| 1. |
- Abe, K., et al.
(author)
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J-PARC Neutrino Beamline Upgrade Technical Design Report
- 2019
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Reports (peer-reviewed)abstract
- In this document, technical details of the upgrade plan of the J-PARC neutrino beamline for the extension of the T2K experiment are described. T2K has proposed to accumulate data corresponding to 2×1022 protons-on-target in the next decade, aiming at an initial observation of CP violation with 3σ or higher significance in the case of maximal CP violation. Methods to increase the neutrino beam intensity, which are necessary to achieve the proposed data increase, are described.
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| 2. |
- Abe, K., et al.
(author)
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Neutron tagging following atmospheric neutrino events in a water Cherenkov detector
- 2022
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In: Journal of Instrumentation. - : Institute of Physics (IOP). - 1748-0221. ; 17:10
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Journal article (peer-reviewed)abstract
- We present the development of neutron-tagging techniques in Super-Kamiokande IV using a neural network analysis. The detection efficiency of neutron capture on hydrogen is estimated to be 26%, with a mis-tag rate of 0.016 per neutrino event. The uncertainty of the tagging efficiency is estimated to be 9.0%. Measurement of the tagging efficiency with data from an Americium-Beryllium calibration agrees with this value within 10%. The tagging procedure was performed on 3,244.4 days of SK-IV atmospheric neutrino data, identifying 18,091 neutrons in 26,473 neutrino events. The fitted neutron capture lifetime was measured as 218 +/- 9 mu s.
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| 3. |
- Menden, MP, et al.
(author)
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Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
- 2019
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 2674-
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Journal article (peer-reviewed)abstract
- The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.
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| 4. |
- Hu, H., et al.
(author)
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X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes
- 2016
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In: Molecular Psychiatry. - : Springer Science and Business Media LLC. - 1359-4184 .- 1476-5578. ; 21:1, s. 133-148
-
Journal article (peer-reviewed)abstract
- X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4(-/-) mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases.
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| 5. |
- Dannetun, Per, et al.
(author)
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Proceedings of the International Conference on Science and Technology of Synthetic Metals The chemical and electronic structure of the interface between aluminum and conjugated polymers or molecules
- 1993
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In: Synthetic metals. - : Elsevier. - 0379-6779 .- 1879-3290. ; 55:1, s. 212-217
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Journal article (peer-reviewed)abstract
- The interaction between aluminum and α-ω-diphenyltetradecaheptaenee (DP7), α-sexithienyl (6T), and poly(p-phenylenevinylene) (PPV), respectively have been studied using both X-ray Photoelectron Spectroscopy (XPS) and Ultraviolet Photoelectron Spectroscopy (UPS). The UPS valence band spectra, are interpreted with the help of quantum chemical calculations based upon Modified Neglect of Diatomic Overlap (MNDO), Valence Effective Hamitonian (VEH) and ab initio Hartree-Fock methods. DP7 is a model molecule for polyacetylene, while 6T is a model molecule (an oligomer) of polythiophene. The results indicate that aluminum reacts strongly with the surfaces of all of the materials studied. The π-electronic structure of each material was strongly modified. Furthermore, aluminum reacts preferentially with the polyene partof DP7, with the vinylene part of PPV, and with the α-carbons of the thiophene nits of 6T.
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| 6. |
- Sieberts, SK, et al.
(author)
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Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis
- 2016
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7, s. 12460-
-
Journal article (peer-reviewed)abstract
- Rheumatoid arthritis (RA) affects millions world-wide. While anti-TNF treatment is widely used to reduce disease progression, treatment fails in ∼one-third of patients. No biomarker currently exists that identifies non-responders before treatment. A rigorous community-based assessment of the utility of SNP data for predicting anti-TNF treatment efficacy in RA patients was performed in the context of a DREAM Challenge (http://www.synapse.org/RA_Challenge). An open challenge framework enabled the comparative evaluation of predictions developed by 73 research groups using the most comprehensive available data and covering a wide range of state-of-the-art modelling methodologies. Despite a significant genetic heritability estimate of treatment non-response trait (h2=0.18, P value=0.02), no significant genetic contribution to prediction accuracy is observed. Results formally confirm the expectations of the rheumatology community that SNP information does not significantly improve predictive performance relative to standard clinical traits, thereby justifying a refocusing of future efforts on collection of other data.
