Sugar-Pucker Force-Induced Transition in Single-Stranded DNA

The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples range from DNA hybridization, DNA ligand binding, DNA unwinding by helicases, etc. To date, ssDNA elasticity has been studied with different methods in molecules of varying sequence and contour length. A dispersion of results has been reported and the value of the persistence length has been found to be larger for shorter ssDNA molecules. We carried out pulling experiments with optical tweezers to characterize the elastic response of ssDNA over three orders of magnitude in length (60–14 k bases). By fitting the force-extension curves (FECs) to the Worm-Like Chain model we confirmed the above trend:the persistence length nearly doubles for the shortest molecule (60 b) with respect to the longest one (14 kb). We demonstrate that the observed trend is due to the different force regimes fitted for long and short molecules, which translates into two distinct elastic regimes at low and high forces. We interpret this behavior in terms of a force-induced sugar pucker conformational transition (C3′-endo to C2′-endo) upon pulling ssDNA.     

Growth condition dependence of unintentional oxygen incorporation in epitaxial GaN

Growth conditions have a tremendous impact on the unintentional background impurity concentration in gallium nitride (GaN) synthesized by molecular beam epitaxy and its resulting chemical and physical properties. In particular for oxygen identified as the dominant background impurity we demonstrate that under optimized growth stoichiometry the growth temperature is the key parameter to control its incorporation and that an increase by 55?°C leads to an oxygen reduction by one order of magnitude. Quantitatively this reduction and the resulting optical and electrical properties are analyzed by secondary ion mass spectroscopy, photoluminescence, capacitance versus voltage measurements, low temperature magneto-transport and parasitic current paths in lateral transistor test structures based on two-dimensional electron gases. At a growth temperature of 665?°C the residual charge carrier concentration is decreased to below 10¹⁵ cm^?3, resulting in insulating behavior and thus making the material suitable for beyond state-of-the-art device applications.     

Visualization of load transfer behaviour between geogrid and sand using PFC

Geogrids have been widely used to improve the soil mechanical behaviour in geotechnical engineering. In order to investigate the load transfer behaviour between the geogrid and sand, a numerical compound tensile test (in sand) with one geogrid tensile member has been carried out using PFC^2D. In this study, sand was modelled as unbonded particles using the linear contact stiffness model, while the geogrid was modelled as bonded particles using the piecewise linear model which has been developed based on the parallel bond model. Calibrations have been performed by comparing the numerical simulation results with the experimental data. The load transfer behaviour between the geogrid and sand has been visualized by geogrid force and displacement distributions along the geogrid, contact force changes in the specimen and rotations of the sand particles in the vicinity of the geogrid at different clamp displacements. The DEM simulation results show that PFC^2D can be used as a practical tool to visualize the load transfer behaviour between the geogrid and sand. Furthermore, the visualization results provide researchers more insights into the interface behaviour between the geogrid and sand at a microscopic scale.     

A case study in the mechanical verification of fault tolerance

To date, there is little evidence that modular reasoning about fault-tolerant systems can simplify the verification process in practice. This question is studied using a prominent example from the fault tolerance literature: the problem of reliable broadcast in point-to-point networks subject to crash failures of processes. The experiences from this case study show how modular specification techniques and rigorous proof re-use can indeed help in such undertakings.