arXiv subjects

Marc Joyeux

Publications and source records attributed to Marc Joyeux.

42 records · Page 3Linked to original sources

arXiv2007

Theoretical investigation of finite size effects at DNA melting

We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both extensive (partition function, entropy, specific heat, etc) and non-extensive (order parameter and correlation length) thermodynamic quantities of finite sequences with open boundary conditions, and applied the modified procedure to two different dynamical models. We showed that rounding of the transition clearly takes place when the length of the sequence is decreased. We also performed a finite-size scaling analysis of the two models and showed that the singular part of the free energy can indeed be expressed in terms of an homogeneous function. However, both the correlation length and the average separation between paired bases diverge at the melting transition, so that it is no longer clear to which of these two quantities the length of the system should be compared. Moreover, Josephson's identity is satisfied for none of the investigated models, so that the derivation of the characteristic exponents which appear, for example, in the expression of the specific heat, requires some care.

physics.bio-ph↗

arXiv2006

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.

physics.chem-ph↗

arXiv2006

On scaling laws at the phase transition of systems with divergent order parameter and/or internal length : the example of DNA denaturation

We used the Transfer-Integral method to compute, with an uncertainty smaller than 5%, the six fundamental characteristic exponents of two dynamical models for DNA thermal denaturation and investigate the validity of the scaling laws. Doubts concerning this point arise because the investigated systems (i) have a divergent internal length, (ii) are described by a divergent order parameter, (iii) are of dimension 1. We found that the assumption that the free energy can be described by a single homogeneous function is robust, despite the divergence of the order parameter, so that Rushbrooke's and Widom's identities are valid relations. Josephson's identity is instead not satisfied. This is probably due to the divergence of the internal length, which invalidates the assumption that the correlation length is solely responsible for singular contributions to thermodynamic quantities. Fisher's identity is even wronger. We showed that this is due to the d=1 dimensionality and obtained an alternative law, which is well satisfied at DNA thermal denaturation.

physics.bio-ph↗

arXiv2006

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.

physics.chem-ph↗

arXiv2005

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.

physics.bio-ph↗

arXiv2005

Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation

We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbour calculations. Within this model, the finiteness of stacking enthalpies is shown to be responsible for the sharpness of calculated melting curves. Transfer-integral and molecular dynamics calculations are performed to demonstrate that the proposed model leads to good agreement with known experimental results for both homogeneous and inhomogeneous DNA.

physics.bio-ph↗