Related papers: Helical structures from an isotropic homopolymer m…
We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters we…
We report the results of Monte Carlo simulations investigating the effect of a spherical confinement within a simple model for a flexible homopolymer. We use the parallel tempering method combined with multi-histogram reweighting analysis…
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…
We present results of Monte Carlo study of the monomer-monomer correlation functions, static structure factor and asphericity characteristics of a single homopolymer in the coil and globular states for three distinct architectures of the…
We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations,…
Using an algorithm for simulating equilibrium configurations, we study a fluctuating helical polymer either (i) contained in a cylindrical pore or (ii) wound around a cylindrical rod. We work in the regime where both the contour length and…
We consider a model for periodic patterns of charges constrained over a cylindrical surface. In particular we focus on patterns of chiral helices, achiral rings or vertical lamellae, with the constraint of global electroneutrality. We study…
We investigate by means of a number of different dynamical Monte Carlo simulation methods the self-assembly of equilibrium polymers in dilute, semidilute and concentrated solutions under good-solvent conditions. In our simulations, both…
We consider the rupture dynamics of a homopolymer chain pulled at one end at a constant loading rate. Our model of the breakable polymer is related to the Rouse chain, with the only difference that the interaction between the monomers is…
Inspired by recent experiments on the spatial organization of bacterial chromosomes, we consider a type of "bottle brush" polymer consisting of a flexible backbone chain, to which flexible side loops are connected. We show that such a model…
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 present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of the individual polymers and their…
Many biological and synthetic materials self-assemble into helical or twisted aggregates. The shape is determined by a complex interplay between elastic forces and the orientation and chirality of the constituent molecules. We study this…
We study the static properties of a semiflexible polymer exposed to a quenched random environment by means of computer simulations. The polymer is modeled as two-dimensional Heisenberg chain. For the random environment we consider hard…
We propose and solve a simple model describing secondary structure formation in random hetero-polymers. It describes monomers with a combination of one-dimensional short-range interactions (representing steric forces and hydrogen bonds) and…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
Mono- and poly-disperse melts of oligomers (average length 10 monomers) of trans-1,4-polyisoprene are simulated in full atomistic detail. The force-field is developed by means of a mixture of ab initio quantum-chemistry and an automatic…
We present a scaling theory describing the collapse of a homopolymer chain in poor solvent. At time t after the beginning of the collapse, the original Gaussian chain of length N is streamlined to form N/g segments of length R(t), each…
Chiral polymers are ubiquitous in nature and in the cellular context they are often found in association with membranes. Here we show that surface bound polymers with an intrinsic twist and anisotropic bending stiffness can exhibit a sharp…
We develop the hybrid Monte Carlo method for simulations of single off-lattice polymer chains. We discuss implementation and choice of simulation parameters in some detail. The performance of the algorithm is tested on models for…