We wish to gratefully acknowledge the original inspiration and extensive support provided to us toward the creation of this system from Dr. Oliver Kreylos of the UC Davis Institute for Data Analysis and Visualization. His advice and assistance were instrumental to our success.
We also wish to thank the NSF BRIGE program for providing funding for this project. This material is based upon work supported by the National Science Foundation under Grant No. 1032653.

1. Install 3D/VR Modeling Software on Modeling PC
<ol>
	<li>Install LINUX base operating system on modeling PC (Ubuntu x86 / AMD64 depending on hardware).</li>
	<li>Modify LINUX base operating system.
	<ol>
		<li>Install libraries and add functionality as necessary.</li>
	</ol>
	</li>
	<li>Install VRUI and NCK 3D/VR modeling software on Modeling PC6.
	<ol>
		<li>Check related websites1,6 to obtain latest versions of all modeling software components.</li>
		<li>Compile, configure and test VRUI.</li>
		<li>Install and test NCK.</li>
	</ol>
	</li>
</ol>
2. Set Up Tracking System1
<ol>
	<li>Mount IR Tracking Cameras4
	<ol>
		<li>Create a rigid camera suspension frame directly above the front edge of the 3D TV near the ceiling for best coverage. Mount 3 cameras on swivel mounts directly above the front corners and the front center of the 3D TV. Ensure that the coverage angle of each camera just grazes the front surface of the TV.</li>
		<li>Aim the cameras to have the widest coverage angle (45 degrees) parallel to the front of the 3D TV. Use a narrower coverage angle (30 degrees) perpendicular to the front of the 3D TV. Allow for maximum overlap within the desired 3D working space. Ensure objects are in view of at least two cameras to be tracked successfully (Figure 3). 
		<img alt="Figure 3" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig3highres.jpg" width="500" /> 
		Figure 3. IR tracking camera coverage to maximize 3D workspace in front of TV. Parts (A) and (B) show front and side view with respect of the 3D/VR Visualization System. <a href="https://www.jove.com/files/ftp_upload/51384/51384fig3highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a></li>
	</ol>
	</li>
	<li>Experiment with alternate camera placement if required to create an adequate 3D workspace. This may be required if the vertical camera mounting distance is constrained.</li>
	<li>Install and Calibrate Tracking Software
	<ol>
		<li>Install the OptiTrack Rigid Body Toolkit on the tracking computer using included installation manual.</li>
		<li>Set Threshold, Exposure, Illumination values dependent on environment and set the Capture Quality to high, as detailed in the tracking software instructions.</li>
		<li>For the Wand Capture, be careful to remove all other reflective material from the 3D workspace. Move smoothly throughout camera overlap working area with the reflective wand. Repeat until standard and mean errors below &#8220;0.5&#8221; are obtained then save the calibration file.</li>
		<li>Set the ground plane to establish a tracked 3D work area coordinate system origin. Define the Wiimote and 3D goggle tracked objects as detailed in the tracking software instructions.</li>
	</ol>
	</li>
	<li>Complete VRUI Calibration
	<ol>
		<li>Set VRUI to accept tracking information from tracking computer.</li>
		<li>Verify tracking functionality in VRUI using DeviceTest calibration utility.</li>
		<li>Align VRUI 3D display and tracking software coordinate systems.</li>
		<li>Set orientation of tracked Wiimote and 3D goggles using AlignTrackingMarkers alignment software.</li>
	</ol>
	</li>
</ol>
3. Prepare 3D Modeling System for Use
<ol>
	<li>Before beginning, remove all reflective jewelry (i.e., watches, earrings, metals, etc.). Do not remove corrective glasses needed to focus on the screen.</li>
	<li>Assemble the equipment for the 3D/VR Visualization System:
	<ol>
		<li>Modeling computer</li>
		<li>Tracking computer</li>
		<li>Large format 3D-capable TV</li>
		<li>Video cable between modeling computer and 3D TV</li>
		<li>3D IR emitter for 3D TV</li>
		<li>Ethernet cables for modeling and tracking computers</li>
		<li>Wiimote with tracking antlers (controller)</li>
		<li>3D goggles with tracking antlers (3D goggles)5</li>
	</ol>
	</li>
	<li>Carefully place controller where it can be reached easily from modeling computer, taking care not to touch or move the spherical IR tracking markers attached to it.</li>
	<li>Carefully place 3D goggles on TV stand (as before, be sure to avoid touching the reflective markers).</li>
	<li>Connect the three USB cables from the IR cameras mounted above the 3D TV to 3 USB ports on the tracking computer, while it is powered OFF.</li>
	<li>Locate the 3D TV remote control and place it in front of 3D TV.</li>
	<li>Connect the video cable to the video card on the modeling computer and the video input of the 3D TV. Also connect the 3D IR emitter for the 3D synchronizing output from the 3D TV, and place emitter on TV stand near side of TV, pointing up toward where goggles will be used. BE VERY CAREFUL NOT to shift the position of the calibrated TV.</li>
	<li>Turn 3D TV ON before powering on the modeling computer to ensure proper recognition by the computer.</li>
	<li>Turn ON modeling computer. After the modeling computer boots to a login prompt, log in on the modeling computer LINUX system to an appropriate account.</li>
