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.模拟PC上安装3D / VR建模软件<ol><li>模拟PC上安装LINUX基本的操作系统（Ubuntu的86 / AMD64取决于硬件）。 </li><li>修改LINUX基本操作系统。 <ol><li>安装库和添加功能是必要的。 </li></ol></li><li>安装VRUI和NCK 3D /模拟PC 6 VR建模软件。 <ol><li>检查相关的网站1,6获得的所有建模软件组件的最新版本。 </li><li>编译，配置和测试VRUI。 </li><li>安装和测试NCK。 </li></ol></li></ol> 2.设置跟踪系统1 <ol><li>安装红外跟踪摄像机4 <ol><li>直接创建一个刚性相机悬挂架3D电视的上限最好覆盖率近前缘上面。安装3个摄像头在旋转支架正上方的前角和3D电视的正前方。确保每个摄像头的覆盖角度正好克拉泽斯电视机的前表面上。 </li><li>对准摄像机具有覆盖范围最广的角度（45度）平行于3D电视的前面。用更窄的覆盖角度（30度）在垂直于3D电视的前面。允许所期望的三维工作空间中的最大重叠。保证对象是鉴于至少两个照相机被成功地跟踪（ 图3）的。 <img alt="图3" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig3highres.jpg" width="500" /> 图3.红外跟踪摄像头的覆盖最大化三维工作空间在电视机前，部分（A）及（B）显示正面和侧面视图就3D / VR可视化系统。 <a href="https://www.jove.com/files/ftp_upload/51384/51384fig3highres.jpg" target="_blank">请点击此处查看该图的放大版本。 。</a> </li></ol></li><li>与备用摄像机安置，如果需要创建一个足够的试验三维工作空间。这可能是必需的，如果摄像机的垂直安装距离的限制。 </li><li>安装和校准跟踪软件<ol><li>安装使用附带的安装手册跟踪计算机上的OptiTrack刚体工具包。 </li><li>设定的阈值，曝光，照度值依赖于环境和设置捕获质量高，在跟踪软件的说明，详细说明。 </li><li>对于棒捕获，要小心从3D空间中删除所有其他反光材料。与反光棒整个摄像头的重叠工作区平稳地移动。重复，直到标准和平均​​低于“0.5”的错误得到然后保存校准文件。 </li><li>设置接地平面，以建立一个三维跟踪工作区坐标系原点。定义的Wiimote和3D眼镜跟踪对象为在跟踪软件的详细说明。 </li></ol></li><li>完整的VRUI校准<ol><li>设置VRUI接受trackin从跟踪计算机G信息。 </li><li>验证使用DeviceTest校准工具跟踪功能的VRUI。 </li><li>对齐VRUI 3D显示和跟踪软件坐标系。 </li><li>使用AlignTrackingMarkers定位软件跟踪的Wiimote和3D眼镜的设置方向。 </li></ol></li></ol> 3.准备三维建模系统使用<ol><li>在开始之前，删除所有反光饰品（如手表，耳环，金属等 ）。不要取下需要关注屏幕上的矫正眼镜。 </li><li>组装设备的3D / VR可视化系统： <ol><li>计算机建模</li><li>跟踪电脑</li><li>大幅面3D功能的电视</li><li>计算机建模和3D电视之间的视频连接线</li><li> 3D红外发射器的3D电视</li><li>以太网电缆建模和跟踪电脑</li><li> Wiimote的跟踪与鹿角（控制器） </li><li>与跟踪鹿角3D眼镜（3D眼镜）5 </li></ol></li><li>小心地控制它可以轻松地从模拟计算机达到，注意不要触摸或移动连接到它的球形IR跟踪标记。 </li><li>小心地在电视上的立场3D眼镜（如前，一定要避免接触反光标记）。 </li><li>从上面装了3D电视跟踪计算机上的3个USB端口，红外摄像机连接三个USB电缆，同时断电。 </li><li>找到3D电视机的遥控器，并将其放置在3D电视前。 </li><li>将视频电缆连接到显卡的建模计算机和3D电视的视频输入。还连接3D红外发射器，用于从3D TV输出的3D同步，并将其放置在发射电视站的电视近前侧，朝上朝向哪里护目镜将被使用。非常小心，不要转移校准电视的位置。 </li><li>建模电脑上连接电源之前打开3D电视确保正确识别由计算机。 </li><li>开启建模计算机。建模计算机启动到登录提示后，计算机建模的Linux系统上登录到相应的帐户。 </li><li>一旦建模电脑桌面可用，使用3D电视机的遥控器来检查视频电缆连接按下“信息/ i”按钮的状态。确保在左上角的电视屏幕上显示“1920×1080 @ 60HZ”。