A Cartesian Fmm-Accelerated Galerkin Boundary Integral Poisson-Boltzmann Solver
نویسندگان
چکیده
The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work developing a Galerkin boundary integral method solving the (PB) equation. solver has combined advantages accuracy, efficiency, memory usage as it applies well-posed formulation to circumvent many numerical difficulties associated PB equation uses O(N) Cartesian Fast Multipole Method (FMM) accelerate GMRES iteration. addition, special treatments such adaptive FMM order, block diagonal preconditioners, discretization, Duffy's transformation are improve performance of solver, which validated on benchmark Kirkwood's sphere series testing proteins.
منابع مشابه
A GPU-accelerated Direct-sum Boundary Integral Poisson-Boltzmann Solver
In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov subspace based linear algebraic solver such as the GMRES. The molecular surfaces are discretized with flat triangles and centroid collocation. To speed up ou...
متن کاملA treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
We present a treecode-accelerated boundary integral (TABI) solver for electrostatics of solvated biomolecules described by the linear Poisson-Boltzmann equation. The method employs a wellconditioned boundary integral formulation for the electrostatic potential and its normal derivative on the molecular surface. The surface is triangulated and the integral equations are discretized by centroid c...
متن کاملDiscontinuous Galerkin Solver for Boltzmann-Poisson Transients
We present results of a discontinuous Galerkin scheme applied to deterministic computations of the transients for the Boltzmann-Poisson system describing electron transport in semiconductor devices. The collisional term models optical-phonon interactions which become dominant under strong energetic conditions corresponding to nano-scale active regions under applied bias. The proposed numerical ...
متن کاملExtreme Scale FMM-Accelerated Boundary Integral Equation Solver for Wave Scattering
Abstract. Algorithmic and architecture-oriented optimizations are essential for achieving performance worthy of anticipated energy-austere exascale systems. In this paper, we present an extreme scale FMM-accelerated boundary integral equation solver for wave scattering, which uses FMM as a matrix-vector multiplication inside the GMRES iterative method. Our FMM Helmholtz kernels are capable of t...
متن کاملGalerkin solver for Boltzmann Poisson systems in nano devices
In this paper, we present results of a discontinuous Galerkin (DG) scheme applied to deterministic computations of the transients for the Boltzmann-Poisson system describing electron transport in semiconductor devices. The collisional term models optical-phonon interactions which become dominant under strong energetic conditions corresponding to nano-scale active regions under applied bias. The...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Social Science Research Network
سال: 2022
ISSN: ['1556-5068']
DOI: https://doi.org/10.2139/ssrn.4203180