study the diaphragmatic mobility by ultrasound. Twenty male Wistar rats were used. The animals were assigned into two equal groups according to the day of euthanasia. The animals were anesthetized and a 1.5 x 1.5 cm of double-layer mesh was inserted between the diaphragm and the liver. For the evaluation of the diaphragm mobility a sonographic method was used. Measurements on specific breathing parameters were taking place. Pathological evaluation took place after the animal's euthanasia. Extra-hepatic granuloma was not differentiated overtime, (χ2=0.04, p>0.05). Neither fibrosis was significantly differentiated, (χ2=0.04, p>0.05). Intra-hepatic granuloma was significantly differentiated overtime, (χ2=10.21, p<0.05). Concerning Te parameter, means were significantly differentiated over time, F (3, 30) = 5.12, (p<0.01). Ttot parameter, it was differentiated over time, F (3, 8)=4.79, (p<0.05). IR parameter was also longitudinally differentiated, F (3, 30)=3.73, (p<0.05). The measurements suggest a transient malfunction of diaphragmatic mobility despite the fact that inflammatory reaction, fibrosis and extra-hepatic granuloma were not significantly differentiated with the passage of time.

Weighted-density functionals for cavity formation and dispersion energies in continuum solvation models

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

Sundararaman, Ravishankar; Gunceler, Deniz; Arias, T. A.

2014-10-07

Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting modelmore » with a single solvent-independent parameter: the electron density threshold (n c), and a single solvent-dependent parameter: the dispersion scale factor (s 6), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s 6 parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.« less

Weighted-density functionals for cavity formation and dispersion energies in continuum solvation models

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

Sundararaman, Ravishankar; Gunceler, Deniz; Arias, T. A.

2014-10-07

Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting modelmore » with a single solvent-independent parameter: the electron density threshold (n{sub c}), and a single solvent-dependent parameter: the dispersion scale factor (s{sub 6}), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s{sub 6} parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.« less

Integrated hydraulic and organophosphate pesticide injection simulations for enhancing event detection in water distribution systems.

PubMed

Schwartz, Rafi; Lahav, Ori; Ostfeld, Avi

2014-10-15

As a complementary step towards solving the general event detection problem of water distribution systems, injection of the organophosphate pesticides, chlorpyrifos (CP) and parathion (PA), were simulated at various locations within example networks and hydraulic parameters were calculated over 24-h duration. The uniqueness of this study is that the chemical reactions and byproducts of the contaminants' oxidation were also simulated, as well as other indicative water quality parameters such as alkalinity, acidity, pH and the total concentration of free chlorine species. The information on the change in water quality parameters induced by the contaminant injection may facilitate on-line detection of an actual event involving this specific substance and pave the way to development of a generic methodology for detecting events involving introduction of pesticides into water distribution systems. Simulation of the contaminant injection was performed at several nodes within two different networks. For each injection, concentrations of the relevant contaminants' mother and daughter species, free chlorine species and water quality parameters, were simulated at nodes downstream of the injection location. The results indicate that injection of these substances can be detected at certain conditions by a very rapid drop in Cl2, functioning as the indicative parameter, as well as a drop in alkalinity concentration and a small decrease in pH, both functioning as supporting parameters, whose usage may reduce false positive alarms. Copyright © 2014 Elsevier Ltd. All rights reserved.

Monitoring mass transport in heterogeneously catalyzed reactions by field-gradient NMR for assessing reaction efficiency in a single pellet

NASA Astrophysics Data System (ADS)

Buljubasich, L.; Blümich, B.; Stapf, S.

2011-09-01

An important aspect in assessing the performance of a catalytically active reactor is the accessibility of the reactive sites inside the individual pellets, and the mass transfer of reactants and products to and from these sites. Optimal design often requires a suitable combination of micro- and macropores in order to facilitate mass transport inside the pellet. In an exothermic reaction, fluid exchange between the pellet and the surrounding medium is enhanced by convection, and often by the occurrence of gas bubbles. Determining mass flow in the vicinity of a pellet thus represents a parameter for quantifying the reaction efficiency and its dependence on time or external reaction conditions. Field gradient Nuclear Magnetic Resonance (NMR) methods are suggested as a tool for providing parameters sensitive to this mass flow in a contact-free and non-invasive way. For the example of bubble-forming hydrogen peroxide decomposition in an alumina pellet, the dependence of the mean-squared displacement of fluid molecules on spatial direction, observation time and reaction time is presented, and multi-pulse techniques are employed in order to separate molecular displacements from coherent and incoherent motion on the timescale of the experiment. The reaction progress is followed until the complete decomposition of H 2O 2.

Kinetic modeling of α-hydrogen abstractions from unsaturated and saturated oxygenate compounds by hydrogen atoms.

PubMed

Paraskevas, Paschalis D; Sabbe, Maarten K; Reyniers, Marie-Françoise; Papayannakos, Nikos G; Marin, Guy B

2014-10-09

Hydrogen-abstraction reactions play a significant role in thermal biomass conversion processes, as well as regular gasification, pyrolysis, or combustion. In this work, a group additivity model is constructed that allows prediction of reaction rates and Arrhenius parameters of hydrogen abstractions by hydrogen atoms from alcohols, ethers, esters, peroxides, ketones, aldehydes, acids, and diketones in a broad temperature range (300-2000 K). A training set of 60 reactions was developed with rate coefficients and Arrhenius parameters calculated by the CBS-QB3 method in the high-pressure limit with tunneling corrections using Eckart tunneling coefficients. From this set of reactions, 15 group additive values were derived for the forward and the reverse reaction, 4 referring to primary and 11 to secondary contributions. The accuracy of the model is validated upon an ab initio and an experimental validation set of 19 and 21 reaction rates, respectively, showing that reaction rates can be predicted with a mean factor of deviation of 2 for the ab initio and 3 for the experimental values. Hence, this work illustrates that the developed group additive model can be reliably applied for the accurate prediction of kinetics of α-hydrogen abstractions by hydrogen atoms from a broad range of oxygenates.

Modeling and optimization aspects of radiation induced grafting of 4-vinylpyridene onto partially fluorinated films

NASA Astrophysics Data System (ADS)

Nasef, Mohamed Mahmoud; Ahmad Ali, Amgad; Saidi, Hamdani; Ahmad, Arshad

2014-01-01

Modeling and optimization aspects of radiation induced grafting (RIG) of 4-vinylpyridine (4-VP) onto partially fluorinated polymers such as poly(ethylene-co-tetrafluoroethene) (ETFE) and poly(vinylidene fluoride) (PVDF) films were comparatively investigated using response surface method (RSM). The effects of independent parameters: absorbed dose, monomer concentration, grafting time and reaction temperature on the response, grafting yield (GY) were correlated through two quadratic models. The results of this work confirm that RSM is a reliable tool not only for optimization of the reaction parameters and prediction of GY in RIG processes, but also for the reduction of the number of the experiments, monomer consumption and absorbed dose leading to an improvement of the overall reaction cost.

Single-particle strength from nucleon transfer in oxygen isotopes: Sensitivity to model parameters

NASA Astrophysics Data System (ADS)

Flavigny, F.; Keeley, N.; Gillibert, A.; Obertelli, A.

2018-03-01

In the analysis of transfer reaction data to extract nuclear structure information the choice of input parameters to the reaction model such as distorting potentials and overlap functions has a significant impact. In this paper we consider a set of data for the (d ,t ) and (d ,3He ) reactions on 14,16,18O as a well-delimited subject for a study of the sensitivity of such analyses to different choices of distorting potentials and overlap functions with particular reference to a previous investigation of the variation of valence nucleon correlations as a function of the difference in nucleon separation energy Δ S =| Sp-Sn| [Phys. Rev. Lett. 110, 122503 (2013), 10.1103/PhysRevLett.110.122503].

Effects of magnetic, radiation and chemical reaction on unsteady heat and mass transfer flow of an oscillating cylinder

NASA Astrophysics Data System (ADS)

Ahmed, Rubel; Rana, B. M. Jewel; Ahmmed, S. F.

2017-06-01

The effects of magnetic, radiation and chemical reaction parameters on the unsteady heat and mass transfer boundary layer flow past an oscillating cylinder is considered. The dimensionless momentum, energy and concentration equations are solved numerically by using explicit finite difference method with the help of a computer programming language Compaq visual FORTRAN 6.6a. The obtained results of this study have been discussed for different values of well-known parameters with different time steps. The effect of these parameters on the velocity field, temperature field and concentration field, skin-friction, Nusselt number, streamlines and isotherms has been studied and results are presented by graphically represented by the tabular form quantitatively. The stability and convergence analysis of the solution parameters that have been used in the mathematical model have been tested.

The relationship between ground reaction force in sit-to-stand movement and lower extremity function in community-dwelling Japanese older adults using long-term care insurance services

PubMed Central

Shen, Shaoshuai; Abe, Takumi; Tsuji, Taishi; Fujii, Keisuke; Ma, Jingyu; Okura, Tomohiro

2017-01-01

[Purpose] The purpose of this study was to investigate which of the four chair-rising methods has low-load and the highest success rate, and whether the GRF parameters in that method are useful for measuring lower extremity function among physically frail Japanese older adults. [Subjects and Methods] Fifty-two individuals participated in this study. The participants voluntarily attempted four types of Sit-to-stand test (one variation without and three variations with the use of their arms). The following parameters were measured: peak reaction force (F/w), two force development rate parameters (RFD1.25/w, RFD8.75/w) and two time-related parameters (T1, T2). Three additional commonly employed clinical tests (One-leg balance with eyes open, Timed up and go and 5-meter walk test) were also conducted. [Results] “Hands on a chair” chair-rising method produced the highest success rate among the four methods. All parameters were highly reliable between testing occasions. T2 showed strongly significant associations with Timed up and go and 5-meter walk test in males. RFD8.75/w showed significant associations with Timed up and go and 5-meter walk test in females. [Conclusion] Ground reaction force parameters in the Sit-to-stand test are a reliable and useful method for assessment of lower extremity function in physically frail Japanese older adults. PMID:28931988

Ground reaction forces on stairs. Part II: knee implant patients versus normals.

PubMed

Stacoff, Alex; Kramers-de Quervain, Inès A; Luder, Gerhard; List, Renate; Stüssi, Edgar

2007-06-01

The goal of this study was to compare selected parameters of vertical ground reaction forces (GRF) of good outcome patients with different prosthesis designs with a matched control group during level walking, stair ascent and descent. Forty subjects, 29 with three main implant designs (including four subjects with a passive knee flexion restriction), and 11 healthy controls were measured with 8-10 repetitions. Vertical ground reaction forces were measured during two consecutive steps with force plates embedded in the walkway and the staircase. Defined parameters of the force signals were used to compare the results of the test groups. The results show, that, postoperatively, good outcome patients produce gait patterns of the vertical ground reaction force which are comparable to normal healthy subjects with the exception of a few distinct differences: a significant reduction (p<0.05) in the vertical loading on the operated side during level walking at take-off, at weight acceptance and take-off during stair ascent of the normal stair. During stair descent, the patients did not reduce load on the operated side, but increased load variation and side-to-side asymmetry; thus, the mechanical loads on the implants were high, which may be important information with respect to loading protocols of knee implant simulators. No systematic differences in any of the test parameters were found between posterior cruciate-retaining (LCS MB and Innex CR) versus non-retaining (LCS RP and Innex UCOR) implant designs. The restricted group showed significant reductions (p<0.05) of several loading parameters as well as an increased side-to-side asymmetry. About one third of the force parameters of the good outcome patients showed a side-to-side asymmetry between two consecutive steps, which was over a proposed level of acceptance.

[Hypersensitivity to mosquito bite manifested as Skeeter síndrome].

