A Computational Framework for Mechanical Response of Macromolecules: Application to the Salt Concentration Dependence of DNA Bendability Export

@article{citeulike:4469868, abstract = {A computational framework is presented for studying the mechanical response of macromolecules. The method combines a continuum mechanics (CM) model for the mechanical properties of the macromolecule with a continuum electrostatic (CE) treatment of solvation. The molecules are represented by their shape and key physicochemical characteristics such as the distribution of materials properties and charge. As a test case, we apply the model to the effect of added salt on the bending of DNA. With a simple representation of DNA, the CM/CE framework using a Debye-H\"{u}ckel model leads to results that are in good agreement with both analytical theories and recent experiments, including a modified Odijk-Skolnick-Fixman theory that takes the finite length of DNA into consideration. Calculations using a more sophisticated CE model (Poisson-Boltzmann), however, suffer from convergence problems, highlighting the importance of balancing numerical accuracy in the CM and CE models when dealing with very large systems, particularly those with a high degree of symmetry.}, author = {Ma, Liang and Yethiraj, Arun and Chen, Xi and Cui, Qiang}, citeulike-article-id = {4469868}, citeulike-linkout-0 = {http://www.cell.com/biophysj/abstract/S0006-3495(09)00551-7}, day = {6}, keywords = {dna-electrostatics, dna\_bending}, month = {May}, number = {9}, pages = {3543--3554}, posted-at = {2009-05-06 10:30:06}, priority = {3}, title = {A Computational Framework for Mechanical Response of Macromolecules: Application to the Salt Concentration Dependence of DNA Bendability}, url = {http://www.cell.com/biophysj/abstract/S0006-3495(09)00551-7}, volume = {96}, year = {2009} }

TY - JOUR ID - citeulike:4469868 L3 - citeulike-article-id:4469868 N2 - A computational framework is presented for studying the mechanical response of macromolecules. The method combines a continuum mechanics (CM) model for the mechanical properties of the macromolecule with a continuum electrostatic (CE) treatment of solvation. The molecules are represented by their shape and key physicochemical characteristics such as the distribution of materials properties and charge. As a test case, we apply the model to the effect of added salt on the bending of DNA. With a simple representation of DNA, the CM/CE framework using a Debye-Hückel model leads to results that are in good agreement with both analytical theories and recent experiments, including a modified Odijk-Skolnick-Fixman theory that takes the finite length of DNA into consideration. Calculations using a more sophisticated CE model (Poisson-Boltzmann), however, suffer from convergence problems, highlighting the importance of balancing numerical accuracy in the CM and CE models when dealing with very large systems, particularly those with a high degree of symmetry. IS - 9 EP - 3554 TI - A Computational Framework for Mechanical Response of Macromolecules: Application to the Salt Concentration Dependence of DNA Bendability VL - 96 SP - 3543 KW - dna-electrostatics KW - dna_bending AU - Ma, Liang AU - Yethiraj, Arun AU - Chen, Xi AU - Cui, Qiang PY - 2009/05/06/ UR - http://www.cell.com/biophysj/abstract/S0006-3495(09)00551-7 ER -