Related papers: Compact phases of polymers with hydrogen bonding
Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
A lattice model of a hetero-polymer with random hydrophilic-hydrophobic charges interacting with the solvent is introduced, whose continnuum counterpart has been proposed by T. Garel, L. Leibler and H. Orland {J. Phys. II France 4, 2139…
Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter $x$ and effective self-attraction promoting…
Molecular dynamic simulations were employed to study a water-like model confined between hydrophobic and hydrophilic plates. The phase behavior of this system is obtained for different distances between the plates and particle-plate…
Hydrogen bonding plays a role in the microphase separation behavior of many block copolymers, such as those used in lithography, where the stronger interactions due to H-bonding can lead to a smaller period for the self-assembled…
We develop the hybrid Monte Carlo method for simulations of single off-lattice polymer chains. We discuss implementation and choice of simulation parameters in some detail. The performance of the algorithm is tested on models for…
We explore the coupling between the helix-coil and coil-globule transitions of a helical polymer using Monte Carlo simulations. A very rich state diagram is found. Each state is characterized by a specific configuration of the chain which…
A system of two self and mutual interacting ring polymers, close together in space, can display several competing equilibrium phases and phase transitions. Using Monte Carlo simulations and combinatorial arguments on a corresponding lattice…
There have been separate studies of the polymer collapse transition, where the collapse was induced by two different types of attraction. In each case, the configurations of the polymer were given by the same subset of random walks being…
We define a lattice model for the interaction of a polymer with water. We solve the model in a suitable approximation. In the case of a non-polar homopolymer, for reasonable values of the parameters, the polymer is found in a non-compact…
We review recent simulation studies of interfaces between immiscible homopolymer phases. Special emphasis is given to the presentation of efficient simulation techniques and powerful methods of data analysis, such as the analysis of…
The collapse and swelling behavior of a generic homopolymer is studied using implicit-solvent, explicit-cosolvent Langevin dynamics computer simulations for varying interaction strengths. The systematic investigation reveals that polymer…
We study the behaviour of a hydrophobic chain near a hydrophobic boundary in two dimensions, using the decorated lattice model of Berkema and Widom [G.T. Barkema and B. Widom, J. Chem. Phys. 113, 2349 (2000)] to obtain effective,…
We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar…
We report the results of Monte Carlo simulations investigating the effect of a spherical confinement within a simple model for a flexible homopolymer. We use the parallel tempering method combined with multi-histogram reweighting analysis…
We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…
The phase structure of self-avoiding polymerized membranes is studied by extensive Hybrid Monte Carlo simulations. Several folding transitions from the flat to a collapsed state are found. Using a suitable order parameter and finite size…
We develop a lattice-based Monte Carlo simulation method for charged mixtures capable of treating dielectric heterogeneities. Using this method, we study oil-water mixtures containing an antagonistic salt, with hydrophilic cations and…
We study numerically a lattice model of semiflexible homopolymers with nearest neighbor attraction and energetic preference for straight joints between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched Rosenbluth…