Wide-field Mueller matrix polarimetry for spectral characterization of basic biological tissues: Muscle, fat, connective tissue, and skin.

This study investigates the polarimetric properties of skin, skeletal muscle, connective tissue, and fat using Mueller matrix imaging. It aims to compare the polarimetric characteristics of these tissues and explore how they evolve with wavelength. Additionally, the temporal evolution of certain tissues during meat aging is studied, providing insights into the dynamic behavior of polarimetric properties over time. The research employs back-scattering configuration and the differential decomposition analysis method of Mueller matrix images. Both in-vivo and ex-vivo experiments were conducted using a consistent instrument setup to ensure reliable analysis. The results reveal wavelength-dependent variations in tissue properties, including an increase in depolarization with wavelength. Significant differences in the polarimetric characteristics of meat tissues, particularly for skeletal muscle, are observed. Over a 24-h period, intensity, diattenuation, and retardation experience alterations, being the decreased retardation in skeletal muscle and the increased retardation in fat the most notable ones.

Dielectric function of vanadium oxide thin films by thermal annealing.

The dielectric function of ${{\rm{VO}}_x}$ and ${{\rm{V}}_2}{{\rm{O}}_5}$ thin films is determined with the use of a spectroscopic Mueller matrix ellipsometer from 1.5 to 5.0 eV. The complex dielectric function of the films is calculated using the measured Mueller matrices filtered with the Cloude decomposition. ${{\rm{VO}}_x}$ shows high absorption in the UV region, a Tauc-Lorentz gap around 2.4 eV, and non-vanishing absorption in the visible. ${{\rm{V}}_2}{{\rm{O}}_5}$ shows a high absorption band centered at 2.87 eV, an indirect optical band gap at 1.95 eV, and a direct optical band gap at 2.33 eV. The ellipsometric characterization is supported by Raman, x-ray photoelectron, and photoluminescence spectroscopy.

Spontaneous mirror-symmetry breaking coupled to top-bottom chirality transfer: from porphyrin self-assembly to scalemic Diels-Alder adducts.

This report shows how the net supramolecular chirality that emerged by spontaneous mirror-symmetry breaking (SMSB) at the mesoscale level can be transferred towards asymmetric solution chemistry. The J-aggregates obtained by self-assembly of an achiral porphyrin act as chiral counteranions in an iminium-promoted Diels-Alder reaction, leading to enantiomeric imbalances in the final adducts.

Quaternion algebra for Stokes-Mueller formalism.

In this paper, we show that the Stokes-Mueller formalism can be reformulated in terms of quaternions and that the quaternion algebra is a suitable alternative presentation of the formalism of Mueller-Jones states that we have recently described [J. Opt. Soc. Am. A34, 80 (2017)JOAOD60740-323210.1364/JOSAA.34.000080]. The vector and matrix states associated with the Mueller matrices of nondepolarizing optical systems are different representations that are isomorphic to the same quaternion state, and this quaternion state turns out to be the rotator of the Stokes quaternion. In this work, we study the properties of this general quaternion state and its application to the calculus of polarization effects. We also show that the coherent linear combination of nondepolarizing optical media states and depolarization phenomena can be reformulated in terms of quaternion states.

Mueller matrix polarimetry on a Young's double-slit experiment analog.

In this Letter we describe an experiment in which coherent light is sent through a calcite crystal that separates the photons by their polarization. The two beams are then let to superpose, and this recombined beam is used to measure the Mueller matrix of the system. Results are interpreted according to our recent formalism of coherent superposition in material media. This is the first experimental implementation of a Young's experiment with complete polarimetry, and it is demonstrated that our method can be used for the experimental synthesis of optical devices with on-demand optical properties.

Hydrodynamic Effects in Soft-matter Self-assembly: The Case of J-Aggregates of Amphiphilic Porphyrins.

Chiral J-aggregates of achiral amphiphilic porphyrins (4-sulfonatophenyl and aryl meso-substituted porphyrins) show several effects under the hydrodynamic forces of common stirring. These effects can be classified as pure mechanic (e. g. elasticity, plasticity and breaking of the self-assembly non-covalent bonding) and chemically selective as detected in the formation/growth of the nanoparticles. Diastereoselective, enantioselective and, depending on the sign of chiral shear forces, even enantiospecific selections have been described. Some types of these effects have been reported in other type of J-aggregates. Reversible and irreversible structural effects have been studied by atomic force imaging. The determination of the optical polarization properties (linear and circular) of their solutions is best done using Mueller matrix polarimetry methods.

Reversible and irreversible emergence of chiroptical signals in J-aggregates of achiral 4-sulfonatophenyl substituted porphyrins: intrinsic chirality vs. chiral ordering in the solution.

Mueller matrix polarimetry distinguishes the different origins of the reversible and irreversible chiroptical effects emerging in stirred solutions of J-aggregate nanoparticles: the reversible effect is due to an anisotropic ordering in the solution and the irreversible one is due to a bias from the racemic composition of intrinsically chiral structures.

Relation between 2D/3D chirality and the appearance of chiroptical effects in real nanostructures.

