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Small Perturbations (small + perturbation)
Selected AbstractsDNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyraseFEBS JOURNAL, Issue 6 2002Jacky L. Snoep DNA of prokaryotes is in a nonequilibrium structural state, characterized as ,active' DNA supercoiling. Alterations in this state affect many life processes and a homeostatic control of DNA supercoiling has been suggested [Menzel, R. & Gellert, M. (1983) Cell34, 105,113]. We here report on a new method for quantifying homeostatic control of the high-energy state of in vivo DNA. The method involves making small perturbation in the expression of topoisomerase I, and measuring the effect on DNA supercoiling of a reporter plasmid and on the expression of DNA gyrase. In a separate set of experiments the expression of DNA gyrase was manipulated and the control on DNA supercoiling and topoisomerase I expression was measured [part of these latter experiments has been published in Jensen, P.R., van der Weijden, C.C., Jensen, L.B., Westerhoff, H.V. & Snoep, J.L. (1999) Eur. J. Biochem.266, 865,877]. Of the two regulatory mechanisms via which homeostasis is,conferred, regulation of enzyme activity or regulation of enzyme expression, we quantified the first to be responsible for 72% and the latter for 28%. The gene expression regulation could be dissected to DNA gyrase (21%) and to topoisomerase I (7%). On a scale from 0 (no homeostatic control) to 1 (full homeostatic control) we quantified the homeostatic control of DNA supercoiling at 0.87. A 10% manipulation of either topoisomerase I or DNA gyrase activity results in a 1.3% change of DNA supercoiling only. We conclude that the homeostatic regulation of the nonequilibrium DNA structure in wild-type Escherichia coli is almost complete and subtle (i.e. involving at least three regulatory mechanisms). [source] Two-dimensional modeling for stability analysis of two-phase stratified flowINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 7 2010Ghassem Heidarinejad Abstract The effect of wavelength and relative velocity on the disturbed interface of two-phase stratified regime is modeled and discussed. To analyze the stability, a small perturbation is imposed on the interface. Growth or decline of the disturbed wave, relative velocity, and surface tension with respect to time will be discussed numerically. Newly developed scheme applied to a two-dimensional flow field and the governing Navier,Stokes equations in laminar regime are solved. Finite volume method together with non-staggered curvilinear grid is a very effective approach to capture interface shape with time. Because of the interface shape, for any time advancement, a new grid is performed separately on each stratified field, liquid, and gas regime. The results are compared with the analytical characteristics method and one-dimensional modeling. This comparison shows that solving the momentum equation including viscosity term leads to physically more realistic results. In addition, the newly developed method is capable of predicting two-phase stratified flow behavior more precisely than one-dimensional modeling. It was perceived that the surface tension has an inevitable role in dissipation of interface instability and convergence of the two-phase flow model. Copyright © 2009 John Wiley & Sons, Ltd. [source] Generic Existence and Robust Nonexistence of Numéraires in Finite Dimensional Securities MarketsMATHEMATICAL FINANCE, Issue 4 2000Bruno Girotto A numéraire is a portfolio that, if prices and dividends are denominated in its units, admits an equivalent martingale measure that transforms all gains processes into martingales. We first supply a necessary and sufficient condition for the generic existence of numéraires in a finite dimensional setting. We then characterize the arbitrage-free prices and dividends for which the absence of numéraires survives any small perturbation preserving no arbitrage. Finally, we identify the cases when any small, but otherwise arbitrary, perturbation of prices and dividends preserves either the existence of numéraires, or their nonexistence under no arbitrage. [source] Reconstructing small perturbations of scatterers from electric or acoustic far-field measurementsMATHEMATICAL METHODS IN THE APPLIED SCIENCES, Issue 11 2008Mikyoung Lim Abstract In this paper, we consider the problem of determining the boundary perturbations of an object from far-field electric or acoustic measurements. Assuming that the unknown scatterer boundary is a small perturbation of a circle, we develop a linearized relationship between the far-field data and the shape of the object. This relationship is used to find the Fourier coefficients of the perturbation of the shape. Copyright © 2008 John Wiley & Sons, Ltd. [source] Convergence rates toward the travelling waves for a model system of the radiating gasMATHEMATICAL METHODS IN THE APPLIED SCIENCES, Issue 6 2007Masataka Nishikawa Abstract The