Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation.

Directory of Open Access Journals (Sweden)

Andrea Ciliberto

2007-03-01

Full Text Available In metabolic networks, metabolites are usually present in great excess over the enzymes that catalyze their interconversion, and describing the rates of these reactions by using the Michaelis-Menten rate law is perfectly valid. This rate law assumes that the concentration of enzyme-substrate complex (C is much less than the free substrate concentration (S0. However, in protein interaction networks, the enzymes and substrates are all proteins in comparable concentrations, and neglecting C with respect to S0 is not valid. Borghans, DeBoer, and Segel developed an alternative description of enzyme kinetics that is valid when C is comparable to S0. We extend this description, which Borghans et al. call the total quasi-steady state approximation, to networks of coupled enzymatic reactions. First, we analyze an isolated Goldbeter-Koshland switch when enzymes and substrates are present in comparable concentrations. Then, on the basis of a real example of the molecular network governing cell cycle progression, we couple two and three Goldbeter-Koshland switches together to study the effects of feedback in networks of protein kinases and phosphatases. Our analysis shows that the total quasi-steady state approximation provides an excellent kinetic formalism for protein interaction networks, because (1 it unveils the modular structure of the enzymatic reactions, (2 it suggests a simple algorithm to formulate correct kinetic equations, and (3 contrary to classical Michaelis-Menten kinetics, it succeeds in faithfully reproducing the dynamics of the network both qualitatively and quantitatively.

Steady state kinetic model for the binding of substrates and allosteric effectors to Escherichia coli phosphoribosyl-diphosphate synthase

DEFF Research Database (Denmark)

Willemoës, Martin; Hove-Jensen, Bjarne; Larsen, Sine

2000-01-01

A steady state kinetic investigation of the Pi activation of 5-phospho-D-ribosyl α-1-diphosphate synthase from Escherichia coli suggests that Pi can bind randomly to the enzyme either before or after an ordered addition of free Mg2+ and substrates. Unsaturation with ribose 5-phosphate increased...... the apparent cooperativity of Pi activation. At unsaturating Pi concentrations partial substrate inhibition by ribose 5-phosphate was observed. Together these results suggest that saturation of the enzyme with Pi directs the subsequent ordered binding of Mg2+ and substrates via a fast pathway, whereas...... saturation with ribose 5-phosphate leads to the binding of Mg2+ and substrates via a slow pathway where Pi binds to the enzyme last. The random mechanism for Pi binding was further supported by studies with competitive inhibitors of Mg2+, MgATP, and ribose 5-phosphate that all appeared noncompetitive when...

Pre-steady state transients in the Drosophila alcohol dehydrogenase catalyzed reaction: isotope effects and stereospecificity

International Nuclear Information System (INIS)

Place, A.R.; Eccleston, J.F.

1987-01-01

The alcohol dehydrogenase (ADH) isolated from Drosophila is unique among alcohol metabolizing enzymes by not requiring metals for catalysis, by showing 4-pro-S (B-sided) hydride transfer stereospecificity, and by possessing a greater catalytic turnover rate for secondary alcohols than for primary alcohols. They have extended their studies on the kinetic mechanism for this enzyme by examining the pre-steady state transients of ternary complex interconversion using stopped-flow fluorescence methods. When enzyme and a 30-fold molar excess of NADH is mixed with excess acetadehyde, methyl ethyl ketone (MEK), or cyclohexanone a rapid (> 100 s -1 ) transient is observe before the steady-state. The rates are insensitive to isotope substitution. With the substrate MEK, the rate and amplitude suggests a single turnover of the enzyme. Similar pre-steady state transients are observed when enzyme and a 50-fold molar excess of NAD + is mixed with ethanol, 2-propanol, and cyclohexanol. The rates show a hyperbolic concentration dependence and a deuterium isotope effect. With d 6 -deuteroethanol the transient no longer occurs in the pre-steady state. When the optical isomers of secondary alcohols are used as substrates, transients are observed only in the R-(-) isomers for all chain lengths. With 2-S(+)-heptanol and 2-S(+)-octanol no transients occur

Some Considerations on the Fundamentals of Chemical Kinetics: Steady State, Quasi-Equilibrium, and Transition State Theory

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Perez-Benito, Joaquin F.

2017-01-01

The elementary reaction sequence A ? I ? Products is the simplest mechanism for which the steady-state and quasi-equilibrium kinetic approximations can be applied. The exact integrated solutions for this chemical system allow inferring the conditions that must fulfill the rate constants for the different approximations to hold. A graphical…

Nonequilibrium steady state of biochemical cycle kinetics under non-isothermal conditions

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Jin, Xiao; Ge, Hao

2018-04-01

The nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but that under non-isothermal conditions has been much less extensively investigated. When the heat exchange between subsystems is slow, the isothermal assumption of the whole system breaks down, as is true for many types of living organisms. Here, starting with a four-state model of molecular transporter across the cell membrane, we generalize the nonequilibrium steady-state theory of isothermal biochemical cycle kinetics to the circumstances with non-uniform temperatures of subsystems in terms of general master equation models. We obtain a new thermodynamic relationship between the chemical reaction rates and thermodynamic potentials in non-isothermal circumstances, based on the overdamped dynamics along the continuous reaction coordinate. We show that the entropy production can vary up to 3% in real cells, even when the temperature difference across the cell membrane is only approximately 1 K. We then decompose the total thermodynamic driving force into its thermal and chemical components and predict that the net flux of molecules transported by the molecular transporter can potentially go against the temperature gradient in the absence of a chemical driving force. Furthermore, we demonstrate that the simple application of the isothermal transition-state rate formula for each chemical reaction in terms of only the reactant’ temperature is not thermodynamically consistent. Therefore, we mathematically derive several revised reaction rate formulas that are not only consistent with the new thermodynamic relationship but also approximate the exact reaction rate better than Kramers’ rate formula under isothermal conditions.

A Poisson-like closed-form expression for the steady-state wealth distribution in a kinetic model of gambling

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Garcia, Jane Bernadette Denise M.; Esguerra, Jose Perico H.

2017-08-01

An approximate but closed-form expression for a Poisson-like steady state wealth distribution in a kinetic model of gambling was formulated from a finite number of its moments, which were generated from a βa,b(x) exchange distribution. The obtained steady-state wealth distributions have tails which are qualitatively similar to those observed in actual wealth distributions.

Fabrication and Characterization of Ultrathin-ring Electrodes for Pseudo-steady-state Amperometric Detection.

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Kitazumi, Yuki; Hamamoto, Katsumi; Noda, Tatsuo; Shirai, Osamu; Kano, Kenji

2015-01-01

The fabrication of ultrathin-ring electrodes with a diameter of 2 mm and a thickness of 100 nm is established. The ultrathin-ring electrodes provide a large density of pseudo-steady-state currents, and realize pseudo-steady-state amperometry under quiescent conditions without a Faraday cage. Under the limiting current conditions, the current response at the ultrathin-ring electrode can be well explained by the theory of the microband electrode response. Cyclic voltammograms at the ultrathin-ring electrode show sigmoidal characteristics with some hysteresis. Numerical simulation reveals that the hysteresis can be ascribed to the time-dependence of pseudo-steady-state current. The performance of amperometry with the ultrathin-ring electrode has been verified in its application to redox enzyme kinetic measurements.

Solution of non-steady-state substrate concentration in the action of biosensor response at mixed enzyme kinetics

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Senthamarai, R.; Jana Ranjani, R.

2018-04-01

In this paper, a mathematical model of an amperometric biosensor at mixed enzyme kinetics and diffusion limitation in the case of substrate inhibition has been developed. The model is based on time dependent reaction diffusion equation containing a non -linear term related to non -Michaelis - Menten kinetics of the enzymatic reaction. Solution for the concentration of the substrate has been derived for all values of parameters using the homotopy perturbation method. All the approximate analytic expressions of substrate concentration are compared with simulation results using Scilab/Matlab program. Finally, we have given a satisfactory agreement between them.

A Kinetic Modelling of Enzyme Inhibitions in the Central Metabolism of Yeast Cells

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Kasbawati; Kalondeng, A.; Aris, N.; Erawaty, N.; Azis, M. I.

2018-03-01

Metabolic regulation plays an important role in the metabolic engineering of a cellular process. It is conducted to improve the productivity of a microbial process by identifying the important regulatory nodes of a metabolic pathway such as fermentation pathway. Regulation of enzymes involved in a particular pathway can be held to improve the productivity of the system. In the central metabolism of yeast cell, some enzymes are known as regulating enzymes that can be inhibited to increase the production of ethanol. In this research we study the kinetic modelling of the enzymes in the central pathway of yeast metabolism by taking into consideration the enzyme inhibition effects to the ethanol production. The existence of positive steady state solution and the stability of the system are also analysed to study the property and dynamical behaviour of the system. One stable steady state of the system is produced if some conditions are fulfilled. The conditions concern to the restriction of the maximum reactions of the enzymes in the pyruvate and acetaldehyde branch points. There exists a certain time of fermentation reaction at which a maximum and a minimum ethanol productions are attained after regulating the system. Optimal ethanol concentration is also produced for a certain initial concentration of inhibitor.

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

International Nuclear Information System (INIS)

Das, Biswajit; Gangopadhyay, Gautam

2012-01-01

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

IBIS, FBR 3-D Steady-State and Kinetics with Thermohydraulic Feedback

International Nuclear Information System (INIS)

Konomura, Mamoru; Tada, Nobuo; Oka, Yoshiaki; An, Shigehiro

1987-01-01

1 - Description of program or function: The IBIS code performs steady state and kinetics calculations based on a three-dimensional nuclear diffusion kinetics with thermal hydraulic feedback. It can calculate the following values in hexagonal-Z geometry of a fast breeder reactor core through the progress of transient: (1) Net reactivity; (2) Total and group-wise delayed neutron fraction; (3) Group-wise delayed neutron precursor concentration; (4) Total power and energy; (5) Space dependent neutron flux in each energy group; (6) Space dependent temperature of each material; (7) Maximum temperature of each material and its location. 2 - Method of solution: The quasi-static method is adopted to solve the three-dimensional nuclear diffusion kinetics problem. The method is the same as employed in the code QX1. The shape function equation is solved with the finite difference treatment as used in the codes CITATION and HONEYCOMB. One-dimensional thermo-hydraulics is solved with a model similar to that given in the code SASLA. Sodium boiling can be taken into account. 3 - Restrictions on the complexity of the problem: The number of neutron energy groups is fixed to 3 groups in the present version of the code

The maximum entropy production and maximum Shannon information entropy in enzyme kinetics

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Dobovišek, Andrej; Markovič, Rene; Brumen, Milan; Fajmut, Aleš

2018-04-01

We demonstrate that the maximum entropy production principle (MEPP) serves as a physical selection principle for the description of the most probable non-equilibrium steady states in simple enzymatic reactions. A theoretical approach is developed, which enables maximization of the density of entropy production with respect to the enzyme rate constants for the enzyme reaction in a steady state. Mass and Gibbs free energy conservations are considered as optimization constraints. In such a way computed optimal enzyme rate constants in a steady state yield also the most uniform probability distribution of the enzyme states. This accounts for the maximal Shannon information entropy. By means of the stability analysis it is also demonstrated that maximal density of entropy production in that enzyme reaction requires flexible enzyme structure, which enables rapid transitions between different enzyme states. These results are supported by an example, in which density of entropy production and Shannon information entropy are numerically maximized for the enzyme Glucose Isomerase.

Concentration profiles near an activated enzyme.

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Park, Soohyung; Agmon, Noam

2008-09-25

When a resting enzyme is activated, substrate concentration profile evolves in its vicinity, ultimately tending to steady state. We use modern theories for many-body effects on diffusion-influenced reactions to derive approximate analytical expressions for the steady-state profile and the Laplace transform of the transient concentration profiles. These show excellent agreement with accurate many-particle Brownian-dynamics simulations for the Michaelis-Menten kinetics. The steady-state profile has a hyperbolic dependence on the distance of the substrate from the enzyme, albeit with a prefactor containing the complexity of the many-body effects. These are most conspicuous for the substrate concentration at the surface of the enzyme. It shows an interesting transition as a function of the enzyme turnover rate. When it is high, the contact concentration decays monotonically to steady state. However, for slow turnover it is nonmonotonic, showing a minimum due to reversible substrate binding, then a maximum due to diffusion of new substrate toward the enzyme, and finally decay to steady state. Under certain conditions one can obtain a good estimate for the critical value of the turnover rate constant at the transition.

DNA Polymerase Fidelity: Comparing Direct Competition of Right and Wrong dNTP Substrates with Steady State and Presteady State Kinetics†

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Bertram, Jeffrey G.; Oertell, Keriann; Petruska, John; Goodman, Myron F.

2009-01-01

DNA polymerase fidelity is defined as the ratio of right (R) to wrong (W) nucleotide incorporations when dRTP and dWTP substrates compete at equal concentrations for primer extension at the same site in the polymerase-primer-template DNA complex. Typically, R incorporation is favored over W by 103 – 105, even in the absence of 3′-exonuclease proofreading. Straightforward in principal, a direct competition fidelity measurement is difficult to perform in practice because detection of a small amount of W is masked by a large amount of R. As an alternative, enzyme kinetics measurements to evaluate kcat/Km for R and W in separate reactions are widely used to measure polymerase fidelity indirectly, based on a steady-state derivation by Fersht. A systematic comparison between direct competition and kinetics has not been made until now. By separating R and W products using electrophoresis, we have successfully made accurate fidelity measurements for directly competing R and W dNTP substrates for 9 of the 12 natural base mispairs. We compare our direct competition results with steady state and presteady state kinetic measurements of fidelity at the same template site, using the proofreading-deficient mutant of Klenow Fragment (KF−) DNA polymerase. All the data are in quantitative agreement. PMID:20000359

Noise-Induced Modulation of the Relaxation Kinetics around a Non-Equilibrium Steady State of Non-Linear Chemical Reaction Networks

OpenAIRE

Ramaswamy, Rajesh; Sbalzarini, Ivo F; González-Segredo, Nélido

2011-01-01

Stochastic effects from correlated noise non-trivially modulate the kinetics of non-linear chemical reaction networks. This is especially important in systems where reactions are confined to small volumes and reactants are delivered in bursts. We characterise how the two noise sources confinement and burst modulate the relaxation kinetics of a non-linear reaction network around a non-equilibrium steady state. We find that the lifetimes of species change with burst input and confinement. Confi...

Extracellular enzyme kinetics scale with resource availability

Science.gov (United States)

Sinsabaugh, Robert L.; Belnap, Jayne; Findlay, Stuart G.; Follstad Shah, Jennifer J.; Hill, Brian H.; Kuehn, Kevin A.; Kuske, Cheryl; Litvak, Marcy E.; Martinez, Noelle G.; Moorhead, Daryl L.; Warnock, Daniel D.

2014-01-01

Microbial community metabolism relies on external digestion, mediated by extracellular enzymes that break down complex organic matter into molecules small enough for cells to assimilate. We analyzed the kinetics of 40 extracellular enzymes that mediate the degradation and assimilation of carbon, nitrogen and phosphorus by diverse aquatic and terrestrial microbial communities (1160 cases). Regression analyses were conducted by habitat (aquatic and terrestrial), enzyme class (hydrolases and oxidoreductases) and assay methodology (low affinity and high affinity substrates) to relate potential reaction rates to substrate availability. Across enzyme classes and habitats, the scaling relationships between apparent Vmax and apparent Km followed similar power laws with exponents of 0.44 to 0.67. These exponents, called elasticities, were not statistically distinct from a central value of 0.50, which occurs when the Km of an enzyme equals substrate concentration, a condition optimal for maintenance of steady state. We also conducted an ecosystem scale analysis of ten extracellular hydrolase activities in relation to soil and sediment organic carbon (2,000–5,000 cases/enzyme) that yielded elasticities near 1.0 (0.9 ± 0.2, n = 36). At the metabolomic scale, the elasticity of extracellular enzymatic reactions is the proportionality constant that connects the C:N:P stoichiometries of organic matter and ecoenzymatic activities. At the ecosystem scale, the elasticity of extracellular enzymatic reactions shows that organic matter ultimately limits effective enzyme binding sites. Our findings suggest that one mechanism by which microbial communities maintain homeostasis is regulating extracellular enzyme expression to optimize the short-term responsiveness of substrate acquisition. The analyses also show that, like elemental stoichiometry, the fundamental attributes of enzymatic reactions can be extrapolated from biochemical to community and ecosystem scales.

Transient competitive complexation in biological kinetic isotope fractionation explains non-steady isotopic effects: Theory and application to denitrification in soils

Energy Technology Data Exchange (ETDEWEB)

Maggi, F.M.; Riley, W.J.

2009-06-01

The theoretical formulation of biological kinetic reactions in isotopic applications often assume first-order or Michaelis-Menten-Monod kinetics under the quasi-steady-state assumption to simplify the system kinetics. However, isotopic e ects have the same order of magnitude as the potential error introduced by these simpli cations. Both formulations lead to a constant fractionation factor which may yield incorrect estimations of the isotopic effect and a misleading interpretation of the isotopic signature of a reaction. We have analyzed the isotopic signature of denitri cation in biogeochemical soil systems by Menyailo and Hungate [2006], where high {sup 15}N{sub 2}O enrichment during N{sub 2}O production and inverse isotope fractionation during N{sub 2}O consumption could not be explained with first-order kinetics and the Rayleigh equation, or with the quasi-steady-state Michaelis-Menten-Monod kinetics. When the quasi-steady-state assumption was relaxed, transient Michaelis-Menten-Monod kinetics accurately reproduced the observations and aided in interpretation of experimental isotopic signatures. These results may imply a substantial revision in using the Rayleigh equation for interpretation of isotopic signatures and in modeling biological kinetic isotope fractionation with first-order kinetics or quasi-steady-state Michaelis-Menten-Monod kinetics.

Determination of kinetic parameters of Fe sup 3+ reduction mediated by a polyaniline film using steady-state and impedance methods

Energy Technology Data Exchange (ETDEWEB)

Deslouis, C. (LP15 du CNRS, Physique des Liquides et Electrochimie, Lab. de l' Univ. Pierre et Marie Curie, 75252 Paris Cedex 05 (FR)); Musiani, M.M.; Pagura, C.; Tribollet, C. (Inst. di Polarografia de Elettrochimica Preparativa del CNR, Corso Stati Uniti, 4, 35020 Camin, Padova (IT))

1991-09-01

This paper discusses the Fe{sup 3+} reduction reaction studied at Pt and polyaniline rotating disk electrodes by steady-state and impedance methods with the aim of testing the possibility of achieving the charge transfer resistance (R{sub ts}) of a redox reaction mediated by a conducting polymer film by ac impedance R{sub ts} was obtained as a function of electrode potential and rotation rate by nonlinear least squares fitting of a previously developed kinetic equation to the experimental data. These R{sub ts} values were combined with steady-state ones to calculate b{sub c} and k{sup 0}.

Explaining the atypical reaction profiles of heme enzymes with a novel mechanistic hypothesis and kinetic treatment.

Directory of Open Access Journals (Sweden)

Kelath Murali Manoj

Full Text Available Many heme enzymes show remarkable versatility and atypical kinetics. The fungal extracellular enzyme chloroperoxidase (CPO characterizes a variety of one and two electron redox reactions in the presence of hydroperoxides. A structural counterpart, found in mammalian microsomal cytochrome P450 (CYP, uses molecular oxygen plus NADPH for the oxidative metabolism (predominantly hydroxylation of substrate in conjunction with a redox partner enzyme, cytochrome P450 reductase. In this study, we employ the two above-mentioned heme-thiolate proteins to probe the reaction kinetics and mechanism of heme enzymes. Hitherto, a substrate inhibition model based upon non-productive binding of substrate (two-site model was used to account for the inhibition of reaction at higher substrate concentrations for the CYP reaction systems. Herein, the observation of substrate inhibition is shown for both peroxide and final substrate in CPO catalyzed peroxidations. Further, analogy is drawn in the "steady state kinetics" of CPO and CYP reaction systems. New experimental observations and analyses indicate that a scheme of competing reactions (involving primary product with enzyme or other reaction components/intermediates is relevant in such complex reaction mixtures. The presence of non-selective reactive intermediate(s affords alternate reaction routes at various substrate/product concentrations, thereby leading to a lowered detectable concentration of "the product of interest" in the reaction milieu. Occam's razor favors the new hypothesis. With the new hypothesis as foundation, a new biphasic treatment to analyze the kinetics is put forth. We also introduce a key concept of "substrate concentration at maximum observed rate". The new treatment affords a more acceptable fit for observable experimental kinetic data of heme redox enzymes.

Stochastic pumping of non-equilibrium steady-states: how molecules adapt to a fluctuating environment.

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Astumian, R D

2018-01-11

In the absence of input energy, a chemical reaction in a closed system ineluctably relaxes toward an equilibrium state governed by a Boltzmann distribution. The addition of a catalyst to the system provides a way for more rapid equilibration toward this distribution, but the catalyst can never, in and of itself, drive the system away from equilibrium. In the presence of external fluctuations, however, a macromolecular catalyst (e.g., an enzyme) can absorb energy and drive the formation of a steady state between reactant and product that is not determined solely by their relative energies. Due to the ubiquity of non-equilibrium steady states in living systems, the development of a theory for the effects of external fluctuations on chemical systems has been a longstanding focus of non-equilibrium thermodynamics. The theory of stochastic pumping has provided insight into how a non-equilibrium steady-state can be formed and maintained in the presence of dissipation and kinetic asymmetry. This effort has been greatly enhanced by a confluence of experimental and theoretical work on synthetic molecular machines designed explicitly to harness external energy to drive non-equilibrium transport and self-assembly.

Stochastic theory of nonequilibrium steady states and its applications. Part I

International Nuclear Information System (INIS)

Zhang Xuejuan; Qian Hong; Qian Min

2012-01-01

The concepts of equilibrium and nonequilibrium steady states are introduced in the present review as mathematical concepts associated with stationary Markov processes. For both discrete stochastic systems with master equations and continuous diffusion processes with Fokker–Planck equations, the nonequilibrium steady state (NESS) is characterized in terms of several key notions which are originated from nonequilibrium physics: time irreversibility, breakdown of detailed balance, free energy dissipation, and positive entropy production rate. After presenting this NESS theory in pedagogically accessible mathematical terms that require only a minimal amount of prerequisites in nonlinear differential equations and the theory of probability, it is applied, in Part I, to two widely studied problems: the stochastic resonance (also known as coherent resonance) and molecular motors (also known as Brownian ratchet). Although both areas have advanced rapidly on their own with a vast amount of literature, the theory of NESS provides them with a unifying mathematical foundation. Part II of this review contains applications of the NESS theory to processes from cellular biochemistry, ranging from enzyme catalyzed reactions, kinetic proofreading, to zeroth-order ultrasensitivity.

Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite load.

Directory of Open Access Journals (Sweden)

Naama Tepper

Full Text Available Steady-state metabolite concentrations in a microorganism typically span several orders of magnitude. The underlying principles governing these concentrations remain poorly understood. Here, we hypothesize that observed variation can be explained in terms of a compromise between factors that favor minimizing metabolite pool sizes (e.g. limited solvent capacity and the need to effectively utilize existing enzymes. The latter requires adequate thermodynamic driving force in metabolic reactions so that forward flux substantially exceeds reverse flux. To test this hypothesis, we developed a method, metabolic tug-of-war (mTOW, which computes steady-state metabolite concentrations in microorganisms on a genome-scale. mTOW is shown to explain up to 55% of the observed variation in measured metabolite concentrations in E. coli and C. acetobutylicum across various growth media. Our approach, based strictly on first thermodynamic principles, is the first method that successfully predicts high-throughput metabolite concentration data in bacteria across conditions.

Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysics

International Nuclear Information System (INIS)

Ge Hao; Qian Min; Qian Hong

2012-01-01

The mathematical theory of nonequilibrium steady state (NESS) has a natural application in open biochemical systems which have sustained source(s) and sink(s) in terms of a difference in their chemical potentials. After a brief introduction in Section , in Part II of this review, we present the widely studied biochemical enzyme kinetics, the workhorse of biochemical dynamic modeling, in terms of the theory of NESS (Section ). We then show that several phenomena in enzyme kinetics, including a newly discovered activation–inhibition switching (Section ) and the well-known non-Michaelis–Menten-cooperativity (Section ) and kinetic proofreading (Section ), are all consequences of the NESS of driven biochemical systems with associated cycle fluxes. Section is focused on nonlinear and nonequilibrium systems of biochemical reactions. We use the phosphorylation–dephosphorylation cycle (PdPC), one of the most important biochemical signaling networks, as an example (Section ). It starts with a brief introduction of the Delbrück–Gillespie process approach to mesoscopic biochemical kinetics (Sections ). We shall discuss the zeroth-order ultrasensitivity of PdPC in terms of a new concept — the temporal cooperativity (Sections ), as well as PdPC with feedback which leads to biochemical nonlinear bistability (Section ). Also, both are nonequilibrium phenomena. PdPC with a nonlinear feedback is kinetically isomorphic to a self-regulating gene expression network, hence the theory of NESS discussed here could have wide applications to many other biochemical systems.

Rethinking fundamentals of enzyme action.

Science.gov (United States)

Northrop, D B

1999-01-01

Despite certain limitations, investigators continue to gainfully employ concepts rooted in steady-state kinetics in efforts to draw mechanistically relevant inferences about enzyme catalysis. By reconsidering steady-state enzyme kinetic behavior, this review develops ideas that allow one to arrive at the following new definitions: (a) V/K, the ratio of the maximal initial velocity divided by the Michaelis-Menten constant, is the apparent rate constant for the capture of substrate into enzyme complexes that are destined to yield product(s) at some later point in time; (b) the maximal velocity V is the apparent rate constant for the release of substrate from captured complexes in the form of free product(s); and (c) the Michaelis-Menten constant K is the ratio of the apparent rate constants for release and capture. The physiologic significance of V/K is also explored to illuminate aspects of antibiotic resistance, the concept of "perfection" in enzyme catalysis, and catalytic proficiency. The conceptual basis of congruent thermodynamic cycles is also considered in an attempt to achieve an unambiguous way for comparing an enzyme-catalyzed reaction with its uncatalyzed reference reaction. Such efforts promise a deeper understanding of the origins of catalytic power, as it relates to stabilization of the reactant ground state, stabilization of the transition state, and reciprocal stabilizations of ground and transition states.

Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models.

Science.gov (United States)

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.

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

Science.gov (United States)

Zhu, Yajun; Zhong, Chengwen; Xu, Kun

2016-06-01

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

Transient competitive complexation in biological kinetic isotope fractionation explains nonsteady isotopic effects: Theory and application to denitrification in soils

Science.gov (United States)

Maggi, Federico; Riley, William J.

2009-12-01

The theoretical formulation of biological kinetic isotope fractionation often assumes first-order or Michaelis-Menten kinetics, the latter solved under the quasi-steady state assumption. Both formulations lead to a constant isotope fractionation factor, therefore they may return incorrect estimations of isotopic effects and misleading interpretations of isotopic signatures when fractionation is not a steady process. We have analyzed the isotopic signature of denitrification in biogeochemical soil systems by Menyailo and Hungate (2006) in which high and variable 15N-N2O enrichment during N2O production and inverse isotope fractionation during N2O consumption could not be explained with first-order kinetics and the Rayleigh equation, or with Michaelis-Menten kinetics. When Michaelis-Menten kinetics were coupled to Monod kinetics to describe biomass and enzyme dynamics, and the quasi-steady state assumption was relaxed, transient Michaelis-Menten-Monod kinetics accurately reproduced the observed concentrations, and variable and inverse isotope fractionations. These results imply a substantial revision in modeling isotopic effects, suggesting that steady state kinetics such as first-order, Rayleigh, and classic Michaelis-Menten kinetics should be superseded by transient kinetics in conjunction with biomass and enzyme dynamics.

Steady-state isotopic transient kinetic analysis investigation of CO-O2 and CO-NO reactions over a commercial automotive catalyst

International Nuclear Information System (INIS)

Oukaci, R.; Blackmond, D.G.; Goodwin, J.G. Jr.; Gallaher, G.R.

1992-01-01

In this paper, steady-state isotopic transient kinetic analysis (SSITKA) is used to study two model reactions, CO oxidation and CO-NO reactions, on a typical formulation of a three-way auto-catalyst. Under steady-state conditions, abrupt switches in the isotopic composition of CO ( 12 C 16 O/ 13 C 18 O) were carried out to produce isotopic transients in both labeled reactants and products. Along with the determination of the average surface lifetimes and concentrations of reaction intermediates, an analysis of the transient responses along the carbon reaction pathway indicated that the distribution of active sites for the formation of CO 2 was bimodal for both reactions. Furthermore, relatively few surface sites contributed to the overall reaction rate

Pre-steady-state kinetic analysis of 1-deoxy-D-xylulose-5-phosphate reductoisomerase from Mycobacterium tuberculosis reveals partially rate-limiting product release by parallel pathways.

Science.gov (United States)

Liu, Juan; Murkin, Andrew S

2012-07-03

As part of the non-mevalonate pathway for the biosynthesis of the isoprenoid precursor isopentenyl pyrophosphate, 1-deoxy-D-xylulose-5-phosphate (DXP) reductoisomerase (DXR) catalyzes the conversion of DXP into 2-C-methyl-D-erythritol 4-phosphate (MEP) by consecutive isomerization and NADPH-dependent reduction reactions. Because this pathway is essential to many infectious organisms but is absent in humans, DXR is a target for drug discovery. In an attempt to characterize its kinetic mechanism and identify rate-limiting steps, we present the first complete transient kinetic investigation of DXR. Stopped-flow fluorescence measurements with Mycobacterium tuberculosis DXR (MtDXR) revealed that NADPH and MEP bind to the free enzyme and that the two bind together to generate a nonproductive ternary complex. Unlike the Escherichia coli orthologue, MtDXR exhibited a burst in the oxidation of NADPH during pre-steady-state reactions, indicating a partially rate-limiting step follows chemistry. By monitoring NADPH fluorescence during these experiments, the transient generation of MtDXR·NADPH·MEP was observed. Global kinetic analysis supports a model involving random substrate binding and ordered release of NADP(+) followed by MEP. The partially rate-limiting release of MEP occurs via two pathways--directly from the binary complex and indirectly via the MtDXR·NADPH·MEP complex--the partitioning being dependent on NADPH concentration. Previous mechanistic studies, including kinetic isotope effects and product inhibition, are discussed in light of this kinetic mechanism.

Co-immobilized Coupled Enzyme Systems in Biotechnology

Science.gov (United States)

2010-01-01

coimmobilized by ~n­ capsulation in silica spheres that were formed by a polymer -templated silicificatiOn reaction (Betancor et al., 2006). Nitrobenzene...F. , FERNANDEZ-LAFUENTE, R. , GUISAN J. M. (2005). Stabilization of enzymes by multipoint immobilization of thiolated proteins on new epoxy-thiol... polymer monoliths in microftuidic devices for steady- state kinetic analysis and spatially separated multi-enzyme reactions. Analytical Chemistry, 79

Cell kinetics of GM-CFC in the steady state

International Nuclear Information System (INIS)

Hagan, M.P.; MacVittie, T.J.; Dodgen, D.P.

1985-01-01

The kinetics of cell turnover for myeloid/monocyte cells that form colonies in agar (GM-CFC) were measured through the progressive increase in their sensitivity to 313-nm light during a period of cell labeling with BrdCyd. Two components of cell killing with distinctly separate labeling kinetics revealed both the presence of two generations within the GM-CFC compartment and the properties of the kinetics of the precursors of the GM-CFC. These precursors of the GM-CFC were not assayable in a routine GM-CFC assay when pregnant mouse uterus extract and mouse L-cell-conditioned medium were used to stimulate colony formation but were revealed by the labeling kinetics of the assayable GM-CFC. Further, these precursor cells appeared to enter the assayable GM-CFC population from a noncycling state. This was evidenced by the failure of the majority of these cells to incorporate BrdCyd during five days of infusion. The half-time for cell turnover within this precursor compartment was measured to be approximately 5.5 days. Further, these normally noncycling cells proliferated rapidly in response to endotoxin. High-proliferative-potential colony-forming cells (HPP-CFC) were tested as a candidate for this precursor population. The results of the determination of the kinetics for these cells showed that the HPP-CFC exist largely in a Go state, existing at an average rate of once every four days. The slow turnover time for these cells and their response to endotoxin challenge are consistent with a close relationship between the HPP-CFC and the Go pool of cells that is the direct precursor of the GM-CFC

Steady state likelihood ratio sensitivity analysis for stiff kinetic Monte Carlo simulations.

Science.gov (United States)

Núñez, M; Vlachos, D G

2015-01-28

Kinetic Monte Carlo simulation is an integral tool in the study of complex physical phenomena present in applications ranging from heterogeneous catalysis to biological systems to crystal growth and atmospheric sciences. Sensitivity analysis is useful for identifying important parameters and rate-determining steps, but the finite-difference application of sensitivity analysis is computationally demanding. Techniques based on the likelihood ratio method reduce the computational cost of sensitivity analysis by obtaining all gradient information in a single run. However, we show that disparity in time scales of microscopic events, which is ubiquitous in real systems, introduces drastic statistical noise into derivative estimates for parameters affecting the fast events. In this work, the steady-state likelihood ratio sensitivity analysis is extended to singularly perturbed systems by invoking partial equilibration for fast reactions, that is, by working on the fast and slow manifolds of the chemistry. Derivatives on each time scale are computed independently and combined to the desired sensitivity coefficients to considerably reduce the noise in derivative estimates for stiff systems. The approach is demonstrated in an analytically solvable linear system.

Noise-induced modulation of the relaxation kinetics around a non-equilibrium steady state of non-linear chemical reaction networks.

Science.gov (United States)

Ramaswamy, Rajesh; Sbalzarini, Ivo F; González-Segredo, Nélido

2011-01-28

Stochastic effects from correlated noise non-trivially modulate the kinetics of non-linear chemical reaction networks. This is especially important in systems where reactions are confined to small volumes and reactants are delivered in bursts. We characterise how the two noise sources confinement and burst modulate the relaxation kinetics of a non-linear reaction network around a non-equilibrium steady state. We find that the lifetimes of species change with burst input and confinement. Confinement increases the lifetimes of all species that are involved in any non-linear reaction as a reactant. Burst monotonically increases or decreases lifetimes. Competition between burst-induced and confinement-induced modulation may hence lead to a non-monotonic modulation. We quantify lifetime as the integral of the time autocorrelation function (ACF) of concentration fluctuations around a non-equilibrium steady state of the reaction network. Furthermore, we look at the first and second derivatives of the ACF, each of which is affected in opposite ways by burst and confinement. This allows discriminating between these two noise sources. We analytically derive the ACF from the linear Fokker-Planck approximation of the chemical master equation in order to establish a baseline for the burst-induced modulation at low confinement. Effects of higher confinement are then studied using a partial-propensity stochastic simulation algorithm. The results presented here may help understand the mechanisms that deviate stochastic kinetics from its deterministic counterpart. In addition, they may be instrumental when using fluorescence-lifetime imaging microscopy (FLIM) or fluorescence-correlation spectroscopy (FCS) to measure confinement and burst in systems with known reaction rates, or, alternatively, to correct for the effects of confinement and burst when experimentally measuring reaction rates.

Absorption kinetics and steady-state plasma concentrations of theophylline following therapeutic doses of two sustained-release preparations

DEFF Research Database (Denmark)

Andersen, O; Nielsen, M K; Eriksen, P B

1983-01-01

Ten healthy volunteers received two sustained-release preparations as a single and multiple dose regimen in an open crossover study. Plasma theophylline concentrations were measured by an enzyme immunoassay. The limited fluctuation of the theophylline levels at steady state, with twice daily...... formulation, whereas this was not the case for the other (r = 0.27 and 0.49). The daily dose necessary to keep the plasma concentration within the therapeutic range of 55-110 mumole/liter varied from 7.9 to 22.9 mg/kg. Only mild side effects were recorded, but they were not correlated to the plasma...... theophylline concentration....

Transition state theory for enzyme kinetics

Science.gov (United States)

Truhlar, Donald G.

2015-01-01

This article is an essay that discusses the concepts underlying the application of modern transition state theory to reactions in enzymes. Issues covered include the potential of mean force, the quantization of vibrations, the free energy of activation, and transmission coefficients to account for nonequilibrium effect, recrossing, and tunneling. PMID:26008760

Occurrence of dead core in catalytic particles containing immobilized enzymes: analysis for the Michaelis-Menten kinetics and assessment of numerical methods.

Science.gov (United States)

Pereira, Félix Monteiro; Oliveira, Samuel Conceição

2016-11-01

In this article, the occurrence of dead core in catalytic particles containing immobilized enzymes is analyzed for the Michaelis-Menten kinetics. An assessment of numerical methods is performed to solve the boundary value problem generated by the mathematical modeling of diffusion and reaction processes under steady state and isothermal conditions. Two classes of numerical methods were employed: shooting and collocation. The shooting method used the ode function from Scilab software. The collocation methods included: that implemented by the bvode function of Scilab, the orthogonal collocation, and the orthogonal collocation on finite elements. The methods were validated for simplified forms of the Michaelis-Menten equation (zero-order and first-order kinetics), for which analytical solutions are available. Among the methods covered in this article, the orthogonal collocation on finite elements proved to be the most robust and efficient method to solve the boundary value problem concerning Michaelis-Menten kinetics. For this enzyme kinetics, it was found that the dead core can occur when verified certain conditions of diffusion-reaction within the catalytic particle. The application of the concepts and methods presented in this study will allow for a more generalized analysis and more accurate designs of heterogeneous enzymatic reactors.

Noise-induced modulation of the relaxation kinetics around a non-equilibrium steady state of non-linear chemical reaction networks.

Directory of Open Access Journals (Sweden)

Rajesh Ramaswamy

2011-01-01

Full Text Available Stochastic effects from correlated noise non-trivially modulate the kinetics of non-linear chemical reaction networks. This is especially important in systems where reactions are confined to small volumes and reactants are delivered in bursts. We characterise how the two noise sources confinement and burst modulate the relaxation kinetics of a non-linear reaction network around a non-equilibrium steady state. We find that the lifetimes of species change with burst input and confinement. Confinement increases the lifetimes of all species that are involved in any non-linear reaction as a reactant. Burst monotonically increases or decreases lifetimes. Competition between burst-induced and confinement-induced modulation may hence lead to a non-monotonic modulation. We quantify lifetime as the integral of the time autocorrelation function (ACF of concentration fluctuations around a non-equilibrium steady state of the reaction network. Furthermore, we look at the first and second derivatives of the ACF, each of which is affected in opposite ways by burst and confinement. This allows discriminating between these two noise sources. We analytically derive the ACF from the linear Fokker-Planck approximation of the chemical master equation in order to establish a baseline for the burst-induced modulation at low confinement. Effects of higher confinement are then studied using a partial-propensity stochastic simulation algorithm. The results presented here may help understand the mechanisms that deviate stochastic kinetics from its deterministic counterpart. In addition, they may be instrumental when using fluorescence-lifetime imaging microscopy (FLIM or fluorescence-correlation spectroscopy (FCS to measure confinement and burst in systems with known reaction rates, or, alternatively, to correct for the effects of confinement and burst when experimentally measuring reaction rates.

Improvement of Student Understanding of How Kinetic Data Facilitates the Determination of Amino Acid Catalytic Function through an Alkaline Phosphatase Structure/Mechanism Bioinformatics Exercise

Science.gov (United States)

Grunwald, Sandra K.; Krueger, Katherine J.

2008-01-01

Laboratory exercises, which utilize alkaline phosphatase as a model enzyme, have been developed and used extensively in undergraduate biochemistry courses to illustrate enzyme steady-state kinetics. A bioinformatics laboratory exercise for the biochemistry laboratory, which complements the traditional alkaline phosphatase kinetics exercise, was…

Thermodynamic activity-based intrinsic enzyme kinetic sheds light on enzyme-solvent interactions.

Science.gov (United States)

Grosch, Jan-Hendrik; Wagner, David; Nistelkas, Vasilios; Spieß, Antje C

2017-01-01

The reaction medium has major impact on biocatalytic reaction systems and on their economic significance. To allow for tailored medium engineering, thermodynamic phenomena, intrinsic enzyme kinetics, and enzyme-solvent interactions have to be discriminated. To this end, enzyme reaction kinetic modeling was coupled with thermodynamic calculations based on investigations of the alcohol dehydrogenase from Lactobacillus brevis (LbADH) in monophasic water/methyl tert-butyl ether (MTBE) mixtures as a model solvent. Substrate concentrations and substrate thermodynamic activities were varied separately to identify the individual thermodynamic and kinetic effects on the enzyme activity. Microkinetic parameters based on concentration and thermodynamic activity were derived to successfully identify a positive effect of MTBE on the availability of the substrate to the enzyme, but a negative effect on the enzyme performance. In conclusion, thermodynamic activity-based kinetic modeling might be a suitable tool to initially curtail the type of enzyme-solvent interactions and thus, a powerful first step to potentially understand the phenomena that occur in nonconventional media in more detail. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:96-103, 2017. © 2016 American Institute of Chemical Engineers.

Cycle kinetics, steady state thermodynamics and motors-a paradigm for living matter physics

International Nuclear Information System (INIS)

Qian, Hong

2005-01-01

An integration of the stochastic mathematical models for motor proteins with Hill's steady state thermodynamics yields a rather comprehensive theory for molecular motors as open systems in the nonequilibrium steady state. This theory, a natural extension of Gibbs' approach to isothermal molecular systems in equilibrium, is compared with other existing theories with dissipative structures and dynamics. The theory of molecular motors might be considered as an archetype for studying more complex open biological systems such as biochemical reaction networks inside living cells

Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase Eta

Science.gov (United States)

Brown, Jessica A.; Zhang, Likui; Sherrer, Shanen M.; Taylor, John-Stephen; Burgers, Peter M. J.; Suo, Zucai

2010-01-01

Understanding polymerase fidelity is an important objective towards ascertaining the overall stability of an organism's genome. Saccharomyces cerevisiae DNA polymerase η (yPolη), a Y-family DNA polymerase, is known to efficiently bypass DNA lesions (e.g., pyrimidine dimers) in vivo. Using pre-steady-state kinetic methods, we examined both full-length and a truncated version of yPolη which contains only the polymerase domain. In the absence of yPolη's C-terminal residues 514–632, the DNA binding affinity was weakened by 2-fold and the base substitution fidelity dropped by 3-fold. Thus, the C-terminus of yPolη may interact with DNA and slightly alter the conformation of the polymerase domain during catalysis. In general, yPolη discriminated between a correct and incorrect nucleotide more during the incorporation step (50-fold on average) than the ground-state binding step (18-fold on average). Blunt-end additions of dATP or pyrene nucleotide 5′-triphosphate revealed the importance of base stacking during the binding of incorrect incoming nucleotides. PMID:20798853

Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase Eta

Directory of Open Access Journals (Sweden)

Jessica A. Brown

2010-01-01

Full Text Available Understanding polymerase fidelity is an important objective towards ascertaining the overall stability of an organism's genome. Saccharomyces cerevisiae DNA polymerase η (yPolη, a Y-family DNA polymerase, is known to efficiently bypass DNA lesions (e.g., pyrimidine dimers in vivo. Using pre-steady-state kinetic methods, we examined both full-length and a truncated version of yPolη which contains only the polymerase domain. In the absence of yPolη's C-terminal residues 514–632, the DNA binding affinity was weakened by 2-fold and the base substitution fidelity dropped by 3-fold. Thus, the C-terminus of yPolη may interact with DNA and slightly alter the conformation of the polymerase domain during catalysis. In general, yPolη discriminated between a correct and incorrect nucleotide more during the incorporation step (50-fold on average than the ground-state binding step (18-fold on average. Blunt-end additions of dATP or pyrene nucleotide 5′-triphosphate revealed the importance of base stacking during the binding of incorrect incoming nucleotides.

Determination of steady state and nonsteady-state glycerol kinetics in humans using deuterium-labeled tracer

International Nuclear Information System (INIS)

Beylot, M.; Martin, C.; Beaufrere, B.; Riou, J.P.; Mornex, R.

1987-01-01

Using deuterium-labeled glycerol as tracer and gas-liquid chromatography-mass spectrometry techniques for the determination of isotopic enrichment, we have developed a simple and ethically acceptable method of determining glycerol appearance rate in humans under steady-state and nonsteady-state conditions. In normal subjects, the appearance rate of glycerol in the post-absorptive state was 2.22 +/- 0.20 mumol X kg-1 X min-1, a value in agreement with those reported in studies with radioactively labeled tracers. The ratio nonesterified fatty acid (NEFA) appearance rate/glycerol appearance rate ranged from 1.95 to 3.40. In insulin-dependent diabetic patients with a mild degree of metabolic control, the appearance rate of glycerol was 2.48 +/- 0.29 mumol X kg-1 X min-1. The volume of distribution of glycerol, determined by the bolus injection technique, was (mean) 0.306 l X kg-1 in normal subjects and 0.308 l X kg-1 in insulin-independent diabetic patients. To evaluate the usefulness of the method for determination of glycerol kinetics in nonsteady-state conditions, we infused six normal subjects with natural glycerol and calculated the isotopically determined glycerol appearance rate using a single compartment model (volume of distribution 0.31 l X kg-1). During these tests, the expected glycerol appearance rates were successively 5.03 +/- 0.33, 7.48 +/- 0.39, 9.94 +/- 0.34, 7.48 +/- 0.39, and 5.03 +/- 0.33 mumol +/- kg-1 X min-1, whereas the corresponding isotopically determined appearance rates were 4.62 +/- 0.45, 6.95 +/- 0.56, 10.85 +/- 0.51, 7.35 +/- 0.34, and 5.28 +/- 0.12 mumol X kg-1 X min-1

The purification and steady-state kinetic behaviour of rabbit heart mitochondrial NAD(P)+ malic enzyme.

OpenAIRE

Davisson, V J; Schulz, A R

1985-01-01

The mitochondrial NAD(P)+ malic enzyme [EC 1.1.1.39, L-malate:NAD+ oxidoreductase (decarboxylating)] was purified from rabbit heart to a specific activity of 7 units (mumol/min)/mg at 23 degrees C. A study of the reductive carboxylation reaction indicates that this enzymic reaction is reversible. The rate of the reductive carboxylation reaction appears to be completely inhibited at an NADH concentration of 0.92 mM. A substrate saturation curve of this reaction with NADH as the varied substrat...

Steady-state cerebral glucose concentrations and transport in the human brain

OpenAIRE

Gruetter, R.; Ugurbil, K.; Seaquist, E. R.

1998-01-01

Understanding the mechanism of brain glucose transport across the blood- brain barrier is of importance to understanding brain energy metabolism. The specific kinetics of glucose transport nave been generally described using standard Michaelis-Menten kinetics. These models predict that the steady- state glucose concentration approaches an upper limit in the human brain when the plasma glucose level is well above the Michaelis-Menten constant for half-maximal transport, K(t). In experiments wh...

Modeling Non-Steady Isotopologue and Isotopomer Speciation and Fractionation during Denitrification in Soils

Science.gov (United States)

Maggi, F.; Riley, W. J.

2009-12-01

The composition and location of 15N atoms on N2O isotopomers and isotopologues during isotope speciation has been used to characterize soil biological N cycling and N2O surface emissions. Although there exist few experimental observations, no attempt has been made to model N2O isotopomer speciation. The mathematical treatment of biological kinetic reactions in isotopic applications normally makes use of first-order and quasi steady-state complexation assumptions without taking into account changes in enzyme concentration, reaction stoichiometry, and isotopologue and isotopomer speciation. When multiatomic isotopically-labeled reactants are used in a multi-molecurar reaction, these assumptions may fail since they always lead to a constant fractionation factor and cannot describe speciation of isotopologues and isotopomers. We have developed a mathematical framework that is capable of describing isotopologue and isotopmer speciation and fractionation under the assumption of non-steady complexation during biological kinetic reactions that overcome the limitations mentioned above. This framework was applied to a case study of non-steady (variable and inverse) isotopic effects observed during N2O production and consumption in soils. Our mathematical treatment has led to generalized kinetic equations which replicate experimental observations with high accuracy and help interpret non-steady isotopic effects and isotopologue and isotopomer speciation. The kinetic equations introduced and applied here have general validity in describing isotopic effects in any biochemical reactions by considering: changing enzyme concentrations, mass and isotope conservation, and reaction stoichiometry. The equations also describe speciation of any isotopologue and isotopomer product from any isotopologue and isotopmer reactant.

An artificial-intelligence technique for qualitatively deriving enzyme kinetic mechanisms from initial-velocity measurements and its application to hexokinase.

Science.gov (United States)

Garfinkel, L; Cohen, D M; Soo, V W; Garfinkel, D; Kulikowski, C A

1989-01-01

We have developed a computer method based on artificial-intelligence techniques for qualitatively analysing steady-state initial-velocity enzyme kinetic data. We have applied our system to experiments on hexokinase from a variety of sources: yeast, ascites and muscle. Our system accepts qualitative stylized descriptions of experimental data, infers constraints from the observed data behaviour and then compares the experimentally inferred constraints with corresponding theoretical model-based constraints. It is desirable to have large data sets which include the results of a variety of experiments. Human intervention is needed to interpret non-kinetic information, differences in conditions, etc. Different strategies were used by the several experimenters whose data was studied to formulate mechanisms for their enzyme preparations, including different methods (product inhibitors or alternate substrates), different experimental protocols (monitoring enzyme activity differently), or different experimental conditions (temperature, pH or ionic strength). The different ordered and rapid-equilibrium mechanisms proposed by these experimenters were generally consistent with their data. On comparing the constraints derived from the several experimental data sets, they are found to be in much less disagreement than the mechanisms published, and some of the disagreement can be ascribed to different experimental conditions (especially ionic strength). PMID:2690819

A steady state model for anaerobic digestion of sewage sludges ...

African Journals Online (AJOL)

A steady state model for anaerobic digestion of sewage sludge is developed that comprises three sequential parts – a kinetic part from which the % COD removal and ... and a carbonate system weak acid/base chemistry part from which the digester pH is calculated from the partial pressure of CO2 and alkalinity generated.

The Path of Carbon in Photosynthesis XVI. Kinetic Relationships of the Intermediates in Steady State Photosynthesis

Science.gov (United States)

Benson, A. A.; Kawaguchi, S.; Hayes, P.; Calvin, M.

1952-06-05

A kinetic study of the accumulation of C{sup 14} in the intermediates of steady state photosynthesis in C{sup 14}O{sub 2} provides information regarding the sequence of reactions involved. The work described applied the radio-chromatographic technique for analysis of the labeled early products. The simultaneous carboxylation reaction resulting in malic acid as well as phosphoglycerate is demonstrated in experiments at high light intensity. A comparison of radioactivities in a number of phosphorylated sugars as a function of time reveals concurrent synthesis of fructose and sedoheptulose phosphates followed by that of ribulose phosphates and later by that of glucose phosphates. The possibility that the cleavage of C{sub 4} compounds to C{sub 2} carbon dioxide acceptors may involve C{sub 7} and C{sub 5} sugars and evidence for this mechanism is presented.

Kinetic memory based on the enzyme-limited competition.

