Related papers: Long range correlations and folding angle in polym…
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…
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…
The properties of polymer composites with nanofiller particles change drastically above a critical filler density known as the percolation threshold. Real nanofillers, such as graphene flakes and cellulose nanocrystals, are not idealized…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the…
We simulate entangled linear polymers in free-standing thin film geometries where the confining dimension is on the same scale or smaller than the bulk chain dimensions. We compare both film-averaged and layer-resolved, spatially…
We study conformations and dynamics of active star polymers. The analysis shows that active star polymers stretching behaviour is quite different from that of active linear chains. The visual inspection of conformations and bond-bond…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: (a) polymer sliding against a hard substrate, and (b) polymer sliding on…
We consider a mean-field model of a polymer with a spherically-symmetric finitely supported potential. We describe how the typical size of the polymer depends on the two parameters: the temperature, which approaches the critical value, and…
There are several simple criteria of folding to a native state in model proteins. One of them involves crossing of a threshold value of the RMSD distance away from the native state. Another checks whether all native contacts are…
The rheological behavior of polymer melts is strongly influenced by parameters such as chain length, chain stiffness, and architecture. In particular, shear thinning, characterized by a power-law decrease in shear viscosity with increasing…
Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
We study jamming in model freely rotating polymers as a function of chain length $N$ and bond angle $\theta_0$. The volume fraction at jamming, $\phi_J(\theta_0)$, is minimal for rigid-rod-like chains ($\theta_0 = 0$), and increases…
In molecular physics, it is often necessary to average over the orientation of molecules when calculating observables, in particular when modelling experiments in the liquid or gas phase. Evaluated in terms of Euler angles, this is closely…
We study a single flexible chain molecule grafted to a membrane which has pores of size slightly larger than the monomer size. On both sides of the membrane there is the same solvent. When this solvent is good, i.e. when the polymer is…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find…
Given the wide range of length scales, the analysis of polymer systems often requires coarse-graining, for which various levels of description may be possible depending on the phenomenon under consideration. Here, we provide a super-coarse…