Related papers: Topological features of proteins from amino acid r…

The topology of many real complex networks has been conjectured to be embedded in hidden metric spaces, where distances between nodes encode their likelihood of being connected. Besides of providing a natural geometrical interpretation of…

Upon loading, atomic networks can feature delayed viscoplastic relaxation. However, the effect of composition and structure on such a relaxation remains poorly understood. Herein, relying on accelerated molecular dynamics simulations and…

Protein function depends on both protein structure and amino acid (aa) sequence. Here we show that modular features of both structure and function can be quantified from the aa sequences alone for the small (40,42 aa) plaque-forming amyloid…

When training transformers on graph-structured data, incorporating information about the underlying topology is crucial for good performance. Topological masking, a type of relative position encoding, achieves this by upweighting or…

In this paper we investigate the role of native geometry on the kinetics of protein folding based on simple lattice models and Monte Carlo simulations. Results obtained within the scope of the Miyazawa-Jernigan indicate the existence of two…

Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…

Quantification and classification of protein structures, such as knotted proteins, often requires noise-free and complete data. Here we develop a mathematical pipeline that systematically analyzes protein structures. We showcase this…

The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…

We solve the problem of determining basic topological properties of flat samples by performing measurements on their outer edge. The global maximum of four probe resistances shows a characteristic behaviour, which is dependent on the genus…

The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…

Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…

To explore the relation between network structure and function, we studied the computational performance of Hopfield-type attractor neural nets with regular lattice, random, small-world and scale-free topologies. The random net is the most…

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…

One of the hallmarks of topological insulators is the correspondence between the value of its bulk topological invariant and the number of topologically protected edge modes observed in a finite-sized sample. This bulk-boundary…

The concept of robustness of regulatory networks has been closely related to the nature of the interactions among genes, and the capability of pattern maintenance or reproducibility. Defining this robustness property is a challenging task,…

We investigate structural transitions in adaptive networks where node states remain fixed and only the connections evolve via state-dependent rewiring. Using a general framework characterized by probabilistic rules for disconnection and…

Studies of how protein fold have shown that the way protein clumps form in the test tube is similar to how proteins form the so-called ``amyloid'' deposits that are the pathological signal of a variety of diseases, among them the memory…

Polymerization and formation of crosslinked polymer networks are important processes in manufacturing, materials fabrication, and in the case of hydrated polymer networks, synthesis of biomedical materials, drug delivery, and tissue…

Networks of elastic fibers are ubiquitous in biological systems and often provide mechanical stability to cells and tissues. Fiber reinforced materials are also common in technology. An important characteristic of such materials is their…

In real networks complex topological features are often associated with a diversity of interactions as measured by the weights of the links. Moreover, spatial constraints may as well play an important role, resulting in a complex interplay…