The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff

@article{citeulike:2837181, abstract = {Using tRNA molecule as an example, we evaluate the applicability of the Poisson-Boltzmann model to highly charged systems such as nucleic acids. Particularly, we describe the effect of explicit crystallographic divalent ions and water molecules, ionic strength of the solvent, and the linear approximation to the Poisson-Boltzmann equation on the electrostatic potential and electrostatic free energy. We calculate and compare typical similarity indices and measures, such as Hodgkin index and root mean square deviation. Finally, we introduce a modification to the nonlinear Poisson-Boltzmann equation, which accounts in a simple way for the finite size of mobile ions, by applying a cutoff in the concentration formula for ionic distribution at regions of high electrostatic potentials. We test the influence of this ionic concentration cutoff on the electrostatic properties of tRNA. {\copyright} 2008 Wiley Periodicals, Inc. J Comput Chem, 2008}, author = {Gruziel, M. and Grochowski, P. and Trylska, J. }, citeulike-article-id = {2837181}, journal = {Journal of Computational Chemistry}, keywords = {electrostatics, nucleic\_acids, solvation}, posted-at = {2008-05-27 11:34:49}, priority = {0}, title = {The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff}, url = {http://www3.interscience.wiley.com/journal/118858882/abstract}, year = {in press} }

TY - JOUR ID - citeulike:2837181 L3 - citeulike-article-id:2837181 TI - The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff JF - Journal of Computational Chemistry N2 - Using tRNA molecule as an example, we evaluate the applicability of the Poisson-Boltzmann model to highly charged systems such as nucleic acids. Particularly, we describe the effect of explicit crystallographic divalent ions and water molecules, ionic strength of the solvent, and the linear approximation to the Poisson-Boltzmann equation on the electrostatic potential and electrostatic free energy. We calculate and compare typical similarity indices and measures, such as Hodgkin index and root mean square deviation. Finally, we introduce a modification to the nonlinear Poisson-Boltzmann equation, which accounts in a simple way for the finite size of mobile ions, by applying a cutoff in the concentration formula for ionic distribution at regions of high electrostatic potentials. We test the influence of this ionic concentration cutoff on the electrostatic properties of tRNA. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 KW - electrostatics KW - nucleic_acids KW - solvation AU - Gruziel, M AU - Grochowski, P AU - Trylska, J PY - in press/// UR - http://www3.interscience.wiley.com/journal/118858882/abstract ER -