Evaluating pathway enumeration algorithms in metabolic engineering case studies

The design of cell factories for the production of compounds involves the search for suitable heterologous pathways. Different strategies have been proposed to infer such pathways, but most are optimization approaches with specific objective functions, not suited to enumerate multiple pathways. In this work, we analyze two pathway enumeration algorithms based on graph representations: the Solution Structure Generation and the Find Path algorithms. Both are capable of enumerating exhaustively multiple pathways using network topology. We study their capabilities and limitations when designing novel heterologous pathways, by applying these methods on two case studies of synthetic metabolic engineering related to the production of butanol and vanillin

Giant nonlinearity and entanglement of single photons in photonic bandgap structures

Giantly enhanced cross-phase modulation with suppressed spectral broadening is predicted between optically-induced dark-state polaritons whose propagation is strongly affected by photonic bandgaps of spatially periodic media with multilevel dopants. This mechanism is shown to be capable of fully entangling two single-photon pulses with high fidelity.Comment: 7 pages, 1 figur

Bright single-photon sources in bottom-up tailored nanowires

The ability to achieve near-unity light extraction efficiency is necessary for a truly deterministic single photon source. The most promising method to reach such high efficiencies is based on embedding single photon emitters in tapered photonic waveguides defined by top-down etching techniques. However, light extraction efficiencies in current top-down approaches are limited by fabrication imperfections and etching induced defects. The efficiency is further tempered by randomly positioned off-axis quantum emitters. Here, we present perfectly positioned single quantum dots on the axis of a tailored nanowire waveguide using bottom-up growth. In comparison to quantum dots in nanowires without waveguide, we demonstrate a 24-fold enhancement in the single photon flux, corresponding to a light extraction efficiency of 42 %. Such high efficiencies in one-dimensional nanowires are promising to transfer quantum information over large distances between remote stationary qubits using flying qubits within the same nanowire p-n junction.Comment: 19 pages, 6 figure

Nanobeam photonic crystal cavity quantum dot laser

The lasing behavior of one dimensional GaAs nanobeam cavities with embedded InAs quantum dots is studied at room temperature. Lasing is observed throughout the quantum dot PL spectrum, and the wavelength dependence of the threshold is calculated. We study the cavity lasers under both 780 nm and 980 nm pump, finding thresholds as low as 0.3 uW and 19 uW for the two pump wavelengths, respectively. Finally, the nanobeam cavity laser wavelengths are tuned by up to 7 nm by employing a fiber taper in near proximity to the cavities. The fiber taper is used both to efficiently pump the cavity and collect the cavity emission.Comment: 8 pages; 6 figure

Towards deterministic optical quantum computation with coherently driven atomic ensembles

Scalable and efficient quantum computation with photonic qubits requires (i) deterministic sources of single-photons, (ii) giant nonlinearities capable of entangling pairs of photons, and (iii) reliable single-photon detectors. In addition, an optical quantum computer would need a robust reversible photon storage devise. Here we discuss several related techniques, based on the coherent manipulation of atomic ensembles in the regime of electromagnetically induced transparency, that are capable of implementing all of the above prerequisites for deterministic optical quantum computation with single photons.Comment: 11 pages, 7 figure

Paternal effect on genomic activation, clinical pregnancy and live birth rate after ICSI with cryopreserved epididymal versus testicular spermatozoa

<p>Abstract</p> <p>Background</p> <p>This study takes an in depth look at embryonic development, implantation, pregnancy and live birth rates with frozen epididymal and testicular sperm from obstructed (OA) and non-obstructed (NOA) patients.</p> <p>Methods</p> <p>Paternal effect of sperm source on zygote formation, embryonic cleavage, and genomic activation were examined. Additional outcome parameters monitored were clinical pregnancy rate (CPR), implantation rate (IR) and live birth rate.</p> <p>Results</p> <p>In this report, we retrospectively analyzed 156 ICSI cycles using cryopreserved epididymal sperm (ES; n = 77) or testicular sperm (TESE; n = 79). The developmental potential of embryos did not appear to be influenced by the type of surgically retrieved sperm. The average number of blastomeres observed on Day 3 was not different among different groups; 7.5 +/- 1.7 (ES), 7.6 +/- 2.1 (TESE-OA) and 6.5 +/- 2.3 (TESE-NOA). Compaction and blastulation rates, both indicators of paternal genomic activation, were similar in embryos derived from ICSI with ES or TESE from OA as well as NOA men. The only parameter significantly affected in NOA-TESE cases was the fertilization rate. CPR and IR with cryopreserved TESE (TESE-OA 59%, 34%, and TESE-NOA 37%, 20%) were also not statistically different, from that achieved with cryopreserved ES (61% and 39%). Live birth rates also appeared to be independent of sperm type. The 87 clinical pregnancies established using cryopreserved TESE and ES, resulted in the birth of 115 healthy infants. No congenital anomalies were noted.</p> <p>Conclusion</p> <p>Zygotic activation seems to be independent of sperm origin and type of azoospermia.</p

Single photon quantum non-demolition in the presence of inhomogeneous broadening

Electromagnetically induced transparency (EIT) has been often proposed for generating nonlinear optical effects at the single photon level; in particular, as a means to effect a quantum non-demolition measurement of a single photon field. Previous treatments have usually considered homogeneously broadened samples, but realisations in any medium will have to contend with inhomogeneous broadening. Here we reappraise an earlier scheme [Munro \textit{et al.} Phys. Rev. A \textbf{71}, 033819 (2005)] with respect to inhomogeneities and show an alternative mode of operation that is preferred in an inhomogeneous environment. We further show the implications of these results on a potential implementation in diamond containing nitrogen-vacancy colour centres. Our modelling shows that single mode waveguide structures of length $200 \mu\mathrm{m}$ in single-crystal diamond containing a dilute ensemble of NV$^-$ of only 200 centres are sufficient for quantum non-demolition measurements using EIT-based weak nonlinear interactions.Comment: 21 pages, 9 figures (some in colour) at low resolution for arXiv purpose

Urban rainwater harvesting systems: Research, implementation and future perspectives.

Published onlineJournal ArticleReviewThis is the author accepted manuscript. The final version is available from IWA Publishing via the DOI in this record.While the practice of rainwater harvesting (RWH) can be traced back millennia, the degree of its modern implementation varies greatly across the world, often with systems that do not maximize potential benefits. With a global focus, the pertinent practical, theoretical and social aspects of RWH are reviewed in order to ascertain the state of the art. Avenues for future research are also identified. A major finding is that the degree of RWH systems implementation and the technology selection are strongly influenced by economic constraints and local regulations. Moreover, despite design protocols having been set up in many countries, recommendations are still often organized only with the objective of conserving water without considering other potential benefits associated with the multiple-purpose nature of RWH. It is suggested that future work on RWH addresses three priority challenges. Firstly, more empirical data on system operation is needed to allow improved modelling by taking into account multiple objectives of RWH systems. Secondly, maintenance aspects and how they may impact the quality of collected rainwater should be explored in the future as a way to increase confidence on rainwater use. Finally, research should be devoted to the understanding of how institutional and socio-political support can be best targeted to improve system efficacy and community acceptance