Computational mechanics reveals nanosecond time correlations in molecular dynamics of liquid systems (original) (raw)
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Physical Review E, 2008
Computer simulated trajectories of bulk water molecules form complex spatiotemporal structures at the picosecond time scale. This intrinsic complexity, which underlies the formation of molecular structures at longer time scales, has been quantified using a measure of statistical complexity. The method estimates the information contained in the molecular trajectory by detecting and quantifying temporal patterns present in the simulated data ͑velocity time series͒. Two types of temporal patterns are found. The first, defined by the short-time correlations corresponding to the velocity autocorrelation decay times ͑Յ0.1 ps͒, remains asymptotically stable for time intervals longer than several tens of nanoseconds. The second is caused by previously unknown longer-time correlations ͑found at longer than the nanoseconds time scales͒ leading to a value of statistical complexity that slowly increases with time. A direct measure based on the notion of statistical complexity that describes how the trajectory explores the phase space and independent from the particular molecular signal used as the observed time series is introduced.
Time correlation functions of simple liquids: A new insight on the underlying dynamical processes
The Journal of Chemical Physics, 2018
Extensive molecular dynamics simulations of liquid sodium have been carried out to evaluate correlation functions of several dynamical quantities. We report the results of a novel analysis of the longitudinal and transverse correlation functions obtained by evaluating directly their self and distinct contributions at different wavevectors k. It is easily recognized that the self-contribution remains close to its k → 0 limit, which turns out to be exactly the autocorrelation function of the single particle velocity. The wavevector dependence of the longitudinal and transverse spectra and their self and distinct parts is also presented. By making use of the decomposition of the velocity autocorrelation spectrum in terms of longitudinal and transverse parts, our analysis is able to recognize the effect of different dynamical processes in different frequency ranges. 1. Introduction. In recent years, the study of dynamical properties of simple monoatomic liquids has received a strong impetus, due to the massive use of new experimental techniques. The large use of X ray [1] and neutron sources [2] along with advanced spectroscopic facilities have allowed the observation of dynamical processes occurring in the terahertz frequency range with surprising good accuracy. Since the seminal works on liquid alkali metals [3], attention has been devoted to other
Application of Statistical Physics to Understand Static and Dynamic Anomalies in Liquid Water
We present an overview of recent research applying ideas of statistical mechanics to try to better understand the statics and especially the dynamic puzzles regarding liquid water. We discuss recent molecular dynamics simulations using the Mahoney-Jorgensen transferable intermolecular potential with five points (TIP5P), which is closer to real water than previously-proposed classical pairwise additive potentials. Simulations of the TIP5P model for a wide range of deeply supercooled states, including both positive and negative pressures, reveal (i) the existence of a non-monotonic temperature of maximum density line and a non-reentrant spinodal, (ii) the presence of a low-temperature phase transition. The take-home message for the static aspects is that what seems to ''matter'' more than previously appreciated is local tetrahedral order, so that liquid water has features in common with SiO 2 and P, as well as perhaps Si and C. To better understand dynamic aspects of water, we focus on the role of the number of diffusive directions in the potential energy landscape. What seems to ''matter'' most is not values of thermodynamic parameters such as temperature T and pressure P, but only the value of a parameter characterizing the potential energy landscape-just as near a critical point what matters is not the values of T and P but rather the values of the correlation length.
Quantifying long time memory in phase space trajectories of molecular liquids
Journal of Molecular Liquids, 2011
A trajectory of liquid water simulated using classical molecular dynamics has been analysed in the framework of symbolic dynamics. The behaviour of symbolic subsequences (words) of nine symbols long has been studied at a very long time of 1 μs. Contrary to naive expectations, the molecular trajectory behaves very differently compared to both a random signal and a random surrogate with spectral properties identical to the molecular trajectory. The molecular system characteristics resemble those of a chaotic map, the Standard map. We conclude that the most probable reason for deviations from randomness in the molecular system is its deterministic dynamics, in particular, the stickiness of periodic islands in the bulk of chaotic motion.
Chemical Physics, 2005
A quantum mechanics/molecular mechanics molecular dynamics simulation was performed for liquid water to investigate structural and dynamical properties of this peculiar liquid. The most important region containing a central reference molecule and all nearest surrounding molecules (first coordination shell) was treated by Hartree-Fock (HF), post-Hartree-Fock [second-order Møller-Plesset perturbation theory (MP2)], and hybrid density functional B3LYP [Becke's three parameter functional (B3) with the correlation functional of Lee, Yang, and Parr (LYP)] methods. In addition, another HF-level simulation (2HF) included the full second coordination shell. Site to site interactions between oxygen-oxygen, oxygen-hydrogen, and hydrogen-hydrogen atoms of all ab initio methods were compared to experimental data. The absence of a second peak and the appearance of a shoulder instead in the gO-O graph obtained from the 2HF simulation is notable, as this feature has been observed so far only for pressurized or heated water. Dynamical data show that the 2HF procedure compensates some of the deficiency of the HF one-shell simulation, reducing the difference between correlated (MP2) and HF results. B3LYP apparently leads to too rigid structures and thus to an artificial slow down of the dynamics.
The Journal of chemical physics, 2010
Experiments and computer simulation studies have revealed existence of rich dynamics in the orientational relaxation of molecules in confined systems such as water in reverse micelles, cyclodextrin cavities, and nanotubes. Here we introduce a novel finite length one dimensional Ising model to investigate the propagation and the annihilation of dynamical correlations in finite systems and to understand the intriguing shortening of the orientational relaxation time that has been reported for small sized reverse micelles. In our finite sized model, the two spins at the two end cells are oriented in the opposite directions to mimic the effects of surface that in real system fixes water orientation in the opposite directions. This produces opposite polarizations to propagate inside from the surface and to produce bulklike condition at the center. This model can be solved analytically for short chains. For long chains, we solve the model numerically with Glauber spin flip dynamics (and also with Metropolis single-spin flip Monte Carlo algorithm). We show that model nicely reproduces many of the features observed in experiments. Due to the destructive interference among correlations that propagate from the surface to the core, one of the rotational relaxation time components decays faster than the bulk. In general, the relaxation of spins is nonexponential due to the interplay between various interactions. In the limit of strong coupling between the spins or in the limit of low temperature, the nature of relaxation of the spins undergoes a qualitative change with the emergence of a homogeneous dynamics where decay is predominantly exponential, again in agreement with experiments.