作者要感谢蒂姆·阿里斯在加州大学默塞德，他在这个项目的援助。在UCM的NSF-币计划在这项工作中的早期部分支持（KAM）。一个NSF-brige是奖励支持的合着者（BND和KAM），提供资金用于这项工作，差旅费会议。 该研究小组希望首先感谢国家科学基金会通过brige是屡获这项工作提供资金。这种材料是基于由美国国家科学基金会资助下，第1032653支持工作。

1.准备NanospringCarver文件和Linux的PC上启动MATLAB 下面的步骤被设计用于一般用户使用的在线26中提供的文件。 <ol><li>解压nanosprings.tar.gz文件归档到“家”或另一种优选目录。 <ol><li>从网上资料库26下载nanosprings.tar.gz文件归档。 </li><li>找到下载的压缩文件并将其移动到标题为“文档/纳米弹簧”首选的工作目录。 </li><li>右键单击nanosprings.tar.gz，然后从右键单击上下文菜单中选择“解压到当前”。 </li></ol></li><li>验证所有必需的文件都存在于当前目录中。这些文件及其用途如下列表： Makefile文件-手动管理文件编译为nanosprings.cpp和Point.cpp Nanosprings.fig -MATLAB GUI内部 Nanosprings.m -MATLAB GUI代码 Point.cpp -点（原子）类定义 Point.h -点（原子）类的头 中分-单机纳米弹簧的可执行文件 example.par -例如参数文件 glasscube.inp - glasscube数据文件 nanosprings.cpp -纳米弹簧的主要代码 nanosprings_diagram.jpg -例如nanospring显示 nanospringsmex.cpp - MATLAB集成nanosprings.cpp nanospringsmex.mexglx - MATLAB集成纳米弹簧的可执行文件 注意：用户需要（在本例中的32位版本）创建了“nanospringsmex.mexglx”的可执行文件的特定的Linux机器被使用。如果还没有完成，验证访问MATLAB“MEX”编译通过键入命令行“， 这MEX”上和验证程序的存在。还通过键入命令行“， 这MATLAB”上验证访问MATLAB程序。使用命令行键入“MEX nanospringsmex.cpp Point.cpp”将打造“nanospringsmex.mexglx”可执行MATLAB集成NanospringCarver文件，如下面的说明进行操作。虽然不是必需的图形用户界面，如果需要的NanospringCarver程序的独立版本可以通过在命令行上输入“make”来创建。这将编译nanosprings.cpp和Point.cpp程序元素共同打造的“ 瓜分 ”的可执行文件。在本教程中，“glasscube.inp”文件中包含位置信息的192,000硅原子和氧原子representin<html>ガ石英玻璃模式，每行含有一个原子的ID，原子类型，以及x，y和z坐标的原子。该文件的第一行是总原子数（192,000）。此文件中的原子坐标是相对值，这如果乘以0.716将代表纳米的距离。 </li><li>在桌面上，打开一个终端窗口。在很多Linux版本实现这一点同时按下“CTRL”，“ALT”和“T”键。 </li><li>将目录更改为到其中的纳米弹簧项目文件被输入提取的文件夹： CD文件/纳米弹簧/ </li><li>接下来，运行命令来编译的二进制文件系统，请键入： MEX nanospringsmex.cpp Point.cpp </li><li>下一步启动MATLAB通过在命令行上输入MATLAB </li></ol> 2.修改和使用图形用户界面（GUI）的NanospringCarver计划ove_content“&gt;按照以下使用在线26中提供的文件中的步骤。 <ol><li>通过点击该指南的图标，在左上角工具栏区域（ 图2）打开在MATLAB指导，以显示与导向快速启动（ 图3），一个新的窗口。 </li></ol><img alt="图2" fo:content-width="6in" src="/files/ftp_upload/51372/51372fig2highres.jpg" width="600" /> 图2：显示如何打开MATLAB的GUIDE MATLAB用户界面 。 <img alt="图3" fo:content-width="6in" src="/files/ftp_upload/51372/51372fig3highres.jpg" width="600" /> 图3：MATLAB GUIDE界面初始化。 <ol start="2"><li>使用“打开现有的图形用户界面”选项卡（ 图4），修改现有的身影。点击“浏览”按钮来搜索现有的GUI图进行修改。选择图中的文件后（Nanosprings.fig，见蓝框），在这两个窗口点击“打开”，以显示与GUI图的新窗口。找到按钮可被用于在左侧面板上的GUI的创建（ 如图5）。 </li></ol><img alt="图4" fo:content-width="6in" src="/files/ftp_upload/51372/51372fig4highres.jpg" width="600" /> 图4：MATLAB向导界面，展示了如何打开现有的图形用户界面的数字文件。 <img alt="图5" fo:content-width="6in" src="/files/ftp_upload/51372/51372fig5highres.jpg" width="600" /> 图5：MATLAB指南界面示出了用于修改现有的GUI图形工具。 <ol start="3"><li>为了运行的图形用户界面，点击“运行”下的“工具“菜单。然后，单击“是”时，弹出窗口提示是否保存这个数字在运行前。一个新的窗口将显示修改后的GUI。 </li><li>如果必要，创建另一GUI，用于使用该图形用户界面，例如，一个不同的特定材料。 </li><li>要设置的例子来说，首先点击“选择输入模型文件”按钮，在界面的顶部，导航到“glasscube.inp”文件。选择该文件，然后单击“打开”，关闭浏览窗口。选定的输入文件和路径，以它现在应该出现在GUI窗口中的“选择输入模型文件”按钮（ 如图6）的权利。 </li></ol><img alt="图6" fo:content-width="6in" src="/files/ftp_upload/51372/51372fig6highres.jpg" width="600" /> 图6：使用图形用户界面来创建一个示例二氧化硅nanospring模式截图。 <ol start="6"><li>接下来，使用“浏览”按钮，在“输出模式”部分中浏览并选择目录到输出模式保存到。确保输出目录正在积极选择，以便为运行被激活，即使是已经列出在所附窗口给该按钮的右输出目录。 注意：列出的“提前参数最小距离”值（在图6 0.209311）中的具体计算为在本实施例中提供的“glasscube.inp”输入文件，并且应保留原样。这个值可以通过运行模型之前在此位置输入的“0”的值作为必要计算在第一次使用一个不同的输入文件。在本实施例中，所有的参数值是在相对单位来匹配输入的原子坐标系统。如果乘以0.716的参数值将代表纳米的距离。&lt;/ LI&gt; <li>按图形用户界面“运行”按钮使用R = 1.0，R = 5.0，P = 1.5，D = 0.209311给定弹簧的参数运行的例子。从MATLAB命令窗口中运行浏览反馈（ 图7）。在反馈中，检查弹簧参数被证实，该输入数据文件被成功地读出，并存储于指定的输出文件的结果“ 模型 ”中描述。 </li></ol><img alt="图7" fo:content-width="5in" src="/files/ftp_upload/51372/51372fig7highres.jpg" width="500" /> 图7：基于GUI的纳米弹簧的运行MATLAB命令窗口的反馈。 注：在上面的例子中，文件“ 模型 ”包含5176原子含有所希望的弹簧，每行一个，与所述第一行给出原子的总数目在该文件中。每一行定义的原子包括原子的ID，原子类型，以及x，y，该原子的Z轴坐标。 <ol start="8"><li>一旦GUI界面完成，用鼠标右键点击“Nanosprings.m”在MATLAB“当前文件夹”窗口中，执行连续运行，选择“运行”，直接调出GUI界面。 注：各种参考文献中列出了27-31基于MATLAB指南和其他信息的基本向导界面。 </li></ol> 3.在一个开放源码的展示台19验证NanospringCarver结果下面的步骤被设计用于可视化和验证由NanospringCarver创建的输出弹簧模型的一般用户。 <ol><li>使用NanospringCarver MATLAB GUI如上所述，生成的文件输入到可视化程序19。当运行可视化程序，使用“点coordin吃了文件“输入选项，按颜色区分原子类型，并选择一个轴网格边界的领域。 </li><li>测量的春款的距离，使他们的记录。 </li><li>比较实测数据对所需的弹簧尺寸及验证弹簧模型的准确性。 </li></ol> 4.使用纳米弹簧的拉伸MD模拟NanospringCarver结果下面的步骤归纳为使用由NanospringCarver作为输入所创建的弹簧模型，以常规的开放源码的MD代码32一般用户。 <ol><li>下载开源MD LAMMPS程序的最新版本。请参考手册和示例相关的在线文档。 </li><li>确定，以制备相应的初始堆积石英玻璃模型，如18之前报道的所需nanospring模型的尺寸。 </li><li>创建使用NanospringCarver MATLAB GUI所需nanospring模型（参见硒ction 2以上）。 </li><li>执行拉伸模拟所需的nanospring，通过拉伸该模型轴向11,13,23。产生nanospring模型的一个代表性的视频被拉伸（参见图8，下面，和动画图1），用于可视化和分析。关于几种nanospring模型在张力下的应力-应变行为和刚度科学结果已在别处23日报道。 </li></ol><img alt="图8" fo:content-width="4in" src="/files/ftp_upload/51372/51372fig8highres.jpg" width="400" /> 图8：拉伸模拟过程中的二氧化硅nanospring的屏幕 （也参见动画图1）。

