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Touching the Essence of Life: Haptic Virtual Proteins for Learning
Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
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.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1332
Keyword [en]
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
Identifiers
URN: urn:nbn:se:liu:diva-58994ISBN: 978-91-7393-341-4 (print)OAI: oai:DiVA.org:liu-58994DiVA: diva2:351561
Public defence
2010-10-01, The Dome Theater, Visualization Center C, Kungsgatan 54, Norrköping, Norrköping, 09:30 (English)
Opponent
Supervisors
Available from: 2010-10-12 Created: 2010-09-06 Last updated: 2016-05-04Bibliographically approved
List of papers
1. Designing and Evaluating a Haptic System for Biomolecular Education
Open this publication in new window or tab >>Designing and Evaluating a Haptic System for Biomolecular Education
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2007 (English)In: IEEE Virtual Reality Conference, 2007. VR '07. / [ed] Sherman, W; Lin, M; Steed, A, Piscataway, NJ, USA: IEEE , 2007, 171-178 p.Conference paper, Published paper (Refereed)
Abstract [en]

In this paper we present an in situ evaluation of a haptic system, with a representative test population, we aim to determine what, if any, benefit haptics can have in a biomolecular education context. We have developed a haptic application for conveying concepts of molecular interactions, specifically in protein-ligand docking. Utilizing a semi-immersive environment with stereo graphics, users are able to manipulate the ligand and feel its interactions in the docking process. The evaluation used cognitive knowledge tests and interviews focused on learning gains. Compared with using time efficiency as the single quality measure this gives a better indication of a system's applicability in an educational environment. Surveys were used to gather opinions and suggestions for improvements. Students do gain from using the application in the learning process but the learning appears to be independent of the addition of haptic feedback. However the addition of force feedback did decrease time requirements and improved the students understanding of the docking process in terms of the forces involved, as is apparent from the students' descriptions of the experience. The students also indicated a number of features which could be improved in future development.

Place, publisher, year, edition, pages
Piscataway, NJ, USA: IEEE, 2007
Keyword
Haptic Interaction, Haptics, Virtual Reality, Computer-assisted instruction, Life Science Education, Protein Interactions, Visualization, Protein-ligand docking
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-39934 (URN)10.1109/VR.2007.352478 (DOI)000245919300022 ()51733 (Local ID)1-4244-0906-3 (ISBN)51733 (Archive number)51733 (OAI)
Conference
IEEE Virtual Reality Conference, Charlotte, NC, USA, 10-14 March 2007
Note

©2009 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. Petter Bivall Persson, Matthew Cooper, Lena Tibell, Shaaron Ainsworth, Anders Ynnerman and Bengt-Harald Jonsson, Designing and Evaluating a Haptic System for Biomolecular Education, 2007, IEEE Virtual Reality Conference 2007, 171-178. http://dx.doi.org/10.1109/VR.2007.352478

Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2016-05-04Bibliographically approved
2. Improved Feature Detection over Large Force Ranges Using History Dependent Transfer Functions
Open this publication in new window or tab >>Improved Feature Detection over Large Force Ranges Using History Dependent Transfer Functions
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2009 (English)In: Third Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environments and Teleoperator Systems, WorldHaptics 2009, IEEE , 2009, 476-481 p.Conference paper, Published paper (Refereed)
Abstract [en]

In this paper we present a history dependent transfer function (HDTF) as a possible approach to enable improved haptic feature detection in high dynamic range (HDR) volume data. The HDTF is a multi-dimensional transfer function that uses the recent force history as a selection criterion to switch between transfer functions, thereby adapting to the explored force range. The HDTF has been evaluated using artificial test data and in a realistic application example, with the HDTF applied to haptic protein-ligand docking. Biochemistry experts performed docking tests, and expressed that the HDTF delivers the expected feedback across a large force magnitude range, conveying both weak attractive and strong repulsive protein-ligand interaction forces. Feature detection tests have been performed with positive results, indicating that the HDTF improves the ability of feature detection in HDR volume data as compared to a static transfer function covering the same range.

