Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization

Summary

Accurate modeling of nanohelical structures is important for predictive simulation studies leading to novel nanotechnology applications.  Currently, software packages and codes are limited in creating atomistic helical models.  We present two procedures designed to create atomistic nanohelical models for simulations, and a graphical interface to enhance research through visualization.

Abstract

Spring-like materials are ubiquitous in nature and of interest in nanotechnology for energy harvesting, hydrogen storage, and biological sensing applications.  For predictive simulations, it has become increasingly important to be able to model the structure of nanohelices accurately.  To study the effect of local structure on the properties of these complex geometries one must develop realistic models.  To date, software packages are rather limited in creating atomistic helical models.  This work focuses on producing atomistic models of silica glass (SiO₂) nanoribbons and nanosprings for molecular dynamics (MD) simulations. Using an MD model of “bulk” silica glass, two computational procedures to precisely create the shape of nanoribbons and nanosprings are presented.  The first method employs the AWK programming language and open-source software to effectively carve various shapes of silica nanoribbons from the initial bulk model, using desired dimensions and parametric equations to define a helix.  With this method, accurate atomistic silica nanoribbons can be generated for a range of pitch values and dimensions.  The second method involves a more robust code which allows flexibility in modeling nanohelical structures.  This approach utilizes a C++ code particularly written to implement pre-screening methods as well as the mathematical equations for a helix, resulting in greater precision and efficiency when creating nanospring models.  Using these codes, well-defined and scalable nanoribbons and nanosprings suited for atomistic simulations can be effectively created.  An added value in both open-source codes is that they can be adapted to reproduce different helical structures, independent of material.  In addition, a MATLAB graphical user interface (GUI) is used to enhance learning through visualization and interaction for a general user with the atomistic helical structures.  One application of these methods is the recent study of nanohelices via MD simulations for mechanical energy harvesting purposes.

Introduction

Helical nanostructures are typically produced in the laboratory using chemical vapor deposition techniques^1-2, while new approaches have been reported in the literature³.  In particular nanosprings and nanoribbons have been studied because of their distinct properties and promising applications in sensors, optics, and electromechanical and fluidic devices^4-7.  Synthesis methods have been reported to produce silica (SiO₂) nanoribbons, making these structures potential building block units for hierarchical systems.  Novel synthesis of 3D silica nanosprings has expanded their applications to chemiresistors when coated with ZnO<....

Protocol

1. Preparing NanospringCarver Files and Starting MATLAB on a LINUX PC

The following steps are designed for a general user to make use of the files provided online²⁶.

1. Unpack the nanosprings.tar.gz file archive into the “Home” or another preferred directory.
   1. Download the nanosprings.tar.gz file archive from the web repository²⁶.
   2. Locate the downloaded archive and move it to a preferred working directory entitled “Documents/Nanosprings”.
   3. Right-click nanosprings.tar.gz and select “extract here” from the right-click context menu.....

Results

The atomistic nanoribbon models created with the first computational procedure (nanoribbons code) and their associated dimensions are shown in Figure 9. The resulting nanospring models using the second computational procedure (nanosprings code) and associated dimensions are shown in Figure 10.

Discussion

Modification of the original approach to create nanohelical structures led to the development of two distinct codes to allow creation of both nanoribbons and nanosprings from an initial bulk silica glass MD model.  The verification of the silica nanoribbon and nanospring models was pursued using different software packages^19-20, which confirmed their dimensional accuracy within the measurement capability of the programs.  Comparison between nanosprings and nanoribbons was also performed by overlaying.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
MATLAB numerical computing software	Mathworks	http://www.mathworks.com/products/matlab/description1.html	See Protocol Introduction and Reference [24]
NanospringCarver program code and files	UC Merced - open source	http://tinyurl.com/qame8dj	See Protocol Section 1 (Step 1.2) and Reference [26]
MATLAB GUI files	UC Merced - open source	http://tinyurl.com/qame8dj	See Protocol Section 1 (Step 1.2) and Reference [26]
Atomistic bulk glass input file	UC Merced - open source	http://tinyurl.com/qame8dj	See Protocol Section 1 (Step 1.2) and Reference [26]
IFrIT visualization software	Open source software	http://sites.google.com/site/ifrithome/	See Protocol Section 3 and Reference [19]
LAMMPS molecular dynamics software	Open source software	http://lammps.sandia.gov/	See Protocol Section 4 and Reference [32]