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Model systems for DNA and its environment: Suitability and accuracy in theoretical calculations
Author(s) -
Pack George R.,
Wong Linda,
Lamm Gene
Publication year - 2009
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.560360703
Subject(s) - monte carlo method , cylinder , statistical physics , counterion , poisson distribution , poisson–boltzmann equation , physics , ion , computational physics , geometry , mathematics , quantum mechanics , statistics
An investigation of the effects of different approximations on the results of Poisson–Boltzmann and Monte Carlo calculations of the accumulation of counterions at the highly charged surface of DNA is presented. Uniformly charged cylinders of various finite lengths are used to model a segment of DNA and the results of Poisson–Boltzmann calculations are compared with those obtained using an infinitely long charged cylinder. Results of Poisson–Boltzmann calculations using all‐atom models of different lengths are also compared in a study of end effects. The use of rigid structures that are significantly shorter than is the persistence length of DNA appears to be justified. Monte Carlo calculations of counterion densities around charged cylinder models have been performed to assess the magnitude of the statistical errors in this approach. Comparison of the calculated local densities at different, symmetrically equivalent, positions indicate that even after 20 million configurations have been sampled there is a small but significant error in the concentrations calculated over regions with a volume of 3.36 Å 3 . Monte Carlo calculations for 1 and 4 Å hard‐sphere counterions are presented with results given after 5 million, 10 million, and 20 million configurations were sampled. The results of these calculations show a strong dependence on the model system used and demonstrate the need for accurate geometric details in the calculations.