Related papers: Quinary lattice model of secondary structures of p…
We consider a lattice polymer model (random walk), in which the walk is allowed to visit lattice bonds at most twice. Such a model might have some relevance to describe statistical properties of RNA molecules. In order to mimic base…
We write exact equations for the thermodynamic properties of a linear polymer molecule confined to walk on a lattice of finite size. The dimension of the space in which the lattice resides can be arbitrary. We also calculate polymer…
There have been separate studies of the polymer collapse transition, where the collapse was induced by two different types of attraction. In each case, the configurations of the polymer were given by the same subset of random walks being…
We investigate the mechanisms underlying selective molecular recognition of single heteropolymers at chemically structured planar surfaces. To this end, we study systems with two-letter (HP) lattice heteropolymers by exact enumeration…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
A simple quasiparticle model, motivated by lowest-order perturbative QCD, is proposed. It is applied to interpret the lattice QCD equation of state. A reasonable reproduction of the lattice data is obtained. In contrast to existing…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
We investigate a Kac-type many particle model that allows a reference-free description of plastic deformation. In the framework of the model a solid body is described by a set of particle positions. A lattice is fitted to the particle…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We…
Simple hidden Markov models are proposed for predicting secondary structure of a protein from its amino acid sequence. Since the length of protein conformation segments varies in a narrow range, we ignore the duration effect of length…
The E. coli chemosensory lattice, consisting of receptors, kinases, and adaptor proteins, is an important test case for biochemical signal processing. Kinase output is characterized by precise adaptation to a wide range of background ligand…
The statistical thermodynamics of binary mixtures of polyatomic species was developed on a generalization in the spirit of the lattice-gas model and the quasi-chemical approximation (QCA). The new theoretical framework is obtained by…
We consider a model of a biomembrane with attached proteins. The membrane is represented by a near spherical continuous surface and attached proteins are described as discrete rigid structures which attach to the membrane at a finite number…
We propose a planar chain system, which is a simple mechanical system with a constraint. It is composed of $N$ masses connected by $N-1$ light links. It can be considered as a model of a chain system, e.g., a polymer, in which each bond is…
In this paper we introduce a novel method of deriving a pairwise potential for protein folding. The potential is obtained by optimization procedure, which simultaneously maximizes the energy gap for {\it all} proteins in the database. To…
We present a simple model for the underlying structure of protein-protein pairwise interaction graphs that is based on the way in which proteins attach to each other in experiments such as yeast two-hybrid assays. We show that data on the…
We present analytic results for a special dimer model on the {\em non-bipartite} and {\em non-planar} checkerboard lattice that does not allow for parallel dimers surrounding diagonal links. We {\em exactly} calculate the number of closed…
We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending…