The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the noncanonical forms A (with a narrow major groove and a large amount of north sugars) or C (with a narrow minor groove and a large share of BII phosphates). To model the formation of such complexes by molecular dynamics methods, the force field is required to reproduce these conformational transitions for a naked DNA. We analyzed the available experimental data on the B–C and B–A transitions under the conditions easily implemented in modeling: in an aqueous NaCl solution. We selected six DNA duplexes which conformations at different salt concentrations are known reliably enough. At low salt concentrations, poly(GC) and poly(A) are in the B-form, classical and slightly shifted to the A-form, respectively. The duplexes ATAT and GGTATACC have a strong and salt concentration dependent bias toward the A-form. The polymers poly(AC) and poly(G) take the C- and A-forms, respectively, at high salt concentrations. The reproduction of the behavior of these oligomers can serve as a test for the balance of interactions between the base stacking and the conformational flexibility of the sugar–phosphate backbone in a DNA force field. We tested the AMBER bsc1 and CHARMM36 force fields and their hybrids, and we failed to reproduce the experiment. In all the force fields, the salt concentration dependence is very weak. The known B-philicity of the AMBER force field proved to result from the B-philicity of its excessively strong base stacking. In the CHARMM force field, the B-form is a result of a fragile balance between the A-philic base stacking (especially for G:C pairs) and the C-philic backbone. Finally, we analyzed some recent simulations of the LacI-, SOX-4-, and Sac7d-DNA complex formation in the framework of the AMBER force field.

The molecular dynamics simulation of longitudinal twisting of graphene nanoribbons hanging from the edge of a flat substrate formed by the surface of a hexagonal boron nitride crystal has been performed. It has been shown that rotation of the free end of a nanoribbon causes twisting of the suspended region accompanied by monotonous sliding of the nanoribbon over the substrate. At the beginning, a regular screw-like shape is formed in the suspended section, next a super-twisted section emerges inside it, further growth of which occurs due to pulling of the nanoribbon from the substrate. After separation from the substrate, the twisted nanoribbon folds into a roll, so that further twisting results only in free rotation of the roll.

Using molecular dynamics simulation, we have shown that multilayer graphene nanoribbons located on the flat surface of the h-BN crystal (on the flat substrate) delaminate due to thermal activation into a parquet of single-layer nanoribbons on the substrate. The delamination of graphene nanoribbons requires overcoming the energy barrier associated with the initial shift of its upper layer. After overcoming the barrier, the delamination proceeds spontaneously with the release of energy. The value of this barrier has been estimated and the delamination of two-layer nanofilms has been simulated. The existence of two delamination scenarios has been shown. The first scenario is the longitudinal (along the long side of the nanoribbon) sliding of the upper layer. The second one is in the sliding of the upper layer with the rotation of the layers relative to each other. The first scenario is common for elongated nanoribbons, the second --- for two-layer graphene flakes having close to a square shape. Keywords: graphene, multilayer nanoribbons, flat substrate, nanoribbon delamination.

The results of numerical simulation of the thermal conductivity of a one-dimensional chain of rotators with a double-barrier interaction potential between the nearest neighbors are presented. It is shown that the internal barrier that separates topologically nonequivalent degenerate states has a substantial effect on the temperature dependence of the thermal conductivity of the chain. At low heights of this barrier in the low-temperature region, the main contribution to the increase in the thermal conductivity is made by nonlinear normal modes. With an increase in the temperature, the increase in the thermal conductivity is limited by the occurrence of local above-barrier transitions that prevent energy transfer along the chain. With an increase in the internal barrier height, the contribution of nonlinear normal modes to the energy transfer process decreases and the system exhibits the temperature behavior typical of systems of conventional rotators.