Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein-ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0

Discovery Learning Experiments in a New Machine Design Laboratory

A new Machine Design Laboratory at Marquette University has been created to foster student exploration with hardware and real-world systems. The Laboratory incorporates areas for teaching and training, and has been designed to promote “hands-on” and “minds-on” learning. It reflects the spirit of transformational learning that is a theme in the College of Engineering. The goal was to create discovery learning oriented experiments for a required junior-level “Design of Machine Elements” course in mechanical engineering that would give students practical experiences and expose them to physical hardware, actual tools, and real-world design challenges. In the experiments students face a range of real-world tasks: identify and select components, measure parameters (dimensions, speed, force), distinguish between normal and used (worn) components and between proper and abnormal behavior, reverse engineer systems, and justify design choices. The experiments serve to motivate the theory and spark interest in the subject of machine design. This paper presents details of the experiments and summarizes student reactions and our experiences in the Machine Design Laboratory. In addition, the paper provides some insights for others who may wish to develop similar types of experiments

An Evaluation in China and the UK of a Virtual Laboratory in Materials Science

This thesis describes the design, development and evaluation of virtual technology-based courseware—Virtual Laboratory in Materials Science used in a tension test that forms part of the course of “Properties of Materials” taught to most first year engineering undergraduates. The effectiveness of this specially developed courseware for virtual laboratory work was evaluated in a pretest—posttest comparative study of the performance of designated subjects between two treatment groups that worked with the courseware and two control groups that worked with a real testing machine. All participants were engineering students studying either with the United Kingdom Open University (UKOU) or with the China Radio & TV University system (CRTVUs). The findings showed that most students enjoyed using the courseware because the simulated real experiment environment can make them feel personally on the scene. Among all the media used in the courseware, 3D and images were more favoured and more helpful to the students in terms of the usability of the courseware. Sounds were not seen as particularly helpful although some participants agreed sounds made the courseware more interesting. The result of the research indicated that using the Virtual Laboratory in Materials Science could make a contribution to students’ understanding of the tensile testing. This evaluation clearly revealed that virtual reality (VR) and virtual environments (VE) technology can facilitate and support engineering course learning or even make learning fun. But when used at times when there were steps that need lots of manipulation, the virtual experiment still had some difficulties that need to be resolved. The research showed that the potential of the virtual testing courseware in promoting concept teaching needs to be tapped further

Hope for the Best, Prepare for the Worst: Response of Tall Steel Buildings to the ShakeOut Scenario Earthquake

This work represents an effort to develop one plausible realization of the effects of the scenario event on tall steel moment-frame buildings. We have used the simulated ground motions with three-dimensional nonlinear finite element models of three buildings in the 20-story class to simulate structural responses at 784 analysis sites spaced at approximately 4 km throughout the San Fernando Valley, the San Gabriel Valley, and the Los Angeles Basin. Based on the simulation results and available information on the number and distribution of steel buildings, the recommended damage scenario for the ShakeOut drill was 5% of the estimated 150 steel moment-frame structures in the 10–30 story range collapsing, 10% red-tagged, 15% with damage serious enough to cause loss of life, and 20% with visible damage requiring building closure

Simulation and Visualization Enhanced Engineering Education- Development and Implementation of Virtual Experiments in a Laboratory Course

This paper presents results from a National Science Foundation grant titled Simulation and Visualization Enhanced Engineering Education , funded by the EEC division. Although the scope of the project is quite broad, embracing a wide range of courses in three engineering disciplines, the present work describes the results obtained from application of simulation and visualization for development and implementation of web-based virtual engineering laboratories. The present work leverages the advancement in hardware and software technologies to map physical experiments into web-based virtual experiments that can be used to enrich student\u27s laboratory experience. Four physical experiments in the thermo-fluids laboratory course have been mapped into virtual experiments, and the newly created virtual experiments have been used by students to conduct pre-lab practice sessions prior to performing corresponding physical experiment sessions. By performing virtual experiments, students learn in more detail about the objectives, procedure and expected outcomes ahead of scheduled physical experiments. Use of virtual experiments in the supplementation mode makes students better learners, and the assessment results show that students are better prepared and get more out of physical laboratory sessions. To test the efficacy of the proposed pre-lab practice session pedagogy, assessment instruments and statistical experimental designs have been developed and implemented to objectively determine whether implemented virtual experiments, used in supplementation mode, enhance student learning compared to the pre-implementation setting (without virtual experiments) and to test if the learning gains are statistically significant or not. The pedagogy of supplementation of physical experiments with pre-lab practice sessions with virtual experiments shows promise, based on results obtained in this project. Impact of various demographic factors such as gender, age, ethnicity, student level etc. on student learning was also analyzed

Cavity induced vibration of flexible hydrofoils

The objective of this work is to investigate the influence of cavity-induced vibrations on the dynamic response and stability of a NACA66 hydrofoil at 8° angle of attack at Re=750 000 via combined experimental measurements and numerical simulations. The rectangular, cantilevered hydrofoil is assumed to be rigid in the chordwise direction, while the spanwise bending and twisting deformations are represented using a two-degrees-of-freedom structural model. The multiphase flow is modeled with an incompressible, unsteady Reynolds Averaged Navier–Stokes solver with the k–ω Shear Stress Transport (SST) turbulence closure model, while the phase evolutions are modeled with a mass-transport equation based cavitation model. The numerical predictions are compared with experimental measurements across a range of cavitation numbers for a rigid and a flexible hydrofoil with the same undeformed geometries. The results showed that foil flexibility can lead to: (1) focusing – locking – of the frequency content of the vibrations to the nearest sub-harmonics of the foil׳s wetted natural frequencies, and (2) broadening of the frequency content of the vibrations in the unstable cavitation regime, where amplifications are observed in the sub-harmonics of the foil natural frequencies. Cavitation was also observed to cause frequency modulation, as the fluid density, and hence fluid induced (inertial, damping, and disturbing) forces fluctuated with unsteady cavitation.The authors gratefully acknowledge Ms. Kelly Cooper (program manager) and the Office of Naval Research (ONR), for their financial support through Grant nos. N00014-11-1-0833 and N0014-12-C-0585, as well as ONR Global and Dr. Woei-Min Lin (program manager) through grant no. N62909-12-1-7076