Related papers: Compact phases of polymers with hydrogen bonding
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Hydrogen bonding is modeled in terms of virtual exchange of protons between water molecules. A simple lattice model is analyzed, using ideas and techniques from the theory of correlated electrons in metals. Reasonable parameters reproduce…
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions…
We investigate the consequences of correlated hopping on the ground state properties of hard-core bosons on a square lattice as revealed by extensive exact diagonalizations and quantum Monte Carlo simulations. While for non interacting…
The phase diagram of lattice hard core bosons with nearest-neighbor interactions allowed to vary independently, from repulsive to attractive, along different crystallographic directions, is studied by Quantum Monte Carlo simulations. We…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide…
We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are…
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…
We study a single statistical amphiphilic copolymer chain AB in a selective solvent (e.g.water). Two situations are considered. In the annealed case, hydrophilic (A) and hydrophobic (B) monomers are at local chemical equilibrium and both…
Recently it has been shown that a two-dimensional model of self-attracting polymers based on attracting segments displays two phase transitions, a theta-like collapse between swollen polymers and a globular state and another between the…
Interest in the protein folding problem has motivated a wide range of theoretical and experimental studies of the kinetics of the collapse of flexible homopolymers. In this Paper a phenomenological model is proposed for the kinetics of the…
Chain molecules play a key role in the polymer field and in living cells. Our focus is on a new homopolymer model of a linear chain molecule subject to an attractive self-interaction promoting compactness. We analyze the model using simple…
Thin films of binary mixtures that interact through isotropic forces and directionally specific "hydrogen bonding" are considered through Monte Carlo simulations. We show, in good agreement with experiment, that the single phase of these…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
We introduce a novel coarse-grained bead-spring model for flexible polymers to systematically examine the effects of an adjusted bonded potential on the formation and stability of structural macrostates in a thermal environment. The density…
We study the model of a partially directed flexible or semi-flexible homopolymer on a square lattice, subject to an externally applied force, in a direction either parallel to, or perpendicular to the preferred direction. The polymer is…
Through Monte Carlo simulations and the Associating Lattice Gas Model, the phases of a two-dimensional fluid under hydrophilic confinement are evaluated. The model, in its unconfined version, reproduces the anomalous behavior of water…