Instantaneous Normal Mode analysis of liquid HF

We present an Instantaneous Normal Modes analysis of liquid HF aimed to clarify the origin of peculiar dynamical properties which are supposed to stem from the arrangement of molecules in linear hydrogen-bonded network. The present study shows that this approach is an unique tool for the understanding of the spectral features revealed in the analysis of both single molecule and collective quantities. For the system under investigation we demonstrate the relevance of hydrogen-bonding ``stretching'' and fast librational motion in the interpretation of these features.Comment: REVTeX, 7 pages, 5 eps figures included. Minor changes in the text and in a figure. Accepted for publication in Phys. Rev. Let

Mean-atom-trajectory model for the velocity autocorrelation function of monatomic liquids

We present a model for the motion of an average atom in a liquid or supercooled liquid state and apply it to calculations of the velocity autocorrelation function $Z(t)$ and diffusion coefficient $D$. The model trajectory consists of oscillations at a distribution of frequencies characteristic of the normal modes of a single potential valley, interspersed with position- and velocity-conserving transits to similar adjacent valleys. The resulting predictions for $Z(t)$ and $D$ agree remarkably well with MD simulations of Na at up to almost three times its melting temperature. Two independent processes in the model relax velocity autocorrelations: (a) dephasing due to the presence of many frequency components, which operates at all temperatures but which produces no diffusion, and (b) the transit process, which increases with increasing temperature and which produces diffusion. Because the model provides a single-atom trajectory in real space and time, including transits, it may be used to calculate all single-atom correlation functions.Comment: LaTeX, 8 figs. This is an updated version of cond-mat/0002057 and cond-mat/0002058 combined Minor changes made to coincide with published versio

Genetic signatures of variation in population size in a native fungal pathogen after the recent intensive plantation of its host tree

Historical fluctuations in forests’ distribution driven by past climate changes and anthropogenic activities can have large impacts on the demographic history of pathogens that have a long co-evolution history with these host trees. Using a population genetic approach, we investigated that hypothesis by reconstructing the demographic history of Armillaria ostoyae, one of the major pathogens of the maritime pine (Pinus pinaster), in the largest monospecific pine planted forest in Europe (south-western France). Genetic structure analyses and approximate Bayesian computation approaches revealed that a single pathogen population underwent a severe reduction in effective size (12 times lower) 1080–2080 generations ago, followed by an expansion (4 times higher) during the last 4 generations. These results are consistent with the history of the maritime pine forest in the region characterized by a strong recession during the last glaciation (~19 000 years ago) and massive plantations during the second half of the nineteenth century. Results suggest that recent and intensive plantations of a host tree population have offered the opportunity for a rapid spread and adaptation of their pathogens

Instantaneous normal mode analysis of correlated cluster motions in hydrogen bonded liquids

We analyze the correlated motions of hydrogen bonded clusters in liquid hydrogen fluoride, methanol, and water using the Instantaneous Normal Mode approach. In the case of hydrogen fluoride and methanol, which form a topologically linear hydrogen bond network, the relevant cluster is a triplet formed by a molecule and its two neighbors. In the case of water, whose hydrogen bond structure has a local tetrahedral symmetry, the basic unit considered is the pentamer formed by a molecule and its four neighbors. For each of these clusters we identify, using symmetry arguments, the a priori modes describing the relative motions of the cluster molecules and introduce suitable projections in order to evaluate how much these modes contribute to the actual motions at different frequencies. In the case of hydrogen fluoride we confirm the assignment of a 50 rad/ps peak observed in the single and collective correlation function spectra to the stretching of the hydrogen bonded network. In the case of methanol the analysis of the correlated motions of the triplets shows that in the intermediate frequency range (around 25 rad/ps) a picture similar to what is observed in hydrogen fluoride applies, whereas the high frequency properties of the liquid (beyond 50 rad/ps) are mostly due to the asymmetric stretching motion. In the case of water we demonstrate that the a priori modes, based on the full tetrahedral symmetry of the water pentamer, do indeed mix strongly under the effect of the interaction with the neighbors. The results are related to the spectroscopic measurement. (C) 2002 American Institute of Physics

The collective dynamical properties of HCl : the transverse current correlations

Results are presented for the transverse current correlation functions and their spectra obtained by molecular dynamics simulation of liquid hydrogen chloride (HCl) at 201 K. To rationalize the results we analyze the data in the framework of the Mori-Zwanig theory and calculate the first order memory functions. This is done both in and exactly from the simulation data and by suitable approximations with one and two decay rates. It is found that the simple viscoelastic approximation with a single relaxation time is not sufficient to describe the dynamics of HCl whereas the extended model with two relaxation-times function accounts quite well for the simulation data in the low wave-number regime. Hydrogen bonding is found to play only a minor role in the dynamics of the liquid and the main features compare well with a simple liquidlike argon. (C) 2001 American Institute of Physics

Dynamics of the hydrogen bond network in liquid water

The dynamics of the hydrogen bonded network in liquid water is studied by means of molecular dynamics simulations for the SPC/E water model at different thermodynamic conditions. The n-folded hydrogen bond coordination of single molecules and the life time of such configurations is studied by correlation functions. A special focus is put on the dynamics of associated trimers. A velocity projection technique is applied to study the trimer dynamics and to interpret the corresponding velocity-autocorrelation function of single molecules. (C) 2002 Elsevier Science B.V. All rights reserved