Biomedical subjects

Marc Joyeux

Publications and source records attributed to Marc Joyeux.

6 recordsLinked to original sources

PubMed2006

Quantum mechanical and quasiclassical investigations of the time domain nonadiabatic dynamics of NO2 close to the bottom of the X 2A1 - A 2B2 conical intersection.

We use the effective Hamiltonian that we recently fitted against the first 306 experimentally observed vibronic transitions of NO2 [Joyeux et al., J. Chem. Phys. 119, 5923 (2003)] to investigate the time domain nonadiabatic dynamics of this molecule on the coupled X 2A1 and A 2B2 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, as for example the projection of the instantaneous probability density on given planes.

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PubMed2006

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, and (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 more wrong. We showed that this is due to the d=1 dimensionality and obtained an alternative law, which is well satisfied at DNA thermal denaturation.

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PubMed2006

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 the 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 CO(2). Based on our analytical solutions of 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 CO(2) and show, through quantum-mechanical propagation, that such a wave packet indeed displays plane switching at energies around 10 000 cm(-1) above the ground state on time scales of about 100 fs.

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PubMed2005

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-neighbor 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 a good agreement with known experimental results for both homogeneous and inhomogeneous DNA.

Anisotropy↗

PubMed2005

Study of vibrational energy localization and redistribution in hydrogen peroxide H2O2 at low energy.

Vibrational energy localization and/or redistribution in hydrogen peroxide H2O2 is studied at about 4000 cm(-1) above the quantum mechanical ground state using the ab initio potential energy surface of Koput, Carter, and Handy [J. Phys. Chem. A 102, 6325 (1998)]. In this work, the recently derived canonical perturbation procedure for floppy molecules serves two purposes. First, from the quantum mechanical point of view, it is shown that the energies of the lowest 130 states are reproduced with an average error smaller than 1.5 cm(-1) by a two-dimensional Hamiltonian, which is a function of the torsion and OO-stretch coordinates and momenta, while the other four degrees of freedom contribute only through powers of good quantum numbers. Moreover, the canonical perturbation procedure is also used in classical mechanics calculations, in order to define meaningful local modes, for which the ingoing and outgoing energy flows are monitored. Almost all the individual trajectories launched on the ab initio surface display the same behavior, that is, the superposition of (a) rapid (few hundreds of femtoseconds) and quasiperiodic energy exchanges between the two OH stretches and between the torsion and OO-stretch, and (b) slower (few to several picoseconds) but erratic-looking energy flows between all degrees of freedom. When averaging over large numbers of trajectories with the same local mode energies at time t=0, one observes instead a smooth and irreversible energy flow between all degrees of freedom, which usually thermalize in the range of several tens of picoseconds, that is, on time scales larger than the 5 ps period associated with the quantum density of states.

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PubMed2004

Semiclassical dynamics of the van der Waals states in O3(X1A1).

We present the analysis and the semiclassical quantization of the van der Waals states of ozone in the ground electronic state X1A1. Progressions of these states dominate the spectrum of O3 at threshold. Periodic orbits are used to perform assignment and quantization of the vibrational states. Semiclassical quantization is numerically accurate despite the fact that the classical phase space is chaotic while the nodal patterns of the quantum mechanical wave functions are regular. The lifetimes of recombination of the van der Waals states into the "normal" ozone are also discussed.

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