The optical activity of fabricated metallic nanostructures is investigated by complete polarimetry. While lattices decorated with nanoscale gammadia etched in thin metallic films have been described as two dimensional, planar nanostructures, they are better described as quasi-planar structures with some three dimensional character. We find that the optical activity of these structures arises not only from the dissymmetric backing by a substrate but, more importantly, from the selective rounding of the nanostructure edges. A true chiroptical response in the far-field is only allowed when the gammadia contain these non-planar features. This is demonstrated by polarimetric measurements in conjunction with electrodynamical simulations based on the discrete dipole approximation that consider non-ideal gammadia. It is also shown that subtle planar dissymmetries in gammadia are sufficient to generate asymmetric transmission of circular polarized light.

Structure vs. excitonic transitions in self-assembled porphyrin nanotubes and their effect on light absorption and scattering.

The optical properties of diprotonated meso-tetrakis(4-sulphonatophenyl)porphyrin (TPPS(4)) J-aggregates of elongated thin particles (nanotubes in solution and ribbons when deposited on solid interfaces) are studied by different polarimetric techniques. The selective light extinction in these structures, which depends on the alignment of the nanoparticle with respect to the polarization of light, is contributed by excitonic absorption bands and by resonance light scattering. The optical response as a function of the polarization of light is complex because, although the quasi-one-dimensional structure confines the local fields along the nanotube axis, there are two orthogonal excitonic bands, of H- and J-character, that can work in favor of or against the field confinement. Results suggest that resonance light scattering is the dominant effect in solid state preparations, i.e. in collective groups (bundles) of ribbons but in diluted solutions, i.e. with isolated nanotubes, the absorption at the excitonic transitions remains dominant and linear dichroism spectra can be a direct probe of the exciton orientations. Therefore, by analyzing scattering and absorption data we can determine the alignment of the excitonic bands within the nanoparticle, i.e. of the orientation of the basic 2D porphyrin architecture in the nanoparticle. This is a necessary first step for understanding the directions of energy transport, charge polarization and non-linear optical properties in these materials.

Optical security verification by synthesizing thin films with unique polarimetric signatures.

This Letter reports the production and optical polarimetric verification of codes based on thin-film technology for security applications. Because thin-film structures display distinctive polarization signatures, this data is used to authenticate the message encoded. Samples are analyzed using an imaging ellipsometer able to measure the 16 components of the Mueller matrix. As a result, the behavior of the thin film under polarized light becomes completely characterized. This information is utilized to distinguish among true and false codes by means of correlation. Without the imaging optics the components of the Mueller matrix become noise-like distributions and, consequently, the message encoded is no longer available. Then, a set of Stokes vectors are generated numerically for any polarization state of the illuminating beam and thus, machine learning techniques can be used to perform classification. We show that successful authentication is possible using the k-nearest neighbors algorithm in thin-films codes that have been anisotropically phase-encoded with pseudorandom phase code.

Mueller matrix microscope with a dual continuous rotating compensator setup and digital demodulation.

In this paper we describe a new Mueller matrix (MM) microscope that generalizes and makes quantitative the polarized light microscopy technique. In this instrument all the elements of the MU are simultaneously determined from the analysis in the frequency domain of the time-dependent intensity of the light beam at every pixel of the camera. The variations in intensity are created by the two compensators continuously rotating at different angular frequencies. A typical measurement is completed in a little over one minute and it can be applied to any visible wavelength. Some examples are presented to demonstrate the capabilities of the instrument.

Achiral-to-chiral transition in benzil solidification: analogies with racemic conglomerates systems showing deracemization.

Experimental results show that benzil (1,2-diphenyl-1,2-ethanedione), an achiral compound that crystallizes as a racemic conglomerate, yields by solidification polycrystalline scalemic mixtures of high enantiomeric excesses. These results are related to those previously reported in this type of compounds on deracemizations of racemic mixtures of crystal enantiomorphs obtained by wet grinding. However, the present results strongly suggest that these experiments cannot be explained without taking into account chiral recognition interactions at the level of precritical clusters. The conditions that would define a general thermodynamic scenario for such deracemizations are discussed.

Alignment and chirality of porphyrin J aggregates formed at the liquid-liquid interface of a centrifugal liquid membrane cell.

Previous direct observations of the J aggregates of diprotonated 5,10,15,20-tetraphenyl-21H,23H-porphine (H4TPP(2+)) formed at the dodecane-water interface in a centrifugal liquid membrane (CLM) cell using conventional CD spectroscopy have shown the existence of circular dichroic signals with a bisignated shape whose sign depends on the rotation direction of the cell. Herein we demonstrate that the determination of the optical Mueller matrix with a two-photoelastic modulator generalized ellipsometer (2-MGE), working in transmission mode, along with the assumption of a two superimposed twin Mueller matrices model (two opposite interfaces in the cylindrical rotation cell) allows us to infer the CD spectra due to overlapping linear polarizations from J aggregates at the front and back liquid-liquid interfaces in the rotating cell. The rotation direction dependence of the CD spectra was thoroughly interpreted by the present model considering the sign and the magnitude of the orientation angle between the front and back J aggregates. The present analysis should help us to understand the optical chirality due to the structural changes in supramolecular and macromolecular systems under flow shear forces as well as changes in birefringence.

