Finite-difference Time-domain (FDTD) Optical Simulations: A Primer for the Life Sciences and Bio-Inspired Engineering

FeSA‐Ir/Metallene Nanozymes Induce Sequential Ferroptosis‐Pyroptosis for Multi‐Immunogenic Responses Against Lung Metastasis

For cancer metastasis inhibition, the combining of nanozymes with immune checkpoint blockade (ICB) therapy remains the major challenge in controllable reactive oxygen species (ROS) generation for creating effective immunogenicity. Herein, new nanozymes with light-controlled ROS production in terms of quantity and variety are developed by conjugating supramolecular-wrapped Fe single atom on iridium metallene with lattice-strained nanoislands (FeSA-Ir@PF NSs). The Fenton-like catalysis of FeSA-Ir@PF NSs effectively produced •OH radicals in dark, which induced ferroptosis and apoptosis of cancer cells. While under second near-infrared (NIR-II) light irradiation, FeSA-Ir@PF NSs showed ultrahigh photothermal conversion efficiency (𝜂, 75.29%), cooperative robust •OH generation, photocatalytic O2 and 1O2 generation, and caused significant pyroptosis of cancer cells. The controllable ROS generation, sequential cancer cells ferroptosis and pyroptosis, led 99.1% primary tumor inhibition and multi-immunogenic responses in vivo. Most importantly, the inhibition of cancer lung metastasis is completely achieved by FeSA-Ir@PF NSs with immune checkpoint inhibitors, as demonstrated in different mice lung metastasis models, including circulating tumor cells (CTCs) model. This work provided new inspiration for developing nanozymes for cancer treatments and metastasis inhibition.

Using high-resolution microscopy data to generate realistic structures for electromagnetic FDTD simulations from complex biological models

Finite-difference time-domain (FDTD) electromagnetic simulations are a computational method that has seen much success in the study of biological optics; however, such simulations are often hindered by the difficulty of faithfully replicating complex biological microstructures in the simulation space. Recently, we designed simulations to calculate the trajectory of electromagnetic light waves through realistically reconstructed retinal photoreceptors and found that cone photoreceptor mitochondria play a substantial role in shaping incoming light. In addition to vision research and ophthalmology, such simulations are broadly applicable to studies of the interaction of electromagnetic radiation with biological tissue. Here, we present our method for discretizing complex 3D models of cellular structures for use in FDTD simulations using MEEP, the MIT Electromagnetic Equation Propagation software, including subpixel smoothing at mesh boundaries. Such models can originate from experimental imaging or be constructed by hand. We also include sample code for use in MEEP. Implementation of this algorithm in new code requires understanding of 3D mathematics and may require several weeks of effort, whereas use of our sample code requires knowledge of MEEP and C++ and may take up to a few hours to prepare a model of interest for 3D FDTD simulation. In all cases, access to a facility supercomputer with parallel processing capabilities is recommended. This protocol offers a practical solution to a significant challenge in the field of computational electrodynamics and paves the way for future advancements in the study of light interaction with biological structures.

Visible and angular interrogation of Kretschmann-based SPR using hybrid Au-ZnO optical sensor for hyperuricemia detection

Uric acid is a waste product of the human body where high levels of it or hyperuricemia can lead to gout, kidney disease and other health issues. In this paper, Finite Difference Time Doman (FDTD) simulation method was used to develop a plasmonic optical sensor to detect uric acid with molarity ranging from 0 to 3.0 mM. A hybrid layer of gold-zinc oxide (Au-ZnO) was used in this Kretschmann-based Surface Plasmon Resonance (K-SPR) technique with angular interrogation at 670 nm and 785 nm visible optical wavelengths. The purpose of this study is to observe the ability of the hybrid material as a sensing performance enhancer for differentiating between healthy and unhealthy uric acid levels based on the refractive index values from previous study. Upon exposure to 670 nm wavelength, the average sensitivity of this sensor was found to be 0.028°/mM with a linearity of 98.67 % and Q-factor value of 0.0053 mM - 1 . While at 785 nm, the average sensitivity is equal to 0.0193°/mM with slightly lower linearity at 94.46 % and Q-factor value of 0.0076 mM - 1 . The results have proven the ability of hybrid material Au-ZnO as a sensing performance enhancer for detecting uric acid when compared with bare Au and can be further explored in experimental work.

Modeling nonlinear optical microscopy in scattering media, part II. Radiation from focal volume to far-field: tutorial

The development and application of nonlinear optical (NLO) microscopy methods in biomedical research has experienced rapid growth over the past three decades. Despite the compelling power of these methods, optical scattering limits their practical use in biological tissues. This tutorial offers a model-based approach illustrating how analytical methods from classical electromagnetism can be employed to comprehensively model NLO microscopy in scattering media. In Part I, we quantitatively model focused beam propagation in non-scattering and scattering media from the lens to focal volume. In Part II, we model signal generation, radiation, and far-field detection. Moreover, we detail modeling approaches for major optical microscopy modalities including classical fluorescence, multi-photon fluorescence, second harmonic generation, and coherent anti-Stokes Raman microscopy.

