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

A Novel Evaluation of Income Class Boundaries Using Inflection Points of Probability Density Functions: A Case Study of Brazil

Categorizing a population into different income classes is important for creating effective policies and analyzing markets. Our study develops a statistical method based on a nationwide survey of income distribution. We use these data to create a cumulative distribution function with a metalogistic distribution and its probability density function. We propose a new way to divide the population into income classes by using the inflection points of the probability density function as the class boundaries. As a case study, we apply this method to income data from Brazil between 2012 and 2022. We identify five income classes, with both their boundaries and the distribution of the population changing over time. To check our approach, we calculate the Gini coefficient and find that our results closely match official figures, with a root mean square deviation of less than 1%. By using individual income instead of family income, we avoid distortions caused by the fact that poorer families tend to be larger than wealthier ones. In the end, we identify five main income classes, with their boundaries shifting each year, reflecting the changing nature of income distribution in society.

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.

Transverse-size critical exponent of directed percolation from Yang-Lee zeros of survival probability

By using transfer-matrix method we compute survival probabilities for the directed percolation problem on strips of a square lattice, and get very precise estimates of their Yang-Lee zeros lying closest to the real axis in the complex plane of occupation probability. This allows us to get accurate values for transverse-size critical exponent and percolation threshold.

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.

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

I compute exact partition function zeros of β hairpins, using both analytic and numerical methods, extending previous work [J. Lee, Phys. Rev. Lett. 110, 248101 (2013)] where only a restricted class of hairpins was considered. The zeros of β hairpins with an odd number of peptide bonds are computed and the difference of the distribution of zeros from those for an even number of peptide bonds is explained in terms of additional entropy of liberating the extra bond at the turn region. Upon the introduction of a hydrophobic core in the central region of the hairpin, the zeros are distributed uniformly on two concentric circles corresponding to the hydrophobic collapse and the transition to the fully folded conformation. One of the circles dissolves as the core moves toward the turn or the tip region, which is explained in terms of the similarity of the intermediate state with the folded or unfolded states. The exact partition function zeros for a hairpin with a more complex structure of native contacts, the 16 C-terminal residues of streptococcal protein G B1, are numerically computed and their loci are closely approximated by concentric circles.