Introduction to nanoXplorer IDE

1.1. Research tutorial

This tutorial provides a step by step walk-through of nanoXplorer IDE's support for researching nanotechnology.

Start >> Selecting a topic

1.1.1. Selecting a topic

In this section you will learn how to select a nanotechnology topic and become familiar with the Topics View.

1. Open the Research Perspective. There are two ways to do this. The fastest way is to use the perspective menu located toward the upper right hand corner of the workspace. Alternatively, select Research from the Open Perspective menu item under the application's Window menu.
   
   
   
                
   
   
   
2. Most likely the Topics View is already open, typically on the left side of the Research Perspective. If it is not open, open it by selecting Window > Show View > Topics.
3. The Topics View organizes nanotechnology topics into a number of categories, each with its own folder. One of the categories is "All Topics" where all available topics can be found. Topics are also grouped alphabetically and by prefix to make them easier to navigate.
   
   
   

   
   Example Topics View
   
   

4. The Topics View acts as the control center for the Research Perspective. Whatever topic is selected in the Topics View the other views respond to that selection by updating their information to reference the currently selected topic. Select any topic, for example "Ab Initio," and see what happens.
   
   
   

Next >> Using nCyclopedia

1.1.2. Using nCyclopedia

In this section you will learn how to view the nCyclopedia entry for a selected nanotechnology topic.

1. If you haven't done so already, open the Research Perspective and select a topic in the Topics View.
2. The nCyclopedia Entry View is typically already open and located in the middle of the Research Perspective. If the nCycloped Entry View is not open, open it by selecting Window > Show View > nCyclopedia Entry . Note that all nCyclopedia entries are stored locally: no Internet connection is required to access the information.
   
   
   
   
   
   
3. Use the toolbar controls to change the size of the text.
4. If the entry contains any links, you may click on them to either change topics (for an internal link) or open an external web page.

Next >> Reading the latest news

1.1.3. Reading the latest news

In this section you will learn how to access the latest news related to the selected nanotechnology topic.

1. If you haven't done so already, open the Research Perspective and select a topic in the Topics View.
2. The News View is typically already open and located in the upper right corner of the Research Perspective. If the News View is not open, open it by selecting Window > Show View > News. Note that for the News View to show any content your computer must have an active connection to the Internet and certain network traffic must be permitted.
   
   
   
   Example News View
   
   
3. A line at the top of the view indicates how many articles were found for your selected nanotechnology topic (if no articles were found, try selecting a more general topic such as "Nanotechnology").
4. Use the scroll bar and the page buttons (on the bottom) to review the available headlines. Use the controls on the toolbar to hide/show context, make the text larger or smaller or change the sorting method.
5. If a news link looks interesting, click on it like you would any web page link. The link should take you to a web page containing the article. Note that you may have to manually bring your web browser to the front if it was already open.
   
   
   

Next >> Searching for images, journal articles and web pages

1.1.4. Searching for images, journal articles and web pages

In this section you will learn how to access search results for images, journal articles and web pages related to the selected nanotechnology topic.

1. If you haven't done so already, open the Research Perspective and select a topic in the Topics View.
2. The Search View is typically already open and located in the bottom right corner of the Research Perspective. If the Search View is not open, open it by selecting Window > Show View > Search.
3. The Search View has tabs on the bottom to enable different kinds of searches, including image, journal article and web pages searches.
   
   
   
   Use the tabs to switch between different types of search results
   
   
4. A line at the top of the view indicates how many articles were found for your selected nanotechnology topic (if no articles were found, try selecting a more general topic such as "Nanotechnology").
5. Use the scroll bar and the page buttons (on the bottom) to review the available headlines. Use the controls on the toolbar to hide/show context and make the text larger or smaller.
6. If a link looks interesting, click on it like you would any web page link. The link should take you to a web page containing the image or article. Note that you may have to manually bring your web browser to the front if it was already open.

