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Ever since its inception, a popular DNA motif called the cross tile has been recognized to self-assemble into addressable 2D templates consisting of periodic square cavities. Although this may be conceptually correct, in reality certain types of cross tiles can only form planar lattices if adjacent tiles are designed to bind in a corrugated manner, in the absence of which they roll up to form 3D nanotube structures. Here we present a theoretical study on why uncorrugated cross tiles self-assemble into counterintuitive 3D nanotube structures and not planar 2D lattices. Coarse-grained normal mode analysis of single and multiple cross tiles within the elastic network model was carried out to expound the vibration modes of the systems. While both single and multiple cross tile simulations produce results conducive to tube formations, the dominant modes of a unit of four cross tiles (one square cavity), termed a quadruplet, fully reflect the symmetries of the actual nanotubes found in experiments and firmly endorse circularization of an array of cross tiles. [ABSTRACT FROM AUTHOR]

In this paper, we present all necessary generalisations to extend the bridging scale, a finite-temperature multiple scale method which couples molecular dynamics (MD) and finite element (FE) simulations, to two dimensions. The crucial development is a numerical treatment of the boundary condition acting upon the reduced atomistic system, as such boundary conditions are analytically intractable beyond simple one-dimension systems. The approach presented in this paper offers distinct advantages compared to previous works, specifically the compact size of the resulting time history kernel, and the fact that the time history kernel can be calculated using an automated numerical procedure for arbitrary multi-dimensional lattice structures and interatomic potentials. We demonstrate the truly two-way nature of the coupled FE and reduced MD equations of motion via two example problems, wave propagation and dynamic crack propagation. Finally, we compare both problems to benchmark full MD simulations to validate the accuracy and efficiency of the proposed method. [ABSTRACT FROM AUTHOR]