Related papers: A Simple Model for the DNA Denaturation Transition
One-dimensional thermodynamic instabilities are phase transitions not prohibited by Landau's argument, because the energy of the domain wall (DW) which separates the two phases is infinite. Whether they actually occur in a given system of…
We investigate polymers pulled away from an interacting surface, where the force is applied to the untethered endpoint and at an angle $\theta$ to the surface. We use the canonical self-avoiding walk model of polymers and obtain the phase…
We investigate the energy relaxation process produced by thermal baths at zero temperature acting on the boundary atoms of chains of classical anharmonic oscillators. Time-dependent perturbation theory allows us to obtain an explicit…
A monolayer of molecules or quantum dots sandwiched between electrodes can be driven out of equilibrium by the application of a bias voltage between the electrodes. We study charge ordering, i.e., the spontaneous formation of a charge…
Our work is motivated by Bourque and Pevzner's (2002) simulation study of the effectiveness of the parsimony method in studying genome rearrangement, and leads to a surprising result about the random transposition walk on the group of…
For the first order transition of the Ising model below $T_c$, Isakov has proven that the free energy possesses an essential singularity in the applied field. Such a singularity in the control parameter, anticipated by condensation theory,…
RNA molecules form a sequence-specific self-pairing pattern at low temperatures. We analyze this problem using a random pairing energy model as well as a random sequence model that includes a base stacking energy in favor of helix…
The denaturation of double-stranded DNA as function of force and temperature is discussed. At room temperature, sequence heterogeneity dominates the physics of single molecule force-extension curves starting about 7 piconewtons of below a…
We investigate a one-dimensional water-like lattice model with Van der Waals and hydrogen-bond interactions, allowing for particle number fluctuations through a chemical potential. The model, defined on a chain with periodic boundary…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
We perform a numerical study of a new microcanonical polymer model on the three dimensional cubic lattice, consisting of ideal chains whose range and number of nearest-neighbor contacts are fixed to given values. Our simulations suggest an…
We investigate the voltage-driven transport of hybridized DNA through membrane channels. As membrane channels are typically too narrow to accommodate hybridized DNA, the dehybridization of the DNA is the critical rate limiting step in the…
This article is dedicated to the study of the 2-dimensional interacting prudent self-avoiding walk (referred to by the acronym IPSAW) and in particular to its collapse transition. The interaction intensity is denoted by $\beta>0$ and the…
Multicanonical ensemble simulations for the simulation of first-order phase transitions suffer from exponential slowing down. Monte Carlo autocorrelation times diverge exponentially with free energy barriers $\Delta F$, which in $L^d$ boxes…
We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
We study the motion of a particle on the two-dimensional honeycomb lattice, whose sites are occupied by either flipping rotators or flipping mirrors, which scatter the particle according to a deterministic rule. For both types of scatterers…
We consider a model of two (fully) compact polymer chains, coupled through an attractive interaction. These compact chains are represented by Hamiltonian paths (HP), and the coupling favors the existence of common bonds between the chains.…
We consider a two dimensional model of non-interacting chains of spinless fermions weakly coupled via a small inter-chain hopping and a repulsive inter-chain interaction. The phase diagram of this model has a surprising feature: an abrupt…
Using a Monte Carlo method, we study the finite-temperature phase transition in the two-dimensional classical Heisenberg model on a triangular lattice with or without easy-plane anisotropy. The model takes account of competing interactions:…