PubMed

Pérez-Vanzzini, Rafael; González-Díaz, Sandra Nora; Arias-Cruz, Alfredo; Palma-Gómez, Samuel; Yong-Rodríguez, Adrián; Gutiérrez-Mujica, José Julio; García-Calderín, Diego; Ibarra, Jesús Arturo

2015-01-01

The reactions to mosquito bites are immunological reactions with involvement of IgE, IgG and T cells mediated hypersensitivity. These reactions are common and range from small local reactions, large local reactions to systemic allergic reactions. Skeeter syndrome is defined as a large local induced inflammatory reaction to mosquito bite and sometimes accompanied by systemic symptoms such as fever and vomiting. Diagnosis is based on clinical history and physical examination, supported by the identification of specific IgE by skin testing. Treatment includes prevention, antihistamines and steroids in some cases. Specific immunotherapy still requires further study. This paper reports two cases of patients with hypersensitivity reactions to mosquito bites, which were evaluated in our center presenting positive skin tests.

A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions

PubMed Central

Saa, Pedro; Nielsen, Lars K.

2015-01-01

Kinetic models provide the means to understand and predict the dynamic behaviour of enzymes upon different perturbations. Despite their obvious advantages, classical parameterizations require large amounts of data to fit their parameters. Particularly, enzymes displaying complex reaction and regulatory (allosteric) mechanisms require a great number of parameters and are therefore often represented by approximate formulae, thereby facilitating the fitting but ignoring many real kinetic behaviours. Here, we show that full exploration of the plausible kinetic space for any enzyme can be achieved using sampling strategies provided a thermodynamically feasible parameterization is used. To this end, we developed a General Reaction Assembly and Sampling Platform (GRASP) capable of consistently parameterizing and sampling accurate kinetic models using minimal reference data. The former integrates the generalized MWC model and the elementary reaction formalism. By formulating the appropriate thermodynamic constraints, our framework enables parameterization of any oligomeric enzyme kinetics without sacrificing complexity or using simplifying assumptions. This thermodynamically safe parameterization relies on the definition of a reference state upon which feasible parameter sets can be efficiently sampled. Uniform sampling of the kinetics space enabled dissecting enzyme catalysis and revealing the impact of thermodynamics on reaction kinetics. Our analysis distinguished three reaction elasticity regions for common biochemical reactions: a steep linear region (0> ΔGr >-2 kJ/mol), a transition region (-2> ΔGr >-20 kJ/mol) and a constant elasticity region (ΔGr <-20 kJ/mol). We also applied this framework to model more complex kinetic behaviours such as the monomeric cooperativity of the mammalian glucokinase and the ultrasensitive response of the phosphoenolpyruvate carboxylase of Escherichia coli. In both cases, our approach described appropriately not only the kinetic behaviour of these enzymes, but it also provided insights about the particular features underpinning the observed kinetics. Overall, this framework will enable systematic parameterization and sampling of enzymatic reactions. PMID:25874556

"In silico" mechanistic studies as predictive tools in microwave-assisted organic synthesis.

PubMed

Rodriguez, A M; Prieto, P; de la Hoz, A; Díaz-Ortiz, A

2011-04-07

Computational calculations can be used as a predictive tool in Microwave-Assisted Organic Synthesis (MAOS). A DFT study on Intramolecular Diels-Alder reactions (IMDA) indicated that the activation energy of the reaction and the polarity of the stationary points are two fundamental parameters to determine "a priori" if a reaction can be improved by using microwave irradiation.

Design study for a magnetically supported reaction wheel

NASA Technical Reports Server (NTRS)

Stocking, G.; Dendy, J.; Sabnis, A.

1974-01-01

Results are described of a study program in which the characteristics of a magnetically supported reaction wheel are defined. Tradeoff analyses are presented for the principal components, which are then combined in several reaction wheel design concepts. A preliminary layout of the preferred configuration is presented along with calculated design and performance parameters. Recommendations are made for a prototype development program.

Effect of modifying agents on the hydrophobicity and yield of zinc borate synthesized by zinc oxide

NASA Astrophysics Data System (ADS)

Acarali, Nil Baran; Bardakci, Melek; Tugrul, Nurcan; Derun, Emek Moroydor; Piskin, Sabriye

2013-06-01

The aim of this study was to synthesize zinc borate using zinc oxide, reference boric acid, and reference zinc borate (reference ZB) as the seed, and to investigate the effects of modifying agents and reaction parameters on the hydrophobicity and yield, respectively. The reaction parameters include reaction time (1-5 h), reactant ratio (H3BO3/ZnO by mass: 2-5), seed ratio (seed crystal/(H3BO3+ZnO) by mass: 0-2wt%), reaction temperature (50-120°C), cooling temperature (10-80°C), and stirring rate (400-700 r/min); the modifying agents involve propylene glycol (PG, 0-6wt%), kerosene (1wt%-6wt%), and oleic acid (OA, 1wt%-6wt%) with solvents (isopropyl alcohol (IPA), ethanol, and methanol). The results of reaction yield obtained from either magnetically or mechanically stirred systems were compared. Zinc borate produced was characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), and contact angle tests to identify the hydrophobicity. In conclusion, zinc borate is synthesized successfully under the optimized reaction conditions, and the different modifying agents with various solvents affect the hydrophobicity of zinc borate.

Thermodynamic Analysis of Chemically Reacting Mixtures-Comparison of First and Second Order Models.

PubMed

Pekař, Miloslav

2018-01-01

Recently, a method based on non-equilibrium continuum thermodynamics which derives thermodynamically consistent reaction rate models together with thermodynamic constraints on their parameters was analyzed using a triangular reaction scheme. The scheme was kinetically of the first order. Here, the analysis is further developed for several first and second order schemes to gain a deeper insight into the thermodynamic consistency of rate equations and relationships between chemical thermodynamic and kinetics. It is shown that the thermodynamic constraints on the so-called proper rate coefficient are usually simple sign restrictions consistent with the supposed reaction directions. Constraints on the so-called coupling rate coefficients are more complex and weaker. This means more freedom in kinetic coupling between reaction steps in a scheme, i.e., in the kinetic effects of other reactions on the rate of some reaction in a reacting system. When compared with traditional mass-action rate equations, the method allows a reduction in the number of traditional rate constants to be evaluated from data, i.e., a reduction in the dimensionality of the parameter estimation problem. This is due to identifying relationships between mass-action rate constants (relationships which also include thermodynamic equilibrium constants) which have so far been unknown.

Stepwise formation of H3O(+)(H2O)n in an ion drift tube: Empirical effective temperature of association/dissociation reaction equilibrium in an electric field.

PubMed

Nakai, Yoichi; Hidaka, Hiroshi; Watanabe, Naoki; Kojima, Takao M

2016-06-14

We measured equilibrium constants for H3O(+)(H2O)n-1 + H2O↔H3O(+)(H2O)n (n = 4-9) reactions taking place in an ion drift tube with various applied electric fields at gas temperatures of 238-330 K. The zero-field reaction equilibrium constants were determined by extrapolation of those obtained at non-zero electric fields. From the zero-field reaction equilibrium constants, the standard enthalpy and entropy changes, ΔHn,n-1 (0) and ΔSn,n-1 (0), of stepwise association for n = 4-8 were derived and were in reasonable agreement with those measured in previous studies. We also examined the electric field dependence of the reaction equilibrium constants at non-zero electric fields for n = 4-8. An effective temperature for the reaction equilibrium constants at non-zero electric field was empirically obtained using a parameter describing the electric field dependence of the reaction equilibrium constants. Furthermore, the size dependence of the parameter was thought to reflect the evolution of the hydrogen-bond structure of H3O(+)(H2O)n with the cluster size. The reflection of structural information in the electric field dependence of the reaction equilibria is particularly noteworthy.

The relevance of TH1 and TH2 cells in immediate and nonimmediate reactions to gelatin-containing vaccine.

PubMed

Ohsaki, M; Tsutsumi, H; Kumagai, T; Yamanaka, T; Wataya, Y; Furukawa, H; Kojima, H; Saito, A; Yano, S; Chiba, S

1999-02-01

The immune mechanism of gelatin allergy, especially the participation of TH1 and TH2 cells and their cytokine secretion, has not been investigated. We investigated the characteristics of T lymphocytes from patients allergic to gelatin-containing vaccine by secondary in vitro stimulation of circulating mononuclear cells with gelatin. We studied 8 children with a history of immediate-type reactions and 8 with nonimmediate-type reactions after inoculation of gelatin-containing vaccine. The expression of IFN-gamma (TH1 ), IL-2 (TH1 ), IL-4 (TH2 ), and IL-13 (TH2 ) mRNA was examined semiquantitatively by using a reverse transcriptase PCR. IgE antibody to bovine gelatin was measured with the fluorometric ELISA system, and gelatin-specific T-cell responses were detected by an in vitro lymphocyte proliferation assay. Patients with an immediate reaction all had gelatin-specific IgE antibody, whereas others did not. However, all patients exhibited positive T-lymphocyte responses specific to gelatin. Lymphocytes from subjects with nonimmediate-type reactions generally expressed very weak or sometimes no IFN-gamma, IL-2, or IL-13 genes and especially no IL-4 gene. On the other hand, the lymphocytes of subjects with immediate-type reactions significantly expressed not only IL-4 and IL-13 but also IFN-gamma and IL-2 mRNA. Our observations suggest that both gelatin-specific TH2 and TH1 responses are involved in the pathogenesis of the immediate reaction to gelatin. The gelatin-specific IL-4 and/or IL-13 responses consistently observed in patients with an immediate reaction may be associated with the production of gelatin-specific IgE antibody.

Transfer functions for protein signal transduction: application to a model of striatal neural plasticity.

PubMed

Scheler, Gabriele

2013-01-01

We present a novel formulation for biochemical reaction networks in the context of protein signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select a set of "source" species, which are interpreted as input signals. Signals are transmitted to all other species in the system (the "target" species) with a specific delay and with a specific transmission strength. The delay is computed as the maximal reaction time until a stable equilibrium for the target species is reached, in the context of all other reactions in the system. The transmission strength is the concentration change of the target species. The computed input-output transfer functions can be stored in a matrix, fitted with parameters, and even recalled to build dynamical models on the basis of state changes. By separating the temporal and the magnitudinal domain we can greatly simplify the computational model, circumventing typical problems of complex dynamical systems. The transfer function transformation of biochemical reaction systems can be applied to mass-action kinetic models of signal transduction. The paper shows that this approach yields significant novel insights while remaining a fully testable and executable dynamical model for signal transduction. In particular we can deconstruct the complex system into local transfer functions between individual species. As an example, we examine modularity and signal integration using a published model of striatal neural plasticity. The modularizations that emerge correspond to a known biological distinction between calcium-dependent and cAMP-dependent pathways. Remarkably, we found that overall interconnectedness depends on the magnitude of inputs, with higher connectivity at low input concentrations and significant modularization at moderate to high input concentrations. This general result, which directly follows from the properties of individual transfer functions, contradicts notions of ubiquitous complexity by showing input-dependent signal transmission inactivation.

Utility of low-dose oral aspirin challenges for diagnosis of aspirin-exacerbated respiratory disease.

PubMed

Jerschow, Elina; Ren, Zhen; Hudes, Golda; Sanak, Marek; Morales, Esperanza; Schuster, Victor; Spivack, Simon D; Rosenstreich, David

2016-04-01

Aspirin-exacerbated respiratory disease (AERD) is diagnosed through graded aspirin challenges that induce hypersensitivity reactions and eicosanoid level changes. It is not known whether diagnostically useful changes also occur after low-dose aspirin challenges that do not induce hypersensitivity reactions. To investigate the utility of low-dose oral aspirin challenges for diagnosing AERD by measuring different clinical parameters and eicosanoid changes. Sixteen patients with AERD and 13 patients with aspirin-tolerant asthma underwent oral challenges with low-dose (20 or 40 mg) aspirin and diagnostic oral graded aspirin challenges (up to 325 mg of aspirin). Forced expiratory volume in 1 second, nasal peak flow, the fraction of exhaled nitric oxide (FeNO), and eicosanoid levels in plasma and urine were analyzed. In patients with AERD but not in those with aspirin-tolerant asthma, 40-mg aspirin challenges induced a significant mean (SEM) decrease from baseline in FeNO (19% [5.1%]; P = .001) without causing any hypersensitivity reaction. The FeNO decrease also occurred after higher-dose aspirin challenges (27.8% [4.9%]; P < .001). The sensitivity and specificity of 40-mg aspirin-induced FeNO changes for identifying AERD were 90% and 100% with an area under the curve of 0.98 (95% CI, 0.92-1.00). The low-dose challenge also induced a significant leukotriene E4 urine increase in patients with AERD (from 6.32 [0.08] to 6.91 [0.15] log-pg/mg creatinine; P < .001), but the sensitivity and specificity of these changes were less than for the FeNO changes. The low-dose aspirin-induced decrease in FeNO in patients with AERD may be useful for the diagnosis of aspirin allergy without inducing a hypersensitivity reaction. clinicaltrials.gov Identifier: NCT01320072. Copyright © 2016 American College of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Concepts, challenges, and successes in modeling thermodynamics of metabolism.

