Related papers: Critical fluctuations in proteins native states
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
Fluctuations may govern the fate of an interacting particle system even on the mean-field level. This is demonstrated via a three species cyclic trapping reaction with a large, yet finite number of particles, where the final number of…
The dependence of the scaling properties of the structure factor on space dimensionality, range of interaction, initial and final conditions, presence or absence of a conservation law is analysed in the framework of the large-N model for…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
Fractal structure of shortest paths depends strongly on interresidue interaction cutoff distance. The dimensionality of shortest paths is calculated as a function of interaction cutoff distance. Shortest paths are self similar with a…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
The order parameter for a continuous transition shows diverging fluctuation near the critical point. Here we show, through numerical simulations and scaling arguments, that the inequality (or variability) between the values of an order…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
We show that in experimental atomic force microscopy studies of the lifetime distribution of mechanically stressed folded proteins the effects of externally applied fluctuations can not be distinguished from those of internally present…
Membrane curvature sensing is essential for a diverse range of biological processes. Recent experiments have revealed that a single nanometer-sized septin protein can distinguish between membrane-coated glass beads of one micron and three…
To understand the finite-size-scaling properties of phases transitions in classical and quantum models in the presence of quenched disorder, it has proven to be fruitful to introduce the notion of a finite-size-pseudo-critical point in each…
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…
We study the effect of membrane proteins on the shape, composition and thermodynamic stability of the surrounding membrane. When the coupling between membrane composition and curvature is strong enough the nearby composition and shape both…
The thermodynamics of excited nuclear systems allows one to explore the second-order phase transition in a two-component quantum mixture. Temperatures and densities are derived from quantum fluctuations of fermions. The pressures are…
The copy number of any protein fluctuates among cells in a population; characterizing and understanding these fluctuations is a fundamental problem in biophysics. We show here that protein distributions measured under a broad range of…
We study the geometrical features of the order parameter's fluctuations near the critical point of mixed-order phase transitions in randomly interdependent spatial networks. In contrast to continuous transitions, where the structure of the…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
The kinetics of dislocations is studied with computer simulation at loadings of different intensity. It is established that the dislocations have a few different structural states. The dislocations "with the micropore" play important role…
While cracking is a complex dynamics that involves material intrinsic properties like grain shape and size distribution, elastic properties of grain and cementing materials, and extrinsic properties of loading, in this work, the focus has…