The Poisson‐Boltzmann equation is a widely used model to study electrostatics in molecular solvation. Its numerical solution using a boundary integral formulation requires a mesh on the molecular surface only, yielding accurate representations of the solute, which is usually a complicated geometry. Here, we utilize adjoint‐based analyses to form two goal‐oriented error estimates that allow us to determine the contribution of each discretization element (panel) to the numerical error in the solvation free energy. This information is useful to identify high‐error panels to then refine them adaptively to find optimal surface meshes. We present results for spheres and real molecular geometries, and see that elements with large error tend to be in regions where there is a high electrostatic potential. We also find that even though both estimates predict different total errors, they have similar performance as part of an adaptive mesh refinement scheme. Our test cases suggest that the adaptive mesh refinement scheme is very effective, as we are able to reduce the error one order of magnitude by increasing the mesh size less than 20% and come out to be more efficient than uniform refinement when computing error estimations. This result sets the basis toward efficient automatic mesh refinement schemes that produce optimal meshes for solvation energy calculations.
Central discontinuous Galerkin methods on overlapping meshes for wave equations
In this paper, we study the central discontinuous Galerkin (DG) method on overlapping meshes for second order wave equations. We consider the first order hyperbolic system, which is equivalent to the second order scalar equation, and construct the corresponding central DG scheme. We then provide the stability analysis and the optimal error estimates for the proposed central DG scheme for one- and multi-dimensional cases with piecewise P k elements. The optimal error estimates are valid for uniform Cartesian meshes and polynomials of arbitrary degree k ≥ 0. In particular, we adopt the techniques in Liu et al . ( SIAM J. Numer. Anal. 56 (2018) 520–541; ESAIM: M2AN 54 (2020) 705–726) and obtain the local projection that is crucial in deriving the optimal order of convergence. The construction of the projection here is more challenging since the unknowns are highly coupled in the proposed scheme. Dispersion analysis is performed on the proposed scheme for one dimensional problems, indicating that the numerical solution with P 1 elements reaches its minimum with a suitable parameter in the dissipation term. Several numerical examples including accuracy tests and long time simulation are presented to validate the theoretical results.
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- NSF-PAR ID:
- 10225997
- Date Published:
- Journal Name:
- ESAIM: Mathematical Modelling and Numerical Analysis
- Volume:
- 55
- Issue:
- 1
- ISSN:
- 0764-583X
- Page Range / eLocation ID:
- 329 to 356
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract This article presents high order accurate discontinuous Galerkin (DG) methods for wave problems on moving curved meshes with general choices of basis and quadrature. The proposed method adopts an arbitrary Lagrangian–Eulerian formulation to map the wave equation from a time‐dependent moving physical domain onto a fixed reference domain. For moving curved meshes, weighted mass matrices must be assembled and inverted at each time step when using explicit time‐stepping methods. We avoid this step by utilizing an easily invertible weight‐adjusted approximation. The resulting semi‐discrete weight‐adjusted DG scheme is provably energy stable up to a term that (for a fixed time interval) converges to zero with the same rate as the optimal error estimate. Numerical experiments using both polynomial and B‐spline bases verify the high order accuracy and energy stability of proposed methods.
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In this paper, we study the error estimates to sufficiently smooth solutions of the nonlinear scalar conservation laws for the semi-discrete central discontinuous Galerkin (DG) finite element methods on uniform Cartesian meshes. A general approach with an explicitly checkable condition is established for the proof of optimal L 2 error estimates of the semi-discrete CDG schemes, and this condition is checked to be valid in one and two dimensions for polynomials of degree up to k = 8. Numerical experiments are given to verify the theoretical results.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1051/m2an/2020069
