Ab initio RNA folding

RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.Comment: 28 pages, 18 figure

Advances in Design by Metallic Materials: Synthesis, Characterization, Simulation and Applications

Very recently, a great deal of attention has been paid by researchers and technologists to trying to eliminate metal materials in the design of products and processes in favor of plastics and composites. After a few years, it is possible to state that metal materials are even more present in our lives and this is especially thanks to their ability to evolve. This Special Issue is focused on the recent evolution of metals and alloys with the scope of presenting the state of the art of solutions where metallic materials have become established, without a doubt, as a successful design solution thanks to their unique properties

Optimisation of ITER Nb3Sn CICCs for coupling loss, transverse electromagnetic load and axial thermal contraction

The ITER cable-in-conduit conductors (CICCs) are built up from sub-cable bundles, wound in different stages, which are twisted to counter coupling loss caused by time-changing external magnet fields. The selection of the twist pitch lengths has major implications for the performance of the cable in the case of strain sensitive superconductors, i.e. Nb3Sn, as the electromagnetic and thermal contraction loads are large but also for the heat load from the AC coupling loss. Reduction of the transverse load and warm-up cool-down degradation can be reached by applying longer twist pitches in a particular sequence for the sub-stages, offering a large cable transverse stiffness, adequate axial flexibility and maximum allowed lateral strand support. Analysis of short sample (TF conductor) data reveals that increasing the twist pitch can lead to a gain of the effective axial compressive strain of more than 0.3 % with practically no degradation from bending. For reduction of the coupling loss, specific choices of the cabling twist sequence are needed with the aim to minimize the area of linked strands and bundles that are coupled and form loops with the applied changing magnetic field, instead of simply avoiding longer pitches. In addition we recommend increasing the wrap coverage of the CS conductor from 50 % to at least 70 %. The models predict significant improvement against strain sensitivity and substantial decrease of the AC coupling loss in Nb3Sn CICCs, but also for NbTi CICCs minimization of the coupling loss can be achieved. Although the success of long pitches to transverse load degradation was already demonstrated, the prediction of the combination with low coupling loss needs to be validated by a short sample test.Comment: to be published in Supercond Sci Techno

Multi-objective optimisation of viscoelastic damping inserts in honeycomb sandwich structures

PublishedArticleAccepted ManuscriptThe Double-Shear Lap Joint (DSLJ) is a novel damping insert sited internally within a structure which is particularly well suited for lightweight sandwich structures with internal voids, such as honeycomb core sandwich panels. In high performance lightweight structures, the insertion of relatively more dense dampers of any type may increase the total mass substantially and alter the mass distribution significantly. The objective herein was to determine the optimum location, number and orientation of DSLJ inserts within a typical sandwich panel, and thereby to assess the efficacy of two different optimisation approaches to this problem; a parametric optimisation and the Adaptive Indicator-Based Evolutionary Algorithm (IBEA). Both approaches were used to maximise the damping while minimising the additional mass of the damping inserts applied to the structure. Although the parametric approach was faster and easier to implement, the Adaptive IBEA identified significantly better configurations in many cases, especially where veering occurred, in one case improving modal loss factors more than fourfold vs the parametric method. Solutions were identified with large increases in modal loss factors but only small increases in mass vs the empty structure.This work was supported by the MEET project (Material for Energy Efficiency in Transport) in the context of the INTERREG IV-A France (Channel) England European cross-border co-operation programme, which is co-financed by the ERDF

Numerical investigation of bone adaptation to exercise and fracture in Thoroughbred racehorses

Third metacarpal bone (MC3) fracture has a massive welfare and economic impact on horse racing, representing 45% of all fatal lower limb fractures, which in themselves represent more than 80% of reasons for death or euthanasia on the UK racecourses. Most of these fractures occur due to the accumulation of tissue fatigue as a result of repetitive loading rather than a specific traumatic event. Despite considerable research in the field, including applying various diagnostic methods, it still remains a challenge to accurately predict the fracture risk and prevent this type of injury. The objective of this thesis is to develop computational tools to quantify bone adaptation and resistance to fracture, thereby providing the basis for a viable and robust solution. Recent advances in subject-specific finite element model generation, for example computed tomography imaging and efficient segmentation algorithms, have significantly improved the accuracy of finite element modelling. Numerical analysis techniques are widely used to enhance understanding of fracture in bones and provide better insight into relationships between load transfer and bone morphology. This thesis proposes a finite element based framework allowing for integrated simulation of bone remodelling under specific loading conditions, followed by the evaluation of its fracture resistance. Accurate representation of bone geometry and heterogeneous material properties are obtained from calibrated computed tomography scans.The material mapping between CT-scan data and discretised geometries for the finite element method is carried out by using Moving Least Squares approximation and L2-projection. Thus is then used for numerical investigations and assessment of density gradients at the common site of fracture. Bone is able to adapt its density to changes in external conditions. This property is one of the most important mechanisms for the development of resistance to fracture. Therefore, a finite element approach for simulating adaptive bone changes (also called bone remodelling) is proposed. The implemented method is based on a phenomenological model of the macroscopic behaviour of bone based on the thermodynamics of open systems. Numerical results showed that the proposed technique has the potential to accurately simulate the long-term bone response to specified training conditions and also improve possible treatment options for bone implants. Assessment of the fracture risk was conducted with crack propagation analysis. The potential of two different approaches was investigated: smeared phase-field and discrete configurational mechanics approach. The popular phase-field method represents a crack by a smooth damage variable leading to a phase-field approximation of the variational formulation for brittle fracture. A robust solution scheme was implemented using a monolithic solution scheme with arc-length control. In the configurational mechanics approach, the driving forces, and fracture energy release rate, are expressed in terms of nodal quantities, enabling a fully implicit formulation for modelling the evolving crack front. The approach was extended for the first time to capture the influence of heterogeneous density distribution. The outcomes of this study showed that discrete and smeared crack approximations are capable of predicting crack paths in three-dimensional heterogeneous bodies with comparable results. However, due to the necessity of using significantly finer meshes, phase-field was found to be less numerically efficient. Finally, the current state of the framework's development was assessed using numerical simulations for bone adaptation and subsequent fracture propagation, including analysis of an equine metacarpal bone. Numerical convergence was demonstrated for all examples, and the use of singularity elements proved to further improve the rate of convergence. It was shown that bone adaptation history and bone density distribution influence both fracture resistance and the resulting crack path. The promising results of this study offer a~novel framework to simulate changes in the bone structure in response to exercise and quantify the likelihood of a fracture

9th EASN International Conference on Innovation in Aviation & Space

This Special Issue book contains selected papers from works presented at the 9th EASN (European Aeronautics Science Network) International Conference on Innovation in Aviation & Space, which was held in Athens, Greece from the 3rd until the 6th of September, 2019. About 450 participants contributed to a high-level scientific gathering, providing some of the latest research results on the topic, as well as some of the latest relevant technological advancements. Eight interesting articles, which cover a wide range of topics including characterization, analysis and design, as well as numerical simulation, are contained in this Special Issue