GPU‐accelerated direct numerical simulations of decaying compressible turbulence employing a GKM‐based solver

Gas Kinetic Method‐based flow solvers have become popular in recent years owing to their robustness in simulating high Mach number compressible flows. We evaluate the performance of the newly developed analytical gas kinetic method (AGKM) by Xuan et al. in performing direct numerical simulation of canonical compressible turbulent flow on graphical processing unit (GPU)s. We find that for a range of turbulent Mach numbers, AGKM results shows excellent agreement with high order accurate results obtained with traditional Navier–Stokes solvers in terms of key turbulence statistics. Further, AGKM is found to be more efficient as compared with the traditional gas kinetic method for GPU implementation. We present a brief overview of the optimizations performed on NVIDIA K20 GPU and show that GPU optimizations boost the speedup up‐to 40x as compared with single core CPU computations. Hence, AGKM can be used as an efficient method for performing fast and accurate direct numerical simulations of compressible turbulent flows on simple GPU‐based workstations. Copyright © 2016 John Wiley & Sons, Ltd.     

State space approach to magnetohydrodynamic flow of perfectly conducting micropolar fluid with stretch

In this work we introduce a model of the boundary layer equations for a perfect conducting micropolar fluid with stretch, bounded by an infinite vertical flat plane surface of a constant temperature. This model is applied to study the effects of free convection currents on the flow of the fluid in the presence of a constant magnetic field. The state space technique is adopted for the solution of a one‐dimensional problem for any set of boundary conditions. The resulting formulation together with the Laplace transform techniques are applied to a thermal shock problem. The inversion of the Laplace transforms is carried out using a numerical approach. Numerical results are given and illustrated graphically for the problem. Copyright © 2011 John Wiley & Sons, Ltd.     

Generation of linear and nonlinear waves in numerical wave tank using clustering technique-volume of fluid method

A two-dimensional (2D) numerical model is developed for the wave simulation and propagation in a wave flume.The fluid flow is assumed to be viscous and incompressible,and the Navier-Stokes and continui...     

Selectivity of seismic electric signal (SES) of the 2000 Izu earthquake swarm: a 3D FEM numerical simulation model

Although seismic electric signal (SES) has been used for short-term prediction of earthquakes, selectivity of SES still remains as one of the mysterious features. As a case study, we made a numerical simulation based on a 3D finite element method (FEM) on the selectivity of SES observed in the case of the 2000 Izu earthquake swarm. Our numerical results indicated that the existence of conductive channel under Niijima island could explain the reported SES selectivity.     

Numerical methods for theoretical analysis of foil bearing dynamics

The bearing under consideration is a self-acting, gas bearing with a flexibly supported foil. In order to conduct the theoretical analysis, three systems were identified: a rotor, a gas film and a flexible structure. Each of these elements has been mathematically analysed and analytical equations have been formulated. It was found, that the gas flow in the bearing can be described by the Reynolds equation, whereas a spring-damper model was selected for the structural analysis. The Reynolds equation is a differential equation the exact solution to which is unknown. The work describes the finite difference method in detail, where the partial derivatives in the Reynolds equation are replaced by a system of algebraic equations. In order to solve the resulting system, the Alternating Direction Implicit method (ADI) was used. Based on that and on the analysis of interactions between the three systems the equations have been computed. The accuracy of methods has been verified by means of series of numerical tests. Chosen results are described in this paper.     

An efficient low‐dissipative WENO filter scheme

This paper presents a simple and efficient procedure developed for tracing discontinuities in flow fields. Numerical experiments are carried out to test the new sensor coupled with the associated nonlinear WENO dissipation filter developed to suppress the numerical dissipation. The tests show that, for a problem containing shocks and vortices, the implementation of the new sensor and an optimized WENO scheme can obtain a stable and highly resolved solution. The numerical experiments demonstrated that the new filter scheme performs efficiently both in parallel and serial running for one‐dimensional inviscid flow problems. Direct numerical simulation of a Mach 5 turbulent boundary layer over a flat plate was carried out to demonstrate the applicability of the scheme to the DNS practices. Copyright © 2011 John Wiley & Sons, Ltd.     

