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Other Publications Birck Nanotechnology Center

October 2008 nanoHUB.org: Advancing Education and Research in Nanotechnology

Gerhard Klimeck School of Electrical and Computer Engineering and Birck Nanotechnology Center, , [email protected]

Michael McLennan Purdue University - Main Campus

Sean B. Brophy Purdue University - Main Campus

George B. Adams III Purdue University - Main Campus

Mark S. Lundstrom Purdue University - Main Campus

Follow this and additional works at: https://docs.lib.purdue.edu/nanodocs

Klimeck, Gerhard; McLennan, Michael; Brophy, Sean B.; Adams, George B. III; and Lundstrom, Mark S., "nanoHUB.org: Advancing Education and Research in Nanotechnology" (2008). Other Nanotechnology Publications. Paper 80. https://docs.lib.purdue.edu/nanodocs/80

This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. H i g h - P e r f o r m a n c e C o m p u t i n g E d u c a t i o n nanoHUB.org: Advancing Education and Research in Nanotechnology

Through the Network for Computational Nanotechnology Web site, nanoHUB.org, tens of thousands of users from 172 countries collaborate, share resources, and solve real nanotechnology problems. The authors share their experiences in developing and using the site’s unique .

n 2002, the US National Science Foun- a history of sharing simulation tools, such as dation established a university network, the Simulation Program with Integrated Circuit called the Network for Computational Emphasis (SPICE).1 The goal was to encourage Nanotechnology (NCN), to support the the development of many tools, tutorials, pod- INational Nanotechnology Initiative. This initia- casts, animations, publications, lecture notes, tive provides a multi-agency framework in support and homework assignments, which we refer to of US government investments in fundamental collectively as “resources.” To achieve this, we nanoscale phenomena research and the transla- needed an infrastructure that would make it easy tion of new understanding to new technology. for a worldwide community of content contribu- NCN aimed to further these goals in three ways: tors to upload and share their resources, receive bringing computational tools online, making the feedback, and make improvements. All of this had tools easy to use, and educating users about the to happen in a self-serve fashion, with very little tools and nanoscience. intervention by NCN staff, so that it could scale Along the way, NCN has created a unique to serve a very large community. cyberinfrastructure to support its Web site, nanoHUB.org hosts nearly 1,000 resources, in- nanoHUB.org, where researchers, educators, and cluding 87 simulation tools (see Figure 1). Many professionals have been collaborating, sharing re- of our resources are published under a Creative sources, and solving nanotechnology problems. Commons 2.5 license (http://creativecommons. In 2007, nanoHUB.org served more than 56,000 org/licenses/by-nc-sa/2.5/), letting others create users from 172 countries. In this article, we share derivative works. NCN staff review contributed our experiences in developing and using this cy- content for appropriateness, completeness, and berinfrastructure, particularly in an educational basic functioning, and we encourage users to context. rate and comment on all resources. Roughly 27

Developing nanoHUB.org 1521-9615/08/$25.00 © 2008 IEEE NCN chose to focus initially on nanoelectron- Copublished by the IEEE CS and the AIP ics, nanoelectromechanical systems, and devices Gerhard Klimeck, Michael McLennan, Sean B. Brophy, for biology and medicine for three reasons: these George B. Adams III, and Mark S. Lundstrom ­areas are developing rapidly, no curricula have been fully established, and has Purdue University

Computing in Science & Engineering This article has been peer-reviewed. 17 Online simulation… …and more

(c) (b)

(d)

(a)

Figure 1. nanoHUB.org provides online simulation and more to a global following. (a) More than 56,000 users in 2007 accessed its resources, including (b) simulations and (c) Flash-based tutorials. Many tutorials are also available as (d) iTunes podcasts, which have attracted more than 6,800 users.