	<li>Once the modeling computer desktop is available, use the 3D TV remote control to check the status of the video cable connection by pressing the &#8220;info/i&#8221; button. Ensure that the TV screen displays &#8220;1920x1080 @ 60hz&#8221; in the upper left corner. If not, reboot the modeling computer to establish correct recognition of the 3D TV. Also be sure TV is in 3D output MODE 2, using the remote control setup menus.</li>
	<li>On the modeling computer desktop, open a terminal window with several tabs.</li>
	<li>On the tracking computer, verify the ethernet adapter IP address by typing &#8220;ipconfig&#8221; in a command window.</li>
	<li>On the modeling computer, open a terminal window tab and check within the VRDevices.cfg file that the &#8220;serverName&#8221; defines the tracking computer ethernet adapter IP address.</li>
	<li>If necessary, alter the &#8220;serverName&#8221; IP address in VRDevices.cfg to match the tracking computer ethernet adapter, and save VRDevices.cfg.</li>
	<li>On the tracking computer, initiate the OptiTrack Rigid Body Tool software.</li>
	<li>Allow the software to open completely, then click the large button near the top menu labeled &#8220;Load Calibration Result&#8221;.</li>
	<li>Browse to and open the appropriate camera calibration file.</li>
	<li>After the file is loaded, click the &#8220;File&#8221; menu and select &#8220;Load rigid body definitions&#8221;.</li>
	<li>Browse to and open the appropriate rigid body definition file for the tracked controller and 3D goggles.</li>
	<li>On the rightmost pane of the tracking software, locate the section labeled &#8220;Streaming&#8221;, expand the section and under the &#8220;VRPN Streaming&#8221; category, verify that the port number listed is 3883, then check the &#8220;Broadcast frame data&#8221; box inside the &#8220;VRPN Streaming Engine&#8221; category.</li>
	<li>At the modeling computer, make sure that the controller is either directly in hand or immediately reachable (2 sec away at the most).</li>
	<li>On the modeling computer, bring up a tab in the terminal window created earlier in this session and navigate to and then initiate the VRDeviceDaemon software, e.g., typing &#8220;./VRDeviceDaemon&#8221;.</li>
	<li>Follow the prompt to &#8220;press buttons 1 &#38; 2 on the Wiimote simultaneously.&#8221; If the activity was successful, the window will now display &#8220;VRDeviceServer: Waiting for client connection&#8221;.</li>
</ol>
4. Test 3D/VR Visualization System Using NCK Software
The following set of instructions outlines how to use the NCK software on-screen menus to establish controller tool functions, and then how to build and manipulate a carbon nanotube in the 3D/VR workspace from constituent carbon atoms (Figure 4). Instructions on how to measure the resulting bond angles and distances (Step 4.4.10) are available online10.
<img alt="Figure 4" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig4highres.jpg" width="500" /> 
Figure 4. Undergraduate student using the 3D/VR Visualization System to study carbon nanotubes (CNTs). Photos (A)-(F) show the building process of a single-walled CNT. <a href="https://www.jove.com/files/ftp_upload/51384/51384fig4highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<ol>
	<li>Within the modeling computer terminal window created in Step 3.11, select the third tab.&#160; To initiate the NCK software, navigate to the NCK installation directory and type: 
	&#8220;./NanotechConstructionKit -rootSection localhost -domainsize 36&#8221;.</li>
	<li>Being very careful not to touch or loosen the attached tracking markers, put on 3D goggles and pick up the controller. Adjust head/goggle viewing position to ensure 3D goggles are receiving 3D TV IR emitter sync signal, allowing 3D/VR viewing of TV display.</li>
	<li>In order to have a toolset to add, move and delete atoms, assign NCK command associations to buttons on the controller as follows:
	<ol>
		<li>Bring up the main NCK on-screen menu by pressing and holding the Home button on the Wiimote, navigating to and selecting the &#8220;Override Tools&#8221; menu item, then releasing the Home button. This allows assignment of commands to different buttons on the controller independently of one another.</li>
		<li>To associate the Wiimote trigger button (on the bottom of the controller) with the action of manipulating atoms within NCK, press and hold the trigger button, navigate the on-screen NCK menu to &#8220;Dragger&#8221; and select &#8220;6-DOF Dragger,&#8221; then release the trigger. The trigger is now associated with the action of manipulating the atoms.</li>
		<li>To assign the function of adding an atom to the &#8220;+&#8221; button on the Wiimote, bring the main menu up by pressing and holding the Home button, navigate to &#8220;Structural Unit Types&#8221;, and select &#8220;Triangle&#8221;, then release the Home button.</li>
		<li>Next press and hold the &#8220;+&#8221; button, navigate to &#8220;Dragger,&#8221; and select &#8220;6-DOF Dragger,&#8221; then release the &#8220;+&#8221; button. The &#8220;+&#8221; button is now associated with creating new atoms of the type selected (carbon atoms represented by triangles, in this case).</li>
		<li>To assign the function of deleting an atom to the &#8220;-&#8221; button on the Wiimote, bring up the main menu by pressing and holding the &#8220;Home&#8221; button, then navigate to &#8220;Structural Unit Types,&#8221; and select &#8220;Delete Selected Units,&#8221; then release the Home button.</li>