present paper is concerned with an asymptotics of a solution to the model system of radiating gas. The previous researches have shown that the solution converges to a travelling wave with a rate (1 + t),1/4 as time t tends to infinity provided that an initial data is given by a small perturbation from the travelling wave in the suitable Sobolev space and the perturbation is integrable. In this paper, we make more elaborate analysis under suitable assumptions on initial data in order to obtain shaper convergence rates than previous researches. The first result is that if the initial data decays at the spatial asymptotic point with a certain algebraic rate, then this rate reflects the time asymptotic convergence rate. Precisely, this convergence rate is completely same as the spatial convergence rate of the initial perturbation. The second result is that if the initial data is given by the Riemann data, an admissible weak solution, which has a discontinuity, converges to the travelling wave exponentially fast. Both of two results are proved by obtaining decay estimates in time through energy methods with suitably chosen weight functions. Copyright © 2006 John Wiley & Sons, Ltd. [source] Variational iteration method for solving the space- and time-fractional KdV equationNUMERICAL METHODS FOR PARTIAL DIFFERENTIAL EQUATIONS, Issue 1 2008Shaher Momani Abstract This paper presents numerical solutions for the space- and time-fractional Korteweg,de Vries equation (KdV for short) using the variational iteration method. The space- and time-fractional derivatives are described in the Caputo sense. In this method, general Lagrange multipliers are introduced to construct correction functionals for the problems. The multipliers in the functionals can be identified optimally via variational theory. The iteration method, which produces the solutions in terms of convergent series with easily computable components, requiring no linearization or small perturbation. The numerical results show that the approach is easy to implement and accurate when applied to space- and time-fractional KdV equations. The method introduces a promising tool for solving many space,time fractional partial differential equations. © 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2007 [source] The Gyldén-type problem revisited: More refined analytical solutionsASTRONOMISCHE NACHRICHTEN, Issue 4 2006A. Pal Abstract We resume and consistently extend our previous researches concerning the Gyldén-type problem (a two-body problem with time-dependent equivalent gravitational parameter). To approach most of the concrete astronomical situations to be modelled in this way, we consider a periodic small perturbation. For the nonresonant case, we present a second-order analytical solution. For the resonant case, we adopt the most realistic astronomical situation: only one dominant term of the Hamiltonian. In this case we point out a fundamental model of resonance, common to every resonant situation, and, moreover, identical to the first fundamental model of resonance . Considering the simplest model of periodic change of the equivalent gravitational parameter, we .nd that all possible resonances are con.ned to the first fundamental model. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Binding of ligands originates small perturbations on the microscopic thermodynamic properties of a multicentre redox proteinFEBS JOURNAL, Issue 9 2005Carlos A. Salgueiro NMR and visible spectroscopy coupled to redox measurements were used to determine the equilibrium thermodynamic properties of the four haems in cytochrome c3 under conditions in which the protein was bound to ligands, the small anion phosphate and the protein rubredoxin with the iron in the active site replaced by zinc. Comparison of these results with data for the isolated cytochrome shows that binding of ligands causes only small changes in the reduction potentials of the haems and their pairwise interactions, and also that the redox-sensitive acid,base centre responsible for the redox,Bohr effect is essentially unaffected. Although neither of the ligands tested is a physiological partner of cytochrome c3, the small changes observed for the thermodynamic properties of cytochrome c3 bound to these ligands vs. the unbound state, indicate that the thermodynamic properties measured for the isolated protein are relevant for a physiological interpretation of the role of this cytochrome in the bioenergetic metabolism of Desulfovibrio. [source] Charge distribution in the water molecule,A comparison of methodsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2005F. Martin Abstract The charge distribution in the water molecule has been analyzed using a broad variety of basis sets, four different quantum mechanical methods (Hartree,Fock, Becke3LYP, MP2, and QCISD), and six population analysis methods (Mulliken, NPA, AIM, CHELPG, Merz,Kollman, and Resp). The influence of the molecular structure on the calculated atomic charges has been studied using small perturbations of the experimentally determined structure. