Related papers: Compact phases of polymers with hydrogen bonding
Hard helices can be regarded as a paradigmatic elementary model for a number of natural and synthetic soft matter systems, all featuring the helix as their basic structural unit: from natural polynucleotides and polypeptides to synthetic…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
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…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
We consider polymers made of magnetic monomers (Ising or Heisenberg-like) in a good solvent. These polymers are modeled as self-avoiding walks on a cubic lattice, and the ferromagnetic interaction between the spins carried by the monomers…
We consider self-avoiding lattice polygons, in the hypercubic lattice, as a model of a ring polymer adsorbed at a surface and either being desorbed by the action of a force, or pushed towards the surface. We show that, when there is no…
The phase diagram of hard helices differs from its hard rods counterpart by the presence of chiral "screw" phases stemming from the characteristic helical shape, in addition to the conventional liquid crystal phases also found for rod-like…
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…
We present Monte Carlo simulation results for square-well homopolymers at a series of bond lengths. Although the model contains only isotropic pairwise interactions, under appropriate conditions this system shows spontaneous chiral symmetry…
The study of the high pressure phase diagram of hydrogen has continued with renewed effort for about one century as it remains a fundamental challenge for experimental and theoretical techniques. Here we employ an efficient molecular…
Ribbons are topological objects of biological and technological importance. Here, we study the folding of thick ribbons with hydrophobic surfaces in a bad solvent in regimes in which either the ribbon's thickness or the solvent molecule…
By means of continuous space Monte Carlo simulation we study conformational structures formed by star and comb heteropolymers during kinetics of folding from the coil to the globule, as well as the corresponding equilibrium states on going…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…
In this article, we report a fully ab initio variational Monte Carlo study of the linear, and periodic chain of Hydrogen atoms, a prototype system providing the simplest example of strong electronic correlation in low dimensions. In…
Hydrophobic interactions are central to biological self-assembly and soft matter organization, yet their microscopic origins remain debated. A key hallmark is the strengthening of attraction between hydrophobic solutes with increasing…
We study the statistical properties of hydrophobic/polar model sequences with unique native states on the square lattice. It is shown that this ensemble of sequences differs from random sequences in significant ways in terms of both the…
We investigate polymers pulled away from an interacting surface, where the force is applied to the untethered endpoint and at an angle $\theta$ to the surface. We use the canonical self-avoiding walk model of polymers and obtain the phase…
The influence of the patchiness and correlations in the distribution of hydrophobic and polar residues at the interface between two rigid biomolecules on their recognition ability is investigated in idealised coarse-grained lattice models.…
We introduce and implement a Monte Carlo scheme to study the equilibrium statistics of polymers in the globular phase. It is based on a model of "interacting elastic lattice polymers" and allows a sufficiently good sampling of long and…