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Orkun Furat

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Applications Biological Physics cond-mat.mtrl-sci Subcellular Processes

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preprint2026arXiv

Statistical analysis of virion-cell interactions mediated by peptide nanofibrils and peptide amphiphiles using STEM tomography

Peptide nanofibrils (PNFs) and peptide amphiphiles (PAs) are promising tools for enhancing viral transduction and gene transfer. However, quantitative insight into how their supramolecular architecture governs virion-cell interactions is limited. Here, we introduce a framework for the acquisition, processing, and statistical analysis of scanning transmission electron microscopy (STEM) tomograms to objectively quantify peptide-virion-cell interactions. Using four transduction-enhancing peptides (D4, Vectofusin-1, palmitic acid-PA (pal-PA), and eicosapentaenoic-PA (eic-PA)), peptide aggregate morphology, interfacial contact areas, and the spatial organization of virions with respect to peptides and cells were analyzed using advanced geometric descriptors. All peptides efficiently captured virions, resulting in few free virions, but they differ in how strictly virions were spatially confined near the cell surface. These differences reflect alternative spatial organization strategies, which are likely crucial factors influencing transduction-enhancing efficacy. Our approach provides a novel, generalizable method to evaluate infection-enhancing nanomaterials and guides the rational design of next-generation peptide assemblies for therapeutic viral delivery.

preprint2023arXiv

Multidimensional characterization of particle morphology and mineralogical composition using CT data and R-vine copulas

Computed tomography (CT) can capture volumes large enough to measure a statistically meaningful number of micron-sized particles with a sufficiently good resolution to allow for the analysis of individual particles. However, the development of methods to efficiently investigate such image data and interpretably model the observed particle features is still an active field of research. When image data of particles exhibiting a wide range of shapes and sizes is considered, traditional image segmentation methods, such as the classic watershed algorithm, struggle to recognize particles with satisfying accuracy. Thus, more advanced methods of machine learning must be utilized for image segmentation to improve the validity of subsequent analyzes. Moreover, CT data does not include information about the mineralogical composition of particles and, therefore, additional SEM-EDS image data has to be acquired. In this paper, micro-CT image data of a particle system mostly consisting of zinnwaldite-quartz composites is considered. First, an image segmentation method is applied which uses deep convolutional neural networks, in particular an adaptation of the U-net architecture. This has the advantage of requiring less hand-labeling than other machine learning methods, while also being more flexible with the possibility of transfer learning. Then, fully parameterized models based on vine copulas are designed to determine multivariate probability distributions of descriptor vectors for the size, shape, texture and composition of particles -- allowing for the estimation and interpretable characterization of interdependencies between particle descriptors. For model fitting, the segmented three-dimensional CT data and co-registered two-dimensional SEM-EDS data are used.