Exact partition function zeros of the Wako-Saitô-Muñoz-Eaton β hairpin model

The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics

Despite the recent advances in the prediction of protein structures by deep neutral networks, the elucidation of protein-folding mechanisms remains challenging. A promising theory for describing protein folding is a coarse-grained statistical mechanical model called the Wako-Saitô-Muñoz-Eaton (WSME) model. The model can calculate the free-energy landscapes of proteins based on a three-dimensional structure with low computational complexity, thereby providing a comprehensive understanding of the folding pathways and the structure and stability of the intermediates and transition states involved in the folding reaction. In this review, we summarize previous and recent studies on protein folding and dynamics performed using the WSME model and discuss future challenges and prospects. The WSME model successfully predicted the folding mechanisms of small single-domain proteins and the effects of amino-acid substitutions on protein stability and folding in a manner that was consistent with experimental results. Furthermore, extended versions of the WSME model were applied to predict the folding mechanisms of multi-domain proteins and the conformational changes associated with protein function. Thus, the WSME model may contribute significantly to solving the protein-folding problem and is expected to be useful for predicting protein folding, stability, and dynamics in basic research and in industrial and medical applications.

Lee-Yang zeros and large-deviation statistics of a molecular zipper

The complex zeros of partition functions were originally investigated by Lee and Yang to explain the behavior of condensing gases. Since then, Lee-Yang zeros have become a powerful tool to describe phase transitions in interacting systems. Today, Lee-Yang zeros are no longer just a theoretical concept; they have been determined in recent experiments. In one approach, the Lee-Yang zeros are extracted from the high cumulants of thermodynamic observables at finite size. Here we employ this method to investigate a phase transition in a molecular zipper. From the energy fluctuations in small zippers, we can predict the temperature at which a phase transition occurs in the thermodynamic limit. Even when the system does not undergo a sharp transition, the Lee-Yang zeros carry important information about the large-deviation statistics and its symmetry properties. Our work suggests an interesting duality between fluctuations in small systems and their phase behavior in the thermodynamic limit. These predictions may be tested in future experiments.

Experimental Determination of Dynamical Lee-Yang Zeros

Statistical physics provides the concepts and methods to explain the phase behavior of interacting many-body systems. Investigations of Lee-Yang zeros-complex singularities of the free energy in systems of finite size-have led to a unified understanding of equilibrium phase transitions. The ideas of Lee and Yang, however, are not restricted to equilibrium phenomena. Recently, Lee-Yang zeros have been used to characterize nonequilibrium processes such as dynamical phase transitions in quantum systems after a quench or dynamic order-disorder transitions in glasses. Here, we experimentally realize a scheme for determining Lee-Yang zeros in such nonequilibrium settings. We extract the dynamical Lee-Yang zeros of a stochastic process involving Andreev tunneling between a normal-state island and two superconducting leads from measurements of the dynamical activity along a trajectory. From the short-time behavior of the Lee-Yang zeros, we predict the large-deviation statistics of the activity which is typically difficult to measure. Our method paves the way for further experiments on the statistical mechanics of many-body systems out of equilibrium.