The interaction networks of structured RNAs

All pairwise interactions occurring between bases which could be detected in three-dimensional structures of crystallized RNA molecules are annotated on new planar diagrams. The diagrams attempt to map the underlying complex networks of base–base interactions and, especially, they aim at conveying key relationships between helical domains: co-axial stacking, bending and all Watson–Crick as well as non-Watson–Crick base pairs. Although such wiring diagrams cannot replace full stereographic images for correct spatial understanding and representation, they reveal structural similarities as well as the conserved patterns and distances between motifs which are present within the interaction networks of folded RNAs of similar or unrelated functions. Finally, the diagrams could help devising methods for meaningfully transforming RNA structures into graphs amenable to network analysis

Observation of the shock wave propagation induced by a high-power laser irradiation into an epoxy material

The propagation of laser-induced shock waves in a transparent epoxy sample is investigated by optical shadowgraphy. The shock waves are generated by a focused laser (3 ns pulse duration—1.2 to 3.4TWcm−2) producing pressure from 44 to 98.9 GPa. It is observed that the shock wave and the release wave created by the shock reverberation at the rear face are both followed by a dark zone in the pictures. This corresponds to the creation of a tensile zone resulting from the crossing on the loading axis of the release waves coming from the edge of the impact area (2D effects). After the laser shock experiment, the residual stresses in the targets are identified and quantified through a photoelasticimetry analysis of the recovered samples. This work results in a new set of original data which can be directly used to validate numerical models implemented to reproduce the behaviour of epoxy under extreme strain rate loading. The residual stresses observed prove that the high-pressure shocks can modify the pure epoxy properties, which could have an influence on the use made of these materials

Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments

The occurrences of two recurrent motifs in ribosomal RNA sequences, the Kink-turn and the C-loop, are examined in crystal structures and systematically compared with sequence alignments of rRNAs from the three kingdoms of life in order to identify the range of the structural and sequence variations. Isostericity Matrices are used to analyze structurally the sequence variations of the characteristic non-Watson–Crick base pairs for each motif. We show that Isostericity Matrices for non-Watson–Crick base pairs provide important tools for deriving the sequence signatures of recurrent motifs, for scoring and refining sequence alignments, and for determining whether motifs are conserved throughout evolution. The systematic use of Isostericity Matrices identifies the positions of the insertion or deletion of one or more nucleotides relative to the structurally characterized examples of motifs and, most importantly, specifies whether these changes result in new motifs. Thus, comparative analysis coupled with Isostericity Matrices allows one to produce and refine structural sequence alignments. The analysis, based on both sequence and structure, permits therefore the evaluation of the conservation of motifs across phylogeny and the derivation of rules of equivalence between structural motifs. The conservations observed in Isostericity Matrices form a predictive basis for identifying motifs in sequences

Dynamic cratering of graphite : experimental results and simulations

The cratering process in brittle materials under hypervelocity impact (HVI) is of major relevance for debris shielding in spacecraft or high-power laser applications. Amongst other materials, carbon is of particular interest since it is widely used as elementary component in composite materials. In this paper we study a porous polycrystalline graphite under HVI and laser impact, both leading to strong debris ejection and cratering. First, we report new experimental data for normal impacts at 4100 and 4200 m s-1 of a 500-μm-diameter steel sphere on a thick sample of graphite. In a second step, dynamic loadings have been performed with a high-power nanosecond laser facility. High-resolution X-ray tomographies and observations with a scanning electron microscope have been performed in order to visualize the crater shape and the subsurface cracks. These two post-mortem diagnostics also provide evidence that, in the case of HVI tests, the fragmented steel sphere was buried into the graphite target below the crater surface. The current study aims to propose an interpretation of the results, including projectile trapping. In spite of their efficiency to capture overall trends in crater size and shape, semi-empirical scaling laws do not usually predict these phenomena. Hence, to offer better insight into the processes leading to this observation, the need for a computational damage model is argued. After discussing energy partitioning in order to identify the dominant physical mechanisms occurring in our experiments, we propose a simple damage model for porous and brittle materials. Compaction and fracture phenomena are included in the model. A failure criterion relying on Weibull theory is used to relate material tensile strength to deformation rate and damage. These constitutive relations have been implemented in an Eulerian hydrocode in order to compute numerical simulations and confront them with experiments. In this paper, we propose a simple fitting procedure of the unknown Weibull parameters based on HVI results. Good agreement is found with experimental observations of crater shapes and dimensions, as well as debris velocity. The projectile inclusion below the crater is also reproduced by the model and a mechanism is proposed for the trapping process. At least two sets of Weibull parameters can be used to match the results. Finally, we show that laser experiment simulations may discriminate in favor of one set of parameters

