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

A complete family of separability criteria

We introduce a new family of separability criteria that are based on the existence of extensions of a bipartite quantum state $\rho$ to a larger number of parties satisfying certain symmetry properties. It can be easily shown that all separable states have the required extensions, so the non-existence of such an extension for a particular state implies that the state is entangled. One of the main advantages of this approach is that searching for the extension can be cast as a convex optimization problem known as a semidefinite program (SDP). Whenever an extension does not exist, the dual optimization constructs an explicit entanglement witness for the particular state. These separability tests can be ordered in a hierarchical structure whose first step corresponds to the well-known Positive Partial Transpose (Peres-Horodecki) criterion, and each test in the hierarchy is at least as powerful as the preceding one. This hierarchy is complete, in the sense that any entangled state is guaranteed to fail a test at some finite point in the hierarchy, thus showing it is entangled. The entanglement witnesses corresponding to each step of the hierarchy have well-defined and very interesting algebraic properties that in turn allow for a characterization of the interior of the set of positive maps. Coupled with some recent results on the computational complexity of the separability problem, which has been shown to be NP-hard, this hierarchy of tests gives a complete and also computationally and theoretically appealing characterization of mixed bipartite entangled states.Comment: 21 pages. Expanded introduction. References added, typos corrected. Accepted for publication in Physical Review

Network Synthesis of Linear Dynamical Quantum Stochastic Systems

The purpose of this paper is to develop a synthesis theory for linear dynamical quantum stochastic systems that are encountered in linear quantum optics and in phenomenological models of linear quantum circuits. In particular, such a theory will enable the systematic realization of coherent/fully quantum linear stochastic controllers for quantum control, amongst other potential applications. We show how general linear dynamical quantum stochastic systems can be constructed by assembling an appropriate interconnection of one degree of freedom open quantum harmonic oscillators and, in the quantum optics setting, discuss how such a network of oscillators can be approximately synthesized or implemented in a systematic way from some linear and non-linear quantum optical elements. An example is also provided to illustrate the theory.Comment: Revised and corrected version, published in SIAM Journal on Control and Optimization, 200

A new bound of the ℒ2[0, T]-induced norm and applications to model reduction

We present a simple bound on the finite horizon ℒ2/[0, T]-induced norm of a linear time-invariant (LTI), not necessarily stable system which can be efficiently computed by calculating the ℋ∞ norm of a shifted version of the original operator. As an application, we show how to use this bound to perform model reduction of unstable systems over a finite horizon. The technique is illustrated with a non-trivial physical example relevant to the appearance of time-irreversible phenomena in statistical physics

Optimal tracking for pairs of qubit states

In classical control theory, tracking refers to the ability to perform measurements and feedback on a classical system in order to enforce some desired dynamics. In this paper we investigate a simple version of quantum tracking, namely, we look at how to optimally transform the state of a single qubit into a given target state, when the system can be prepared in two different ways, and the target state depends on the choice of preparation. We propose a tracking strategy that is proved to be optimal for any input and target states. Applications in the context of state discrimination, state purification, state stabilization and state-dependent quantum cloning are presented, where existing optimality results are recovered and extended.Comment: 15 pages, 8 figures. Extensive revision of text, optimality results extended, other physical applications include