Purity of 3D polarization.

Measures of purity for 3D partially polarized fields, and in particular, the separation into circularly and linearly polarized contributions, are reexamined, and a new degree of total linear polarization introduced. Explicit expressions for the characteristic decomposition in terms of coherency matrix elements are presented, including the special case of an intrinsic coherency matrix. Parameterization of the coherency matrix in terms of ellipticity, and the directions of the ellipse normal and major axis are investigated. Phase consistency is discussed. A comprehensive collection of results regarding intrinsic polarization properties is presented.

Charged dielectric spheres interacting in electrolytic solution: A linearized Poisson-Boltzmann equation model.

We present an analytical theory of electrostatic interactions of two spherical dielectric particles of arbitrary radii and dielectric constants, immersed into a polarizable ionic solvent (assuming that the linearized Poisson-Boltzmann framework holds) and bearing arbitrary charge distributions expanded in multipolar terms. The presented development entails a novel two-center re-expansion analytical theory that expands upon and improves the existing ones, bypassing the conventional expansions in modified Bessel functions. On this basis, we develop a specific matrix formalism that facilitates the construction of asymptotic expansions in ascending order of Debye screening terms of potential coefficients, which are then employed to find exact closed-form expressions for the total electrostatic energy. In particular, this work allows us to explicitly and precisely quantify the k-screened terms of the potential coefficients and mutual interaction energy. Specific cases of monopolar and dipolar distributions are described in particular detail. Comprehensive numerical examples and tests of series convergence and the relative balance of leading and higher-order terms of the mutual interaction energy are presented depending on the inter-particle distance and particles' radii. The results of this work find application in soft matter modeling and, in particular, in computational biophysics and colloid science, where the availability of increasingly larger experimental structures at the atomic-level resolution makes numerical treatment challenging and calls for more efficient expressions and an increased range of validity.

Phasor approach of Mueller matrix optical scanning microscopy for biological tissue imaging.

Mueller matrix microscopy is an advanced imaging technique providing a full characterization of the optical polarization fingerprint of a sample. The Lu-Chipman (LC) decomposition, a method based on the modeling of elementary polarimetric arrangements and matrix inversions, is the gold standard to extract each polarimetric component separately. However, this models the optical system as a small number of discrete optical elements and requires a priori knowledge of the order in which these elements occur. In stratified media or when the ordering is not known, the interpretation of the LC decomposition becomes difficult. In this work, we propose a new, to our knowledge, representation dedicated to the study of biological tissues that combines Mueller matrix microscopy with a phasor approach. We demonstrate that this method provides an easier and direct interpretation of the retardance images in any birefringent material without the use of mathematical assumptions regarding the structure of the sample and yields comparable contrast to the LC decomposition. By validating this approach through numerical simulations, we demonstrate that it is able to give access to localized structural information, resulting in a simple determination of the birefringent parameters at the microscopic level. We apply our novel, to our knowledge, method to typical biological tissues that are of interest in the field of biomedical diagnosis.

Polarimetric optical scanning microscopy of zebrafish embryonic development using the coherency matrix.

Many of the most important resolution improvements in optical microscopy techniques are based on the reduction of scattering effects. The main benefit of polarimetry-based imaging to this end is the discrimination between scattering phenomena originating from complex systems and the experimental noise. The determination of the coherency matrix elements from the experimental Mueller matrix can take advantage of scattering measurements to obtain additional information on the structural organization of a sample. We analyze the contrast mechanisms extracted from (a) the coherency matrix elements, (b) its eigenvalues and (c) the indices of polarimetric purity at different stages of zebrafish embryos, based on previous work using Mueller matrix optical scanning microscopy. We show that the use of the coherency matrix and related decompositions leads to an improvement in the imaging contrast, without requiring any complicated algebraic operations or any a priori knowledge of the sample, in contrast to standard polarimetric methods.

The role of histone tails in nucleosome stability: An electrostatic perspective.

We propose a methodology for the study of protein-DNA electrostatic interactions and apply it to clarify the effect of histone tails in nucleosomes. This method can be used to correlate electrostatic interactions to structural and functional features of protein-DNA systems, and can be combined with coarse-grained representations. In particular, we focus on the electrostatic field and resulting forces acting on the DNA. We investigate the electrostatic origins of effects such as different stages in DNA unwrapping, nucleosome destabilization upon histone tail truncation, and the role of specific arginines and lysines undergoing Post-Translational Modifications. We find that the positioning of the histone tails can oppose the attractive pull of the histone core, locally deform the DNA, and tune DNA unwrapping. Small conformational variations in the often overlooked H2A C-terminal tails had significant electrostatic repercussions near the DNA entry and exit sites. The H2A N-terminal tail exerts attractive electrostatic forces towards the histone core in positions where Polymerase II halts its progress. We validate our results with comparisons to previous experimental and computational observations.

Eigenvectors of polarization coherency matrices.

Calculation of the eigenvectors of two- and three-dimensional coherency matrices, and the four-dimensional coherency matrix associated with a Mueller matrix, is considered, especially for algebraic cases, in the light of recently published algorithms. The preferred approach is based on a combination of an evaluation of the characteristic polynomial and an adjugate matrix. The diagonal terms of the coherency matrix are given in terms of the characteristic polynomial of reduced matrices as functions of the eigenvalues of the coherency matrix. The analogous polynomial form for the off-diagonal elements of the coherency matrix is also presented. Simple expressions are given for the pure component in the characteristic decomposition.

Polarization in reflectance imaging.

