Limitations of Passive Protection of Quantum Information

The ability to protect quantum information from the effect of noise is one of the major goals of quantum information processing. In this article, we study limitations on the asymptotic stability of quantum information stored in passive N-qubit systems. We consider the effect of small imperfections in the implementation of the protecting Hamiltonian in the form of perturbations or weak coupling to a ground state environment. We prove that, regardless of the protecting Hamiltonian, there exists a perturbed evolution that necessitates a final error correcting step when the state of the memory is read. Such an error correction step is shown to require a finite error threshold, the lack thereof being exemplified by the 3D compass model. We go on to present explicit weak Hamiltonian perturbations which destroy the logical information stored in the 2D toric code in a time O(log(N)).Comment: 17 pages and appendice

RecA and DNA recombination: a review of molecular mechanisms

International audienceRecombinases are responsible for homologous recombination and maintenance of genome integrity. In Escherichia coli, the recombinase RecA forms a nucleoprotein filament with the ssDNA present at a DNA break and searches for a homologous dsDNA to use as a template for break repair. During the first step of this process, the ssDNA is bound to RecA and stretched into a Watson-Crick base-paired triplet conformation. The RecA nucleoprotein filament also contains ATP and Mg 2+ , two cofactors required for RecA activity. Then, the complex starts a homology search by interacting with and stretching dsDNA. Thanks to supercoiling, intersegment sampling and RecA clustering, a genome-wide homology search takes place at a relevant metabolic timescale. When a region of homology 8 to 20 base pairs in length is found and stabilized, DNA strand exchange proceeds, forming a heteroduplex complex that is resolved through a combination of DNA synthesis, ligation and resolution. RecA activities can take place without ATP hydrolysis, but this latter activity is necessary to improve and accelerate the process. Protein flexibility and monomer-monomer interactions are fundamental for RecA activity, which functions cooperatively. A structure/function relationship analysis suggests that the recombinogenic activity can be improved and that recombinases have an inherently large recombination potential. Understanding this relationship is essential for designing RecA derivatives with enhanced activity for biotechnology applications. For example, this protein is a major actor in the recombinase polymerase isothermal amplification (RPA) used in point-of-care diagnostics

Group field theories for all loop quantum gravity

Group field theories represent a 2nd quantized reformulation of the loop quantum gravity state space and a completion of the spin foam formalism. States of the canonical theory, in the traditional continuum setting, have support on graphs of arbitrary valence. On the other hand, group field theories have usually been defined in a simplicial context, thus dealing with a restricted set of graphs. In this paper, we generalize the combinatorics of group field theories to cover all the loop quantum gravity state space. As an explicit example, we describe the GFT formulation of the KKL spin foam model, as well as a particular modified version. We show that the use of tensor model tools allows for the most effective construction. In order to clarify the mathematical basis of our construction and of the formalisms with which we deal, we also give an exhaustive description of the combinatorial structures entering spin foam models and group field theories, both at the level of the boundary states and of the quantum amplitudes.Comment: version published in New Journal of Physic

Mechanistic behaviour and molecular interactions of heat shock protein 47 (HSP47)

This project involves the study of heat shock protein 47 (HSP47), which is a molecular chaperone crucial for collagen biosynthesis. It exhibits a high degree of sequence homology with members of the serine protease inhibitor (serpin) superfamily, though HSP47 does not possess the inhibitory activity. It is a single-substrate chaperone, and binds only to collagen. ‘Knock-out’ of the hsp47 gene impairs the secretion of correctly folded collagen triple helix molecules leading to embryonic lethality in mice. Thus the aim of this project was to elucidate the specific mechanism that governs the binding to and release from collagen at the molecular level, known as the ‘pH-switch mechanism’. Emphasis is given on histidine (His) residues as the HSP47-collagen dissociation pH is similar to the pKa of the imidazole side chain of His residues. Site directed mutagenesis was used to mutate surface His residues, based on a mouse HSP47 homology model. The effects of the mutations on the behaviour of HSP47 were then assessed by collagen binding assays and structural analyses with circular dichroism (CD). All mutants were found to have good solubility and retain their binding ability to collagen like wild-type HSP47 in batch assay, but perturbed behaviour was seen in column experiment. Mutation of His residue at position 191 (H191) causes the shift in the collagen dissociation pH, while mutation of H197 and/or 198 disrupt the specific HSP47-collagen interaction. H191, 197 and 198 are predicted to be located in the region near the C-terminus of strand 3 of β-sheet A (s3A) in the homology model, a region specifically known as the ‘breach cluster’ in serpin nomenclature. The extent of conformational rearrangement of this region was further investigated by means of intrinsic tryptophan fluorescence spectroscopy using a series of single tryptophan (Trp) mutants. Results from analyses performed on the mutants did not contradict the observation seen in His mutational work, as Trp residues in the ‘breach’ cluster are likely to be located in the dynamic region of HSP47 pH-triggered conformational change. In conclusion, this study establishes the importance of His residues in the ‘breach cluster’ to HSP47 pH-switch behaviour. Finally, a model for HSP47 pH-switch mechanism was proposed from data obtained via mutagenesis experiments. The model is hoped to assist future research into HSP47 cellular behaviour and will also be of great use in therapeutic applications involving the molecular chaperone