Related papers: Long range correlations and folding angle in polym…
We study the dynamics of a polymer when it is quenched from a $\theta$ solvent into a good or bad solvent by means of a Langevin equation. The variation of the radius of gyration is studied as a function of time. For the first stage of…
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…
Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape.…
Chirality in polymeric systems enables a wide range of emergent optical, mechanical, and transport phenomena, yet a unified framework that quantitatively connects molecular-scale geometry to chiral behavior remains lacking. Existing…
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…
By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
The conformational behavior of a coarse-grained finite polymer chain near an attractive spherical surface was investigated by means of multicanonical Monte Carlo computer simulations. In a detailed analysis of canonical equilibrium data…
Through extensive molecular simulations we determine a phase diagram of attractive, flexible polymer chains in two and three dimensions. A surprisingly rich collection of distinct crystal morphologies appear, which can be finely tuned…
We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…
The present research is dedicated to provide deeper understanding of the impact of complex architecture of branched polymers on their behaviour in solvents. The folding dynamics of macromolecules and hydrodynamics of polymer fluids are…
We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…
The statistical mechanics of a linear non-interacting polymer chain with a large number of monomers is considered with fixed angular momentum. The radius of gyration for a linear polymer is derived exactly by functional integration. This…
Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
Stretched polymers with attractive interaction are studied in two and three dimensions. They are described by biased self-avoiding random walks with nearest neighbour attraction. The bias corresponds to opposite forces applied to the first…
Random heteropolymers are a minimal description of biopolymers and can provide a theoretical framework to the investigate the formation of loops in biophysical experiments. A two--state model provides a consistent and robust way to study…
Polymer mixtures fractionate between phases depending on their molecular weight. Consequently, by varying solvent conditions, a polydisperse polymer sample can be separated between phases so as to achieve a particular molecular weight…
We study winding angles of oriented polymers with orientation-dependent interaction in two dimensions. Using exact analytical calculations, computer simulations, and phenomenological arguments, we succeed in finding the variance of the…