Condensed Matter Theory

Abstract:

We consider the time evolution of local observables after an interaction quench in the repulsive Lieb-Liniger model. The system is initialized in the ground state for vanishing interaction and then time-evolved with the Lieb-Liniger Hamiltonian for large, finite interacting strength c. We employ the Quench Action approach to express the full time evolution of local observables in terms of sums over energy eigenstates and then derive the leading terms of a 1/c expansion for several one and two-point functions as a function of time t >0 after the quantum quench. We observe delicate cancellations of contributions to the spectral sums that depend on the details of the choice of representative state in the Quench Action approach and our final results are independent of this choice. Our results provide a highly non-trivial confirmation of the typicality assumptions underlying the Quench Action approach.

Abstract:

A bstract Thymine dimers are a major mutagenic photoproduct induced by UV radiation. While they have been the subject of extensive theoretical and experimental investigations, questions of how DNA supercoiling affects local defect properties, or, conversely, how the presence of such defects changes global supercoiled structure, are largely unexplored. Here we introduce a model of thymine dimers in the oxDNA forcefield, parametrised by comparison to melting experiments and structural measurements of the thymine dimer induced bend angle. We performed extensive molecular dynamics simulations of double-stranded DNA as a function of external twist and force. Compared to undamaged DNA, the presence of a thymine dimer lowers the supercoiling densities at which plectonemes and bubbles occur. For biologically relevant supercoiling densities and forces, thymine dimers can preferentially segregate to the tips of the plectonemes, where they enhance the probability of a localized tip-bubble. This mechanism increases the probability of highly bent and denatured states at the thymine dimer site, which may facilitate repair enzyme binding. Thymine dimer-induced tip-bubbles also pin plectonemes, which may help repair enzymes to locate damage. We hypothesize that the interplay of supercoiling and local defects plays an important role for a wider set of DNA damage repair systems.