如果没有，请重新启动计算机建模，以树立正确识别3D电视。还可以肯定的电视是3D输出模式2，使用遥控器设置菜单。 </li><li>在模拟计算机桌面上，有几个标签中打开一个终端窗口。 </li><li>在跟踪计算机上，通过在命令窗口下键入“ipconfig”验证以太网适配器的IP地址。 </li><li>在模拟计算机上，打开一个终端窗口选项卡，并选中VRDevices.cfg文件中的“服务器名”定义跟踪计算机以太网适配器的IP地址。 </li><li>如果有必要，改变在VRDevices.cfg的“服务器名”IP地址匹配跟踪计算机以太网适配器，并保存VRDevices.cfg。 </li><li>在跟踪计算机上，启动OptiTrack刚体工具软件。 </li><li>让软件完全打开，然后单击接近顶部菜单标有“负载校准结果”大按钮。 </li><li>浏览并打开相应的摄像机标定文件。 </li><li>加载该文件后，单击“文件”菜单，选择“加载刚体的定义”。 </li><li>浏览并打开相应的刚体定义文件的跟踪控制器和3D眼镜。 </li><li>在跟踪软件的最右边的窗格中，找到标有“流媒体”的部分，展开部分，根据“VRPN流”类别中，验证列出的端口号是3883，然后勾选“宽投VRPN流引擎“类别”内盒“帧数据。 </li><li>在模拟计算机，请确保该控制器可以直接在手或立即到达（2秒走在最）。 </li><li>在模拟计算机，调出选项卡在本届会议早些时候创建的终端窗口并导航到，然后启动VRDeviceDaemon软件，例如输入“./VRDeviceDaemon”。 </li><li>按照提示如果活动是成功的，该窗口将显示“请按按钮1和2的W​​iimote的同时进行。”“VRDeviceServer：等待客户端连接”。 </li></ol> 4.测试3D / VR可视化系统使用NCK软件下面的指令集概述了如何使用NCK软件屏幕上的菜单来建立控制器工具功能，以及如何构建和操纵碳nanotu在从构成碳原子数（ 图4）的3D / VR的工作区。可在线10如何衡量所产生的键角和距离（步骤4.4.10）指令。 <img alt="图4" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig4highres.jpg" width="500" /> 图4.本科学生使用3D / VR可视化系统研究碳纳米管（CNT）的照片（A） - （F）显示单壁碳纳米管的建设过程中<a href="https://www.jove.com/files/ftp_upload/51384/51384fig4highres.jpg" target="_blank">，请点击这里查看该图的放大版本。 。</a> <ol><li>在步骤3.11创建的模拟计算机终端窗口中，选择第三个选项卡。要启动NCK软件，导航到NCK的安装目录，然后键入： “./NanotechConstructionKit -rootSection本地主机-domainsize 36“。 </li><li>非常小心，不要触摸或松开连接跟踪标记，戴上3D眼镜，拿起控制器。调整头/护目镜观看位置，以确保3D眼镜正在接受3D电视的红外发射器同步信号，使3D / VR观看电视显示屏。 </li><li>为了有一个工具来添加，移动和删除原子，分配NCK命令协会按钮控制器上进行如下： <ol><li>调出主NCK屏幕菜单通过按住遥控器手柄上的Home键，导航到并选择“覆盖工具”菜单项，然后释放Home键。这使得命令不同的按钮的分配彼此独立控制器上。 </li><li>到Wiimote的触发按钮（在控制器的底部）与内NCK，按操纵原子操作相关联，并按住扳机按钮，导航屏幕上的NCK菜单＆＃8220;牵引机“，然后选择”6-DOF牵引机“，然后松开扳机。触发现在与操纵原子的动作相关联。 </li><li>分配添加原子上的Wiimote的“+”按钮的功能，把主菜单由按住Home键，导航到“结构单元类型”，然后选择“三角”，然后松开Home键。 </li><li>接下来按住“+”按钮，定位到“牵引机”，然后选择“6-DOF牵引机”，然后松开“+”按钮。的“+”按钮现在与创建所选类型的新原子（由三角形表示的碳原子数，在这种情况下）相关联。 </li><li>要指定删除一个原子的功能“ - ”关于Wiimote的按钮，调出主菜单，按住“主页”按钮，然后导航到“结构单元类型”，然后选择＆＃8220;删除选定的单位，“然后松开Home键。 </li><li>接下来，按住“ - ”按钮，定位到“牵引机”，然后选择“6-DOF牵引机”，并发布了“ - ”按钮。在“ - ”按钮现在删除原子有关。 </li><li>遵循相同的程序来分配的“锁定选定单元”的功能的“1”的Wiimote按钮，“解锁所选单元”的“2”的控制器按钮。 </li></ol></li><li>一旦控制器按钮已配置，使用NCK如下创建一个碳纳米管： <ol><li>使用“+”按钮，两个3键三角形碳原子添加到NCK的工作区。