Visual Simulation Tools: Solutions to Shift the Education Paradigm 

 Judith Light Feather, President, The NanoTechnology Group Inc.
 

Advances in microscopy and optical lenses have opened the ‘window to nature’ allowing us to see how the world actually works at the atomic level. This scale of science is all-encompassing and demands collaboration between physics, chemistry, biology, engineering and information technology, along with simulation and modeling software technicians.

Our organization is constantly searching for solutions to provide more visual elements to include in the curriculum development for students to understand and work at the atomic scale of science.   Most of the simulation programs are designed for the university level research students and professors. Some of the programs we have found are at the pre-launch testing phase, while others are ready for commercialization. All of the companies are offering large discounts and/or free trial offers for education and government use of the software.   We have placed a few of them prior to this article on our website for access and have recently been introduced to several other new programs designed for specific areas of research in nano science.  

All of the tools are necessary for the various focuses of research and study at the atomic level. It is imperative that visual simulation tools and programs are adopted into all education programs as viable solutions.

Introducing the first systems engineering software for nanodevice design

Recently, I was introduced to Vic Peña, CEO of nanoTITAN Inc., whose company has developed a systems engineering software for nanodevice design and communication.   Mr. Peña has an excellent background in visualization tools from his years at TASC, a subsidiary of Northrup/Grumman. During our conversation he also stated that when he and his partner, Rob Bishop, nanoTITAN’s CTO, left TASC, it became their largest client for the new software programs that are specific data visualization tools in myriad applications. These tools became the foundation for their flagship product, nanoXplorer™.

nanoTITAN was incorporated on January 19, 2001—at the dawn of the new millennium— in the Commonwealth of Virginia. According to Mr. Peña, their mission is to be the premier provider of software, information and services to the nanotechnology community and to assume a central role in the evolution of nanotechnology from basic research to profitable application: "Enabling the Diamond Age."

Since I was interested in visual simulation software for education, my first question was, ”What level of student would this system be practical for in the area of education, or did you just design it for commercial applications in the industry?“

”Basically, we target students at the university level and especially those conducting research. However, it can also be adaptable for workforce technician training at Community Colleges and maybe the few Advanced Technical High Schools who would like to develop an introductory level course“, stated Peña.

”What if the graduate students that had the program in a university lab, could provide a few sample files of the early basic research from the program, which could then be developed into Introductory curriculum for high schools?, I inquired. ”It may be an avenue to explore with universities who are using the system“, replied Peña.  

”What is the difference between your system for designing molecular devices and other simulation software that models molecular motors at the nanoscale“ was my next question.

”Simulation programs are usually designed for specific purposes and the categories are so broad when involving chemistry, biology and physics at the nanoscale. Therefore, instead of working in a single focus area, we decided to tackle the issue of ‘whole system thinking’ software applications that can handle a research project from the first molecule to the prototype device stage for commercialization in materials science, hence our systems approach“, stated Peña.

”Our philosophy is one of incremental growth in capability—‘three yards and a cloud of dust,’ if you will, which is why we are aiming at becoming the Nanoinformatics leader. If you take the whole systems approach from the beginning, the growth stems from the essential needs of an early stage industry’s growth.   Our software designs will incorporate that growth which all starts in the research labs at universities as well as governments and corporations,“ he explained.   ”You also must realize that our software is designed for all areas of research in materials science, so I recommend other programs to universities that are working on research of electrical nanoscale devices, such as Atomistix in Denmark. They excel in this area of electronics simulation software,“

”In conclusion, we are still the only simulation developer that has taken on the whole system approach, and materials science is a very important research area for nanoscale products entering the marketplace in this decade. Our nanoinformatics system will help move the current research and development of nanomaterials into the marketplace with an accurate prototype that will enhance the cost effectiveness of the commercialization process. This stage is a requirement for all research funding awarded to universities as government grants. Nanoinformatics includes the components that protect the Intellectual Property (IP) for the Patent process within the system for each research project creating an ecological economy from concept stage in the lab to market.“

The components of Nanoinformatics

Nanoinformatics starts with nanoXplorer—the essential software resource for the nanotechnology workgroup. Researchers and engineers can use nanoXplorer to explore, exchange and engineer the full range of their nanodevice inspirations, from concept to commercialization. Built on the principles of life cycle systems engineering, nanoXplorer complements chemical analysis and simulation software by providing management of all aspects of a nanodevice. The user of this program is presented with in-depth information, which includes the chemical structure, properties, operational characteristics, interface and connection details and visualizations of the molecular nanodevice.

