本研究使用了先进光源的资源, 这是一个能源部的科学用户设施根据合同没有。DE-AC02-05CH11231。我们还想确认 Drs. l. Dobrzhinetskaya 和罗伊为碳硅石样品提供了帮助, c. 斯图尔特为她的橄榄蜗牛壳数据, h. 沈为橄榄蜗牛壳的准备, 和周和陈教授对橄榄蜗牛的 EDS 测量壳。

1. 设置光束线和收集数据
注: 校准标准和样品以同样的方式收集, 主要区别在处理方法。
<ol><li>装上样品并关闭实验箱。
	<ol>
<li>将一个样本附加到运动底座的上半部分 (见材料表), 这样, ROI 相对于底座垂直偏移至少15毫米。 注: 标准块存在于光束线中, 用于样品 < 20 毫米厚。运动学基础的下半部分永久安装在光束线的舞台系统上。</li>
		<li>将样品和底座放在实验箱内的舞台顶部。关闭实验笼。</li>
	</ol></li>
	<li>打开光束线控制和数据采集软件。
	<ol>
<li>打开光束线控制程序。单击左上角的箭头以初始化程序。等待右侧的所有信号灯变绿, 表示软件已初始化。</li>
		<li>单击任何光束线组件以初始化该组件的控制面板。这主要适用于翻译阶段和狭缝控制。</li>
		<li>从桌面上初始化 x 射线衍射扫描软件。 注意: 只有在光束线控件程序完全打开后才能进行此操作, 否则程序无法正确通信, 映射过程将无法正常工作。</li>
	</ol></li>
	<li>将样品带入 x 射线束的焦距。
	<ol>
<li>通过点击标记为 "激光" 的按钮打开对准激光器。</li>
		<li>通过使用 "舞台对齐" 菜单并单击向上和向下箭头, 将样本的 ROI 在粗略对准摄像机的近似视觉焦点内, 平移上 x、y 和 z 阶段。通过键入所需的值, 调整每台电机可以慢速行驶的距离。 注意: 这些阶段是机动和控制与光束线软件。</li>
		<li>在看细对焦相机时, 平移上 z 马达, 直到激光光斑与屏幕上的标记对齐。 注意: 如果对每个样本执行这种机动操作, 所有采样到探测器的参数将保持不变。</li>
	</ol></li>
	<li>选择白色 (多色) 光或单色模式。
	<ol>
<li>在实验箱入口处的轧辊缝, 以确定最终的焦点 demagnification, 从而在样品上的光束大小。注意: 它们作为 x 射线的源点, 在聚焦于单色器下游的一组 KB 镜像之前。卷缝尺寸可以增加, 以增加流量 (例如在单色模式) 的费用增加的横梁尺寸的样品。</li>
		<li>确保使用正确的辊缝设置: 8 µm x 16 µm 为白色光束应用或100µm x 100 µm 为单色应用。</li>
		<li>对于在单色模式下进行的实验, 在增加辊缝尺寸之前, 在6000和 2.2万 eV 之间输入能量, 将单色仪移动到所需的能量。</li>
	</ol></li>
	<li>使用预聚焦 M201 镜调整光束强度。
	<ol>
<li>打开控制菜单, 进入马达 |显示。从马达列表中选择M201 间距。在5计数增量中慢跑, 直到离子腔 (IC) 计数值最大化为止。</li>
		<li>马达有很长的反弹, 所以慢慢地执行这个过程。</li>
	</ol></li>
	<li>使用 XRF 绘制样本。
	<ol>
<li>从扫描中初始化荧光映射|x 射线扫描菜单。将 XRF 测量的文件名和文件夹位置更改为正确的名称。</li>
		<li>增加8元素的兴趣, 通过键入在2-20 凯文之间的能量范围, 其中包括一个主要的发射线的特定元素。 注: 如果系统在单色模式下运行, 则元素能量范围必须至少为1凯文以下的单色能量用于产生荧光线, 以诱导荧光过程 (见 Beckhoff等。16)。</li>
		<li>使用上 x 和 y 马达, 定义一个矩形区域, 映射将通过使用舞台软件驱动到两个对立的角来进行。在 "设置" 菜单中单击 "设置为当前 Pos ", 将它们设置为开始和结束位置。 注: 地图可在各阶段的行程限制范围内任意大小。</li>
		<li>输入扫描的速度或停留时间。通过按 "开始" 和 "结束" 按钮, 验证映射是否覆盖了示例的 ROI, 以查看已选择用于定义映射的对角相反的角。</li>
		<li>单击 "开始" 按钮开始扫描。此时, 将继续测量, 直到扫描完所有点。 注意: 该程序将保存值的文本文件, 其中每一行对应于一个马达位置, 每列对应的读数, 如电机, 总输入光束强度, 测量元素强度等.这些可以在任何 replotted图形程序。测量程序还实时显示元素映射。</li>
	</ol></li>
	<li>用 x 射线衍射图来绘制样品。
	<ol>
<li>在 x 射线衍射扫描窗口中键入数据收集过程的用户名, 以生成要在其中写入所有数据的主文件夹。</li>
		<li>键入示例名称。 注意: 该示例的所有衍射模式都将位于该名称的文件夹中, 并且它们将被标记为 sample_name_xxxxx. tif, 其中的 xxxx 是一个数字字符串, 通常从00001开始。</li>
		<li>确保选择 "上 x" 和 "上 Y" 作为 X 和 Y 扫描马达。该系统的设计, 以扫描许多可用的光束线马达, 取决于正在进行的实验类型。对于大多数情况, 扫描将执行 xy, xz, 或在单色能量 (映射单晶峰值位置; 这是一个1D 扫描)。</li>
		<li>键入地图的 x 和 y 的起始位置和终点。</li>
		<li>键入 x 和 y 步长, 以及模式曝光时间。 注: 使用全白光束进行的单晶扫描速度更快, 因为光束通量是比单色扫描大的数量级。因此, 单晶模式的暴露倾向于 < 1 秒, 而单色扫描曝光 (如粉末衍射) 往往是 > 十年代。输入步骤大小和曝光时间后, 程序将估计收集整个地图所需的总扫描时间。</li>
		<li>单击 "播放" 按钮启动映射。 注意: 该程序现在将自动移动到指定的马达位置/地图像素并记录一个衍射图案, 然后通过每个像素进行进度, 直到映射完全记录为. tif 文件序列。</li>
	</ol></li>
</ol>2. 使用光束线开发的 X 射线 Microdiffraction 分析软件 (圣诞)17的工艺数据
<ol><li>加载模式
	<ol>
<li>打开圣诞节17。通过进入文件来加载衍射图案|加载图像并选择一个模式。通过图像来减去探测器的背景|适合和删除背景。</li>
		<li>通过参数来加载校准文件|校准参数。单击 "加载校验" 并选择适当的校准参数文件。 注: 校准参数文件将包含诸如像素大小比 (始终固定)、探测器距离 (采样点和检测中心之间的焦距)、探测器角位置、xcent (x 探测器中心) 等信息,ycent (在 y 的探测器中心), 音高, 偏航, 和滚动的探测器, 样本方向, 以及波长, 如果使用单色光。</li>
	</ol></li>
	<li>处理单晶数据。
	<ol>
<li>索引模式<ol>