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| 7. |
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| 8. |
- Babst, F., et al.
(author)
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When tree rings go global: Challenges and opportunities for retro- and prospective insight
- 2018
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In: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791. ; 197, s. 1-20
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Journal article (peer-reviewed)abstract
- The demand for large-scale and long-term information on tree growth is increasing rapidly as environmental change research strives to quantify and forecast the impacts of continued warming on forest ecosystems. This demand, combined with the now quasi-global availability of tree-ring observations, has inspired researchers to compile large tree-ring networks to address continental or even global-scale research questions. However, these emergent spatial objectives contrast with paleo-oriented research ideas that have guided the development of many existing records. A series of challenges related to how, where, and when samples have been collected is complicating the transition of tree rings from a local to a global resource on the question of tree growth. Herein, we review possibilities to scale tree-ring data (A) from the sample to the whole tree, (B) from the tree to the site, and (C) from the site to larger spatial domains. Representative tree-ring sampling supported by creative statistical approaches is thereby key to robustly capture the heterogeneity of climate-growth responses across forested landscapes. We highlight the benefits of combining the temporal information embedded in tree rings with the spatial information offered by forest inventories and earth observations to quantify tree growth and its drivers. In addition, we show how the continued development of mechanistic tree-ring models can help address some of the non-linearities and feedbacks that complicate making inference from tree-ring data. By embracing scaling issues, the discipline of dendrochronology will greatly increase its contributions to assessing climate impacts on forests and support the development of adaptation strategies. © 2018 Elsevier Ltd
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| 9. |
- Gorman, Jeffrey, et al.
(author)
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Deoxyribonucleic Acid Encoded and Size-Defined π-Stacking of Perylene Diimides
- 2022
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In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 144:1, s. 368-376
-
Journal article (peer-reviewed)abstract
- Natural photosystems use protein scaffolds to control intermolecular interactions that enable exciton flow, charge generation, and long-range charge separation. In contrast, there is limited structural control in current organic electronic devices such as OLEDs and solar cells. We report here the DNA-encoded assembly of pi-conjugated perylene diimides (PDIs) with deterministic control over the number of electronically coupled molecules. The PDIs are integrated within DNA chains using phosphoramidite coupling chemistry, allowing selection of the DNA sequence to either side, and specification of intermolecular DNA hybridization. In this way, we have developed a "toolbox" for construction of any stacking sequence of these semiconducting molecules. We have discovered that we need to use a full hierarchy of interactions: DNA guides the semiconductors into specified close proximity, hydrophobic-hydrophilic differentiation drives aggregation of the semiconductor moieties, and local geometry and electrostatic interactions define intermolecular positioning. As a result, the PDIs pack to give substantial intermolecular pi wave function overlap, leading to an evolution of singlet excited states from localized excitons in the PDI monomer to excimers with wave functions delocalized over all five PDIs in the pentamer. This is accompanied by a change in the dominant triplet forming mechanism from localized spin-orbit charge transfer mediated intersystem crossing for the monomer toward a delocalized excimer process for the pentamer. Our modular DNA-based assembly reveals real opportunities for the rapid development of bespoke semiconductor architectures with molecule-by-molecule precision.
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| 10. |
- Orsborne, Sarah R.E., et al.
(author)
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Photogeneration of Spin Quintet Triplet-Triplet Excitations in DNA-Assembled Pentacene Stacks
- 2023
-
In: Journal of the American Chemical Society. - : American Chemical Society. - 0002-7863 .- 1520-5126. ; 145:9, s. 5431-5438
-
Journal article (peer-reviewed)abstract
- Singlet fission (SF), an exciton-doubling process observed in certain molecular semiconductors where two triplet excitons are generated from one singlet exciton, requires correctly tuned intermolecular coupling to allow separation of the two triplets to different molecular units. We explore this using DNA-encoded assembly of SF-capable pentacenes into discrete π-stacked constructs of defined size and geometry. Precise structural control is achieved via a combination of the DNA duplex formation between complementary single-stranded DNA and the local molecular geometry that directs the SF chromophores into a stable and predictable slip-stacked configuration, as confirmed by molecular dynamics (MD) modeling. Transient electron spin resonance spectroscopy revealed that within these DNA-assembled pentacene stacks, SF evolves via a bound triplet pair quintet state, which subsequently converts into free triplets. SF evolution via a long-lived quintet state sets specific requirements on intermolecular coupling, rendering the quintet spectrum and its zero-field-splitting parameters highly sensitive to intermolecular geometry. We have found that the experimental spectra and zero-field-splitting parameters are consistent with a slight systematic strain relative to the MD-optimized geometry. Thus, the transient electron spin resonance analysis is a powerful tool to test and refine the MD-derived structure models. DNA-encoded assembly of coupled semiconductor molecules allows controlled construction of electronically functional structures, but brings with it significant dynamic and polar disorders. Our findings here of efficient SF through quintet states demonstrate that these conditions still allow efficient and controlled semiconductor operation and point toward future opportunities for constructing functional optoelectronic systems.
