Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization

The overall goal of this procedure is to create atomistic models of helical, nano springs and nano ribbons using an open source code for molecular dynamics or MD simulations. This video describes how to prepare silica glass nano springing models by first preparing an appropriate atomistic bulk silica input file, along with the open source nano springing carver program files. The second step is to start MATLAB on a Linux PC and use the nano springing carver graphical user interface to generate a desired nano springing model.

Next, the nanos springing carver results are verified in an open source visualizer. The final step is to use the results in MD tensile simulations of springs. Ultimately, a variety of well-defined and scalable nano helical models can be effectively generated for MD simulations toward materials innovation research.

I first came up with idea of using this method back when I was performing molecular dynamic simulations of nanostructures such nano wires and others. As you may know, spring-like materials are very abundant in nature, and so it's important to try and study such geometries and especially for simul, for applications that have to do with energy harvesting, hydrogen storage and biological sensing and others. And currently there are commercial packages and codes available in the market.

However, they're quite limited in in the types of geometries you can create. And so optimistic helical models are not readily easy, easy to accomplish. So we hope that these type of efforts help future studies demonstrating this procedure will be Max Larner, who is a graduate student in my laboratory.

The files used in this video are provided online at the Davila Group website. See the text protocol accompanying this video for the URL. To begin, download the nano springs dot tar dot gz file archive from the web repository.

Locate the downloaded archive and move it to a preferred working directory. Entitled Documents slash Nanos Springs. Right click nano springs tar dot gz, and select extract here.

From the right click context menu, verify that all of the required files are present in the current directory. See the text protocol for a list of those files and their purpose on the desktop. Open a terminal window and change the directory to the folder into which the Nano Springs project files were extracted.

Next, run the command to compile the binary for the system by typing me Nano Springs, me CPP Point cpp. Then initiate MATLAB by typing MATLAB on the command line using the files provided online. Open the guide in MATLAB by clicking the guide icon on the top left toolbar area.

To display a new window with guide quickstart. Use the open existing gooey tab to modify an existing figure. Click on the browse button to search for the existing gooey figure to be modified.

After selecting the figure file, click on open in both windows to display a new window with the gooey figure in order to run the gooey click on run under the tools menu. And yes, when a popup window prompts whether to save the figure before running a new window displays the modified gooey. To set up the example run first, click on the select input model file button at the top of the gooey and navigate to the Glass cube IP file.

After selecting the input file, the path to it should appear in the gooey window to the right of the selected input model file button. Next, navigate to the output model section and use the browse button to browse for and select the directory to save the output model. Run the example using the given spring parameters by pressing the gooey run button.

In the MATLAB feedback, verify the number of input atoms selected for the spring model and the spring model parameters. Once the gooey interface is finalized, perform successive runs by right clicking on nano springs dot M in the MATLAB current folder window and selecting run. To bring up the gooey interface directly to visualize and verify the output spring models created by nano springing carver.

Use the nano springing carver MATLAB GUI to generate files as before for input into the visualization program. Measure distances in the spring models and make a record of them. Compare measured data against desired spring dimensions and verify spring model accuracy to use the spring models created by nano springing carver as input to a conventional open source molecular dynamics code.

First, download the latest version of the open source molecular dynamics program. Lamps, determine the dimensions of the desired nano springing model in order to prepare the appropriate initial bulk silica glass model. Then create the desired nano springing model using the nano springing carver MATLAB gui.

As before, perform tensile simulations on the desired nano springing by stretching the model. Axially produce a representative video of the nanos springing model being stretched for visualization and analysis. The computational methods presented in this procedure allow creation of silica, nano springs and nano ribbons suitable for atomistic simulations.

Shown here is an atomistic model of a silicon nano ribbon with a nano ribbon radius of 1.07 nanometers, A radius of helix of 5.37 nanometers and a pitch of 7.16 nanometers. Snapshots illustrate distinct views of the nano structure. This figure shows different views of an atomistic model of a silicon nano springing with a wire radius of 1.07 nanometers, a radius of helix of 4.29 nanometers, and a pitch of 4.29 nanometers.

After watching this video, people should expect to be able to create a helical nano springs using this open source code that we developed for future molecular dynamic simulations. In summary, the methods that were presented in this video will facilitate anyone to study nano lysis via simulations, and in that way, feature studies that include the design of nano devices will be possible.