Literature DB >> 18235844

Extending the Fast Multipole Method for Charges inside a Dielectric Sphere in an Ionic Solvent: High Order Image Approximations for Reaction Fields.

Shaozhong Deng1, Wei Cai.   

Abstract

As a sequel to our previous paper on extending the Fast Multipole Method (FMM) for charges inside a dielectric sphere [J. Comput. Phys. 223 (2007) 846-864], this paper further extends the FMM to the electrostatic calculation for charges inside a dielectric sphere immersed in an ionic solvent, a scenery with more relevance in biological applications. The key findings include two fourth-order multiple discrete image approximations in terms of u=λa to the reaction field induced by the ionic solvent, provided that u=λa < 1 where λ is the inverse Debye screening length of the ionic solvent and a is the radius of the dielectric sphere. A 10(-4) relative accuracy in the reaction field of a source charge within the sphere can be achieved with only 3-4 point image charges. Together with the image charges, the FMM can be used to speed up the calculation of electrostatic interactions of charges in a dielectric sphere immersed in an ionic solvent.

Year:  2007        PMID: 18235844      PMCID: PMC2219213          DOI: 10.1016/j.jcp.2007.09.001

Source DB:  PubMed          Journal:  J Comput Phys        ISSN: 0021-9991            Impact factor:   3.553


  14 in total

Review 1.  Molecular dynamics simulations of biomolecules: long-range electrostatic effects.

Authors:  C Sagui; T A Darden
Journal:  Annu Rev Biophys Biomol Struct       Date:  1999

Review 2.  The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology.

Authors:  F Fogolari; A Brigo; H Molinari
Journal:  J Mol Recognit       Date:  2002 Nov-Dec       Impact factor: 2.137

3.  Poisson-Boltzmann methods for biomolecular electrostatics.

Authors:  Nathan A Baker
Journal:  Methods Enzymol       Date:  2004       Impact factor: 1.600

Review 4.  Recent advances in the development and application of implicit solvent models in biomolecule simulations.

Authors:  Michael Feig; Charles L Brooks
Journal:  Curr Opin Struct Biol       Date:  2004-04       Impact factor: 6.809

5.  An efficient hybrid explicit/implicit solvent method for biomolecular simulations.

Authors:  Michael S Lee; Freddie R Salsbury; Mark A Olson
Journal:  J Comput Chem       Date:  2004-12       Impact factor: 3.376

Review 6.  Improving implicit solvent simulations: a Poisson-centric view.

Authors:  Nathan A Baker
Journal:  Curr Opin Struct Biol       Date:  2005-04       Impact factor: 6.809

Review 7.  Electrostatics calculations: latest methodological advances.

Authors:  Patrice Koehl
Journal:  Curr Opin Struct Biol       Date:  2006-03-15       Impact factor: 6.809

Review 8.  Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

Authors:  R M Levy; E Gallicchio
Journal:  Annu Rev Phys Chem       Date:  1998       Impact factor: 12.703

9.  Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.

Authors:  R Abagyan; M Totrov
Journal:  J Mol Biol       Date:  1994-01-21       Impact factor: 5.469

10.  Calculation of the electric potential in the active site cleft due to alpha-helix dipoles.

Authors:  J Warwicker; H C Watson
Journal:  J Mol Biol       Date:  1982-06-05       Impact factor: 5.469

View more
  10 in total

1.  An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions.

Authors:  Yuchun Lin; Andrij Baumketner; Shaozhong Deng; Zhenli Xu; Donald Jacobs; Wei Cai
Journal:  J Chem Phys       Date:  2009-10-21       Impact factor: 3.488

2.  New Versions of Image Approximations to the Ionic Solvent Induced Reaction Field.

Authors:  Changfeng Xue; Shaozhong Deng
Journal:  Comput Phys Commun       Date:  2008-02-01       Impact factor: 4.390

3.  A Sixth-order Image Approximation to the Ionic Solvent Induced Reaction Field.

Authors:  Ming Xiang; Shaozhong Deng; Wei Cai
Journal:  J Sci Comput       Date:  2009-12-01       Impact factor: 2.592

4.  Ionic solvation studied by image-charge reaction field method.

Authors:  Yuchun Lin; Andrij Baumketner; Wei Song; Shaozhong Deng; Donald Jacobs; Wei Cai
Journal:  J Chem Phys       Date:  2011-01-28       Impact factor: 3.488

Review 5.  Biomolecular electrostatics and solvation: a computational perspective.

Authors:  Pengyu Ren; Jaehun Chun; Dennis G Thomas; Michael J Schnieders; Marcelo Marucho; Jiajing Zhang; Nathan A Baker
Journal:  Q Rev Biophys       Date:  2012-11       Impact factor: 5.318

6.  ICSM: An order N method for calculating electrostatic interactions added to TINKER.

Authors:  Katherine Baker; Andrij Baumketner; Yuchun Lin; Shaozhong Deng; Donald Jacobs; Wei Cai
Journal:  Comput Phys Commun       Date:  2012-08-14       Impact factor: 4.390

7.  Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations.

Authors:  Zhenli Xu; Wei Cai
Journal:  SIAM Rev Soc Ind Appl Math       Date:  2011-11-07       Impact factor: 10.780

8.  Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules.

Authors:  Peihua Qin; Zhenli Xu; Wei Cai; Donald Jacobs
Journal:  Commun Comput Phys       Date:  2009-11       Impact factor: 3.246

9.  Image charge approximations of reaction fields in solvents with arbitrary ionic strength.

Authors:  Zhenli Xu; Shaozhong Deng; Wei Cai
Journal:  J Comput Phys       Date:  2009-04-01       Impact factor: 3.553

10.  A fast and accurate computational method for the linear-combination-based isotropic periodic sum.

Authors:  Kazuaki Z Takahashi; Takuma Nozawa; Kenji Yasuoka
Journal:  Sci Rep       Date:  2018-08-08       Impact factor: 4.379

  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.