Lidar, D. A. ; Thirumalai, D. ; Elber, R. ; Gerber, R. B. Fractal analysis of protein potential energy landscapes.
PHYSICAL REVIEW E 1999,
59, 2231-2243.
AbstractThe fractal properties of the total potential energy V as a function of time t are studied for a number of systems, including realistic models of proteins (pancreatic polypeptide, bovine pancreatic trypsine inhibitor, and myoglobin). The fractal dimension of-V(t), characterized by the exponent gamma, is almost independent of temperature, and increases with time, more slowly the larger the protein. Perhaps the most striking observation of this study is the apparent universality of the fractal dimension, which depends only weakly on the type of molecular system. We explain this behavior by assuming that fractality is caused by a self-generated dynamical noise, a consequence of intermode coupling due to anharmonicity. Global topological features of the potential energy landscape are found to have little effect on the observed fractal behavior. [S1063-651X(99)11402-8].
Wilkie, J. ; Ratner, M. A. ; Gerber, R. B. Jastrow corrected time-dependent self-consistent field approximation.
JOURNAL OF CHEMICAL PHYSICS 1999,
110, 7610-7621.
AbstractAn improved approximation to the time-dependent Schrodinger equation is developed by correcting the time-dependent self-consistent field ansatz with a Jastrow prefactor defined via a set of variationally determined time-dependent parameters and a linearly independent set of prespecified spatial functions. The method is applicable in any number of dimensions, conserves norm and energy, is without parametric singularities, possesses an internal estimate of the accuracy, and has computational costs that scale algebraically with the number of degrees of freedom. The new formalism is applied to a two-dimensional double well potential to demonstrate the improved accuracy of the method. An extension of the method to electronically nonadiabatic problems is also presented. (C) 1999 American Institute of Physics. [S0021-9606(99)01616-5].
Chaban, G. M. ; Jung, J. O. ; Gerber, R. B. Ab initio calculation of anharmonic vibrational states of polyatomic systems: Electronic structure combined with vibrational self-consistent field.
JOURNAL OF CHEMICAL PHYSICS 1999,
111, 1823-1829.
AbstractAn algorithm for first-principles calculation of vibrational spectroscopy of polyatomic molecules is proposed, which combines electronic ab initio codes with the vibrational self-consistent field (VSCF) method, and with a perturbation-theoretic extension of VSCF. The integrated method directly uses points on the potential energy surface, computed from the electronic ab initio code, in the VSCF part. No fitting of an analytic potential function is involved. A key element in the approach is the approximation that only interactions between pairs of normal modes are important, while interactions of triples or more can be neglected. This assumption was found to hold well in applications. The new algorithm was applied to the fundamental vibrational excitations of H(2)O, Cl(-)(H(2)O), and (H(2)O)(2), using the Moller-Plesset method for the electronic structure. The vibrational frequencies found are in very good accord with experiments. Estimates suggest that this electronic ab initio/VSCF approach should be feasible, with reasonable computational resources, for all-mode calculations of vibrational energies and wave functions for systems of up to 10-15 atoms. The new method can be also very useful for testing the accuracy of electronic structure codes by comparing with experimental vibrational spectroscopy. (C) 1999 American Institute of Physics. [S0021-9606(99)01928-5].
Jungwirth, P. ; Roeselova, M. ; Gerber, R. B. Optimal coordinates for separable approximations in quantum dynamics of polyatomic systems: Coordinate choice criteria and error estimates.
JOURNAL OF CHEMICAL PHYSICS 1999,
110, 9833-9841.
