Simulations of electromagnetic effects in high frequency capacitively coupled discharges using the Darwin approximation

The Darwin approximation is investigated for its possible use in simulation of electromagnetic effects in large size, high frequency capacitively coupled discharges. The approximation is utilized within the framework of two different fluid models which are applied to typical cases showing pronounced standing wave and skin effects. With the first model it is demonstrated that Darwin approximation is valid for treatment of such effects in the range of parameters under consideration. The second approach, a reduced nonlinear Darwin approximation-based model, shows that the electromagnetic phenomena persist in a more realistic setting. The Darwin approximation offers a simple and efficient way of carrying out electromagnetic simulations as it removes the Courant condition plaguing explicit electromagnetic algorithms and can be implemented as a straightforward modification of electrostatic algorithms. The algorithm described here avoids iterative schemes needed for the divergence cleaning and represents a fast and efficient solver, which can be used in fluid and kinetic models for self-consistent description of technical plasmas exhibiting certain electromagnetic activity

Models of organometallic complexes for optoelectronic applications

Organometallic complexes have potential applications as the optically active components of organic light emitting diodes (OLEDs) and organic photovoltaics (OPV). Development of more effective complexes may be aided by understanding their excited state properties. Here we discuss two key theoretical approaches to investigate these complexes: first principles atomistic models and effective Hamiltonian models. We review applications of these methods, such as, determining the nature of the emitting state, predicting the fraction of injected charges that form triplet excitations, and explaining the sensitivity of device performance to small changes in the molecular structure of the organometallic complexes.Comment: To appear in themed issue of J. Mat. Chem. on the modelling of material

Surface Dependent Electron and Negative Ion Density in Inductively Coupled Discharges

Electron and negative ion density have been measured in a modfied Applied Materials DPS metal etch chamber using gas mixtures of BCl{sub 3}, Cl{sub 2} and Ar. Measurements were performed for four dflerent substrate types to examine the influence of surface material on the bulk plasma properties; aluminurq alumina, photoresist and 50 percent patterned aluminum / photoresist. Electron densities in the Cl{sub 2} / BCl{sub 3} mixtures varied from 0.25 to 4 x 10{sup 11} cm{sup -3}. Photodetachment measurements of the negative ion density indicate that the negative ion density was smaller than the electron density and that the electron to negative ion density ratio varied between 1 and 6. The presence of photoresist had a dominant intluence on the electron and negative ion density compared to alumina and aluminum surfaces. In most cases, the electron density above wafers covered with photoresist was a factor of two lower while the negative ion density was a factor of two higher than the aluminum or alumina surfaces

Surface dependent electron and negative ion density in inductively coupled discharges

Electron and negative ion density have been measured in a modfied Applied Materials DPS metal etch chamber using gas mixtures of BCl{sub 3}, Cl{sub 2} and Ar. Measurements were performed for four dflerent substrate types to examine the influence of surface material on the bulk plasma properties; aluminurq alumina, photoresist and 50 percent patterned aluminum / photoresist. Electron densities in the Cl{sub 2} / BCl{sub 3} mixtures varied from 0.25 to 4 x 10{sup 11} cm{sup -3}. Photodetachment measurements of the negative ion density indicate that the negative ion density was smaller than the electron density and that the electron to negative ion density ratio varied between 1 and 6. The presence of photoresist had a dominant intluence on the electron and negative ion density compared to alumina and aluminum surfaces. In most cases, the electron density above wafers covered with photoresist was a factor of two lower while the negative ion density was a factor of two higher than the aluminum or alumina surfaces

The Role of Protein Kinase A Regulation of the E6 PDZ-Binding Domain during the Differentiation-Dependent Life Cycle of Human Papillomavirus Type 18

Human papillomavirus (HPV) E6 proteins of high-risk alpha types target a select group of PSD95/DLG1/ZO1 (PDZ) domain-containing proteins by using a C-terminal PDZ-binding motif (PBM), an interaction that can be negatively regulated by phosphorylation of the E6 PBM by protein kinase A (PKA). Here, we have mutated the canonical PKA recognition motif that partially overlaps with the E6 PBM in the HPV18 genome (E6153PKA) and compared the effect of this mutation on the HPVl8 life cycle in primary keratinocytes with the wild-type genome and with a second mutant genome that lacks the E6 PBM (E6ΔPDZ). Loss of PKA recognition of E6 was associated with increased growth of the genome-containing cells relative to cells carrying the wild-type genome, and upon stratification, a more hyperplastic phenotype, with an increase in the number of S-phase competent cells in the upper suprabasal layers, while the opposite was seen with the E6ΔPDZ genome. Moreover, the growth of wild-type genome-containing cells was sensitive to changes in PKA activity, and these changes were associated with increased phosphorylation of the E6 PBM. In marked contrast to E6ΔPDZ genomes, the E6153PKA mutation exhibited no deleterious effects on viral genome amplification or expression of late proteins. Our data suggest that the E6 PBM function is differentially regulated by phosphorylation in the HPV18 life cycle. We speculate that perturbation of protein kinase signaling pathways could lead to changes in E6 PBM function, which in turn could have a bearing on tumor promotion and progression

