Algebraic Statistics of Poincaré Recurrences in a DNA Molecule

Power-law trapping in the volume-preserving Arnold-Beltrami-Childress map

Understanding stickiness and power-law behavior of Poincaré recurrence statistics is an open problem for higher-dimensional systems, in contrast to the well-understood case of systems with two degrees of freedom. We study such intermittent behavior of chaotic orbits in three-dimensional volume-preserving maps using the example of the Arnold-Beltrami-Childress map. The map has a mixed phase space with a cylindrical regular region surrounded by a chaotic sea for the considered parameters. We observe a characteristic overall power-law decay of the cumulative Poincaré recurrence statistics with significant oscillations superimposed. This slow decay is caused by orbits which spend long times close to the surface of the regular region. Representing such long-trapped orbits in frequency space shows clear signatures of partial barriers and reveals that coupled resonances play an essential role. Using a small number of the most relevant resonances allows for classifying long-trapped orbits. From this the Poincaré recurrence statistics can be divided into different exponentially decaying contributions, which very accurately explains the overall power-law behavior including the oscillations.

Weak nanoscale chaos and anomalous relaxation in DNA

Anomalous nonexponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA base pairs exhibits a slow power-law relaxation attributable to weak Hamiltonian chaos, with parameters similar to experimental data. Here, the relationship is studied between this motion and spectroscopic signals measured in DNA with a small molecular photoprobe inserted into the base-pair stack. To this end, the earlier computational approach in combination with an analytical theory is applied to the experimental DNA fragment. It is found that the intensity of breathing dynamics is strongly increased in the internal base pairs that flank the photoprobe, with anomalous relaxation quantitatively close to that in terminal base pairs. A physical mechanism is proposed to explain the coupling between the relaxation of base-pair breathing and the experimental response signal. It is concluded that the algebraic relaxation observed experimentally is very likely a manifestation of weakly chaotic dynamics of hydrogen-bond breathing in the base pairs stacked to the photoprobe and that the weak nanoscale chaos can represent an ubiquitous hidden source of nonexponential relaxation in ultrafast spectroscopy.

Anomalous dynamics and the choice of Poincaré recurrence set

We investigate the dependence of Poincaré recurrence-time statistics on the choice of recurrence set by sampling the dynamics of two- and four-dimensional Hamiltonian maps. We derive a method that allows us to visualize the direct relation between the shape of a recurrence set and the values of its return probability distribution in arbitrary phase-space dimensions. Such a procedure, which is shown to be quite effective in the detection of tiny regions of regular motion, allows us to explain why similar recurrence sets have very different distributions and how to modify them in order to enhance their return probabilities. Applied to data, this enables us to understand the coexistence of extremely long, transient powerlike decays whose anomalous exponent depends on the chosen recurrence set.