Extreme bendability of DNA double helix due to bending asymmetry

Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study (B. Eslami-Mossallam and M. Ejtehadi, Phys. Rev. E 80, 011919 (2009)). Exploiting a coarse grained representation of DNA molecule at base pair (bp) level, and using the Monte Carlo simulation method in combination with the umbrella sampling technique, we calculate the loop formation probability of DNA in the AER model. We show that, for DNA molecule has a larger J-factor compared to the WLC model which is in excellent agreement with recent experimental data.Comment: 8 pages, 9 figure

Synchronization dynamics of two nanomechanical membranes within a Fabry-Perot cavity

Spontaneous synchronization is a significant collective behavior of weakly coupled systems. Due to their inherent nonlinear nature, optomechanical systems can exhibit self-sustained oscillations which can be exploited for synchronizing different mechanical resonators. In this paper, we explore the synchronization dynamics of two membranes coupled to a common optical field within a cavity, and pumped with a strong blue-detuned laser drive. We focus on the system quantum dynamics in the parameter regime corresponding to synchronization of the classical motion of the two membranes. With an appropriate definition of the phase difference operator for the resonators, we study synchronization in the quantum case through the covariance matrix formalism. We find that for sufficiently large driving, quantum synchronization is robust with respect to quantum fluctuations and to thermal noise up to not too large temperatures. Under synchronization, the two membranes are never entangled, while quantum discord behaves similarly to quantum synchronization, that is, it is larger when the variance of the phase difference is smaller