Related papers: Compact phases of polymers with hydrogen bonding
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…
The phase diagram for a two-dimensional self-avoiding walk model on the square lattice incorporating attractive short-ranged interactions between parallel sections of walk is derived using numerical transfer matrix techniques. The model…
We present a Monte Carlo study of a lattice gas driven out of equilibrium by a local hopping bias. Sites can be empty or occupied by one of two types of particles, which are distinguished by their response to the hopping bias. All particles…
We address the problem of inverse polymer swelling. This phenomenon, in which a collapsed polymer chain swells upon decreasing temperature, can be observed experimentally in so-called thermoreversible homopolymers in aqueous solution, and…
We present studies of an effective model which is a simple generalization of the standard model of a local pair superconductor with on-site pairing (i.e., the model of hard core bosons on a lattice) to the case of finite pair binding…
By taking into account base-base stacking interactions we improve the Generalized Model of Polypeptide Chain (GMPC). Based on a one-dimensional Potts-like model with many-particle interactions, the GMPC describes the helix-coil transition…
We use complete enumeration and Monte Carlo techniques to study two-dimensional self-avoiding polymer chains with quenched ``charges'' $\pm 1$. The interaction of charges at neighboring lattice sites is described by $q_i q_j$. We find that…
We present an overview of the recent progress that has been made in understanding the origin of hydrophobic interactions. We discuss the different character of the solvation behavior of apolar solutes at small and large length scales. We…
Globular proteins as well as recently synthesized colloids engineered with differently charged surface regions have in common a reduced bonding valence and a complex interaction pattern dominated by like-charge attraction and…
A theoretical model for the effect of water hydrogen bonding on the thermodynamics of hydrophobic hydration is proposed as a combination of the classical density functional theory with the recently developed probabilistic approach to water…
Motivated by the rich phase diagram of the high temperature superconductors, we introduce a toy model with three state variables which can be interpreted as two state particles and holes. The Hamiltonian has a term which favors…
We use quantum Monte Carlo simulations to obtain zero-temperature state diagrams for strongly correlated lattice bosons in one and two dimensions under the influence of a harmonic confining potential. Since harmonic traps generate a…
We study the nature of the ground state of the strongly-coupled two dimensional extended boson Hubbard model on a square lattice. We demonstrate that strong but finite on-site interaction U along with a comparable nearest-neighbor repulsion…
This paper reviews recent Monte Carlo simulation studies of the glassy behavior in thin polymer films. The simulations employ a version of the bond-fluctuation lattice model, in which the glass transition is driven by the competition…
We report Monte Carlo simulations of the self-assembly of supramolecular polymers based on a model of patchy particles. We find a first-order phase transition, characterized by hysteresis and nucleation, toward a solid bundle of polymers,…
Motivated by the idea that intrinsically disordered proteins (IDPs) condense into liquid-like droplets within cells, we carry out Monte Carlo simulations of a polymer lattice model to study the relationship between charge patterning and…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
In this work, we report our results on the phase transition of a flexible homopolymer from a stretched chain to a compact globule. The Wang-landau method is used to study the thermodynamic properties of a the chain up to 512 monomers. We…
We investigate the isotropic-to-nematic phase transition in systems of hard helical particles, using Onsager theory and Monte Carlo computer simulations. Motivation of this work resides in the ubiquity of the helical shape motif in many…
The stability of a $\beta$-sheeted conformation and its transition into a random coil are studied with a 2D lattice biopolymer model. At low temperature and low external force, the polymer folds back and forth on itself and forms a…