Remarks on discrete and continuous large-scale models of DNA dynamics.
We present a comparison of the continuous versus discrete models of large-scale DNA conformation, focusing on issues of relevance to molecular dynamics. Starting from conventional expressions for elastic potential energy, we derive elastic dynamic equations in terms of Cartesian coordinates of the helical axis curve, together with a twist function representing the helical or excess twist. It is noted that the conventional potential energies for the two models are not consistent. In addition, we derive expressions for random Brownian forcing for the nonlinear elastic dynamics and discuss the nature of such forces in a continuous system.
Klapper
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Department of Mathematical Sciences, Montana State University, Bozeman 59717, USA. klapper@math.montana.edu
Qian
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H
D001703:Biophysics / Q000379:methods; D004247:DNA / Q000737:chemistry*; D004548:Elasticity; D008956:Models, Chemical; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D013314:Stress, Mechanical; D013816:Thermodynamics
D004247:DNA