1,220 research outputs found
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
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