Related papers: Statistical properties of contact vectors
This paper investigates the structure-property relations of thin-walled lattices under dynamic longitudinal compression, characterized by their cross-sections and heights. These relations elucidate the interactions of different geometric…
Last decade, numerous giant data center networks are built to provide increasingly fashionable web applications. For two integers $m\geq 0$ and $n\geq 2$, the $m$-dimensional DCell network with $n$-port switches $D_{m,n}$ and…
Neural networks are often represented as graphs of connections between neurons. However, despite their wide use, there is currently little understanding of the relationship between the graph structure of the neural network and its…
We study the dynamics and equilibrium profile shapes of contact lines for wetting in the case of a spatially inhomogeneous solid wall with stripe defects. Using a phase-field model with conserved dynamics, we first numerically determine the…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…
For a closed connected manifold N, we establish the existence of geometric structures on various subgroups of the contactomorphism group of the standard contact jet space J^1N, as well as on the group of contactomorphisms of the standard…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Monte Carlo simulations show that long-range interactions play a major role in determining the folding rates of 48-mer three-dimensional lattice polymers modelled by the Go potential. For three target structures with different native…
An $r$-identifying code on a graph $G$ is a set $C\subset V(G)$ such that for every vertex in $V(G)$, the intersection of the radius-$r$ closed neighborhood with $C$ is nonempty and different. Here, we provide an overview on codes for the…
Understanding the structures why links are formed is an important and prominent research topic. In this paper, we therefore consider the link prediction problem in face-to-face contact networks, and analyze the predictability of new and…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
In this paper we study properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…
The simplest approximation of interaction potential between amino-acids in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation.…
Previous research has shown a strong correlation of protein folding rates to the native state geometry, yet a complete explanation for this dependence is still lacking. Here we study the rate-geometry relationship with a simple statistical…
Jamming is a phenomenon shared by a wide variety of systems, such as granular materials, foams, and glasses in their high density regime. This has motivated the development of a theoretical framework capable of explaining many of their…
Using remarkably simple experimental techniques it is possible to gently break a metallic contact and thus form conducting nanowires. During the last stages of the pulling a neck-shaped wire connects the two electrodes, the diameter of…
In this study, we propose a Kernel-PCA model designed to capture structure-function relationships in a protein. This model also enables ranking of reaction coordinates according to their impact on protein properties. By leveraging machine…
A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly…
High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…
This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…