Space-time correlations of fluctuating velocities in turbulent shear flows

Space-time correlations or Eulerian two-point two-time correlations of fluctuating velocities are analytically and numerically investigated in turbulent shear flows. An elliptic model for the space-time correlations in the inertial range is developed from the similarity assumptions on the isocorrelation contours: they share a uniform preference direction and a constant aspect ratio. The similarity assumptions are justified using the Kolmogorov similarity hypotheses and verified using the direct numerical simulation DNS of turbulent channel flows. The model relates the space-time correlations to the space correlations via the convection and sweeping characteristic velocities. The analytical expressions for the convection and sweeping velocities are derived from the Navier-Stokes equations for homogeneous turbulent shear flows, where the convection velocity is represented by the mean velocity and the sweeping velocity is the sum of the random sweeping velocity and the shearinduced velocity. This suggests that unlike Taylor’s model where the convection velocity is dominating and Kraichnan and Tennekes’ model where the random sweeping velocity is dominating, the decorrelation time scales of the space-time correlations in turbulent shear flows are determined by the convection velocity, the random sweeping velocity, and the shear-induced velocity. This model predicts a universal form of the spacetime correlations with the two characteristic velocities. The DNS of turbulent channel flows supports the prediction: the correlation functions exhibit a fair good collapse, when plotted against the normalized space and time separations defined by the elliptic model.

Subgrid-scale contributions to Lagrangian time correlations in isotropic turbulence

The application of large-eddy simulation (LES) to particle-laden turbulence raises such a fundamental question as whether the LES with a subgrid scale (SGS) model can correctly predict Lagrangian time correlations (LTCs). Most of the currently existing SGS models are constructed based on the energy budget equations. Therefore, they are able to correctly predict energy spectra, but they may not ensure the correct prediction on the LTCs. Previous researches investigated the effect of the SGS modeling on the Eulerian time correlations. This paper is devoted to study the LTCs in LES. A direct numerical simulation (DNS) and the LES with a spectral eddy viscosity model are performed for isotropic turbulence and the LTCs are calculated using the passive vector method. Both a priori and a posteriori tests are carried out. It is observed that the subgrid-scale contributions to the LTCs cannot be simply ignored and the LES overpredicts the LTCs than the DNS. It is concluded from the straining hypothesis that an accurate prediction of enstrophy spectra is most critical to the prediction of the LTCs.

Switch Region for Pathogenic Structural Change in Conformational Disease and Its Prediction

Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs) and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1) influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1) it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2) it provides an ideal target for clinical treatment.

A block SPP algorithm for multidimensional tridiagonal equations with optimal message vector length

A parallel strategy for solving multidimensional tridiagonal equations is investigated in this paper. We present in detail an improved version of single parallel partition (SPP) algorithm in conjunction with message vectorization, which aggregates several communication messages into one to reduce the communication cost. We show the resulting block SPP can achieve good speedup for a wide range of message vector length (MVL), especially when the number of grid points in the divided direction is large. Instead of only using the largest possible MVL, we adopt numerical tests and modeling analysis to determine an optimal MVL so that significant improvement in speedup can be obtained.

Work and energy equations and the principle of generalized effective stress for unsaturated soils

The effective stress principle has been efficiently applied to saturated soils in the soil mechanics and geotechnical engineering practice; however, its applicability to unsaturated soils is still under debate. The appropriate selection of stress state variables is essential for the construction of constitutive models for unsaturated soils. Owing to the complexity of unsaturated soils, it is difficult to determine the deformation and strength behaviors of unsaturated soils uniquely with the previous single-effective-stress variable theory and two-effective-stress-variable theory in all the situations. In this paper, based on the porous media theory, the specific expression of work is proposed, and the effective stress of unsaturated soils conjugated with the displacement of the soil skeleton is further derived. In the derived work and energy balance equations, the energy dissipation in unsaturated soils is taken into account. According to the derived work and energy balance equations, all of the three generalized stresses and the conjugated strains have effects on the deformation of unsaturated soils. For considering these effects, a principle of generalized effective stress to describe the behaviors of unsaturated soils is proposed. The proposed principle of generalized effective stress may reduce to the previous effective stress theory of single-stress variable or the two-stress variables under certain conditions. This principle provides a helpful reference for the development of constitutive models for unsaturated soils.

Periodic solutions of integro-differential equations which arise in population dynamics

The problem of the existence and stability of periodic solutions of infinite-lag integra-differential equations is considered. Specifically, the integrals involved are of the convolution type with the dependent variable being integrated over the range (- ∞,t), as occur in models of population growth. It is shown that Hopf bifurcation of periodic solutions from a steady state can occur, when a pair of eigenvalues crosses the imaginary axis. Also considered is the existence of traveling wave solutions of a model population equation allowing spatial diffusion in addition to the usual temporal variation. Lastly, the stability of the periodic solutions resulting from Hopf bifurcation is determined with aid of a Floquet theory.

The first chapter is devoted to linear integro-differential equations with constant coefficients utilizing the method of semi-groups of operators. The second chapter analyzes the Hopf bifurcation providing an existence theorem. Also, the two-timing perturbation procedure is applied to construct the periodic solutions. The third chapter uses two-timing to obtain traveling wave solutions of the diffusive model, as well as providing an existence theorem. The fourth chapter develops a Floquet theory for linear integro-differential equations with periodic coefficients again using the semi-group approach. The fifth chapter gives sufficient conditions for the stability or instability of a periodic solution in terms of the linearization of the equations. These results are then applied to the Hopf bifurcation problem and to a certain population equation modeling periodically fluctuating environments to deduce the stability of the corresponding periodic solutions.