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作者宣称，他们有没有竞争的财务权益。

修改原来的方法来创建导致两种不同的代码开发，使双方建立纳米带和纳米弹簧从最初的散装石英玻璃MD模式nanohelical结构。使用不同的软件包19-20，其内的程序的测量能力证实其尺寸精度的二氧化硅纳米带和nanospring模型的验证是追求的。还通过从不同的侧面和角度，这导致了额外的几何验证覆盖在模型进行纳米弹簧和纳米带的比较。由于其可扩展性，与任何散装材料模型的大小和潜在用?...

A correction was made to <a href="/video/51372">Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization</a>. Online article is missing its 29th author reference.
The reference section has added:
29. MathWorks. Use and create MATLAB MEX-files [Internet]. [Massachusetts]: MathWorks; [cited 2013 May 30]. Available from: http://
www.mathworks.com/help/matlab/call-mex-files-1.html (2014).

A correction was made to <a href="/video/51372">Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization</a>. Online article is missing its 29th author reference.

Erratum: Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization

螺旋形的纳米结构通常产生在实验室使用化学气相沉积技术1-2，而新的方法已经在文献中报道3。特别是纳米弹簧和纳米带进行了研究，因为其独特的性质和在传感器，光学和机电和流体装置4-7具有应用前景的。合成方法已被报道，以产生二氧化硅（SiO 2）的纳米带，使得这些结构潜在积木单元分层系统。三维硅纳米弹簧新的合成时使用ZnO 8或纳米颗粒用于诊断9-10涂扩大其应用到化学电阻。 在二氧化硅纳米弹簧和纳米带的力学性能试验研究很少，主要是由于在操作和测试方法和equipme电流限制新台币。调查的纳米结构和纳米弹簧的纳米力学使用的理论和模拟11-14已有报道。有些模拟13集中在非晶纳米弹簧的纳米力学行为，因为他们可以探索制度通过试验没有完全访问。金属纳米弹簧的原子论研究已在文献中报道，调查大小弹性特性15的依赖，以及最近的螺旋形的结晶二氧化硅的纳米结构的纳米力学14。也已在不同的材料进行nanospring结构的实验测试，如螺旋形的碳纳米结构和碳纳米卷16-17。尽管知识收集迄今为止，这些新的纳米结构的机械性能的更完整的理解是需要未来的纳米器件的制造工作。 由于二氧化硅克MD研究姑娘（非晶体硅）nanohelices还很有限，这种结构的原子建模需要创建自定义的代码。创建石英玻璃螺旋MD机型没有其他替代方法已经确定迄今在最近的文献检索。在这项工作中，一个自下而上的方法，以螺旋石英玻璃的纳米结构，包括纳米弹簧和纳米带的原子模型是对追求未来大规模MD纳米机械模拟。一般的处理方法包括建立一个MD“散”石英玻璃模型如先前报道18，并通过为此开发了两种强大的可适应的计算机代码雕刻出这种“批量”样不同的螺旋纳米结构。这两种计算方法提供了一个独特的方式创造纳米带和nanospring车型以极高的效率和原子论的细节;这些结构适合于大规模的原子论模拟。