Science.gov (United States)

Hatakeyama, Tetsuhiro S; Kaneko, Kunihiko

2014-08-01

Cellular memory, which allows cells to retain information from their environment, is important for a variety of cellular functions, such as adaptation to external stimuli, cell differentiation, and synaptic plasticity. Although posttranslational modifications have received much attention as a source of cellular memory, the mechanisms directing such alterations have not been fully uncovered. It may be possible to embed memory in multiple stable states in dynamical systems governing modifications. However, several experiments on modifications of proteins suggest long-term relaxation depending on experienced external conditions, without explicit switches over multi-stable states. As an alternative to a multistability memory scheme, we propose "kinetic memory" for epigenetic cellular memory, in which memory is stored as a slow-relaxation process far from a stable fixed state. Information from previous environmental exposure is retained as the long-term maintenance of a cellular state, rather than switches over fixed states. To demonstrate this kinetic memory, we study several models in which multimeric proteins undergo catalytic modifications (e.g., phosphorylation and methylation), and find that a slow relaxation process of the modification state, logarithmic in time, appears when the concentration of a catalyst (enzyme) involved in the modification reactions is lower than that of the substrates. Sharp transitions from a normal fast-relaxation phase into this slow-relaxation phase are revealed, and explained by enzyme-limited competition among modification reactions. The slow-relaxation process is confirmed by simulations of several models of catalytic reactions of protein modifications, and it enables the memorization of external stimuli, as its time course depends crucially on the history of the stimuli. This kinetic memory provides novel insight into a broad class of cellular memory and functions. In particular, applications for long-term potentiation are discussed

Enzyme-catalyzed synthesis and kinetics of ultrasonic-assisted biodiesel production from waste tallow.

Science.gov (United States)

Adewale, Peter; Dumont, Marie-Josée; Ngadi, Michael

2015-11-01

The use of ultrasonic processing was evaluated for its ability to achieve adequate mixing while providing sufficient activation energy for the enzymatic transesterification of waste tallow. The effects of ultrasonic parameters (amplitude, cycle and pulse) and major reaction factors (molar ratio and enzyme concentration) on the reaction kinetics of biodiesel generation from waste tallow bio-catalyzed by immobilized lipase [Candida antarctica lipase B (CALB)] were investigated. Three sets of experiments namely A, B, and C were conducted. In experiment set A, two factors (ultrasonic amplitude and cycle) were investigated at three levels; in experiment set B, two factors (molar ratio and enzyme concentration) were examined at three levels; and in experiment set C, two factors (ultrasonic amplitude and reaction time) were investigated at five levels. A Ping Pong Bi Bi kinetic model approach was employed to study the effect of ultrasonic amplitude on the enzymatic transesterification. Kinetic constants of transesterification reaction were determined at different ultrasonic amplitudes (30%, 35%, 40%, 45%, and 50%) and enzyme concentrations (4, 6, and 8 wt.% of fat) at constant molar ratio (fat:methanol); 1:6, and ultrasonic cycle; 5 Hz. Optimal conditions for ultrasound-assisted biodiesel production from waste tallow were fat:methanol molar ratio, 1:4; catalyst level 6% (w/w of fat); reaction time, 20 min (30 times less than conventional batch processes); ultrasonic amplitude 40% at 5 Hz. The kinetic model results revealed interesting features of ultrasound assisted enzyme-catalyzed transesterification (as compared to conventional system): at ultrasonic amplitude 40%, the reaction activities within the system seemed to be steady after 20 min which means the reaction could proceed with or without ultrasonic mixing. Reversed phase high performance liquid chromatography indicated the biodiesel yield to be 85.6±0.08%. Copyright © 2015 Elsevier B.V. All rights reserved.

Internal Diffusion-Controlled Enzyme Reaction: The Acetylcholinesterase Kinetics.

Science.gov (United States)

Lee, Sangyun; Kim, Ji-Hyun; Lee, Sangyoub

2012-02-14

Acetylcholinesterase is an enzyme with a very high turnover rate; it quenches the neurotransmitter, acetylcholine, at the synapse. We have investigated the kinetics of the enzyme reaction by calculating the diffusion rate of the substrate molecule along an active site channel inside the enzyme from atomic-level molecular dynamics simulations. In contrast to the previous works, we have found that the internal substrate diffusion is the determinant of the acetylcholinesterase kinetics in the low substrate concentration limit. Our estimate of the overall bimolecular reaction rate constant for the enzyme is in good agreement with the experimental data. In addition, the present calculation provides a reasonable explanation for the effects of the ionic strength of solution and the mutation of surface residues of the enzyme. The study suggests that internal diffusion of the substrate could be a key factor in understanding the kinetics of enzymes of similar characteristics.

The steady-state tokamak program

International Nuclear Information System (INIS)

Politzer, D.A.; Nevins, W.M.

1992-01-01

This paper reports on a steady-state tokamak experiment (STE) needed to develop the technology and physics data base required for construction of a steady-state fusion power demonstration reactor in the early 21st century. The STE will provide an integrated facility for the development and demonstration of steady-state and particle handling, low-activation high-heat-flux components and materials, efficient current drive, and continuous plasma performance in steady-state, with reactor-like plasma conditions under severe conditions of heat and particle bombardment of the wall. The STE facility will also be used to develop operation and control scenarios for ITER

Mesoscopic dynamics of diffusion-influenced enzyme kinetics.

Science.gov (United States)

Chen, Jiang-Xing; Kapral, Raymond

2011-01-28

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

Mesoscopic dynamics of diffusion-influenced enzyme kinetics

Science.gov (United States)

Chen, Jiang-Xing; Kapral, Raymond

2011-01-01

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

Mechanism for multiplicity of steady states with distinct cell concentration in continuous culture of mammalian cells.

Science.gov (United States)

Yongky, Andrew; Lee, Jongchan; Le, Tung; Mulukutla, Bhanu Chandra; Daoutidis, Prodromos; Hu, Wei-Shou

2015-07-01

Continuous culture for the production of biopharmaceutical proteins offers the possibility of steady state operations and thus more consistent product quality and increased productivity. Under some conditions, multiplicity of steady states has been observed in continuous cultures of mammalian cells, wherein with the same dilution rate and feed nutrient composition, steady states with very different cell and product concentrations may be reached. At those different steady states, cells may exhibit a high glycolysis flux with high lactate production and low cell concentration, or a low glycolysis flux with low lactate and high cell concentration. These different steady states, with different cell concentration, also have different productivity. Developing a mechanistic understanding of the occurrence of steady state multiplicity and devising a strategy to steer the culture toward the desired steady state is critical. We establish a multi-scale kinetic model that integrates a mechanistic intracellular metabolic model and cell growth model in a continuous bioreactor. We show that steady state multiplicity exists in a range of dilution rate in continuous culture as a result of the bistable behavior in glycolysis. The insights from the model were used to devise strategies to guide the culture to the desired steady state in the multiple steady state region. The model provides a guideline principle in the design of continuous culture processes of mammalian cells. © 2015 Wiley Periodicals, Inc.

VALIDITY OF EXCESS ENTROPY PRODUCTION CRITERION OF THERMODYNAMIC STABILITY FOR NONEQUILIBRIUM STEADY STATES

Institute of Scientific and Technical Information of China (English)

吴金平

1991-01-01

The relation between the excess entropy production criterion of thermodynamic stabilityfor nonequilibrium states and kinetic linear stability principle is discussed. It is shown thatthe condition required by the excess entropy production criterion generally is sufficient, butnot necessary to judge the system stability. The condition required by the excess entropyproduction criterion is stronger than that of the linear stability principle. Only when theproduct matrix between the linearized matrix of kinetic equations and matrix of quadraticform of second-order excess entropy is symmetric, is the condition required by the excessentropy production criterion that the steady steate is asymptotically stable (δ_xP>0) necessaryand sufficient. The counterexample given by Fox to prove that the excess entropy, (δ~2S)ss,is not a Liapunov function is incorrect. Contradictory to his conclusion, the counterexampleis just a positive one that proves that the excess entropy is a Liapunov function. Moreover,the excess entropy production criterion is not limited by symmetric conditions of the linear-ized matrix of kinetic equations. The excess entropy around nonequilibrium steady states,(δ~2S)ss, is a Liapunov function of thermodynamic system.

Sulfur isotopic and proteomic profiles of sulfate reducers grown under differential steady-states

Science.gov (United States)

Leavitt, W.; Venceslau, S.; Waldbauer, J.; Smith, D. A.; Boidi, F. J.; Bradley, A. S.

2016-12-01

Microbial sulfate reducers (MSR) drive the Earth's biogeochemical sulfur cycle. At the heart of this energy metabolism is a cascade of redox transformations coupling organic carbon and/or hydrogen oxidation to the dissimilatory reduction of sulfate to sulfide. The product sulfide is depleted in the heavier isotopes of sulfur, relative to the reactant sulfate, consistent with a normal kinetic isotope effect. However, the magnitude of the net fractionation during MSR can range over a range of 70 permil, consistent with a multi-step set of reactions. This range in MSR fractionation has been shown to mainly depend on: i) the cell-specific sulfate reduction rate (csSRR), and ii) the ambient sulfate concentration. However, the fractionation under identical conditions differs among strains (Bradley et al. 2016. Geobio), and so must also be mediated by strain-specific processes, such as the nature and quantity of individual proteins involved in sulfate reduction, electron transport, and growth. In recent work we have examined the influence of electron donor, electron acceptor, and co-limitation under controlled steady-state culture conditions in order better inform models of MSR isotope fractionation, and the physiological and isotopic response to differential environmental forcings (e.g. Leavitt et al. (2013) PNAS). Recent models of the fractionation response to MSR rate (c.f. Bradley 2016; Wing & Halevy, 2016) make specific predictions for the responses of the cellular metabolome and proteome. Here we compare the steady-state S-isotopic fractionation and proteome of `fast' versus `slow' grown D. vulgaris, using replicate chemostats under electron donor limitation. We observe clear and statistically robust changes in some key central MSR and C-metabolism enzymes, though a host of the critical energy-transfer enzymes show no statistically discernable change. We discuss these results in light of recent theoretical advances and their relevance to modern and ancient

Steady-state kinetics of substrate binding and iron release in tomato ACC oxidase.

Science.gov (United States)

Thrower, J S; Blalock, R; Klinman, J P

2001-08-14

1-Aminocyclopropane-1-carboxylate oxidase (ACC oxidase) catalyzes the last step in the biosynthetic pathway of the plant hormone, ethylene. This unusual reaction results in the oxidative ring cleavage of 1-aminocyclopropane carboxylate (ACC) into ethylene, cyanide, and CO2 and requires ferrous ion, ascorbate, and molecular oxygen for catalysis. A new purification procedure and assay method have been developed for tomato ACC oxidase that result in greatly increased enzymatic activity. This method allowed us to determine the rate of iron release from the enzyme and the effect of the activator, CO2, on this rate. Initial velocity studies support an ordered kinetic mechanism where ACC binds first followed by O2; ascorbate can bind after O2 or possibly before ACC. This kinetic mechanism differs from one recently proposed for the ACC oxidase from avocado.

Thermodynamic Activity-Based Progress Curve Analysis in Enzyme Kinetics.

Science.gov (United States)

Pleiss, Jürgen

2018-03-01

Macrokinetic Michaelis-Menten models based on thermodynamic activity provide insights into enzyme kinetics because they separate substrate-enzyme from substrate-solvent interactions. Kinetic parameters are estimated from experimental progress curves of enzyme-catalyzed reactions. Three pitfalls are discussed: deviations between thermodynamic and concentration-based models, product effects on the substrate activity coefficient, and product inhibition. Copyright © 2017 Elsevier Ltd. All rights reserved.

Large deviation theory for the kinetics and energetics of turnover of enzyme catalysis in a chemiostatic flow

Science.gov (United States)

Das, Biswajit; Gangopadhyay, Gautam

2018-05-01

In the framework of large deviation theory, we have characterized nonequilibrium turnover statistics of enzyme catalysis in a chemiostatic flow with externally controllable parameters, like substrate injection rate and mechanical force. In the kinetics of the process, we have shown the fluctuation theorems in terms of the symmetry of the scaled cumulant generating function (SCGF) in the transient and steady state regime and a similar symmetry rule is reflected in a large deviation rate function (LDRF) as a property of the dissipation rate through boundaries. Large deviation theory also gives the thermodynamic force of a nonequilibrium steady state, as is usually recorded experimentally by a single molecule technique, which plays a key role responsible for the dynamical symmetry of the SCGF and LDRF. Using some special properties of the Legendre transformation, here, we have provided a relation between the fluctuations of fluxes and dissipation rates, and among them, the fluctuation of the turnover rate is routinely estimated but the fluctuation in the dissipation rate is yet to be characterized for small systems. Such an enzymatic reaction flow system can be a very good testing ground to systematically understand the rare events from the large deviation theory which is beyond fluctuation theorem and central limit theorem.

On the precision of quasi steady state assumptions in stochastic dynamics

Science.gov (United States)

Agarwal, Animesh; Adams, Rhys; Castellani, Gastone C.; Shouval, Harel Z.

2012-07-01

Many biochemical networks have complex multidimensional dynamics and there is a long history of methods that have been used for dimensionality reduction for such reaction networks. Usually a deterministic mass action approach is used; however, in small volumes, there are significant fluctuations from the mean which the mass action approach cannot capture. In such cases stochastic simulation methods should be used. In this paper, we evaluate the applicability of one such dimensionality reduction method, the quasi-steady state approximation (QSSA) [L. Menten and M. Michaelis, "Die kinetik der invertinwirkung," Biochem. Z 49, 333369 (1913)] for dimensionality reduction in case of stochastic dynamics. First, the applicability of QSSA approach is evaluated for a canonical system of enzyme reactions. Application of QSSA to such a reaction system in a deterministic setting leads to Michaelis-Menten reduced kinetics which can be used to derive the equilibrium concentrations of the reaction species. In the case of stochastic simulations, however, the steady state is characterized by fluctuations around the mean equilibrium concentration. Our analysis shows that a QSSA based approach for dimensionality reduction captures well the mean of the distribution as obtained from a full dimensional simulation but fails to accurately capture the distribution around that mean. Moreover, the QSSA approximation is not unique. We have then extended the analysis to a simple bistable biochemical network model proposed to account for the stability of synaptic efficacies; the substrate of learning and memory [J. E. Lisman, "A mechanism of memory storage insensitive to molecular turnover: A bistable autophosphorylating kinase," Proc. Natl. Acad. Sci. U.S.A. 82, 3055-3057 (1985)], 10.1073/pnas.82.9.3055. Our analysis shows that a QSSA based dimensionality reduction method results in errors as big as two orders of magnitude in predicting the residence times in the two stable states.

Kinetics and comparison of δ-aminolevulinic-acid-induced endogenous protoporphyrin-IX in single cell by steady state and multiphoton fluorescence imaging

Science.gov (United States)

Ganesan, Singaravelu; Elangovan, Masilamani; Periasamy, Ammasi

2001-04-01

Photodynamic Therapy has emerged as a new modality in the treatment of various nonmalignant and malignant diseases. It involves the systemic administration of tumor specific photo-sensitizers with the subsequent application of visible light. This combination causes the generation of cytotoxic species, which damage sensitive targets, producing cell injury and tumor destruction. Although, photofrin is the only photosensitizer currently approved for PDT and tumor detection, its concomitant cutaneous photosensitization poses a significant problem. Hence, δ-aminoleuvulinic acid (δ-ALA) a precursor for the endogenous production of Protoporphyrin IX, through heme biosynthesis pathway, has gained significant importance in the Photodynamic Therapy. Though δ-ALA is present naturally in the cells, exogenous δ-ALA helps to synthesis more of PpIX in the tumor cells, as the fast growing tumor cells take up the administered δ-ALA more than the normal cells. Based on these facts, many invasive studies have been reported on the kinetics of δ-ALA at cellular level by chemical extraction of PpIX from the cells. In the present study we have studied the kinetics of δ-ALA induced PpIX fluorescence from Hela cells by perchloric/Methanol extraction method. However, the amount of PpIX synthesized in the cells at different point of incubation time by noninvasive methods has not been reported. Hence we have also used a noninvasive technique of measuring the kinetics δ-ALA induced PPIX fluorescence from Hela, an epithelial cell derived from human cervical cancer by both single photon (steady state) and multi photon excitation. From the studies it is observed that the δ-ALA induced PpIX is more at 2 hours incubation time for 2 mM of δ-ALA concentration. Further, it is observed that with steady state fluorescence imaging method, the excitation light itself cause the Photodynamic damage, due to the prolonged exposure of the cells than in multi photon excitation, leading to the rounding

Determination of Model Kinetics for Forced Unsteady State Operation of Catalytic CH4 Oxidation

Directory of Open Access Journals (Sweden)

Effendy Mohammad

2016-01-01

Full Text Available The catalytic oxidation of methane for abating the emission vented from coal mine or natural gas transportation has been known as most reliable method. A reverse flow reactor operation has been widely used to oxidize this methane emission due to its capability for autothermal operation and heat production. The design of the reverse flow reactor requires a proper kinetic rate expression, which should be developed based on the operating condition. The kinetic rate obtained in the steady state condition cannot be applied for designing the reactor operated under unsteady state condition. Therefore, new approach to develop the dynamic kinetic rate expression becomes indispensable, particularly for periodic operation such as reverse flow reactor. This paper presents a novel method to develop the kinetic rate expression applied for unsteady state operation. The model reaction of the catalytic methane oxidation over Pt/-Al2O3 catalyst was used with kinetic parameter determined from laboratory experiments. The reactor used was a fixed bed, once-through operation, with a composition modulation in the feed gas. The switching time was set at 3 min by varying the feed concentration, feed flow rate, and reaction temperature. The concentrations of methane in the feed and product were measured and analysed using gas chromatography. The steady state condition for obtaining the kinetic rate expression was taken as a base case and as a way to judge its appropriateness to be applied for dynamic system. A Langmuir-Hinshelwood reaction rate model was developed. The time period during one cycle was divided into some segments, depending on the ratio of CH4/O2. The experimental result shows that there were kinetic regimes occur during one cycle: kinetic regime controlled by intrinsic surface reaction and kinetic regime controlled by external diffusion. The kinetic rate obtained in the steady state operation was not appropriate when applied for unsteady state operation

Neuroreceptor quantitation in vivo by the steady-state principle using constant infusion or bolus injection of radioactive tracers

DEFF Research Database (Denmark)

Lassen, N A

1992-01-01

The approaches hitherto used for measuring the kinetic constants Kd and Bmax of neuroreceptors in vivo all violate the steady state of the system. This complicates the kinetic analysis as approximations must be made, introducing errors of unknown magnitude. The present study presents the theory...

Dissipative dark matter halos: The steady state solution. II.

Science.gov (United States)

Foot, R.

2018-05-01

Within the mirror dark matter model and dissipative dark matter models in general, halos around galaxies with active star formation (including spirals and gas-rich dwarfs) are dynamical: they expand and contract in response to heating and cooling processes. Ordinary type II supernovae (SNe) can provide the dominant heat source, which is possible if kinetic mixing interaction exists with strength ɛ ˜10-9- 10-10 . Dissipative dark matter halos can be modeled as a fluid governed by Euler's equations. Around sufficiently isolated and unperturbed galaxies the halo can relax to a steady state configuration, where heating and cooling rates locally balance and hydrostatic equilibrium prevails. These steady state conditions can be solved to derive the physical properties, including the halo density and temperature profiles, for model galaxies. Here, we consider idealized spherically symmetric galaxies within the mirror dark particle model, as in our earlier paper [Phys. Rev. D 97, 043012 (2018), 10.1103/PhysRevD.97.043012], but we assume that the local halo heating in the SN vicinity dominates over radiative sources. With this assumption, physically interesting steady state solutions arise which we compute for a representative range of model galaxies. The end result is a rather simple description of the dark matter halo around idealized spherically symmetric systems, characterized in principle by only one parameter, with physical properties that closely resemble the empirical properties of disk galaxies.

Kinetics of enzyme action: essential principles for drug hunters

National Research Council Canada - National Science Library

Stein, Ross L

2011-01-01

... field. Beginning with the most basic principles pertaining to simple, one-substrate enzyme reactions and their inhibitors, and progressing to a thorough treatment of two-substrate enzymes, Kinetics of Enzyme Action...

A Comprehensive Enzyme Kinetic Exercise for Biochemistry

Science.gov (United States)

Barton, Janice S.

2011-01-01

This article describes a comprehensive treatment of experimental enzyme kinetics strongly coupled to electronic data acquisition and use of spreadsheets to organize data and perform linear and nonlinear least-squares analyses, all in a manner that promotes development of important reasoning skills. Kinetic parameters are obtained for the stable…

Enzyme Mechanism and Slow-Onset Inhibition of Plasmodium falciparum Enoyl-Acyl Carrier Protein Reductase by an Inorganic Complex

Science.gov (United States)

de Medeiros, Patrícia Soares de Maria; Ducati, Rodrigo Gay; Basso, Luiz Augusto; Santos, Diógenes Santiago; da Silva, Luiz Hildebrando Pereira

2011-01-01

Malaria continues to be a major cause of children's morbidity and mortality worldwide, causing nearly one million deaths annually. The human malaria parasite, Plasmodium falciparum, synthesizes fatty acids employing the Type II fatty acid biosynthesis system (FAS II), unlike humans that rely on the Type I (FAS I) pathway. The FAS II system elongates acyl fatty acid precursors of the cell membrane in Plasmodium. Enoyl reductase (ENR) enzyme is a member of the FAS II system. Here we present steady-state kinetics, pre-steady-state kinetics, and equilibrium fluorescence spectroscopy data that allowed proposal of P. falciparum ENR (PfENR) enzyme mechanism. Moreover, building on previous results, the present study also evaluates the PfENR inhibition by the pentacyano(isoniazid)ferrateII compound. This inorganic complex represents a new class of lead compounds for the development of antimalarial agents focused on the inhibition of PfENR. PMID:21603269

Current IUBMB recommendations on enzyme nomenclature and kinetics

Directory of Open Access Journals (Sweden)

Athel Cornish-Bowden

2014-05-01

Full Text Available The International Union of Biochemistry (IUB, now IUBMB prepared recommendations for describing the kinetic behaviour of enzymes in 1981. Despite the more than 30 years that have passed since these have not subsequently been revised, though in various respects they do not adequately cover current needs. The IUBMB is also responsible for recommendations on the naming and classification of enzymes. In contrast to the case of kinetics, these recommendations are kept continuously up to date.

On enzyme kinetic parameters modification of gamma irradiation

International Nuclear Information System (INIS)

Ferdes, O.S.; Ferdes, M.; Turcu, G.R.

1993-01-01

To elucidate the molecular mechanisms of gamma-ray action on biomolecules there were investigated the modifications in activity and other kinetic parameters for some enzymes irradiated in pure dry state at relative high doses. There were considered bacterial and fungal α-amylases, glucoamylase and Mucor sp. protease irradiated by a 60 Co gamma-ray source in the dose range 1.0-30.0 kGy, at different dose-rates between 0.5-2.0 kGy/h, at room temperature. Considering the enzyme inactivation in this dose range, the dose-effect relationships have an expected form and depend on the irradiation conditions but not significantly on the dose rate. The catalytic properties of enzymes were modified by irradiation. By usual methods it is evidenced a direct correlation between the enzymatic activities, Michaelis-Menten constant, K m , reaction velocities, v, and the irradiation dose. These experimental findings can support a self-consistent theoretical approach on biophysical radiation action on biological active molecules like enzymes. At the same time, some enzyme behaviour to irradiation could be considered like a good biological indicator of radiation response. (Author) 4 Figs., 19 Refs

Diffusion-driven steady states of the Z-pinch

International Nuclear Information System (INIS)

Lehnert, B.

1988-01-01

Steady states of a Z-pinch where no electric field is imposed along the pinch axis by external means are investigated. In this case, diffusion-driven states become possible when imposed volume sources of particles and heat drive a radial diffusion velocity that, in its turn, generates the electric plasma current. The particle sources can be from pellet injection or a neutral gas blanket, and the heat sources provided by thermonuclear reactions or auxiliary heating. The present analysis and associated kinetic considerations indicate that steady diffusion-driven operation should become possible for certain classes of plasma profiles, without running into singularity problems at the pinch axis. Such operation leads to higher axial currents in a Z-pinch without an axial magnetic field than in a tokamaklike case under similar plasma conditions. The technical difficulty in realizing a volume distribution of particle sinks introduces certain constraints on the plasma and current profiles. This fact has to be taken into account in a stability analysis. Neoclassical or anomalous diffusion will increase the diffusion velocity of the plasma but is not expected to affect the main physical features of the present results

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

International Nuclear Information System (INIS)

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti

2016-01-01

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

Energy Technology Data Exchange (ETDEWEB)

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti, E-mail: arti@iitm.ac.in [Department of Chemistry, Indian Institute of Technology, Madras, Chennai 600036 (India)

2016-08-28

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

Science.gov (United States)

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti

2016-08-01

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

steady – state performance of induction and transfer state

African Journals Online (AJOL)

eobe

This paper presents paper presents paper presents the steady the steady the steady–state performance state performance state performance comparison comparison comparison between polyphase induction motor and polyphase between polyphase induction motor and polyphase. TF motor operating in. TF motor ...

A Sensitive and Robust Enzyme Kinetic Experiment Using Microplates and Fluorogenic Ester Substrates

Science.gov (United States)

Johnson, R. Jeremy; Hoops, Geoffrey C.; Savas, Christopher J.; Kartje, Zachary; Lavis, Luke D.

2015-01-01

Enzyme kinetics measurements are a standard component of undergraduate biochemistry laboratories. The combination of serine hydrolases and fluorogenic enzyme substrates provides a rapid, sensitive, and general method for measuring enzyme kinetics in an undergraduate biochemistry laboratory. In this method, the kinetic activity of multiple protein…

An effective rate equation approach to reaction kinetics in small volumes: theory and application to biochemical reactions in nonequilibrium steady-state conditions.

Science.gov (United States)

Grima, R

2010-07-21

Chemical master equations provide a mathematical description of stochastic reaction kinetics in well-mixed conditions. They are a valid description over length scales that are larger than the reactive mean free path and thus describe kinetics in compartments of mesoscopic and macroscopic dimensions. The trajectories of the stochastic chemical processes described by the master equation can be ensemble-averaged to obtain the average number density of chemical species, i.e., the true concentration, at any spatial scale of interest. For macroscopic volumes, the true concentration is very well approximated by the solution of the corresponding deterministic and macroscopic rate equations, i.e., the macroscopic concentration. However, this equivalence breaks down for mesoscopic volumes. These deviations are particularly significant for open systems and cannot be calculated via the Fokker-Planck or linear-noise approximations of the master equation. We utilize the system-size expansion including terms of the order of Omega(-1/2) to derive a set of differential equations whose solution approximates the true concentration as given by the master equation. These equations are valid in any open or closed chemical reaction network and at both the mesoscopic and macroscopic scales. In the limit of large volumes, the effective mesoscopic rate equations become precisely equal to the conventional macroscopic rate equations. We compare the three formalisms of effective mesoscopic rate equations, conventional rate equations, and chemical master equations by applying them to several biochemical reaction systems (homodimeric and heterodimeric protein-protein interactions, series of sequential enzyme reactions, and positive feedback loops) in nonequilibrium steady-state conditions. In all cases, we find that the effective mesoscopic rate equations can predict very well the true concentration of a chemical species. This provides a useful method by which one can quickly determine the

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

Directory of Open Access Journals (Sweden)

Supaporn Kradtap Hartwell

2012-01-01

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

Pre-Steady State Kinetic Investigation of the Incorporation of Anti-Hepatitis B Nucleotide Analogs Catalyzed by Non-Canonical Human DNA Polymerases

Science.gov (United States)

Brown, Jessica A.; Pack, Lindsey R.; Fowler, Jason D.; Suo, Zucai

2011-01-01

Antiviral nucleoside analogs have been developed to inhibit the enzymatic activities of the hepatitis B virus (HBV) polymerase, thereby preventing the replication and production of HBV. However, the usage of these analogs can be limited by drug toxicity because the 5′-triphosphates of these nucleoside analogs (nucleotide analogs) are potential substrates for human DNA polymerases to incorporate into host DNA. Although they are poor substrates for human replicative DNA polymerases, it remains to be established whether these nucleotide analogs are substrates for the recently discovered human X- and Y-family DNA polymerases. Using pre-steady state kinetic techniques, we have measured the substrate specificity values for human DNA polymerases β, λ, η, ι, κ, and Rev1 incorporating the active forms of the following anti-HBV nucleoside analogs approved for clinical use: adefovir, tenofovir, lamivudine, telbivudine, and entecavir. Compared to the incorporation of a natural nucleotide, most of the nucleotide analogs were incorporated less efficiently (2 to >122,000) by the six human DNA polymerases. In addition, the potential for entecavir and telbivudine, two drugs which possess a 3′-hydroxyl, to become embedded into human DNA was examined by primer extension and DNA ligation assays. These results suggested that telbivudine functions as a chain terminator while entecavir was efficiently extended by the six enzymes and was a substrate for human DNA ligase I. Our findings suggested that incorporation of anti-HBV nucleotide analogs catalyzed by human X- and Y-family polymerases may contribute to clinical toxicity. PMID:22132702

Pseudo Steady-State Free Precession for MR-Fingerprinting.

Science.gov (United States)

Assländer, Jakob; Glaser, Steffen J; Hennig, Jürgen

2017-03-01

This article discusses the signal behavior in the case the flip angle in steady-state free precession sequences is continuously varied as suggested for MR-fingerprinting sequences. Flip angle variations prevent the establishment of a steady state and introduce instabilities regarding to magnetic field inhomogeneities and intravoxel dephasing. We show how a pseudo steady state can be achieved, which restores the spin echo nature of steady-state free precession. Based on geometrical considerations, relationships between the flip angle, repetition and echo time are derived that suffice to the establishment of a pseudo steady state. The theory is tested with Bloch simulations as well as phantom and in vivo experiments. A typical steady-state free precession passband can be restored with the proposed conditions. The stability of the pseudo steady state is demonstrated by comparing the evolution of the signal of a single isochromat to one resulting from a spin ensemble. As confirmed by experiments, magnetization in a pseudo steady state can be described with fewer degrees of freedom compared to the original fingerprinting and the pseudo steady state results in more reliable parameter maps. The proposed conditions restore the spin-echo-like signal behavior typical for steady-state free precession in fingerprinting sequences, making this approach more robust to B 0 variations. Magn Reson Med 77:1151-1161, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Multimode optical fibers: steady state mode exciter.

Science.gov (United States)

Ikeda, M; Sugimura, A; Ikegami, T

1976-09-01

The steady state mode power distribution of the multimode graded index fiber was measured. A simple and effective steady state mode exciter was fabricated by an etching technique. Its insertion loss was 0.5 dB for an injection laser. Deviation in transmission characteristics of multimode graded index fibers can be avoided by using the steady state mode exciter.

Steady-State Creep of Asphalt Concrete

Directory of Open Access Journals (Sweden)

Alibai Iskakbayev

2017-02-01

Full Text Available This paper reports the experimental investigation of the steady-state creep process for fine-grained asphalt concrete at a temperature of 20 ± 2 °С and under stress from 0.055 to 0.311 MPa under direct tension and was found to occur at a constant rate. The experimental results also determined the start, the end point, and the duration of the steady-state creep process. The dependence of these factors, in addition to the steady-state creep rate and viscosity of the asphalt concrete on stress is satisfactorily described by a power function. Furthermore, it showed that stress has a great impact on the specific characteristics of asphalt concrete: stress variation by one order causes their variation by 3–4.5 orders. The described relations are formulated for the steady-state of asphalt concrete in a complex stressed condition. The dependence is determined between stress intensity and strain rate intensity.

Diffusion in coronas around clinopyroxene: modelling with local equilibrium and steady state, and a non-steady-state modification to account for zoned actinolite-hornblende

Science.gov (United States)

Ashworth, J. R.; Birdi, J. J.; Emmett, T. F.

1992-01-01

Retrograde coronas of Caledonian age, between clinopyroxene and plagioclase in the Jotun Nappe Complex, Norway, illustrate the effects of diffusion kinetics on mineral distributions among layers and on the compositions of hornblende-actinolite. One corona type comprises a symplectite of epidote + quartz adjacent to plagioclase, and a less well-organized intergrowth of amphibole + quartz replacing clinopyroxene. The observed mineral proportions imply an open-system reaction, but the similarity of Al/Si ratios in reactant plagioclase and product symplectite indicates approximate conservation of Al2O3 and SiO2. The largest inferred open-system flux is a loss of CaO, mostly derived from consumption of clinopyroxene. The approximate layer structure, Pl|Ep + Qtz|Hbl + Qtz|Act±Hbl + Qtz|Cpx, is modelled using the theory of steady-state diffusion-controlled growth with local equilibrium. To obtain a solution, it is necessary to use a reactant plagioclase composition which takes into account aluminous (epidote) inclusions. The results indicate that, in terms of Onsager diffusion coefficients L ii , Ca is more mobile than AL ( L CaCa/ L AlAl≳3.) (where ≳ means greater than or approximately equal to). This behaviour of Ca is comparable with that of Mg in previously studied coronas around olivine. Si is non-diffusing in the present modelling, because of silica saturation. Oxidation of some Fe2+ to Fe3+ occurs within the corona. Mg diffuses towards its source (clinopyroxene) to maintain local equilibrium. Other coronas consist of two layers, hornblende adjacent to plagioclase and zoned amphibole + quartz adjacent to clinopyroxene. In the zoned layer, actinolitic hornblende forms relict patches, separated from quartz blebs by more aluminous hornblende. A preliminary steady-state, local-equilibrium model of grain-boundary diffusion explains the formation of low-Al and high-Al layers as due to Al immobility. Zoning and replacement are qualitatively explained in terms of

Mechanistic studies with solubilized rat liver steroid 5 alpha-reductase: Elucidation of the kinetic mechanism

International Nuclear Information System (INIS)

Levy, M.A.; Brandt, M.; Greway, A.T.

1990-01-01

A solubilized preparation of steroid 5 alpha-reductase from rat liver has been used in studies focused toward an understanding of the kinetic mechanism associated with enzyme catalysis. From the results of analyses with product and dead-end inhibitors, a preferentially ordered binding of substrates and release of products from the surface of the enzyme is proposed. The observations from these experiments were identical with those using the steroid 5 alpha-reductase activity associated with rat liver microsomes. The primary isotope effects on steady-state kinetic parameters when [4S-2H]NADPH was used also were consistent with an ordered kinetic mechanism. Normal isotope effects were observed for all three kinetic parameters (Vm/Km for both testosterone and NADPH and Vm) at all substrate concentrations used experimentally. Upon extrapolation to infinite concentration of testosterone, the isotope effect on Vm/Km for NADPH approached unity, indicating that the nicotinamide dinucleotide phosphate is the first substrate binding to and the second product released from the enzyme. The isotope effects on Vm/Km for testosterone at infinite concentration of cofactor and on Vm were 3.8 +/- 0.5 and 3.3 +/- 0.4, respectively. Data from the pH profiles of these three steady-state parameters and the inhibition constants (1/Ki) of competitive inhibitors versus both substrates indicate that the binding of nicotinamide dinucleotide phosphate involves coordination of its anionic 2'-phosphate to a protonated enzyme-associated base with an apparent pK near 8.0. From these results, relative limits have been placed on several of the internal rate constants used to describe the ordered mechanism of the rat liver steroid 5 alpha-reductase

Steady state analysis of Boolean molecular network models via model reduction and computational algebra.

Science.gov (United States)

Veliz-Cuba, Alan; Aguilar, Boris; Hinkelmann, Franziska; Laubenbacher, Reinhard

2014-06-26

A key problem in the analysis of mathematical models of molecular networks is the determination of their steady states. The present paper addresses this problem for Boolean network models, an increasingly popular modeling paradigm for networks lacking detailed kinetic information. For small models, the problem can be solved by exhaustive enumeration of all state transitions. But for larger models this is not feasible, since the size of the phase space grows exponentially with the dimension of the network. The dimension of published models is growing to over 100, so that efficient methods for steady state determination are essential. Several methods have been proposed for large networks, some of them heuristic. While these methods represent a substantial improvement in scalability over exhaustive enumeration, the problem for large networks is still unsolved in general. This paper presents an algorithm that consists of two main parts. The first is a graph theoretic reduction of the wiring diagram of the network, while preserving all information about steady states. The second part formulates the determination of all steady states of a Boolean network as a problem of finding all solutions to a system of polynomial equations over the finite number system with two elements. This problem can be solved with existing computer algebra software. This algorithm compares favorably with several existing algorithms for steady state determination. One advantage is that it is not heuristic or reliant on sampling, but rather determines algorithmically and exactly all steady states of a Boolean network. The code for the algorithm, as well as the test suite of benchmark networks, is available upon request from the corresponding author. The algorithm presented in this paper reliably determines all steady states of sparse Boolean networks with up to 1000 nodes. The algorithm is effective at analyzing virtually all published models even those of moderate connectivity. The problem for

Dynamical and technological consequences of multiple isolas of steady states in a catalytic fluidised-bed reactor

Directory of Open Access Journals (Sweden)

Bizon Katarzyna

2017-09-01

Full Text Available Steady-state characteristics of a catalytic fluidised bed reactor and its dynamical consequences are analyzed. The occurrence of an untypical steady-state structure manifesting in a form of multiple isolas is described. A two-phase bubbling bed model is used for a quantitative description of the bed of catalyst. The influence of heat exchange intensity and a fluidisation ratio onto the generation of isolated solution branches is presented for two kinetic schemes. Dynamical consequences of the coexistence of such untypical branches of steady states are presented. The impact of linear growth of the fluidisation ratio and step change of the cooling medium temperature onto the desired product yield is analyzed. The results presented in this study confirm that the identification of a region of the occurrence of multiple isolas is important due to their strong impact both on the process start-up and its control.

Enzyme-catalyzed and binding reaction kinetics determined by titration calorimetry.

Science.gov (United States)

Hansen, Lee D; Transtrum, Mark K; Quinn, Colette; Demarse, Neil

2016-05-01

Isothermal calorimetry allows monitoring of reaction rates via direct measurement of the rate of heat produced by the reaction. Calorimetry is one of very few techniques that can be used to measure rates without taking a derivative of the primary data. Because heat is a universal indicator of chemical reactions, calorimetry can be used to measure kinetics in opaque solutions, suspensions, and multiple phase systems and does not require chemical labeling. The only significant limitation of calorimetry for kinetic measurements is that the time constant of the reaction must be greater than the time constant of the calorimeter which can range from a few seconds to a few minutes. Calorimetry has the unique ability to provide both kinetic and thermodynamic data. This article describes the calorimetric methodology for determining reaction kinetics and reviews examples from recent literature that demonstrate applications of titration calorimetry to determine kinetics of enzyme-catalyzed and ligand binding reactions. A complete model for the temperature dependence of enzyme activity is presented. A previous method commonly used for blank corrections in determinations of equilibrium constants and enthalpy changes for binding reactions is shown to be subject to significant systematic error. Methods for determination of the kinetics of enzyme-catalyzed reactions and for simultaneous determination of thermodynamics and kinetics of ligand binding reactions are reviewed. Copyright © 2015 Elsevier B.V. All rights reserved.

Reexamining Michaelis-Menten Enzyme Kinetics for Xanthine Oxidase

Science.gov (United States)

Bassingthwaighte, James B.; Chinn, Tamara M.

2013-01-01

Abbreviated expressions for enzyme kinetic expressions, such as the Michaelis-Menten (M-M) equations, are based on the premise that enzyme concentrations are low compared with those of the substrate and product. When one does progress experiments, where the solute is consumed during conversion to form a series of products, the idealized conditions…

Mathematical treatment of isotopologue and isotopomer speciation and fractionation in biochemical kinetics

Science.gov (United States)

Maggi, Federico; Riley, William J.

2010-03-01

We present a mathematical treatment of the kinetic equations that describe isotopologue and isotopomer speciation and fractionation during enzyme-catalyzed biochemical reactions. These equations, presented here with the name GEBIK (general equations for biochemical isotope kinetics) and GEBIF (general equations for biochemical isotope fractionation), take into account microbial biomass and enzyme dynamics, reaction stoichiometry, isotope substitution number, and isotope location within each isotopologue and isotopomer. In addition to solving the complete GEBIK and GEBIF, we also present and discuss two approximations to the full solutions under the assumption of biomass-free and enzyme steady-state, and under the quasi-steady-state assumption as applied to the complexation rate. The complete and approximate approaches are applied to observations of biological denitrification in soils. Our analysis highlights that the full GEBIK and GEBIF provide a more accurate description of concentrations and isotopic compositions of substrates and products throughout the reaction than do the approximate forms. We demonstrate that the isotopic effects of a biochemical reaction depend, in the most general case, on substrate and complex concentrations and, therefore, the fractionation factor is a function of time. We also demonstrate that inverse isotopic effects can occur for values of the fractionation factor smaller than 1, and that reactions that do not discriminate isotopes do not necessarily imply a fractionation factor equal to 1.

A simple steady-state model for carry-over of aflatoxins from feed to cow's milk.

NARCIS (Netherlands)

Eijkeren, Jan C H van; Bakker, Martine I; Zeilmaker, Marco J

2006-01-01

A simple steady-state model is derived from two kinetic one-compartment models for the disposition of aflatoxin B1 (AFB1) and aflatoxin M1 (AFM1) in the lactating cow. The model relates daily intake of AFB1 in feed of dairy cattle and the cow's lactation status to resulting concentrations of AFM1 in

Probing the molecular mechanism of action of the HIV-1 reverse transcriptase inhibitor 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA) using pre-steady-state kinetics

OpenAIRE

Muftuoglu, Yagmur; Sohl, Christal D.; Mislak, Andrea C.; Mitsuya, Hiroaki; Sarafianos, Stefan G.; Anderson, Karen S.

2014-01-01

The novel antiretroviral 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA) is a potent nucleoside HIV-1 reverse transcriptase (RT) inhibitor (NRTI). Unlike other FDA-approved NRTIs, EFdA contains a 3′-hydroxyl. Pre-steady-state kinetics showed RT preferred incorporating EFdA-TP over native dATP. Moreover, RT slowly inserted nucleotides past an EFdA-terminated primer, resulting in delayed chain termination with unaffected fidelity. This is distinct from KP1212, another 3′-hydroxyl-containing RT inh...

Steady-State Performance of Kalman Filter for DPLL

Institute of Scientific and Technical Information of China (English)

QIAN Yi; CUI Xiaowei; LU Mingquan; FENG Zhenming

2009-01-01

For certain system models, the structure of the Kalman filter is equivalent to a second-order vari-able gain digital phase-locked loop (DPLL). To apply the knowledge of DPLLs to the design of Kalman filters, this paper studies the steady-state performance of Kalman filters for these system models. The results show that the steady-state Kalman gain has the same form as the DPLL gain. An approximate simple form for the steady-state Kalman gain is used to derive an expression for the equivalent loop bandwidth of the Kalman filter as a function of the process and observation noise variances. These results can be used to analyze the steady-state performance of a Kalman filter with DPLL theory or to design a Kalman filter model with the same steady-state performance as a given DPLL.

Global Kinetic Analysis of Mammalian E3 Reveals pH-dependent NAD+/NADH Regulation, Physiological Kinetic Reversibility, and Catalytic Optimum*

Science.gov (United States)

Moxley, Michael A.; Beard, Daniel A.; Bazil, Jason N.

2016-01-01

Mammalian E3 is an essential mitochondrial enzyme responsible for catalyzing the terminal reaction in the oxidative catabolism of several metabolites. E3 is a key regulator of metabolic fuel selection as a component of the pyruvate dehydrogenase complex (PDHc). E3 regulates PDHc activity by altering the affinity of pyruvate dehydrogenase kinase, an inhibitor of the enzyme complex, through changes in reduction and acetylation state of lipoamide moieties set by the NAD+/NADH ratio. Thus, an accurate kinetic model of E3 is needed to predict overall mammalian PDHc activity. Here, we have combined numerous literature data sets and new equilibrium spectroscopic experiments with a multitude of independently collected forward and reverse steady-state kinetic assays using pig heart E3. The latter kinetic assays demonstrate a pH-dependent transition of NAD+ activation to inhibition, shown here, to our knowledge, for the first time in a single consistent data set. Experimental data were analyzed to yield a thermodynamically constrained four-redox-state model of E3 that simulates pH-dependent activation/inhibition and active site redox states for various conditions. The developed model was used to determine substrate/product conditions that give maximal E3 rates and show that, due to non-Michaelis-Menten behavior, the maximal flux is different compared with the classically defined kcat. PMID:26644471

Instability of the Null Steady State: The Fundamental Problem of Inhibiting Malignant Cell Growth

Science.gov (United States)

Varfolomeev, S. D.; Lukovenkov, A. V.

2018-07-01

Mathematical modeling of the process of inhibiting malignant growth by common chemotherapeutic agents and biological therapeutics is used to investigate the effect kinetic parameters of the model have on the outcome of treatment. It is shown that the ultimate suppression of growth, i.e., the formation of a stable steady-state with no cancer cells, cannot be attained if only the means of classical chemotherapy are used.

New Tore Supra steady state operating scenario

International Nuclear Information System (INIS)

Martin, G.; Parlange, F.; van Houtte, D.; Wijnands, T.

1995-01-01

This document deals with plasma control in steady state conditions. A new plasma control systems enabling feedback control of global plasma equilibrium parameters has been developed. It also enables to operate plasma discharge in steady state regime. (TEC). 4 refs., 5 figs

Enzyme kinetic characterization of protein tyrosine phosphatases

DEFF Research Database (Denmark)

Peters, Günther H.J.; Branner, S.; Møller, K. B.

2003-01-01

Protein tyrosine phosphatases (PTPs) play a central role in cellular signaling processes, resulting in an increased interest in modulating the activities of PTPs. We therefore decided to undertake a detailed enzyme kinetic evaluation of various transmembrane and cytosolic PTPs (PTPalpha, PTPbeta...

Steady state neutral beam injector

International Nuclear Information System (INIS)

Mattoo, S.K.; Bandyopadhyay, M.; Baruah, U.K.; Bisai, N.; Chakbraborty, A.K.; Chakrapani, Ch.; Jana, M.R.; Bajpai, M.; Jaykumar, P.K.; Patel, D.; Patel, G.; Patel, P.J.; Prahlad, V.; Rao, N.V.M.; Rotti, C.; Singh, N.P.; Sridhar, B.

2000-01-01

Learning from operational reliability of neutral beam injectors in particular and various heating schemes including RF in general on TFTR, JET, JT-60, it has become clear that neutral beam injectors may find a greater role assigned to them for maintaining the plasma in steady state devices under construction. Many technological solutions, integrated in the present day generation of injectors have given rise to capability of producing multimegawatt power at many tens of kV. They have already operated for integrated time >10 5 S without deterioration in the performance. However, a new generation of injectors for steady state devices have to address to some basic issues. They stem from material erosion under particle bombardment, heat transfer > 10 MW/m 2 , frequent regeneration of cryopanels, inertial power supplies, data acquisition and control of large volume of data. Some of these engineering issues have been addressed to in the proposed neutral beam injector for SST-1 at our institute; the remaining shall have to wait for the inputs of the database generated from the actual experience with steady state injectors. (author)

A cross-bridge based model of force depression: Can a single modification address both transient and steady-state behaviors?

Science.gov (United States)

Corr, David T; Herzog, Walter

2016-03-21

Force depression (FD), the reduction of isometric force following active shortening, is a phenomenon of skeletal muscle that has received significant attention in biomechanical and physiological literature, yet the mechanisms underlying FD remain unknown. Recent experiments identified a slower rate of force redevelopment with increasing amounts of steady-state FD, suggesting that FD may be caused, at least in part, by a decrease in cross-bridge binding rate (Corr and Herzog, 2005; Koppes et al., 2014). Herein, we develop a cross-bridge based model of FD in which the binding rate function, f, decreases with the mechanical work performed during shortening. This modification incorporates a direct relationship between steady-state FD and muscle mechanical work (Corr and Herzog, 2005; Herzog et al., 2000; Kosterina et al., 2008), and is consistent with a proposed mechanism attributing FD to stress-induced inhibition of cross-bridge attachments (Herzog, 1998; Maréchal and Plaghki, 1979). Thus, for an increase in mechanical work, the model should predict a slower force redevelopment (decreased attachment rate) to a more depressed steady-state force (fewer attached cross-bridges), and a reduction in contractile element stiffness (Ford et al., 1981). We hypothesized that since this modification affects the cross-bridge kinetics, a corresponding model would be able to account for both transient and steady-state FD behaviors. Comparisons to prior experiments (Corr and Herzog, 2005; Herzog et al., 2000; Kosterina et al., 2008) show that both steady-state and transient aspects of FD, as well as the relationship of FD with respect to speed and amplitude of shortening, are well captured by this model. Thus, this relatively simple cross-bridge based model of FD lends support to a mechanism involving the inhibition of cross-bridge binding, and indicates that cross-bridge kinetics may play a critical role in FD. Copyright © 2016 Elsevier Ltd. All rights reserved.

Measurement of non-steady-state free fatty acid turnover

International Nuclear Information System (INIS)

Jensen, M.D.; Heiling, V.; Miles, J.M.

1990-01-01

The accuracy of non-steady-state equations for measuring changes in free fatty acid rate of appearance (Ra) is unknown. In the present study, endogenous lipolysis (traced with [ 14 C]-linoleate) was pharmacologically suppressed in six conscious mongrel dogs. A computer-responsive infusion pump was then used to deliver an intravenous oleic acid emulsion in both constant and linear gradient infusion modes. Both non-steady-state equations with various effective volumes of distribution (V) and steady-state equations were used to measure oleate Ra [( 14 C]oleate). Endogenous lipolysis did not change during the experiment. When oleate Ra increased in a linear gradient fashion, only non-steady-state equations with a large (150 ml/kg) V resulted in erroneous values (9% overestimate, P less than 0.05). In contrast, when oleate Ra decreased in a similar fashion, steady-state and standard non-steady-state equations (V = plasma volume = 50 ml/kg) overestimated total oleate Ra (18 and 7%, P less than 0.001 and P less than 0.05, respectively). Overall, non-steady-state equations with an effective V of 90 ml/kg (1.8 x plasma volume) allowed the most accurate estimates of oleate Ra

[Enzyme kinetic glucose determination by the glucose dehydrogenase method. Enzyme kinetic substrate determination using competitive inhibitors, II (author's transl)].

Science.gov (United States)

Müller-Matthesius, R

1975-05-01

The sensitivity of enzyme kinetic substrate determinations can be improved with the aid of competitive inhibitors. As an example, the determination of glucose dehydrogenase in the presence of potassium thiocyanate is described. The method has the advantage of rapid operation with satisfactory precision.

Dissipative dark matter halos: The steady state solution

Science.gov (United States)

Foot, R.

2018-02-01

Dissipative dark matter, where dark matter particle properties closely resemble familiar baryonic matter, is considered. Mirror dark matter, which arises from an isomorphic hidden sector, is a specific and theoretically constrained scenario. Other possibilities include models with more generic hidden sectors that contain massless dark photons [unbroken U (1 ) gauge interactions]. Such dark matter not only features dissipative cooling processes but also is assumed to have nontrivial heating sourced by ordinary supernovae (facilitated by the kinetic mixing interaction). The dynamics of dissipative dark matter halos around rotationally supported galaxies, influenced by heating as well as cooling processes, can be modeled by fluid equations. For a sufficiently isolated galaxy with a stable star formation rate, the dissipative dark matter halos are expected to evolve to a steady state configuration which is in hydrostatic equilibrium and where heating and cooling rates locally balance. Here, we take into account the major cooling and heating processes, and numerically solve for the steady state solution under the assumptions of spherical symmetry, negligible dark magnetic fields, and that supernova sourced energy is transported to the halo via dark radiation. For the parameters considered, and assumptions made, we were unable to find a physically realistic solution for the constrained case of mirror dark matter halos. Halo cooling generally exceeds heating at realistic halo mass densities. This problem can be rectified in more generic dissipative dark matter models, and we discuss a specific example in some detail.

Probing the molecular mechanism of action of the HIV-1 reverse transcriptase inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) using pre-steady-state kinetics.

Science.gov (United States)

Muftuoglu, Yagmur; Sohl, Christal D; Mislak, Andrea C; Mitsuya, Hiroaki; Sarafianos, Stefan G; Anderson, Karen S

2014-06-01

The novel antiretroviral 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) is a potent nucleoside HIV-1 reverse transcriptase (RT) inhibitor (NRTI). Unlike other FDA-approved NRTIs, EFdA contains a 3'-hydroxyl. Pre-steady-state kinetics showed RT preferred incorporating EFdA-TP over native dATP. Moreover, RT slowly inserted nucleotides past an EFdA-terminated primer, resulting in delayed chain termination with unaffected fidelity. This is distinct from KP1212, another 3'-hydroxyl-containing RT inhibitor considered to promote viral lethal mutagenesis. New mechanistic features of RT inhibition by EFdA are revealed. Copyright © 2014 Elsevier B.V. All rights reserved.

