ISSN:
1089-7690
Source:
AIP Digital Archive
Topics:
Physics
,
Chemistry and Pharmacology
Notes:
Brownian dynamics simulations of a three-bead and a ten-bead model of a flexible linear macromolecule in solution are performed. Dynamic forward depolarized light scattering autocorrelation functions are calculated from these dynamic simulations to a delay time of 30 μs and are analyzed by the program contin, yielding the simplest distribution of decay times that is consistent with the simulated data. The distribution of decay times obtained from the simulations of the three-bead model are compared with those obtained from the calculations of Roitman and Zimm on the dynamic behavior of a three-bead trumbell. The simulations and the theory of Roitman and Zimm show excellent agreement. The distribution of decay times obtained from the simulations of the ten-bead model with a persistence length of 600 A(ring) is compared with previously published transient electric birefringence data from a 367 base pair monodisperse DNA fragment, again showing excellent agreement. Results from dynamic simulations of the ten-bead model with varying persistence length are then favorably compared with new transient electric birefringence data from the 367 base pair DNA fragment, obtained at varying ionic strength. The simulations of a model with a persistence length of 900 A(ring) agree with the transient electric birefringence results from the DNA in a 1.4 mM ionic strength solution, showing the behavior of a slightly flexible rod. Simulations of a model with persistence length of 400 A(ring) agree with the transient electric birefringence results from the DNA in a 4.4 mM ionic strength solution, showing behavior more indicative of a semistiff worm-like chain. Simulations of ensembles of rigid three-bead and ten-bead models yield dynamics quite different from their flexible counterparts. This raises concerns about the use of ensembles of rigid shapes as models for rotational dynamics of flexible molecules. These studies independently confirm the behavior predicted by the Roitman–Zimm calculations for the trumbell and demonstrate that Brownian dynamics simulations of a ten-bead model of DNA reproduce the dynamic decay spectrum and the dependence of that decay spectrum on chain stiffness, as measured by transient electric birefringence.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1063/1.455043
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