Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study.

Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.

Publisher Correction: Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study.

This paper was originally published under standard Springer Nature copyright. As of the date of this correction, the Analysis is available online as an open-access paper with a CC-BY license. No other part of the paper has been changed.

Investigation of Relationship between Hemodynamic and Morphometric Characteristics of Aortas in Pediatric Patients.

Background: The utilization of hemodynamic parameters, whose estimation is often cumbersome, can fasten diagnostics and decision-making related to congenital heart diseases. The main goal of this study is to investigate the relationship between hemodynamic and morphometric features of the thoracic aorta and to construct corresponding predictive models. Methods: Multi-slice spiral computed tomography images of the aortas of patients with coarctation diagnoses and patients without cardiac or vascular diseases were evaluated to obtain numerical models of the aorta and branches of the aortic arch. Hemodynamic characteristics were estimated in key subdomains of the aorta and three branches using computational fluid dynamics methods. The key morphometric features (diameters) were calculated at locations in proximity to the domains, where hemodynamic characteristics are evaluated. Results: The functional dependencies for velocities and pressure on the corresponding diameters have been fitted, and a metamodel has been constructed employing the predicted values from these models. Conclusions: The metamodel demonstrated high accuracy in classifying aortas into their respective types, thereby confirming the adequacy of the predicted hemodynamic characteristics by morphometric characteristics. The proposed methodology is applicable to other heart diseases without fundamental changes.

Effective Boundary Conditions and Stochastic Crack Distribution for Modelling Guided Waves Scattering by a Partially Closed Interfacial Delamination in a Laminate.

Cohesive and adhesive bindings degrade during operation and maintenance even if contacting materials in a manufactured laminated structure are perfectly matched at the interfaces. Two modelling approaches for describing partially closed delaminations or imperfect contact zones, which often occurs at the interfaces, are examined and considered. To confirm the adequateness of the applicability of the effective spring boundary conditions for guided wave scattering by a finite length delamination, guided wave propagation through a damaged zone with a distribution of micro-cracks is compared with an equivalent cohesive zone model, where the spring stiffnesses for the effective boundary conditions are calculated using the properties of the considered crack distribution. Two kinds of local interfacial decohesion zones with an imperfect contact at the interfaces are considered: uniform partially closed delaminations and bridged cracks. The possibility of the employment of the effective spring boundary conditions to substitute a distribution of micro-cracks is analysed and discussed. Two algorithms of generation of a distribution of open micro-cracks providing characteristics equivalent to the effective boundary conditions are presented and examined. The influence of the characteristics of a delamination on wave characteristics (eigenfrequencies, eigenforms, transmission coefficient) is investigated for several kinds of partially closed delaminations.

Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α.

The dynamic architecture of chromatin fibers, a key determinant of genome regulation, is poorly understood. Here, we employ multimodal single-molecule Förster resonance energy transfer studies to reveal structural states and their interconversion kinetics in chromatin fibers. We show that nucleosomes engage in short-lived (micro- to milliseconds) stacking interactions with one of their neighbors. This results in discrete tetranucleosome units with distinct interaction registers that interconvert within hundreds of milliseconds. Additionally, we find that dynamic chromatin architecture is modulated by the multivalent architectural protein heterochromatin protein 1α (HP1α), which engages methylated histone tails and thereby transiently stabilizes stacked nucleosomes. This compacted state nevertheless remains dynamic, exhibiting fluctuations on the timescale of HP1α residence times. Overall, this study reveals that exposure of internal DNA sites and nucleosome surfaces in chromatin fibers is governed by an intrinsic dynamic hierarchy from micro- to milliseconds, allowing the gene regulation machinery to access compact chromatin.