Tutorial: Machine-Learning-Based CREASE-2D Analysis of 2D SAXS Profiles to Characterize Anisotropic Nanostructures in Soft Materials

Abstract

We present a tutorial to guide users on how to extend the Computational Reverse Engineering Analysis of Scattering Experiments-2D (CREASE-2D) framework to interpret their experimental two-dimensional small-angle scattering (SAS) data from soft materials (e.g., polymers, peptide amphiphiles, biomolecular fibrils). Unlike most traditional SAS analysis approaches, which typically rely on azimuthally averaged one-dimensional (1D) profiles, CREASE-2D utilizes the complete 2D scattering profile to reveal information about anisotropy in the structure. In past applications, CREASE has provided insights into complex structural features, including the cross-sectional shapes of assembled nanostructures and dispersity in these features, which are difficult to discern with existing analytical models. While (1D-) CREASE has been applied to SANS and SAXS data, this tutorial shares the steps for implementing CREASE-2D using an example of a dipeptide solution system, for which we have SAXS data. We present details for these steps involved in using CREASE-2D to interpret SAXS profiles: how to preprocess SAXS data, define relevant structural features, generate three-dimensional real-space structures for specific values of these features, train a machine learning (ML) surrogate model to predict scattering profiles for given structural features, and optimize these features using genetic algorithms (GA). Then, we use these steps to interpret complex 2D-SAXS data collected from dipeptide solutions that, in microscopy images, exhibit nanoscale structures that could be elliptical tubes/flat tapes/cylinders or a combination of these cross sections. Open-source codes, computational hardware, and software requirements, as well as the strengths and limitations of this protocol, are also presented. We expect researchers working with (soft) biomaterials, peptide amphiphiles, amphiphilic polymer solutions, polymer nanocomposites, and blends of particles/polymers will find this CREASE-2D method and this tutorial of use.