NanoHUB

Last updated
nanoHUB.org
NanoHUB N COLOR HIRES.png
The nanoHUB.org logo
Type of site
Scientific research support
URL www.nanohub.org
CommercialNo
Launched2002

nanoHUB.org is a science and engineering gateway comprising community-contributed resources and geared toward education, 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). NCN supports research efforts in nanoelectronics; nanomaterials; nanoelectromechanical systems (NEMS); nanofluidics; nanomedicine, nanobiology; and nanophotonics.

Contents

History

The Network for Computational Nanotechnology was established in 2002 [2] to create a resource for nanoscience and nanotechnology via online services for research, education, and professional collaboration. Initially 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 now operates entirely at Purdue.

The US National Science Foundation (NSF) provided grants of approximately $14 million from 2002 through 2010, with principal investigator Mark S. Lundstrom. [3] Continuing US NSF grants have been awarded since 2007 with principal investigator Gerhard Klimeck and co-principal investigator Alejandro Strachan, with total funding of over $20 million. [4]

Resources

The Web portal of NCN is nanoHUB.org and is an instance of a HUBzero hub. It offers simulation tools, course materials, lectures, seminars, tutorials, user groups, and online meetings. [5] [6] 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. [7]

Main resource types: [8]

Simulation tools

The nanoHUB provides in-browser simulation tools geared toward nanotechnology, electrical engineering, materials science, 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 can develop and contribute their own tools for live deployment.

Examples of tools include: [9]

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
computes and visualizes 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 band structures.
nano-Materials Simulation Toolkit
uses molecular dynamics to simulate materials at the atomic scale.
DFT calculations with Quantum ESPRESSO
uses density functional theory to simulate the electronic structure of materials.

Infrastructure

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. [10]

Jupyter notebooks

To complement the existing Rappture GUI tools within nanoHUB, the more recent browser based Jupyter notebooks are also available on nanoHUB, since 2017. Jupyter in nanoHUB offer new possibilities using the existing scientific software, and most notably all Rappture tools, within nanoHUB with the notebooks of interspersed code (e.g. Python, text, and multimedia.

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 their 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. [11]

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 hundreds of times in the scientific literature, peaking in 2009. [12] [13] 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? ]

nanoHUB-U

The nanoHUB-U [14] online course initiative was developed to enable students to study a subject in a five-week framework roughly equivalent to a 1-credit class. No credit is given – quizzes and exams are simple and are intended to be aids to learning rather than rigorous tests for acquired skills. In the spirit of a research university, nanoHUB-U courses aim to bring new advances and understanding from research into the curriculum; in addition, simulation (often from nanoHUB) are heavily included in the courses. Every effort is made to present courses in a way that is accessible to beginning graduate students with a variety of different backgrounds with a minimum number of prerequisites. The ideal nanoHUB-U course is accessible to any students with an undergraduate degree in engineering or the physical sciences. Courses include nanoelectronics, nanoscale materials, and nanoscale characterization. nanoHUB-U courses are now a part of edX.

See also

Related Research Articles

<span class="mw-page-title-main">Virtual Network Computing</span> Graphical desktop-sharing system

Virtual Network Computing (VNC) is a graphical desktop-sharing system that uses the Remote Frame Buffer protocol (RFB) to remotely control another computer. It transmits the keyboard and mouse input from one computer to another, relaying the graphical-screen updates, over a network.

The Center for Nanophase Materials Sciences is the first of the five Nanoscale Science Research Centers sponsored by the United States Department of Energy. It is located in Oak Ridge, Tennessee and is a collaborative research facility for the synthesis, characterization, theory/ modeling/ simulation, and design of nanoscale materials. It is co-located with Spallation Neutron Source.

E-Science or eScience is computationally intensive science that is carried out in highly distributed network environments, or science that uses immense data sets that require grid computing; the term sometimes includes technologies that enable distributed collaboration, such as the Access Grid. The term was created by John Taylor, the Director General of the United Kingdom's Office of Science and Technology in 1999 and was used to describe a large funding initiative starting in November 2000. E-science has been more broadly interpreted since then, as "the application of computer technology to the undertaking of modern scientific investigation, including the preparation, experimentation, data collection, results dissemination, and long-term storage and accessibility of all materials generated through the scientific process. These may include data modeling and analysis, electronic/digitized laboratory notebooks, raw and fitted data sets, manuscript production and draft versions, pre-prints, and print and/or electronic publications." In 2014, IEEE eScience Conference Series condensed the definition to "eScience promotes innovation in collaborative, computationally- or data-intensive research across all disciplines, throughout the research lifecycle" in one of the working definitions used by the organizers. E-science encompasses "what is often referred to as big data [which] has revolutionized science... [such as] the Large Hadron Collider (LHC) at CERN... [that] generates around 780 terabytes per year... highly data intensive modern fields of science...that generate large amounts of E-science data include: computational biology, bioinformatics, genomics" and the human digital footprint for the social sciences.

