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

Interactive Chemical Reactivity Exploration

Elucidating chemical reactivity in complex molecular assemblies of a few hundred atoms is, despite the remarkable progress in quantum chemistry, still a major challenge. Black-box search methods to find intermediates and transition-state structures might fail in such situations because of the high-dimensionality of the potential energy surface. Here, we propose the concept of interactive chemical reactivity exploration to effectively introduce the chemist's intuition into the search process. We employ a haptic pointer device with force-feedback to allow the operator the direct manipulation of structures in three dimensions along with simultaneous perception of the quantum mechanical response upon structure modification as forces. We elaborate on the details of how such an interactive exploration should proceed and which technical difficulties need to be overcome. All reactivity-exploration concepts developed for this purpose have been implemented in the Samson programming environment.Comment: 36 pages, 14 figure

Usability Assessment of a Multimodal Visual-Haptic Framework for Chemistry Education

In this work, we assess the usability of a virtual environment where the force of interaction between the electrostatic field around the molecule and a charge associated to the proxy of a haptic device can be felt. Feedbacks to user are provided in a multimodal visual and haptic way, and auxiliary information are also rendered

Immersive Interactive Quantum Mechanics for Teaching and Learning Chemistry

The impossibility of experiencing the molecular world with our senses hampers teaching and understanding chemistry because very abstract concepts (such as atoms, chemical bonds, molecular structure, reactivity) are required for this process. Virtual reality, especially when based on explicit physical modeling (potentially in real time), offers a solution to this dilemma. Chemistry teaching can make use of advanced technologies such as virtual-reality frameworks and haptic devices. We show how an immersive learning setting could be applied to help students understand the core concepts of typical chemical reactions by offering a much more intuitive approach than traditional learning settings. Our setting relies on an interactive exploration and manipulation of a chemical system; this system is simulated in real-time with quantum chemical methods, and therefore, behaves in a physically meaningful way.Comment: 16 pages, 4 figure

Applying forces to elastic network models of large biomolecules using a haptic feedback device

Elastic network models of biomolecules have proved to be relatively good at predicting global conformational changes particularly in large systems. Software that facilitates rapid and intuitive exploration of conformational change in elastic network models of large biomolecules in response to externally applied forces would therefore be of considerable use, particularly if the forces mimic those that arise in the interaction with a functional ligand. We have developed software that enables a user to apply forces to individual atoms of an elastic network model of a biomolecule through a haptic feedback device or a mouse. With a haptic feedback device the user feels the response to the applied force whilst seeing the biomolecule deform on the screen. Prior to the interactive session normal mode analysis is performed, or pre-calculated normal mode eigenvalues and eigenvectors are loaded. For large molecules this allows the memory and number of calculations to be reduced by employing the idea of the important subspace, a relatively small space of the first M lowest frequency normal mode eigenvectors within which a large proportion of the total fluctuation occurs. Using this approach it was possible to study GroEL on a standard PC as even though only 2.3% of the total number of eigenvectors could be used, they accounted for 50% of the total fluctuation. User testing has shown that the haptic version allows for much more rapid and intuitive exploration of the molecule than the mouse version

Teaching complex theoretical multi-step problems in ICT networking through 3D printing and augmented reality

This paper presents a pilot study rationale and research methodology using a mixed media visualisation (3D printing and Augmented Reality simulation) learning intervention to help students in an ICT degree represent theoretical complex multi-step problems without a corresponding real world physical analog model. This is important because these concepts are difficult to visualise without a corresponding mental model. The proposed intervention uses an augmented reality application programmed with free commercially available tools, tested through an action research methodology, to evaluate the effectiveness of the mixed media visualisation techniques to teach ICT students networking. Specifically, 3D models of network equipment will be placed in a field and then the augmented reality app can be used to observe packet traversal and routing between the different devices as data travels from the source to the destination. Outcomes are expected to be an overall improvement in final skill level for all students