Related papers: Bethe approximation for a DNA-like self-avoiding w…
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 detailed study of a model for strongly-interacting fermions with exclusion rules and lattice $\mathcal N=2$ supersymmetry is presented. A submanifold in the space of parameters of the model where it is Bethe-ansatz solvable is identified.…
The cations, in form of salt, present in the solution containing DNA play a crucial role in the opening of two strands of DNA. We use a simple non linear model and investigate the role of these cations on the mechanical unzipping of DNA.…
Theoretical description of anisotropic systems, such as layered superconductors and coupled spin chains, is often a challenge due to the different natures of interactions along different directions. As a model of such a system, we present…
We study the phase diagram at finite temperature of a system of Fermi particles on the sites of the Bethe lattice with coordination number z and interacting through onsite U and nearest-neighbor V interactions. This is a physical…
Replication and transcription are two important processes in living systems. To execute such processes, various proteins work far away from equilibrium in a staggered way. Motivated by this, aspects of hysteresis during unzipping of DNA…
This study presents a computational framework to investigate and predict the complicated multiphase properties of eco-friendly lead-free piezoelectric materials, which are crucial for sustainable technological progress. Although their…
We study the Bethe approximation for a system of long rigid rods of fixed length k, with only excluded volume interaction. For large enough k, this system undergoes an isotropic-nematic phase transition as a function of density of the rods.…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
We study an active random walker model in which a particle's motion is determined by a self-generated field. The field encodes information about the particle's path history. This leads to either self-attractive or self-repelling behavior.…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
The melting phase diagram of a double-stranded DNA in poor solvent is studied using the pruned and enriched Rosenbluth method on a simple cubic lattice. As the solvent quality is changed from good to poor, there is a non-monotonic change in…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
We study heat transport in semiconductor nanostructures by solving the Boltzmann Transport Equation (BTE) by means of the Discrete Ordinate Method (DOM). Relaxation time and phase and group velocitiy spectral dependencies are taken into…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and…
We introduce the phase model on a lattice and solve it using the algebraic Bethe ansatz. Time-dependent temperature correlation functions of phase operators and the "darkness formation probability" are calculated in the thermodynamical…
This research incorporates Bayesian game theory into pedestrian evacuation in an agent-based model. Three pedestrian behaviours were compared: Random Follow, Shortest Route and Bayesian Nash Equilibrium (BNE), as well as combinations of…
Using a theoretical model for spontaneous partial DNA unwrapping from histones, we study the transient exposure of protein-binding DNA sites within nucleosomes. We focus on the functional dependence of the rates for site exposure and…