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Touching the Essence of Life : Haptic Virtual Proteins for Learning
... Their system utilized a modified Argonne E-3 Remote Manipulator (ARM) for ligand movement and force feedback display, and managed to accelerate the docking of small rigid molecules by a factor of two. Subsequent works investigated the benefits of haptics in computer-aided drug design [13], in rational drug design [14], in computer-aided molecular design [15], for the study of protein-drug and protein-protein interactions [9,16,17], and in e-learning and education [18][19][20][21]. These studies indicated that hapticsassisted docking can help users' (experts or students of structural biol ogy) learn about the process of molecular binding, and experts to improve upon docking conformations that have not been (or could not be) verified experimentally. ...
Interactive haptics-assisted docking provides a virtual environment for the study of molecular complex formation. It enables the user to interact with the virtual molecules, experience the interaction forces via their sense of touch, and gain insights about the docking process itself. Here we use a recently developed haptics software tool, Haptimol_RD, for the rigid docking of protein subunits to form complexes. Dimers, both homo and hetero, are loaded into the software with their subunits separated in space for the purpose of assessing whether they can be brought back into the correct docking pose via rigid-body movements. Four dimers were classified into two types: two with an interwinding subunit interface and two with a non-interwinding subunit interface. It was found that the two with an interwinding interface could not be docked whereas the two with the non-interwinding interface could be. For the two that could be docked a “sucking” effect could be felt on the haptic device when the correct binding pose was approached which is associated with a minimum in the interaction energy. It is clear that for those that could not be docked, the conformation of one or both of the subunits must change upon docking. This leads to the steric-based concept of a locked or non-locked interface. Non-locked interfaces have shapes that allow the subunits to come together or come apart without the necessity of intra-subunit conformational change, whereas locked interfaces require a conformational change within one or both subunits for them to be able to come apart.
... al. [21]. Force grid systems usually treat both molecules or just the receptor as rigid structures, and pre-compute a 3D force grid of the van der Waals (vdW) and/or electrostatic 50 forces around the receptor [21,22,23,24,25,26] or the receptor's active site [27]. ...
Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loop should run at rates of 500Hz to 1kHz. We present an adaptive force calculation approach that can be executed in parallel on a wide range of Graphics Processing Units (GPUs) for interactive haptics-assisted docking with wider applicability to molecular simulations. Prior to the interactive session either a regular grid or an octree is selected according to the available GPU memory to determine the set of interatomic interactions within a cutoff distance. The total force is then calculated from this set. The approach can achieve force updates in less than 2ms for molecular structures comprising hundreds of thousands of atoms each, with performance improvements of up to 90 times the speed of current CPU-based force calculation approaches used in interactive docking. Furthermore, it overcomes several computational limitations of previous approaches such as pre-computed force grids, and could potentially be used to model receptor flexibility at haptic refresh rates.
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The drive to make human-computer interactions more efficient and effortless has pushed interface designers to think about new methods of information transmission, display and manipulation. The incorporation of haptic feedback cues into the computer interfacing schematic allows the tactile channel to be opened up as a means of complementing and challenging the data provided by the senses of seeing and hearing. In this article, using the Novint Corporation's Falcon three-dimensional touch interface as a case study, the author examines the strategic aims of animating and scaling computer-generated space for the haptic. Spaces of heterogeneous scales, from the microscopic to the macroscopic, can be rendered as analogous force sensations using the Falcon's three-dimensional workspace. The author argues that the project of incorporating complex touch feedback into computing entails not just a transformation of spatiotemporal field accessed by touch, but a wholesale redefinition and rearticulation of touch as a category of human experience.
Cagatay Basdogan 2 C o l l e g e o f E n g i n e e r i n g , K o c U n i v e r s i t y, I s ta n b u l , 3 4 4 5 0 C o l l e g e o f E n g i n e e r i n g , K o c U n i v e r s i t y, I s ta n b u l , 3 4 4 5 0 ABSTRACT In this paper, we present computationally efficient methods for visualization and simulation of molecular interactions in virtual environments with haptic feedback. In our simulations, the haptic device is used to guide a rigid ligand molecule into a receptor site while the molecular forces acting on the ligand molecule are scaled and reflected to the user in real-time. We demonstrate that the presence of a haptic interface accelerates the binding process and reduce the binding errors if it is used as a precursor to estimate the initial configuration of the ligand molecule at the binding site. After placement and rough alignment of the ligand molecule inside the binding cavity with the help of a haptic device, we use a novel computational approach to determine the final binding configuration of the ligand molecule. In this approach, the ligand molecule is treated as a rigid body seeking for the lowest potential configuration. The intermediate rigid body configurations of the ligand molecule is calculated in a least square sense using the new positions of its atoms moving under the influence of molecular interaction forces. The proposed approach is computationally more efficient than the molecular simulation methods that utilize the standard rigid-body formulations. We also present new methods for haptic visualization of a protein surface interactively to search for potential binding sites.