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| 11. |
- Parker, P, et al.
(author)
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Progress in integrated assessment and modelling
- 2002
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In: Environmental Modelling & Software. - 1364-8152. ; 17:3, s. 209-217
-
Journal article (peer-reviewed)abstract
- Environmental processes have been modelled for decades. However. the need for integrated assessment and modeling (IAM) has,town as the extent and severity of environmental problems in the 21st Century worsens. The scale of IAM is not restricted to the global level as in climate change models, but includes local and regional models of environmental problems. This paper discusses various definitions of IAM and identifies five different types of integration that Lire needed for the effective solution of environmental problems. The future is then depicted in the form of two brief scenarios: one optimistic and one pessimistic. The current state of IAM is then briefly reviewed. The issues of complexity and validation in IAM are recognised as more complex than in traditional disciplinary approaches. Communication is identified as a central issue both internally among team members and externally with decision-makers. stakeholders and other scientists. Finally it is concluded that the process of integrated assessment and modelling is considered as important as the product for any particular project. By learning to work together and recognise the contribution of all team members and participants, it is believed that we will have a strong scientific and social basis to address the environmental problems of the 21st Century.
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| 12. |
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| 13. |
- Wang, T, et al.
(author)
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Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders
- 2020
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1, s. 4932-
-
Journal article (peer-reviewed)abstract
- Most genes associated with neurodevelopmental disorders (NDDs) were identified with an excess of de novo mutations (DNMs) but the significance in case–control mutation burden analysis is unestablished. Here, we sequence 63 genes in 16,294 NDD cases and an additional 62 genes in 6,211 NDD cases. By combining these with published data, we assess a total of 125 genes in over 16,000 NDD cases and compare the mutation burden to nonpsychiatric controls from ExAC. We identify 48 genes (25 newly reported) showing significant burden of ultra-rare (MAF < 0.01%) gene-disruptive mutations (FDR 5%), six of which reach family-wise error rate (FWER) significance (p < 1.25E−06). Among these 125 targeted genes, we also reevaluate DNM excess in 17,426 NDD trios with 6,499 new autism trios. We identify 90 genes enriched for DNMs (FDR 5%; e.g., GABRG2 and UIMC1); of which, 61 reach FWER significance (p < 3.64E−07; e.g., CASZ1). In addition to doubling the number of patients for many NDD risk genes, we present phenotype–genotype correlations for seven risk genes (CTCF, HNRNPU, KCNQ3, ZBTB18, TCF12, SPEN, and LEO1) based on this large-scale targeted sequencing effort.
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| 14. |
- Andaji-Garmaroudi, Z., et al.
(author)
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Elucidating and Mitigating Degradation Processes in Perovskite Light-Emitting Diodes
- 2020
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In: Advanced Energy Materials. - : Wiley-VCH Verlag. - 1614-6832 .- 1614-6840. ; 10:48
-
Journal article (peer-reviewed)abstract
- Halide perovskites have attracted substantial interest for their potential as disruptive display and lighting technologies. However, perovskite light-emitting diodes (PeLEDs) are still hindered by poor operational stability. A fundamental understanding of the degradation processes is lacking but will be key to mitigating these pathways. Here, a combination of in operando and ex situ measurements to monitor the performance degradation of (Cs0.06FA0.79MA0.15)Pb(I0.85Br0.15)3 PeLEDs over time is used. Through device, nanoscale cross-sectional chemical mapping, and optical spectroscopy measurements, it is revealed that the degraded performance arises from an irreversible accumulation of bromide content at one interface, which leads to barriers to injection of charge carriers and thus increased nonradiative recombination. This ionic segregation is impeded by passivating the perovskite films with potassium halides, which immobilizes the excess halide species. The passivated PeLEDs show enhanced external quantum efficiency (EQE) from 0.5% to 4.5% and, importantly, show significantly enhanced stability, with minimal performance roll-off even at high current densities (>200 mA cm−2). The decay half-life for the devices under continuous operation at peak EQE increases from <1 to ≈15 h through passivation, and ≈200 h under pulsed operation. The results provide generalized insight into degradation pathways in PeLEDs and highlight routes to overcome these challenges.