A Review of Urban Water Body Challenges and Approaches: (1) Rehabilitation and Remediation

We review how urbanization alters aquatic ecosystems, as well as actions that managers can take to remediate urban waters. Urbanization affects streams by fundamentally altering longitudinal and lateral processes that in turn alter hydrology, habitat, and water chemistry; these effects create physical and chemical stressors that in turn affect the biota. Urban streams often suffer from multiple stressor effects that have collectively been termed an “urban stream syndrome,” in which no single factor dominates degraded conditions. Resource managers have multiple ways of combating the urban stream syndrome. These approaches range from whole-watershed protection to reach-scale habitat rehabilitation, but the prescription must be matched to the scale of the factors that are causing the problem, and results will likely not be immediate because of lengthy recovery times. Although pristine or reference conditions are far from attainable, urban stream rehabilitation is a worthy goal because appropriate actions can provide ecosystem improvements as well as increased ecosystem service benefits for human society

Ambient fabrication of flexible and large-area organic light-emitting devices using slot-die coating

The grand vision of manufacturing large-area emissive devices with low-cost roll-to-roll coating methods, akin to how newspapers are produced, appeared with the emergence of the organic light-emitting diode about 20 years ago. Today, small organic light-emitting diode displays are commercially available in smartphones, but the promise of a continuous ambient fabrication has unfortunately not materialized yet, as organic light-emitting diodes invariably depend on the use of one or more time- and energy-consuming process steps under vacuum. Here we report an all-solution-based fabrication of an alternative emissive device, a light-emitting electrochemical cell, using a slot-die roll-coating apparatus. The fabricated flexible sheets exhibit bidirectional and uniform light emission, and feature a fault-tolerant >1-μm-thick active material that is doped in situ during operation. It is notable that the initial preparation of inks, the subsequent coating of the constituent layers and the final device operation all could be executed under ambient air