In this historical and observational study, we describe how scientists use representations and tools in the chemistry laboratory, and we derive implications from these findings for the design of educational environments. In our observations we found that chemists use representations and tools to mediate between the physical substances that they study and the aperceptual chemical entities and processes that underlie and account for the material qualities of these physical substances. There are 2 important, interrelated aspects of this mediational process: the material and the social. The 1st emphasizes the surface features of both physical phenomena and symbolic representations, features that can be perceived and manipulated. The 2nd underscores the inherently semiotic, rhetorical process whereby chemists claim that representations stand for unseen entities and processes. In elaborating on our analyses, we • Examine the historical origins and contemporary practices of representation use in one particular domain - chemistry - to look at how developments in the design of representations advance the development of a scientific community, as well as the understanding of scientists engaged in laboratory practice. • Examine representations spontaneously generated by chemists, as well as those generated by their tools or instruments, and look at how scientists - individually and collaboratively - coordinate these 2 types of representations with the material substances of their investigations to understand the structures and processes that underlie them. • Draw implications from the study of scientists to make recommendations for the design of learning environments and symbol systems that can support the use of representations by students to understand the structures and processes that underlie their scientific investigations and to engage them in the practices of knowledge-building communities.
As human beings, we can interact with our environment through the sense of touch, which helps us to build an understanding of objects and events. The implications of touch for cognition are recognized by many educators who advocate the use of "hands-on" instruction. But is it possible to know some- thing more completely by touching it? Does touch promote the construction ofnmore connected and meaningful understandings? Current technology makes the addition of touch to computer-generated environments possible, but the educational implications of this innovation are still largely unknown. This article is a baseline review that examines the role of touch in cognition and learning and explores the research investigating the efficacy of the haptic augmentation of instruction.
Bodily manipulations, such as juggling, suggest a well‐synchronized physical interaction as if the person were a physics expert. The juggler uses “knowledge” that is rooted in bodily experience, to interact with the environment. Such enacted bodily knowledge is powerful, efficient, predictive, and relates to sensory perception of the dynamics of objects. This paper describes results of an empirical study in physics learning, aimed at exploring links between sensory input, visual representations, and corresponding conceptual learning in physics. The central finding is that through sensory interaction (e.g., touch, vision) with a physical system in the physics laboratory, learners spontaneously generate a novel reference‐system of pictorial representations, typical to the situation explored. Results show that in collaborative hands‐on problem‐solving in physics, a pictorial referential communication system is generated. Elements of the pictorial communication system were found to be one of three: photographic, metaphoric, or symbolic. The constituents of the communication system are socially shared, hence valid, are used repeatedly when similar experience happens, therefore consistent. Thus visual‐spatial representations of non‐explicit knowledge turn into pictorial representations for communication. It is powerful because it allows access and retrieval of tacit knowledge, inaccessible by symbolic interaction.
In two experiments, we examined how professional chemists (i.e., experts) and undergraduate chemistry students (i.e., novices) respond to a variety of chemistry representations (video segments, graphs, animations, and equations). In the first experiment, we provided subjects with a range of representations and asked them to group them together in any way that made sense to them. Both experts and novices created chemically meaningful groupings. Novices formed smaller groupings and more often used same-media representations. Experts used representations in multiple media to form larger groups. The reasons experts gave for their groupings were judged to be conceptual, while those of novices were judged to be based on surface features. In the second experiment, subjects were asked to transform a range of representations into specified alternative representations (e.g., given an equation and asked to draw a graph). Experts were better than novices in providing equivalent representations, particularly verbal descriptions for any given representation. We discuss the role that surface features of representations play in the understanding of chemistry, and we emphasize the importance of developing representational competence in chemistry students. We draw implications for the role that multiple representations—particularly linguistic ones—should play in chemistry curriculum, instruction, and assessment. © 1997 John Wiley & Sons, Inc. J Res Sci Teach 34: 949–968, 1997.
