Related papers: Long range correlations and folding angle in polym…
We point out that the correlation between folding times and $\sigma = (T_{\theta } - T_{f})/T_{\theta }$ in protein-like heteropolymer models where $T_{\theta }$ and $T_{f}$ are the collapse and folding transition temperatures was already…
We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined into nano-channels and under periodic compression. We…
The process of adsorption on a planar repulsive, "marginal" and attractive wall of long-flexible polymer chains with excluded volume interactions is investigated. The performed scaling analysis is based on formal analogy between the polymer…
A polymer folding model on the square lattice is constructed with attractive contact interactions of strength 1/c^2, 0<c<1. The corresponding model on a dynamical random lattice, with freely fluctuating co-ordination number at each vertex,…
While proteins have been treated as particles with a spherically symmetric interaction, of course in reality the situation is rather more complex. A simple step towards higher complexity is to treat the proteins as non--spherical particles…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
We show that non-entangled polymers display an elastic-like behaviour at a macroscopic scale (probed at some 0.100 mm thickness) up to at least hundred degrees above the glass transition temperature. This observation, found under…
We computed the phase-separation behavior and effective interactions of colloid-polymer mixtures in the "protein limit", where the polymer radius of gyration is much larger than the colloid radius. For ideal polymers, the critical colloidal…
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 investigate the time evolution of the heteropolymer model introduced by Iori, Marinari and Parisi to describe some of the features of protein folding mechanisms. We study how the (folded) shape of the chain evolves in time. We find that…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
We study the conformational properties of complex Gaussian polymers containing $f_c$ linear branches and $f_r$ closed loops, periodically tethered at $n$ branching points to either a linear polymer backbone (generalized bottlebrush…
Brownian motion and viscoelasticity of semiflexible polymers is a subject that has been studied for many years. Still, rigorous analysis has been hindered due to the difficulty in handling the constraint that polymer chains cannot be…
In suitable environments, proteins, nucleic acids and certain synthetic polymers fold into unique conformations. This work shows that it is possible to construct lattice models of foldable heteropolymers by expressing the energy only in…
The calculation of Euclidean distance between points is generalized to one-dimensional objects such as strings or polymers. Necessary and sufficient conditions for the minimal transformation between two polymer configurations are derived.…
In this paper we study the shape characteristics of a polymer chain in a good solvent using a mesoscopic level of modelling. The dissipative particle dynamics simulations are performed in the $3D$ space at a range of chain lengths $N$. The…
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…
In the context of the coloured stochastic vertex model in a quadrant, we identify a family of observables whose averages are given by explicit contour integrals. The observables are certain linear combinations of $q$-moments of the coloured…
In our original article (Phys. Chem. Chem. Phys., 2012, 14, 60446053) a convergence problem resulted in an averaging error in computing the entropy from a set of Wang-Landau Monte-Carlo simulations. Here we report corrected results for the…