Nanohub
Encyclopedia
nanoHUB.org is science cyberinfrastructure
comprising community-contributed resources and geared toward educational applications, professional networking, and interactive simulation tools for nanotechnology
. 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
.
The US National Science Foundation
(NSF) provided grants of about $14 million from 2002 through 2010, with principal investigator
Mark Lundstrom.
The Web portal
of NCN is nanoHUB.org. It offers simulation tools, course materials, lectures, seminars, tutorials, user groups, and online meetings.
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.
Resources include:
Examples of tools include:
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.
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.
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, the Open Science Grid, and other national grid computing
resources.
The software later became supported by a consortium and used for some other projects.
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:
(GUI) for the tool automatically .
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.
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.
As a scientific resource, nanoHUB was cited hundrends of times in the scientific literature, peaking in 2009.
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.
Cyberinfrastructure
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...
comprising community-contributed resources and geared toward educational applications, professional networking, and interactive simulation tools for nanotechnology
Nanotechnology
Nanotechnology is the study of manipulating matter on an atomic and molecular scale. Generally, nanotechnology deals with developing materials, devices, or other structures possessing at least one dimension sized from 1 to 100 nanometres...
. Funded by the United States National Science Foundation
National Science Foundation
The National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health...
(NSF), it is a product of the Network for Computational Nanotechnology (NCN), a multi-university initiative of eight member institutions including Purdue University
Purdue University
Purdue University, located in West Lafayette, Indiana, U.S., is the flagship university of the six-campus Purdue University system. Purdue was founded on May 6, 1869, as a land-grant university when the Indiana General Assembly, taking advantage of the Morrill Act, accepted a donation of land and...
, the University of California at Berkeley, the University of Illinois at Urbana-Champaign
University of Illinois at Urbana-Champaign
The University of Illinois at Urbana–Champaign is a large public research-intensive university in the state of Illinois, United States. It is the flagship campus of the University of Illinois system...
, Massachusetts Institute of Technology
Massachusetts Institute of Technology
The Massachusetts Institute of Technology is a private research university located in Cambridge, Massachusetts. MIT has five schools and one college, containing a total of 32 academic departments, with a strong emphasis on scientific and technological education and research.Founded in 1861 in...
, the Molecular Foundry
Molecular Foundry
- The Molecular Foundry : is a nanoscience user facility located at the Lawrence Berkeley National Laboratory in Berkeley, California, and is one of five nanoscale science research centers sponsored by the United States Department of Energy...
at Lawrence Berkeley National Laboratory
Lawrence Berkeley National Laboratory
The Lawrence Berkeley National Laboratory , is a U.S. Department of Energy national laboratory conducting unclassified scientific research. It is located on the grounds of the University of California, Berkeley, in the Berkeley Hills above the central campus...
, Norfolk State University
Norfolk State University
Norfolk State University is a four-year, state-supported, coed, liberal arts, historically black university located in Norfolk, Virginia. It is member school of the Thurgood Marshall Scholarship Fund and the Virginia High-Tech Partnership.-Academics:...
, Northwestern University
Northwestern University
Northwestern University is a private research university in Evanston and Chicago, Illinois, USA. Northwestern has eleven undergraduate, graduate, and professional schools offering 124 undergraduate degrees and 145 graduate and professional degrees....
, and the University of Texas at El Paso
University of Texas at El Paso
The University of Texas at El Paso is a four-year state university, and is a component institution of the University of Texas System. Its campus is located on the bank of the Rio Grande in El Paso, Texas. The school was founded in 1914 as The Texas State School of Mines and Metallurgy,...
. 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
Nanoelectronics
Nanoelectronics refer to the use of nanotechnology on electronic components, especially transistors. Although the term nanotechnology is generally defined as utilizing technology less than 100 nm in size, nanoelectronics often refer to transistor devices that are so small that inter-atomic...
; nanoelectromechanical systems (NEMS); nanofluidics
Nanofluidics
Nanofluidics is the study of the behavior, manipulation, and control of fluids that are confined to structures of nanometer characteristic dimensions...
; nanomedicine
Nanomedicine
Nanomedicine is the medical application of nanotechnology. Nanomedicine ranges from the medical applications of nanomaterials, to nanoelectronic biosensors, and even possible future applications of molecular nanotechnology. Current problems for nanomedicine involve understanding the issues related...
, biology
Biology
Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, origin, evolution, distribution, and taxonomy. Biology is a vast subject containing many subdivisions, topics, and disciplines...
; and nanophotonics
Nanophotonics
Nanophotonics or Nano-optics is the study of the behavior of light on the nanometer scale. It is considered as a branch of optical engineering which deals with optics, or the interaction of light with particles or substances, at deeply subwavelength length scales...
.
Infrastructure
The Network for Computational Nanotechnology was established in 2002.The US National Science Foundation
National Science Foundation
The National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health...
(NSF) provided grants of about $14 million from 2002 through 2010, with principal investigator
Principal investigator
A principal investigator is the lead scientist or engineer for a particular well-defined science project, such as a laboratory study or clinical trial....
Mark Lundstrom.
The Web portal
Web portal
A web portal or links page is a web site that functions as a point of access to information in the World Wide Web. A portal presents information from diverse sources in a unified way....
of NCN is nanoHUB.org. It offers simulation tools, course materials, lectures, seminars, tutorials, user groups, and online meetings.
Interactive simulation tools are accessible from web browsers and run via a distributed computing network at Purdue University
Purdue University
Purdue University, located in West Lafayette, Indiana, U.S., is the flagship university of the six-campus Purdue University system. Purdue was founded on May 6, 1869, as a land-grant university when the Indiana General Assembly, taking advantage of the Morrill Act, accepted a donation of land and...
, as well as the TeraGrid
TeraGrid
TeraGrid is an e-Science grid computing infrastructure combining resources at eleven partner sites. The project started in 2001 and operated from 2004 through 2011....
and Open Science Grid. These resources are provided by hundreds of member contributors in the nanoscience community.
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
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:
SCHRED: calculates envelope wavefunctions and the corresponding bound-state energies in a typical Metal-Oxide-Semiconductor
MOSFET
The metal–oxide–semiconductor field-effect transistor is a transistor used for amplifying or switching electronic signals. The basic principle of this kind of transistor was first patented by Julius Edgar Lilienfeld in 1925...
(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
Schrödinger equation
The Schrödinger equation was formulated in 1926 by Austrian physicist Erwin Schrödinger. Used in physics , it is an equation that describes how the quantum state of a physical system changes in time....
.
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
Drift velocity
The drift velocity is the average velocity that a particle, such as an electron, attains due to an electric field. It can also be referred to as Axial Drift Velocity since particles defined are assumed to be moving along a plane. In general, an electron will 'rattle around' in a conductor at the...
, electron average energy and electron mobility
Electron mobility
In solid-state physics, the electron mobility characterizes how quickly an electron can move through a metal or semiconductor, when pulled by an electric field. In semiconductors, there is an analogous quantity for holes, called hole 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
Effective mass
In solid state physics, a particle's effective mass is the mass it seems to carry in the semiclassical model of transport in a crystal. It can be shown that electrons and holes in a crystal respond to electric and magnetic fields almost as if they were particles with a mass dependence in their...
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
Molecular dynamics
Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
to simulate materials at the nano and micro-scale.
ninithi
Ninithi
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...
: 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.
HUBzero
HUBzero, the software develeoped for nanoHUB, was created by researchers at Purdue UniversityPurdue University
Purdue University, located in West Lafayette, Indiana, U.S., is the flagship university of the six-campus Purdue University system. Purdue was founded on May 6, 1869, as a land-grant university when the Indiana General Assembly, taking advantage of the Morrill Act, accepted a donation of land and...
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.
HUBzero allows individuals to create web sites that connect a community in scientific research and educational activities. HUBzero sites combine Web 2.0
Web 2.0
The term Web 2.0 is associated with web applications that facilitate participatory information sharing, interoperability, user-centered design, and collaboration on the World Wide Web...
concepts with middleware that provides access to interactive simulation tools including access to TeraGrid, the Open Science Grid, and other national grid computing
Grid computing
Grid computing is a term referring to the combination of computer resources from multiple administrative domains to reach a common goal. The grid can be thought of as a distributed system with non-interactive workloads that involve a large number of files...
resources.
The software later became supported by a consortium and used for some other projects.
The web site built from open-source software
Open-source software
Open-source software is computer software that is available in source code form: the source code and certain other rights normally reserved for copyright holders are provided under a software license that permits users to study, change, improve and at times also to distribute the software.Open...
: the Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
operating system, the Apache web server, the MySQL
MySQL
MySQL officially, but also commonly "My Sequel") is a relational database management system that runs as a server providing multi-user access to a number of databases. It is named after developer Michael Widenius' daughter, My...
database, the Joomla content management system, and the PHP
PHP
PHP is a general-purpose server-side scripting language originally designed for web development to produce dynamic web pages. For this purpose, PHP code is embedded into the HTML source document and interpreted by a web server with a PHP processor module, which generates the web page document...
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 InterfaceGraphical user interface
In computing, a graphical user interface is a type of user interface that allows users to interact with electronic devices with images rather than text commands. GUIs can be used in computers, hand-held devices such as MP3 players, portable media players or gaming devices, household appliances and...
(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
WebDAV
Web-based Distributed Authoring and Versioning is a set of methods based on the Hypertext Transfer Protocol that facilitates collaboration between users in editing and managing documents and files stored on World Wide Web servers...
support on Windows, Macintosh, and Linux operating systems to access theier nanoHUB files on a local desktop.
Middleware
The web serverWeb server
Web server can refer to either the hardware or the software that helps to deliver content that can be accessed through the Internet....
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
Unix
Unix is a multitasking, multi-user computer operating system originally developed in 1969 by a group of AT&T employees at Bell Labs, including Ken Thompson, Dennis Ritchie, Brian Kernighan, Douglas McIlroy, and Joe Ossanna...
systems, Xen
Xen
Xen is a virtual-machine monitor providing services that allow multiple computer operating systems to execute on the same computer hardware concurrently....
virtual machines, and a form of virtualization based on OpenVZ
OpenVZ
OpenVZ is an operating system-level virtualization technology based on the Linux kernel and operating system. OpenVZ allows a physical server to run multiple isolated operating system instances, known as containers, Virtual Private Servers , or Virtual Environments...
. 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 was cited hundrends of times in the scientific literature, peaking in 2009.
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.
See also
- Materials informaticsMaterials informaticsMaterials informatics is a field of study that applies the principles of informatics to materials science and engineering to better understand the use, selection, development, and discovery of materials...
- Integrated computational materials engineeringIntegrated computational materials engineeringIntegrated Computational Materials Engineering is an approach to design products, the materials that comprise them, and their associated materials processing methods by linking materials models at multiple length scales. Key words are "Integrated", involving integrating models at multiple length...
- Multiscale modelingMultiscale modelingIn engineering, mathematics, physics, meteorology and computer science, multiscale modeling is the field of solving physical problems which have important features at multiple scales, particularly multiple spatial and temporal scales. Important problems include scale linking...