A virtual world for exploring the interactions of atoms is described. The program was created in order to provide an alternative to traditional meth- ods of teaching chemistry to pre-college students. A haptic interface allows a user of the program to experience a recreation of the forces that would be pre- sent during real world atomic interactions. A first order simulation of atomic in- teraction is described, sufficiently simple that real-time calculations may be performed with the model. The program underwent preliminary testing during a hands-on demonstration. Based on initial feedback from users, an experiment was designed to evaluate the benefits of haptic feedback in assembling mole- cules. The results show that by providing force feedback, it is possible to de- crease the amount of time required to create a simple molecule in a virtual envi- ronment. The next phase of testing will be to demonstrate the utility of the simulator in an elementary school classroom.
Internet-based telepresence and teleaction systems require packet-based transmission of haptic data and typically gener-ate high packet rates between operator and teleoperator. This leads to the necessity of packet rate reduction techniques. The so-called deadband approach presented earlier by the authors uses a psychophysically motivated scheme based on Weber's difference threshold (just noticable difference -JND) where force sample values are only transmitted if the change ex-ceeds this threshold. This approach has been extended to three dimensions resulting in an additional perceptual domain -namely force direction. An experimental evaluation with hu-man subjects was conducted in order to examine the change of the JND in 3D when force magnitude and force direction are combined. Our results show that the extension into dimen-sions yields to an increased JND in certain cases. Thus, higher compression ratios of haptic data and reduction in number of packets sent over the network can be reached.
This chapter examines the role that representations and visualizations can play in the chemical curriculum. Two types of curricular
goals are examined: students’ acquisition of important chemical concepts and principles and students’ participation in the
investigative practices of chemistry—“students becoming chemists.” Literature in learning theory and research support these
two goals and this literature is reviewed. The first goal relates to cognitive theory and the way that representations and
visualizations can support student understanding of concepts related to molecular entities and processes that are not otherwise
available for direct perception. The second goal relates to situative theory and the role that representations and visualizations
play in development of representational competence and the social and physical processes of collaboratively constructing an
understanding of chemical processes in the laboratory. We analyze research on computer-based molecular modeling, simulations,
and animations from these two perspectives and make recommendations for instruction and future research.
This paper introduces a novel algorithm for haptic interaction with an adaptive simulation of articulated-body dynamics. Our algorithm has a multi-threaded structure, which allows us to separate the force feedback computation from the adaptive dynamics simulation. The algorithm we propose for force feedback computation has a logarithmic complexity in the number of degrees of freedom in the articulated body. We have implemented our approach and tested it on a 3.0GHz dual processor Xeon PC. The preliminary benchmarks presented here demonstrate that our multi-threaded approach, as well as the logarithmic complexity of the force feedback computation, allow us to interact in a stable way with large articulated bodies that have complex dynamics (such as articulated-body models of proteins). Whatever the update rate of the adaptive simulation loop, the force feedback computation is performed in a few tens of microseconds.
This paper presents a new method for a six degrees of freedom haptic feedback in molecular docking simulations in virtual reality. The proposed method allows real-time haptic interaction even in the case of classical molecular simulation which implies notoriously long computation time. These simulations are classically used by the pharmaceutical industry (Sanofi-Aventis) and are based on the energetic description of atoms to estimate the interaction between a ligand and a protein. The haptic control scheme uses wave variables for a stable and robust teleoperation, and a transcription of the calculated energy into forces and torques for the manipulation of a flexible ligand around the binding site of a flexible molecule. This method can then be used with any energetic force field using a minimization process, thus avoiding the fastidious optimization of molecular simulation programs.
Prior studies have shown that local surface orientation is a dominant source of information for haptic curvature perception in static conditions. We show that this dominance holds for dynamic touch, just as was shown earlier for static touch. Using an apparatus specifically developed for this purpose, we tested this hypothesis by providing observers with two independently controlled sources of geometric information. The robotic-like apparatus could accurately control the position of a contact surface independently from its orientation in space, while allowing subjects to freely and actively explore virtual shapes in the lateral direction. In the first experiment, we measured discrimination thresholds for the two types of shape information and compared the discrimination of real shapes to that of virtual shapes. The results confirmed the dominance of local surface orientation. We propose a model that predicts cue dominance for different scales of exploration. In the second experiment, we investigated whether a virtual curved surface felt as curved as a real curved surface. We found that observers did not systematically judge either of the two kinds of stimuli to be more curved than the other. More importantly, we found that points of subjective curvedness were not influenced by the availability of height information.
We present a framework for studying ligand binding which is based on techniques recently developed in the robotics motion planning community. We are interested in locating binding sites on the protein for ligand molecule. Our work investigates the performance of a fully automated motion planner, as well as the effects of supplementary user input collected using a haptic device. Our results applying an obstacle-based probabilistic roadmap motion planning algorithm (OBPRM) to some protein-ligand complexes are encouraging. The framework successfully identified potential building sites for all complexes studied. We find that user input helps the planner, and haptic device helps the user to understand the protein structure by enabling them to feel the difficult-to-visualize forces.
External representations (pictures, diagrams, graphs, concrete models) have always been valuable tools for the science teacher. The formation of personal, internal, representations – visualizations – from them plays a key role in all learning, especially in that of science. The use of personal computers and sophisticated software has expanded into the areas of simulation, virtual reality, and animation, and students now engage in the creation of models, a key aspect of scientific methodology. Several academic disciplines underlie these developments, yet act independently of each other, to the detriment of an attainment of what is possible. This book brings together the insights of practicing scientists, science education researchers, computer specialists, and cognitive scientists, to produce a coherent overview. It links presentations about the cognitive theory of representation and visualization, its implications for science curriculum design, and for learning and teaching in classrooms and laboratories.
A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the free energy change upon binding. Interestingly, this method applies a Lamarckian model of genetics, in which environmental adaptations of an individual's phenotype are reverse transcribed into its genotype and become heritable traits (sic). We consider three search methods, Monte Carlo simulated annealing, a traditional genetic algorithm, and the Lamarckian genetic algorithm, and compare their performance in dockings of seven protein–ligand test systems having known three-dimensional structure. We show that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTODOCK, and that the Lamarckian genetic algorithm is the most efficient, reliable, and successful of the three. The empirical free energy function was calibrated using a set of 30 structurally known protein–ligand complexes with experimentally determined binding constants. Linear regression analysis of the observed binding constants in terms of a wide variety of structure-derived molecular properties was performed. The final model had a residual standard error of 9.11 kJ mol⁻¹ (2.177 kcal mol⁻¹) and was chosen as the new energy function. The new search methods and empirical free energy function are available in AUTODOCK, version 3.0. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1639–1662, 1998
Chi (2005) proposed that students experience difficulty in learning about physics concepts such as light, heat, or electric current because they attribute to these concepts an inappropriate ontological status of material substances rather than the more veridical status of emergent processes. Conceptual change could thus be facilitated by training students in the appropriate ontology prior to physics instruction. We tested this prediction by developing a computer-based module whereby participants learned about emergent processes. Control participants completed a computer-based task that was uninformative with respect to ontology. Both groups then studied a physics text concerned with electricity, including explanations and a posttest. Verbal explanations and qualitative problem solutions revealed that experimental students gained a deeper understanding of electric current.
Physical models of biomolecular components and their interactions are extraordinarily useful aids in understanding complex biological structure and organization. With our collaborators at The Scripps Research Institute (TSRI) and the University of Utah we are exploring the production of such models through autofabrication technology, and augmenting them with a variety of interface modalities, including augmented visual overlays, haptic interaction, voice command input, auditory displays, and "data probe" interaction. Our multi- modality mixed reality approach is integrated around PMV, TSRI's Python-based molecular visualization software. Results of this collaborative development project are proving useful for both molecular biology research and teaching.
Discriminability along the dimension of meaningfulness, as defined by Noble's m′ scale, was studied in two experiments. In a pilot experiment, an attempt to establish the just noticeable difference (j.n.d.) at two portions of the scale (high and medium) was unsuccessful since the j.n.d. apparently exceeded the range of scale values used (1/6 of the scale). Therefore, the first experiment made use of a much larger portion of the scale (2/3) and a single j.n.d. was calculated at .96, a value representing 1/5 of the entire scale. The Ss in the second study were run individually as opposed to the group situation of the first. The difference threshold in the second experiment was smaller, about 1/7 of the whole scale. Reasons for the differences among the pilot study and the two experiments were discussed, and suggestions made about the use of m′ as an independent variable, in light of the large j.n.d.
This paper presents a computer-aided design system for molecular docking and nanoscale assembly . A lab-built 5-DOF (degree of freedom) haptic device and the driving computational engine have been developed to provide force-torque feedback to the users for computer-aided molecular design (CAMD). The developed haptic force-torque feedback will enable researchers to visualize, touch, manipulate and assemble molecules in a virtual environment. The presented techniques can be used in the computer-aided molecular design to provide the researchers a real- time tool to better understand molecular interactions and to evaluate possible pharmaceutical drugs and nanoscale devices. Computer implementation and illustrative examples are also presented in this paper.
