Related papers: DNA bubble dynamics as a quantum Coulomb problem
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…
We study the equilibrium statistical mechanics of classical two-dimensional Coulomb systems living on a pseudosphere (an infinite surface of constant negative curvature). The Coulomb potential created by one point charge exists and goes to…
We numerically model decaying quantum turbulence in two-dimensional disk-shaped Bose-Einstein condensates, and investigate the effects of finite temperature on the turbulent dynamics. We prepare initial states with a range of condensate…
We study the time evolution in system of $N$ bosons with a relativistic dispersion law interacting through an attractive Coulomb potential with coupling constant $G$. We consider the mean field scaling where $N$ tends to infinity, $G$ tends…
We investigate the nonlinear dynamics of a damped Peyrard-Bishop DNA model taking into account long-range interactions with distance dependence |l|^-s on the elastic coupling constant between different DNA base pairs. Considering both…
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…
We have studied properties of quantum charge fluids interacting with random impurities or heavy polarons using a microscopic Hamiltonian with the full many-body Coulomb interaction with the use of variational many-body formalism. At zero…
We study the real time dynamics of a quantum system with potential barrier coupled to a heat-bath environment. Employing the path integral approach an evolution equation for the time dependent density matrix is derived. The time evolution…
The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses…
We use differential dynamic microscopy and particle tracking to determine the dynamical characteristics of a coarsening foam in reciprocal and direct space. At all wavevectors $q$ investigated, the intermediate scattering function exhibits…
We demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathing dynamics is followed in accordance with the stochastic…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
We study the large distance behavior of a steady distribution of two Brownian particles under external driving in a two-dimensional space. Employing a method of perturbative system reduction, we analyze a Fokker-Planck equation that…
We investigate the real-time evolution of lattice bosons in two spatial dimensions whose dynamics is governed by a Markovian quantum master equation. We employ the Wigner-Weyl phase space quantization and derive the functional integral for…
Molecular dynamics simulation is used to investigate the crystallization of a classical two-dimensional electron system, in which electrons interact with the Coulomb repulsion. From the positional and the orientational correlation…
Two conducting quantum systems coupled only via interactions can exhibit the phenomenon of Coulomb drag, in which a current passed through one layer can pull a current along in the other. However, in systems with particle-hole symmetry --…
We investigate system-environment correlations based on the exact dynamics of a qubit and its environment in the framework of pure decoherence (phase damping). We focus on the relation of decoherence and the build-up of system-reservoir…
We propose a new strategy to improve the self-assembly properties of DNA-functionalised colloids. The problem that we address is that DNA-functionalised colloids typically crystallize in a narrow temperature window, if at all. The…
We study the non-equilibrium dynamics of the Luttinger model after a quantum quench, when the initial state is a finite temperature thermal equilibrium state. The diagonal elements of the density matrix in the steady state show thermal…
Inspired by one--dimensional light--particle systems, the dynamics of a non-Hamiltonian system with long--range forces is investigated. While the molecular dynamics does not reach an equilibrium state, it may be approximated in the…