The Sinclair and Kennaugh matrices are widely used in the remote sensing discipline for signals detected in the backward direction. The connections between the Jones matrix and the Sinclair matrix, and between the Mueller matrix and the Kennaugh matrix, are explored. Different operations on the Jones matrix and their corresponding effects on the Mueller matrix, coherency matrix, and coherence vector are derived. As an example, the Sinclair matrix leads to a Mueller-Sinclair matrix, and a transformed coherence vector. The Kennaugh matrix is not, however, a Mueller matrix, but can be determined from the Mueller or Mueller-Sinclair matrices. We consider backscattering through a medium on a perfect mirror. We propose that backscattering from a uniform medium can be modeled as an effective uniform medium situated on a perfectly reflective substrate, and the elementary polarization properties derived. In this way, the concept of a uniform polarizing medium can be extended to the reflectance geometry. An experimental Mueller matrix from the literature is considered as an example.

Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment.

Understanding the mechanisms that trigger chromatin compaction, its patterns, and the factors they depend on, is a fundamental and still open question in Biology. Chromatin compacts and reinforces DNA and is a stable but dynamic structure, to make DNA accessible to proteins. In recent years, computational advances have provided larger amounts of data and have made large-scale simulations more viable. Experimental techniques for the extraction and reconstitution of chromatin fibers have improved, reinvigorating theoretical and experimental interest in the topic and stimulating debate on points previously considered as certainties regarding chromatin. A great assortment of approaches has emerged, from all-atom single-nucleosome or oligonucleosome simulations to various degrees of coarse graining, to polymer models, to fractal-like structures and purely topological models. Different fiber-start patterns have been studied in theory and experiment, as well as different linker DNA lengths. DNA is a highly charged macromolecule, making ionic and electrostatic interactions extremely important for chromatin topology and dynamics. Indeed, the repercussions of varying ionic concentration have been extensively examined at the computational level, using all-atom, coarse-grained, and continuum techniques. The presence of high-curvature AT-rich segments in DNA can cause conformational variations, attesting to the fact that the role of DNA is both structural and electrostatic. There have been some tentative attempts to describe the force fields governing chromatin conformational changes and the energy landscapes of these transitions, but the intricacy of the system has hampered reaching a consensus. The study of chromatin conformations is an intrinsically multiscale topic, influenced by a wide range of biological and physical interactions, spanning from the atomic to the chromosome level. Therefore, powerful modeling techniques and carefully planned experiments are required for an overview of the most relevant phenomena and interactions. The topic provides fertile ground for interdisciplinary studies featuring a synergy between theoretical and experimental scientists from different fields and the cross-validation of respective results, with a multi-scale perspective. Here, we summarize some of the most representative approaches, and focus on the importance of electrostatics and solvation, often overlooked aspects of chromatin modeling.

Zebrafish structural development in Mueller-matrix scanning microscopy.

Zebrafish are powerful animal models for understanding biological processes and the molecular mechanisms involved in different human diseases. Advanced optical techniques based on fluorescence microscopy have become the main imaging method to characterize the development of these organisms at the microscopic level. However, the need for fluorescence probes and the consequent high light doses required to excite fluorophores can affect the biological process under observation including modification of metabolic function or phototoxicity. Here, without using any labels, we propose an implementation of a Mueller-matrix polarimeter into a commercial optical scanning microscope to characterize the polarimetric transformation of zebrafish preserved at different embryonic developmental stages. By combining the full polarimetric measurements with statistical analysis of the Lu and Chipman mathematical decomposition, we demonstrate that it is possible to quantify the structural changes of the biological organization of fixed zebrafish embryos and larvae at the cellular scale. This convenient implementation, with low light intensity requirement and cheap price, coupled with the quantitative nature of Mueller-matrix formalism, can pave the way for a better understanding of developmental biology, in which label-free techniques become a standard tool to study organisms.

Eigenvalues of the coherency matrix for exact backscattering.

An important approach to interpretation of the Mueller matrix is based on the eigenvalues of the coherency matrix, given by the roots of a quartic characteristic equation. For the case of backscattering, one eigenvalue is zero from reciprocity arguments, and the characteristic equation reduces to a cubic. These two approaches (quartic and cubic) to calculation of the eigenvalues for exact backscattering are analytically considered and compared. As expected, the cubic approach is usually simpler, but for the special case of two zero eigenvalues, either approach reduces to the predictions of the simple quadratic characteristic equation. Either approach can be used for numerical calculation of the eigenvalues. The variation in different purity measures with the values of the Mueller matrix elements is presented. An experimental Mueller matrix for backscattering from a turbid chiral medium is investigated.

Coherency and differential Mueller matrices for polarizing media.

The elements of the coherency matrix give the strength of the components of a Mueller matrix in the coherency basis. The Z-matrix (called the polarization-coupling matrix or state-generating matrix) represents a partial sum of the coherency expansion. For transmission through a deterministic medium, the coherency elements can be used directly as generators to calculate the development of polarization upon propagation. The commutation properties of the coherency elements are investigated. New matrices that we call the W-matrix and the X-matrix, both different representations of the Z-matrix in a Jones basis, are introduced. The W-matrix controls the transformation of the Jones vector and also the covariance matrix. The product of the X-matrix with its complex conjugate gives the matrix representation of the Mueller matrix in the Jones basis. The development of Mueller matrix and coherency matrix elements upon propagation through some examples of a uniform medium is investigated. It is shown that the coherency matrix is more easily interpreted than the Mueller matrix. Analytic expressions are presented to calculate the elementary polarization properties from coherency matrix elements or Mueller matrix parameters.