Related papers: Relationship Between Structural Fractal and Possib…
Inhomogeneities in deposition may lead to formation of rough surfaces, whose height fluctuations can be probed directly by scanning microscopy, or indirectly by scattering. Analytical or numerical treatments of simple growth models suggest…
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,…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
We study numerically the coarsening kinetics of a two-dimensional ferromagnetic system with aleatory bond dilution. We show that interfaces between domains of opposite magnetisation are fractal on every lengthscale, but with different…
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…
A fast and accurate grid-based method with low memory requirement is presented to calculate volume characteristics in molecular systems. The distribution of volume and packing density is characterized in globular proteins, where void space…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
There are three important types of structural properties that remain unchanged under the structural transformation of condensed matter physics and chemistry. They are the properties that remain unchanged under the structural periodic…
One of the most puzzling and unsolved challenges in molecular biology is understanding how proteins fold. Despite having advanced predictive tools that can accurately estimate the native structures of proteins, we still lack a comprehensive…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
The aim of this review article is to give a comprehensive description of the scaling properties detected for the distribution of cosmic structures. Due to the great variety of statistical methods to describe the large-scale structure of the…
We investigate the influence of fractal structure on material properties. We calculate the statistical correlation functions of fractal media defined by level-cut Gaussian random fields. This allows the modeling of both surface fractal and…
The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times,…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
We investigate a recent suggestion that the spatial distribution of earthquake hypocenters makes a fractal set with a structure and fractal dimensionality close to those of the backbone of critical percolation clusters, by analyzing four…
Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape.…
The some dynamic properties of a random heteropolymer in the condensed state are studied in the mode coupling approximation. In agreement with recent report a dynamic friction increasing is predicted for the random heteropolymer with…
We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
The fractal nature of graphs has traditionally been investigated by using the nodes of networks as the basic units. Here, instead, we propose to concentrate on the graph edges, and introduce a practical and computationally not demanding…