Nonlinear Enzyme Kinetics Can Lead to High Metabolic Flux Control Coefficients: Implications for the Evolution of Dominance

In a classic study, Kacser & Burns (1981, Genetics 97, 639-666) demonstrated that given certain plausible assumptions, the flux in a metabolic pathway was more or less indifferent to the activity of any of the enzymes in the pathway taken singly. It was inferred from this that the observed dominance of most wild-type alleles with respect to loss-of-function mutations did not require an adaptive, meaning selectionist, explanation. Cornish-Bowden (1987, J. theor. Biol. 125, 333-338) showed that the Kacser-Burns inference was not valid when substrate concentrations were large relative to the relevant Michaelis constants. We find that in a randomly constructed functional pathway, even when substrate levels are small, one can expect high values of control coefficients for metabolic flux in the presence of significant nonlinearities as exemplified by enzymes with Hill coefficients ranging from two to six, or by the existence of oscillatory loops. Under these conditions the flux can be quite sensitive to changes in enzyme activity as might be caused by inactivating one of the two alleles in a diploid. Therefore, the phenomenon of dominance cannot be a trivial ''default'' consequence of physiology but must be intimately linked to the manner in which metabolic networks have been moulded by natural selection.

3-D kinematical conservation laws (KCL): Evolution of a surface in R-3 - in particular propagation of a nonlinear wavefront

3-D KCL are equations of evolution of a propagating surface (or a wavefront) Omega(t), in 3-space dimensions and were first derived by Giles, Prasad and Ravindran in 1995 assuming the motion of the surface to be isotropic. Here we discuss various properties of these 3-D KCL.These are the most general equations in conservation form, governing the evolution of Omega(t) with singularities which we call kinks and which are curves across which the normal n to Omega(t) and amplitude won Omega(t) are discontinuous. From KCL we derive a system of six differential equations and show that the KCL system is equivalent to the ray equations of 2, The six independent equations and an energy transport equation (for small amplitude waves in a polytropic gas) involving an amplitude w (which is related to the normal velocity m of Omega(t)) form a completely determined system of seven equations. We have determined eigenvalues of the system by a very novel method and find that the system has two distinct nonzero eigenvalues and five zero eigenvalues and the dimension of the eigenspace associated with the multiple eigenvalue 0 is only 4. For an appropriately defined m, the two nonzero eigenvalues are real when m > 1 and pure imaginary when m < 1. Finally we give some examples of evolution of weakly nonlinear wavefronts.

Evolution and decay of cylindrical and spherical nonlinear acoustic waves generated by a sinusoidal source

The present work gives a comprehensive numerical study of the evolution and decay of cylindrical and spherical nonlinear acoustic waves generated by a sinusoidal source. Using pseudospectral and predictor–corrector implicit finite difference methods, we first reproduced the known analytic results of the plane harmonic problem to a high degree of accuracy. The non-planar harmonic problems, for which the amplitude decay is faster than that for the planar case, are then treated. The results are correlated with the known asymptotic results of Scott (1981) and Enflo (1985). The constant in the old-age formula for the cylindrical canonical problem is found to be 1.85 which is rather close to 2, ‘estimated’ analytically by Enflo. The old-age solutions exhibiting strict symmetry about the maximum are recovered; these provide an excellent analytic check on the numerical solutions. The evolution of the waves for different source geometries is depicted graphically.

Finite volume evolution Galerkin method for hyperbolic conservation laws with spatially varying flux functions

We present a generalization of the finite volume evolution Galerkin scheme [M. Lukacova-Medvid'ova,J. Saibertov'a, G. Warnecke, Finite volume evolution Galerkin methods for nonlinear hyperbolic systems, J. Comp. Phys. (2002) 183 533-562; M. Luacova-Medvid'ova, K.W. Morton, G. Warnecke, Finite volume evolution Galerkin (FVEG) methods for hyperbolic problems, SIAM J. Sci. Comput. (2004) 26 1-30] for hyperbolic systems with spatially varying flux functions. Our goal is to develop a genuinely multi-dimensional numerical scheme for wave propagation problems in a heterogeneous media. We illustrate our methodology for acoustic waves in a heterogeneous medium but the results can be generalized to more complex systems. The finite volume evolution Galerkin (FVEG) method is a predictor-corrector method combining the finite volume corrector step with the evolutionary predictor step. In order to evolve fluxes along the cell interfaces we use multi-dimensional approximate evolution operator. The latter is constructed using the theory of bicharacteristics under the assumption of spatially dependent wave speeds. To approximate heterogeneous medium a staggered grid approach is used. Several numerical experiments for wave propagation with continuous as well as discontinuous wave speeds confirm the robustness and reliability of the new FVEG scheme.

