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.

<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>

Les auteurs déclarent qu&#39;ils ne ont aucun intérêt financier concurrentes.

Éléments essentiels à la réussite de l&#39;installation et l&#39;utilisation du système de visualisation 3D / VR sont détaillées dans l&#39;environnement physique et de conception et de considérations spéciales dans les matériaux supplémentaires. Considérations d&#39;installation importants incluent la hauteur d&#39;affichage 3D pour la commodité de permanent à long terme ou de l&#39;usage assis, maximisés suivi caméra montée hauteur pour créer un grand espace 3D de tr...

La science des matériaux est un domaine interdisciplinaire qui examine les relations structure-propriété dans la matière pour leur application à de nombreux domaines de la science et de l&#39;ingénierie. Comme les relations structure-propriété sont étudiées par des simulations informatiques, en plus de l&#39;expérimentation, des outils informatiques offrent des caractéristiques complémentaires qui peuvent améliorer les efforts de recherche. Alors que les nanomatériaux sont d&#39;intérêt pour les scientifiques et ont une valeur rédemptrice pour leur impact social potentiel, ce régime de taille se heurte à de nombreux défis trouvés notamment dans l&#39;expérimentation. Les simulations informatiques permettent aux scientifiques et ingénieurs d&#39;effectuer des tests spécialisés dans une grande variété d&#39;environnements limités seulement par le temps et les ressources de calcul. Dynamique moléculaire (MD) simulations permettent en temps opportun et des échelles de longueur d&#39;étudier les phénomènes d&#39;intérêt dans de nombreux nanomatériaux. Simulations développer l&#39;étude des matériaux en éliminant les contraintes de til laboratoire de physique, mais de nombreux outils informatiques manquent accessibles, des interfaces intuitives pour la recherche. Amélioration de l&#39;affichage graphique des modèles, algorithmes de calcul efficaces, et l&#39;unité de traitement graphique (GPU) informatique basée compléter les efforts actuels de simulation. Ces nouveaux dispositifs graphiques combinent avec des unités centrales de traitement efficace pour permettre des calculs mathématiques intensifs à accomplir par le GPU. Il en résulte une accélération efficace de calcul de l&#39;ordre de 10x accompagnée d&#39;une réduction de la consommation de puissance allant jusqu&#39;à 20x. Le but de ce projet de recherche était de développer et mettre en œuvre un nouvel outil pour les enquêtes sur les nanosciences qui se connecte directement une interface interactive à des simulations MD, l&#39;analyse en science des matériaux et la visualisation 3D. Ce système innovant avec des capacités uniques et puissantes analyse a été utilisé pour la recherche à l&#39;échelle nanométrique et de l&#39;éducation à l&#39;UC Merced, avec des implications directes à d&#39;autres rel<html> domaines de la tige és tels que la nanotechnologie, la physique, la biologie et la géologie et bénéfice ultime à l&#39;éducation et la société. Le système de visualisation 3D / VR a été mis en œuvre à la fois comme un instrument de recherche et d&#39;enseignement qui permet la création et la manipulation de structures atomiques dans une réalité virtuelle 3D interactive (VR) environnement. Le système a été créé à partir d&#39;un ensemble de coût relativement faible et les composants accessibles suivant le modèle développé à l&#39;origine par le Dr Oliver Kreylos à l&#39;UC Davis 1. Ci-dessous une photo de la mise en page finale 3D / Système de visualisation VR, avec des composants importants marqués (Figure 1). Ce système a été initialement créé à des fins d&#39;éducation à l&#39;UC Merced en 2009. La mise en œuvre du système 3D d&#39;origine / VR a donné lieu à des publications évaluées par les pairs 2-3. Tableau 1 ci-dessous résume les principales caractéristiques pour chaque élément du système de visualisation 3D / VR. MÉNAGEMENT &quot;fo: keep-together.within-page =&quot; always &quot;&gt; <img alt="Figure 1" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig1highres.jpg" width="500" /> Figure 1. 3D / Système de visualisation VR et composantes principales (gauche) dans le Laboratoire de recherche Davila à UCM et les dispositifs de visualisation (à droite). <a href="https://www.jove.com/files/ftp_upload/51384/51384fig1highres.jpg" target="_blank">Se il vous plaît cliquer ici pour voir une version plus grande de cette figure.