We used all-atom molecular dynamics simulation to investigate the elastic properties of double-stranded DNA (dsDNA). We focused on the influences of temperature on the stretch, bend, and twist elasticities, as well as the twist–stretch coupling, of the dsDNA over a wide range of temperature. The results showed that the bending and twist persistence lengths, together with the stretch and twist moduli, decrease linearly with temperature. However, the twist–stretch coupling behaves in a positive correction and enhances as the temperature increases. The potential mechanisms of how temperature affects dsDNA elasticity and coupling were investigated by using the trajectories from atomistic simulation, in which thermal fluctuations in structural parameters were analyzed in detail. We analyzed the simulation results by comparing them with previous simulation and experimental data, which are in good agreement. The prediction about the temperature dependence of dsDNA elastic properties provides a deeper understanding of DNA elasticities in biological environments and potentially helps in the further development of DNA nanotechnology.

Coarse-grained molecular dynamics simulations are used to investigate the conformations of binary semiflexible ring polymers (SRPs) of two different lengths confined in a hard sphere. Segregated structures of SRPs in binary mixtures are strongly dependent upon the number density of system (ρ), the bending energy of long SRPs (K_b, long), and the chain length ratio of long to short SRPs (α). With a low ρ or a weak K_b, long at a small ratio α, long SRPs are immersed randomly in the matrix of short SRPs. As ρ and bending energy of long SRPs (K_b, long) are increased up to a certain value for a large ratio α, a nearly complete segregation between long and short SRPs is observed, which can be further characterized by the ratio of tangential and radial components of long SRPs velocity. These explicit segregated structures of the two components in spherical confinement are induced by a delicate competition between the entropic excluded volume (depletion) effects and bending contributions.

The sliding dynamics of one- or multi-ring structures along a semiflexible cyclic polymer in radial poly[n]catenanes is investigated using molecular dynamics simulations. The fixed and fluctuating (non-fixed) semiflexible central cyclic polymers are considered, respectively. With increasing bending energy of the central cyclic polymer, for the fixed case, the diffusion coefficient increases monotonically due to the reduction of the tortuous sliding path, while for the fluctuating case, the diffusion coefficient decreases. This indicates that the contribution of the polymer fluctuation is suppressed by a further increase in the stiffness of the central cyclic chain. Compared with the one ring case, the mean-square displacement of the multiple rings exhibits a unique sub-diffusive behavior at intermediate time scales due to the repulsion between two neighboring rings. In addition, for the multi-ring system, the whole set of rings exhibit relatively slower diffusion, but faster local dynamics of threading rings and rotational diffusion of the central cyclic polymer arise. These results may help us to understand the diffusion motion of rings in radial poly[n]catenanes from a fundamental point of view and control the sliding dynamics in molecular designs.

The effects of topological constraints on penetration structures of semi-flexible ring polymers in a melt are investigated using molecular dynamics simulations, considering simultaneously the effects of the chain stiffness. Three topology types of rings are considered: 0₁-knot (the unknotted), 3₁-knot and 6₁-knot ring polymers, respectively. With the improved algorithm to detect and quantify the inter-ring penetration (or inter-ring threading), the degree of ring threading does not increase monotonously with the chain stiffness, existing a peak value at the intermediate stiffness. It indicates that rings interpenetrate most at intermediate stiffness where there is a balance between coil expansion (favoring penetrations) and stiffness (inhibiting penetrations). Meanwhile, the inter-ring penetration would be suppressed with the knot complexity of the rings. The analysis of effective potential between the rings provides a better understanding for this non-monotonous behavior in inter-ring penetration.

Using the single-site Gutzwiller method, we theoretically study the ground state and the interspecies entanglement properties of interexchange symmetric multicomponent (two- and three-component) bosonic mixtures in an optical lattice, and the results are generalized to an $n$-component $(n=2,3,4,...)$ system. We compute the mean-field phase diagram, the interspecies entanglement entropy, and the ground-state spectral decomposition. Three phases—namely, the $n$-component superfluid state (nSF), the $n$-component Mott insulator state (nMI), and the supercounterfluid state (SCF)—are observed. Interestingly, we find that there are $n-1$ SCF lobes to separate every two neighboring nMI lobes in the phase diagram. More importantly, we derive the exact general expression of the interspecies entanglement entropy for the SCF phase. In addition, we also investigate the demixing effect of an $n$-component mixture and demonstrate that the mixing-demixing critical point is independent of $n$.