Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Mar 1:1:10.2478/mlbmb-2013-0002.
doi: 10.2478/mlbmb-2013-0002.

Progress in developing Poisson-Boltzmann equation solvers

Chuan Li  1 , Lin Li, Marharyta Petukh, Emil Alexov
Affiliations

Progress in developing Poisson-Boltzmann equation solvers

Chuan Li et al. Mol Based Math Biol. .

Abstract

This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nano-objects.

Keywords: Continuum electrostatics; Poisson-Boltzmann equation; dielectric constant; molecular surface; numerical techniques.

PubMed Disclaimer

Figures

Figure 1
Figure 1
A two dielectric media problem. The space is divided into 3 regions by the molecular surface(solid curve) and the ion-exclusion layer (broken curve): Ω1(molecule), Ω2(stern layer) and Ω3(water environment). Mobile ions, carrying either positive or negative charges, are only present in the water phase.
Figure 2
Figure 2
The continuum electrostatic model for macromolecule immersed in water phase. The water phase is colored in blue and the molecule is colored in orange. A. the immediate shell of water molecule surrounding the macromolecule. B. A cavity inside the macromolecule filled with water. C. The macromolecule interior with inhomogeneous dielectric distribution indicated with grey color.
Figure 3
Figure 3
Dielectric constant distribution map for the reaction center protein calculated with Gaussian approach implemented in DelPhi. The reaction center protein is in a cartoon presentation; A plane of dielectric distribution is also shown in this figure.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Abraham MJ, Gready JE. Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5. Journal of computational chemistry. 2011;32:2031–2040. - PubMed
    1. Adir N, et al. Co-crystallization and characterization of the photosynthetic reaction center-cytochrome c2 complex from Rhodobacter sphaeroides. Biochemistry. 1996;35:2535–47. - PubMed
    1. Aksoylu B, et al. Goal-Oriented Adaptivity and Multilevel Preconditioning for the Poisson-Boltzmann Equation. Journal of Scientific Computing. 2012:1–24.
    1. Alexov E. Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: comparing experimental with computed pK(a)s. Proteins-Structure Function and Bioinformatics. 2003;50:94–103. - PubMed
    1. Alexov E, et al. Progress in the prediction of pKa values in proteins. Proteins-Structure Function and Bioinformatics. 2011;79:3260–75. - PMC - PubMed

LinkOut - more resources

-