Analytical models of icosahedral shells for 3D optical imaging of viruses

Abstract: A modulated icosahedral shell with an inclusion is a concise description of many viruses, including recently-discovered large double-stranded DNA ones. Many X-ray scattering patterns of such viruses show major polygonal fringes, which can be reproduced in image reconstruction with a homogeneous icosahedral shell. A key question regarding a low-resolution reconstruction is how to introduce further changes to the 3D profile in an efficient way with only a few parameters. Here, we derive and compile different analytical models of such an object with consideration of practical optical setups and typical structures of such viruses. The benefits of such models include 1) inherent filtering and suppressing different numerical errors of a discrete grid, 2) providing a concise and meaningful set of descriptors for feature extraction in high-throughput classification/sorting and higher-resolution cumulative reconstructions, 3) disentangling (physical) resolution from (numerical) discretization step and having a vector graphics format for visualization or further analysis at arbitrary scales, 4) eliminating the phase-retrieval step and enforcing transparent, relevant, and controlled type/level of a-priori information in a real-space formulation, and 5) evaluating the reflections and surface resonances of an icosahedral object, and hence corrections for the common scattering model.