相关论文: Statistical Properties of Contact Maps
Based on a newly developed contact-density chain-growth algorithm, we have simulated a nongrafted peptide in the vicinity of different attractive substrates. We analyzed the specificity of the peptide adsorption by focussing on the…
Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence information remains very challenging. Recently evolutionary coupling (EC) analysis, which predicts contacts by…
Face-to-face interactions reveal recurring patterns, suggesting the possibility of shared underlying mechanisms. More specifically, inter-contact durations, contact durations and number of contacts per edge share similar heavy-tail…
Long-distance characteristics of small-world networks have been studied by means of self-avoiding walks (SAW's). We consider networks generated by rewiring links in one- and two-dimensional regular lattices. The number of SAW's $u_n$ was…
Darwinian evolution can be illustrated as an uphill walk in a landscape, where the surface consists of genotypes, the height coordinates represent fitness, and each step corresponds to a point mutation. Epistasis, roughly defined as the…
Evaluating accessible conformational space is computationally expensive and thermal motions are partly neglected in computer models of molecular interactions. This produces error into the estimates of binding strength. We introduce a method…
The set of visited sites and the number of visited sites are two basic properties of the random walk trajectory. We consider two independent random walks on a hyper-cubic lattice and study ordering probabilities associated with these…
The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native…
We use a one-dimensional random walk on $D$-dimensional hyper-spheres to determine the critical behavior of statistical systems in hyper-spherical geometries. First, we demonstrate the properties of such walk by studying the phase diagram…
We consider the enumeration of walks on the non-negative lattice $\mathbb{N}^d$, with steps defined by a set $\mathcal{S} \subset \{-1, 0, 1\}^d \setminus \{\mathbf{0}\}$. Previous work in this area has established asymptotics for the…
We reduce the problem of counting self-avoiding walks in the square lattice to a problem of counting the number of integral points in multidimensional domains. We obtain an asymptotic estimate of the number of self-avoiding walks of length…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…
It is known that the limiting behavior of the contact process strongly depends upon the geometry of the graph on which particles evolve: while the contact process on the regular lattice exhibits only two phases, the process on homogeneous…
Lattice paths effectively model phenomena in chemistry, physics and probability theory. Asymptotic enumeration of lattice paths is linked with entropy in the physical systems being modeled. Lattice paths restricted to different regions of…
The walk distances in graphs are defined as the result of appropriate transformations of the $\sum_{k=0}^\infty(tA)^k$ proximity measures, where $A$ is the weighted adjacency matrix of a graph and $t$ is a sufficiently small positive…
Simplified representations of macromolecules help in rationalising and understanding the outcome of atomistic simulations, and serve to the construction of effective, coarse-grained models. The number and distribution of coarse-grained…
Returning walks on a lattice are sequences of moves that start at a given lattice site and return to the same site after $n$ steps. Determining the total number of returning walks of a given length $n$ is a typical graph-theoretical problem…
We present an algorithm for the exhaustive enumeration of all monomer sequences and conformations of short lattice proteins as described by the hydrophobic-polar (HP) model. The algorithm is used for an exact identification of all designing…
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…
A recently developed model of random walks on a $D$-dimensional hyperspherical lattice, where $D$ is {\sl not} restricted to integer values, is used to study polymer growth near a $D$-dimensional attractive hyperspherical boundary. The…