Mechanical persistence length

Recently a very detailed study on the single chain dynamic structure factor of short chain PIB (M =3870) melts was undertaken with the aim to identify the leading effects limiting the applicability of the Rouse model toward short length scales [217]. This study was later followed by experiments on PDMS (M =6460), a polymer that has very low rotational barriers [219]. Finally, in order to access directly the intrachain relaxation mechanism experiments comparing PDMS and PIB in solution were also carried out [186]. The structural parameters for both chains were virtually identical, Rg=19.2 (21.3 A). Also their characteristic ratios C =6.73 (6.19) are very similar, i.e. the polymers have nearly equal contour length L and identical persistence lengths, thus their conformation are the same. The rotational barriers on the other hand are 3-3.5 kcal/mol for PIB and about 0.1 kcal/mol for PDMS. We first describe in some detail the study on the PIB melt compared with the PDMS melt and then discuss the results. 

A theoretical analysis of the possible conformations of polylp-phenylene terephthalate) (PPTA) and polylp-phenylene isophthalate) (PPIA) is performed on the basis of molecular mechanics and molecular dynamics trajectories. The dependence of the persistence length on the fluctuations of the torsional angle around the ester bond is discussed for PPTA in the frame of the RIS model. Realistic parameters like bond length and bond angles are provided by computer simulations using MD. 

Flory, P. J., Statistical Mechanics of Chain Molecules, Hanser Publisher, New York (1989). To express the stiffness of a chain, the worm-like chain is a useful model, which is characterized by two parameters the persistence length Ip and the contour length L. In the limit of L/lp —> oo, the Kuhn segment length as defined by Eq. (1.32) is twice the persistence length. 

The OxDNA model provides a good representation of the DNA thermodynamics, while also providing an accurate description of the structural and mechanical properties of dsDNA B-DNA and ssDNA. Moreover, the ssDNA correctly describes the formation of hairpins or other ssDNA secondary structures through the stacking interactions of the intra-strand sites. This model accurately reproduces the persistence lengths of the ssDNA and dsDNA and... 

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