Related papers: Pseudoknots in a Homopolymer
We analyze the crystallization and collapse transition of a simple model for flexible polymer chains on simple cubic and face-centered cubic lattices by means of sophisticated chain-growth methods. In contrast to bond-fluctuation polymer…
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 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 analyze static properties of a strongly confined semiflexible polymer, i.e. either trapped in a closed space or compressed by external forces, in an athermal solvent. Like a flexible polymer case, we can resort to an analogy with the…
The presence of slipknots in configurations of proteins and DNA has been shown to affect their functionality, or alter it entirely. Historically, polymers are modeled as polygonal chains in space. As an alternative to space curves, we…
A cascade of phase transitions from square to hexagonal lattice is studied in 2D system of particles interacting via core-softened potential. Due to the presence of two length-scales of repulsion, different local configurations with four,…
In this paper we complete the study of the phase diagram and conformational states of a stiff homopolymer. It is known that folding of a sufficiently stiff chain results in formation of a torus. We find that the phase diagram obtained from…
We examine the behavior of entanglement entropy of a subsystem $A$ in a fully backreacted holographic model of a $1+1$ dimensional $p$ wave superconductor across the phase transition. For a given temperature, the system goes to a…
We suggest a theory of internal coherent tunneling in the pseudogap region where the applied voltage is below the free electron gap. We consider quasi 1D systems where the gap is originated by a lattice dimerization like in polyacethylene,…
Whenever a symmetry in the ground state of a system is broken, topological defects will exist. These defects are essential for understanding phase transitions in low dimensional systems[1]. Excitingly in some unique condensed matter systems…
We propose and solve a simple model describing secondary structure formation in random hetero-polymers. It describes monomers with a combination of one-dimensional short-range interactions (representing steric forces and hydrogen bonds) and…
We report on self-assembly, clustering, and conformational phases of peptides on inorganic semiconductor surfaces. The peptide-covered surface fraction can differ by a factor of 25, depending mainly on surface and peptide polarity. Low…
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…
The physics of the pseudo-gap phase of high temperature cuprate superconductors has been an enduring mystery in the past thirty years. The ubiquitous presence of the pseudo-gap phase in under-doped cuprates suggests that its understanding…
We present a computer simulation study of the compact self-avoiding loops as regards their length and topological state. We use a Hamiltonian closed path on the cubic-shaped segment of a 3D cubic lattice as a model of a compact polymer. The…
The universality of the swelling of the radius of gyration of a homopolymer relative to its value in the $\theta$ state, independent of polymer-solvent chemistry, in the crossover regime between $\theta$ and athermal solvent conditions, is…
Self-buckling is an interesting phenomenon that is easily found around us, either in nature or in objects made by human. Palm fronds which initially directed upward when they were short and turned into bending after appreciably longer is an…
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…
Local moment formation is ubiquitous in disordered semiconductors such as Si:P, where it is observed both in the metallic and the insulating regimes. Here, we focus on local moment behavior in disordered insulators, which arises from…
The analysis performed as well as extensive numerical simulations have revealed the possibility of the generation of homoclinic orbits as a result of homoclinic bifurcation in a porous pellet. A method has been proposed for the development…