--- _id: '8268' abstract: - lang: eng text: 'Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality.' acknowledgement: The authors would like to thank Dr. Michiel Brentjens at the Netherlands Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab gratefully acknowledge the support from the Swiss Data Science Center, Alibaba, Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich Insurance, Chinese Scholarship Council, and the Department of Computer Science at ETH Zurich. article_processing_charge: No article_type: original author: - first_name: Nezihe Merve full_name: Gurel, Nezihe Merve last_name: Gurel - first_name: Kaan full_name: Kara, Kaan last_name: Kara - first_name: Alen full_name: Stojanov, Alen last_name: Stojanov - first_name: Tyler full_name: Smith, Tyler last_name: Smith - first_name: Thomas full_name: Lemmin, Thomas last_name: Lemmin - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Markus full_name: Puschel, Markus last_name: Puschel - first_name: Ce full_name: Zhang, Ce last_name: Zhang citation: ama: 'Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 2020;68:4268-4282. doi:10.1109/TSP.2020.3010355' apa: 'Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A., … Zhang, C. (2020). Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2020.3010355' chicago: 'Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin, Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing. IEEE, 2020. https://doi.org/10.1109/TSP.2020.3010355.' ieee: 'N. M. Gurel et al., “Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications,” IEEE Transactions on Signal Processing, vol. 68. IEEE, pp. 4268–4282, 2020.' ista: 'Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M, Zhang C. 2020. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 68, 4268–4282.' mla: 'Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing, vol. 68, IEEE, 2020, pp. 4268–82, doi:10.1109/TSP.2020.3010355.' short: N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M. Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282. date_created: 2020-08-16T22:00:56Z date_published: 2020-07-20T00:00:00Z date_updated: 2023-08-22T08:40:08Z day: '20' department: - _id: DaAl doi: 10.1109/TSP.2020.3010355 external_id: arxiv: - '1802.04907' isi: - '000562044500001' intvolume: ' 68' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.04907 month: '07' oa: 1 oa_version: Preprint page: 4268-4282 publication: IEEE Transactions on Signal Processing publication_identifier: eissn: - '19410476' issn: - 1053587X publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: 'Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 68 year: '2020' ... --- _id: '8271' acknowledgement: We thank Dr. Gai Huang for his comments and help. We apologize to authors whose work could not be cited due to space limitation. No conflict of interest declared. article_processing_charge: No article_type: original author: - first_name: Peng full_name: He, Peng last_name: He - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: Guanghui full_name: Xiao, Guanghui last_name: Xiao citation: ama: He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 2020;13(9):1238-1240. doi:10.1016/j.molp.2020.07.006 apa: He, P., Zhang, Y., & Xiao, G. (2020). Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.07.006 chicago: He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.07.006. ieee: P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution of allotetraploid cotton species,” Molecular Plant, vol. 13, no. 9. Elsevier, pp. 1238–1240, 2020. ista: He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 13(9), 1238–1240. mla: He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” Molecular Plant, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40, doi:10.1016/j.molp.2020.07.006. short: P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240. date_created: 2020-08-16T22:00:57Z date_published: 2020-09-07T00:00:00Z date_updated: 2023-08-22T08:40:35Z day: '07' department: - _id: JiFr doi: 10.1016/j.molp.2020.07.006 external_id: isi: - '000566895400007' pmid: - '32688032' intvolume: ' 13' isi: 1 issue: '9' language: - iso: eng month: '09' oa_version: None page: 1238-1240 pmid: 1 publication: Molecular Plant publication_identifier: eissn: - '17529867' issn: - '16742052' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Origin of a subgenome and genome evolution of allotetraploid cotton species type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2020' ... --- _id: '8101' abstract: - lang: eng text: By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature. acknowledgement: "We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin, and Bilge Baytekin for helpful discussions.