Related papers: Compact phases of polymers with hydrogen bonding
By means of Monte Carlo computer simulations in the isothermal-isobaric ensemble, we investigated the interaction of a hydrophobic ligand with the hydrophobic surfaces of various curvatures (planar, convex and concave). A simple…
We present a Bethe approximation to study lattice models of linear polymers. The approach is variational in nature and based on the cluster variation method (CVM). We focus on a model with $(i)$ a nearest neighbor attractive energy…
The adsorption of a collagen fragment on both a hydrophobic, hydrogen-terminated and a hydrophilic, natively oxidised Si surface is investigated using all-atom molecular dynamics. While favourable direct protein-surface interactions via…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
This report deals with phase transition in Bond Fluctuation Model (BFM) of a linear homo polymer on a two dimensional square lattice. Each monomer occupies a unit cell of four lattice sites. The condition that a lattice site can at best be…
We consider a model of two (fully) compact polymer chains, coupled through an attractive interaction. These compact chains are represented by Hamiltonian paths (HP), and the coupling favors the existence of common bonds between the chains.…
We investigate the cooperative effects of a single finite chain of monomers near an attractive substrate by first constructing a conformational pseudo-phase diagram based on the thermal fluctuations of energetic and structural quantities.…
Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures…
We study the dynamics of water confined between hydrophobic flat surfaces at low temperature. At different pressures, we observe different behaviors that we understand in terms of the hydrogen bonds dynamics. At high pressure, the formation…
We obtain the solution of models of self-avoiding walks with attractive interactions on Husimi lattices built with squares. Two attractive interactions are considered: between monomers on first-neighbor sites and not consecutive along a…
We report on self-assembly, clustering, and conformational phases of peptides on inorganic semiconductor surfaces. The peptide-covered surface fraction can differ by a factor of 25, depending mainly on surface and peptide polarity. Low…
We study simple lattice systems to demonstrate the influence of interpenetrating bond networks on phase behavior. We promote interpenetration by using a Hamiltonian with a weakly repulsive interaction with nearest neighbors and an…
We study the ground-state physics of a single-component Haldane model on a hexagonal two-leg ladder geometry with a particular focus on strongly interacting bosonic particles. We concentrate our analysis on the regime of less than one…
The density of electronic one-particle states in monolayer graphene is studied by performing the Hybrid Monte-Carlo simulations of the tight-binding model for electrons on the pi orbitals of carbon atoms which make up the graphene lattice.…
Motivated by recent experimental results in ultra-thin helimagnetic Holmium films, we have performed an extensive classical Monte Carlo simulation of films of different thickness, assuming a Hamiltonian with six inter-layer exchange…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…
We improve a lattice model of water introduced by Sastry, Debenedetti, Sciortino, and Stanley to give insight on experimental thermodynamic anomalies in supercooled phase, taking into account the correlations between intra-molecular…
Current major approaches to access surface hydrophobicity include directly introducing hydrophobic nonpolar groups/molecules into surface or elaborately fabricating surface roughness. Here, for the first time, molecular dynamics simulations…
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…
In this work we analyze a particular setup with ultracold atoms trapped in state-dependent lattices. We show that any asymmetry in the contact interaction translates into one of two classes of correlated hopping. After deriving the…