Flexibility of short-strand RNA in aqueous solution as revealed by molecular dynamics simulation:are A′-RNA and A-RNA distinct conformational structures?

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A'-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA namely major groove width, inclination and the number of base pairs in a helical twist over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A'-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors). © CSIRO 2009.

Hairpin vortex solution in planar Couette flow: a tapestry of knotted vortices

A numerical continuation method has been carried out seeking solutions for two distinct flow configurations, planar Couette flow (PCF) and laterally heated flow in a vertical slot (LHF). We found that the spanwise vortex solution in LHF identifies a new solution in PCF. The vortical structure of our new solution has the shape of a hairpin observed ubiquitously in high-Reynolds-number turbulent flow, and we believe this discovery may provide the paradigm for a hierarchical organization of coherent structures in turbulent shear layers.

Optical chemsensor based on etched tilted Bragg grating structures in multimode fiber

We present a simple optical chemsensor device based on tilted Bragg grating structures ultraviolet-inscribed in conventional multimode fiber and sensitized by a hydrofluoric (HF)-etching treatment. The transition behaviors of fiber Bragg gratings (FBGs) from normal to tilted structures and their spectral evolution under HF-etching have been studied. The etched devices have been used to measure the concentrations of sugar solution, showing a potential capability of detecting concentration changes as small as 0.5%, which is an order of magnitude lower than that of previously reported FBG sensors in single-mode fiber.

Temporal finite elements in the dynamic analysis of structures

This thesis demonstrates that the use of finite elements need not be confined to space alone, but that they may also be used in the time domain, It is shown that finite element methods may be used successfully to obtain the response of systems to applied forces, including, for example, the accelerations in a tall structure subjected to an earthquake shock. It is further demonstrated that at least one of these methods may be considered to be a practical alternative to more usual methods of solution. A detailed investigation of the accuracy and stability of finite element solutions is included, and methods of applications to both single- and multi-degree of freedom systems are described. Solutions using two different temporal finite elements are compared with those obtained by conventional methods, and a comparison of computation times for the different methods is given. The application of finite element methods to distributed systems is described, using both separate discretizations in space and time, and a combined space-time discretization. The inclusion of both viscous and hysteretic damping is shown to add little to the difficulty of the solution. Temporal finite elements are also seen to be of considerable interest when applied to non-linear systems, both when the system parameters are time-dependent and also when they are functions of displacement. Solutions are given for many different examples, and the computer programs used for the finite element methods are included in an Appendix.

Dissipative nonlinear structures in optical fiber systems II : self-similar parabolic pulses in active fibers

In this second talk on dissipative structures in fiber applications, we overview theoretical aspects of the generation, evolution and characterization of self-similar parabolic-shaped pulses in fiber amplifier media. In particular, we present a perturbation analysis that describes the structural changes induced by third-order fiber dispersion on the parabolic pulse solution of the nonlinear Schrödinger equation with gain. Promising applications of parabolic pulses in optical signal post-processing and regeneration in communication systems are also discussed.

Dissipative nonlinear structures in optical fiber systems II:self-similar parabolic pulses in active fibers

In this second talk on dissipative structures in fiber applications, we overview theoretical aspects of the generation, evolution and characterization of self-similar parabolic-shaped pulses in fiber amplifier media. In particular, we present a perturbation analysis that describes the structural changes induced by third-order fiber dispersion on the parabolic pulse solution of the nonlinear Schrödinger equation with gain. Promising applications of parabolic pulses in optical signal post-processing and regeneration in communication systems are also discussed.

Optical chemsensor based on etched tilted Bragg grating structures in multimode fiber

We present a simple optical chemsensor device based on tilted Bragg grating structures ultraviolet-inscribed in conventional multimode fiber and sensitized by a hydrofluoric (HF)-etching treatment. The transition behaviors of fiber Bragg gratings (FBGs) from normal to tilted structures and their spectral evolution under HF-etching have been studied. The etched devices have been used to measure the concentrations of sugar solution, showing a potential capability of detecting concentration changes as small as 0.5%, which is an order of magnitude lower than that of previously reported FBG sensors in single-mode fiber.

Metrology enhanced tooling for aerospace (META):strategies for improved accuracy of jig built structures

The accuracy of many aerospace structures is limited by the accuracy of assembly tooling which is in turn limited by the accuracy of the measurements used to set the tooling. Further loss of accuracy results from different rates of thermal expansion for the components and tooling. This paper describes improved tooling designs and setting processes which have the potential to significantly improve the accuracy of aerospace structures. The most advanced solution described is environmentally isolated interferometer networks embedded within tooling combined with active compensation of component pick-ups. This would eliminate environmental effects on measurements while also allowing compensation for thermal expansion. A more immediately realizable solution is the adjustment of component pick-ups using micrometer jacking screws allowing multilateration to be employed during the final stages of the setting process to generate the required offsets. Copyright © 2011 SAE International.