x11vnc is a Virtual Network Computing (VNC) server program. It allows remote access from a remote client to a computer hosting an X Window session and the x11vnc software, continuously polling the X server's frame buffer for changes. This allows the user to control their X11 desktop from a remote computer either on the user's own network, or from over the Internet as if the user were sitting in front of it. x11vnc can also poll non-X11 frame buffer devices, such as webcams or TV tuner cards, iPAQ, Neuros OSD, the Linux console, and the Mac OS X graphics display. x11vnc is part of the LibVNCServer project and is free software available under the GNU General Public License. x11vnc was written by Karl Runge.

United States federal research funders use the term cyberinfrastructure to describe research environments that support advanced data acquisition, data storage, data management, data integration, data mining, data visualization and other computing and information processing services distributed over the Internet beyond the scope of a single institution. In scientific usage, cyberinfrastructure is a technological and sociological solution to the problem of efficiently connecting laboratories, data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.

<span class="mw-page-title-main">Metasploit Project</span> Computer security testing tool

The Metasploit Project is a computer security project that provides information about security vulnerabilities and aids in penetration testing and IDS signature development. It is owned by Boston, Massachusetts-based security company Rapid7.

Rocks Cluster Distribution is a Linux distribution intended for high-performance computing (HPC) clusters. It was started by National Partnership for Advanced Computational Infrastructure and the San Diego Supercomputer Center (SDSC) in 2000. It was initially funded in part by an NSF grant (2000–07), but was funded by the follow-up NSF grant through 2011.

A home server is a computing server located in a private computing residence providing services to other devices inside or outside the household through a home network or the Internet. Such services may include file and printer serving, media center serving, home automation control, web serving, web caching, file sharing and synchronization, video surveillance and digital video recorder, calendar and contact sharing and synchronization, account authentication, and backup services.

<span class="mw-page-title-main">Computer cluster</span> Set of computers configured in a distributed computing system

A computer cluster is a set of computers that work together so that they can be viewed as a single system. Unlike grid computers, computer clusters have each node set to perform the same task, controlled and scheduled by software.

Web-based simulation (WBS) is the invocation of computer simulation services over the World Wide Web, specifically through a web browser. Increasingly, the web is being looked upon as an environment for providing modeling and simulation applications, and as such, is an emerging area of investigation within the simulation community.

<span class="mw-page-title-main">Open Cobalt</span> Software for creating virtual worlds

Open Cobalt is a free and open-source software platform for constructing, accessing, and sharing virtual worlds both on local area networks or across the Internet, with no need for centralized servers.

<span class="mw-page-title-main">BioSLAX</span>

BioSLAX is a Live CD/Live DVD/Live USB comprising a suite of more than 300 bioinformatics tools and application suites. It has been released by the Bioinformatics Resource Unit of the Life Sciences Institute (LSI), National University of Singapore (NUS) and is bootable from any PC that allows a CD/DVD or USB boot option and runs the compressed Slackware flavour of the Linux Operating System (OS), also known as Slax. Slax was created by Tomáš Matějíček in the Czech Republic using the Linux Live Scripts which he also developed. The BioSLAX derivative was created by Mark De Silva, Lim Kuan Siong and Tan Tin Wee.

Techila Distributed Computing Engine is a commercial grid computing software product. It speeds up simulation, analysis and other computational applications by enabling scalability across the IT resources in user's on-premises data center and in the user's own cloud account. Techila Distributed Computing Engine is developed and licensed by Techila Technologies Ltd, a privately held company headquartered in Tampere, Finland. The product is also available as an on-demand solution in Google Cloud Launcher, the online marketplace created and operated by Google. According to IDC, the solution enables organizations to create HPC infrastructure without the major capital investments and operating expenses required by new HPC hardware.

Integrated computational materials engineering (ICME) involves the integration of experimental results, design models, simulations, and other computational data related to a variety of materials used in multiscale engineering and design. Central to the achievement of ICME goals has been the creation of a cyberinfrastructure, a Web-based, collaborative platform which provides the ability to accumulate, organize and disseminate knowledge pertaining to materials science and engineering to facilitate this information being broadly utilized, enhanced, and expanded.