此外，定制的图形用户界面，用于促进建立所述螺旋结构的可视化。 最初在室温下创建的“散装”石英玻璃模型的结构。大规模的分子动力学模拟的进行使用Garofalini为此原子间作用势类似于以前的研究18，它是相对高效的计算，并适用于大系统。最初的“批量”石英玻璃的结构包括一个立方体的模型（14.3 X 14.3 X 14.3纳米3），其中包含192,000原子。的“散装”石英玻璃模型平衡在300K为0.5纳秒使用周期边界条件，得到的初始状态。 两种计算方法的设计和利用，以创造原子二氧化硅纳米带和nanospring车型。第一种方法包括雕刻出由硅石纳米带使用定义的螺旋线的参数方程的“散装”结构，其几何形状（间距，螺旋线的半径，和导线半径）。这个过程包括使用AWK编程语言，Linux操作系统，开源可视化软件19。一般的迭代过程来创建纳米带的原子论模型包括：（1）选择的原子中的“散装”石英玻璃模型，（2）计算从所选择的原子的距离的点在空间上的预先定义的螺旋形函数， （3）该距离进行比较，以所期望的纳米带的半径，和（4）丢弃或保持原子中的输出数据的模式。详细的一步一步的说明对这一方法包括在可扩展的开放式源 ​​代码补充材料 。用这种方法，使用不同的螺距，螺旋和纳米带的半径值半径，随后被测量创建了几个二氧化硅纳米带为防止与分子分析和可视化软件19-20所需的尺寸值精度。功能性几何形状（间距高价值和纳米带的半径值低）生成的二氧化硅纳米带的原子模型。一些伪像，由原子排除错误的，导致欠光滑纳米带表面，在非常高的纳米带的半径值和极低的音调值的变化。类似的方法已被用于在创建的二氧化硅纳米线21-23的过程。 这里介绍的第二种方法包括雕刻出的二氧化硅纳米弹簧从“本体”的二氧化硅结构通过实施预筛选方法，以提高效率，除了数学方程为一个螺旋线。这个过程需要创造一个更强大的C ++代码以允许在模拟这些螺旋形的纳米结构具有更大的灵活性。迭代方法创建atomis纳米弹簧的抽搐模型包括：（1）丢弃保证落在螺旋路径以外的所有原子，（2）确定性螺旋路径上选择一个点，（3）进行比较的特定距离内的所有原子到这个所选择的点，和（4 ）丢弃或存放在输出数据模型中的每个原子。甲一步一步说明对这一方法也被包括在补充材料。使用这种方法，几个二氧化硅nanospring模型具有不同的尺寸（半径线，螺旋线的半径，和nanospring的间距）中得到的可扩展开放式源 ​​代码在图1中所示的高精度石英nanospring模型，用该方法有效地获得，没有证据发现在极端的nanospring（低和高）的间距值的工件。的创建和使用此方法的图形用户界面中的协议部分中进行说明。 图1：表示特征尺寸，其中r，R和 P分别表示所述电线的半径，螺旋线的半径，和音调的一般螺旋结构 H表示螺旋结构23的总高度。 这个协议描述了如何准备NanospringCarver文件，一个LINUX 25电脑上运行的MATLAB 24，并 ​​使用图形用户界面来制备原子论nanospring模型。这些以前无法获得的模型作为基础，新的分子动力学（MD）模拟23对材料的创新研究。 一般的一步一步的过程来创建原子nanospring模型涉及到使用下列内容：（一）NanospringCarver（V 0.5测试版）的代码（开放式酸行政长官在C ++语言），（二）大宗石英玻璃模型（输入文件），（三）MATLAB的GUI界面和相关文件，并使用Linux的PC上的本地牌照（D）MATLAB软件（第7版）。项（a） - （c）项（NanospringCarver代码，石英玻璃模型，MATLAB GUI文件）可以自由地在网上下载26。 MATLAB（矩阵实验室）是一种高级语言进行数值计算，可视化，和来自MathWorks公司24，它主要用于数据可视化和分析，图像处理和计算生物学的应用程序开发。