		<li>Next, press and hold the &#8220;-&#8221; button, navigate to &#8220;Dragger,&#8221; then &#8220;6-DOF Dragger,&#8221; and release the &#8220;-&#8220; button. The &#8220;-&#8221; button is now associated with deleting atoms.</li>
		<li>Follow a similar procedure to assign the functions of &#8220;Lock Selected Units&#8221; to the &#8220;1&#8221; Wiimote button, and &#8220;Unlock Selected Units&#8221; to the &#8220;2&#8221; controller button.</li>
	</ol>
	</li>
	<li>Once the controller buttons have been configured, create a carbon nanotube using NCK as follows:
	<ol>
		<li>Using the &#8220;+&#8221; button, add two 3-bond triangular carbon atoms to the NCK workspace. Manipulate these using the trigger button until they join at a vertex.</li>
		<li>Add 4 more carbon atoms to create a hexagonal star shape.</li>
		<li>Using the &#8220;Home&#8221; menu, navigate to &#8220;I/O Menus&#8221;, then &#8220;Save Units .</li>
		<li>Move the 6 pointed structure away from its current position.</li>
		<li>Using the &#8220;Home&#8221; menu, navigate to &#8220;I/O Menus&#8221;, then &#8220;Load Units .</li>
		<li>Repeat the last 2 steps until a 6 by 6 sheet of hexagonal 6-atom rings has been created (Figure 5A).</li>
		<li>Using the &#8220;1&#8221; button, lock one atom in the top row, and an opposing atom in the bottom row. The locked atoms will be marked with a pink color (Figure 5B).</li>
		<li>Using the trigger button, carefully move one of the locked atoms in a circular arc until its free vertex approaches the free vertex of the opposing locked atom. A green line will appear between the vertices when they are close enough that atomic attraction will cause them to join with a bond (Figure 5C). Once successfully joined, unlock both of the atoms using the &#8220;2&#8221; button.</li>
		<li>Continue similarly locking, joining, and unlocking opposing atomic vertices in the carbon sheet, effectively &#8220;zipping&#8221; the sheet into a final carbon nanotube (Figures 5D-5F). 
		<img alt="Figure 5" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig5highres.jpg" width="500" /> 
		Figure 5. Step-wise creation of a single-walled CNT showing (A) a 6 x 6 sheet (graphene) of hexagonal carbon rings, (B) opposing carbon atoms &#8220;locked&#8221; (shown as pink triangles) to allow easier manipulation against realistic interatomic forces, (C) carbon (graphene) sheet carefully curved to allow bonding between atoms on opposing sides, (D) two additional opposing carbon atoms locked to assist further carbon sheet curvature, (E) additional opposing carbon atoms bonded to continue carbon sheet curvature into a nanotube, and (F) final CNT formed after sequential bonding of opposing atoms of the original carbon sheet (graphene). <a href="https://www.jove.com/files/ftp_upload/51384/51384fig5highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a></li>
		<li>When the nanotube is complete, use on-screen measurement tools to confirm structural angles and distances10.</li>
	</ol>
	</li>
</ol>
5. Visualization of Molecular Dynamics Simulation Models
<ol>
	<li>Import an initial crystalline SiO2 cubical model into the 3D/VR NCK software, and investigate the initial structure (see Figure 2A).</li>
	<li>Open-source programs MDCASK11 and LAMMPS12 were targeted because of features that are well-suited to this research focus. The latter program is used in this work given its varied interatomic potentials and GPU computing capability. Using the LAMMPS MD package12, run a simulated melt/quench procedure on this initial structure to produce an amorphous SiO2 structure. Details on this simulated procedure can be found in previous publications13-15.</li>
	<li>Import the resulting new amorphous (disordered) SiO2 model into the 3D/VR NCK software and investigate the structure (see Figure 2B).</li>
	<li>Create a SiO2 nanospring/nanoribbon out of the new amorphous solid using the open source code NanospringCarver16 and associated instructional documentation17 (Figure 6). <img alt="Figure 6" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig6highres.jpg" width="500" /> 
	Figure 6. Illustration of the step-by-step atom selection process at different stages in the creation of a nanospring using the NanospringCarver program. Parts (A-D) indicate 25%, 50%, 75% and 100% completion of this process17. <a href="https://www.jove.com/files/ftp_upload/51384/51384fig6highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a></li>
	<li>Use the LAMMPS MD package to perform tensile simulations on the nanospring/nanoribbon (Figure 7). Details on this procedure can be found in a previous publication15. 
	<img alt="Figure 7" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig7highres.jpg" width="500" /> 
	Figure 7. Snapshot image from LAMMPS MD silica helical nanostructure (nanoribbon) tensile simulation results.</li>
	<li>Use the open source software tools VMD (Visualize Molecular Dynamics)18 ImageMagick19, and FFmpeg20 to create snapshots and animation of the helical nanostructure throughout this simulation (Animated Figure 1), for presentation in the 3D/VR Visualization System. <a href="https://www.jove.com/files/ftp_upload/51384/51384fig7highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a></li>
</ol>
<a href="https://www.jove.com/files/ftp_upload/51384/Animated_Fig1-movie NR-0140_frames.mov" target="_blank">Animated Figure 1</a>. Animation of helical nanostructure tensile simulation.

