Nonlinear Dependence (nonlinear + dependence)

Distribution by Scientific Domains

Selected Abstracts

Characterization of the NAD+ binding site of Candida boidinii formate dehydrogenase by affinity labelling and site-directed mutagenesis

FEBS JOURNAL, Issue 22 2000
Nikolas E. Labrou
The 2,,3,-dialdehyde derivative of ADP (oADP) has been shown to be an affinity label for the NAD+ binding site of recombinant Candida boidinii formate dehydrogenase (FDH). Inactivation of FDH by oADP at pH 7.6 followed biphasic pseudo first-order saturation kinetics. The rate of inactivation exhibited a nonlinear dependence on the concentration of oADP, which can be described by reversible binding of reagent to the enzyme (Kd = 0.46 mm for the fast phase, 0.45 mm for the slow phase) prior to the irreversible reaction, with maximum rate constants of 0.012 and 0.007 min,1 for the fast and slow phases, respectively. Inactivation of formate dehydrogenase by oADP resulted in the formation of an enzyme,oADP product, a process that was reversed after dialysis or after treatment with 2-mercaptoethanol (> 90% reactivation). The reactivation of the enzyme by 2-mercaptoethanol was prevented if the enzyme,oADP complex was previously reduced by NaBH4, suggesting that the reaction product was a stable Schiff's base. Protection from inactivation was afforded by nucleotides (NAD+, NADH and ADP) demonstrating the specificity of the reaction. When the enzyme was completely inactivated, approximately 1 mol of [14C]oADP per mol of subunit was incorporated. Cleavage of [14C]oADP-modified enzyme with trypsin and subsequent separation of peptides by RP-HPLC gave only one radioactive peak. Amino-acid sequencing of the radioactive tryptic peptide revealed the target site of oADP reaction to be Lys360. These results indicate that oADP inactivates FDH by specific reaction at the nucleotide binding site, with negative cooperativity between subunits accounting for the appearance of two phases of inactivation. Molecular modelling studies were used to create a model of C. boidinii FDH, based on the known structure of the Pseudomonas enzyme, using the modeller 4 program. The model confirmed that Lys360 is positioned at the NAD+ -binding site. Site-directed mutagenesis was used in dissecting the structure and functional role of Lys360. The mutant Lys360,Ala enzyme exhibited unchanged kcat and Km values for formate but showed reduced affinity for NAD+. The molecular model was used to help interpret these biochemical data concerning the Lys360,Ala enzyme. The data are discussed in terms of engineering coenzyme specificity. [source]

Spin states in polynuclear clusters: The [Fe2O2] core of the methane monooxygenase active site

Carmen Herrmann
Abstract The ability to provide a correct description of different spin states of mono- and polynuclear transition metal complexes is essential for a detailed investigation of reactions that are catalyzed by such complexes. We study the energetics of different total and local spin states of a dinuclear oxygen-bridged iron(IV) model for the intermediate Q of the hydroxylase component of methane monooxygenase by means of spin-unrestricted Kohn,Sham density functional theory. Because it is known that the spin state total energies depend systematically on the density functional, and that this dependence is intimately connected to the exact exchange admixture of present-day hybdrid functionals, we compare total energies, local and total spin values, and Heisenberg coupling constants calculated with the established functionals BP86 and B3LYP as well as with a modified B3LYP version with an exact exchange admixture ranging from 0 to 24%. It is found that exact exchange enhances local spin polarization. As the exact exchange admixture increases, the high-spin state is energetically favored, although the Broken-Symmetry state always is the ground state. Instead of the strict linear variation of the energy splittings observed for mononuclear complexes, a slightly nonlinear dependence is found. The Heisenberg coupling constants JFe1Fe2,evaluated according to three different proposals from the literature,are found to vary from ,129 to ,494cm,1 accordingly. The experimental finding that intermediate Q has an antiferromagnetic ground state is thus confirmed. 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1223,1239, 2006 [source]

Estimation and forecasting in first-order vector autoregressions with near to unit roots and conditional heteroscedasticity

Theologos Pantelidis
Abstract This paper investigates the effects of imposing invalid cointegration restrictions or ignoring valid ones on the estimation, testing and forecasting properties of the bivariate, first-order, vector autoregressive (VAR(1)) model. We first consider nearly cointegrated VARs, that is, stable systems whose largest root, lmax, lies in the neighborhood of unity, while the other root, lmin, is safely smaller than unity. In this context, we define the ,forecast cost of type I' to be the deterioration in the forecasting accuracy of the VAR model due to the imposition of invalid cointegration restrictions. However, there are cases where misspecification arises for the opposite reasons, namely from ignoring cointegration when the true process is, in fact, cointegrated. Such cases can arise when lmax equals unity and lmin is less than but near to unity. The effects of this type of misspecification on forecasting will be referred to as ,forecast cost of type II'. By means of Monte Carlo simulations, we measure both types of forecast cost in actual situations, where the researcher is led (or misled) by the usual unit root tests in choosing the unit root structure of the system. We consider VAR(1) processes driven by i.i.d. Gaussian or GARCH innovations. To distinguish between the effects of nonlinear dependence and those of leptokurtosis, we also consider processes driven by i.i.d. t(2) innovations. The simulation results reveal that the forecast cost of imposing invalid cointegration restrictions is substantial, especially for small samples. On the other hand, the forecast cost of ignoring valid cointegration restrictions is small but not negligible. In all the cases considered, both types of forecast cost increase with the intensity of GARCH effects. Copyright 2009 John Wiley & Sons, Ltd. [source]

