Name: scalable nanohelices for predictive studies and enhanced 3d visualization
Uploaded: 2014-11-12T15:00:00
Description: Watch this Scientific Journal Video about Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization at JoVE.com

The authors want to thank Tim Allis at UC Merced for his assistance in this project.&#160; The NSF-COINS program at UCM supported (KAM) in an early part of this work.&#160; An NSF-BRIGE award supported co-authors (BND and KAM), providing funds for this work and travel expenses to conferences.
The research group wishes to acknowledge primarily the National Science Foundation for funding this work via a BRIGE award.&#160; This material is based upon work supported by the National Science Foundation under Grant No. 1032653.

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.
<ol>
	<li>Unpack the nanosprings.tar.gz file archive into the &#8220;Home&#8221; or another preferred directory.
	<ol>
		<li>Download the nanosprings.tar.gz file archive from the web repository26.</li>
		<li>Locate the downloaded archive and move it to a preferred working d...

<ol>
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R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chapter+1:+Bio+Sensors,+Diagnostics+&amp;+Imaging.">Chapter 1: Bio Sensors, Diagnostics &amp; Imaging.</a> Nanotechnology 2010: Bio Sensors, Instruments, Medical, Environment and Energy. , 19 (2010).</li><li>Sai, V. V. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Silica+nanosprings+coated+with+noble+metal+nanoparticles:+highly+active+SERS+substrates.">Silica nanosprings coated with noble metal nanoparticles: highly active SERS substrates.</a> J. Phys. Chem. C. 115 (2), 453-459 (2010).</li><li>Fonseca, d. a., Galv&#227;o, A. F., S, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanical+properties+of+nanosprings.">Mechanical properties of nanosprings.</a> Phys. Rev.Lett. 92 (17), 175502-175505 (2004).</li><li>Zhang, G., Zhao, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanical+characteristics+of+nanoscale+springs.">Mechanical characteristics of nanoscale springs.</a> J. Appl. Phys. 95 (1), 267-271 (2004).</li><li>Fonseca, d. a., Malta, A. F., Galv&#227;o, C. P., S, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanical+properties+of+amorphous+nanosprings.">Mechanical properties of amorphous nanosprings.</a> Nanotechnology. 17 (22), 5620-5626 (2006).</li><li>Mohedas, I., Garcia, A. P., Buehler, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanomechanics+of+biologically+inspired+helical+silica+nanostructures.">Nanomechanics of biologically inspired helical silica nanostructures.</a> Proceedings of the Institution of Mechanical Engineers, Part N: J. Nanoengineering and Nanosystems. 224 (3), 93-100 (2010).</li><li>Chang, I. L., Yeh, M. -. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+atomistic+study+of+nanosprings.">An atomistic study of nanosprings.</a> J. Appl. Phys. 104 (2), 0243051-0243056 (2008).</li><li>Poggi, M. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measuring+the+compression+of+a+carbon+nanospring.">Measuring the compression of a carbon nanospring.</a> Nano Lett. 4 (6), 1009-1016 (2004).</li><li>Chen, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanics+of+a+carbon+nanocoil.">Mechanics of a carbon nanocoil.</a> Nano Lett. 3 (9), 1299-1304 (2003).</li><li>D&#225;vila, L. P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transformations+in+the+medium-range+order+of+fused+silica+under+high+pressure.">Transformations in the medium-range order of fused silica under high pressure.</a> Phys. Rev. Lett. 91 (20), 2055011-2055014 (2003).</li><li>. Nick Gnedin&#8217;s Ionization FRont Interactive Tool (IFrIT) v. 3.2.8 - A general purpose visualization software [Internet] Available from: <a target="_blank" href="https://sites.google.com/site/ifrithome/">https://sites.google.com/site/ifrithome/</a> (2013)</li><li>Silva, E. C. C. M., Tong, L., Yip, S., Van Vliet, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Size+effects+on+the+stiffness+of+silica+nanowires.">Size effects on the stiffness of silica nanowires.</a> Small. 2 (2), 239-243 (2006).</li><li>D&#225;vila, L. P., Leppert, V. J., Bringa, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+mechanical+behavior+and+nanostructure+of+silica+nanowires+via+simulations.">The mechanical behavior and nanostructure of silica nanowires via simulations.</a> Scripta Mater. 60 (10), 843-846 (2009).</li><li>Doblack, B. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> The structure and properties of silica glass nanostructures using novel computational systems [thesis]. , 55-55 (2013).</li><li>Nanospring Models via MATLAB and NanospringCarver. Davila group website [Internet] Available from: <a target="_blank" href="https://eng.ucmerced.edu/people/ldavila/home/nanospring-models-via-matlab-nanospringcarver-dissemination-of-research-results-and-products">https://eng.ucmerced.edu/people/ldavila/home/nanospring-models-via-matlab-nanospringcarver-dissemination-of-research-results-and-products</a> (2013)</li><li>. Blinkdagger - An Engineering and MATLAB blog [Internet] Available from: <a target="_blank" href="https://eng.ucmerced.edu/people/ldavila/home/nanospring-models-via-matlab-nanospringcarver-dissemination-of-research-results-and-products">https://eng.ucmerced.edu/people/ldavila/home/nanospring-models-via-matlab-nanospringcarver-dissemination-of-research-results-and-products</a> (2014)</li></ol>

