Some Further Results for the Stationary Points and Dynamics of Supercooled Liquids

We present some new theoretical and computational results for the stationary points of bulk systems. First we demonstrate how the potential energy surface can be partitioned into catchment basins associated with every stationary point using a combination of Newton-Raphson and eigenvector-following techniques. Numerical results are presented for a 256-atom supercell representation of a binary Lennard-Jones system. We then derive analytical formulae for the number of stationary points as a function of both system size and the Hessian index, using a framework based upon weakly interacting subsystems. This analysis reveals a simple relation between the total number of stationary points, the number of local minima, and the number of transition states connected on average to each minimum. Finally we calculate two measures of localisation for the displacements corresponding to Hessian eigenvectors in samples of stationary points obtained from the Newton-Raphson-based geometry optimisation scheme. Systematic differences are found between the properties of eigenvectors corresponding to positive and negative Hessian eigenvalues, and localised character is most pronounced for stationary points with low values of the Hessian index.Comment: 16 pages, 2 figure

Rearrangements and Tunneling Splittings in Small Water Clusters

Recent far-infrared vibration-rotation tunneling (FIR-VRT) experiments pose new challenges to theory because the interpretation and prediction of such spectra requires a detailed understanding of the potential energy surface (PES) away from minima. In particular we need a global description of the PES in terms of a complete reaction graph. Hence all the transition states and associated mechanisms which might give rise to observable tunneling splittings must be characterized. It may be possible to guess the detailed permutations of atoms from the transition state alone, but experience suggests this is unwise. In this contribution a brief overview of the issues involved in treating the large amplitude motions of such systems will be given, with references to more detailed discussions and some specific examples. In particular we will consider the effective molecular symmetry group, the classification of rearrangement mechanisms, the location of minima and transition states and the calculation of reaction pathways. The application of these theories to small water clusters ranging from water dimer to water hexamer will then be considered. More details can be found in recent reviews.Comment: 15 pages, 5 figures. This paper was prepared in August 1997 for the proceedings volume of the NATO-ASI meeting on "Recent Theoretical and Experimental Advances in Hydrogen Bonded Clusters" edited by Sotiris Xantheas, which has so far not appeare

Theoretical study of finite temperature spectroscopy in van der Waals clusters. II Time-dependent absorption spectra

Using approximate partition functions and a master equation approach, we investigate the statistical relaxation toward equilibrium in selected CaAr$_n$ clusters. The Gaussian theory of absorption (previous article) is employed to calculate the average photoabsorption intensity associated with the 4s^2-> 4s^14p^1 transition of calcium as a function of time during relaxation. In CaAr_6 and CaAr_10 simple relaxation is observed with a single time scale. CaAr_13 exhibits much slower dynamics and the relaxation occurs over two distinct time scales. CaAr_37 shows much slower relaxation with multiple transients, reminiscent of glassy behavior due to competition between different low-energy structures. We interpret these results in terms of the underlying potential energy surfaces for these clusters.Comment: 10 pages, 9 figure

Protein Structure Prediction Using Basin-Hopping

Associative memory Hamiltonian structure prediction potentials are not overly rugged, thereby suggesting their landscapes are like those of actual proteins. In the present contribution we show how basin-hopping global optimization can identify low-lying minima for the corresponding mildly frustrated energy landscapes. For small systems the basin-hopping algorithm succeeds in locating both lower minima and conformations closer to the experimental structure than does molecular dynamics with simulated annealing. For large systems the efficiency of basin-hopping decreases for our initial implementation, where the steps consist of random perturbations to the Cartesian coordinates. We implemented umbrella sampling using basin-hopping to further confirm when the global minima are reached. We have also improved the energy surface by employing bioinformatic techniques for reducing the roughness or variance of the energy surface. Finally, the basin-hopping calculations have guided improvements in the excluded volume of the Hamiltonian, producing better structures. These results suggest a novel and transferable optimization scheme for future energy function development