This paper investigates Rayleigh wave interaction with simulated, surface breaking cracks using a finite element method, in which the scattered wave modes giving rise to the in-plane and out-of-plane displacements are presented. By looking at the contribution from all of the transmitted, reflected, and mode-converted signals at the crack, the magnitude of signal enhancement in the near field and the mechanism by which this occurs can be fully explained. Furthermore, oscillations in the Rayleigh wave reflection and transmission coefficients with crack depth in the far field can be explained by means of multiple reflected and transmitted wave modes at the crack, whose relative amplitudes are dependent on the crack depth. Results agree with previously published experimental measurements.

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We present a reliable and accurate solution to the induced fit docking problem for protein-ligand binding by combining ligand-based pharmacophore docking (Phase), rigid receptor docking (Glide), and protein structure prediction (Prime) with explicit solvent molecular dynamics simulations. We provide an in-depth description of our novel methodology and present results for 41 targets consisting of 415 cross-docking cases divided amongst a training and test set. For both the training and test-set, we compute binding modes with a ligand-heavy atom RMSD to within 2.5 Å or better in over 90% of cross-docking cases compared to less than 70% of cross-docking cases using our previously published induced-fit docking algorithm and less than 41% using rigid receptor docking. Applications of the predicted ligand-receptor structure in free energy perturbation calculations is demonstrated for both public data and in active drug discovery projects, both retrospectively and prospectively.

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