NUMERICAL SOLUTION OF STEADY STATE DISPERSION FLOW MODEL FOR LACTOSE-LACTASE HYDROLYSIS WITH DIFFERENT KINETICS IN FIXED BED

Directory of Open Access Journals (Sweden)

OLAOSEBIKAN ABIDOYE OLAFADEHAN

2010-06-01

Full Text Available A detailed computational procedure for evaluating lactose hydrolysis with immobilized enzyme in a packed bed tubular reactor under dispersion flow conditions is presented. The dispersion flow model for lactose hydrolysis using different kinetics, taking cognizance of external mass transfer resistances, was solved by the method of orthogonal collocation. The reliability of model simulations was tested using experimental data from a laboratory packed bed column, where the -galactosidase of Kluyveromyces fragilis was immobilized on spherical chitosan beads. Comparison of the simulated results with experimental exit conversion shows that the dispersion flow model and using Michaelis-Menten kinetics with competitive product (galactose inhibition are appropriate to interpret the experimental results and simulate the process of lactose hydrolysis in a fixed bed.

Quasi-steady-state voltammetry of rapid electron transfer reactions at the macroscopic substrate of the scanning electrochemical microscope.

Science.gov (United States)

Nioradze, Nikoloz; Kim, Jiyeon; Amemiya, Shigeru

2011-02-01

We report on a novel theory and experiment for scanning electrochemical microscopy (SECM) to enable quasi-steady-state voltammetry of rapid electron transfer (ET) reactions at macroscopic substrates. With this powerful approach, the substrate potential is cycled widely across the formal potential of a redox couple while the reactant or product of a substrate reaction is amperometrically detected at the tip in the feedback or substrate generation/tip collection mode, respectively. The plot of tip current versus substrate potential features the retraceable sigmoidal shape of a quasi-steady-state voltammogram although a transient voltammogram is obtained at the macroscopic substrate. Finite element simulations reveal that a short tip-substrate distance and a reversible substrate reaction (except under the tip) are required for quasi-steady-state voltammetry. Advantageously, a pair of quasi-steady-state voltammograms is obtained by employing both operation modes to reliably determine all transport, thermodynamic, and kinetic parameters as confirmed experimentally for rapid ET reactions of ferrocenemethanol and 7,7,8,8-tetracyanoquinodimethane at a Pt substrate with ∼0.5 μm-radius Pt tips positioned at 90 nm-1 μm distances. Standard ET rate constants of ∼7 cm/s were obtained for the latter mediator as the largest determined for a substrate reaction by SECM. Various potential applications of quasi-steady-state voltammetry are also proposed.

Implications of steady-state operation on divertor design

International Nuclear Information System (INIS)

Sevier, D.L.; Reis, E.E.; Baxi, C.B.; Silke, G.W.; Wong, C.P.C.; Hill, D.N.

1996-01-01

As fusion experiments progress towards long pulse or steady state operation, plasma facing components are undergoing a significant change in their design. This change represents the transition from inertially cooled pulsed systems to steady state designs of significant power handling capacity. A limited number of Plasma Facing Component (PFC) systems are in operation or planning to address this steady state challenge at low heat flux. However in most divertor designs components are required to operate at heat fluxes at 5 MW/m 2 or above. The need for data in this area has resulted in a significant amount of thermal/hydraulic and thermal fatigue testing being done on prototypical elements. Short pulse design solutions are not adequate for longer pulse experiments and the areas of thermal design, structural design, material selection, maintainability, and lifetime prediction are undergoing significant changes. A prudent engineering approach will guide us through the transitional phase of divertor design to steady-state power plant components. This paper reviews the design implications in this transition to steady state machines and the status of the community efforts to meet evolving design requirements. 54 refs., 5 figs., 2 tabs

Kinetics of Single-Enzyme Reactions on Vesicles: Role of Substrate Aggregation

Science.gov (United States)

Zhdanov, Vladimir P.

2015-03-01

Enzymatic reactions occurring in vivo on lipid membranes can be influenced by various factors including macromolecular crowding in general and substrate aggregation in particular. In academic studies, the role of these factors can experimentally be clarified by tracking single-enzyme kinetics occurring on individual lipid vesicles. To extend the conceptual basis for such experiments, we analyze herein the corresponding kinetics mathematically with emphasis on the role of substrate aggregation. In general, the aggregation may occur on different length scales. Small aggregates may e.g. contain a few proteins or peptides while large aggregates may be mesoscopic as in the case of lipid domains which can be formed in the membranes composed of different lipids. We present a kinetic model describing comprehensively the effect of aggregation of the former type on the dependence of the reaction rate on substrate membrane concentration. The results obtained with physically reasonable parameters indicate that the aggregation-related deviations from the conventional Michaelis-Menten kinetics may be appreciable. Special Issue Comments: This theoretical article is focused on single-enzyme reactions occurring in parallel with substrate aggregation on individual vesicles. This subject is related to a few Special Issue articles concerning enzyme dynamics6,7 and function8 and mathematical aspects of stochastic kinetics.9

Steady-State Process Modelling

DEFF Research Database (Denmark)

Cameron, Ian; Gani, Rafiqul

2011-01-01

illustrate the “equation oriented” approach as well as the “sequential modular” approach to solving complex flowsheets for steady state applications. The applications include the Williams-Otto plant, the hydrodealkylation (HDA) of toluene, conversion of ethylene to ethanol and a bio-ethanol process....

Design of Infusion Schemes for Neuroreceptor Imaging: Application to [11C]Flumazenil-PET Steady-State Study

Directory of Open Access Journals (Sweden)

Ling Feng

2016-01-01

Full Text Available This study aims at developing a simulation system that predicts the optimal study design for attaining tracer steady-state conditions in brain and blood rapidly. Tracer kinetics was determined from bolus studies and used to construct the system. Subsequently, the system was used to design inputs for bolus infusion (BI or programmed infusion (PI experiments. Steady-state quantitative measurements can be made with one short scan and venous blood samples. The GABAA receptor ligand [C11]Flumazenil (FMZ was chosen for this purpose, as it lacks a suitable reference region. Methods. Five bolus [C11]FMZ-PET scans were conducted, based on which population-based PI and BI schemes were designed and tested in five additional healthy subjects. The design of a PI was assisted by an offline feedback controller. Results. The system could reproduce the measurements in blood and brain. With PI, [C11]FMZ steady state was attained within 40 min, which was 8 min earlier than the optimal BI (B/I ratio = 55 min. Conclusions. The system can design both BI and PI schemes to attain steady state rapidly. For example, subjects can be [C11]FMZ-PET scanned after 40 min of tracer infusion for 40 min with venous sampling and a straight-forward quantification. This simulation toolbox is available for other PET-tracers.

Steady-state and transient hydrocarbon production in graphite by low energy impact of atomic and molecular deuterium projectiles

International Nuclear Information System (INIS)

Zhang, H.; Meyer, F.W.

2009-01-01

We report measurements of steady-state yields of methyl, methane and heavier hydrocarbons for deuterium atomic and molecular ions incident on ATJ graphite, HOPG, and a-C:D thin films in the energy range 10-200 eV/D. The yields were determined using a QMS technique in conjunction with calibrated hydrocarbon leaks. We have also studied transient hydrocarbon production and hydrogen (deuterium) re-emission for 80 and 150 eV/D D + , D 2 + , and D 3 + projectiles incident on ATJ graphite surfaces pre-loaded to steady state by 20 eV/D beams of the corresponding species. Immediately after starting the higher-energy beams, transient hydrocarbon and D 2 re-emission yields significantly larger than steady-state values were observed, which exponentially decayed as a function of beam fluence. The initial yield values were related to the starting hydrocarbon and deuterium densities in the prepared sample, while the exponential decay constants provided information on the hydrocarbon kinetic release and hydrogen (deuterium) detrapping cross-sections.

Use of Mushroom Tyrosinase to Introduce Michaelis-Menten Enzyme Kinetics to Biochemistry Students

Science.gov (United States)

Flurkey, William H.; Inlow, Jennifer K.

2017-01-01

An inexpensive enzyme kinetics laboratory exercise for undergraduate biochemistry students is described utilizing tyrosinase from white button mushrooms. The exercise can be completed in one or two three-hour lab sessions. The optimal amounts of enzyme, substrate (catechol), and inhibitor (kojic acid) are first determined, and then kinetic data is…

Pellet injectors for steady state plasma fuelling

International Nuclear Information System (INIS)

Vinyar, I.; Geraud, A.; Yamada, H.; Lukin, A.; Sakamoto, R.; Skoblikov, S.; Umov, A.; Oda, Y.; Gros, G.; Krasilnikov, I.; Reznichenko, P.; Panchenko, V.

2005-01-01

Successful steady state operation of a fusion reactor should be supported by repetitive pellet injection of solidified hydrogen isotopes in order to produce high performance plasmas. This paper presents pneumatic pellet injectors and its implementation for long discharge on the LHD and TORE SUPRA, and a new centrifuge pellet injector test results. All injectors are fitted with screw extruders well suited for steady state operation

Probing the molecular mechanism of action of the HIV-1 reverse transcriptase inhibitor 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA) using pre-steady-state kinetics

Science.gov (United States)

Muftuoglu, Yagmur; Sohl, Christal D.; Mislak, Andrea C.; Mitsuya, Hiroaki; Sarafianos, Stefan G.; Anderson, Karen S.

2014-01-01

The novel antiretroviral 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA) is a potent nucleoside HIV-1 reverse transcriptase (RT) inhibitor (NRTI). Unlike other FDA-approved NRTIs, EFdA contains a 3′-hydroxyl. Pre-steady-state kinetics showed RT preferred incorporating EFdA-TP over native dATP. Moreover, RT slowly inserted nucleotides past an EFdA-terminated primer, resulting in delayed chain termination with unaffected fidelity. This is distinct from KP1212, another 3′-hydroxyl-containing RT inhibitor considered to promote viral lethal mutagenesis. New mechanistic features of RT inhibition by EFdA are revealed. PMID:24632447

Transition-state analysis of a Vmax mutant of AMP nucleosidase by the application of heavy-atom kinetic isotope effects

International Nuclear Information System (INIS)

Parkin, D.W.; Mentch, F.; Banks, G.A.; Horenstein, B.A.; Schramm, V.L.

1991-01-01

The transition state of the V max mutant of AMP nucleosidase from Azotobacter vinelandii has been characterized by heavy-atom kinetic isotope effects in the presence and absence of MgATP, the allosteric activator. The enzyme catalyzes hydrolysis of the N-glycosidic bond of AMP at approximately 2% of the rate of the normal enzyme with only minor changes in the K m for substrate, the activation constant for MgATP, and the K i for formycin 5'-phosphate, a tight-binding competitive inhibitor. Isotope effects were measured as a function of the allosteric activator concentration that increases the turnover number of the enzyme from 0.006 s -1 . The kinetic isotope effects were measured with the substrates [1'- 3 H]AMP, [2'- 2 H]AMP, [9- 15 N]AMP, and [1',9- 14 C, 15 N]AMP. All substrates gave significant kinetic isotope effects in a pattern that establishes that the reaction expresses intrinsic kinetic isotope effects in the presence or absence of MgATP. Transition-state analysis using bond-energy and bond-order vibrational analysis indicated that the transition state for the mutant enzyme has a similar position in the reaction coordinate compared to that for the normal enzyme. The mutant enzyme is less effective in stabilizing the carbocation-like intermediate and in the ability to protonate N7 of adenine to create a better leaving group. This altered transition-state structure was confirmed by an altered substrate specificity for the mutant protein

A Hands-On Classroom Simulation to Demonstrate Concepts in Enzyme Kinetics

Science.gov (United States)

Junker, Matthew

2010-01-01

A classroom exercise is described to introduce enzyme kinetics in an undergraduate biochemistry or chemistry course. The exercise is a simulation in which a student acts as an enzyme that "catalyzes" the unscrewing of a nut from a bolt. With other students assisting, the student enzyme carries out reactions with bolt-nut substrates under different…

Automated Determination of Oxygen-Dependent Enzyme Kinetics in a Tube-in-Tube Flow Reactor.

Science.gov (United States)

Ringborg, Rolf H; Toftgaard Pedersen, Asbjørn; Woodley, John M

2017-09-08

Enzyme-mediated oxidation is of particular interest to synthetic organic chemists. However, the implementation of such systems demands knowledge of enzyme kinetics. Conventionally collecting kinetic data for biocatalytic oxidations is fraught with difficulties such as low oxygen solubility in water and limited oxygen supply. Here, we present a novel method for the collection of such kinetic data using a pressurized tube-in-tube reactor, operated in the low-dispersed flow regime to generate time-series data, with minimal material consumption. Experimental development and validation of the instrument revealed not only the high degree of accuracy of the kinetic data obtained, but also the necessity of making measurements in this way to enable the accurate evaluation of high K MO enzyme systems. For the first time, this paves the way to integrate kinetic data into the protein engineering cycle.

Steady-State Clozapine and Norclozapine Pharmacokinetics in Maori and European Patients.

Science.gov (United States)

Menkes, David B; Glue, Paul; Gale, Christopher; Lam, Frederic; Hung, Cheung-Tak; Hung, Noelyn

2018-01-01

Clozapine is the most effective drug for treatment-resistant schizophrenia, but its use is limited by toxicity. Because ethnicity has been reported to affect clozapine metabolism, we compared its steady state pharmacokinetics in New Zealand Maori and European patients. Clozapine and norclozapine steady state bioavailability was assessed over 24h under fasting and fed conditions in 12 Maori and 16 European patients treated for chronic psychotic illnesses with stable once-daily clozapine doses. Plasma clozapine and norclozapine concentrations were assessed using liquid chromatography with tandem mass spectrometry; pharmacokinetic parameters were calculated using standard non-compartmental methods, and compared using unpaired t-tests. Mean pharmacokinetic parameters (AUC, C max and C min ) for clozapine and norclozapine were virtually identical in Maori and European subjects, under both fed and fasted conditions. Clozapine bioavailability does not vary between Maori and European patients, and thus does not need to be considered in prescribing decisions. Additional studies are needed to identify if there are differences between Maori and European populations for drugs metabolized by other enzyme pathways. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

BR2 reactor core steady state transient modeling

International Nuclear Information System (INIS)

Makarenko, A.; Petrova, T.

2000-01-01

A coupled neutronics/hydraulics/heat-conduction model of the BR2 reactor core is under development at SCK-CEN. The neutron transport phenomenon has been implemented as steady state and time dependent nodal diffusion. The non-linear heat conduction equation in-side fuel elements is solved with a time dependent finite element method. To allow coupling between functional modules and to simulate subcooled regimes, a simple single-phase hydraulics has been introduced, while the two-phase hydraulics is under development. Multiple tests, general benchmark cases as well as calculation/experiment comparisons demonstrated a good accuracy of both neutronic and thermal hydraulic models, numerical reliability and full code portability. A refinement methodology has been developed and tested for better neutronic representation in hexagonal geometry. Much effort is still needed to complete the development of an extended cross section library with kinetic data and two-phase flow representation. (author)

Steady state compact toroidal plasma production

Science.gov (United States)

Turner, William C.

1986-01-01

Apparatus and method for maintaining steady state compact toroidal plasmas. A compact toroidal plasma is formed by a magnetized coaxial plasma gun and held in close proximity to the gun electrodes by applied magnetic fields or magnetic fields produced by image currents in conducting walls. Voltage supply means maintains a constant potential across the electrodes producing an increasing magnetic helicity which drives the plasma away from a minimum energy state. The plasma globally relaxes to a new minimum energy state, conserving helicity according to Taylor's relaxation hypothesis, and injecting net helicity into the core of the compact toroidal plasma. Controlling the voltage so as to inject net helicity at a predetermined rate based on dissipative processes maintains or increases the compact toroidal plasma in a time averaged steady state mode.

Proteomic analyses for profiling regulated proteins/enzymes by Fucus vesiculosus fucoidan in B16 melanoma cells: A combination of enzyme kinetics functional study.

Science.gov (United States)

Wang, Zhi-Jiang; Zheng, Li; Yang, Jun-Mo; Kang, Yani; Park, Yong-Doo

2018-06-01

Fucoidans are complex sulfated polysaccharides that have a wide range of biological activities. Previously, we reported the various effects of Fucus vesiculosus fucoidan on tyrosinase and B16 melanoma cells. In this study, to identify fucoidan-targeted proteins in B16 melanoma cells, we performed a proteomics study and integrated enzyme kinetics. We detected 19 candidate proteins dysregulated by fucoidan treatment. Among the probed proteins, the enzyme kinetics of two candidate enzymes, namely lactate dehydrogenase (LDH) as an upregulated protein and superoxide dismutase (SOD) as a downregulated enzyme, were determined. The enzyme kinetics results showed that Fucus vesiculosus fucoidan significantly inhibited LDH catalytic function while it did not affect SOD activity even at a high dose, while only slightly decreased activity (up to 10%) at a low dose. Based on our previous and present observations, fucoidan could inhibit B16 melanoma cells growth via regulating proteins/enzymes expression levels such as LDH and SOD known as cell survival biomarkers. Interestingly, both expression level and enzyme catalytic activity of LDH were regulated by fucoidan, which could directly induce the apoptotic effect on B16 melanoma cells along with SOD downregulation. This study highlights how combining proteomics with enzyme kinetics can yield valuable insights into fucoidan targets. Copyright © 2018 Elsevier B.V. All rights reserved.

Bioethanol from lignocellulose - pretreatment, enzyme immobilization and hydrolysis kinetics

DEFF Research Database (Denmark)

Tsai, Chien Tai

, the cost of enzyme is still the bottle neck, re-using the enzyme is apossible way to reduce the input of enzyme in the process. In the point view of engineering, the prediction of enzymatic hydrolysis kinetics under different substrate loading, enzyme combination is usful for process design. Therefore...... lignocellulose is the required high cellulase enzyme dosages that increase the processing costs. One method to decrease the enzyme dosage is to re-use BG, which hydrolyze the soluble substrate cellobiose. Based on the hypothesis that immobilized BG can be re-used, how many times the enzyme could be recycled...... liquid and pretreatment time can be reduced, the influence of substrate concentration, pretreatment time and temperature were investigated and optimized. Pretreatment of barley straw by [EMIM]Ac, correlative models were constructed using 3 different pretreatment parameters (temperature, time...

Modeling physiological processes in plankton on enzyme kinetic principles

Directory of Open Access Journals (Sweden)

Ted Packard

2004-04-01

Full Text Available Many ecologically important chemical transformations in the ocean are controlled by biochemical enzyme reactions in plankton. Nitrogenase regulates the transformation of N2 to ammonium in some cyanobacteria and serves as the entryway for N2 into the ocean biosphere. Nitrate reductase controls the reduction of NO3 to NO2 and hence new production in phytoplankton. The respiratory electron transfer system in all organisms links the carbon oxidation reactions of intermediary metabolism with the reduction of oxygen in respiration. Rubisco controls the fixation of CO2 into organic matter in phytoplankton and thus is the major entry point of carbon into the oceanic biosphere. In addition to these, there are the enzymes that control CO2 production, NH4 excretion and the fluxes of phosphate. Some of these enzymes have been recognized and researched by marine scientists in the last thirty years. However, until recently the kinetic principles of enzyme control have not been exploited to formulate accurate mathematical equations of the controlling physiological expressions. Were such expressions available they would increase our power to predict the rates of chemical transformations in the extracellular environment of microbial populations whether this extracellular environment is culture media or the ocean. Here we formulate from the principles of bisubstrate enzyme kinetics, mathematical expressions for the processes of NO3 reduction, O2 consumption, N2 fixation, total nitrogen uptake.

Steady-state molecular dynamics simulation of vapor to liquid nucleation with Mc Donald's demon

International Nuclear Information System (INIS)

Horsch, M.; Miroshnichenko, S.; Vrabec, J.

2009-01-01

Grand canonical MD with McDonald's demon is discussed in the present contribution and applied for sampling both nucleation kinetics and steady-state properties of a supersaturated vapor. The idea behind the new approach is to simulate the production of clusters up to a given size for a specified supersaturation. The classical nucleation theory is found to overestimate the free energy of cluster formation and deviate by two orders of magnitude from the nucleation rate below the triple point at high supersaturations.

Core signalling motif displaying multistability through multi-state enzymes

DEFF Research Database (Denmark)

Feng, Song; Saez Cornellana, Meritxell; Wiuf, Carsten Henrik

2016-01-01

Bistability, and more generally multistability, is a key system dynamics feature enabling decision-making and memory in cells. Deciphering the molecular determinants of multistability is thus crucial for a better understanding of cellular pathways and their (re)engineering in synthetic biology....... Here, we show that a key motif found predominantly in eukaryotic signalling systems, namely a futile signalling cycle, can display bistability when featuring a two-state kinase. We provide necessary and sufficient mathematical conditions on the kinetic parameters of this motif that guarantee...... the existence of multiple steady states. These conditions foster the intuition that bistability arises as a consequence of competition between the two states of the kinase. Extending from this result, we find that increasing the number of kinase states linearly translates into an increase in the number...

Interactions of solid and liquid lithium with steady state hydrogen and helium plasmas

International Nuclear Information System (INIS)

Hirooka, Y.; Nishikawa, M.; Ohgaki, H.; Ohtsuka, Y.

2005-01-01

A variety of innovative Plasma-Facing Component (PFC) concepts, employing moving solid or liquid surfaces, have recently been proposed in order to resolve technical issues, associated with the applications of currently used PFCs in future steady state fusion devices. As the first step to evaluate the concept using flowing-liquids for PFCs, steady state hydrogen and helium plasma interactions with solid and standing liquid lithium have been investigated in the present work, using the H α and He-I spectroscopy at the ion bombarding energies up to 150eV and at the lithium temperatures between room temperature and 480 deg C. Data indicate that hydrogen recycling over liquid lithium is clearly reduced, relative to that over solid lithium, whereas helium recycling does not show the same trend. From the kinetic analysis of these recycling time constant data, the activation energies for the overall recycling processes have been evaluated to be 0.02±0.01eV, both for hydrogen and helium plasmas. Also, it has been found that the activation energy is nearly independent of ion bombarding energy. (author)

Steady State Shift Damage Localization

DEFF Research Database (Denmark)

Sekjær, Claus; Bull, Thomas; Markvart, Morten Kusk

2017-01-01

The steady state shift damage localization (S3DL) method localizes structural deterioration, manifested as either a mass or stiffness perturbation, by interrogating the damage-induced change in the steady state vibration response with damage patterns cast from a theoretical model. Damage is, thus...... the required accuracy when examining complex structures, an extensive amount of degrees of freedom (DOF) must often be utilized. Since the interrogation matrix for each damage pattern depends on the size of the system matrices constituting the FE-model, the computational time quickly becomes of first......-order importance. The present paper investigates two sub-structuring approaches, in which the idea is to employ Craig-Bampton super-elements to reduce the amount of interrogation distributions while still providing an acceptable localization resolution. The first approach operates on a strict super-element level...

Quantum thermodynamics of nanoscale steady states far from equilibrium

Science.gov (United States)

Taniguchi, Nobuhiko

2018-04-01

We develop an exact quantum thermodynamic description for a noninteracting nanoscale steady state that couples strongly with multiple reservoirs. We demonstrate that there exists a steady-state extension of the thermodynamic function that correctly accounts for the multiterminal Landauer-Büttiker formula of quantum transport of charge, energy, or heat via the nonequilibrium thermodynamic relations. Its explicit form is obtained for a single bosonic or fermionic level in the wide-band limit, and corresponding thermodynamic forces (affinities) are identified. Nonlinear generalization of the Onsager reciprocity relations are derived. We suggest that the steady-state thermodynamic function is also capable of characterizing the heat current fluctuations of the critical transport where the thermal fluctuations dominate. Also, the suggested nonequilibrium steady-state thermodynamic relations seemingly persist for a spin-degenerate single level with local interaction.

Misconceptions regarding basic thermodynamics and enzyme kinetics have led to erroneous conclusions regarding the metabolic importance of lactate dehydrogenase isoenzyme expression.

Science.gov (United States)

Bak, Lasse K; Schousboe, Arne

2017-11-01

Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate involving the coenzyme NAD + . Part of the foundation for the proposed shuttling of lactate from astrocytes to neurons during brain activation is the differential distribution of LDH isoenzymes between the two cell types. In this short review, we outline the basic kinetic properties of the LDH isoenzymes expressed in neurons and astrocytes, and argue that the distribution of LDH isoenzymes does not in any way govern directional flow of lactate between the two cellular compartments. The two main points are as follows. First, in line with the general concept of chemical catalysis, enzymes do not influence the thermodynamic equilibrium of a chemical reaction but merely the speed at which equilibrium is obtained. Thus, differential distribution of LDH isoenzymes with different kinetic parameters does not predict which cells are producing and which are consuming lactate. Second, the thermodynamic equilibrium of the reaction is toward the reduced substrate (i.e., lactate), which is reflected in the concentrations measured in brain tissue, suggesting that the reaction is at near-equilibrium at steady state. To conclude, the cellular distribution of LDH isoenzymes is of little if any consequence in determining any directional flow of lactate between neurons and astrocytes. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Steady states in conformal theories

CERN Multimedia

CERN. Geneva

2015-01-01

A novel conjecture regarding the steady state behavior of conformal field theories placed between two heat baths will be presented. Some verification of the conjecture will be provided in the context of fluid dynamics and holography.

Enzyme kinetics of hevamine, a chitinase from the rubber tree Hevea brasiliensis

NARCIS (Netherlands)

Bokma, Evert; Barends, Thomas; Terwisscha van Scheltinga, Anke C.; Dijkstra, Bauke W.; Beintema, Jaap J.

2000-01-01

The enzyme kinetics of hevamine, a chitinase from the rubber tree Hevea brasiliensis, were studied in detail with a new enzyme assay. In this assay, the enzyme reaction products were derivatized by reductive coupling to a chromophore, Products mere separated by HPLC and the amount of product was

Differences between automatically detected and steady-state fractional flow reserve.

Science.gov (United States)

Härle, Tobias; Meyer, Sven; Vahldiek, Felix; Elsässer, Albrecht

2016-02-01

Measurement of fractional flow reserve (FFR) has become a standard diagnostic tool in the catheterization laboratory. FFR evaluation studies were based on pressure recordings during steady-state maximum hyperemia. Commercially available computer systems detect the lowest Pd/Pa ratio automatically, which might not always be measured during steady-state hyperemia. We sought to compare the automatically detected FFR and true steady-state FFR. Pressure measurement traces of 105 coronary lesions from 77 patients with intermediate coronary lesions or multivessel disease were reviewed. In all patients, hyperemia had been achieved by intravenous adenosine administration using a dosage of 140 µg/kg/min. In 42 lesions (40%) automatically detected FFR was lower than true steady-state FFR. Mean bias was 0.009 (standard deviation 0.015, limits of agreement -0.02, 0.037). In 4 lesions (3.8%) both methods lead to different treatment recommendations, in all 4 cases instantaneous wave-free ratio confirmed steady-state FFR. Automatically detected FFR was slightly lower than steady-state FFR in more than one-third of cases. Consequently, interpretation of automatically detected FFR values closely below the cutoff value requires special attention.

Steady state and transient power handling in JET

International Nuclear Information System (INIS)

Matthews, G.F.

2002-01-01

Recent JET experiments and analysis have demonstrated the importance of edge collisionality for the physics of divertor power loading both during and between ELMs. Since collisionality decreases strongly with machine size, JET routinely operates in an ITER relevant regime which is difficult or impossible to access in smaller devices. This new understanding has enabled us to develop more physically justifiable scalings for static and transient power deposition in ITER and demonstrates a need for kinetic models when simulating edge behaviour in JET and ITER. Steady state power loading in ITER is likely to be within limits provided that the divertor plasma is kept in the high recycling or detached regime. Extrapolations of the typical type I ELMs found in JET to ITER highlight the importance of developing regimes characterised by small ELMs, if surface ablation is to be avoided. Disruptive power loads measured in the JET divertor appear far more benign than would be expected from current ITER assumptions. (author)

New types of experimental data shape the use of enzyme kinetics for dynamic network modeling.

Science.gov (United States)

Tummler, Katja; Lubitz, Timo; Schelker, Max; Klipp, Edda

2014-01-01

Since the publication of Leonor Michaelis and Maude Menten's paper on the reaction kinetics of the enzyme invertase in 1913, molecular biology has evolved tremendously. New measurement techniques allow in vivo characterization of the whole genome, proteome or transcriptome of cells, whereas the classical enzyme essay only allows determination of the two Michaelis-Menten parameters V and K(m). Nevertheless, Michaelis-Menten kinetics are still commonly used, not only in the in vitro context of enzyme characterization but also as a rate law for enzymatic reactions in larger biochemical reaction networks. In this review, we give an overview of the historical development of kinetic rate laws originating from Michaelis-Menten kinetics over the past 100 years. Furthermore, we briefly summarize the experimental techniques used for the characterization of enzymes, and discuss web resources that systematically store kinetic parameters and related information. Finally, describe the novel opportunities that arise from using these data in dynamic mathematical modeling. In this framework, traditional in vitro approaches may be combined with modern genome-scale measurements to foster thorough understanding of the underlying complex mechanisms. © 2013 FEBS.

Steady State versus Pulsed Tokamak DEMO

Energy Technology Data Exchange (ETDEWEB)

Orsitto, F.P., E-mail: francesco.orsitto@enea.it [Associazione EURATOM-ENEA Unita Tecnica Fusione, Frascati (Italy); Todd, T. [CCFE/Fusion Association, Culham Science Centre, Abingdon (United Kingdom)

2012-09-15

Full text: The present report deals with a Review of problems for a Steady state(SS) DEMO, related argument is treated about the models and the present status of comparison between the characteristics of DEMO pulsed versus a Steady state device.The studied SS DEMO Models (SLIM CS, PPCS model C EU-DEMO, ARIES-RS) are analyzed from the point of view of the similarity scaling laws and critical issues for a steady state DEMO. A comparison between steady state and pulsed DEMO is therefore carried out: in this context a new set of parameters for a pulsed (6 - 8 hours pulse) DEMO is determined working below the density limit, peak temperature of 20 keV, and requiring a modest improvement in the confinement factor(H{sub IPBy2} = 1.1) with respect to the H-mode. Both parameters density and confinement parameter are lower than the DEMO models presently considered. The concept of partially non-inductive pulsed DEMO is introduced since a pulsed DEMO needs heating and current drive tools for plasma stability and burn control. The change of the main parameter design for a DEMO working at high plasma peak temperatures T{sub e} {approx} 35 keV is analyzed: in this range the reactivity increases linearly with temperature, and a device with smaller major radius (R = 7.5 m) is compatible with high temperature. Increasing temperature is beneficial for current drive efficiency and heat load on divertor, being the synchrotron radiation one of the relevant components of the plasma emission at high temperatures and current drive efficiency increases with temperature. Technology and engineering problems are examined including efficiency and availability R&D issues for a high temperature DEMO. Fatigue and creep-fatigue effects of pulsed operations on pulsed DEMO components are considered in outline to define the R&D needed for DEMO development. (author)

LANSCE steady state unperturbed thermal neutron fluxes at 100 μA

International Nuclear Information System (INIS)

Russell, G.J.

1989-01-01

The ''maximum'' unperturbed, steady state thermal neutron flux for LANSCE is calculated to be 2 /times/ 10 13 n/cm 2 -s for 100 μA of 800-MeV protons. This LANSCE neutron flux is a comparable entity to a steady state reactor thermal neutron flux. LANSCE perturbed steady state thermal neutron fluxes have also been calculated. Because LANSCE is a pulsed neutron source, much higher ''peak'' (in time) neutron fluxes can be generated than at a steady state reactor source. 5 refs., 5 figs

Steady-state kinetics of proguanil and its active metabolite, cycloguanil, in man.

Science.gov (United States)

Edstein, M D; Veenendaal, J R; Scott, H V; Rieckmann, K H

1988-01-01

The pharmacokinetics of proguanil and its active metabolite, cycloguanil, were determined at steady-state in 6 healthy male volunteers after daily administration of 2 Paludrine tablets (200 mg proguanil hydrochloride). A maximum plasma proguanil concentration of 130.3 +/- 16.0 ng/ml (mean +/- SD) was reached at 3.8 +/- 1.3 h while a maximum cycloguanil concentration of 52.0 +/- 15.2 ng/ml was obtained at 5.3 +/- 1.0 h after dosing. The elimination half-lives of proguanil and cycloguanil were 14.5 +/- 3.0 h and 11.7 +/- 3.1 h, respectively. The plasma clearance of proguanil was 1.43 +/- 0.33 l/h/kg and the apparent volume of distribution was 30.7 +/- 12.3 l/kg. Renal clearance of proguanil (0.33 +/- 0.19 l/h/kg) was about 23% of the plasma clearance and 35.6 +/- 9.6% of the oral dose was recovered as proguanil and cycloguanil.

An Integrated Circuit for Chip-Based Analysis of Enzyme Kinetics and Metabolite Quantification.

Science.gov (United States)

Cheah, Boon Chong; Macdonald, Alasdair Iain; Martin, Christopher; Streklas, Angelos J; Campbell, Gordon; Al-Rawhani, Mohammed A; Nemeth, Balazs; Grant, James P; Barrett, Michael P; Cumming, David R S

2016-06-01

We have created a novel chip-based diagnostic tools based upon quantification of metabolites using enzymes specific for their chemical conversion. Using this device we show for the first time that a solid-state circuit can be used to measure enzyme kinetics and calculate the Michaelis-Menten constant. Substrate concentration dependency of enzyme reaction rates is central to this aim. Ion-sensitive field effect transistors (ISFET) are excellent transducers for biosensing applications that are reliant upon enzyme assays, especially since they can be fabricated using mainstream microelectronics technology to ensure low unit cost, mass-manufacture, scaling to make many sensors and straightforward miniaturisation for use in point-of-care devices. Here, we describe an integrated ISFET array comprising 2(16) sensors. The device was fabricated with a complementary metal oxide semiconductor (CMOS) process. Unlike traditional CMOS ISFET sensors that use the Si3N4 passivation of the foundry for ion detection, the device reported here was processed with a layer of Ta2O5 that increased the detection sensitivity to 45 mV/pH unit at the sensor readout. The drift was reduced to 0.8 mV/hour with a linear pH response between pH 2-12. A high-speed instrumentation system capable of acquiring nearly 500 fps was developed to stream out the data. The device was then used to measure glucose concentration through the activity of hexokinase in the range of 0.05 mM-231 mM, encompassing glucose's physiological range in blood. Localised and temporal enzyme kinetics of hexokinase was studied in detail. These results present a roadmap towards a viable personal metabolome machine.

Enzyme activity and kinetics in substrate-amended river sediments

Energy Technology Data Exchange (ETDEWEB)

Duddridge, J E; Wainwright, M

1982-01-01

In determining the effects of heavy metals in microbial activity and litter degradation in river sediments, one approach is to determine the effects of these pollutants on sediment enzyme activity and synthesis. Methods to assay amylase, cellulase and urease activity in diverse river sediments are reported. Enzyme activity was low in non-amended sediments, but increased markedly when the appropriate substrate was added, paralleling both athropogenic and natural amendment. Linear relationships between enzyme activity, length of incubation, sample size and substrate concentration were established. Sediment enzyme activity generally obeyed Michaelis-Menton kinetics, but of the three enzymes, urease gave least significant correlation coefficients when the data for substrate concentration versus activity was applied to the Eadie-Hofstee transformation of the Michaelis-Menten equation. K/sub m/ and V/sub max/ for amylase, cellulase and urease in sediments are reported. (JMT)

Calculation analysis on steady state natural circulation characteristics

International Nuclear Information System (INIS)

Wang Fei; Nie Changhua; Huang Yanping

2005-01-01

The calculation results of single-phase steady state natural circulation characteristics by using Retran02 code have been presented, good agreement is achieved between the verified calculation result and the experimental data which were conducted at a test facility. Based on the calculation model, some sensibility analyses were made and much deeper understanding for single-phase steady state natural circulation characteristics was obtained. (author)

Selection of steady states in planar Darcy convection

International Nuclear Information System (INIS)

Tsybulin, V.G.; Karasoezen, B.; Ergenc, T.

2006-01-01

The planar natural convection of an incompressible fluid in a porous medium is considered. We study the selection of steady states under temperature perturbations on the boundary. A selection map is introduced in order to analyze the selection of a steady state from a continuous family of equilibria which exists under zero boundary conditions. The results of finite-difference modeling for a rectangular enclosure are presented

Steady-state oxygen-solubility in niobium

International Nuclear Information System (INIS)

Schulze, K.; Jehn, H.

1977-01-01

During annealing of niobium in oxygen in certain temperature and pressure ranges steady states are established between the absorption of molecular oxygen and the evaporation of volatile oxides. The oxygen concentration in the niobium-oxygen α-solid solution is a function of oxygen pressure and temperature and has been redetermined in the ranges 10 -5 - 10 -2 Pa O 2 and 2,070 - 2,470 K. It follows differing from former results the equation csub(o) = 9.1 x 10 -6 x sub(po2) x exp (502000/RT) with csub(o) in at.-ppm, sub(po2) in Pa, T in K, R = 8.31 J x mol -1 x K -1 . The existence of steady states is limited to a temperature range from 1870 to 2470 K and to oxygen concentrations below the solubility limit given by solidus and solvus lines in the T-c diagram. In the experiments high-purity niobium wires with a specific electrical ratio rho (273 K)/rho(4.2 K) > 5,000 have been gassed under isothermal-isobaric conditions until the steady state has been reached. The oxygen concentration has been determined analytically by vacuum fusion extraction with platinum-flux technique as well as by electrical residual resistivity measurements at 4.2 K. (orig.) [de

Steady-state entanglement activation in optomechanical cavities

Science.gov (United States)

Farace, Alessandro; Ciccarello, Francesco; Fazio, Rosario; Giovannetti, Vittorio

2014-02-01

Quantum discord, and related indicators, are raising a relentless interest as a novel paradigm of nonclassical correlations beyond entanglement. Here, we discover a discord-activated mechanism yielding steady-state entanglement production in a realistic continuous-variable setup. This comprises two coupled optomechanical cavities, where the optical modes (OMs) communicate through a fiber. We first use a simplified model to highlight the creation of steady-state discord between the OMs. We show next that such discord improves the level of stationary optomechanical entanglement attainable in the system, making it more robust against temperature and thermal noise.

Kinetics of leather dyeing pretreated with enzymes: role of acid protease.

Science.gov (United States)

Kanth, Swarna Vinodh; Venba, Rajangam; Jayakumar, Gladstone Christopher; Chandrababu, Narasimhan Kannan

2009-04-01

In the present investigation, kinetics of dyeing involving pretreatment with acid protease has been presented. Application of acid protease in dyeing process resulted in increased absorption and diffusion of dye into the leather matrix. Enzyme treatment at 1% concentration, 60 min duration and 50 degrees C resulted in maximum of 98% dye exhaustion and increased absorption rate constants. The final exhaustion (C(infinity)) for the best fit of CI Acid Black 194 dye has been 98.5% with K and r2 values from the modified Cegarra-Puente isotherm as 0.1033 and 0.0631. CI Acid Black 194 being a 2:1 metal complex acid dye exhibited higher absorption rate than the acid dye CI Acid Black 210. A reduction in 50% activation energy calculated from Arrhenius equation has been observed in enzyme assisted dyeing process of both the dyes that substantiates enhanced dye absorption. The absorption rate constant calculated with modified Cegarra-Puente equation confirm higher rate constants and faster kinetics for enzyme assisted dyeing process. Enzyme treated leather exhibited richness of color and shade when compared with control. The present study substantiates the essential role of enzyme pretreatment as an eco-friendly leather dyeing process.

Numerical method for three dimensional steady-state two-phase flow calculations

International Nuclear Information System (INIS)

Raymond, P.; Toumi, I.

1992-01-01

This paper presents the numerical scheme which was developed for the FLICA-4 computer code to calculate three dimensional steady state two phase flows. This computer code is devoted to steady state and transient thermal hydraulics analysis of nuclear reactor cores 1,3 . The first section briefly describes the FLICA-4 flow modelling. Then in order to introduce the numerical method for steady state computations, some details are given about the implicit numerical scheme based upon an approximate Riemann solver which was developed for calculation of flow transients. The third section deals with the numerical method for steady state computations, which is derived from this previous general scheme and its optimization. We give some numerical results for steady state calculations and comparisons on required CPU time and memory for various meshing and linear system solvers

Development of synchronous generator saturation model from steady-state operating data

Energy Technology Data Exchange (ETDEWEB)

Jadric, Martin; Despalatovic, Marin; Terzic, Bozo [FESB University of Split, Faculty of Electrical Engineering, Mechanical Engineering and Naval Architecture, Split (Croatia)

2010-11-15

A new method to estimate and model the saturated synchronous reactances of hydroturbine generators from operating data is presented. For the estimation process, measurements of only the generator steady-state variables are required. First, using a specific procedure, the field to armature turns ratio is estimated from measured steady-state variables at constant power generation and various excitation conditions. Subsequently, for each set of steady-state operating data, saturated synchronous reactances are identified. Fitting surfaces, defined as polynomial functions in two variables, are later used to model these saturated reactances. It is shown that the simpler polynomial functions may be used to model saturation at the steady-state than at the dynamic conditions. The developed steady-state model is validated with measurements performed on the 34 MVA hydroturbine generator. (author)

Steady state and transient critical heat flux examinations

International Nuclear Information System (INIS)

Szabados, L.

1978-02-01

In steady state conditions within the P.W.R. parameter range the critical heat flux correlations based on local parameters reproduce the experimental data with less deviations than those based on system parameters. The transient experiments were restricted for the case of power transients. A data processing method for critical heat flux measurements has been developed and the applicability of quasi steady state calculation has been verified. (D.P.)

The steady-state kinetics of the NADH-dependent nitrite reductase from Escherichia coli K 12. Nitrite and hydroxylamine reduction.

Science.gov (United States)

Jackson, R H; Cole, J A; Cornish-Bowden, A

1981-01-01

The reduction of both NO2- and hydroxylamine by the NADH-dependent nitrite reductase of Escherichia coli K 12 (EC 1.6.6.4) appears to follow Michaelis-Menten kinetics over a wide range of NADH concentrations. Substrate inhibition can, however, be detected at low concentrations of the product NAD+. In addition, NAD+ displays mixed product inhibition with respect to NADH and mixed or uncompetitive inhibition with respect to hydroxylamine. These inhibition characteristics are consistent with a mechanism in which hydroxylamine binds during catalysis to a different enzyme form from that generated when NAD+ is released. The apparent maximum velocity with NADH as varied substrate increases as the NAD+ concentration increases from 0.05 to 0.7 mM with 1 mM-NO2- or 100 mM-hydroxylamine as oxidized substrate. This increase is more marked for hydroxylamine reduction than for NO2- reduction. Models incorporating only one binding site for NAD can account for the variation in the Michaelis-Menten parameters for both NADH and hydroxylamine with [NAD+] for hydroxylamine reduction. According to these models, activation of the reaction occurs by reversal of an over-reduction of the enzyme by NADH. If the observed activation of the enzyme by NAD+ derives both from activation of the generation of the enzyme-hydroxylamine complex from the enzyme-NO2- complex during NO2- reduction and from activation of the reduction of the enzyme-hydroxylamine complex to form NH4+, then the variation of Vapp. for NO2- or hydroxylamine with [NAD+] is consistent with the occurrence of the same enzyme-hydroxylamine complex as an intermediate in both reactions. PMID:6279095

Measurement of Enzyme Kinetics by Use of a Blood Glucometer: Hydrolysis of Sucrose and Lactose

Science.gov (United States)

Heinzerling, Peter; Schrader, Frank; Schanze, Sascha

2012-01-01

An alternative analytical method for measuring the kinetic parameters of the enzymes invertase and lactase is described. Invertase hydrolyzes sucrose to glucose and fructose and lactase hydrolyzes lactose to glucose and galactose. In most enzyme kinetics studies, photometric methods or test strips are used to quantify the derivates of the…

The Markov process admits a consistent steady-state thermodynamic formalism

Science.gov (United States)

Peng, Liangrong; Zhu, Yi; Hong, Liu

2018-01-01

The search for a unified formulation for describing various non-equilibrium processes is a central task of modern non-equilibrium thermodynamics. In this paper, a novel steady-state thermodynamic formalism was established for general Markov processes described by the Chapman-Kolmogorov equation. Furthermore, corresponding formalisms of steady-state thermodynamics for the master equation and Fokker-Planck equation could be rigorously derived in mathematics. To be concrete, we proved that (1) in the limit of continuous time, the steady-state thermodynamic formalism for the Chapman-Kolmogorov equation fully agrees with that for the master equation; (2) a similar one-to-one correspondence could be established rigorously between the master equation and Fokker-Planck equation in the limit of large system size; (3) when a Markov process is restrained to one-step jump, the steady-state thermodynamic formalism for the Fokker-Planck equation with discrete state variables also goes to that for master equations, as the discretization step gets smaller and smaller. Our analysis indicated that general Markov processes admit a unified and self-consistent non-equilibrium steady-state thermodynamic formalism, regardless of underlying detailed models.

Contour analysis of steady state tokamak reactor performance

International Nuclear Information System (INIS)

Devoto, R.S.; Fenstermacher, M.E.

1990-01-01

A new method of analysis for presenting the possible operating space for steady state, non-ignited tokamak reactors is proposed. The method uses contours of reactor performance and plasma characteristics, fusion power gain, wall neutron flux, current drive power, etc., plotted on a two-dimensional grid, the axes of which are the plasma current I p and the normalized beta, β n = β/(I p /aB 0 ), to show possible operating points. These steady state operating contour plots are called SOPCONS. This technique is illustrated in an application to a design for the International Thermonuclear Experimental Reactor (ITER) with neutral beam, lower hybrid and bootstrap current drive. The utility of the SOPCON plots for pointing out some of the non-intuitive considerations in steady state reactor design is shown. (author). Letter-to-the-editor. 16 refs, 3 figs, 1 tab

Rate kernel theory for pseudo-first-order kinetics of diffusion-influenced reactions and application to fluorescence quenching kinetics.

Science.gov (United States)

Yang, Mino

2007-06-07

Theoretical foundation of rate kernel equation approaches for diffusion-influenced chemical reactions is presented and applied to explain the kinetics of fluorescence quenching reactions. A many-body master equation is constructed by introducing stochastic terms, which characterize the rates of chemical reactions, into the many-body Smoluchowski equation. A Langevin-type of memory equation for the density fields of reactants evolving under the influence of time-independent perturbation is derived. This equation should be useful in predicting the time evolution of reactant concentrations approaching the steady state attained by the perturbation as well as the steady-state concentrations. The dynamics of fluctuation occurring in equilibrium state can be predicted by the memory equation by turning the perturbation off and consequently may be useful in obtaining the linear response to a time-dependent perturbation. It is found that unimolecular decay processes including the time-independent perturbation can be incorporated into bimolecular reaction kinetics as a Laplace transform variable. As a result, a theory for bimolecular reactions along with the unimolecular process turned off is sufficient to predict overall reaction kinetics including the effects of unimolecular reactions and perturbation. As the present formulation is applied to steady-state kinetics of fluorescence quenching reactions, the exact relation between fluorophore concentrations and the intensity of excitation light is derived.

Modelling of different enzyme productions by solid-state fermentation on several agro-industrial residues.

Science.gov (United States)

Diaz, Ana Belen; Blandino, Ana; Webb, Colin; Caro, Ildefonso

2016-11-01

A simple kinetic model, with only three fitting parameters, for several enzyme productions in Petri dishes by solid-state fermentation is proposed in this paper, which may be a valuable tool for simulation of this type of processes. Basically, the model is able to predict temporal fungal enzyme production by solid-state fermentation on complex substrates, maximum enzyme activity expected and time at which these maxima are reached. In this work, several fermentations in solid state were performed in Petri dishes, using four filamentous fungi grown on different agro-industrial residues, measuring xylanase, exo-polygalacturonase, cellulose and laccase activities over time. Regression coefficients after fitting experimental data to the proposed model turned out to be quite high in all cases. In fact, these results are very interesting considering, on the one hand, the simplicity of the model and, on the other hand, that enzyme activities correspond to different enzymes, produced by different fungi on different substrates.

Solution of generalized control system equations at steady state

International Nuclear Information System (INIS)

Vilim, R.B.

1987-01-01

Although a number of reactor systems codes feature generalized control system models, none of the models offer a steady-state solution finder. Indeed, if a transient is to begin from steady-state conditions, the user must provide estimates for the control system initial conditions and run a null transient until the plant converges to steady state. Several such transients may have to be run before values for control system demand signals are found that produce the desired plant steady state. The intent of this paper is (a) to present the control system equations assumed in the SASSYS reactor systems code and to identify the appropriate set of initial conditions, (b) to describe the generalized block diagram approach used to represent these equations, and (c) to describe a solution method and algorithm for computing these initial conditions from the block diagram. The algorithm has been installed in the SASSYS code for use with the code's generalized control system model. The solution finder greatly enhances the effectiveness of the code and the efficiency of the user in running it

Steady-state spheromak reactor studies

International Nuclear Information System (INIS)

Krakowski, R.A.; Hagenson, R.L.

1985-01-01

After summarizing the essential elements of a gun-sustained spheromak, the potential for a steady-state is explored by means of a comprehensive physics/engineering/costing model. A range of cost-optimized reactor design points is presented, and the sensitivity of cost to key physics, engineering, and operational variables is reported

A Numerical Procedure for Model Identifiability Analysis Applied to Enzyme Kinetics

DEFF Research Database (Denmark)

Daele, Timothy, Van; Van Hoey, Stijn; Gernaey, Krist

2015-01-01

The proper calibration of models describing enzyme kinetics can be quite challenging. In the literature, different procedures are available to calibrate these enzymatic models in an efficient way. However, in most cases the model structure is already decided on prior to the actual calibration...... and Pronzato (1997) and which can be easily set up for any type of model. In this paper the proposed approach is applied to the forward reaction rate of the enzyme kinetics proposed by Shin and Kim(1998). Structural identifiability analysis showed that no local structural model problems were occurring......) identifiability problems. By using the presented approach it is possible to detect potential identifiability problems and avoid pointless calibration (and experimental!) effort....

High-throughput functional screening of steroid substrates with wild-type and chimeric P450 enzymes.

Science.gov (United States)

Urban, Philippe; Truan, Gilles; Pompon, Denis

2014-01-01

The promiscuity of a collection of enzymes consisting of 31 wild-type and synthetic variants of CYP1A enzymes was evaluated using a series of 14 steroids and 2 steroid-like chemicals, namely, nootkatone, a terpenoid, and mifepristone, a drug. For each enzyme-substrate couple, the initial steady-state velocity of metabolite formation was determined at a substrate saturating concentration. For that, a high-throughput approach was designed involving automatized incubations in 96-well microplate with sixteen 6-point kinetics per microplate and data acquisition using LC/MS system accepting 96-well microplate for injections. The resulting dataset was used for multivariate statistics aimed at sorting out the correlations existing between tested enzyme variants and ability to metabolize steroid substrates. Functional classifications of both CYP1A enzyme variants and steroid substrate structures were obtained allowing the delineation of global structural features for both substrate recognition and regioselectivity of oxidation.