AbstractA considerable effort has been recently directed toward developing separable (mean-field) approximations for quantum molecular dynamics, such as the time-dependent self-consistent field (TDSCF) or the classical separable potential (CSP) methods. Unlike numerically exact solutions of the time-dependent Schrodinger equation, the accuracy of separable quantum dynamical simulations crucially depends on the choice of the coordinate frame. Since the approximate methods replace exact interactions between individual degrees of freedom by mean-field couplings, the goal is to work with coordinates which separate modes as well as possible. Unfortunately, for a larger system no practical way to optimize coordinates for mean-field quantum dynamics exists. Here, we suggest a simple and practical method for estimating the error of separable simulations, which allows us to select from a given set the optimal coordinate frame, or to identify modes, the couplings between which have to be treated more accurately. In the spirit of the CSP method, the time-dependent error estimate is based on differences between the exact and mean-field Hamiltonians along a swarm of classical trajectories. This makes it possible to very simply determine optimal coordinates for CSP or TDSCF propagation before actually performing any quantum simulation. The present methodology is applied to realistic and experimentally relevant systems, namely to the ultrafast relaxation following electron photodetachment in I- Ar-n (n=2 and 12) and Cl-H2O clusters. It is shown that the accuracy of separable quantum methods is strongly system and coordinate dependent. Comparison with numerically exact results shows that the suggested error measure correlates well with the actual error of the approximate quantum propagation, the accuracy of which can be consequently improved significantly, practically without additional computational effort. Finally, the feasibility of the proposed method for simulations of large polyatomic systems is demonstrated. (C) 1999 American Institute of Physics. [S0021-9606(99)00820-X].
Niv, M. Y. ; Krylov, A. I. ; Gerber, R. B. ; Buck, U. Photodissociation of HCl adsorbed on the surface of an Ar-12 cluster: Nonadiabatic molecular dynamics simulations.
JOURNAL OF CHEMICAL PHYSICS 1999,
110, 11047-11053.
AbstractThe photodissociation of HCl adsorbed on the surface of an Ar-12 cluster is studied by semiclassical molecular dynamics simulations, using a surface-hopping approach for the nonadiabatic transitions. The DIM method is used to construct the 12 potential energy surfaces that are involved, and the nonadiabatic couplings. The results are compared with previous studies on HCl embedded inside Ar clusters and on the triatomic Ar-HCl cluster. The main findings are the following: (1) There is a yield of about 1% for recombination onto the ground electronic state of HCl, roughly the same as for HCl embedded inside Ar-12. (2) Photodissociation lifetimes much longer than for Ar-HCl are found. (3) The kinetic energy distribution of the H atom shows large energy transfer to the cluster, greater than in the case of HCl in the embedded geometry in (Ar)(12)HCl. (4) An interesting mechanism leads to the formation of some fraction of very ``hot'' Cl atoms. (5) About 10% of the Cl is left trapped in (Ar)(m)Cl clusters. (6) The branching ratio P-1/2:P-3/2 for the Cl atoms that leave the cluster shows electronic cooling compared to the isolated HCl molecule case. The results throw light on the role of local geometry in photodissociation/recombination processes, and in particular on the mechanisms pertinent in the case of surface-adsorbed species. The nature of the results, showing strong cage effects at the surface geometries is to a large extent a consequence of the encapsulation of the H atom, obtained for the structure of the (Ar)(12) HCl cluster. (C) 1999 American Institute of Physics. [S0021-9606(99)70222-9].
Brudermann, J. ; Buck, U. ; Fredj, E. ; Gerber, R. B. ; Ratner, M. A. Vibrational excitation in He+(H2O)(11) collisions: Quantum calculations and experiment.
JOURNAL OF CHEMICAL PHYSICS 1999,
111, 10069-10076.
AbstractHelium atoms are scattered from a beam of water clusters with mean size (n) over bar = 10 in an angular and velocity resolved collision experiment. The measured peaks are identified as elastic scattering, rotationally inelastic scattering of monomers, and vibrational excitation of the clusters. To interpret the latter processes quantum calculations are performed for He+(H2O)(11) collisions using the TDSCF approximation which includes the anharmonic force field of the water clusters and energy transfer between the modes. By comparison of the calculated and experimental results, the most probable excitations correspond to energy transfer for around 7 meV and, with smaller intensities, up to 20 meV. The excitations correspond to shearing modes of the outer rings and the middle ring of the highly nonrigid cluster against each other. (C) 1999 American Institute of Physics. [S0021-9606(99)01546-9].