nanoHUB

nanoHUB.org

The nanoHUB.org logo
URL	nanohub.org
Commercial?	No
Type of site	Scientific research support
Launched	2002

nanoHUB.org is science cyberinfrastructure comprising community-contributed resources and geared toward educational applications, professional networking, and interactive simulation tools for nanotechnology.^[1] Funded by the United States National Science Foundation (NSF), it is a product of the Network for Computational Nanotechnology (NCN), a multi-university initiative of eight member institutions including Purdue University, the University of California at Berkeley, the University of Illinois at Urbana-Champaign, Massachusetts Institute of Technology, the Molecular Foundry at Lawrence Berkeley National Laboratory, Norfolk State University, Northwestern University, and the University of Texas at El Paso. NCN was established to create a resource for nanoscience and nanotechnology via on-line services for research, education, and professional collaboration. NCN supports research efforts in nanoelectronics; nanoelectromechanical systems (NEMS); nanofluidics; nanomedicine, biology; and nanophotonics.

Infrastructure

The Network for Computational Nanotechnology was established in 2002.^[2] The US National Science Foundation (NSF) provided grants of about $14 million from 2002 through 2010, with principal investigator Mark Lundstrom.^[3]

The Web portal of NCN is nanoHUB.org. It offers simulation tools, course materials, lectures, seminars, tutorials, user groups, and online meetings.^[4][5] Interactive simulation tools are accessible from web browsers and run via a distributed computing network at Purdue University, as well as the TeraGrid and Open Science Grid. These resources are provided by hundreds of member contributors in the nanoscience community.^[6]

Resources include:^[7]

• Online Seminars
• Online Group Meeting Rooms
• Virtual Linux Workspaces that facilitate tool development within an in-browser Linux machine
• Online Workshops
• User Groups
• Interactive Simulation Tools for nanotechnology and related fields
• Lectures, Podcasts & Learning Materials in multiple formats
• Course Curricula for educators
• News & Events for Nanotechnology

Simulation tools

The nanoHUB provides in-browser simulation tools geared toward nanotechnology, electrical engineering, chemistry, and semiconductor education. nanoHUB simulations are available to users as both stand-alone tools and part of structured teaching and learning curricula comprising numerous tools. Users develop and contribute their own tools for live deployment.

Examples of tools include:^[8]

SCHRED

calculates envelope wavefunctions and the corresponding bound-state energies in a typical Metal-Oxide-Semiconductor (MOS) or Semiconductor-Oxide-Semiconductor (SOS) structure and a typical SOI structure by solving self-consistently the one-dimensional (1D) Poisson equation and the 1D Schrödinger equation.

Quantum Dot Lab

computes the eigenstates of a particle in a box of various shapes including domes and pyramids.

Bulk Monte Carlo Tool

calculates the bulk values of the electron drift velocity, electron average energy and electron mobility for electric fields applied in arbitrary crystallographic direction in both column 4 (Si and Ge) and III-V (GaAs, SiC and GaN) materials.

Crystal Viewer

helps in visualizing various types of Bravais lattices, planes and Miller indices needed for many material, electronics and chemistry courses. Also large bulk systems for different materials (Silicon, InAs, GaAs, diamond, graphene, Buckyball) can be viewed using this tool.

Band Structure Lab

uses the sp3s*d5 tight binding method to compute E(k) for bulk, planar, and nanowire semiconductors. Using this tool, researchers may compute and visualize the band structures of bulk semiconductors, thin films, and nanowires for various materials, growth orientations, and strain conditions. Physical parameters such as the bandgap and effective mass can also be obtained from the computed E(k). The bandedges and effective masses of the bulk materials and the nanostructures structures can be analyzed as a function of various strain conditions.

nano-Materials Simulation Toolkit

which uses molecular dynamics to simulate materials at the nano and micro-scale.

ninithi

which can be used to visualize the 3D molecular geometries of graphene/nano-ribbons,carbon nanotubes and fullerenes. Ninithi also provides features to simulate the electronic band structures of graphene and carbon nanotubes.^[9]