Steady state of tapped granular polygons

International Nuclear Information System (INIS)

Carlevaro, Carlos M; Pugnaloni, Luis A

2011-01-01

The steady state packing fraction of a tapped granular bed is studied for different grain shapes via a discrete element method. Grains are monosized regular polygons, from triangles to icosagons. Comparisons with disc packings show that the steady state packing fraction as a function of the tapping intensity presents the same general trends in polygon packings. However, better packing fractions are obtained, as expected, for shapes that can tessellate the plane (triangles, squares and hexagons). In addition, we find a sharp transition for packings of polygons with more than 13 vertices signaled by a discontinuity in the packing fraction at a particular tapping intensity. Density fluctuations for most shapes are consistent with recent experimental findings in disc packing; however, a peculiar behavior is found for triangles and squares

Nonequilibrium steady states and resonant tunneling in time-periodically driven systems with interactions

Science.gov (United States)

Qin, Tao; Hofstetter, Walter

2018-03-01

Time-periodically driven systems are a versatile toolbox for realizing interesting effective Hamiltonians. Heating, caused by excitations to high-energy states, is a challenge for experiments. While most setups so far address the relatively weakly interacting regime, it is of general interest to study heating in strongly correlated systems. Using Floquet dynamical mean-field theory, we study nonequilibrium steady states (NESS) in the Falicov-Kimball model, with time-periodically driven kinetic energy or interaction. We systematically investigate the nonequilibrium properties of the NESS. For a driven kinetic energy, we show that resonant tunneling, where the interaction is an integer multiple of the driving frequency, plays an important role in the heating. In the strongly correlated regime, we show that this can be well understood using Fermi's golden rule and the Schrieffer-Wolff transformation for a time-periodically driven system. We furthermore demonstrate that resonant tunneling can be used to control the population of Floquet states to achieve "photodoping." For driven interactions introduced by an oscillating magnetic field near a widely adopted Feshbach resonance, we find that the double occupancy is strongly modulated. Our calculations apply to shaken ultracold-atom systems and to solid-state systems in a spatially uniform but time-dependent electric field. They are also closely related to lattice modulation spectroscopy. Our calculations are helpful to understand the latest experiments on strongly correlated Floquet systems.

Pre-steady-state kinetic studies of redox reactions catalysed by Bacillus subtilis ferredoxin-NADP(+) oxidoreductase with NADP(+)/NADPH and ferredoxin.

Science.gov (United States)

Seo, Daisuke; Soeta, Takahiro; Sakurai, Hidehiro; Sétif, Pierre; Sakurai, Takeshi

2016-06-01

Ferredoxin-NADP(+) oxidoreductase ([EC1.18.1.2], FNR) from Bacillus subtilis (BsFNR) is a homodimeric flavoprotein sharing structural homology with bacterial NADPH-thioredoxin reductase. Pre-steady-state kinetics of the reactions of BsFNR with NADP(+), NADPH, NADPD (deuterated form) and B. subtilis ferredoxin (BsFd) using stopped-flow spectrophotometry were studied. Mixing BsFNR with NADP(+) and NADPH yielded two types of charge-transfer (CT) complexes, oxidized FNR (FNR(ox))-NADPH and reduced FNR (FNR(red))-NADP(+), both having CT absorption bands centered at approximately 600n m. After mixing BsFNR(ox) with about a 10-fold molar excess of NADPH (forward reaction), BsFNR was almost completely reduced at equilibrium. When BsFNR(red) was mixed with NADP(+), the amount of BsFNR(ox) increased with increasing NADP(+) concentration, but BsFNR(red) remained as the major species at equilibrium even with about 50-fold molar excess NADP(+). In both directions, the hydride-transfer was the rate-determining step, where the forward direction rate constant (~500 s(-1)) was much higher than the reverse one (reaction. The characteristics of the BsFNR reactions with NADP(+)/NADPH were compared with those of other types of FNRs. Copyright © 2016 Elsevier B.V. All rights reserved.

Modeling nitrous oxide production and reduction in soil through explicit representation of denitrification enzyme kinetics.

Science.gov (United States)

Zheng, Jianqiu; Doskey, Paul V

2015-02-17

An enzyme-explicit denitrification model with representations for pre- and de novo synthesized enzymes was developed to improve predictions of nitrous oxide (N2O) accumulations in soil and emissions from the surface. The metabolic model of denitrification is based on dual-substrate utilization and Monod growth kinetics. Enzyme synthesis/activation was incorporated into each sequential reduction step of denitrification to regulate dynamics of the denitrifier population and the active enzyme pool, which controlled the rate function. Parameterizations were developed from observations of the dynamics of N2O production and reduction in soil incubation experiments. The model successfully reproduced the dynamics of N2O and N2 accumulation in the incubations and revealed an important regulatory effect of denitrification enzyme kinetics on the accumulation of denitrification products. Pre-synthesized denitrification enzymes contributed 20, 13, 43, and 62% of N2O that accumulated in 48 h incubations of soil collected from depths of 0-5, 5-10, 10-15, and 15-25 cm, respectively. An enzyme activity function (E) was defined to estimate the relative concentration of active enzymes and variation in response to environmental conditions. The value of E allows for activities of pre-synthesized denitrification enzymes to be differentiated from de novo synthesized enzymes. Incorporating explicit representations of denitrification enzyme kinetics into biogeochemical models is a promising approach for accurately simulating dynamics of the production and reduction of N2O in soils.

Calculations of steady-state and reactivity insertion transients in a research reactor simulating the PWR

International Nuclear Information System (INIS)

Mladin, Mirea; Mladin, Daniela; Prodea, Ilie

2010-01-01

In 2008, IAEA started a Coordinated Research Project for benchmarking the thermalhydraulic and neutronic computer codes for research reactor analysis against the experimental data. In this framework, for the first year of research contract, the Institute for Nuclear Research engaged in steady-state analysis of SPERT-III reactor and also in the simulation of the reactivity insertion tests performed in this reactor during mid sixties. In the first part, the paper describes a Monte Carlo input model of the oxide core selected for investigation and the results of the steady-state neutronic calculations with respect to hot and cold core reactivity excess and control rods worth. Also, prompt neutron life and reactivity feed-back coefficients were examined. These results were compared with the data provided in the reactor specification document concerning neutronic design calculated data. The second part of the paper is dedicated to calculation of the reactivity insertion transients with RELAP5 and CATHARE2 thermalhydraulic codes, both including point reactor kinetics models, and to comparison with experimental data. (authors)

Steady-state propagation of interface corner crack

DEFF Research Database (Denmark)

Veluri, Badrinath; Jensen, Henrik Myhre

2013-01-01

Steady-state propagation of interface cracks close to three-dimensional corners has been analyzed. Attention was focused on modeling the shape of the interface crack front and calculating the critical stress for steady-state propagation of the crack. The crack propagation was investigated...... on the finite element method with iterative adjustment of the crack front to estimate the critical delamination stresses as a function of the fracture criterion and corner angles. The implication of the results on the delamination is discussed in terms of crack front profiles and the critical stresses...... for propagation and the angle of intersection of the crack front with the free edge....

Steady-state leaching of tritiated water from silica gel

DEFF Research Database (Denmark)

Das, H.A.; Hou, Xiaolin

2009-01-01

Aqueous leaching of tritium from silica gel, loaded by absorption of water vapor, makes part of reactor de-commissioning. It is found to follow the formulation of steady-state diffusion.......Aqueous leaching of tritium from silica gel, loaded by absorption of water vapor, makes part of reactor de-commissioning. It is found to follow the formulation of steady-state diffusion....

Quasi steady-state aerodynamic model development for race vehicle simulations

Science.gov (United States)

Mohrfeld-Halterman, J. A.; Uddin, M.

2016-01-01

Presented in this paper is a procedure to develop a high fidelity quasi steady-state aerodynamic model for use in race car vehicle dynamic simulations. Developed to fit quasi steady-state wind tunnel data, the aerodynamic model is regressed against three independent variables: front ground clearance, rear ride height, and yaw angle. An initial dual range model is presented and then further refined to reduce the model complexity while maintaining a high level of predictive accuracy. The model complexity reduction decreases the required amount of wind tunnel data thereby reducing wind tunnel testing time and cost. The quasi steady-state aerodynamic model for the pitch moment degree of freedom is systematically developed in this paper. This same procedure can be extended to the other five aerodynamic degrees of freedom to develop a complete six degree of freedom quasi steady-state aerodynamic model for any vehicle.

SigrafW: An Easy-to-Use Program for Fitting Enzyme Kinetic Data

Science.gov (United States)

Leone, Francisco Assis; Baranauskas, Jose Augusto; Furriel, Rosa Prazeres Melo; Borin, Ivana Aparecida

2005-01-01

SigrafW is Windows-compatible software developed using the Microsoft[R] Visual Basic Studio program that uses the simplified Hill equation for fitting kinetic data from allosteric and Michaelian enzymes. SigrafW uses a modified Fibonacci search to calculate maximal velocity (V), the Hill coefficient (n), and the enzyme-substrate apparent…

Realizing steady-state tokamak operation for fusion energy

International Nuclear Information System (INIS)

Luce, T. C.

2011-01-01

Continuous operation of a tokamak for fusion energy has clear engineering advantages but requires conditions beyond those sufficient for a burning plasma. The fusion reactions and external sources must support both the pressure and the current equilibrium without inductive current drive, leading to demands on stability, confinement, current drive, and plasma-wall interactions that exceed those for pulsed tokamaks. These conditions have been met individually, and significant progress has been made in the past decade to realize scenarios where the required conditions are obtained simultaneously. Tokamaks are operated routinely without disruptions near pressure limits, as needed for steady-state operation. Fully noninductive sustainment with more than half of the current from intrinsic currents has been obtained for a resistive time with normalized pressure and confinement approaching those needed for steady-state conditions. One remaining challenge is handling the heat and particle fluxes expected in a steady-state tokamak without compromising the core plasma performance.

Steady State Advanced Tokamak (SSAT): The mission and the machine

International Nuclear Information System (INIS)

Thomassen, K.; Goldston, R.; Nevins, B.; Neilson, H.; Shannon, T.; Montgomery, B.

1992-03-01

Extending the tokamak concept to the steady state regime and pursuing advances in tokamak physics are important and complementary steps for the magnetic fusion energy program. The required transition away from inductive current drive will provide exciting opportunities for advances in tokamak physics, as well as important impetus to drive advances in fusion technology. Recognizing this, the Fusion Policy Advisory Committee and the US National Energy Strategy identified the development of steady state tokamak physics and technology, and improvements in the tokamak concept, as vital elements in the magnetic fusion energy development plan. Both called for the construction of a steady state tokamak facility to address these plan elements. Advances in physics that produce better confinement and higher pressure limits are required for a similar unit size reactor. Regimes with largely self-driven plasma current are required to permit a steady-state tokamak reactor with acceptable recirculating power. Reliable techniques of disruption control will be needed to achieve the availability goals of an economic reactor. Thus the central role of this new tokamak facility is to point the way to a more attractive demonstration reactor (DEMO) than the present data base would support. To meet the challenges, we propose a new ''Steady State Advanced Tokamak'' (SSAT) facility that would develop and demonstrate optimized steady state tokamak operating mode. While other tokamaks in the world program employ superconducting toroidal field coils, SSAT would be the first major tokamak to operate with a fully superconducting coil set in the elongated, divertor geometry planned for ITER and DEMO

Assessing Quasi-Steady State in Evaporation of Sessile Drops by Diffusion Models

Science.gov (United States)

Martin, Cameron; Nguyen, Hoa; Kelly-Zion, Peter; Pursell, Chris

2017-11-01

The vapor distributions surrounding sessile drops of methanol are modeled as the solutions of the steady-state and transient diffusion equations using Matlab's PDE Toolbox. The goal is to determine how quickly the transient diffusive transport reaches its quasi-steady state as the droplet geometry is varied between a Weber's disc, a real droplet shape, and a spherical cap with matching thickness or contact angle. We assume that the only transport mechanism at work is diffusion. Quasi-steady state is defined using several metrics, such as differences between the transient and steady-state solutions, and change in the transient solution over time. Knowing the vapor distribution, the gradient is computed to evaluate the diffusive flux. The flux is integrated along the surface of a control volume surrounding the drop to obtain the net rate of diffusion out of the volume. Based on the differences between the transient and steady-state diffusive fluxes at the discrete points along the control-volume surface, the time to reach quasi-steady state evaporation is determined and is consistent with other proposed measurements. By varying the dimensions of the control volume, we can also assess what regimes have equivalent or different quasi-steady states for different droplet geometries. Petroleum Research Fund.

Structural and Kinetic Properties of the Aldehyde Dehydrogenase NahF, a Broad Substrate Specificity Enzyme for Aldehyde Oxidation.

Science.gov (United States)

Coitinho, Juliana B; Pereira, Mozart S; Costa, Débora M A; Guimarães, Samuel L; Araújo, Simara S; Hengge, Alvan C; Brandão, Tiago A S; Nagem, Ronaldo A P

2016-09-27

The salicylaldehyde dehydrogenase (NahF) catalyzes the oxidation of salicylaldehyde to salicylate using NAD(+) as a cofactor, the last reaction of the upper degradation pathway of naphthalene in Pseudomonas putida G7. The naphthalene is an abundant and toxic compound in oil and has been used as a model for bioremediation studies. The steady-state kinetic parameters for oxidation of aliphatic or aromatic aldehydes catalyzed by 6xHis-NahF are presented. The 6xHis-NahF catalyzes the oxidation of aromatic aldehydes with large kcat/Km values close to 10(6) M(-1) s(-1). The active site of NahF is highly hydrophobic, and the enzyme shows higher specificity for less polar substrates than for polar substrates, e.g., acetaldehyde. The enzyme shows α/β folding with three well-defined domains: the oligomerization domain, which is responsible for the interlacement between the two monomers; the Rossmann-like fold domain, essential for nucleotide binding; and the catalytic domain. A salicylaldehyde molecule was observed in a deep pocket in the crystal structure of NahF where the catalytic C284 and E250 are present. Moreover, the residues G150, R157, W96, F99, F274, F279, and Y446 were thought to be important for catalysis and specificity for aromatic aldehydes. Understanding the molecular features responsible for NahF activity allows for comparisons with other aldehyde dehydrogenases and, together with structural information, provides the information needed for future mutational studies aimed to enhance its stability and specificity and further its use in biotechnological processes.

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

Science.gov (United States)

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

2011-07-01

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

Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate.

Science.gov (United States)

Tian, Yang; Suk, Dae-Hwan; Cai, Feng; Crich, David; Mesecar, Andrew D

2008-11-25

o-Succinylbenzoyl-CoA (OSB-CoA) synthetase (EC 6.2.1.26) catalyzes the ATP-dependent condensation of o-succinylbenzoate (OSB) and CoA to form OSB-CoA, the fourth step of the menaquinone biosynthetic pathway in Bacillus anthracis. Gene knockout studies have highlighted this enzyme as a potential target for the discovery of new antibiotics. Here we report the first studies on the kinetic mechanism of B. anthracis OSB-CoA synthetase, classifying it as an ordered bi uni uni bi ping-pong mechanism. Through a series of pre-steady-state and steady-state kinetic studies in conjunction with direct binding studies, it is demonstrated that CoA, the last substrate to bind, strongly activates the first half-reaction after the first round of turnover. The activation of the first half-reaction is most likely achieved by CoA stabilizing conformations of the enzyme in the "F" form, which slowly isomerize back to the E form. Thus, the kinetic mechanism of OSB-CoA synthetase may be more accurately described as an ordered bi uni uni bi iso ping-pong mechanism. The substrate specificity of OSB-CoA synthetase was probed using a series of OSB analogues with alterations in the carboxylate groups. OSB-CoA shows a strong preference for OSB over all of the analogues tested as none were active except 4-[2-(trifluoromethyl)phenyl]-4-oxobutyric acid which exhibited a 100-fold decrease in k(cat)/K(m). On the basis of an understanding of OSB-CoA synthetase's kinetic mechanism and substrate specificity, a reaction intermediate analogue of OSB-AMP, 5'-O-{N-[2-(trifluoromethyl)phenyl]-4-oxobutyl}adenosine sulfonamide (TFMP-butyl-AMS), was designed and synthesized. This inhibitor was found to be an uncompetitive inhibitor to CoA and a mixed-type inhibitor to ATP and OSB with low micromolar inhibition constants. Collectively, these results should serve as an important forerunner to more detailed and extensive inhibitor design studies aimed at developing lead compounds against the OSB-CoA synthetase

Steady state theta pinch concept for slow formation of FRC

International Nuclear Information System (INIS)

Hirano, K.

1987-05-01

A steady state high beta plasma flow through a channel along the magnetic field increasing downstream can be regarded as a ''steady state theta pinch'', because if we see the plasma riding on the flow we should observe very similar process taking place in a theta pinch. Anticipating to produce an FRC without using very high voltage technics such as the ones required in a conventional theta pinch, we have studied after the analogy a ''steady state reversed field theta pinch'' which is brought about by steady head-on collision of counter plasma streams along the channel as ejected from two identical co-axial plasma sources mounted at the both ends of the apparatus. The ideal Poisson and shock adiabatic flow models are employed for the analysis of the steady colliding process. It is demonstrated that an FRC involving large numbers of particles is produced only by the weak shock mode which is achieved in case energetic plasma flow is decelerated almost to be stagnated through Poisson adiabatic process before the streams are collided. (author)

A new perspective on steady-state cosmology: from Einstein to Hoyle

OpenAIRE

O'Raifeartaigh, Cormac; Mitton, Simon

2015-01-01

We recently reported the discovery of an unpublished manuscript by Albert Einstein in which he attempted a 'steady-state' model of the universe, i.e., a cosmic model in which the expanding universe remains essentially unchanged due to a continuous formation of matter from empty space. The manuscript was apparently written in early 1931, many years before the steady-state models of Fred Hoyle, Hermann Bondi and Thomas Gold. We compare Einstein’s steady-state cosmology with that of Hoyle, Bondi...

Spectroscopic and Kinetic Characterization of Peroxidase-Like π-Cation Radical Pinch-Porphyrin-Iron(III Reaction Intermediate Models of Peroxidase Enzymes

Directory of Open Access Journals (Sweden)

Samuel Hernández Anzaldo

2016-06-01

Full Text Available The spectroscopic and kinetic characterization of two intermediates from the H2O2 oxidation of three dimethyl ester [(proto, (meso, (deuteroporphyrinato (picdien]Fe(III complexes ([FePPPic], [FeMPPic] and [FeDPPic], respectively pinch-porphyrin peroxidase enzyme models, with s = 5/2 and 3/2 Fe(III quantum mixed spin (qms ground states is described herein. The kinetic study by UV/Vis at λmax = 465 nm showed two different types of kinetics during the oxidation process in the guaiacol test for peroxidases (1–3 + guaiacol + H2O2 → oxidation guaiacol products. The first intermediate was observed during the first 24 s of the reaction. When the reaction conditions were changed to higher concentration of pinch-porphyrins and hydrogen peroxide only one type of kinetics was observed. Next, the reaction was performed only between pinch-porphyrins-Fe(III and H2O2, resulting in only two types of kinetics that were developed during the first 0–4 s. After this time a self-oxidation process was observed. Our hypotheses state that the formation of the π-cation radicals, reaction intermediates of the pinch-porphyrin-Fe(III family with the ligand picdien [N,N’-bis-pyridin-2-ylmethyl-propane-1,3-diamine], occurred with unique kinetics that are different from the overall process and was involved in the oxidation pathway. UV-Vis, 1H-NMR and ESR spectra confirmed the formation of such intermediates. The results in this paper highlight the link between different spectroscopic techniques that positively depict the kinetic traits of artificial compounds with enzyme-like activity.

High-Throughput Functional Screening of Steroid Substrates with Wild-Type and Chimeric P450 Enzymes

Directory of Open Access Journals (Sweden)

Philippe Urban

2014-01-01

Full Text Available The promiscuity of a collection of enzymes consisting of 31 wild-type and synthetic variants of CYP1A enzymes was evaluated using a series of 14 steroids and 2 steroid-like chemicals, namely, nootkatone, a terpenoid, and mifepristone, a drug. For each enzyme-substrate couple, the initial steady-state velocity of metabolite formation was determined at a substrate saturating concentration. For that, a high-throughput approach was designed involving automatized incubations in 96-well microplate with sixteen 6-point kinetics per microplate and data acquisition using LC/MS system accepting 96-well microplate for injections. The resulting dataset was used for multivariate statistics aimed at sorting out the correlations existing between tested enzyme variants and ability to metabolize steroid substrates. Functional classifications of both CYP1A enzyme variants and steroid substrate structures were obtained allowing the delineation of global structural features for both substrate recognition and regioselectivity of oxidation.

Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics

Energy Technology Data Exchange (ETDEWEB)

Li, Minjing [School; Qian, Wei-jun [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Gao, Yuqian [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Shi, Liang [School; Liu, Chongxuan [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; School

2017-09-28

The kinetics of biogeochemical processes in natural and engineered environmental systems are typically described using Monod-type or modified Monod-type models. These models rely on biomass as surrogates for functional enzymes in microbial community that catalyze biogeochemical reactions. A major challenge to apply such models is the difficulty to quantitatively measure functional biomass for constraining and validating the models. On the other hand, omics-based approaches have been increasingly used to characterize microbial community structure, functions, and metabolites. Here we proposed an enzyme-based model that can incorporate omics-data to link microbial community functions with biogeochemical process kinetics. The model treats enzymes as time-variable catalysts for biogeochemical reactions and applies biogeochemical reaction network to incorporate intermediate metabolites. The sequences of genes and proteins from metagenomes, as well as those from the UniProt database, were used for targeted enzyme quantification and to provide insights into the dynamic linkage among functional genes, enzymes, and metabolites that are necessary to be incorporated in the model. The application of the model was demonstrated using denitrification as an example by comparing model-simulated with measured functional enzymes, genes, denitrification substrates and intermediates

Soluble and immobilized catalase. Effect of pressure and inhibition on kinetics and deactivation.

Science.gov (United States)

Vasudevan, P T; Thakur, D S

1994-12-01

This article examines the effect of pressure on the steady-state kinetics and long-term deactivation of the enzyme catalase supported on porous alumina. The reaction studied is the decomposition of hydrogen peroxide. The results of studies carried out in a continuous stirred-tank reactor under isothermal conditions are presented and compared with results obtained for soluble catalase. For soluble catalase, it is found that in the range of pressures studied, the oxygen flow rate increases with increase in pressure up to a certain value and then decreases. Hydrogen peroxide concentration appears to have a strong influence on pressure effects. With immobilized catalase, the pressure effects are not as prominent. Fluorescent microscopy studies of the immobilized enzyme suggest that this is probably because of pore diffusional limitations.

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

Science.gov (United States)

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

2014-01-01

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

Empirical evaluation of a virtual laboratory approach to teach lactate dehydrogenase enzyme kinetics.

Science.gov (United States)

Booth, Christine; Cheluvappa, Rajkumar; Bellinson, Zack; Maguire, Danni; Zimitat, Craig; Abraham, Joyce; Eri, Rajaraman

2016-06-01

Personalised instruction is increasingly recognised as crucial for efficacious learning today. Our seminal work delineates and elaborates on the principles, development and implementation of a specially-designed adaptive, virtual laboratory. We strived to teach laboratory skills associated with lactate dehydrogenase (LDH) enzyme kinetics to 2nd-year biochemistry students using our adaptive learning platform. Pertinent specific aims were to:(1)design/implement a web-based lesson to teach lactate dehydrogenase(LDH) enzyme kinetics to 2nd-year biochemistry students(2)determine its efficacious in improving students' comprehension of enzyme kinetics(3)assess their perception of its usefulness/manageability(vLab versus Conventional Tutorial). Our tools were designed using HTML5 technology. We hosted the program on an adaptive e-learning platform (AeLP). Provisions were made to interactively impart informed laboratory skills associated with measuring LDH enzyme kinetics. A series of e-learning methods were created. Tutorials were generated for interactive teaching and assessment. The learning outcomes herein were on par with that from a conventional classroom tutorial. Student feedback showed that the majority of students found the vLab learning experience "valuable"; and the vLab format/interface "well-designed". However, there were a few technical issues with the 1st roll-out of the platform. Our pioneering effort resulted in productive learning with the vLab, with parity with that from a conventional tutorial. Our contingent discussion emphasises not only the cornerstone advantages, but also the shortcomings of the AeLP method utilised. We conclude with an astute analysis of possible extensions and applications of our methodology.

Toroidal visco-resistive magnetohydrodynamic steady states contain vortices

International Nuclear Information System (INIS)

Bates, J.W.; Montgomery, D.C.

1998-01-01

Poloidal velocity fields seem to be a fundamental feature of resistive toroidal magnetohydrodynamic (MHD) steady states. They are a consequence of force balance in toroidal geometry, do not require any kind of instability, and disappear in the open-quotes straight cylinderclose quotes (infinite aspect ratio) limit. If a current density j results from an axisymmetric toroidal electric field that is irrotational inside a torus, it leads to a magnetic field B such that ∇x(jxB) is nonvanishing, so that the Lorentz force cannot be balanced by the gradient of any scalar pressure in the equation of motion. In a steady state, finite poloidal velocity fields and toroidal vorticity must exist. Their calculation is difficult, but explicit solutions can be found in the limit of low Reynolds number. Here, existing calculations are generalized to the more realistic case of no-slip boundary conditions on the velocity field and a circular toroidal cross section. The results of this paper strongly suggest that discussions of confined steady states in toroidal MHD must include flows from the outset. copyright 1998 American Institute of Physics

Transient and steady-state currents in epoxy resin

International Nuclear Information System (INIS)

Guillermin, Christophe; Rain, Pascal; Rowe, Stephen W

2006-01-01

Charging and discharging currents have been measured in a diglycidyl ether of bisphenol-A epoxy resin with and without silica fillers, below and above its glass transition temperature T g = 65 deg. C. Both transient and steady-state current densities have been analysed. The average applied fields ranged from 3 to 35 kV mm -1 with a sample thickness of 0.5 mm. Above T g , transient currents suggested a phenomenon of charge injection forming trapped space charges even at low fields. Steady-state currents confirmed that the behaviour was not Ohmic and suggested Schottky-type injection. Below T g , the current is not controlled by the metal-dielectric interface but by the conduction in the volume: the current is Ohmic at low fields and both transient and steady-state currents suggest a phenomenon of space-charge limited currents at high fields. The field threshold is similar in the filler-free and the filled resin. Values in the range 12-17 kV mm -1 have been measured

Transient and steady-state currents in epoxy resin

Energy Technology Data Exchange (ETDEWEB)

Guillermin, Christophe [Schneider Electric Industries S.A.S., 37 quai Paul-Louis Merlin, 38050 Grenoble Cedex 9 (France); Rain, Pascal [Laboratoire d' Electrostatique et de Materiaux Dielectriques (LEMD), CNRS, 25 avenue des Martyrs, 38042 Grenoble Cedex 9 (France); Rowe, Stephen W [Schneider Electric Industries S.A.S., 37 quai Paul-Louis Merlin, 38050 Grenoble Cedex 9 (France)

2006-02-07

Charging and discharging currents have been measured in a diglycidyl ether of bisphenol-A epoxy resin with and without silica fillers, below and above its glass transition temperature T{sub g} = 65 deg. C. Both transient and steady-state current densities have been analysed. The average applied fields ranged from 3 to 35 kV mm{sup -1} with a sample thickness of 0.5 mm. Above T{sub g}, transient currents suggested a phenomenon of charge injection forming trapped space charges even at low fields. Steady-state currents confirmed that the behaviour was not Ohmic and suggested Schottky-type injection. Below T{sub g}, the current is not controlled by the metal-dielectric interface but by the conduction in the volume: the current is Ohmic at low fields and both transient and steady-state currents suggest a phenomenon of space-charge limited currents at high fields. The field threshold is similar in the filler-free and the filled resin. Values in the range 12-17 kV mm{sup -1} have been measured.

Efficient steady-state solver for hierarchical quantum master equations

Science.gov (United States)

Zhang, Hou-Dao; Qiao, Qin; Xu, Rui-Xue; Zheng, Xiao; Yan, YiJing

2017-07-01

Steady states play pivotal roles in many equilibrium and non-equilibrium open system studies. Their accurate evaluations call for exact theories with rigorous treatment of system-bath interactions. Therein, the hierarchical equations-of-motion (HEOM) formalism is a nonperturbative and non-Markovian quantum dissipation theory, which can faithfully describe the dissipative dynamics and nonlinear response of open systems. Nevertheless, solving the steady states of open quantum systems via HEOM is often a challenging task, due to the vast number of dynamical quantities involved. In this work, we propose a self-consistent iteration approach that quickly solves the HEOM steady states. We demonstrate its high efficiency with accurate and fast evaluations of low-temperature thermal equilibrium of a model Fenna-Matthews-Olson pigment-protein complex. Numerically exact evaluation of thermal equilibrium Rényi entropies and stationary emission line shapes is presented with detailed discussion.

Steady state flow evaluations for passive auxiliary feedwater system of APR

International Nuclear Information System (INIS)

Park, Jongha; Kim, Jaeyul; Seong, Hoje; Kang, Kyoungho

2012-01-01

This paper briefly introduces a methodology to evaluate steady state flow of APR+ Passive Auxiliary Feedwater System (PAFS). The PAFS is being developed as a safety grade passive system to completely replace the existing active Auxiliary Feedwater System (AFWS). Natural circulation cooling can be generally classified into the single-phase, two-phase, and boiling-condensation modes. The PAF is designed to be operated in a boiling-condensation natural circulation mode. The steady-state flow rate should be equal to the steady-state boiling/condensation rate determined by the steady-state energy and momentum balances in the PAFS. The determined steady-state flow rate can be used in the design optimization for the natural circulation loop of the PAFS through the steady-state momentum balance. Since the retarding force, which is to be balanced by the driving force in the natural circulation system design depends on the reliable evaluation of the success of a natural circulation system design depends on the reliable evaluation of the pressure loss coefficients. In PAFS, the core decay heat is released by natural circulation flow between the S G secondary side and the Passive Condensation Heat Exchanger (PCHX) that is immersed in the Passive Condensation Cooling Tank (PCCT). The PCCT is located on the top of Auxiliary building The driving force is determined by the difference between the S/G (heat Source) secondary water level and condensation liquid (heat sink) level. It will overcome retarding force at flowrate in the system, which is determined by vaporization and condensation of the steam which is generated at the S/G by the latent heat in system. In this study, the theoretical method to estimate the steady state flow rate in boiling-condensation natural circulation system is developed and compared with test results

Einstein's steady-state theory: an abandoned model of the cosmos

Science.gov (United States)

O'Raifeartaigh, Cormac; McCann, Brendan; Nahm, Werner; Mitton, Simon

2014-09-01

We present a translation and analysis of an unpublished manuscript by Albert Einstein in which he attempted to construct a `steady-state' model of the universe. The manuscript, which appears to have been written in early 1931, demonstrates that Einstein once explored a cosmic model in which the mean density of matter in an expanding universe is maintained constant by the continuous formation of matter from empty space. This model is very different to previously known Einsteinian models of the cosmos (both static and dynamic) but anticipates the later steady-state cosmology of Hoyle, Bondi and Gold in some ways. We find that Einstein's steady-state model contains a fundamental flaw and suggest that it was abandoned for this reason. We also suggest that he declined to explore a more sophisticated version because he found such theories rather contrived. The manuscript is of historical interest because it reveals that Einstein debated between steady-state and evolving models of the cosmos decades before a similar debate took place in the cosmological community.

Steady state in a gas of inelastic rough spheres heated by a uniform stochastic force

Energy Technology Data Exchange (ETDEWEB)

Vega Reyes, Francisco, E-mail: fvega@unex.es; Santos, Andrés, E-mail: andres@unex.es [Departamento de Física and Instituto de Computación Científica Avanzada (ICCAEx), Universidad de Extremadura, 06071 Badajoz (Spain)

2015-11-15

We study here the steady state attained in a granular gas of inelastic rough spheres that is subject to a spatially uniform random volume force. The stochastic force has the form of the so-called white noise and acts by adding impulse to the particle translational velocities. We work out an analytical solution of the corresponding velocity distribution function from a Sonine polynomial expansion that displays energy non-equipartition between the translational and rotational modes, translational and rotational kurtoses, and translational-rotational velocity correlations. By comparison with a numerical solution of the Boltzmann kinetic equation (by means of the direct simulation Monte Carlo method), we show that our analytical solution provides a good description that is quantitatively very accurate in certain ranges of inelasticity and roughness. We also find three important features that make the forced granular gas steady state very different from the homogeneous cooling state (attained by an unforced granular gas). First, the marginal velocity distributions are always close to a Maxwellian. Second, there is a continuous transition to the purely smooth limit (where the effects of particle rotations are ignored). And third, the angular translational-rotational velocity correlations show a preference for a quasiperpendicular mutual orientation (which is called “lifted-tennis-ball” behavior)

Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate †

Science.gov (United States)

Tian, Yang; Suk, Dae-Hwan; Cai, Feng; Crich, David; Mesecar, Andrew D.

2009-01-01

O-succinylbenzoyl-CoA (OSB-CoA) synthetase (EC 6.2.1.26) catalyzes the ATP-dependent condensation of o-succinylbenzoate (OSB) and CoA to form OSB-CoA, the fourth step of the menaquinone biosynthetic pathway in Bacillus anthracis. Gene knockout studies have highlighted this enzyme as a potential target for the discovery of new antibiotics. Here we report the first studies on the kinetic mechanism of B. anthracis OSB-CoA synthetase, classifying it as an ordered Bi Uni Uni Bi ping-pong mechanism. Through a series of pre-steady-state and steady-state kinetic studies in conjunction with direct-binding studies, it is demonstrated that CoA, the last substrate to bind, strongly activates the first half-reaction after the first round of turnover. The activation of the first-half reaction is most likely achieved by CoA stabilizing conformations of the enzyme in the ‘F’ form, which slowly isomerize back to the E form. Thus, the kinetic mechanism of OSB-CoA synthetase may be more accurately described as an ordered Bi Uni Uni Bi Iso ping-pong mechanism. The substrate specificity of OSB-CoA synthetase was probed using a series of OSB analogs with alterations in the carboxylate groups. OSB-CoA shows a strong preference for OSB over all of the analogs tested as none were active except 4-(2-trifluoromethylphenyl)-4-oxobutyric acid which exhibited a 100-fold decrease in kcat/Km. Based on an understanding of OSB-CoA synthetase’s kinetic mechanism and substrate specificity, a reaction intermediate analog of OSB-AMP, 5’-O-(N-(2-trifluoromethylphenyl)-4-oxobutyl) adenosine sulfonamide (TFMP-butyl-AMS), was designed and synthesized. This inhibitor was found to be an uncompetitive inhibitor to CoA and a mixed-type inhibitor to ATP and OSB with low micromolar inhibition constants. Collectively, these results should serve as an important forerunner to more detailed and extensive inhibitor design studies aimed at developing lead compounds against the OSB-CoA synthetase class of

Modeling capsid kinetics assembly from the steady state distribution of multi-sizes aggregates

Energy Technology Data Exchange (ETDEWEB)

Hozé, Nathanaël; Holcman, David

2014-01-24

The kinetics of aggregation for particles of various sizes depends on their diffusive arrival and fusion at a specific nucleation site. We present here a mean-field approximation and a stochastic jump model for aggregates at equilibrium. This approach is an alternative to the classical Smoluchowski equations that do not have a close form and are not solvable in general. We analyze these mean-field equations and obtain the kinetics of a cluster formation. Our approach provides a simplified theoretical framework to study the kinetics of viral capsid formation, such as HIV from the self-assembly of the structural proteins Gag.

Simulations of KSTAR high performance steady state operation scenarios

International Nuclear Information System (INIS)

Na, Yong-Su; Kessel, C.E.; Park, J.M.; Yi, Sumin; Kim, J.Y.; Becoulet, A.; Sips, A.C.C.

2009-01-01

We report the results of predictive modelling of high performance steady state operation scenarios in KSTAR. Firstly, the capabilities of steady state operation are investigated with time-dependent simulations using a free-boundary plasma equilibrium evolution code coupled with transport calculations. Secondly, the reproducibility of high performance steady state operation scenarios developed in the DIII-D tokamak, of similar size to that of KSTAR, is investigated using the experimental data taken from DIII-D. Finally, the capability of ITER-relevant steady state operation is investigated in KSTAR. It is found that KSTAR is able to establish high performance steady state operation scenarios; β N above 3, H 98 (y, 2) up to 2.0, f BS up to 0.76 and f NI equals 1.0. In this work, a realistic density profile is newly introduced for predictive simulations by employing the scaling law of a density peaking factor. The influence of the current ramp-up scenario and the transport model is discussed with respect to the fusion performance and non-inductive current drive fraction in the transport simulations. As observed in the experiments, both the heating and the plasma current waveforms in the current ramp-up phase produce a strong effect on the q-profile, the fusion performance and also on the non-inductive current drive fraction in the current flattop phase. A criterion in terms of q min is found to establish ITER-relevant steady state operation scenarios. This will provide a guideline for designing the current ramp-up phase in KSTAR. It is observed that the transport model also affects the predictive values of fusion performance as well as the non-inductive current drive fraction. The Weiland transport model predicts the highest fusion performance as well as non-inductive current drive fraction in KSTAR. In contrast, the GLF23 model exhibits the lowest ones. ITER-relevant advanced scenarios cannot be obtained with the GLF23 model in the conditions given in this work

Deduction of kinetic mechanism in multisubstrate enzyme reactions from tritium isotope effects. Application to dopamine beta-hydroxylase

International Nuclear Information System (INIS)

Klinman, J.P.; Humphries, H.; Voet, J.G.

1980-01-01

Primary tritium isotope effects have been measured for the hydroxylation of [2-3H] dopamine catalyzed by dopamine beta-hydroxylase. Experimental values vary from 8.8 +/- 1.4 at 0.02 mM oxygen to 4.1 +/- 0.6 at 1.0 mM oxygen. It is shown that the observed dependence of the isotope effect on oxygen concentration provides unequivocal evidence for a kinetically significant dissociation of both dopamine and oxygen from enzyme, ternary complex. This approach, which is applicable to any multisubstrate enzyme characterized by detectable kinetic isotope effects, provides an alternate to classical methods for the elucidation of kinetic order in enzyme-catalyzed reactions

Superconducting magnets and cryogenics for the steady state superconducting tokamak SST-1

International Nuclear Information System (INIS)

Saxena, Y.C.

2000-01-01

SST-1 is a steady state superconducting tokamak for studying the physics of the plasma processes in tokamak under steady state conditions and to learn technologies related to the steady state operation of the tokamak. SST-1 will have superconducting magnets made from NbTi based conductors operating at 4.5 K temperature. The design of the superconducting magnets and the cryogenic system of SST-1 tokamak are described. (author)

Drying characteristic, enzyme inactivation and browning pigmentation kinetics of controlled humidity-convective drying of banana slices

Science.gov (United States)

Sarpong, Frederick; Yu, Xiaojie; Zhou, Cunshan; Oteng-Darko, Patricia; Amenorfe, Leticia Peace; Wu, Bengang; Bai, Junwen; Ma, Haile

2018-04-01

Investigating the kinetics of enzyme activities and browning indexes in food are very essential in understanding the enzyme inactivation and browning pigmentation reaction during drying processing. In order to understand and predict accurately the enzyme inactivation and browning pigmentation of banana slices using Relative Humidity (RH)-convective hot air dryer aided by ultrasound (US) pretreatment, this study was conducted. Drying was carried out with 20 kHz frequency of US-pretreatment using three durations (10 20 and 30 min) and RH (10 20 and 30%) conditions at 70 °C and 2.0 m/s air velocity. The kinetic study of both enzyme inactivation and browning pigmentation results were compared to their relevance of fit in terms of coefficient of correlation (R2), the root mean square error (RMSE) and the reduced chi-square (χ 2). First order and second-order polynomial kinetic model fitted well for enzyme inactivation and browning indexes respectively. Both enzymes inactivation kinetics and enzymatic browning index (EBI) declined significantly (p drying time in all drying conditions and rate of decrease intensified in longer US-pretreatment duration and lower RH conditions. However, shorter US-pretreatment duration and higher RH conditions reduced the non- enzymatic browning index (NBI) significantly. Again, longer US-pretreatment duration and lower RH shortened the drying time but adversely created more microspores from the micrograph study. Longer US pretreatment and lower RH decrease significantly (p < 0.05) the L* and b* values whereas the a* values was increased.

Steady-state models in electrophoresis: from isotachophoresis to capillary zone electrophoresis

NARCIS (Netherlands)

Beckers, J.L.

1995-01-01

Although all electrophoretic techniques are closely allied and controlled by the same rules, we often distinguish between steady-state and dynamic models in the modeling of electrophoretic processes, whereby steady-state models are applied for isotachophoresis (ITP) and dynamic models are applied

X-Ray Spectral Analysis of the Steady States of GRS1915+105

Science.gov (United States)

Peris, Charith S.; Remillard, Ronald A.; Steiner, James F.; Vrtilek, Saeqa D.; Varnière, Peggy; Rodriguez, Jerome; Pooley, Guy

2016-05-01

We report on the X-ray spectral behavior within the steady states of GRS1915+105. Our work is based on the full data set of the source obtained using the Proportional Counter Array (PCA) on the Rossi X-ray Timing Explorer (RXTE) and 15 GHz radio data obtained using the Ryle Telescope. The steady observations within the X-ray data set naturally separated into two regions in the color-color diagram and we refer to these regions as steady-soft and steady-hard. GRS1915+105 displays significant curvature in the coronal component in both the soft and hard data within the RXTE/PCA bandpass. A majority of the steady-soft observations displays a roughly constant inner disk radius ({R}{{in}}), while the steady-hard observations display an evolving disk truncation which is correlated to the mass accretion rate through the disk. The disk flux and coronal flux are strongly correlated in steady-hard observations and very weakly correlated in the steady-soft observations. Within the steady-hard observations, we observe two particular circumstances when there are correlations between the coronal X-ray flux and the radio flux with log slopes η ˜ 0.68+/- 0.35 and η ˜ 1.12+/- 0.13. They are consistent with the upper and lower tracks of Gallo et al. (2012), respectively. A comparison of the model parameters to the state definitions shows that almost all of the steady-soft observations match the criteria of either a thermal or steep power-law state, while a large portion of the steady-hard observations match the hard-state criteria when the disk fraction constraint is neglected.

Physical design of MW-class steady-state spherical tokamak, QUEST

International Nuclear Information System (INIS)

Hanada, K.; Sato, K.N.; Zushi, H.; Nakamura, K.; Sakamoto, M.; Idei, H.; Hasegawa, M.; Kawasaki, S.; Nakashima, H.; Higashijima, A.; Higashizono, Y.; Yoshida, N.; Takase, Y.; Ejiri, A.; Ogawa, Y.; Ono, Y.; Yoshida, Z.; Mitarai, O.; Maekawa, T.; Kishimoto, Y.; Ishiguro, M.; Yoshinaga, T.; Igami, H.; Hirooka, Y.; Komori, A.; Motojima, O.; Sudo, S.; Yamada, H.; Ando, A.; Asakura, Nobuyuki; Matsukawa, Makoto; Ishida, A.; Ohno, N.; Peng, M.

2008-10-01

QUEST (R=0.68 m, a=0.4 m) focuses on the steady state operation of the spherical tokamak (ST) by controlled PWI and electron Bernstain wave (EBW) current drive (CD). The QUEST project will be developed along two phases, phase I: steady state operation with plasma current, I p =20-30 kA on open divertor configuration and phase II: steady state operation with I p = 100 kA and β of 10% in short pulse on closed divertor configuration. Feasibility of the missions on QUEST was investigated and the suitable machine size of QUEST was decided based on the physical view of plasma parameters. Electron Bernstein wave (EBW) current drive are planned to establish the maintenance of plasma current in steady state. Mode conversion efficiency to EBW was calculated and the conversion of 95% will be expected. A new type antenna for QUEST has been fabricated to excite EBW effectively. The situation of heat and particle handling is challenging, and W and high temperature wall is adopted. The start-up scenario of plasma current was investigated based on the driven current by energetic electron and the most favorable magnetic configuration for start-up is proposed. (author)

Basin stability measure of different steady states in coupled oscillators

Science.gov (United States)

Rakshit, Sarbendu; Bera, Bidesh K.; Majhi, Soumen; Hens, Chittaranjan; Ghosh, Dibakar

2017-04-01

In this report, we investigate the stabilization of saddle fixed points in coupled oscillators where individual oscillators exhibit the saddle fixed points. The coupled oscillators may have two structurally different types of suppressed states, namely amplitude death and oscillation death. The stabilization of saddle equilibrium point refers to the amplitude death state where oscillations are ceased and all the oscillators converge to the single stable steady state via inverse pitchfork bifurcation. Due to multistability features of oscillation death states, linear stability theory fails to analyze the stability of such states analytically, so we quantify all the states by basin stability measurement which is an universal nonlocal nonlinear concept and it interplays with the volume of basins of attractions. We also observe multi-clustered oscillation death states in a random network and measure them using basin stability framework. To explore such phenomena we choose a network of coupled Duffing-Holmes and Lorenz oscillators which are interacting through mean-field coupling. We investigate how basin stability for different steady states depends on mean-field density and coupling strength. We also analytically derive stability conditions for different steady states and confirm by rigorous bifurcation analysis.

Molecular control of steady-state dendritic cell maturation and immune homeostasis.

Science.gov (United States)

Hammer, Gianna Elena; Ma, Averil

2013-01-01

Dendritic cells (DCs) are specialized sentinels responsible for coordinating adaptive immunity. This function is dependent upon coupled sensitivity to environmental signs of inflammation and infection to cellular maturation-the programmed alteration of DC phenotype and function to enhance immune cell activation. Although DCs are thus well equipped to respond to pathogens, maturation triggers are not unique to infection. Given that immune cells are exquisitely sensitive to the biological functions of DCs, we now appreciate that multiple layers of suppression are required to restrict the environmental sensitivity, cellular maturation, and even life span of DCs to prevent aberrant immune activation during the steady state. At the same time, steady-state DCs are not quiescent but rather perform key functions that support homeostasis of numerous cell types. Here we review these functions and molecular mechanisms of suppression that control steady-state DC maturation. Corruption of these steady-state operatives has diverse immunological consequences and pinpoints DCs as potent drivers of autoimmune and inflammatory disease.

Dark Entangled Steady States of Interacting Rydberg Atoms

DEFF Research Database (Denmark)

Dasari, Durga; Mølmer, Klaus

2013-01-01

their short-lived excited states lead to rapid, dissipative formation of an entangled steady state. We show that for a wide range of physical parameters, this entangled state is formed on a time scale given by the strengths of coherent Raman and Rabi fields applied to the atoms, while it is only weakly...

Indicators for suicide substrate inactivation: A kinetic investigation

Indian Academy of Sciences (India)

Sharmistha Dhatt

2017-11-20

Nov 20, 2017 ... practical ones, that can decisively conclude enzyme inactivation are considered. Steady-state approximation ... nase 1 and 2 enzymes), Exemesteme - a drug used in the treatment of breast cancer (inhibitor of aromatase enzyme), AZT and .... for a next indicator that can serve as a diagnostic tool for enzyme ...

Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints.

Science.gov (United States)

Fiedler, Anna; Raeth, Sebastian; Theis, Fabian J; Hausser, Angelika; Hasenauer, Jan

2016-08-22

Ordinary differential equation (ODE) models are widely used to describe (bio-)chemical and biological processes. To enhance the predictive power of these models, their unknown parameters are estimated from experimental data. These experimental data are mostly collected in perturbation experiments, in which the processes are pushed out of steady state by applying a stimulus. The information that the initial condition is a steady state of the unperturbed process provides valuable information, as it restricts the dynamics of the process and thereby the parameters. However, implementing steady-state constraints in the optimization often results in convergence problems. In this manuscript, we propose two new methods for solving optimization problems with steady-state constraints. The first method exploits ideas from optimization algorithms on manifolds and introduces a retraction operator, essentially reducing the dimension of the optimization problem. The second method is based on the continuous analogue of the optimization problem. This continuous analogue is an ODE whose equilibrium points are the optima of the constrained optimization problem. This equivalence enables the use of adaptive numerical methods for solving optimization problems with steady-state constraints. Both methods are tailored to the problem structure and exploit the local geometry of the steady-state manifold and its stability properties. A parameterization of the steady-state manifold is not required. The efficiency and reliability of the proposed methods is evaluated using one toy example and two applications. The first application example uses published data while the second uses a novel dataset for Raf/MEK/ERK signaling. The proposed methods demonstrated better convergence properties than state-of-the-art methods employed in systems and computational biology. Furthermore, the average computation time per converged start is significantly lower. In addition to the theoretical results, the

Online quench-flow electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for elucidating kinetic and chemical enzymatic reaction mechanisms.

Science.gov (United States)

Clarke, David J; Stokes, Adam A; Langridge-Smith, Pat; Mackay, C Logan

2010-03-01

We have developed an automated quench-flow microreactor which interfaces directly to an electrospray ionization (ESI) mass spectrometer. We have used this device in conjunction with ESI Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) to demonstrate the potential of this approach for studying the mechanistic details of enzyme reactions. For the model system chosen to test this device, namely, the pre-steady-state hydrolysis of p-nitrophenyl acetate by the enzyme chymotrypsin, the kinetic parameters obtained are in good agreement with those in the literature. To our knowledge, this is the first reported use of online quench-flow coupled with FTICR MS. Furthermore, we have exploited the power of FTICR MS to interrogate the quenched covalently bound enzyme intermediate using top-down fragmentation. The accurate mass capabilities of FTICR MS permitted the nature of the intermediate to be assigned with high confidence. Electron capture dissociation (ECD) fragmentation allowed us to locate the intermediate to a five amino acid section of the protein--which includes the known catalytic residue, Ser(195). This experimental approach, which uniquely can provide both kinetic and chemical details of enzyme mechanisms, is a potentially powerful tool for studies of enzyme catalysis.

Communication: Limitations of the stochastic quasi-steady-state approximation in open biochemical reaction networks

Science.gov (United States)

Thomas, Philipp; Straube, Arthur V.; Grima, Ramon

2011-11-01

It is commonly believed that, whenever timescale separation holds, the predictions of reduced chemical master equations obtained using the stochastic quasi-steady-state approximation are in very good agreement with the predictions of the full master equations. We use the linear noise approximation to obtain a simple formula for the relative error between the predictions of the two master equations for the Michaelis-Menten reaction with substrate input. The reduced approach is predicted to overestimate the variance of the substrate concentration fluctuations by as much as 30%. The theoretical results are validated by stochastic simulations using experimental parameter values for enzymes involved in proteolysis, gluconeogenesis, and fermentation.

A steady state theory for processive cellulases

DEFF Research Database (Denmark)

Cruys-Bagger, Nicolaj; Olsen, Jens Elmerdahl; Præstgaard, Eigil

2013-01-01

coefficient’, which represents the probability of the enzyme dissociating from the substrate strand before completing n sequential catalytic steps, where n is the mean processivity number measured experimentally. Typical processive cellulases have high substrate affinity, and therefore this probability is low....... This has significant kinetic implications, for example the maximal specific rate (Vmax/E0) for processive cellulases is much lower than the catalytic rate constant (kcat). We discuss how relationships based on this theory may be used in both comparative and mechanistic analyses of cellulases....

A design of steady state fusion burner

International Nuclear Information System (INIS)

Hasegawa, Akira; Hatori, Tadatsugu; Itoh, Kimitaka; Ikuta, Takashi; Kodama, Yuji.

1975-01-01

We present a brief design of a steady state fusion burner in which a continuous burning of nuclear fuel may be achieved with output power of a gigawatt. The laser fusion is proposed to ignite the fuel. (auth.)

Enzyme catalyzed oxidative gelation of sugar beet pectin: Kinetics and rheology

DEFF Research Database (Denmark)

Abang Zaidel, Dayang Norulfairuz; Chronakis, Ioannis S.; Meyer, Anne S.

2012-01-01

Sugar beet pectin (SBP) is a marginally utilized co-processing product from sugar production from sugar beets. In this study, the kinetics of oxidative gelation of SBP, taking place via enzyme catalyzed cross-linking of ferulic acid moieties (FA), was studied using small angle oscillatory...

