Related papers: Side chain and backbone ordering in a polypeptide

In this paper we summarize some results of our theoretical investigations of helix-coil transition both in single-strand (polypeptides) and two-strand (polynucleotides) macromolecules. The Hamiltonian does not contain any parameter designed…

Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…

We study the conformations of polymer chains in a poor solvent, with and without bending rigidity, by means of a simple statistical mechanics model. This model can be exactly solved for chains of length up to N=55 using exact enumeration…

When gold is deposited on Si(553), the surface self-assembles to form a periodic array of steps with nearly perfect structural order. In scanning tunneling microscopy these steps resemble quasi-one-dimensional atomic chains. At temperatures…

We develop a theoretical description of the topological disentanglement occurring when torus knots reach the ends of a semi-flexible polymer under tension. These include decays into simpler knots and total unknotting. The minimal number of…

We consider various two-leg ladder models exhibiting gapped phases. All of these phases have short-ranged valence bond ground states, and they all exhibit string order. However, we show that short-ranged valence bond ground states divide…

In this supporting material for the main paper (the preceding submission), we show, in addition to the related information for the experiments, additional discussion that cannot fit in the main paper (due to the space constraint). It…

Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…

We study the electronic properties of coupled parallel Polyyne chains in a couple of symmetric stacking arrangements, namely the AA stacking and the stacking AB, with the single and triple carbon bonds of one chain aligned (AA) and…

Motivated by the structure of networks of cross-linked cytoskeletal biopolymers, we study the orientationally ordered phases in two-dimensional networks of randomly cross-linked semiflexible polymers. We consider permanent cross-links which…

We propose an experimental scheme to effectively assemble chains of dipolar gases with an uniform length in a multi-layer system. The obtained dipolar chains can form a chain crystal with the system temperature easily controlled by the…

We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers,…

We study long polymer chains in a poor solvent, confined to the space between two parallel hard walls. The walls are energetically neutral and pose only a geometric constraint which changes the properties of the coil-globule (or…

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…

We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is…

In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…

We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by…

Using multicanonical simulations, the authors study the effect of charged end groups on helix formation in alanine based polypeptides. They confirm earlier reports that neutral polyalanine exhibits a pronounced helix-coil transition in gas…

We study equilibrium shapes and shape transformations of a confined semiflexible chain inside a soft lipid tubule using simulations and continuum theories. The deformed tubular shapes and chain conformations depend on the relative magnitude…

X-shaped liquid crystalline molecules (XLCMs) are obtained by tethering two flexible end A-blocks and two flexible side B-blocks to a rigid backbone (R). A rich array of ordered structures can be formed from XLCMs, driven by the competition…