Related papers: Secondary Structures in Long Compact Polymers
Monte Carlo simulations and finite-size scaling analysis have been carried out to study the critical behavior in a two-dimensional system of particles with two bonding sites that, by decreasing temperature or increasing density, polymerize…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
In this chapter we review the rich behavior of polymer chains embedded in a quenched random environment. We first consider the problem of a Gaussian chain free to move in a random potential with short-ranged correlations. We derive the…
Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance…
Rigid particles pack into structures, such as sand dunes on the beach, whose overall stability is determined by the average number of contacts between particles. However, when packing spatially extended objects with flexible shapes,…
We discuss various ensembles of homogeneous complex networks and a Monte-Carlo method of generating graphs from these ensembles. The method is quite general and can be applied to simulate micro-canonical, canonical or grand-canonical…
The demand for innovative synthetic polymers with improved properties is high, but their structural complexity and vast design space hinder rapid discovery. Machine learning-guided molecular design is a promising approach to accelerate…
We propose a new toy model of a heteropolymer chain capable of forming planar secondary structures typical for RNA molecules. In this model the sequential intervals between neighboring monomers along a chain are considered as quenched…
Processes on different length scales affect the dynamics of chain molecules. In this work, we focus on structures on the scale of a monomer and investigate polyolefins, i.e. hydrocarbon chains with different small scale architectures. We…
Using a mapping of compact polymers on the Manhattan lattice to spanning trees, we calculate exactly the average number of bends at infinite temperature. We then find, in a high temperature approximation, the energy of the system as a…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
We report several important observations that underscore the distinctions between the constrained-path Monte Carlo method and the continuum and lattice versions of the fixed-node method. The main distinctions stem from the differences in…
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a randomly cross-linked (RCL) polymer model, where…
Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind…
In this article, a novel cluster analysis algorithm was employed in the study of polymer coil to globule transition via single chain Monte Carlo simulations. The algorithm, which has been recently applied in Molecular Dynamics simulations…
We study autocorrelation times of physical observables in lattice QCD as a function of the molecular dynamics trajectory length in the hybrid Monte-Carlo algorithm. In an interval of trajectory lengths where energy and reversibility…
We study a Monte Carlo algorithm that is based on a specific (randomly shifted and dilated) lattice point set. The main result of this paper is that the mean squared error for a given compactly supported, square-integrable function is…
We present a Monte Carlo simulation of a polymer nematic for varying volume fractions, concentrating on the structure function of the sample. We achieve nematic ordering with stiff polymers made of spherical monomers that would otherwise…
Assuming Gaussian chain statistics along the chain contour, we generate by means of a proper fractal generator hyperbranched polymer trees which are marginally compact. Static and dynamical properties, such as the radial intrachain pair…
We study the behavior of self avoiding polymers in a background of vertically aligned rods that are either frozen into random positions or free to move horizontally. We find that in both cases the polymer chains are highly elongated, with…