Deep Learning Based Inversion of Locally Anisotropic Weld Properties from Ultrasonic Array Data

The ability to reliably detect and characterise defects embedded in austenitic steel welds depends on prior knowledge of microstructural descriptors, such as the orientations of the weld’s locally anisotropic grain structure. These orientations are usually unknown but it has been shown recently that they can be estimated from ultrasonic scattered wave data. However, conventional algorithms used for solving this inverse problem incur a significant computational cost. In this paper, we propose a framework which uses deep neural networks (DNNs) to reconstruct crystallographic orientations in a welded material from ultrasonic travel time data, in real-time. Acquiring the large amount of training data required for DNNs experimentally is practically infeasible for this problem, therefore a model based training approach is investigated instead, where a simple and efficient analytical method for modelling ultrasonic wave travel times through given weld geometries is implemented. The proposed method is validated by testing the trained networks on data arising from sophisticated finite element simulations of wave propagation through weld microstructures. The trained deep neural network predicts grain orientations to within 3° and in near real-time (0.04 s), presenting a significant step towards realising real-time, accurate characterisation of weld microstructures from ultrasonic non-destructive measurements. The subsequent improvement in defect imaging is then demonstrated via use of the DNN predicted crystallographic orientations to correct the delay laws on which the total focusing method imaging algorithm is based. An improvement of up to 5.3 dB in the signal-to-noise ratio is achieved

Analysis of the Shadow-Sausage Effect Caustic

We analyze the optical caustic produced by light refracted at the curved meniscus surrounding a cylindrical rod standing partially out of a liquid-filled container. When the rod is tilted from the vertical or when light is diagonally incident, the caustic is a four-cusped astroid with two of its cusps obscured by the rod\u27s shadow. If a portion of the flat end of the rod is raised above the water level, the caustic evolves into a pattern of five interlocking cusps. The five cusps result from symmetry breaking of a three-cusped surface perturbation caustic. (C) 2003 Optical Society of America

Interactivity:the missing link between virtual reality technology and drug discovery pipelines

The potential of virtual reality (VR) to contribute to drug design and development has been recognised for many years. Hardware and software developments now mean that this potential is beginning to be realised, and VR methods are being actively used in this sphere. A recent advance is to use VR not only to visualise and interact with molecular structures, but also to interact with molecular dynamics simulations of 'on the fly' (interactive molecular dynamics in VR, IMD-VR), which is useful not only for flexible docking but also to examine binding processes and conformational changes. iMD-VR has been shown to be useful for creating complexes of ligands bound to target proteins, e.g., recently applied to peptide inhibitors of the SARS-CoV-2 main protease. In this review, we use the term 'interactive VR' to refer to software where interactivity is an inherent part of the user VR experience e.g., in making structural modifications or interacting with a physically rigorous molecular dynamics (MD) simulation, as opposed to simply using VR controllers to rotate and translate the molecule for enhanced visualisation. Here, we describe these methods and their application to problems relevant to drug discovery, highlighting the possibilities that they offer in this arena. We suggest that the ease of viewing and manipulating molecular structures and dynamics, and the ability to modify structures on the fly (e.g., adding or deleting atoms) makes modern interactive VR a valuable tool to add to the armoury of drug development methods.Comment: 19 pages, 3 figure

Free energy along drug-protein binding pathways interactively sampled in virtual reality

We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined approach as iMD-VR-FE. Stage one involves using a state-of-the-art iMD-VR framework to generate a diverse range of protein-ligand unbinding pathways, benefitting from the sophistication of human spatial and chemical intuition. Stage two involves using the iMD-VR-sampled pathways as initial guesses for defining a path-based reaction coordinate from which we can obtain a corresponding free energy profile using FE methods. To investigate the performance of the method, we apply iMD-VR-FE to investigate the unbinding of a benzamidine ligand from a trypsin protein. The binding free energy calculated using iMD-VR-FE is similar for each pathway, indicating internal consistency. Moreover, the resulting free energy profiles can distinguish energetic differences between pathways corresponding to various protein-ligand conformations (e.g., helping to identify pathways that are more favourable) and enable identification of metastable states along the pathways. The two-step iMD-VR-FE approach offers an intuitive way for researchers to test hypotheses for candidate pathways in biomolecular systems, quickly obtaining both qualitative and quantitative insight

Real-time super-resolution mapping of locally anisotropic grain orientations for ultrasonic non-destructive evaluation of crystalline material

Estimating the spatially varying microstructures of heterogeneous and locally anisotropic media non-destructively is necessary for the accurate detection of flaws and reliable monitoring of manufacturing processes. Conventional algorithms used for solving this inverse problem come with significant computational cost, particularly in the case of high-dimensional, nonlinear tomographic problems, and are thus not suitable for near-real-time applications. In this paper, for the first time, we propose a framework which uses deep neural networks (DNNs) with full aperture, pitch-catch and pulse-echo transducer configurations, to reconstruct material maps of crystallographic orientation. We also present the first application of generative adversarial networks (GANs) to achieve super-resolution of ultrasonic tomographic images, providing a factor-four increase in image resolution and up to a 50% increase in structural similarity. The importance of including appropriate prior knowledge in the GAN training data set to increase inversion accuracy is demonstrated: known information about the material's structure should be represented in the training data. We show that after a computationally expensive training process, the DNNs and GANs can be used in less than 1 second (0.9 s on a standard desktop computer) to provide a high-resolution map of the material's grain orientations, addressing the challenge of significant computational cost faced by conventional tomography algorithms

Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution

Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly widely utilized in studies of reactions in enzymes and other large systems. Here, we apply a range of QM/MM methods to investigate the Claisen rearrangement of chorismate to prephenate, in solution, and in the enzyme chorismate mutase. Using projector-based embedding in a QM/MM framework, we apply treatments up to the CCSD­(T) level. We test a range of density functional QM/MM methods and QM region sizes. The results show that the calculated reaction energetics are significantly more sensitive to the choice of density functional than they are to the size of the QM region in these systems. Projector-based embedding of a wave function method in DFT reduced the 13 kcal/mol spread in barrier heights calculated at the DFT/MM level to a spread of just 0.3 kcal/mol, essentially eliminating dependence on the functional. Projector-based embedding of correlated ab initio methods provides a practical method for achieving high accuracy for energy profiles derived from DFT and DFT/MM calculations for reactions in condensed phases