<li>通过参数来加载标准的晶体结构文件 (. cri) |晶体结构并选择合适的文件。如果必须计算应力值, 则加载刚度文件 (. stf), 其中包含材料的三阶弹性张量矩阵。 注意:. cri 文件将包含空间组号、所有六格参数、威科夫原子位置和原子类型的数目、分数坐标和旺季。</li>
			<li>要计算晶粒方向, 请转到参数 |劳厄的晶体取向参数。在平面和平面方向上键入 "hkl 平面法线"。</li>
			<li>通过分析来查找示例峰值|峰值搜索。<ol>
<li>根据衍射模式的强度, 选择一个峰值阈值 (例如,信号/噪声比) 到介于5和50之间的值。</li>
				<li>单击 "转到" 按钮以启动峰值搜索。添加任何未被程序选中的峰值, 并删除任何死峰。</li>
			</ol>
</li>
			<li>通过分析来初始化索引|劳厄索引。</li>
		</ol>
</li>
		<li>确定应变和/或应力。<ol>
<li>如果不需要量化压力, 请跳过此步骤。否则, 转到参数 |晶体结构和加载与晶体结构相关的刚度文件 (. stf)。 注: 该文件由三阶刚度张量矩阵组成, 用于特定材料。示例提供了圣诞软件。</li>
			<li>选择应力参数。<ol>
<li>转到参数 |应变/校准劳厄细化参数。一个新的窗口将打开, 与校准参数的实验系统在右侧和应变细化参数的左侧。</li>
				<li>为样品选择适当的应变细化参数。</li>
				<li>如果需要对晶体方向进行细化, 请确保还选择了 "细化方向" 框。</li>
			</ol>
</li>
			<li>通过分析来初始化应变计算|应变细化/校准。</li>
		</ol>
</li>
		<li>计算并显示2D 地图。<ol>
<li>从自动化分析中打开分析过程|设置劳厄模式的自动分析。将会打开一个新窗口。<ol>
<li>在 "图像文件参数" 下, 单击 "..." 按钮, 然后选择映射序列中的第一个文件。在 "结束工业" 下, 输入序列中最后一个文件的编号。该步骤通常设置为1。如果这是真的, # 点现在应该是地图像素的总数量。在 "保存文件参数" 下, 输入文件名。 注意: 可以忽略该路径, 因为在群集计算的情况下不会读取它。</li>
				<li>设置 NERSC 参数。<ol>
<li>在 " NERSC 目录" 下, 键入用户目录。当用户从 NERSC 中征求群集访问权限时, 将分配此项。</li>
					<li>在 "图像目录" 下, 输入数据当前所在的群集上的文件位置。</li>
					<li>在 "保存目录" 下, 输入要保存处理的文件的群集上的文件位置。</li>
					<li>在 " Nb" 节点下, 输入要用于计算的节点数。 注意: 映射点的总数应由节点数整除。</li>
					<li>单击 "创建 NERSC 文件" 以生成指令文件并保存它。此文件将以. dat 格式。</li>
				</ol>
</li>
			</ol>
</li>
			<li>将. dat 文件上载到 NERSC 群集。 注意: 通常, 这是通过数据传输程序 (如 WinSCP) 完成的。</li>
			<li>从终端窗口 (登录到 NERSC 帐户), 运行可执行文件 XMASparamsplit_new .exe。出现提示时, 键入 NERSC 文件的名称。 注意: 程序现在将执行, 节点将被分配来按顺序处理每个图像文件。节点完成计算后, 数据将被添加到名为 "示例名称" 的序列文件中. 将. 序列文件复制到本地计算机。</li>
			<li>打开. 序列号文件。<ol>
<li>在圣诞节, 点击分析 |读取分析顺序列表。这将打开一个新窗口。</li>
				<li>通过单击 "加载为", 然后从本地计算机中选择. 序列文件, 加载. 序列号列表。</li>
				<li>点击显示显示地图;这将打开一个新窗口。要选择哪个列将对应于 2D z 图的 z 值, 请从下拉菜单中选择它。</li>
				<li>若要导出数据, 请单击 "另存为" 列表, 另存为 .txt 或. dat 文件。 注意: 如果需要, 此文件的内容可以上载到另一个绘图程序中。</li>
			</ol>
</li>
		</ol>
</li>
	</ol></li>
	<li>处理粉末衍射数据。 注: 有几种不同类型的分析可能。这些下降大致分为三个不同的类别: 完整模式的整合, 在 2θ, 映射相分布使用一个典型的峰值, 一个特定的阶段, 或映射的首选方向的一个峰值。<ol>
<li>将整个模式整合为2θ的功能。<ol>
<li>转到分析 |2theta 集成。选择一个覆盖图案中的角度的2θ范围, 可以通过悬停在图案的任何像素上并读取显示的2θ值来找到。</li>
			<li>选择χ (方位) 范围。 注意: 在这里, 可以选择整个方位范围, 或者只是某些区域, 具体取决于用户的喜好。</li>
			<li>单击 "转到集成"。单击 "保存" 以保存模式。</li>
		</ol>
</li>
		<li>通过在2θ上集成一个峰值并将其映射到2D 地图, 来映射相位位置。<ol>
<li>选择2θ和χ范围, 如上一步所列 (但此时间仅限于整个模式的子集)。 注: 通常只有一个峰值, 代表特定阶段的兴趣, 被选中。理想的峰值预计不会与其他阶段重叠。</li>
			<li>选择合适的函数 (高斯或洛伦兹), 然后单击 "转到" 按钮以适应峰值。在继续之前, 请确保合适的情况良好。</li>
			<li>要映射相位位置, 请转到 "自动分析" | "设置 twotheta 分析;将会打开一个新窗口。选择路径、开始和结束编号以及结果文件名, 然后单击箭头开始扫描。 注意: 该程序现在将映射每个模式上的以前适合的峰值, 并将映射峰值的强度、宽度、位置和 d 间距记录到结果文件中。然后, 生成的文件 (通常是文本文件) 可以上载到任何绘图程序中, 并由用户绘制。</li>
		</ol>
</li>
		<li>通过在χ中集成一个峰值并在2D 地图上映射, 来映射首选方向。<ol>
<li>转到分析 |沿 Chi 积分。将会打开一个新窗口。与以前一样, 选择覆盖峰值的2θ和χ范围, 以显示首选方向。</li>
			<li>选择合适的函数 (高斯或洛伦兹), 然后按 "转到" 按钮进行调整。 注意: 该程序现在将χ分成几个箱, 并将计算每个 bin 在指定的2θ范围内的总强度。结果将是一个情节的强度作为χ的功能。当合适时, 它会指示最高强度的角方向。</li>
			<li>要映射所有文件, 请转到 "自动分析" | "设置阶段-chi 分析。选择路径、开始和结束编号以及结果文件名, 然后单击箭头开始扫描。 注意: 该程序将在所有模式下映射相同的峰值, 并生成一个包含结果的文本文件, 作为马达位置的函数。然后可以在任何绘图程序中绘制这些图。</li>
		</ol>
</li>
	</ol></li>
</ol>