Mesh-free approximations via the error reproducing kernel method and applications to nonlinear systems developing shocks

Error estimates for the error reproducing kernel method (ERKM) are provided. The ERKM is a mesh-free functional approximation scheme [A. Shaw, D. Roy, A NURBS-based error reproducing kernel method with applications in solid mechanics, Computational Mechanics (2006), to appear (available online)], wherein a targeted function and its derivatives are first approximated via non-uniform rational B-splines (NURBS) basis function. Errors in the NURBS approximation are then reproduced via a family of non-NURBS basis functions, constructed using a polynomial reproduction condition, and added to the NURBS approximation of the function obtained in the first step. In addition to the derivation of error estimates, convergence studies are undertaken for a couple of test boundary value problems with known exact solutions. The ERKM is next applied to a one-dimensional Burgers equation where, time evolution leads to a breakdown of the continuous solution and the appearance of a shock. Many available mesh-free schemes appear to be unable to capture this shock without numerical instability. However, given that any desired order of continuity is achievable through NURBS approximations, the ERKM can even accurately approximate functions with discontinuous derivatives. Moreover, due to the variation diminishing property of NURBS, it has advantages in representing sharp changes in gradients. This paper is focused on demonstrating this ability of ERKM via some numerical examples. Comparisons of some of the results with those via the standard form of the reproducing kernel particle method (RKPM) demonstrate the relative numerical advantages and accuracy of the ERKM.

Third post-Newtonian angular momentum flux and the secular evolution of orbital elements for inspiralling compact binaries in quasi-elliptical orbits

The angular-momentum flux from an inspiralling binary system of compact objects moving in quasi-elliptical orbits is computed at the third post-Newtonian (3PN) order using the multipolar post-Minkowskian wave generation formalism. The 3PN angular-momentum flux involves the instantaneous, tail, and tail-of-tails contributions as for the 3PN energy flux, and in addition a contribution due to nonlinear memory. We average the angular-momentum flux over the binary's orbit using the 3PN quasi-Keplerian representation of elliptical orbits. The averaged angular-momentum flux provides the final input needed for gravitational-wave phasing of binaries moving in quasi-elliptical orbits. We obtain the evolution of orbital elements under 3PN gravitational radiation reaction in the quasi-elliptic case. For small eccentricities, we give simpler limiting expressions relevant for phasing up to order e(2). This work is important for the construction of templates for quasi-eccentric binaries, and for the comparison of post-Newtonian results with the numerical relativity simulations of the plunge and merger of eccentric binaries.

Nonlinear structural dynamical system identification using adaptive particle filters

The problem of identifying parameters of nonlinear vibrating systems using spatially incomplete, noisy, time-domain measurements is considered. The problem is formulated within the framework of dynamic state estimation formalisms that employ particle filters. The parameters of the system, which are to be identified, are treated as a set of random variables with finite number of discrete states. The study develops a procedure that combines a bank of self-learning particle filters with a global iteration strategy to estimate the probability distribution of the system parameters to be identified. Individual particle filters are based on the sequential importance sampling filter algorithm that is readily available in the existing literature. The paper develops the requisite recursive formulary for evaluating the evolution of weights associated with system parameter states. The correctness of the formulations developed is demonstrated first by applying the proposed procedure to a few linear vibrating systems for which an alternative solution using adaptive Kalman filter method is possible. Subsequently, illustrative examples on three nonlinear vibrating systems, using synthetic vibration data, are presented to reveal the correct functioning of the method. (c) 2007 Elsevier Ltd. All rights reserved.

A nonlinear theory of wake development

A simple new series, using an expansion of the velocity profile in parabolic cylinder functions, has been developed to describe the nonlinear evolution of a steady, laminar, incompressible wake from a given arbitrary initial profile. The first term in this series is itself found to provide a very satisfactory prediction of the decay of the maximum velocity defect in the wake behind a flat plate or aft of the recirculation zone behind a symmetric blunt body. A detailed analysis, including higher order terms, has been made of the flat plate wake with a Blasius profile at the trailing edge. The same method yields, as a special case, complete results for the development of linearized wakes with arbitrary initial profile under the influence of arbitrary pressure gradients. Finally, for purposes of comparison, a simple approximate solution is obtained using momentum integral methods, and found to predict satisfactorily the decay of the maximum velocity defect. © 1970 Wolters-Noordhoff Publishing.