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| 15. |
- Bröms, P., et al.
(author)
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Optical absorption studies of sodium doped poly(cyanoterephthalylidene)
- 1994
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In: Synthetic metals. - : Elsevier. - 0379-6779 .- 1879-3290. ; 67:1-3, s. 93-96
-
Journal article (peer-reviewed)abstract
- The effects of doping poly(cyanoterephthalylidene) with sodium in ultrahighvacuum been studied by optical absorption spectroscopy. Upon doping, new optical transitions are observed within the bandgap; the characteristics of these transitions are consistent with the formation of bipolarons. The optical absorption results are confirmed by direct measurements of the doping-induced gap states using ultraviolet photoelectron spectroscopy.
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| 16. |
- Cacialli, F., et al.
(author)
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Synthesis and characterisation of poly(distyrylbenzene-block-hexa(ethylene oxide)) and its fluorinated analogue - Two new block copolymers and their application in electroluminescent devices
- 2002
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In: Polymer. - 0032-3861 .- 1873-2291. ; 43:12, s. 3555-3561
-
Journal article (peer-reviewed)abstract
- Two new soluble block copolymers are reported in which chromophores and hexa(ethylene oxide) units alternate along the polymer backbone. In polymer 1 the chromophore was the distyrylbenzene unit. The polymer was synthesised via the Wittig reaction and the ionization potential of 5.4 ± 0.2 eV was measured by cyclic voltammetry and photoelectron spectroscopy. Polymer 1 showed a high solid-state photoluminescence efficiency (34%) and was used to make efficient (0.5 cd/A) light emitting diodes (LEDs). Polymer 1 was also used in light emitting cells, these showed luminescence in reverse bias and a reduced turn-on voltage compared to the LEDs. Polymer 2, in which the chromophore was dodecafluoro-distryrylbenzene, was prepared via the Horner-Wittig reaction and showed an ionization potential of 6.25 ± 0.15 eV and a solid-state photoluminescence efficiency of 17%. It was used as electron-conducting layer in a LED but failed to give significant electroluminescence. The optical energy gap for both polymers was 3.0 eV. © 2002 Published by Elsevier Science Ltd.
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| 17. |
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| 18. |
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| 19. |
- Dannetun, Per, et al.
(author)
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New Results on Metal-Polymer Interfaces
- 1993
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In: Molecular Crystals and Liquid Crystals. - : Taylor & Francis. - 1542-1406 .- 1563-5287. ; 228:1, s. 43-48
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Journal article (peer-reviewed)abstract
- New results on studies of the early stages of formation of the aluminum-poly(p-phenylenevinylene) interface are presented.
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| 20. |
- Kim, J.S., et al.
(author)
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Kelvin probe and ultraviolet photoemission measurements of indium tin oxide work function: : a comparison
- 2000
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In: Synthetic metals. - 0379-6779 .- 1879-3290. ; 111-112, s. 311-314
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Journal article (peer-reviewed)abstract
- We report a comparison of the work functions of thin films of indium tin oxide (ITO), carried out by means of ultraviolet photoelectron spectroscopy (UPS) and by measurements of the contact potential difference with respect to a gold reference electrode (Kelvin probe (KP) method). We investigated commercially available ITOs both "as-received", and after certain surface treatments, such as oxygen plasma. First, we find measurable discrepancies between KP values measured with three different instruments, and between the KP and the UPS values. Secondly, and unexpectedly, we find that the KP, although more sensitive than UPS, does not detect certain differences between ITOs with different surface treatments. We discuss the results in view of the different environments in which the measurements are carried out (UHV for the UPS and air/Ar for the Kelvin method), of the effects which may be induced by the high-energy photon irradiation in the UPS measurement, and of the stability of the gold probe work function in gas ambient. We conclude that UPS is better-suited for absolute work function determination, although KP remains a convenient and inexpensive tool for fast screening of contact potential differences. (C) 2000 Elsevier Science S.A. All rights reserved.