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

scalable nanohelices for predictive studies and enhanced 3d visualization

弹簧状材料是无处不在的能量采集，储氢，以及生物传感应用纳米技术的兴趣的性质和。用于预测性模拟中，它已成为日益重要的是能够以nanohelices的结构精确地模拟。研究局部结构对这些复杂的几何形状必须制定切合实际的模型性能的影响。迄今为止，软件包相当有限，创造原子论螺旋模型。这项工作的重点是生产石英玻璃的原子模型（SiO 2）的纳米带和纳米弹簧的分子动力学（MD）模拟。使用“批量”石英玻璃，两种计算过程的MD模型来精确地产生纳米带和纳米弹簧的形状呈现。第一种方法采用AWK编程语言和开源软件来有效地瓜分二氧化硅纳米带的各种形状的我nitial批量模型，使用所需的尺寸和参数方程定义一个螺旋。用这种方法，可以为一系列音调值和尺寸来生成准确的原子论二氧化硅纳米带。第二种方法是一种更健壮的代码，它允许灵活地建模nanohelical结构。该方式利用特别写入执行预筛选方法以及数学方程为一个螺旋线，在创建nanospring模型时产生更大的精度和效率的C ++代码。使用这些代码，定义良好的和可扩展的纳米带和纳米弹簧适于原子仿真可以有效地创建。在两个开放源码的附加价值在于它们可适于再现不同螺旋结构，独立的材料制成。此外，一个MATLAB的图形用户界面（GUI），用于增强通过可视化和交互学习与原子论直升机一般用户CAL结构。这些方法的一个应用是nanohelices通过分子动力学模拟的最近研究了机械能收获的目的。

与第一计算过程（纳米带码）产生的原子论模型纳米带及其相关的尺寸如图9所示。使用的第二计算过程（纳米弹簧代码）和相关联的尺寸所得nanospring模型示于图10中 。 <img alt="图9" fo:content-width="5in" src="/files/ftp_upload/51372/51372fig9highres.jpg" width="500" /> 二氧化硅纳米带的图9原子论模型与所需尺寸：r（下...

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

Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization

nanohelical结构的精确建模是预测模拟研究导致了新的纳米技术应用很重要。目前，软件包和代码创建原子论螺旋模型的限制。我们提出旨在打造原子论nanohelical模型模拟两个程序，和一个图形界面，以提高通过可视化的研究。

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 ...

scalable-nanohelices-for-predictive-studies-enhanced-3d

Research

JoVE Journal

Engineering

10.4K 次观看.  University of California Merced.  nanohelical结构的精确建模是预测模拟研究导致了新的纳米技术应用很重要。目前，软件包和代码创建原子论螺旋模型的限制。我们提出旨在打造原子论nanohelical模型模拟两个程序，和一个图形界面，以提高通过可视化的研究。 

视频: Scalable Nanohelices for Predictive Studies and Enhanced 3D Visualization

High-resolution, High-speed, Three-dimensional Video Imaging with Digital Fringe Projection Techniques

Digital fringe projection (DFP) techniques provide dense 3D measurements of dynamically changing surfaces.&#160;Like the human eyes and brain, DFP uses triangulation between matching points in two views of the same scene at different angles to compute depth.&#160;However, unlike a stereo-based method, DFP uses a digital video projector to replace one of the cameras1. The projector rapidly projects a known sinusoidal pattern onto the subject, and the surface of the subject distorts these patterns in the camera&#8217;s field of view. Three distorted patterns (fringe images) from the camera can be used to compute the depth using triangulation.
Unlike other 3D measurement methods, DFP techniques lead to systems that tend to be faster, lower in equipment cost, more flexible, and easier to develop.&#160;DFP systems can also achieve the same measurement resolution as the camera.&#160;For this reason, DFP and other digital structured light techniques have recently been the focus of intense research (as summarized in1-5). Taking advantage of DFP, the graphics processing unit, and optimized algorithms, we have developed a system capable of 30&#160;Hz 3D video data acquisition, reconstruction, and display for over 300,000 measurement points per frame6,7.&#160;Binary defocusing DFP methods can achieve even greater speeds8.
Diverse applications can benefit from DFP techniques. Our collaborators have used our systems for facial function analysis9, facial animation10, cardiac mechanics studies11, and fluid surface measurements, but many other potential applications exist.&#160;This video will teach the fundamentals of DFP techniques and illustrate the design and operation of a binary defocusing DFP system.

