Related papers: Solvation model dependency of helix-coil transitio…
The folding transition of single, long semiflexible polymers was studied with special emphasis on the chain length effect using Monte Carlo simulations. While a relatively short chain (10-25 Kuhn segments) undergoes a large discrete…
For a model deca-alanine peptide the cavity (ideal hydrophobic) contribution to hydration favors the helix state in the coil-to-helix transition and the paired helix bundle in the assembly of two helices. The energetic contributions of…
The helix-coil transition is modified by grafting to a surface. This modification is studied for short peptides capable of forming $\alpha$-helices. Three factors are involved: (i) the grafting can induced change of the boundary free energy…
The investigation of freezing transitions of single polymers is computationally demanding, since surface effects dominate the nucleation process. In recent studies we have systematically shown that the freezing properties of flexible,…
The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide…
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…
We have simulated 10-residue polyalanine chain by multicanonical method to visualize the 3D topographic picture of the free energy landscape over the whole range of temperatures, hence to show the funnel along the folding pathway…
We present results from all-atom molecular dynamics simulations for the nonequilibrium dynamics of the collapse and helix-coil transition in polyalanine. In particular, we compare the influence of three different thermostats, viz., the…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…
The conformations of semiflexible (bio)polymers are studied in flow through geometrically structured microchannels. Using mesoscale hydrodynamics simulations, we show that the polymer undergoes a rod-to-helix transition as it moves from the…
Helix-coil transition in polypeptides is an example of a spin model with a preferred spin direction, in the sense that a theoretical formulation of this problem requires to assign a preferred value of spin to the helical conformation in…
We calculate the Yang-Lee zeros for characteristic temperatures of the helix-coil transition in a continuum model of polyalanine. The distribution of these zeros differs from predictions of the Zimm-Bragg theory and supports recent claims…
The extension elasticity of rod-coil mutliblock copolymers is analyzed for two experimentally accessible situations. In the quenched case, when the architecture is fixed by the synthesis, the force law is distinguished by a sharp change in…
A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate…
The influence of monomer-monomer interactions on the scaling exponents and shape characteristics of a single polymer chain in a selective solvent is investigated using Langevin dynamics simulations. By systematically increasing the…
Biological molecules can form hydrogen bonds between nearby residues, leading to helical secondary structures. The associated reduction of configurational entropy leads to a temperature dependence of this effect: the "helix-coil…
We study polymer-polymer phase separation in a common good solvent by means of Monte Carlo simulations of the bond-fluctuation model. Below a critical, chain-length dependent concentration, no phase separation occurs. For higher…
Systematic microcanonical inflection-point analysis of precise numerical results obtained in extensive generalized-ensemble Monte Carlo simulations reveals a bifurcation of the coil-globule transition line for polymers with a bending…
Most helix-coil transition theories can be characterized by a set of three parameters: energetic, describing the (free) energy cost of forming a helical state in one repeating unit; entropic, accounting for the decrease of entropy due to…
The nature of the globule-coil transition of surface-confined polymers has been an issue of debate. Here this 2D collapse transition is studied through a partially directed lattice model. In the general case of polymers with positive…