percent of the content has received ratings (using at all Top 50 US engineering schools2 and more a five-star scale), and 46 percent of the ratings than 14 percent of all .edu domains. (See www. have associated comments. Content with many nanohub.org/usage for additional usage details, favorable ratings tends to bubble up in search re- updated monthly.) sults, whereas content with poor ratings is harder to find. To date, NCN has pursued tool quality Cyberinfrastructure by engaging selected research groups for tool de- nanoHUB.org simulation tools aren’t the batch- velopment. NCN member sites have encouraged mode services common on the Web; rather, the majority of other content, such as research they’re intuitive, interactive graphical tools that seminars, tutorials, short courses, homework ex- make it easy for users to learn and explore. Users ercises, and animations. can launch simulations from their Web browser The nanoHUB.org user community grew simply by clicking the “Simulate” button and can from 1,000 users in 2002 to more than 56,000 in change any parameter, launch another simulation, 2007. Some 5,800 registered users logged in and and quickly compare results. About one-third of ran more than 240,000 simulation jobs in 2007. the nanoHUB.org tools deliver results in less than We identify unregistered users by IP address and 10 seconds, about one-half in less than one min- count them only if they aren’t a Web-crawling ute. Computationally demanding simulation jobs robot and if they download a resource or spend dispatch to grid computing resources, including more than 15 minutes browsing the site. Roughly the NSF TeraGrid (www.teragrid.org), Open Sci- 85 percent of our registered users and 91 per- ence Grid (www.opensciencegrid.org), and virtual cent of unregistered users are affiliated with an clusters powered by Violin software.3 Intensive educational institution. nanoHUB.org has users volume rendering and flow-visualization tasks dis-

18 Computing in Science & Engineering patch seamlessly to a specialized rendering cluster.4 over its associated control. The GUI can include nanoHUB.org middleware hides grid computing’s embedded notes in HTML format, with links to complexity, handling authentication, authoriza- tutorials and documentation. Rappture recogniz- tion, file transfer, and visualization, and letting the es various output types and automatically invokes user focus on conducting experiments and learn- the appropriate visualization engine. In the past ing new concepts. Irrespective of the computation three years, more than 200 developers have used time, users can set up and analyze their numeri- Rappture on more than 190 projects. Typical proj- cal experiments’ results interactively in a friendly ects have required a few days of programmer time GUI without installing any software. nanoHUB. to create the Rappture interface that readied a raw org can achieve such ease of use for numerous tools simulation code for nanoHUB.org deployment. because of its unique cyberinfrastructure. Rappture also provides a consistent and acces- nanoHUB.org is built on the open source sible presentation, which is extremely important LAMP (Linux, Apache, MySQL, and PHP) plat- in an educational setting. Instructors interested form5 and the Joomla (www.joomla.org) content in constructing a coherent sequence of learning management system. Launching a tool session in- experiences for students need a common interface vokes a Joomla component that we developed. The for all the tools. For example, the design project component then communicates with our middle- for a course might require the synthesis of results ware to launch a tool session on a cluster of avail- from several simulation tools. With a consistent able machines and emits a Web page containing a interface, learners will apply their intellectual en- virtual network computing applet6 that connects ergy to investigating their questions rather than back to the live tool session. To users, it appears to learning new interfaces. that a simple Java applet is running in their Web browser—and indeed it is—but nanoHUB.org Role in Education is serving the tool (which could be a community Early on, NCN identified users at academic insti- code consisting of a few hundred thousand lines tutions—both educators and researchers—as our of source code developed in tens of person years) target audience and set out to meet their needs. and the computing cycles from a much more so- Many educators and students don’t have adminis- phisticated platform, which can scale to handle trator privileges to install software on their com- very large jobs (such as memory-intensive jobs puters. For tools to be used in the classroom, they that require large amounts of RAM or highly par- must be available on all platforms, including Win- allel jobs that might require many CPUs). dows, Mac OS X, and Linux, without user-based To drastically reduce the programmer hours installation. They must be easy to use and time ef- needed to create friendly GUIs to a wide vari- ficient. They should have integrated visualization ety of powerful simulation codes, NCN created capabilities so that, with minimal effort, students an open source toolkit called Rappture (Rapid can generate, view, compare, and capture many App­ lication Infrastructure; http://rappture.org). different results for further use. The tools must Rappture-based tools are ordinary applications have supporting materials so that students can that run on Windows, Mac OS X, and Linux jump quickly from a result to a seminar that ex- platforms, irrespective of any Web deployment. plains underlying concepts. As the Science Envi- Coupled with our unique middleware, however, ronment for Ecological Knowledge and SciDesign nanoHUB.org delivers them via any Java-enabled projects in this issue show (see p. 28), tools alone browser; no extra work is required to deploy a are insufficient for community adoption; a rich powerful Linux-based tool online. Not only is set of resources supporting tool use is necessary. the resulting tool easy to use, but it’s also easy to Web-based resources such as nanoHUB.org can develop, typically by graduate students deeply in- provide anytime, anywhere support to distrib- volved with the underlying theory code or under- uted educational initiatives, such as Ohio’s inter- graduate students working in a team with expert ­institution undergraduate minor in computational graduate students. science (see p. 12). They can also level the field for Rappture programmers describe the input pa- access by users from diverse backgrounds and in- rameters and output results for a simulation code stitutions who want to gain experience with HPC, as a hierarchy of data objects in an XML file such as the experience reported in this issue by (www.w3.org/XML). Rappture reads that file and David Joiner and colleagues (see p. 40). generates a GUI automatically, producing a tool Experienced computational scientists in nano- such as the one in Figure 2. Each input and output science, and their graduate students, can advance has a description that pops up when users mouse their learning through nanoHUB.org resources

