5 research outputs found
Towards more realistic dynamical models for DNA secondary structure
We propose a dynamical model for the secondary structure of DNA, which is
based on the finite stacking enthalpies used in thermodynamics calculations. In
this model, the two strands can separate and the bases are allowed to rotate
perpendicular to the sequence axis. We show, through molecular dynamics
simulations, that the model has the correct behaviour at the denaturation
transition.Comment: accepted for publication in Chemical Physics Letter
1/f fluctuations of DNA temperature at thermal denaturation
We theoretically investigated the temperature fluctuations of DNA close to
denaturation and observed a strong enhancement of these fluctuations at the
critical temperature. Although in a much lower frequency range, such a sharp
increase was also reported in the recent experimental work of Nagapriya et al
[Phys. Rev. Lett. 96, 038102 (2006)]. We showed that there is instead no
enhancement of temperature fluctuations when the dissipation coefficient in
Langevin equations is assumed to be larger than a few tens of ps-1, and pointed
out the possible role of the solvent in real experiments. We sought for a
possible correlation between the growth of large bubbles and the enhancement of
temperature fluctuations but found no direct evidence thereof. Finally, we
showed that neither the enhancement of fluctuations nor the 1/f dependence are
observed at the scale of a single base pair, while these properties show up
when summing the contributions of a large number of base pairs. We therefore
conclude that both effects result from collective motions that are facilitated
by the divergence of the correlation length at denaturation
Quantum mechanical and quasiclassical investigation of the time domain nonadiabatic dynamics of NO2 close to the bottom of the X2A1-A2B2 conical intersection
We use the effective Hamiltonian that we recently fitted against the first
306 experimentally observed vibronic transitions of NO2 [J. Chem. Phys. 119,
5923 (2003)] to investigate the time domain nonadiabatic dynamics of this
molecule on the coupled X2A1 and A2B2 electronic states, using both quantum
mechanical and quasiclassical techniques. From the quantum mechanical point of
view, we show that the transfer of population to the electronic ground state
originating from a wave packet launched on the excited state occurs in a
stepwise fashion. The evolution of wave packets launched on the electronic
ground state is instead more complex because the crossing seam is located close
to the bottom of the electronic excited state. We next use the mapping
formalism, which replaces the discrete electronic degrees of freedom by
continuous ones, to obtain a classical description of the coupled electronic
states. We propagate gaussian swarms of trajectories to show that this approach
can be used to calculate the populations in each electronic state. We finally
propose a very simple trajectory surface hopping model, which assumes that
trajectories have a constant probability to jump onto the other state in a
particular region of the phase space and a null hopping probability outside
from this region. Quasiclassical calculations show that this model enables a
precise estimation of complex quantities, like for example the projection of
the instantaneous probability density on given planes.Comment: accepted for publication in J. Chem. Phy
Classical and quantum mechanical plane switching in CO2
Classical plane switching takes place in systems with a pronounced 1:2
resonance, where the degree of freedom with lowest frequency is
doubly-degenerate. Under appropriate conditions, one observes a periodic and
abrupt precession of the plane in which the doubly-degenerate motion takes
place. In this article, we show that quantum plane switching exists in CO2 :
Based on our analytical solutions of the classical Hamilton's equations of
motion, we describe the dependence on vibrational angular momentum and energy
of the frequency of switches and the plane switching angle. Using these
results, we find optimal initial wave packet conditions for CO2 and show,
through quantum mechanical propagation, that such a wave packet indeed displays
plane switching at energies around 10000 cm-1 above the ground state on time
scales of about 100 fs.Comment: accepted for publication in the Journal of Chemical Physic