Related papers: Compact phases of polymers with hydrogen bonding
The two dimensional square lattice hard-core boson Hubbard model with near neighbor interactions has a `checkerboard' charge density wave insulating phase at half-filling and sufficiently large intersite repulsion. When doped, rather than…
We report dynamic Monte Carlo simulation on conformational transition of H-shaped branched polymers by varying main chain (backbone) and side chain (branch) length. H-shaped polymers in comparison with equivalent linear polymers exhibit a…
The some dynamic properties of a random heteropolymer in the condensed state are studied in the mode coupling approximation. In agreement with recent report a dynamic friction increasing is predicted for the random heteropolymer with…
Despite of many efforts, we still lack a clear picture on how heavy electrons emerge and develop on the Kondo lattice. Here we introduce a key concept named the hybridization bond phase and propose a scenario based on phase correlation to…
We study the localisation of lattice polymer models near a permeable interface in two dimensions. Localisation can arise due to an interaction between the polymer and the interface, and can be altered by a preference for the bulk solvent on…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
Applying the contact density chain-growth algorithm to lattice heteropolymers, we identify the conformational transitions of a nongrafted hydrophobic-polar heteropolymer with 103 residues in the vicinity of a polar, a hydrophobic, and a…
In this work, results are presented of Hybrid-Monte-Carlo simulations of the tight-binding Hamiltonian of graphene, coupled to an instantaneous long-range two-body potential which is modeled by a Hubbard-Stratonovich auxiliary field. We…
A microscopic model is proposed for the interactions between sickle hemoglobin molecules based on information from the protein data bank. A Monte Carlo simulation of a simplified two patch model is carried out, with the goal of…
Atomic-scale helices exist as motifs for several material lattices. We examine a tight-binding model for a single one-dimensional monatomic chain with a p-orbital basis coiled into a helix. A topologically nontrivial phase emerging from…
We theoretically investigate qualitative features of the field-temperature ($H$-$T$) phase diagram of superconductors with strong attractive interaction lying in the BCS-BEC crossover regime. Starting with a simple attractive Hubbard model,…
Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type of energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we…
A generic lattice model for systems containing particles interacting with short-range attraction long-range repulsion (SALR) potential that can be solved exactly in one dimension is introduced. We assume attraction J_1 between the first…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…
We present a theoretical model for predicting the phase behavior of polymer solutions in which phase separation competes with oligomerization. Specifically, we consider scenarios in which the assembly of polymer chains into stoichiometric…
We study a solution of interacting semiflexible polymers with curvature energy in poor-solvent conditions on the d-dimensional cubic lattice using mean-field theory and Monte Carlo computer simulations. Building upon past studies on a…
We study a two-species bosonic Hubbard model on a two-dimensional square lattice by means of quantum Monte Carlo simulations. In addition to the usual contact repulsive interactions between the particles, the Hamiltonian has an…
An earlier one-dimensional lattice model of hydrophobic attraction is extended to two and three dimensions and studied by Monte Carlo simulation. The solvent-mediated contribution to the potential of mean force between hydrophobic solute…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…