## Abstract We present a new hybrid explicit/implicit solvent method for dynamics simulations of macromolecular systems. The method models explicitly the hydration of the solute by either a layer or sphere of water molecules, and the generalized Born (GB) theory is used to treat the bulk continuum
A parallel implicit/explicit hybrid time domain method for computational electromagnetics
β Scribed by Z. Q. Xie; O. Hassan; K. Morgan
- Publisher
- John Wiley and Sons
- Year
- 2009
- Tongue
- English
- Weight
- 440 KB
- Volume
- 80
- Category
- Article
- ISSN
- 0029-5981
- DOI
- 10.1002/nme.2654
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β¦ Synopsis
Abstract
The numerical solution of Maxwell's curl equations in the time domain is achieved by combining an unstructured mesh finite element algorithm with a cartesian finite difference method. The practical problem area selected to illustrate the application of the approach is the simulation of threeβdimensional electromagnetic wave scattering. The scattering obstacle and the free space region immediately adjacent to it are discretized using an unstructured mesh of linear tetrahedral elements. The remainder of the computational domain is filled with a regular cartesian mesh. These two meshes are overlapped to create a hybrid mesh for the numerical solution. On the cartesian mesh, an explicit finite difference method is adopted and an implicit/explicit finite element formulation is employed on the unstructured mesh. This approach ensures that computational efficiency is maintained if, for any reason, the generated unstructured mesh contains elements of a size much smaller than that required for accurate wave propagation. A perfectly matched layer is added at the artificial far field boundary, created by the truncation of the physical domain prior to the numerical solution. The complete solution approach is parallelized, to enable largeβscale simulations to be effectively performed. Examples are included to demonstrate the numerical performance that can be achieved. Copyright Β© 2009 John Wiley & Sons, Ltd.
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