Science for All Americans declares that an understanding of the nature of science is one criterion of scientific literacy. Unfortunately practising science teachers often misunderstand and misrepresent the nature of their disciplines. In this study we have attempted to construct an understanding of preservice elementary teachers' views by analysing their written responses to questions about the nature of science. We used analytic induction to derive categories and themes from the data and then formulated generalizations from these themes. Our findings reveal that out students have realist and positivist views of the scientific enterprise, and that they place little emphasis on the social or creative dimensions of the discipline. These preservice teachers will soon offer young children their first experiences with school science; their beliefs about the nature of science have implications for their science teaching and for their students' science learning.
This paper examines the role of tactile perception in conceptual construction of forces and fields. The learning environment includes a simulation of a force field. The force applied by the field on an object is transferred to the learner's hand through a tactile interface designed as a trackball. The learner experiences varying resistance from the trackball when moving an object on the screen. The forces are actually “felt”, exerted on the screen-object as if the learner's hand is immersed in the “field.” We hypothesize that a tactile interface acts as an agent aimed at recruiting the body non-propositional knowledge, for construction of formal physics knowledge on fields of forces. Twelve subjects were asked to explore the structure of several invisible fields through tactile interface, then to design a series of situations that generate current and that energetically trap a particle in a particular area. The results of the study show that s tudents with no background in physics constructed a graphical representation of a field force of a single and double center of forces similar to the formal physics representation, though they had no conceptual background (i.e., vectors, field lines). Based on the tactile information, they constructed a representation of force as a vector, of force lines, equal-force lines (potential lines for particular cases), potential well (“trap”) and motion of a charged particle in a field of forces. We show that computer tactile interface acts as a trigger for access to non-propositional knowledge employed in everyday bodily activity, but not in formal learning. The computer environment turns into a virtual environment, carrying the features of perception within “reality”, providing opportunities for conceptual construction.
MENTAL imagery is thought to play a key role in certain aspects of visual perception and to depend on neural activity in visual cortex. We asked whether tactile discrimination of grating orientation, which appears to involve visual mental imagery, recruits visual cortical areas. (H2O)-O-15 positron emission tomography was performed in humans during presentation of gratings to the right index fingerpad. Selective attention to grating orientation significantly increased regional cerebral blood flow, relative to a control task involving selective attention to grating dimensions, in a region located in left parieto-occipital cortex. We propose that this activation reflects the use of imagery-related visuo-spatial processes to enable the tactile discrimination of orientation.
In this article, we examine the role of visuospatial cognition in chemistry learning. We review three related kinds of literature: correlational studies of spatial abilities and chemistry learning, students' conceptual errors and difficulties understanding visual representations, and visualization tools that have been designed to help overcome these limitations. On the basis of our review, we conclude that visuospatial abilities and more general reasoning skills are relevant to chemistry learning, some of students' conceptual errors in chemistry are due to difficulties in operating on the internal and external visuospatial representations, and some visualization tools have been effective in helping students overcome the kinds of conceptual errors that may arise through difficulties in using visuospatial representations. To help students understand chemistry concepts and develop representational skills through supporting their visuospatial thinking, we suggest five principles for designing chemistry visualization tools: (1) providing multiple representations and descriptions, (2) making linked referential connections visible, (3) presenting the dynamic and interactive nature of chemistry, (4) promoting the transformation between 2D and 3D, and (5) reducing cognitive load by making information explicit and integrating information for students.
Susan Lederman (SL) is an invited member of the International Council of Research Fellows for the Braille Research Center and a Fellow of he Canadian Psychology Association. She was also an Associate of the Canadian Institute for Advanced Research in the Robotics and Artificial Intelligence Programme for 8 years. A Professor in the Departments of Psychology and Computing & Information Science at Queen's University at Kingston (Ontario, Canada), she has written and coauthored numerous articles on tactile psychophysics, haptic perception and cognition, motor control, and haptic applications in robotics, teleoperation, and virtual environments. She is currently the coorganizer of the Annual Symposium a Haptic Interfaces for Teleoperation and Virtual Environment Systems. René Verry (RV) is a psychology professor at Millikin University (Decatur, IL), where she teaches a variety of courses in the experimental core, including Sensation and Perception. She chose the often-subordinated somatic senses as the focus of her interview, and recruited Susan Lederman as our research specialist.