Systematic estimation of state noise statistics for extended Kalman filters

AICHE JOURNAL, Issue 2 2000
Jaleel Valappil
The successful application of model-based control depends on the information about the states of the dynamic system. State-estimation methods, like extended Kalman filters (EKF), are useful for obtaining reliable estimates of the states from a limited number of measurements. They also can handle the model uncertainties and the effect of unmeasured disturbances. The main issue in applying EKF remains that one needs to specify the confidence in the model in terms of process noise covariance matrix. The information about the model uncertainties can effectively and systematically calculate the process noise covariance matrix for an EKF. Two systematic approaches are used for this calculation. The first is based on a Taylor series expansion of the nonlinear equations around the nominal parameter values, while the second accounts for the nonlinear dependence of the system on the fitted parameters by Monte Carlo simulations that can easily be performed on-line. The value of the process noise covariance matrix obtained is not limited to a diagonal form and depends on the current state of the dynamic system. Thus the a-priori information regarding the uncertainty in the model is utilized and the need for extensive tuning of the EKF is eliminated. The application of these techniques to example processes is also discussed. The accuracy of this methodology is compared very favorably with the traditional methods of trial-and-error tuning of EKF. [source]

Possible anomalous Hall effect of Be/Si pair delta-doped GaAs structures

J. P. Noh
Abstract Beryllium/Silicon pair delta-doped GaAs structures grown by molecular-beam epitaxy exhibit Hall resistance which has highly nonlinear dependence on the applied magnetic field. The dependence of the occurrence of the nonlinear Hall resistance on the sample structure is investigated. A significantly large increase in the non-linearity and magnitude of the Hall resistance is observed from a sample structure whose buffer layer is grown under the low As flux and thick buffer layer condition. The non-linearity of the Hall resistance is found to depend on a single parameter B /T, where B and T are the magnetic field and temperature, respectively. From another sample structure in which an AlGaAs barrier with a single Be delta-doped layer is placed near the Be/Si pair delta-doped layer, a similar nonlinear Hall resistance is observed. On the basis of these results, it is suggested that the anomalous Hall effect results from interplay between itinerant holes in the valence band and localized spins in the delta-doped layer in these structures. ( 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Mixing efficiency in a pin mixing section for single-screw extruders

W. G. Yao
Non-Newtonian, non-isothermal, 3D finite-element simulation of mixing performance in a pin mixing section with different axial gaps in the pins has been carried out according to their realistic configurations. The quantitative evaluation of mixing ability was based on the theory of kinematics of fluid mixing. To learn and to compare the local mixing performance in a standard screw and a pin mixing section, the local mixing efficiency distribution proposed by Ottino was calculated. Also, the RTDs of these mixers were calculated in an attemt to measure mixing. The integration of the two, namely, the integrating local mixing efficiency along a number of particle pathlines from entrance to exit, together with statistical treatment, which was referred as integral mixing efficiency, then gives a quantitative judgment of the total mixing ability of a continuous mixer. The calculated results showed a nonlinear dependence of the mixing ability of a pin mixing section on the axial gap of the pins. Finally, the calculation results were compared with the experimental ones obtained in our previous study. [source]

Nonlinear dynamics in high-frequency intraday financial data: Evidence for the UK long gilt futures market

David G. McMillan
Recent research investigating the properties of high-frequency financial data has suggested that the stochastic nonlinearity widely present in such data may be characterized by heterogeneous components in conditional volatility, and nonlinear dependence of threshold autoregressive form due to market frictions. This article tests for the presence of such effects in intraday long gilt futures returns on the UK LIFFE market. Tests against the null of linearity indicate the significance of smooth transition autoregressive nonlinearities in such returns at the 5-min frequency, which entails a first-order autoregressive process with switching intercept. This nonlinear structure is robust to the presence of asymmetric and component structures in conditional variance, and consistent with the existence of heterogeneous traders facing different levels of transaction costs, noise trader risk, or capital constraints. 2002 Wiley Periodicals, Inc. Jrl Fut Mark 22:1037,1057, 2002 [source]