这些使用触发按钮，直到他们在一个顶点加入操纵。 </li><li>添加4个碳原子创建一个六角星形。 </li><li>使用“家”菜单，导航到“I / O菜单”，然后选择“保存单位。 </li><li>移动6尖结构远离其当前位置。 </li><li>使用“家”菜单，导航到“I / O菜单”，然后选择“载入单位。 </li><li>直到6由6片的六角形-6-原子环已创建（ 图5A）重复最后2个步骤。 </li><li>使用“1”的按钮时，锁定一个原子顶行中，且最底行中的相对原子。锁定的原子将被标记为粉红色（ 图5B）。 </li><li>使用触发按钮，小心地将锁定原子之一以圆弧直到其自由顶点接近相对的锁定原子的自由顶点。绿色行会当他们是足够接近，原子的吸引力会导致他们加入一个键（ 图5C）的顶点之间出现。一旦成功加入，解开两者都使用了“2”键的原子。 </li><li>继续同样锁定，加入和解锁反对原子弹版本践中的碳片材，有效地“压缩和解”片材成最终的碳纳米管（ 图5D-5F）。 <img alt="图5" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig5highres.jpg" width="500" /> 图5.逐步建立一个单壁CNT显示出（A） 的一个6×6片（石墨烯）的六方碳环，（B）的相对的碳原子“锁定”（示出为粉红色三角形），以允许对更容易操纵现实原子间力，（C）的碳（石墨）片小心弯曲以允许原子之间的结合上相对的侧面，（D）的锁定，以协助进一步碳片曲率两个附加的相对碳原子，（E）的附加 ​​的相对碳原子键合到碳继续原来的C的相对原子的连续键合后形成的片材的曲率成纳米管，和（F）最终的CNT阿尔邦板材（石墨烯）。 <a href="https://www.jove.com/files/ftp_upload/51384/51384fig5highres.jpg" target="_blank">请点击此处查看该图的放大版本。</a> </li><li>当纳米管完成后，使用屏幕上的测量工具，以确定结构的角度和距离10。 </li></ol></li></ol> 5.可视化的分子动力学模拟模型<ol><li>导入初始结晶二氧化硅立方体模型到3D / VR NCK软件，并调查最初的结构（ 见图2A）。 </li><li>开源程序MDCASK 11和12 LAMMPS进行了针对性的，因为这是非常适合这项研究的重点功能。后者计划用于这项工作赋予其不同的原子间电势和GPU的计算能力。使用LAMMPS MD包12中 ，运行一个模拟的熔体/淬火过程在此初始结构，以产生无定形的SiO 2 ST<html> ructure。在这个模拟过程的详细信息可以在以前的出版物13-15找到。 </li><li>导入生成新的非晶（无序）的SiO 2模型到3D / VR NCK软件和调查结构（ 见图 2b）。 </li><li>创建的SiO 2 nanospring /纳米带出了新的无定形固体使用开放源代码NanospringCarver 16和相关指导性文件17（ 图6）。 <img alt="图6" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig6highres.jpg" width="500" /> 图6.图示在创建使用NanospringCarver程序nanospring的不同阶段的一步一步原子选择处理的部件：（A - D）表示25％，50％，该方法的75％和100％的完成17。目标=“_空白”&gt;点击此处查看该图的放大版本。 </li><li>使用LAMMPS MD包上的nanospring /纳米带（ 图7）进行拉伸模拟。在此过程的详细信息可以在以前的出版物15被发现。 <img alt="图7" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig7highres.jpg" width="500" /> 从LAMMPS MD二氧化硅纳米螺旋（纳米带）拉伸仿真结果如图7快照图像。 </li><li>使用开源软件工具VMD（可视化分子动力学）18 ImageMagick的19，和FFmpeg的20创建快照和螺旋纳米结构的动画贯穿这个模拟（ 动画图1），用于演示的3D / VR可视化系统。 <a href="https://www.jove.com/files/ftp_upload/51384/51384fig7highres.jpg" target="_blank">请点击这里查看大V</a>版为这个数字的。 </li></ol> <a href="https://www.jove.com/files/ftp_upload/51384/Animated_Fig1-movie NR-0140_frames.mov" target="_blank">动画图1</a> 。动画螺旋纳米结构拉伸模拟。