Large curricular changes of the 1960s brought about by the ChemStudy and Chemical Bond Approach initiatives were generally successful, but they also created learning problems. These were well recognized by a series of surveys in 1971. Recent surveys (2008) show that the same chemical difficulties for learners are still present in most “modern” curricula at all levels. This is despite the efforts of many international research projects designed to improve the learning of chemistry. The common factor in all these problem areas for chemistry students is information overload. The effect of having these problematic topics in the curriculum is to drive students away from chemistry. We have come to accept that these topics are fundamental to learning chemistry, but are they so essential? Are we blindly teaching them because they have “always been taught”? This paper suggests a bold approach, which questions the inclusion of these problematic topics and suggests models by which a pragmatic revision can take place without dilution or trivialization of chemistry as a discipline. Urgent joint action by the ACS, the Royal Society of Chemistry, and other international chemical societies is recommended.Keywords (Audience): First-Year Undergraduate/General; Graduate Education/Research; High School/Introductory Chemistry; Second-Year Undergraduate; Upper-Division Undergraduate
This study analyzes the impact of an integrated sensory model within a thermal equilibrium visualization. We hypothesized that this intervention would not only help students revise their disruptive experientially supported ideas about why objects feel hot or cold, but also increase their understanding of thermal equilibrium. The analysis synthesizes test data and interviews to measure the impact of this strategy. Results show that students in the experimental tactile group significantly outperform their control group counterparts on posttests and delayed posttests, not only on tactile explanations, but also on thermal equilibrium explanations. Interview transcripts of experimental and control group students corroborate these findings. Discussion addresses improving the tactile model as well as application of the strategy to other science topics. The discussion also considers possible incorporation of actual kinetic or thermal haptic feedback to reinforce the current audio and visual feedback of the visualization. This research builds on the conceptual change literature about the nature and role of students' experientially supported ideas as well as our understanding of curriculum and visualization design to support students in learning about thermodynamics, a science topic on which students perform poorly as shown by the National Assessment of Educational Progress (NAEP) and Third International Mathematics and Science Study (TIMSS) studies. © 2003 Wiley Periodicals, Inc. J Res Sci Teach 41: 1–23, 2004
Many students have difficulty learning symbolic and molecular representations of chemistry. This study investigated how students developed an understanding of chemical representations with the aid of a computer-based visualizing tool, eChem, that allowed them to build molecular models and view multiple representations simultaneously. Multiple sources of data were collected with the participation of 71 eleventh graders at a small public high school over a 6-week period. The results of pre- and posttests showed that students' understanding of chemical representations improved substantially (p < .001, effect size = 2.68-. The analysis of video recordings revealed that several features in eChem helped students construct models and translate representations. Students who were highly engaged in discussions while using eChem made referential linkages between visual and conceptual aspects of representations. This in turn may have deepened their understanding of chemical representations and concepts. The findings also suggest that computerized models can serve as a vehicle for students to generate mental images. Finally, students demonstrated their preferences of certain types of representations and did not use all types of three-dimensional models interchangeably. © 2001 John Wiley & Sons, Inc. J Res Sci Teach 38: 821–842, 2001
This study investigated the impact of haptic augmentation of a science inquiry program on students' learning about viruses and nanoscale science. The study assessed how the addition of different types of haptic feedback (active touch and kinesthetic feedback) combined with computer visualizations influenced middle and high school students' experiences. The influences of a PHANToM (a sophisticated haptic desktop device), a Sidewinder (a haptic gaming joystick), and a mouse (no haptic feedback) interface were compared. The levels of engagement in the instruction and students' attitudes about the instructional program were assessed using a combination of constructed response and Likert scale items. Potential cognitive differences were examined through an analysis of spontaneously generated analogies that appeared during student discourse. Results showed that the addition of haptic feedback from the haptic-gaming joystick and the PHANToM provided a more immersive learning environment that not only made the instruction more engaging but may also influence the way in which the students construct their understandings about abstract science concepts. © 2005 Wiley Periodicals, Inc. Sci Ed90:111–123, 2006
The rapid pace of development is bringing advanced technologies to the World Wide Web (WWW), and, as a result, schools have access to new tools for science investigations. In this exploratory study, we investigated how an educational experience organized around students' use of a WWW-controllable atomic force microscope (AFM) influenced students' understandings of viruses. The context for the study was a weeklong unit on viruses for two high school biology classes which incorporated student use of the WWW controllable AFM. We also investigated how the haptic (involving kinesthetics and touch) experiences afforded by this tool might influence students' knowledge of viruses, microscopy, and nanometer scale. Fifty students from two high school biology classes participated in a series of instructional activities and pre- and postassessments (knowledge test, opinion questionnaire, and interviews). Results showed that students' understandings of microscale, virus morphology, and dimensionality changed as a result of the experiences. Students' conceptions moved from a two-dimensional textbook-like image of a virus to a three-dimensional image of an adenovirus. The results of this preliminary study suggest that the use of the technology as a tool for learning about morphology of materials too small to see may be beneficial. © 2003 Wiley Periodicals, Inc. J Res Sci Teach 40: 303–322, 2003
This chapter presents evidence for the development of visualizationbreak through touch when in circumstances where no visual
information is provided. Results reported here show that local touch is translated into gestalt whole visualized patterns.