HUBzero

HUBzero, the software develeoped for nanoHUB, was created by researchers at Purdue University in conjunction with the NSF-sponsored Network for Computational Nanotechnology. It was based on the Purdue University Network Computing Hubs (PUNCH) project that had begun in the 1990s under Mark Lundstrom, Josef Fortes, and Nirav Kapadia.^[7] HUBzero allows individuals to create web sites that connect a community in scientific research and educational activities. HUBzero sites combine Web 2.0 concepts with middleware that provides access to interactive simulation tools including access to TeraGrid,^[10] the Open Science Grid, and other national grid computing resources. The software later became supported by a consortium and used for some other projects.^[11][12]

The web site built from open-source software: the Linux operating system, the Apache web server, the MySQL database, the Joomla content management system, and the PHP web scripting language. The HUBzero software allows individuals to access simulation tools and share information. Sites using the hub infrastructure are standardized with the following modules:

• Interactive simulation tools, hosted on the hub cluster and delivered to web browsers
• Simulation tool development area, including source code control and bug tracking
• Animated presentations delivered in Flash format
• Mechanism for uploading and sharing resources
• 5-star ratings and user feedback for resources
• User support area, with question-and-answer forum
• Statistics about users and usage patterns

Rappture Toolkit

The Rappture (Rapid APPlication infrastrucTURE) toolkit provides the basic infrastructure for the development of a large class of scientific applications, allowing scientists to focus on their core algorithm. It does so in a language-neutral fashion, so one may access Rappture in a variety of programming environments, including C/C++, Fortran and Python. To use Rappture, a developer describes all of the inputs and outputs for the simulator, and Rappture generates a Graphical User Interface (GUI) for the tool automatically ^[13].

Workspaces

A workspace is an in-browser Linux desktop that provides access to NCN's Rappture toolkit, along with computational resources available on the NCN, Open Science Grid, and TeraGrid networks. One can use these resources to conduct research, or as a development area for new simulation tools. One may upload code, compile it, test it, and debug it. Once code is tested and working properly in a workspace, it can be deployed as a live tool on nanoHUB.

A user can use normal Linux tools to transfer data into and out of a workspace. For example, sftp [e-mail] will establish a connection with a nanoHUB file share. Users can also use built-in WebDAV support on Windows, Macintosh, and Linux operating systems to access theier nanoHUB files on a local desktop.

Middleware

The web server uses a daemon to dynamically relay incoming VNC connections to the execution host on which an application session is running. Instead of using the port router to set up a separate channel by which a file import or export operation is conducted, it uses VNC to trigger an action on the browser which relays a file transfer through the main nanoHUB web server. The primary advantage of consolidating these capabilities into the web server is that it limits the entry point to the nanoHUB to one address: www.nanohub.org. This simplifies the security model as well as reduces on the number of independent security certificates to manage.

One disadvantage of consolidating most communication through the web server is the lack of scalability when too much data is transferred by individual users. In order to avoid a network traffic jam, the web server can be replicated and clustered into one name by means of DNS round-robin selection.

The backend execution hosts that support Maxwell can operate with conventional Unix systems, Xen virtual machines, and a form of virtualization based on OpenVZ. For each system, a VNC server is pre-started for every session. When OpenVZ is used, that VNC server is started inside of a virtual container. Processes running in that container cannot see other processes on the physical system, see the CPU load imposed by other users, dominate the resources of the physical machine, or make outbound network connections. By selectively overriding the restrictions imposed by OpenVZ, it is possible to synthesize a fully private environment for each application session that the user can use remotely.^[14]

Usage

The majority of users come from academic institutions using nanoHUB as part of their research and educational activities. Users also come from national labs and private industry. As a scientific resource, nanoHUB was cited hundrends of times in the scientific literature, peaking in 2009.^[15][16] Approximately sixty percent of the citations stem from authors not affiliated with the NCN. More than 200 of the citations refer to nanotechnology research, with more than 150 of them citing concrete resource usage. Twenty citations elaborate on nanoHUB use in education and more than 30 refer to nanoHUB as an example of national cyberinfrastructure.^[when?]

