Oscillator Polarizabilities Research Articles

Optical Properties of DNA in Aqueous Solution

In the study of DNA electric birefringence, it is usual to use theories that consider that molecules in solution are small in relation to the light wavelength. In this work, we study the DNA electric birefringence using a broken-rod macroion (BRM) model composed of two cylindrical arms which does not restrict the size of the molecules. To achieve this, we include the inhomogeneity effect of the light electric field through the molecule and the interaction between its different parts. To analyze the interaction between a molecule and the incident beam of light, we apply the discrete dipole approximation (DDA), according to which each molecule is described as a finite array of electronic coupled oscillators. The electric birefringence is calculated from the oscillator polarizability. This is obtained from experimental data of electric birefringence saturation and from the increment of the solution refraction index in relation to that of the solvent. Furthermore, the oscillator polarizability is also estimated from DNA absorption spectrum using the Kronig-Kramers relations. This allows us to analyze the contributions of the different absorption bands of DNA to the electric birefringence. We analyze the influence of the inhomogeneity of the light electric field and of the intramolecular interactions in the characterization of DNA optical properties using electric birefringence measurements.

Nucleic acid vibrational circular dichroism, absorption, and linear dichroism spectra. I. A DeVoe theory approach

Infrared (IR) vibrational circular dichroism (VCD), absorption, and linear dichroism (LD) spectra of four homopolyribonucleotides, poly(rA), poly(rG), poly(rC), and poly(rU), have been calculated, in the 1750-1550 cm-1 spectral region, using the DeVoe polarizability theory. A newly derived algorithm, which approximates the Hilbert transform of imaginaries to reals, was used in the calculations to obtain real parts of oscillator polarizabilities associated with each normal mode. The calculated spectra of the polynucleotides were compared with previously measured solution spectra. The good agreement between calculated and measured polynucleotide spectra indicates, for the first time, that the DeVoe theory is a useful means of calculating the VCD and IR absorption spectra of polynucleotides. For the first time, calculated DeVoe theory VCD and IR absorption spectra of oriented polynucleotides are presented. The calculated VCD spectra for the oriented polynucleotides are used to predict the spectra for such measurements made in the future. The calculated IR spectra for the oriented polynucleotides are useful in interpreting the linear dichroism of the polynucleotides.

Erratum: Dynamical interaction of an atomic oscillator with squeezed radiation inside a cavity

The dynamical interaction of an oscillator with squeezed radiation inside a cavity is considered. Exact solution of the dynamical equation is presented using the Wigner function for the combined system of the atomic oscillator and the squeezed radiation. This solution enables us to study (i) relaxation of the oscillator for arbitrary bandwidth of the squeezed radiation, and (ii) effects of squeezed radiation on vacuum-field Rabi splittings. Explicit results for fluctuation spectra and the oscillator polarizabilities are given. New resonances in the fluctuation spectra appear as the radiation in the cavity becomes more and more squeezed. Strong narrowing of the vacuum-field Rabi splitting due to squeezed radiation is predicted. Very large enhancement of the oscillator polarizability at Rabi side peaks is also predicted. The modification of the cavity output due to the atomic oscillator is discussed.

Dynamical interaction of an atomic oscillator with squeezed radiation inside a cavity.

The dynamical interaction of an oscillator with squeezed radiation inside a cavity is considered. Exact solution of the dynamical equation is presented using the Wigner function for the combined system of the atomic oscillator and the squeezed radiation. This solution enables us to study (i) relaxation of the oscillator for arbitrary bandwidth of the squeezed radiation, and (ii) effects of squeezed radiation on vacuum-field Rabi splittings. Explicit results for fluctuation spectra and the oscillator polarizabilities are given. New resonances in the fluctuation spectra appear as the radiation in the cavity becomes more and more squeezed. Strong narrowing of the vacuum-field Rabi splitting due to squeezed radiation is predicted. Very large enhancement of the oscillator polarizability at Rabi side peaks is also predicted. The modification of the cavity output due to the atomic oscillator is discussed.

Circular dichroism calculations for double‐stranded polynucleotides of repeating sequence

AbstractOptical property calculations are presented for poly(A·U), poly[(A‐U)·(A‐U)], poly(G·C), and poly[(G‐C)·(G‐C)] in RNA, B‐DNA, and C‐DNA conformations. An all‐order classical coupled oscillator polarizability theory was used, and an effective dielectric constant of 2 was assumed. The calculated CD spectra were found to be sensitive to both geometry and sequence. Agreement with the measured CD spectra of poly(A·U), poly(G·C), and poly(dG·dC) is very good. Calculations for other sequences and geometries are less satisfactory and are particularly poor for poly[(G‐C)·(G‐C)] in RNA geometry and poly(A·T) in B‐DNA geometry. Attempts to improve agreement with measured spectra by varying monomer properties have been only partially successful for these calculations, but they illustrate the types of changes that may prove to be necessary. Calculations using other published X‐ray coordinates for certain deoxypolynucleotides of simple sequence, some of which are quite different from B‐DNA coordinates, did not result in better agreement with measured spectra. Finally, the dependence of the calculated CD on chain length is examined. Results show that non‐nearest neighbor interactions can be important when runs of 3 or more identical base pairs appear in a given sequence.

Polynucleotide circular dichroism calculations: use of an all-order classical coupled oscillator polarizability theory.

AbstractAn all‐order classical coupled oscillator theory in which monomer band shapes are explicity taken into account is applied to the calculations of polynucleotide circular dichroism. Calculations are shown for ApA and oligoadenylic acid of varying chain lengths, in both RNA and B‐DNA geometry, and the advantages of this theory are assessed. By introducing an effective dielectric constant, good agreement with measured spectra is obtained. Variations in monomer parameters are tested in an attempt to eliminate remaining discrepancies between calculated and measured spectra.