Kinetics based reaction optimization of enzyme catalysed reduction of formaldehyde to methanol with synchronous cofactor regeneration

DEFF Research Database (Denmark)

Marpani, Fauziah Binti; Sárossy, Zsuzsa; Pinelo, Manuel

2017-01-01

regeneration of the reducing equivalents during reaction is required. Herein, we report the optimization of the enzymatic conversion of formaldehyde (CHOH) to CH3 OH by alcohol dehydrogenase, the final step of the enzymatic redox reaction of CO2 to CH3 OH, with kinetically synchronous enzymatic cofactor...... regeneration using either glucose dehydrogenase (System I) or xylose dehydrogenase (System II). A mathematical model of the enzyme kinetics was employed to identify the best reaction set-up for attaining optimal cofactor recycling rate and enzyme utilization efficiency. Targeted process optimization...... experiments were conducted to verify the kinetically modelled results. Repetitive reaction cycles were shown to enhance the yield of CH3 OH, increase the total turnover number (TTN) and the biocatalytic productivity rate (BPR) value for both system I and II whilst minimizing the exposure of the enzymes...

Steady State Dynamic Operating Behavior of Universal Motor

Directory of Open Access Journals (Sweden)

Muhammad Khan Burdi

2015-01-01

Full Text Available A detailed investigation of the universal motor is developed and used for various dynamic steady state and transient operating conditions of loads. In the investigation, output torque, motor speed, input current, input/output power and efficiency are computed, compared and analyzed for different loads. While this paper discusses the steady-state behavior of the universal motor, another companion paper, ?Transient dynamic behavior of universal motor?, will discuss its transient behavior in detail. A non-linear generalized electric machine model of the motor is considered for the analysis. This study was essential to investigate effect of output load on input current, power, speed and efficiency of the motor during operations. Previously such investigation is not known

Quasi-steady state natural convection in a tilted porous layer

Energy Technology Data Exchange (ETDEWEB)

Robillard, L.; Vasseur, P. (Ecole Polytechnique, Montreal, PQ (Canada))

1992-12-01

Natural convection in an inclined porous layer heated or cooled on one side, when its other walls are insulated, has several important engineering applications. These include solar power collection, regenerative heat exchangers, and high performance insulation for buildings and cold storage. Although the problem is basically an unsteady state one, it is known that if the heating (or cooling) process is maintained for a sufficiently long time, a quasi-steady state is approached. Quasi-steady state laminar natural convection in an inclined porous layer is studied analytically and numerically. On the basis of the Darcy-Oberbeck-Boussinesq equations, the problem is solved analytically in the limit of a thin porous layer heated on one side by a heat flux while the other boundaries are maintained adiabatic. For quasi-steady state, the flow and temperature fields overall heat transfer rates are obtained in terms of the controlling parameters and the onset of convection in a bottom heated horizantal system is predicted. It is also demonstrated for the case of a bottom-heated layer that for sufficiently small inclinations, multiple unicellular quasi-steady states exist, some of which are unstable. A numerical study of the same phenomenon, obtained by solving the complete set of governing equations, is conducted. Good agreement is found between the analytical predictions and the numerical simulation. 22 refs., 6 figs.

The alteration of intracellular enzymes. III. The effect of temperature on the kinetics of altered and unaltered yeast catalase.

Science.gov (United States)

FRASER, M J; KAPLAN, J G

1955-03-20

1. The very large increase in catalase activity (Euler effect) which follows treatment of yeast cells with CHCl(3), UV and n-propanol is accompanied by highly significant changes in kinetic properties. With respect to the enzymatic decomposition of H(2)O(2), the thermodynamic constants of the activation process micro, DeltaHdouble dagger, DeltaSdouble dagger, DeltaFdouble dagger, decrease, following treatment of the intracellular enzyme, by 4.5 kcal., 4.5 kcal., 10.1 e.u. and 1.7 kcal., respectively, all these differences being significant at the 1 per cent level. 2. Similar differences exist between the untreated, intracellular enzyme on the one hand, and the extracted yeast and crystalline beef liver catalases on the other. Significant differences in these thermodynamic constants do not exist among the treated intracellular, extracted yeast, and crystalline liver catalases. 3. These data provide unequivocal confirmation of the phenomenon of enzyme alteration reported previously, and confirm previous evidence that the extracted and crystalline enzymes have also undergone enzyme alteration and have properties which are identical with, or very similar to, those of the catalase altered in situ. 4. With respect to the process of heat destruction of catalase, the greatly diminished stability to heat of the altered enzymes, previously reported, has been confirmed. The thermodynamic constants of activation of this process have likewise changed following alteration, in the case of micro, DeltaHdouble dagger, and DeltaSdouble dagger an increase of 20.6 kcal., 20.6 kcal., and 70 e.u., respectively, and of DeltaFdouble dagger a decrease of 2.8 kcal. 5. All these data have been shown to be consistent with, and in some cases predictable from, the interfacial hypothesis, which states that the unaltered catalase exists within the cell adsorbed to some interface, in a partially, but reversibly, unfolded configuration of relatively low specificity; enzyme alteration consists, in

Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes.

Science.gov (United States)

Gao, Jiali; Major, Dan T; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu

2008-01-01

A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.

Automated Determination of Oxygen-Dependent Enzyme Kinetics in a Tube-in-Tube Flow Reactor

DEFF Research Database (Denmark)

Ringborg, Rolf Hoffmeyer; Pedersen, Asbjørn Toftgaard; Woodley, John

2017-01-01

revealed not only the high degree of accuracy of the kinetic data obtained, but also the necessity of making measurements in this way to enable the accurate evaluation of high KMO enzyme systems. For the first time, this paves the way to integrate kinetic data into the protein engineering cycle....

Dual kinetic curves in reversible electrochemical systems.

Directory of Open Access Journals (Sweden)

Michael J Hankins

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

On Steady-State Tropical Cyclones

Science.gov (United States)

2014-01-01

Press: London. Marks FD, Black PG, Montgomery MT, Burpee RW. 2008. Structure of the eye and eyewall of Hurricane Hugo (1989). Mon. Weather Rev. 136: 1237... hurricanes ; tropical cyclones; typhoons; steady-state Received 18 April 2013; Revised 25 November 2013; Accepted 29 December 2013; Published online in Wiley...the concept of the ‘mature stage’ of a hurricane vortex. The definition of the ‘mature stage’ is commonly based on the time period in which the maximum

STEADY-STATE RELATIVISTIC STELLAR DYNAMICS AROUND A MASSIVE BLACK HOLE

Energy Technology Data Exchange (ETDEWEB)

Bar-Or, Ben; Alexander, Tal [Department of Particle Physics and Astrophysics, Weizmann Institute of Science, P.O. Box 26, Rehovot 76100 (Israel)

2016-04-01

A massive black hole (MBH) consumes stars whose orbits evolve into the small phase-space volume of unstable orbits, the “loss cone,” which take them into the MBH, or close enough to interact strongly with it. The resulting phenomena, e.g., tidal heating and disruption, binary capture and hyper-velocity star ejection, gravitational wave (GW) emission by inspiraling compact remnants, or hydrodynamical interactions with an accretion disk, can produce observable signatures and thereby reveal the MBH, affect its mass and spin evolution, test strong gravity, and probe stars and gas near the MBH. These continuous stellar loss and resupply processes shape the central stellar distribution. We investigate relativistic stellar dynamics near the loss cone of a non-spinning MBH in steady state, analytically and by Monte Carlo simulations of the diffusion of the orbital parameters. These take into account Newtonian mass precession due to enclosed stellar mass, in-plane precession due to general relativity, dissipation by GW, uncorrelated two-body relaxation, correlated resonant relaxation (RR), and adiabatic invariance due to secular precession, using a rigorously derived description of correlated post-Newtonian dynamics in the diffusion limit. We argue that general maximal entropy considerations strongly constrain the orbital diffusion in steady state, irrespective of the relaxation mechanism. We identify the exact phase-space separatrix between plunges and inspirals, and predict their steady-state rates. We derive the dependence of the rates on the mass of the MBH, show that the contribution of RR in steady state is small, and discuss special cases where unquenched RR in restricted volumes of phase-space may affect the steady state substantially.

40 CFR Appendix II to Part 1039 - Steady-State Duty Cycles

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Steady-State Duty Cycles II Appendix... Appendix II to Part 1039—Steady-State Duty Cycles (a) The following duty cycles apply for constant-speed engines: (1) The following duty cycle applies for discrete-mode testing: D2 mode number Engine speed...

Analysis of steady state creep of southeastern New Mexico bedded salt

International Nuclear Information System (INIS)

Herrmann, W.; Wawersik, W.R.; Lauson, H.S.

1980-03-01

Steady state creep rates have been obtained from a large suite of existing experimental creep data relating to bedded rock salt from the Salado formation of S.E. New Mexico. Experimental conditions covered an intermediate temperature range from 22 0 C to 200 0 C, and shear stresses from 1000 psi (7 MPa) to 6000 psi (31 MPa). An expression, based on a single diffusion controlled dislocation climb mechanism, has been found to fit the observed dependence of steady state creep rate on shear stress and temperature, yielding an activation energy of 12 kcal/mole (50 kJ/mole) and a stress exponent of 4.9. Multiple regression analysis revealed a dependence on stratigraphy, but no statistically significant dependence on pressure of specimen size. No consistent dilatancy or compaction associated with steady state creep was found, although some individual specimens dilated or compacted during creep. The steady state creep data were found to agree very well with creep data for both bedded and dome salt from a variety of other locations

Chlorine decay under steady and unsteady-state hydraulic conditions

DEFF Research Database (Denmark)

Stoianov, Ivan; Aisopou, Angeliki

2014-01-01

This paper describes a simulation framework for the scale-adaptive hydraulic and chlorine decay modelling under steady and unsteady-state flows. Bulk flow and pipe wall reaction coefficients are replaced with steady and unsteady-state reaction coefficients. An unsteady decay coefficient is defined...... which depends upon the absolute value of shear stress and the rate of change of shear stress for quasi-unsteady and unsteady-state flows. A preliminary experimental and analytical investigation was carried out in a water transmission main. The results were used to model monochloramine decay...... and these demonstrate that the dynamic hydraulic conditions have a significant impact on water quality deterioration and the rapid loss of disinfectant residual. © 2013 The Authors....

Steady-state heat transfer in an inverted U-tube steam generator

International Nuclear Information System (INIS)

Boucher, T.J.

1986-01-01

Experimental results are presented involving U-tube steam generator tube bundle local heat transfer and fluid conditions during steady-state, full-power operations performed at high temperatures and pressures with conditions typical of a pressurized water reactor (15.0 MPa primary pressure, 600 K hot-leg fluid temperatures, 6.2 MPa secondary pressure). The MOD-2C facility represents the state-of-the-art in measurement of tube local heat transfer data and average tube bundle secondary fluid density at several elevations, which allows an estimate of the axial heat transfer and void distributions during steady-state and transient operations. The method of heat transfer data reduction is presented and the heat flux, secondary convective heat transfer coefficient, and void fraction distributions are quantified for steady-state, full-power operations

40 CFR Appendix II to Part 1042 - Steady-State Duty Cycles

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Steady-State Duty Cycles II Appendix..., App. II Appendix II to Part 1042—Steady-State Duty Cycles (a) The following duty cycles apply as specified in § 1042.505(b)(1): (1) The following duty cycle applies for discrete-mode testing: E3 mode No...

Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data

Directory of Open Access Journals (Sweden)

Klipp Edda

2006-12-01

Full Text Available Abstract Background Translating a known metabolic network into a dynamic model requires reasonable guesses of all enzyme parameters. In Bayesian parameter estimation, model parameters are described by a posterior probability distribution, which scores the potential parameter sets, showing how well each of them agrees with the data and with the prior assumptions made. Results We compute posterior distributions of kinetic parameters within a Bayesian framework, based on integration of kinetic, thermodynamic, metabolic, and proteomic data. The structure of the metabolic system (i.e., stoichiometries and enzyme regulation needs to be known, and the reactions are modelled by convenience kinetics with thermodynamically independent parameters. The parameter posterior is computed in two separate steps: a first posterior summarises the available data on enzyme kinetic parameters; an improved second posterior is obtained by integrating metabolic fluxes, concentrations, and enzyme concentrations for one or more steady states. The data can be heterogenous, incomplete, and uncertain, and the posterior is approximated by a multivariate log-normal distribution. We apply the method to a model of the threonine synthesis pathway: the integration of metabolic data has little effect on the marginal posterior distributions of individual model parameters. Nevertheless, it leads to strong correlations between the parameters in the joint posterior distribution, which greatly improve the model predictions by the following Monte-Carlo simulations. Conclusion We present a standardised method to translate metabolic networks into dynamic models. To determine the model parameters, evidence from various experimental data is combined and weighted using Bayesian parameter estimation. The resulting posterior parameter distribution describes a statistical ensemble of parameter sets; the parameter variances and correlations can account for missing knowledge, measurement

Emergence of advance waves in a steady-state universe

Energy Technology Data Exchange (ETDEWEB)

Hobart, R.H.

1979-10-01

In standard Wheeler-Feynman electrodynamics advanced waves from any source are absolutely canceled by the advanced waves from the absorber responding to that source. The present work shows this cancellation fails over cosmic distances in a steady-state universe. A test of the view proposed earlier, in a paper which assumed failure of cancellation ad hoc, that zero-point fluctuations of the electromagnetic field are such emergent advanced waves, is posed. The view entails anomalous slowing of spontaneous transition rates at longer emission wavelengths; available data go against this, furnishing additional argument against the suspect assumption that the universe is steady-state.

Emergence of advance waves in a steady-state universe

International Nuclear Information System (INIS)

Hobart, R.H.

1979-01-01

In standard Wheeler-Feynman electrodynamics advanced waves from any source are absolutely canceled by the advanced waves from the absorber responding to that source. The present work shows this cancellation fails over cosmic distances in a steady-state universe. A test of the view proposed earlier, in a paper which assumed failure of cancellation ad hoc, that zero-point fluctuations of the electromagnetic field are such emergent advanced waves, is posed. The view entails anomalous slowing of spontaneous transition rates at longer emission wavelengths; available data go against this, furnishing additional argument against the suspect assumption that the universe is steady-state

Structural and kinetic analysis of the unnatural fusion protein 4-coumaroyl-CoA ligase::stilbene synthase

Energy Technology Data Exchange (ETDEWEB)

Wang, Yechun; Yi, Hankuil; Wang, Melissa; Yu, Oliver; Jez, Joseph M. (WU); (Danforth)

2012-10-24

To increase the biochemical efficiency of biosynthetic systems, metabolic engineers have explored different approaches for organizing enzymes, including the generation of unnatural fusion proteins. Previous work aimed at improving the biosynthesis of resveratrol, a stilbene associated a range of health-promoting activities, in yeast used an unnatural engineered fusion protein of Arabidopsis thaliana (thale cress) 4-coumaroyl-CoA ligase (At4CL1) and Vitis vinifera (grape) stilbene synthase (VvSTS) to increase resveratrol levels 15-fold relative to yeast expressing the individual enzymes. Here we present the crystallographic and biochemical analysis of the 4CL::STS fusion protein. Determination of the X-ray crystal structure of 4CL::STS provides the first molecular view of an artificial didomain adenylation/ketosynthase fusion protein. Comparison of the steady-state kinetic properties of At4CL1, VvSTS, and 4CL::STS demonstrates that the fusion protein improves catalytic efficiency of either reaction less than 3-fold. Structural and kinetic analysis suggests that colocalization of the two enzyme active sites within 70 {angstrom} of each other provides the basis for enhanced in vivo synthesis of resveratrol.

Steady-state Operational Characteristics of Ghana Research ...

African Journals Online (AJOL)

Steady state operational characteristics of the 30 kW tank-in-pool type reactor named Ghana Research Reactor-1 were investigated after a successful on-site zero power critical experiments. The steadystate operational character-istics determined were the thermal neutron fluxes, maximum period of operation at nominal ...

Evidence for forcing-dependent steady states in a turbulent swirling flow.

Science.gov (United States)

Saint-Michel, B; Dubrulle, B; Marié, L; Ravelet, F; Daviaud, F

2013-12-06

We study the influence on steady turbulent states of the forcing in a von Karman flow, at constant impeller speed, or at constant torque. We find that the different forcing conditions change the nature of the stability of the steady states and reveal dynamical regimes that bear similarities to low-dimensional systems. We suggest that this forcing dependence may be applicable to other turbulent systems.

Constructive interference in steady-state/FIESTA-C clinical applications in neuroimaging

International Nuclear Information System (INIS)

Kulkami, Makarand

2011-01-01

Full text: High spatial resolution is one of the major problems in neuroimaging, par ticularly in cranial and spinal nerve imaging. Constructive interference in steady-state/fast imaging employing steady-state acquisition with phase cycling is a robust sequence in imaging the cranial and spinal nerve patholo gies. This pictorial review is a concise article about the applications of this sequence in neuroimaging with clinical examples.

Optimal control of transitions between nonequilibrium steady states.

Directory of Open Access Journals (Sweden)

Patrick R Zulkowski

Full Text Available Biological systems fundamentally exist out of equilibrium in order to preserve organized structures and processes. Many changing cellular conditions can be represented as transitions between nonequilibrium steady states, and organisms have an interest in optimizing such transitions. Using the Hatano-Sasa Y-value, we extend a recently developed geometrical framework for determining optimal protocols so that it can be applied to systems driven from nonequilibrium steady states. We calculate and numerically verify optimal protocols for a colloidal particle dragged through solution by a translating optical trap with two controllable parameters. We offer experimental predictions, specifically that optimal protocols are significantly less costly than naive ones. Optimal protocols similar to these may ultimately point to design principles for biological energy transduction systems and guide the design of artificial molecular machines.

The non-local Fisher–KPP equation: travelling waves and steady states

International Nuclear Information System (INIS)

Berestycki, Henri; Nadin, Grégoire; Perthame, Benoit; Ryzhik, Lenya

2009-01-01

We consider the Fisher–KPP equation with a non-local saturation effect defined through an interaction kernel φ(x) and investigate the possible differences with the standard Fisher–KPP equation. Our first concern is the existence of steady states. We prove that if the Fourier transform φ-circumflex(ξ) is positive or if the length σ of the non-local interaction is short enough, then the only steady states are u ≡ 0 and u ≡ 1. Next, we study existence of the travelling waves. We prove that this equation admits travelling wave solutions that connect u = 0 to an unknown positive steady state u ∞ (x), for all speeds c ≥ c * . The travelling wave connects to the standard state u ∞ (x) ≡ 1 under the aforementioned conditions: φ-circumflex(ξ) > 0 or σ is sufficiently small. However, the wave is not monotonic for σ large

Current drive efficiency requirements for an attractive steady-state reactor

Energy Technology Data Exchange (ETDEWEB)

Tonon, G

1994-12-31

The expected values of the figure of merit and the electrical efficiency of various non-inductive current drive methods are considered. The main experimental results achieved today with neutral beams and radiofrequency systems are summarized. Taking into account the simplified energy flow diagram of a steady state reactor, the figure of merit and the electrical efficiency values which are necessary in order to envisage an attractive steady-state reactor are determined. These values are compared to the theoretical predictions. (author). 16 refs., 11 figs., 2 tabs.

Current drive efficiency requirements for an attractive steady-state reactor

International Nuclear Information System (INIS)

Tonon, G.

1994-01-01

The expected values of the figure of merit and the electrical efficiency of various non-inductive current drive methods are considered. The main experimental results achieved today with neutral beams and radiofrequency systems are summarized. Taking into account the simplified energy flow diagram of a steady state reactor, the figure of merit and the electrical efficiency values which are necessary in order to envisage an attractive steady-state reactor are determined. These values are compared to the theoretical predictions. (author). 16 refs., 11 figs., 2 tabs

Kinetics based reaction optimization of enzyme catalyzed reduction of formaldehyde to methanol with synchronous cofactor regeneration.

Science.gov (United States)

Marpani, Fauziah; Sárossy, Zsuzsa; Pinelo, Manuel; Meyer, Anne S

2017-12-01

Enzymatic reduction of carbon dioxide (CO 2 ) to methanol (CH 3 OH) can be accomplished using a designed set-up of three oxidoreductases utilizing reduced pyridine nucleotide (NADH) as cofactor for the reducing equivalents electron supply. For this enzyme system to function efficiently a balanced regeneration of the reducing equivalents during reaction is required. Herein, we report the optimization of the enzymatic conversion of formaldehyde (CHOH) to CH 3 OH by alcohol dehydrogenase, the final step of the enzymatic redox reaction of CO 2 to CH 3 OH, with kinetically synchronous enzymatic cofactor regeneration using either glucose dehydrogenase (System I) or xylose dehydrogenase (System II). A mathematical model of the enzyme kinetics was employed to identify the best reaction set-up for attaining optimal cofactor recycling rate and enzyme utilization efficiency. Targeted process optimization experiments were conducted to verify the kinetically modeled results. Repetitive reaction cycles were shown to enhance the yield of CH 3 OH, increase the total turnover number (TTN) and the biocatalytic productivity rate (BPR) value for both system I and II whilst minimizing the exposure of the enzymes to high concentrations of CHOH. System II was found to be superior to System I with a yield of 8 mM CH 3 OH, a TTN of 160 and BPR of 24 μmol CH 3 OH/U · h during 6 hr of reaction. The study demonstrates that an optimal reaction set-up could be designed from rational kinetics modeling to maximize the yield of CH 3 OH, whilst simultaneously optimizing cofactor recycling and enzyme utilization efficiency. © 2017 Wiley Periodicals, Inc.

Burn cycle requirements comparison of pulsed and steady-state tokamak reactors

International Nuclear Information System (INIS)

Brooks, J.N.; Ehst, D.A.

1983-12-01

Burn cycle parameters and energy transfer system requirements were analyzed for an 8-m commercial tokamak reactor using four types of cycles: conventional, hybrid, internal transformer, and steady state. Not surprisingly, steady state is the best burn mode if it can be achieved. The hybrid cycle is a promising alternative to the conventional. In contrast, the internal transformer cycle does not appear attractive for the size tokamak in question

Dual role of imidazole as activator/inhibitor of sweet almond (Prunus dulcis β-glucosidase

Directory of Open Access Journals (Sweden)

Sara Caramia

2017-07-01

Full Text Available The activity of Prunus dulcis (sweet almond β-glucosidase at the expense of p-nitrophenyl-β-d-glucopyranoside at pH 6 was determined, both under steady-state and pre-steady-state conditions. Using crude enzyme preparations, competitive inhibition by 1–5 mM imidazole was observed under both kinetic conditions tested. However, when imidazole was added to reaction mixtures at 0.125–0.250 mM, we detected a significant enzyme activation. To further inspect this effect exerted by imidazole, β-glucosidase was purified to homogeneity. Two enzyme isoforms were isolated, i.e. a full-length monomer, and a dimer containing a full-length and a truncated subunit. Dimeric β-glucosidase was found to perform much better than the monomeric enzyme, independently of the kinetic conditions used to assay enzyme activity. In addition, the sensitivity towards imidazole was found to differ between the two isoforms. While monomeric enzyme was indeed found to be relatively insensitive to imidazole, dimeric β-glucosidase was observed to be significantly activated by 0.125–0.250 mM imidazole under pre-steady-state conditions. Further, steady-state assays revealed that the addition of 0.125 mM imidazole to reaction mixtures increases the Km of dimeric enzyme from 2.3 to 6.7 mM. The activation of β-glucosidase dimer by imidazole is proposed to be exerted via a conformational transition poising the enzyme towards proficient catalysis.

Dual role of imidazole as activator/inhibitor of sweet almond (Prunus dulcis) β-glucosidase.

Science.gov (United States)

Caramia, Sara; Gatius, Angela Gala Morena; Dal Piaz, Fabrizio; Gaja, Denis; Hochkoeppler, Alejandro

2017-07-01

The activity of Prunus dulcis (sweet almond) β-glucosidase at the expense of p -nitrophenyl-β-d-glucopyranoside at pH 6 was determined, both under steady-state and pre-steady-state conditions. Using crude enzyme preparations, competitive inhibition by 1-5 mM imidazole was observed under both kinetic conditions tested. However, when imidazole was added to reaction mixtures at 0.125-0.250 mM, we detected a significant enzyme activation. To further inspect this effect exerted by imidazole, β-glucosidase was purified to homogeneity. Two enzyme isoforms were isolated, i.e. a full-length monomer, and a dimer containing a full-length and a truncated subunit. Dimeric β-glucosidase was found to perform much better than the monomeric enzyme, independently of the kinetic conditions used to assay enzyme activity. In addition, the sensitivity towards imidazole was found to differ between the two isoforms. While monomeric enzyme was indeed found to be relatively insensitive to imidazole, dimeric β-glucosidase was observed to be significantly activated by 0.125-0.250 mM imidazole under pre-steady-state conditions. Further, steady-state assays revealed that the addition of 0.125 mM imidazole to reaction mixtures increases the K m of dimeric enzyme from 2.3 to 6.7 mM. The activation of β-glucosidase dimer by imidazole is proposed to be exerted via a conformational transition poising the enzyme towards proficient catalysis.

40 CFR 1033.515 - Discrete-mode steady-state emission tests of locomotives and locomotive engines.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Discrete-mode steady-state emission... Procedures § 1033.515 Discrete-mode steady-state emission tests of locomotives and locomotive engines. This... a warm-up followed by a sequence of nominally steady-state discrete test modes, as described in...

Stochastic simulation of enzyme-catalyzed reactions with disparate timescales.

Science.gov (United States)

Barik, Debashis; Paul, Mark R; Baumann, William T; Cao, Yang; Tyson, John J

2008-10-01

Many physiological characteristics of living cells are regulated by protein interaction networks. Because the total numbers of these protein species can be small, molecular noise can have significant effects on the dynamical properties of a regulatory network. Computing these stochastic effects is made difficult by the large timescale separations typical of protein interactions (e.g., complex formation may occur in fractions of a second, whereas catalytic conversions may take minutes). Exact stochastic simulation may be very inefficient under these circumstances, and methods for speeding up the simulation without sacrificing accuracy have been widely studied. We show that the "total quasi-steady-state approximation" for enzyme-catalyzed reactions provides a useful framework for efficient and accurate stochastic simulations. The method is applied to three examples: a simple enzyme-catalyzed reaction where enzyme and substrate have comparable abundances, a Goldbeter-Koshland switch, where a kinase and phosphatase regulate the phosphorylation state of a common substrate, and coupled Goldbeter-Koshland switches that exhibit bistability. Simulations based on the total quasi-steady-state approximation accurately capture the steady-state probability distributions of all components of these reaction networks. In many respects, the approximation also faithfully reproduces time-dependent aspects of the fluctuations. The method is accurate even under conditions of poor timescale separation.

Comparing a Dynamic Fed-Batch and a Continuous Steady-State Simulation of Ethanol Fermentation in a Distillery to a Stoichiometric Conversion Simulation

OpenAIRE

Fonseca, G.C.; Costa, C.B.B.; Cruz, A.J.G.

2017-01-01

Abstract An autonomous sugarcane bioethanol plant was simulated in EMSO software, an equation oriented process simulator. Three types of fermentation units were simulated: a six parallel fed-batch reactor system, a set of four CSTR in steady state and one consisting of a single stoichiometric reactor. Stoichiometric models are less accurate than kinetic-based fermentation models used for fed-batch and continuous fermenter simulations, since they do not account for inhibition effects and depen...

The effects of intrinsic noise on the behaviour of bistable cell regulatory systems under quasi-steady state conditions.

Science.gov (United States)

de la Cruz, Roberto; Guerrero, Pilar; Spill, Fabian; Alarcón, Tomás

2015-08-21

We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady state approximation based on the semi-classical approximation of the partial differential equation for the generating function associated with the chemical master equation. Such approximation proceeds by optimising an action functional whose associated set of Euler-Lagrange (Hamilton) equations provides the most likely fluctuation path. We show that, under appropriate conditions granting time scale separation, the Hamiltonian can be re-scaled so that the set of Hamilton equations splits up into slow and fast variables, whereby the quasi-steady state approximation can be applied. We analyse two particular examples of systems whose mean-field limit has been shown to exhibit bi-stability: an enzyme-catalysed system of two mutually inhibitory proteins and a gene regulatory circuit with self-activation. Our theory establishes that the number of molecules of the conserved species is order parameters whose variation regulates bistable behaviour in the associated systems beyond the predictions of the mean-field theory. This prediction is fully confirmed by direct numerical simulations using the stochastic simulation algorithm. This result allows us to propose strategies whereby, by varying the number of molecules of the three conserved chemical species, cell properties associated to bistable behaviour (phenotype, cell-cycle status, etc.) can be controlled.

The effects of intrinsic noise on the behaviour of bistable cell regulatory systems under quasi-steady state conditions

Energy Technology Data Exchange (ETDEWEB)

Cruz, Roberto; Alarcón, Tomás de la [Centre de Recerca Matemàtica. Edifici C, Campus de Bellaterra, 08193 Bellaterra (Barcelona) (Spain); Departament de Matemàtiques, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona) (Spain); Guerrero, Pilar [Department of Mathematics, University College London, Gower Street, London WC1E 6BT (United Kingdom); Spill, Fabian [Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215 (United States); Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States)

2015-08-21

We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady state approximation based on the semi-classical approximation of the partial differential equation for the generating function associated with the chemical master equation. Such approximation proceeds by optimising an action functional whose associated set of Euler-Lagrange (Hamilton) equations provides the most likely fluctuation path. We show that, under appropriate conditions granting time scale separation, the Hamiltonian can be re-scaled so that the set of Hamilton equations splits up into slow and fast variables, whereby the quasi-steady state approximation can be applied. We analyse two particular examples of systems whose mean-field limit has been shown to exhibit bi-stability: an enzyme-catalysed system of two mutually inhibitory proteins and a gene regulatory circuit with self-activation. Our theory establishes that the number of molecules of the conserved species is order parameters whose variation regulates bistable behaviour in the associated systems beyond the predictions of the mean-field theory. This prediction is fully confirmed by direct numerical simulations using the stochastic simulation algorithm. This result allows us to propose strategies whereby, by varying the number of molecules of the three conserved chemical species, cell properties associated to bistable behaviour (phenotype, cell-cycle status, etc.) can be controlled.

Influence of longitudinal position on the evolution of steady-state signal in cardiac cine balanced steady-state free precession imaging.

Science.gov (United States)

Spear, Tyler J; Stromp, Tori A; Leung, Steve W; Vandsburger, Moriel H

2017-11-01

Emerging quantitative cardiac magnetic resonance imaging (CMRI) techniques use cine balanced steady-state free precession (bSSFP) to measure myocardial signal intensity and probe underlying physiological parameters. This correlation assumes that steady-state is maintained uniformly throughout the heart in space and time. To determine the effects of longitudinal cardiac motion and initial slice position on signal deviation in cine bSSFP imaging by comparing two-dimensional (2D) and three-dimensional (3D) acquisitions. Nine healthy volunteers completed cardiac MRI on a 1.5-T scanner. Short axis images were taken at six slice locations using both 2D and 3D cine bSSFP. 3D acquisitions spanned two slices above and below selected slice locations. Changes in myocardial signal intensity were measured across the cardiac cycle and compared to longitudinal shortening. For 2D cine bSSFP, 46% ± 9% of all frames and 84% ± 13% of end-diastolic frames remained within 10% of initial signal intensity. For 3D cine bSSFP the proportions increased to 87% ± 8% and 97% ± 5%. There was no correlation between longitudinal shortening and peak changes in myocardial signal. The initial slice position significantly impacted peak changes in signal intensity for 2D sequences ( P  cine bSSFP that is only restored at the center of a 3D excitation volume. During diastole, a transient steady-state is established similar to that achieved with 3D cine bSSFP regardless of slice location.

The mechanisms of Excited states in enzymes

DEFF Research Database (Denmark)

Petersen, Frederic Nicolas Rønne; Bohr, Henrik

2010-01-01

Enzyme catalysis is studied on the basis of excited state processes, which are of electronic, vibrational and thermal nature. The ways of achieving the excited state, such as photo-absorption and ligand binding, are discussed and exemplified by various cases of enzymes.......Enzyme catalysis is studied on the basis of excited state processes, which are of electronic, vibrational and thermal nature. The ways of achieving the excited state, such as photo-absorption and ligand binding, are discussed and exemplified by various cases of enzymes....

Progress and prospect of true steady state operation with RF

Directory of Open Access Journals (Sweden)

Jacquinot Jean

2017-01-01

Full Text Available Operation of fusion confinement experiments in full steady state is a major challenge for the development towards fusion energy. Critical to achieving this goal is the availability of actively cooled plasma facing components and auxiliary systems withstanding the very harsh plasma environment. Equally challenging are physics issues related to achieving plasma conditions and current drive efficiency required by reactor plasmas. RF heating and current drive systems have been key instruments for obtaining the progress made until today towards steady state. They hold all the records of long pulse plasma operation both in tokamaks and in stellarators. Nevertheless much progress remains to be made in particular for integrating all the requirements necessary for maintaining in steady state the density and plasma pressure conditions of a reactor. This is an important stated aim of ITER and of devices equipped with superconducting magnets. After considering the present state of the art, this review will address the key issues which remain to be solved both in physics and technology for reaching this goal. They constitute very active subjects of research which will require much dedicated experimentation in the new generation of superconducting devices which are now in operation or becoming close to it.

Steady-state spheromak

International Nuclear Information System (INIS)

Jarboe, T.R.

1982-01-01

A major effort is being made in the national program to make the operation of axisymmetric, toroidal confinement systems steady state by the application of expensive rf current drive. Described here is a method by which such a confinement system, the spheromak, can be refluxed indefinitely through the application of dc power. As a step towards dc sustainment we have operated the present CTX source in the slow source mode with a longer power application time (approx. 0.1 ms) and successfully generated long-lived spheromaks. If the erosion of the electrodes can be controlled as well as it is with MPD arcs then dc operation should be very clean. If only a small fraction (approx. 10% for an experiment) of the poloidal flux of the spheromak connects to the source then the dc sustainment can be very efficient. The amount of connecting flux that is necessary for sustainment needs to be determined experimentally

The Steady State Calculation for SMART with MIDAS/SMR

International Nuclear Information System (INIS)

Park, Jong Hwa; Kim, Dong Ha; Chung, Young Jong; Park, Sun Hee; Cho, Seong Won

2010-01-01

KAERI is developing a new concept of reactor that all the main components such as the steam generator, the coolant pumps and the pressurizer are located inside the reactor vessel. Before the severe accident sequences are estimated, it is prerequisite that MIDAS code predicts the steady state conditions properly. But MIDAS code does not include the heat transfer model for the helical tube. Therefore, the heat transfer models for the helical tube from TASS/SMR-S were implemented into MIDAS code. To estimate the validity of the implemented heat transfer correlations for the helical tube and the input data, the steady state was recalculated with MIDAS/SMR based on design level 2 and compared with the design values

On the optimization of a steady-state bootstrap-reactor

International Nuclear Information System (INIS)

Polevoy, A.R.; Martynov, A.A.; Medvedev, S.Yu.

1993-01-01

A commercial fusion tokamak-reactor may be economically acceptable only for low recirculating power fraction r 0 ≡ P CD /P α BS ≡I BS /I > 0.9 to sustain the steady-state operation mode for high plasma densities > 1.5 10 20 m -3 , fulfilled the divertor conditions. This paper presents the approximate expressions for the optimal set of reactor parameters for r BS /I∼1, based on the self-consistent plasma simulations by 1.5D ASTRA code. The linear MHD stability analysis for ideal n=1 kink and ballooning modes has been carried out to determine the conditions of stabilization for bootstrap steady state tokamak reactor BSSTR configurations. (author) 10 refs., 1 tab

Some Investigations on Protease Enzyme Production Kinetics Using Bacillus licheniformis BBRC 100053 and Effects of Inhibitors on Protease Activity

Directory of Open Access Journals (Sweden)

Zahra Ghobadi Nejad

2014-01-01

Full Text Available Due to great commercial application of protease, it is necessary to study kinetic characterization of this enzyme in order to improve design of enzymatic reactors. In this study, mathematical modeling of protease enzyme production kinetics which is derived from Bacillus licheniformis BBRC 100053 was studied (at 37°C, pH 10 after 73 h in stationary phase, and 150 rpm. The aim of the present paper was to determine the best kinetic model and kinetic parameters for production of protease and calculating Ki (inhibition constant of different inhibitors to find the most effective one. The kinetic parameters Km (Michaelis-Menten constant and Vm (maximum rate were calculated 0.626 mM and 0.0523 mM/min. According to the experimental results, using DFP (diisopropyl fluorophosphate and PMSF (phenylmethanesulfonyl fluoride as inhibitors almost 50% of the enzyme activity could be inhibited when their concentrations were 0.525 and 0.541 mM, respectively. Ki for DFP and PMSF were 0.46 and 0.56 mM, respectively. Kinetic analysis showed that the Lineweaver-Burk model was the best fitting model for protease production kinetics DFP was more effective than PMSF and both of them should be covered in the group of noncompetitive inhibitors.

Steady-state creep of discontinuous fibre composites

International Nuclear Information System (INIS)

Boecker Pedersen, O.

1975-07-01

A review is given of the relevant literature on creep of composites, including a presentation of existing models for the steady-state creep of composites containing aligned discontinuous fibres where creep of the matrix and fibres is assumed to follow a power law. A model is suggested for predicting the composite creep law from a matrix creep law given in a general form, in the case where the fibres do not creep. The composite creep law predicted by this model is compared with those predicted by previous models, when these are extended to comprise a general matrix creep law. Experimentally, pure copper and composites consisting of aligned discontinuous tungsten fibres in a copper matrix were creep tested at a temperature of 500 deg C. The results indicate a relatively low stress sensitivity of the steady-state creep-rate for pure copper and relatively high stress sensitivity for the composites. This may be explained by the creep models based upon a general matrix creep law. A quantitative prediction shows promising agreement with the present experimental results. (author)

Steady state statistical correlations predict bistability in reaction motifs.

Science.gov (United States)

Chakravarty, Suchana; Barik, Debashis

2017-03-28

Various cellular decision making processes are regulated by bistable switches that take graded input signals and convert them to binary all-or-none responses. Traditionally, a bistable switch generated by a positive feedback loop is characterized either by a hysteretic signal response curve with two distinct signaling thresholds or by characterizing the bimodality of the response distribution in the bistable region. To identify the intrinsic bistability of a feedback regulated network, here we propose that bistability can be determined by correlating higher order moments and cumulants (≥2) of the joint steady state distributions of two components connected in a positive feedback loop. We performed stochastic simulations of four feedback regulated models with intrinsic bistability and we show that for a bistable switch with variation of the signal dose, the steady state variance vs. covariance adopts a signatory cusp-shaped curve. Further, we find that the (n + 1)th order cross-cumulant vs. nth order cross-cumulant adopts a closed loop structure for at least n = 3. We also propose that our method is capable of identifying systems without intrinsic bistability even though the system may show bimodality in the marginal response distribution. The proposed method can be used to analyze single cell protein data measured at steady state from experiments such as flow cytometry.

Understanding void fraction in steady state and dynamic environments

International Nuclear Information System (INIS)

Chexal, B.; Maulbetsch, J.; Harrison, J.; Petersen, C.; Jensen, P.; Horowitz, J.

1997-01-01

Understanding void fraction behavior in steady-state and dynamic environments is important to accurately predict the thermal-hydraulic behavior of two-phase or two-component systems. The Chexal-Lellouche (C-L) void fraction mode described herein covers the full range of pressures, flows, void fractions, and fluid types (steam-water, air-water, and refrigerants). A drift flux model formulation is used which covers the complete range of concurrent and countercurrent flows. The (1996) model revises the earlier C-L void fraction correlation, improves the capability of the model in countercurrent flow based on the incorporation of additional data, and improves the characteristics of the correlation that are important in transient programs. The model has been qualified with data from a number of steady state two-phase and two-component tests, and has been incorporated into the transient analysis code RELAP5 and RETRAN-3D and evaluated with a variety of transient and steady state tests. A 'plug-in' module for the void fraction correlation has been developed and implemented in RELAP5 and RETRAN-3D. The module is available as source code for inclusion into other thermal-hydraulic programs and can be used in any program that utilizes the same interface variables

Catalysis of Silver catfish Major Hepatic Glutathione Transferase proceeds via rapid equilibrium sequential random Mechanism

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Ayodele O. Kolawole

Full Text Available Fish hepatic glutathione transferases are connected with the elimination of intracellular pollutants and detoxification of organic micro-pollutants in their aquatic ecosystem. The two-substrate steady state kinetic mechanism of Silver catfish (Synodontis eupterus major hepatic glutathione transferases purified to apparent homogeneity was explored. The enzyme was dimeric enzyme with a monomeric size of 25.6 kDa. Initial-velocity studies and Product inhibition patterns by methyl glutathione and chloride with respect to GSH-CDNB; GSH-ρ-nitrophenylacetate; and GSH-Ethacrynic acid all conforms to a rapid equilibrium sequential random Bi Bi kinetic mechanism rather than steady state sequential random Bi Bi kinetic. α was 2.96 ± 0.35 for the model. The pH profile of Vmax/KM (with saturating 1-chloro-2,4-dinitrobenzene and variable GSH concentrations showed apparent pKa value of 6.88 and 9.86. Inhibition studies as a function of inhibitor concentration show that the enzyme is a homodimer and near neutral GST. The enzyme poorly conjugates 4-hydroxylnonenal and cumene hydroperoxide and may not be involved in oxidative stress protection. The seGST is unique and overwhelmingly shows characteristics similar to those of homodimeric class Pi GSTs, as was indicated by its kinetic mechanism, substrate specificity and inhibition studies. The rate- limiting step, probably the product release, of the reaction is viscosity-dependent and is consequential if macro-viscosogen or micro-viscosogen. Keywords: Silver catfish, Glutathione transferase, Steady-state, Kinetic mechanism, Inhibition

Developing a Steady-state Kinetic Model for Industrial Scale Semi-Regenerative Catalytic Naphtha Reforming Process

Directory of Open Access Journals (Sweden)

Seif Mohaddecy, R.

2014-05-01

Full Text Available Due to the demand for high octane gasoline as a transportation fuel, the catalytic naphtha reformer has become one of the most important processes in petroleum refineries. In this research, the steady-state modelling of a catalytic fixed-bed naphtha reforming process to predict the momentous output variables was studied. These variables were octane number, yield, hydrogen purity, and temperature of all reforming reactors. To do such a task, an industrial scale semi-regenerative catalytic naphtha reforming unit was studied and modelled. In addition, to evaluate the developed model, the predicted variables i.e. outlet temperatures of reactors, research octane number, yield of gasoline and hydrogen purity were compared against actual data. The results showed that there is a close mapping between the actual and predicted variables, and the mean relative absolute deviation of the mentioned process variables were 0.38 %, 0.52 %, 0.54 %, 0.32 %, 4.8 % and 3.2 %, respectively.

Extracting Steady State Components from Synchrophasor Data Using Kalman Filters

Directory of Open Access Journals (Sweden)

Farhan Mahmood

2016-04-01

Full Text Available Data from phasor measurement units (PMUs may be exploited to provide steady state information to the applications which require it. As PMU measurements may contain errors and missing data, the paper presents the application of a Kalman Filter technique for real-time data processing. PMU data captures the power system’s response at different time-scales, which are generated by different types of power system events; the presented Kalman Filter methods have been applied to extract the steady state components of PMU measurements that can be fed to steady state applications. Two KF-based methods have been proposed, i.e., a windowing-based KF method and “the modified KF”. Both methods are capable of reducing noise, compensating for missing data and filtering outliers from input PMU signals. A comparison of proposed methods has been carried out using the PMU data generated from a hardware-in-the-loop (HIL experimental setup. In addition, a performance analysis of the proposed methods is performed using an evaluation metric.

Interfacial binding of cutinase rather than its catalytic activity determines the steady state interfacial tension during oil drop lipid hydrolysis.

Science.gov (United States)

Flipsen, J A; van Schaick, M A; Dijkman, R; van der Hijden, H T; Verheij, H M; Egmond, M R

1999-02-01

Hydrolysis of triglycerides by cutinase from Fusarium solani pisi causes in oil drop tensiometer experiments a decrease of the interfacial tension. A series of cutinase variants with amino acid substitutions at its molecular surface yielded different values of the steady state interfacial tension. This tension value poorly correlated with the specific activity as such nor with the total activity (defined as the specific activity multiplied by the amount of enzyme bound) of the cutinase variants. Moreover, it appeared that at activity levels above 15% of that of wild type cutinase the contribution of hydrolysis to the decrease of the tension is saturating. A clear positive correlation was found between the interfacial tension plateau value and the interfacial binding of cutinase, as determined with attenuated total reflection Fourier transformed infrared spectroscopy (ATR-FTIR). These results indicate that the interfacial steady state level is not determined by the rate of hydrolysis, but mainly by the interfacial binding of cutinase.

Analysis of physical properties controlling steady-state infiltration rates on tropical savannah soils

International Nuclear Information System (INIS)

Mbagwu, J.S.C.

1993-10-01

A knowledge of physical properties influencing the steady-state infiltration rates (ic) of soils is needed for the hydrologic modelling of the infiltration process. In this study evidence is provided to show that effective porosity (Pe) (i.e. the proportion of macro pore spaces with equivalent radius of > 15 μm) and dry bulk density are the most important soil physical properties controlling the steady-state infiltration rates on a tropical savannah with varying land use histories. At a macro porosity value of ≤ 5.0% the steady-state infiltration rate is zero. Total porosity and the proportion of water-retaining pores explained only a small fraction of the variation in this property. Steady-state infiltration rates can also be estimated from either the saturated hydraulic conductivity (Ks) by the equation, i c = 31.1 + 1.06 (Ks), (R 2 = 0.8104, p ≤ 0.001) or the soil water transmissivity (A) by the equation, i c = 30.0 + 29.9(A), (R 2 = 0.8228, ρ ≤ 0.001). The Philip two-parameter model under predicted steady-state infiltration rates generally. Considering the ease of determination and reliability it is suggested that effective porosity be used to estimate the steady-state infiltration rates of these other soils with similar characteristics. The model is, i c 388.7(Pe) - 10.8(R 2 = 0.7265, p ≤ 0.001) where i c is in (cm/hr) and Pe in (cm 3 /cm 3 ). (author). 20 refs, 3 figs, 4 tabs

Full transmission modes and steady states in defect gratings,

NARCIS (Netherlands)

van Groesen, Embrecht W.C.; Sopaheluwakan, A.; Andonowati, A.; de Ridder, R.M; Altena, G; Geuzebroek, D.H.; Dekker, R

2003-01-01

For a symmetric grating structure with a defect, we show that a fully transmitted defect mode in the band gap can be obtained as a superposition of two steady states: an amplified and an attenuated defect state. Without scanning the whole band gap by transmission calculations, this simplifies the

Bioaccumulation factors and the steady state assumption for cesium isotopes in aquatic foodwebs near nuclear facilities.

Science.gov (United States)

Rowan, D J

2013-07-01

Steady state approaches, such as transfer coefficients or bioaccumulation factors, are commonly used to model the bioaccumulation of (137)Cs in aquatic foodwebs from routine operations and releases from nuclear generating stations and other nuclear facilities. Routine releases from nuclear generating stations and facilities, however, often consist of pulses as liquid waste is stored, analyzed to ensure regulatory compliance and then released. The effect of repeated pulse releases on the steady state assumption inherent in the bioaccumulation factor approach has not been evaluated. In this study, I examine the steady state assumption for aquatic biota by analyzing data for two cesium isotopes in the same biota, one isotope in steady state (stable (133)Cs) from geologic sources and the other released in pulses ((137)Cs) from reactor operations. I also compare (137)Cs bioaccumulation factors for similar upstream populations from the same system exposed solely to weapon test (137)Cs, and assumed to be in steady state. The steady state assumption appears to be valid for small organisms at lower trophic levels (zooplankton, rainbow smelt and 0+ yellow perch) but not for older and larger fish at higher trophic levels (walleye). Attempts to account for previous exposure and retention through a biokinetics approach had a similar effect on steady state, upstream and non-steady state, downstream populations of walleye, but were ineffective in explaining the more or less constant deviation between fish with steady state exposures and non-steady state exposures of about 2-fold for all age classes of walleye. These results suggest that for large, piscivorous fish, repeated exposure to short duration, pulse releases leads to much higher (137)Cs BAFs than expected from (133)Cs BAFs for the same fish or (137)Cs BAFs for similar populations in the same system not impacted by reactor releases. These results suggest that the steady state approach should be used with caution in any

Purification of SUMO conjugating enzymes and kinetic analysis of substrate conjugation

Science.gov (United States)

Yunus, Ali A.; Lima, Christopher D.

2009-01-01

SUMO conjugation to protein substrates requires the concerted action of a dedicated E2 ubiquitin conjugation enzyme (Ubc9) and associated E3 ligases. Although Ubc9 can directly recognize and modify substrate lysine residues that occur within a consensus site for SUMO modification, E3 ligases can redirect specificity and enhance conjugation rates during SUMO conjugation in vitro and in vivo. In this chapter, we will describe methods utilized to purify SUMO conjugating enzymes and model substrates which can be used for analysis of SUMO conjugation in vitro. We will also describe methods to extract kinetic parameters during E3-dependent or E3-independent substrate conjugation. PMID:19107417

Assessment of peripheral skeletal muscle microperfusion in a porcine model of peripheral arterial stenosis by steady-state contrast-enhanced ultrasound and Doppler flow measurement.

Science.gov (United States)

Naehle, Claas P; Steinberg, Verena A; Schild, Hans; Mommertz, Gottfried

2015-05-01

Noninvasive measurement of peripheral muscle microperfusion could potentially improve diagnosis, management, and treatment of peripheral arterial disease (PAD) and thus improve patient care. Contrast-enhanced ultrasound (CEUS) as a noninvasive diagnostic tool allows quantification of muscle perfusion. Increasing data on bolus technique CEUS reflecting microperfusion are becoming available, but only limited data on steady-state CEUS for assessment of muscle microperfusion are available. Therefore, the aim of this study was to evaluate steady-state CEUS for assessment of peripheral muscle microperfusion in a PAD animal model. In a porcine animal model, peripheral muscle microperfusion was quantified by steady-state CEUS replenishment kinetics (mean transit time [mTT] and wash-in rate [WiR]) of the biceps femoris muscle during intravenous steady-state infusion of INN-sulfur hexafluoride (SonoVue; Bracco, Geneva, Switzerland). In addition, macroperfusion was quantified at the external femoral artery with a Doppler flow probe. Peripheral muscle microperfusion and Doppler flow measurements were performed bilaterally at rest and under adenosine stress (70 μg/kg body weight) before and after unilateral creation of a moderate external iliac artery stenosis. All measurements could be performed completely in 10 pigs. Compared with baseline measurements, peripheral muscle microperfusion decreased significantly during adenosine stress (rest vs adenosine stress: mTT, 7.8 ± 3.3 vs 21.2 ± 17.8 s, P = .0006; WiR, 58.4 ± 38.1 vs 25.3 ± 15.6 arbitrary units [a.u.]/s, P flow, 122.3 ± 31.4 vs 83.6 ± 28.1 mL/min, P = .0067) and after stenosis creation (no stenosis vs stenosis: mTT, 8.1 ± 3.1 vs 29.2 ± 18.0 s, P = .0469; WiR, 53.0 ± 22.7 vs 13.6 ± 8.4 a.u./s, P = .0156; Doppler flow, 124.2 ± 41.8 vs 65.9 ± 40.0 mL/min, P = .0313). After stenosis creation, adenosine stress led to a further significant decrease of peripheral muscle microperfusion but had no effect on

Steady states of a diode with counterstreaming electron and positron beams

Energy Technology Data Exchange (ETDEWEB)

Ender, A. Ya.; Kuznetsov, V. I., E-mail: victor.kuznetsov@mail.ioffe.ru; Gruzdev, A. A. [Russian Academy of Sciences, Ioffe Institute (Russian Federation)

2016-10-15

Steady states of a plasma layer with counterstreaming beams of oppositely charged particles moving without collisions in a self-consistent electric field are analyzed. The study is aimed at clarifying the mechanism of generation and reconstruction of pulsar radiation. Such a layer also models the processes occurring in Knudsen plasma diodes with counterstreaming electron and ion beams. The steady-state solutions are exhaustively classified. The existence of several solutions at the same external parameters is established.