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A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nacre+tablet+thickness+records+formation+temperature+in+modern+and+fossil+shells.">Nacre tablet thickness records formation temperature in modern and fossil shells.</a> Earth Planet Sc Lett. 460, 281-292 (2017).</li><li>Mass, T., 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=Amorphous+calcium+carbonate+particles+form+coral+skeletons.">Amorphous calcium carbonate particles form coral skeletons.</a> P Natl Acad Sci. 114 (37), E7670-E7678 (2017).</li><li>Marcus, M. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Parrotfish+Teeth:+Stiff+Biominerals+Whose+Microstructure+Makes+Them+Tough+and+Abrasion-Resistant+To+Bite+Stony+Corals.">Parrotfish Teeth: Stiff Biominerals Whose Microstructure Makes Them Tough and Abrasion-Resistant To Bite Stony Corals.</a> ACS Nano. 11 (12), 11856-11865 (2017).</li><li>Kunz, M., 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=A+dedicated+superbend+x-ray+microdiffraction+beamline+for+materials,+geo-,+and+environmental+sciences+at+the+advanced+light+source.">A dedicated superbend x-ray microdiffraction beamline for materials, geo-, and environmental sciences at the advanced light source.</a> Rev Sci Instrum. 80 (3), 035108 (2009).</li><li>Beckhoff, B., Kanngie&#223;er, B., Langhoff, N., Wedell, R., Wolff, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Handbook of Practical X-Ray Fluorescence Analysis. , (2007).</li><li>Tamura, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=XMAS:+A+Versatile+Tool+for+Analyzing+Synchrotron+X-ray+Microdiffraction+Data.">XMAS: A Versatile Tool for Analyzing Synchrotron X-ray Microdiffraction Data.</a> Strain and Dislocation Gradients from Diffraction. , 125-155 (2014).</li><li>Dobrzhinetskaya, L., 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=Moissanite+(SiC)+with+metal-silicide+and+silicon+inclusions+from+tuff+of+Israel:+Raman+spectroscopy+and+electron+microscope+studies.">Moissanite (SiC) with metal-silicide and silicon inclusions from tuff of Israel: Raman spectroscopy and electron microscope studies.</a> Lithos. , (2017).</li><li>Thibault, N. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Morphological+and+structural+crystallography+and+optical+properties+of+silicon+carbide+(SiC):+Part+II:+Structural+crystallography+and+optical+properties.">Morphological and structural crystallography and optical properties of silicon carbide (SiC): Part II: Structural crystallography and optical properties.</a> American Mineralogist. 29 (9-10), 327-362 (1944).</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=.">.</a> Electron Backscatter Diffraction in Materials Science. , (2009).</li></ol>

