Journal Article

Exploring the landscape of model representations

Foley, Thomas T., Shell, M. Scott, Noid, W. G., Kidder, Katherine M.

2020

Overview

The success of any physical model critically depends upon adopting an appropriate representation for the phenomenon of interest. Unfortunately, it remains generally challenging to identify the essential degrees of freedom or, equivalently, the proper order parameters for describing complex phenomena. Here we develop a statistical physics framework for exploring and quantitatively characterizing the space of order parameters for representing physical systems. Specifically, we examine the space of low-resolution representations that correspond to particle-based coarse-grained (CG) models for a simple microscopic model of protein fluctuations. We employ Monte Carlo (MC) methods to sample this space and determine the density of states for CG representations as a function of their ability to preserve the configurational information, I, and large-scale fluctuations, 𝓠, of the microscopic model. These two metrics are uncorrelated in high-resolution representations but become anticorrelated at lower resolutions. Moreover, our MC simulations suggest an emergent length scale for coarse-graining proteins, as well as a qualitative distinction between good and bad representations of proteins. Finally, we relate our work to recent approaches for clustering graphs and detecting communities in networks.

• Publisher: National Academy of Sciences
• Subject: Biological Sciences / Biophysics and Computational Biology / Chemistry / Clustering / Fluctuations / Granulation / Mathematical models / Models, Chemical / Monte Carlo Method / Monte Carlo simulation / Neural Networks, Computer / Order parameters / Phase Transition / Physical Sciences / Protein Conformation / Proteins / Representations