Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions

Sequence-based contact prediction has shown considerable promise in assisting non-homologous structure modeling, but it often requires many homologous sequences and a sufficient number of correct contacts to achieve correct folds. Here, we developed a method, C-QUARK, that integrates multiple deep-learning and coevolution-based contact-maps to guide the replica-exchange Monte Carlo fragment assembly simulations. The method was tested on 247 non-redundant proteins, where C-QUARK could fold 75% of the cases with TM-scores (template-modeling scores) ≥0.5, which was 2.6 times more than that achieved by QUARK. For the 59 cases that had either low contact accuracy or few homologous sequences, C-QUARK correctly folded 6 times more proteins than other contact-based folding methods. C-QUARK was also tested on 64 free-modeling targets from the 13th CASP (critical assessment of protein structure prediction) experiment and had an average GDT_TS (global distance test) score that was 5% higher than the best CASP predictors. These data demonstrate, in a robust manner, the progress in modeling non-homologous protein structures using low-accuracy and sparse contact-map predictions.

Theoretical Study on Proton Diffusivity in Y-Doped BaZrO3 with Realistic Dopant Configurations

We theoretically revisit the proton diffusivity in yttrium-doped barium zirconate (Y-doped BaZrO₃) with realistic dopant configurations under processing conditions. In a recent study employing the replica exchange Monte Carlo method, the equilibrium Y configurations at typical sintering temperatures were shown to deviate from the random configuration assumed in earlier theoretical studies. In the present study, we took this observation into account and evaluated the effect of the Y configuration on the proton diffusivity. Using the master equation approach based on local diffusion barriers calculated from first principles, the proton diffusivities under realistic Y configurations were estimated to be higher than those in the random configuration. This is explained by the fact that realistic Y configurations have fewer trap sites with deep potential wells compared to the random configuration due to the isolation trend of Y dopants. In addition, the effects of proton-proton interaction and the abundance of preferential conduction pathways are discussed; it is found that both are relatively minor factors compared to the trap site effect in determining the dependence of the proton diffusivity on the Y configurations.<br>

Theoretical Study on Proton Diffusivity in Y-Doped BaZrO3 with Realistic Dopant Configurations

We theoretically revisit the proton diffusivity in yttrium-doped barium zirconate (Y-doped BaZrO₃) with realistic dopant configurations under processing conditions. In a recent study employing the replica exchange Monte Carlo method, the equilibrium Y configurations at typical sintering temperatures were shown to deviate from the random configuration assumed in earlier theoretical studies. In the present study, we took this observation into account and evaluated the effect of the Y configuration on the proton diffusivity. Using the master equation approach based on local diffusion barriers calculated from first principles, the proton diffusivities under realistic Y configurations were estimated to be higher than those in the random configuration. This is explained by the fact that realistic Y configurations have fewer trap sites with deep potential wells compared to the random configuration due to the isolation trend of Y dopants. In addition, the effects of proton-proton interaction and the abundance of preferential conduction pathways are discussed; it is found that both are relatively minor factors compared to the trap site effect in determining the dependence of the proton diffusivity on the Y configurations.<br>

Comparison of Conformational Phase Behavior for Flexible and Semiflexible Polymers

We employ the recently introduced generalized microcanonical inflection point method for the statistical analysis of phase transitions in flexible and semiflexible polymers and study the impact of the bending stiffness upon the character and order of transitions between random-coil, globules, and pseudocrystalline conformations. The high-accuracy estimates of the microcanonical entropy and its derivatives required for this study were obtained by extensive replica-exchange Monte Carlo simulations. We observe that the transition behavior into the compact phases changes qualitatively with increasing bending stiffness. Whereas the Θ collapse transition is less affected, the first-order liquid-solid transition characteristic for flexible polymers ceases to exist once bending effects dominate over attractive monomer-monomer interactions.

Theoretical Study on Proton Diffusivity in Y-Doped BaZrO3 with Realistic Dopant Configurations

We theoretically revisit the proton diffusivity in yttrium-doped barium zirconate (Y-doped BaZrO₃) with realistic dopant configurations under processing conditions. In a recent study employing the replica exchange Monte Carlo method, the equilibrium Y configurations at typical sintering temperatures were shown to deviate from the random configuration assumed in earlier theoretical studies. In the present study, we took this observation into account and evaluated the effect of the Y configuration on the proton diffusivity. Using the master equation approach based on local diffusion barriers calculated from first principles, the proton diffusivities under realistic Y configurations were estimated to be higher than those in the random configuration. This is explained by the fact that realistic Y configurations have fewer trap sites with deep potential wells compared to the random configuration due to the isolation trend of Y dopants. In addition, the effects of proton-proton interaction and the abundance of preferential conduction pathways are discussed; it is found that both are relatively minor factors compared to the trap site effect in determining the dependence of the proton diffusivity on the Y configurations.<br>

Theoretical Study on Proton Diffusivity in Y-Doped BaZrO3 with Realistic Dopant Configurations

We theoretically revisit the proton diffusivity in yttrium-doped barium zirconate (Y-doped BaZrO₃) with realistic dopant configurations under processing conditions. In a recent study employing the replica exchange Monte Carlo method, the equilibrium Y configurations at typical sintering temperatures were shown to deviate from the random configuration assumed in earlier theoretical studies. In the present study, we took this observation into account and evaluated the effect of the Y configuration on the proton diffusivity. Using the master equation approach based on local diffusion barriers calculated from first principles, the proton diffusivities under realistic Y configurations were estimated to be higher than those in the random configuration. This is explained by the fact that realistic Y configurations have fewer trap sites with deep potential wells compared to the random configuration due to the isolation trend of Y dopants. In addition, the effects of proton-proton interaction and the abundance of preferential conduction pathways are discussed; it is found that both are relatively minor factors compared to the trap site effect in determining the dependence of the proton diffusivity on the Y configurations.<br>

Theoretical Study on Proton Diffusivity in Y-Doped BaZrO3 with Realistic Dopant Configurations

We theoretically revisit the proton diffusivity in yttrium-doped barium zirconate (Y-doped BaZrO₃) with realistic dopant configurations under processing conditions. In a recent study employing the replica exchange Monte Carlo method, the equilibrium Y configurations at typical sintering temperatures were shown to deviate from the random configuration assumed in earlier theoretical studies. In the present study, we took this observation into account and evaluated the effect of the Y configuration on the proton diffusivity. Using the master equation approach based on local diffusion barriers calculated from first principles, the proton diffusivities under realistic Y configurations were estimated to be higher than those in the random configuration. This is explained by the fact that realistic Y configurations have fewer trap sites with deep potential wells compared to the random configuration due to the isolation trend of Y dopants. In addition, the effects of proton-proton interaction and the abundance of preferential conduction pathways are discussed; it is found that both are relatively minor factors compared to the trap site effect in determining the dependence of the proton diffusivity on the Y configurations.<br>

Calculation of Order Parameter and Critical Exponents of the Spin Glass in the Frame of Edwards-Anderson Model

It is well known that critical phenomena occur in condensed matter under certain conditions, when an abrupt change in its properties occurs. In the vicinity of critical points, various phenomena may arise. The critical region can be described by a set of state parameters (order parameters), which allow one to obtain information about the anomalous behavior of thermodynamic averages, internal processes, and the nature of the objects of study. The abnormal nonlinear behavior of state parameters is described by critical exponents. In this article, we considered spin glass on the example of the Edwards-Anderson model. For the simulation, the replica-exchange Monte-Carlo method was used. Critical exponents were obtained to describe the behavior of the model in the critical region.