作者没有什么可透露的。

我们提出了一种联合 x 射线衍射和 XRF 分析的晶体样品在 ALS 光束线12.3.2 的方法。虽然劳厄衍射、粉末衍射和 XRF 本身都不是新颖的方法, 但光束线12.3.2 结合了微米尺度的 x 射线光束大小、扫描阶段系统与探测器曝光触发相关联, 并全面分析软件, 以允许在实验室仪器上不可能的实验。光束线中的光子通量比实验室仪器所能达到的数量级要高一些。此外, 典型的劳厄衍射实验室仪器仅设计用于单晶体...

晶体样品经常显示微米尺度上的异质性。在地球科学中, 矿物的识别, 它们的晶体结构, 以及它们在2D 系统中的相位关系, 对于理解一个特定系统的物理和化学是很重要的, 需要一个空间分辨的定量技术。例如, 可以根据局部2D 区域内的相分布来检查矿物之间的关系。这可能会影响到在岩石体内可能发生的历史和化学相互作用。或者, 一个单一矿物的物质结构可以被审查;这可能决定矿物可能已经或目前正在遭受的变形类型 (例如, 在原位变形实验的情况下, 像钻石铁砧单元的设备)。在地学中, 这些分析通常是使用扫描电子显微镜 (SEM) 与能量或波长色散 x 射线光谱 (E/WDS) 和电子背向散射衍射 (EBSD) 相结合进行的。然而, 样品的制备可能是困难的, 涉及广泛的抛光和安装真空测量。此外, EBSD 是一种表面技术, 需要相对浊的晶体, 这并不总是情况下, 地质材料可能经历了隆起, 侵蚀, 或压缩。
使用 2D x 射线 microdiffraction 和 XRF 映射的空间分辨特性, 如 ALS 的光束线12.3.2 所提供的, 是一种快速而直接的方法, 用于制作单个或多相系统的大面积图, 其中晶体尺寸在少量纳米 (在多晶样品的情况下) 到上百个微米。与其他常用技术相比, 该方法具有许多优点。不同于其他2D 晶体制图技术, 如 EBSD, microdiffraction 样品可以测量在环境条件下, 因此不需要特殊的准备, 因为没有真空室。Microdiffraction 适用于原始的水晶, 以及那些经历过严重的应变或塑性变形的晶体。像薄切片这样的样品通常被检查, 如嵌在环氧树脂中的材料, 甚至是不变的岩石或谷物。数据收集速度快, 通常小于0.5 秒/像素的劳厄衍射, 不到1分钟/像素的粉末衍射, 和小于 0.1 s/像素的 XRF。数据存储在本地, 临时存放在本地存储上, 并且更永久性地保存在国家能源研究科学计算 (NERSC) 中心, 便于下载。衍射数据处理可以在局部群上或 NERSC 群中进行, 在20分钟以下。这使得数据收集和分析的快速吞吐量, 以及与实验室仪器相比, 在短时间内进行大面积测量。
该方法具有广泛的应用价值, 在材料科学和工程中得到了广泛应用, 分析了从3维印刷金属1、2到太阳能电池板变形3的各种情况, 以应变拓扑材料4, 到记忆合金相变5, 到高压行为的纳米晶材料6,7。最近的地球科学项目包括分析各种石英样品中的应变8,9的火山胶凝过程10,11, 以及生物矿物, 如方解石和文石在壳和珊瑚12,13或磷灰石在牙齿14, 和额外的研究陨石相分布, 矿物结构识别的新矿物, 和塑性变形响应的高压二氧化硅也被收集。在光束线12.3.2 使用的技术适用于范围广泛的样品, 与矿物学或岩石学群落中的任何人有关。在这里, 我们概述了光束线12.3.2 的数据采集和分析协议, 并提出了几个应用, 以证明联合 XRF 和劳厄/粉 microdiffraction 技术在地球科学领域的实用性。
在进入实验细节之前, 讨论终端站的设置 (参见图 1和图 4中的 Kunz等) 是密切相关的。15). x 射线光束退出储存环, 并使用环形镜 (M201) 定向, 其目的是将光源重新聚焦在实验笼的入口处。它通过一组辊缝, 作为一个次要的来源点。然后 monochromatized (或不) 取决于实验类型, 然后通过一组克里斯·柯克帕特里克-贝兹 (KB) 镜像, 在通过第二套狭缝并聚焦于微米尺寸。然后光束通过一个离子室, 其信号用于确定光束强度。附着在离子室是一个针孔, 它阻止散射信号撞击到探测器上。聚焦光束然后遇到样本。样品放在一个舞台的顶部, 由8马达组成: 一组粗 (下) x, y, z 马达, 一组精细 (上部) x, y, z 马达, 和两个旋转马达 (Φ和χ)。它可以可视化与三光学摄像头: 一个低变焦, 放置在离子室的顶部, 一个具有高变焦, 放置在一个近似45°角度的 x 射线光束的平面上, 和第二个高变焦相机放置在90°角度, 关于 tx 射线光束。最后一个最适合垂直方向的样品 (例如, 用于传输模式实验), 而成像是使用附着在针孔上的楔形镜面进行的。x 射线衍射探测器位于较大的旋转阶段, 可控制探测器的角度和垂直位移。还存在一种用于收集 XRF 的硅漂移探测器。样品可以以任何方式制备, 只要所暴露的感兴趣区域 (ROI) 是平坦的 (在微米级), 并发现或覆盖在不超过50-100 µm 的 x 射线透明材料, 如聚酰亚胺胶带。
下面概述的过程描述了在反射几何中发生的实验, 并假定 z 方向是正常的样本, x 和 y 分别是水平和垂直扫描方向。然而, 由于舞台和探测器系统的灵活性, 在传输几何中进行了一些实验, 其中 x 和 z 方向为水平和垂直扫描方向, y 与直接光束平行 (见杰克逊等等。10,11)。

<table><tbody><tr><td>ThorLabs KB3x3 kinematic base, top half</td><td>ThorLabs</td><td>KBT3X3</td><td>Several of these bases are available for borrowing. The base must be the imperial and not the metric type, otherwise it will not properly fit on the stage.</td></tr><tr><td>Scotch double sided tape</td><td></td><td></td><td>Available at any office supply store, and also at the beamline</td></tr><tr><td>Polyimide/Kapton tape</td><td>Dupont</td><td></td><td>Several widths are commercially available. Any width that is enough to cover the sample is fine.</td></tr><tr><td>Samples</td><td></td><td></td><td>Provided by user, site of interest should be polished if larger mapping is desired.</td></tr><tr><td>Software: XMAS</td><td></td><td></td><td>Downloadable here https://sites.google.com/a/lbl.gov/bl12-3-2/user-resources</td></tr><tr><td>Software: IDL 6.2</td><td>Harris Geospatial Solutions</td><td></td><td></td></tr><tr><td>X-ray Diffraction Detector</td><td>DECTRIS Pilatus 1M&amp;nbsp;</td><td></td><td>hybrid pixel array detector</td></tr><tr><td>Huber stage</td><td></td><td></td><td>stage for detector</td></tr><tr><td>Vortex silicon drift detector&amp;nbsp;</td><td></td><td></td><td>silicon drift detector</td></tr><tr><td>IgorPro v. 6.37</td><td></td><td></td><td>Plotting software</td></tr></tbody></table>

synchrotron x-ray microdiffraction and fluorescence imaging of mineral and rock samples

在本报告中, 我们描述了获取和处理 x 射线 microfluorescence (μXRF) 和劳厄和粉末 microdiffraction 二维 (2D) 地图在光束线12.3.2 的先进光源 (ALS) 的详细程序, 劳伦斯伯克利国家实验室。测量可以在任何小于10厘米 x 10 厘米 x 5 厘米的样品上执行, 并具有平坦暴露的表面。实验几何是用标准材料 (XRF 的元素标准, 和晶体样品如 Si, 石英, 或 Al2O3的衍射) 来校准的。样品与 x 射线束的焦距对齐, 并执行光栅扫描, 其中每个像素对应一个测量,例如,一个 XRF 光谱或一个衍射图案。然后使用内部开发的软件 "圣诞" 处理这些数据, 它输出文本文件, 其中每一行对应于一个像素位置。碳硅石和橄榄蜗牛壳的代表性数据展示了数据质量、收集和分析策略。

劳厄 Microdiffraction
最近对天然碳硅石 (SiC) 样品18进行了测量和分析。该样品包括一个嵌在环氧树脂插头的凝灰岩, 然后切割和抛光, 以揭露 ROI。用光学显微镜和拉曼光谱 (图 1a) 鉴定了三碳硅石颗粒。其中一粒, SiC 2 (图 1b), 被认为含有本机硅 (Si)<sup class=...

Watch this Scientific Journal Video about Synchrotron X-ray Microdiffraction and Fluorescence Imaging of Mineral and Rock Samples at JoVE.com

Synchrotron X-ray Microdiffraction and Fluorescence Imaging of Mineral and Rock Samples

我们描述了一个光束线的设置, 目的是进行快速的二维 x 射线荧光和 x 射线 microdiffraction 映射的单晶或粉末样品使用劳厄 (多色辐射) 或粉末 (单色辐射) 衍射。生成的地图提供了有关应变、方向、相分布和塑性变形的信息。

矿物和岩石样品的同步辐射 x 射线 Microdiffraction 和荧光成像

In this report, we describe a detailed procedure for acquiring and processing&#160;x-ray microfluorescence (&#956;XRF), and Laue and powder ...

synchrotron-x-ray-microdiffraction-fluorescence-imaging-mineral-rock

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Chemistry

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Electronic Structure of Atoms

SCIENTISTS IN ACTION

8.9K 次观看.  Lawrence Berkeley National Laboratory. 我们描述了一个光束线的设置, 目的是进行快速的二维 x 射线荧光和 x 射线 microdiffraction 映射的单晶或粉末样品使用劳厄 (多色辐射) 或粉末 (单色辐射) 衍射。生成的地图提供了有关应变、方向、相分布和塑性变形的信息。

视频: Synchrotron X-ray Microdiffraction and Fluorescence Imaging of Mineral and Rock Samples