</a> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td> Article </td><td> Composant </td><td> Fonctionnalité dans le système </td></tr><tr><td> Un </td><td> TV 3D </td><td> Affichage 3D de structures moléculaires modélisées et les menus à l&#39;écran. </td></tr><tr><td> B </td><td> Infrarouge (IR) caméras de suivi 4 </td><td> Caméras IR positions de piste des lunettes de vision Wiimote et 3D dans le mode d&#39;espace de travail en face de la télévision 3D, permettant virTual manipulation 3D des structures affichées. </td></tr><tr><td> C </td><td> Suivi PC </td><td> Exécute IR logiciel de suivi de la caméra et transmet positions de lunettes Wiimote et 3D à l&#39;ordinateur de modélisation. </td></tr><tr><td> Ré </td><td> Wiimote </td><td> Utilisé pour la gestion à l&#39;écran de logiciels de modélisation et de manipuler des structures dans un environnement virtuel en 3D. </td></tr><tr><td> E </td><td> Lunettes 3D 5 </td><td> Synchronisé avec le signal TV 3D IR, permettra vue 3D de la structure. Position suivis par les caméras IR pour vision précise de 3D. </td></tr><tr><td> Fa </td><td> Modélisation PC </td><td> Exécute NCK / VRUI modélisation 3D et l&#39;affichage des logiciels 6, accepte les signaux lunettes / position et de contrôle Wiimote pour créer précise vue 3D de la structure moléculaire. </td></tr></tbody></table> Tableau 1. Fonctionnalité des principaux éléments du système de visualisation 3D / VR au UCM. Description du système de visualisation 3D / VR et composants de base: / VR Visualisation Présentation du système 3D - La 3D / VR Visualization System se compose d&#39;un ensemble de caméras infrarouges et un logiciel de suivi fonctionnant en liaison avec le logiciel de modélisation 3D pour permettre à un utilisateur de créer de façon interactive 3D des structures moléculaires. Les caméras et les logiciels IR suivre la position 3D d&#39;une Wiimote et 3D lunettes de vision en utilisant des marqueurs infrarouges, et passent à présent le logiciel de modélisation. Le logiciel de modélisation utilise les signaux de commande Wiimote et le mouvement pour générer des structures moléculaires 3D visible en utilisant la combinaison d&#39;un grand format de la télévision 3D avec des lunettes 3D synchronisés et à chenilles. Il en résulte un espace de travail 3D réalité virtuelle à l&#39;intérieur de laquelle l&#39;utilisateur peut créer et manipuler dynamiquement les structures moléculaires virtuelles qui reflètent le comportement physique du monde réel sur la base de forces inter-atomiques utilisés dans le logiciel de modélisation (figure 2). Considerati spécialesons pour la mise en place de ce système peut être trouvé dans les matériaux supplémentaires. <img alt="Figure 2" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig2highres.jpg" width="500" /> Figure 2. Étude nanomatériaux de silice en utilisant le système de visualisation 3D / VR. (A) Un chercheur crée un modèle de cristobalite initial (cristallin) avant simulations à base de GPU. (B) Lors de l&#39;exécution d&#39;une procédure simulée MD fondre trempe sur le modèle représenté en (a), un autre chercheur obtient un modèle de verre de silice (non cristalline). <a href="https://www.jove.com/files/ftp_upload/51384/51384fig2highres.jpg" target="_blank">Se il vous plaît cliquer ici pour voir une version plus grande de cette figure.</a> 3D / VR Visualisation Enhancement System - MD Simulation Capability: Dynamique moléculaire des systèmes de simulation sont couramment mises en œuvre dans unMode multi-nodal, ce est une grande charge de travail est distribué ou parallélisée parmi des dizaines de milliers de processeurs. Récemment, des possibilités supplémentaires pour le calcul scientifique accélérée ont surgi sur l&#39;évolution du traitement de l&#39;infographie. Ces progrès incluent une interface logicielle permettant aux scientifiques de profiter de la nature hautement parallèle de la puissance de traitement intrinsèque à puces graphiques. Avec l&#39;avènement de l&#39;Unified Device Architecture Compute ou CUDA 7, les scientifiques peuvent utiliser les GPU 8 pour améliorer la vitesse à laquelle les problèmes sont résolus, tout en réduisant le coût des infrastructures. Un GPU typique peut avoir l&#39;équivalent de centaines de milliers de noyaux ou «nœuds» de traitement des informations, et comme ceux-ci peuvent être utilisés chacun en parallèle, une solution bien codée peut fournir jusqu&#39;à 1,000x accélération débit contre son homologue multi-core . Bien que pas tous les problèmes est bien adapté à cette approche, simulations de DM actuelles ont vu jusqu&#39;à 15x performances débit gagne 9. Détails sur le système de visualisation MD-GPU amélioration 3D / VR peuvent être trouvés dans les matériaux supplémentaires.

