Touching the Essence of Life : Haptic Virtual Proteins for Learning

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 molec ...

[1]  R. Moreno Cognitive load theory: more food for thought , 2010 .

[2]  Xing-Dong Yang,et al.  Perception of haptic force magnitude during hand movements , 2008, 2008 IEEE International Conference on Robotics and Automation.

[3]  A. Clark An embodied cognitive science? , 1999, Trends in Cognitive Sciences.

[4]  Xing-Dong Yang,et al.  The Effects of Hand Motion on Haptic Perception of Force Direction , 2008, EuroHaptics.

[5]  Thomas R. Tretter,et al.  Haptic Augmentation of Science Instruction: Does Touch Matter? , 2006 .

[6]  Kenneth M Merz,et al.  Haptic applications for molecular structure manipulation. , 2007, Journal of molecular graphics & modelling.

[7]  Yong-Gu Lee,et al.  Smoothing haptic interaction using molecular force calculations , 2004, Comput. Aided Des..

[8]  Erica Harvey,et al.  Haptic representation of the atom , 2000, 2000 IEEE Conference on Information Visualization. An International Conference on Computer Visualization and Graphics.

[9]  Allison M. Okamura,et al.  Feeling is Believing: Using a Force‐Feedback Joystick to Teach Dynamic Systems , 2000 .

[10]  Miriam Reiner,et al.  Visualization : theory and practice in science education , 2008 .

[11]  S. Ainsworth,et al.  Multiple Forms of Dynamic Representation. , 2004 .

[12]  J. Richardson,et al.  Teaching molecular 3‐D literacy , 2002 .

[13]  M A Srinivasan,et al.  Development and evaluation of an epidural injection simulator with force feedback for medical training. , 2001, Studies in health technology and informatics.

[14]  Stéphane Redon,et al.  A Force-Feedback Algorithm for Adaptive Articulated-Body Dynamics Simulation , 2007, Proceedings 2007 IEEE International Conference on Robotics and Automation.

[15]  野間 春生,et al.  Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems 参加報告 , 1997 .

[16]  Joseph Krajcik,et al.  Promoting understanding of chemical representations: Students' use of a visualization tool in the classroom , 2001 .

[17]  Scott T. Grafton,et al.  Involvement of visual cortex in tactile discrimination of orientation , 1999, Nature.

[18]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1974, Nature.

[19]  Miriam Reiner,et al.  Seeing Through Touch: The Role of Haptic Information in Visualization , 2008 .

[20]  Susana K. Lai-Yuen,et al.  Computer-aided molecular design (CAMD) with force-torque feedback , 2005, Ninth International Conference on Computer Aided Design and Computer Graphics (CAD-CG'05).

[21]  J. Edward Colgate,et al.  Psychophysical evaluation of a variable friction tactile interface , 2009, Electronic Imaging.

[22]  Douglas B. Clark,et al.  Helping students revise disruptive experientially supported ideas about thermodynamics: Computer visualizations and tactile models , 2004 .

[23]  Anders Ynnerman,et al.  Improved feature detection over large force ranges using history dependent transfer functions , 2009, World Haptics 2009 - Third Joint EuroHaptics conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems.

[24]  R. J. Irwin,et al.  Differential thresholds for limb movement measured using adaptive techniques , 1992, Perception & psychophysics.

[25]  Frederick P. Brooks,et al.  Force display performs better than visual display in a simple 6-D docking task , 1989, Proceedings, 1989 International Conference on Robotics and Automation.

[26]  Paul P. Maglio,et al.  On Distinguishing Epistemic from Pragmatic Action , 1994, Cogn. Sci..

[27]  Shaaron Ainsworth,et al.  The functions of multiple representations , 1999, Comput. Educ..

[28]  David S. Goodsell,et al.  Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4 , 1996, J. Comput. Aided Mol. Des..

[29]  Nancy M. Amato,et al.  Ligand Binding with OBPRM and Haptic User Input: Enhancing Automatic Motion Planning with Virtual Touch , 2000 .

[30]  R. Kozma,et al.  Multimedia and understanding: Expert and novice responses to different representations of chemical phenomena , 1997 .

[31]  Kirsten Rassmus-Gröhn,et al.  User Centered Design of Non-Visual Audio-Haptics , 2008 .

[32]  Miriam Reiner,et al.  The role of haptics in immersive telecommunication environments , 2004, IEEE Transactions on Circuits and Systems for Video Technology.

