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Francesco S. Pavone

Publications and source records attributed to Francesco S. Pavone.

4 recordsLinked to original sources

A unified perspective on wavelength selection for molecular composition inference from diffuse spectroscopy

Optical monitoring of living tissue targeting quantification of molecular composition is an active area of research. In the case of broadband spectroscopy, one can attempt to extract molecular, or more precisely, chromophore concentration from a broad-range spectrum of the reflected light. However, selecting the shortest wavelength range sufficient for quantitative optical monitoring remains an open problem. Various wavelength optimization methods are scattered throughout the literature, however, there is no unified view to date. Our work's motivation is to construct a wavelength selection framework by unifying existing selection approaches and propose a novel projection-based method that allows for the pre-identification of a wavelength range that is adequate for the final selection. The framework specifically focuses on proposing different methods that quantify match or mismatch between the chosen light-matter interaction model, defined by the chosen endmembers (e.g. molecular chromophores), and the measured intensity from the spectroscopic data. To evaluate the framework, we perform a retrospective analysis on a broadband spectroscopy dataset of piglets during an induced hypoxia-ischemia state. Overall, we show that our novel projection-based method can be used for band selection, and that existing approaches can be used in conjunction to select an optimal minimal wavelength set that satisfies biophysical model constraints.

physics.optics

Finite-Difference Time-Domain simulations of transmission microscopy enable a better interpretation of 3D nerve fiber architectures in the brain

In many laboratories, conventional bright-field transmission microscopes are available to study the structure and organization principles of fibrous tissue samples, but they usually provide only 2D information. To access the third (out-of-plane) dimension, more advanced techniques are employed. An example is 3D Polarized Light Imaging (3D-PLI), which measures the birefringence of histological brain sections to derive the spatial nerve fiber orientations. Here, we show how light scattering in transmission microscopy measurements can be leveraged to gain 3D structural information about fibrous tissue samples like brain tissue. For this purpose, we developed a simulation framework using finite-difference time-domain (FDTD) simulations and high performance computing, which can easily be adapted to other microscopy techniques and tissue types with comparable fibrous structures (e.g., muscle fibers, collagen, or artificial fibers). As conventional bright-field transmission microscopy provides usually only 2D information about tissue structures, a three-dimensional reconstruction of fibers across several sections is difficult. By combining our simulations with experimental studies, we show that the polarization-independent transmitted light intensity (transmittance) contains 3D information: We demonstrate in several experimental studies on brain sections from different species (rodent, monkey, human) that the transmittance decreases significantly (by more than 50%) with the increasing out-of-plane angle of the nerve fibers. Our FDTD simulations show that this decrease is mainly caused by polarization-independent light scattering in combination with the finite numerical aperture of the imaging system. This allows to use standard transmission microscopy techniques to obtain 3D information about the fiber inclination and to detect steep fibers, without need for additional measurements.

physics.med-ph

Calibration of optical tweezers with positional detection in the back-focal-plane

We explain and demonstrate a new method of force- and position-calibration for optical tweezers with back-focal-plane photo detection. The method combines power spectral measurements of thermal motion and the response to a sinusoidal motion of a translation stage. It consequently does not use the drag coefficient of the trapped ob ject as an input. Thus, neither the viscosity, nor the size of the trapped ob ject, nor its distance to nearby surfaces need to be known. The method requires only a low level of instrumentation and can be applied in situ in all spatial dimensions. It is both accurate and precise: true values are returned, with small error-bars. We tested this experimentally, near and far from surfaces. Both position- and force-calibration were accurate to within 3%. To calibrate, we moved the sample with a piezo-electric translation stage, but the laser beam could be moved instead, e.g. by acousto-optic deflectors. Near surfaces, this precision requires an improved formula for the hydrodynamical interaction between an infinite plane and a micro-sphere in non-constant motion parallel to it. We give such a formula.

physics.bio-ph

Stepwise bending of DNA by a single TATA-box Binding Protein

The TATA-box Binding Protein (TBP) is required by all three eukaryotic RNA polymerases for the initiation of transcription from most promoters. TBP recognizes, binds to, and bends promoter sequences called ``TATA-boxes'' in the DNA. We present results from the study of individual Saccharomyces cerevisia TBPs interacting with single DNA molecules containing a TATA-box. Using video microscopy, we observed the Brownian motion of beads tethered by short surface-bound DNA. When TBP binds to and bends the DNA, the conformation of the DNA changes and the amplitude of Brownian motion of the tethered bead is reduced compared to that of unbent DNA. We detected individual binding and dissociation events and derived kinetic parameters for the process. Dissociation was induced by increasing the salt concentration or by directly pulling on the tethered bead using optical tweezers. In addition to the well-defined free and bound classes of Brownian motion, we observed another two classes of motion. These extra classes were identified with intermediate states on a three-step, linear binding pathway. Biological implications of the intermediate states are discussed.

physics.bio-ph