Related papers: RNAlike polymer model: exact calculation on the Be…
We consider a ${\rm A}_m{\rm B}_n$ diblock copolymer, whose links are capable of forming local reversible bonds with each other. We assume that the resulting structure of the bonds is RNA--like, i.e. topologically isomorphic to a tree. We…
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…
We study the population dynamics of a ring-shaped optical lattice with a high number of particles per site and a low, below ten, number of wells. Using a localized on-site basis defined in terms of stationary states, we were able to…
We introduce a two-dimensional walk model in which a random walker can only move on the first quarter of a two-dimensional plane. We calculate the partition function of this walk model using a transfer matrix method and show that the model…
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…
Proteins in photosynthetic membranes can organize into patterned arrays that span the membrane's lateral size. Attractions between proteins in different layers of a membrane stack can play a key role in this ordering, as was suggested by…
We study energy relaxation in a phenomenological model for polymer built from rheological considerations: a one dimensional nonlinear lattice with dissipative couplings. These couplings are well known in polymer's community to be possibly…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
Lattice molecule models are proposed in order to study statistical mechanics of glass transition in finite dimensions. Molecules in the models are represented by hard Wang tiles and their density is controlled by a chemical potential. An…
We study a lattice-gas model of penetrable particles on a square-lattice substrate with same-site and nearest-neighbor interactions. Penetrability implies that the number of particles occupying a single lattice site is unlimited and the…
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…
Stretched polymers with attractive interaction are studied in two and three dimensions. They are described by biased self-avoiding random walks with nearest neighbour attraction. The bias corresponds to opposite forces applied to the first…
We introduce a 2-dimensional lattice model of granular matter. We use a combination of proof and simulation to demonstrate an order/disorder phase transition in the model, to which we associate the granular phenomenon of random close…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…
We investigate a system of two atoms in an optical lattice, performing a quantum walk by state-dependent shift operations and a coin operation acting on the internal states. The atoms interact, e.g., by cold collisions, whenever they are in…
We reconsider model II of [J. Chem. Phys. 1968, 49, 1778--1783], a two-dimensional lattice-gas system featuring a crystalline phase and two distinct fluid phases (liquid and vapor). In this system, a particle prevents other particles from…
In the standard approach to lattice proteins the models based on nearest neighbor interaction are used. In this kind of models it is difficult to explain the existence of secondary structures --- special preferred conformations of protein…
We study magnetic polymers, defined as self-avoiding walks where each monomer $i$ carries a "spin'' $s_i$ and interacts with its first neighbor monomers, let us say $j$, via a coupling constant $J(s_i,s_j)$. Ising-like [$s_i = \pm 1$, with…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…