Kinetic control of the supramolecular chirality of porphyrin J-aggregates.

The aggregation of achiral sulfonatophenyl- and phenyl-meso-substituted diprotonated porphyrins to chiral J-aggregates is a hierarchical noncovalent polymerization process preceded by a critical nucleation stage. This allows significant enantiomeric excesses by the formation of a few primary nuclei and the control of their growth by the effect that flows (imperfect mixing) have on the secondary nucleation of the J-aggregate particles. In addition, the results strongly suggest that when only one species of aggregate predominates, the CD signals of the three excitonic bands in the visible region (around 420, 490, and 700 nm) show the same sign. Thus, differences on their relative sign would be due to the presence of different species.

Chirality generated by flows in pseudocyanine dye J-aggregates: revisiting 40 years old reports.

Spontaneous symmetry breaking in J-aggregates of cyanine dyes has a long history in chemical literature. In 1976, Honda and Hada claimed that they had achieved chiral induction (CD) by stirring J-aggregates of pseudocyanine. However, this report is controversial, as the combinations of linear dichroism and birefringence can lead to artifactual circular dichroic signals that are unrelated to molecular chirality. A Mueller matrix spectroscopy study, with an approach for the application of a gradient of the shear rate (solution layer between a rotating and a fixed disk) that differs from the simple vortex stirring used in the original report, shows that true CD can be induced in the sample. The phenomenon is discussed, taking into account the flow dynamics that allows the alignment of the aggregate particles and the gradient of shear rates that determines their folding/torsion, which leads to a chiral excitonic transition.

Emergence of supramolecular chirality by flows.

Hydrodynamic forces in stirred solutions induce chirality in some supramolecular species of J-aggregates, as detected at the level of the electronic transition. However, the mechanism that explains the phenomenon remains to be elucidated, although the basic effect of hydrodynamic gradients of the shear rate is most probably the folding or bending of the nanoparticles in solution. Herein, we demonstrate a correlation between chiral flows in different regions of circular and square stirred cuvettes and the emergence of true circular dichroism (CD). The results show that chaotic flows lead to a racemic mixture of chiral shaped supramolecular species, and vortical flows to scalemic mixtures. In a magnetically stirred flask the descending and ascending flows are of different chiral sign and the CD reading depends on the weighting of these two flows of inverse chiral sign. The effect of the gradient of shear rates of the flows leading to chiral shape objects depends on the shape of the cuvette, which suggests that the flask shape and the controlled addition of reagents in defined regions of the stirred solutions may exert a control in self-assembly processes.

Analytic inversion of the Mueller-Jones polarization matrices for homogeneous media.

In this Letter we present the equations to calculate the six independent polarization effects of an arbitrary normalized Mueller-Jones matrix corresponding to homogenous media. A comparison between this method and other inversion procedures is discussed, and the application of the analytic inversion to experimental Mueller matrices is illustrated.

Chiral biases in solids by effect of shear gradients: a speculation on the deterministic origin of biological homochirality.

We present an experimental approach to the study of the chirality of three CM2 meteorite solid samples by direct measurement of the optical activity (circular birefringence; CB). The measurements are based on transmission two modulator generalized ellipsometry in conjuction with microscope optics to map the CB of the samples. In spite of the complexity of such optical analysis, these first results indicate the presence of optically active areas in the meteorite solid matrix. In the case of the Murchison sample the statistics of the CB mapping shows a bimodal distribution with a bias to negative CB values. The composition of the active areas probably corresponds to serpentines and other poorly identified phyllosilicate phases. The results are compatible with the hypothesis that in a mineral-based scenario for the origin of life a CB sign bias in the chiral fractures originated by mechanical and flow shear gradients on clays could be later transferred to the reactions of the absorbed organic compounds.

Determination of the components of the gyration tensor of quartz by oblique incidence transmission two-modulator generalized ellipsometry.

The two independent components of the gyration tensor of quartz, g(11) and g(33), have been spectroscopically measured using a transmission two-modulator generalized ellipsometer. The method is used to determine the optical activity in crystals in directions other than the optic axis, where the linear birefringence is much larger than the optical activity.

Reversible mechanical induction of optical activity in solutions of soft-matter nanophases.

Nanophases of J-aggregates of several achiral amphiphilic porphyrins, which have thin long acicular shapes (nanoribbons), show the immediate and reversible formation of a stationary mechano-chiral state in the solution by vortex stirring, as detected by their circular dichroic signals measured by 2-modulator generalized ellipsometry. The results suggest that when a macroscopic chiral force creates supramolecular chirality, it also creates an enantiomeric excess of screw distortions, which may be detected by their excitonic absorption. An explanation on the effect of the shear flow gradients is proposed on the basis of the orientation of the rotating particles in the vortex and the size, shape, and mechanical properties of the nanoparticles.