A fast algorithm for particle simulations
Journal of Computational Physics
The electric potential of a macromolecule in a solvent: A fundamental approach
Journal of Computational Physics
Applied Numerical Mathematics - Special issue on massively parallel computing and applications
A fast hierarchical algorithm for 3-D capacitance extraction
DAC '98 Proceedings of the 35th annual Design Automation Conference
A multiscale method for fast capacitance extraction
Proceedings of the 36th annual ACM/IEEE Design Automation Conference
A fast adaptive multipole algorithm for calculating screened Coulomb (Yukawa) interactions
Journal of Computational Physics - Special issue on computational molecular biophysics
IES3: Efficient Electrostatic and Electromagnetic Simulation
IEEE Computational Science & Engineering
A new version of the fast multipole method for screened Coulomb interactions in three dimensions
Journal of Computational Physics
Fast methods for simulation of biomolecule electrostatics
Proceedings of the 2002 IEEE/ACM international conference on Computer-aided design
Journal of Computational Physics
Handbook of Mathematical Functions, With Formulas, Graphs, and Mathematical Tables,
Handbook of Mathematical Functions, With Formulas, Graphs, and Mathematical Tables,
A boundary element formulation of protein electrostatics with explicit ions
Journal of Computational Physics
A precorrected-FFT method for electrostatic analysis of complicated 3-D structures
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
A Cartesian treecode for screened coulomb interactions
Journal of Computational Physics
A Sixth-order Image Approximation to the Ionic Solvent Induced Reaction Field
Journal of Scientific Computing
Journal of Computational Physics
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In this paper, we present an efficient and accurate numerical algorithm for calculating the electrostatic interactions in biomolecular systems. In our scheme, a boundary integral equation (BIE) approach is applied to discretize the linearized Poisson-Boltzmann (PB) equation. The resulting integral formulas are well conditioned for single molecule cases as well as for systems with more than one macromolecule, and are solved efficiently using Krylov subspace based iterative methods such as generalized minimal residual (GMRES) or biconjugate gradient stabilized (BiCGStab) methods. In each iteration, the convolution type matrix-vector multiplications are accelerated by a new version of the fast multipole method (FMM). The implemented algorithm is asymptotically optimal O(N) both in CPU time and memory usage with optimized prefactors. Our approach enhances the present computational ability to treat electrostatics of large scale systems in protein-protein interactions and nano particle assembly processes. Applications including calculating the electrostatics of the nicotinic acetylcholine receptor (nAChR) and interactions between protein Sso7d and DNA are presented.