Synthesis and Microdiffraction at Extreme Pressures and Temperatures

High pressure compounds and polymorphs are investigated for a broad range of purposes such as determine structures and processes of deep planetary interiors, design materials with novel properties, understand the mechanical behavior of materials exposed to very high stresses as in explosions or impacts. Synthesis and structural analysis of materials at extreme conditions of pressure and temperature entails remarkable technical challenges. In the laser heated diamond anvil cell (LH-DAC), very high pressure is generated between the tips of two opposing diamond anvils forced against each other; focused infrared laser beams, shined through the diamonds, allow to reach very high temperatures on samples absorbing the laser radiation. When the LH-DAC is installed in a synchrotron beamline that provides extremely brilliant x-ray radiation, the structure of materials under extreme conditions can be probed in situ. LH-DAC samples, although very small, can show highly variable grain size, phase and chemical composition. In order to obtain the high resolution structural analysis and the most comprehensive characterization of a sample, we collect diffraction data in 2D grids and combine powder, single crystal and multigrain diffraction techniques. Representative results obtained in the synthesis of a new iron oxide, Fe4O5 1 will be shown.

The laser heated diamond anvil cell combined with synchrotron micro-diffraction techniques allows researchers to explore the nature and properties of new phases of matter at extreme pressure and temperature (PT) conditions. Heterogeneous samples can be characterized in situ under high pressure by 2D mapping and combined powder, single-crystal and multigrain diffraction approaches.

在极端的压力和温度的合成和Microdiffraction

High pressure compounds and polymorphs are investigated for a broad range of purposes such as determine structures and processes of deep planetary ...

科研

工程学

Preparing Adherent Cells for X-ray Fluorescence Imaging by Chemical Fixation

X-ray fluorescence imaging allows us to non-destructively measure the spatial distribution and concentration of multiple elements simultaneously over large or small sample areas. It has been applied in many areas of science, including materials science, geoscience, studying works of cultural heritage, and in chemical biology. In the case of chemical biology, for example, visualizing the metal distributions within cells allows us to study both naturally-occurring metal ions in the cells, as well as exogenously-introduced metals such as drugs and nanoparticles. Due to the fully hydrated nature of nearly all biological samples, cryo-fixation followed by imaging under cryogenic temperature represents the ideal imaging modality currently available. However, under the circumstances that such a combination is not easily accessible or practical, aldehyde based chemical fixation remains useful and sometimes inevitable. This article describes in as much detail as possible in the preparation of adherent mammalian cells by chemical fixation for X-ray fluorescent imaging.

Here, we present a protocol on how to determine the quantity and distribution of metals in a sample using synchrotron X-ray fluorescence. We focus on adherent cells, and describe the chemical fixation method to prepare this sample. We then describe how to mount and image the sample using synchrotron X-rays.

化学固定准备贴壁细胞的X射线荧光成像

X-ray fluorescence imaging allows us to non-destructively measure the spatial distribution and concentration of multiple elements simultaneously over ...

化学

Microcrystallography of Protein Crystals and In Cellulo Diffraction

The advent of high-quality microfocus beamlines at many synchrotron facilities has permitted the routine analysis of crystals smaller than 10 &#181;m in their largest dimension, which used to represent a challenge. We present two alternative workflows for the structure determination of protein microcrystals by X-ray crystallography with a particular focus on crystals grown in vivo. The microcrystals are either extracted from cells by sonication and purified by differential centrifugation, or analyzed in cellulo after cell sorting by flow cytometry of crystal-containing cells. Optionally, purified crystals or crystal-containing cells are soaked in heavy atom solutions for experimental phasing. These samples are then prepared for diffraction experiments in a similar way by application onto a micromesh support and flash cooling in liquid nitrogen. We briefly describe and compare serial diffraction experiments of isolated microcrystals and crystal-containing cells using a microfocus synchrotron beamline to produce datasets suitable for phasing, model building and refinement.
These workflows are exemplified with crystals of the Bombyx mori cypovirus 1 (BmCPV1) polyhedrin produced by infection of insect cells with a recombinant baculovirus. In this case study, in cellulo analysis is more efficient than analysis of purified crystals and yields a structure in ~8 days from expression to refinement.

Microcrystallography of Protein Crystals and In Cellulo Diffraction

A protocol is presented for X-ray crystallography using protein microcrystals. Two examples analyzing in vivo-grown microcrystals after purification or in cellulo are compared.

蛋白晶体的微结晶和<em&gt;在Cellulo</em&gt;衍射

The advent of high-quality microfocus beamlines at many synchrotron facilities has permitted the routine analysis of crystals smaller than 10 &#181;m in ...

生物化学

Dynamic Pore-scale Reservoir-condition Imaging of Reaction in Carbonates Using Synchrotron Fast Tomography

Underground storage permanence is a major concern for carbon capture and storage. Pumping CO2 into carbonate reservoirs has the potential to dissolve geologic seals and allow CO2 to escape. However, the dissolution processes at reservoir conditions are poorly understood. Thus, time-resolved experiments are needed to observe and predict the nature and rate of dissolution at the pore scale. Synchrotron fast tomography is a method of taking high-resolution time-resolved images of complex pore structures much more quickly than traditional &#181;-CT. The Diamond Lightsource Pink Beam was used to dynamically image dissolution of limestone in the presence of CO2-saturated brine at reservoir conditions. 100 scans were taken at a 6.1 &#181;m resolution over a period of 2 hours. The images were segmented and the porosity and permeability were measured using image analysis and network extraction. Porosity increased uniformly along the length of the sample; however, the rate of increase of both porosity and permeability slowed at later times.

