Related papers: The nonlinear elasticity of an $\alpha$-helical po…
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…
I propose a variation of the standard worm--like chain model to account for internal order parameter (helix/coil) fields on the polymer chain. This internal order parameter field influences polymer conformational statistics by locally…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
Recent developments of microscopic mechanical experiments allow the manipulation of individual polymer molecules in two main ways: \textit{uniform} stretching by external forces and \textit{non-uniform} stretching by external fields. Many…
We study the mechanical and conformational properties of networks of helical polymers with a combination of Monte Carlo simulations based on the Wang-Landau algorithm and the Three-chain Model. We find that the stress-strain behavior of…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We explore the coupling between the helix-coil and coil-globule transitions of a helical polymer using Monte Carlo simulations. A very rich state diagram is found. Each state is characterized by a specific configuration of the chain which…
Single-chain elasticity of polyethylene at $\theta$ point up to 90% of stretching with respect to its contour length is computed by Monte-Carlo simulation of an atomistic model in continuous space. The elasticity law together with the…
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
We present a study of the bend angle distribution of semiflexible polymers of short and intermediate lengths within the wormlike chain model. This enables us to calculate the elastic response of a stiff molecule to a bending moment. Our…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
The structure of a polystyrene matrix filled with tightly cross-linked polystyrene nanoparticles, forming an athermal nanocomposite system, is investigated by means of a Monte Carlo sampling formalism. The polymer chains are represented as…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
We introduce a simple geometric model for a double-stranded and double-helical polymer. We study the statistical mechanics of such polymers using both analytical techniques and simulation. Our model has a single energy-scale which…
We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an $\alpha$-helix conformation. The polypeptide is assumed to be adsorbed…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
We simulate structural phase behavior of polymer-grafted colloidal particles by molecular Monte Carlo technique. Interparticle potential, which has a finite repulsive square-step outside a rigid core of the colloid, was previously confirmed…
We study structural phase transition of polymer-grafted colloidal particles by Monte Carlo simulations on hard spherical particles. The interaction potential, which has a weak repulsive step outside the hard core, was validated with use of…