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 97,105, 2005 [source] A priori information in a regularized sinogram-based method for removing ring artefacts in tomographyJOURNAL OF SYNCHROTRON RADIATION, Issue 4 2010Sofya Titarenko Ring artefacts in X-ray computerized tomography reconstructions are considered. The authors propose a ring artefact removal method based on a priori information regarding the sinogram including smoothness along the horizontal coordinate, symmetry of the first and the final rows and consideration of small perturbations during acquisition. The method does not require prior reconstruction of the original or corrected sinograms. Its numerical implementation is based on quadratic programming. Its efficacy is examined with regard to experimental data sets collected on graphite and bone. [source] Multidimensional Hele-Shaw flows modelling Stokesian fluidsMATHEMATICAL METHODS IN THE APPLIED SCIENCES, Issue 5 2009Joachim Escher Abstract We consider here an n -dimensional periodic flow describing the motion of an incompressible Stokesian fluid in a Hele-Shaw cell. The free surface separating the fluid from air, at pressure normalized to be zero, is moving under the influence of gravity and surface tension. We prove the existence of a unique classical Hölder solution for small perturbations of cylinders. Moreover, we evidence the existence of a single steady state and prove its exponential stability. Copyright © 2008 John Wiley & Sons, Ltd. [source] Reconstructing small perturbations of scatterers from electric or acoustic far-field measurementsMATHEMATICAL METHODS IN THE APPLIED SCIENCES, Issue 11 2008Mikyoung Lim Abstract In this paper, we consider the problem of determining the boundary perturbations of an object from far-field electric or acoustic measurements. Assuming that the unknown scatterer boundary is a small perturbation of a circle, we develop a linearized relationship between the far-field data and the shape of the object. This relationship is used to find the Fourier coefficients of the perturbation of the shape. Copyright © 2008 John Wiley & Sons, Ltd. [source] The structured total least-squares approach for non-linearly structured matricesNUMERICAL LINEAR ALGEBRA WITH APPLICATIONS, Issue 4 2002P. Lemmerling Abstract In this paper, an extension of the structured total least-squares (STLS) approach for non-linearly structured matrices is presented in the so-called ,Riemannian singular value decomposition' (RiSVD) framework. It is shown that this type of STLS problem can be solved by solving a set of Riemannian SVD equations. For small perturbations the problem can be reformulated into finding the smallest singular value and the corresponding right singular vector of this Riemannian SVD. A heuristic algorithm is proposed. Some examples of Vandermonde-type matrices are used to demonstrate the improved accuracy of the obtained parameter estimator when compared to other methods such as least squares (LS) or total least squares (TLS). Copyright © 2002 John Wiley & Sons, Ltd. [source] Dynamical modeling of chaos single-screw extruder and its three-dimensional numerical analysisPOLYMER ENGINEERING & SCIENCE, Issue 3 2000W. R. Hwang The Chaos Screw (CS) nonlinear dynamical model is proposed to describe the development of chaos in a single-screw extrusion process and the model is verified by three-dimensional numerical simulations. The only-barrier channel is the unperturbed Hamiltonian system, which consists of two homoclinic orbits and nested elliptic tori of nonlinear oscillation in periodic (extended) state space. A periodically inserted no-barrier zone represents a perturbation. For small perturbations, homoclinic tangle leads to the Cantor set near the homoclinic fixed point and elliptic rotations are changed into the resonance bands or KAM tori, depending on the commensurability of frequency ratio of the corresponding orbits. A finite element method of multivariant Q,1+PO elements is applied to solve the velocity fields and a 4th order Runge-Kutta method is used for the particle tracing. The resulting Poincaré section verifies the proposed dynamical model, showing the resonance band corresponding to rotation number 1/3 under small perturbations. As the strength of perturbation increases, the Poincaré sections indicate wider stochastic regions in which random particle motions take place. [source] Analysis of fluid-structure interaction in low pressure MEMS by Integral EquationsPROCEEDINGS IN APPLIED MATHEMATICS & MECHANICS, Issue 1 2008Attilio FrangiArticle first published online: 25 FEB 200 The evaluation of gas dissipation occurring in inertial polysilicon MEMS is addressed focusing the attention on the free,molecule flow. In this regime, which is very often of interest for industrial applications, collisions between molecules can be neglected and the momentum transfer to the moving shuttle can be easily computed. Since the surfaces of silicon MEMS are generally very rough, a complete diffusion model is adopted to describe the wall,molecule interaction. A Boundary Integral Equation approach is proposed and it is shown that the introduction of the key assumption of small perturbations is crucial in the development of a robust and fast numerical tool. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Inverse problem in seismic imagingPROCEEDINGS IN APPLIED MATHEMATICS & MECHANICS, Issue 1 2007Maria Cameron We address the problem of estimating sound speeds (seismic velocities) inside the earth which is necessary for obtaining seismic images in regular Cartesian coordinates. The main goals are to develop algorithms to convert time migration velocities to true seismic velocities, and to convert time-migrated images to depth images in regular Cartesian coordinates. Our main results are three-fold. First, we establish a theoretical relation between the seismic velocities and the time migration velocities using the paraxial ray tracing theory. Second, we formulate an appropriate inverse problem describing the relation between time migration velocities and depth velocities and show that this problem is mathematically ill-posed, i.e., unstable to small perturbations. Third, we develop numerical algorithms to solve regularized versions of these equations which can be used to recover smoothed velocity variations. Our algorithms consist of efficient time-to-depth conversion algorithms based on Dijkstra-like Fast Marching Methods, as well as level set and ray tracing algorithms for transforming Dix velocities into seismic velocities. Our algorithms are applied to both two-dimensional and three-dimensional problems and we test them on a collection of both synthetic examples and field data. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Tropical-cyclone intensification and predictability in a minimal three-dimensional modelTHE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 636 2008Seoleun Shin Abstract We investigate the amplification and predictability of tropical cyclones in the context of a minimal, three-dimensional numerical model. In the prototype problem for intensification, starting with a tropical storm strength vortex in a quiescent environment on an f -plane, the emergent flow in the inner region of the vortex becomes highly asymmetric and dominated by deep convective vortex structures, even though the problem as posed is essentially axisymmetric. The details of the intensification process, including the asymmetric structures that develop, are highly sensitive to small perturbations in the low-level moisture field at the initial time. This sensitivity is manifest in a significant spread in the intensity of vortices from an ensemble of calculations in which random moisture perturbations are added in the lowest model level. Similar experiments are carried out on a ,-plane and in the case where there is an anticyclonic shear flow at upper levels. The former set shows no significant difference from the f -plane calculations in the evolution of intensity, but the latter set shows a significantly weaker vortex, contrary to a broadly held hypothesis that upper-level outflow channels are favourable to intensification. Copyright © 2008 Royal Meteorological Society [source] Critical catalytic functional groups in the mechanism of aspartate-,-semialdehyde dehydrogenaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2004Julio Blanco Aspartate-,-semialdehyde dehydrogenase (ASADH) catalyzes the reductive dephosphorylation of ,-aspartyl phosphate to l -aspartate-,-semialdehyde in the aspartate biosynthetic pathway. This pathway is not found in humans or other eukaryotic organisms, yet is required for the production of threonine, isoleucine, methionine and lysine in most microorganisms. The mechanism of this enzyme has been examined through the structures of two active-site mutants of ASADH from Haemophilus influenzae. Replacement of the enzyme active-site cysteine with serine (C136S) leads to a dramatic loss of catalytic activity caused by the expected decrease in nucleophilicity, but also by a change in the orientation of the serine hydroxyl group relative to the cysteine thiolate. In contrast, in the H277N active-site mutant the introduced amide is oriented in virtually the same position as that of the histidine imidazole ring. However, a shift in the position of the bound reaction intermediate to accommodate this shorter asparagine side chain, coupled with the inability of this introduced amide to serve as a proton acceptor, results in a 100-fold decrease in the catalytic efficiency of H277N relative to the native enzyme. These mutant enzymes have the same overall fold and high structural identity to native ASADH. However, small perturbations in the positioning of essential catalytic groups or reactive intermediates have dramatic effects on catalytic efficiency. [source] | ||||||||||||||||