Feasibility study for improved steady-state initialization algorithms for the RELAP5 computer code

International Nuclear Information System (INIS)

Paulsen, M.P.; Peterson, C.E.; Katsma, K.R.

1993-04-01

A design for a new steady-state initialization method is presented that represents an improvement over the current method used in RELAP5. Current initialization methods for RELAP5 solve the transient fluidflow balance equations simulating a transient to achieve steady-state conditions. Because the transient solution is used, the initial conditions may change from the desired values requiring the use of controllers and long transient running times to obtain steady-state conditions for system problems. The new initialization method allows the user to fix thermal-hydraulic values in volumes and junctions where the conditions are best known and have the code compute the initial conditions in other areas of the system. The steady-state balance equations and solution methods are presented. The constitutive, component, and specialpurpose models are reviewed with respect to modifications required for the new steady-state initialization method. The requirements for user input are defined and the feasibility of the method is demonstrated with a testbed code by initializing some simple channel problems. The initialization of the sample problems using, the old and the new methods are compared

Time Reversibility, Correlation Decay and the Steady State Fluctuation Relation for Dissipation

Directory of Open Access Journals (Sweden)

Denis J. Evans

2013-04-01

Full Text Available Steady state fluctuation relations for nonequilibrium systems are under intense investigation because of their important practical implications in nanotechnology and biology. However the precise conditions under which they hold need clarification. Using the dissipation function, which is related to the entropy production of linear irreversible thermodynamics, we show time reversibility, ergodic consistency and a recently introduced form of correlation decay, called T-mixing, are sufficient conditions for steady state fluctuation relations to hold. Our results are not restricted to a particular model and show that the steady state fluctuation relation for the dissipation function holds near or far from equilibrium subject to these conditions. The dissipation function thus plays a comparable role in nonequilibrium systems to thermodynamic potentials in equilibrium systems.

Efficient decoding with steady-state Kalman filter in neural interface systems.

Science.gov (United States)

Malik, Wasim Q; Truccolo, Wilson; Brown, Emery N; Hochberg, Leigh R

2011-02-01

The Kalman filter is commonly used in neural interface systems to decode neural activity and estimate the desired movement kinematics. We analyze a low-complexity Kalman filter implementation in which the filter gain is approximated by its steady-state form, computed offline before real-time decoding commences. We evaluate its performance using human motor cortical spike train data obtained from an intracortical recording array as part of an ongoing pilot clinical trial. We demonstrate that the standard Kalman filter gain converges to within 95% of the steady-state filter gain in 1.5±0.5 s (mean ±s.d.). The difference in the intended movement velocity decoded by the two filters vanishes within 5 s, with a correlation coefficient of 0.99 between the two decoded velocities over the session length. We also find that the steady-state Kalman filter reduces the computational load (algorithm execution time) for decoding the firing rates of 25±3 single units by a factor of 7.0±0.9. We expect that the gain in computational efficiency will be much higher in systems with larger neural ensembles. The steady-state filter can thus provide substantial runtime efficiency at little cost in terms of estimation accuracy. This far more efficient neural decoding approach will facilitate the practical implementation of future large-dimensional, multisignal neural interface systems.

The quasi-steady state of the valley wind system

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Juerg eSchmidli

2015-12-01

Full Text Available The quasi-steady-state limit of the diurnal valley wind system is investigated overidealized three-dimensional topography. Although this limit is rarely attained inreality due to ever-changing forcings, the investigation of this limit canprovide valuable insight, in particular on the mass and heat fluxes associatedwith the along-valley wind. We derive a scaling relation for the quasi-steady-state along-valleymass flux as a function of valley geometry, valley size, atmospheric stratification,and surface sensible heat flux forcing. The scaling relation is tested by comparisonwith the mass flux diagnosed from numerical simulations of the valleywind system. Good agreement is found. The results also provide insight into the relationbetween surface friction and the strength of the along-valley pressure gradient.

Asymmetric effect of mechanical stress on the forward and reverse reaction catalyzed by an enzyme.

Directory of Open Access Journals (Sweden)

Collin Joseph

Full Text Available The concept of modulating enzymatic activity by exerting a mechanical stress on the enzyme has been established in previous work. Mechanical perturbation is also a tool for probing conformational motion accompanying the enzymatic cycle. Here we report measurements of the forward and reverse kinetics of the enzyme Guanylate Kinase from yeast (Saccharomyces cerevisiae. The enzyme is held in a state of stress using the DNA spring method. The observation that mechanical stress has different effects on the forward and reverse reaction kinetics suggests that forward and reverse reactions follow different paths, on average, in the enzyme's conformational space. Comparing the kinetics of the stressed and unstressed enzyme we also show that the maximum speed of the enzyme is comparable to the predictions of the relaxation model of enzyme action, where we use the independently determined dissipation coefficient [Formula: see text] for the enzyme's conformational motion. The present experiments provide a mean to explore enzyme kinetics beyond the static energy landscape picture of transition state theory.

A Review of Fusion and Tokamak Research Towards Steady-State Operation: A JAEA Contribution

Directory of Open Access Journals (Sweden)

Mitsuru Kikuchi

2010-11-01

Full Text Available Providing a historical overview of 50 years of fusion research, a review of the fundamentals and concepts of fusion and research efforts towards the implementation of a steady state tokamak reactor is presented. In 1990, a steady-state tokamak reactor (SSTR best utilizing the bootstrap current was developed. Since then, significant efforts have been made in major tokamaks, including JT-60U, exploring advanced regimes relevant to the steady state operation of tokamaks. In this paper, the fundamentals of fusion and plasma confinement, and the concepts and research on current drive and MHD stability of advanced tokamaks towards realization of a steady-state tokamak reactor are reviewed, with an emphasis on the contributions of the JAEA. Finally, a view of fusion energy utilization in the 21st century is introduced.

Finite element modelling of creep process - steady state stresses and strains

Directory of Open Access Journals (Sweden)

Sedmak Aleksandar S.

2014-01-01

Full Text Available Finite element modelling of steady state creep process has been described. Using an analogy of visco-plastic problem with a described procedure, the finite element method has been used to calculate steady state stresses and strains in 2D problems. An example of application of such a procedure have been presented, using real life problem - cylindrical pipe with longitudinal crack at high temperature, under internal pressure, and estimating its residual life, based on the C*integral evaluation.

Multiple solutions of steady-state Poisson–Nernst–Planck equations with steric effects

International Nuclear Information System (INIS)

Lin, Tai-Chia; Eisenberg, Bob

2015-01-01

Experiments measuring currents through single protein channels show unstable currents. Channels switch between ‘open’ or ‘closed’ states in a spontaneous stochastic process called gating. Currents are either (nearly) zero or at a definite level, characteristic of each type of protein, independent of time, once the channel is open. The steady state Poisson–Nernst–Planck equations with steric effects (PNP-steric equations) describe steady current through the open channel quite well, in a wide variety of conditions. Here we study the existence of multiple solutions of steady state PNP-steric equations to see if they themselves, without modification or augmentation, can describe two levels of current. We prove that there are two steady state solutions of PNP-steric equations for (a) three types of ion species (two types of cations and one type of anion) with a positive constant permanent charge, and (b) four types of ion species (two types of cations and their counter-ions) with a constant permanent charge but no sign condition. The excess currents (due to steric effects) associated with these two steady state solutions are derived and expressed as two distinct formulas. Our results indicate that PNP-steric equations may become a useful model to study spontaneous gating of ion channels. Spontaneous gating is thought to involve small structural changes in the channel protein that perhaps produce large changes in the profiles of free energy that determine ion flow. Gating is known to be modulated by external structures. Both can be included in future extensions of our present analysis. (paper)

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

Science.gov (United States)

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

2001-02-01

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

40 CFR 86.1363-2007 - Steady-state testing with a discrete-mode cycle.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 19 2010-07-01 2010-07-01 false Steady-state testing with a discrete-mode cycle. 86.1363-2007 Section 86.1363-2007 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Exhaust Test Procedures § 86.1363-2007 Steady-state testing with a discrete-mode cycle. This section...

Decarboxylation of Malate in the Crassulacean Acid Metabolism Plant Bryophyllum (Kalanchoe) fedtschenkoi (Role of NAD-Malic Enzyme).

Science.gov (United States)

Cook, R. M.; Lindsay, J. G.; Wilkins, M. B.; Nimmo, H. G.

1995-01-01

The role of NAD-malic enzyme (NAD-ME) in the Crassulacean acid metabolism plant Bryophyllum (Kalanchoe) fedtschenkoi was investigated using preparations of intact and solubilized mitochondria from fully expanded leaves. Intact, coupled mitochondria isolated during the day or night did not differ in their ability to take up [14C]malic acid from the surrounding medium or to respire using malate or succinate as substrate. However, intact mitochondria isolated from plants during the day decarboxylated added malate to pyruvate significantly faster than mitochondria isolated from plants at night. NAD-ME activity in solubilized mitochondrial extracts showed hysteretic kinetics and was stimulated by a number of activators, including acetyl-coenzyme A, fructose-1,6-bisphosphate, and sulfate ions. In the absence of these effectors, reaction progress curves were nonlinear, with a pronounced acceleration phase. The lag period before a steady-state rate was reached in assays of mitochondrial extracts decreased during the photoperiod and increased slowly during the period of darkness. However, these changes in the kinetic properties of the enzyme could not account for the changes in the rate of decarboxylation of malate by intact mitochondria. Gel-filtration experiments showed that mitochondrial extracts contained three forms of NAD-ME with different molecular weights. The relative proportions of the three forms varied somewhat throughout the light/dark cycle, but this did not account for the changes in the kinetics behavior of the enzyme during the diurnal cycle. PMID:12228671

Quantitative kinetics of proteolytic enzymes determined by a surface concentration-based assay using peptide arrays.

Science.gov (United States)

Jung, Se-Hui; Kong, Deok-Hoon; Park, Seoung-Woo; Kim, Young-Myeong; Ha, Kwon-Soo

2012-08-21

Peptide arrays have emerged as a key technology for drug discovery, diagnosis, and cell biology. Despite the promise of these arrays, applications of peptide arrays to quantitative analysis of enzyme kinetics have been limited due to the difficulty in obtaining quantitative information of enzymatic reaction products. In this study, we developed a new approach for the quantitative kinetics analysis of proteases using fluorescence-conjugated peptide arrays, a surface concentration-based assay with solid-phase peptide standards using dry-off measurements, and compared it with an applied concentration-based assay. For fabrication of the peptide arrays, substrate peptides of cMMP-3, caspase-3, caspase-9, and calpain-1 were functionalized with TAMRA and cysteine, and were immobilized onto amine-functionalized arrays using a heterobifunctional linker, N-[γ-maleimidobutyloxy]succinimide ester. The proteolytic activities of the four enzymes were quantitatively analyzed by calculating changes induced by enzymatic reactions in the concentrations of peptides bound to array surfaces. In addition, this assay was successfully applied for calculating the Michaelis constant (K(m,surf)) for the four enzymes. Thus, this new assay has a strong potential for use in the quantitative evaluation of proteases, and for drug discovery through kinetics studies including the determination of K(m) and V(max).

Herd-Level Modeling and Steady-State Livestock Productivity ...

African Journals Online (AJOL)

... an outline of the scope for applications and addresses the prospects for refinement and model extensions. The algorithms for use in development of steady state derivations include transition of matrices in a Markov Chain approach, continuous differential equations and actuarial approach built on life and fecundity tables.

Principle of Entropy Maximization for Nonequilibrium Steady States

DEFF Research Database (Denmark)

Shapiro, Alexander; Stenby, Erling Halfdan

2002-01-01

The goal of this contribution is to find out to what extent the principle of entropy maximization, which serves as a basis for the equilibrium thermodynamics, may be generalized onto non-equilibrium steady states. We prove a theorem that, in the system of thermodynamic coordinates, where entropy...

Steady-state operation of spheromaks by inductive techniques

International Nuclear Information System (INIS)

Janos, A.

1984-04-01

A method to maintain a steady-state spheromak configuration inductively using the S-1 Spheromak device is described. The S-1 Spheromak formation apparatus can be utilized to inject magnetic helicity continuously (C.W., not pulsed or D.C.) into the spheromak configuration after equilibrium is achieved in the linked mode of operation. Oscillation of both poloidal- and toroidal-field currents in the flux core (psi-phi Pumping), with proper phasing, injects a net time-averaged helicity into the plasma. Steady-state maintenance relies on flux conversion, which has been earlier identified. Relevant experimental data from the operation of S-1 are described. Helicity flow has been measured and the proposed injection scheme simulated. In a reasonable time practical voltages and frequencies can inject an amount of helicity comparable to that in the initial plasma. Plasma currents can be maintained or increased. This pumping technique is similar to F-THETA Pumping of a Reversed-Field-Pinch but is applied to this inverse-pinch formation

Antioxidant pool in beer and kinetics of EPR spin-trapping.

Science.gov (United States)

Kocherginsky, Nikolai M; Kostetski, Yuri Yu; Smirnov, Alex I

2005-08-24

The kinetics of spin-trap adduct formation in beer oxidation exhibits an induction period if the reaction is carried out at elevated temperatures and in the presence of air. This lag period lasts until the endogenous antioxidants are almost completely depleted, and its duration is used as an indicator of the flavor stability and shelf life of beer. This paper demonstrates that the total kinetics of the process can be characterized by three parameters-the lag period, the rate of spin-trap adduct formation, and, finally, the steady-state spin-adduct concentration. A steady-state chain reaction mechanism is described, and quantitative estimates of the main kinetic parameters such as the initiation rate, antioxidant pool, effective content of organic molecules participating in the chain reactions, and the rate constant of the 1-hydroxyethyl radical EtOH(*) spin-adduct disappearance are given. An additional new dimensionless parameter is suggested to characterize the antioxidant pool-the product of the lag time and the rate of spin-trap radical formation immediately after the lag time, normalized by the steady-state concentration of the adducts. The results of spin-tapping EPR experiments are compared with the nitroxide reduction kinetics measured in the same beer samples. It is shown that although the kinetics of nitroxide reduction in beer can be used to evaluate the reducing power of beer, the latter parameter does not correlate with the antioxidant pool. The relationship of free radical processes, antioxidant pool, reducing power, and beer staling is discussed.

Steady-state solidification of aqueous ammonium chloride

Science.gov (United States)

Peppin, S. S. L.; Huppert, Herbert E.; Worster, M. Grae

We report on a series of experiments in which a Hele-Shaw cell containing aqueous solutions of NH4Cl was translated at prescribed rates through a steady temperature gradient. The salt formed the primary solid phase of a mushy layer as the solution solidified, with the salt-depleted residual fluid driving buoyancy-driven convection and the development of chimneys in the mushy layer. Depending on the operating conditions, several morphological transitions occurred. A regime diagram is presented quantifying these transitions as a function of freezing rate and the initial concentration of the solution. In general, for a given concentration, increasing the freezing rate caused the steady-state system to change from a convecting mushy layer with chimneys to a non-convecting mushy layer below a relatively quiescent liquid, and then to a much thinner mushy layer separated from the liquid by a region of active secondary nucleation. At higher initial concentrations the second of these states did not occur. At lower concentrations, but still above the eutectic, the mushy layer disappeared. A simple mathematical model of the system is developed which compares well with the experimental measurements of the intermediate, non-convecting state and serves as a benchmark against which to understand some of the effects of convection. Movies are available with the online version of the paper.

Kinetic investigation of heterogeneous catalytic reactions by means of the kinetic isotope method

Energy Technology Data Exchange (ETDEWEB)

Bauer, F; Dermietzel, J [Akademie der Wissenschaften der DDR, Leipzig. Zentralinstitut fuer Isotopen- und Strahlenforschung

1978-09-01

The application of the kinetic isotope method to heterogeneous catalytic processes is possible for surface compounds by using the steady-state relation. However, the characterization of intermediate products becomes ambiguous if sorption rates are of the same order of magnitude as surface reactions rates. The isotopic exchange reaction renders possible the estimation of sorption rates.

Statistical steady states in turbulent droplet condensation

Science.gov (United States)

Bec, Jeremie; Krstulovic, Giorgio; Siewert, Christoph

2017-11-01

We investigate the general problem of turbulent condensation. Using direct numerical simulations we show that the fluctuations of the supersaturation field offer different conditions for the growth of droplets which evolve in time due to turbulent transport and mixing. This leads to propose a Lagrangian stochastic model consisting of a set of integro-differential equations for the joint evolution of the squared radius and the supersaturation along droplet trajectories. The model has two parameters fixed by the total amount of water and the thermodynamic properties, as well as the Lagrangian integral timescale of the turbulent supersaturation. The model reproduces very well the droplet size distributions obtained from direct numerical simulations and their time evolution. A noticeable result is that, after a stage where the squared radius simply diffuses, the system converges exponentially fast to a statistical steady state independent of the initial conditions. The main mechanism involved in this convergence is a loss of memory induced by a significant number of droplets undergoing a complete evaporation before growing again. The statistical steady state is characterised by an exponential tail in the droplet mass distribution.

The renneting of milk : a kinetic study of the enzymic and aggregation reactions

NARCIS (Netherlands)

Hooydonk, van A.C.M.

1987-01-01

The rennet-induced clotting of milk was studied under various conditions. The kinetics of the enzymic and aggregation reactions was analysed separately and, where possible, related to the physico-chemical properties of the casein micelle and its environment.

The effects of important

ATC calculation with steady-state security constraints using Benders decomposition

International Nuclear Information System (INIS)

Shaaban, M.; Yan, Z.; Ni, Y.; Wu, F.; Li, W.; Liu, H.

2003-01-01

Available transfer capability (ATC) is an important indicator of the usable amount of transmission capacity accessible by assorted parties for commercial trading, ATC calculation is nontrivial when steady-state security constraints are included. In hie paper, Benders decomposition method is proposed to partition the AC problem with steady-state security constraints into a base case master problem and a series of subproblems relevant to various contingencies to include their impacts on ATC. The mathematical model is formulated and the two solution schemes are presented. Computer testing on the 4-bus system and IEEE 30-bus system shows the effectiveness of the proposed method and the solution schemes. (Author)

Enzymes as Biocatalysts for Lipid-based Bioproducts Processing

DEFF Research Database (Denmark)

Cheong, Ling-Zhi; Guo, Zheng; Fedosov, Sergey

2012-01-01

Bioproducts are materials, chemicals and energy derived from renewable biological resources such as agriculture, forestry, and biologically-derived wastes. To date, the use of enzymes as biocatalysts for lipid-based bioproducts processing has shown marked increase. This is mainly due to the fact...... that cost benefit derived from enzymatic processing such as enzyme specificity, higher product purity and lesser or none toxic waste disposal has surpassed the cost of biocatalysts itself. This chapter provided insights into distinct enzymes characteristics essential in industrial processing especially...... enzymes kinetics. Understanding of enzyme kinetics is important especially in designing efficient reaction set-ups including type of bioreactors, reaction conditions and reusability of biocatalysts to ensure efficient running cost. A brief review of state-of-the-art in industrial applications of enzymes...

How should we understand non-equilibrium many-body steady states?

Science.gov (United States)

Maghrebi, Mohammad; Gorshkov, Alexey

: Many-body systems with both coherent dynamics and dissipation constitute a rich class of models which are nevertheless much less explored than their dissipationless counterparts. The advent of numerous experimental platforms that simulate such dynamics poses an immediate challenge to systematically understand and classify these models. In particular, nontrivial many-body states emerge as steady states under non-equilibrium dynamics. In this talk, I use a field-theoretic approach based on the Keldysh formalism to study nonequilibrium phases and phase transitions in such models. I show that an effective temperature generically emerges as a result of dissipation, and the universal behavior including the dynamics near the steady state is described by a thermodynamic universality class. In the end, I will also discuss possibilities that go beyond the paradigm of an effective thermodynamic behavior.

An implicit steady-state initialization package for the RELAP5 computer code

International Nuclear Information System (INIS)

Paulsen, M.P.; Peterson, C.E.; Odar, F.

1995-08-01

A direct steady-state initialization (DSSI) method has been developed and implemented in the RELAP5 hydrodynamic analysis program. It provides a means for users to specify a small set of initial conditions which are then propagated through the remainder of the system. The DSSI scheme utilizes the steady-state form of the RELAP5 balance equations for nonequilibrium two-phase flow. It also employs the RELAP5 component models and constitutive model packages for wall-to-phase and interphase momentum and heat exchange. A fully implicit solution of the linearized hydrodynamic equations is implemented. An implicit coupling scheme is used to augment the standard steady-state heat conduction solution for steam generator use. It solves the primary-side tube region energy equations, heat conduction equations, wall heat flux boundary conditions, and overall energy balance equation as a coupled system of equations and improves convergence. The DSSI method for initializing RELAP5 problems to steady-state conditions has been compared with the transient solution scheme using a suite of test problems including; adiabatic single-phase liquid and vapor flow through channels with and without healing and area changes; a heated two-phase test bundle representative of BWR core conditions; and a single-loop PWR model

Kinetic isotope effect studies on milk xanthine oxidase and on chicken liver xanthine dehydrogenase

International Nuclear Information System (INIS)

D'Ardenne, S.C.; Edmondson, D.E.

1990-01-01

The effect of isotopic substitution of the 8-H of xanthine (with 2 H and 3 H) on the rate of oxidation by bovine xanthine oxidase and by chicken xanthine dehydrogenase has been measured. V/K isotope effects were determined from competition experiments. No difference in H/T (V/K) values was observed between xanthine oxidase and xanthine dehydrogenase. Xanthine dehydrogenase exhibited a larger T/D (V/K) value than that observed for xanthine oxidase. Observed H/T (V/K) values for either enzyme are less than those H/T (V/K) values calculated with D/T (V/K) data. These discrepancies are suggested to arise from the presence of a rate-limiting step(s) prior to the irreversible C-H bond cleavage step in the mechanistic pathways of both enzymes. These kinetic complexities preclude examination of whether tunneling contributes to the reaction coordinate for the H-transfer step in each enzyme. No observable exchange of tritium with solvent is observed during the anaerobic incubation of [8- 3 H]xanthine with either enzyme, which suggests the reverse commitment to catalysis (C r ) is essentially zero. With the assumption of adherence to reduced mass relationships, the intrinsic deuterium isotope effect ( D k) for xanthine oxidation is calculated. By the use of these values and steady-state kinetic data, the minimal rate for the hydrogen-transfer step is calculated to be ∼75-fold faster than k cat for xanthine oxidase and ∼10-fold faster than k cat for xanthine dehydrogenase. Values calculated for each enzyme were found to be identical within experimental uncertainty

Computational multiple steady states for enzymatic esterification of ethanol and oleic acid in an isothermal CSTR.

Science.gov (United States)

Ho, Pang-Yen; Chuang, Guo-Syong; Chao, An-Chong; Li, Hsing-Ya

2005-05-01

The capacity of complex biochemical reaction networks (consisting of 11 coupled non-linear ordinary differential equations) to show multiple steady states, was investigated. The system involved esterification of ethanol and oleic acid by lipase in an isothermal continuous stirred tank reactor (CSTR). The Deficiency One Algorithm and the Subnetwork Analysis were applied to determine the steady state multiplicity. A set of rate constants and two corresponding steady states are computed. The phenomena of bistability, hysteresis and bifurcation are discussed. Moreover, the capacity of steady state multiplicity is extended to the family of the studied reaction networks.

A quaternionic map for the steady states of the Heisenberg spin-chain

Energy Technology Data Exchange (ETDEWEB)

Mehta, Mitaxi P., E-mail: mitaxi.mehta@ahduni.edu.in [IICT, Ahmedabad University, Opp. IIM, Navrangpura, Ahmedabad (India); Dutta, Souvik; Tiwari, Shubhanshu [BITS-Pilani, K.K. Birla Goa campus, Goa (India)

2014-01-17

We show that the steady states of the classical Heisenberg XXX spin-chain in an external magnetic field can be found by iterations of a quaternionic map. A restricted model, e.g., the xy spin-chain is known to have spatially chaotic steady states and the phase space occupied by these chaotic states is known to go through discrete changes as the field strength is varied. The same phenomenon is studied for the xxx spin-chain. It is seen that in this model the phase space volume varies smoothly with the external field.

A quaternionic map for the steady states of the Heisenberg spin-chain

International Nuclear Information System (INIS)

Mehta, Mitaxi P.; Dutta, Souvik; Tiwari, Shubhanshu

2014-01-01

We show that the steady states of the classical Heisenberg XXX spin-chain in an external magnetic field can be found by iterations of a quaternionic map. A restricted model, e.g., the xy spin-chain is known to have spatially chaotic steady states and the phase space occupied by these chaotic states is known to go through discrete changes as the field strength is varied. The same phenomenon is studied for the xxx spin-chain. It is seen that in this model the phase space volume varies smoothly with the external field.

Characterization of electron states in dense plasmas and its use in atomic kinetics modeling

International Nuclear Information System (INIS)

Fisher, D.V.; Maron, Y.

2003-01-01

We describe a self-consistent statistical approach to account for plasma density effects in collisional-radiative kinetics. The approach is based on the characterization of three distinct types of electron states, namely, bound, collectivized, and free, and on the formalism of the effective statistical weights (ESW) of the bound states. The present approach accounts for individual and collective effects of the surrounding electrons and ions on atomic (ionic) electron states. High-accuracy expressions for the ESWs of bound states have been derived. The notions of ionization stage population, free electron density, and rate coefficient are redefined in accordance with the present characterization scheme. The modified expressions for the probabilities of electron-impact induced transitions as well as spontaneous and induced radiative transitions are then obtained. The influence of collectivized states on a dense plasma ionization composition is demonstrated to be strong. Examples of calculated ESWs and populations of ionic quantum states for steady state and transient plasmas are given

A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles.

Science.gov (United States)

Kitayama, Tomoya; Kinoshita, Ayako; Sugimoto, Masahiro; Nakayama, Yoichi; Tomita, Masaru

2006-07-17

In order to improve understanding of metabolic systems there have been attempts to construct S-system models from time courses. Conventionally, non-linear curve-fitting algorithms have been used for modelling, because of the non-linear properties of parameter estimation from time series. However, the huge iterative calculations required have hindered the development of large-scale metabolic pathway models. To solve this problem we propose a novel method involving power-law modelling of metabolic pathways from the Jacobian of the targeted system and the steady-state flux profiles by linearization of S-systems. The results of two case studies modelling a straight and a branched pathway, respectively, showed that our method reduced the number of unknown parameters needing to be estimated. The time-courses simulated by conventional kinetic models and those described by our method behaved similarly under a wide range of perturbations of metabolite concentrations. The proposed method reduces calculation complexity and facilitates the construction of large-scale S-system models of metabolic pathways, realizing a practical application of reverse engineering of dynamic simulation models from the Jacobian of the targeted system and steady-state flux profiles.

A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles

Directory of Open Access Journals (Sweden)

Sugimoto Masahiro

2006-07-01

Full Text Available Abstract Background In order to improve understanding of metabolic systems there have been attempts to construct S-system models from time courses. Conventionally, non-linear curve-fitting algorithms have been used for modelling, because of the non-linear properties of parameter estimation from time series. However, the huge iterative calculations required have hindered the development of large-scale metabolic pathway models. To solve this problem we propose a novel method involving power-law modelling of metabolic pathways from the Jacobian of the targeted system and the steady-state flux profiles by linearization of S-systems. Results The results of two case studies modelling a straight and a branched pathway, respectively, showed that our method reduced the number of unknown parameters needing to be estimated. The time-courses simulated by conventional kinetic models and those described by our method behaved similarly under a wide range of perturbations of metabolite concentrations. Conclusion The proposed method reduces calculation complexity and facilitates the construction of large-scale S-system models of metabolic pathways, realizing a practical application of reverse engineering of dynamic simulation models from the Jacobian of the targeted system and steady-state flux profiles.

Caseoperoxidase, mixed β-casein-SDS-hemin-imidazole complex: a nano artificial enzyme.

Science.gov (United States)

Moosavi-Movahedi, Zainab; Gharibi, Hussein; Hadi-Alijanvand, Hamid; Akbarzadeh, Mohammad; Esmaili, Mansoore; Atri, Maliheh S; Sefidbakht, Yahya; Bohlooli, Mousa; Nazari, Khodadad; Javadian, Soheila; Hong, Jun; Saboury, Ali A; Sheibani, Nader; Moosavi-Movahedi, Ali A

2015-01-01

A novel peroxidase-like artificial enzyme, named "caseoperoxidase", was biomimetically designed using a nano artificial amino acid apo-protein hydrophobic pocket. This four-component nano artificial enzyme containing heme-imidazole-β-casein-SDS exhibited high activity growth and k(cat) performance toward the native horseradish peroxidase demonstrated by the steady state kinetics using UV-vis spectrophotometry. The hydrophobicity and secondary structure of the caseoperoxidase were studied by ANS fluorescence and circular dichroism spectroscopy. Camel β-casein (Cβ-casein) was selected as an appropriate apo-protein for the heme active site because of its innate flexibility and exalted hydrophobicity. This selection was confirmed by homology modeling method. Heme docking into the newly obtained Cβ-casein structure indicated one heme was mainly incorporated with Cβ-casein. The presence of a main electrostatic site for the active site in the Cβ-casein was also confirmed by experimental methods through Wyman binding potential and isothermal titration calorimetry. The existence of Cβ-casein protein in this biocatalyst lowered the suicide inactivation and provided a suitable protective role for the heme active-site. Additional experiments confirmed the retention of caseoperoxidase structure and function as an artificial enzyme.

Steady state ion acceleration by a circularly polarized laser pulse

International Nuclear Information System (INIS)

Zhang Xiaomei; Shen Baifei; Cang Yu; Li Xuemei; Jin Zhangying; Wang Fengchao

2007-01-01

The steady state ion acceleration at the front of a cold solid target by a circularly polarized flat-top laser pulse is studied with one-dimensional particle-in-cell (PIC) simulation. A model that ions are reflected by a steady laser-driven piston is used by comparing with the electrostatic shock acceleration. A stable profile with a double-flat-top structure in phase space forms after ions enter the undisturbed region of the target with a constant velocity

A Novel Chronic Opioid Monitoring Tool to Assess Prescription Drug Steady State Levels in Oral Fluid.

Science.gov (United States)

Shaparin, Naum; Mehta, Neel; Kunkel, Frank; Stripp, Richard; Borg, Damon; Kolb, Elizabeth

2017-11-01

Interpretation limitations of urine drug testing and the invasiveness of blood toxicology have motivated the desire for the development of simpler methods to assess biologically active drug levels on an individualized patient basis. Oral fluid is a matrix well-suited for the challenge because collections are based on simple noninvasive procedures and drug concentrations better correlate to blood drug levels as oral fluid is a filtrate of the blood. Well-established pharmacokinetic models were utilized to generate oral fluid steady state concentration ranges to assess the interpretive value of the alternative matrix to monitor steady state plasma oxycodone levels. Paired oral fluid and plasma samples were collected from patients chronically prescribed oxycodone and quantitatively analyzed by liquid chromatography tandem mass spectrometry. Steady state plasma concentration ranges were calculated for each donor and converted to an equivalent range in oral fluid. Measured plasma and oral fluid oxycodone concentrations were compared with respective matrix-matched steady state ranges, using each plasma steady state classification as the control. A high degree of correlation was observed between matrices when classifying donors according to expected steady state oxycodone concentration. Agreement between plasma and oral fluid steady state classifications was observed in 75.6% of paired samples. This study supports novel application of basic pharmacokinetic knowledge to the pain management industry, simplifying and improving individualized drug monitoring and risk assessment through the use of oral fluid drug testing. Many benefits of established therapeutic drug monitoring in plasma can be realized in oral fluid for patients chronically prescribed oxycodone at steady state. © 2017 American Academy of Pain Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Poiseuille flow of soft glasses in narrow channels: from quiescence to steady state.

Science.gov (United States)

Chaudhuri, Pinaki; Horbach, Jürgen

2014-10-01

Using numerical simulations, the onset of Poiseuille flow in a confined soft glass is investigated. Starting from the quiescent state, steady flow sets in at a time scale which increases with a decrease in applied forcing. At this onset time scale, a rapid transition occurs via the simultaneous fluidization of regions having different local stresses. In the absence of steady flow at long times, creep is observed even in regions where the local stress is larger than the bulk yielding threshold. Finally, we show that the time scale to attain steady flow depends strongly on the history of the initial state.

Steady-state bifurcations of the three-dimensional Kolmogorov problem

Directory of Open Access Journals (Sweden)

Zhi-Min Chen

2000-08-01

Full Text Available This paper studies the spatially periodic incompressible fluid motion in $mathbb R^3$ excited by the external force $k^2(sin kz, 0,0$ with $kgeq 2$ an integer. This driving force gives rise to the existence of the unidirectional basic steady flow $u_0=(sin kz,0, 0$ for any Reynolds number. It is shown in Theorem 1.1 that there exist a number of critical Reynolds numbers such that $u_0$ bifurcates into either 4 or 8 or 16 different steady states, when the Reynolds number increases across each of such numbers.

Existence and instability of steady states for a triangular cross-diffusion system: A computer-assisted proof

Science.gov (United States)

Breden, Maxime; Castelli, Roberto

2018-05-01

In this paper, we present and apply a computer-assisted method to study steady states of a triangular cross-diffusion system. Our approach consist in an a posteriori validation procedure, that is based on using a fixed point argument around a numerically computed solution, in the spirit of the Newton-Kantorovich theorem. It allows to prove the existence of various non homogeneous steady states for different parameter values. In some situations, we obtain as many as 13 coexisting steady states. We also apply the a posteriori validation procedure to study the linear stability of the obtained steady states, proving that many of them are in fact unstable.

Steady-state heat transfer in an inverted U-tube steam generator

International Nuclear Information System (INIS)

Boucher, T.J.

1987-01-01

Experimental results are presented involving U-tube steam generator tube bundle local heat transfer and fluid conditions during stead-state, full-power operations performed at high temperatures and pressures with conditions typical of a pressurized water reactor (15.0 MPa primary pressure, 600 K steam generator inlet plenum fluid temperatures, 6.2 MPa secondary pressure). The Semiscale (MOD-2C facility represents the state-of-the-art in measurement of tube local heat transfer data and average tube bundle secondary fluid density at several elevations, which allows an estimate of the axial heat transfer and void distributions during steady-state and transient operations. The method of heat transfer data reduction is presented and the heat flux, secondary convective heat transfer coefficient, and void fraction distributions are quantified for steady-state, full-power operations

Enzyme Kinetics By Directly Imaging A Porous Silicon Microfluidic Reactor Using Desorption/Ionization on Silicon Mass Spectrometry

NARCIS (Netherlands)

Nichols, K.P.F.; Azoz, Seyla; Gardeniers, Johannes G.E.

2008-01-01

Enzyme kinetics were obtained in a porous silicon microfluidic channel by combining an enzyme and substrate droplet, allowing them to react and deposit a small amount of residue on the channel walls, and then analyzing this residue by directly ionizing the channel walls using a matrix assisted laser

Kinetic model for an up-flow anaerobic packed bed bioreactor: Dairy ...

African Journals Online (AJOL)

Kinetic studies of anaerobic digestion process of cheese whey were conducted in a pilot-scale up-flow anaerobic packed bed bioreactor (UAPB). An influent COD concentration of 59419 mg/l was utilized at steady state condition. Logistic and Monod kinetic models were employed to describe microbial activities of cheese ...

Expression and kinetic properties of a recombinant 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase isoenzyme of human liver.

Science.gov (United States)

Deyashiki, Y; Tamada, Y; Miyabe, Y; Nakanishi, M; Matsuura, K; Hara, A

1995-08-01

Human liver cytosol contains multiple forms of 3 alpha-hydroxysteroid dehydrogenase and dihydrodiol dehydrogenase with hydroxysteroid dehydrogenase activity, and multiple cDNAs for the enzymes have been cloned from human liver cDNA libraries. To understand the relationship of the multiple enzyme froms to the genes, a cDNA, which has been reported to code for an isoenzyme of human liver 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase, was expressed in Escherichia coli. The recombinant enzyme showed structural and functional properties almost identical to those of the isoenzyme purified from human liver. In addition, the recombinant isoenzyme efficiently reduced 5 alpha-dihydrotestosterone and 5 beta-dihydrocortisone, the known substrates of human liver 3 alpha-hydroxysteroid dehydrogenase and chlordecone reductase previously purified, which suggests that these human liver enzymes are identical. Furthermore, the steady-state kinetic data for NADP(+)-linked (S)-1-indanol oxidation by the recombinant isoenzyme were consistent with a sequential ordered mechanism in which NADP+ binds first. Phenolphthalein inhibited this isoenzyme much more potently than it did the other human liver dihydrodiol dehydrogenases, and was a competitive inhibitor (Ki = 20 nM) that bound to the enzyme-NADP+ complex.

Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes

Czech Academy of Sciences Publication Activity Database

Müller, Stefan; Regensburger, G.; Steuer, Ralf

2014-01-01

Roč. 347, APR 2014 (2014), s. 182-190 ISSN 0022-5193 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : metabolic optimization * enzyme kinetics * oriented matroid * elementary vector * conformal sum Subject RIV: EI - Biotechnology ; Bionics Impact factor: 2.116, year: 2014

An accelerator based steady state neutron source

International Nuclear Information System (INIS)

Burke, R.J.; Johnson, D.L.

1985-01-01

Using high current, c.w. linear accelerator technology, a spallation neutron source can achieve much higher average intensities than existing or proposed pulsed spallation sources. With about 100 mA of 300 MeV protons or deuterons, the Accelerator Based Neutron Research Facility (ABNR) would initially achieve the 10 16 n/cm 2 .s thermal flux goal of the advanced steady state neutron source, and upgrading could provide higher steady state fluxes. The relatively low ion energy compared to other spallation sources has an important impact on R and D requirements as well as capital cost, for which a range of $300-450M is estimated by comparison to other accelerator-based neutron source facilities. The source is similar to a reactor source in most respects. It has some higher energy neutrons but fewer gamma rays, and the moderator region is free of many of the design constraints of a reactor, which helps to implement sources for various neutron energy spectra, many beam tubes, etc. With the development of multi-beam concept and the basis for currents greater than 100 mA that is assumed in the R and D plan, the ABNR would serve many additional uses, such as fusion materials development, production of proton-rich isotopes, and other energy and defense program needs

Reliable and Efficient Procedure for Steady-State Analysis of Nonautonomous and Autonomous Systems

Directory of Open Access Journals (Sweden)

J. Dobes

2012-04-01

Full Text Available The majority of contemporary design tools do not still contain steady-state algorithms, especially for the autonomous systems. This is mainly caused by insufficient accuracy of the algorithm for numerical integration, but also by unreliable steady-state algorithms themselves. Therefore, in the paper, a very stable and efficient procedure for the numerical integration of nonlinear differential-algebraic systems is defined first. Afterwards, two improved methods are defined for finding the steady state, which use this integration algorithm in their iteration loops. The first is based on the idea of extrapolation, and the second utilizes nonstandard time-domain sensitivity analysis. The two steady-state algorithms are compared by analyses of a rectifier and a C-class amplifier, and the extrapolation algorithm is primarily selected as a more reliable alternative. Finally, the method based on the extrapolation naturally cooperating with the algorithm for solving the differential-algebraic systems is thoroughly tested on various electronic circuits: Van der Pol and Colpitts oscillators, fragment of a large bipolar logical circuit, feedback and distributed microwave oscillators, and power amplifier. The results confirm that the extrapolation method is faster than a classical plain numerical integration, especially for larger circuits with complicated transients.

Steady-state hydrodynamic instabilities of active liquid crystals: hybrid lattice Boltzmann simulations.

Science.gov (United States)

Marenduzzo, D; Orlandini, E; Cates, M E; Yeomans, J M

2007-09-01

We report hybrid lattice Boltzmann (HLB) simulations of the hydrodynamics of an active nematic liquid crystal sandwiched between confining walls with various anchoring conditions. We confirm the existence of a transition between a passive phase and an active phase, in which there is spontaneous flow in the steady state. This transition is attained for sufficiently "extensile" rods, in the case of flow-aligning liquid crystals, and for sufficiently "contractile" ones for flow-tumbling materials. In a quasi-one-dimensional geometry, deep in the active phase of flow-aligning materials, our simulations give evidence of hysteresis and history-dependent steady states, as well as of spontaneous banded flow. Flow-tumbling materials, in contrast, rearrange themselves so that only the two boundary layers flow in steady state. Two-dimensional simulations, with periodic boundary conditions, show additional instabilities, with the spontaneous flow appearing as patterns made up of "convection rolls." These results demonstrate a remarkable richness (including dependence on anchoring conditions) in the steady-state phase behavior of active materials, even in the absence of external forcing; they have no counterpart for passive nematics. Our HLB methodology, which combines lattice Boltzmann for momentum transport with a finite difference scheme for the order parameter dynamics, offers a robust and efficient method for probing the complex hydrodynamic behavior of active nematics.

Preclusion of switch behavior in reaction networks with mass-action kinetics

DEFF Research Database (Denmark)

Feliu, Elisenda; Wiuf, C.

2012-01-01

We study networks taken with mass-action kinetics and provide a Jacobian criterion that applies to an arbitrary network to preclude the existence of multiple positive steady states within any stoichiometric class for any choice of rate constants. We are concerned with the characterization...... precludes the existence of degenerate steady states. Further, we relate injectivity of a network to that of the network obtained by adding outflow, or degradation, reactions for all species....

Kinetics of the H 2O 2-dependent ligninase-catalyzed oxidation of veratryl alcohol in the presence of cationic surfactant studied by spectrophotometric technique

Science.gov (United States)

Liu, Airong; Huang, Xirong; Song, Shaofang; Wang, Dan; Lu, Xuemei; Qu, Yinbo; Gao, Peiji

2003-09-01

The kinetics of ligninase-catalyzed oxidation of veratryl alcohol (VA) by H 2O 2 in the aqueous medium containing cationic surfactant cetyltrimethylammonium bromide (CTAB) has been investigated using spectrophotometric technique. Steady-state kinetic studies at different concentrations of CTAB indicate that the reaction follows a ping pong mechanism and the mechanism always holds but the kinetic parameters vary with CTAB concentrations. CTAB is a weak inhibitor for ligninase; it lowers the maximum initial velocity. CTAB also causes the Michaelis constant of H 2O 2 to decrease dramatically and that of VA to increase markedly. Based on the changes in kinetic parameters of the enzyme-catalyzed reaction at different CTAB concentrations (lower than, near to and larger than its critical micelle concentration) and the effects of the CTAB monomer and the micelles on the spectra of VA and its corresponding aldehyde, a conclusion could be made that modification of the enzymatic protein by the surfactant monomer should be responsible for the above-mentioned results.

Dust remobilization in fusion plasmas under steady state conditions

NARCIS (Netherlands)

Tolias, P.; Ratynskaia, S.; de Angeli, M.; De Temmerman, G.; Ripamonti, D.; Riva, G.; I. Bykov,; Shalpegin, A.; Vignitchouk, L.; Brochard, F.; Bystrov, K.; Bardin, S.; Litnovsky, A.

2016-01-01

The first combined experimental and theoretical studies of dust remobilization by plasma forces are reported. The main theoretical aspects of remobilization in fusion devices under steady state conditions are analyzed. In particular, the dominant role of adhesive forces is highlighted and generic

Combined Steady-State and Dynamic Heat Exchanger Experiment

Science.gov (United States)

Luyben, William L.; Tuzla, Kemal; Bader, Paul N.

2009-01-01

This paper describes a heat-transfer experiment that combines steady-state analysis and dynamic control. A process-water stream is circulated through two tube-in-shell heat exchangers in series. In the first, the process water is heated by steam. In the second, it is cooled by cooling water. The equipment is pilot-plant size: heat-transfer areas…

Steady-state equations of even flux and scattering

International Nuclear Information System (INIS)

Verwaerde, D.

1985-11-01

Some mathematical properties of steady-state equation of even flux are shown in variational formalism. This theoretical frame allows to study the existence of a solution and its asymptotical behavior in opaque media (i.e. the relation with scattering equation). At last it allows to qualify the convergence velocity of resolution iterative processes used practically [fr

Hydrodynamics of stratified epithelium: Steady state and linearized dynamics

Science.gov (United States)

Yeh, Wei-Ting; Chen, Hsuan-Yi

2016-05-01

A theoretical model for stratified epithelium is presented. The viscoelastic properties of the tissue are assumed to be dependent on the spatial distribution of proliferative and differentiated cells. Based on this assumption, a hydrodynamic description of tissue dynamics at the long-wavelength, long-time limit is developed, and the analysis reveals important insights into the dynamics of an epithelium close to its steady state. When the proliferative cells occupy a thin region close to the basal membrane, the relaxation rate towards the steady state is enhanced by cell division and cell apoptosis. On the other hand, when the region where proliferative cells reside becomes sufficiently thick, a flow induced by cell apoptosis close to the apical surface enhances small perturbations. This destabilizing mechanism is general for continuous self-renewal multilayered tissues; it could be related to the origin of certain tissue morphology, tumor growth, and the development pattern.

Theory of minimum dissipation of energy for the steady state

International Nuclear Information System (INIS)

Chu, T.K.

1992-02-01

The magnetic configuration of an inductively driven steady-state plasma bounded by a surface (or two adjacent surfaces) on which B·n = 0 is force-free: ∇xB = 2αB, where α is a constant, in time and in space. α is the ratio of the Poynting flux to the magnetic helicity flux at the boundary. It is also the ratio of the dissipative rates of the magnetic energy to the magnetic helicity in the plasma. The spatial extent of the configuration is noninfinitesimal. This global constraint is a result of the requirement that, for a steady-state plasma, the rate of change of the vector potential, ∂A/∂t, is constant in time and uniform in space

Electron flow in multicenter enzymes: theory, applications, and consequences on the natural design of redox chains.

Science.gov (United States)

Léger, Christophe; Lederer, Florence; Guigliarelli, Bruno; Bertrand, Patrick

2006-01-11

In protein film voltammetry, a redox enzyme is directly connected to an electrode; in the presence of substrate and when the driving force provided by the electrode is appropriate, a current flow reveals the steady-state turnover. We show that, in the case of a multicenter enzyme, this signal reports on the energetics and kinetics of electron transfer (ET) along the redox chain that wires the active site to the electrode, and this provides a new strategy for studying intramolecular ET. We propose a model which takes into account all the enzyme's redox microstates, and we prove it useful to interpret data for various enzymes. Several general ideas emerge from this analysis. Considering the reversibility of ET is a requirement: the usual picture, where ET is depicted as a series of irreversible steps, is oversimplified and lacks the important features that we emphasize. We give justification to the concept of apparent reduction potential on the time scale of turnover and we explain how the value of this potential relates to the thermodynamic and kinetic properties of the system. When intramolecular ET does not limit turnover, the redox chain merely mediates the driving force provided by the electrode or the soluble redox partner, whereas when intramolecular ET is slow, the enzyme behaves as if its active active site had apparent redox properties which depend on the reduction potentials of the relays. This suggests an alternative to the idea that redox chains are optimized in terms of speed: evolutionary pressure may have resulted in slowing down intramolecular ET in order to tune the enzyme's "operating potential".

Plasma flow reactor for steady state monitoring of physical and chemical processes at high temperatures.

Science.gov (United States)

Koroglu, Batikan; Mehl, Marco; Armstrong, Michael R; Crowhurst, Jonathan C; Weisz, David G; Zaug, Joseph M; Dai, Zurong; Radousky, Harry B; Chernov, Alex; Ramon, Erick; Stavrou, Elissaios; Knight, Kim; Fabris, Andrea L; Cappelli, Mark A; Rose, Timothy P

2017-09-01

We present the development of a steady state plasma flow reactor to investigate gas phase physical and chemical processes that occur at high temperature (1000 flow injector). We have modeled the system using computational fluid dynamics simulations that are bounded by measured temperatures. In situ line-of-sight optical emission and absorption spectroscopy have been used to determine the structures and concentrations of molecules formed during rapid cooling of reactants after they pass through the plasma. Emission spectroscopy also enables us to determine the temperatures at which these dynamic processes occur. A sample collection probe inserted from the open end of the reactor is used to collect condensed materials and analyze them ex situ using electron microscopy. The preliminary results of two separate investigations involving the condensation of metal oxides and chemical kinetics of high-temperature gas reactions are discussed.

Exact steady state manifold of a boundary driven spin-1 Lai–Sutherland chain

International Nuclear Information System (INIS)

Ilievski, Enej; Prosen, Tomaž

2014-01-01

We present an explicit construction of a family of steady state density matrices for an open integrable spin-1 chain with bilinear and biquadratic interactions, also known as the Lai–Sutherland model, driven far from equilibrium by means of two oppositely polarizing Markovian dissipation channels localized at the boundary. The steady state solution exhibits n+1 fold degeneracy, for a chain of length n, due to existence of (strong) Liouvillian U(1) symmetry. The latter can be exploited to introduce a chemical potential and define a grand canonical nonequilibrium steady state ensemble. The matrix product form of the solution entails an infinitely-dimensional representation of a non-trivial Lie algebra (semidirect product of sl 2 and a non-nilpotent radical) and hints to a novel Yang–Baxter integrability structure

Exact steady state manifold of a boundary driven spin-1 Lai–Sutherland chain

Energy Technology Data Exchange (ETDEWEB)

Ilievski, Enej; Prosen, Tomaž

2014-05-15

We present an explicit construction of a family of steady state density matrices for an open integrable spin-1 chain with bilinear and biquadratic interactions, also known as the Lai–Sutherland model, driven far from equilibrium by means of two oppositely polarizing Markovian dissipation channels localized at the boundary. The steady state solution exhibits n+1 fold degeneracy, for a chain of length n, due to existence of (strong) Liouvillian U(1) symmetry. The latter can be exploited to introduce a chemical potential and define a grand canonical nonequilibrium steady state ensemble. The matrix product form of the solution entails an infinitely-dimensional representation of a non-trivial Lie algebra (semidirect product of sl{sub 2} and a non-nilpotent radical) and hints to a novel Yang–Baxter integrability structure.

Integration of steady-state and temporal gene expression data for the inference of gene regulatory networks.

Science.gov (United States)

Wang, Yi Kan; Hurley, Daniel G; Schnell, Santiago; Print, Cristin G; Crampin, Edmund J

2013-01-01

We develop a new regression algorithm, cMIKANA, for inference of gene regulatory networks from combinations of steady-state and time-series gene expression data. Using simulated gene expression datasets to assess the accuracy of reconstructing gene regulatory networks, we show that steady-state and time-series data sets can successfully be combined to identify gene regulatory interactions using the new algorithm. Inferring gene networks from combined data sets was found to be advantageous when using noisy measurements collected with either lower sampling rates or a limited number of experimental replicates. We illustrate our method by applying it to a microarray gene expression dataset from human umbilical vein endothelial cells (HUVECs) which combines time series data from treatment with growth factor TNF and steady state data from siRNA knockdown treatments. Our results suggest that the combination of steady-state and time-series datasets may provide better prediction of RNA-to-RNA interactions, and may also reveal biological features that cannot be identified from dynamic or steady state information alone. Finally, we consider the experimental design of genomics experiments for gene regulatory network inference and show that network inference can be improved by incorporating steady-state measurements with time-series data.

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

DEFF Research Database (Denmark)

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

2017-01-01

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

Digital simulation of chronoamperometry at a disk electrode under a flat polymer film containing an enzyme

DEFF Research Database (Denmark)

Britz, Dieter; Strutwolf, Jörg

2015-01-01

Current-time and steady state current behaviour were simulated for an ultramicrodisk electrode (UMDE) inlaid flush with an insulating plane and overlaid by a flat film of polymer containing an enzyme, of various film thicknesses and essentially infinite extent. Steady state currents go through a maxim...

