Related papers: Random Matrix Solution of a Polymer Collapse Model
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
A linear copolymer made of two reciprocally attracting N-monomer blocks collapses to a compact phase through a novel transition, whose exponents are determined with extensive MC simulations in two and three dimensions. In the former case,…
Long linear polymers in dilute solutions are known to undergo a collapse transition from a random coil (expand itself) to a compact ball (fold itself up) when the temperature is lowered, or the solvent quality deteriorates. A natural model…
We consider a directed variant of the negative-weight percolation model in a two-dimensional, periodic, square lattice. The problem exhibits edge weights which are taken from a distribution that allows for both positive and negative values.…
We study the XY model on a lattice with fluctuating connectivity. The expectation is that at an appropriate critical point such a system corresponds to a compactified boson coupled to 2d quantum gravity. Our simulations focus, in…
The dynamics of compaction of hard cross-shaped pentamers on the 2D square lattice is investigated. The addition of new particles is controlled by diffusive relaxation. It is shown that the filling process terminates at a glassy phase with…
A model is discussed where all operators are constructed from a quantum scalar field whose energy spectrum takes on all real values. The Schr\"odinger picture wave function depends upon space and time coordinates for each particle, as well…
We develop off-lattice simulations of semiflexible polymer chains subjected to applied mechanical forces using Markov Chain Monte Carlo. Our approach models the polymer as a chain of fixed-length bonds, with configurations updated through…
We have studied the transition in shape of two dimensional polyampholytes using Monte Carlo simulation. We observe that polymers with randomly charged monomers get into a globular shape at lower temperatures, provided that their total…
We study the model of a partially directed flexible or semi-flexible homopolymer on a square lattice, subject to an externally applied force, in a direction either parallel to, or perpendicular to the preferred direction. The polymer is…
Two-dimensional Rydberg atoms are modeled at low temperatures by means of the classical Monte Carlo method. The Coulomb repulsion of charged ions competing with the repulsive van der Waals long-range tail is modeled by a number of…
For $n\in [-2,2]$ the $O(n)$ model on a random lattice has critical points to which a scaling behaviour characteristic of 2D gravity interacting with conformal matter fields with $c\in [-\infty,1]$ can be associated. Previously we have…
We introduce in this paper two dimensional lattice models whose continuum limit belongs to the $N=2$ series. The first kind of model is integrable and obtained through a geometrical reformulation, generalizing results known in the $k=1$…
We study a classical model of fully-packed loops on the square lattice, which interact through attractive loop segment interactions between opposite sides of plaquettes. This study is motivated by effective models of interacting quantum…
We propose and solve a simple model describing secondary structure formation in random hetero-polymers. It describes monomers with a combination of one-dimensional short-range interactions (representing steric forces and hydrogen bonds) and…
This thesis deals with some $(1+1)$-dimensional lattice path models from the KPZ universality class: the directed random polymer with inverse-gamma weights (known as log-gamma polymer) and its zero temperature degeneration, i.e. the last…
While the structure of chromatin has been studied in great detail on length scales below 30 nm, amazingly little is known about the higher-order folding motifs of chromatin in interphase. Recent experiments give evidence that the folding…
We introduce a random matrix framework for studying statistical-mechanical lattice systems through spectral observables. Equilibrium configurations sampled from a Boltzmann measure are mapped to matrix ensembles whose covariance structure…
Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures…
We consider polymers in which M randomly selected pairs of monomers are restricted to be in contact. Analytical arguments and numerical simulations show that an ideal (Gaussian) chain of N monomers remains expanded as long as M<<N; its mean…