William L. Nichols

Rotational energy distributions for homonuclear diatomic beams scattered from solid surfaces: A hard-cube model

Rotational energy distributions of diatomic molecular beams scattered from solid surfaces are calculated with a hard‐cube model previously used to compute scattering patterns. The extent of energy transfer between rotational and translational degrees of freedom in a scattering system is examined. Both rotationally cold and hot incident beams are considered. The calculations are all numerical.

CORRELATIONS BETWEEN ANGULAR MOMENTUM ORIENTATION AND EXIT VELOCITY IN GAS-SURFACE SCATTERING : A PROBE OF THE DEPENDENCE OF COLLISION DYNAMICS ON THE POSITION OF IMPACT

The scattering of rotationally cold N2 from Ag(111) results in angular momentum alignment and orientation of the scattered molecules; measurement of the angular momentum polarization as a function of exit angle, final J state, and exit translation energy provides direct information on the dynamics of the collisions. In this paper, the orientation of the angular momentum vector of the scattered N2 molecules, A{1}1−(J) has been measured for slow, medium, and fast groups of molecules in single rotational states at fixed exit angles. With normal incidence scattering (θi=0°) and off‐normal detection, for a given final J state, the ‘‘slow’’ molecules have a higher probability of tumbling backwards (‘‘back spin’’) than the ‘‘fast’’ molecules. Conversely, for glancing incidence scattering (θi=30°) with quasi‐specular detection, the opposite trend is observed: the slow molecules have a higher probability of tumbling forwards (‘‘top spin’’) than the fast molecules. These experiments were simulated and analyzed usin...

Protein structural alignment for detection of maximally conserved regions

An algorithm for comparison of homologous protein structures and for study of conformational changes in proteins, has been developed. The method is based on identification of pieces of the two molecules that have similar shapes, as determined by the local conformation of the polypeptide chain. Pieces that superpose within a specified tolerance are assembled into domains based on similar transformations for superposition. The result is sets of pieces that represent conserved structural elements and conserved spatial relationships between structural elements within the proteins being compared. A similarity criterion based on maximum distance rather than on root mean square deviation reduces bias by outliers. The utility of the method is demonstrated by using examples from the protein kinase family.

One-phonon scattering of He from the LiF(001)〈100〉 Rayleigh mode

Abstract The one-phonon cross-section from the Rayleigh mode calculated with a point-ion lattice dynamical theory accounts for all salient inelastic scattering intensities seen in He-LiF(001)〈100〉 measurements published by Brusdeylins, Doak and Toennies [J. Chem. Phys. 75 (1981) 1784]. Scattering cross-sections are found by the Rayleigh method, wherein the repulsive part of the scattering potential is approximated as a hard-wall. The solution is in the form of a perturbation expansion in the elastic corrugation and phonon motion of the surface. For each phonon order the solution is infinite in the elastic corrugation. Resonant intensity enhancement occurs either through selective desorption or selective adsorption, both of which have amplitudes which explicitly appear in the perturbation expansion and can be separately calculated. Intensity enhancement also occurs by kinematical focusing. We find a new type of kinematical focusing in addition to that discussed by Benedek [Phys. Rev. Letters 35 (1975) 234].