September/October 2008 19 (b)

(c)

(a)

Figure 2. Instant GUI. Rappture generates the GUI for a tool on the basis of a description of its inputs and outputs. Users can change any input parameter, run simulations, and compare results with (a) intuitive sliders or data overlay. This example compares the (b) conduction band edge and (c) charge distribution in a resonant tunneling diode7 for a simple linear potential drop and a charge self-consistent potential.

with little additional pedagogical support. Based the tool sessions live, projecting on a screen so that on resource ratings and comments, users can suc- students can follow along. With its integrated vi- cessfully leverage their prior knowledge to com- sualization capabilities, nanoHUB.org becomes a prehend the new content knowledge and conduct vivid whiteboard of sorts for instructors, as Figure research with the simulations tools. In this way, 3 shows. They can demonstrate their own thought the available resources are helping to educate the processes as they run experiments and interpret nanotechnology research community and to con- results. Instructors can pose “What if?” questions duct research. to students, ask them to generate predictions, and Graduate students new to nanoscience and then provide explanations while examining the computational inquiry require more guidance results. This cognitive apprenticeship lets instructors through formal educational settings. Multiple assume the mentor role, introducing students to pedagogical approaches can involve using simula- the discipline and its methods.8 tion tools to support student learning in the class- If live simulation runs would take too much room, for both homework assignments and design time, instructors can easily prepare any num- projects. Each of these uses has a slightly different ber of runs before class because closing a Web use model. browser doesn’t close tool sessions. Tools remain active and, upon reconnecting to nanoHUB.org, Classroom Learning show on the users’ “My nanoHUB” page under For classroom demonstrations, instructors can run the “My Sessions” heading. Clicking on a session

20 Computing in Science & Engineering (a) (b) (c)

(d) (e)

Figure 3. 3D nanoHUB.org simulation images. (a) An electrostatic potential from ,9 (b) (5, 0) and (10, 2) carbon nanotubes in CNTbands,10 (c) A (10, 2)B Carbon Nano Ribbon in CNTbands, (d) a Gramicidin in BioMOCA,11 and (e) an eigenstate in Quantum Dot Lab.12 Users can rotate, zoom, insert cut planes, as in (e), and interactively manipulate all images. Users can download the images with a simple click of a button. name quickly revives the tool session. So, instruc- from the smaller investigations conducted in the tors can present examples smoothly to maintain homework problems. Students often work in teams engaging classroom dynamics with students. and must share their tool sessions with each other and with the instructor to work out problems. Us- Homework Assignments ers can share any nanoHUB.org tool session by For homework assignments, students use the tools entering the nanoHUB.org login name for one to explore the relationships between input and or more users (with equal security privileges) and output parameters. They can compare the results clicking the “Share” button. of an analytical solution calculated by hand to the numerical results obtained from nanoHUB.org, or Feedback they can seek to understand input and output re- NCN faculty are investigating our resources’ lationship trends. Through these methods, learn- benefits for educating a wide range of learners ers can begin to unpack the black-box simulation and examining how experts use nanoHUB.org re- model and notice subtle changes in its character- sources to build new knowledge. Toward that end, istics. These experiences develop students’ ability NCN developed a short student survey to provide to systematically investigate questions rather than an initial glimpse into how students perceive the use trial-and-error strategies. utility and usability of nanoHUB.org resources in their courses and for their future goals. Design Projects NCN recently surveyed more than 100 gradu- Design projects provide students with the oppor- ate students in electrical engineering, bioengi- tunity to synthesize everything they’ve learned neering, and material sciences courses. These

