Related papers: Controlling Secondary Structures of Bio-Polymers w…
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…
A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearest-neighbor interaction of a Morse-like potential…
The Cellular Potts model, also known as the Glazier-Graner-Hogeweg model, is a lattice-based approach by which biological tissues at the level of individual cells can be numerically studied. Traditionally, a square or hexagonal underlying…
We present Monte Carlo simulations of a three-state lattice gas, half-filled with two types of particles which attract one another, irrespective of their identities. A bias drives the two particle species in opposite directions,…
Applying the contact density chain-growth algorithm to lattice heteropolymers, we identify the conformational transitions of a nongrafted hydrophobic-polar heteropolymer with 103 residues in the vicinity of a polar, a hydrophobic, and a…
Mechanically bonded membranes of interlocked ring polymers are a significant generalization of conventional elastic sheets, where connectivity is provided by covalent bonding, and represent a promising class of topological meta-materials.…
In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher…
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…
A model for a monolayer of two types of particles spontaneously forming ordered patterns is studied by a mesoscopic theory and by MC simulations. We assume hard-cores of the same size for both components, short-range attraction long-range…
Polymer chains decorated with a fraction of monomers capable of forming reversible bonds form transient polymer networks that are important in soft and biological systems. If chains are flexible and the attractive monomers are all of the…
We propose a mean-field model to explore the equilibrium coupling between micelle aggregation and lattice choice in neutral copolymer and selective solvent mixtures. We find both thermotropic and lyotropic transitions from face-centered…
Triangular lattice models for pattern formation by hard-core soft-shell particles at interfaces are introduced and studied in order to determine the effect of the shell thickness and structure. In model I, we consider particles with…
We consider various lattice models of polymers: lattice trees, lattice animals, and self-avoiding walks. The polymer interacts with a surface (hyperplane), receiving a unit energy reward for each site in the surface. There is an adsorption…
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…
The shape of biological shells, such as cell nuclei, membranes, and vesicles, often deviates from a perfect sphere due to an interplay of complex interactions with a myriad of molecular structures. In particular, semiflexible biopolymers…
We present a mesoscopic lattice model for non-ideal fluid flows with directional interactions, mimicking the effects of hydrogen-bonds in water. The model supports a rich and complex structural dynamics of the orientational order parameter,…
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…
It was recently proposed to use the stray magnetic fields of superconducting vortex lattices to trap ultracold atoms for building quantum emulators. This calls for new methods for engineering and manipulating of the vortex states. One of…
We use a coarse grained molecular model of supported lipid bilayers to study the formation of adhesion domains. We find that this process is a first order phase transition, triggered by a combination of pairwise short range attractive…
Dynamical control of the nonlinear optical properties of solids -- with light itself -- will be essential for future ultrafast photonic technologies. Previously, methods to modulate nonlinear processes including second-harmonic generation…