It further shows that haptics, perception through touch, has semantics and that specific force patterns that constitute haptic
interactions act as elements of information that are translated into visual images. It is shown that regions in the occipital
brain, especially the Lateral Occipital Tactile-Visual Area, are activated when subjects attempt to recognize a shape haptically.
Visualization of haptic patterns provides holistic gestalt views based on local haptic sensory cues. Haptic information contributes
the micro details to visualization while the macro details are contributed by the human-visual system. It is further concluded
that these findings about the processes of touch – visualization have major implications for design of cognitive technology
with the intention of improving learning. A combination of touch and visual cues is advantageous to learning, providing more
than each for the construction of a meaningful image of the world.
What are interactive multimodal learning environments and how should they be designed to promote students’ learning? In this
paper, we offer a cognitive–affective theory of learning with media from which instructional design principles are derived.
Then, we review a set of experimental studies in which we found empirical support for five design principles: guided activity,
reflection, feedback, control, and pretraining. Finally, we offer directions for future instructional technology research.
Early research with multimedia environments questioned whether these environments are effective in supporting learning. More
recently it has been acknowledged that this question should really be about the specific conditions and reasons why multimedia
is effective. However, while the argument has become more sophisticated, the techniques for evaluating learning with multimedia
environments have not always followed suit. The dominant approach at present involves factorial designs with novices as participants,
learning something for a short period of time with outcomes tested by an immediate pen and paper post-test. In this chapter,
the positive aspects of this approach are reviewed, but it will be argued that such an approach limits the questions that
can be answered. Four important such questions about learning with multimedia are proposed and then the chapter describes
a range of methodologies that can be used to answer them.
KeywordsExperimental methods-Flexible designs-Evaluation-Microgenetic
Modelling as an element in scientific methodology and models as the outcome of modelling are both important aspects of the
conduct of science and hence of science education. The chapter is concerned with the challenges that students face in understanding
the three ‘levels’ at which models can be represented – ‘macro’, ‘sub-micro’, ‘symbolic’ – and the relationships between them.
A model can, at a given level, be expressed in ‘external representations’ – those versions physically available to others
– and in ‘internal representations’ – those versions available mentally to an individual person. The making of meaning for
any such representation is ‘visualization’. It is of such importance in science and hence in science education that the acquisition
of fluency in visualization is highly desirable and may be called ‘metavisual capability’ or ‘metavisualization’. Criteria
for the attainment of metavisualization are proposed. Two approaches to the ontological categorization of representations
are put forward, one based on the purpose which the representation is intended to serve, the other based on the dimensionality
– 1D, 2D, 3D – of the representation. For the latter scheme, the requirements for metavisualization are discussed in some
detail in terms of its components. General approaches to the development of metavisualization are outlined. Multi-disciplinary
teams are needed if the research and development needed to improve visualization in science education is to take place.
Cognitive load is a theoretical notion with an increasingly central role in the educational research literature. The basic
idea of cognitive load theory is that cognitive capacity in working memory is limited, so that if a learning task requires
too much capacity, learning will be hampered. The recommended remedy is to design instructional systems that optimize the
use of working memory capacity and avoid cognitive overload. Cognitive load theory has advanced educational research considerably
and has been used to explain a large set of experimental findings. This article sets out to explore the open questions and
the boundaries of cognitive load theory by identifying a number of problematic conceptual, methodological and application-related
issues. It concludes by presenting a research agenda for future studies of cognitive load.
KeywordCognitive load theory
Over the last decade we have witnessed the emergence of technologies such as libraries, Object Orientation, software architecture and visual programming. The common goal of these technologies is to achieve software reuse. Even though, many significant advances have been made in areas such as library design, domain analysis, metric of reuse and organization for reuse, there are still unresolved problems such as component inter-operability and framework design[1]. We have investigated the use of interpreted languages to create a programmable, dynamic environment in which components can be tied together at a high level. This work has demonstrated the benefits of such an approach and has taught us about the features of the interpreted language that are key to a successful component integration.
