Condensed Matter Theory

Abstract:

We introduce a pair of time-reversible models defined on the discrete space-time lattice with 3 states per site, specifically, a vacancy and a particle of two flavours (species). The local update rules reproduce the rule 54 reversible cellular automaton when only a single species of particles is present, and satisfy the requirements of flavour exchange (C), space-reversal (P), and time-reversal (T) symmetries. We find closed-form expressions for three local conserved charges and provide an explicit matrix product form of the grand canonical Gibbs states, which are identical for both models. For one of the models this family of Gibbs states seems to be a complete characterisation of equilibrium (i.e. space and time translation invariant) states, while for the other model we empirically find a sequence of local conserved charges, one for each support size larger than 2, hinting to its algebraic integrability. Finally, we numerically investigate the behaviour of spatio-temporal correlation functions of charge densities, and test the prediction of nonlinear fluctuating hydrodynamics for the model with exactly three local charges. The numerically observed 'sound velocity' deviates from the hydrodynamic prediction. The deviations are either significant, or they decay extremely slowly with the simulation time, which leaves us with an open question for the mechanism of such a glassy behaviour in a deterministic locally interacting system.

Abstract:

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, parametrized 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.

Abstract:

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, parametrized 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.