\r\nThis project has received funding from the European Unions Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411." article_number: '082602' article_processing_charge: Yes article_type: original author: - first_name: Galien M full_name: Grosjean, Galien M id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425 last_name: Grosjean orcid: 0000-0001-5154-417X - first_name: Sebastian full_name: Wald, Sebastian id: 133F200A-B015-11E9-AD41-0EDAE5697425 last_name: Wald - first_name: Juan Carlos A full_name: Sobarzo Ponce, Juan Carlos A id: 4B807D68-AE37-11E9-AC72-31CAE5697425 last_name: Sobarzo Ponce - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 2020;4(8). doi:10.1103/PhysRevMaterials.4.082602 apa: Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., & Waitukaitis, S. R. (2020). Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.4.082602 chicago: Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials. American Physical Society, 2020. https://doi.org/10.1103/PhysRevMaterials.4.082602. ieee: G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively consistent scale-spanning model for same-material tribocharging,” Physical Review Materials, vol. 4, no. 8. American Physical Society, 2020. ista: Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 4(8), 082602. mla: Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials, vol. 4, no. 8, 082602, American Physical Society, 2020, doi:10.1103/PhysRevMaterials.4.082602. short: G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review Materials 4 (2020). date_created: 2020-07-07T11:33:54Z date_published: 2020-08-17T00:00:00Z date_updated: 2023-08-22T08:41:32Z day: '17' ddc: - '530' department: - _id: ScWa doi: 10.1103/PhysRevMaterials.4.082602 ec_funded: 1 external_id: arxiv: - '2006.07120' isi: - '000561897000001' file: - access_level: open_access checksum: 288fef1eeb6540c6344bb8f7c8159dc9 content_type: application/pdf creator: ggrosjea date_created: 2020-08-17T15:54:20Z date_updated: 2020-08-17T15:54:20Z file_id: '8277' file_name: Grosjean2020.pdf file_size: 853753 relation: main_file success: 1 file_date_updated: 2020-08-17T15:54:20Z has_accepted_license: '1' intvolume: ' 4' isi: 1 issue: '8' keyword: - electric charge - tribocharging - soft matter - granular materials - polymers language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Physical Review Materials publication_identifier: issn: - 2475-9953 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '12697' relation: popular_science status: public scopus_import: '1' status: public title: Quantitatively consistent scale-spanning model for same-material tribocharging tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 4 year: '2020' ... --- _id: '8325' abstract: - lang: eng text: "Let \U0001D439:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. " acknowledgement: We thank Andrea Sportiello for sharing his insights on perturbative regimes of the Abelian sandpile model which was the starting point of our work. We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who participated on the initial state of this project, when we had nothing except the computer simulation and pictures. We thank Mikhail Raskin for providing us the code on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak, Danila Cherkashin asked us a lot of questions and listened to us; not all of their questions found answers here, but we are going to treat them in subsequent papers. article_processing_charge: No article_type: original author: - first_name: Nikita full_name: Kalinin, Nikita last_name: Kalinin - first_name: Mikhail full_name: Shkolnikov, Mikhail id: 35084A62-F248-11E8-B48F-1D18A9856A87 last_name: Shkolnikov orcid: 0000-0002-4310-178X citation: ama: Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 2020;378(9):1649-1675. doi:10.1007/s00220-020-03828-8 apa: Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-020-03828-8 chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-020-03828-8. ieee: N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020. ista: Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675. mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics, vol. 378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:10.1007/s00220-020-03828-8. short: N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 1649–1675. date_created: 2020-08-30T22:01:13Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-08-22T09:00:03Z day: '01' department: - _id: TaHa doi: 10.1007/s00220-020-03828-8 ec_funded: 1 external_id: arxiv: - '1711.04285' isi: - '000560620600001' intvolume: ' 378' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.04285 month: '09' oa: 1 oa_version: Preprint page: 1649-1675 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Communications in Mathematical Physics publication_identifier: eissn: - '14320916' issn: - '00103616' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Sandpile solitons via smoothing of superharmonic functions type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 378 year: '2020' ... --- _id: '8318' abstract: - lang: eng text: Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I. acknowledgement: This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster. article_number: '4135' article_processing_charge: No article_type: original author: - first_name: Javier full_name: Gutierrez-Fernandez, Javier id: 