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.&#160; The verification of the silica nanoribbon and nanospring models was pursued using different software packages19-20, which confirmed their dimensional accuracy within the measurement capability of the programs.&#160; Comparison between nanosprings and nanoribbons was also performed by overlaying...

Helical nanostructures are typically produced in the laboratory using chemical vapor deposition techniques1-2, while new approaches have been reported in the literature3.&#160; In particular nanosprings and nanoribbons have been studied because of their distinct properties and promising applications in sensors, optics, and electromechanical and fluidic devices4-7.&#160; Synthesis methods have been reported to produce silica (SiO2) nanoribbons, making these structures potential building block units for hierarchical systems.&#160; Novel synthesis of 3D silica nanosprings has expanded their applications to chemiresistors when coated with ZnO8 or nanoparticles for diagnostic applications9-10.
Experimental studies on the mechanical properties of silica nanosprings and nanoribbons are scarce, primarily due to current limitations in manipulation and testing methods and equipment.&#160; Investigations into the nanomechanics of nanostructures and nanosprings have been reported using theory and simulations11-14.&#160; Some simulations13 have focused on nanomechanical behavior of amorphous nanosprings because they can explore regimes not fully accessible through experimentation.&#160; Atomistic studies of metallic nanosprings have been reported in literature to investigate the size dependence of elastic properties15, and more recently the nanomechanics of helical crystalline silica nanostructures14.&#160; Experimental testing of nanospring structures has also been performed in different materials such as helical carbon nanostructures and carbon nanocoils16-17.&#160; Despite the knowledge gathered thus far, a more complete understanding of the mechanical properties of these novel nanostructures is needed for future nanodevice fabrication efforts.
As MD studies of silica glass (non-crystalline silica) nanohelices are still quite limited, the atomistic modeling of such structures requires the creation of customized codes.&#160; No other alternative methods of creating silica glass helical MD models have been identified thus far upon recent literature search.&#160; In this work, a bottom-up approach to the atomistic modeling of helical silica glass nanostructures including nanosprings and nanoribbons is pursued for future large-scale MD nanomechanical simulations.&#160; The general approach involves the creation of an MD &#8220;bulk&#8221; silica glass model as reported previously18, and carving out various helical nanostructures from this &#8220;bulk&#8221; sample via two robust and adaptable computer codes developed for this purpose.&#160; Both computational procedures offer a distinct way to create nanoribbon and nanospring models with great efficiency and atomistic detail; these structures are suitable for large-scale atomistic simulations.&#160; In addition, a customized graphical user interface is used to facilitate creation and visualization of the helical structures.
The structure of the &#8220;bulk&#8221; silica glass model is initially created at room temperature.&#160; Large-scale MD simulations are conducted for this purpose using the Garofalini interatomic potential similar to prior studies18, which is relatively efficient computationally and appropriate for large systems. The initial &#8220;bulk&#8221; silica glass structure consists of a cubical model (14.3 x 14.3 x 14.3 nm3) which contains 192,000 atoms.&#160; The &#8220;bulk&#8221; silica glass model is equilibrated at 300 K for 0.5 nsec to obtain the initial state using periodic boundary conditions.
Two computational procedures are designed and utilized to create atomistic silica nanoribbon and nanospring models.&#160; The first method involves carving out silica nanoribbons from the &#8220;bulk&#8221; structure using the parametric equations that define a helix, and its geometry (pitch, radius of helix, and wire radius).&#160; This procedure includes using the AWK programming language, the LINUX operating system, and open-source visualization software19.&#160; The general iterative procedure to create atomistic models of nanoribbons involves: (1) selecting an atom in the &#8220;bulk&#8221; silica glass model, (2) calculating the distance from the selected atom to a point in space on a pre-defined helical function, (3) comparing this distance to the radius of the desired nanoribbon, and (4) discarding or keeping the atom in an output data model.&#160; A detailed step-by-step description for this method is included in the Scalable Open-Source Codes Supplemental Material.&#160; With this method, several silica nanoribbons were created using different pitch, radius of helix and nanoribbon radius values, which were measured subsequently for accuracy against the desired dimensional values with molecular analysis and visualization software19-20.&#160; Atomistic models of silica nanoribbons were generated with functional geometries (high values of pitch and low values of nanoribbon radius).&#160; Some artifacts, consisting of atoms excluded in error, leading to a less smooth nanoribbon surface, were observed at exceedingly high nanoribbon radius values and extremely low pitch values.&#160; Similar methods have been used in the process of creating silica nanowires21-23.