PubMed

Cannon, William R

2014-01-01

The modeling of the chemical reactions involved in metabolism is a daunting task. Ideally, the modeling of metabolism would use kinetic simulations, but these simulations require knowledge of the thousands of rate constants involved in the reactions. The measurement of rate constants is very labor intensive, and hence rate constants for most enzymatic reactions are not available. Consequently, constraint-based flux modeling has been the method of choice because it does not require the use of the rate constants of the law of mass action. However, this convenience also limits the predictive power of constraint-based approaches in that the law of mass action is used only as a constraint, making it difficult to predict metabolite levels or energy requirements of pathways. An alternative to both of these approaches is to model metabolism using simulations of states rather than simulations of reactions, in which the state is defined as the set of all metabolite counts or concentrations. While kinetic simulations model reactions based on the likelihood of the reaction derived from the law of mass action, states are modeled based on likelihood ratios of mass action. Both approaches provide information on the energy requirements of metabolic reactions and pathways. However, modeling states rather than reactions has the advantage that the parameters needed to model states (chemical potentials) are much easier to determine than the parameters needed to model reactions (rate constants). Herein, we discuss recent results, assumptions, and issues in using simulations of state to model metabolism.

First-order kinetic gas generation model parameters for wet landfills.

PubMed

Faour, Ayman A; Reinhart, Debra R; You, Huaxin

2007-01-01

Landfill gas collection data from wet landfill cells were analyzed and first-order gas generation model parameters were estimated for the US EPA landfill gas emissions model (LandGEM). Parameters were determined through statistical comparison of predicted and actual gas collection. The US EPA LandGEM model appeared to fit the data well, provided it is preceded by a lag phase, which on average was 1.5 years. The first-order reaction rate constant, k, and the methane generation potential, L(o), were estimated for a set of landfills with short-term waste placement and long-term gas collection data. Mean and 95% confidence parameter estimates for these data sets were found using mixed-effects model regression followed by bootstrap analysis. The mean values for the specific methane volume produced during the lag phase (V(sto)), L(o), and k were 33 m(3)/Megagrams (Mg), 76 m(3)/Mg, and 0.28 year(-1), respectively. Parameters were also estimated for three full scale wet landfills where waste was placed over many years. The k and L(o) estimated for these landfills were 0.21 year(-1), 115 m(3)/Mg, 0.11 year(-1), 95 m(3)/Mg, and 0.12 year(-1) and 87 m(3)/Mg, respectively. A group of data points from wet landfills cells with short-term data were also analyzed. A conservative set of parameter estimates was suggested based on the upper 95% confidence interval parameters as a k of 0.3 year(-1) and a L(o) of 100 m(3)/Mg if design is optimized and the lag is minimized.

Oxidation of alkylarenes to the corresponding acids using aqueous potassium permanganate by hydrodynamic cavitation.

PubMed

Ambulgekar, G V; Samant, S D; Pandit, A B

2004-05-01

Oxidation of toluene using aqueous potassium permanganate was studied under heterogeneous condition in the presence of hydrodynamic cavitation and compared with the results of the reaction under acoustic cavitation. Various parameters, such as quantity of potassium permanganate, toluene to aqueous phase ratio, reaction time and cavitation parameters such as orifice plate, and pump discharge pressure were optimized. The reaction was found to be considerably accelerated at ambient temperature in the presence of cavitation. On comparison, it was found that when 1 kJ of energy was passed to the reaction mixture in the case of acoustic cavitation, the product obtained was 4.63 x 10(-6) mol, whereas when 1 kJ of energy was passed to the reaction mixture in the case of hydrodynamic cavitation the product obtained was 2.70 x 10(-5) mol. Hence, about six times more product would be obtained in the case of hydrodynamic cavitation than in the case of acoustic cavitation at same energy dissipation. It has been observed that further optimization is possible.

Influence of vegetable oils fatty acid composition on reaction temperature and glycerides conversion to biodiesel during transesterification.

PubMed

Pinzi, S; Gandía, L M; Arzamendi, G; Ruiz, J J; Dorado, M P

2011-01-01

Presence of unreacted glycerides in biodiesel may reduce drastically its quality. This is why conversion of raw material in biodiesel through transesterification needs to readjust reaction parameter values to complete. In the present work, monitoring of glycerides transformation in biodiesel during the transesterification of vegetable oils was carried out. To check the influence of the chemical composition on glycerides conversion, selected vegetable oils covered a wide range of fatty acid composition. Reactions were carried out under alkali-transesterification in the presence of methanol. In addition, a multiple regression model was proposed. Results showed that kinetics depends on chemical and physical properties of the oils. It was found that the optimal reaction temperature depends on both length and unsaturation degree of vegetable oils fatty acid chains. Vegetable oils with higher degree of unsaturation exhibit faster monoglycerides conversion to biodiesel. It can be concluded that fatty acid composition influences reaction parameters and glycerides conversion, hence biodiesel yield and economic viability. Copyright © 2010 Elsevier Ltd. All rights reserved.

Dimethyl sulfoxide could be a useful probe to evaluate unusual skin angioneurotic reaction and epidermal permeability.

PubMed

Chen, Shuang Y; Wang, Xue M; Liu, Yan Q; Gao, Yan R; Liu, Xiao P; Li, Shu Y; Dong, Ya Q

2014-03-01

Dimethyl sulfoxide (DMSO) has been suggested as a traditional chemical probe for assessing skin susceptibility and barrier function. The purpose of this study was to determine the role of DMSO test for the evaluation of unusual skin angioneurotic reaction and epidermal permeability. Thirty healthy volunteers were exposed to 98% DMSO on the flexor forearm skin for three exposure durations (5 min, 10 min and 15 min). Clinical visual score and biological physical parameters were obtained. The volunteers were divided into two groups according to the clinical visual scoring. The skin parameters were subsequently analyzed. There was a significant correlation between clinical visual score and biological physical parameters. The skin color parameters (a*, oxyhemoglobin, erythema and melanin index) and blood flow values were significant between two groups regardless of duration of DMSO exposure, and a significant difference between density values could also be detected if we regrouped the volunteers according to the sting-producing score. Our results also suggested there was no correlation between questionnaire score and clinical visual score or other parameters. Application of 98% DMSO for 10 min combined with a* (at 30 min) and blood flow (at 10 min) values could help us to identify persons with a hyper-angionerotic reaction to chemical stimulus. The penetrative activity of DMSO correlated with the thickness of the individual's skin.

Materials from Mussel-Inspired Chemistry for Cell and Tissue Engineering Applications.

PubMed

Madhurakkat Perikamana, Sajeesh Kumar; Lee, Jinkyu; Lee, Yu Bin; Shin, Young Min; Lee, Esther J; Mikos, Antonios G; Shin, Heungsoo

2015-09-14

Current advances in biomaterial fabrication techniques have broadened their application in different realms of biomedical engineering, spanning from drug delivery to tissue engineering. The success of biomaterials depends highly on the ability to modulate cell and tissue responses, including cell adhesion, as well as induction of repair and immune processes. Thus, most recent approaches in the field have concentrated on functionalizing biomaterials with different biomolecules intended to evoke cell- and tissue-specific reactions. Marine mussels produce mussel adhesive proteins (MAPs), which help them strongly attach to different surfaces, even under wet conditions in the ocean. Inspired by mussel adhesiveness, scientists discovered that dopamine undergoes self-polymerization at alkaline conditions. This reaction provides a universal coating for metals, polymers, and ceramics, regardless of their chemical and physical properties. Furthermore, this polymerized layer is enriched with catechol groups that enable immobilization of primary amine or thiol-based biomolecules via a simple dipping process. Herein, this review explores the versatile surface modification techniques that have recently been exploited in tissue engineering and summarizes polydopamine polymerization mechanisms, coating process parameters, and effects on substrate properties. A brief discussion of polydopamine-based reactions in the context of engineering various tissue types, including bone, blood vessels, cartilage, nerves, and muscle, is also provided.

New Biofuel Integrating Glycerol into Its Composition Through the Use of Covalent Immobilized Pig Pancreatic Lipase

PubMed Central

Luna, Diego; Posadillo, Alejandro; Caballero, Verónica; Verdugo, Cristóbal; Bautista, Felipa M.; Romero, Antonio A.; Sancho, Enrique D.; Luna, Carlos; Calero, Juan

2012-01-01

By using 1,3-specific Pig Pancreatic lipase (EC 3.1.1.3 or PPL), covalently immobilized on AlPO4/Sepiolite support as biocatalyst, a new second-generation biodiesel was obtained in the transesterification reaction of sunflower oil with ethanol and other alcohols of low molecular weight. The resulting biofuel is composed of fatty acid ethyl esters and monoglycerides (FAEE/MG) blended in a molar relation 2/1. This novel product, which integrates glycerol as monoacylglycerols (MG) into the biofuel composition, has similar physicochemical properties compared to those of conventional biodiesel and also avoids the removal step of this by-product. The biocatalyst was found to be strongly fixed to the inorganic support (75%). Nevertheless, the efficiency of the immobilized enzyme was reduced to half (49.1%) compared to that of the free PPL. The immobilized enzyme showed a remarkable stability as well as a great reusability (more than 40 successive reuses) without a significant loss of its initial catalytic activity. Immobilized and free enzymes exhibited different reaction mechanisms, according to the different results in the Arrhenius parameters (Ln A and Ea). However, the use of supported PPL was found to be very suitable for the repetitive production of biofuel due to its facile recyclability from the reaction mixture. PMID:22949849

Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring*

PubMed Central

Lawless, Craig; Holman, Stephen W.; Brownridge, Philip; Lanthaler, Karin; Harman, Victoria M.; Watkins, Rachel; Hammond, Dean E.; Miller, Rebecca L.; Sims, Paul F. G.; Grant, Christopher M.; Eyers, Claire E.; Beynon, Robert J.

2016-01-01

Defining intracellular protein concentration is critical in molecular systems biology. Although strategies for determining relative protein changes are available, defining robust absolute values in copies per cell has proven significantly more challenging. Here we present a reference data set quantifying over 1800 Saccharomyces cerevisiae proteins by direct means using protein-specific stable-isotope labeled internal standards and selected reaction monitoring (SRM) mass spectrometry, far exceeding any previous study. This was achieved by careful design of over 100 QconCAT recombinant proteins as standards, defining 1167 proteins in terms of copies per cell and upper limits on a further 668, with robust CVs routinely less than 20%. The selected reaction monitoring-derived proteome is compared with existing quantitative data sets, highlighting the disparities between methodologies. Coupled with a quantification of the transcriptome by RNA-seq taken from the same cells, these data support revised estimates of several fundamental molecular parameters: a total protein count of ∼100 million molecules-per-cell, a median of ∼1000 proteins-per-transcript, and a linear model of protein translation explaining 70% of the variance in translation rate. This work contributes a “gold-standard” reference yeast proteome (including 532 values based on high quality, dual peptide quantification) that can be widely used in systems models and for other comparative studies. PMID:26750110

Evaluation of the Pool Critical Assembly Benchmark with Explicitly-Modeled Geometry using MCNP6

DOE PAGES

Kulesza, Joel A.; Martz, Roger Lee

2017-03-01

Despite being one of the most widely used benchmarks for qualifying light water reactor (LWR) radiation transport methods and data, no benchmark calculation of the Oak Ridge National Laboratory (ORNL) Pool Critical Assembly (PCA) pressure vessel wall benchmark facility (PVWBF) using MCNP6 with explicitly modeled core geometry exists. As such, this paper provides results for such an analysis. First, a criticality calculation is used to construct the fixed source term. Next, ADVANTG-generated variance reduction parameters are used within the final MCNP6 fixed source calculations. These calculations provide unadjusted dosimetry results using three sets of dosimetry reaction cross sections of varyingmore » ages (those packaged with MCNP6, from the IRDF-2002 multi-group library, and from the ACE-formatted IRDFF v1.05 library). These results are then compared to two different sets of measured reaction rates. The comparison agrees in an overall sense within 2% and on a specific reaction- and dosimetry location-basis within 5%. Except for the neptunium dosimetry, the individual foil raw calculation-to-experiment comparisons usually agree within 10% but is typically greater than unity. Finally, in the course of developing these calculations, geometry that has previously not been completely specified is provided herein for the convenience of future analysts.« less

Modeling of Flow, Transport and Controlled Sedimentation Phenomena during Mixing of Salt Solutions in Complex Porous Formations

NASA Astrophysics Data System (ADS)

Skouras, Eugene D.; Jaho, Sofia; Pavlakou, Efstathia I.; Sygouni, Varvara; Petsi, Anastasia; Paraskeva, Christakis A.

