Related papers: Side-chain and backbone ordering in Homopolymers

We report results from multicanonical simulations of polyglutamic acid chains of length of ten residues. For this simple polypeptide we observe a decoupling of backbone and side-chain ordering in the folding process. While the details of…

We investigate the relation between backbone and side-chain ordering in a small protein. For this purpos e we have performed multicanonical simulations of the villin headpiece subdomain HP-36, an often used to y model in protein studies.…

Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short…

Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…

We study a homopolymer model of a protein chain, where each monomer carries a dipole moment. To mimic the geometry of the peptidic bond, these dipoles are constrained to be locally perpendicular to the chain. The tensorial character of the…

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 thermodynamics of a homopolymeric chain with both Van der Waals and highly-directional hydrogen bond interaction is studied. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give raise to…

We have performed parallel tempering Monte Carlo simulations using a simple continuum heteropolymer model for proteins. All ten heteropolymer sequences which we have studied have shown first-order transitions at low temperature to ordered…

Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…

Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…

Mesogens, which are typically stiff rodlike or disklike molecules, are able to self-organize into liquid crystal (LC) phases in a certain temperature range. Such mesogens, or LC groups, can be attached to polymer chains in various…

In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher…

Exchanging hydrophobic alkyl-based side chains to hydrophilic glycol-based side chains is a widely adopted method for improving mixed-transport device performance, despite the impact on solid state packing and polymer-electrolyte…

We investigate the addition of stiffness to the lattice model of hydrogen-bonded polymers in two and three dimensions. We find that, in contrast to polymers that interact via a homogeneous short-range interaction, the collapse transition is…

What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…

The processability and optoelectronic properties of organic semiconductors can be tuned and manipulated via chemical design. The substitution of the alkyl side chains by oligoethers has recently been successful for applications such as…

In organic optoelectronics, order of conjugated molecules is required for good charge transport, but strong aggregation behavior may generate grain boundaries and trapping, opposing those benefits. Side chains on a polymer's backbone are…

We study the interplay of intrinsic-electronic and environmental factors on long-range charge transport across molecular chains with up to $N\sim 80$ monomers. We describe the molecular electronic structure of the chain with a tight-binding…

The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…

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…