<ol>
	<li>Doblack, B. N., Flores, C., Matlock, T., D&#225;vila, L. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+emergence+of+immersive+low-cost+3D+virtual+reality+environments+for+interactive+learning+in+materials+science+and+engineering.">The emergence of immersive low-cost 3D virtual reality environments for interactive learning in materials science and engineering.</a> Mater. Res. Soc. Symp. Proc. 1320, (2011).</li><li>Flores, C., Matlock, T., D&#225;vila, L. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhancing+materials+research+through+innovative+3D+environments+and+interactive+manuals+for+data+visualization+and+analysis.">Enhancing materials research through innovative 3D environments and interactive manuals for data visualization and analysis.</a> Mater. Res. Soc. Symp. Proc. 1472, (2012).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=3D+goggle+source.">3D goggle source.</a> , (2013).</li><li>. &#8220;3D/VR Visualization System - Startup and Shutdown Protocol&#8221; and &#8220;3D/VR Visualization System &#8211; CNT Modeling Example&#8221; documents Available from: <a target="_blank" href="https://eng.ucmerced.edu/people/ldavila/home/3d-vr-visualization-system-dissemination-of-research-results-and-products">https://eng.ucmerced.edu/people/ldavila/home/3d-vr-visualization-system-dissemination-of-research-results-and-products</a> (2013)</li><li>. MDCASK molecular dynamics code Available from: <a target="_blank" href="https://asc.llnl.gov/computing_resources/purple/archive/benchmarks/mdcask">https://asc.llnl.gov/computing_resources/purple/archive/benchmarks/mdcask</a> (2013)</li><li>Feuston, B. P., Garofalini, S. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Empirical+three-body+potential+for+vitreous+silica.">Empirical three-body potential for vitreous silica.</a> J. Chem. Phys. 89 (9), 5818-5824 (1988).</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>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. , (2013).</li><li>Meagher, K. A., Doblack, B. N., Ramirez, M., D&#225;vila, L. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Scalable+nanohelices+for+predictive+studies+and+enhanced+3D+visualization.">Scalable nanohelices for predictive studies and enhanced 3D visualization.</a> J. Vis. Exp. In-Press, .</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=University+of+California+Television+(UCTV).">University of California Television (UCTV).</a> Our Digital Life series: The Future: Teaching and Life-Saving Tools episode. , (2013).</li></ol>

