In this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions with persistent homology analysis, so as to construct a series of multiscale persistent functions, particularly multiscale persistent entropies, for structure characterization. To clarify the fundamental idea of our method, the multiscale persistent entropy model is discussed in great detail. Mathematically, unlike the previous persistent entropy or topological entropy, a special resolution parameter is incorporated into our model. Various scales can be achieved by tuning its value. Physically, our multiscale persistent entropy can be used in conformation entropy evaluation. More specifically, it is found that our method incorporates in it a natural classification scheme. This is achieved through a density filtration of a multiscale rigidity function built from bond and/or dihedral angle distributions. To further validate our model, a systematical comparison with the traditional entropy evaluation model is done. It is found that our model is able to preserve the intrinsic topological features of biomolecular data much better than traditional approaches, particularly for resolutions in the mediate range. Moreover, our method can be successfully used in protein classification. For a test database with around nine hundred proteins, a clear separation between all-alpha and all-beta proteins can be achieved, using only the dihedral and pseudo-bond angle information. Finally, a special protein structure index (PSI) is proposed, for the first time, to describe the "regularity" of protein structures. Essentially, PSI can be used to describe the "regularity" information in any systems.

Based on a global estimate of the heat kernel, some important inequalities such as Poincaré inequality and log-Sobolev inequality, furthermore a tight logarithm Sobolev inequality are presented on graphs, just under a positive curvature condition CDE'(n,K) with some K > 0. As consequences, we obtain exponential integrability of integrable Lipschitz functions and moment bounds at the same assumption on graphs.

This paper is concerned with an interior penalty discontinuous Galerkin (IPDG) method based on a flexible type of non-polynomial local approximation space for the Helmholtz equation with varying wavenumber. The local approximation space consists of multiple polynomial-modulated phase functions which can be chosen according to the phase information of the solution. We obtain some {approximation} properties for this space and \textit{a prior} $L^2$ error estimates for the \textit{h}-convergence of the IPDG method using duality argument. We also provide ample numerical examples to show that, building phase information into the local spaces often gives more accurate results comparing to using the standard polynomial spaces.

In this paper, high order central finite difference schemes in a finite interval are analyzed for the diffusion equation. Boundary conditions of the initial-boundary value problem (IBVP) are treated by the simplified inverse Lax-Wendroff (SILW) procedure. For the fully discrete case, a third order explicit Runge-Kutta method is used as an example for the analysis. Stability is analyzed by both the GKS (Gustafsson, Kreiss and Sundstr\"om) theory and the eigenvalue visualization method on both semi-discrete and fully discrete schemes. The two different analysis techniques yield consistent results. Numerical tests are performed to demonstrate and validate the analysis results.

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