Spatially Resolving Size Effects on Diffusivity in Nanoporous Extracellular Matrix-like Materials with Fluorescence Correlation Spectroscopy Super-Resolution Optical Fluctuation Imaging

Super-resolving particle diffusion heterogeneity in porous hydrogels via high-speed 3D active-feedback single-particle tracking microscopy

Nanoparticle diffusion in 3D porous structures is critical to understanding natural and synthetic systems but remains underexplored due to limitations in traditional microscopy methods. Here, we use 3D Single-Molecule Active-feedback Real-time Tracking (3D-SMART) microscopy to resolve nanoparticle dynamics in agarose gels with unprecedented spatiotemporal resolution. We highlight 'hopping diffusion', where particles intermittently escape confinement pockets, providing insights into hydrogel microstructure. Long, highly sampled trajectories enable extraction of kinetic parameters, confinement sizes, and thermodynamic barriers. This study demonstrates 3D-SMART's ability to probe particle-environment interactions at super-resolution (∼10 nm in XY and ∼30 nm in Z) in 3D, offering new perspectives on nanoparticle diffusion and the structural dynamics of porous materials, with implications for drug delivery, material science, and biological systems.

Effect of polyacrylamide gel elasticity on collagen type II fibril assembly

Collagen type II fibrils provide structural integrity to the articular cartilage extracellular matrix. However, the conditions that control the fibril radial size scale, distribution, and formation inside of dense networks are not well understood. We have investigated how surrounding elastic networks affect fibril formation by observing the structure and dynamics of collagen type II in model polyacrylamide gels of varying moduli. Cryogenic transmission electron microscopy (cryo-TEM) is used to image the fibril structure and is verified qualitatively with optical microscopy of fluorescently-tagged collagen within the gels. Using fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI), the diffusion dynamics of the collagen in low pH and neutral pH conditions are determined. Overall, the fibril bundle diameter and concentration were found to decrease as a function of gel modulus. The single fibril diameter remains constant at 30 nm within the gels; however, the diameter was found to be smaller when compared to in solution. Additionally, the mode of diffusion of the collagen triple helices changes within gel environments, decreasing the diffusion coefficient. Understanding the intricate relationship between network topology and collagen type II fibril formation is crucial in gaining deeper insights into the transport phenomena within complex acellular tissues that are necessary for the development of future therapeutic materials.

Cross-Correlation Increases Sampling in Diffusion-Based Super-Resolution Optical Fluctuation Imaging

Correlation signal processing of optical three-dimensional (x, y, t) data can produce super-resolution images. The second-order cross-correlation function XC 2 has been documented to produce super-resolution imaging with static and blinking emitters but not for diffusing emitters. Here, we both analytically and numerically demonstrate cross-correlation analysis for diffusing particles. We then expand our fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) analysis to use cross-correlation as a postprocessing computational technique to extract both dynamic and structural information on particle diffusion in nanoscale structures simultaneously. Cross-correlation maintains the same super-resolution as auto-correlation while also increasing the sampling rates to reduce aliasing for spatial information in both simulated and experimental data. Our work demonstrates how fcsSOFI with cross-correlation can be a powerful signal-processing tool to resolve the nanoscale dynamics and structure in samples relevant to biological and soft materials.

A practical guide to light-sheet microscopy for nanoscale imaging: Looking beyond the cell

We present a comprehensive guide to light-sheet microscopy (LSM) to assist scientists in navigating the practical implementation of this microscopy technique. Emphasizing the applicability of LSM to image both static microscale and nanoscale features, as well as diffusion dynamics, we present the fundamental concepts of microscopy, progressing through beam profile considerations, to image reconstruction. We outline key practical decisions in constructing a home-built system and provide insight into the alignment and calibration processes. We briefly discuss the conditions necessary for constructing a continuous 3D image and introduce our home-built code for data analysis. By providing this guide, we aim to alleviate the challenges associated with designing and constructing LSM systems and offer scientists new to LSM a valuable resource in navigating this complex field.

Cross-correlation increases sampling in diffusion-based super-resolution optical fluctuation imaging

Correlation signal processing of optical three-dimensional (x, y, t) data can produce super-resolution images. The second order cross-correlation function XC 2 has been documented to produce super-resolution imaging with static and blinking emitters but not for diffusing emitters. Here, we both analytically and numerically demonstrate cross-correlation analysis for diffusing particles. We then expand our fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) analysis to use cross-correlation as a post-processing computational technique to extract both dynamic and structural information of particle diffusion in nanoscale structures simultaneously. We further show how this method increases sampling rates and reduces aliasing for spatial information in both simulated and experimental data. Our work demonstrates how fcsSOFI with cross-correlation can be a powerful signal-processing tool to resolve the nanoscale dynamics and structure in samples relevant to biological and soft materials.

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