A real-time molecular docking system is developed that uses an
electrically coupled remote manipulator as a force display. The system,
which uses integrates interactive computer graphics and high-speed
calculation of the interaction forces between a drug and a receptor site
in a molecule, is designed to be a tool for molecular scientists. The
manipulator is used to generate the forces and torques exerted on the
drug molecule when it is aligned with the receptor site by the user's
hand. The manipulator serves both as an input device for 6-D
manipulation and as an output device for generating forces. Preliminary
testing indicates that the system might enhance the biochemist's
understanding and performance
A simplified docking problem is studied. The user attempts to find
the potential-energy minimum in a 6-D space defined by six Hooke's-law
springs attached to a manipulable object. This space has no other local
minima. A pilot-controlled experiment with seven subjects, twelve trials
each, showed that performance with a force display is better
( p <0.01) than performance with a visual display alone, and
that subjects are able to find the zero-force position more than twice
as fast with a force display alone than with a visual display alone.
Also described is a way of graphically representing the resultants of a
set of forces and torques acting on a body. Even though the experiment
shows force display to be more effective, it also shows that the simple
6-D docking task can reliably be done with this visual display alone
This paper presents a new method for haptic feedback in molecular docking simulations as applied to the design of new drugs. These simulations, typically used by the pharmaceutical industry, for example Sanofi-Aventis, are based on the description of atomic energies to estimate the interactions between a ligand and a protein. The main drawback is that forces and torques cannot be calculated using a simple derivation. Moreover, when considering flexible ligand–protein docking, it is essential to take into account the delay in the molecular simulator’s response, as it may lead to an unstable bilateral control scheme. The proposed method allows for stable haptic feedback using wave variables. For the operator to feel the molecular interactions, this method builds a local energy model based on the interatomic interactions and on the haptic device’s displacement. The interaction wrench can be obtained using an analytic derivation of the energy model. Consequently, the teleoperation system is software independent, and can be extended to any bio-application, provided that it is energy based. Additionally, it ensures stable six degrees of freedom manipulation, therefore allowing comprehensive and stable haptic feedback.
The terms dynamic representation and animation are often used as if they are synonymous, but in this paper we argue that there are multiple ways to represent phenomena that change over time. Time-persistent representations show a range of values over time. Time-implicit representations also show a range of values but not the specific times when the values occur. Time-singular representations show only a single point of time. In this paper, we examine the use of dynamic representations in instructional simulations. We argue that the three types of dynamic representations have distinct advantages compared to static representations. We also suggest there are specific cognitive tasks associated with their use. Furthermore, dynamic representations of different form are often displayed simultaneously. We conclude that to understand learning with multiple dynamic representations, it is crucial to consider the way in which time is displayed.
This paper presents a new method for smoothing haptic interaction with molecular force calculations that uses Lennard-Jones forcefield. The gradient of the forcefield is used unaltered when the distance between two atoms is greater than the sum of their van der Waals radii. However, when they are smaller, a hard-surface wall implemented using a spring model is used to repel two atoms. This eliminates the instability when two atoms are in contact in the presence of forcefields that have strong gradients. This method is tested on rigid hydrocarbon molecules with no bond creation or breaking.
We present data and argument to show that in Tetris—a real‐time, interactive video game—certain cognitive and perceptual problems are more quickly, easily, and reliably solved by performing actions in the world than by performing computational actions in the head alone. We have found that some of the translations and rotations made by players of this video game are best understood as actions that use the world to improve cognition. These actions are not used to implement a plan, or to implement a reaction; they are used to change the world in order to simplify the problem‐solving task. Thus, we distinguish pragmatic actions—actions performed to bring one physically closer to a goal—from epistemic actions—actions performed to uncover informatioan that is hidden or hard to compute mentally.
To illustrate the need for epistemic actions, we first develop a standard information‐processing model of Tetris cognition and show that it cannot explain performance data from human players of the game—even when we relax the assumption of fully sequential processing. Standard models disregard many actions taken by players because they appear unmotivated or superfluous. However, we show that such actions are actually far from superfluous; they play a valuable role in improving human performance. We argue that traditional accounts are limited because they regard action as having a single function: to change the world. By recognizing a second function of action—an epistemic function—we can explain many of the actions that a traditional model cannot. Although our argument is supported by numerous examples specifically from Tetris, we outline how the new category of epistemic action can be incorporated into theories of action more generally.