Eigenvalues of kinematical conservation laws (KCL) based 3-D weakly nonlinear ray theory (WNLRT)

System of kinematical conservation laws (KCL) govern evolution of a curve in a plane or a surface in space, even if the curve or the surface has singularities on it. In our recent publication K. R. Arun, P. Prasad, 3-D kinematical conservation laws (KCL): evolution of a surface in R-3-in particular propagation of a nonlinear wavefront, Wave Motion 46 (2009) 293-311] we have developed a mathematical theory to study the successive positions and geometry of a 3-D weakly nonlinear wavefront by adding an energy transport equation to KCL. The 7 x 7 system of equations of this KCL based 3-D weakly nonlinear ray theory (WNLRT) is quite complex and explicit expressions for its two nonzero eigenvalues could not be obtained before. In this short note, we use two different methods: (i) the equivalence of KCL and ray equations and (ii) the transformation of surface coordinates, to derive the same exact expressions for these eigenvalues. The explicit expressions for nonzero eigenvalues are important also for checking stability of any numerical scheme to solve 3-D WNLRT. (C) 2010 Elsevier Inc. All rights reserved.

Application of nonlinear filtering to credit risk

Merton's model views equity as a call option on the asset of the firm. Thus the asset is partially observed through the equity. Then using nonlinear filtering an explicit expression for likelihood ratio for underlying parameters in terms of the nonlinear filter is obtained. As the evolution of the filter itself depends on the parameters in question, this does not permit direct maximum likelihood estimation, but does pave the way for the `Expectation-Maximization' method for estimating parameters. (C) 2010 Elsevier B.V. All rights reserved.

Evolution in the time series of vortex velocity fluctuations across different regimes of vortex flow

Investigations of vortex velocity fluctuation in time domain have revealed a presence of low frequency velocity fluctuations which evolve with the different driven phases of the vortex state in a single crystal of 2H-NbSe2. The observation of velocity fluctuations with a characteristic low frequency is associated with the onset of nonlinear nature of vortex flow deep in the driven elastic vortex state. (C) 2009 Elsevier B.V. All rights reserved.

Model Hamiltonians for nonlinear optical properties of conjugated polymers

Quantum cell models for delocalized electrons provide a unified approach to the large NLO responses of conjugated polymers and pi-pi* spectra of conjugated molecules. We discuss exact NLO coefficients of infinite chains with noninteracting pi-electrons and finite chains with molecular Coulomb interactions V(R) in order to compare exact and self-consistent-field results, to follow the evolution from molecular to polymeric responses, and to model vibronic contributions in third-harmonic-generation spectra. We relate polymer fluorescence to the alternation delta of transfer integrals t(1+/-delta) along the chain and discuss correlated excited states and energy thresholds of conjugated polymers.

Kinetics of hydrogen evolution on submicron size Co, Ni, Pd and CoNi alloy powder electrodes by d.c. polarization and a.c. impedance studies

Submicron size Co, Ni and Co-Ni alloy powders have been synthesized by the polyol method using the corresponding metal malonates and Pd powder by reduction of PdOx in methanol. The kinetics of the hydrogen evolution reaction ( HER) in 6 M KOH electrolyte have been studied on electrodes made from the pressed powders. The d.c. polarization measurements have resulted in a value close to 120 mV decade(-1) for the Tafel slope, suggesting that the HER follows the Volmer-Heyrovsky mechanism. The values of exchange current density (i(o)) are in the range 1-10 mA cm(-2) for electrodes fabricated in the study. The a.c. impedance spectra measured at several potentials in the HER region showed a single semicircle in the Nyquist plots. Exchange current density (i(o)) and energy transfer coefficient (alpha) have been calculated by employing a nonlinear least square-fitting program.

Continuous-time Single Network Adaptive Critic for Regulator Design of Nonlinear Control Affine Systems

An optimal control law for a general nonlinear system can be obtained by solving Hamilton-Jacobi-Bellman equation. However, it is difficult to obtain an analytical solution of this equation even for a moderately complex system. In this paper, we propose a continuoustime single network adaptive critic scheme for nonlinear control affine systems where the optimal cost-to-go function is approximated using a parametric positive semi-definite function. Unlike earlier approaches, a continuous-time weight update law is derived from the HJB equation. The stability of the system is analysed during the evolution of weights using Lyapunov theory. The effectiveness of the scheme is demonstrated through simulation examples.

Transverse single spin asymmetry in e plus p(up arrow) -> e plus J/psi plus X and transverse momentum dependent evolution of the Sivers function

We extend our analysis of transverse single spin asymmetry in electroproduction of J/psi to include the effect of the scale evolution of the transverse momentum dependent (TMD) parton distribution functions and gluon Sivers function. We estimate single spin asymmetry for JLab, HERMES, COMPASS, and eRHIC energies using the color evaporation model of charmonium production, using an analytically obtained approximate solution of TMD evolution equations discussed in the literature. We find that there is a reduction in the asymmetry compared with our predictions for the earlier case considered by us, wherein the Q(2) dependence came only from DGLAP evolution of the unpolarized gluon densities and a different parametrization of the TMD Sivers function was used.