Related papers: Compact phases of polymers with hydrogen bonding
We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not unexpectedly, found to exhibit a pronounced peak well below the…
The thermodynamics of a homopolymeric chain with both Van der Waals and highly-directional hydrogen bond interaction is studied. The effect of hydrogen bonds is to reduce dramatically the entropy of low-lying states and to give raise to…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
We investigate a lattice model of polymers where the nearest-neighbour monomer-monomer interaction strengths differ according to whether the local configurations have so-called ``hydrogen-like'' formations or not. If the interaction…
We study a single self avoiding hydrophilic hydrophobic polymer chain, through Monte Carlo lattice simulations. The affinity of monomer $i$ for water is characterized by a (scalar) charge $\lambda_{i}$, and the monomer-water interaction is…
The presence of ordered structures such as helices in collapsed states of polymer chains is still an open question challenging physics and biology. In this work, we present a potential model for polymer chains with monomers that are not…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
We investigate the addition of stiffness to the lattice model of hydrogen-bonded polymers in two and three dimensions. We find that, in contrast to polymers that interact via a homogeneous short-range interaction, the collapse transition is…
We present results for a lattice model of bio-polymers where the type of $\beta$-sheet formation can be controlled by different types of hydrogen bonds depending on the relative orientation of close segments of the polymer. Tuning these…
We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…
We have performed chain-growth simulations of minimalistic hybrid lattice models for polymers interacting with interfaces of attractive solid substrates in order to gain insights into the conformational transitions of the polymers in the…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
We introduce a polymer model where the transition from swollen to compact configurations is due to interactions between the monomers and the solvent. These interactions are the origin of the effective attractive interactions between…
A two-dimensional square-lattice model for the formation of secondary structures in proteins, the hydrogen-bonding model, is extended to include the effects of solvent quality. This is achieved by allowing configuration-dependent…
Conformational phases of a semiflexible off-lattice homopolymer model near an attractive substrate are investigated by means of multicanonical computer simulations. In our polymer-substrate model, nonbonded pairs of monomers as well as…
We have performed parallel tempering Monte Carlo simulations using a simple continuum heteropolymer model for proteins. All ten heteropolymer sequences which we have studied have shown first-order transitions at low temperature to ordered…
The phase structure of a homopolymer chain is investigated in terms of a universal theoretical model, designed to describe the infrared limit of slow spatial variations. The effects of chirality are studied and compared with the influence…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
We report Monte Carlo simulations of a lattice-polymer model that can account for both polymer crystallization and liquid-liquid demixing in solutions of semiflexible homopolymers. In our model, neighboring polymer segments can have…
A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative…