Disentangling Rotational Dynamics and Ordering Transitions in a System of Self-Organizing Protein Nanorods <i>via</i> Rotationally Invariant Latent Representations
Sergei V. Kalinin, Shuai Zhang, Mani Valleti, Harley Pyles, David Baker, James J. De Yoreo, Maxim Ziatdinov
Abstract
The dynamics of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally invariant variational autoencoder-based analysis of orientation and shape evolution. The latter allows for disentanglement of the particle orientation from other degrees of freedom and compensates for lateral shifts. The disentangled representations in the latent space encode the rich spectrum of local transitions that can now be visualized and explored via continuous variables. The time dependence of ensemble averages allows insight into the time dynamics of the system and, in particular, illustrates the presence of the potential ordering transition. Finally, analysis of the latent variables along the single-particle trajectory allows tracing these parameters on a single-particle level. The proposed approach is expected to be universally applicable for the description of the imaging data in optical, scanning probe, and electron microscopy seeking to understand the dynamics of complex systems where rotations are a significant part of the process.