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Designing atomically precise nanocomponents is meaningless if the resulting components are unrealistic in terms of stability or function. Therefore, simulation plays a key role in the design process. Just as airplane and automobile designers must take into careful account the stresses, temperatures and other factors that will impact the operation of each individual component - down to each nut and bolt - so too must the nanoengineer examine all aspects of of the nanocomponents that she designs. Nature has the last word on whether a particular atomic structure will behave as desired or even hold together at all. nanoXplorer IDE includes simulations for approximating nature, so that nanoengineers can be confident in their designs. Simulations are easy to configure, launch and manage. Results remain available as long as needed and can be viewed in a variety of ways. Most importantly, the simulation capabilities are tightly integrated into the design environment, improving efficiency and the user experience.
 Geometry Optimization/Energy Minimization
Designing nanoscale components, one must position every atom where it needs it to be to support the overall function of the component. But at the end of this design process the laws of nature must be given equal time. The process of minimizing the energy of a system is called geometry optimization. The optimized geometry may or may not be what you thought when you designed the nanocomponent. If your component is not stable, you'll need to make some changes. nanoXplorer IDE includes an easy-to-use and configure geometry optimization simulation so that you can perform reality-checks on your nanocomponent designs. On Windows, nanoXplorer IDE also makes the Open Babel minimization simulation capability (obminimize) available--providing verified and validated results you can trust.
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 Automatic Atom Typing
When using a molecular mechanics force field to calculate relative system energies each atom is assigned a type, which takes into account its relationship with its particular neighbors in the atomic system. The accuracy of the results are typically quite sensitive to the atom type assignments, so it's important to type each atom with care. Those with experience performing these types of calculations know that the atom typing step can be time-consuming and susceptible to human error. nanoXplorer IDE's molecular mechanics simulator addresses both shortcomings. Each atom and it's neighbors are analyzed automatically in order to determine the closest match for a particular atom amongst the tens or hundreds of atom types defined by the selected force field. This ensures better accuracy and eliminates a manually intensive step, speeding up the whole process.
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 Simulation Management
With nanoXplorer IDE you can run multiple simulations at a time, with feedback on progress, easy access to intermediate and final results, the ability to pause and restart as necessary and keep simulation results as long as desired. The Simulation Manager ties all of these capabilities together to maximize your efficiency. New simulations can be created easily; a new simulation wizard guides you through selecting and configuring the simulation you would like to run.
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 Simulation Plug-ins
nanoXplorer IDE includes the basic simulation capabilities needed to ensure that your nanoscale designs are feasible and stable. We also include an extension point where you can integrate your own simulations into the nanoXplorer environment. Integrating a new simulation requires some Java coding and probably some data format translations, but nothing too difficult. The benefits of doing so are the benefits of the integrated development environment (IDE)... higher productivity and better work flow. |
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