September/October 2008 21 students agree that the tools are accessible and ior at the molecular and atomic levels.14 Further the graphical outputs are easy to interpret. In research is under way. addition, they report that their interaction with the simulations facilitates their own question For Education, Research, or Both generation and self-exploration to generate new Early on, NCN tried to classify tools as being knowledge. They also agree that simulations help for education or for research, but we learned them comprehend nano concepts better than lec- that with ready access and nanoHUB.org’s ease tures and readings do.13 Most encouraging are of use, the distinction isn’t clear. For example, students’ reports that these tools align with their CNTbands10 was created for classroom use interests, and they anticipate using these re- and provides a simple density of states, disper- sources in their own research. Therefore, these sion calculation, and 3D visualization of various introductions to nanoscience through expert- carbon nanotubes, yet scientific literature has level tools have a positive impact in advancing cited it five times (www.nanohub.org/tools/cnt the research community. Continuing work will bands-ext/#citations) for its use in research. A focus on how learners develop their ability to Stanford University student began using the think and reason with the tools relative to the Resonant Tunneling Diodes simulator in a nano­ way experts use the tools. technology class taught by H.-S. P. Wong in Undergraduate students surveyed reported ex- 2005 and went on to use that tool in his own periences in their courses similar to the graduate research project.15 Schred,16 a 1D Schrödinger- students’ experiences. We have reports from 100 ­Poisson Solver for Silicon devices, also has 80 students using nanoHUB.org in chemistry and ­citations in the research literature, which indi- nanodevices. They agree that demonstrations cates serious research use, yet instructors have repeatedly used it in the classroom. Overall, Most encouraging are students’ reports scientific literature has cited nanoHUB.org and its tools more than 265 times (www.nano- that these tools align with their interests, hub.org/citations), and roughly 60 percent of these citations are from authors unaffiliated and they anticipate using these resources with the NCN. NCN has received many testi- monials from professors about nanoHUB.org’s in their own research. usefulness in education and research (http:// nanohub.org/about/quotes). Even tutorial materi- als have been cited.17,18 Researchers are recogniz- with simulations helped their comprehension of ing nanoHUB.org as a new way of publishing. the concepts more than traditional lectures and readings. They found the resources easy to use and accessible. However, undergraduates were s we continue to make improvements, split on their perception of simulations as “highly ­nanoHUB.org remains a work in relevant to my area of interest,” and response vari- progress. By developing our cyber- ance was quite large. Related to this response is infrastructure in close collaboration their perception of their ability to interpret tool Awith users—especially professors and their stu- results and generate their own questions. These dents—NCN maintains contact with community results could be because undergraduate courses needs and values. are less specialized than graduate courses and that nanoHUB.org is changing how users and devel- these students need more instruction on how to opers in research and education alike access and use these tools to support inquiry. use simulation tools and associated material. The Undergraduate students are still developing underlying cyberinfrastructure is now a generic the foundational technology and information lit- package called HUBzero (http://hubzero.org). We eracy skills necessary to comprehend the assign- believe the “HUB” concept is transferable to many ments and tools appropriate for graduate students. engineering and science disciplines, and we’re ac- Therefore, new learning modules and instruc- tively deploying new HUBs for discovery and learn- tional approaches are needed to accommodate the ing. The HUB concept will greatly expand the user possibly wide variance of undergraduate learners’ base for modeling and simulation, and open new ability to reason with the tools—for example, we possibilities for many people who would otherwise see great potential in visualizations to develop avoid computing. We plan an open source software learners’ mental representations of system behav- release of HUBzero for fall 2009.

