Comment on "Bubble nucleation and cooperativity in DNA melting" [Phys. Rev. Letters 94, 035504 (2005), arXiv:cond-mat/0412591]

The conclusions presented in this Letter arXiv:cond-mat/0412591 rely on not converged calculations and should be considered with caution.Comment: accepted as a "Comment" in PR

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

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

Fractional bidromy in the vibrational spectrum of HOCl

We introduce the notion of fractional bidromy which is the combination of fractional monodromy and bidromy, two recent generalizations of Hamiltonian monodromy. We consider the vibrational spectrum of the HOCl molecule which is used as an illustrative example to show the presence of nontrivial fractional bidromy. To our knowledge, this is the first example of a molecular system where such a generalized monodromy is exhibited.Comment: 9 pages, 2 figue