The second method presented here includes carving out silica nanosprings from the &#8220;bulk&#8221; silica structure by implementing pre-screening methods to increase efficiency in addition to the mathematical equations for a helix.&#160; This procedure required creating a more robust C++ code to allow greater flexibility in modeling these helical nanostructures.&#160; The iterative method to create atomistic models of nanosprings includes: (1) discarding all atoms guaranteed to fall outside the helical path, (2) deterministically selecting a point on the helical path, (3) comparing all atoms within a specific distance to this selected point, and (4) discarding or storing each atom in an output data model.&#160; A step-by-step description for this method is also included in the Scalable Open-Source Codes Supplemental Material.&#160; With this method, several silica nanospring models were obtained with varied dimensions (wire radius, radius of helix, and pitch of nanospring) as shown in Figure 1.&#160; Highly precise silica nanospring models were obtained efficiently with this method, with no evidence of artifacts found at extreme (low and high) pitch values for the nanospring.&#160; The creation and use of the graphical user interface for this method is described in the Protocol section.
<img alt="Figure 1" fo:content-width="4in" src="/files/ftp_upload/51372/51372fig1highres.jpg" width="400" /> 
Figure 1: A general helical structure showing characteristic dimensions, where r, R and p represent the wire radius, radius of helix, and pitch respectively. H denotes the total height of the helical structure23.
This protocol describes how to prepare the NanospringCarver files, running MATLAB24 on a LINUX25 PC, and use a graphical user interface to prepare atomistic nanospring models.&#160; These previously unavailable models serve as the basis for novel molecular dynamics (MD) simulations23 toward materials innovation research.
The general step-by-step procedure to create atomistic nanospring models involves using the following elements: (a) NanospringCarver (v. 0.5 beta) code (open-source in C++ language), (b) bulk silica glass model (input file), (c) MATLAB GUI interface and related files, and (d) MATLAB software (version 7) using a local license on a LINUX PC.&#160; Items (a)-(c) above (NanospringCarver code, silica glass model, MATLAB GUI files) are free to download online26.&#160; MATLAB (Matrix Laboratory) is a high-level language for numerical computation, visualization, and application development from MathWorks24, which is mostly used for data visualization and analysis, image processing, and computational biology.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>MATLAB numerical computing software</td>
			<td>Mathworks</td>
			<td><a href="http://www.mathworks.com/products/matlab/description1.html">http://www.mathworks.com/products/matlab/description1.html</a></td>
			<td>See Protocol Introduction and Reference [24]</td>
		</tr>
		<tr>
			<td>NanospringCarver program code and files</td>
			<td>UC Merced - open source</td>
			<td><a href="http://tinyurl.com/qame8dj">http://tinyurl.com/qame8dj</a></td>
			<td>See Protocol Section 1 (Step 1.2) and Reference [26]</td>
		</tr>
		<tr>
			<td>MATLAB GUI files</td>
			<td>UC Merced - open source</td>
			<td><a href="http://tinyurl.com/qame8dj">http://tinyurl.com/qame8dj</a></td>
			<td>See Protocol Section 1 (Step 1.2) and Reference [26]</td>
		</tr>
		<tr>
			<td>Atomistic bulk glass input file</td>
			<td>UC Merced - open source</td>
			<td><a href="http://tinyurl.com/qame8dj">http://tinyurl.com/qame8dj</a></td>
			<td>See Protocol Section 1 (Step 1.2) and Reference [26]</td>
		</tr>
		<tr>
			<td>IFrIT visualization software</td>
			<td>Open source software</td>
			<td><a href="http://sites.google.com/site/ifrithome/">http://sites.google.com/site/ifrithome/</a></td>
			<td>See Protocol Section 3 and Reference [19]</td>
		</tr>
		<tr>
			<td>LAMMPS molecular dynamics software</td>
			<td>Open source software</td>
			<td><a href="http://www.lammps.sandia.gov/">http://www.lammps.sandia.gov/</a></td>
			<td>See Protocol Section 4 and Reference [32]</td>
		</tr>
	</tbody>
</table>

