Related papers: Statistical mechanics of columnar DNA assemblies
We experimentally demonstrate that spin dynamics and the phase diagram of spinor condensates can be conveniently tuned by a two-dimensional optical lattice. Spin population oscillations and a lattice-tuned separatrix in phase space are…
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
This article studies the statistical mechanics of elastica as a model of the shapes of the supercoiled DNA, and shows that its excited states can be characterized by the focusing modified KdV (MKdV) equation due to thermal fluctuation.…
Previous Monte Carlo investigations by Wojciechowski \emph{et al.} have found two unusual phases in two-dimensional systems of anisotropic hard particles: a tetratic phase of four-fold symmetry for hard squares [Comp. Methods in Science and…
We present the phase diagram and critical properties of a coupled $XY$-Ising model on a triangular lattice using the mean-field approximation, the Migdal-Kadanoff scheme of renormalization group and Monte-Carlo simulations. The topology of…
Using density-functional theory, we have analyzed the phase behavior of binary mixtures of hard rods of different lengths and diameters. Previous studies have shown a strong tendency of smectic phases of these mixtures to segregate and, in…
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 determine the arrangement of spins in the ground state of the XY model with quenched, random fields, on a fully connected graph. Two types of disordered fields are considered, namely randomly oriented magnetic fields, and randomly…
Frustrated spin systems can show phases with spontaneous breaking of spin-rotational symmetry without the formation of local magnetic order. We study the dynamic response of the spin-nematic phase of one-dimensional spin-1/2 systems,…
The dynamical behavior of a harmonic chain in a spatially periodic potential (Frenkel-Kontorova model, discrete sine-Gordon equation) under the influence of an external force and a velocity proportional damping is investigated. We do this…
The helical distribution of the electronic density in chiral molecules, such as DNA and bacteriorhodopsin, has been suggested to induce a spin-orbit coupling interaction that may lead to the so-called chirality-induced spin selectivity…
Nonlinear molecular excitations in DNA have traditionally been modelled using the nonlinear Schr\"odinger equation (NLSE). An alternative approach is based on the plane-base rotator model and the SU(2)/U(1) generalized spin coherent states,…
Recently, it has been recognized that phase transitions play an important role in the probabilistic analysis of combinatorial optimization problems. However, there are in fact many other relations that lead to close ties between computer…
Motivated by recent experiments on the itinerant helimagnet MnSi, we study general properties of helical spin crystals - magnetic structures obtained by superposing distinct spin spirals. An effective Landau description of helical spin…
We present the results of our numerical analysis of a "composite" model of DNA which generalizes a well-known elementary torsional model of Yakushevich by allowing bases to move independently from the backbone. The model shares with the…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…