The authors declare that they have no competing financial interests.

Critical elements in the successful installation and usage of the 3D/VR Visualization System are detailed in the Physical Environment and Design Considerations and Special Considerations in supplemental materials. Important installation considerations include 3D display height for comfortable long-term standing or seated usage, maximized tracking camera mounted height to create a large 3D working area, stable tracking camera and 3D display support to maintain configuration over time, and...

Materials science is an interdisciplinary field that examines the structure-property relationships in matter for their application to many areas of science and engineering. As structure-property relationships are investigated through computer simulations in addition to experimentation, computational tools offer complementary features that can enhance research efforts. While nanomaterials are of interest to scientists and have redeeming value for their potential social impact, this size regime is fraught with many challenges found particularly in experimentation.
Computer simulations allow scientists and engineers to perform specialized tests in a large variety of environments limited only by time and computational resources. Molecular dynamics (MD) simulations allow the appropriate time and length scales to study the phenomena of interest in many nanomaterials. Simulations expand the study of materials by removing the constraints of the physical laboratory, however many computational tools lack accessible, intuitive interfaces for research. Enhancement with the graphical display of models, efficient computational algorithms, and graphical processing unit (GPU) based computing complement current simulation efforts. These new graphics devices combine with central processing units efficiently to allow mathematically intensive calculations to be accomplished by the GPU. The result is an effective acceleration of computation on the order of 10x accompanied by a reduction in power consumption of up to 20x.
The goal of this research project was to develop and implement a novel tool for nanoscience investigation that directly connects an interactive interface to MD simulations, materials science analysis and 3D visualization. This innovative system with unique and powerful analysis capabilities has been used for nanoscale research and education at UC Merced, with direct implications to other related STEM fields such as nanotechnology, physics, biology, and geology, and ultimate benefit to education and society.
The 3D/VR Visualization System was implemented as both a research and teaching instrument which allows creation and manipulation of atomic structures in an interactive 3D virtual reality (VR) environment. The system was created from a set of relatively low-cost and accessible components following the model originally developed by Dr. Oliver Kreylos at UC Davis1.
Below is a photo of the final 3D/VR Visualization System layout, with important components labeled (Figure 1). This system was originally established for education purposes at UC Merced in 2009. The implementation of the original 3D/VR system resulted in peer-reviewed publications2-3. Table 1 below summarizes key characteristics for each element of the 3D/VR Visualization System.
<img alt="Figure 1" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig1highres.jpg" width="500" /> 
Figure 1. 3D/VR Visualization System and main components (left) in the Davila Research Laboratory at UCM and visualization devices (right). <a href="https://www.jove.com/files/ftp_upload/51384/51384fig1highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Item</td>
			<td>Component</td>
			<td>Functionality in System</td>
		</tr>
		<tr>
			<td>A</td>
			<td>3D TV</td>
			<td>3D display of modeled molecular structures and on-screen menus.</td>
		</tr>
		<tr>
			<td>B</td>
			<td>Infrared (IR) tracking cameras4</td>
			<td>IR cameras track positions of the Wiimote and 3D viewing goggles in the user workspace in front of 3D TV, allowing virtual 3D manipulation of displayed structures.</td>
		</tr>
		<tr>
			<td>C</td>
			<td>Tracking PC</td>
			<td>Runs IR camera tracking software and transmits Wiimote and 3D goggle positions to modeling computer.</td>
		</tr>
		<tr>
			<td>D</td>
			<td>Wiimote</td>
			<td>Used for on-screen management of modeling software and to manipulate structures in 3D virtual environment.</td>
		</tr>
		<tr>
			<td>E</td>
			<td>3D goggles5</td>
			<td>Synchronized with 3D TV IR signal, allow 3D view of structure. Position tracked by IR cameras for accurate 3D view.</td>
		</tr>
		<tr>
			<td>F</td>
			<td>Modeling PC</td>
			<td>Runs NCK/VRUI 3D modeling and display software6, accepts goggle / Wiimote position and control signals to create accurate 3D molecular structure view.</td>
		</tr>
	</tbody>
</table>
Table 1. Functionality of main elements of the 3D/VR Visualization System at UCM.
Description of 3D/VR Visualization System and Basic Components:
3D/VR Visualization System Overview &#8212; The 3D/VR Visualization System consists of a set of IR cameras and tracking software operating in conjunction with 3D modeling software to allow a user to interactively create 3D molecular structures. The IR cameras and software track the 3D location of a Wiimote and 3D viewing goggles using IR markers, and pass this to the modeling software. The modeling software uses the Wiimote control signals and movement to generate 3D molecular structures viewable using the combination of a 3D-capable large format television with synchronized and tracked 3D goggles. This results in a 3D virtual reality workspace within which the user can dynamically create and manipulate virtual molecular structures which reflect real-world physical behavior based on inter-atomic forces used in the modeling software (Figure 2). Special considerations for setting up this system can be found in supplemental materials.
<img alt="Figure 2" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig2highres.jpg" width="500" /> 
Figure 2. Investigating silica nanomaterials using the 3D/VR Visualization System. (a) A researcher creates an initial cristobalite model (crystalline) before GPU-based simulations. (b) Upon performing a simulated MD melt-quench procedure on model shown in (a), another researcher obtains a silica glass model (non-crystalline). <a href="https://www.jove.com/files/ftp_upload/51384/51384fig2highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
3D/VR Visualization System Enhancement &#8212; MD Simulation Capability:
Molecular dynamics simulation systems are commonly implemented in a multi-nodal fashion, that is, a large workload is distributed or parallelized among tens to thousands of processors. Recently, additional opportunities for accelerated scientific computing have arisen out of developments in computer graphics processing. These advances include a software interface allowing scientists to take advantage of the highly parallel nature of the processing power intrinsic to graphics chips. With the advent of the Compute Unified Device Architecture or CUDA7, scientists can use GPUs8 to enhance the speed at which problems are solved while reducing the cost of infrastructure. A typical GPU may have the equivalent of hundreds to thousands of cores or &#8220;nodes&#8221; for processing information, and as these can each be used in parallel, a well-coded solution may provide up to 1,000x throughput acceleration against its multi-core counterpart. Though not every problem is well-suited to this approach, current MD simulations have seen up to 15x throughput performance gains9. Details on the 3D/VR visualization system MD-GPU enhancement can be found in supplemental materials.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Samsung 61&#34; 3D-capable high definition DLP TV</td>
			<td>Samsung</td>
			<td><a href="http://www.samsung.com/us/video/tvs">http://www.samsung.com/us/video/tvs</a></td>
			<td>See Protocol Section 3 (Step 3.2)&#160; (Large format 3D-capable TV)</td>
		</tr>
		<tr>
			<td>Alienware Area51 750i modeling computer</td>
			<td>Alienware</td>
			<td><a href="http://www.alienware.com/">http://www.alienware.com</a></td>
			<td>See Protocol Section 1 (Step 1.1)&#160; (Modeling computer)</td>
		</tr>
		<tr>
			<td>HP EliteBook 8530w tracking computer</td>
			<td>HP</td>
			<td><a href="http://www.hp.com/">http://www.hp.com</a></td>
			<td>See Protocol Section 2 (Step 2.3)&#160; (Tracking computer)</td>
		</tr>
		<tr>
			<td>V100:R2 IR tracking cameras (3)</td>
			<td>Naturalpoint</td>
			<td><a href="http://www.naturalpoint.com/optitrack/products/v100-r2/">http://www.naturalpoint.com/optitrack/products/v100-r2/</a></td>
			<td>See Protocol Section 2 (Step 2.1) and Reference [4]&#160; (Tracking cameras)</td>
		</tr>
		<tr>
			<td>OptiTrack Tracking Tools IR tracking software</td>
			<td>Naturalpoint</td>
			<td><a href="http://www.naturalpoint.com/optitrack/software/">http://www.naturalpoint.com/optitrack/software/</a></td>
			<td>See Protocol Section 2 (Step 2.3) and Reference [4]&#160; (Tracking software)</td>
		</tr>
		<tr>
			<td>3D Goggles and 3D TV IR sync emitter</td>
			<td>Ilixco</td>
			<td><a href="http://www.i-glassesstore.com/dlp3d-wireless-2set.html">http://www.i-glassesstore.com/dlp3d-wireless-2set.html</a></td>
			<td>See Protocol Section 3 (Step 3.2) and Reference [5]&#160; (3D goggles)</td>
		</tr>
		<tr>
			<td>Wiimote 3D controller</td>
			<td>Nintendo</td>
			<td><a href="http://www.nintendo.com/wii">http://www.nintendo.com/wii</a></td>
			<td>See Protocol Section 3 (Step 3.2)&#160; (Wiimote)</td>
		</tr>
		<tr>
			<td>VRUI, NCK and associated 3D/VR modeling software</td>
			<td>Open source software</td>
			<td><a href="http://idav.ucdavis.edu/~okreylos/ResDev/NanoTech/index.html">http://idav.ucdavis.edu/~okreylos/ResDev/NanoTech/index.html</a></td>
			<td>See Protocol Section 1 (Step 1.3) and References [1,6]&#160; (VRUI, NCK)</td>
		</tr>
		<tr>
			<td>LAMMPS molecular dynamics software</td>
			<td>Open source software</td>
			<td><a href="http://lammps.sandia.gov/">http://lammps.sandia.gov/&#160;</a></td>
			<td>See Protocol Section 5 (Step 5.2) and Reference [12]&#160; (LAMMPS)</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 5 (Step 5.4) and References [16-17]&#160; (NanospringCarver)</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 5 (Step 5.4) and References [16-17]&#160; (NanospringCarver)</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 5 (Step 5.4) and References [16-17]&#160; (NanospringCarver)</td>
		</tr>
	</tbody>
</table>