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| 21. |
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| 22. |
- Howard, Ian A., et al.
(author)
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Charge Recombination and Exciton Annihilation Reactions in Conjugated Polymer Blends
- 2010
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In: Journal of the American Chemical Society. - 0002-7863. ; 132:1, s. 328-335
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Journal article (peer-reviewed)abstract
- Bimolecular interactions between excitations in conjugated polymer thin films are important because they influence the efficiency of many optoelectronic devices that require high excitation densities. Using time-resolved optical spectroscopy, we measure the bimolecular interactions of charges, singlet excitons, and triplet excitons in intimately mixed polyfluorene blends with band-edge offsets optimized for photoinduced electron transfer. Bimolecular charge recombination and triplet−triplet annihilation are negligible, but exciton−charge interactions are efficient. The annihilation of singlet excitons by charges occurs on picosecond time-scales and reaches a rate equivalent to that of charge transfer. Triplet exciton annihilation by charges occurs on nanosecond time-scales. The surprising absence of nongeminate charge recombination is shown to be due to the limited mobility of charge carriers at the heterojunction. Therefore, extremely high densities of charge pairs can be maintained in the blend. The absence of triplet−triplet annihilation is a consequence of restricted triplet diffusion in the blend morphology. We suggest that the rate and nature of bimolecular interactions are determined by the stochastic excitation distribution in the polymer blend and the limited connectivity between the polymer domains. A model based on these assumptions quantitatively explains the effects. Our findings provide a comprehensive framework for understanding bimolecular recombination and annihilation processes in nanostructured materials.
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| 23. |
- Lombeck, F., et al.
(author)
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On the Effect of Prevalent Carbazole Homocoupling Defects on the Photovoltaic Performance of PCDTBT:PC71BM Solar Cells
- 2016
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In: Advanced Energy Materials. - : Wiley. - 1614-6840 .- 1614-6832. ; 6:21
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Journal article (peer-reviewed)abstract
- The photophysical properties and solar cell performance of the classical donor-acceptor copolymer PCDTBT(poly(N-9-heptadecanyl-2,7-carbazole-alt -5,5-(4,7-di-2-thienyl-2,1,3-benzothiadiazole))) in relation to unintentionally formed main chain defects are investigated. Carbazole-carbazole homocouplings (Cbz hc) are found to significant extent in PCDTBT made with a variety of Suzuki polycondensation conditions. Cbz hc vary between 0 and 8 mol% depending on the synthetic protocol used, and are quantified by detailed nuclear magnetic resonance spectroscopy including model compounds, which allows to establish a calibration curve from optical spectroscopy. The results are corroborated by extended time-dependent density functional theory investigations on the structural, electronic, and optical properties of regularly alternating and homocoupled chains. The photovoltaic properties of PCDTBT:fullerene blend solar cells significantly depend on the Cbz hc content for constant molecular weight, whereby an increasing amount of Cbz hc leads to strongly decreased short circuit currents J(SC). With increasing Cbz hc content, J(SC) decreases more strongly than the intensity of the low energy absorption band, suggesting that small losses in absorption cannot explain the decrease in J(SC) alone, rather than combined effects of a more localized LUMO level on the TBT unit and lower hole mobilities found in highly defective samples. Homocoupling-free PCDTBT with optimized molecular weight yields the highest efficiency up to 7.2% without extensive optimization.
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| 24. |
- Markmann, James F., et al.
(author)
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Executive Summary of IPITA-TTS Opinion Leaders Report on the Future of beta-Cell Replacement
- 2016
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In: Transplantation. - 0041-1337 .- 1534-6080. ; 100:7, s. E25-E31
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Research review (peer-reviewed)abstract
- The International Pancreas and Islet Transplant Association (IPITA), in conjunction with the Transplantation Society (TTS), convened a workshop to consider the future of pancreas and islet transplantation in the context of potential competing technologies that are under development, including the artificial pancreas, transplantation tolerance, xenotransplantation, encapsulation, stem cell derived beta cells, beta cell proliferation, and endogenous regeneration. Separate workgroups for each topic and then the collective group reviewed the state of the art, hurdles to application, and proposed research agenda for each therapy that would allow widespread application. Herein we present the executive summary of this workshop that focuses on obstacles to application and the research agenda to overcome them; the full length article with detailed background for each topic is published as an online supplement to Transplantation.
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| 25. |
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