Place, publisher, year, edition, pages
IEEE, 2009
Keyword
Haptics, Virtual Reality, Scientific Visualization
National Category
Interaction Technologies
Identifiers
urn:nbn:se:liu:diva-45355 (URN)10.1109/WHC.2009.4810843 (DOI)81912 (Local ID)978-1-4244-3858-7 (ISBN)81912 (Archive number)81912 (OAI)
Conference
Third Joint EuroHaptics conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems. World Haptics 2009.Salt Lake City, UT, USA, 18-20 March 2009
Projects
VisMolLS
Note

©2009 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. Petter Bivall Persson, Gunnar E. Höst, Matthew D. Cooper, Lena A. E. Tibell and Anders Ynnerman, Improved Feature Detection over Large Force Ranges Using History Dependent Transfer Functions, 2009, Third Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environments and Teleoperator Systems, WorldHaptics 2009, 476-481. http://dx.doi.org/10.1109/WHC.2009.4810843

Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2016-05-04Bibliographically approved
3. Do Haptic Representations Help Complex Molecular Learning?
Open this publication in new window or tab >>Do Haptic Representations Help Complex Molecular Learning?
2011 (English)In: Science Education, ISSN 0036-8326, E-ISSN 1098-237X, Vol. 95, no 4, 700-719 p.Article in journal (Refereed) Published
Abstract [en]

This study explored whether adding a haptic interface (that provides users with somatosensory information about virtual objects by force and tactile feedback) to a three-dimensional (3D) chemical model enhanced students' understanding of complex molecular interactions. Two modes of the model were compared in a between-groups pre- and posttest design. In both modes, users could move and rotate virtual 3D representations of the chemical structures of the two molecules, a protein and a small ligand molecule. In addition, in a haptic mode users could feel the interactions (repulsive and attractive) between molecules as forces with a haptic device. Twenty postgraduate students (10 in each condition) took pretests about the process of protein--ligand recognition before exploring the model in ways suggested by structured worksheets and then completing a posttest. Analysis addressed quantitative learning outcomes and more qualitatively students' reasoning during the learning phase. Results showed that the haptic system helped students learn more about the process of protein–ligand recognition and changed the way they reasoned about molecules to include more force-based explanations. It may also have protected students from drawing erroneous conclusions about the process of protein–ligand recognition observed when students interacted with only the visual model.

Keyword
Haptic learning, multimodality, molecular interactions, protein-ligand docking
National Category
Didactics Biochemistry and Molecular Biology Media and Communication Technology
Identifiers
urn:nbn:se:liu:diva-60354 (URN)10.1002/sce.20439 (DOI)
Projects
VisMolLS
Available from: 2010-10-12 Created: 2010-10-12 Last updated: 2017-12-12
4. Using logging data to visualize and explore students’ interaction and learning with a haptic virtual model of protein-ligand docking
Open this publication in new window or tab >>Using logging data to visualize and explore students’ interaction and learning with a haptic virtual model of protein-ligand docking
(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
Interactive learning environments; multimedia systems; pedagogical issues; postsecondary education; virtual reality
National Category
Natural Sciences
Identifiers
urn:nbn:se:liu:diva-60355 (URN)
Available from: 2010-10-12 Created: 2010-10-12 Last updated: 2016-05-04
5. Haptic Just Noticeable Difference in Continuous Probing of Volume Data
Open this publication in new window or tab >>Haptic Just Noticeable Difference in Continuous Probing of Volume Data
2010 (English)Report (Other academic)
Abstract [en]

Just noticeable difference (JND) describes how much two perceptual sensory inputs must differ in order to be distinguishable from each other. Knowledge of the JND is vital when two features in a dataset are to be separably represented. JND has received a lot of attention in haptic research and this study makes a contribution to the field by determining JNDs during users' probing of volumetric data at two force levels. We also investigated whether these JNDs were affected by where in the haptic workspace the probing occurred. Reference force magnitudes were 0.1 N and 0.8 N, and the volume data was presented in rectangular blocks positioned at the eight corners of a cube 10 cm3 in size. Results showed that the JNDs varied significantly for the two force levels, with mean values of 38.5% and 8.8% obtained for the 0.1 N and 0.8 N levels, respectively, and that the JND was influenced by where the data was positioned.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2010. 19 p.
Series
Technical reports in Computer and Information Science, ISSN 1654-7233 ; 6
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-58011 (URN)
Available from: 2010-07-16 Created: 2010-07-16 Last updated: 2010-10-12Bibliographically approved

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  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
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Output format
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