1.2. Nanodevice design tutorial

This tutorial takes you step-by-step through creating a nanodevice design, including creating a NanoFile, adding nanoscale components, editing those components and saving the design.

Start >> Open the Design Perspective

1.2.1. Open the Design Perspective

The Design Perspective is the home of many of the Views and Editors that you will use during the design process, so start this tutorial by opening it, if it is not already open.

There are two ways to open the Design Perspective. The fastest way is to use the perspective menu located toward the upper right hand corner of the workspace. Alternatively, select Design from the Open Perspective menu item under the application's Window menu.

The Design Perspective is the default perspective of nanoXplorer IDE.

     

Next >> Open the Workspace View

1.2.2. Open the Workspace View

The Workspace View shows you the resources that you have in your workspace. In particular it is able to look inside NanoFiles (nanodevice design files) and see their contents. It also serves as a sort of control panel for the design process so let's open that, if it is not already visible, by selecting Window > Show View > Workspace.

An example Workspace View

Next >> Create a new project

1.2.3. Create a new project

Projects are a convenient way to organize nanodevice designs and related files. While the workspace includes a default project, create a new one for this tutorial.

• Select File > New > Project... from the main application menu.
• Use the New Project Wizard to name and create the new project.

Next >> Create a new folder

1.2.4. Create a new folder

Folders provide a way to further organize files. Create a new folder in our new project and name it "tutorial."

• Select File > New > Folder... from the main application menu.
• Use the New Folder Wizard to set its parent project and name and create the folder.

Next >> Create a new NanoFile

1.2.5. Create a new NanoFile

A NanoFile is a special file that contains nanodevice designs and related information. Create a new NanoFile so that you can begin creating a new nanodevice design.

There are two ways to create a new NanoFile:

1. Use the File > New > Other...menu command from nanoXplorer IDE's main menu bar.
2. Select the NanoFile wizard in the dialog.
3. Select a name and parent for the new NanoFile and press the Finish button.

or

1. Open the Design Perspective.
2. Open the Workspace View, if necessary.
3. Press the New NanoFile button () on the Workspace View toolbar.
4. Select a name and parent for the new NanoFile and press the Finish button.

Both of these actions will create a new NanoFile and place it in the workspace at the specified location. If the Workspace View is open, the NanoFile will be immediately visible in the project, folder and file hierarchy.

Next >> Open the NanoFile

1.2.6. Open the NanoFile

You created a NanoFile in the previous step; now you would like to open it for editing.

Simply locate the Nanofile in the Workspace View and double-click on it. This will open the NanoFile Editor for that NanoFile. Be patient; it may take a few moments for the Editor window to come up as it needs to load the advanced three-dimensional interactive environment.

The NanoFile Editor, once visible, will show empty space because you haven't added anything yet.

Next >> Add components to the NanoFile

1.2.7. Add components to the NanoFile

To keep this basic tutorial simple, you will only add one component to the NanoFile. In a real design process, of course, this is where most of the hard work would take place. Selecting, modifying, positioning, orienting, and connecting components with atomistic precision could take days for a complex nanodevice design.

Double-click the Nanotube widget in the Widgets View. This should open the New Nanotube Wizard. If you want to try and set parameters for the nanotube, go ahead and do so, however, for the tutorial all you need to do is press "Finish" to create the default nanotube.

• For just a taste of the editing capabilites at your disposal, try moving the nanotube (grab the nanotube with left mouse button and drag it somewhere). Or you can change the orientation by dragging with the right mouse button.
• If you want to change your viewpoint, drag on the scene background.
• Try to bring up the context menu (right-click on Windows and Linux) for some of the atoms and bonds in the nanotube.

More comprehensive information about the NanoFile Editor is offered outside this tutorial.

Next >> Save the NanoFile

1.2.8. Save the NanoFile

Now that you have edited the NanoFile, you may want to save the changes. Make sure the NanoFile Editor has focus (for example, by clicking on its tab) and press the save button on the main application toolbar.

Close the editor window and open the NanoFile a second time. The nanotube should be there just as you left it.