scalable nanohelices for predictive studies and enhanced 3d visualization

Spring-like materials are ubiquitous in nature and of interest in nanotechnology for energy harvesting, hydrogen storage, and biological sensing applications.&#160; For predictive simulations, it has become increasingly important to be able to model the structure of nanohelices accurately.&#160; To study the effect of local structure on the properties of these complex geometries one must develop realistic models.&#160; To date, software packages are rather limited in creating atomistic helical models.&#160; This work focuses on producing atomistic models of silica glass (SiO2) nanoribbons and nanosprings for molecular dynamics (MD) simulations. Using an MD model of &#8220;bulk&#8221; silica glass, two computational procedures to precisely create the shape of nanoribbons and nanosprings are presented.&#160; 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.&#160; With this method, accurate atomistic silica nanoribbons can be generated for a range of pitch values and dimensions.&#160; The second method involves a more robust code which allows flexibility in modeling nanohelical structures.&#160; 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.&#160; Using these codes, well-defined and scalable nanoribbons and nanosprings suited for atomistic simulations can be effectively created.&#160; An added value in both open-source codes is that they can be adapted to reproduce different helical structures, independent of material.&#160; 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.&#160; One application of these methods is the recent study of nanohelices via MD simulations for mechanical energy harvesting purposes.

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.
<img alt="Figure 9" fo:content-width="5in" src="/files/ftp_upload/51372/51372fig9highres.jpg" width="500" /> 
Figure 9...

Watch this Scientific Journal Video about Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization at JoVE.com

Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization

Accurate modeling of nanohelical structures is important for predictive simulation studies leading to novel nanotechnology applications.&#160; Currently, software packages and codes are limited in creating atomistic helical models.&#160; We present two procedures designed to create atomistic nanohelical models for simulations, and a graphical interface to enhance research through visualization.

Spring-like materials are ubiquitous in nature and of interest in nanotechnology for energy harvesting, hydrogen storage, and biological sensing ...

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