@Article{CiCP-19-3,
author = {},
title = {Automated Parallel and Body-Fitted Mesh Generation in Finite Element Simulation of Macromolecular Systems},
journal = {Communications in Computational Physics},
year = {2016},
volume = {19},
number = {3},
pages = {582--602},
abstract = {<p style="text-align: justify;">Mesh generation is a bottleneck for finite element simulations of
biomolecules. A robust and efficient approach, based on the immersed boundary
method proposed in [8], has been developed and implemented to generate large-scale
mesh body-fitted to molecular shape for general parallel finite element simulations.
The molecular Gaussian surface is adopted to represent the molecular surface, and
is finally approximated by piecewise planes via the tool phgSurfaceCut in PHG [43],
which is improved and can reliably handle complicated molecular surfaces, through
mesh refinement steps. A coarse background mesh is imported first and then is distributed
into each process using a mesh partitioning algorithm such as space filling
curve [5] or METIS [22]. A bisection method is used for the mesh refinements according
to the molecular PDB or PQR file which describes the biomolecular region. After
mesh refinements, the mesh is optionally repartitioned and redistributed for load balancing.
For finite element simulations, the modification of region mark and boundary
types is done in parallel. Our parallel mesh generation method has been successfully
applied to a sphere cavity model, a DNA fragment, a gramicidin A channel and a huge
Dengue virus system. The results of numerical experiments show good parallel efficiency. Computations of electrostatic potential and solvation energy also validate the
method. Moreover, the meshing process and adaptive finite element computation can
be integrated as one PHG project to avoid the mesh importing and exporting costs,
and improve the convenience of application as well.</p>},
issn = {1991-7120},
doi = {https://doi.org/10.4208/cicp.161114.021015a},
url = {https://global-sci.com/article/80266/automated-parallel-and-body-fitted-mesh-generation-in-finite-element-simulation-of-macromolecular-systems}
}