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Biomedical subjects

S N Volkov

Publications and source records attributed to S N Volkov.

15 recordsLinked to original sources

Nonlinear optical interactions of wave packets in photonic crystals: Hamiltonian dynamics of effective fields.

We develop an effective-field formalism that is suitable for describing nonlinear interactions of multiple wave packets in photonic crystals of arbitrary dimensionality. The theory is valid for "high-contrast" variations of the refractive index in the photonic crystal, provided dispersion and absorption effects can be neglected; it is based on a Hamiltonian formulation of the underlying Maxwell equations. We show that the dynamical equations for the effective fields are similar to those commonly used in nonlinear optics of homogeneous media, but with coefficients determined from the photonic band structure. We can introduce an effective energy density and an effective Poynting vector, expressed in terms of the effective fields, that satisfy a continuity equation. We illustrate our approach with a solution of the problem of degenerate optical parametric amplification in the undepleted pump approximation, and by considering the linear electro-optic effect as a quadratic nonlinear optical process.

Journal Article↗

Exciton coherence and electron energy loss spectroscopy of conjugated molecules.

Signatures of the exciton coherence size, which controls the nonlinear optical response and luminescence of conjugated systems, in the electronic dynamic structure factor S(q,omega) are calculated. We find that for small molecules the momentum dependence of the lowest exciton resonance is purely geometric, reflecting the molecular size rather than a universal exciton size, as suggested recently. For long chains the q dependence is determined by the interplay of the exciton size and the bond-alternation length scales.

Journal Article↗

Theory of low-frequency vibrations in DNA macromolecules.

To describe low-frequency dynamics of DNA macromolecules a model is developed taking into account the hydrogen bond stretching in base pairs, the backbone flexibility and intranucleoside mobility. For double-stranded DNA the normal vibrations are found and the structure of low-frequency spectrum is determined. The agreement between theory and Raman spectroscopy data for B-DNA is demonstrated. Conformational dependences of vibration spectrum during the B----A and helix----coil DNA transitions are studied. The contribution coming from low-frequency mobility to the nucleic-protein recognition processes is discussed.

DNA↗

Conformational transition dynamics and the mechanism of long-range effects in DNA.

A two-component model is proposed to describe the conformational dynamics of DNA macromolecule. A hypothesis on the mechanism of long-distance action transfer in DNA by local conformational transitions is presented. The conditions under which local transitions of B-A type are transmitted along a DNA chain are established.

Chemical Phenomena↗

[Theoretical study of the hypochromic effect in polynucleotides].

The first UV-absorption band hypochromicity of poly(dA)-poly(dT), poly(dG)-poly(dC), poly(dA), poly(dT), poly(dG), poly(dC), is calculated with the help of the perturbation theory. The wave functions of the bases are computed by Pariser--Parr--Pople's method taking into account all the singly excited configurations. The results obtained show a good correlation between the theoretical and experimental values of hypochromicity. A considerable influence of the vaccum electron transitions on the hypochromicity of polynucleotides is revealed. The origin of the hypochromic effect in the double-stranded polynucleotides is investigated. It is shown that intrastrand interactions between the bases make the main contribution to hypochromicity (60-76%), while the contribution of the Watson-Crick pairs is small (2-12%). The essential part of hypochromicity (22-28%) is due to the interstrand interactions between the bases which are not coupled by hydrogen bonds. The discussion of the experimental data shows that the present theoretical investigation could serve as a basis for correct treatment of experimental results.

Binding Sites↗

[Conformational stimulation in DNA type macromolecules].

A concept for the description of structural elements mobility of a DNA-type macromolecule is suggested. The possible existence of conformational excitations weakly sensitive to a macromolecule heterogeneity in DNA is shown. The dependence of the macromolecule low-energy excitation spectrum on the nucleotide content is found and its sensitivity to thermal action is predicted.

DNA↗

[Conformation oscillations of DNA].

A conformational mobility model is proposed to describe the low-frequency DNA structure dynamics. The transverse oscillations of structure elements in a double-stranded chain are studied. The frequency of DNA long-wave conformational oscillations are estimated and the theory is shown to agree with experiment. DNA low-frequency Raman spectra are interpreted.

DNA↗

[Mechanism of hydrogen exchange in DNA].

The hydrogen exchange mechanism of DNA bases imino- and amino protons is explained according to a suggested exchangeable state model. This state can be formed as a result of significant structural fluctuations which are not complete base pair openings. The exchangeable state model represents the hydrogen-bonded complex of two nucleotide bases and one water molecule made up dynamically. Quantum-mechanical calculations for the values of energy as the function of H-bond proton positions in the complex were carried out and the two-proton positions in the complex were carried out and the two-proton transfer is shown to be possible. The suggested model allows to give a noncontradictary interpretation of the hydrogen exchange data in double-helical polynucleotides.

DNA↗

[Effect of double helix conformation transitions on DNA hypochromism].

The sensitivity of the first UV-absorption band hypochromism of DNA to changes in double helix form has been investigated theoretically. The hypochromism of DNA is studied within the perturbation theory and the nearest neighbour approximation. The heterogeneity of DNA is taken into account by introducing the nearest neighbour frequencies. The electronic characteristics of monomers (nucleotide bases) are calculated by the quantum mechanical PPP CI method. The hypochromism of A-, B-, C-, D- and T-forms of DNA is calculated. A slight dependence of the hypochromism on double helix conformation is obtained. This result is in agreement with experimental data. The reasons for the observed non-sensitivity of the DNA UV-absorption spectrum to conformational transitions within a two-stranded structure are explained. It is shown that the theory leads to an agreement with experiments because a large number of electronic transitions in nucleotide bases and the heterogeneity of DNA are taken into account.

Base Sequence↗