Spall fracture and twinning in laser shock-loaded single-crystal magnesium

As a major failure process in materials subjected to dynamic loading, spall fracture is one of the most widely studied issues in shock physics. To investigate its dependence on the microstructure, including both initial and shock-induced features, laser shock experiments were performed on single crystal magnesium. Shock loading was applied in directions parallel and perpendicular to the c-axis of the crystals. Both the spall strength and the fracture surface morphology are found to depend on the direction of the shock application with respect to crystal orientations. The results complement data obtained previously over ranges of lower strain rates. A detailed analysis of the residual microstructure and crack patterns in the recovered samples shows strong correlations between damage localization and twins, both pre-existing and shock-induced. Thus, cracks match specific twinning directions, which is discussed on the basis of deformation mechanisms reported under quasi-static loading conditions, either prismatic slip or twinning depending on local orientations

Investigating Ramp Wave Propagation inside Silica Glass with Laser Experiments and Molecular Simulations

Under elastic shock compression silica glass exhibits a very specific behaviour. A shock propagating inside a material is usually seen as the propagation of a discontinuity. However in silica glass, shocks are unstable and lead to the propagation of a ramp wave where the shock front becomes gradually larger over time. Ramp waves were already reported in the literature, however their origin remain uncertain. This work presents an original study combining laser shock-induced experiments and molecular dynamics simulation aiming to improve the understanding of the mechanisms involved. Experimental ramp waves were directly observed using shadowgraphy technique allowing for an estimation of the head and tail velocities. Molecular dynamics simulations were carried out in order to reproduce ramp waves and to gain insight into the material properties. Ramp waves were observed for both elastic and plastic shockwaves. In the latter case, the plastic waves were preceded by an elastic ramp precursor. The sound speed, related to the material compressibility, was found to decrease with increasing pressure, as observed experimentally for quasi-static hydrostatic loading, thus providing an explanation for the instabilities that lead to the propagation of ramp waves

The UA_handle: a versatile submotif in stable RNA architectures†

Stable RNAs are modular and hierarchical 3D architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions. Sequence and atomic structure analysis has revealed a novel submotif involving a minimal set of five nucleotides, termed the UA_handle motif (5′XU/ANnX3′). It consists of a U:A Watson–Crick: Hoogsteen trans base pair stacked over a classic Watson–Crick base pair, and a bulge of one or more nucleotides that can act as a handle for making different types of long-range interactions. This motif is one of the most versatile building blocks identified in stable RNAs. It enters into the composition of numerous recurrent motifs of greater structural complexity such as the T-loop, the 11-nt receptor, the UAA/GAN and the G-ribo motifs. Several structural principles pertaining to RNA motifs are derived from our analysis. A limited set of basic submotifs can account for the formation of most structural motifs uncovered in ribosomal and stable RNAs. Structural motifs can act as structural scaffoldings and be functionally and topologically equivalent despite sequence and structural differences. The sequence network resulting from the structural relationships shared by these RNA motifs can be used as a proto-language for assisting prediction and rational design of RNA tertiary structures

Engineering cooperative tecto–RNA complexes having programmable stoichiometries

High affinity and specificity RNA–RNA binding interfaces can be constructed by combining pairs of GNRA loop/loop–receptor interaction motifs. These interactions can be fused using flexible four-way junction motifs to create divalent, self-assembling scaffolding units (‘tecto-RNA’) that have favorable properties for nanomedicine and other applications. We describe the design and directed assembly of tecto-RNA units ranging from closed, cooperatively assembling ring-shaped complexes of programmable stoichiometries (dimers, trimers and tetramers) to open multimeric structures. The novelty of this work is that tuning of the stoichiometries of self-assembled complexes is achieved by precise positioning of the interaction motifs in the monomer units rather than changing their binding specificities. Structure-probing and transmission electron microscopy studies as well as thermodynamic analysis support formation of closed cooperative complexes that are highly resistant to nuclease digestion. The present designs provide two helical arms per RNA monomer for further functionalization aims

Experimental and numerical investigations of shock and shear wave propagation induced by femtosecond laser irradiation in epoxy resins

In this work, original shock experiments are presented. Laser-induced shock and shear wave propagations have been observed in an epoxy resin, in the case of femtosecond laser irradiation. A specific time-resolved shadowgraphy setup has been developed using the photoelasticimetry principle to enhance the shear wave observation. Shear waves have been observed in epoxy resin after laser irradiation. Their propagation has been quantified in comparison with the main shock propagation. A discussion, hinging on numerical results, is finally given to improve understanding of the phenomenon