Rotamer decomposition and protein dynamics: Efficiently analyzing dihedral populations from molecular dynamics

Molecular mechanics methods have matured into powerful methods to understand the dynamics and flexibility of macromolecules and especially proteins. As multinanosecond to microsecond length molecular dynamics (MD) simulations become commonplace, advanced analysis tools are required to generate scientifically useful information from large amounts of data. Some of the key degrees of freedom to understand protein flexibility and dynamics are the amino acid residue side chain dihedral angles. In this work, we present an easily automated way to summarize and understand the relevant dihedral populations. A tremendous reduction in complexity is achieved by describing dihedral timeseries in terms of histograms decomposed into Gaussians. Using the familiar and widely studied protein lysozyme, it is demonstrated that our approach captures essential properties of protein structure and dynamics. A simple classification scheme is proposed that indicates the rotational state population for each dihedral angle of interest and allows a decision if a given side chain or peptide backbone fragment remains rigid during the course of an MD simulation, adopts a converged distribution between conformational substates or has not reached convergence yet. © 2012 Wiley Periodicals, Inc.     

A numerically stable restrained electrostatic potential charge fitting method

Inspired by the idea of charge decomposition in calculation of the dipole preserving and polarization consistent charges (Zhang et al., J. Comput. Chem. 2011, 32, 2127), we have proposed a numerically stable restrained electrostatic potential (ESP)‐based charge fitting method for protein. The atomic charge is composed of two parts. The dominant part is fixed to a predefined value (e.g., AMBER charge), and the residual part is to be determined by restrained fitting to residual ESP on grid points around the molecule. Nonuniform weighting factors as a function of the dominant charge are assigned to the atoms. Because the residual part is several folds to several orders smaller than the dominant part, the impact of ill‐conditioning is alleviated. This charge fitting method can be used in quantum mechanical/molecular mechanical (QM/MM) simulations and similar studies, where QM calculated electronic properties are frequently mapped to partial atomic charges. © 2012 Wiley Periodicals, Inc.     

Threshold flexoelectric deformations in homeotropic nematic layers

Elastic deformations of nematic liquid crystal layers subjected to a d.c. electric field were studied numerically. The flexoelectric properties of the nematic material and the presence of ionic space charge were taken into account. Homeotropic alignment with finite surface anchoring strength was assumed. The director orientation and the electric potential distribution were calculated; the space charge density was also determined. It was found that the threshold voltage strongly depended on the parameters of the system. In particular, a threshold as low as a few tenths of a volt occurred under suitable circumstances. In the case of a negative dielectric anisotropy, Δ ε, such low values of the threshold voltage existed when the ion concentration was sufficiently high, and given sufficiently large magnitudes of the flexoelectric coefficients and a sufficiently small anchoring energy. If the ion concentration was low or if the flexoelectric coefficients were small or if the surface anchoring was strong, the threshold was equal to several volts. In the case of positive dielectric anisotropy, the threshold amounted to several tenths of a volt for a weakly anisotropic and highly conductive material. If the dielectric anisotropy was sufficiently high or if the ion concentration was sufficiently low, the threshold voltage increased with Δ ε and reached tens of volts. These results can be explained as the effect of the inhomogeneous electric field arising in the vicinity of the surfaces, due to the ionic space charge redistributed by the external voltage. They are qualitatively consistent with earlier experiments which show the effect of the ion concentration on the elastic deformations in flexoelectric nematics. They correspond also with theoretical results concerning the effect of the electric field produced by the surface polarization or by the adsorption of ions.     

Construction of conformal mappings by generalized polarization tensors

We present a new systematic method to compute the Riemann mapping from the outside of the unit disc to the outside of a simply connected domain. We derive explicit relations between the coefficients of the Riemann mapping and the generalized polarization tensors associated with the domain. Because the generalized polarization tensors can be computed numerically, we are able to compute the coefficients of the Riemann mapping using these relations. Effectiveness of the method is validated by numerical examples. Copyright © 2014 John Wiley & Sons, Ltd.