2015-04-01

The deposition of salts in porous media is a major engineering phenomenon encountered in a plethora of industrial and environmental applications where in some cases is desirable and in other not (oil production, geothermal systems, soil stabilization etc). Systematic approach of these problems requires knowledge of the key mechanisms of precipitating salts within the porous structures, in order to develop new methods to control the process. In this work, the development and the solution of spatiotemporally variable mass balances during salt solution mixing along specific pores were performed. Both analytical models and finite differences CFD models were applied for the study of flow and transport with simultaneous homogeneous and heterogeneous nucleation (by crystal growth on the surface of the pores) in simple geometries, while unstructured finite elements and meshless methods were developed and implemented for spatial discretization, reconstruction, and solution of transport equations and homogeneous / heterogeneous reactions in more complex geometries. At initial stages of this work, critical problem parameters were identified, such as the characteristics of the porosity, the number of dissolved components, etc. The parameters were then used for solving problems which correspond to available experimental data. For each combination of ions and materials, specific data and process characteristics were included: (a) crystal kinetics (nucleation, growth rates or reaction surface rates of crystals, critical suspension concentrations), (b) physico-chemical properties (bulk density, dimensions of generated crystals, ion diffusion coefficients in the solution), (c) operating parameters (macroscopic velocity, flow, or pressure gradient of the solution, ion concentration) (d) microfluidic data (geometry, flow area), (e) porosity data in Darcy description (initial porosity, specific surface area, tortuosity). During the modeling of flow and transport in three-dimensional pore network, the dependence of the mass balance in all major directions is taken into account, either as a three-dimensional network of pores with specific geometry (cylinders, sinusoidal cells), or as a homogeneous random medium (Darcy description). The distribution of the crystals along the porous medium was calculated in the case of selective crystallization on the walls, which is the predominant effect to date in the experiments. The crystals distribution was also examined in the case where crystallization was carried out in the bulk solution. Salts sedimentation experiments were simulated both in an unsaturated porous medium and in a medium saturated with an oil phase. A comparison of the simulation results with corresponding experimental results was performed in order to design improved selective sedimentation of salts systems in porous formations. ACKNOWLEDGMENTS This research was partially funded by the European Union (European Social Fund-ESF) and Greek National Funds through the Operational program "Education and Lifelong Learning" under the action Aristeia II (Code No 4420).

Development of a chemiluminescent and bioluminescent system for the detection of bacteria in wastewater effluent

NASA Technical Reports Server (NTRS)

Thomas, R. R.

1975-01-01

Automated chemiluminescent and bioluminescent sensors were developed for continuous monitoring of microbial levels in wastewater effluent. Development of the chemiluminescent system included optimization of reagent concentrations as well as two new techniques which will allow for increased sensitivity and specificity. The optimal reagent concentrations are 0.0025 M luminol and 0.0125 M sodium perborate in 0.75N sodium hydroxide before addition of sample. The methods developed to increase specificity include (1) extraction of porphyrins from bacteria collected in a filter using 0.1N NaOH - 50 percent Ethanol, and (2) use of the specific reaction rate characteristics for the different luminol catalysts. Since reaction times are different for each catalyst, the reaction can be made specific for bacteria by measuring only the light emission from the particular reaction time zone specific for bacteria. Developments of the bioluminescent firefly luciferase system were in the area of flow system design.

A Measurement Plane for Optical Networks to Manage Emergency Events

NASA Astrophysics Data System (ADS)

Tego, E.; Carciofi, C.; Grazioso, P.; Petrini, V.; Pompei, S.; Matera, F.; Attanasio, V.; Nastri, E.; Restuccia, E.

2017-11-01

In this work, we show a wide geographical area optical network test bed, adopting the mPlane measurement plane for monitoring its performance and to manage software defined network approaches, with some specific tests and procedures dedicated to respond to disaster events and to support emergency networks. Such a test bed includes FTTX accesses, and it is currently implemented to support future 5G wireless services with slicing procedures based on Carrier Ethernet. The characteristics of this platform have been experimentally tested in the case of a damage-causing link failure and traffic congestion, showing a fast reactions to these disastrous events, allowing the user to recharge the initial QoS parameters.

In vitro folding of inclusion body proteins.

PubMed

Rudolph, R; Lilie, H

1996-01-01

Insoluble, inactive inclusion bodies are frequently formed upon recombinant protein production in transformed microorganisms. These inclusion bodies, which contain the recombinant protein in an highly enriched form, can be isolated by solid/liquid separation. After solubilization, native proteins can be generated from the inactive material by using in vitro folding techniques. New folding procedures have been developed for efficient in vitro reconstitution of complex hydrophobic, multidomain, oligomeric, or highly disulfide-bonded proteins. These protocols take into account process parameters such as protein concentration, catalysis of disulfide bond formation, temperature, pH, and ionic strength, as well as specific solvent ingredients that reduce unproductive side reactions. Modification of the protein sequence has been exploited to improve in vitro folding.

Frequency response of electrochemical cells

NASA Technical Reports Server (NTRS)

Thomas, Daniel L.

1990-01-01

The main objective was to examine the feasibility of using frequency response techniques (1) as a tool in destructive physical analysis of batteries, particularly for estimating electrode structural parameters such as specific area, porosity, and tortuosity and (2) as a non-destructive testing technique for obtaining information such as state of charge and acceptability for space flight. The phenomena that contribute to the frequency response of an electrode include: (1) double layer capacitance; (2) Faradaic reaction resistance; (3) mass transfer of Warburg impedance; and (4) ohmic solution resistance. Nickel cadmium cells were investigated in solutions of KOH. A significant amount of data was acquired. Quantitative data analysis, using the developed software, is planned for the future.

Gene cloning and overexpression of a geranylgeranyl diphosphate synthase of an extremely thermophilic bacterium, Thermus thermophilus.

PubMed

Ohto, C; Ishida, C; Koike-Takeshita, A; Yokoyama, K; Muramatsu, M; Nishino, T; Obata, S

1999-02-01

A geranylgeranyl diphosphate (GGPP) synthase gene of an extremely thermophilic bacterium, Thermus thermophilus, was cloned and sequenced. T. thermophilus GGPP synthase, overexpressed in Escherichia coli cells as a glutathione S-transferase fusion protein, was purified and characterized. The fusion protein, retaining thermostability, formed a homodimer, and showed higher specific activity than did a partially purified thermostable enzyme previously reported. Optimal reaction conditions and kinetic parameters were also examined. The deduced amino acid sequence indicated that T. thermophilus GGPP synthase was excluded from the group of bacterial type GGPP synthases and lacked the insertion amino acid residues in the first aspartate-rich motif as do archaeal and eukaryotic short-chain prenyltransferases.

Estimation of beech pyrolysis kinetic parameters by Shuffled Complex Evolution.

PubMed

Ding, Yanming; Wang, Changjian; Chaos, Marcos; Chen, Ruiyu; Lu, Shouxiang

2016-01-01

The pyrolysis kinetics of a typical biomass energy feedstock, beech, was investigated based on thermogravimetric analysis over a wide heating rate range from 5K/min to 80K/min. A three-component (corresponding to hemicellulose, cellulose and lignin) parallel decomposition reaction scheme was applied to describe the experimental data. The resulting kinetic reaction model was coupled to an evolutionary optimization algorithm (Shuffled Complex Evolution, SCE) to obtain model parameters. To the authors' knowledge, this is the first study in which SCE has been used in the context of thermogravimetry. The kinetic parameters were simultaneously optimized against data for 10, 20 and 60K/min heating rates, providing excellent fits to experimental data. Furthermore, it was shown that the optimized parameters were applicable to heating rates (5 and 80K/min) beyond those used to generate them. Finally, the predicted results based on optimized parameters were contrasted with those based on the literature. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effect of ozonolysis pretreatment parameters on the sugar release, ozone consumption and ethanol production from sugarcane bagasse.

PubMed

Travaini, Rodolfo; Barrado, Enrique; Bolado-Rodríguez, Silvia

2016-08-01

A L9(3)(4) orthogonal array (OA) experimental design was applied to study the four parameters considered most important in the ozonolysis pretreatment (moisture content, ozone concentration, ozone/oxygen flow and particle size) on ethanol production from sugarcane bagasse (SCB). Statistical analysis highlighted ozone concentration as the highest influence parameter on reaction time and sugars release after enzymatic hydrolysis. The increase on reaction time when decreasing the ozone/oxygen flow resulted in small differences of ozone consumptions. Design optimization for sugars release provided a parameters combination close to the best experimental run, where 77.55% and 56.95% of glucose and xylose yields were obtained, respectively. When optimizing the grams of sugar released by gram of ozone, the highest influence parameter was moisture content, with a maximum yield of 2.98gSUGARS/gO3. In experiments on hydrolysates fermentation, Saccharomyces cerevisiae provided ethanol yields around 80%, while Pichia stipitis was completely inhibited. Copyright © 2016 Elsevier Ltd. All rights reserved.

A fluorescence high throughput screening method for the detection of reactive electrophiles as potential skin sensitizers

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

Avonto, Cristina; Chittiboyina, Amar G.; Rua, Diego

2015-12-01

Skin sensitization is an important toxicological end-point in the risk assessment of chemical allergens. Because of the complexity of the biological mechanisms associated with skin sensitization, integrated approaches combining different chemical, biological and in silico methods are recommended to replace conventional animal tests. Chemical methods are intended to characterize the potential of a sensitizer to induce earlier molecular initiating events. The presence of an electrophilic mechanistic domain is considered one of the essential chemical features to covalently bind to the biological target and induce further haptenation processes. Current in chemico assays rely on the quantification of unreacted model nucleophiles aftermore » incubation with the candidate sensitizer. In the current study, a new fluorescence-based method, ‘HTS-DCYA assay’, is proposed. The assay aims at the identification of reactive electrophiles based on their chemical reactivity toward a model fluorescent thiol. The reaction workflow enabled the development of a High Throughput Screening (HTS) method to directly quantify the reaction adducts. The reaction conditions have been optimized to minimize solubility issues, oxidative side reactions and increase the throughput of the assay while minimizing the reaction time, which are common issues with existing methods. Thirty-six chemicals previously classified with LLNA, DPRA or KeratinoSens™ were tested as a proof of concept. Preliminary results gave an estimated 82% accuracy, 78% sensitivity, 90% specificity, comparable to other in chemico methods such as Cys-DPRA. In addition to validated chemicals, six natural products were analyzed and a prediction of their sensitization potential is presented for the first time. - Highlights: • A novel fluorescence-based method to detect electrophilic sensitizers is proposed. • A model fluorescent thiol was used to directly quantify the reaction products. • A discussion of the reaction workflow and critical parameters is presented. • The method could provide a useful tool to complement existing chemical assays.« less

Cyclic Square Wave Voltammetry of Surface-Confined Quasireversible Electron Transfer Reactions.

PubMed

Mann, Megan A; Bottomley, Lawrence A

2015-09-01

The theory for cyclic square wave voltammetry of surface-confined quasireversible electrode reactions is presented and experimentally verified. Theoretical voltammograms were calculated following systematic variation of empirical parameters to assess their impact on the shape of the voltammogram. From the trends obtained, diagnostic criteria for this mechanism were deduced. These criteria were experimentally confirmed using two well-established surface-confined analytes. When properly applied, these criteria will enable non-experts in voltammetry to assign the electrode reaction mechanism and accurately measure electrode reaction kinetics.

