Oakley H. Crawford

Electron affinities of polar molecules

All molecules having dipole moments greater than 1.625 D (0.639 ea0) have positive electron affinities in the Born–Oppenheimer approximation (i.e., when the nuclei are stationary). However, when nuclear motion is treated exactly, the above sufficient condition for binding an extra electron is modified. We have determined the magnitudes of Born–Oppenheimer electron affinities which are required in order to insure that the negative ions of polar molecules (μ≳1.625 D) are still stable when the nuclei are free to move.

Radiation from oscillating dipoles embedded in a layered system

Maxwell’s equations are solved for the radiation due to a source consisting of an oscillating point dipole located in a layered system. Solutions are developed first for the related problem of the fields generated in the system by a distant dipole source, and the problem of interest is then solved by application of the Lorentz reciprocity theorem. The effects of extremely thin layers are considered in detail. Some of the results are illustrated by calculations of the emission from dipoles located in, or near, a film covering a plane‐bounded silver metal substrate. It is found that the surface selection rule for absorption, emission, or Raman scattering is not valid for molecules contained in this film.

Application of PROSPECT in CASP4: Characterizing protein structures with new folds

In the Fourth Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP4), we predicted all 43 targets using our threading application PROSPECT. PROSPECT guarantees to find an optimal alignment between a protein sequence and a structural fold for a general energy function with pairwise contact potential. For each prediction, it gives a reliability assessment based on a neural network approach. In addition, PROSPECT has been added to the Genomic Integrated Supercomputing Toolkit (GIST) and is deployed on terascale computing resources. Structural predictions in CASP4 included three categories, that is comparative modeling, fold recognition, and prediction for structures with new folds. In the fold recognition category, PROSPECT correctly identified 8 of a total of 22 and finished the sixth in the total scores among 127 assessed groups. In the “new fold” category, it found important structural features for most targets, and its overall performance is among the best of all prediction methods. Our CASP4 performance demonstrates that PROSPECT is a powerful tool to quickly characterize structures with new folds, and it may provide useful structural restraints for ab initio prediction methods. Proteins 2001;Suppl 5:140–148.

Resonant-coherent excitation of channeled ions.

A first-principles calculation of the resonant-coherent excitation of planar-channeled hydrogenic ions is presented. The interplay between coherent interaction with the periodic crystal lattice potential and inelastic electron-electron collisions is shown to be crucial in both intraionic transitions and electron loss from the ion. The magnitude of resonant-coherent excitation is predicted to oscillate with the amplitude of the oscillations of the ion trajectory. Good agreement is found with experiments.

A computational method for NMR-constrained protein threading.

Protein threading provides an effective method for fold recognition and backbone structure prediction. But its application is currently limited due to its level of prediction accuracy and scope of applicability. One way to significantly improve its usefulness is through the incorporation of underconstrained (or partial) NMR data. It is well known that the NMR method for protein structure determination applies only to small proteins and that its effectiveness decreases rapidly as the protein mass increases beyond about 30 kD. We present, in this paper, a computational framework for applying underconstrained NMR data (that alone are insufficient for structure determination) as constraints in protein threading and also in all-atom model construction. In this study, we consider both secondary structure assignments from chemical shifts and NOE distance restraints. Our results have shown that both secondary structure assignments and a small number of long-range NOEs can significantly improve the threading quality in both fold recognition and threading-alignment accuracy, and can possibly extend threadings scope of applicability from homologs to analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a great amount of structural information, equivalent to that provided by many NMR data; and hence can help reduce the number of NMR data typically required for an accurate structure determination. This new technique can potentially accelerate current NMR structure determination processes and possibly expand NMRs capability to larger proteins.

Resonant coherent excitation of O7+, F8+, and C5+ in the 〈100〉 axial channel in gold

Abstract Previous studies have shown that when an ion moves in an axial channel with a velocity, v , such that hKv/ d = ΔE ij , transitions are coherently induced. K is an integer, d is the longitudinal atomic spacing in the channel, and ΔE ij , is an ionic transition energy. Since the ionization cross section for an excited state is much greater than that for the ground state, the effect for 1s → 2p transitions is observed as a minimum in the surviving, one-electron charge-state fraction as the velocity is scanned through a resonance. Resonant coherent excitation (RCE) for the following one-electron ions, moving in the 〈100〉 axial channel in gold, are reported here: O 7+ , K = 2, 85.9 MeV; F 8+ , K = 2, 163.6 MeV; and C 5+ , K = 1, 81.6 MeV. The K = 2 resonances have a single narrow dip superimposed on a broad minimum, in contrast to the doublet minimum previously observed for lower Z ions. Comparison is made to predictions based on the positions of the Stark components deduced from the rainbow scattering theory. A similar comparison is made for the stronger and broader K = 1 resonance of C 5+ .

The non-linear wake in a hydrodynamical model

Abstract A hydrodynamical model is used to calculate the non-linear wake and stopping power of a moving charge, Z, in an electron gas for intermediate and high velocities (v ≥ 1.5vB). In this work, the non-linear hydrodynamic equations for the induced density in the electron gas are expanded in a perturbation series in powers of the nuclear charge, Z and solved to second order in Z. Results for the induced second-order potential and the Z3-stopping power are given for an electron gas simulatingaluminum.

Resonant coherent excitation in planar channeling

Abstract Planar channeled ions (velocity = ν ) experience a coherent periodic perturbation of frequency ν = υ / d , where d is the distance along the ion path between planes orthogonal to the channeling plane. The velocity at which a given RCE harmonic, ( l , k ), occurs is tuneable with θ. This additional degree of freedom allows the measurement of (1) velocity dependence of the static and dynamic ( (wake) field on the ion, and (2) coincidences in velocity for more than one resonance. Using the enhanced ionization technique, we report on RCE for N 5+ and N 6+ in (100) planar channeling in Au.

Protein structure determination using protein threading and sparse NMR data (extended abstract)

It is well known that the NMR method for protein structure determination applies to small proteins and that its effectiveness decreases very rapidly as the molecular weight increases beyond about 30 kD. We have recently developed a method for protein structure determination that can fully utilize partial NMR data as calculation constraints. The core of the method is a threading algorithm that guarantees to find a globally optimal alignment between a query sequence and a template structure, under distance constraints specified by NMR/NOE data. Our preliminary tests have demonstrated that a small number of NMR/NOE distance restraints can significantly improve threading performance in both fold recognition and threading-alignment accuracy, and can possibly extend threadings scope of applicability from structural homologs to structural analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a significant amount of structural information, equivalent to that provided by the NMR method with many NMR/NOE restraints; and hence can greatly reduce the amount of NMR data typically required for accurate structure determination. Our prelimenary study suggest that a small number of NOE restraints may suffice to determine adequately the all-atom structure when those restraints are incorporated in a procedure combining threading, modeling of loops and sidechains, and molecular dynamics simulation. Potentially, this new technique can expand NMRs capability to larger proteins.

Nonlinear effects in interactions of swift ions with solids

When a charged particle penetrates a solid, the response of the electrons is nonlinear in the charge of the projectile, except in the high-velocity limit. This response is of interest in connection with the wake of induced electron density and its various consequences, including energy loss of the particle. In this work, several theoretical approaches to the nonlinear wake of swift particles in an electron gas are compared. These include a hydrodynamical model, a many-body perturbation-theory formulation using a random-phase approximation, the time-dependent Hartree approximation, and two methods within time-dependent density functional theory.