Related papers: Statistical Properties of Contact Maps
This note aims to bring attention to a simple class of discrete dynamical systems exhibiting some complex behaviour. Each of these systems is defined as a self-mapping of the unit square and is obtained by coupling two families of…
We consider the partially asymmetric simple exclusion process (PASEP) when its steady-state probability distribution function can be written in terms of a linear superposition of product measures with a finite number of shocks. In this case…
Fix two lattice paths $P$ and $Q$ from $(0,0)$ to $(m,r)$ that use East and North steps with $P $ never going above $Q$. Bonin et al. show that the lattice paths that go from $(0,0)$ to $(m,r)$ and remain bounded by $P$ and $Q$ can be…
Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D…
The contact process on an infinite homogeneous tree is shown to exhibit at least two phase transitions as the infection parameter lambda is varied. For small values of lambda a single infection eventually dies out. For larger lambda the…
We consider the problem of morphing between contact representations of a plane graph. In an $\mathcal F$-contact representation of a plane graph $G$, vertices are realized by internally disjoint elements from a family $\mathcal F$ of…
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…
The random walk with choice is a well known variation to the random walk that first selects a subset of $d$ neighbours nodes and then decides to move to the node which maximizes the value of a certain metric; this metric captures the number…
Using molecular dynamics simulation of a standard bead-spring model we investigate the density crossover scaling of strictly two-dimensional self-avoiding polymer chains focusing on properties related to the contact exponent set by the…
A map is a connected topological graph cellularly embedded in a surface and a complete map is a cellularly embedded complete graph in a surface. In this paper, all automorphisms of complete maps of order n are determined by permutations on…
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…
Directed paths have been used extensively in the scientific literature as a model of a linear polymer. Such paths models in particular the conformational entropy of a linear polymer and the effects it has on the free energy. These directed…
We study a model for a random walk of two classes of particles (A and B). Where both species are present in the same site, the motion of A's takes precedence over that of B's. The model was originally proposed and analyzed in Maragakis et…
One of the most powerful techniques to study protein structures is to look for recurrent fragments (also called substructures or spatial motifs), then use them as patterns to characterize the proteins under study. An emergent trend consists…
Entropies based on walks on graphs and on their line-graphs are defined. They are based on the summation over diagonal and off-diagonal elements of the thermal Green's function of a graph also known as the communicability. The walk…
Conventional cell tracking methods detect multiple cells in each frame (detection) and then associate the detection results in successive time-frames (association). Most cell tracking methods perform the association task independently from…
We work with combinatorial maps to represent graph embeddings into surfaces up to isotopy. The surface in which the graph is embedded is left implicit in this approach. The constructions herein are proof-relevant and stated with a subset of…
In $2013$ a novel self-assembly strategy for polypeptide nanostructure design which could lead to significant developments in biotechnology was presented in [Design of a single-chain polypeptide tetrahedron assembled from coiled-coil…
Uncovering the mechanism behind the scaling law in human trajectories is of fundamental significance in understanding many spatio-temporal phenomena. In combination of the exploration and the preferential returns, we propose a simple…
We map the conformation space of a simple lattice polymer chain to a network, where (i) the vertices of the network have a one-to-one correspondence to the conformations of the chain, and (ii) a link between two vertices indicates the…