An asymptotic analysis of supersonic reacting mixing layers

NASA Technical Reports Server (NTRS)

Jackson, T. L.; Hussaini, M. Y.

1987-01-01

The purpose of this paper is to present an asymptotic analysis of the laminar mixing of the simultaneous chemical reaction between parallel supersonic streams of two reacting species. The study is based on a one-step irreversible Arrhenius reaction and on large activation energy asymptotics. Essentially it extends the work of Linan and Crespo to include the effect of free shear and Mach number on the ignition regime, the deflagration regime and the diffusion flame regime. It is found that the effective parameter is the product of the characteristic Mach number and a shear parameter.

Kinetic of antigent-antibody reactions with scattering method

NASA Astrophysics Data System (ADS)

Bilyi, Olexander I.; Kiselyov, Yevgen M.; Novikov, Volodymyr P.

2001-07-01

The immune reactions of interaction antigen-antibody represent specific effect of an antigene with an antibody, which outcome are the complex immune aggregates forming precipitate in case of a soluble antigene, or agglutinate in case of a corpuscular antigene. Immunological methods which uses in the quality of carrier protein latex's polymeric microspheresis, gained name and method latex agglutination. Polymeric microspheresis have the array of advantages before biological carries, which consist in the opportunity of the variation of attributes surface and size microspheresis in the broad band of meanings with the preservation of narrow distribution particles behind measurements, the putting of functional groups, necessary for bunch with ligand on stage their synthesis, in ragidity at storage. The quantitative evaluation of parameters of a response of interaction antigen-antibody in immunology is possible by optical methods on a measurement of a modification of intensity of a light stream of a solution in an outcome of a course of a reaction. Concentration of immune complexes determine both on slacking a taking place stream of light, and on a modification of intensity of a stream of light scattering suspended particles in a solution. The process light scattering by colloidal aggregates are formed from suspension microspheresis with adsorbed on their surface protein is described. In report the physics principle of registration immune reaction by light scattering methods is concerned. The results of the effectiveness latex's preparation created on basis of the polymeric carries is described.

Proxy-based accelerated discovery of Fischer–Tropsch catalysts† †Electronic supplementary information (ESI) available: Details of synthesis, analysis and testing, validation experiments for high-throughput XRD and gas treatment, details of statistical analysis and calculations, tabulation of synthesis parameters and XRD results, alternatives to Fig. 3 highlighting different data points, FTS testing results displayed graphically. See DOI: 10.1039/c4sc02116a Click here for additional data file.

PubMed Central

Boldrin, Paul; Gallagher, James R.; Combes, Gary B.; Enache, Dan I.; James, David; Ellis, Peter R.; Kelly, Gordon; Claridge, John B.

2015-01-01

Development of heterogeneous catalysts for complex reactions such as Fischer–Tropsch synthesis of fuels is hampered by difficult reaction conditions, slow characterisation techniques such as chemisorption and temperature-programmed reduction and the need for long term stability. High-throughput (HT) methods may help, but their use has until now focused on bespoke micro-reactors for direct measurements of activity and selectivity. These are specific to individual reactions and do not provide more fundamental information on the materials. Here we report using simpler HT characterisation techniques (XRD and TGA) along with ageing under Fischer–Tropsch reaction conditions to provide information analogous to metal surface area, degree of reduction and thousands of hours of stability testing time for hundreds of samples per month. The use of this method allowed the identification of a series of highly stable, high surface area catalysts promoted by Mg and Ru. In an advance over traditional multichannel HT reactors, the chemical and structural information we obtain on the materials allows us to identify the structural effects of the promoters and their effects on the modes of deactivation observed. PMID:29560180

In vitro and in vivo evaluation of the inflammatory potential of various nanoporous hydroxyapatite biomaterials.

PubMed

Velard, Frédéric; Schlaubitz, Silke; Fricain, Jean-Christophe; Guillaume, Christine; Laurent-Maquin, Dominique; Möller-Siegert, Janina; Vidal, Loïc; Jallot, Edouard; Sayen, Stéphanie; Raissle, Olivier; Nedelec, Jean-Marie; Vix-Guterl, Cathie; Anselme, Karine; Amédée, Joëlle; Laquerrière, Patrice

2015-01-01

To discriminate the most important physicochemical parameters for bone reconstruction, the inflammatory potential of seven nanoporous hydroxyapatite powders synthesized by hard or soft templating was evaluated both in vitro and in vivo. After physical and chemical characterization of the powders, we studied the production of inflammatory mediators by human primary monocytes after 4 and 24 h in contact with powders, and the host response after 2 weeks implantation in a mouse critical size defect model. In vitro results highlighted increases in the secretion of TNF-α, IL-1, -8, -10 and proMMP-2 and -9 and decreases in the secretion of IL-6 only for powders prepared by hard templating. In vivo observations confirmed an extensive inflammatory tissue reaction and a strong resorption for the most inflammatory powder in vitro. These findings highlight that the most critical physicochemical parameters for these nanoporous hydroxyapatite are, the crystallinity that controls dissolution potential, the specific surface area and the size and shape of crystallites.

Dynamic absorption coefficients of chemically amplified resists and nonchemically amplified resists at extreme ultraviolet

NASA Astrophysics Data System (ADS)

Fallica, Roberto; Stowers, Jason K.; Grenville, Andrew; Frommhold, Andreas; Robinson, Alex P. G.; Ekinci, Yasin

2016-07-01

The dynamic absorption coefficients of several chemically amplified resists (CAR) and non-CAR extreme ultraviolet (EUV) photoresists are measured experimentally using a specifically developed setup in transmission mode at the x-ray interference lithography beamline of the Swiss Light Source. The absorption coefficient α and the Dill parameters ABC were measured with unprecedented accuracy. In general, the α of resists match very closely with the theoretical value calculated from elemental densities and absorption coefficients, whereas exceptions are observed. In addition, through the direct measurements of the absorption coefficients and dose-to-clear values, we introduce a new figure of merit called chemical sensitivity to account for all the postabsorption chemical reaction ongoing in the resist, which also predicts a quantitative clearing volume and clearing radius, due to the photon absorption in the resist. These parameters may help provide deeper insight into the underlying mechanisms of the EUV concepts of clearing volume and clearing radius, which are then defined and quantitatively calculated.

Bites of the European pigeon tick (Argas reflexus): Risk of IgE-mediated sensitizations and anaphylactic reactions.

PubMed

Kleine-Tebbe, Jörg; Heinatz, Anja; Gräser, Inken; Dautel, Hans; Hansen, Gitte Nordskov; Kespohl, Sabine; Rihs, Hans-Peter; Raulf-Heimsoth, Monika; Vater, Günther; Rytter, Manfred; Haustein, Uwe-Fritjof

2006-01-01

Local and systemic reactions can occur after bites of Argas reflexus (Argas), a soft tick parasitizing pigeons. Risk assessment of IgE-mediated sensitizations and systemic reactions after Argas bites. Case histories, skin prick tests (SPTs) with a whole-body extract of Argas containing major allergen Arg r 1, and common inhalants and specific IgE measurements were obtained from 148 subjects who had had Argas bites and 20 volunteers as a control group. Systemic reactions (urticaria, angioedema, dyspnea, cardiovascular dysregulation, unconsciousness) were reported in 12 of 148 (8%); 146 of 148 (99%) had local reactions. Atopy was found in 37 of 146 (25%) with local reactions and 3 of 12 (25%) with systemic reactions. SPT to Argas was positive in 24 of 148 (16%) with a high proportion of atopics 10 of 24 (42%); specific IgE to Argas was detectable in 12 of 135 (8% of 148) with moderate concordance to systemic reactions. No positive SPT or specific IgE results to Argas were obtained in the control group. Immunoblotting of 23 sera revealed an IgE-binding protein in 19 of 23 sera (82%) at 22 kd, indicating a major allergen of Argas. Severe anaphylactic reactions were infrequently (approximately 8%) found after bites of the soft tick Argas reflexus. Atopy is a risk factor for skin sensitizations to Argas, but not for systemic reactions after bites by Argas. Using a whole-body extract of Argas, diagnosis through SPT and specific IgE is hampered by false-negative and irrelevant positive results, particularly in atopy.

Correcting reaction rates measured by saturation-transfer magnetic resonance spectroscopy

NASA Astrophysics Data System (ADS)

Gabr, Refaat E.; Weiss, Robert G.; Bottomley, Paul A.

2008-04-01

Off-resonance or spillover irradiation and incomplete saturation can introduce significant errors in the estimates of chemical rate constants measured by saturation-transfer magnetic resonance spectroscopy (MRS). Existing methods of correction are effective only over a limited parameter range. Here, a general approach of numerically solving the Bloch-McConnell equations to calculate exchange rates, relaxation times and concentrations for the saturation-transfer experiment is investigated, but found to require more measurements and higher signal-to-noise ratios than in vivo studies can practically afford. As an alternative, correction formulae for the reaction rate are provided which account for the expected parameter ranges and limited measurements available in vivo. The correction term is a quadratic function of experimental measurements. In computer simulations, the new formulae showed negligible bias and reduced the maximum error in the rate constants by about 3-fold compared to traditional formulae, and the error scatter by about 4-fold, over a wide range of parameters for conventional saturation transfer employing progressive saturation, and for the four-angle saturation-transfer method applied to the creatine kinase (CK) reaction in the human heart at 1.5 T. In normal in vivo spectra affected by spillover, the correction increases the mean calculated forward CK reaction rate by 6-16% over traditional and prior correction formulae.

Modeled Neutron and Charged-Particle Induced Nuclear Reaction Cross Sections for Radiochemistry in the Region of Yttrium, Zirconium, Niobium, and Molybdenum

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

Hoffman, R D; Kelley, K; Dietrich, F S

2006-06-13

We have developed a set of modeled nuclear reaction cross sections for use in radiochemical diagnostics. Systematics for the input parameters required by the Hauser-Feshbach statistical model were developed and used to calculate neutron, proton, and deuteron induced nuclear reaction cross sections for targets ranging from strontium (Z = 38) to rhodium (Z = 45).

A Nonlinear, Multiinput, Multioutput Process Control Laboratory Experiment

ERIC Educational Resources Information Center

Young, Brent R.; van der Lee, James H.; Svrcek, William Y.

2006-01-01

Experience in using a user-friendly software, Mathcad, in the undergraduate chemical reaction engineering course is discussed. Example problems considered for illustration deal with simultaneous solution of linear algebraic equations (kinetic parameter estimation), nonlinear algebraic equations (equilibrium calculations for multiple reactions and…

Human beings' adaptability to extreme environmental changes from medical and physical points of view

NASA Astrophysics Data System (ADS)

Khabarova, Olga; Ragulskaya, Maria; Dimitrova, Svetla; Safaraly-Oghlu Babayev, Elchin; Samsonov, Sergey; Med. Dimitry Markov, Of; Nazarova, Of Med. Olga N.; Rudenchik, Evgeny

The question about features of human reaction on the sharp environmental physical activity (EPA) changes is considered by international group of physicists and physicians on the base of results of monitoring of human health state in different cities spread on latitude and longitude. The typical reaction of human body on the influences, exceeding the organisms' ability to adaptation, is of stress-reaction character. From medical point of view there is no significant difference for human body -what external (EPA) agent shocked an organism (emotional or some physical threats). First attempt of the organism to restore its homeostasis is stress-reaction, being universal for many stress-factors. Its main stages (such as alarm, resistance, and exhaustion) are detectable by different medical equipments, but we tried to find universal, non-traumatic method of daily measurements, enough sensitive and appropriate for observation of people reaction both on weather and space weather (geomagnetic activity) changes. The experiment was based on a method of electrical conductivity measurements of biologically active (acupunctural) points of human skin. The used method (electroacupunctural method by Dr. R.Voll) is very sensitive to current state of an organism and characterize the functional condition of different organs and systems of human body and allows to express so-called "group's health status" in the units, suitable for comparison with meteorological and heliogeophysical parameters. We conduct the parallel investigations as a part of collaborative study in different geographic latitudes-longitudes (Baku:40° 23'43"N -49° 52'56"E, Troitsk (Moscow region): 55° 28'40"N -37° 18'42"E, Yakutsk: 62° 02'00"N -129° 44'00"E). Measurements were carried out on daily basis with permanent group of functionally healthy persons (Moscow -19, Yakutsk -22, CityBaku -12 volunteers). Daily monitoring of nervous, endocrinological, lymphatic systems, blood, lungs, thick and thin intestine, heart and parenhimatic organs, allergy and hypophisis was conducted simultaneously with analyses of space weather (parameters of solar and geomagnetic activities) as well as local meteorological parameters (temperature, atmospheric pressure, humidity, wind speed, etc.). It was proved that it is possible to consider not only weather changes but also geomagnetic field variations as a stressor. It is concluded that : 1. human reaction on the sharp changes of selected external (environmental) physical activity parameters goes like typical stress-reaction; 2. features of stress-reaction depend on history of previous failures of an organism and on state of external background (frequent stresses deplete human organism possibility to adaptation); 3. features of stress-reaction depend on the geographic location (latitude). Possible physi-cal explanation of human organism stress-reaction on changes of geomagnetic oscillatory regime and atmospheric thermobaric variations is discussed.