While there is no ”official“ definition of ”nanodevice,“ in the nanoXplorer software it has the specific meaning of a molecular device, comprised by components with nanoscale dimensions that have a particular purpose or function. ”Nanoscale“ indicates a size ranging from a small molecule (each atom is about one tenth of a nanometer—or one Angstrom) to about 100 times larger than that, or the approximate size of typical virus. These are not strict thresholds in practice, but offer a good framework for a universal understanding of the scale involved.

An example of a very simple existing nanodevice is a carbon nanotube. Though only a single molecule, it can be used for a variety of purposes as a result of its unique properties. For example, it may be used as a component in electronics due to its ability to act as a conductor or semiconductor (depending on its configuration), it has incredible tensile strength making it ideal for reinforcing materials and can even emit photons under certain conditions, leading to its use in certain display technologies just coming to market. More complex examples of nanodevices can be found both in nature (for example, ion channels) and on the drawing boards of many leading edge laboratories.

nanoXplorer is the first software application to make the nanodevice its central paradigm In order to handle multiple levels of complexity, nanoXplorer models nanodevices as a hierarchical collection of components broken down into three levels.

The Component Toolbar provides easy access to all of the components that a user can include in a nanodevice. This includes all of the levels of the nanodevice model hierarchy: nanosystems, molecular devices, device components, molecules and volumes—as well as interfaces and connections. It also includes custom configuration tools for specific molecules of special interest to nanotechnologists: nanotubes, buckyballs, DNA and dendritic polymers.

Data Protection in the program

The digital rights feature enables a user to prohibit third parties from certain actions (display, edit, save, aggregate) as they pertain to a particular piece of the nanodevice design. Permission to perform those actions may be granted subject to certain constraints and requirements. Constraints may include a cap on the number of uses or sunrise/sunset times. Requirements may include the need to accept an agreement or make payment.

By enabling a system where information can be protected and offered for compensation, nanoTITAN is planting the seeds for e-commerce in nanodevice designs.

Intuitive Interactive 3D environment

The Structure Panel provides fine control over the structure of a nanodevice through an intuitive interactive 3D environment. It is very easy to add new atoms and bonds, or delete them—or even edit the atom type or bond order, in place. This interactivity feature makes this program one of the most advanced molecular design tools on the market, where molecular design is a crucial element of nanodevice design. The flexible Pattern Tool also allows a user to specify a rectangular, cylindrical or spherical pattern of objects. This can help the nanodevice designer quickly create large devices that have repeating elements.

Supported data types include nanodevice designs (nanoML), molecules (e.g., CML, PDB), trajectories, images, videos, numerical data files (NetCDF) and text files. Any data incorporated into the nanodevice design is saved along with it (in nanoML) and is available each time the nanodevice design is opened for viewing. Thus the Data Panel is a powerful tool for both analysis and collaboration. Simulated and experimental data can be easily organized and shared with peers. Helpful images, animations and miscellaneous files can accompany a design to make sure the essential design elements are not lost. Students and novices can come up to speed quickly.

The Operation Panel captures the functionality of the nanodevice being designed. Eight categories of operational capability are summarized in the display and may be edited by the user.

1. Chronometry -- indicates the ability of the nanodevice to sense or keep time.

2. Communication -- indicates the ability to transmit and receive data.

3. Computation -- captures its suitability to be used as a component of a computational device.

4. Energy -- refers to its ability to convert energy from one type to another as well as its ability to generate power or requirement for power to operate.

5. Motility -- indicates its ability to move in various environments.

6. Safety -- is a consideration with nanodevices, particularly with regard to replication, environmental impact and biohazard.

7. Sensing -- captures the nanodevices ability to sense things about or in its environment.

8. Transport -- indicates whether the nanodevice can move other things.

The Assembly Panel captures information about a Nanodevice's interfaces and (for a Nanosystem) the connections between subsystems. A nanodevice can have any number of interfaces, which in turn can have any number of ”joins.“ A ”join“ has a particular type (chemical, electromagnetic, physical or remote) and position.

The Display Panel captures visualizations of the nanodevice and can be used to convey important information to others that will view a nanodevice design. A standard 3D view is always included, but the user can add additional 3D views as desired, with a high degree of flexibility in what is displayed. The user can also capture or load 2D images for inclusion in the nanodevice.

