相关论文: The nonlinear elasticity of an $\alpha$-helical po…

We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local…

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…

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…

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…

$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…

By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…

A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from…

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…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…

We analyze the stretching elasticity of a wormlike chain with a tension discontinuity resulting from a Hookean spring connecting its backbone to a fixed point. The elasticity of isolated semiflexible filaments has been the subject in a…

Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…

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…

Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…

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…

Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address…

The longitudinal response of single semiflexible polymers to sudden changes in externally applied forces is known to be controlled by the propagation and relaxation of backbone tension. Under many experimental circumstances, realized, e.g.,…

The elastic properties of two-component bilayer membranes are studied using a coarse grain model for amphiphilic molecules. The two species of amphiphiles considered here differ only in their length. Molecular Dynamics simulations are…

Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…

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…