The code DYN3DR for steady-state and transient analyses of light water reactor cores with Cartesian geometry

International Nuclear Information System (INIS)

Grundmann, U.

1995-11-01

The code DYN3D/M2 was developed for 3-dimensional steady-state and transient analyses of reactor cores with hexagonal fuel assemblies. The neutron kinetics of the new version DYN3DR is based on a nodal method for the solution of the 3-dimensional 2-group neutron diffusion equation for Cartesian geometry. The thermal-hydraulic model FLOCAL simulating the two phase flow of coolant and the fuel rod behaviour is used in the two versions. The fundamentals for the solution of the neutron diffusion equations in DYN3DR are described. The 3-dimensional NEACRP benchmarks for rod ejections in LWR with quadratic fuel assemblies were calculated and the results were compared with the published solutions. The developed algorithm for neutron kinetics are suitable for using parallel processing. The behaviour of speed-up versus the number of processors is demonstrated for calculations of a static neutron flux distribution using a workstation with 4 processors. (orig.) [de

Effects of design variables predicted by a steady - state thermal performance analysis model of a loop heat pipe

International Nuclear Information System (INIS)

Jung, Eui Guk; Boo, Joon Hong

2008-01-01

This study deals with a mathematical modeling for the steady-state temperature characteristics of an entire loop heat pipe. The lumped layer model was applied to each node for temperature analysis. The flat type evaporator and condenser in the model had planar dimensions of 40 mm (W) x 50 mm (L). The wick material was a sintered metal and the working fluid was methanol. The molecular kinetic theory was employed to model the phase change phenomena in the evaporator and the condenser. Liquid-vapor interface configuration was expressed by the thin film theories available in the literature. Effects of design factors of loop heat pipe on the thermal performance were investigated by the modeling proposed in this study

Direct measurement of newly synthesized ATP dissociation kinetics in sarcoplasmic reticulum ATPase

International Nuclear Information System (INIS)

Teruel-Puche, J.; Kurzmack, M.; Inesi, G.

1987-01-01

Incubation of SR vesicles with Ca 2+ and ( 32 P)acetylphosphate, yields steady state levels of ( 32 P)phosphorylated enzyme (ATPase) intermediate and high concentrations of Ca 2+ in the lumen of the vesicles. At this time, addition of ADP (and EGTA to lower the Ca 2+ concentration in the medium outside the vesicles) results in single cycle formation of (γ- 32 P)ATP by transfer of ( 32 P)phosphate from the enzyme intermediate to ADP. The phosphoenzyme decay and ATP formation exhibit a fast component within the first 20 msec following addition of ADP, and a slower component reaching an asymptote in approximately 100 msec. They have now measured by a rapid filtration method the fraction of newly synthesized ATP which is bound to the enzyme, as opposed to the fraction dissociated into the medium. They find that nearly all the ATP formed during the initial burst is still bound to the enzyme within the initial 20 msec of reaction. Dissociation of newly synthesized ATP occurs then with approximately 13 sec -1 rate constant, permitting reequilibration of the system and further formation of ATP. The rate limiting effect of ATP dissociation and other partial reactions on the slow component of single cycle ATP synthesis is evaluated by appropriate kinetic simulations

Purification, kinetic behavior, and regulation of NAD(P)+ malic enzyme of tumor mitochondria.

Science.gov (United States)

Moreadith, R W; Lehninger, A L

1984-05-25

The purification and kinetic characterization of an NAD(P)+-malic enzyme from 22aH mouse hepatoma mitochondria are described. The enzyme was purified 328-fold with a final yield of 51% and specific activity of 38.1 units/mg of protein by employing DEAE-cellulose chromatography and an ATP affinity column. Sephadex G-200 chromatography yielded a native Mr = 240,000. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a major subunit with Mr = 61,000, suggesting a tetrameric structure, and also showed that the preparation contained less than 10% polypeptide impurities. Use of the ATP affinity column required the presence of MnCl2 and fumarate (an allosteric activator) in the elution buffers. In the absence of fumarate, the Michaelis constants for malate, NAD+, and NADP+ were 3.6 mM, 55 microM, and 72 microM, respectively; in the presence of fumarate (2 mM), the constants were 0.34 mM, 9 microM, and 13 microM, respectively. ATP was shown to be an allosteric inhibitor, competitive with malate. However, the inhibition by ATP displayed hyperbolic competitive kinetics with a KI (ATP) of 80 microM (minus fumarate) and 0.5 mM (plus 2 mM fumarate). The allosteric properties of the enzyme are integrated into a rationale for its specific role in the pathways of malate and glutamate oxidation in tumor mitochondria.

Algorithm for determining two-periodic steady-states in AC machines directly in time domain

Directory of Open Access Journals (Sweden)

Sobczyk Tadeusz J.

2016-09-01

Full Text Available This paper describes an algorithm for finding steady states in AC machines for the cases of their two-periodic nature. The algorithm enables to specify the steady-state solution identified directly in time domain despite of the fact that two-periodic waveforms are not repeated in any finite time interval. The basis for such an algorithm is a discrete differential operator that specifies the temporary values of the derivative of the two-periodic function in the selected set of points on the basis of the values of that function in the same set of points. It allows to develop algebraic equations defining the steady state solution reached in a chosen point set for the nonlinear differential equations describing the AC machines when electrical and mechanical equations should be solved together. That set of those values allows determining the steady state solution at any time instant up to infinity. The algorithm described in this paper is competitive with respect to the one known in literature an approach based on the harmonic balance method operated in frequency domain.

Analysis on the steady-state coherent synchrotron radiation with strong shielding

International Nuclear Information System (INIS)

Li, R.; Bohn, C.L.; Bisognano, J.J.

1997-01-01

There are several papers concerning shielding of coherent synchrotron radiation (CSR) emitted by a Gaussian line charge on a circular orbit centered between two parallel conducting plates. Previous asymptotic analyses in the frequency domain show that shielded steady-state CSR mainly arises from harmonics in the bunch frequency exceeding the threshold harmonic for satisfying the boundary conditions at the plates. In this paper the authors extend the frequency-domain analysis into the regime of strong shielding, in which the threshold harmonic exceeds the characteristic frequency of the bunch. The result is then compared to the shielded steady-state CSR power obtained using image charges

Steady-state entanglement and thermalization of coupled qubits in two common heat baths

Science.gov (United States)

Hu, Li-Zhen; Man, Zhong-Xiao; Xia, Yun-Jie

2018-03-01

In this work, we study the steady-state entanglement and thermalization of two coupled qubits embedded in two common baths with different temperatures. The common bath is relevant when the two qubits are difficult to be isolated to only contact with their local baths. With the quantum master equation constructed in the eigenstate representation of the coupled qubits, we have demonstrated the variations of steady-state entanglement with respect to various parameters of the qubits' system in both equilibrium and nonequilibrium cases of the baths. The coupling strength and energy detuning of the qubits as well as the temperature gradient of the baths are found to be beneficial to the enhancement of the entanglement. We note a dark state of the qubits that is free from time-evolution and its initial population can greatly influence the steady-state entanglement. By virtues of effective temperatures, we also study the thermalization of the coupled qubits and their variations with energy detuning.

The technology and science of steady-state operation in magnetically confined plasmas

International Nuclear Information System (INIS)

Becoulet, A; Hoang, G T

2008-01-01

The steady-state operation of magnetically confined fusion plasmas is considered as one of the 'grand challenges' of future decades, if not the ultimate goal of the research and development activities towards a new source of energy. Reaching such a goal requires the high-level integration of both science and technology aspects of magnetic fusion into self-consistent plasma regimes in fusion-grade devices. On the physics side, the first constraint addresses the magnetic confinement itself which must be made persistent. This means to either rely on intrinsically steady-state configurations, like the stellarator one, or turn the inductively driven tokamak configuration into a fully non-inductive one, through a mix of additional current sources. The low efficiency of the external current drive methods and the necessity to minimize the re-circulating power claim for a current mix strongly weighted by the internal 'pressure driven' bootstrap current, itself strongly sensitive to the heat and particle transport properties of the plasma. A virtuous circle may form as the heat and particle transport properties are themselves sensitive to the current profile conditions. Note that several other factors, e.g. plasma rotation profile, magneto-hydro-dynamics activity, also influence the equilibrium state. In the present tokamak devices, several examples of such 'advanced tokamak' physics research demonstrate the feasibility of steady-state regimes, though with a number of open questions still under investigation. The modelling activity also progresses quite fast in this domain and supports understanding and extrapolation. This high level of physics sophistication of the plasma scenario however needs to be combined with steady-state technological constraints. The technology constraints for steady-state operation are basically twofold: the specific technologies required to reach the steady-state plasma conditions and the generic technologies linked to the long pulse operation of a

A displacement based FE formulation for steady state problems

NARCIS (Netherlands)

Yu, Y.

2005-01-01

In this thesis a new displacement based formulation is developed for elasto-plastic deformations in steady state problems. In this formulation the displacements are the primary variables, which is in contrast to the more common formulations in terms of the velocities as the primary variables. In a

Kinetic study of the effects of calcium ions on cationic artichoke (Cynara scolymus L.) peroxidase: calcium binding, steady-state kinetics and reactions with hydrogen peroxide.

Science.gov (United States)

Hiner, Alexander N P; Sidrach, Lara; Chazarra, Soledad; Varón, Ramón; Tudela, José; García-Cánovas, Francisco; Rodríguez-López, José Neptuno

2004-01-01

The apparent catalytic constant (k(cat)) of artichoke (Cynara scolymus L.) peroxidase (AKPC) with 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) increased 130-fold in the presence of calcium ions (Ca2+) but the affinity (K(m)) of the enzyme for ABTS was 500 times lower than for Ca2+-free AKPC. AKPC is known to exhibit an equilibrium between 6-aquo hexa-coordinate and penta-coordinate forms of the haem iron that is modulated by Ca2+ and affects compound I formation. Measurements of the Ca2+ dissociation constant (K(D)) were complicated by the water-association/dissociation equilibrium yielding a global value more than 1000 times too high. The value for the Ca2+ binding step alone has now been determined to be K(D) approximately 10 nM. AKPC-Ca2+ was more resistant to inactivation by hydrogen peroxide (H(2)O(2)) and exhibited increased catalase activity. An analysis of the complex H(2)O(2) concentration dependent kinetics of Ca2+-free AKPC is presented.

Importance sampling large deviations in nonequilibrium steady states. I

Science.gov (United States)

Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T.

2018-03-01

Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.

Importance sampling large deviations in nonequilibrium steady states. I.

Science.gov (United States)

Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T

2018-03-28

Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.

Kinetic proofreading at single molecular level: aminoacylation of tRNA(Ile and the role of water as an editor.

Directory of Open Access Journals (Sweden)

Mantu Santra

Full Text Available Proofreading/editing in protein synthesis is essential for accurate translation of information from the genetic code. In this article we present a theoretical investigation of efficiency of a kinetic proofreading mechanism that employs hydrolysis of the wrong substrate as the discriminatory step in enzyme catalytic reactions. We consider aminoacylation of tRNA(Ile which is a crucial step in protein synthesis and for which experimental results are now available. We present an augmented kinetic scheme and then employ methods of stochastic simulation algorithm to obtain time dependent concentrations of different substances involved in the reaction and their rates of formation. We obtain the rates of product formation and ATP hydrolysis for both correct and wrong substrates (isoleucine and valine in our case, respectively, in single molecular enzyme as well as ensemble enzyme kinetics. The present theoretical scheme correctly reproduces (i the amplitude of the discrimination factor in the overall rates between isoleucine and valine which is obtained as (1.8×10(2.(4.33×10(2 = 7.8×10(4, (ii the rates of ATP hydrolysis for both Ile and Val at different substrate concentrations in the aminoacylation of tRNA(Ile. The present study shows a non-michaelis type dependence of rate of reaction on tRNA(Ile concentration in case of valine. The overall editing in steady state is found to be independent of amino acid concentration. Interestingly, the computed ATP hydrolysis rate for valine at high substrate concentration is same as the rate of formation of Ile-tRNA(Ile whereas at intermediate substrate concentration the ATP hydrolysis rate is relatively low. We find that the presence of additional editing domain in class I editing enzyme makes the kinetic proofreading more efficient through enhanced hydrolysis of wrong product at the editing CP1 domain.

A novel multivariate STeady-state index during general ANesthesia (STAN).

Science.gov (United States)

Castro, Ana; de Almeida, Fernando Gomes; Amorim, Pedro; Nunes, Catarina S

2017-08-01

The assessment of the adequacy of general anesthesia for surgery, namely the nociception/anti-nociception balance, has received wide attention from the scientific community. Monitoring systems based on the frontal EEG/EMG, or autonomic state reactions (e.g. heart rate and blood pressure) have been developed aiming to objectively assess this balance. In this study a new multivariate indicator of patients' steady-state during anesthesia (STAN) is proposed, based on wavelet analysis of signals linked to noxious activation. A clinical protocol was designed to analyze precise noxious stimuli (laryngoscopy/intubation, tetanic, and incision), under three different analgesic doses; patients were randomized to receive either remifentanil 2.0, 3.0 or 4.0 ng/ml. ECG, PPG, BP, BIS, EMG and [Formula: see text] were continuously recorded. ECG, PPG and BP were processed to extract beat-to-beat information, and [Formula: see text] curve used to estimate the respiration rate. A combined steady-state index based on wavelet analysis of these variables, was applied and compared between the three study groups and stimuli (Wilcoxon signed ranks, Kruskal-Wallis and Mann-Whitney tests). Following institutional approval and signing the informed consent thirty four patients were enrolled in this study (3 excluded due to signal loss during data collection). The BIS index of the EEG, frontal EMG, heart rate, BP, and PPG wave amplitude changed in response to different noxious stimuli. Laryngoscopy/intubation was the stimulus with the more pronounced response [Formula: see text]. These variables were used in the construction of the combined index STAN; STAN responded adequately to noxious stimuli, with a more pronounced response to laryngoscopy/intubation (18.5-43.1 %, [Formula: see text]), and the attenuation provided by the analgesic, detecting steady-state periods in the different physiological signals analyzed (approximately 50 % of the total study time). A new multivariate approach for

Revealing kinetics and state-dependent binding properties of IKur-targeting drugs that maximize atrial fibrillation selectivity

Science.gov (United States)

Ellinwood, Nicholas; Dobrev, Dobromir; Morotti, Stefano; Grandi, Eleonora

2017-09-01

The KV1.5 potassium channel, which underlies the ultra-rapid delayed-rectifier current (IKur) and is predominantly expressed in atria vs. ventricles, has emerged as a promising target to treat atrial fibrillation (AF). However, while numerous KV1.5-selective compounds have been screened, characterized, and tested in various animal models of AF, evidence of antiarrhythmic efficacy in humans is still lacking. Moreover, current guidelines for pre-clinical assessment of candidate drugs heavily rely on steady-state concentration-response curves or IC50 values, which can overlook adverse cardiotoxic effects. We sought to investigate the effects of kinetics and state-dependent binding of IKur-targeting drugs on atrial electrophysiology in silico and reveal the ideal properties of IKur blockers that maximize anti-AF efficacy and minimize pro-arrhythmic risk. To this aim, we developed a new Markov model of IKur that describes KV1.5 gating based on experimental voltage-clamp data in atrial myocytes from patient right-atrial samples in normal sinus rhythm. We extended the IKur formulation to account for state-specificity and kinetics of KV1.5-drug interactions and incorporated it into our human atrial cell model. We simulated 1- and 3-Hz pacing protocols in drug-free conditions and with a [drug] equal to the IC50 value. The effects of binding and unbinding kinetics were determined by examining permutations of the forward (kon) and reverse (koff) binding rates to the closed, open, and inactivated states of the KV1.5 channel. We identified a subset of ideal drugs exhibiting anti-AF electrophysiological parameter changes at fast pacing rates (effective refractory period prolongation), while having little effect on normal sinus rhythm (limited action potential prolongation). Our results highlight that accurately accounting for channel interactions with drugs, including kinetics and state-dependent binding, is critical for developing safer and more effective pharmacological anti

Kinetics and spatial distribution of enzymes of carbon, nitrogen and phosphorus cycles in earthworm biopores

Science.gov (United States)

Hoang Thi Thu, Duyen; Razavi, Bahar S.

2016-04-01

Earthworms boost microbial activities and consequently form hotspots in soil. The distribution of enzyme activities inside the earthworm biopores is completely unknown. For the first time, we analyzed enzyme kinetics and visualized enzyme distribution inside and outside biopores by in situ soil zymography. Kinetic parameters (Vmax and Km) of 6 enzymes β-glucosidase (GLU), cellobiohydrolase (CBH), xylanase (XYL), chitinase (NAG), leucine aminopeptidase (LAP) and acid phosphatase (APT) were determined in biopores formed by Lumbricus terrestris L.. The spatial distributions of GLU, NAG and APT become visible via zymograms in comparison between earthworm-inhabited and earthworm-free soil. Zymography showed heterogeneous distribution of hotspots in the rhizosphere and biopores. The hotspot areas were 2.4 to 14 times larger in the biopores than in soil without earthworms. The significantly higher Vmax values for GLU, CBH, XYL, NAG and APT in biopores confirmed the stimulation of enzyme activities by earthworms. For CBH, XYL and NAG, the 2- to 3-fold higher Km values in biopores indicated different enzyme systems with lower substrate affinity compared to control soil. The positive effects of earthworms on Vmax were cancelled by the Km increase for CBH, XYL and NAG at a substrate concentration below 20 μmol g-1 soil. The change of enzyme systems reflected a shift in dominant microbial populations toward species with lower affinity to holo-celluloses and to N-acetylglucosamine, and with higher affinity to proteins as compared to the biopores-free soil. We conclude that earthworm biopores are microbial hotspots with much higher and dense distribution of enzyme activities compared to bulk soil. References Spohn M, Kuzyakov Y. (2014) Spatial and temporal dynamics of hotspots of enzyme activity in soil as affected by living and dead roots - a soil zymography analysis, Plant Soil 379: 67-77. Blagodatskaya, E., Kuzyakov, Y., 2013. Review paper: Active microorganisms in soil

Intrinsic Noise Profoundly Alters the Dynamics and Steady State of Morphogen-Controlled Bistable Genetic Switches.

Directory of Open Access Journals (Sweden)

Ruben Perez-Carrasco

2016-10-01

Full Text Available During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signalling molecules-morphogens-guide this process by controlling downstream transcriptional networks. A mechanism commonly used in these networks to convert the continuous information provided by the gradient into discrete transitions between adjacent cell types is the genetic toggle switch, composed of cross-repressing transcriptional determinants. Previous analyses have emphasised the steady state output of these mechanisms. Here, we explore the dynamics of the toggle switch and use exact numerical simulations of the kinetic reactions, the corresponding Chemical Langevin Equation, and Minimum Action Path theory to establish a framework for studying the effect of gene expression noise on patterning time and boundary position. This provides insight into the time scale, gene expression trajectories and directionality of stochastic switching events between cell states. Taking gene expression noise into account predicts that the final boundary position of a morphogen-induced toggle switch, although robust to changes in the details of the noise, is distinct from that of the deterministic system. Moreover, the dramatic increase in patterning time close to the boundary predicted from the deterministic case is substantially reduced. The resulting stochastic switching introduces differences in patterning time along the morphogen gradient that result in a patterning wave propagating away from the morphogen source with a velocity determined by the intrinsic noise. The wave sharpens and slows as it advances and may never reach steady state in a biologically relevant time. This could explain experimentally observed dynamics of pattern formation. Together the analysis reveals the importance of dynamical transients for understanding morphogen-driven transcriptional networks and indicates that gene expression noise can

Intrinsic Noise Profoundly Alters the Dynamics and Steady State of Morphogen-Controlled Bistable Genetic Switches

Science.gov (United States)

Page, Karen M.

2016-01-01

During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signalling molecules—morphogens—guide this process by controlling downstream transcriptional networks. A mechanism commonly used in these networks to convert the continuous information provided by the gradient into discrete transitions between adjacent cell types is the genetic toggle switch, composed of cross-repressing transcriptional determinants. Previous analyses have emphasised the steady state output of these mechanisms. Here, we explore the dynamics of the toggle switch and use exact numerical simulations of the kinetic reactions, the corresponding Chemical Langevin Equation, and Minimum Action Path theory to establish a framework for studying the effect of gene expression noise on patterning time and boundary position. This provides insight into the time scale, gene expression trajectories and directionality of stochastic switching events between cell states. Taking gene expression noise into account predicts that the final boundary position of a morphogen-induced toggle switch, although robust to changes in the details of the noise, is distinct from that of the deterministic system. Moreover, the dramatic increase in patterning time close to the boundary predicted from the deterministic case is substantially reduced. The resulting stochastic switching introduces differences in patterning time along the morphogen gradient that result in a patterning wave propagating away from the morphogen source with a velocity determined by the intrinsic noise. The wave sharpens and slows as it advances and may never reach steady state in a biologically relevant time. This could explain experimentally observed dynamics of pattern formation. Together the analysis reveals the importance of dynamical transients for understanding morphogen-driven transcriptional networks and indicates that gene expression noise can qualitatively

A Data Filter for Identifying Steady-State Operating Points in Engine Flight Data for Condition Monitoring Applications

Science.gov (United States)

Simon, Donald L.; Litt, Jonathan S.

2010-01-01

This paper presents an algorithm that automatically identifies and extracts steady-state engine operating points from engine flight data. It calculates the mean and standard deviation of select parameters contained in the incoming flight data stream. If the standard deviation of the data falls below defined constraints, the engine is assumed to be at a steady-state operating point, and the mean measurement data at that point are archived for subsequent condition monitoring purposes. The fundamental design of the steady-state data filter is completely generic and applicable for any dynamic system. Additional domain-specific logic constraints are applied to reduce data outliers and variance within the collected steady-state data. The filter is designed for on-line real-time processing of streaming data as opposed to post-processing of the data in batch mode. Results of applying the steady-state data filter to recorded helicopter engine flight data are shown, demonstrating its utility for engine condition monitoring applications.

Comparison of pulsed three-dimensional CEST acquisition schemes at 7 tesla : steady state versus pseudosteady state

NARCIS (Netherlands)

Khlebnikov, Vitaly; Geades, Nicolas; Klomp, DWJ; Hoogduin, Hans; Gowland, Penny; Mougin, Olivier

PURPOSE: To compare two pulsed, volumetric chemical exchange saturation transfer (CEST) acquisition schemes: steady state (SS) and pseudosteady state (PS) for the same brain coverage, spatial/spectral resolution and scan time. METHODS: Both schemes were optimized for maximum sensitivity to amide

Steady-state and dynamic models for particle engulfment during solidification

Science.gov (United States)

Tao, Yutao; Yeckel, Andrew; Derby, Jeffrey J.

2016-06-01

Steady-state and dynamic models are developed to study the physical mechanisms that determine the pushing or engulfment of a solid particle at a moving solid-liquid interface. The mathematical model formulation rigorously accounts for energy and momentum conservation, while faithfully representing the interfacial phenomena affecting solidification phase change and particle motion. A numerical solution approach is developed using the Galerkin finite element method and elliptic mesh generation in an arbitrary Lagrangian-Eulerian implementation, thus allowing for a rigorous representation of forces and dynamics previously inaccessible by approaches using analytical approximations. We demonstrate that this model accurately computes the solidification interface shape while simultaneously resolving thin fluid layers around the particle that arise from premelting during particle engulfment. We reinterpret the significance of premelting via the definition an unambiguous critical velocity for engulfment from steady-state analysis and bifurcation theory. We also explore the complicated transient behaviors that underlie the steady states of this system and posit the significance of dynamical behavior on engulfment events for many systems. We critically examine the onset of engulfment by comparing our computational predictions to those obtained using the analytical model of Rempel and Worster [29]. We assert that, while the accurate calculation of van der Waals repulsive forces remains an open issue, the computational model developed here provides a clear benefit over prior models for computing particle drag forces and other phenomena needed for the faithful simulation of particle engulfment.

Tore-Supra infrared thermography system, a real steady-state diagnostic

International Nuclear Information System (INIS)

Guilhem, D.; Bondil, J.L.; Bertrand, B.; Desgranges, C.; Lipa, M.; Messina, P.; Missirlian, M.; Portafaix, C.; Reichle, R.; Roche, H.; Saille, A.

2005-01-01

Tore-Supra Tokamak (I p = 1.5 MA, B t = 4 T) has been constructed with a steady-state magnetic field using super-conducting magnets and water-cooled plasma facing components (PFCs) for high-performance long pulse plasma discharges. When not actively cooled, plasma facing components can only accumulate a limited amount of energy since the temperature increases continuously during the discharge until radiation cooling equals the incoming heat flux. Such an environment is found in the JET Tokamak [JET Team, IAEA-CN-60/A1-3, Seville, 1994] and on TRIAM [M. Sakamoto, H. Nakashima, S. Kawasaki, A. Iyomasa, S.V. Kulkarni, M. Hasegawa, E. Jotaki, H. Zushi, K. Nakamura, K. Hanada, S. Itoh, Static and dynamic properties of wall recycling in TRIAM-1M, J. Nucl. Mater. 313-316 (2003) 519-523] [Y. Kamada, et al., Nucl. Fusion 3 (1999) 1845]. In Tore-Supra, the surface temperature of the actively cooled plasma facing components reach steady state within a second. We present here the Tore-Supra thermographic system, made of seven endoscope bodies equipped so far with eight infrared (IR) cameras. It has to be noted that this diagnostic is the first diagnostic to be actively cooled, as required for steady state. The main purpose of such a diagnostic is to prevent the plasma to damage the actively cooled plasma facing components (ACPFCs), which consist of the toroidal pumped limiter (TPL), 7 m 2 , and of five radio-frequency antennae, 1.5 m 2 each

Effective reaction rates in diffusion-limited phosphorylation-dephosphorylation cycles

Science.gov (United States)

Szymańska, Paulina; Kochańczyk, Marek; Miekisz, Jacek; Lipniacki, Tomasz

2015-02-01

We investigate the kinetics of the ubiquitous phosphorylation-dephosphorylation cycle on biological membranes by means of kinetic Monte Carlo simulations on the triangular lattice. We establish the dependence of effective macroscopic reaction rate coefficients as well as the steady-state phosphorylated substrate fraction on the diffusion coefficient and concentrations of opposing enzymes: kinases and phosphatases. In the limits of zero and infinite diffusion, the numerical results agree with analytical predictions; these two limits give the lower and the upper bound for the macroscopic rate coefficients, respectively. In the zero-diffusion limit, which is important in the analysis of dense systems, phosphorylation and dephosphorylation reactions can convert only these substrates which remain in contact with opposing enzymes. In the most studied regime of nonzero but small diffusion, a contribution linearly proportional to the diffusion coefficient appears in the reaction rate. In this regime, the presence of opposing enzymes creates inhomogeneities in the (de)phosphorylated substrate distributions: The spatial correlation function shows that enzymes are surrounded by clouds of converted substrates. This effect becomes important at low enzyme concentrations, substantially lowering effective reaction rates. Effective reaction rates decrease with decreasing diffusion and this dependence is more pronounced for the less-abundant enzyme. Consequently, the steady-state fraction of phosphorylated substrates can increase or decrease with diffusion, depending on relative concentrations of both enzymes. Additionally, steady states are controlled by molecular crowders which, mostly by lowering the effective diffusion of reactants, favor the more abundant enzyme.

Three-dimensional stellarator equilibrium as an ohmic steady state

International Nuclear Information System (INIS)

Park, W.; Monticello, D.A.; Strauss, H.; Manickam, J.

1985-07-01

A stable three-dimensional stellarator equilibrium can be obtained numerically by a time-dependent relaxation method using small values of dissipation. The final state is an ohmic steady state which approaches an ohmic equilibrium in the limit of small dissipation coefficients. We describe a method to speed up the relaxation process and a method to implement the B vector . del p = 0 condition. These methods are applied to obtain three-dimensional heliac equilibria using the reduced heliac equations

Comparison of Steady-State SVC Models in Load Flow Calculations

DEFF Research Database (Denmark)

Chen, Peiyuan; Chen, Zhe; Bak-Jensen, Birgitte

2008-01-01

This paper compares in a load flow calculation three existing steady-state models of static var compensator (SVC), i.e. the generator-fixed susceptance model, the total susceptance model and the firing angle model. The comparison is made in terms of the voltage at the SVC regulated bus, equivalent...... SVC susceptance at the fundamental frequency and the load flow convergence rate both when SVC is operating within and on the limits. The latter two models give inaccurate results of the equivalent SVC susceptance as compared to the generator model due to the assumption of constant voltage when the SVC...... is operating within the limits. This may underestimate or overestimate the SVC regulating capability. Two modified models are proposed to improve the SVC regulated voltage according to its steady-state characteristic. The simulation results of the two modified models show the improved accuracy...

Rapid mixing and short storage timescale in the magma dynamics of a steady-state volcano

Science.gov (United States)

Petrone, Chiara Maria; Braschi, Eleonora; Francalanci, Lorella; Casalini, Martina; Tommasini, Simone

2018-06-01

Steady-state volcanic activity implies equilibrium between the rate of magma replenishment and eruption of compositionally homogeneous magmas, lasting for tens to thousands of years in an open conduit system. The Present-day activity of Stromboli volcano (Aeolian Islands, Southern Italy) has long been recognised as typical of a steady-state volcano, with a shallow magmatic reservoir (highly porphyritic or hp-magma) continuously refilled by more mafic magma (with low phenocryst content or lp-magma) at a constant rate and accompanied by mixing, crystallisation and eruption. Our aim is to clarify the timescale and dynamics of the plumbing system at the establishment of the Present-day steady-state activity (volcanoes.

Neutron kinetics developments of the SIMMER-III safety code for APS application

International Nuclear Information System (INIS)

Rineiski, A.; Kiefhaber, E.; Merk, B.; Maschek, W.

2000-01-01

Recent developments extending the capabilities of the SIMMER-III code for dealing with transients and accidents in an ADS are presented. The impact of weighting functions on the point-kinetics parameters at steady-state is shown. Some preliminary results of using a space-time kinetics model for beam-trip related transients are highlighted. (orig.)

Comparing Non-Steady State Emissions under Start-Up and Shut-Down Operating Conditions with Steady State Emissions for Several Industrial Sectors: A Literature Review

Directory of Open Access Journals (Sweden)

Juwairia Obaid

2017-02-01

Full Text Available This study investigates the emissions of various industrial facilities under start-up, shut-down, and normal operations. The industries that have been investigated include power and/or heat generation, energy-from-waste generation, nuclear power generation, sulphuric acid production, ethylene production, petrochemical production, and waste incineration. The study investigated multiple facilities worldwide for each of these industrial categories. The different potential contaminants characteristic of each industry type have been investigated and the emissions of these contaminants under non-steady state have been compared to the steady state emissions. Where available, trends have been developed to identify the circumstances, i.e., the industrial sector and contaminant, under which the assessment and consideration of emissions from start-up and shut-down events is necessary for each industry. These trends differ by industrial sector and contaminant. For example, the study shows that sulphur dioxide (SO2 emissions should be assessed for the start-up operations of sulphuric acid production plants, but may not need to be assessed for the start-up operations of a conventional power generation facility. The trends developed as part of this research paper will help air permit applicants to effectively allocate their resources when assessing emissions related to non-steady state operations. Additionally, it will ensure that emissions are assessed for the worst-case scenario. This is especially important when emissions under start-up and shut-down operations have the potential to exceed enforceable emission limits. Thus, assessing emissions for the worst-case scenario can help in preventing the emissions from adversely impacting public health and the environment.

Steady-state modeling of reactive distillation columns - doi: 10.4025/actascitechnol.v34i1.9535

Directory of Open Access Journals (Sweden)

Vilmar Steffen

2011-11-01

Full Text Available An algorithm for the solution of the mathematical model featuring reactive distillation process in steady-state columns is analyzed. It has been presumed that each stage’s outlet streams in the model were in phase equilibrium conditions and that chemical kinetics was described by a reaction rate model. Within the context of the developed algorithm a procedure to solve a set of equations in a sequential form and a methodology to produce the initial estimates was defined. Broyden’s method was employed to solve the equations that model the chemical reactions. Algorithm was evaluated by study cases of 2-pentene metathesis and MTBE synthesis. The simulation results were close to results available in the literature and the proposed algorithm proved to be efficient since in both cases the convergence towards a solution was found.

A steady-state fluid model of the coaxial plasma gun

International Nuclear Information System (INIS)

Herziger, G.; Krompholz, H.; Schneider, W.; Schoenbach, K.

1979-01-01

The plasma layer in a coaxial plasma gun is considered as a shock front driven by expanding magnetic fields. Analytical steady-state solutions of the fluid equations yield the plasma properties, allowing the scaling of plasma focus devices. (Auth.)

Development of repetitive railgun pellet accelerator and steady-state pellet supply system

International Nuclear Information System (INIS)

Oda, Y.; Onozuka, M.; Azuma, K.; Kasai, S.; Hasegawa, K.

1995-01-01

A railgun system for repetitive high-speed pellet acceleration and steady-state pellet supply system has been developed and investigated. Using a 2m-long railgun system, the hydrogen pellet was accelerated to 2.6km/sec by the supplied energy of 1.7kJ. It is expected that the hydrogen pellet can be accelerated to 3km/sec using the present pneumatic pellet accelerator and a 2m-long augment railgun. Screw-driven hydrogen-isotope filament extruding system has been fabricated and will be tested to examine its applicability to the steady-state extrusion of the solid hydrogen-isotope filament

Development of repetitive railgun pellet accelerator and steady-state pellet supply system

Energy Technology Data Exchange (ETDEWEB)

Oda, Y.; Onozuka, M.; Azuma, K. [Mitsubishi Heavy Industries, Ltd., Kobe (Japan); Kasai, S.; Hasegawa, K. [Japan Atomic Energy Research Inst., Naka (Japan)

1995-12-31

A railgun system for repetitive high-speed pellet acceleration and steady-state pellet supply system has been developed and investigated. Using a 2m-long railgun system, the hydrogen pellet was accelerated to 2.6km/sec by the supplied energy of 1.7kJ. It is expected that the hydrogen pellet can be accelerated to 3km/sec using the present pneumatic pellet accelerator and a 2m-long augment railgun. Screw-driven hydrogen-isotope filament extruding system has been fabricated and will be tested to examine its applicability to the steady-state extrusion of the solid hydrogen-isotope filament.

Local wettability reversal during steady-state two-phase flow in porous media.

Science.gov (United States)

Sinha, Santanu; Grøva, Morten; Ødegården, Torgeir Bryge; Skjetne, Erik; Hansen, Alex

2011-09-01

We study the effect of local wettability reversal on remobilizing immobile fluid clusters in steady-state two-phase flow in porous media. We consider a two-dimensional network model for a porous medium and introduce a wettability alteration mechanism. A qualitative change in the steady-state flow patterns, destabilizing the percolating and trapped clusters, is observed as the system wettability is varied. When capillary forces are strong, a finite wettability alteration is necessary to move the system from a single-phase to a two-phase flow regime. When both phases are mobile, we find a linear relationship between fractional flow and wettability alteration.

An equation oriented approach to steady state flowsheeting of methanol synthesis loop

International Nuclear Information System (INIS)

Fathikalajahi, J.; Baniadam, M.; Rahimpour, M.R.

2008-01-01

An equation-oriented approach was developed for steady state flowsheeting of a commercial methanol plant. The loop consists of fixed bed reactor, flash separator, preheater, coolers, and compressor. For steady sate flowsheeting of the plant mathematical model of reactor and other units are needed. Reactor used in loop is a Lurgi type and its configuration is rather complex. Previously reactor and flash separator are modeled as two important units of plant. The model is based on mass and energy balances in each equipment and utilizing some auxiliary equations such as rate of reaction and thermodynamics model for activity coefficients of liquid. In order to validate the mathematical model for the synthesis loop, some simulation data were performed using operating conditions and characteristics of the commercial plant. The good agreement between the steady state simulation results and the plant data shows the validity of the model

Coagulation profile of children with sickle cell anemia in steady state ...

African Journals Online (AJOL)

Background: Sickle cell anemia is associated with a hypercoagulable state that may lead to alterations in a coagulation profile. Measurements of coagulation factors are known to have some predictive value for clinical outcome. Objectives: To determine the coagulation profile of children with SCA in steady state and crisis ...

Determination of the Steady State Leakage Current in Structures with Ferroelectric Ceramic Films

Science.gov (United States)

Podgornyi, Yu. V.; Vorotilov, K. A.; Sigov, A. S.

2018-03-01

Steady state leakage currents have been investigated in capacitor structures with ferroelectric solgel films of lead zirconate titanate (PZT) formed on silicon substrates with a lower Pt electrode. It is established that Pt/PZT/Hg structures, regardless of the PZT film thickness, are characterized by the presence of a rectifying contact similar to p-n junction. The steady state leakage current in the forward direction increases with a decrease in the film thickness and is determined by the ferroelectric bulk conductivity.

Modeling the kinetics of volatilization from glass melts

NARCIS (Netherlands)

Beerkens, R.G.C.

2001-01-01

A model description for the evaporation kinetics from glass melts in direct contact with static atmospheres or flowing gas phases is presented. The derived models and equations are based on the solution of the second Ficks' diffusion law and quasi-steady-state mass transfer relations, taking into

steady and dynamic states analysis of induction motor: fea approach

African Journals Online (AJOL)

HOD

The flux levels at these loading conditions were also monitored. Key words: Three phase Induction Motor, Steady state and Dynamic Response, Flux Levels, FEA, Loading conditions. 1. INTRODUCTION ..... Boston: Computational Mechanics Publications;. New York: ... for Electrical Engineers, Cambridge University. Press ...

Post-CHF heat transfer during steady-state and transient conditions

International Nuclear Information System (INIS)

Fung, K.K.

1978-06-01

This review extends previous reviews of steady-state post-CHF literature by Groeneveld, Gardiner, and Fung by including more recent data. A review of the literature on transient post-CHF data is also included by extending the work of Yadigaroglu

Paracetamol decreases steady-state exposure to lamotrigine by induction of glucuronidation in healthy subjects

DEFF Research Database (Denmark)

Gastrup, Sandra; Stage, Tore Bjerregaard; Fruekilde, Palle Bach Nielsen

2016-01-01

AIM: Patients receiving lamotrigine therapy frequently use paracetamol concomitantly. While one study suggests a possible, clinically relevant drug-drug interaction, practical recommendations of the concomitant use are inconsistent. We performed a systematic pharmacokinetic study in healthy...... volunteers to quantify the effect of 4-day treatment of paracetamol on the metabolism of steady-state lamotrigine. METHODS: Twelve healthy, male volunteers participated in an open-label, sequential interaction study. Lamotrigine was titrated to steady state (100 mg daily) over 36 days, and blood and urine...... sampling was performed in a non-randomised order with and without paracetamol (1 g four times daily). The primary endpoint was change in steady-state area under the plasma concentration-time curve of lamotrigine. Secondary endpoints were changes in total apparent oral clearance, renal clearance...

Distraction task rather than focal attention modulates gamma activity associated with auditory steady-state responses (ASSRs)

DEFF Research Database (Denmark)

Griskova-Bulanova, Inga; Ruksenas, Osvaldas; Dapsys, Kastytis

2011-01-01

To explore the modulation of auditory steady-state response (ASSR) by experimental tasks, differing in attentional focus and arousal level.......To explore the modulation of auditory steady-state response (ASSR) by experimental tasks, differing in attentional focus and arousal level....

Enzyme Kinetics Experiment with the Multienzyme Complex Viscozyme L and Two Substrates for the Accurate Determination of Michaelian Parameters

Science.gov (United States)

Guerra, Nelson Pérez

2017-01-01

A laboratory experiment in which students study the kinetics of the Viscozyme-L-catalyzed hydrolysis of cellulose and starch comparatively was designed for an upper-division biochemistry laboratory. The main objective of this experiment was to provide an opportunity to perform enhanced enzyme kinetics data analysis using appropriate informatics…

Thymidine kinase 2 enzyme kinetics elucidate the mechanism of thymidine-induced mitochondrial DNA depletion.

Science.gov (United States)

Sun, Ren; Wang, Liya

2014-10-07

Mitochondrial thymidine kinase 2 (TK2) is a nuclear gene-encoded protein, synthesized in the cytosol and subsequently translocated into the mitochondrial matrix, where it catalyzes the phosphorylation of thymidine (dT) and deoxycytidine (dC). The kinetics of dT phosphorylation exhibits negative cooperativity, but dC phosphorylation follows hyperbolic Michaelis-Menten kinetics. The two substrates compete with each other in that dT is a competitive inhibitor of dC phosphorylation, while dC acts as a noncompetitive inhibitor of dT phosphorylation. In addition, TK2 is feedback inhibited by dTTP and dCTP. TK2 also phosphorylates a number of pyrimidine nucleoside analogues used in antiviral and anticancer therapy and thus plays an important role in mitochondrial toxicities caused by nucleoside analogues. Deficiency in TK2 activity due to genetic alterations causes devastating mitochondrial diseases, which are characterized by mitochondrial DNA (mtDNA) depletion or multiple deletions in the affected tissues. Severe TK2 deficiency is associated with early-onset fatal mitochondrial DNA depletion syndrome, while less severe deficiencies result in late-onset phenotypes. In this review, studies of the enzyme kinetic behavior of TK2 enzyme variants are used to explain the mechanism of mtDNA depletion caused by TK2 mutations, thymidine overload due to thymidine phosphorylase deficiency, and mitochondrial toxicity caused by antiviral thymidine analogues.

Steady state solution of the Poisson-Nernst-Planck equations

International Nuclear Information System (INIS)

Golovnev, A.; Trimper, S.

2010-01-01

The exact steady state solution of the Poisson-Nernst-Planck equations (PNP) is given in terms of Jacobi elliptic functions. A more tractable approximate solution is derived which can be used to compare the results with experimental observations in binary electrolytes. The breakdown of the PNP for high concentration and high applied voltage is discussed.

Spatial variability of steady-state infiltration into a two-layer soil system on burned hillslopes

Science.gov (United States)

Kinner, D.A.; Moody, J.A.

2010-01-01

Rainfall-runoff simulations were conducted to estimate the characteristics of the steady-state infiltration rate into 1-m2 north- and south-facing hillslope plots burned by a wildfire in October 2003. Soil profiles in the plots consisted of a two-layer system composed of an ash on top of sandy mineral soil. Multiple rainfall rates (18.4-51.2 mm h-1) were used during 14 short-duration (30 min) and 2 long-duration simulations (2-4 h). Steady state was reached in 7-26 min. Observed spatially-averaged steady-state infiltration rates ranged from 18.2 to 23.8 mm h-1 for north-facing and from 17.9 to 36.0 mm h-1 for south-facing plots. Three different theoretical spatial distribution models of steady-state infiltration rate were fit to the measurements of rainfall rate and steady-state discharge to provided estimates of the spatial average (19.2-22.2 mm h-1) and the coefficient of variation (0.11-0.40) of infiltration rates, overland flow contributing area (74-90% of the plot area), and infiltration threshold (19.0-26 mm h-1). Tensiometer measurements indicated a downward moving pressure wave and suggest that infiltration-excess overland flow is the runoff process on these burned hillslope with a two-layer system. Moreover, the results indicate that the ash layer is wettable, may restrict water flow into the underlying layer, and increase the infiltration threshold; whereas, the underlying mineral soil, though coarser, limits the infiltration rate. These results of the spatial variability of steady-state infiltration can be used to develop physically-based rainfall-runoff models for burned areas with a two-layer soil system. ?? 2010 Elsevier B.V.

MARS input data for steady-state calculation of ATLAS

International Nuclear Information System (INIS)

Park, Hyun Sik; Euh, D. J.; Choi, K. Y.; Kwon, T. S.; Jeong, J. J.; Baek, W. P.

2004-12-01

An integral effect test loop for Pressurized Water Reactors (PWRs), the ATLAS (Advanced Thermal-hydraulic Test Loop for Accident Simulation), is under construction by Thermal-Hydraulics Safety Research Division in Korea Atomic Energy Research Institute (KAERI). This report includes calculation sheets of the input for the best-estimate system analysis code, the MARS code, based on the ongoing design features of ATLAS. The ATLAS facility has been designed to have the length scale of 1/2 and area scale of 1/144 compared with the reference plant, APR1400. The contents of this report are divided into three parts: (1) core and reactor vessel, (2) steam generator and steam line, and (3) primary piping, pressurizer and reactor coolant pump. The steady-state analysis for the ATLAS facility will be performed based on these calculation sheets, and its results will be applied to the detailed design of ATLAS. Additionally, the calculation results will contribute to getting optimum test conditions and preliminary operational test conditions for the steady-state and transient experiments

Thermodynamic simulation and evaluation of sugar refinery evaporators using a steady state modelling approach

International Nuclear Information System (INIS)

Lewis, A.E.; Khodabocus, F.; Dhokun, V.; Khalife, M.

2010-01-01

In a sugar refinery, the juice is concentrated through evaporation, with the objective of concentrating the juice to syrup as rapidly as possible. Because the heat of vaporization of water is relatively high, the evaporation process can be highly energy intensive, and therefore the economical use of steam is important in the refinery. This paper reports on the development of a simulation model for the evaporation sections of two Mauritian sugar refineries. The first objective was to use the simulation model to carry out an energy balance over the evaporators in order to assess the economy of steam usage over the refinery. The second objective was to examine to what extent a fundamental steady state model, based on thermodynamics (not kinetics) was capable of predicting the material and energy flows in two operating sugar refineries and thereby to evaluate the applicability of the modelling framework. The simulation model was validated using historical data as well as data from the plant DCS system. The simulation results generally correlated well with the measured values, except for one of the evaporators on one refinery. Some suggestions were made as to the cause of the discrepancy. On balance, it was found that both refineries are extremely efficient in terms of steam and equipment usage and that there is not much scope for energy optimisation within the present configuration - nor for much spare steam capacity for an additional refinery. It was also shown that steady state process simulation, using thermodynamic models, can generate a very useful representation of a working refinery. Besides being able to use the model to 'benchmark' the operation and thus evaluate its performance as a whole as well as across individual units, it could also be used to evaluate refinery performance across refineries, nationally as well as globally.

Advanced control scenario of high-performance steady-state operation for JT-60 superconducting tokamak

International Nuclear Information System (INIS)

Tamai, H.; Kurita, G.; Matsukawa, M.; Urata, K.; Sakurai, S.; Tsuchiya, K.; Morioka, A.; Miura, Y.M.; Kizu, K.; Kamada, Y.; Sakasai, A.; Ishida, S.

2004-01-01

Plasma control on high-β N steady-state operation for JT-60 superconducting modification is discussed. Accessibility to high-β N exceeding the free-boundary limit is investigated with the stabilising wall of reduced-activated ferritic steel and the active feedback control of the in-vessel non-axisymmetric field coils. Taking the merit of superconducting magnet, advanced plasma control for steady-state high performance operation could be expected. (authors)

Kinetics of solid state phase transformations: Measurement and ...

Indian Academy of Sciences (India)

Administrator

heating or cooling rate can also exert a crucial influence on the kinetic outcome is stressed. The kinetic ... A simple and general modelling methodology for understanding the kinetics of ... state is of interest on both basic and applied grounds.

Steady-state pharmacokinetics of pravastatin in children with familial hypercholesterolaemia

NARCIS (Netherlands)

Wiersma, Heleen E.; Wiegman, Albert; Koopmans, Richard P.; Bakker, Henk D.; Kastelein, John J. P.; van Boxtel, Chris J.

2004-01-01

Objective: To determine pharmacokinetic data for pravastatin in children, since current data are insufficient in this age group. Subjects and methods: A 2-week, multiple-dose, steady-state pharmacokinetic study was carried out with pravastatin 20mg daily in 24 children with familial

Optimising performance in steady state for a supermarket refrigeration system

DEFF Research Database (Denmark)

Green, Torben; Kinnaert, Michel; Razavi-Far, Roozbeh

2012-01-01

Using a supermarket refrigeration system as an illustrative example, the paper postulates that by appropriately utilising knowledge of plant operation, the plant wide performance can be optimised based on a small set of variables. Focusing on steady state operations, the total system performance...

Iterative Observer-based Estimation Algorithms for Steady-State Elliptic Partial Differential Equation Systems

KAUST Repository

Majeed, Muhammad Usman

2017-07-19

Steady-state elliptic partial differential equations (PDEs) are frequently used to model a diverse range of physical phenomena. The source and boundary data estimation problems for such PDE systems are of prime interest in various engineering disciplines including biomedical engineering, mechanics of materials and earth sciences. Almost all existing solution strategies for such problems can be broadly classified as optimization-based techniques, which are computationally heavy especially when the problems are formulated on higher dimensional space domains. However, in this dissertation, feedback based state estimation algorithms, known as state observers, are developed to solve such steady-state problems using one of the space variables as time-like. In this regard, first, an iterative observer algorithm is developed that sweeps over regular-shaped domains and solves boundary estimation problems for steady-state Laplace equation. It is well-known that source and boundary estimation problems for the elliptic PDEs are highly sensitive to noise in the data. For this, an optimal iterative observer algorithm, which is a robust counterpart of the iterative observer, is presented to tackle the ill-posedness due to noise. The iterative observer algorithm and the optimal iterative algorithm are then used to solve source localization and estimation problems for Poisson equation for noise-free and noisy data cases respectively. Next, a divide and conquer approach is developed for three-dimensional domains with two congruent parallel surfaces to solve the boundary and the source data estimation problems for the steady-state Laplace and Poisson kind of systems respectively. Theoretical results are shown using a functional analysis framework, and consistent numerical simulation results are presented for several test cases using finite difference discretization schemes.

Progress towards Steady State on NSTX

International Nuclear Information System (INIS)

Gates, D.A.; Kessel, C.; Menard, J.; Taylor, G.; Wilson, J.R.

2005-01-01

In order to reduce recirculating power fraction to acceptable levels, the spherical torus concept relies on the simultaneous achievement of high toroidal β and high bootstrap fraction in steady state. In the last year, as a result of plasma control system improvements, the achievable plasma elongation on the National Spherical Torus Experiment (NSTX) has been raised from κ ∼ 2.1 to κ ∼ 2.6--approximately a 25% increase. This increase in elongation has lead to a doubling increase in the toroidal β for long-pulse discharges. The increase in β is associated with an increase in plasma current at nearly fixed poloidal β, which enables higher β t with nearly constant bootstrap fraction. As a result, for the first time in a spherical torus, a discharge with a plasma current of 1 MA has been sustained for 1 second. Data is presented from NSTX correlating the increase in performance with increased plasma shaping capability. In addition to improved shaping, H-modes induced during the current ramp phase of the plasma discharge have been used to reduce flux consumption during and to delay the onset of MHD instabilities. A modeled integrated scenario, which has 100% non-inductive current drive with very high toroidal β, will also be presented. The NSTX poloidal field coils are currently being modified to produce the plasma shape which is required for this scenario, which requires high triangularity ((delta) ∼ 0.8) at elevated elongation (κ ∼ 2.5). The other main requirement for steady state on NSTX is the ability to drive a fraction of the total plasma current with radio-frequency waves. The results of High Harmonic Fast Wave heating and current drive studies as well as electron Bernstein Wave emission studies will be presented

Theoretical analysis of steady state operating forces in control valves

Directory of Open Access Journals (Sweden)

Basavaraj Hubballi

2018-01-01

Full Text Available The controlling components, such as valves are used to regulate controlled fluid power. It is not always possible to calculate valve forces accurately, and with some types of valves even the existence of certain types of forces cannot be predicted with certainty. In many cases, however, the analysis can be made fairly completely and accurately. The assumption of steady state conditions is valid for the valve alone, but transient effects in the rest of the system may be large. These effects are particularly important with regard to the instability of valves, where the system may react on the valve in such a way as to make it squeal or oscillate, sometimes with large amplitude. The origin of the steady state flow force understood from a brief qualitative explanation. The following paper will summarize much of what is known about valve forces in the spool type controlling element.

