Breakdown of the few-level approximation in collective systems

The validity of the few-level approximation in dipole-dipole interacting collective systems is discussed. As example system, we study the archetype case of two dipole-dipole interacting atoms, each modelled by two complete sets of angular momentum multiplets. We establish the breakdown of the few-level approximation by first proving the intuitive result that the dipole-dipole induced energy shifts between collective two-atom states depend on the length of the vector connecting the atoms, but not on its orientation, if complete and degenerate multiplets are considered. A careful analysis of our findings reveals that the simplification of the atomic level scheme by artificially omitting Zeeman sublevels in a few-level approximation generally leads to incorrect predictions. We find that this breakdown can be traced back to the dipole-dipole coupling of transitions with orthogonal dipole moments. Our interpretation enables us to identify special geometries in which partial few-level approximations to two- or three-level systems are valid

Coherent control in a decoherence-free subspace of a collective multi-level system

Decoherence-free subspaces (DFS) in systems of dipole-dipole interacting multi-level atoms are investigated theoretically. It is shown that the collective state space of two dipole-dipole interacting four-level atoms contains a four-dimensional DFS. We describe a method that allows to populate the antisymmetric states of the DFS by means of a laser field, without the need of a field gradient between the two atoms. We identify these antisymmetric states as long-lived entangled states. Further, we show that any single-qubit operation between two states of the DFS can be induced by means of a microwave field. Typical operation times of these qubit rotations can be significantly shorter than for a nuclear spin system.Comment: 15 pages, 11 figure

Lifetimes of Confined Acoustic Phonons in Ultra-Thin Silicon Membranes

We study the relaxation of coherent acoustic phonon modes with frequencies up to 500 GHz in ultra-thin free-standing silicon membranes. Using an ultrafast pump-probe technique of asynchronous optical sampling, we observe that the decay time of the first-order dilatational mode decreases significantly from \sim 4.7 ns to 5 ps with decreasing membrane thickness from \sim 194 to 8 nm. The experimental results are compared with theories considering both intrinsic phonon-phonon interactions and extrinsic surface roughness scattering including a wavelength-dependent specularity. Our results provide insight to understand some of the limits of nanomechanical resonators and thermal transport in nanostructures

Role of the CipA Scaffoldin Protein in Cellulose Solubilization, as Determined by Targeted Gene Deletion and Complementation in Clostridium thermocellum

The CipA scaffoldin protein plays a key role in the Clostridium thermocellum cellulosome. Previous studies have revealed that mutants deficient in binding or solubilizing cellulose also exhibit reduced expression of CipA. To confirm that CipA is, in fact, necessary for rapid solubilization of crystalline cellulose, the gene was deleted from the chromosome using targeted gene deletion technologies. The CipA deletion mutant exhibited a 100-fold reduction in cellulose solubilization rate, although it was eventually able to solubilize 80% of the 5 g/liter cellulose initially present. The deletion mutant was complemented by a copy of cipA expressed from a replicating plasmid. In this strain, Avicelase activity was restored, although the rate was 2-fold lower than that in the wild type and the duration of the lag phase was increased. The cipA coding sequence is located at the beginning of a gene cluster containing several other genes thought to be responsible for the structural organization of the cellulosome, including olpB, orf2p, and olpA. Tandem mass spectrometry revealed a 10-fold reduction in the expression of olpB, which may explain the lower growth rate. This deletion experiment adds further evidence that CipA plays a key role in cellulose solubilization by C. thermocellum, and it raises interesting questions about the differential roles of the anchor scaffoldin proteins OlpB, Orf2p, and SdbA

Measuring the quantum efficiency of single radiating dipoles using a scanning mirror

Using scanning probe techniques, we show the controlled manipulation of the radiation from single dipoles. In one experiment we study the modification of the fluorescence lifetime of a single molecular dipole in front of a movable silver mirror. A second experiment demonstrates the changing plasmon spectrum of a gold nanoparticle in front of a dielectric mirror. Comparison of our data with theoretical models allows determination of the quantum efficiency of each radiating dipole.Comment: 4 pages, 4 figure

Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis

Background: The gutless marine worm Olavius algarvensis has a completely reduced digestive and excretory system, and lives in an obligate nutritional symbiosis with bacterial symbionts. While considerable knowledge has been gained of the symbionts, the host has remained largely unstudied. Here, we generated transcriptomes and proteomes of O. algarvensis to better understand how this annelid worm gains nutrition from its symbionts, how it adapted physiologically to a symbiotic lifestyle, and how its innate immune system recognizes and responds to its symbiotic microbiota. Results: Key adaptations to the symbiosis include (i) the expression of gut-specific digestive enzymes despite the absence of a gut, most likely for the digestion of symbionts in the host's epidermal cells; (ii) a modified hemoglobin that may bind hydrogen sulfide produced by two of the worm's symbionts; and (iii) the expression of a very abundant protein for oxygen storage, hemerythrin, that could provide oxygen to the symbionts and the host under anoxic conditions. Additionally, we identified a large repertoire of proteins involved in interactions between the worm's innate immune system and its symbiotic microbiota, such as peptidoglycan recognition proteins, lectins, fibrinogen-related proteins, Toll and scavenger receptors, and antimicrobial proteins. Conclusions: We show how this worm, over the course of evolutionary time, has modified widely-used proteins and changed their expression patterns in adaptation to its symbiotic lifestyle and describe expressed components of the innate immune system in a marine oligochaete. Our results provide further support for the recent realization that animals have evolved within the context of their associations with microbes and that their adaptive responses to symbiotic microbiota have led to biological innovations

An ultra-sensitive pulsed balanced homodyne detector: Application to time-domain quantum measurements

A pulsed balanced homodyne detector has been developed for precise measurements of electric field quadratures of pulsed optical quantum states. A high level of common mode suppression (> 85 dB) and low electronic noise (730 electrons per pulse) provide a signal to noise ratio of 14 dB for the measurement of the quantum noise of individual pulses. Measurements at repetition rates up to 1 MHz are possible. As a test, quantum tomography of the coherent state is performed and the Wigner function and the density matrix are reconstructed with a 99.5% fidelity. The detection system can also be used for ultrasensitive balanced detection in cw mode, e.g. for weak absorption measurements.Comment: 3 pages, submitted to Optics Letter

Consequences of hydroxyl generation by the silica/water reaction

Water diffusing into silica surfaces gives rise for several effectson diffusion behaviour and mechanical properties. Water added to silica glass increases its specific volume so that the silica expands near the surface. Mechanical boundary conditions give rise for compressive “swelling stresses”. This fact provides a tool for the interpretation of many experimental observations from literature

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea

The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANME partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors