ArticleBiophysical journal2009
A computational framework for mechanical response of macromolecules: application to the salt concentration dependence of DNA bendability.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Enriched gradient recovery for interface solutions of the Poisson-Boltzmann equation.Journal of computational physics · 2020Article
- The structure and intermolecular forces of DNA condensates.Nucleic acids research · 2016Article
- Article
- Comment on "Modulating DNA configuration by interfacial traction: an elastic rod model to characterize DNA folding and unfolding".Journal of biological physics · 2014Article
- Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A.Biophysical journal · 2013Article
- Structural and functional consequences of phosphate-arsenate substitutions in selected nucleotides: DNA, RNA, and ATP.The journal of physical chemistry. B · 2012Article
- Disruption and formation of surface salt bridges are coupled to DNA binding by the integration host factor: a computational analysis.Biochemistry · 2011Article
- Chemically accurate coarse graining of double-stranded DNA.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
Corrections and comments
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Authors and funding
4 authors.
Funding
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.
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Registered trials
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