Related papers: Combinatorics and topological weights of chromatin…
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local,…
The interplay of topological constraints and Coulomb interactions in static and dynamic properties of charged polymers is investigated by numerical simulations and scaling arguments. In the absence of screening, the long-range interaction…
Upon a matrix representation of a binary bipartite network, via the permutation invariance, a coupling geometry is computed to approximate the minimum energy macrostate of a network's system. Such a macrostate is supposed to constitute the…
We numerically examine the nonlinear rubber elasticity of topologically constrained polymer networks. We propose a simple and effective model based on Graessley and Pearson's topological model (GP model) for describing the topological…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
The topological interaction arising in interlinked polymeric rings such as DNA catenanes is considered. More specifically, the free energy for a pair of linked random walk rings is derived where the distance $R$ between two segments each of…
As complex networks find applications in a growing range of disciplines, the diversity of naturally occurring and model networks being studied is exploding. The adoption of a well-developed collection of network taxonomies is a natural…
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and…
Real-world networks process structured connections since they have non-trivial vertex degree correlation and clustering. Here we propose a toy model of structure formation in real-world weighted network. In our model, a network evolves by…
Leveraging topological properties in the response of electromagnetic systems can greatly enhance their potential. Although the investigation of singularity-based electromagnetics and non-Hermitian electronics has considerably increased in…
The classification of topological materials is revisited using advanced computational workflows that integrate hybrid density functional theory calculations with exact Hartree-Fock exchange. Unlike previous studies, our workflow optimizes…
When two periodic potentials compete in materials, one may adopt the other, which straightforwardly generates topological defects. Of particular interest are domain walls in charge-, dipole-, and spin-ordered systems, which govern…
We present a unified framework to systematically embed complex knotted and linked structures, beyond the torus family, into diverse topological phases, including Hopf insulators, classical spin liquids, topological semimetals, and…
We have developed different network approaches to complex patterns of frictional interfaces (contact areas developments). Here, we analyze the dynamics of static friction. We found, under the correlation measure, the fraction of triangles…
Geometry can be used to explain many properties commonly observed in real networks. It is therefore often assumed that real networks, especially those with high average local clustering, live in an underlying hidden geometric space.…
Being ubiquitous, solitons have particle-like properties, exhibiting behaviour often associated with atoms. Bound solitons emulate dynamics of molecules, though solitonic analogues of polymeric materials have not been considered yet. Here…
Impact of an intruder on granular matter leads to formation of mesoscopic force networks seen particularly clearly in the recent experiments carried out with photoelastic particles, e.g., Clark et al., Phys. Rev. Lett., 114 144502 (2015).…
Gaining insight about ensembles of magnetic configurations, that could originate the confining string tension between quarks, constitutes a major concern in current lattice investigations. This interest also applies to a different approach,…
The structure of the network can be described by motifs, which are subgraphs that often repeat themselves. In order to understand the structure of network motifs, it is of great importance to study subgraphs from the perspective of…
We address the role of topology in the energy transport process that occurs in networks of photosynthetic complexes. We take inspiration from light harvesting networks present in purple bacteria and simulate an incoherent dissipative energy…