Explicit consideration of topological and parameter uncertainty gives new insights into a well-established model of glycolysis.

PubMed

Achcar, Fiona; Barrett, Michael P; Breitling, Rainer

2013-09-01

Previous models of glycolysis in the sleeping sickness parasite Trypanosoma brucei assumed that the core part of glycolysis in this unicellular parasite is tightly compartimentalized within an organelle, the glycosome, which had previously been shown to contain most of the glycolytic enzymes. The glycosomes were assumed to be largely impermeable, and exchange of metabolites between the cytosol and the glycosome was assumed to be regulated by specific transporters in the glycosomal membrane. This tight compartmentalization was considered to be essential for parasite viability. Recently, size-specific metabolite pores were discovered in the membrane of glycosomes. These channels are proposed to allow smaller metabolites to diffuse across the membrane but not larger ones. In light of this new finding, we re-analyzed the model taking into account uncertainty about the topology of the metabolic system in T. brucei, as well as uncertainty about the values of all parameters of individual enzymatic reactions. Our analysis shows that these newly-discovered nonspecific pores are not necessarily incompatible with our current knowledge of the glycosomal metabolic system, provided that the known cytosolic activities of the glycosomal enzymes play an important role in the regulation of glycolytic fluxes and the concentration of metabolic intermediates of the pathway. © 2013 FEBS.

Correspondence between discrete and continuous models of excitable media: trigger waves

NASA Technical Reports Server (NTRS)

Chernyak, Y. B.; Feldman, A. B.; Cohen, R. J.

1997-01-01

We present a theoretical framework for relating continuous partial differential equation (PDE) models of excitable media to discrete cellular automata (CA) models on a randomized lattice. These relations establish a quantitative link between the CA model and the specific physical system under study. We derive expressions for the CA model's plane wave speed, critical curvature, and effective diffusion constant in terms of the model's internal parameters (the interaction radius, excitation threshold, and time step). We then equate these expressions to the corresponding quantities obtained from solution of the PDEs (for a fixed excitability). This yields a set of coupled equations with a unique solution for the required CA parameter values. Here we restrict our analysis to "trigger" wave solutions obtained in the limiting case of a two-dimensional excitable medium with no recovery processes. We tested the correspondence between our CA model and two PDE models (the FitzHugh-Nagumo medium and a medium with a "sawtooth" nonlinear reaction source) and found good agreement with the numerical solutions of the PDEs. Our results suggest that the behavior of trigger waves is actually controlled by a small number of parameters.

Double stratification effects in chemically reactive squeezed Sutterby fluid flow with thermal radiation and mixed convection

NASA Astrophysics Data System (ADS)

Ahmad, S.; Farooq, M.; Javed, M.; Anjum, Aisha

2018-03-01

A current analysis is carried out to study theoretically the mixed convection characteristics in squeezing flow of Sutterby fluid in squeezed channel. The constitutive equation of Sutterby model is utilized to characterize the rheology of squeezing phenomenon. Flow characteristics are explored with dual stratification. In flowing fluid which contains heat and mass transport, the first order chemical reaction and radiative heat flux affect the transport phenomenon. The systems of non-linear governing equations have been modulating which then solved by mean of convergent approach (Homotopy Analysis Method). The graphs are reported and illustrated for emerging parameters. Through graphical explanations, drag force, rate of heat and mass transport are conversed for different pertinent parameters. It is found that heat and mass transport rate decays with dominant double stratified parameters and chemical reaction parameter. The present two-dimensional examination is applicable in some of the engineering processes and industrial fluid mechanics.

Ground Reaction Forces and Gait Parameters during Motorized and Non-Motorized Treadmill Walking and Runing on the International Space Station Treadmill

NASA Technical Reports Server (NTRS)

Hagan, Ronald Donald; Norcross, Jason; DeWitt, John; Lee, Stuart M.; McCleary, Frank; Edwards, W. Brent

2006-01-01

Both motorized (T-M) and non-motorized (T-NM) treadmill locomotion are used on the International Space Station (ISS) as countermeasures to the deleterious effects of prolonged weightlessness. However, the ground reaction forces (GRF) and gait parameters of these exercise modes have not been examined. The purpose of this study was to determine if differences in GRF and gait parameters exist while walking (1.34 m/s) and running (3.13 m/s) on T-M and T-NM. Dissimilar GRF and gait parameters suggest that T-M and T-NM locomotion may elicit different physiologic effects. T-NM may result in a reduced stimulus to bone formation due to a lower LR, but an increased energy cost as a result of shorter, more frequent strides. Therefore, the usage of each mode should depend upon the desired training stimulus.

Analysis of Mathematical Modelling on Potentiometric Biosensors

PubMed Central

Mehala, N.; Rajendran, L.

2014-01-01

A mathematical model of potentiometric enzyme electrodes for a nonsteady condition has been developed. The model is based on the system of two coupled nonlinear time-dependent reaction diffusion equations for Michaelis-Menten formalism that describes the concentrations of substrate and product within the enzymatic layer. Analytical expressions for the concentration of substrate and product and the corresponding flux response have been derived for all values of parameters using the new homotopy perturbation method. Furthermore, the complex inversion formula is employed in this work to solve the boundary value problem. The analytical solutions obtained allow a full description of the response curves for only two kinetic parameters (unsaturation/saturation parameter and reaction/diffusion parameter). Theoretical descriptions are given for the two limiting cases (zero and first order kinetics) and relatively simple approaches for general cases are presented. All the analytical results are compared with simulation results using Scilab/Matlab program. The numerical results agree with the appropriate theories. PMID:25969765

Analysis of mathematical modelling on potentiometric biosensors.

PubMed

Mehala, N; Rajendran, L

2014-01-01

A mathematical model of potentiometric enzyme electrodes for a nonsteady condition has been developed. The model is based on the system of two coupled nonlinear time-dependent reaction diffusion equations for Michaelis-Menten formalism that describes the concentrations of substrate and product within the enzymatic layer. Analytical expressions for the concentration of substrate and product and the corresponding flux response have been derived for all values of parameters using the new homotopy perturbation method. Furthermore, the complex inversion formula is employed in this work to solve the boundary value problem. The analytical solutions obtained allow a full description of the response curves for only two kinetic parameters (unsaturation/saturation parameter and reaction/diffusion parameter). Theoretical descriptions are given for the two limiting cases (zero and first order kinetics) and relatively simple approaches for general cases are presented. All the analytical results are compared with simulation results using Scilab/Matlab program. The numerical results agree with the appropriate theories.

Convective boundary conditions effect on peristaltic flow of a MHD Jeffery nanofluid

NASA Astrophysics Data System (ADS)

Kothandapani, M.; Prakash, J.

2016-03-01

This work is aimed at describing the influences of MHD, chemical reaction, thermal radiation and heat source/sink parameter on peristaltic flow of Jeffery nanofluids in a tapered asymmetric channel along with slip and convective boundary conditions. The governing equations of a nanofluid are first formulated and then simplified under long-wavelength and low-Reynolds number approaches. The equation of nanoparticles temperature and concentration is coupled; hence, homotopy perturbation method has been used to obtain the solutions of temperature and concentration of nanoparticles. Analytical solutions for axial velocity, stream function and pressure gradient have also constructed. Effects of various influential flow parameters have been pointed out through with help of the graphs. Analysis indicates that the temperature of nanofluids decreases for a given increase in heat transfer Biot number and chemical reaction parameter, but it possesses converse behavior in respect of mass transfer Biot number and heat source/sink parameter.

Determining Spacecraft Reaction Wheel Friction Parameters

NASA Technical Reports Server (NTRS)

Sarani, Siamak

2009-01-01

Software was developed to characterize the drag in each of the Cassini spacecraft's Reaction Wheel Assemblies (RWAs) to determine the RWA friction parameters. This tool measures the drag torque of RWAs for not only the high spin rates (greater than 250 RPM), but also the low spin rates (less than 250 RPM) where there is a lack of an elastohydrodynamic boundary layer in the bearings. RWA rate and drag torque profiles as functions of time are collected via telemetry once every 4 seconds and once every 8 seconds, respectively. Intermediate processing steps single-out the coast-down regions. A nonlinear model for the drag torque as a function of RWA spin rate is incorporated in order to characterize the low spin rate regime. The tool then uses a nonlinear parameter optimization algorithm based on the Nelder-Mead simplex method to determine the viscous coefficient, the Dahl friction, and the two parameters that account for the low spin-rate behavior.

Chemically reactive species in squeezed flow through modified Fourier's and Fick's laws

NASA Astrophysics Data System (ADS)

Farooq, M.; Ahmad, S.; Javed, M.; Anjum, Aisha

2018-02-01

The squeezing flow of a Newtonian fluid with variable viscosity over a stretchable sheet embedded in Darcy porous medium is addressed. Cattaneo-Christov double diffusion models are adopted to disclose the salient features of heat and mass transport via variable thermal conductivity and variable mass diffusivity instead of conventional Fourier's and Fick's laws. Further, the concept of heat generation/absorption coefficient and first-order chemical reaction are also imposed to illustrate the characteristics of heat and mass transfer. Highly nonlinear computations are developed in dimensionless form and analyzed via the homotopic technique. The variation of flow parameters on velocity, concentration, and temperature distributions are sketched and disclosed physically. The results found that both concentration and temperature distributions decay for higher solutal and thermal relaxation parameters, respectively. Moreover, a higher chemical reaction parameter results in the reduction of the concentration field whereas the temperature profile enhances for a higher heat generation/absorption parameter.

Kinetics, mechanism, and spectroscopy of the reversible binding of nitric oxide to aquated iron(II). An undergraduate text book reaction revisited.

PubMed

Wanat, Alicja; Schneppensieper, Thorsten; Stochel, Grazyna; van Eldik, Rudi; Bill, Eckhard; Wieghardt, Karl

2002-01-14

A detailed kinetic and mechanistic analysis of the classical "brown-ring" reaction of [Fe(H(2)O)(6)](2+) with NO was performed using stopped-flow and laser flash photolysis techniques at ambient and high pressure. The kinetic parameters for the "on" and "off" reactions at 25 degrees C were found to be k(on) = 1.42 x 10(6) M(-1) s(-1), DeltaH(++)(on) = 37.1 +/- 0.5 kJ mol(-1), DeltaS(++)(on) = -3 +/- 2 J K(-1) mol(-1), DeltaV(++)(on) = +6.1 +/- 0.4 cm(3) mol(-1), and k(off) = 3240 +/- 750 s(-1), DeltaH(++)(off) = 48.4 +/- 1.4 kJ mol(-1), DeltaS(++)(off) = -15 +/- 5 J K(-1) mol(-1), DeltaV(++)(off) = +1.3 +/- 0.2 cm(3) mol(-1). These parameters suggest that both reactions follow an interchange dissociative (I(d)) ligand substitution mechanism, which correlates well with the suggested mechanism for the water exchange reaction on [Fe(H(2)O)(6)](2+). In addition, Mössbauer spectroscopy and EPR measurements were performed on the reaction product [Fe(H(2)O)(5)(NO)](2+). The Mössbauer and EPR parameters closely resemble those of the [FeNO](7) units in any of the other well-characterized nitrosyl complexes. It is concluded that its electronic structure is best described by the presence of high-spin Fe(III) antiferromagnetically coupled to NO(-) (S = 1) yielding the observed spin quartet ground state (S = (3)/(2)), i.e., [Fe(III)(H(2)O)(5)(NO(-))](2+), and not [Fe(I)(H(2)O)(5)(NO(+))](2+) as usually quoted in undergraduate text books.