This video describes the fundamentals of digital fringe projection techniques, which provide dense 3D measurements of dynamically changing surfaces.&#160;It also demonstrates the design and operation of a high-speed binary defocusing system based on these techniques.

Digital fringe projection (DFP) techniques provide dense 3D measurements of dynamically changing surfaces.&#160;Like the human eyes and brain, DFP uses ...

科研

工程学

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 ...

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.

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 ...

Micro-masonry for 3D Additive Micromanufacturing

Transfer printing is a method to transfer solid micro/nanoscale materials (herein called &#8216;inks&#8217;) from a substrate where they are generated to a different substrate by utilizing elastomeric stamps. Transfer printing enables the integration of heterogeneous materials to fabricate unexampled structures or functional systems that are found in recent advanced devices such as flexible and stretchable solar cells and LED arrays. While transfer printing exhibits unique features in material assembly capability, the use of adhesive layers or the surface modification such as deposition of self-assembled monolayer (SAM) on substrates for enhancing printing processes hinders its wide adaptation in microassembly of microelectromechanical system (MEMS) structures and devices. To overcome this shortcoming, we developed an advanced mode of transfer printing which deterministically assembles individual microscale objects solely through controlling surface contact area without any surface alteration. The absence of an adhesive layer or other modification and the subsequent material bonding processes ensure not only mechanical bonding, but also thermal and electrical connection between assembled materials, which further opens various applications in adaptation in building unusual MEMS devices.

This paper introduces a 3D additive micromanufacturing strategy (termed &#8216;micro-masonry&#8217;) for the flexible fabrication of microelectromechanical system (MEMS) structures and devices. This approach involves transfer printing-based assembly of micro/nanoscale materials in conjunction with rapid thermal annealing-enabled material bonding techniques.

微砌筑的3D添加剂Micromanufacturing

Transfer printing is a method to transfer solid micro/nanoscale materials (herein called &#8216;inks&#8217;) from a substrate where they are generated to ...

Surface Enhanced Raman Spectroscopy Detection of Biomolecules Using EBL Fabricated Nanostructured Substrates

Fabrication and characterization of conjugate nano-biological systems interfacing metallic nanostructures on solid supports with immobilized biomolecules is reported. The entire sequence of relevant experimental steps is described, involving the fabrication of nanostructured substrates using electron beam lithography, immobilization of biomolecules on the substrates, and their characterization utilizing surface-enhanced Raman spectroscopy (SERS). Three different designs of nano-biological systems are employed, including protein A, glucose binding protein, and a dopamine binding DNA aptamer. In the latter two cases, the binding of respective ligands, D-glucose and dopamine, is also included. The three kinds of biomolecules are immobilized on nanostructured substrates by different methods, and the results of SERS imaging are reported. The capabilities of SERS to detect vibrational modes from surface-immobilized proteins, as well as to capture the protein-ligand and aptamer-ligand binding are demonstrated. The results also illustrate the influence of the surface nanostructure geometry, biomolecules immobilization strategy, Raman activity of the molecules and presence or absence of the ligand binding on the SERS spectra acquired.

We describe the fabrication and characterization of nano-biological systems interfacing nanostructured substrates with immobilized proteins and aptamers. The relevant experimental steps involving lithographic fabrication of nanostructured substrates, bio-functionalization, and surface-enhanced Raman spectroscopy (SERS) characterization, are reported. SERS detection of surface-immobilized proteins, and probing of protein-ligand and aptamer-ligand binding is demonstrated.

表面增强拉曼光谱检测生物分子利用EBL装配纳米衬底

Fabrication and characterization of conjugate nano-biological systems interfacing metallic nanostructures on solid supports with immobilized biomolecules ...