Synchrotron fast tomography was used to dynamically image dissolution of limestone in the presence of CO2-saturated brine at reservoir conditions. 100 scans were taken at a 6.1 &#181;m resolution over a period of 2 h.

用同步快速反应层析成像动态孔隙规模油藏条件下成像碳酸盐

Underground storage permanence is a major concern for carbon capture and storage. Pumping CO2 into carbonate reservoirs has the potential to dissolve ...

Stress Distribution During Cold Compression of Rocks and Mineral Aggregates Using Synchrotron-based X-Ray Diffraction

We report detailed procedures for performing compression experiments on rocks and mineral aggregates within a multi-anvil deformation apparatus (D-DIA) coupled with synchrotron X-radiation. A cube-shaped sample assembly is prepared and compressed, at room temperature, by a set of four X-ray transparent sintered diamond anvils and two tungsten carbide anvils, in the lateral and the vertical planes, respectively. All six anvils are housed within a 250-ton hydraulic press and driven inward simultaneously by two wedged guide blocks. A horizontal energy dispersive X-ray beam is projected through and diffracted by the sample assembly. The beam is commonly in the mode of either white or monochromatic X-ray. In the case of white X-ray, the diffracted X-rays are detected by a solid-state detector array that collects the resulting energy dispersive diffraction pattern. In the case of monochromatic X-ray, the diffracted pattern is recorded using a two-dimensional (2-D) detector, such as an imaging plate or a charge-coupled device (CCD) detector. The 2-D diffraction patterns are analyzed to derive lattice spacings. The elastic strains of the sample are derived from the atomic lattice spacing within grains. The stress is then calculated using the predetermined elastic modulus and the elastic strain. Furthermore, the stress distribution in two-dimensions allow for understanding how stress is distributed in different orientations. In addition, a scintillator in the X-ray path yields a visible light image of the sample environment, which allows for the precise measurement of sample length changes during the experiment, yielding a direct measurement of volume strain on the sample. This type of experiment can quantify the stress distribution within geomaterials, which can ultimately shed light on the mechanism responsible for compaction. Such knowledge has the potential to significantly improve our understanding of key processes in rock mechanics, geotechnical engineering, mineral physics, and material science applications where compactive processes are important.

We report detailed procedures for compression experiments on rocks and mineral aggregates within a multi-anvil deformation apparatus coupled with synchrotron X-radiation. Such experiments allow quantification of the stress distribution within samples, that ultimately sheds light on compaction processes in geomaterials.

基于同步辐射 x 射线衍射的岩石和矿物团聚体冷压缩应力分布

We report detailed procedures for performing compression experiments on rocks and mineral aggregates within a multi-anvil deformation apparatus (D-DIA) ...

环境科学

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The devices are patterned from epoxy glue using soft lithography and are suitable for in situ X-ray diffraction experiments at room temperature. The sample wells are lidded on both sides with polymeric polyimide foil windows that allow diffraction data collection with low X-ray background. This fabrication method is undemanding and inexpensive. After the sourcing of a SU-8 master wafer, all fabrication can be completed outside of a cleanroom in a typical research lab environment. The chip design and fabrication protocol utilize capillary valving to microfluidically split an aqueous reaction into defined nanoliter sized droplets. This loading mechanism avoids the sample loss from channel dead-volume and can easily be performed manually without using pumps or other equipment for fluid actuation. We describe how isolated nanoliter sized drops of protein solution can be monitored in situ by dynamic light scattering to control protein crystal nucleation and growth. After suitable crystals are grown, complete X-ray diffraction datasets can be collected using goniometer based in situ fixed target serial X-ray crystallography at room temperature. The protocol provides custom scripts to process diffraction datasets using a suite of software tools to solve and refine the protein crystal structure. This approach avoids the artefacts possibly induced during cryo-preservation or manual crystal handling in conventional crystallography experiments. We present and compare three protein structures that were solved using small crystals with dimensions of approximately 10-20 &#181;m grown in chip. By crystallizing and diffracting in situ, handling and hence mechanical disturbances of fragile crystals is minimized. The protocol details how to fabricate a custom X-ray transparent microfluidic chip suitable for in situ serial crystallography. As almost every crystal can be used for diffraction data collection, these microfluidic chips are a very efficient crystal delivery method.

Microfluidic Chips for In Situ Crystal X-ray Diffraction and In Situ Dynamic Light Scattering for Serial Crystallography

This protocol describes in detail how to fabricate and operate microfluidic devices for X-ray diffraction data collection at room temperature. Additionally, it describes how to monitor protein crystallization by dynamic light scattering and how to process and analyze obtained diffraction data.

用于原位晶体 x 射线衍射和原位的微流控芯片系列晶体学的动态光散射

This protocol describes fabricating microfluidic devices with low X-ray background optimized for goniometer based fixed target serial crystallography. The ...

