Computing Electrostatics of COVID-19 Proteins with Parallelized Boundary Integral Poisson-Boltzmann Solvers
arxiv(2023)
摘要
The Poisson-Boltzmann (PB) model governs the electrostatics of solvated
biomolecules, i.e., potential, field, energy, and force. These quantities can
provide useful information about protein properties, functions, and dynamics.
In this project, we investigate the practical application of the PB model on
selected proteins that play significant roles in the spread, treatment, and
prevention of COVID-19 virus diseases. To this end, we solved the boundary
integral form of the PB equation on the molecular surfaces of the selected
proteins. For each selected protein, the simulation produces the electrostatic
solvation energy as a global measurement and electrostatic surface potential
for local details.
By considering the advantages of current algorithms and computer hardware, we
focus on the parallelization of the treecode-accelerated boundary integral
(TABI) solver using the Message Passing Interface (MPI) on CPUs and the
parallelized direct-sum boundary integral (DSBI) solver using KOKKOS on GPUs.
We provide guidance for users when the DSBI solver on GPU or the TABI solver
with MPI on CPU should be used depending on the size of the problem.
Specifically, when the number of unknowns is smaller than a predetermined
threshold, the GPU-accelerated DSBI solver converges rapidly thus has the
potential to perform PB model-based molecular dynamics or Monte Carlo
simulation.
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