3D Printing of Biomolecular Models for Research and Pedagogy

The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D structures are most often perceived using the two-dimensional and exclusively visual medium of the computer screen. Converting digital 3D molecular data into real objects enables information to be perceived through an expanded range of human senses, including direct stereoscopic vision, touch, and interaction. Such tangible models facilitate new insights, enable hypothesis testing, and serve as psychological or sensory anchors for conceptual information about the functions of biomolecules. Recent advances in consumer 3D printing technology enable, for the first time, the cost-effective fabrication of high-quality and scientifically accurate models of biomolecules in a variety of molecular representations. However, the optimization of the virtual model and its printing parameters is difficult and time consuming without detailed guidance. Here, we provide a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy using open source or low-cost software and low-cost 3D printers that use fused filament fabrication technology.

Physical models of biomolecules can facilitate an understanding of their structure-function for the researcher, aid in communication between researchers, and serve as an educational tool in pedagogical endeavors. Here, we provide detailed guidance for the 3D printing of accurate models of biomolecules using fused filament fabrication desktop 3D printers.

生物分子模型的3D打印技术的研究与教学

The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D ...

Scalable Solution-processed Fabrication Strategy for High-performance, Flexible, Transparent Electrodes with Embedded Metal Mesh

Here, the authors report the embedded metal-mesh transparent electrode (EMTE), a new transparent electrode (TE) with a metal mesh completely embedded in a polymer film. This paper also presents a low-cost, vacuum-free fabrication method for this novel TE; the approach combines lithography, electroplating, and imprint transfer (LEIT) processing. The embedded nature of the EMTEs offers many advantages, such as high surface smoothness, which is essential for organic electronic device production; superior mechanical stability during bending; favorable resistance to chemicals and moisture; and strong adhesion with plastic film. LEIT fabrication features an electroplating process for vacuum-free metal deposition and is favorable for industrial mass production. Furthermore, LEIT allows for the fabrication of metal mesh with a high aspect ratio (i.e., thickness to linewidth), significantly enhancing its electrical conductance without adversely losing optical transmittance. We demonstrate several prototypes of flexible EMTEs, with sheet resistances lower than 1 &#937;/sq and transmittances greater than 90%, resulting in very high figures of merit (FoM) &#8211; up to 1.5 x 104 &#8211; which are amongst the best values in the published literature.

This protocol describes a solution-based fabrication strategy for high-performance, flexible, transparent electrodes with fully-embedded, thick metal mesh. Flexible transparent electrodes fabricated by this process demonstrate among the highest reported performances, including ultra-low sheet resistance, high optical transmittance, mechanical stability under bending, strong substrate adhesion, surface smoothness, and environmental stability.

具有嵌入式金属网的高性能，灵活，透明电极的可扩展解决方案处理制造策略

Here, the authors report the embedded metal-mesh transparent electrode (EMTE), a new transparent electrode (TE) with a metal mesh completely embedded in a ...

Scalable Quantum Integrated Circuits on Superconducting Two-Dimensional Electron Gas Platform

To form a coherent quantum transport in hybrid superconductor-semiconductor (S-Sm) junctions, the formation of a homogeneous and barrier-free interface between two different materials is necessary. The S-Sm junction with high interface transparency will then facilitate the observation of the induced hard superconducting gap, which is the key requirement to access the topological phases (TPs) and observation of exotic quasiparticles such as Majorana zero modes (MZM) in hybrid systems. A material platform that can support observation of TPs and allows the realization of complex and branched geometries is therefore highly demanding in quantum processing and computing science and technology. Here, we introduce a two-dimensional material system and study the proximity induced superconductivity in semiconducting two-dimensional electron gas (2DEG) that is the basis of a hybrid quantum integrated circuit (QIC). The 2DEG is a 30 nm thick In0.75Ga0.25As quantum well that is buried between two In0.75Al0.25As barriers in a heterostructure. Niobium (Nb) films are used as the superconducting electrodes to form Nb- In0.75Ga0.25As -Nb Josephson junctions (JJs) that are symmetric, planar and ballistic. Two different approaches were used to form the JJs and QICs. The long junctions were fabricated photolithographically, but e-beam lithography was used for short junctions&#8217; fabrication. The coherent quantum transport measurements as a function of temperature in the presence/absence of magnetic field B are discussed. In both device fabrication approaches, the proximity induced superconducting properties were observed in the In0.75Ga0.25As 2DEG. It was found that e-beam lithographically patterned JJs of shorter lengths result in observation of induced superconducting gap at much higher temperature ranges. The results that are reproducible and clean suggesting that the hybrid 2D JJs and QICs based on In0.75Ga0.25As quantum wells could be a promising material platform to realize the real complex and scalable electronic and photonic quantum circuitry and devices.

