Volume 3, Issue 5
Poisson-Boltzmann Theory of Bionanosystems

A. Sayyed-Ahmad, Y. Miao & P. Ortoleva

DOI:

Commun. Comput. Phys., 3 (2008), pp. 1100-1116.

Published online: 2008-03

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  • Abstract

ThestructureandfunctionofBNS(bionanosystems) suchasmacromolecules, viruses and ribosomes are strongly affected by electrostatic interactions. Yet their supra-millionatomsizemakesthemdifficulttosimulateviaastraightforwardPoissonBoltzmann (PB) approach. Here we explore a multiscale approach that results in a coarse-grained PB equation that follows rigorously fromthe all-atomPB equation. The derivation of the coarse-grainedequation follows froman ansatz on the dependenceof the electrical potential in two distinct ways, i.e. one reflecting atomic-scale variations and the other capturing nanometer-scale features. With this ansatz and a series expansion of the potential in a length-scale ratio, the coarse-grained PB equation is obtained. This multiscale methodology and an efficient computational methodology provide a way to efficiently simulate BNS electrostatics with atomic-scale resolution for the first time, avoiding the need for excessive supercomputer resources. The coarse-grained PB equation contains a tensorial dielectric constant that mediates the channeling of the electric field along macromolecules in an aqueous medium. The multiscale approach and novel salinity connections to the PB equation presented here should enhance the accuracy and wider applicability of PB modeling. 

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@Article{CiCP-3-1100, author = {A. Sayyed-Ahmad, Y. Miao and P. Ortoleva}, title = {Poisson-Boltzmann Theory of Bionanosystems}, journal = {Communications in Computational Physics}, year = {2008}, volume = {3}, number = {5}, pages = {1100--1116}, abstract = {

ThestructureandfunctionofBNS(bionanosystems) suchasmacromolecules, viruses and ribosomes are strongly affected by electrostatic interactions. Yet their supra-millionatomsizemakesthemdifficulttosimulateviaastraightforwardPoissonBoltzmann (PB) approach. Here we explore a multiscale approach that results in a coarse-grained PB equation that follows rigorously fromthe all-atomPB equation. The derivation of the coarse-grainedequation follows froman ansatz on the dependenceof the electrical potential in two distinct ways, i.e. one reflecting atomic-scale variations and the other capturing nanometer-scale features. With this ansatz and a series expansion of the potential in a length-scale ratio, the coarse-grained PB equation is obtained. This multiscale methodology and an efficient computational methodology provide a way to efficiently simulate BNS electrostatics with atomic-scale resolution for the first time, avoiding the need for excessive supercomputer resources. The coarse-grained PB equation contains a tensorial dielectric constant that mediates the channeling of the electric field along macromolecules in an aqueous medium. The multiscale approach and novel salinity connections to the PB equation presented here should enhance the accuracy and wider applicability of PB modeling. 

}, issn = {1991-7120}, doi = {https://doi.org/}, url = {http://global-sci.org/intro/article_detail/cicp/7890.html} }
TY - JOUR T1 - Poisson-Boltzmann Theory of Bionanosystems AU - A. Sayyed-Ahmad, Y. Miao & P. Ortoleva JO - Communications in Computational Physics VL - 5 SP - 1100 EP - 1116 PY - 2008 DA - 2008/03 SN - 3 DO - http://dor.org/ UR - https://global-sci.org/intro/cicp/7890.html KW - AB -

ThestructureandfunctionofBNS(bionanosystems) suchasmacromolecules, viruses and ribosomes are strongly affected by electrostatic interactions. Yet their supra-millionatomsizemakesthemdifficulttosimulateviaastraightforwardPoissonBoltzmann (PB) approach. Here we explore a multiscale approach that results in a coarse-grained PB equation that follows rigorously fromthe all-atomPB equation. The derivation of the coarse-grainedequation follows froman ansatz on the dependenceof the electrical potential in two distinct ways, i.e. one reflecting atomic-scale variations and the other capturing nanometer-scale features. With this ansatz and a series expansion of the potential in a length-scale ratio, the coarse-grained PB equation is obtained. This multiscale methodology and an efficient computational methodology provide a way to efficiently simulate BNS electrostatics with atomic-scale resolution for the first time, avoiding the need for excessive supercomputer resources. The coarse-grained PB equation contains a tensorial dielectric constant that mediates the channeling of the electric field along macromolecules in an aqueous medium. The multiscale approach and novel salinity connections to the PB equation presented here should enhance the accuracy and wider applicability of PB modeling. 

A. Sayyed-Ahmad, Y. Miao & P. Ortoleva. (1970). Poisson-Boltzmann Theory of Bionanosystems. Communications in Computational Physics. 3 (5). 1100-1116. doi:
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