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-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.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Ma L,Yethiraj A,Chen X,Cui Qdoi
10.1016/j.bpj.2009.01.047subject
Has Abstractpub_date
2009-05-06 00:00:00pages
3543-54issue
9eissn
0006-3495issn
1542-0086pii
S0006-3495(09)00551-7journal_volume
96pub_type
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