Time-resolved fluorescence study of the single tryptophan in thiocyanate and azide derivatives of horseradish peroxidase: Implication for a p H-induced conformational change in the heme cavity

Detailed pH-dependent steady state and picosecond time-resolved tryptophan fluorescence studies on thiocyanate and azide complexes of horseradish peroxidase have been carried out. The fluorescence decay of the single tryptophan in these species was fitted to a discrete three exponential model. Maximum entropy method analysis also gave three distinct regions of lifetime distributions. The fast subnanosecond lifetime component was found to have > 97% amplitude contribution while other two longer lifetime components have small contributions. Small contributions from the nanosecond lifetime components possibly arise from apoprotein impurity or some small amount of disordered heme conformer of the protein. pH dependence of the fast picosecond lifetime components was found to show a systematic behavior which has been interpreted in the light of obligatory conformation change associated with activation of the enzyme at low pH.     

Trefftz,collocation, and other boundary methods—A comparison

In this article we survey the Trefftz method (TM), the collocation method (CM), and the collocation Trefftz method (CTM). We also review the coupling techniques for the interzonal conditions, which include the indirect Trefftz method, the original Trefftz method, the penalty plus hybrid Trefftz method, and the direct Trefftz method. Other boundary methods are also briefly described. Key issues in these algorithms, including the error analysis, are addressed. New numerical results are reported. Comparisons among TMs and other numerical methods are made. It is concluded that the CTM is the simplest algorithm and provides the most accurate solution with the best numerical stability. © 2006 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2007     

Solution of the hyperbolic mild‐slope equation using the finite volume method

A finite volume solver for the 2D depth‐integrated harmonic hyperbolic formulation of the mild‐slope equation for wave propagation is presented and discussed. The solver is implemented on unstructured triangular meshes and the solution methodology is based upon a Godunov‐type second‐order finite volume scheme, whereby the numerical fluxes are computed using Roe's flux function. The eigensystem of the mild‐slope equations is derived and used for the construction of Roe's matrix. A formulation that updates the unknown variables in time implicitly is presented, which produces a more accurate and reliable scheme than hitherto available. Boundary conditions for different types of boundaries are also derived. The agreement of the computed results with analytical results for a range of wave propagation/transformation problems is very good, and the model is found to be virtually paraxiality‐free. Copyright © 2003 John Wiley & Sons, Ltd.     

Implementation of some higher-order convection schemes on non-uniform grids

A generalized formulation is applied to implement the quadratic upstream interpolation (QUICK) scheme, the second-order upwind (SOU) scheme and the second-order hybrid scheme (SHYBRID) on non-uniform grids. The implementation method is simple. The accuracy and efficiency of these higher-order schemes on non-uniform grids are assessed. Three well-known bench mark convection-diffusion problems and a fluid flow problem are revisited using non-uniform grids. These are: (1) transport of a scalar tracer by a uniform velocity field; (2) heat transport in a recirculating flow; (3) two-dimensional non-linear Burgers equations; and (4) a two-dimensional incompressible Navier-Stokes flow which is similar to the classical lid-driven cavity flow. The known exact solutions of the last three problems make it possible to thoroughly evaluate accuracies of various uniform and non-uniform grids. Higher accuracy is obtained for fewer grid points on non-uniform grids. The order of accuracy of the examined schemes is maintained for some tested problems if the distribution of non-uniform grid points is properly chosen.     

Monte Carlo Hamiltonian: Linear Potentials

We further study the validity of the Monte Carlo Hamiltonian method. The advantage of the method,in comparison with the standard Monte Carlo Lagrangian approach, is its capability to study the excited states. Weconsider two quantum mechanical models: a symmetric one V(x) = |x|/2; and an asymmetric one V(x) = ∞, forx ＜ 0 and V(x) = x, for x ≥ 0. The results for the spectrum, wave functions and thermodynamical observables are inagreement with the analytical or Runge-Kutta calculations.     

Extension of a combined analytical/numerical initial value problem solver for unsteady periodic flow

Here we describe analytical and numerical modifications that extend the Differential Reduced Ejector/ mixer Analysis (DREA), a combined analytical/numerical, multiple species ejector/mixing code developed for preliminary design applications, to apply to periodic unsteady flow. An unsteady periodic flow modelling capability opens a range of pertinent simulation problems including pulse detonation engines (PDE), internal combustion engine ICE applications, mixing enhancement and more fundamental fluid dynamic unsteadiness, e.g. fan instability/vortex shedding problems. Although mapping between steady and periodic forms for a scalar equation is a classical problem in applied mathematics, we will show that extension to systems of equations and, moreover, problems with complex initial conditions are more challenging. Additionally, the inherent large gradient initial condition singularities that are characteristic of mixing flows and that have greatly influenced the DREA code formulation, place considerable limitations on the use of numerical solution methods. Fortunately, using the combined analytical–numerical form of the DREA formulation, a successful formulation is developed and described. Comparison of this method with experimental measurements for jet flows with excitation shows reasonable agreement with the simulation. Other flow fields are presented to demonstrate the capabilities of the model. As such, we demonstrate that unsteady periodic effects can be included within the simple, efficient, coarse grid DREA implementation that has been the original intent of the DREA development effort, namely, to provide a viable tool where more complex and expensive models are inappropriate. Copyright © 2002 John Wiley & Sons, Ltd.     

A marker method for the solution of the damped Burgers' equation

A new method for the solution of the damped Burgers' equation is described. The marker method relies on the definition of a convective field associated with the underlying partial differential equation; the information about the approximate solution is associated with the response of an ensemble of markers to this convective field. Some key aspects of the method, such as the selection of the shape function and the initial loading, are discussed in some details. The marker method is applicable to a general class of nonlinear dispersive partial differential equations. © 2005 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2006     

Light Scattering by Cylindrical Fibers with High Aspect Ratio Using the Null‐Field Method with Discrete Sources

The problem of computing light scattering by cylindrical fibers with high aspect ratio in the framework of the Null‐Field method with discrete sources is treated. Numerical experiments for investigating the scattering properties of two fiber geometries are performed using distributed spherical vector wave functions as discrete sources.     

Decay of confined,two-dimensional,spatially periodic arrays of vortices: A numerical investigation

The disarrangement of a perturbed lattice of vortices was studied numerically. The basic state is an exponentially decaying, exact solution of the Navier-Stokes equations. Square arrays of vortices with even numbers of vortex cells along each side were perturbed and their evolution was investigated. Whether the energy in the perturbation grows somewhat before it decays or decays monotonically depends on the initial strength of the vortices of the basic state, the extent of lateral confinement and the structure of the perturbation. The critical condition for temporally local instability, i.e. the critical amplitude of the basic state that must be exceeded to allow energy transfer from the basic state to the perturbation, is discussed. In the strongly confined case of a square lattice of four vortices the appearance of enchancement of global rotation is the result of energy transfer from the basic state to a temporally local unstable mode. Energy is transferred from the basic state to larger-scaled structures (inverse cascade) only if the scales of the larger structures are inherently contained in the initial structure of the perturbation. The initial structure of the double array of vortices is not maintained except for a very special form of perturbation. The facts that large scales decay more slowly than small scales and that, when non-linearities are sufficiently strong, energy is transferred from one scale to another explain the differences in the disarrangement process for different initial strengths of the vortices of the basic state. The stronger vortices, i.e. the vortices perturbed in a manner that increases their strength, tend to dominate the weaker vortices. The pairing and subsequent merging (or capture) of vortices of like sense into larger-scale vortices are described in terms of peaks in the evolution of the square root of the palinstrophy divided by the enstrophy.