相关论文: Pseudoknots in a Homopolymer
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
The phase structure of a homopolymer chain is investigated in terms of a universal theoretical model, designed to describe the infrared limit of slow spatial variations. The effects of chirality are studied and compared with the influence…
Interest in the protein folding problem has motivated a wide range of theoretical and experimental studies of the kinetics of the collapse of flexible homopolymers. In this Paper a phenomenological model is proposed for the kinetics of the…
We study numerically the tightness of prime flat knots in a model of self-attracting polymers with excluded volume. We find that these knots are localised in the high temperature swollen regime, but become delocalised in the low temperature…
Recently it has been shown that a two-dimensional model of self-attracting polymers based on attracting segments displays two phase transitions, a theta-like collapse between swollen polymers and a globular state and another between the…
We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not unexpectedly, found to exhibit a pronounced peak well below the…
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible…
An extensive study of single block copolymer knots containing two kinds of monomers $A$ and $B$ is presented. The knots are in a solution and their monomers are subjected to short range interactions that can be attractive or repulsive. In…
We consider the extended Hubbard diamond chain with an arbitrary number of particles driven by chemical potential. The interaction between dimer diamond chain and nodal couplings is considered in the atomic limit (no hopping), while the…
Mesoscopic structure of the periodically alternating layers of stretched homopolymer chains surrounded by perpendicularly oriented oligomeric tails is studied for the systems with both strong (ionic) and weak (hydrogen) interactions. We…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
We use complete enumeration and Monte Carlo techniques to study two-dimensional self-avoiding polymer chains with quenched ``charges'' $\pm 1$. The interaction of charges at neighboring lattice sites is described by $q_i q_j$. We find that…
Pseudodiagrams are knot or link diagrams where some of the crossing information is missing. Pseudoknots are equivalence classes of pseudodiagrams, where equivalence is generated by a natural set of Reidemeister moves. In this paper, we…
Random heteropolymers are a minimal description of biopolymers and can provide a theoretical framework to the investigate the formation of loops in biophysical experiments. A two--state model provides a consistent and robust way to study…
We study the statistical mechanics of double-stranded semi-flexible polymers using both analytical techniques and simulation. We find a transition at some finite temperature, from a type of short range order to a fundamentally different…
Recently it has been shown that a two-dimensional model of self-attracting polymers based on attracting segments with the addition of stiffness displays three phases: a swollen phase, a globular, liquid-like phase, and an anisotropic…
We propose a new analytic approach to study the phase diagram of random heteropolymers, based on the cavity method. For copolymers we analyze the nature and phenomenology of the glass transition as a function of sequence correlations.…
We examine the effects of a phenomenological pseudogap on the T=0 K phase diagram of a high temperature superconductor within a self-consistent model which exhibits a d-wave pairing symmetry. At the mean-field level the presence of a…
The two-dimensional attractive Hubbard model is studied in the weak to intermediate coupling regime by employing a non-perturbative approach. It is first shown that this approach is in quantitative agreement with Monte Carlo calculations…