Modeling nonlinear optical microscopy in scattering media, part I. Propagation from lens to focal volume: tutorial

The development and application of nonlinear optical (NLO) microscopy methods in biomedical research have experienced rapid growth over the past three decades. Despite the compelling power of these methods, optical scattering limits their practical use in biological tissues. This tutorial offers a model-based approach illustrating how analytical methods from classical electromagnetism can be employed to comprehensively model NLO microscopy in scattering media. In Part I, we quantitatively model focused beam propagation in non-scattering and scattering media from the lens to focal volume. In Part II, we model signal generation, radiation, and far-field detection. Moreover, we detail modeling approaches for major optical microscopy modalities including classical fluorescence, multi-photon fluorescence, second harmonic generation, and coherent anti-Stokes Raman microscopy.

Design methodologies and engineering applications for ecosystem biomimicry: an interdisciplinary review spanning cyber, physical, and cyber-physical systems

Ecosystem biomimicry is a promising pathway for sustainable development. However, while typical form- and process-level biomimicry is prevalent, system-level ecosystem biomimicry remains a nascent practice in numerous engineering fields. This critical review takes an interdisciplinary approach to synthesize trends across case studies, evaluate design methodologies, and identify future opportunities when applying ecosystem biomimicry to engineering practices, including cyber systems (CS), physical systems (PS), and cyber-physical systems (CPS). After systematically sourcing publications from major databases, the papers were first analyzed at a meta level for their bibliographic context and for statistical correlations among categorical variables. Then, we investigated deeper into the engineering applications and design methodologies. Results indicate that CPS most frequently mimic organisms and ecosystems, while CS and PS frequently mimic populations-communities and molecules-tissues-organ systems, respectively (statistically highly significant). An indirect approach is most often used for mimicry at organizational levels from populations to ecosystems, while a direct approach frequently suits levels from molecules to organisms (highly significant). Dominant themes across engineering applications include symbiotic organism search algorithms for CS and ecological network analysis for CPS, while PS are highly diverse. For design methodologies, this work summarizes and details ten well-documented biomimetic process models among literature, which addresses an outdated concern for a lack of systematic methods for ecosystem biomimicry. In addition to the Biomimetics Standard ISO 18458, these methods include the Natural Step and Techno-Ecological Synergy framework, among others. Further, the analyses revealed future opportunities from less utilized design methods (e.g. interdisciplinary teams tackling indirect, ecosystem-level projects) to well-established engineering concepts ready for technological advancement (e.g. implementing membrane computing for physical applications). For future studies, this review provides a comprehensive reference for ecosystem biomimetic design practices and application opportunities across multiple engineering domains.

Robust Full-Spectral Color Tuning of Photonic Colloids

Creation of color through photonic morphologies manufactured by molecular self-assembly is a promising approach, but the complexity and lack of robustness of the fabrication processes have limited their technical exploitation. Here, it is shown that photonic spheres with full-color tuning across the entire visible spectrum can be readily and reliably achieved by the emulsification of solutions containing a block copolymer (BCP) and two swelling additives. Solvent diffusion out of the emulsion droplets gives rise to 20-150 µm-sized spheres with an onion-like lamellar morphology. Controlling the lamellar thickness by differential swelling with the two additives enables color tuning of the Bragg interference-based reflection band across the entire visible spectrum. By studying five different systems, a set of important principles for manufacturing photonic colloids is established. Two swelling additives are required, one of which must exhibit strong interactions with one of the BCP blocks. The additives should be chosen to enhance the dielectric contrast, and the formation kinetics of the spheres must be sufficiently slow to enable the emergence of the photonic morphology. The proposed approach is versatile and robust and allows the scalable production of photonic pigments with possible future applications in inks for cosmetics and arts, coatings, and displays.

A new approach for microstructure imaging

A recurring issue with microstructure studies is specimen lighting. In particular, microscope lighting must be deployed in such a way as to highlight biological elements without enhancing caustic effects and diffraction. We describe here a high frequency technique due to address this lighting issue. First, an extensive study is undertaken concerning asymptotic equations in order to identify the most promising algorithm for 3D microstructure analysis. Ultimately, models based on virtual light rays are discarded in favor of a model that considers the joint computation of phase and irradiance. This paper maintains the essential goal of the study concerning biological microstructures but offers several supplementary notes on computational details which provide perspectives on analyses of the arrangements of numerous objects in biological tissues.