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Using logging data to visualize and explore students’ interaction and learning with a haptic virtual model of protein-ligand docking
Linköping University, Department of Science and Technology. Linköping University, The Institute of Technology.
Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.ORCID iD: 0000-0002-4694-5611
(English)Manuscript (preprint) (Other academic)
Abstract [en]

This study explores students’ interaction and learning with a haptic virtual model of biomolecular recognition. Twenty students assigned to a haptics or no-haptics condition performed a protein-ligand docking task where interaction was captured in log files. Any improvement in understanding of recognition was measured by comparing written responses to a conceptual question before and after interaction. A log-profiling tool visualized students’ traversal of the ligand while multivariate parallel coordinate analyses uncovered trends in the data. Students who experienced force feedback (haptics) displayed docked positions that were more clustered in comparison with no-haptics students, coupled to docking profiles that depicted a more focused traversal of the ligand. Students in the no-haptics condition employed double the amount of behaviours concerned with switching between multiple visual representations offered by the system. In the no-haptics group, this visually intense processing was associated with ‘fitting’ the ligand closer distances to the surface of the protein. A negative relationship between high representational switching activity and learning gain as well as spatial aptitude was also revealed. From an information-processing perspective, visual and haptic coordination could permit engagement of each perceptual channel simultaneously, in effect offloading the visual pathway by placing less strain on visual working memory.

Keyword [en]
Interactive learning environments; multimedia systems; pedagogical issues; postsecondary education; virtual reality
National Category
Natural Sciences
URN: urn:nbn:se:liu:diva-60355OAI: diva2:356435
Available from: 2010-10-12 Created: 2010-10-12 Last updated: 2016-05-04
In thesis
1. Touching the Essence of Life: Haptic Virtual Proteins for Learning
Open this publication in new window or tab >>Touching the Essence of Life: Haptic Virtual Proteins for Learning
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This dissertation presents research in the development and use of a multi-modal visual and haptic virtual model in higher education. The model, named Chemical Force Feedback (CFF), represents molecular recognition through the example of protein-ligand docking, and enables students to simultaneously see and feel representations of the protein and ligand molecules and their force interactions. The research efforts have been divided between educational research aspects and development of haptic feedback techniques.

The CFF model was evaluated in situ through multiple data-collections in a university course on molecular interactions. To isolate possible influences of haptics on learning, half of the students ran CFF with haptics, and the others used the equipment with force feedback disabled. Pre- and post-tests showed a significant learning gain for all students. A particular influence of haptics was found on students reasoning, discovered through an open-ended written probe where students' responses contained elaborate descriptions of the molecular recognition process.

Students' interactions with the system were analyzed using customized information visualization tools. Analysis revealed differences between the groups, for example, in their use of visual representations on offer, and in how they moved the ligand molecule. Differences in representational and interactive behaviours showed relationships with aspects of the learning outcomes.

The CFF model was improved in an iterative evaluation and development process. A focus was placed on force model design, where one significant challenge was in conveying information from data with large force differences, ranging from very weak interactions to extreme forces generated when atoms collide. Therefore, a History Dependent Transfer Function (HDTF) was designed which adapts the translation of forces derived from the data to output forces according to the properties of the recently derived forces. Evaluation revealed that the HDTF improves the ability to haptically detect features in volumetric data with large force ranges.

To further enable force models with high fidelity, an investigation was conducted to determine the perceptual Just Noticeable Difference (JND) in force for detection of interfaces between features in volumetric data. Results showed that JNDs vary depending on the magnitude of the forces in the volume and depending on where in the workspace the data is presented.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2010. 78 p.
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1332
Haptics, Educational Research, Biomolecular Education, Life Science, JND, Just Noticeable Difference, Protein-ligand Docking, Haptic docking, Visualization, Haptic Transfer Functions, Volume Data Haptics, History Dependent Transfer Function, Log file analysis, Molecular Recognition, Force Feedback, Virtual Reality
National Category
Other Computer and Information Science
urn:nbn:se:liu:diva-58994 (URN)978-91-7393-341-4 (ISBN)
Public defence
2010-10-01, The Dome Theater, Visualization Center C, Kungsgatan 54, Norrköping, Norrköping, 09:30 (English)
Available from: 2010-10-12 Created: 2010-09-06 Last updated: 2016-05-04Bibliographically approved

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Schönborn, Konrad J.Bivall, PetterTibell, Lena A. E.
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