Related papers: Combinatorics and topological weights of chromatin…

We discuss the extension of loop quantum gravity to topspin networks, a proposal which allows topological information to be encoded in spin networks. We will show that this requires minimal changes to the phase space, C*-algebra and Hilbert…

In an increasingly interconnected world, understanding and summarizing the structure of these networks becomes increasingly relevant. However, this task is nontrivial; proposed summary statistics are as diverse as the networks they…

The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms leading to the…

A general relation for the dependence of nearest neighbor degree correlations on degree is derived. Dependence of local clustering on degree is shown to be the sole determining factor of assortative versus disassortative mixing in networks.…

Networked structures arise in a wide array of different contexts such as technological and transportation infrastructures, social phenomena, and biological systems. These highly interconnected systems have recently been the focus of a great…

It has long been observed that trimethylamin N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work of the two osmolytes, various…

In this study, we performed comprehensive morphological investigations of the spontaneous formations of effective network structures among elements in coupled logistic maps, specifically with a delayed connection change. Our proposed model…

Based on a local greedy numerical algorithm, we compute the topology of weighted, directed, and of unlimited extension networks of non identical Kuramoto oscillators which simultaneously satisfy 2 criteria: i) global frequency…

Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…

Elucidating the physics of a concentrated suspension of ring polymers, or of an ensemble of ring polymers in a complex environment, is an important outstanding question in polymer physics. Many of the characteristic features of these…

More than two decades ago, combinatorial topology was shown to be useful for analyzing distributed fault-tolerant algorithms in shared memory systems and in message passing systems. In this work, we show that combinatorial topology can also…

Numerical studies of the average size of trivially knotted polymer loops with no excluded volume are undertaken. Topology is identified by Alexander and Vassiliev degree 2 invariants. Probability of a trivial knot, average gyration radius,…

Network analysis is a powerful way of modeling chromatin interactions. Assortativity is a network property used in social sciences to identify factors affecting how people establish social ties. We propose a new approach, using chromatin…

We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to…

Granular materials exhibit intricate force networks, often concentrated in chains rather than being uniformly distributed. These meso-scale structures are complex to characterize, owing to their heterogeneous and anisotropic nature. We…

The viscous flow of polymer chains in dense melts is dominated by topological constraints whenever the single chain contour length, N, becomes larger than the characteristic scale Ne, defining comprehensively the macroscopic rheological…

Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…

We derive an exact representation of the topological effect on the dynamics of sequence processing neural networks within signal-to-noise analysis. A new network structure parameter, loopiness coefficient, is introduced to quantitatively…

A variant of coupled-cluster theory is described here, wherein the degrees of freedom are fluctuations of fragments between internally correlated states. The effects of intra-fragment correlation on the inter-fragment interaction are…

Chimera states, marked by the coexistence of order and disorder in systems of coupled oscillators, have captivated researchers with their existence and intricate patterns. Despite ongoing advances, a fully understanding of the genesis of…