Tensor Networks with a Twist: Anyon-permuting domain walls and defects in PEPS

We study the realization of anyon-permuting symmetries of topological phases on the lattice using tensor networks. Working on the virtual level of a projected entangled pair state, we find matrix product operators (MPOs) that realize all unitary topological symmetries for the toric and color codes. These operators act as domain walls that enact the symmetry transformation on anyons as they cross. By considering open boundary conditions for these domain wall MPOs, we show how to introduce symmetry twists and defect lines into the state.Comment: 11 pages, 6 figures, 2 appendices, v2 published versio

Photon statistics and dynamics of Fluorescence Resonance Energy Transfer

We report high time-resolution measurements of photon statistics from pairs of dye molecules coupled by fluorescence resonance energy transfer (FRET). In addition to quantum-optical photon antibunching, we observe photon bunching on a timescale of several nanoseconds. We show by numerical simulation that configuration fluctuations in the coupled fluorophore system could account for minor deviations of our data from predictions of basic Forster theory. With further characterization we believe that FRET photon statistics could provide a unique tool for studying DNA mechanics on timescales from 10^-9 to 10^-3 s.Comment: 4 pages, 4 figures, submitted to Physical Review Letter

All bipartite entangled states display some hidden nonlocality

We show that a violation of the Clauser-Horne-Shimony-Holt (CHSH) inequality can be demonstrated in a certain kind of Bell experiment for all bipartite entangled states. Our protocol allows local filtering measurements and involves shared ancilla states that do not themselves violate CHSH. Our result follows from two main steps. We first provide a simple characterization of the states that violate the CHSH-inequality after local filtering operations in terms of witness-like operators. Second, we prove that for each entangled state $\sigma$, there exists another state $\rho$ not violating CHSH, such that $\rho\otimes\sigma$ violates CHSH. Hence, in this scenario, $\sigma$ cannot be substituted by classical correlations without changing the statistics of the experiment; we say that $\sigma$ is not simulable by classical correlations and our result is that entanglement is equivalent to non-simulability.Comment: 5 pages, 1 figur

Ribonucleolytic resection is required for repair of strand displaced nonhomologous end-joining intermediates

Nonhomologous end-joining (NHEJ) pathways repair DNA double-strand breaks (DSBs) in eukaryotes and many prokaryotes, although it is not reported to operate in the third domain of life, archaea. Here, we describe a complete NHEJ complex, consisting of DNA ligase (Lig), polymerase (Pol), phosphoesterase (PE), and Ku from a mesophillic archaeon, Methanocella paludicola (Mpa). Mpa Lig has limited DNA nick-sealing activity but is efficient in ligating nicks containing a 3′ ribonucleotide. Mpa Pol preferentially incorporates nucleoside triphosphates onto a DNA primer strand, filling DNA gaps in annealed breaks. Mpa PE sequentially removes 3′ phosphates and ribonucleotides from primer strands, leaving a ligatable terminal 3′ monoribonucleotide. These proteins, together with the DNA end-binding protein Ku, form a functional NHEJ break-repair apparatus that is highly homologous to the bacterial complex. Although the major roles of Pol and Lig in break repair have been reported, PE’s function in NHEJ has remained obscure. We establish that PE is required for ribonucleolytic resection of RNA intermediates at annealed DSBs. Polymerase-catalyzed strand-displacement synthesis on DNA gaps can result in the formation of nonligatable NHEJ intermediates. The function of PE in NHEJ repair is to detect and remove inappropriately incorporated ribonucleotides or phosphates from 3′ ends of annealed DSBs to configure the termini for ligation. Thus, PE prevents the accumulation of abortive genotoxic DNA intermediates arising from strand displacement synthesis that otherwise would be refractory to repair

Semiclassical theory of cavity-assisted atom cooling

We present a systematic semiclassical model for the simulation of the dynamics of a single two-level atom strongly coupled to a driven high-finesse optical cavity. From the Fokker-Planck equation of the combined atom-field Wigner function we derive stochastic differential equations for the atomic motion and the cavity field. The corresponding noise sources exhibit strong correlations between the atomic momentum fluctuations and the noise in the phase quadrature of the cavity field. The model provides an effective tool to investigate localisation effects as well as cooling and trapping times. In addition, we can continuously study the transition from a few photon quantum field to the classical limit of a large coherent field amplitude.Comment: 10 pages, 8 figure