Quantum integrated circuits (QICs) consisting of array of planar and ballistic Josephson junctions (JJs) based on In0.75Ga0.25As two-dimensional electron gas (2DEG) is demonstrated. Two different methods for fabrication of the two-dimensional (2D) JJs and QICs are discussed followed by the demonstration of quantum transport measurements in sub-Kelvin temperatures.

超导二维电子气体平台上的可扩展量子集成电路

To form a coherent quantum transport in hybrid superconductor-semiconductor (S-Sm) junctions, the formation of a homogeneous and barrier-free interface ...

Scalable Stamp Printing and Fabrication of Hemiwicking Surfaces

Hemiwicking is a process where a fluid wets a patterned surface beyond its normal wetting length due to a combination of capillary action and imbibition. This wetting phenomenon is important in many technical fields ranging from physiology to aerospace engineering. Currently, several different techniques exist for fabricating hemiwicking structures. These conventional methods, however, are often time consuming and are difficult to scale-up for large areas or are difficult to customize for specific, nonhomogeneous patterning geometries. The presented protocol provides researchers with a simple, scalable, and cost-effective method for fabricating micro-patterned hemiwicking surfaces. The method fabricates wicking structures through the use of stamp printing, polydimethylsiloxane (PDMS) molding, and thin-film surface coatings. The protocol is demonstrated for hemiwicking with ethanol on PDMS micropillar arrays coated with a 70 nm thick aluminum thin-film.

A simple protocol is provided for the fabrication of hemiwicking structures of varying sizes, shapes, and materials. The protocol uses a combination of physical stamping, PDMS molding, and thin-film surface modifications via common materials deposition techniques.

可缩放邮票印刷及不堪砌面的制作

Hemiwicking is a process where a fluid wets a patterned surface beyond its normal wetting length due to a combination of capillary action and imbibition. ...

3D Printing - Evaluating Particle Emissions of a 3D Printing Pen

Three-dimensional (3D) printing as a type of additive manufacturing shows continuing increase in application and consumer popularity. The fused filament fabrication (FFF) is an inexpensive method used most frequently by consumers. Studies with 3D printers have shown that during the printing process particulate and volatile substances are released. Handheld 3D printing pens also use the FFF method but the consumer&#8217;s proximity to the 3D pens gives reason to higher exposure compared to a 3D printer. At the same time, 3D printing pens are often marketed for children who could be more sensitive to the printing emission. The aim of this study was to implement a low cost method to analyze the emissions of 3D printing pens. Polylactide (PLA) and acrylonitrile butadiene styrene (ABS) filaments of different colors were tested. In addition, filaments containing metal and carbon nanotubes (CNTs) were analyzed. An 18.5 L chamber and sampling close to the emission source was used to characterize emissions and concentrations near the breathing zone of the user.
Particle emissions and particle size distributions were measured and the potential release of metal particles and CNTs investigated. Particle number concentrations were found in a range of 105 - 106 particles/cm3, which is comparable to previous reports from 3D printers. Transmission electron microscopy (TEM) analysis showed nanoparticles of the different thermoplastic materials as well as of metal particles and CNTs. High contents of metal were observed by inductively coupled plasma mass spectrometry (ICP-MS).
These results call for a cautious use of 3D pens due to potential risk to the consumers.

This protocol presents a method to analyze the emission of 3D printing pens. Particle concentration and particle size distribution of the released particle is measured. Released particles are further analyzed with transmission electron microscopy (TEM). Metal content in filaments is quantified by inductively coupled plasma mass spectrometry (ICP-MS).

3D 打印 - 评估 3D 打印笔的粒子排放

Three-dimensional (3D) printing as a type of additive manufacturing shows continuing increase in application and consumer popularity. The fused filament ...