Modeling the thermal evolution of enzyme-created bubbles in DNA

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 are carried out by assembled complexes with enzymes that separate selected regions of NAs. Within the frame of a nonlinear dynamics approach we model the structure of the DNA duplex by a nonlinear network of coupled oscillators. We show that in fact from certain local structural distortions there originate oscillating localized patterns, that is radial and torsional breathers, which are associated with localized H-bond deformations, being reminiscent of the replication bubble. We further study the temperature dependence of these oscillating bubbles. To this aim the underlying nonlinear oscillator network of the DNA duplex is brought in contact with a heat bath using the Nos$\rm{\acute{e}}$-Hoover-method. Special attention is paid to the stability of the oscillating bubbles under the imposed thermal perturbations. It is demonstrated that the radial and torsional breathers, sustain the impact of thermal perturbations even at temperatures as high as room temperature. Generally, for nonzero temperature the H-bond breathers move coherently along the double chain whereas at T=0 standing radial and torsional breathers result.Comment: 19 pages, 7 figure

Renormalisation group determination of the order of the DNA denaturation transition

We report on the nature of the thermal denaturation transition of homogeneous DNA as determined from a renormalisation group analysis of the Peyrard-Bishop-Dauxois model. Our approach is based on an analogy with the phenomenon of critical wetting that goes further than previous qualitative comparisons, and shows that the transition is continuous for the average base-pair separation. However, since the range of universal critical behaviour appears to be very narrow, numerically observed denaturation transitions may look first-order, as it has been reported in the literature.Comment: 6 pages; no figures; to appear in Europhysics Letter

Discovery of a new radio galaxy within the error box of the unidentified gamma-ray source 3EG J1735-1500

We report the discovery of a new radio galaxy within the location error box of the gamma-ray source 3EG J1735-1500. The galaxy is a double-sided jet source forming a large angle with the line of sight. Optical observations reveal a V ~ 18 magnitude galaxy at the position of the radio core. Although the association with the EGRET source is not confirmed at the present stage, because there is a competing, alternative gamma-ray candidate within the location error contours which is also studied here, the case deserves further attention. The new radio galaxy can be used to test the recently proposed possibility of gamma-ray emitting radio galaxies beyond the already known case of Centaurus A.Comment: 12 pages, 3 figures. Accepted for publication in Ap

Determining the dimensionality of bipartite orbital-angular-momentum entanglement using multi-sector phase masks

The Shannon dimensionality of orbital-angular-momentum (OAM) entanglement produced in spontaneous parametric down-conversion can be probed by using multi-sector phase analysers [1]. We demonstrate a spatial light modulator-based implementation of these analysers, and use it to measure a Schmidt number of about 50

Hybrid Architecture for Engineering Magnonic Quantum Networks

We show theoretically that a network of superconducting loops and magnetic particles can be used to implement magnonic crystals with tunable magnonic band structures. In our approach, the loops mediate interactions between the particles and allow magnetic excitations to tunnel over long distances. As a result, different arrangements of loops and particles allow one to engineer the band structure for the magnonic excitations. Furthermore, we show how magnons in such crystals can serve as a quantum bus for long-distance magnetic coupling of spin qubits. The qubits are coupled to the magnets in the network by their local magnetic-dipole interaction and provide an integrated way to measure the state of the magnonic quantum network.Comment: Manuscript: 4 pages, 3 figures. Supplemental Material: 9 pages, 4 figures. V2: Published version in PRA: 14 pages + 8 figures. Substantial rearrangement of the content of the previous versio

Dynamics of Entanglement Transfer Through Multipartite Dissipative Systems

We study the dynamics of entanglement transfer in a system composed of two initially correlated three-level atoms, each located in a cavity interacting with its own reservoir. Instead of tracing out reservoir modes to describe the dynamics using the master equation approach, we consider explicitly the dynamics of the reservoirs. In this situation, we show that the entanglement is completely transferred from atoms to reservoirs. Although the cavities mediate this entanglement transfer, we show that under certain conditions, no entanglement is found in cavities throughout the dynamics. Considering the entanglement dynamics of interacting and non-interacting bipartite subsystems, we found time windows where the entanglement can only flow through interacting subsystems, depending on the system parameters.Comment: 8 pages, 11 figures, publishe in Physical Review

Characterization of high-dimensional entangled systems via mutually unbiased measurements

Mutually unbiased bases (MUBs) play a key role in many protocols in quantum science, such as quantum key distribution. However, defining MUBs for arbitrary high-dimensional systems is theoretically difficult, and measurements in such bases can be hard to implement. We show experimentally that efficient quantum state reconstruction of a high-dimensional multi-partite quantum system can be performed by considering only the MUBs of the individual parts. The state spaces of the individual subsystems are always smaller than the state space of the composite system. Thus, the benefit of this method is that MUBs need to be defined for the small Hilbert spaces of the subsystems rather than for the large space of the overall system. This becomes especially relevant where the definition or measurement of MUBs for the overall system is challenging. We illustrate this approach by implementing measurements for a high-dimensional system consisting of two photons entangled in the orbital angular momentum (OAM) degree of freedom, and we reconstruct the state of this system for dimensions of the individual photons from d=2 to 5.Comment: 8 page