Condensed Matter Theory

Abstract:

We study interacting bosons on a lattice in a magnetic field. When the number of flux quanta per plaquette is close to a rational fraction, the low-energy physics is mapped to a multispecies continuum model: bosons in the lowest Landau level where each boson is given an internal degree of freedom, or pseudospin. We find that the interaction potential between the bosons involves terms that do not conserve pseudospin, corresponding to umklapp processes, which in some cases can also be seen as BCS-type pairing terms. We argue that in experimentally realistic regimes for bosonic atoms in optical lattices with synthetic magnetic fields, these terms are crucial for determining the nature of allowed ground states. In particular, we show numerically that certain paired wave functions related to the Moore-Read Pfaffian state are stabilized by these terms, whereas certain other wave functions can be destabilized when umklapp processes become strong. © 2012 American Physical Society.

Abstract:

Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a cruciform can proceed through a cooperative mechanism. Firstly, a twist-induced denaturation bubble must diffuse so that its midpoint is near the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must be large enough to allow one of the arms to form a small number of hairpin bonds. Once the first arm is partially formed, the second arm can rapidly grow to a similar size. Because bubbles can twist back on themselves, they need considerably fewer bases to resolve torsional stress than the final cruciform state does. The initially stabilised cruciform therefore continues to grow, which typically proceeds synchronously, reminiscent of the S-type mechanism of cruciform formation. By using umbrella sampling techniques we calculate, for different temperatures and superhelical densities, the free energy as a function of the number of bonds in each cruciform along the correlated but non-synchronous nucleation pathways we observed in direct simulations.