Related papers: RNAlike polymer model: exact calculation on the Be…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
Formation of RNA secondary structures is an example of the sequence-structure problem omnipresent in biopolymers. A theoretical question of recent interest is whether a random RNA sequence undergoes a finite temperature glass transition. We…
We study the lattice random walk dynamics in a heterogeneous space of two media separated by an interface and having different diffusivity and bias. Depending on the position of the interface, there exist two exclusive ways to model the…
We consider a one-dimensional classical many-body system with interaction potential of Lennard-Jones type in the thermodynamic limit at low temperature $1/\beta\in(0,\infty)$. The ground state is a periodic lattice. We show that when the…
The phase diagram for a two-dimensional self-avoiding walk model on the square lattice incorporating attractive short-ranged interactions between parallel sections of walk is derived using numerical transfer matrix techniques. The model…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
We calculate properties of dipolar interacting ultracold molecules or Rydberg atoms in a semi-synthetic three-dimensional configuration -- one synthetic dimension plus a two-dimensional real space optical lattice or periodic microtrap array…
Recent advances in Generalized Ensemble simulations and microcanonical analysis allowed the investigation of structural transitions in polymer models over a broad range of local bending and torsion strengths. It is reasonable to argue that…
We show how the use of variational states to approximate the ground state of a system can be employed to study a multi-mode Dicke model. One of the main contributions of this work is the introduction of a not very commonly used quantity,…
We consider the Ising model on the two-dimensional square lattice where on each horizontal line, called "layer", the interaction is given by a ferromagnetic Kac potential with coupling strength $J_\gamma(x,y)=\gamma J(\gamma(x-y))$, where…
In the framework of Husimi and Bethe lattices, we investigate a generalized polymer model that incorporates as special cases different models previously studied in the literature, namely, the standard interacting self-avoiding walk, the…
The dynamics of dry active matter have implications for a diverse collection of biological phenomena spanning a range of length and time scales, such as animal flocking, cell tissue dynamics, and swarming of inserts and bacteria. Uniting…
The unfolding of a polymer below the $\theta$ point when pulled by an external force is studied both in d=2 on the lattice and in $d=3$ off lattice. A ground state analysis of finite length chains shows that the globule unfolds via multiple…
The ground state fidelity per lattice site is shown to be able to detect quantum phase transitions for the Kitaev model on the honeycomb lattice, a prototypical example of quantum lattice systems with topological order. It is found that, in…
Translocation through a nanopore is a new experimental technique to probe physical properties of biomolecules. A bulk of theoretical and computational work exists on the dependence of the time to translocate a single unstructured molecule…
Various interacting lattice path models of polymer collapse in two dimensions demonstrate different critical behaviours. This difference has been without a clear explanation. The collapse transition has been variously seen to be in the…
We introduce a lattice model of glass transition in polymer globules. This model exhibits a novel scenario of ergodicity breaking in which the disjoint regions of phase space do not arise uniformly, but as small chambers whose number…
We present a lattice model for polymer solutions, explicitly incorporating interactions with a bath of solvent and cosolvent molecules. By exploiting the well-known analogy between polymer systems and the $O(n)$-vector spin model in the…
After a general introduction to the field, we describe some recent results concerning disorder effects on both `random walk models', where the random walk is a dynamical process generated by local transition rules, and on `polymer models',…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…