In this paper, we apply the local discontinuous Galerkin (LDG) method to solve the classical Keller-Segel (KS) chemotaxis model. The exact solution of the KS chemotaxis model may exhibit blow-up patterns with certain initial conditions, and is not easy to approximate numerically. Moreover, it has been proved that there exists a definition of free energy of the KS system which dissipates with respect to time. We will construct a consistent numerical energy and prove the energy dissipation with the LDG discretization. Several numerical experiments in one and two space dimensions will be given. Especially, for solutions with blow-up (converge to Dirac delta functions), the densities of KS model are computed to be strictly positive in the numerical experiments and the energies are also numerically observed to be strictly positive and decreasing as are seen in the figures. Therefore, the scheme is stable for the KS model with blow-up solutions.

We present a new Matched Interface and Boundary (MIB) regularization method for treating charge singularity in solvated biomolecules whose electrostatics are described by the Poisson–Boltzmann (PB) equation. In a regularization method, by decomposing the potential function into two or three components, the singular component can be analytically represented by the Green’s function, while other components possess a higher regularity. Our new regularization combines the efficiency of two-component schemes with the accuracy of the three-component schemes. Based on this regularization, a new MIB finite difference algorithm is developed for solving both linear and nonlinear PB equations, where the nonlinearity is handled by using the inexact-Newton’s method. Compared with the existing MIB PB solver based on a three-component regularization, the present algorithm is simpler to implement by circumventing the work to solve a boundary value Poisson equation inside the molecular interface and to compute related interface jump conditions numerically. Moreover, the new MIB algorithm becomes computationally less expensive, while maintains the same second order accuracy. This is numerically verified by calculating the electrostatic potential and solvation energy on the Kirkwood sphere on which the analytical solutions are available and on a series of proteins with various sizes.

The matrix completion problem is to recover a low-rank matrix from a subset of its entries. The main solution strategy for this problem has been based on nuclear-norm minimization which requires computing singular value decompositionsa task that is increasingly costly as matrix sizes and ranks increase. To improve the capacity of solving large-scale problems, we propose a low-rank factorization model and construct a nonlinear successive over-relaxation (SOR) algorithm that only requires solving a linear least squares problem per iteration. Extensive numerical experiments show that the algorithm can reliably solve a wide range of problems at a speed at least several times faster than many nuclear-norm minimization algorithms. In addition, convergence of this nonlinear SOR algorithm to a stationary point is analyzed.

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The Laplace-Beltrami operator (LBO) is a fundamental object associated to Riemannian manifolds, which encodes all intrinsic geometry of the manifolds and has many desirable prop- erties. Recently, we proposed a novel numerical method, Point Integral method (PIM), to discretize the Laplace-Beltrami operator on point clouds [28]. In this paper, we analyze the convergence of Point Integral method (PIM) for Poisson equation with Neumann boundary condition on submanifolds isometrically embedded in Euclidean spaces.