Finite-difference Time-domain (FDTD) Optical Simulations: A Primer for the Life Sciences and Bio-Inspired Engineering
Finite-difference Time-domain (FDTD) Optical Simulations: A Primer for the Life Sciences and Bio-Inspired Engineering
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DOI：
10.1016/j.micron.2021.103160
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发表时间：
2021-10-19
期刊：
影响因子：
2.4
通讯作者：
Aizenberg, Joanna
中科院分区：
文献类型：
--
作者：
McCoy, Dakota E.;Shneidman, Anna, V;Aizenberg, Joanna
从阳光斑驳的森林到海洋深处的发光生物，光影响着地球上的大多数生态系统。生物学家长期以来一直在研究纳米和微米尺度的生物适应性，以使用越来越复杂的显微镜，光谱学和其他分析设备来操纵光。结合实验工具，光与物体相互作用的模拟可以帮助研究人员确定观察到的结构的影响，并探索变化如何影响光学功能。特别是，时域有限差分（FDTD）方法被广泛用于整个纳米光子学社区，以有效地模拟光与各种材料和光学器件的相互作用。最近，FDTD已被用于表征自然界中的光学适应，例如鱼类和其他生物的伪装，性别选择的鸟类和蜘蛛的颜色以及植物的光合效率。FDTD在生物工程中也很常见，因为生物工程结构的设计可以通过FDTD模拟来指导和优化。参数扫描是FDTD的一个特别有用的应用，它允许研究人员探索自然和合成系统中的一系列变量和修改（例如，研究改变结构的尺寸、形状或折射率的光学效应）。在这里，我们回顾了FDTD模拟在生物学中的应用，并提出了一个简短的方法引物为生命科学家量身定制，重点放在商业软件Lumerical FDTD。我们给予特别注意的FDTD是否是正确的工具使用，如何使用实验技术来获取和导入感兴趣的结构，以及如何获得它们的光学特性，如折射率和吸收。本入门旨在帮助研究人员理解FDTD，实现建模光学效应的方法，并了解该工具的优点和局限性。总之，FDTD非常适合（i）表征光学适应性和（ii）提供机械解释;通过这样做，它有助于（iii）得出进化理论的结论和（iv）激发基于自然结构的新技术。
Light influences most ecosystems on earth, from sun-dappled forests to bioluminescent creatures in the ocean deep. Biologists have long studied nano- and micro-scale organismal adaptations to manipulate light using evermore sophisticated microscopy, spectroscopy, and other analytical equipment. In combination with experimental tools, simulations of light interacting with objects can help researchers determine the impact of observed structures and explore how variations affect optical function. In particular, the finite-difference time-domain (FDTD) method is widely used throughout the nanophotonics community to efficiently simulate light interacting with a variety of materials and optical devices. More recently, FDTD has been used to characterize optical adaptations in nature, such as camouflage in fish and other organisms, colors in sexually-selected birds and spiders, and photosynthetic efficiency in plants. FDTD is also common in bioengineering, as the design of biologicallyinspired engineered structures can be guided and optimized through FDTD simulations. Parameter sweeps are a particularly useful application of FDTD, which allows researchers to explore a range of variables and modifications in natural and synthetic systems (e.g., to investigate the optical effects of changing the sizes, shape, or refractive indices of a structure). Here, we review the use of FDTD simulations in biology and present a brief methods primer tailored for life scientists, with a focus on the commercially available software Lumerical FDTD. We give special attention to whether FDTD is the right tool to use, how experimental techniques are used to acquire and import the structures of interest, and how their optical properties such as refractive index and absorption are obtained. This primer is intended to help researchers understand FDTD, implement the method to model optical effects, and learn about the benefits and limitations of this tool. Altogether, FDTD is well-suited to (i) characterize optical adaptations and (ii) provide mechanistic explanations; by doing so, it helps (iii) make conclusions about evolutionary theory and (iv) inspire new technologies based on natural structures.