DockPro: A VR-Based Tool for Protein-Protein Docking Problem

Proteins are large molecules that are vital for all living organisms and they are essential components of many industrial products. The process of binding a protein to another is called protein-protein docking. Many automated algorithms have been proposed to find docking configurations that might yield promising protein-protein complexes. However, these automated methods are likely to come up with false positives and have high computational costs. Consequently, Virtual Reality has been used to take advantage of user's experience on the problem; and proposed applications can be further improved. Haptic devices have been used for molecular docking problems; but they are inappropriate for protein-protein docking due to their workspace limitations. Instead of haptic rendering of forces, we provide a novel visual feedback for simulating physicochemical forces of proteins. We propose an interactive 3D application, DockPro, which enables domain experts to come up with dockings of protein-protein couples by using magnetic trackers and gloves in front of a large display

Touching proteins with virtual bare hands : visualizing protein–drug complexes and their dynamics in self-made virtual reality using gaming hardware

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more accessible and intuitive visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). While bespoke commercial VR suites are available, in this work, we present a freely available software pipeline for visualising protein structures through VR. New consumer hardware, such as the HTC Vive and the Oculus Rift utilized in this study, are available at reasonable prices. As an instructive example, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-led drug design by exposing molecular interactions that might be hidden in the less informative static models. This is a paradigmatic test case scenario for many similar applications in computer-aided molecular studies and design

Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

A Comparative Study of Desktop, Fishtank, and Cave Systems for the Exploration of Volume Rendered Confocal Data Sets

We present a participant study that compares biological data exploration tasks using volume renderings of laser confocal microscopy data across three environments that vary in level of immersion: a desktop, fishtank, and cave system. For the tasks, data, and visualization approach used in our study, we found that subjects qualitatively preferred and quantitatively performed better in the cave compared with the fishtank and desktop. Subjects performed real-world biological data analysis tasks that emphasized understanding spatial relationships including characterizing the general features in a volume, identifying colocated features, and reporting geometric relationships such as whether clusters of cells were coplanar. After analyzing data in each environment, subjects were asked to choose which environment they wanted to analyze additional data sets in - subjects uniformly selected the cave environment

Psychological benefits and educational potential of physically immersive artificial environment pedagogy

Over the last decade, physically immersive artificial environments (PIAEs) have proliferated. These environments afford greater interactivity, which has been shown to increase learner understanding, knowledge retention, and interest in the subject (Bonwell & Eison, 1991, p. 3; Prince, 2004). It would follow, then, that PIAEs would have similar educational benefits. However, little research has been done to prove that such benefits exist. Immersive environments include 2-demensional and 2.5-dimensional on-screen displays, semi-immersive screens, and physically immersive setups, such as CAVE and blue-c (Display Systems: 3D & Advanced, 2008; Gross, n.d.). There are many perceived benefits to immersive environments. At present, their novelty seems to hold students\u27 attention better than traditional environments. PIAEs may improve students\u27 attitude toward the domain; provide contextual learning, constructivism, and experiential learning; allow students to visit physically inaccessible environments; and provide concrete representations of abstract concepts. Student interaction and multimodal interaction may be increased and students\u27 spatial abilities may increase in physically immersive environments. A physically immersive artificial environment was developed at RIT, for which the students of two classes used and created immersive content. These students were tested to determine whether they exhibited differences in their science related attitudes, mental rotation abilities, and spatial orientation abilities after using the PIAE for a 10-week period. The study found inconclusive evidence regarding changes in science related attitudes and spatial orientation abilities, but did find evidence in support of the hypothesis that experiences in a physically immersive environment increase students\u27 mental rotation abilities. The study lays the groundwork for further research into the educational benefits of physically immersive artificial environments

Immersive Visualization in Biomedical Computational Fluid Dynamics and Didactic Teaching and Learning

Virtual reality (VR) can stimulate active learning, critical thinking, decision making and improved performance. It requires a medium to show virtual content, which is called a virtual environment (VE). The MARquette Visualization Lab (MARVL) is an example of a VE. Robust processes and workflows that allow for the creation of content for use within MARVL further increases the userbase for this valuable resource. A workflow was created to display biomedical computational fluid dynamics (CFD) and complementary data in a wide range of VE’s. This allows a researcher to study the simulation in its natural three-dimensional (3D) morphology. In addition, it is an exciting way to extract more information from CFD results by taking advantage of improved depth cues, a larger display canvas, custom interactivity, and an immersive approach that surrounds the researcher. The CFD to VR workflow was designed to be basic enough for a novice user. It is also used as a tool to foster collaboration between engineers and clinicians. The workflow aimed to support results from common CFD software packages and across clinical research areas. ParaView, Blender and Unity were used in the workflow to take standard CFD files and process them for viewing in VR. Designated scripts were written to automate the steps implemented in each software package. The workflow was successfully completed across multiple biomedical vessels, scales and applications including: the aorta with application to congenital cardiovascular disease, the Circle of Willis with respect to cerebral aneurysms, and the airway for surgical treatment planning. The workflow was completed by novice users in approximately an hour. Bringing VR further into didactic teaching within academia allows students to be fully immersed in their respective subject matter, thereby increasing the students’ sense of presence, understanding and enthusiasm. MARVL is a space for collaborative learning that also offers an immersive, virtual experience. A workflow was created to view PowerPoint presentations in 3D using MARVL. A resulting Immersive PowerPoint workflow used PowerPoint, Unity and other open-source software packages to display the PowerPoint presentations in 3D. The Immersive PowerPoint workflow can be completed in under thirty minutes

Modeling and Simulation in Engineering

This book provides an open platform to establish and share knowledge developed by scholars, scientists, and engineers from all over the world, about various applications of the modeling and simulation in the design process of products, in various engineering fields. The book consists of 12 chapters arranged in two sections (3D Modeling and Virtual Prototyping), reflecting the multidimensionality of applications related to modeling and simulation. Some of the most recent modeling and simulation techniques, as well as some of the most accurate and sophisticated software in treating complex systems, are applied. All the original contributions in this book are jointed by the basic principle of a successful modeling and simulation process: as complex as necessary, and as simple as possible. The idea is to manipulate the simplifying assumptions in a way that reduces the complexity of the model (in order to make a real-time simulation), but without altering the precision of the results