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

The Analysis of design and manufacturing tasks using haptic and immersive VR - Some case studies

The use of virtual reality in interactive design and manufacture has been researched extensively but the practical application of this technology in industry is still very much in its infancy. This is surprising as one would have expected that, after some 30 years of research commercial applications of interactive design or manufacturing planning and analysis would be widespread throughout the product design domain. One of the major but less well known advantages of VR technology is that logging the user gives a great deal of rich data which can be used to automatically generate designs or manufacturing instructions, analyse design and manufacturing tasks, map engineering processes and, tentatively, acquire expert knowledge. The authors feel that the benefits of VR in these areas have not been fully disseminated to the wider industrial community and - with the advent of cheaper PC-based VR solutions - perhaps a wider appreciation of the capabilities of this type of technology may encourage companies to adopt VR solutions for some of their product design processes. With this in mind, this paper will describe in detail applications of haptics in assembly demonstrating how user task logging can lead to the analysis of design and manufacturing tasks at a level of detail not previously possible as well as giving usable engineering outputs. The haptic 3D VR study involves the use of a Phantom and 3D system to analyse and compare this technology against real-world user performance. This work demonstrates that the detailed logging of tasks in a virtual environment gives considerable potential for understanding how virtual tasks can be mapped onto their real world equivalent as well as showing how haptic process plans can be generated in a similar manner to the conduit design and assembly planning HMD VR tool reported in PART A. The paper concludes with a view as to how the authors feel that the use of VR systems in product design and manufacturing should evolve in order to enable the industrial adoption of this technology in the future

A real-time proximity querying algorithm for haptic-based molecular docking

Intermolecular binding underlies every metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow us to study the binding process. Haptic-based docking provides an immersive virtual docking environment where the user can interact with and guide the molecules to their binding pose. Moreover, it allows human perception, intuition and knowledge to assist and accelerate the docking process, and reduces incorrect binding poses. Crucial for interactive docking is the real-time calculation of interaction forces. For smooth and accurate haptic exploration and manipulation, force-feedback cues have to be updated at a rate of 1 kHz. Hence, force calculations must be performed within 1ms. To achieve this, modern haptic-based docking approaches often utilize pre-computed force grids and linear interpolation. However, such grids are time-consuming to pre-compute (especially for large molecules), memory hungry, can induce rough force transitions at cell boundaries and cannot be applied to flexible docking. Here we propose an efficient proximity querying method for computing intermolecular forces in real time. Our motivation is the eventual development of a haptic-based docking solution that can model molecular flexibility. Uniquely in a haptics application we use octrees to decompose the 3D search space in order to identify the set of interacting atoms within a cut-off distance. Force calculations are then performed on this set in real time. The implementation constructs the trees dynamically, and computes the interaction forces of large molecular structures (i.e. consisting of thousands of atoms) within haptic refresh rates. We have implemented this method in an immersive, haptic-based, rigid-body, molecular docking application called Haptimol_RD. The user can use the haptic device to orientate the molecules in space, sense the interaction forces on the device, and guide the molecules to their binding pose. Haptimol_RD is designed to run on consumer level hardware, i.e. there is no need for specialized/proprietary hardware

Prop-Based Haptic Interaction with Co-location and Immersion: an Automotive Application

Most research on 3D user interfaces aims at providing only a single sensory modality. One challenge is to integrate several sensory modalities into a seamless system while preserving each modality's immersion and performance factors. This paper concerns manipulation tasks and proposes a visuo-haptic system integrating immersive visualization, tactile force and tactile feedback with co-location. An industrial application is presented

On singular values decomposition and patterns for human motion analysis and simulation

We are interested in human motion characterization and automatic motion simulation. The apparent redun- dancy of the humanoid w.r.t its explicit tasks lead to the problem of choosing a plausible movement in the framework of redun- dant kinematics. This work explores the intrinsic relationships between singular value decomposition at kinematic level and optimization principles at task level and joint level. Two task- based schemes devoted to simulation of human motion are then proposed and analyzed. These results are illustrated by motion captures, analyses and task-based simulations. Pattern of singular values serve as a basis for a discussion concerning the similarity of simulated and real motions