<span class="mw-page-title-main">Ninithi</span>

Ninithi is free and open source modelling software that can be used to visualize and analyze carbon materials used in nanotechnology. Users of ninithi can 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. The software was developed by Lanka Software Foundation, in Sri Lanka and released in 2010 under the GPL licence. Ninithi is written in the Java programming language and available for both Microsoft Windows and Linux platforms.

<span class="mw-page-title-main">Gerhard Klimeck</span>

Gerhard Klimeck is a German-American scientist and author in the field of nanotechnology. He is a professor of Electrical and Computer Engineering at Purdue University School of Electrical and Computer Engineering.

Mark S. Lundstrom is an American electrical engineering researcher, educator, and author. He is known for contributions to the theory, modeling, and understanding of semiconductor devices, especially nanoscale transistors, and as the creator of the nanoHUB, a major online resource for nanotechnology. Lundstrom is Don and Carol Scifres Distinguished Professor of Electrical and Computer Engineering and in 2020 served as Acting Dean of the College of Engineering at Purdue University, in West Lafayette, Indiana.

HUBzero is an open source software platform for building websites that support scientific activities.

<span class="mw-page-title-main">Alejandro Strachan</span>

Alejandro Strachan is a scientist in the field of computational materials and a professor of materials engineering at Purdue University. Before joining Purdue University, he was a staff member at Los Alamos National Laboratory.

Science gateways provide access to advanced resources for science and engineering researchers, educators, and students. Through streamlined, online, user-friendly interfaces, gateways combine a variety of cyberinfrastructure (CI) components in support of a community-specific set of tools, applications, and data collections.: In general, these specialized, shared resources are integrated as a Web portal, mobile app, or a suite of applications. Through science gateways, broad communities of researchers can access diverse resources which can save both time and money for themselves and their institutions. As listed below, functions and resources offered by science gateways include shared equipment and instruments, computational services, advanced software applications, collaboration capabilities, data repositories, and networks.

References

  1. Sebastien Goasguen; Krishna Madhavan; David Wolinsky; Renato Figueiredo; Jaime Frey; Alain Roy; Paul Ruth; Dongyan Xu (2008). "Middleware Integration and Deployment Strategies for Cyberinfrastructures". Advances in Grid and Pervasive Computing. Lecture Notes in Computer Science. Vol. 5036. pp. 187–198. doi:10.1007/978-3-540-68083-3_20. ISBN   978-3-540-68081-9.
  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 & Engineering. IEEE Computer Society. 10 (5): 17–23. Bibcode:2008CSE....10e..17K. doi:10.1109/MCSE.2008.120. S2CID   2020684.
  3. "Network for Computational Nanotechnology". Award Abstract #0228390. National Science Foundation. September 10, 2002. Retrieved September 19, 2011.
  4. "Network for Computational Nanotechnology Cyber Platform". Award Abstract #1227110. National Science Foundation. November 20, 2012. Retrieved February 6, 2019.
  5. "nanoHUB.org" . Retrieved 8 October 2014.
  6. "Virtual World Is Sign Of Future For Scientists, Engineers". News release. Science Daily. July 18, 2008. Retrieved September 19, 2011.
  7. "Contributors". nanoHUB.org official web site. Retrieved September 19, 2011.
  8. Diana G. Oblinger (August 2007). "nanoHUB" (PDF). ELI Paper 7. Educause Learning Initiative. Archived from the original (PDF) on October 5, 2011. Retrieved September 19, 2011.
  9. "nanoFORGE: Available tools". nanoHUB web site. Retrieved September 19, 2011.
  10. "infrastructure:rappture" . Retrieved 8 October 2014.
  11. Sebastien Goasguen (2007). "Grid Architecture for Scientitic Communities". Grid-based Problem Solving Environments. IFIP the International Federation for Information Processing. Vol. 239. International Federation for Information Processing. p. 397. doi:10.1007/978-0-387-73659-4_23. ISBN   978-0-387-73658-7. S2CID   35004767.
  12. "Citations". nanoHUB.org web site. Retrieved September 19, 2011.
  13. James R. Bottum; James F. Davis; Peter M. Siegel; Brad Wheeler & Diana G. Oblinger (July–August 2008). "Cyberinfrastructure: In Tune for the Future". Educause Review. Vol. 43, no. 4. Archived from the original on September 7, 2008. Retrieved September 19, 2011.
  14. "Group: NanoHUB-U".

Further reading