Z. J. Wang

Mohammad Alhawwary, Z. J. Wang

Large eddy simulation (LES) has been increasingly used to tackle vortex-dominated turbulent flows. In LES, the quality of the simulation results hinges upon the quality of the numerical discretizations in both space and time. It is in this context we perform a Fourier analysis of several popular methods in LES including the discontinuous Galerkin (DG), finite difference (FD), and compact difference (CD) methods. We begin by reviewing the semi-discrete versions of all methods under-consideration, followed by a fully-discrete analysis with explicit Runge-Kutta (RK) time integration schemes. In this regard, we are able to unravel the true dispersion/dissipation behavior of DG and Runge-Kutta DG (RKDG) schemes for the entire wavenumber range. The physical-mode is verified to be a good approximation for the asymptotic behavior of these DG schemes in the low wavenumber range. After that, we proceed to compare the DG, FD, and CD methods in dispersion and dissipation properties. Numerical tests are conducted using the linear advection equation to verify the analysis. In comparing different methods, it is found that the overall numerical dissipation strongly depends on the time step. Compact difference (CD) and central finite difference (FD) schemes, in some particular settings, can have more numerical dissipation than the DG scheme with an upwind flux. This claim is then verified through a numerical test using the Burgers' equation.

Shu-Jie Li, Li-Shi Luo, Z. J. Wang et al.

An exponential time-integrator scheme of second-order accuracy based on the predictor-corrector methodology, denoted PCEXP, is developed to solve multi-dimensional nonlinear partial differential equations pertaining to fluid dynamics. The effective and efficient implementation of PCEXP is realized by means of the Krylov method. The linear stability and truncation error are analyzed through a one-dimensional model equation. The proposed PCEXP scheme is applied to the Euler equations discretized with a discontinuous Galerkin method in both two and three dimensions. The effectiveness and efficiency of the PCEXP scheme are demonstrated for both steady and unsteady inviscid flows. The accuracy and efficiency of the PCEXP scheme are verified and validated through comparisons with the explicit third-order total variation diminishing Runge-Kutta scheme (TVDRK3), the implicit backward Euler (BE) and the implicit second-order backward difference formula (BDF2). For unsteady flows, the PCEXP scheme generates a temporal error much smaller than the BDF2 scheme does, while maintaining the expected acceleration at the same time. Moreover, the PCEXP scheme is also shown to achieve the computational efficiency comparable to the implicit schemes for steady flows.

Lu Han, G. C. Shan, B. F. Chu et al.

The novel coronavirus disease, named COVID-19, emerged in China in December 2019, and has rapidly spread around the world. It is clearly urgent to fight COVID-19 at global scale. The development of methods for identifying drug uses based on phenotypic data can improve the efficiency of drug development. However, there are still many difficulties in identifying drug applications based on cell picture data. This work reported one state-of-the-art machine learning method to identify drug uses based on the cell image features of 1024 drugs generated in the LINCS program. Because the multi-dimensional features of the image are affected by non-experimental factors, the characteristics of similar drugs vary greatly, and the current sample number is not enough to use deep learning and other methods are used for learning optimization. As a consequence, this study is based on the supervised ITML algorithm to convert the characteristics of drugs. The results show that the characteristics of ITML conversion are more conducive to the recognition of drug functions. The analysis of feature conversion shows that different features play important roles in identifying different drug functions. For the current COVID-19, Chloroquine and Hydroxychloroquine achieve antiviral effects by inhibiting endocytosis, etc., and were classified to the same community. And Clomiphene in the same community inibited the entry of Ebola Virus, indicated a similar MoAs that could be reflected by cell image.

Mohammad Alhawwary, Z. J. Wang

In this paper, we study the stability (in terms of the maximum time step) and accuracy (in terms of the wavenumber-diffusion properties) for several popular discontinuous Galerkin (DG) viscous flux formulations. The considered methods include the symmetric interior penalty formulation (SIPG), the first and second approaches of Bassi and Rebay (BR1, BR2), and the local discontinuous Galerkin method (LDG). For the purpose of stability, we consider the von Neumann stability analysis method for uniform grids with a periodic boundary condition. In addition, the combined-mode analysis approach previously introduced for the wave equation is utilized to analyze the dissipative error. This new approach can be used to study the performance of a particular DG and Runge-Kutta DG (RKDG) scheme for the entire extended wavenumber range. Thus, more insights into the robustness as well as accuracy and efficiency can be obtained. For instance, the LDG method provides larger dissipation for high-wavenumber components than the BR1 and BR2 approaches for short time simulations in addition to a lower error bound for long time simulations. The BR1 approach with added dissipation can have desirable properties and stability similar to BR2. For BR2, the penalty parameter can be adjusted to enhance the performance of the scheme. The results are verified through canonical numerical tests.