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作者宣称，他们有没有竞争的财务权益。

在成功安装了3D / VR可视化系统的部署和使用的关键要素是在物理环境和设计考虑 ，并特别注意事项的补充材料的详细。重要的安装注意事项，包括3D显示器高度舒适的长期站立或坐着的使用，最大限度地跟踪摄像机安装高度，创造了大量的3D工作区，稳定跟踪摄像头和3D显示的支持，以保持配置随着时间的推移，以及去除红外线反射元素从3D工作区域。正如前面提到的安?...

材料科学是一个跨学科领域的检查结构 - 性能关系，无论他们的应用科学和工程的许多领域。由于结构与性能的关系，通过计算机模拟，除了实验研究，计算工具提供了互补的功能，可以增强研究工作。虽然纳米材料感兴趣的科学家和有兑换价值为他们潜在的社会影响，这种规模的制度充满了发现特别是在实验许多挑战。 计算机模拟使科学家和工程师在种类繁多的只有时间和计算资源有限的环境中进行专门的测试。分子动力学（MD）模拟允许适当的时间和长度尺度来研究感兴趣的现象在许多纳米材料。模拟扩大材料的研究，通过去除T的限制他的物理实验室，然而，许多计算工具缺乏方便，直观的界面进行研究。加强与模型的图形显示，高效的计算算法和图形处理单元（GPU）的计算补充当前模拟的努力。这些新的图形设备与中央处理单元相结合高效，让数学密集型计算由GPU来完成。其结果是计算的10倍伴随在高达20倍的功率消耗的降低的数量级上的有效加速。 这一研究项目的目标是开发和实施了一种新的工具，纳米科学的调查，直接连接的人机交互界面，MD模拟，材料科学分析和三维可视化。该创新系统具有独特而强大的分析功能已被用于在UC Merced的纳米研究和教育，直接影响到其他相对<html> ated STEM领域，如纳米技术，物理，生物，地质，并最终受益于教育和社会。 在3D / VR可视化系统实施既是科研和教学仪器，它允许创建和操纵原子结构中的交互式三维虚拟现实（VR）环境。该系统是由最初由奥利弗Kreylos博士在加州大学戴维斯分校1开发的模型下面一组相对低的成本和可获得的组件创建。 下面是一个照片的最终3D / VR的可视化系统的布局，与标记的重要组成部分（ 图1）。该系统最初是建立在教育的目的在加州默塞德在2009年的原始3D / VR系统的实施，导致在同行评审的出版物2-3。下面的表1总结了3D / VR可视化系统中的每个元素的关键特性。 ntent“FO：保持together.within页=”总是“&gt; <img alt="图1" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig1highres.jpg" width="500" /> 图1. 3D / VR可视化系统，并在UCM和可视化设备（右）的主要成分（左）在达维拉研究实验室。 <a href="https://www.jove.com/files/ftp_upload/51384/51384fig1highres.jpg" target="_blank">请点击此处查看该图的放大版本。</a> <table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td> 项目 </td><td> 部件 </td><td> 功能在系统 </td></tr><tr><td>一</td><td> 3D电视</td><td> 3D显示模拟的分子结构和屏幕上的菜单。 </td></tr><tr><td> B </td><td>红外（IR）跟踪摄像机4 </td><td>红外摄像机在3D电视前的用户工作区的Wiimote和3D眼镜观看的轨道位置，让VIR图阿尔3D操作显示结​​构。 </td></tr><tr><td> Ç </td><td>跟踪PC </td><td>运行红外摄像机跟踪软件，并发送的Wiimote和3D眼镜持仓建模计算机。 </td></tr><tr><td> ð </td><td>的Wiimote </td><td>用于建模软件的屏幕上的管理和操作结构在三维虚拟环境。 </td></tr><tr><td> Ë </td><td> 3D眼镜5 </td><td>同步的3D电视IR信号，使结构的三维视图。位置由红外摄像头进行精确的三维视图跟踪。 </td></tr><tr><td> ˚F </td><td>造型PC </td><td>运行NCK / VRUI 3D建模和显示软件6，接受护目镜/ Wiimote的位置和控制信号，创建精确的三维分子结构的视图。 </td></tr></tbody></table> 表1.功能的3D / VR可视化系统在UCM的主要元素。 DESCRIPTIOñ3D / VR可视化系统和基本组件： 3D / VR可视化系统概述 -在3D / VR可视化系统包括一套红外摄像机和跟踪软件与三维建模软件一起运行，以允许用户以交互方式创建三维分子结构。红外相机和软件跟踪使用IR标记物的Wiimote和3D眼镜观看3D的位置，并通过这个来建模软件。建模软件使用Wiimote的控制信号和动作与同步和跟踪3D眼镜使用3D功能的大幅面电视的结合，生成三维分子结构可见。这导致在一个三维虚拟现实工作空间中，用户可以动态地创建和操作基于在建模软件使用原子间力反映真实世界物理行为（ 图2）虚拟分子结构。特别considerati附件设立该系统可以在补充材料中找到。 <img alt="图2" fo:content-width="5in" src="/files/ftp_upload/51384/51384fig2highres.jpg" width="500" /> 图2.调查采用3D / VR可视化系统二氧化硅纳米材料。 （ 一 ）研究人员创建了基于GPU的仿真之前的初始方石英模型（结晶）。 （b）当在（A），另一位研究员获得石英玻璃模型（非结晶）所示模型进行了模拟MD熔融淬火的过程。 <a href="https://www.jove.com/files/ftp_upload/51384/51384fig2highres.jpg" target="_blank">请点击此处查看该图的放大版本。</a> 3D / VR可视化系统增强- MD模拟能力： 分子动力学模拟系统中普遍采用的多节点的方式，就是一个大的工作量分配或并行间几十到上千处理器。近日，加速科学​​计算额外的机会已经出现了事态发展计算机图形处理。这些进展包括软件接口，使科学家们采取的处理能力固有的图形芯片的高度并行特性的优势。与统一计算设备架构或CUDA 7的出现，科学家可以利用GPU的8，以提高在该同时减少的基础设施成本的问题得到解决的速度。一个典型的GPU可以具有数百到数千芯或“节点”的用于处理信息的等效，而且因为这些可以并行每个被使用的，以及编码的溶液可以提供高达1,000倍针对其多核对应吞吐量加速度。虽然不是所有的问题是非常适合于这种方法，当前MD模​​拟已经看到高达15X吞吐量性能提升9。在3D / VR的可视化系统的MD-GPU的增强的细节可以在补充材料中找到。

