Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
2015 | 3 | 1 |
Tytuł artykułu

A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations

Treść / Zawartość
Warianty tytułu
Języki publikacji
Numerically solving the Poisson-Boltzmann equation is a challenging task due to the existence of the dielectric interface, singular partial charges representing the biomolecule, discontinuity of the electrostatic field, infinite simulation domains, etc. Boundary integral formulation of the Poisson-Boltzmann equation can circumvent these numerical challenges and meanwhile conveniently use the fast numerical algorithms and the latest high performance computers to achieve combined improvement on both efficiency and accuracy. In the past a few years, we developed several boundary integral Poisson-Boltzmann solvers in pursuing accuracy, efficiency, and the combination of both. In this paper, we summarize the features and functions of these solvers, and give instructions and references for potential users. Meanwhile, we quantitatively report the solvation free energy computation of these boundary integral PB solvers benchmarked with Matched Interface Boundary Poisson-Boltzmann solver (MIBPB), a current 2nd order accurate finite difference Poisson-Boltzmann solver.
Opis fizyczny
  • Department of Mathematics, Southern Methodist University, Dallas, TX 75275 USA
  • [1] Baker, N. A. (2005). Improving implicit solvent simulations: a Poisson-centric view. Current Opinion in Structural Biology, 15(2):137–43. [Crossref]
  • [2] Baker, N. A., Sept, D., Holst, M. J., and Mccammon, J. A. (2001a). The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. IBM Journal of Research and Development, 45(3-4):427–438. [Crossref]
  • [3] Baker, N. A., Sept, D., Joseph, S., Holst, M. J., and McCammon, J. A. (2001b). Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of the United States of America, 98(18):10037– 10041.
  • [4] Barnes, J. and Hut, P. (1986). A hierarchical o(n log n) force-calculation algorithm. Nature, 324(6096):446–449.
  • [5] Bordner, A. J. and Huber, G. A. (2003). Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces onmacromolecules in solution. Journal of Computational Chemistry, 24(3):353–367. [Crossref]
  • [6] Boschitsch, A. H. and Fenley, M. O. (2004). Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation. Journal of Computational Chemistry, 25(7):935–955. [Crossref][WoS]
  • [7] Boschitsch, A. H., Fenley, M. O., and Zhou, H.-X. (2002). Fast boundary element method for the linear Poisson-Boltzmann equation. The Journal of Physical Chemistry B, 106(10):2741–2754.
  • [8] Connolly, M. L. (1985). Depth buffer algorithms for molecular modeling. J. Mol. Graphics, 3:19–24. [Crossref]
  • [9] Cortis, C. M. and Friesner, R. A. (1997). Numerical solution of the Poisson-Boltzmann equation using tetrahedral finite-element meshes. Journal of Computational Chemistry, 18:1591–1608. [Crossref]
  • [10] Fogolari, F., Brigo, A., and Molinari, H. (2002). The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology. Journal of Molecular Recognition, 15(6):377–92. [Crossref]
  • [11] Geng, W. (2013). Parallel higher-order boundary integral electrostatics computation on molecular surfaces with curved triangulation. Journal of Computational Physics, 241(0):253 – 265. [WoS]
  • [12] Geng,W. and Jacob, F. (2013). A GPU-accelerated direct-sumboundary integral Poisson-Boltzmann solver . Computer Physics Communications, 184(6):1490 – 1496. [WoS]
  • [13] Geng, W. and Krasny, R. (2013). A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules. Journal of Computational Physics, 247(0):62 – 78. [WoS]
  • [14] Geng, W., Yu, S., and Wei, G. W. (2007). Treatment of charge singularities in implicit solvent models. Journal of Chemical Physics, 127:114106.
  • [15] Holst, M. and Saied, F. (1993). Multigrid solution of the Poisson-Boltzmann equation. Journal of Computational Chemistry, 14(1):105–13. [Crossref]
  • [16] Holst, M. J. (1994). The Poisson-Boltzmann Equation: Analysis and Multilevel Numerical Solution. PhD thesis, UIUC.
  • [17] Honig, B. and Nicholls, A. (1995). Classical electrostatics in biology and chemistry. Science, 268(5214):1144–9.
  • [18] Im, W., Beglov, D., and Roux, B. (1998). Continuum solvation model: electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Computer Physics Communications, 111(1-3):59–75. [Crossref]
  • [19] Juffer, A., E., B., van Keulen, B., van der Ploeg, A., and Berendsen, H. (1991). The electric potential of a macromolecule in a solvent: a fundamental approach. J. Comput. Phys., 97:144–171.
  • [20] Kirkwood, J. G. (1934). Theory of solution of molecules containing widely separated charges with special application to zwitterions. J. Comput. Phys., 7:351 – 361.
  • [21] Lee, B. and Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J Mol Biol, 55(3):379–400. [Crossref]
  • [22] Li, P., Johnston, H., and Krasny, R. (2009). A Cartesian treecode for screened Coulomb interactions. J. Comput. Phys., 228(10):3858–3868. [WoS]
  • [23] Liang, J. and Subranmaniam, S. (1997). Computation of molecular electrostatics with boundary element methods. Biophys. J., 73:1830–1841.
  • [24] Lu, B., Cheng, X., Huang, J., and McCammon, J. A. (2006). Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proceedings of the National Academy of Sciences, 103(51):19314–19319.
  • [25] Lu, B. Z., Zhou, Y. C., Holst, M. J., and McCammon, J. A. (2008). Recent progress in numerical methods for the Poisson- Boltzmann equation in biophysical applications. Communications in Computational Physics, 3(5):973–1009.
  • [26] Lu, Q. and Luo, R. (2003). A Poisson-Boltzmann dynamics method with nonperiodic boundary condition. Journal of Chemical Physics, 119(21):11035–11047.
  • [27] Luo, R., David, L., and Gilson, M. K. (2002). Accelerated Poisson-Boltzmann calculations for static and dynamic systems. Journal of Computational Chemistry, 23(13):1244–53. [Crossref]
  • [28] Rocchia, W., Alexov, E., and Honig, B. (2001). Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions. J. Phys. Chem., 105:6507–6514.
  • [29] Saad, Y. and Schultz, M. (1986). GMRES: a generalized minimal residual algorithm for solving nonsymmetric linear systems. SIAM Journal on Scientific and Statistical Computing, 7(3):856–869. [Crossref]
  • [30] Sanner, M. F., Olson, A. J., and Spehner, J. C. (1996). Reduced surface: An eflcient way to compute molecular surfaces. Biopolymers, 38:305–320.
  • [31] Vorobjev, Y. N. and Scheraga, H. A. (1997). A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent. Journal of Computational Chemistry, 18(4):569–583. [Crossref]
  • [32] Zauhar, R. J. and Morgan, R. S. (1985). A new method for computing the macromolecular electric potential. Journal of Molecular Biology, 186(4):815–20. [Crossref]
  • [33] Zauhar, R. J. and Morgan, R. S. (1988). The rigorous computation of themolecular electric potential. Journal of Computational Chemistry, 9(2):171–187. [Crossref]
Typ dokumentu
Identyfikator YADDA
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.