The evolution of environmental and genetic sex determination in fluctuating environments.

PubMed

Van Dooren, Tom J M; Leimar, Olof

2003-12-01

Twenty years ago, Bulmer and Bull suggested that disruptive selection, produced by environmental fluctuations, can result in an evolutionary transition from environmental sex determination (ESD) to genetic sex determination (GSD). We investigated the feasibility of such a process, using mutation-limited adaptive dynamics and individual-based computer simulations. Our model describes the evolution of a reaction norm for sex determination in a metapopulation setting with partial migration and variation in an environmental variable both within and between local patches. The reaction norm represents the probability of becoming a female as a function of environmental state and was modeled as a sigmoid function with two parameters, one giving the location (i.e., the value of the environmental variable for which an individual has equal chance of becoming either sex) and the other giving the slope of the reaction norm for that environment. The slope can be interpreted as being set by the level of developmental noise in morph determination, with less noise giving a steeper slope and a more switchlike reaction norm. We found convergence stable reaction norms with intermediate to large amounts of developmental noise for conditions characterized by low migration rates, small differential competitive advantages between the sexes over environments, and little variation between individual environments within patches compared to variation between patches. We also considered reaction norms with the slope parameter constrained to a high value, corresponding to little developmental noise. For these we found evolutionary branching in the location parameter and a transition from ESD toward GSD, analogous to the original analysis by Bulmer and Bull. Further evolutionary change, including dominance evolution, produced a polymorphism acting as a GSD system with heterogamety. Our results point to the role of developmental noise in the evolution of sex determination.

An improved swarm optimization for parameter estimation and biological model selection.

PubMed

Abdullah, Afnizanfaizal; Deris, Safaai; Mohamad, Mohd Saberi; Anwar, Sohail

2013-01-01

One of the key aspects of computational systems biology is the investigation on the dynamic biological processes within cells. Computational models are often required to elucidate the mechanisms and principles driving the processes because of the nonlinearity and complexity. The models usually incorporate a set of parameters that signify the physical properties of the actual biological systems. In most cases, these parameters are estimated by fitting the model outputs with the corresponding experimental data. However, this is a challenging task because the available experimental data are frequently noisy and incomplete. In this paper, a new hybrid optimization method is proposed to estimate these parameters from the noisy and incomplete experimental data. The proposed method, called Swarm-based Chemical Reaction Optimization, integrates the evolutionary searching strategy employed by the Chemical Reaction Optimization, into the neighbouring searching strategy of the Firefly Algorithm method. The effectiveness of the method was evaluated using a simulated nonlinear model and two biological models: synthetic transcriptional oscillators, and extracellular protease production models. The results showed that the accuracy and computational speed of the proposed method were better than the existing Differential Evolution, Firefly Algorithm and Chemical Reaction Optimization methods. The reliability of the estimated parameters was statistically validated, which suggests that the model outputs produced by these parameters were valid even when noisy and incomplete experimental data were used. Additionally, Akaike Information Criterion was employed to evaluate the model selection, which highlighted the capability of the proposed method in choosing a plausible model based on the experimental data. In conclusion, this paper presents the effectiveness of the proposed method for parameter estimation and model selection problems using noisy and incomplete experimental data. This study is hoped to provide a new insight in developing more accurate and reliable biological models based on limited and low quality experimental data.

Thermal decomposition of sewage sludge under N2, CO2 and air: Gas characterization and kinetic analysis.

PubMed

Hernández, Ana Belén; Okonta, Felix; Freeman, Ntuli

2017-07-01

Thermochemical valorisation processes that allow energy to be recovered from sewage sludge, such as pyrolysis and gasification, have demonstrated great potential as convenient alternatives to conventional sewage sludge disposal technologies. Moreover, these processes may benefit from CO 2 recycling. Today, the scaling up of these technologies requires an advanced knowledge of the reactivity of sewage sludge and the characteristics of the products, specific to the thermochemical process. In this study the behaviour of sewage sludge during thermochemical conversion, under different atmospheres (N 2 , CO 2 and air), was studied, using TGA-FTIR, in order to understand the effects of different atmospheric gases on the kinetics of degradation and on the gaseous products. The different steps observed during the solid degradation were related with the production of different gaseous compounds. A higher oxidative degree of the atmosphere surrounding the sample resulted in higher reaction rates and a shift of the degradation mechanisms to lower temperatures, especially for the mechanisms taking place at temperatures above 400 °C. Finally, a multiple first-order reaction model was proposed to compare the kinetic parameters obtained under different atmospheres. Overall, the highest activation energies were obtained for combustion. This work proves that CO 2 , an intermediate oxidative atmosphere between N 2 and air, results in an intermediate behaviour (intermediate peaks in the derivative thermogravimetric curves and intermediate activation energies) during the thermochemical decomposition of sewage sludge. Overall, it can be concluded that the kinetics of these different processes require a different approach for their scaling up and specific consideration of their characteristic reaction temperatures and rates should be evaluated. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Computational Tool to Detect and Avoid Redundancy in Selected Reaction Monitoring

PubMed Central

Röst, Hannes; Malmström, Lars; Aebersold, Ruedi

2012-01-01

Selected reaction monitoring (SRM), also called multiple reaction monitoring, has become an invaluable tool for targeted quantitative proteomic analyses, but its application can be compromised by nonoptimal selection of transitions. In particular, complex backgrounds may cause ambiguities in SRM measurement results because peptides with interfering transitions similar to those of the target peptide may be present in the sample. Here, we developed a computer program, the SRMCollider, that calculates nonredundant theoretical SRM assays, also known as unique ion signatures (UIS), for a given proteomic background. We show theoretically that UIS of three transitions suffice to conclusively identify 90% of all yeast peptides and 85% of all human peptides. Using predicted retention times, the SRMCollider also simulates time-scheduled SRM acquisition, which reduces the number of interferences to consider and leads to fewer transitions necessary to construct an assay. By integrating experimental fragment ion intensities from large scale proteome synthesis efforts (SRMAtlas) with the information content-based UIS, we combine two orthogonal approaches to create high quality SRM assays ready to be deployed. We provide a user friendly, open source implementation of an algorithm to calculate UIS of any order that can be accessed online at http://www.srmcollider.org to find interfering transitions. Finally, our tool can also simulate the specificity of novel data-independent MS acquisition methods in Q1–Q3 space. This allows us to predict parameters for these methods that deliver a specificity comparable with that of SRM. Using SRM interference information in addition to other sources of information can increase the confidence in an SRM measurement. We expect that the consideration of information content will become a standard step in SRM assay design and analysis, facilitated by the SRMCollider. PMID:22535207

Development of polymerase chain reaction-based diagnostic tests for detection of Malsoor virus & adenovirus isolated from Rousettus species of bats in Maharashtra, India.

PubMed

Shete, Anita M; Yadav, Pragya; Kumar, Vimal; Nikam, Tushar; Mehershahi, Kurosh; Kokate, Prasad; Patil, Deepak; Mourya, Devendra T

2017-01-01

Bats are recognized as important reservoirs for emerging infectious disease and some unknown viral diseases. Two novel viruses, Malsoor virus (family Bunyaviridae, genus, Phlebovirus) and a novel adenovirus (AdV) (family, Adenoviridae genus, Mastadenovirus), were identified from Rousettus bats in the Maharashtra State of India. This study was done to develop and optimize real time reverse transcription - polymerase chain reaction (RT-PCR) assays for Malsoor virus and real time and nested PCR for adenovirus from Rousettus bats. For rapid and accurate screening of Malsoor virus and adenovirus a nested polymerase chain reaction and TaqMan-based real-time PCR were developed. Highly conserved region of nucleoprotein gene of phleboviruses and polymerase gene sequence from the Indian bat AdV isolate polyprotein gene were selected respectively for diagnostic assay development of Malsoor virus and AdV. Sensitivity and specificity of assays were calculated and optimized assays were used to screen bat samples. Molecular diagnostic assays were developed for screening of Malsoor virus and AdV and those were found to be specific. Based on the experiments performed with different parameters, nested PCR was found to be more sensitive than real-time PCR; however, for rapid screening, real-time PCR can be used and further nested PCR can be used for final confirmation or in those laboratories where real-time facility/expertise is not existing. This study reports the development and optimization of nested RT-PCR and a TaqMan-based real-time PCR for Malsoor virus and AdV. The diagnostic assays can be used for rapid detection of these novel viruses to understand their prevalence among bat population.

Semi-Supervised Recurrent Neural Network for Adverse Drug Reaction mention extraction.

PubMed

Gupta, Shashank; Pawar, Sachin; Ramrakhiyani, Nitin; Palshikar, Girish Keshav; Varma, Vasudeva

2018-06-13

Social media is a useful platform to share health-related information due to its vast reach. This makes it a good candidate for public-health monitoring tasks, specifically for pharmacovigilance. We study the problem of extraction of Adverse-Drug-Reaction (ADR) mentions from social media, particularly from Twitter. Medical information extraction from social media is challenging, mainly due to short and highly informal nature of text, as compared to more technical and formal medical reports. Current methods in ADR mention extraction rely on supervised learning methods, which suffer from labeled data scarcity problem. The state-of-the-art method uses deep neural networks, specifically a class of Recurrent Neural Network (RNN) which is Long-Short-Term-Memory network (LSTM). Deep neural networks, due to their large number of free parameters rely heavily on large annotated corpora for learning the end task. But in the real-world, it is hard to get large labeled data, mainly due to the heavy cost associated with the manual annotation. To this end, we propose a novel semi-supervised learning based RNN model, which can leverage unlabeled data also present in abundance on social media. Through experiments we demonstrate the effectiveness of our method, achieving state-of-the-art performance in ADR mention extraction. In this study, we tackle the problem of labeled data scarcity for Adverse Drug Reaction mention extraction from social media and propose a novel semi-supervised learning based method which can leverage large unlabeled corpus available in abundance on the web. Through empirical study, we demonstrate that our proposed method outperforms fully supervised learning based baseline which relies on large manually annotated corpus for a good performance.

Spectral Induced Polarization approaches to characterize reactive transport parameters and processes

NASA Astrophysics Data System (ADS)

Schmutz, M.; Franceschi, M.; Revil, A.; Peruzzo, L.; Maury, T.; Vaudelet, P.; Ghorbani, A.; Hubbard, S. S.

2017-12-01

For almost a decade, geophysical methods have explored the potential for characterization of reactive transport parameters and processes relevant to hydrogeology, contaminant remediation, and oil and gas applications. Spectral Induced Polarization (SIP) methods show particular promise in this endeavour, given the sensitivity of the SIP signature to geological material electrical double layer properties and the critical role of the electrical double layer on reactive transport processes, such as adsorption. In this presentation, we discuss results from several recent studies that have been performed to quantify the value of SIP parameters for characterizing reactive transport parameters. The advances have been realized through performing experimental studies and interpreting their responses using theoretical and numerical approaches. We describe a series of controlled experimental studies that have been performed to quantify the SIP responses to variations in grain size and specific surface area, pore fluid geochemistry, and other factors. We also model chemical reactions at the interface fluid/matrix linked to part of our experimental data set. For some examples, both geochemical modelling and measurements are integrated into a SIP physico-chemical based model. Our studies indicate both the potential of and the opportunity for using SIP to estimate reactive transport parameters. In case of well sorted granulometry of the samples, we find that the grain size characterization (as well as the permeabililty for some specific examples) value can be estimated using SIP. We show that SIP is sensitive to physico-chemical conditions at the fluid/mineral interface, including the different pore fluid dissolved ions (Na+, Cu2+, Zn2+, Pb2+) due to their different adsorption behavior. We also showed the relevance of our approach to characterize the fluid/matrix interaction for various organic contents (wetting and non-wetting oils). We also discuss early efforts to jointly interpret SIP and other information for improved estimation, approaches to use SIP information to constrain mechanistic flow and transport models, and the potential to apply some of the approaches to field scale applications.