<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

Le développement croissant de l&#39;informatique (matériel et logiciel) dans les dernières décennies a eu un impact de la recherche scientifique dans de nombreux domaines, y compris la science des matériaux, la biologie, la chimie et la physique parmi beaucoup d&#39;autres. Un nouveau système de calcul pour la simulation précise et rapide et 3D / VR visualisation des nanostructures est présenté ici, l&#39;aide de l&#39;open-source dynamique moléculaire (MD) programme informatique LAMMPS. Cette méthode de calcul alternatif utilise des processeurs graphiques modernes, la technologie NVIDIA CUDA et codes scientifiques spécialisés pour surmonter les obstacles de vitesse de traitement communs aux méthodes de calcul traditionnelles. En conjonction avec un système de réalité virtuelle utilisée pour modéliser les matériaux, cette amélioration permet l&#39;ajout de capacité de simulation MD accéléré. La motivation est de fournir un environnement de recherche roman qui permet simultanément la visualisation, la simulation, la modélisation et l&#39;analyse. L&#39;objectif de la recherche est d&#39;étudier la structure et les propriétés de l&#39;azote inorganiqueanostructures (par exemple, nanosprings de verre de silice) dans des conditions différentes en utilisant ce système de calcul innovante. Le travail présenté décrit une description du système de visualisation 3D / VR et les composants de base, un aperçu des considérations importantes comme l&#39;environnement physique, de détails sur la configuration et l&#39;utilisation du nouveau système, une procédure générale pour l&#39;amélioration MD accélérée, informations techniques et remarques pertinentes. L&#39;impact de ce travail est la création d&#39;un système informatique unique combinant des matériaux à l&#39;échelle nanométrique simulation, la visualisation et l&#39;interactivité dans un environnement virtuel, qui est à la fois un instrument de recherche et d&#39;enseignement à l&#39;UC Merced.

Cette 3D / VR Visualization System offre de nouvelles possibilités pour la conduite des études de sciences des matériaux. Comme cet environnement immersif fonctionne en temps réel, sous la forme d&#39;entrée et d&#39;affichage 3D, le chercheur est présenté avec un instrument entièrement interactif nanométriques 2. En suivant le protocole présenté ici, un nanoruban hélicoïdal de silice a été créée dans cette étape par étape. Un aperçu de cette structure produite à partir LAMMPS MD est repr...

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.

Roman 3D / VR environnement interactif pour MD simulations, visualisation et d&#39;analyse

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 vues.  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.

Vidéo: 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.

Fabrication, l&#39;exploitation et la visualisation des écoulements en surface à ondes acoustiques axées microfluidique-Acoustiques contre-courant

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

Recherche

Ingénierie

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.

Nanohelices évolutives pour les études de prévision et le renforcement de la visualisation 3D

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.

Selective Area Modification de la Silicon mouillabilité de surface par irradiation laser pulsé UV en milieu liquide

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.

Plasmonique et Piégeage Libération de Nanoparticules dans un environnement de surveillance

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.

Fabrication à haute température de nanostructurés yttriée-Zircon (YSZ) par scellants<em&gt; In Situ</em&gt; Carbon Templating xérogels

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.

Lignes directrices et l’expérience à l’aide d’imagerie biomarqueur Explorer (IBEX) pour 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 ...

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).

Analyse de l’applicabilité des méthodes d’évaluation des paramètres morphologiques des barres d’acier corrodé

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.

Surveillance des fissures dans les tests de fatigue par résonance des spécimens soudés à l'aide de la corrélation d'image numérique

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.

Chirurgie et traitement des échantillons pour l’imagerie corrélative de la valve pulmonaire murine

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.

Système d’expérimentation en ligne interactif et visualisé pour l’enseignement et la recherche en ingénierie

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