相关论文: Fractal globule as an artificial molecular machine
Highly nonlinear behavior of a system of discrete sites on a lattice is observed when a specific feedback loop is introduced into models employing coupled map lattices, quantum cellular automata, or the real-valued analogues of the latter.…
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 have developed different network approaches to analyze complex patterns of frictional interfaces (contact area developments). Network theory is a fundamental tool for the modern understanding of complex systems in which, by a simple…
We investigate two and three-dimensional shell-structured-inflatable froths, which can be constructed by a recursion procedure adding successive layers of cells around a germ cell. We prove that any froth can be reduced into a system of…
We describe an example of a structurally stable heteroclinic network for which nearby orbits exhibit irregular but sustained switching between the various sub-cycles in the network. The mechanism for switching is the presence of spiralling…
This work reports an extensive study of three-dimensional topological ordered phases that, in one of the directions behave like usual topological order concerning mobility of excitations, but in the perpendicular plane manifest type-II…
Thin elastic solids are easily deformed into a myriad of three-dimensional shapes, which may contain sharp localized structures as in a crumpled candy wrapper, or have smooth and diffuse features like the undulating edge of a flower.…
Chromosomes in the nucleus assemble into hierarchies of 3D domains that, during interphase, share essential features with a knot-free condensed polymer known as the fractal globule (FG). The FG-like chromosome likely affects macromolecular…
In this article, we present a novel box-covering algorithm for analyzing the fractal properties of complex networks. Unlike traditional algorithms that impose a predetermined box size, our approach assigns nodes to boxes identified by their…
Network self-similarity or fractality are widely accepted as an important topological property of metabolic networks; however, recent studies cast doubt on the reality of self-similarity in the networks. Therefore, we perform a…
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…
The spring network model constitutes the backbone in the representations of a host of physical systems. In this work, we report the disturbance-driven microscopic dynamics of an isolated, closed spring network of spherical topology in…
Entangled networks are ubiquitous in tissues, polymers, and fabrics. However, their mechanics remain insufficiently understood due to the complexity of the topological constraints at the network level. Here, we develop a mathematical…
Polymer's network is treated as an anisotropic fractal with fractional dimensionality D = 1 + \epsilon close to one. Percolation model on such a fractal is studied. Using the real space renormalization group approach of Migdal and Kadanoff…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…
For a given pcf self-similar fractal, a certain network (weighted graph) is constructed whose ideal boundary is (homeomorphic to) the fractal. This construction is the first representation of a connected self-similar fractal as the boundary…
The tube model is a central concept in polymer physics, and allows to reduce the complex many-filament problem of an entangled polymer solution to a single filament description. We investigate the probability distribution function of…
Covering a network with the minimum possible number of boxes can reveal interesting features for the network structure, especially in terms of self-similar or fractal characteristics. Considerable attention has been recently devoted to this…
Active fluids, composed of individual self-propelled agents, can generate complex large-scale coherent flows. A particularly important laboratory realization of such an active fluid is a system composed of microtubules, aligned in a…
Molecular simulations provide a powerful means to unravel the complex relationships between network architecture and the mechanical response of polymer networks, with a particular emphasis on rupture and fracture phenomena. Although…