22 Computing in Science & Engineering Acknowledgments nology of the Network for Computational Nano- We gratefully acknowledge the work of the technology (NCN) and professor of electrical and nanoHUB.org software team and the more than 440 computer engineering at Purdue University. He content contributors to date, as well as the leader- leads the development and deployment of Web- ship of the US National Science Foundation program based simulation tools hosted on nanoHUB.org. His managers and directors and Purdue University ad- research interests include modeling nanoelectronic ministration, who saw this work’s potential. NSF devices, parallel cluster computing, and genetic al- awards EEC-0228390, EEC-0634750, OCI-0438246, gorithms. Klimeck has a PhD in electrical engineer- and OCI-0721680 fund NCN. ing from Purdue and is a senior member of the IEEE as well as a member of the American Physical Soci- References ety, Eta Kappa Nu, and Tau Beta Pi. Contact him at [email protected]. 1. L.W. Nagel, “SPICE2: A Computer Program to Simulate Circuits,” tech. memo ERL-M520, Electronic Research Lab., Univ. of California, Berkeley, May 1975. Michael McLennan is a senior research scientist in 2. “America’s Best Graduate Schools 2007,” US News & World the Rosen Center for Advanced Computing at Pur- Report, vol. 140, no. 13, 2007, p. 59. due University. He’s also the software architect for 3. P. Ruth et al., “Virtual Distributed Environments in a Shared nanoHUB.org and creator of the Rappture toolkit. His Infrastructure,” Computer, vol. 38, no. 5, 2005, pp. 63–69. research interests include GUI design and software ar- 4. W. Qiao et al., “Hub-Based Simulation and Graphics Hardware Accelerated Visualization for Nanotechnology chitecture. McLennan has a PhD in electrical engineer- ­Applications,” IEEE Trans. Visualization and Computer Graph- ing from Purdue and is a member of the IEEE, Eta Kappa ics, vol. 12, no. 5, 2006, pp. 1061–1068. Nu, and Tau Beta Pi. Contact him at mmclennan@ 5. G. Lawton, “LAMP Lights Enterprise Development Efforts,” purdue.edu. Computer, vol. 38, no. 9, 2005, pp. 18–20. 6. T. Richardson et al., “Virtual Network Computing,” IEEE Internet Computing, vol. 2, no. 1, 1998, pp. 33–38. Sean P. Brophy is assistant professor in the School 7. M. McLennan, “Resonant Tunneling Diode Simulator,“ of Engineering Education at Purdue University and 2005; doi: 10254/nanohub-r230.2. is part of the education team at NCN. His research 8. A. Collins, J.S. Brown, and A. Holum, “Cognitive Apprentice- interests include using simulations and models to ship: Making Thinking Visible,” Am. Educator, vol. 6, no. 11, teach difficult engineering concepts, defining meth- 1991, pp. 38–46. ods for formative assessment in and out of the 9. E. Polizzi et al., “Nanowire,“ 2006; doi: 10254/nanohub -r1307.3. classroom, and understanding adaptive expertise 10. Y. Yoon et al., “CNTbands,“ 2006; doi: 10254/nanohub development and constructing learning environ- -r1838.3. ments that lead to adaptive expertise. Brophy has 11. R. Toghraee and U. Ravaioli, “BioMOCA,“ 2008; doi: 10254/ a PhD in education and human development from nanohub-r1497.1. Vanderbilt University. Contact him at sbrophy@ 12. G. Klimeck et al., “Quantum Dot Lab,“ 2005; doi: 10254/ purdue.edu. nanohub-r450.4. 13. A. Magana, S.B. Brophy, and G. Bodner, “Professors’ In- structional Approaches and Students’ Perceptions of nano- George B. Adams III is the associate director for NCN HUB.org Simulations as Learning Tools,” Proc. Ann. Conf. Am. programs at Purdue University. In 2000, he helped Soc. for Eng. Education, Am. Soc. for Eng. Education, 2008; organize the planning team for what has become the http://asee.org/conferences/v2search.cfm. Birck Nanotechnology Center at Purdue. His research 14. P.N. Johnson-Laird, “Mental Models in Cognitive Science,” Cognitive Science: A Multidisciplinary Journal, vol. 4, 1980, pp. interests include nanotechnology, computer architec- 71–115. ture, and algorithms. Adams has a PhD in electrical 15. D. Akinwande and H.-S.P. Wong, “A Composite Circuit Mod- engineering from Purdue and is a senior member of el for NDR Devices in Random Access Memory Cells,” IEEE the IEEE as well as a member of Eta Kappa Nu and Trans. Electron Devices, vol. 54, no. 4, 2007, pp. 776–783. Tau Beta Pi. Contact him at [email protected]. 16. D. Vasileska et al., “Schred,“ 2006; doi: 10254/nanohub -r221.2. 17. M.A. Alam, “On the Reliability of Micro-Electronic Devices: Mark S. Lundstrom is NCN’s director and the Don An Introductory Lecture on Negative Bias Temperature and Carol Scifres Distinguished Professor of Electri- Instability,” Nanotechnology 501 Lecture Series, 2005; www. cal and Computer Engineering at Purdue University. nanohub.org/resources/193/. His research interests are on the physics and ultimate 18. S.V. Kumar, C.H. Kim, and S.S. Sapatnekar, “An Analytical Model for Negative Bias Temperature Instability,” Proc. limits of nanoscale electronic devices. Lundstrom has 2006 IEEE/ACM Int’l Conf. Computer-Aided Design, ACM Press, a PhD from Purdue and is a fellow of the IEEE, the 2006, pp. 493–496. American Physical Society, and the American Asso- ciation for the Advancement of Science. Contact him Gerhard Klimeck is the associate director for tech- at [email protected].

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