novel 3d/vr interactive environment for md simulations, visualization and analysis

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

This 3D/VR Visualization System presents new opportunities for conducting materials science studies. As this immersive environment operates in real time, in the form of 3D input and display, the researcher is presented with a fully interactive nanoscaled instrument2. By following the protocol presented here, a silica helical nanoribbon was created in this step-by-step fashion. A snapshot of this structure produced from LAMMPS MD is shown in Figure 7. This structure was subjected to simulated t...

Watch this Scientific Journal Video about Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis at JoVE.com

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

A new computational system featuring GPU-accelerated molecular dynamics simulation and 3D/VR visualization, analysis and manipulation of nanostructures has been implemented, representing a novel approach to advance materials research and promote innovative investigation and alternative methods to learn about material structures with dimensions invisible to the human eye.

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials ...

novel-3dvr-interactive-environment-for-md-simulations-visualization

Research

JoVE Journal

Engineering

11.8K Views.  University of California Merced. A new computational system featuring GPU-accelerated molecular dynamics simulation and 3D/VR visualization, analysis and manipulation of nanostructures has been implemented, representing a novel approach to advance materials research and promote innovative investigation and alternative methods to learn about material structures with dimensions invisible to the human eye.

Video: Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Fabrication, Operation and Flow Visualization in Surface-acoustic-wave-driven Acoustic-counterflow Microfluidics

Surface acoustic waves (SAWs) can be used to drive liquids in portable microfluidic chips via the acoustic counterflow phenomenon. In this video we present the fabrication protocol for a multilayered SAW acoustic counterflow device. The device is fabricated starting from a lithium niobate (LN) substrate onto which two interdigital transducers (IDTs) and appropriate markers are patterned. A polydimethylsiloxane (PDMS) channel cast on an SU8 master mold is finally bonded on the patterned substrate. Following the fabrication procedure, we show the techniques that allow the characterization and operation of the acoustic counterflow device in order to pump fluids through the PDMS channel grid. We finally present the procedure to visualize liquid flow in the channels. The protocol is used to show on-chip fluid pumping under different flow regimes such as laminar flow and more complicated dynamics characterized by vortices and particle accumulation domains.

In this video we first describe fabrication and operation procedures of a surface acoustic wave (SAW) acoustic counterflow device. We then demonstrate an experimental setup that allows for both qualitative flow visualization and quantitative analysis of complex flows within the SAW pumping device.

Surface acoustic waves (SAWs) can be used to drive liquids in portable microfluidic chips via the acoustic counterflow phenomenon. In this video we ...

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.

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 ...

Selective Area Modification of Silicon Surface Wettability by Pulsed UV Laser Irradiation in Liquid Environment

The wettability of silicon (Si) is one of the important parameters in the technology of surface functionalization of this material and fabrication of biosensing devices. We report on a protocol of using KrF and ArF lasers irradiating Si (001) samples immersed in a liquid environment with low number of pulses and operating at moderately low pulse fluences to induce Si wettability modification. Wafers immersed for up to 4 hr in a 0.01% H2O2/H2O solution did not show measurable change in their initial contact angle (CA) ~75&#176;. However, the 500-pulse KrF and ArF lasers irradiation of such wafers in a microchamber filled with 0.01% H2O2/H2O solution at 250 and 65 mJ/cm2, respectively, has decreased the CA to near 15&#176;, indicating the formation of a superhydrophilic surface. The formation of OH-terminated Si (001), with no measurable change of the wafer&#8217;s surface morphology, has been confirmed by X-ray photoelectron spectroscopy and atomic force microscopy measurements. The selective area irradiated samples were then immersed in a biotin-conjugated fluorescein-stained nanospheres solution for 2 hr, resulting in a successful immobilization of the nanospheres in the non-irradiated area. This illustrates the potential of&#160;the method for selective area biofunctionalization and fabrication of advanced Si-based biosensing architectures. We also describe a similar protocol of irradiation of wafers immersed in methanol (CH3OH) using ArF laser operating at pulse fluence of 65 mJ/cm2 and in situ formation of a strongly hydrophobic surface of Si (001) with the CA of 103&#176;. The XPS results indicate ArF laser induced formation of Si&#8211;(OCH3)x compounds responsible for the observed hydrophobicity. However, no such compounds were found by XPS on the Si surface irradiated by KrF laser in methanol, demonstrating the inability of the KrF laser to photodissociate methanol and create -OCH3 radicals.