[33]  Stéphane Régnier,et al.  Stable six degrees of freedom haptic feedback for flexible ligand-protein docking , 2009, Comput. Aided Des..

[34]  John Kenneth Salisbury,et al.  Haptic Feedback Enhances Force Skill Learning , 2007, Second Joint EuroHaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems (WHC'07).

[35]  Roberta L. Klatzky,et al.  Measuring just noticeable differences for haptic force feedback: implications for rehabilitation , 2002, Proceedings 10th Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems. HAPTICS 2002.

[36]  Heather Carnahan,et al.  Evidence for haptic memory , 2009, World Haptics 2009 - Third Joint EuroHaptics conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems.

[37]  John K. Gilbert,et al.  Visualization: An Emergent Field of Practice and Enquiry in Science Education , 2008 .

[38]  Miriam Reiner,et al.  Sensory Cues, Visualization and Physics Learning , 2009 .

[39]  Anders Ynnerman,et al.  Designing and Evaluating a Haptic System for Biomolecular Education , 2007, 2007 IEEE Virtual Reality Conference.

[40]  R. Kozma,et al.  The Roles of Representations and Tools in the Chemistry Laboratory and Their Implications for Chemistry Learning , 2000 .

[41]  Aleš Křenek,et al.  Haptic visualization of molecular model , 2007 .

[42]  R E Johnston,et al.  Visual psychophysics and medical imaging: nonparametric adaptive method for rapid threshold estimation in sensitivity experiments. , 1990, IEEE transactions on medical imaging.

[43]  Thomas Huk,et al.  Who benefits from learning with 3D models? the case of spatial ability , 2006, J. Comput. Assist. Learn..

[44]  Nancy M. Amato,et al.  Ligand binding with OBPRM and user input , 2001, Proceedings 2001 ICRA. IEEE International Conference on Robotics and Automation (Cat. No.01CH37164).

[45]  Charles D. Hansen,et al.  A constraint-based technique for haptic volume exploration , 2003, IEEE Visualization, 2003. VIS 2003..

[46]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..

[47]  David S. Ebert,et al.  Multi-modal perceptualization of volumetric data and its application to molecular docking , 2005, First Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems. World Haptics Conference.

[48]  Michael Goldfarb,et al.  The effect of force saturation on the haptic perception of detail , 2002 .

[49]  Yuan-Shin Lee,et al.  Interactive Computer-Aided Design for Molecular Docking and Assembly , 2006 .

[50]  Michel F. Sanner,et al.  Role of haptics in teaching structural molecular biology , 2003, 11th Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems, 2003. HAPTICS 2003. Proceedings..

[51]  G. Höst Engineering carbonic anhydrase for highly selective ester hydrolysis , 2007 .

[52]  Sandra K. Abell,et al.  What is science?: preservice elementary teachers’ conceptions of the nature of science , 1994 .

[53]  M F Sanner,et al.  Python: a programming language for software integration and development. , 1999, Journal of molecular graphics & modelling.

[54]  M. G. Jones,et al.  Haptics in Education: Exploring an Untapped Sensory Modality , 2006 .

[55]  G. Bower,et al.  THE PSYCHOLOGY OF LEARNING AND M·OTIVATION , 2001 .

[56]  Richard E. Mayer,et al.  Seeking a science of instruction , 2010 .

[57]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[58]  Jing Wang,et al.  Visual Haptic-Based Biomolecular Docking and Its Applications in E-Learning , 2009, Trans. Edutainment.

[59]  Allison M. Okamura,et al.  Educational Haptics , 2007, AAAI Spring Symposium: Semantic Scientific Knowledge Integration.

[60]  R. Mayer,et al.  Interactive Multimodal Learning Environments , 2007 .

[61]  Anatole Lécuyer,et al.  Improving Perception and Understanding of Nanoscale Phenomena Using Haptics and Visual Analogy , 2008, EuroHaptics.

[62]  Hiroshi Tanaka,et al.  Concept and prototype of protein-ligand docking simulator with force feedback technology , 2002, Bioinform..

[63]  Frederick P. Brooks,et al.  Using a manipulator for force display in molecular docking , 1988, Proceedings. 1988 IEEE International Conference on Robotics and Automation.

[64]  E. Fava Sensation & Perception , 2004, NeuroImage.

[65]  Jerome Smith,et al.  A just noticeable difference for meaningfulness , 1969 .