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

PubMed

Du, Bin; Zielinski, Daniel C; Kavvas, Erol S; Dräger, Andreas; Tan, Justin; Zhang, Zhen; Ruggiero, Kayla E; Arzumanyan, Garri A; Palsson, Bernhard O

2016-06-06

The mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question. In this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations. Overall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches.

Cometary Evolution: Clues on Physical Properties from Chondritic Interplanetary Dust Particles

NASA Technical Reports Server (NTRS)

Rietmeijer, Frans J. M.; Mackinnon, Ian D. R.

1989-01-01

The degree of diversity or similarity detected in comets depends primarily on the lifetimes of the individual cometary nuclei at the time of analysis. It is inherent in our understanding of cometary orbital dynamics and the seminal model of comet origins by Oort that cometary evolution is the natural order of events in our Solar System. Thus, predictions of cometary behaviour in terms of bulk physical, mineralogical or chemical parameters should contain an appreciation of temporal variation(s). Previously, Rietmeijer and Mackinnon developed mineralogical bases for the chemical evolution of cometary nuclei primarily with regard to the predominantly silicate fraction of comet nuclei. We suggested that alteration of solids in cometary nuclei should be expected and that indications of likely reactants and products can be derived from judicious comparison with terrestrial diagenetic environments which include hydrocryogenic and low-temperature aqueous alterations. In a further development of this concept, Rietmeijer provides indirect evidence for the formation of sulfides and oxides in comet nuclei. Furthermore, Rietmeijer noted that timescales for hydrocryogenic and low-temperature reactions involving liquid water are probably adequate for relatively mature comets, e.g. P/comet Halley. In this paper, we will address the evolution of comet nuclei physical parameters such as solid particle grain size, porosity and density. In natural environments, chemical evolution (e.g. mineral reactions) is often accompanied by changes in physical properties. These concurrent changes are well-documented in the terrestrial geological literature, especially in studies of sediment diagenesis and we suggest that similar basic principles apply within the upper few meters of active comet nuclei. The database for prediction of comet nuclei physical parameters is, in principle, the same as used for the proposition of chemical evolution. We use detailed mineralogical studies of chondritic interplanetary dust particles (IDPS) as a guide to the likely constitution of mature comets traversing the inner Solar System. While there is, as yet, no direct proof that a specific sub-group or type of chondritic IDP is derived from a specific comet, it is clear that these particles are extraterrestrial in origin and that a certain portion of the interplanetary flux received by the Earth is cometary in origin. Two chondritic porous (CP) MPs, sample numbers W7010A2 and W7029Cl, from the Johnson Space Center Cosmic Dust Collection have been selected for this study of putative cometary physical parameters. This particular type of particle is considered a likely candidate for a cometary origin on the basis of mineralogy, bulk composition and morphology. While many IDPs have been subjected to intensive study over the past decade, we can develop a physical parameter model on only these two CP IDPs because few others have been studied in sufficient detail.

Cometary Evolution: Clues on Physical Properties from Chondritic Interplanetary Dust Particles

NASA Technical Reports Server (NTRS)

Reitmeijer, Frans J. M.; Mackinnon, Ian D. R.

1997-01-01

The degree of diversity or similarity detected in comets depends primarily on the lifetimes of the individual cometary nuclei at the time of analysis. It is inherent in our understanding of cometary orbital dynamics and the seminal model of comet origins that cometary evolution is the natural order of events in our Solar System. Thus, predictions of cometary behaviour in terms of bulk physical, mineralogical or chemical parameters should contain an appreciation of temporal variation(s). Previously, Rietmeijer and Mackinnon [1987] developed mineralogical bases for the chemical evolution of cometary nuclei primarily with regard to the predominantly silicate fraction of comet nuclei. We suggested that alteration of solids in cometary nuclei should be expected and that indications of likely reactants and products can be derived from judicious comparison with terrestrial diagenetic environments which include hydrocryogenic and low-temperature aqueous alterations. In a further development of this concept, Rietmeijer [1988] provides indirect evidence for the formation of sulfides and oxides in comet nuclei. Furthermore, Rietmeijer [1988] noted that timescales for hydrocryogenic and low-temperature reactions involving liquid water are probably adequate for relatively mature comets, e.g. P/comet Halley. In this paper, we will address the evolution of comet nuclei physical parameters such as solid particle grain size, porosity and density. In natural environments, chemical evolution (e.g. mineral reactions) is often accompanied by changes in physical properties. These concurrent changes are well-documented in the terrestrial geological literature, especially in studies of sediment diagenesis and we suggest that similar basic principles apply within the upper few meters of active comet nuclei. The database for prediction of comet nuclei physical parameters is, in principle, the same as used for the proposition of chemical evolution. We use detailed mineralogical studies of chondritic interplanetary dust particles (IDPS) as a guide to the likely constitution of mature comets traversing the inner Solar System. While there is, as yet, no direct proof that a specific sub-group or type of chondritic IDP is derived from a specific comet, it is clear that these particles are extraterrestrial in origin and that a certain portion of the interplanetary flux received by the Earth is cometary in origin. Two chondritic porous (CP) IDPS, sample numbers W701OA2 and W7029CI, from the Johnson Space Center Cosmic Dust Collection have been selected for this study of putative cometary physical parameters. This particular type of particle is considered a likely candidate for a cometary origin on the basis of mineralogy, bulk composition and morphology. While many IDPs have been subjected to intensive study over the past decade, we can develop a physical parameter model on only these two CP IDPs because few others have been studied in sufficient detail.

40 CFR 258.54 - Detection monitoring program.

Code of Federal Regulations, 2010 CFR

2010-07-01

... FOR MUNICIPAL SOLID WASTE LANDFILLS Ground-Water Monitoring and Corrective Action § 258.54 Detection... reaction products in the unsaturated zone beneath the MSWLF unit; (iii) The detectability of indicator parameters, waste constituents, and reaction products in the ground water; and (iv) The concentration or...

Study of dynamics of glucose-glucose oxidase-ferricyanide reaction

NASA Astrophysics Data System (ADS)

Nováková, A.; Schreiberová, L.; Schreiber, I.

2011-12-01

This work is focused on dynamics of the glucose-glucose oxidase-ferricyanide enzymatic reaction with or without sodium hydroxide in a continuous-flow stirred tank reactor (CSTR) and in a batch reactor. This reaction exhibits pH-variations having autocatalytic character and is reported to provide nonlinear dynamic behavior (bistability, excitability). The dynamical behavior of the reaction was examined within a wide range of inlet parameters. The main inlet parameters were the ratio of concentrations of sodium hydroxide and ferricyanide and the flow rate. In a batch reactor we observed an autocatalytic drop of pH from slightly basic to medium acidic values. In a CSTR our aim was to find bistability in the presence of sodium hydroxide. However, only a basic steady state was found. In order to reach an acidic steady state, we investigated the system in the absence of sodium hydroxide. Under these conditions the transition from the basic to the acidic steady state was observed when inlet glucose concentration was increased.

Influence of the reaction conditions on the enzyme catalyzed transesterification of castor oil: A possible step in biodiesel production.

PubMed

Andrade, Thalles A; Errico, Massimiliano; Christensen, Knud V

2017-11-01

The identification of the influence of the reaction parameters is of paramount importance when defining a process design. In this work, non-edible castor oil was reacted with methanol to produce a possible component for biodiesel blends, using liquid enzymes as the catalyst. Temperature, alcohol-to-oil molar ratio, enzyme and added water contents were the reaction parameters evaluated in the transesterification reactions. The optimal conditions, giving the optimal final FAME yield and FFA content in the methyl ester-phase was identified. At 35°C, 6.0 methanol-to-oil molar ratio, 5wt% of enzyme and 5wt% of water contents, 94% of FAME yield and 6.1% of FFA in the final composition were obtained. The investigation was completed with the analysis of the component profiles, showing that at least 8h are necessary to reach a satisfactory FAME yield together with a minor FFA content. Copyright © 2017 Elsevier Ltd. All rights reserved.

Reactive flow model development for PBXW-126 using modern nonlinear optimization methods

NASA Astrophysics Data System (ADS)

Murphy, M. J.; Simpson, R. L.; Urtiew, P. A.; Souers, P. C.; Garcia, F.; Garza, R. G.

1996-05-01

The initiation and detonation behavior of PBXW-126 has been characterized and is described. PBXW-126 is a composite explosive consisting of approximately equal amounts of RDX, AP, AL, and NTO with a polyurethane binder. The three term ignition and growth of reaction model parameters (ignition+two growth terms) have been found using nonlinear optimization methods to determine the "best" set of model parameters. The ignition term treats the initiation of up to 0.5% of the RDX. The first growth term in the model treats the RDX growth of reaction up to 20% reacted. The second growth term treats the subsequent growth of reaction of the remaining AP/AL/NTO. The unreacted equation of state (EOS) was determined from the wave profiles of embedded gauge tests while the JWL product EOS was determined from cylinder expansion test results. The nonlinear optimization code, NLQPEB/GLO, was used to determine the "best" set of coefficients for the three term Lee-Tarver ignition and growth of reaction model.

Monitoring mass transport in heterogeneously catalyzed reactions by field-gradient NMR for assessing reaction efficiency in a single pellet.

PubMed

Buljubasich, L; Blümich, B; Stapf, S

2011-09-01

An important aspect in assessing the performance of a catalytically active reactor is the accessibility of the reactive sites inside the individual pellets, and the mass transfer of reactants and products to and from these sites. Optimal design often requires a suitable combination of micro- and macropores in order to facilitate mass transport inside the pellet. In an exothermic reaction, fluid exchange between the pellet and the surrounding medium is enhanced by convection, and often by the occurrence of gas bubbles. Determining mass flow in the vicinity of a pellet thus represents a parameter for quantifying the reaction efficiency and its dependence on time or external reaction conditions. Field gradient Nuclear Magnetic Resonance (NMR) methods are suggested as a tool for providing parameters sensitive to this mass flow in a contact-free and non-invasive way. For the example of bubble-forming hydrogen peroxide decomposition in an alumina pellet, the dependence of the mean-squared displacement of fluid molecules on spatial direction, observation time and reaction time is presented, and multi-pulse techniques are employed in order to separate molecular displacements from coherent and incoherent motion on the timescale of the experiment. The reaction progress is followed until the complete decomposition of H2O2. Copyright © 2011 Elsevier Inc. All rights reserved.

A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems

PubMed Central

Lo, Wing-Cheong; Chen, Long; Wang, Ming; Nie, Qing

2012-01-01

An inhomogeneous steady state pattern of nonlinear reaction-diffusion equations with no-flux boundary conditions is usually computed by solving the corresponding time-dependent reaction-diffusion equations using temporal schemes. Nonlinear solvers (e.g., Newton’s method) take less CPU time in direct computation for the steady state; however, their convergence is sensitive to the initial guess, often leading to divergence or convergence to spatially homogeneous solution. Systematically numerical exploration of spatial patterns of reaction-diffusion equations under different parameter regimes requires that the numerical method be efficient and robust to initial condition or initial guess, with better likelihood of convergence to an inhomogeneous pattern. Here, a new approach that combines the advantages of temporal schemes in robustness and Newton’s method in fast convergence in solving steady states of reaction-diffusion equations is proposed. In particular, an adaptive implicit Euler with inexact solver (AIIE) method is found to be much more efficient than temporal schemes and more robust in convergence than typical nonlinear solvers (e.g., Newton’s method) in finding the inhomogeneous pattern. Application of this new approach to two reaction-diffusion equations in one, two, and three spatial dimensions, along with direct comparisons to several other existing methods, demonstrates that AIIE is a more desirable method for searching inhomogeneous spatial patterns of reaction-diffusion equations in a large parameter space. PMID:22773849