1.3. What is nanoXplorer IDE?

Nanoinformatics starts with nanoXplorer IDE â??the essential software resource for the nanotechnology workgroup. Researchers and engineers use nanoXplorer to realize the full range of their nanodevice inspirations, from concept to commercialization. nanoXplorer IDE is a complete design, analysis and research environment priced to fit comfortably in your workgroupâ??s budget.

With nanoXplorer IDE, you can:

• Design, visualize and communicate your nanoscale device ideas

• Interactively model your device through the advanced nVisualizerâ?¢ 3D interface for atomically precise, intuitive control of structure and content

• Simulate nanoscale devices and subcomponents using a variety of techniques

• Access the latest nanotechnology-related information and data right on your desktop with nCyclopedia and integrated research tools

• Model complex nanosystems using hierarchical components

• Integrate your own design, simulation, data and visualization plug-ins, leveraging nanoXplorerâ??s unique extensibility

• Create nanotubes, buckyballs, DNA and other common nanoscale entities with the help of easy to use wizards

• Manage experimental and simulated data, including images, videos, molecular trajectories, multidimensional data sets and custom 3D views

• Save your designs in nanoML®, the de facto language for nanodevice specifications

• Deploy on your workgroupâ??s Windows®, Linux and Solarisâ?¢ workstations

• Integrate with CVS and other configuration management systems to support shared design documents and data

1.4. Using nanoXplorer IDE

nanoXplorer IDE is built upon a strong foundation of the Java Platform and the Eclipse Rich Client Platform. This architecture provides a very robust and capable user interface. There are some key elements to the user interface that you will need to understand in order to get the most out of nanoXplorer IDE; these are workspaces, the workbench, perspectives, views and editors.

Workspaces

A Workspace is simply the "stuff" on which you are currently working and corresponds directly to a folder on your computer. nanoXplorer IDE allows you to switch Workspaces, so you can have more than one work area on your computer and you may be prompted to select a Workspace when you first launch nanoXplorer IDE.

The Workbench

The Workbench is essentially just another name for the entire user interface. It's main purpose is to provide top level actions, functionality and window management and holds whatever Perspectives have been defined.

More information about the Workbench is available here.

Perspectives

A perspective is a set of views (and perhaps editors) and actions that are particularly useful for accomplishing certain tasks or when acting in a certain role. nanoXplorer IDE provides a number of different persectives, including

• Design Perspective - nanodevice design editors and views
• Analysis Perspective - simulation and analysis tools
• Research Perspective - tools for researching nanotechnology
• Resource Perspective - workspace resource management

More information about perspectives is available here.

Views and Editors

Views and editors are the workhorses of the user interface. A View typically displays information, while an Editor enables content changes. Views can be opened any time from the Window menu. Editors must be opened on a particular resource in the Workspace, typically by double-clicking it. Read more about Views and Editors.

Consider looking through the Workbench User Guide to familiarize yourself with the many productivity enhancing aspects of the Workbench.

1.5. Simulation tutorial

This tutorial takes you step-by-step through creating, configuring and running a simulation, and then viewing its results.

Note that this tutorial requires an existing NanoFile with some molecular content in your workspace. See the Nanodevice Design Tutorial if you need to create a NanoFile.

Start >> Open the Analysis Perspective

1.5.1. Open the Analysis Perspective

The Analysis Perspective contains a default set of views useful for performing nanoscale analysis and simulation.

There are two ways to open the Analysis Perspective:

• use the perspective menu located toward the upper right hand corner of the workspace
• use the application menu bar... Window > Open Perspective > Analysis.
  
  
  
               

   

Next >> Open the Simulation Manager View

1.5.2. Open the Simulation Manager View

The Simulation Manager View has a button to create new simulations. If it is not already visible in the Analysis Perspective, open it using the application menu bar:

• Window > Show View > Simulation Manager

An example Simulation Manager View showing toolbar buttons and two completed simulations

Next >> Open the New Simulation Wizard

1.5.3. Open the New Simulation Wizard

The New Simulation Wizard is used to create all new simulations within nanoXplorer IDE. To open it, press the "New Simulation" () button on the Simulation Manager View toolbar.

