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A new algorithm is presented for finding the global minimum, and other low-lying minima, of a potential energy surface (PES) of biological molecules. The algorithm synergetically combines three well-known global optimization methods: the diffusion equation method (DEM), which involves smoothing the PES; a simulated annealing (SA) algorithm; and evolutionary… (More)

The harmonic approximation for the potential energy of proteins is known to be inadequate for the calculation of many protein properties. To study the effect of anharmonic terms on protein vibrations, the anharmonic wave functions for the ground state and low-lying excited states of the bovine pancreatic trypsin inhibitor (BPTI) were calculated. The results… (More)

The study of evaporation of water from biological macromolecules is important for the understanding of electrospray mass spectrometry experiments. In electrospray ionization (ESI), electrically charged nanoscale droplets are formed from solutions of, for example, proteins. Then evaporation of the solvent leads to dry protein ions that can be analyzed in the… (More)

Anharmonic vibrational spectroscopy calculations using MP2 and B3LYP computed potential surfaces are carried out for a series of molecules, and frequencies and intensities are compared with those from experiment. The vibrational self-consistent field with second-order perturbation correction (VSCF-PT2) is used in computing the spectra. The test calculations… (More)

The dynamics of Cl͑ 2 P͒ atoms in a solid Ar matrix is studied, with emphasis on electronic energy relaxation of excited states, and on p-orbital reorientation effects. The method used follows Tully's approach for nonadiabatic molecular dynamics simulations, which treats the electronic degrees of freedom quantum-mechanically, and the atomic motions… (More)

Photodissociation experiments were carried out at 193 nm for single HCl molecules which are adsorbed on the surface of large Ar n clusters and small (HCl)m complexes which are embedded in the interior of these clusters. For the surface case the size dependence is measured for the average sizes n=140-1000. No cage exit events are observed in agreement with… (More)

- A. I. Ktylov, R. B. Gerber
- 1999

Photodissociation of ICN by UV excitation in solid and liquid Ar is studied by molecular dynamics simulations. The focus is on the differences between the cage effects on the CN photoproduct in the two phases, and on the excited state isomerization ICN*-t INC* dynamics in the solid matrix. Nonadiabatic transitions are neglected in this first study. The main… (More)

- A T Yinnon, D A Lidar, I Farbman, R B Gerber, P Zeppenfeld, M A Krzyzowski +1 other
- 1997

A theoretical study is made on He scattering from three basic classes of disordered adlayers: (a) Translationally random adsorbates, (b) disordered compact islands and (c) fractal submonolayers. The implications of the results to experimental studies of He scattering from disordered surfaces are discussed, and a combined experimental-theoretical study is… (More)

- A. T. Yinnon, R. B. Gerber, P. Zeppenfeld, G. Comsa
- 1997

An approach based on He scattering is used to develop an atomic-level structural model for an epitaxially grown disordered sub-monolayer of Ag on Pt(111) at 38K. Quantum scattering calculations are used to fit structural models to the measured angular intensity distribution of He atoms scattered from this system. The structure obtained corresponds to… (More)

- D A Hamburger, R B Gerber
- 1995

The information content and properties of the cross section for atom scattering from a defect on a flat surface are investigated. Using the Sudden approximation, a simple expression is obtained that relates the cross section to the underlying atom/defect interaction potential. An approximate inversion formula is given, that determines the shape function of… (More)