Chemical education using feelable molecules

Artificial Life and Robotics, 2019

Purpose To provide a virtual reality 3D user interface with comprehensive molecular modeling, we have developed a novel haptic rendering system with a fingertip haptic rendering device and a hand-tracking Leap Motion controller. Methods The system handles virtual molecular objects with real hands motion captured by the Leap Motion controller in a virtual reality environment. The fingertip haptic rendering device attached on each finger and a wrist gives haptic display, when virtual hands manipulating virtual molecular objects. Results Based on preliminary software development studies using existing 3D graphics toolkit such as CHAI3D and Unity, the fingertip haptic rendering device works with a reasonable performance for a polygon surface model and a ribbon model, but not for an atomic model due to the low rendering performance. On the other hand, the device provides us a grasping feeling of a large molecule represented by an atomic model, when used with the particle simulation system running on graphics library, DirectX 12. The haptic rendering performances, among the three software systems are discussed.

Lecture Notes in Computer Science, 2009

The science of haptics has received an enormous attention in the last decade. One of the major application trends of haptics technology is data visualization and training. In this paper, we present our work towards developing a hapticallyenhanced model for manipulation and tactile exploration of molecules. The graphic models of molecules is extracted using file formats widely used in chemical and biological field. The addition of haptic interface enables users to feel the interaction forces between the explored molecule and a simple probe molecule (such as water, or basic electronic charge). Since the interaction forces are very small, the forces felt by the user are scaled accordingly. The haptic device used is the Sensable PHANTOM R Omni. The developed tool can be used for teaching and scientific purposes due to its high reliance on both theoretical and experimental data.

2015

In recent years the field of alternative haptic interface is expanding and improvements are being made by developing, testing and refining devices along with software to give users the possibility of interacting with three dimensional virtual objects in an intuitive way. Such technology can play a significant role in education, especially as complements of MOOCs delivery. This paper presents a description of an educational haptic system for chemistry experiment simulations and molecular visualization that can complement a virtual delivery system by providing hands-on experiences. It also describes some didactic scenarios and discusses current results and future works.

ChemPhysChem, 2014

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 transitionstate 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.

2021

Over the past 15 years we have been developing tools for interacting with biomolecules using haptics. Interactions with biomolecules in the virtual world are made via a haptic-feedback device that is able to resist inputs from the user or even act to move the user’s hand in response to molecular forces. Here we highlight the key methodological advances made in the development of these tools including Haptimol ISAS, a tool for interacting with a molecule’s solvent accessible surface, Haptimol ENM, a tool for applying forces to an elastic network model of a biomolecule, DockIT (formerly Haptimol RD), for interactive rigid docking, and Haptimol FlexiDock, for interactive docking that models flexibility in the receptor molecule

2008

Three-dimensional functions that represent atomic orbitals are traditionally difficult for chemistry students to conceptualize. Large sections of undergraduate physical chemistry texts are devoted to breaking apart and simplifying electron density functions so they can be visually represented. Traditional methodologies include skins (isosurfaces and enclosures of certain probabilities), three-dimensional projections (color, contours, slices) and two-dimensional graphs. Preliminary work with the Phantom 3d haptic interface suggests that haptics are an important addition to the chemist's tool set for representing atomic orbitals. With the Phantom, users simply move through real three-dimensional space and perceive the electron density as the force on the Phantom's pen. In our work, the force is proportional to the probability density function for the electron at any point, given by the square of the wavefunction describing a particular atomic orbital (ψ2 (r, θ, φ)). Nodes ar...

Computers & Education, 2011

This study explores tertiary students' interaction with a haptic virtual model representing the specific binding of two biomolecules, a core concept in molecular life science education. Twenty students assigned to a haptics (experimental) or no-haptics (control) condition performed a "docking" task where users sought the most favourable position between a ligand and protein molecule, while students' interactions with the model were logged. Improvement in students' understanding of biomolecular binding was previously measured by comparing written responses to a target conceptual question before and after interaction with the model. A log-profiling tool visualized students' movement of the ligand molecule during the docking task. Multivariate parallel coordinate analyses explored any relationships in the entire student data set. The haptics group produced a tighter constellation of collected final docked ligand positions in comparison with no-haptics students, coupled to docking profiles that depicted a more fine-tuned ligand traversal. Students in the no-haptics condition employed double the amount of interactive behaviours concerned with switching between different visual chemical representations offered by the model. In the no-haptics group, this visually intense processing was synonymous with erroneously 'fitting' the ligand closer distances to the protein surface. Students who showed higher learning gains tended to engage fewer visual representational switches, and were from the haptics group, while students with a higher spatial ability also engaged fewer visual representational switches, irrespective of assigned condition. From an information-processing standpoint, visual and haptic coordination may offload the visual pathway by placing less strain on visual working memory. From an embodied cognition perspective, visual and tactile sensorimotor interactions in the macroworld may provide access to constructing knowledge about submicroscopic phenomena. The results have cognitive and practical implications for the use of multimodal virtual reality technologies in educational contexts.

Many biological activities take place through the physicochemical interaction of two molecules. This interaction occurs when one of the molecules finds a suitable location on the surface of the other for binding. This process is known as molecular docking and it has applications to drug design. If we can determine which drug molecule binds to a particular protein and how the protein interacts with the bonded molecule, we can possibly enhance or inhibit its activities. This information, in turn, can be used to develop new drugs that are more effective against diseases. In this paper, we propose a new approach based on human-computer interaction paradigm for the solution of rigid-body molecular docking problem. In our approach, a rigid ligand molecule (i.e. drug) manipulated by the user is inserted into the cavities of a rigid protein molecule to search for the binding cavity while the molecular interaction forces are conveyed to the user via a haptic device for guidance. We developed a new visualization concept, Active Haptic Workspace (AHW), for the efficient exploration of the large protein surface in high resolution using a haptic device having a small workspace. After the discovery of the true binding site and the rough alignment of the ligand molecule inside the cavity by the user, its final configuration is calculated off-line through time-stepping molecular dynamics (MD) simulations. At each time step, the optimum rigid-body transformations of the ligand molecule are calculated using a new approach, which minimizes the distance error between the previous rigid-body coordinates of its atoms and their new coordinates calculated by the MD simulations. The simulations are continued until the ligand molecule arrives to the lowest energy configuration. Our experimental studies conducted with six human subjects testing six different molecular complexes demonstrate that given a ligand molecule and five potential binding sites on a protein surface, the subjects can successfully identify the true binding site using visual and haptic cues. Moreover, they can roughly align the ligand molecule inside the binding cavity such that the final configuration of the ligand molecule can be determined via the proposed MD simulations.

Lecture Notes in Computer Science, 2015

Currently, first-year chemistry students learn about three-dimensional molecular structures using a combination of lectures, tutorials, and practical hands-on experience with molecular chemistry kits. We have developed a basic 3D molecule construction simulation, called MolyPoly. The system was designed to augment the teaching of organic chemistry by helping students grasp the concepts of chemistry through visualisation in an immersive environment, 3D natural interaction, and audio lesson feedback. This paper presents the results of a pilot study conducted with a first-year chemistry class at the University of Tasmania. Participating students were split into two groups: MolyPoly group (no lecturer in the sessions) and traditional classroom group during the four insemester classroom sessions over a period of two weeks. We present our comparative analyses over the knowledge-based pretest and posttest of the two groups, by discussing the overall improvement as well as investigating the improvement over the test questions with different knowledge difficulty levels and different required spatial knowledge.

BMC Structural Biology, 2009

Background From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere ...