Condensed Matter Theory

Abstract:

I solve a quantum chain whose Hamiltonian is comprised solely of local four-fermi operators by constructing free-fermion raising and lowering operators. The free-fermion operators are both non-local and highly non-linear in the local fermions. This construction yields the complete spectrum of the Hamiltonian and an associated classical transfer matrix. The spatially uniform system is gapless with dynamical critical exponent z=3/2, while staggering the couplings gives a more conventional free-fermion model with an Ising transition. The Hamiltonian is equivalent to that of a spin-1/2 chain with next-nearest-neighbour interactions, and has a supersymmetry generated by a sum of fermion trilinears. The supercharges are part of a large non-abelian symmetry algebra that results in exponentially large degeneracies. The model is integrable for either open or periodic boundary conditions but the free-fermion construction only works for the former, while for the latter the extended symmetry is broken and the degeneracies split.

Abstract:

DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. While the wormlike chain model provides a good description of small to moderate bending fluctuations, it is expected to break down for large bending. Recent cyclization experiments on strongly bent shorter molecules indeed suggest enhanced flexibility over and above that expected from the wormlike chain. Here, we use a coarse-grained model of DNA to investigate the subtle thermodynamics of DNA cyclization for molecules ranging from 30 to 210 base pairs. As the molecules get shorter, we find increasing deviations between our computed equilibrium j-factor and the classic wormlike chain predictions of Shimada and Yamakawa for a torsionally aligned looped molecule. These deviations are due to sharp kinking, first at nicks, and only subsequently in the body of the duplex. At the shortest lengths, substantial fraying at the ends of duplex domains is the dominant method of relaxation. We also estimate the dynamic j-factor measured in recent FRET experiments. We find that the dynamic j-factor is systematically larger than its equilibrium counterpart-with the deviation larger for shorter molecules-because not all the stress present in the fully cyclized state is present in the transition state. These observations are important for the interpretation of recent cyclization experiments, suggesting that measured anomalously high j-factors may not necessarily indicate non-WLC behavior in the body of duplexes.