Related papers: Statistical Properties of Contact Maps

Contact path geometries are curved geometric structures on a contact manifold comprising smooth families of paths modeled on the family of all isotropic lines in the projectivization of a symplectic vector space. Locally such a structure is…

We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries.…

We provide a naturally isomorphic description of the persistence map from merge trees to barcodes in terms of a monotone map from the partition lattice to the subset lattice. Our description is local, which offers the potential to speed up…

We study the localisation of lattice polymer models near a permeable interface in two dimensions. Localisation can arise due to an interaction between the polymer and the interface, and can be altered by a preference for the bulk solvent on…

In this work, Transition Probability Matrix (TPM) is proposed as a new method for extracting the features of nodes in the graph. The proposed method uses random walks to capture the connectivity structure of a node's close neighborhood. The…

In this paper we present a novel framework for sequence to shape maps. These combinatorial maps realize exponentially many shapes, and have preimages which contain extended connected subgraphs of diameter n (neutral networks). We prove that…

Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique…

We study the two-species symbiotic contact process (2SCP), recently proposed in [de Oliveira, Santos and Dickman, Phys. Rev. E {\bf 86}, 011121 (2012)] . In this model, each site of a lattice may be vacant or host single individuals of…

We consider two or more simple symmetric walks on some graphs, e.g. the real line, the plane or the two dimensional comb lattice, and investigate the properties of the distance among the walkers.

In polymer physics it is typically assumed that excluded volume interactions are effectively screened in polymer melts. Hence, chains could be described by an effective random walk without excluded volume interactions. In this letter, we…

Throughout developmental biology and ecology, transport can be driven by nonlocal interactions. Examples include cells that migrate based on contact with pseudopodia extended from other cells, and animals that move based on their vision of…

Polymer chains undergoing a continuous adsorption-desorption transition are studied through extensive computer simulations. A three-dimensional self-avoiding walk lattice model of a polymer chain grafted onto a surface has been treated for…

The solvability of the three-dimensional O($N$) scalar field theory in the large $N$ limit makes it an ideal toy model exhibiting "walking" behavior, expected in some SU($N$) gauge theories with a large number of fermion flavors. We study…

We consider a mortal random walker on a family of hierarchical graphs in the presence of some trap sites. The configuration comprising the graph, the starting point of the walk, and the locations of the trap sites is taken to be exactly…

In this work, we present a simple and efficient generator of polymeric linear chains, based on a random self-avoiding walk process. The chains are generated using a discrete process of growth, in cubic networks and in a finite time, without…

Movement is a fundamental behaviour of organisms that brings about beneficial encounters with resources and mates, but at the same time exposes the organism to dangerous encounters with predators. The movement patterns adopted by organisms…

We define the crossing graph of a given embedded graph (such as a road network) to be a graph with a vertex for each edge of the embedding, with two crossing graph vertices adjacent when the corresponding two edges of the embedding cross…

We study the metric structure of walks on graphs, understood as Lipschitz sequences. To this end, a weighted metric is introduced to handle sequences, enabling the definition of distances between walks based on stepwise vertex distances and…

Laman graphs naturally arise in structural mechanics and rigidity theory. Specifically, they characterize minimally rigid planar bar-and-joint systems which are frequently needed in robotics, as well as in molecular chemistry and polymer…

We show that the contact map of the native structure of globular proteins can be reconstructed starting from the sole knowledge of the contact map's principal eigenvector, and present an exact algorithm for this purpose. Our algorithm…