Chaos and resonances in the classical scattering of a positron by a model diatomic molecule.

PURPOSE: A recently proposed model potential to study quantum scattering of a positron from a hydrogen molecule is used to solve the Hamilton equations for scattering trajectories. In the present classical description, the positron can transfer energy to the vibrational mode of the molecule, remaining trapped for a while before escaping to infinity. Such vibrational resonances may correspond to trajectories which are embedded in phase-space regions of chaotic scattering.

Cation valence dependence of hydrogen bond and stacking potentials in DNA mesoscopic models.

Monovalent and divalent cations play a crucial role in living cells and for molecular techniques such as PCR. Here we evaluate DNA melting temperatures in magnesium (Mg2+) and magnesium­potassium (Mg2++ K+) buffers with a mesoscopic model that allows us to estimate hydrogen bonds and stacking interaction potentials. The Mg2+ and Mg2++ K+ results are compared to previous calculations for sodium ions (Na+), in terms of equivalent sodium concentration and ionic strength. Morse potentials, related to hydrogen bonding, were found to be essentially constant and unaffected by cation conditions. However, for stacking interactions we find a clear dependence with ionic strength and cation valence. The highest ionic strength variations, for both hydrogen bonds and stacking interactions, was found at the sequence terminals. This suggests that end-to-end interactions in DNA will be strongly dependent on cation valence and ionic strength.