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L L Van Zandt

Publications and source records attributed to L L Van Zandt.

At least 19 recordsLinked to original sources
PubMed1994

Local modes in a DNA polymer with hydrogen bond defect.

Vibrations of a homopolymer DNA with localized hydrogen bond defects have been examined using the recently developed decaying mode theory for long-chain polymers with local structural defects. For a poly(dA)-poly(dT) homopolymer having perturbed hydrogen bonds in one base pair, a localized mode at 63.2 cm-1 has been found. This mode has a very nearly pure H-bond stretch or "breathing" character, although the backbones do not separate. This agrees in frequency with a similar result found by other authors using a different approach. We search the full microwave frequency range for other local modes for several models of weakened H bonds. Besides the local mode with breathing characteristics, local modes with other characteristic motions were found, but only for asymmetrically perturbed bonds. We find in general that local modes are not very robust, requiring quite specific, narrow ranges in parameter space. They are also not abundant, there being only three in our most prolific model.

Biophysical Phenomena↗
PubMed1994

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.

Algorithms↗
PubMed1992

Plasmon interpretation of 25 cm-1 mode in DNA.

An extension of the effective field approach for the normal mode dynamics of dissolved DNA polymers has been applied to study the vibrational modes of DNA-hydration sheath-counterion system, to include the effect of site bound counterions on the system dynamics. An alternative interpretation has been suggested for a 25 cm-1 mode recently observed in DNA samples and interpreted earlier as an interhelical mode. Analysing the eigenvectors this mode is found to possess a large electric dipole moment with longitudinal collective oscillations of the system. These characteristics identify this mode as a collective plasmon mode. Possible physical reasons for the existence of this character have been presented.

Computer Simulation↗
PubMed1991

Low-frequency parameterization of hydrogen bonding.

We review the model of the hydrogen bond developed by Lippincott and Schroeder and discuss the frequency range in which it is valid, specifically in the optical and near infrared range. We then show why and how to modify the Lippincott and Schroeder formulate to apply to the far infrared and lower ranges. The contrasts between the old and modified systems, particularly with respect to the effective force constants are worked out and plotted for an example.

DNA↗
PubMed1990

Modeling hydrogen bonds in three dimensions.

The effective potential between two hydrogen bonded atoms is calculated on the basis of the Lippencott-Schroeder bent bond model, taken to be a typical model interaction. We differ from other calculations in that the minimum energy configuration for the proton is treated adiabatically, its position being recomputed at each value of the larger atoms separation. We find the typical hard core to have been a consequence of an artificial restriction of the proton to a fixed angle with the larger atom axis, basically a one-dimensional assumption. Free to move in three dimensions, the proton is squeezed off the axis as the separation narrows, and the hard core feature is gone. Depending on the degree of bond bending, the anharmonicity of the bond may be diminished, eliminated, or even reversed.

Computer Simulation↗
PubMed1989

Phonon interpretation of inelastic neutron scattering in DNA crystals.

The calculated spectrum of longitudinal compressional waves on DNA polymer chains is shown to be in excellent agreement with recently performed inelastic neutron scattering measurements in hydrated, oriented DNA crystals. This opens up a previously unexplored frequency regime of DNA science and establishes the validity of the phonon extended wave description of DNA elementary excitations in this region.

DNA↗
PubMed1989

Temperature and concentration behavior of anomalous microwave resonances in DNA.

We have calculated the expected absorption of microwave radiation in the gigaHertz frequency range by fixed-length DNA polymer molecules dissolved in saline solution. While the effects of counterions and solvent dynamics have been accounted for in detail, the features of the absorption are completely dominated by the interaction between the charged polymer and the so-called first hydration layer, that is, the nearest layer of solvent water molecules not actually bonded to the polymer. The relevant parameters of the interaction are the strength of the water-to-polymer coupling and the average persistence time of the individual water-to-polymer bonds. These are presumably hydrogen bonds to the oxygen atoms of the backbone phosphate structure. Using a given parameterization we can obtain the structured absorption corresponding to compressional wave phonon excitations on the polymer, "organ pipe" modes, such as have been claimed to be seen by Edwards, Davis, Swicord, and Saffer. While further studies have not confirmed these resonances, at some frequency and hydration these modes must become visible because of the high relaxation time measured by Lindsay, the existence of the resonances in relatively dry fibers and films of DNA, and the existence of underdamped modes in the ir spectrum of DNA in solution. We have examined the effects of varying salt concentration and the system temperature.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA↗
PubMed1987

Why structured water causes sharp absorption by DNA at microwave frequencies.

Aqueous solutions of oligopolymer DNA have been observed by G.S. Edwards, C.C. Davis, M.L. Swicord and J.D. Saffer, Phys. Rev. Lett. 53, 1284 (1984) 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. Although hydrodynamic coupling of such vibrations to the surrounding solvent would preclude the existence of sharp resonances, the molecular nature of the solvent in the near neighborhood of the polymer and- paradoxically- the strong water/polymer interactions provide a means for effectively decoupling the polymer motion from the dissipation of the liquid. Recent measurements of DNA/water relaxation times allow estimating numerical values in a parameterization of the decoupling effect. The resulting predicted frequency dependence explains many of the smaller features of Edwards' experiment as well as the overall anomaly. A simple model gives a surprisingly complete account of the features of the data using only values determined from other experiments.

DNA↗
PubMed1986

A theorem on Boussinesq solitons or why soliton formation sharpens resonant absorption and why this has nothing to do with real polymers.

Soliton formation has been proposed as an explanation for anomalously sharp resonances observed in DNA microwave absorption. We give an elementary, physical explanation of why line narrowing occurs for Boussinesq solitons. We consider real atoms bound by realistic chemical bonds and show that even under the assumption of the most favorable possible conditions, the soliton narrowing mechanism is a maximum correction of only a few percent. At each step of the argument, the simple calculations we show are either exact-in the sense of following the Boussinesq equation - or err on the side of emphasizing the soliton lifetime enhancement. Thus our results serve as an upper bound to any enhancement effects.

DNA↗
PubMed1986

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.

DNA↗
PubMed1981

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

A Green's 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).

DNA↗
PubMed1979

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.

DNA↗