L. L. Van Zandt

Resonant and localized breathing modes in terminal regions of the DNA double helix

A Greens function approach is used in constructing a dynamic model of a semi-infinite length of the DNA homopolymer B poly(d) . poly(d). Considerable attention is focused on the hydrogen bond stretching close to the terminus. A melting (or breathing) coordinate (M) is defined as an average over the three linking hydrogen bond stretches in a unit cell. The thermal mean squared amplitude of (M) is enhanced at the chain end compared with the interior. Spectral branches at 69, 80 and 105 cm-1, as well as a local mode at 75 cm-1, are primary contributors to the enhancement. We suggest that this fact can affect the thermal melting of a DNA double helical homopolymer, enhancing the tendency to start from an end (if one is available). We show how certain infinite chain modes with small (M) amplitude can turn into breathing modes near the terminus, and suggest that the same phenomenon may occur near other specific base-pair sequences. There is also considerable attention paid to the low microwave region from approximately 0 to 1.75 cm-1. The thermally activated modes in this frequency region contribute approximately (0.02 A)2 to [M2(0)] at 40 K, approximately two orders of magnitude greater than for [M2(infinity)]. Most important however, is the existence of narrow resonant modes in this frequency region. Particularly pronounced resonances near 0.03 cm-1 and 0.08 cm-1 (approximately 0.9 and 2.4 GHz) amplify M2(0) at the terminus by about for orders of magnitude over the infinite chain value M2(infinity).

Breathing modes and induced resonant melting of the double helix

Abstract Breathing modes are found in double helical DNA which can induce melting by excessive stretching of H-bonds. Energy for such melting may be supplied by splitting of nucleoside triphosphate bonds.

Localized charge carrier transport in pure single crystals of NiO

Abstract Results of Seebeck and resistivity measurements on carefully grown pure single crystals of NiO are shown to be inconsistent with predictions based on itinerant carrier models. A new model for hopping conduction, which contains a dependence of the hopping activation energy on spin ordering, is proposed and used to predict accurately the observed magnitude and temperature dependence of the resistivity in NiO.

Surface conduction versus bulk conduction in pure stoichiometric NiO crystals

Abstract From the measurement of three-probe resistivities, which are much larger than two-probe resistivities, we conclude that annealed, nominally pure and nearly stoichiometric NiO single crystals normally have a low-resistivity surface layer which masks the behaviour of the bulk in most electrical measurements. Bulk resistivities larger than 1016 Ω cm have been measured below 100°C. It is possible that the results of nearly all previous Hall, resistivity and thermoelectric-power measurements made on high-resistivity samples are indicative of the surface rather than the bulk properties of NiO.

Vibrational Local Modes in DNA Polymer

Where the translational symmetry of a long polymer chain is interrupted, characteristic vibrations of the molecule are possible in which only those atoms at or relatively near the defect site partake of the motion. This contrasts with the more common vibrational states in which the motion propagates along the chain as a sound wave. Examples of readily producible local defects include broken bonds, missing atoms or groups, and extra links as are found, e.g., in thymine dimers. For each different defect, the spectrum of local mode frequencies is characteristic of its structure. Hence the local modes give direct information about the nature of the defect and can serve as a diagnostic signature of the polymer chain lesion. We have developed and are using algorithms and fortran code to predict the existence and nature of local modes based on their atomic structures. We have studied examples of different defects and found their eigen-frequencies and eigenvectors. For the simplest case of a broken hydrogen bond in a single A-T unit in a long homopolymer dA.dT chain, we display stereo views of the vibrating unit side-by-side with the undisturbed molecule for the three local modes occurring below 300 cm-1 in frequency.

Theory of the Schwarz‐Hora Effect

The theory of electrons scattered by light in the presence of a thin dielectric slab is developed and applied to some recent experiments of Schwarz and Hora. The experimental results are explained and some new effects predicted.

Displacements of backbone vibrational modes of A-DNA and B-DNA

We display the displacement vectors or eigenvectors of calculations of the A- and B-DNA backbones. These calculations are based on a refinement scheme that simultaneously fit several backbone modes of A-DNA, B-DNA, and A-RNA. We discuss the role of symmetry operations in mode calculations and the relevance of these displacement vectors to the interpretation of linear dichroism measurements performed on the A- and B-DNA helix.

Theory of the anomalous resonant absorption of DNA at microwave frequencies.

Aqueous solutions of oligopolymer DNA have been observed by Edwards, Davis, Swicord & Saffer to show structured absorption of microwave energy in the region of several gigahertz characteristic of an ordered series of compressional normal mode vibrations propagating on the polymer chain. Hydrodynamic coupling of such vibrations to the surrounding solvent would preclude the existence of sharp resonances. The inclusion of electromagnetic interactions with surrounding counter ions yields a richer space of possibilities for complex behavior of the combined system. A well defined resonant absorption peak appears when the molecular motion and the nearby solvent motion are even slightly decoupled. The microwave electric fields in the vicinity of the molecule provide a mechanism for such a decoupling not present for the case of electrically neutral solvent.

Atomic motions and high frequency cutoff in biological macromolecules

Abstract We point out that the structure of a class of biological macromolecules permits a reduction of the complete atomic dynamical description into motions of subunits consisting of mutually rigidly bound atomic subgroups with relatively weak, flexible joints connecting them. As an example performing an analysis of the DNA normal mode vibrations, we find a distinct bifurcation of the phonon frequency spectrum into two regions. Below a sharp cutoff at about 380 cm −1 the vibrations consist nearly entirely of simple translations and rotations of the subgroups, and are thus potentially capable of metabolic involvement. Above the cutoff, a subunit as a whole is essentially stationary, showing internal vibration only.

INTENSITY RELATIONSHIPS IN THE SCHWARZ‐HORA EFFECT

The dependence of the intensity of the reemitted radiation in the Schwarz‐Hora effect as a function of electron beam intensity, coherence time, energy spread, and beam length is calculated. Sufficient information is given to provide for experimental confirmation or rejection of the hypothesis that radiation occurs by virtual excitation of and longitudinal dipole radiation from target ions. Two terms, one quadratic and one linear in the beam current, are found.