BENDANDI A.

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,...

Depolarization has been found to be a useful contrast mechanism in biological and medical imaging. The Mueller matrix can be used to describe polarization effects of a depolarizing material. An historical review of relevant polarization algebra, measures of depolarization, and purity spaces is presented, and the connections with the eigenvalues...

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...

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...

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...

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...

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...

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....