Analyzing Stability and Feasibility

The program includes molecular mechanics simulation for performing geometry optimization/ energy minimization for large molecules (such as molecular devices). This is useful for analyzing the structural stability and feasibility of a particular design. It also includes a fully-integrated version of the Nano-Hive Nanospace Simulator, a flexible open-source tool for analyzing the physical world at the nanometer scale. With Nano-Hive it is possible to calculate spatial and temporal properties of nanodevice components, including molecular trajectories that display atomic positions as a function of time. Nano-Hive can also perform electrostatic potential calculations of interest in many areas of nanotechnology. The simulation capabilities can be extended by wrapping any 3rd party simulation, simply by creating user interface and data handling components that adhere to nanoXplorer's simulation API.  

Built in Language

NanoML is an XML-based markup language for specifying nanodevice designs. It includes the chemical structure of the nanodevice, but goes far beyond that to include properties and operational characteristics, visualizations, digital rights, interface information and more. As such it is the ideal vehicle for transmitting information about nanodevice designs to colleagues and the public in general.   NanoML serves as the foundation file format for both nanoXplorer and the Nanodevice Database. NanoML is a registered trademark of nanoTITAN.

Included in the nanoXplorer programs are the following components:

nCyclopedia, a nanotechnology Wiki available on the nanoTITAN web site and nCyclopedia Plus™, an enhanced selection of news, articles and data for nanotechnology topics available exclusively from nanoXplorer 2005.

nVisualizer™, a powerful data visualization application that offers clients an easy to use tool for converting digital data into any combination of 3D, 2D and aural elements. Its component architecture allows rapid development of interactive information spaces.

Open source Java™ libraries of general use to scientists, engineers and developers, including the popular Quantity LIbrary, which models numerous physical quantities, their units and operations. nanoTITAN is partnered with Nano-Hive™, incorporating its Nanospace Simulator technology into nanoXplorer 2005, leveraging its powerful and extensible simulation capabilities. nanoTITAN is partnered with TASC, Inc., a Northrop Grumman Company, to provide visualization.

Now educators and students can enter the nanoscale together with nanoXplorer 2005’ Professional with features that enable 2-way collaboration between educators, colleagues and students providing real-time dynamic sharing of nanodevice designs and related data with licensing fees customized to your needs.

Education Discounts Available – Approx. 33% for universities and government use.

A Free test download is also available at:

www.nanoTITAN.com

Nanorex Developer of Nanoengineer is now making Computational tools for structural DNA nanotechnology

Nanoengineer 1 is for Everyone...

NanoEngineer-1 isn't just for people with powerful supercomputers at large universities. Actually, NanoEngineer-1 was created for anyone with a personal computer. Have a PC running Windows? No problem.  A Mac user? Download and install NanoEngineer-1! Oh, you have a Unix box. That's OK, we've got that covered, too.  Visit our site today.

http://nanoengineer-1.com/content/index.php  

Open-Source computational tools for SDN

Nanorex is developing open-source computational tools to support research in structural DNA nanotechnology (SDN). To do this, we are extending our existing application, NanoEngineer-1, to provide a foundation of tools for visualization, modeling, and manipulation of DNA, and to make it a framework that can support and integrate other computational tools developed by the SDN community. This work is part of our broader mission to support the development of advanced nanosystems. We've entered a process of collaborative development that will help the SDN research community integrate its diverse tools for design, modeling, and analysis, making them more useful and more widely available. Working with the rest of the SDN community, we'd like to make this process serve everyone's needs at multiple levels, both as users and as developers.

Their mission is to support the design and development of advanced nanosystems

Self-assembled atomically precise nanosystems hold great promise in many areas, both experimental and practical. Among the products will be systems that help researchers build more advanced systems. We expect structural DNA nanotechnology to play a central role in next-generation nanosystems.

Our mission is to support the design and development of advanced nanosystems through computational tools. In all areas of technology, tools for design and modeling help researchers to solidify their ideas into concrete representations and to evaluate and revise them. This speeds the cycle of design, fabrication, and testing at the center of the development process. SDN will be no exception.

DNA structures can provide frameworks for next-generation nanosystems

Three lines of research are converging to create a capability for systematic design of complex, atomically precise nanosystems. SDN has a crucial role in this prospective development.

