Base sequence dependent sliding of proteins on DNA

The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random walk usually assumed. The general validity and the implications of the results are discussed.Comment: 12 pages, 3 figure

Scaling of the von Neumann entropy across a finite temperature phase transition

The spectrum of the reduced density matrix and the temperature dependence of the von Neumann entropy (VNE) are analytically obtained for a system of hard core bosons on a complete graph which exhibits a phase transition to a Bose-Einstein condensate at $T=T_c$. It is demonstrated that the VNE undergoes a crossover from purely logarithmic at T=0 to purely linear in block size $n$ behaviour for $T\geq T_{c}$. For intermediate temperatures, VNE is a sum of two contributions which are identified as the classical (Gibbs) and the quantum (due to entanglement) parts of the von Neumann entropy.Comment: 4 pages, 2 figure

Phase diagram of two-lane driven diffusive systems

We consider a large class of two-lane driven diffusive systems in contact with reservoirs at their boundaries and develop a stability analysis as a method to derive the phase diagrams of such systems. We illustrate the method by deriving phase diagrams for the asymmetric exclusion process coupled to various second lanes: a diffusive lane; an asymmetric exclusion process with advection in the same direction as the first lane, and an asymmetric exclusion process with advection in the opposite direction. The competing currents on the two lanes naturally lead to a very rich phenomenology and we find a variety of phase diagrams. It is shown that the stability analysis is equivalent to an `extremal current principle' for the total current in the two lanes. We also point to classes of models where both the stability analysis and the extremal current principle fail

Entanglement of eta-pairing state with off-diagonal long-range order

Off-diagonal long-range order (ODLRO) is a quantum phenomenon not describable in classical mechanical terms. It is believed to be one characteristic of superconductivity. The quantum state constructed by eta-pairing which demonstrates ODLRO is an eigenstate of the three-dimensional Hubbard model. Entanglement is a key concept of the quantum information processing and has no classical counterpart. We study the entanglement property of eta-pairing quantum state. The concurrence is a well-known measure of quantum entanglement. We show that the concurrence of entanglement between one-site and the rest sites is exactly the correlation function of the ODLRO for the eta-pairing state in the thermodynamic limit. So, when the eta-pairing state is entangled, it demonstrates ODLRO and is thus in superconducting phase, if it is a separable state, there is no ODLRO. In the thermodynamic limit, the entanglement between M-site and other sites of the eta-pairing state does not vanish. Other types of ODLRO of eta-pairing state are presented. We show that the behavior of the ODLRO correlation functions is equivalent to that of the entanglement of the eta-pairing state. The scaling of the entropy of the entanglement for the eta-pairing state is studied.Comment: 4 pages, 4 eps figure

On the entanglement entropy for a XY spin chain

The entanglement entropy for the ground state of a XY spin chain is related to the corner transfer matrices of the triangular Ising model and expressed in closed form.Comment: 4 pages, 2 figure

Behavior of magnetic currents in anisotropic Heisenberg spin chains out of equilibrium

The behavior of the magnetic currents in one-dimensional Heisenberg XXZ spin chains kept out of equilibrium by boundary driving fields is investigated. In particular, the dependence of the spin currents on the anisotropy parameter Delta and on the boundary fields is studied both analytically and numerically in the framework of the Lindblad master equation formalism. We show that the spin current can be maximized with appropriate choices of the boundary fields, and for odd system sizes, N, we demonstrate the existence of additional symmetries that cause the current to be an odd function of Delta. From direct numerical integrations of the quantum master equation, we find that for an arbitrary N the current J(z)(N) vanishes for Delta = 0, while for Delta negative it alternates its sign with the system size. In the gapless critical region |Delta| 1 we find that J(z) (N) similar to exp(-alpha N). A simple mean-field approach, which predicts rather well the values of J(z) (N) for the gapped region and the values of the absolute current maxima in the critical region, is developed. The existence of two different stationary solutions for the mean-field density matrix in the whole parameter range is also demonstrated

A Model of Sequence-Dependent Protein Diffusion along DNA

We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. Hydrogen bonds formed at the target site are used as the main sequence-dependent interaction between protein and DNA. The resulting dynamical properties and the possibility of an experimental verification are discussed in details. We show that, while at large times the process reaches a linear diffusion regime, it initially displays a sub-diffusive behavior. The sub-diffusive regime can last sufficiently long to be of biological interest