scholarly journals Ability of the Poisson–Boltzmann equation to capture molecular dynamics predicted ion distribution around polyelectrolytes

2017 ◽  
Vol 19 (36) ◽  
pp. 24583-24593 ◽  
Author(s):  
Piotr Batys ◽  
Sohvi Luukkonen ◽  
Maria Sammalkorpi
Keyword(s):  
Molecular Dynamics ◽  
Boltzmann Equation ◽  
Charge Density ◽  
Layer Thickness ◽  
Mean Field ◽  
Ion Distribution ◽  
Line Charge ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

Ion condensation around polyelectrolytes is examined computationally at all-atom and mean field detail levels to extract the practical limits of a PB model; the condensed ion layer thickness is found to depend solely on polyelectrolyte line charge density.

DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi

2013 ◽  
Vol 13 (1) ◽  
pp. 256-268 ◽  
Author(s):  
Lane W. Votapka ◽  
Luke Czapla ◽  
Maxim Zhenirovskyy ◽  
Rommie E. Amaro
Keyword(s):  
Molecular Dynamics ◽  
Influenza Virus ◽  
Boltzmann Equation ◽  
General Theory ◽  
Electrostatic Interactions ◽  
Biological Interest ◽  
Single Structure ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation ◽  
Electrostatic Calculations

AbstractA new VMD plugin that interfaces with DelPhi to provide ensemble-averaged electrostatic calculations using the Poisson-Boltzmann equation is presented. The general theory and context of this approach are discussed, and examples of the plugin interface and calculations are presented. This new tool is applied to systems of current biological interest, obtaining the ensemble-averaged electrostatic properties of the two major influenza virus glycoproteins, hemagglutinin and neuraminidase, from explicitly solvated all-atom molecular dynamics trajectories. The differences between the ensemble-averaged electrostatics and those obtained from a single structure are examined in detail for these examples, revealing how the plugin can be a powerful tool in facilitating the modeling of electrostatic interactions in biological systems.

scholarly journals Nonlinear screening of charged macromolecules

2011 ◽  
Vol 369 (1935) ◽  
pp. 322-334 ◽  
Author(s):  
Gabriel Téllez
Keyword(s):  
Boltzmann Equation ◽  
Mean Field ◽  
Field Approach ◽  
Interesting Insight ◽  
Hückel Theory ◽  
Charge Renormalization ◽  
Poisson Boltzmann ◽  
Charged Macromolecules ◽  
Poisson Boltzmann Equation ◽  
Physical Phenomena

We present several aspects of the screening of charged macromolecules in an electrolyte. After a review of the basic mean field approach, based on the linear Debye–Hückel theory, we consider the case of highly charged macromolecules, where the linear approximation breaks down and the system is described by the full nonlinear Poisson–Boltzmann equation. Some analytical results for this nonlinear equation give some interesting insight on physical phenomena like the charge renormalization and the Manning counterion condensation.

The interaction of two charged spheres in the Poisson–Boltzmann equation

1981 ◽  
Vol 59 (13) ◽  
pp. 1860-1864 ◽  
Author(s):  
Joseph E. Ledbetter ◽  
Thomas L. Croxton ◽  
Donald A. McQuarrie
Keyword(s):  
Boltzmann Equation ◽  
Charge Density ◽  
Surface Charge ◽  
Electrostatic Potential ◽  
Surface Charge Density ◽  
Ionic Solution ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation ◽  
Good Agreement ◽  
Charged Spheres

The Poisson–Boltzmann equation for two large charged spheres immersed in an ionic solution with either constant surface charge density or constant surface potential is solved numerically. The repulsion between the spheres is calculated from the electrostatic potential in the double layer surrounding the spheres. Good agreement between this numerically calculated force and the force computed using the Derjaguin formula for spheres with constant surface charge density is found at small separations of the spheres.

scholarly journals Monte Carlo methods for linear and non-linear Poisson-Boltzmann equation

2015 ◽  
Vol 48 ◽  
pp. 420-446 ◽  
Author(s):  
Mireille Bossy ◽  
Nicolas Champagnat ◽  
Hélène Leman ◽  
Sylvain Maire ◽  
Laurent Violeau ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Boltzmann Equation ◽  
Monte Carlo Methods ◽  
Non Linear ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation
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