See also

• Materials informatics
• Integrated computational materials engineering
• Multiscale modeling

References

1. ^ Sebastien Goasguen, Krishna Madhavan, David Wolinsky, Renato Figueiredo, Jaime Frey, Alain Roy, Paul Ruth and Dongyan Xu (2008). "Middleware Integration and Deployment Strategies for Cyberinfrastructures". Advances in Grid and Pervasive Computing. Lecture Notes in Computer Science. 5036. pp. 187–198. doi:10.1007/978-3-540-68083-3_20. 
2. ^ Gerhard Klimeck, Michael McLennan, Sean P. Brophy,George B. Adams III, Mark S. Lundstrom (September/October 2008). "nanoHUB.org: Advancing Education and Research in Nanotechnology". Computing in Science and Engineering (IEEE Computer Society) 10 (5). doi:10.1109/MCSE.2008.120. 
3. ^ "Network for Computational Nanotechnology". Award Abstract #0228390. National Science Foundation. September 10, 2002. http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0228390. Retrieved September 19, 2011. 
4. ^ http://www.nanohub.org/resources
5. ^ "Virtual World Is Sign Of Future For Scientists, Engineers". News release (Science Daily). July 18, 2008. http://www.sciencedaily.com/releases/2008/07/080716161557.htm. Retrieved September 19, 2011. 
6. ^ "Contributors". nanoHUB.org official web site. http://nanohub.org/members/contributors. Retrieved September 19, 2011. 
7. ^ ^{a b} Diana G. Oblinger (August 2007). "nanoHUB". ELI Paper 7. Educause Learning Initiative. http://net.educause.edu/ir/library/pdf/eli3015.pdf. Retrieved September 19, 2011. 
8. ^ "nanoFORGE: Available tools". nanoHUB web site. http://nanohub.org/tools. Retrieved September 19, 2011. 
9. ^ Chanaka Suranjith Rupasinghe, Mufthas Rasikim. "ninithi". Lanka Software Foundation. http://nanohub.org/resources/8987. Retrieved September 19, 2011. 
10. ^ Charlie Catlett, Sebastien Goasguen, Jim Marsteller, Stuart Martin, Don Middleton, Kevin J. Price, Anurag Shankar, Von Welch, Nancy Wilkins-Diehr (November 12, 2006). "Science Gateways on the TeraGrid" (ppt). Presentation at GCE06, Second International Workshop in Grid Computing Environments. Tampa, Florida. http://library.rit.edu/oajournals/index.php/gce/article/view/68/59. Retrieved September 19, 2011. 
11. ^ "HUBzero - Platform for Scientific Collaboration". Official web site. Purdue University. http://hubzero.org. Retrieved September 19, 2011. 
12. ^ Michael McLennan and Greg Kline (February 28, 2011). "HUBzero Paving the Way for the Third Pillar of Science". HPC in the Cloud. http://www.hpcinthecloud.com/hpccloud/2011-02-28/hubzero_paving_the_way_for_the_third_pillar_of_science.html. Retrieved September 19, 2011. 
13. ^ http://rappture.org
14. ^ Sebastien Goasguen (2007). "Grid Architecture for Scientitic Communities". Grid-based Problem Solving Environments. 239. International Federation for Information Processing. doi:10.1007/978-0-387-73659-4_23. 
15. ^ "Citations". nanoHUB.org web site. http://www.nanohub.org/citations. Retrieved September 19, 2011. 
16. ^ James R. Bottum, James F. Davis, Peter M. Siegel, Brad Wheeler, and Diana G. Oblinger (July/August 2008). "Cyberinfrastructure: In Tune for the Future". Educause Review 43 (4). http://connect.educause.edu/Library/EDUCAUSE+Review/CyberinfrastructureInTune/46966. Retrieved September 19, 2011. 

Further reading

• EDUCAUSE Review, vol. 42, no. 6 - nanoHUB: Community & Collaboration
• Publications related to HUBzero
• Federal Resources for Educational Excellence
• IBM.com: nanoHUB Does Remote Computing Right
• Alan Henry (August 28, 2007). "Scientists Connect at nanoHUB". Appscout. Archived from the original on July 16, 2011. http://web.archive.org/web/20110716175111/http://www.appscout.com/2007/08/scientists_connect_at_nanohub.php/.