We report on a process of in situ alteration of HF treated Si (001) surface into a hydrophilic or hydrophobic state by irradiating samples in microfluidic chambers filled with&#160;H2O2/H2O solution (0.01%-0.5%) or methanol solutions using pulsed UV laser of a relative low pulse fluence.

The wettability of silicon (Si) is one of the important parameters in the technology of surface functionalization of this material and fabrication of ...

Plasmonic Trapping and Release of Nanoparticles in a Monitoring Environment

Plasmonic tweezers use surface plasmon polaritons to confine polarizable nanoscale objects. Among the various designs of plasmonic tweezers, only a few can observe immobilized particles. Moreover, a limited number of studies have experimentally measured the exertable forces on the particles. The designs can be classified as the protruding nanodisk type or the suppressed nanohole type. For the latter, microscopic observation is extremely challenging. In this paper, a new plasmonic tweezer system is introduced to monitor particles, both in directions parallel and orthogonal to the symmetric axis of a plasmonic nanohole structure. This feature enables us to observe the movement of each particle near the rim of the nanohole. Furthermore, we can quantitatively estimate the maximal trapping forces using a new fluidic channel.

A microchip fabrication process that incorporates plasmonic tweezers is presented here. The microchip enables the imaging of a trapped particle to measure maximal trapping forces.

Plasmonic tweezers use surface plasmon polaritons to confine polarizable nanoscale objects. Among the various designs of plasmonic tweezers, only a few ...

High Temperature Fabrication of Nanostructured Yttria-Stabilized-Zirconia (YSZ) Scaffolds by In Situ Carbon Templating Xerogels

We demonstrate a method for the high temperature fabrication of porous, nanostructured yttria-stabilized-zirconia (YSZ, 8 mol% yttria - 92 mol% zirconia) scaffolds with tunable specific surface areas up to 80 m2&#183;g-1. An aqueous solution of a zirconium salt, yttrium salt, and glucose is mixed with propylene oxide (PO) to form a gel. The gel is dried under ambient conditions to form a xerogel. The xerogel is pressed into pellets and then sintered in an argon atmosphere. During sintering, a YSZ ceramic phase forms and the organic components decompose, leaving behind amorphous carbon. The carbon formed in situ serves as a hard template, preserving a high surface area YSZ nanomorphology at sintering temperature. The carbon is subsequently removed by oxidation in air at low temperature, resulting in a porous, nanostructured YSZ scaffold. The concentration of the carbon template and the final scaffold surface area can be systematically tuned by varying the glucose concentration in the gel synthesis. The carbon template concentration was quantified using thermogravimetric analysis (TGA), the surface area and pore size distribution was determined by physical adsorption measurements, and the morphology was characterized using scanning electron microscopy (SEM). Phase purity and crystallite size was determined using X-ray diffraction (XRD). This fabrication approach provides a novel, flexible platform for realizing unprecedented scaffold surface areas and nanomorphologies for ceramic-based electrochemical energy conversion applications, e.g. solid oxide fuel cell (SOFC) electrodes.

High Temperature Fabrication of Nanostructured Yttria-Stabilized-Zirconia YSZ Scaffolds by In Situ Carbon Templating Xerogels

A protocol for fabricating porous, nanostructured yttria-stabilized-zirconia (YSZ) scaffolds at temperatures between 1,000 &#176;C and 1,400 &#176;C is presented.

We demonstrate a method for the high temperature fabrication of porous, nanostructured yttria-stabilized-zirconia (YSZ, 8 mol% yttria - 92 mol% zirconia) ...

Guidelines and Experience Using Imaging Biomarker Explorer (IBEX) for Radiomics

Imaging Biomarker Explorer (IBEX) is an open-source tool for medical imaging radiomics work. The purpose of this paper is to describe how to use IBEX's graphical user interface (GUI) and to demonstrate how IBEX calculated features have been used in clinical studies. IBEX allows for the import of DICOM images with DICOM radiation therapy structure files or Pinnacle files. Once the images are imported, IBEX has tools within the Data Selection GUI to manipulate the viewing of the images, measure voxel values and distances, and create and edit contours. IBEX comes with 27 preprocessing and 132 feature choices to design feature sets. Each preprocessing and feature category has parameters that can be altered. The output from IBEX is a spreadsheet that contains: 1) each feature from the feature set calculated for each contour in a data set, 2) image information about each contour in a data set, and 3) a summary of the preprocessing and features used with their selected parameters. Features calculated from IBEX have been used in studies to test the variability of features under different imaging conditions and in survival models to improve current clinical models.

Guidelines and Experience Using Imaging Biomarker Explorer IBEX for Radiomics

We describe IBEX, an open-source tool designed for medical imaging radiomics studies, and how to use this tool. In addition, some published works that have used IBEX for uncertainty analysis and model building are showcased.

