Article

Fast methods for simulation of biomolecule electrostatics

Authors:

Shihhsien S. Kuo,

Michael D. Altman,

Jaydeep P. Bardhan,

Jacob K. WhiteAuthors Info & Claims

ICCAD '02: Proceedings of the 2002 IEEE/ACM international conference on Computer-aided design

Pages 466 - 473

https://doi.org/10.1145/774572.774640

Published: 10 November 2002 Publication History

Abstract

Computer simulation is an important tool for improving our understanding of biomolecule electrostatics, in part to aid in drug design. However, the numerical techniques used in these simulation tools do not exploit fast solver approaches widely used in analyzing integrated circuit interconnects. In this paper we describe one popular formulation used to analyze biomolecule electrostatics, present an integral formulation of the problem, and apply the precorrected-FFT method to accelerate the solution of the integral equations.

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Cited By

Bardhan J(2014)Boundary-Integral and Boundary-Element Methods for Biomolecular Electrostatics: Progress, Challenges, and Important Lessons from CEBA 2013Computational Electrostatics for Biological Applications10.1007/978-3-319-12211-3_6(121-141)Online publication date: 30-Nov-2014
https://doi.org/10.1007/978-3-319-12211-3_6
Bardhan JAltman MTidor BWhite J(2009)“Reverse-Schur” Approach to Optimization with Linear PDE Constraints: Application to Biomolecule Analysis and DesignJournal of Chemical Theory and Computation10.1021/ct90011745:12(3260-3278)Online publication date: 30-Oct-2009
https://doi.org/10.1021/ct9001174
Lu BCheng XHuang JMcCammon J(2009)An Adaptive Fast Multipole Boundary Element Method for Poisson−Boltzmann ElectrostaticsJournal of Chemical Theory and Computation10.1021/ct900083k5:6(1692-1699)Online publication date: 21-May-2009
https://doi.org/10.1021/ct900083k
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Index Terms

Fast methods for simulation of biomolecule electrostatics

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cover image ACM Conferences

ICCAD '02: Proceedings of the 2002 IEEE/ACM international conference on Computer-aided design

November 2002

793 pages

ISBN:0780376072

DOI:10.1145/774572

General Chair:
Lawrence T. Pileggi
Carnegie Mellon Univ., Pittsburgh, PA
,
Program Chair:
Andreas Kuehlmann
Cadence Berkeley Labs., Berkeley, CA

Copyright © 2002 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 10 November 2002

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ICCAD02: 2002 IEEE / ACM International Conference on Computer Aided Design

November 10 - 14, 2002

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Cited By

Bardhan J(2014)Boundary-Integral and Boundary-Element Methods for Biomolecular Electrostatics: Progress, Challenges, and Important Lessons from CEBA 2013Computational Electrostatics for Biological Applications10.1007/978-3-319-12211-3_6(121-141)Online publication date: 30-Nov-2014
https://doi.org/10.1007/978-3-319-12211-3_6
Bardhan JAltman MTidor BWhite J(2009)“Reverse-Schur” Approach to Optimization with Linear PDE Constraints: Application to Biomolecule Analysis and DesignJournal of Chemical Theory and Computation10.1021/ct90011745:12(3260-3278)Online publication date: 30-Oct-2009
https://doi.org/10.1021/ct9001174
Lu BCheng XHuang JMcCammon J(2009)An Adaptive Fast Multipole Boundary Element Method for Poisson−Boltzmann ElectrostaticsJournal of Chemical Theory and Computation10.1021/ct900083k5:6(1692-1699)Online publication date: 21-May-2009
https://doi.org/10.1021/ct900083k
Kuo STidor BWhite J(2008)A meshless, spectrally accurate, integral equation solver for molecular surface electrostaticsACM Journal on Emerging Technologies in Computing Systems10.1145/1350763.13507664:2(1-30)Online publication date: 23-Apr-2008
https://dl.acm.org/doi/10.1145/1350763.1350766
Lu BCheng XAndrew McCammon J(2007)"New-version-fast-multipole-method" accelerated electrostatic calculations in biomolecular systemsJournal of Computational Physics10.1016/j.jcp.2007.05.026226:2(1348-1366)Online publication date: 1-Oct-2007
https://dl.acm.org/doi/10.1016/j.jcp.2007.05.026
Kuo SWhite JHassoun S(2006)A spectrally accurate integral equation solver for molecular surface electrostaticsProceedings of the 2006 IEEE/ACM international conference on Computer-aided design10.1145/1233501.1233689(899-906)Online publication date: 5-Nov-2006
https://dl.acm.org/doi/10.1145/1233501.1233689
Khattri S(2006)Computationally efficient technique for nonlinear poisson-boltzmann equationProceedings of the 6th international conference on Computational Science - Volume Part I10.1007/11758501_123(860-863)Online publication date: 28-May-2006
https://dl.acm.org/doi/10.1007/11758501_123
Altman MBardhan JTidor BWhite J(2006)FFTSVD: A FAST MULTISCALE BOUNDARY ELEMENT METHOD SOLVER SUITABLE FOR BIO-MEMS AND BIOMOLECULE SIMULATIONDesign Automation Methods and Tools for Microfluidics-Based Biochips10.1007/1-4020-5123-9_6(143-168)Online publication date: 2006
https://doi.org/10.1007/1-4020-5123-9_6

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