| 1. |
- Ramilowski, JA, et al.
(författare)
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Functional annotation of human long noncoding RNAs via molecular phenotyping
- 2020
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Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 30:7, s. 1060-1072
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Tidskriftsartikel (refereegranskat)abstract
- Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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| 2. |
- Hoffmann, M., et al.
(författare)
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Magnetic and Electronic Properties of Complex Oxides from First-Principles
- 2020
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Ingår i: Physica status solidi. B, Basic research. - : Wiley-VCH Verlag. - 0370-1972 .- 1521-3951.
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Tidskriftsartikel (refereegranskat)abstract
- The theoretical treatment of complex oxide structures requires a combination of efficient methods to calculate structural, electronic, and magnetic properties, due to special challenges such as strong correlations and disorder. In terms of a multicode approach, this study combines various complementary first-principles methods based on density functional theory to exploit their specific strengths. Pseudopotential methods, known for giving reliable forces and total energies, are used for structural optimization. The optimized structure serves as input for the Green's function and linear muffin-tin orbital methods. Those methods are powerful for the calculation of magnetic ground states and spectroscopic properties. Within the multicode approach, disorder is investigated by means of the coherent potential approximation within a Green's function method or by construction of special quasirandom structures in the framework of the pseudopotential methods. Magnetic ground states and phase transitions are studied using an effective Heisenberg model treated in terms of a Monte Carlo method, where the magnetic exchange parameters are calculated from first-principles. The performance of the multicode approach is demonstrated with different examples, including defect formation, strained films, and surface properties.
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| 3. |
- Kern, S., et al.
(författare)
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Reflection-enhanced gain in traveling-wave parametric amplifiers
- 2023
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Ingår i: Physical Review B. - 2469-9969 .- 2469-9950. ; 107:17
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Tidskriftsartikel (refereegranskat)abstract
- The operating principle of traveling-wave parametric amplifiers is typically understood in terms of the standard coupled mode theory, which describes the evolution of forward propagating waves without any reflections, i.e., for perfect impedance matching. However, in practice, superconducting microwave amplifiers are unmatched nonlinear finite-length devices, where the reflecting waves undergo complex parametric processes, not described by the standard coupled mode theory. Here, we present an analytical solution for the TWPA gain, which includes the interaction of reflected waves. These reflections result in corrections to the well-known results of the standard coupled mode theory, which are obtained for both three-wave and four-wave mixing processes. Due to these reflections, the gain is enhanced and unwanted nonlinear phase modulations are suppressed. Predictions of the model are experimentally demonstrated on two types of unmatched TWPA, based on coplanar waveguides with a central wire consisting of (i) a high kinetic inductance superconductor, and (ii) an array of 2000 Josephson junctions.
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