Nanohub

Nanohub

nanoHUB.org is a Web 2.0 science cyberinfrastructure made up of community contributed resources and geared toward educational applications, professional networking, and interactive simulation tools for nanotechnology. Funded by the 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, 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, NEMS, nanofluidics, nanomedicine/biology, and nanophotonics.

Resources

nanoHUB.org is NCN's gateway for delivery and hosting of simulation tools, course materials, lectures, seminars, tutorials, user groups, and online meetings. nanoHUB hosts approximately 1200 user-contributed resources which focus on nanotechnology education and simulation for topics related to nanotechnology. nanoHUB 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 approximately 500 member contributors in the nanoscience community.

nanoHUB resources include:

  • 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

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. As of 9/18/2008, nanoHUB hosts 124 distinct simulation tools. nanoHUB users develop and contribute their own tools for live deployment.

Examples of some tools include:


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


Quantum Dot Lab, which computes the eigenstates of a particle in a box of various shapes including domes and pyramids.


Bulk Monte Carlo Tool, which 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 which 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.

Infrastructure

nanoHUB utilizes numerous resources for the development, deployment, and presentation of simulations and related materials. These include the HUBzero, the RAPPTURE interface, and Maxwell's Daemon middleware.

HUBzero

nanoHUB is powered by the HUBzero software developed at Purdue University. 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 a middleware that provides access to interactive simulation tools. These tools are research codes with access to TeraGrid, the Open Science Grid, and other national Grid computing resources.

HUBzero was created by researchers at Purdue University in conjunction with the NSF-sponsored Network for Computational Nanotechnology. The hub is a web site built from a conglomeration of open source packages—the Linux operating system, an Apache web server, a MySQL database, PHP web scripting, and the Joomla content management system. The HUBzero software utilizes the basic infrastructure to create an environment in which individuals can access simulation tools and share information. Sites utilizing 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 toolkit (RapidAPPlication infrastrucTURE) 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 .

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 yourlogin@sftp.nanohub.org 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 transfered 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.

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 is cited over 260 times in the scientific literature . Approximately 60 percent of the citations stem from authors not affiliated with the NCN. Over 200 of the citations refer to nanotechnology research, with over 150 of them citing concrete resource usage. 20 citations elaborate on nanoHUB use in education and over 30 refer to nanoHUB as an example of a national cyberinfrastructure. The goals of this cyberinfrastructure are to enhance the scientific discovery process, as well as enable new venues for discovery throughout the scientific community .

References

Further Reading

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