[66]  Ruth B. Ekstrom,et al.  Manual for kit of factor-referenced cognitive tests , 1976 .

[67]  Y. Matsuoka,et al.  The tolerance for visual feedback distortions in a virtual environment , 2002, Physiology & Behavior.

[68]  H. Levitt Transformed up-down methods in psychoacoustics. , 1971, The Journal of the Acoustical Society of America.

[69]  Scott T. Grafton,et al.  Feeling with the mind's eye , 1997, Neuroreport.

[70]  D. Goodsell,et al.  Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.

[71]  Anatole Lécuyer,et al.  Virtual technical trainer: learning how to use milling machines with multi-sensory feedback in virtual reality , 2005, IEEE Proceedings. VR 2005. Virtual Reality, 2005..

[72]  Suzanne Weghorst Augmented Tangible Molecular Models , 2003 .

[73]  Chris Harding,et al.  Improving Introductory Calculus Education with 3-D Visualizationand Virtual Touch (Haptics) , 2007, Second International Multi-Symposiums on Computer and Computational Sciences (IMSCCS 2007).

[74]  Lois W. Sayrs Interviews : an introduction to qualitative research interviewing , 1996 .

[75]  Gábor Székely,et al.  Computationally efficient techniques for data-driven haptic rendering , 2009, World Haptics 2009 - Third Joint EuroHaptics conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems.

[76]  Alain Micaelli,et al.  6 DOF haptic feedback for molecular docking using wave variables , 2007, Proceedings 2007 IEEE International Conference on Robotics and Automation.

[77]  Trevor R Anderson,et al.  The importance of visual literacy in the education of biochemists * , 2006, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[78]  René Verry,et al.  Don't Take Touch for Granted: An Interview with Susan Lederman , 1998 .

[80]  Jimmy Johansson,et al.  Efficient Information Visualization of Multivariate and Time-Varying Data , 2008 .

[81]  P. Shah,et al.  Exploring visuospatial thinking in chemistry learning , 2004 .

[82]  James D. Slotta,et al.  Helping Students Understand Challenging Topics in Science Through Ontology Training , 2006 .

[83]  A. H. Johnstone,et al.  You Can’t Get There from Here1 , 2010 .

[84]  MICHAEL J. JACOBSON,et al.  Problem solving, cognition, and complex systems: Differences between experts and novices , 2001, Complex..

[85]  Vincent Hayward,et al.  Local Surface Orientation Dominates Haptic Curvature Discrimination , 2009, IEEE Transactions on Haptics.

[86]  M. F.,et al.  Bibliography , 1985, Experimental Gerontology.

[87]  Allison M. Okamura,et al.  Virtual Environment for Exploring Atomic Bonding , 2004 .

[88]  Cagatay Basdogan,et al.  Haptics in minimally invasive surgical simulation and training , 2004, IEEE Computer Graphics and Applications.

[89]  M K Kaiser,et al.  How baseball outfielders determine where to run to catch fly balls. , 1995, Science.

[90]  Klaus Schulten,et al.  A system for interactive molecular dynamics simulation , 2001, I3D '01.

[91]  Miriam Reiner,et al.  Conceptual Construction of Fields Through Tactile Interface , 1999, Interact. Learn. Environ..

[92]  Erk Subasi,et al.  A New Haptic Interaction and Visualization Approach for Rigid Molecular Docking in Virtual Environments , 2008, PRESENCE: Teleoperators and Virtual Environments.

[93]  Roberta L. Klatzky,et al.  JND Analysis of Texture Roughness Perception using a Magnetic Levitation Haptic Device , 2007, Second Joint EuroHaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems (WHC'07).

[94]  M. Gail Jones,et al.  Learning at the nanoscale: The impact of students' use of remote microscopy on concepts of viruses, scale, and microscopy , 2003 .

[95]  T. Jong Cognitive load theory, educational research, and instructional design: some food for thought , 2010 .

[96]  Robert B. Kozma,et al.  Students Becoming Chemists: Developing Representationl Competence , 2005 .

[97]  Mark Wright,et al.  The Effect of Haptic Feedback and Stereo Graphics in a 3D Target Acquisition Task , 2002 .

[98]  Frederick P. Brooks,et al.  Project GROPEHaptic displays for scientific visualization , 1990, SIGGRAPH.

[99]  Shaaron Ainsworth How Should We Evaluate Multimedia Learning Environments , 2008 .