Literature DB >> 20459161

Multiscale analytic continuation approach to nanosystem simulation: applications to virus electrostatics.

Abhishek Singharoy1, Anastasia M Yesnik, Peter Ortoleva.   

Abstract

Electrostatic effects in nanosystems are understood via a physical picture built on their multiscale character and the distinct behavior of mobile ions versus charge groups fixed to the nanostructure. The Poisson-Boltzmann equation is nondimensionalized to introduce a factor lambda that measures the density of mobile ion charge versus that due to fixed charges; the diffusive smearing and volume exclusion effects of the former tend to diminish its value relative to that from the fixed charges. We introduce the ratio sigma of the average nearest-neighbor atom distance to the characteristic size of the features of the nanostructure of interest (e.g., a viral capsomer). We show that a unified treatment (i.e., lambda proportional to sigma) and a perturbation expansion around sigma=0 yields, through analytic continuation, an approximation to the electrostatic potential of high accuracy and computational efficiency. The approach was analyzed via Padé approximants and demonstrated on viral system electrostatics; it can be generalized to accommodate extended Poisson-Boltzmann models, and has wider applicability to nonequilibrium electrodiffusion and many-particle quantum systems.

Mesh:

Year:  2010        PMID: 20459161      PMCID: PMC2878355          DOI: 10.1063/1.3424771

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  18 in total

1.  Electrostatics of nanosystems: application to microtubules and the ribosome.

Authors:  N A Baker; D Sept; S Joseph; M J Holst; J A McCammon
Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-21       Impact factor: 11.205

2.  Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation.

Authors:  Alexander H Boschitsch; Marcia O Fenley
Journal:  J Comput Chem       Date:  2004-05       Impact factor: 3.376

3.  Nanoparticle dynamics: a multiscale analysis of the Liouville equation.

Authors:  Peter J Ortoleva
Journal:  J Phys Chem B       Date:  2005-11-17       Impact factor: 2.991

4.  Viral structural transitions: an all-atom multiscale theory.

Authors:  Yinglong Miao; Peter J Ortoleva
Journal:  J Chem Phys       Date:  2006-12-07       Impact factor: 3.488

5.  All-atom multiscaling and new ensembles for dynamical nanoparticles.

Authors:  Yinglong Miao; Peter Ortoleva
Journal:  J Chem Phys       Date:  2006-07-28       Impact factor: 3.488

6.  Stochastic dynamics of bionanosystems: Multiscale analysis and specialized ensembles.

Authors:  S Pankavich; Y Miao; J Ortoleva; Z Shreif; P Ortoleva
Journal:  J Chem Phys       Date:  2008-06-21       Impact factor: 3.488

7.  The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff.

Authors:  Magdalena Gruziel; Pawel Grochowski; Joanna Trylska
Journal:  J Comput Chem       Date:  2008-09       Impact factor: 3.376

8.  DNA bending by small, mobile multivalent cations.

Authors:  I Rouzina; V A Bloomfield
Journal:  Biophys J       Date:  1998-06       Impact factor: 4.033

9.  Importance of Vp1 calcium-binding residues in assembly, cell entry, and nuclear entry of simian virus 40.

Authors:  Peggy P Li; Akira Naknanishi; Mary A Tran; Ken-Ichiro Ishizu; Masaaki Kawano; Martin Phillips; Hiroshi Handa; Robert C Liddington; Harumi Kasamatsu
Journal:  J Virol       Date:  2003-07       Impact factor: 5.103

10.  Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids.

Authors:  Robert Konecny; Joanna Trylska; Florence Tama; Deqiang Zhang; Nathan A Baker; Charles L Brooks; J A McCammon
Journal:  Biopolymers       Date:  2006-06-05       Impact factor: 2.505

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  3 in total

1.  Order parameters for macromolecules: application to multiscale simulation.

Authors:  A Singharoy; S Cheluvaraja; P Ortoleva
Journal:  J Chem Phys       Date:  2011-01-28       Impact factor: 3.488

2.  Multiscale simulation of microbe structure and dynamics.

Authors:  Harshad Joshi; Abhishek Singharoy; Yuriy V Sereda; Srinath C Cheluvaraja; Peter J Ortoleva
Journal:  Prog Biophys Mol Biol       Date:  2011-07-23       Impact factor: 3.667

3.  Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies.

Authors:  Abhishek Singharoy; Harshad Joshi; Yinglong Miao; Peter J Ortoleva
Journal:  J Phys Chem B       Date:  2012-03-09       Impact factor: 2.991

  3 in total

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