Imaging Biomarker Explorer (IBEX) is an open-source tool for medical imaging radiomics work. The purpose of this paper is to describe how to use IBEX's ...

Applicability Analysis of Assessment Methods for Morphological Parameters of Corroded Steel Bars

The irregular and uneven residual sections along the length of a corroded steel bar substantially change its mechanical properties and significantly dominate the safety and performance of an existing concrete structure. As a result, it is important to measure the geometry and amount of corrosion of a steel bar in a structure properly to assess the residual bearing capacity and service life of the structure. This paper introduces and compares five different methods for measuring the geometry and amount of corrosion of a steel bar. A single 500 mm long and 14 mm diameter steel bar is the specimen that is subjected to accelerated corrosion in this protocol. Its morphology and the amount of corrosion were carefully measured before and after using mass loss measurements, a Vernier caliper, drainage measurements, 3D scanning, and X-ray micro-computed tomography (XCT). The applicability and suitability of these different methods were then evaluated. The results show that the Vernier caliper is the best choice for measuring the morphology of a non-corroded bar, while 3D scanning is the most suitable for quantifying the morphology of a corroded bar.

This paper measures the geometry and the amount of corrosion of a steel bar using different methods: mass loss, calipers, drainage measurements, 3D scanning, and X-ray micro-computed tomography (XCT).

The irregular and uneven residual sections along the length of a corroded steel bar substantially change its mechanical properties and significantly ...

Crack Monitoring in Resonance Fatigue Testing of Welded Specimens Using Digital Image Correlation

A procedure using digital image correlation (DIC) to detect cracks on welded specimens during fatigue tests on resonance testing machines is presented. It is intended as a practical and reproducible procedure to identify macroscopic cracks at an early stage and monitor crack propagation during fatigue tests. It consists of strain field measurements at the weld using DIC. Images are taken at fixed load cycle intervals. Cracks become visible in the computed strain field as elevated strains. This way, the whole width of a small-scale specimen can be monitored to detect where and when a crack initiates. Subsequently, it is possible to monitor the development of the crack length. Because the resulting images are saved, the results are verifiable and comparable. The procedure is limited to cracks initiating at the surface and is intended for fatigue tests under laboratory conditions. By visualizing the crack, the presented procedure allows direct observation of macrocracks from their formation until rupture of the specimen.

Digital image correlation is used in fatigue tests on a resonance testing machine to detect macroscopic cracks and monitor crack propagation in welded specimens. Cracks on the specimen surface become visible as increased strains.

A procedure using digital image correlation (DIC) to detect cracks on welded specimens during fatigue tests on resonance testing machines is presented. It ...

Surgery and Sample Processing for Correlative Imaging of the Murine Pulmonary Valve

The underlying causes of heart valve related-disease (HVD) are elusive. Murine animal models provide an excellent tool for studying HVD, however, the surgical and instrumental expertise required to accurately quantify the structure and organization across multiple length scales have stunted its advancement. This work provides a detailed description of the murine dissection, en bloc staining, sample processing, and correlative imaging procedures for depicting the heart valve at different length scales. Hydrostatic transvalvular pressure was used to control the temporal heterogeneity by chemically fixing the heart valve conformation. Micro-computed tomography (&#181;CT) was used to confirm the geometry of the heart valve and provide a reference for the downstream sample processing needed for the serial block face scanning electron microscopy (SBF-SEM). High-resolution serial SEM images of the extracellular matrix (ECM) were taken and reconstructed to provide a local 3D representation of its organization. &#181;CT and SBF-SEM imaging methods were then correlated to overcome the spatial variation across the pulmonary valve. Though the work presented is exclusively on the pulmonary valve, this methodology could be adopted for describing the hierarchical organization in biological systems and is pivotal for the structural characterization across multiple length scales.

Here, we describe a correlative workflow for the excision, pressurization, fixation, and imaging of the murine pulmonary valve to determine the gross conformation and local extracellular matrix structures.

The underlying causes of heart valve related-disease (HVD) are elusive. Murine animal models provide an excellent tool for studying HVD, however, the ...

Interactive and Visualized Online Experimentation System for Engineering Education and Research

Experimentation is crucial in engineering education. This work explores visualized experiments in online laboratories for teaching and learning and also research. Interactive and visualizing features, including theory-guided algorithm implementation, web-based algorithm design, customizable monitoring interface, and three-dimensional (3-D) virtual test rigs are discussed. To illustrate the features and functionalities of the proposed laboratories, three examples, including the first-order system exploration using a circuit-based system with electrical elements, web-based control algorithm design for virtual and remote experimentation, are provided. Using user-designed control algorithms, not only can simulations be conducted, but real-time experiments can also be conducted once the designed control algorithms have been compiled into executable control algorithms. The proposed online laboratory also provides a customizable monitoring interface, with which users can customize their user interface using provided widgets such as the textbox, chart, 3-D, and camera widget. Teachers can use the system for online demonstration in the classroom, students for after-class experimentation, and researchers to verify control strategies.

This work describes an online experimentation system that provides visualized experiments, including the visualization of theories, concepts, and formulas, visualizing the experimental process with three-dimensional (3-D) virtual test rigs, and visualizing the control and monitoring system using widgets such as charts and cameras.

Experimentation is crucial in engineering education. This work explores visualized experiments in online laboratories for teaching and learning and also ...