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Comparison of three-dimensional Poisson solution methods for particle-based simulation and inhomogeneous dielectrics

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      Electrostatics of nanosystems: application to microtubules and the ribosome.

      Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the Poisson-Boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. Here we present the application of numerical methods to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size. As a demonstration of this methodology, electrostatic potentials have been calculated for large microtubule and ribosome structures. The results point to the likely role of electrostatics in a variety of activities of these structures.
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        GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems

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          What is "liquid"? Understanding the states of matter

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            Author and article information

            Journal
            PLEEE8
            Physical Review E
            Phys. Rev. E
            American Physical Society (APS)
            1539-3755
            1550-2376
            July 2012
            July 12 2012
            : 86
            : 1
            10.1103/PhysRevE.86.011912
            © 2012

            http://link.aps.org/licenses/aps-default-license

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