Multipurpose silicon photonics signal processor core

[EN] Integrated photonics changes the scaling laws of information and communication systems offering architectural choices that combine photonics with electronics to optimize performance, power, footprint, and cost. Application-specific photonic integrated circuits, where particular circuits/chips are designed to optimally perform particular functionalities, require a considerable number of design and fabrication iterations leading to long development times. A different approach inspired by electronic Field Programmable Gate Arrays is the programmable photonic processor, where a common hardware implemented by a two-dimensional photonic waveguide mesh realizes different functionalities through programming. Here, we report the demonstration of such reconfigurable waveguide mesh in silicon. We demonstrate over 20 different functionalities with a simple seven hexagonal cell structure, which can be applied to different fields including communications, chemical and biomedical sensing, signal processing, multiprocessor networks, and quantum information systems. Our work is an important step toward this paradigm.J.C. acknowledges funding from the ERC Advanced Grant ERC-ADG-2016-741415 UMWP-Chip, I.G. acknowledges the funding through the Spanish MINECO Ramon y Cajal program. D.P. acknowledges financial support from the UPV through the FPI predoctoral funding scheme. D.J.T. acknowledges funding from the Royal Society for his University Research Fellowship.Pérez-López, D.; Gasulla Mestre, I.; Crudgington, L.; Thomson, DJ.; Khokhar, AZ.; Li, K.; Cao, W.... (2017). Multipurpose silicon photonics signal processor core. Nature Communications. 8(1925):1-9. https://doi.org/10.1038/s41467-017-00714-1S1981925Doerr, C. R. & Okamoto, K. Advances in silica planar lightwave circuits. J. Lightw. Technol. 24, 4763–4789 (2006).Coldren, L. A. et al. High performance InP-based photonic ICs—A tutorial. J. Lightw. Technol 29, 554–570 (2011).Soref, R. The past, present, and future of silicon photonics. IEEE J. Sel. Top. Quantum Electron. 12, 1678–1687 (2006).Bogaerts, W. Design challenges in silicon photonics. IEEE J. Sel. Top. Quantum Electron. 20, 8202008 (2014).Bogaerts, W. et al. Nanophotonic waveguides in silicon-on-insulator fabricated with CMOS technology. J. Lightw. Technol. 23, 401–412 (2005).Smit, M. K. et al. An introduction to InP-based generic integration technology. Semicond. Sci. Technol. 29, 083001 (2014).Leinse, A. et al. TriPleX waveguide platform: low-loss technology over a wide wavelength range. Proc. SPIE 8767, 87670E (2013).Kish, F. et al. From visible light-emitting diodes to large-scale III–V photonic integrated circuits. Proc. IEEE 101, 2255–2270 (2013).Heck, M. J. R. et al. Hybrid silicon photonic integrated circuit technology. IEEE J. Sel. Top. Quantum Electron. 19, 6100117 (2013).Sacher, W. et al. Multilayer silicon nitride-on-silicon integrated photonic platforms and devices. J. Lightw. Technol. 33, 901–910 (2015).Asghari, M. Silicon photonics: A low cost integration platform for datacom and telecom applications. In OFC/NFOEC 2008 – 2008 Conference on Optical Fiber Communication/National Fiber Optic Engineers Conference 1–10 (San Diego, USA, 2008).Melati, D. et al. Integrated all-optical MIMO demultiplexer for mode- and wavelength-division-multiplexed transmission. Opt. Lett. 42, 342–345 (2017).Waterhouse, R. & Novak, D. Realizing 5G: microwave photonics for 5G mobile wireless systems. IEEE Microw. Mag. 16, 84–92 (2015).Marpaung, D. et al. Integrated microwave photonics. Laser Photon. Rev. 7, 506–538 (2013).Iezekiel, S., Burla, M., Klamkin, J., Marpaung, D. & Capmany, J. RF engineering meets optoelectronics: Progress in integrated microwave photonics. IEEE Microw. Mag. 16, 28–45 (2015).Technology focus on microwave photonics. Nat. Photon. 5, 723 (2011).Ghelfi, P. et al. A fully photonics-based coherent radar system. Nature 507, 341–345 (2014).Heideman, R. G. TriPleX™-based integrated optical ring resonators for lab-ona-chip-and environmental detection. IEEE J. Sel. Top. Quantum Electron. 18, 1583–1596 (2012).Estevez, M. C., Alvarez, M. & Lechuga, L. Integrated optical devices for lab-on-a-chip biosensing applications. Laser Photon. Rev. 6, 463–487 (2012).Almeida, V. R., Barrios, C. A., Panepucci, R. & Lipson, M. All-optical control of light on a silicon chip. Nature 431, 1081–1084 (2004).Norberg, E. J., Guzzon, R. S., Parker, J. S., Johansson, L. A. & Coldren, L. A. Programmable photonic microwave filters monolithically integrated in InP/InGaAsP. J. Lightw. Technol. 29, 1611–1619 (2011).Wang, J. et al. Reconfigurable radio-frequency arbitrary waveforms synthesized in a silicon photonic chip. Nat. Commun. 6, 5957 (2015).Hill, M. T. et al. A fast low power optical memory based on coupled micro-ring lasers. Nature 432, 206–209 (2004).Slavík, R. et al. Photonic temporal integrator for all-optical computing. Opt. Express 16, 18202–18214 (2008).Sun, C. et al. A monolithically-integrated chip-to-chip optical link in bulk CMOS. IEEE J. Solid-State Circ. 50, 828–844 (2015).Sun, C. et al. Single-chip microprocessor that communicates directly using light. Nature 528, 534–538 (2015).Assefa, S. et al. in Optical Fibre Communication Conference OMM6, https://www.osapublishing.org/abstract.cfm?uri=OFC-2011-OMM6 (Optical Society of America, 2011).Peruzzo, A. et al. Multimode quantum interference of photons in multiport integrated devices. Nat. Commun. 2, 224 (2011).Bonneau, D. et al. Quantum interference and manipulation of entanglement in silicon wire waveguide quantum circuits. N. J. Phys. 14, 045003 (2012).Metcalf, B. J. et al. Multiphoton quantum interference in a multiport integrated photonic device. Nat. Commun. 4, 1356 (2013).Muñoz, P. et al. in 16th International Conference on Transparent Optical Networks (ICTON), 1–4 (Graz, 2014).Ribeiro, A. et al. Demonstration of a 4×4-port universal linear circuit. Optica 3, 1348–1357 (2016).Liu, W. et al. A fully reconfigurable photonic integrated signal processor. Nat. Photon 10, 190–195 (2016).Graydon, O. Birth of the programmable optical chip. Nat. Photon 10, 1 (2016).Pérez, D., Gasulla, I. & Capmany, J. Software-defined reconfigurable microwave photonics processor. Opt. Express 23, 14640–14654 (2015).Miller, D. A. B. Self-configuring universal linear optical component. Photon. Res. 1, 1–15 (2013).Miller, D. A. B. Self-aligning universal beam coupler. Opt. Express 21, 6360–6370 (2013).Clements, W. R. et al. Optimal design for universal multiport interferometers. Optica 3, 1460–1465 (2016).Zhuang, L., Roeloffzen, C. G. H., Hoekman, M., Boller, K.-J. & Lowery, A. J. Programmable photonic signal processor chip for radiofrequency applications. Optica 2, 854–859 (2015).Capmany, J., Gasulla, I. & Pérez, D. Microwave photonics: The programmable processor. Nat. Photon. 10, 6–8 (2016).Pérez, D., Gasulla., Capmany, J. & Soref, R. A. Reconfigurable lattice mesh designs for programmable photonic processors. Opt. Express 24, 12093–12106 (2016).Madsen, C. K. & Zhao, J. H. Optical Filter Design and Analysis: A Signal Processing Approach. 1st edn. (Wiley, 1999).Jinguji, K. Synthesis of coherent two-port lattice-form optical delay-line circuit. J. Lightw. Technol. 13, 73–82 (1995).Jinguji, K. Synthesis of coherent two-port Optical delay-line circuit with ring waveguides. J. Lightw. Technol. 14, 1882–1898 (1996).Madsen, C. K. General IIR optical filter design for WDM applications using all-pass filters. J. Lightw. Technol. 18, 860–868 (2000).Burla, M. et al. On-chip CMOS compatible reconfigurable optical delay line with separate carrier tuning for microwave photonic signal processing. Opt. Express 19, 21475–21484 (2011).Yariv, A. et al. Coupled resonator optical waveguides: a proposal and analysis. Opt. Lett. 24, 711–713 (1999).Hebner, J. E. et al. Distributed and localized feedback in microresonator sequences for linear and nonlinear optics. J. Opt. Soc. Am. B. 21, 1665–1673 (2004).Fandiño, J. S. et al. A monolithic integrated photonic microwave filter. Nat. Photon. 11, 124–129 (2017).Miller, D. A. B. All linear optical devices are mode converters. Opt. Express 20, 23985–23993 (2012).Reck, M. et al. Experimental realization of any discrete unitary operator. Phys. Rev. Lett. 73, 58–61 (1994).Carolan, J. et al. Universal linear optics. Science 349, 711 (2015).Nielsen, M. A. & Chuang, I. L. Quantum Computation and Quantum Information. 1st edn. (Cambridge University Press, 2001).Miller, D. A. B. Perfect optics with imperfect components. Optica 2, 747–750 (2015).Grillanda, S. et al. Non-invasive monitoring and control in silicon photonics using CMOS integrated electronics. Optica 1, 129–136 (2014)