The first page of the New Simulation Wizard

Next >> Select a Simulation

1.5.4. Select a simulation

The available simulations are presented in a drop-down menu. For this tutorial, select "nanoXplorer Geometry Optimization."

Select a simulation from the drop-down menu

Next >> Configure the Simulation

1.5.5. Configure the simulation

Each type of simulation will present its own pages for configuration in the New Simulation Wizard. Assuming you selected the "nanoXplorer Geometry Optimization" simulation, press "Next" to advance to the geometry optimization configuration pages. Configure the simulation as follows:

• Select the atomic system you wish to simulate (either from the current workspace or from a file):
  

• Go to the next page.
• Select an energy (and energy gradient) calculator. Choose the MM3 parameterized force field for this tutorial:
  

• Go to the next page.
• Configure the optimization algorithm's search parameters (using the default parameters is fine):
  

Next >> Run the Simulation

1.5.6. Run the Simulation

Change the name of the simulation, if desired. To run the simulation, press the "Finish" button on the New Simulation Wizard. If you don't want the simulation to run right away deselect the associated check box first.

Next >> View the Simulation Results

1.5.7. View the Simulation Results

Open the Simulation View for the simulation to view its results and configuration information by pressing the Open Simulation Information button () on the Simulation Manager toolbar.

Example Simulation View showing optimized geometry result

2.1. Researching nanotechnology

The field of nanotechnology is both very broad and rapidly evolving. These circumstances make it quite difficult for scientists, engineers, students and teachers of nanotechnology to have a complete understanding of the advances that impact their areas of interest. nanoXplorer IDE fills the need for a central place for researching various aspects of nanotechnology. Its Research Perspective supplies various informational views on a continually expanding number of nanotechnology topics in broadly-defined categories ranging from basic science to societal impacts.

The integrated nCyclopedia (nanotechnology encyclopedia) provides in depth information on each topic, while supporting views provide additional information such as the latest news and related information out on the Internet. Taken together, the Research Perspective becomes an information portal to a succession of selected nanotechnology topics, leading to increased understanding and awareness.

Topics
nCyclopedia
News
Search

2.2. Nanoscale device design

The promise of nanotechnology is that someday we'll be able to create a myriad of nanoscale devices that can do everything from prevent disease to clean our environment to suffuse our surroundings with massive computing power... and all that would make possible.

Manufacturing technology will have to come a long way before such things are possible. However, designing such nanodevices is possible today, if one does not worry about the hard problems involved in going from blueprint to real world and the mass production that would have to be available for nanoscale devices to make any meaningful impact. Moreover, some simpler real world nanotechnology applications are available today and enhancing actual products, such as nanoparticle coatings, nanofibers in textiles and nanoscale electronic components. Clearly we are at the beginning of a technological revolution that will transform the world, but the scientists and engineers who are trying to turn these possibilities into realities need tools to help them.

The process of nanoscale device design is similar to aircraft design, automobile design and even, in some respects, software design. It requires hierarchical organization, libraries of reusable parts, advanced visualization and interactivity, teams working together, subsystems of varying complexity and the interfaces between them, and a file format for capturing the design, among many other things.

nanoXplorer IDE sits at the cross-section of chemistry and engineering, providing all the tools to do realistic work with nanoscale components while preserving the function of macroscale computer-aided design systems. It enables teams to work with nanoscale device designs efficiently and powerfully, supporting the design process from the very first inkling of an idea all the way to full-fledged complex design that has been simulated in its target environment and is ready for real world prototyping by some yet to be realized desktop nanoscale device factory.

2.3. The Nanodevice Model

A nanodevice may be defined as "molecules with a purpose." It is a device in the sense that it can be used for something (whether simple or complex) and it is "nano" in the sense that it is characterized by parts that are best measured in nanometers (one billionth of a meter, about the size of a small molecule). The term usually implies that human engineering has played some part in its conception, though some interesting nanodevices are also found in nature. This definition encompasses everything from simple nanowires that do nothing but conduct electricity to complex "nanobots" that are perhaps mobile, autonomous and capable of various functions. Thus nanodevices are both routinely available in today's labs and speculative engineering that will unfold over decades to come. nanoXplorer IDE enables design of the full range of nanodevices.

nanoXplorer models nanodevices as a hierarchical collection of nanosystems, connections, molecular devices, interfaces, device components, molecular components and spatial components. Each is described below:

• Nanosystem - the top-most level of the hierarchy, contains subsystems and subdevices
• Molecular Device - consists of device components
• Device Component - consists of molecules and volumes
• Molecule - small or large
• Volume - region of space with particular properties and appearance
• Interface (not shown) - a nanodevice component may include any number of interfaces
• Connection (not shown) - a connection between two nanodevice component interfaces

2.4. Simulation

Simulations approximate the behavior of real systems and are often used during the design process to explore how different design decisions affect performance and functionality.

nanoXplorer IDE provides an extensible simulation framework for analyzing nanoscale systems, supporting nanoengineering and exploring nanoscale science. This extensible framework allows anyone to add their own simulations to the powerful nanoXplorer Integrated Development Environment (IDE).

3.1. Running nanoXplorer IDE

To run nanoXplorer IDE, follow these steps:

1. If necessary, install nanoXplorer IDE.
   1. Download nanoXplorer IDE from the nanoTITAN web site.
   2. Decompress the downloaded Zip file into a new directory, preserving the folder hierarchy. Download and install WinZip if you don't yet have a tool that can decompress a Zip file.
2. Using your file system browser, go into the top level folder where nanoXplorer IDE was installed.
3. Double-click on the nanoXplorer IDE executable to launch the application.

Note that on most operating systems you can create a shortcut to the application on your desktop, for example by dragging the executable icon and dropping it on the desktop background.

3.2. Opening the License Manager Wizard

The License Manager Wizard provides feedback on license status, allows activation of a node license and assists with license purchases and support extensions. To open the License Manager Wizard:

1. Press the Open License Manager Wizard button () on the application toolbar, or
2. Select Window > License Manager... from the application's main menu bar

First page of the License Manager Wizard

3.3. Activating a node license

Upon purchase of a node license you will receive an activation key. To enter this key and activate you rlicense:

1. Open the License Manager Wizard by choosing the Window > License Manager... menu item (or pressing the License Manager button on the main toolbar)
2. Select the "I have purchased a node license and have my activation key" option and proceed to the next page
3. Type (or copy and paste) the key string into the "Activation Key" field of the License Manager, fill in the other requested information and then press the "Activate Node License" button immediately to the right. The License Manager Wizard will indicate whether the upgrade was successful.
   

If for some reason the transmission fails repeatedly or you do not have an Internet connection on the installation machine, you may mail the activation information from a different computer.

1. Proceed to the next page to troubleshoot the activation request.
2. Copy the information provided, preferably saving it to a file
3. Send the information in an email to support@nanotitan.com from any machine. The license key and instructions on how to install it will then be sent to the email address provided (so make sure that it's correct and that its the one where you wish to receive the key).

3.4. Purchasing a license

To purchase one or more licenses for nanoXplorer IDE:

1. Visit the nanoTITAN web site and follow the links to buy the licenses. There are also purchase order forms available for download.
2. Once a node license purchase has been processed, an email will be sent to you containing an activation key.
   - Network licenses will require communication between nanoTITAN and a technical contact in order to define the networks on which nanoXplorer will be allowed to run, however no key is required to activate a network license once it has been properly configured.
3. Enter the activation key in the License Manager.

4.1.1.1. License Manager Wizard

You will require a license for every computer on which you wish to run nanoXplorer (beyond the evaluation period). Purchase node or network licenses on the nanoTITAN web site.