Sample Preparation and Transfer Protocol for In-Vacuum Long-Wavelength Crystallography on Beamline I23 at Diamond Light Source

Long-wavelength macromolecular crystallography (MX) exploits the anomalous scattering properties of elements, such as sulfur, phosphorus, potassium, chlorine, or calcium, that are often natively present in macromolecules. This enables the direct structure solution of proteins and nucleic acids via experimental phasing without the need of additional labelling. To eliminate the significant air absorption of X-rays in this wavelength regime, these experiments are performed in a vacuum environment. Beamline I23 at Diamond Light Source, UK, is the first synchrotron instrument of its kind, designed and optimized for MX experiments in the long wavelength range towards 5 &#197;. 
To make this possible, a large vacuum vessel encloses all endstation components of the sample environment. The necessity to maintain samples at cryogenic temperatures during storage and data collection in vacuum requires the use of thermally conductive sample holders. This facilitates efficient heat removal to ensure sample cooling to approximately 50 K. The current protocol describes the procedures used for sample preparation and transfer of samples into vacuum on beamline I23. Ensuring uniformity in practices and methods already established within the macromolecular crystallography community, sample cooling to liquid nitrogen temperature can be performed in any laboratory setting equipped with standard MX tools. 
Cryogenic storage and transport of samples only require standard commercially available equipment. Specialized equipment is required for the transfer of cryogenically cooled crystals from liquid nitrogen into the vacuum endstation. Bespoke sample handling tools and a dedicated Cryogenic Transfer System (CTS) have been developed in house. Diffraction data collected on samples prepared using this protocol show excellent merging statistics, indicating that the quality of samples is unaltered during the procedure. This opens unique opportunities for in-vacuum MX in a wavelength range beyond standard synchrotron beamlines.

Here, we present a protocol for cryogenic sample preparation and transfer of crystals into the vacuum endstation on beamline I23 at Diamond Light Source, for long-wavelength macromolecular X-ray crystallography experiments.

金刚石光源下光束线I23真空长波长晶体学的样品制备和转移实验方案

Long-wavelength macromolecular crystallography (MX) exploits the anomalous scattering properties of elements, such as sulfur, phosphorus, potassium, ...

A 3D Cartographic Description of the Cell by Cryo Soft X-ray Tomography

Imaging techniques are fundamental in order to understand cell organization and machinery in biological research and the related fields. Among these techniques, cryo soft X-ray tomography (SXT) allows imaging whole cryo-preserved cells in the water window X-ray energy range (284-543 eV), in which carbon structures have intrinsically higher absorption than water, allowing the 3D reconstruction of the linear absorption coefficient of the material contained in each voxel. Quantitative structural information at the level of whole cells up to 10 &#181;m thick is then achievable this way, with high throughput and spatial resolution down to 25-30 nm half-pitch. Cryo-SXT has proven itself relevant to current biomedical research, providing 3D information on cellular infection processes (virus, bacteria, or parasites), morphological changes due to diseases (such as recessive genetic diseases) and helping us understand drug action at the cellular level, or locating specific structures in the 3D cellular environment. In addition, by taking advantage of the tunable wavelength at synchrotron facilities, spectro-microscopy or its 3D counterpart, spectro-tomography, can also be used to image and quantify specific elements in the cell, such as calcium in biomineralization processes. Cryo-SXT provides complementary information to other biological imaging techniques such as electron microscopy, X-ray fluorescence or visible light fluorescence, and is generally used as a partner method for 2D or 3D correlative imaging at cryogenic conditions in order to link function, location, and morphology.

Here, a protocol describing the sample preparation and data collection steps required in cryo soft X-ray tomography (SXT) to image the ultrastructure of whole cryo-preserved cells at a resolution of 25 nm half pitch, is presented.

通过冷冻软X射线断层扫描对细胞进行3D制图描述

Imaging techniques are fundamental in order to understand cell organization and machinery in biological research and the related fields. Among these ...

生物学

X-ray Fluorescence (XRF)

Source: Laboratory of Dr. Lydia Finney &#8212; Argonne National Laboratory
X-ray fluorescence is an induced, emitted radiation that can be used to generate spectroscopic information. X-ray fluorescence microscopy is a non-destructive imaging technique that uses the induced fluorescence emission of metals to identify and quantify their spatial distribution.

X-ray Fluorescence XRF: Elemental Analysis by Emitted Fluorescent X-Ray

X 射线荧光光谱 (XRF)

Source: Laboratory of Dr. Lydia Finney &#8212; Argonne National Laboratory
X-ray fluorescence is an induced, emitted radiation that can be used to ...

教育

JoVE Science Education

分析化学

Single Crystal and Powder X-ray Diffraction

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
X-ray crystallography is a technique that uses X-rays to study the structure of molecules. X-ray diffraction (XRD) experiments are routinely carried out with either single-crystal or powdered samples.
Single-crystal XRD:
Single-crystal XRD allows for absolute structure determination. With single-crystal XRD data, the exact atomic positions can be observed, and thus bond lengths and angles can be determined. This technique provides the structure within a single crystal, which does not necessarily represent the bulk of the material. Therefore, additional bulk characterization methods must be utilized to prove the identity and purity of a compound.
Powder XRD:
Unlike single-crystal XRD, powder XRD looks at a large sample of polycrystalline material and therefore is considered a bulk characterization technique. The powder pattern is considered a &#34;fingerprint&#34; for a given material; it provides information about the phase (polymorph) and crystallinity of the material. Typically, powder XRD is used to study minerals, zeolites, metal-organic frameworks (MOFs), and other extended solids. Powder XRD can also be used to establish bulk purity of molecular species.
Previously, we have seen how to grow X-ray quality crystals (see video in Essentials of Organic Chemistry series). Here we will learn the principles behind XRD. We will then collect both single-crystal and powder data on Mo2(ArNC(H)NAr)4, where Ar = p-MeOC6H5.

单晶和粉末 X 射线衍射

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
X-ray crystallography is a technique that uses X-rays to study the ...