Chain length dependence of folding transition in a semiflexible homo-polymer chain: Appearance of a core–shell structure

Abstract

The folding transition of single, long semiflexible polymers was studied with special emphasis on the chain length effect using Monte Carlo simulations. While a relatively short chain (10-25 Kuhn segments) undergoes a large discrete transition between swollen coil and compact toroid conformations, a long chain (50 Kuhn segments) exhibits an intrachain segregated state between the disordered coil and ordered toroid.

Phase diagram for a single flexible Stockmayer polymer at zero field

“…Those partially collapsed structures resemble vaguely the core-shell structures found in non-magnetic semiflexible attractive chains 27 . Nonetheless, in the present case we have a core plus some loose tails rather than a shell surrounding a core.…”

“…As it is shown in Figure 5, for the case η = 0.1, the main part of the filament adopts a structure that resembles a tight helix, while the ends of the chain arrange in such a way that the two ends stay in close contact. These helicoidal states are related to the toroidal conformations observed in non-magnetic semi-flexible chains where local chain stiffness helps to stabilise those structures 22,27 . In our case, the magnetic interactions tend to force a nose-tail orientation of the dipoles that, in addition, will induce a local chain stiffness 3 .…”

“…The range of temperatures sampled is T ∈ [0. 27,5], where the upper boundary T = 5 has been chosen because the most interesting features were found in all cases to occur well below such value. It is worth to remark that the value of the parameters chosen for the simulations correspond to values close to those one can expect in experiments, thus, for instance, the relative strength of the magnetic forces involved compared to the thermal fluctuations coincide with that corresponding to ferrofluid particles made of magnetite with σ e ∼ 20 − 25nm.…”

“…Several studies have shown semiflexible chains to possess toroidal or disklike phases. 22,[24][25][26][27][28] Helix structures have also been found for some very specific square-well potentials.29 Related to this, helical long-lived transient states have also been identified for chains with truncated Lennard-Jones potentials. 30 For magnetic chains the number of studies is much lower.…”

In Vitro Murine Leukemia Retroviral Integration and Structure Fluctuation of Target DNA

“…Our idea was that several DNA structures favorable for integration, including the cruciform structure, were yielded during the fluctuation. Once generated by fluctuation, such secondary structure is relatively stable, because the contained Mg 2+ neutralized the negative charge on the DNA strand and stabilized the secondary structure as displayed in Figure 4E [22] , [23] . The interactions of Mg 2+ and the DNA fragment gave rise to a large structural deformation at the base pair region.…”