Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models
Coarse-grained molecular simulation models have provided immense, often general, insight into the complex behavior of condensed-phase systems but suffer from a lost connection to the true dynamical properties of the underlying system. In general, the physics that is built into a model shapes the free-energy landscape, restricting the attainable static and kinetic properties. In this work, we perform a detailed investigation into the property interrelationships resulting from these restrictions, for a representative system of the helix-coil transition. Inspired by high-throughput studies, we systematically vary force-field parameters and monitor their structural, kinetic, and thermodynamic properties. The focus of our investigation is a simple coarse-grained model, which accurately represents the underlying structural ensemble, i.e., effectively avoids sterically-forbidden configurations. As a result of this built-in physics, we observe a rather large restriction in the topology of the networks characterizing the simulation kinetics. When screening across force-field parameters, we find that structurally accurate models also best reproduce the kinetics, suggesting structural-kinetic relationships for these models. Additionally, an investigation into thermodynamic properties reveals a link between the cooperativity of the transition and the network topology at a single reference temperature.
This work systematically vary force-field parameters and monitor their structural, kinetic, and thermodynamic properties, and finds that structurally accurate models also best reproduce the kinetics, suggesting structural-kinetic relationships for these models.
@article{Rudzinski_2018, title={Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models}, volume={148}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.5025125}, DOI={10.1063/1.5025125}, number={20}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Rudzinski, Joseph F. and Bereau, Tristan}, year={2018}, month=may }
