Quantum walks of correlated particles

Quantum walks of correlated particles offer the possibility to study large-scale quantum interference, simulate biological, chemical and physical systems, and a route to universal quantum computation. Here we demonstrate quantum walks of two identical photons in an array of 21 continuously evanescently-coupled waveguides in a SiOxNy chip. We observe quantum correlations, violating a classical limit by 76 standard deviations, and find that they depend critically on the input state of the quantum walk. These results open the way to a powerful approach to quantum walks using correlated particles to encode information in an exponentially larger state space

Quantum walk on distinguishable non-interacting many-particles and indistinguishable two-particle

We present an investigation of many-particle quantum walks in systems of non-interacting distinguishable particles. Along with a redistribution of the many-particle density profile we show that the collective evolution of the many-particle system resembles the single-particle quantum walk evolution when the number of steps is greater than the number of particles in the system. For non-uniform initial states we show that the quantum walks can be effectively used to separate the basis states of the particle in position space and grouping like state together. We also discuss a two-particle quantum walk on a two- dimensional lattice and demonstrate an evolution leading to the localization of both particles at the center of the lattice. Finally we discuss the outcome of a quantum walk of two indistinguishable particles interacting at some point during the evolution.Comment: 8 pages, 7 figures, To appear in special issue: "quantum walks" to be published in Quantum Information Processin

Universal digital quantum simulation with trapped ions

A digital quantum simulator is an envisioned quantum device that can be pro- grammed to efficiently simulate any other local system. We demonstrate and investigate the digital approach to quantum simulation in a system of trapped ions. Using sequences of up to 100 gates and 6 qubits, the full time dynamics of a range of spin systems are digitally simulated. Interactions beyond those naturally present in our simulator are accurately reproduced and quantitative bounds are provided for the overall simulation quality. Our results demon- strate the key principles of digital quantum simulation and provide evidence that the level of control required for a full-scale device is within reach.Comment: 12 pages, 4 figures (main article) + 31 pages, 9 figures (supplementary online material

Comparative study of the extracellular proteome of Sulfolobus species reveals limited secretion

Although a large number of potentially secreted proteins can be predicted on the basis of genomic distribution of signal sequence-bearing proteins, protein secretion in Archaea has barely been studied. A proteomic inventory and comparison of the growth medium proteins in three hyperthermoacidophiles, i.e., Sulfolobus solfataricus, S. acidocaldarius and S. tokodaii, indicates that only few proteins are freely secreted into the growth medium and that the majority originates from cell envelope bound forms. In S. acidocaldarius both cell-associated and secreted α-amylase activities are detected. Inactivation of the amyA gene resulted in a complete loss of activity, suggesting that the same protein is responsible for the a-amylase activity at both locations. It is concluded that protein secretion in Sulfolobus is a limited process, and it is suggested that the S-layer may act as a barrier for the free diffusion of folded proteins into the medium

A unified model for BAM function that takes into account type Vc secretion and species differences in BAM composition

Transmembrane proteins in the outer membrane of Gram-negative bacteria are almost exclusively β-barrels. They are inserted into the outer membrane by a conserved and essential protein complex called the BAM (for β-barrel assembly machinery). In this commentary, we summarize current research into the mechanism of this protein complex and how it relates to type V secretion. Type V secretion systems are autotransporters that all contain a β-barrel transmembrane domain inserted by BAM. In type Vc systems, this domain is a homotrimer. We argue that none of the current models are sufficient to explain BAM function particularly regarding type Vc secretion. We also find that current models based on the well-studied model system Escherichia coli mostly ignore the pronounced differences in BAM composition between different bacterial species. We propose a more holistic view on how all OMPs, including autotransporters, are incorporated into the lipid bilayer

Live Flow Cytometry Analysis of c-di-GMP Levels in Single Cell Populations.

Second-generation RNA-based fluorescent biosensors have been developed that enable flow cytometry experiments to monitor the population dynamics of c-di-GMP signaling in live bacteria. These experiments are high-throughput, provide information at the single-cell level, and can be performed on cells grown in complex media and/or under anaerobic conditions. Here, we describe flow cytometry methods for three applications: (1) high-throughput screening for diguanylate cyclase activity, (2) analyzing c-di-GMP levels under anaerobic conditions, and (3) monitoring cell population dynamics of c-di-GMP levels upon environmental changes. These methods showcase RNA-based fluorescent biosensors as versatile tools for studying c-di-GMP signaling in bacteria

Isothermal Titration Calorimetry to Determine Apparent Dissociation Constants (K d) and Stoichiometry of Interaction (n) of C-di-GMP Binding Proteins

Isothermal titration calorimetry (ITC) is a commonly used biophysical technique that enables the quantitative characterization of intermolecular interactions in solution. Based on enthalpy changes (ΔH) upon titration of the binding partner (e.g., a small-molecule ligand such as c-di-GMP) to the molecule of interest (e.g., a receptor protein), the resulting binding isotherms provide information on the equilibrium association/dissociation constants (K a, K d) and stoichiometry of binding (n), as well as on changes in the Gibbs free energy (ΔG) and entropy (ΔS) along the interaction. Here we present ITC experiments used for the characterization of c-di-GMP binding proteins and discuss advantages and potential caveats in the interpretation of results