Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?

Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base-pairing and base-pair stacking interactions, and a threshold external force is needed to pull the hairpinned structure into a random coiled one. The base-pair stacking interaction in the ssDNA chain makes this hairpin-coil conversion a discontinuous (first-order) phase transition process characterized by a force plateau in the force-extension curve, while lowering this potential below some critical level turns this transition into continuous (second-order) type, no matter how strong the base-pairing interaction is. The phase diagram (including hairpin-I, -II, and random coil) is discussed as a function of stacking potential and external force. These results are in quantitative agreement with recent experimental observations of different ssDNA sequences, and they reveal the necessity to consider the base-pair stacking interactions in order to understand the structural formation of RNA, a polymer designed by nature itself. The theoretical method used may be extended to study the long-range interaction along double-stranded DNA caused by the topological constraint of fixed linking number.Comment: 8 pages using Revte

Engineering topological phases in the Luttinger semimetal α\alpha-Sn

$\alpha$-Sn is well known as a typical Luttinger semimetal with a quadratic band touching at the $\Gamma$ point. Based on the effective $k\cdot p$ analysis as well as first-principles calculations, we demonstrate that multiple topological phases with a rich diagram, including topological insulator, Dirac semimetal, and Weyl semimetal phases, can be induced and engineered in $\alpha$-Sn by external strains, magnetic fields, and circularly polarized light (CPL). Intriguingly, not only the conventional type-I Weyl nodes, but also type-II Weyl nodes and double-Weyl nodes can be generated directly from the quadratic semimetal by applying a magnetic field or CPL. Our results apply equally well to other Luttinger semimetals with similar crystal and electronic structures, and thus open an avenue for realizing and engineering multiple topological phases on a versatile platform.Comment: 15 pages, 6 figure

Anomalous Edge Transport in the Quantum Anomalous Hall State

We predict by first-principles calculations that thin films of Cr-doped (Bi,Sb)$_2$Te$_3$ magnetic topological insulator have gapless non-chiral edge states coexisting with the chiral edge state. Such gapless non-chiral states are not immune to backscattering, which would explain dissipative transport in the quantum anomalous Hall (QAH) state observed in this system experimentally. Here we study the edge transport with both chiral and non-chiral states by Landaur-B\"{u}ttiker formalism, and find that the longitudinal resistance is nonzero whereas Hall resistance is quantized to $h/e^2$. In particular, the longitudinal resistance can be greatly reduced by adding an extra floating probe even if it is not used, while the Hall resistance remains at the quantized value. We propose several transport experiments to detect the dissipative non-chiral edge channels. These results will facilitate the realization of pure dissipationless transport of QAH states in magnetic topological insulators.Comment: 4.8 pages, 4 figure