Related papers: Remark on Protein Collapse from a Random Walk
We consider a model of two (fully) compact polymer chains, coupled through an attractive interaction. These compact chains are represented by Hamiltonian paths (HP), and the coupling favors the existence of common bonds between the chains.…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Using exact enumeration methods and Monte Carlo simulations we study the phase diagram relative to the conformational transitions of a two dimensional diblock copolymer. The polymer is made of two homogeneous strands of monomers of…
We considered diffusion-driven processes on small-world networks with distance-dependent random links. The study of diffusion on such networks is motivated by transport on randomly folded polymer chains, synchronization problems in…
A simple model of globular proteins which incorporates anisotropic attractions is proposed. It is closely related to models used to model simple hydrogen-bonding molecules such as water. Theories for both the fluid and solid phases are…
We consider the phase transition in the system of n simultaneously developing random walks on the halfline x>=0. All walks are independent on each others in all points except the origin x=0, where the point well is located. The well depth…
This investigation is motivated by a result we proved recently for the random transposition random walk: the distance from the starting point of the walk has a phase transition from a linear regime to a sublinear regime at time $n/2$. Here,…
In this work, we report our results on the phase transition of a flexible homopolymer from a stretched chain to a compact globule. The Wang-landau method is used to study the thermodynamic properties of a the chain up to 512 monomers. We…
We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the…
Chain molecules play a key role in the polymer field and in living cells. Our focus is on a new homopolymer model of a linear chain molecule subject to an attractive self-interaction promoting compactness. We analyze the model using simple…
In this article we study a one dimensional model for a polymer in a poor solvent: the random walk on $\mathbb{Z}$ penalized by its range. More precisely, we consider a Gibbs transformation of the law of the simple symmmetric random walk by…
A comprehensive, semi-quantitative model for the thermodynamics of hydrophobic solvation is presented. The model is based on a very simple premise suggested by the scaled particle theory and treats both solute and solvent molecules as hard…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
Extensive Monte Carlo data analysis gives clear evidence that collapsed linear polymers in two dimensions fall in the universality class of athermal, dense self-avoiding walks, as conjectured by B.Duplantier [Phys.Rev.Lett. 71, 4274…
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…
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 show that Wang-Landau sampling, combined with suitable Monte Carlo trial moves, provides a powerful method for both the ground state search and the determination of the density of states for the hydrophobic-polar (HP) protein model and…
The random walk with hyperbolic probabilities that we are introducing is an example of stochastic diffusion in a one-dimensional heterogeneous media. Although driven by site-dependent one-step transition probabilities, the process retains…
We consider the motion of a particle in a periodic two dimensional flow perturbed by small (molecular) diffusion. The flow is generated by a divergence free zero mean vector field. The long time behavior corresponds to the behavior of the…
We estimate the probability regarding polymerization of a macromolecule which is made of distinct monomers. The lattice model of the random walk has been used to mimic the conformations of an ideal chain in two and three dimensions. It has…