Radial distribution function of semiflexible oligomers with stretching flexibility

摘要

The radial distribution of the end-to-end distance R-ee is crucial for quantifying the global size and flexibility of a linear polymer. For semiflexible polymers, several analytical formulas have been derived for the radial distribution of R-ee ignoring the stretching flexibility. However, for semiflexible oligomers, such as DNA or RNA, the stretching flexibility can be rather pronounced and can significantly affect the radial distribution of R-ee. In this study, we obtained an extended formula that includes the stretch modulus to describe the distribution of R-ee for semiflexible oligomers on the basis of previous formulas for semiflexible polymers without stretching flexibility. The extended formula was validated by extensive Monte Carlo simulations over wide ranges of the stretch modulus and persistence length, as well as all-atom molecular dynamics simulations of short DNAs and RNAs. Additionally, our analyses showed that the effect of stretching flexibility on the distribution of R-ee becomes negligible for DNAs longer than similar to 130 base pairs and RNAs longer than similar to 240 base pairs. Published by AIP Publishing.