Related papers: On Heteropolymer Shape Dynamics
We have analyzed the dependence of average ground state energy per monomer, $e$, of the complex of two random heteropolymers with quenched sequences, on chain length, $n$, in the ensemble of chains with uniform distribution of primary…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
Recent measurements of the force versus extension curves in stretched single stranded DNA, under conditions where the hydrogen bonding between complementary bases is inhibited, provide a new handle for the study of self-avoiding effects in…
We consider a random walk in a random potential, which models a situation of a random polymer and we study the annealed and quenched costs to perform long crossings from a point to a hyperplane. These costs are measured by the so called…
We study the time evolution of the R\'enyi entanglement entropies following a quantum quench in a two-dimensional (2D) free-fermion system. By employing dimensional reduction, we effectively transform the 2D problem into decoupled chains, a…
The dynamical correlations of a model consisting of particles constrained on the line and interacting with a nearest--neighbour Lennard--Jones potential are computed by molecular--dynamics simulations. A drastic qualitative change of the…
We introduce a simple theoretical model, the Freely Jointed Chain with quenched hinges (qFJC), which captures the quenched disorder in the local bending stiffness of the polymer. In this article, we analyze the tensile elasticity of the…
Shape transformations in driven and damped molecular chains are considered. Closed chains of weakly coupled molecular subunits under the action of spatially homogeneous time-periodic external field are studied. The coupling between the…
The effect of topology on the collapse transition and instantaneous shape of an energy polydisperse polymer (a model heteropolymer) is studied by means of computer simulations. In particular, we consider three different chain topology,…
We investigate the effects of quenched disorder, in the form of site and bond dilution, on the physics of the $S=1/2$ antiferromagnetic Heisenberg model on even-leg ladders. Site dilution is found to prune rung singlets and thus create…
In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…
We consider general disordered models of pinning of directed polymers on a defect line. This class contains in particular the $(1+1)$--dimensional interface wetting model, the disordered Poland--Scheraga model of DNA denaturation and other…
A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
We study the ground-state properties of one-dimensional fluids of classical (i.e., non-quantum) particles interacting pairwisely via a potential, at the fixed particle density $\rho$. Restricting ourselves to periodic configurations of…
The dynamics of polymer-nanoparticle (NP) mixtures, which involves multiple scales and system-specific variables, has posed a long-standing challenge on its theoretical description. In this paper, we construct a microscopic theory for…
We consider the continuous time version of the Random Walk Pinning Model (RWPM), studied in [5,6,7]. Given a fixed realization of a random walk Y$ on Z^d with jump rate rho (that plays the role of the random medium), we modify the law of a…
We describe method to discuss thermodynamics of a defected semi-flexible homo-polymer chain in the two and three dimensions using fully directed self-avoiding walk lattice model. The defects are located along a line and these defects are…
We have developed a theory of polymer entanglement using an extended Cahn-Hilliard functional, with two extra terms. One is a nonlocal attractive term, operating over mesoscales, which is interpreted as giving rise to entanglement, and the…