Select an action

Select an action and press "Next."

Activate a node license

Copy and paste your activation key into the text box, enter the other required information and then press the "Activate Node License" button.

Enter a code

You may receive a special code to enter into the license manager (for troubleshooting or installing a license off-line, for example). Copy and paste your code into the text box and then press the "Submit Code" button.

Purchasing a license

This page directs you to the nanoTITAN web site where licenses can be purchased electronically or purchase orders and price lists are available.

Extending support subscription

The intial purchase of a nanoXplorer IDE license includes one year of free support and upgrades. Thereafter, the support subscription must be renewed to continue enjoying these services. This page directs you to the nanoTITAN web site where extensions can be purchased.

5. What's new

What's new in 3.3.3.20080825

This is a Stable maintenance release. Improvements include:

• Corrected problem with execution of OpenBabel energy minimization on some platforms
• Optimized and corrected some incorrect bonds in the Diamond creation wizard
• Changed the initial viewpoint when opening scenes
• Fixed bug in boolean geometry editing (used for Diamond and Graphite creation)
• Fixed bug in label management of coordinates and offsets.
• Changed labels from autosized to fixed size in NanotubeZoo sample file. Also added tethers.

What's new in 3.3.2.20080819

This is a Stable release. Significant changes from the last Stable release, by category, are described below:

• General
• Design
• Visualization
• Simulation
• Integration
• Research

6. System requirements

nanoXplorer IDE is an advanced application built with the latest Java technology. It may be necessary to configure or upgrade your system before running the application.

Hardware requirements

• Minimum recommended system:
  • 1.5 GHz Pentium CPU or equivalent
  • 512 MB RAM
  • 3D Graphics Accelerator
• 100 MB free disk space for installation
• Note: users processing large nanodevices and/or molecules will benefit most from additional RAM, more advanced graphics accelerators and multiple/faster CPUs.
  

Software requirements

nanoXplorer IDE runs on the Java Platform and therefore requires that Java SE be downloaded and properly installed before nanoXplorer is executed:

• Java SE 6, or later
  (JRE 6+ or JDK 6+)
  Available from Sun Microsystems (point your browser to http://java.sun.com to download the latest version.

• One of the supported operating systems (Windows, Linux/GTK... see the nanoXplorer IDE download page for available versions).

Other requirements

• Various functionality in nanoXplorer IDE requires an Internet connection, however the application will run without one.
• The nanoXplorer user interface is optimized for screen resolutions greater than 1024x768.
  
  
  
  
  

7. Privacy

At nanoTITAN, Inc. we take your privacy seriously. We will never share or sell your personal information, including your email address, for any reason, except as required by law.

What information do we collect?

The License Manager is used to submit information for registering your version of nanoXplorer with nanoTITAN. The information collected includes name, organization, email, and current key. A valid email address is required--nanoTITAN will send the permanent key requested during registration to the email provided. The current key is also necessary for validation purposes. Name and organization are supplemental, though we strongly recommend entering valid values in these fields in order to facilitate future upgrade and support requests.

How do we use that information?

We use the information that is collected to:

• generate a permanent key for your machine
• email the permanent key to you
• maintain a database of registered users for support and maintenance

We will not share or sell your personal information, including your email address, to other companies for any reason, except as required by law.

8. Support

Email support

Send your bugs, problem reports and feature requests to support@nanotitan.com. Please be as detailed as possible in order to help us resolve the problem. Your request for support will be handled on a priority basis (registered users have priority; be sure to include your name and key so that nanoTITAN can verify your registration status). Open the License Manager (Window > License Manager...) to see your key.

If you have an active Internet connection while nanoXplorer IDE is running you can also access the on-line support web page through the Welcome screen (Help > Welcome, Web Resources).

Help documentation

Users are encouraged to use the application User Guide (Help > Help Contents) before contacting nanoTITAN (have you tried the search function?).

Web site

Users may also wish to visit the software support section of our web site to look for further information regarding a specific problem or upgrade before submitting a problem report.