<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

的计算，在过去的几十年（硬件和软件）的日益发展已经影响了科研在许多领域，包括材料科学，生物学，化学和物理之间等等。一种新的计算体系，为准确，快速的模拟和纳米结构的3D / VR可视化在这里呈现，采用开源分子动力学（MD）计算机程序LAMMPS。这种替代计算方法采用现代图形处理器，NVIDIA CUDA技术和专门的科学规范，克服常见的传统计算方法处理速度的障碍。在与用于建模材料的虚拟现实系统相结合，这种增强允许添加的加速MD模拟能力。动机是提供一种新的研究环境，其同时允许可视化，仿真，建模和分析。这项研究的目的是探讨无机氮的结构和性能anostructures（ 如石英玻璃纳米弹簧）采用这种创新的计算系统在不同条件下。提出的工作概述如物理环境的3D / VR可视化系统和基本成分，重要的考虑因素的概述的说明，对新系统的安装和使用的信息，用于加速的MD增强的一般程序，技术信息，和相关的言论。这项工作的影响是建立一个独特的计算系统，在虚拟环境中，这既是一种研究和教学仪器在加州大学默塞德结合纳米材料模拟，可视化和交互性。

这种3D / VR可视化系统提出了开展材料科学的研究，新的机遇。作为这种身临其境环境实时操作，在3D输入和显示的形式，研究者提出了完全交互式纳米尺度的仪器2。按照这里介绍的协议，二氧化硅螺旋纳米带在此一步一步的方式被创建。从LAMMPS MD产生这种结构的快照显示在图7。这种结构进行模拟拉伸测试，并且该模拟的结果示于动画图1，它示出了在拉伸力的结?...

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.

新颖的3D / VR互动环境MD模拟，可视化和分析

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 次观看.  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.

视频: 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.

制造，操作和表面声波驱动声逆流微流体流动可视化

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

科研

工程学

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.

可扩展的Nanohelices的预测研究和增强的3D可视化

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.

硅表面润湿性的选择区域改性脉冲紫外激光照射在液体环境

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.

电浆捕获和纳米粒子的释放在监控环境

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.

通过纳米氧化钇稳定的二氧化锆（YSZ）的支架的高温加工<em&gt;原位</em&gt;碳模板干凝胶

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.

使用成像生物标志物探险家 (野山羊) Radiomics 的指南和经验

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).

钢筋形态参数评价方法的适用性分析

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.

使用数字图像相关性对焊接试样共振疲劳测试中的裂纹监测

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.

穆林肺瓣膜相关成像的手术和样品处理

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.

工程教育研究互动可视化在线实验系统

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