Degradation of p53 by Human Alphapapillomavirus E6 Proteins Shows a Stronger Correlation with Phylogeny than Oncogenicity

Human Papillomavirus (HPV) E6 induced p53 degradation is thought to be an essential activity by which high-risk human Alphapapillomaviruses (alpha-HPVs) contribute to cervical cancer development. However, most of our understanding is derived from the comparison of HPV16 and HPV11. These two viruses are relatively distinct viruses, making the extrapolation of these results difficult. In the present study, we expand the tested strains (types) to include members of all known HPV species groups within the Alphapapillomavirus genus.We report the biochemical activity of E6 proteins from 27 HPV types representing all alpha-HPV species groups to degrade p53 in human cells. Expression of E6 from all HPV types epidemiologically classified as group 1 carcinogens significantly reduced p53 levels. However, several types not associated with cancer (e.g., HPV53, HPV70 and HPV71) were equally active in degrading p53. HPV types within species groups alpha 5, 6, 7, 9 and 11 share a most recent common ancestor (MRCA) and all contain E6 ORFs that degrade p53. A unique exception, HPV71 E6 ORF that degraded p53 was outside this clade and is one of the most prevalent HPV types infecting the cervix in a population-based study of 10,000 women. Alignment of E6 ORFs identified an amino acid site that was highly correlated with the biochemical ability to degrade p53. Alteration of this amino acid in HPV71 E6 abrogated its ability to degrade p53, while alteration of this site in HPV71-related HPV90 and HPV106 E6s enhanced their capacity to degrade p53.These data suggest that the alpha-HPV E6 proteins' ability to degrade p53 is an evolved phenotype inherited from a most recent common ancestor of the high-risk species that does not always segregate with carcinogenicity. In addition, we identified an amino-acid residue strongly correlated with viral p53 degrading potential