Special structures

The first line of research is the development of a wide range of atomically precise functional components -- organometallic complexes, magic-size quantum dots, nanotubes and fibers, engineered surfaces, and so forth. These have functions ranging from chemical catalysis to electro-optical transduction to structural support. This wide range of functions, however, is offset by a major limitation: each of these functional components is a special structure, either unique or part of a small family, not a member of a designable class of billions of possible structures. This limitation makes it almost impossible to design components that will self-assemble to form complex, atomically precise systems. By themselves, these special structures are simply too constrained to provide the necessary diversity of selectively complementary surfaces.

Engineered proteins

The second line of research is the development of polymers made from a diverse set of monomers that fold to make specific 3D structures. Protein engineering is the advanced technology of this sort, and it has progressed to the point where researchers routinely design novel structures that are more stable than those found in nature. Artificial and natural examples show that proteins can perform a wide range of functions, and can bind proteins, nucleic acids, and an enormous range of other atomically precise structures, both biological and non-biological. Proteins therefore provide a solution to the problem of assembling the special, highly functional structures discussed above. Protein molecules can be effective structures: they have strengths and stiffnesses like those of epoxies, polycarbonates, and other engineering polymers. However, these useful properties are offset by a slow design, fabrication, and testing cycle (several months) and by the small size of individual proteins (a few nanometers). They are attractive as components and linkers, but less attractive as a way to combine components to make large systems.

Structural DNA

The third line is SDN itself, which now can be used to implement a large growing range of structures on a scale of tens to thousands of nanometers. Like proteins, but unlike the special, highly functional structures, DNA is a modular system that can be used to make a set of structures of combinatorial size, with billions of possible design choices for strands just a few nanometers long. Unlike proteins, DNA structures can be made with a fast design, fabrication, and testing cycle (no more than a few days, in some instances), and they can easily be thousands of times larger in volume. They can provide specific binding sites for proteins or DNA-tagged structures, holding hundreds or thousands of components in specific spatial geometries.

These lines of development are complementary, the first providing diverse elements of high functionality, the second providing components that can bind them precisely, and the third providing structures that can organize them in large numbers to form complex patterns. The resulting ability to build modular composite nanosystems opens the door to an as-yet unimaginable range of experimental and practical applications. SDN plays a vital role in this prospect: it is literally what holds it all together.

Structural DNA nanotechnology is a point of high leverage for computational tools

DNA structures are a good target for computer-aided design tools. They are regular enough that they can be designed and using relatively abstract representations, yet complex enough that computer support for visualization is essential. With DNA as a medium, designers can arrange and rearrange parts in a systematic way, much as they would in designing conventional macroscopic objects.

Special structures, by contrast, leave little scope for design, and while proteins have enormous scope for design, the process has special difficulties. Where a designer can rearrange DNA strands by following simple rules, relying on the regularities of helical structure and paired bases, a protein designer must use a computational search process to find combinations of side chains that fit together. This makes even the simplest design steps more difficult to plan and implement.

The development of modular composite nanosystems will require computational support for designs that include special structures and proteins, and some support may be possible at an early date. SDN design is the natural starting point, however, and is a rich field in itself.

An open-source framework will enable collaborative development of software tools

The growing SDN community has developed many software tools, and will develop many more in the years to come. Nanorex is developing open-source software that provides tools for visualization, modeling, and manipulation of DNA structures, and that provides interfaces for integrating these capabilities with existing and future software tools developed within the SDN community.

Because the core software is open source (NanoEngineer-1 is under GPL), all participants can be confident that it won't become expensive, and that any team that is working to extend it must continue to satisfy the broader community. Nanorex can't take down the project by failing, going bad, or trying to squeeze money out of the software itself -- in the worst case, the work would simply continue under new leadership.

Researchers will want to keep control of the tools they create, both to ensure their quality and to get proper credit when they are used. These tools can be treated as distinct open-source projects, giving researchers full control of the content of software that appears under their names. User interface conventions in NanoEngineer-1 will give clear credit to the creator of a tool when it is used. Rather than absorbing contributions and making them invisible, the project will offer researchers a new distribution channel that can make their work better known, better supported, and more widely used.

Our mission is to support the design and development of advanced nanosystems, and we see SDN is a central part of that development. No single research group or company could possibly provide all the necessary tools, so the choice is whether to have a jumble of incompatible pieces of software, each implementing a limited user interface, or to find a way to bring these tools together to form a more integrated system with powerful capabilities. We think that the general approach described here will enable the second, superior option. The approach itself, of course, is also open to contributions and revision by the community of users and contributors in the SDN research community. 

http://nanoengineer-1.com/content/index.php