The relative importance of kinetic mechanisms and variable enzyme abundances for the regulation of hepatic glucose metabolism--insights from mathematical modeling.

Science.gov (United States)

Bulik, Sascha; Holzhütter, Hermann-Georg; Berndt, Nikolaus

2016-03-02

Adaptation of the cellular metabolism to varying external conditions is brought about by regulated changes in the activity of enzymes and transporters. Hormone-dependent reversible enzyme phosphorylation and concentration changes of reactants and allosteric effectors are the major types of rapid kinetic enzyme regulation, whereas on longer time scales changes in protein abundance may also become operative. Here, we used a comprehensive mathematical model of the hepatic glucose metabolism of rat hepatocytes to decipher the relative importance of different regulatory modes and their mutual interdependencies in the hepatic control of plasma glucose homeostasis. Model simulations reveal significant differences in the capability of liver metabolism to counteract variations of plasma glucose in different physiological settings (starvation, ad libitum nutrient supply, diabetes). Changes in enzyme abundances adjust the metabolic output to the anticipated physiological demand but may turn into a regulatory disadvantage if sudden unexpected changes of the external conditions occur. Allosteric and hormonal control of enzyme activities allow the liver to assume a broad range of metabolic states and may even fully reverse flux changes resulting from changes of enzyme abundances alone. Metabolic control analysis reveals that control of the hepatic glucose metabolism is mainly exerted by enzymes alone, which are differently controlled by alterations in enzyme abundance, reversible phosphorylation, and allosteric effects. In hepatic glucose metabolism, regulation of enzyme activities by changes of reactants, allosteric effects, and reversible phosphorylation is equally important as changes in protein abundance of key regulatory enzymes.

Is steady-state capitalism viable? A review of the issues and an answer in the affirmative.

Science.gov (United States)

Lawn, Philip

2011-02-01

Most ecological economists believe that the transition to a steady-state economy is necessary to ensure ecological sustainability and to maximize a nation's economic welfare. While some observers agree with the necessity of the steady-state economy, they are nonetheless critical of the suggestion made by ecological economists-in particular, Herman Daly-that a steady-state economy is compatible with a capitalist system. First, they believe that steady-state capitalism is based on the untenable assumption that growth is an optional rather than in-built element of capitalism. Second, they argue that capitalist notions of efficient resource allocation are too restrictive to facilitate the transition to an "ecological" or steady-state economy. I believe these observers are outright wrong with their first criticism and, because they misunderstand Daly's vision of a steady-state economy, are misplaced with their second criticism. The nature of a capitalist system depends upon the institutional framework that supports and shapes it. Hence, a capitalist system can exist in a wide variety of forms. Unfortunately, many observers fail to recognize that the current "growth imperative" is the result of capitalist systems everywhere being institutionally designed to grow. They need not be designed this way to survive and thrive. Indeed, because continued growth is both existentially undesirable and ecologically unsustainable, redesigning capitalist systems through the introduction of Daly-like institutions would prove to be capitalism's savior. What's more, it would constitute humankind's best hope of achieving sustainable development. © 2011 New York Academy of Sciences.

Blood-organ transfer kinetics

International Nuclear Information System (INIS)

Skrable, K.W.; Chabot, G.E.; French, C.S.; Wrenn, M.E.; Lipsztein, J.; Sasso, T.L.; Durbin, P.W.

1980-01-01

Exact and approximate kinetics equations relating to the transfer and elimination of radionuclides from the blood and various organs in the body are presented. These expressions may be used to estimate the instantaneous activity or the total number of disintegrations of a radionuclide in the blood or various organs of reference in the body, hence, also the respective dose rates and doses. The exact kinetics equations may be used to relate measurements of radionuclides in excreta to burdens in the body. They do give better results for exposure intervals long compared to the effective mean lives of the radionuclide in the various organs of reference, and they yield the exact steady state expressions. Fortunately, this condition is often satisfied for the relatively long standard exposure interval of 50 years that is applied to occupational exposure. In addition, the steady state expressions may be used along with metabolic data of the distribution of elements in the body, diet and excreta to estimate values of the rate constants used in both the exact and approximate expressions. A comparison of the exact and approximate expressions is given for the uranium metabolic model of Wrenn et al. and a comparison is made with current ICRP models. (author)

Stabilizing the border steady-state solution of two interacting ...

African Journals Online (AJOL)

In this paper, we have successfully developed a feedback control which has been used to stabilize an unstable steady-state solution (0, 3.3534). This convergence has occurred when the values of the final time are 190, 200, 210 and 220 which corresponds to the scenario when the value of the step length of our simulation ...

Ideal MHD stability and performance of ITER steady-state scenarios with ITBs

Science.gov (United States)

Poli, F. M.; Kessel, C. E.; Chance, M. S.; Jardin, S. C.; Manickam, J.

2012-06-01

Non-inductive steady-state scenarios on ITER will need to operate with internal transport barriers (ITBs) in order to reach adequate fusion gain at typical currents of 9 MA. The large pressure gradients at the location of the internal barrier are conducive to the development of ideal MHD instabilities that may limit the plasma performance and may lead to plasma disruptions. Fully non-inductive scenario simulations with five combinations of heating and current drive sources are presented in this work, with plasma currents in the range 7-10 MA. For each configuration the linear, ideal MHD stability is analysed for variations of the Greenwald fraction and of the pressure peaking factor around the operating point, aiming at defining an operational space for stable, steady-state operations at optimized performance. It is shown that plasmas with lower hybrid heating and current drive maintain the minimum safety factor above 1.5, which is desirable in steady-state operations to avoid neoclassical tearing modes. Operating with moderate ITBs at 2/3 of the minor radius, these plasmas have a minimum safety factor above 2, are ideal MHD stable and reach Q ≳ 5 operating above the ideal no-wall limit.

Coherent control of long-distance steady-state entanglement in lossy resonator arrays

Science.gov (United States)

Angelakis, D. G.; Dai, L.; Kwek, L. C.

2010-07-01

We show that coherent control of the steady-state long-distance entanglement between pairs of cavity-atom systems in an array of lossy and driven coupled resonators is possible. The cavities are doped with atoms and are connected through waveguides, other cavities or fibers depending on the implementation. We find that the steady-state entanglement can be coherently controlled through the tuning of the phase difference between the driving fields. It can also be surprisingly high in spite of the pumps being classical fields. For some implementations where the connecting element can be a fiber, long-distance steady-state quantum correlations can be established. Furthermore, the maximal of entanglement for any pair is achieved when their corresponding direct coupling is much smaller than their individual couplings to the third party. This effect is reminiscent of the establishment of coherence between otherwise uncoupled atomic levels using classical coherent fields. We suggest a method to measure this entanglement by analyzing the correlations of the emitted photons from the array and also analyze the above results for a range of values of the system parameters, different network geometries and possible implementation technologies.

Producing a steady-state population inversion

International Nuclear Information System (INIS)

Richards, R.K.; Griffin, D.C.

1986-03-01

An observed steady-state transition at 17.5 nm is identified as the 2p 5 3s3p 4 S/sub 3/2/ → 2p 6 3p 2 P/sub 3/2/ transition in Na-like aluminum. The upper level is populated by electron inner shell ionization of metastable Mg-like aluminum. From the emission intensity, the rate coefficient for populating the upper level is calculated to be approximately 5 x 10 -10 ) cm 3 /sec. Since the upper level is quasimetastable with a lifetime 22 times longer than the lower level, it may be possible to produce a population inversion, if a competing process to populate the lower level can be reduced

Steady-State Ion Beam Modeling with MICHELLE

Science.gov (United States)

Petillo, John

2003-10-01

There is a need to efficiently model ion beam physics for ion implantation, chemical vapor deposition, and ion thrusters. Common to all is the need for three-dimensional (3D) simulation of volumetric ion sources, ion acceleration, and optics, with the ability to model charge exchange of the ion beam with a background neutral gas. The two pieces of physics stand out as significant are the modeling of the volumetric source and charge exchange. In the MICHELLE code, the method for modeling the plasma sheath in ion sources assumes that the electron distribution function is a Maxwellian function of electrostatic potential over electron temperature. Charge exchange is the process by which a neutral background gas with a "fast" charged particle streaming through exchanges its electron with the charged particle. An efficient method for capturing this is essential, and the model presented is based on semi-empirical collision cross section functions. This appears to be the first steady-state 3D algorithm of its type to contain multiple generations of charge exchange, work with multiple species and multiple charge state beam/source particles simultaneously, take into account the self-consistent space charge effects, and track the subsequent fast neutral particles. The solution used by MICHELLE is to combine finite element analysis with particle-in-cell (PIC) methods. The basic physics model is based on the equilibrium steady-state application of the electrostatic particle-in-cell (PIC) approximation employing a conformal computational mesh. The foundation stems from the same basic model introduced in codes such as EGUN. Here, Poisson's equation is used to self-consistently include the effects of space charge on the fields, and the relativistic Lorentz equation is used to integrate the particle trajectories through those fields. The presentation will consider the complexity of modeling ion thrusters.

The Effects of High Intensity Interval Training vs Steady State Training on Aerobic and Anaerobic Capacity.

Science.gov (United States)

Foster, Carl; Farland, Courtney V; Guidotti, Flavia; Harbin, Michelle; Roberts, Brianna; Schuette, Jeff; Tuuri, Andrew; Doberstein, Scott T; Porcari, John P

2015-12-01

High intensity interval training (HIIT) has become an increasingly popular form of exercise due to its potentially large effects on exercise capacity and small time requirement. This study compared the effects of two HIIT protocols vs steady-state training on aerobic and anaerobic capacity following 8-weeks of training. Fifty-five untrained college-aged subjects were randomly assigned to three training groups (3x weekly). Steady-state (n = 19) exercised (cycle ergometer) 20 minutes at 90% of ventilatory threshold (VT). Tabata (n = 21) completed eight intervals of 20s at 170% VO2max/10s rest. Meyer (n = 15) completed 13 sets of 30s (20 min) @ 100% PVO2 max/ 60s recovery, average PO = 90% VT. Each subject did 24 training sessions during 8 weeks. There were significant (p Tabata protocol was significantly less enjoyable (p HIIT protocols are time efficient, they are not superior to conventional exercise training in sedentary young adults. Key pointsSteady state training equivalent to HIIT in untrained studentsMild interval training presents very similar physiologic challenge compared to steady state trainingHIIT (particularly very high intensity variants were less enjoyable than steady state or mild interval trainingEnjoyment of training decreases across the course of an 8 week experimental training program.

Iterative Observer-based Estimation Algorithms for Steady-State Elliptic Partial Differential Equation Systems

KAUST Repository

Majeed, Muhammad Usman

2017-01-01

the problems are formulated on higher dimensional space domains. However, in this dissertation, feedback based state estimation algorithms, known as state observers, are developed to solve such steady-state problems using one of the space variables as time

Analysis of steady state and transient two-phase flows in downwardly inclined lines

International Nuclear Information System (INIS)

Crawford, T.J.

1983-01-01

A study of steady-state and transient two-phase flows in downwardly inclined lines is described. Steady-state flow patterns maps are presented using Freon-113 as the working fluid to provide new high density vapors. These flow maps with high density vapor serve to significantly extend the investigations of steady-state downward two-phase flow patterns. Physical models developed which successfully predicted the onset or location of various flow pattern transitions. A new simplified criterion that would be useful to designers and experimenters is offered for the onset of dispersed flow. A new empirical holdup correlation and a new bubble diameter/flow rate correlation are also proposed. Flow transients in vertical downward lines were studied to investigate the possible formation of intermediate or spurious flow patterns that would not be seen at steady-state conditions. Void fraction behavior during the transients was modeled by using the dynamic slip equation from the transient analysis code RETRAN. Physical models of interfacial area were developed and compared with models and data from literature. There was satisfactory agreement between the models of the present study and the literature models and data. The concentration parameter of the drift flux model was evaluated for vertical downward flow. These new values of the flow dependent parameter were different from those previously proposed in the literature for use in upward flows, and made the drift flux model suitable for use in upward or downward flow lines

S3C: EBT Steady-State Shooting code description and user's guide

International Nuclear Information System (INIS)

Downum, W.B.

1983-09-01

The Oak Ridge National Laboratory (ORNL) one-dimensional (1-D) Steady-State Shooting code (S3C) for ELMO Bumpy Torus (EBT) plasmas is described. Benchmark calculations finding the steady-state density and electron and ion temperature profiles for a known neutral density profile and known external energy sources are carried out. Good agreement is obtained with results from the ORNL Radially Resolved Time Dependent 1-D Transport code for an EBT-Q type reactor. The program logic is described, along with the physics models in each code block and the variable names used. Sample input and output files are listed, along with the main code

Steady-state ozone concentrations in radiation induced noble gas-oxygen discharges

International Nuclear Information System (INIS)

Elsayed-Ali, H.E.; Miley, G.H.

1985-01-01

Measurements of steady-state ozone concentrations in continuous radiation induced noble gas-O/sub 2/ and noble gas-o/sub 2/-SF/sub 6/ mixtures has been accomplished. The discharges were created through the bombardment of the gases with energetic particles from the boron-10 (n,α) lithium-7 nuclear reaction. Three noble gases were studied, He, Ne, and Ar at partial pressures of few hundred Torr. The dose rates studied were in the order of 10/sup 15/ eV . cm/sup -3/ . s/sup -1/. The experimental apparatus and procedure were previously described. The experimentally observed steady-state ozone concentrations in noble gas-O/sub 2/ discharges were about an order of magnitude lower than that observed for oxygen radiolysis at similar dose rates. These results were physically explained by an enhanced role of negative ionic reactions with ozone causing its destruction. In noble gas-O/sub 2/-SF/sub 6/ mixtures, the steady-state ozone concentrations were found to be significantly higher (3-6 times) than that without the SF/sub 6/ addition. This observation was contrary to only a small increase observed after SF/sub 6/ addition to a few hundred Torr oxygen and is explained by an enhanced rate of electron dissociative attachment of ozone in noble gas-O/sub 2/ discharges

Transient and Steady-State Responses of an Asymmetric Nonlinear Oscillator

Directory of Open Access Journals (Sweden)

Alex Elías-Zúñiga

2013-01-01

oscillator that describes the motion of a damped, forced system supported symmetrically by simple shear springs on a smooth inclined bearing surface. We also use the percentage overshoot value to study the influence of damping and nonlinearity on the transient and steady-state oscillatory amplitudes.

Capitalist Diversity and De-growth Trajectories to Steady-state Economies

DEFF Research Database (Denmark)

Buch-Hansen, Hubert

2014-01-01

Growth-critical scholarship has done much to both expose the environmentally unsustainable nature of the capitalist growth-economies of the overdeveloped part of the world and to develop an alternative vision of a degrowth transition leading to a steady-state economy. However, this scholarship fa...

Indirect MRI of 17 o-labeled water using steady-state sequences: Signal simulation and preclinical experiment.

Science.gov (United States)

Kudo, Kohsuke; Harada, Taisuke; Kameda, Hiroyuki; Uwano, Ikuko; Yamashita, Fumio; Higuchi, Satomi; Yoshioka, Kunihiro; Sasaki, Makoto

2018-05-01

Few studies have been reported for T 2 -weighted indirect 17 O imaging. To evaluate the feasibility of steady-state sequences for indirect 17 O brain imaging. Signal simulation, phantom measurements, and prospective animal experiments were performed in accordance with the institutional guidelines for animal experiments. Signal simulations of balanced steady-state free precession (bSSFP) were performed for concentrations of 17 O ranging from 0.037-1.600%. Phantom measurements with concentrations of 17 O water ranging from 0.037-1.566% were also conducted. Six healthy beagle dogs were scanned with intravenous administration of 20% 17 O-labeled water (1 mL/kg). Dynamic 3D-bSSFP scans were performed at 3T MRI. 17 O-labeled water was injected 60 seconds after the scan start, and the total scan duration was 5 minutes. Based on the result of signal simulation and phantom measurement, signal changes in the beagle dogs were measured and converted into 17 O concentrations. The 17 O concentrations were averaged for every 15 seconds, and compared to the baseline (30-45 sec) with Dunnett's multiple comparison tests. Signal simulation revealed that the relationships between 17 O concentration and the natural logarithm of relative signals were linear. The intraclass correlation coefficient between relative signals in phantom measurement and signal simulations was 0.974. In the animal experiments, significant increases in 17 O concentration (P O. At the end of scanning, mean respective 17 O concentrations of 0.084 ± 0.026%, 0.117 ± 0.038, 0.082 ± 0.037%, and 0.049 ± 0.004% were noted for the cerebral cortex, cerebellar cortex, cerebral white matter, and ventricle. Dynamic steady-state sequences were feasible for indirect 17 O imaging, and absolute quantification was possible. This method can be applied for the measurement of permeability and blood flow in the brain, and for kinetic analysis of cerebrospinal fluid. 2 Technical Efficacy: Stage 1 J. Magn. Reson

Restitution slope is principally determined by steady-state action potential duration.

Science.gov (United States)

Shattock, Michael J; Park, Kyung Chan; Yang, Hsiang-Yu; Lee, Angela W C; Niederer, Steven; MacLeod, Kenneth T; Winter, James

2017-06-01

The steepness of the action potential duration (APD) restitution curve and local tissue refractoriness are both thought to play important roles in arrhythmogenesis. Despite this, there has been little recognition of the apparent association between steady-state APD and the slope of the restitution curve. The objective of this study was to test the hypothesis that restitution slope is determined by APD and to examine the relationship between restitution slope, refractoriness and susceptibility to VF. Experiments were conducted in isolated hearts and ventricular myocytes from adult guinea pigs and rabbits. Restitution curves were measured under control conditions and following intervention to prolong (clofilium, veratridine, bretylium, low [Ca]e, chronic transverse aortic constriction) or shorten (catecholamines, rapid pacing) ventricular APD. Despite markedly differing mechanisms of action, all interventions that prolonged the action potential led to a steepening of the restitution curve (and vice versa). Normalizing the restitution curve as a % of steady-state APD abolished the difference in restitution curves with all interventions. Effects on restitution were preserved when APD was modulated by current injection in myocytes pre-treated with the calcium chelator BAPTA-AM - to abolish the intracellular calcium transient. The non-linear relation between APD and the rate of repolarization of the action potential is shown to underpin the common influence of APD on the slope of the restitution curve. Susceptibility to VF was found to parallel changes in APD/refractoriness, rather than restitution slope. Steady-state APD is the principal determinant of the slope of the ventricular electrical restitution curve. In the absence of post-repolarization refractoriness, factors that prolong the action potential would be expected to steepen the restitution curve. However, concomitant changes in tissue refractoriness act to reduce susceptibility to sustained VF. Dependence on

Preliminary design study of a steady state tokamak device

International Nuclear Information System (INIS)

Miya, Naoyuki; Nakajima, Shinji; Ushigusa, Kenkichi; and athors)

1992-09-01

Preliminary design study has been made for a steady tokamak with the plasma current of 10MA, as the next to the JT-60U experimental programs. The goal of the research program is the integrated study of steady state, high-power physics and technology. Present candidate design is to use superconducting TF and PF magnet systems and long pulse operation of 100's-1000's of sec with non inductive current drive mainly by 500keV negative ion beam injection of 60MW. Low activation material such as titanium alloy is chosen for the water tank type vacuum vessel, which is also the nuclear shield for the superconducting coils. The present preliminary design study shows that the device can meet the existing JT-60U facility capability. (author)

Dynamic fluid connectivity during steady-state multiphase flow in a sandstone.

Science.gov (United States)

Reynolds, Catriona A; Menke, Hannah; Andrew, Matthew; Blunt, Martin J; Krevor, Samuel

2017-08-01

The current conceptual picture of steady-state multiphase Darcy flow in porous media is that the fluid phases organize into separate flow pathways with stable interfaces. Here we demonstrate a previously unobserved type of steady-state flow behavior, which we term "dynamic connectivity," using fast pore-scale X-ray imaging. We image the flow of N 2 and brine through a permeable sandstone at subsurface reservoir conditions, and low capillary numbers, and at constant fluid saturation. At any instant, the network of pores filled with the nonwetting phase is not necessarily connected. Flow occurs along pathways that periodically reconnect, like cars controlled by traffic lights. This behavior is consistent with an energy balance, where some of the energy of the injected fluids is sporadically converted to create new interfaces.

Steady state operation of tokamaks. Proceedings of a technical committee meeting

International Nuclear Information System (INIS)

2000-10-01

The first IAEA Technical Committee Meeting (TCM) on Steady State Operation of Tokamaks was organized to discuss the operations of present long-pulse tokamaks (TRIAM-1M, TORE SUPRA, MT-7, HT-7M, HL-1M) and the plans for future steady-state tokamaks such as SST-1, CIEL, and HT-7U. This meeting, held from 13-15 October 1998, was hosted by the Academia Sinica Institute of Plasma Physics (ASIPP), Hefei, China. Participants from China, France, India, Japan, the Russian Federation, and the IAEA participated in the meeting. There were 18 individual presentations plus general discussions on many topics, including superconducting magnet systems, cryogenics, plasma position control, non-inductive current drive, auxiliary heating, plasma-wall interactions, high heat flux components, particle control, and data acquisition

Kinetic and CD/MCD spectroscopic studies of the atypical, three-His-ligated, non-heme Fe2+ center in diketone dioxygenase: the role of hydrophilic outer shell residues in catalysis.

Science.gov (United States)

Straganz, Grit D; Diebold, Adrienne R; Egger, Sigrid; Nidetzky, Bernd; Solomon, Edward I

2010-02-09

Diketone cleaving enzyme (Dke1) is a dioxygenase with an atypical, three-histidine-ligated, mononuclear non-heme Fe(2+) center. To assess the role in enzyme catalysis of the hydrophilic residues in the active site pocket, residues Glu98, Arg80, Tyr70, and Thr107 were subjected to mutational analysis. Steady state and pre-steady state kinetics indicated a role for Glu98 in promoting both substrate binding and O(2) reduction. Additionally, the Glu98 substitution eliminated the pH dependence of substrate binding (k(cat)(app)/K(M)(app)-pH profile) present in wild-type Dke1 (pK(a) = 6.3 +/- 0.4 and 8.4 +/- 0.4). MCD spectroscopy revealed that the Glu98 --> Gln mutation leads to the conversion of the six-coordinate (6C) resting Fe(2+) center present in the wild-type enzyme at pH 7.0 to a mixture of five-coordinate (5C) and 6C sites. The 6C geometry was restored with a pH shift to 9.5 which also resulted in ligand field (LF) energy splittings identical to that found for wild-type (WT) Dke1 at pH 9.5. In WT Dke1, these LF transitions are shifted up in energy by approximately 300 cm(-1) at pH 9.5 relative to pH 7.0. These data, combined with CD pH titrations which reveal a pK(a) of approximately 8.2 for resting WT Dke1 and the Glu98 --> Gln variant, indicate the deprotonation of a metal-ligated water. Together, the kinetic and spectroscopic data reveal a stabilizing effect of Glu98 on the 6C geometry of the metal center, priming it for substrate ligation. Arg80 and Tyr70 are shown to promote O(2) reduction, while Thr107 stabilizes the Fe(II) cofactor.

Steady State and Transient Analysis of Induction Motor Driving a ...

African Journals Online (AJOL)

The importance of using a digital computer in studying the performance of Induction machine under steady and transient states is presented with computer results which show the transient behaviour of 3-phase machine during balanced and unbalanced conditions. The computer simulation for these operating conditions is ...

Data system design considerations for a pseudo-steady-state device

International Nuclear Information System (INIS)

Wing, W.R.

1981-01-01

The Advanced Toroidal Facility is being designed to run in a steady state. This places stringent requirements on a data system, since it must provide steady-state support that is equivalent to the support users are accustomed to from pulsed experiments; i.e., enough capacity to reduce diagnostic data for live presentation. Parameters such as density, position, and temperature must be presented live (i.e., within 0.1 s). Quantities such as plasma shape or internal structure should be available with a minimum of delay. The traditional solution to providing such capabilities is to use distributed processing to off-load data acquisition from the analysis computers. However, this suffers in a real-time environment because of the necessity of moving large quantities of data from acquisition to analysis. We expect to solve the problem by using a pipelined design that will acquire data directly into shared memory, where any one of four CPU's (VAX 11/780's) can proceed with analysis

Steady-state evoked potentials possibilities for mental-state estimation

Science.gov (United States)

Junker, Andrew M.; Schnurer, John H.; Ingle, David F.; Downey, Craig W.

1988-01-01

The use of the human steady-state evoked potential (SSEP) as a possible measure of mental-state estimation is explored. A method for evoking a visual response to a sum-of-ten sine waves is presented. This approach provides simultaneous multiple frequency measurements of the human EEG to the evoking stimulus in terms of describing functions (gain and phase) and remnant spectra. Ways in which these quantities vary with the addition of performance tasks (manual tracking, grammatical reasoning, and decision making) are presented. Models of the describing function measures can be formulated using systems engineering technology. Relationships between model parameters and performance scores during manual tracking are discussed. Problems of unresponsiveness and lack of repeatability of subject responses are addressed in terms of a need for loop closure of the SSEP. A technique to achieve loop closure using a lock-in amplifier approach is presented. Results of a study designed to test the effectiveness of using feedback to consciously connect humans to their evoked response are presented. Findings indicate that conscious control of EEG is possible. Implications of these results in terms of secondary tasks for mental-state estimation and brain actuated control are addressed.

Substrate inhibition kinetics of phenol degradation by binary mixed ...

African Journals Online (AJOL)

Steady states of a continuous culture with an inhibitory substrate were used to estimate kinetic parameters under substrate limitation (chemo stat operation). Mixed cultures of an indigenous Pseudomonas fluorescence and Pseudomonas aeruginosa were grown in continuous culture on phenol as the sole source of carbon ...

Disassembly of Faceted Macrosteps in the Step Droplet Zone in Non-Equilibrium Steady State

Directory of Open Access Journals (Sweden)

Noriko Akutsu

2017-02-01

Full Text Available A Wulff figure—the polar graph of the surface tension of a crystal—with a discontinuity was calculated by applying the density matrix renormalization group method to the p-RSOS model, a restricted solid-on-solid model with a point-contact-type step–step attraction. In the step droplet zone in this model, the surface tension is discontinuous around the (111 surface and continuous around the (001 surface. The vicinal surface of 4H-SiC crystal in a Si–Cr–C solution is thought to be in the step droplet zone. The dependence of the vicinal surface growth rate and the macrostep size 〈 n 〉 on the driving force Δ μ for a typical state in the step droplet zone in non-equilibrium steady state was calculated using the Monte Carlo method. In contrast to the known step bunching phenomenon, the size of the macrostep was found to decrease with increasing driving force. The detachment of elementary steps from a macrostep was investigated, and it was found that 〈 n 〉 satisfies a scaling function. Moreover, kinetic roughening was observed for | Δ μ | > Δ μ R , where Δ μ R is the crossover driving force above which the macrostep disappears.

Thermal Conductivity of EB-PVD Thermal Barrier Coatings Evaluated by a Steady-State Laser Heat Flux Technique

Science.gov (United States)

Zhu, Dongming; Miller, Robert A.; Nagaraj, Ben A.; Bruce, Robert W.

2000-01-01

The thermal conductivity of electron beam-physical vapor deposited (EB-PVD) Zr02-8wt%Y2O3 thermal barrier coatings was determined by a steady-state heat flux laser technique. Thermal conductivity change kinetics of the EB-PVD ceramic coatings were also obtained in real time, at high temperatures, under the laser high heat flux, long term test conditions. The thermal conductivity increase due to micro-pore sintering and the decrease due to coating micro-delaminations in the EB-PVD coatings were evaluated for grooved and non-grooved EB-PVD coating systems under isothermal and thermal cycling conditions. The coating failure modes under the high heat flux test conditions were also investigated. The test technique provides a viable means for obtaining coating thermal conductivity data for use in design, development, and life prediction for engine applications.

Progress on advanced tokamak and steady-state scenario development on DIII-D and NSTX

Energy Technology Data Exchange (ETDEWEB)

Doyle, E J [Department of Electrical Engineering and PSTI, University of California, Los Angeles, California 90095 (United States); Garofalo, A M [Columbia University, New York, New York 10027 (United States); Greenfield, C M [General Atomics, San Diego, California 92186-5608 (United States); Kaye, S M [Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543-0451 (United States); Menard, J E [Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543-0451 (United States); Murakami, M [Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Sabbagh, S A [Columbia University, New York, New York 10027 (United States); Austin, M E [University of Texas-Austin, Austin, Texas 78712 (United States); Bell, R E [Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543-0451 (United States); Burrell, K H [General Atomics, San Diego, California 92186-5608 (United States); Ferron, J R [General Atomics, San Diego, California 92186-5608 (United States); Gates, D A [Princeton Plasma Physics Lab., Princeton, New Jersey 08543-0451 (United States); Groebner, R J; Hyatt, A W; Luce, T C; Petty, C C; Wade, M R; Waltz, R E [General Atomics, San Diego, California 92186-5608 (United States); Jayakumar, R J [Lawrence Livermore National Lab., Livermore, California 94550 (United States); Kinsey, J E [Lehigh Univ., Bethlehem, Pennsylvania 18015 (United States); LeBlanc, B P [Princeton Plasma Physics Lab., Princeton, New Jersey 08543-0451 (United States); McKee, G R [Univ. of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Okabayashi, M [Princeton Plasma Physics Lab., Princeton, New Jersey 08543-0451 (United States); Peng, Y-K M [Oak Ridge National Lab., Oak Ridge, Tennessee 37831 (United States); Politzer, P A [General Atomics, San Diego, California 92186-5608 (United States); Rhodes, T L [Dept. of Electrical Engineering and PSTI, Univ. of California, Los Angeles, California 90095 (United States)

2006-12-15

Advanced tokamak (AT) research seeks to develop steady-state operating scenarios for ITER and other future devices from a demonstrated scientific basis. Normalized target parameters for steady-state operation on ITER are 100% non-inductive current operation with a bootstrap current fraction f{sub BS} {>=} 60%, q{sub 95} {approx} 4-5 and G {identical_to}{beta}{sub N}H{sub scaling}/q{sub 95}{sup 2} {>=}0.3. Progress in realizing such plasmas is considered in terms of the development of plasma control capabilities and scientific understanding, leading to improved AT performance. NSTX has demonstrated active resistive wall mode stabilization with low, ITER-relevant, rotation rates below the critical value required for passive stabilization. On DIII-D, experimental observations and GYRO simulations indicate that ion internal transport barrier (ITB) formation at rational-q surfaces is due to equilibrium zonal flows generating high local E ? B shear levels. In addition, stability modelling for DIII-D indicates a path to operation at {beta}{sub N} {>=} 4 with q{sub min} {>=} 2, using broad, hollow current profiles to increase the ideal wall stability limit. Both NSTX and DIII-D have optimized plasma performance and expanded AT operational limits. NSTX now has long-pulse, high performance discharges meeting the normalized targets for an spherical torus-based component test facility. DIII-D has developed sustained discharges combining high beta and ITBs, with performance approaching levels required for AT reactor concepts, e.g. {beta}{sub N} = 4, H{sub 89} = 2.5, with f{sub BS} > 60%. Most importantly, DIII-D has developed ITER steady-state demonstration discharges, simultaneously meeting the targets for steady-state Q {>=} 5 operation on ITER set out above, substantially increasing confidence in ITER meeting its steady-state performance objective.

Thermal hydraulic and neutron kinetic coupled simulation of the IPR-R1 Triga reactor

Energy Technology Data Exchange (ETDEWEB)

Reis, Patricia A.L.; Costa, Antonella L.; Pereira, Claubia; Silva, Clarysson A.M. da; Veloso, Maria Auxiliadora F.; Soares, Humbero V., E-mail: patricialire@yahoo.com.br, E-mail: antonella@nuclear.ufmg.br, E-mail: claubia@nuclear.ufmg.br, E-mail: clarysson@nuclear.ufmg.br, E-mail: dora@nuclear.ufmg.br, E-mail: betovitor@ig.com.br [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Departamento de Engenharia Nuclear; Instituto Nacional de Ciencias e Tecnologia de Reatores Nucleares Inovadores (INCT/CNPq Rede), Rio de Janeiro, RJ (Brazil)

2013-07-01

The nuclear industry and the scientific community have turned the attention for the development of coupled 3D neutron kinetics (NK) and thermal-hydraulic (TH) system codes to investigate specific nuclear reactor transients. Improving in theoretical investigations of complex phenomena in nuclear reactor technology have been increased thanks to numerical methods and computational resources incorporated in nuclear codes. This paper presents a model for the IPR-R1 TRIGA research reactor using the RELAP5-3D 3.0 code. The development and the assessment of the thermal-hydraulic RELAP5 code model for the IPR-R1 have been validated for steady state and transient situations and the results were published in preceding works. Results of RELAP5-3D steady state and a transient case presented in this paper show good agreement with experimental data, validating then this model for point kinetic calculations. To supply adequate cross sections to the NK code, the WIMSD5 is being used. First results of steady state calculation using the 3D neutron modeling are being presented in this paper. (author)

Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation

Directory of Open Access Journals (Sweden)

Nag Ambarish

2011-06-01

Full Text Available Abstract Background Higher plants and algae are able to fix atmospheric carbon dioxide through photosynthesis and store this fixed carbon in large quantities as starch, which can be hydrolyzed into sugars serving as feedstock for fermentation to biofuels and precursors. Rational engineering of carbon flow in plant cells requires a greater understanding of how starch breakdown fluxes respond to variations in enzyme concentrations, kinetic parameters, and metabolite concentrations. We have therefore developed and simulated a detailed kinetic ordinary differential equation model of the degradation pathways for starch synthesized in plants and green algae, which to our knowledge is the most complete such model reported to date. Results Simulation with 9 internal metabolites and 8 external metabolites, the concentrations of the latter fixed at reasonable biochemical values, leads to a single reference solution showing β-amylase activity to be the rate-limiting step in carbon flow from starch degradation. Additionally, the response coefficients for stromal glucose to the glucose transporter kcat and KM are substantial, whereas those for cytosolic glucose are not, consistent with a kinetic bottleneck due to transport. Response coefficient norms show stromal maltopentaose and cytosolic glucosylated arabinogalactan to be the most and least globally sensitive metabolites, respectively, and β-amylase kcat and KM for starch to be the kinetic parameters with the largest aggregate effect on metabolite concentrations as a whole. The latter kinetic parameters, together with those for glucose transport, have the greatest effect on stromal glucose, which is a precursor for biofuel synthetic pathways. Exploration of the steady-state solution space with respect to concentrations of 6 external metabolites and 8 dynamic metabolite concentrations show that stromal metabolism is strongly coupled to starch levels, and that transport between compartments serves to

Comparing Interval Management Control Laws for Steady-State Errors and String Stability

Science.gov (United States)

Weitz, Lesley A.; Swieringa, Kurt A.

2018-01-01

Interval Management (IM) is a future airborne spacing concept that leverages avionics to provide speed guidance to an aircraft to achieve and maintain a specified spacing interval from another aircraft. The design of a speed control law to achieve the spacing goal is a key aspect in the research and development of the IM concept. In this paper, two control laws that are used in much of the contemporary IM research are analyzed and compared to characterize steady-state errors and string stability. Numerical results are used to illustrate how the choice of control laws gains impacts the size of steady-state errors and string performance and the potential trade-offs between those performance characteristics.

Magnetic sensor for steady state tokamak

Energy Technology Data Exchange (ETDEWEB)

Neyatani, Yuzuru; Mori, Katsuharu; Oguri, Shigeru; Kikuchi, Mitsuru [Japan Atomic Energy Research Inst., Naka, Ibaraki (Japan). Naka Fusion Research Establishment

1996-06-01

A new type of magnetic sensor has been developed for the measurement of steady state magnetic fields without DC-drift such as integration circuit. The electromagnetic force induced to the current which leads to the sensor was used for the measurement. For the high frequency component which exceeds higher than the vibration frequency of sensor, pick-up coil was used through the high pass filter. From the results using tokamak discharges, this sensor can measure the magnetic field in the tokamak discharge. During {approx}2 hours measurement, no DC drift was observed. The sensor can respond {approx}10ms of fast change of magnetic field during disruptions. We confirm the extension of measured range to control the current which leads to the sensor. (author).

Perspectives on electrostatics and conformational motions in enzyme catalysis.

Science.gov (United States)

Hanoian, Philip; Liu, C Tony; Hammes-Schiffer, Sharon; Benkovic, Stephen

2015-02-17

CONSPECTUS: Enzymes are essential for all living organisms, and their effectiveness as chemical catalysts has driven more than a half century of research seeking to understand the enormous rate enhancements they provide. Nevertheless, a complete understanding of the factors that govern the rate enhancements and selectivities of enzymes remains elusive, due to the extraordinary complexity and cooperativity that are the hallmarks of these biomolecules. We have used a combination of site-directed mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear magnetic resonance (NMR), vibrational and fluorescence spectroscopies, resonance energy transfer, and computer simulations to study the implications of conformational motions and electrostatic interactions on enzyme catalysis in the enzyme dihydrofolate reductase (DHFR). We have demonstrated that modest equilibrium conformational changes are functionally related to the hydride transfer reaction. Results obtained for mutant DHFRs illustrated that reductions in hydride transfer rates are correlated with altered conformational motions, and analysis of the evolutionary history of DHFR indicated that mutations appear to have occurred to preserve both the hydride transfer rate and the associated conformational changes. More recent results suggested that differences in local electrostatic environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination of primary and solvent kinetic isotope effects, we demonstrated that the reaction mechanism is consistent across a broad pH range, and computer simulations suggested that deprotonation of the active site Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into the ecDHFR active site provided an experimental tool for interrogating these microenvironments and for investigating changes in electrostatics along the DHFR catalytic cycle

Blood flow patterns during incremental and steady-state aerobic exercise.

Science.gov (United States)

Coovert, Daniel; Evans, LeVisa D; Jarrett, Steven; Lima, Carla; Lima, Natalia; Gurovich, Alvaro N

2017-05-30

Endothelial shear stress (ESS) is a physiological stimulus for vascular homeostasis, highly dependent on blood flow patterns. Exercise-induced ESS might be beneficial on vascular health. However, it is unclear what type of ESS aerobic exercise (AX) produces. The aims of this study are to characterize exercise-induced blood flow patterns during incremental and steady-state AX. We expect blood flow pattern during exercise will be intensity-dependent and bidirectional. Six college-aged students (2 males and 4 females) were recruited to perform 2 exercise tests on cycleergometer. First, an 8-12-min incremental test (Test 1) where oxygen uptake (VO2), heart rate (HR), blood pressure (BP), and blood lactate (La) were measured at rest and after each 2-min step. Then, at least 48-hr. after the first test, a 3-step steady state exercise test (Test 2) was performed measuring VO2, HR, BP, and La. The three steps were performed at the following exercise intensities according to La: 0-2 mmol/L, 2-4 mmol/L, and 4-6 mmol/L. During both tests, blood flow patterns were determined by high-definition ultrasound and Doppler on the brachial artery. These measurements allowed to determine blood flow velocities and directions during exercise. On Test 1 VO2, HR, BP, La, and antegrade blood flow velocity significantly increased in an intensity-dependent manner (repeated measures ANOVA, pflow velocity did not significantly change during Test 1. On Test 2 all the previous variables significantly increased in an intensity-dependent manner (repeated measures ANOVA, pflow patterns during incremental and steady-state exercises include both antegrade and retrograde blood flows.

Concept study of the Steady State Tokamak Reactor (SSTR)

International Nuclear Information System (INIS)

1991-06-01

The Steady State Tokamak Reactor (SSTR) concept has been proposed as a realistic fusion power reactor to be built in the near future. An overall concept of SSTR is introduced which is based on a small extension of the present day physics and technologies. The major feature of SSTR is the maximum utilization of a bootstrap current in order to reduce the power required for the steady state operation. This requirement leads to the choice of moderate current (12 MA), and high βp (2.0) for the device, which are achieved by selecting high aspect ratio (A=4) and high toroidal magnetic field (16.5 T). A negative-ion-based neutral beam injection system is used both for heating and central current drive. Notable engineering features of SSTR are: the use of a uniform vacuum vessel and periodical replacements of the first wall and blanket layers and significant reduction of the electromagnetic force with the use of functionally gradient material. It is shown that a tokamak machine comparable to ITER in size can become a power reactor capable of generating about 1 GW of electricity with a plant efficiency of ∼30%. (author)

Steady-state pattern electroretinogram and short-duration transient visual evoked potentials in glaucomatous and healthy eyes.

Science.gov (United States)

Amarasekera, Dilru C; Resende, Arthur F; Waisbourd, Michael; Puri, Sanjeev; Moster, Marlene R; Hark, Lisa A; Katz, L Jay; Fudemberg, Scott J; Mantravadi, Anand V

2018-01-01

This study evaluates two rapid electrophysiological glaucoma diagnostic tests that may add a functional perspective to glaucoma diagnosis. This study aimed to determine the ability of two office-based electrophysiological diagnostic tests, steady-state pattern electroretinogram and short-duration transient visual evoked potentials, to discern between glaucomatous and healthy eyes. This is a cross-sectional study in a hospital setting. Forty-one patients with glaucoma and 41 healthy volunteers participated in the study. Steady-state pattern electroretinogram and short-duration transient visual evoked potential testing was conducted in glaucomatous and healthy eyes. A 64-bar-size stimulus with both a low-contrast and high-contrast setting was used to compare steady-state pattern electroretinogram parameters in both groups. A low-contrast and high-contrast checkerboard stimulus was used to measure short-duration transient visual evoked potential parameters in both groups. Steady-state pattern electroretinogram parameters compared were MagnitudeD, MagnitudeD/Magnitude ratio, and the signal-to-noise ratio. Short-duration transient visual evoked potential parameters compared were amplitude and latency. MagnitudeD was significantly lower in glaucoma patients when using a low-contrast (P = 0.001) and high-contrast (P state pattern electroretinogram stimulus. MagnitudeD/Magnitude ratio and SNR were significantly lower in the glaucoma group when using a high-contrast 64-bar-size stimulus (P state pattern electroretinogram was effectively able to discern between glaucomatous and healthy eyes. Steady-state pattern electroretinogram may thus have a role as a clinically useful electrophysiological diagnostic tool. © 2017 Royal Australian and New Zealand College of Ophthalmologists.

Steady-state free precession with myocardial tagging: CSPAMM in a single breathhold.

Science.gov (United States)

Zwanenburg, Jaco J M; Kuijer, Joost P A; Marcus, J Tim; Heethaar, Robert M

2003-04-01

A method is presented that combines steady-state free precession (SSFP) cine imaging with myocardial tagging. Before the tagging preparation at each ECG-R wave, the steady-state magnetization is stored as longitudinal magnetization by an alpha/2 flip-back pulse. Imaging is continued immediately after tagging preparation, using linearly increasing startup angles (LISA) with a rampup over 10 pulses. Interleaved segmented k-space ordering is used to prevent artifacts from the increasing signal during the LISA rampup. First, this LISA-SSFP method was evaluated regarding ghost artifacts from the steady-state interruption by comparing LISA with an alpha/2 startup method. Next, LISA-SSFP was compared with spoiled gradient echo (SGRE) imaging, regarding tag contrast-to-noise ratio and tag persistence. The measurements were performed in phantoms and in six subjects applying breathhold cine imaging with tagging (temporal resolution 51 ms). The results show that ghost artifacts are negligible for the LISA method. Compared to the SGRE reference, LISA-SSFP was two times faster, with a slightly better tag contrast-to-noise. Additionally, the tags persisted 126 ms longer with LISA-SSFP than with SGRE imaging. The high efficiency of LISA-SSFP enables the acquisition of complementary tagged (CSPAMM) images in a single breathhold. Copyright 2003 Wiley-Liss, Inc.

Uptake kinetics of metals by the earthworm Eisenia fetida exposed to field-contaminated soils

Energy Technology Data Exchange (ETDEWEB)

Nahmani, Johanne, E-mail: nahmani@univ-metz.f [Laboratoire Interactions Ecotoxicite, Biodiversite, Ecosystemes, CNRS UMR 7146, Universite Paul Verlaine - Metz, Rue du General Delestraint, 57070 Metz (France); Department of Soil Science, School of Human and Environmental Sciences, University of Reading, Whiteknights, Reading, Berkshire RG6 6DW (United Kingdom); Hodson, Mark E. [Department of Soil Science, School of Human and Environmental Sciences, University of Reading, Whiteknights, Reading, Berkshire RG6 6DW (United Kingdom); Devin, Simon [Laboratoire Interactions Ecotoxicite, Biodiversite, Ecosystemes, CNRS UMR 7146, Universite Paul Verlaine - Metz, Rue du General Delestraint, 57070 Metz (France); Vijver, Martina G. [Leiden University, Institute of Environmental Sciences (CML), P.O. Box 9518, 2300 RA Leiden (Netherlands)

2009-10-15

It is well known that earthworms can accumulate metals. However, most accumulation studies focus on Cd-, Cu-, Pb- or Zn-amended soils, additionally few studies consider accumulation kinetics. Here we model the accumulation kinetics of 18 elements by Eisenia fetida, exposed to 8 metal-contaminated and 2 uncontaminated soils. Tissue metal concentration was determined after 3, 7, 14, 21, 28 and 42 days. Metal elimination rate was important in determining time to reach steady-state tissue metal concentration. Uptake flux to elimination rate ratios showed less variation and lower values for essential than for non-essential metals. In theory kinetic rate constants are dependent only on species and metal. Therefore it should be possible to predict steady-state tissue metal concentrations on the basis of very few measurements using the rate constants. However, our experiments show that it is difficult to extrapolate the accumulation kinetic constants derived using one soil to another. - Earthworm metal uptake and elimination constants derived from a one-compartment model show little systematic variation with soil properties.

Steady-State Characterization of Bacteriorhodopsin-D85N Photocycle

Science.gov (United States)

Timucin, Dogan A.; Downie, John D.; Norvig, Peter (Technical Monitor)

1999-01-01

An operational characterization of the photocycle of the genetic mutant D85N of bacteriorhodopsin, BR-D85N, is presented. Steady-state bleach spectra and pump-probe absorbance data are obtained with thick hydrated films containing BR-D85N embedded in a gelatin host. Simple two- and three-state models are used to analyze the photocycle dynamics and extract relevant information such as pure-state absorption spectra, photochemical-transition quantum efficiencies, and thermal lifetimes of dominant states appearing in the photocycle, the knowledge of which should aid in the analysis of optical recording and retrieval of data in films incorporating this photochromic material. The remarkable characteristics of this material and their implications from the viewpoint of optical data storage and processing are discussed.

Minimal gain marching schemes: searching for unstable steady-states with unsteady solvers

Science.gov (United States)

de S. Teixeira, Renan; S. de B. Alves, Leonardo

2017-12-01

Reference solutions are important in several applications. They are used as base states in linear stability analyses as well as initial conditions and reference states for sponge zones in numerical simulations, just to name a few examples. Their accuracy is also paramount in both fields, leading to more reliable analyses and efficient simulations, respectively. Hence, steady-states usually make the best reference solutions. Unfortunately, standard marching schemes utilized for accurate unsteady simulations almost never reach steady-states of unstable flows. Steady governing equations could be solved instead, by employing Newton-type methods often coupled with continuation techniques. However, such iterative approaches do require large computational resources and very good initial guesses to converge. These difficulties motivated the development of a technique known as selective frequency damping (SFD) (Åkervik et al. in Phys Fluids 18(6):068102, 2006). It adds a source term to the unsteady governing equations that filters out the unstable frequencies, allowing a steady-state to be reached. This approach does not require a good initial condition and works well for self-excited flows, where a single nonzero excitation frequency is selected by either absolute or global instability mechanisms. On the other hand, it seems unable to damp stationary disturbances. Furthermore, flows with a broad unstable frequency spectrum might require the use of multiple filters, which delays convergence significantly. Both scenarios appear in convectively, absolutely or globally unstable flows. An alternative approach is proposed in the present paper. It modifies the coefficients of a marching scheme in such a way that makes the absolute value of its linear gain smaller than one within the required unstable frequency spectra, allowing the respective disturbance amplitudes to decay given enough time. These ideas are applied here to implicit multi-step schemes. A few chosen test cases

Steady-state pulses and superradiance in short-wavelength, swept-gain amplifiers

International Nuclear Information System (INIS)

Bonifacio, R.; Hopf, F.A.; Meystre, P.; Scully, M.O.

1975-01-01

The steady-state behavior of amplifiers in which the excitation is swept at the speed of light is discussed in the semiclassical approximation. In the present work the case where the decay time of the population is comparable to that of the polarization is examined. Pulse propagation is shown to obey a generalized sine-Gordon equation which contains the effects of atomic relaxations. The analytical expression of the steady-state pulses (SSP) gives two threshold conditions. In the region of limited gain the SSP is a broad pulse with small area which can be obtained by small signal theory. In the second region of high gain the SSP is the superradiant π pulse. Its pulse power is not limited as in usual superradiant theory because, as is shown, for a swept excitation the cooperation-length limit does not exist

The single-process biochemical reaction of Rubisco: a unified theory and model with the effects of irradiance, CO₂ and rate-limiting step on the kinetics of C₃ and C₄ photosynthesis from gas exchange.

Science.gov (United States)

Farazdaghi, Hadi

2011-02-01

Photosynthesis is the origin of oxygenic life on the planet, and its models are the core of all models of plant biology, agriculture, environmental quality and global climate change. A theory is presented here, based on single process biochemical reactions of Rubisco, recognizing that: In the light, Rubisco activase helps separate Rubisco from the stored ribulose-1,5-bisphosphate (RuBP), activates Rubisco with carbamylation and addition of Mg²(+), and then produces two products, in two steps: (Step 1) Reaction of Rubisco with RuBP produces a Rubisco-enediol complex, which is the carboxylase-oxygenase enzyme (Enco) and (Step 2) Enco captures CO₂ and/or O₂ and produces intermediate products leading to production and release of 3-phosphoglycerate (PGA) and Rubisco. PGA interactively controls (1) the carboxylation-oxygenation, (2) electron transport, and (3) triosephosphate pathway of the Calvin-Benson cycle that leads to the release of glucose and regeneration of RuBP. Initially, the total enzyme participates in the two steps of the reaction transitionally and its rate follows Michaelis-Menten kinetics. But, for a continuous steady state, Rubisco must be divided into two concurrently active segments for the two steps. This causes a deviation of the steady state from the transitional rate. Kinetic models are developed that integrate the transitional and the steady state reactions. They are tested and successfully validated with verifiable experimental data. The single-process theory is compared to the widely used two-process theory of Farquhar et al. (1980. Planta 149, 78-90), which assumes that the carboxylation rate is either Rubisco-limited at low CO₂ levels such as CO₂ compensation point, or RuBP regeneration-limited at high CO₂. Since the photosynthesis rate cannot increase beyond the two-process theory's Rubisco limit at the CO₂ compensation point, net photosynthesis cannot increase above zero in daylight, and since there is always respiration at

Kinetic studies of the inhibition of a human liver 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase isozyme by bile acids and anti-inflammatory drugs.

Science.gov (United States)

Miyabe, Y; Amano, T; Deyashiki, Y; Hara, A; Tsukada, F

1995-01-01

We have investigated the steady-state kinetics for a cytosolic 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase isozyme of human liver and its inhibition by several bile acids and anti-inflammatory drugs such as indomethacin, flufemanic acid and naproxen. Initial velocity and product inhibition studies performed in the NADP(+)-linked (S)-1-indanol oxidation at pH 7.4 were consistent with a sequential ordered mechanism in which NADP+ binds first and leaves last. The bile acids and drugs, competitive inhibitors with respect to the alcohol substrate, exhibited uncompetitive inhibition with respect to the coenzyme, with Ki values less than 1 microM, whereas indomethacin exhibited noncompetitive inhibition (Ki < 24 microM). The kinetics of the inhibition by a mixture of the two inhibitors suggests that bile acids and drugs, except indomethacin, bind to overlapping sites at the active center of the enzyme-coenzyme binary complex.