A fast solver for nonlocal electrostatic theory in biomolecular science and engineering

Biological molecules perform their functions surrounded by water and mobile ions, which strongly influence molecular structure and behavior. The electrostatic interactions between a molecule and solvent are particularly difficult to model theoretically, due to the forces' long range and the col...

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Bibliographic Details
Published in:2011 48th ACM/EDAC/IEEE Design Automation Conference (DAC) pp. 801 - 805
Main Authors: Bardhan, Jaydeep P., Hildebrandt, Andreas
Format: Conference Proceeding
Language:English
Published: New York, NY, USA ACM 05.06.2011
IEEE
Series:ACM Conferences
Subjects:
Applied computing > Physical sciences and engineering > Chemistry
Biological system modeling
Computational modeling
Computing methodologies > Modeling and simulation > Model development and analysis > Modeling methodologies
Electric potential
Electrostatics
Equations
I.6.5 [Model Development]: Methodologies
J.2 [Physical Sciences and Engineering]: Chemistry
Mathematical model
Solvents
ISBN:1450306365, 9781450306362
ISSN:0738-100X
Online Access:Get full text
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Summary:Biological molecules perform their functions surrounded by water and mobile ions, which strongly influence molecular structure and behavior. The electrostatic interactions between a molecule and solvent are particularly difficult to model theoretically, due to the forces' long range and the collective response of many thousands of solvent molecules. The dominant modeling approaches represent the two extremes of the trade-off between molecular realism and computational efficiency: all-atom molecular dynamics in explicit solvent, and macroscopic continuum theory (the Poisson or Poisson--Boltzmann equation). We present the first fast-solver implementation of an advanced nonlocal continuum theory that combines key advantages of both approaches. In particular, molecular realism is included by limiting solvent dielectric response on short length scales, using a model for nonlocal dielectric response allows the resulting problem (a linear integro-differential Poisson equation) to be reformulated as a system of coupled boundary-integral equations using double reciprocity. Whereas previous studies using the nonlocal theory had been limited to small model problems, owing to computational cost, our work opens the door to studying much larger problems including rational drug design, protein engineering, and nanofluidics.
ISBN:1450306365
9781450306362
ISSN:0738-100X
DOI:10.1145/2024724.2024904