Polarization- and Chaos-Game-Based Fingerprinting of Molecular Targets of Listeria Monocytogenes Vaccine and Fully Virulent Strains.

Two approaches to the synthesis of 2D binary identifiers ("fingerprints") of DNA-associated symbol sequences are considered in this paper. One of these approaches is based on the simulation of polarization-dependent diffraction patterns formed by reading the modeled DNA-associated 2D phase-modulating structures with a coherent light beam. In this case, 2D binarized distributions of close-to-circular extreme polarization states are applied as fingerprints of analyzed nucleotide sequences. The second approach is based on the transformation of the DNA-associated chaos game representation (CGR) maps into finite-dimensional binary matrices. In both cases, the differences between the structures of the analyzed and reference symbol sequences are quantified by calculating the correlation coefficient of the synthesized binary matrices. A comparison of the approaches under consideration is carried out using symbol sequences corresponding to nucleotide sequences of the hly gene from the vaccine and wild-type strains of Listeria monocytogenes as the analyzed objects. These strains differ in terms of the number of substituted nucleotides in relation to the vaccine strain selected as a reference. The results of the performed analysis allow us to conclude that the identification of structural differences in the DNA-associated symbolic sequences is significantly more efficient when using the binary distributions of close-to-circular extreme polarization states. The approach given can be applicable for genetic differentiation immunized from vaccinated animals (DIVA).

Reference-free path length interferometry of random media with the intensity moments analysis.

Stochastic interference of partially coherent light multiple scattered by a random medium is considered. The relationship between the second- and third-order moments of intensity fluctuations in random interference patterns, the coherence function of probe radiation, and the probability density of path differences for the interfering partial waves in the medium are established. The obtained relationships were verified using the statistical analysis of spectrally selected fluorescence radiation emitted by the laser-pumped dye-doped random medium. Rhodamine 6G water solution was applied as the doping agent for the ensembles of densely packed silica grains which were pumped by the CW radiation (532 nm) from the diode-pumped solid state laser. Experimentally observed abrupt decay of the second- and third-order moments of fluorescence intensity fluctuations for the wavelengths ranging from 620 nm to 680 nm is interpreted in terms of amplification of spontaneous emission at large dye concentrations. This paper discusses the new optical probe of random media defined as "the reference-free path length interferometry with the intensity moments analysis".