3D9511BA-F248-11E8-B48F-1D18A9856A87 last_name: Gutierrez-Fernandez - first_name: Karol full_name: Kaszuba, Karol id: 3FDF9472-F248-11E8-B48F-1D18A9856A87 last_name: Kaszuba - first_name: Gurdeep S. full_name: Minhas, Gurdeep S. last_name: Minhas - first_name: Rozbeh full_name: Baradaran, Rozbeh last_name: Baradaran - first_name: Margherita full_name: Tambalo, Margherita id: 4187dfe4-ec23-11ea-ae46-f08ab378313a last_name: Tambalo - first_name: David T. full_name: Gallagher, David T. last_name: Gallagher - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17957-0 apa: Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17957-0 chicago: Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0. ieee: J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer Nature, 2020. ista: Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135. mla: Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:10.1038/s41467-020-17957-0. short: J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020). date_created: 2020-08-30T22:01:10Z date_published: 2020-08-18T00:00:00Z date_updated: 2023-08-22T09:03:00Z day: '18' ddc: - '570' department: - _id: LeSa doi: 10.1038/s41467-020-17957-0 external_id: isi: - '000607072900001' pmid: - '32811817' file: - access_level: open_access checksum: 52b96f41d7d0db9728064c08da00d030 content_type: application/pdf creator: cziletti date_created: 2020-08-31T13:40:00Z date_updated: 2020-08-31T13:40:00Z file_id: '8326' file_name: 2020_NatComm_Gutierrez-Fernandez.pdf file_size: 7527373 relation: main_file success: 1 file_date_updated: 2020-08-31T13:40:00Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/ scopus_import: '1' status: public title: Key role of quinone in the mechanism of respiratory complex I tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8320' abstract: - lang: eng text: The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications. acknowledgement: We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay. article_processing_charge: No article_type: original author: - first_name: S. A. full_name: Mukba, S. A. last_name: Mukba - first_name: Petr full_name: Vlasov, Petr id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87 last_name: Vlasov - first_name: P. M. full_name: Kolosov, P. M. last_name: Kolosov - first_name: E. Y. full_name: Shuvalova, E. Y. last_name: Shuvalova - first_name: T. V. full_name: Egorova, T. V. last_name: Egorova - first_name: E. Z. full_name: Alkalaeva, E. Z. last_name: Alkalaeva citation: ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 2020;54(4):475-484. doi:10.1134/S0026893320040111' apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111' chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111.' ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.' ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.' mla: 'Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:10.1134/S0026893320040111.' short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484. date_created: 2020-08-30T22:01:11Z date_published: 2020-08-19T00:00:00Z date_updated: 2023-08-22T09:01:03Z day: '19' department: - _id: FyKo doi: 10.1134/S0026893320040111 external_id: isi: - '000562110300001' intvolume: ' 54' isi: 1 issue: '4' language: - iso: eng month: '08' oa_version: None page: 475-484 publication: Molecular Biology publication_identifier: eissn: - '16083245' issn: - '00268933' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8321' relation: original status: public scopus_import: '1' status: public title: 'Expanding the genetic code: Unnatural base pairs in biological systems' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 54 year: '2020' ... --- _id: '8321' abstract: - lang: eng text: The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications. article_processing_charge: No article_type: original author: - first_name: S. A. full_name: Mukba, S. A. last_name: Mukba - first_name: Petr full_name: Vlasov, Petr id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87 last_name: Vlasov - first_name: P. M. full_name: Kolosov, P. M. last_name: Kolosov - first_name: E. Y. full_name: Shuvalova, E. Y. last_name: Shuvalova - first_name: T. V. full_name: Egorova, T. V. last_name: Egorova - first_name: E. Z. full_name: Alkalaeva, E. Z. last_name: Alkalaeva citation: ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126' apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420040126' chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420040126.' ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.' ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541.' mla: 'Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126.' short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541. date_created: 2020-08-30T22:01:11Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T09:01:02Z day: '01' department: - _id: FyKo doi: 10.31857/S0026898420040126 external_id: pmid: - '32799218' intvolume: ' 54' issue: '4' language: - iso: rus month: '07' oa_version: None page: 531-541 pmid: 1 publication: Molekuliarnaia biologiia publication_identifier: issn: - '00268984' publication_status: published publisher: Russian Academy of Sciences quality_controlled: '1' related_material: record: - id: '8320' relation: translation status: public scopus_import: '1' status: public title: 'Expanding the genetic code: Unnatural base pairs in biological systems' type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 54 year: '2020' ... --- _id: '8323' article_processing_charge: No article_type: letter_note author: - first_name: János full_name: Pach, János id: E62E3130-B088-11EA-B919-BF823C25FEA4 last_name: Pach citation: ama: Pach J. A farewell to Ricky Pollack. Discrete and Computational Geometry. 2020;64:571-574. doi:10.1007/s00454-020-00237-5 apa: Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00237-5 chicago: Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5. ieee: J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 571–574, 2020. ista: Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574. mla: Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 571–74, doi:10.1007/s00454-020-00237-5. short: J. Pach, Discrete and Computational Geometry 64 (2020) 571–574. date_created: 2020-08-30T22:01:12Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-08-22T09:05:04Z day: '01' department: - _id: HeEd doi: 10.1007/s00454-020-00237-5 external_id: isi: - '000561483500001' intvolume: ' 64' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00454-020-00237-5 month: '10' oa: 1 oa_version: None page: 571-574 publication: Discrete and Computational Geometry publication_identifier: eissn: - '14320444' issn: - '01795376' publication_status: published publisher: Springer Nature scopus_import: '1' status: public title: A farewell to Ricky Pollack type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 64 year: '2020' ... --- _id: '8336' abstract: - lang: eng text: Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: This paper is dedicated to deceased P. Galuszka for his support and contribution to the project. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material. The work was supported from ERDF project “Plants as a tool for sustainable global development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S (K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria (H.S.). article_number: '4285' article_processing_charge: No article_type: original author: - first_name: Karolina full_name: Kubiasova, Karolina id: 946011F4-3E71-11EA-860B-C7A73DDC885E last_name: Kubiasova orcid: 0000-0001-5630-9419 - first_name: Juan C full_name: Montesinos López, Juan C id: 310A8E3E-F248-11E8-B48F-1D18A9856A87 last_name: Montesinos López orcid: 0000-0001-9179-6099 - first_name: Olga full_name: Šamajová, Olga last_name: Šamajová - first_name: Jaroslav full_name: Nisler, Jaroslav last_name: Nisler - first_name: Václav full_name: Mik, Václav last_name: Mik - first_name: Hana full_name: Semeradova, Hana id: 42FE702E-F248-11E8-B48F-1D18A9856A87 last_name: Semeradova - first_name: Lucie full_name: Plíhalová, Lucie last_name: Plíhalová - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Peter full_name: Marhavý, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavý orcid: 0000-0001-5227-5741 - first_name: Nicola full_name: Cavallari, Nicola id: 457160E6-F248-11E8-B48F-1D18A9856A87 last_name: Cavallari - first_name: David full_name: Zalabák, David last_name: Zalabák - first_name: Karel full_name: Berka, Karel last_name: Berka - first_name: Karel full_name: Doležal, Karel last_name: Doležal - first_name: Petr full_name: Galuszka, Petr last_name: Galuszka - first_name: Jozef full_name: Šamaj, Jozef last_name: Šamaj - first_name: Miroslav full_name: Strnad, Miroslav last_name: Strnad - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ondřej full_name: Plíhal, Ondřej last_name: Plíhal - first_name: Lukáš full_name: Spíchal, Lukáš last_name: Spíchal citation: ama: Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 2020;11. doi:10.1038/s41467-020-17949-0 apa: Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V., Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17949-0 chicago: Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler, Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17949-0. ieee: K. Kubiasova et al., “Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 11, 4285. mla: Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications, vol. 11, 4285, Springer Nature, 2020, doi:10.1038/s41467-020-17949-0. short: K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová, L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal, P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications 11 (2020). date_created: 2020-09-06T22:01:12Z date_published: 2020-08-27T00:00:00Z date_updated: 2023-08-22T09:09:06Z day: '27' ddc: - '580' department: - _id: EvBe doi: 10.1038/s41467-020-17949-0 ec_funded: 1 external_id: isi: - '000567931000002' pmid: - '32855390' file: - access_level: open_access checksum: 7494b7665b3d2bf2d8edb13e4f12b92d content_type: application/pdf creator: dernst date_created: 2020-09-10T08:05:19Z date_updated: 2020-09-10T08:05:19Z file_id: '8357' file_name: 2020_NatureComm_Kubiasova.pdf file_size: 3455704 relation: main_file success: 1 file_date_updated: 2020-09-10T08:05:19Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 261821BC-B435-11E9-9278-68D0E5697425 grant_number: '24746' name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis. - _id: 253E54C8-B435-11E9-9278-68D0E5697425 grant_number: ALTF710-2016 name: Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8337' abstract: - lang: eng text: Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses. acknowledged_ssus: - _id: Bio acknowledgement: 'We thank Bruno Müller and Aaron Rashotte for critical discussions and provision of plant lines used in this work, Roger Granbom and Tamara Hernández Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic) for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre and the IST Austria Bio-Imaging facility are acknowledged for support. The work was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.), Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.), the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811) (E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic via the European Regional Development Fund-Project “Plants as a tool for sustainable global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M., L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P., K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J. was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading to these results received funding from European Union’s Horizon 2020 programme (ERC grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.' article_number: '4284' article_processing_charge: No article_type: original author: - first_name: Ioanna full_name: Antoniadi, Ioanna last_name: Antoniadi - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Zuzana full_name: Gelová, Zuzana id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425 last_name: Gelová orcid: 0000-0003-4783-1752 - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: Ondřej full_name: Plíhal, Ondřej last_name: Plíhal - first_name: Radim full_name: Simerský, Radim last_name: Simerský - first_name: Václav full_name: Mik, Václav last_name: Mik - first_name: Thomas full_name: Vain, Thomas last_name: Vain - first_name: Eduardo full_name: Mateo-Bonmatí, Eduardo last_name: Mateo-Bonmatí - first_name: Michal full_name: Karady, Michal last_name: Karady - first_name: Markéta full_name: Pernisová, Markéta last_name: Pernisová - first_name: Lenka full_name: Plačková, Lenka last_name: Plačková - first_name: Korawit full_name: Opassathian, Korawit last_name: Opassathian - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Karel full_name: Doležal, Karel last_name: Doležal - first_name: Karin full_name: Ljung, Karin last_name: Ljung - first_name: Colin full_name: Turnbull, Colin last_name: Turnbull citation: ama: Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 2020;11. doi:10.1038/s41467-020-17700-9 apa: Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský, R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17700-9 chicago: Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17700-9. ieee: I. Antoniadi et al., “Cell-surface receptors enable perception of extracellular cytokinins,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 11, 4284. mla: Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications, vol. 11, 4284, Springer Nature, 2020, doi:10.1038/s41467-020-17700-9. short: I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský, V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian, J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications 11 (2020). date_created: 2020-09-06T22:01:13Z date_published: 2020-08-27T00:00:00Z date_updated: 2023-08-22T09:10:32Z day: '27' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41467-020-17700-9 ec_funded: 1 external_id: isi: - '000567931000001' file: - access_level: open_access checksum: 5b96f39b598de7510cfefefb819b9a6d content_type: application/pdf creator: dernst date_created: 2020-12-10T12:23:56Z date_updated: 2020-12-10T12:23:56Z file_id: '8936' file_name: 2020_NatureComm_Antoniadi.pdf file_size: 3526415 relation: main_file success: 1 file_date_updated: 2020-12-10T12:23:56Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Cell-surface receptors enable perception of extracellular cytokinins tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8067' abstract: - lang: eng text: "With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the\r\nmid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7." alternative_title: - IST Austria Technical Report article_processing_charge: No author: - first_name: Alberto full_name: Varzi, Alberto last_name: Varzi - first_name: Katharina full_name: Thanner, Katharina last_name: Thanner - first_name: Roberto full_name: Scipioni, Roberto last_name: Scipioni - first_name: Daniele full_name: Di Lecce, Daniele last_name: Di Lecce - first_name: Jusef full_name: Hassoun, Jusef last_name: Hassoun - first_name: Susanne full_name: Dörfler, Susanne last_name: Dörfler - first_name: Holger full_name: Altheus, Holger last_name: Altheus - first_name: Stefan full_name: Kaskel, Stefan last_name: Kaskel - first_name: Christian full_name: Prehal, Christian last_name: Prehal - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Varzi A, Thanner K, Scipioni R, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria doi:10.15479/AT:ISTA:8067 apa: Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (n.d.). Current status and future perspectives of Lithium metal batteries. IST Austria. https://doi.org/10.15479/AT:ISTA:8067 chicago: Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, n.d. https://doi.org/10.15479/AT:ISTA:8067. ieee: A. Varzi et al., Current status and future perspectives of Lithium metal batteries. IST Austria. ista: Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. Current status and future perspectives of Lithium metal batteries, IST Austria, 63p. mla: Varzi, Alberto, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, doi:10.15479/AT:ISTA:8067. short: A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Current Status and Future Perspectives of Lithium Metal Batteries, IST Austria, n.d. date_created: 2020-06-30T07:37:39Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T09:20:36Z day: '01' ddc: - '540' department: - _id: StFr doi: 10.15479/AT:ISTA:8067 file: - access_level: open_access checksum: d183ca1465a1cbb4f8db27875cd156f7 content_type: application/pdf creator: dernst date_created: 2020-07-02T07:36:04Z date_updated: 2020-07-14T12:48:08Z file_id: '8076' file_name: 20200612_JPS_review_Li_metal_submitted.pdf file_size: 2612498 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' keyword: - Battery - Lithium metal - Lithium-sulphur - Lithium-air - All-solid-state language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '63' publication_identifier: issn: - 2664-1690 publication_status: submitted publisher: IST Austria related_material: record: - id: '8361' relation: later_version status: public status: public title: Current status and future perspectives of Lithium metal batteries type: technical_report user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '8361' abstract: - lang: eng text: With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, Li metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries. A particular attention is paid to recent developments of these battery technologies and their current state with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7. acknowledgement: A.V. and K.T. acknowledge, respectively, the financial support of the Helmholtz Association and BMW AG. J.H. acknowledges the collabo-ration project “Accordo di Collaborazione Quadro 2015” between Uni-versity of Ferrara (Department of Chemical and Pharmaceutical Sciences) and Sapienza University of Rome (Department of Chemistry). S.D., H.A. and S.K. thank the Fraunhofer Gesellschaft, Technische Uni-versit ̈at Dresden and would like to acknowledge European Union’s Horizon 2020 research and innovation programme under grant agree-ment No 814471. S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 636069) and IST Austria. article_number: '228803' article_processing_charge: No article_type: original author: - first_name: Alberto full_name: Varzi, Alberto last_name: Varzi orcid: 0000-0001-5069-0589 - first_name: Katharina full_name: Thanner, Katharina last_name: Thanner orcid: 0000-0001-5394-2323 - first_name: Roberto full_name: Scipioni, Roberto last_name: Scipioni orcid: 0000-0003-1926-421X - first_name: Daniele full_name: Di Lecce, Daniele last_name: Di Lecce - first_name: Jusef full_name: Hassoun, Jusef last_name: Hassoun - first_name: Susanne full_name: Dörfler, Susanne last_name: Dörfler - first_name: Holger full_name: Altheus, Holger last_name: Altheus - first_name: Stefan full_name: Kaskel, Stefan last_name: Kaskel - first_name: Christian full_name: Prehal, Christian last_name: Prehal orcid: 0000-0003-0654-0940 - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Varzi A, Thanner K, Scipioni R, et al. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 2020;480(12). doi:10.1016/j.jpowsour.2020.228803 apa: Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (2020). Current status and future perspectives of lithium metal batteries. Journal of Power Sources. Elsevier. https://doi.org/10.1016/j.jpowsour.2020.228803 chicago: Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. “Current Status and Future Perspectives of Lithium Metal Batteries.” Journal of Power Sources. Elsevier, 2020. https://doi.org/10.1016/j.jpowsour.2020.228803. ieee: A. Varzi et al., “Current status and future perspectives of lithium metal batteries,” Journal of Power Sources, vol. 480, no. 12. Elsevier, 2020. ista: Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. 2020. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 480(12), 228803. mla: Varzi, Alberto, et al. “Current Status and Future Perspectives of Lithium Metal Batteries.” Journal of Power Sources, vol. 480, no. 12, 228803, Elsevier, 2020, doi:10.1016/j.jpowsour.2020.228803. short: A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Journal of Power Sources 480 (2020). date_created: 2020-09-10T10:48:40Z date_published: 2020-12-31T00:00:00Z date_updated: 2023-08-22T09:20:37Z day: '31' department: - _id: StFr doi: 10.1016/j.jpowsour.2020.228803 external_id: isi: - '000593857300001' intvolume: ' 480' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.jpowsour.2020.228803 month: '12' oa: 1 oa_version: Published Version publication: Journal of Power Sources publication_identifier: issn: - 0378-7753 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '8067' relation: earlier_version status: public status: public title: Current status and future perspectives of lithium metal batteries type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 480 year: '2020' ... --- _id: '14028' abstract: - lang: eng text: 'The present review addresses the technical advances and the theoretical developments to realize and rationalize attosecond-science experiments that reveal a new dynamical time scale (10−15-10−18 s), with a particular emphasis on molecular systems and the implications of attosecond processes for chemical dynamics. After a brief outline of the theoretical framework for treating non-perturbative phenomena in Section 2, we introduce the physical mechanisms underlying high-harmonic generation and attosecond technology. The relevant technological developments and experimental schemes are covered in Section 3. Throughout the remainder of the chapter, we report on selected applications in molecular attosecond physics, thereby addressing specific phenomena mediated by purely electronic dynamics: charge localization in molecular hydrogen, charge migration in biorelevant molecules, high-harmonic spectroscopy, and delays in molecular photoionization.' article_processing_charge: No author: - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: Baykusheva DR, Wörner HJ. Attosecond molecular spectroscopy and dynamics. doi:10.48550/arXiv.2002.02111 apa: Baykusheva, D. R., & Wörner, H. J. (n.d.). Attosecond molecular spectroscopy and dynamics. https://doi.org/10.48550/arXiv.2002.02111 chicago: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular Spectroscopy and Dynamics,” n.d. https://doi.org/10.48550/arXiv.2002.02111. ieee: D. R. Baykusheva and H. J. Wörner, “Attosecond molecular spectroscopy and dynamics.” . ista: Baykusheva DR, Wörner HJ. Attosecond molecular spectroscopy and dynamics. 10.48550/arXiv.2002.02111. mla: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. Attosecond Molecular Spectroscopy and Dynamics. doi:10.48550/arXiv.2002.02111. short: D.R. Baykusheva, H.J. Wörner, (n.d.). date_created: 2023-08-10T06:47:45Z date_published: 2020-02-01T00:00:00Z date_updated: 2023-08-22T09:17:34Z day: '01' doi: 10.48550/arXiv.2002.02111 extern: '1' external_id: arxiv: - '2002.02111' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2002.02111 month: '02' oa: 1 oa_version: Preprint page: '2002.02111' publication_status: submitted status: public title: Attosecond molecular spectroscopy and dynamics type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8529' abstract: - lang: eng text: Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform. acknowledged_ssus: - _id: NanoFab acknowledgement: We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET). article_number: '4460' article_processing_charge: No article_type: original author: - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 - first_name: Matthias full_name: Wulf, Matthias id: 45598606-F248-11E8-B48F-1D18A9856A87 last_name: Wulf orcid: 0000-0001-6613-1378 - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: William J full_name: Hease, William J id: 29705398-F248-11E8-B48F-1D18A9856A87 last_name: Hease orcid: 0000-0001-9868-2166 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 2020;11. doi:10.1038/s41467-020-18269-z apa: Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18269-z chicago: Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18269-z. ieee: G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460. mla: Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Nature Communications, vol. 11, 4460, Springer Nature, 2020, doi:10.1038/s41467-020-18269-z. short: G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020). date_created: 2020-09-18T10:56:20Z date_published: 2020-09-08T00:00:00Z date_updated: 2023-08-22T09:27:12Z day: '08' ddc: - '530' department: - _id: JoFi doi: 10.1038/s41467-020-18269-z ec_funded: 1 external_id: isi: - '000577280200001' file: - access_level: open_access checksum: 88f92544889eb18bb38e25629a422a86 content_type: application/pdf creator: dernst date_created: 2020-09-18T13:02:37Z date_updated: 2020-09-18T13:02:37Z file_id: '8530' file_name: 2020_NatureComm_Arnold.pdf file_size: 1002818 relation: main_file success: 1 file_date_updated: 2020-09-18T13:02:37Z has_accepted_license: '1' intvolume: ' 11' isi: 1 keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 257EB838-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '732894' name: Hybrid Optomechanical Technologies - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies - _id: 2671EB66-B435-11E9-9278-68D0E5697425 name: Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-020-18912-9 - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/ record: - id: '13056' relation: research_data status: public status: public title: Converting microwave and telecom photons with a silicon photonic nanomechanical interface tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8535' abstract: - lang: eng text: We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation. acknowledged_ssus: - _id: ScienComp acknowledgement: We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385. article_number: '65' article_processing_charge: No article_type: original author: - first_name: Tomas full_name: Skrivan, Tomas id: 486A5A46-F248-11E8-B48F-1D18A9856A87 last_name: Skrivan - first_name: Andreas full_name: Soderstrom, Andreas last_name: Soderstrom - first_name: John full_name: Johansson, John last_name: Johansson - first_name: Christoph full_name: Sprenger, Christoph last_name: Sprenger - first_name: Ken full_name: Museth, Ken last_name: Museth - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: 'Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392466' apa: 'Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., & Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392466' chicago: 'Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger, Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392466.' ieee: 'T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan, “Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.' ista: 'Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 39(4), 65.' mla: 'Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” ACM Transactions on Graphics, vol. 39, no. 4, 65, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392466.' short: T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020). date_created: 2020-09-20T22:01:37Z date_published: 2020-07-08T00:00:00Z date_updated: 2023-08-22T09:28:27Z day: '08' ddc: - '000' department: - _id: ChWo doi: 10.1145/3386569.3392466 ec_funded: 1 external_id: isi: - '000583700300038' file: - access_level: open_access checksum: c3a680893f01cc4a9e961ff0a4cfa12f content_type: application/pdf creator: dernst date_created: 2020-09-21T07:51:44Z date_updated: 2020-09-21T07:51:44Z file_id: '8541' file_name: 2020_ACM_Skrivan.pdf file_size: 20223953 relation: main_file success: 1 file_date_updated: 2020-09-21T07:51:44Z has_accepted_license: '1' intvolume: ' 39' isi: 1 issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: ACM Transactions on Graphics publication_identifier: eissn: - '15577368' issn: - '07300301' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 39 year: '2020' ... --- _id: '8539' abstract: - lang: eng text: Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions. - lang: fre text: "Les bases stables cohomologiques et K-théoriques proviennent de l’étude de la cohomologie quantique et de la K-théorie quantique. La formule de restriction pour les bases stables cohomologiques a joué un rôle important dans le calcul de la connexion quantique du fibré cotangent de variétés de drapeaux partielles. Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette description algébrique et la méthode des polynômes de racine, nous donnons une formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la formule de restriction pour les variétés de drapeaux partielles. Nous construisons également une relation entre la base stable et la base de Casselman dans les représentations de la série principale du groupe dual de Langlands p-adique. Comme une application, nous donnons une formule close pour la matrice de transition entre la base de Casselman et les fonctions caractéristiques. " article_processing_charge: No article_type: original author: - first_name: C. full_name: Su, C. last_name: Su - first_name: Gufang full_name: Zhao, Gufang id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87 last_name: Zhao - first_name: C. full_name: Zhong, C. last_name: Zhong citation: ama: Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 2020;53(3):663-671. doi:10.24033/asens.2431 apa: Su, C., Zhao, G., & Zhong, C. (2020). On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. Société Mathématique de France. https://doi.org/10.24033/asens.2431 chicago: Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure. Société Mathématique de France, 2020. https://doi.org/10.24033/asens.2431. ieee: C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer resolution,” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3. Société Mathématique de France, pp. 663–671, 2020. ista: Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671. mla: Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3, Société Mathématique de France, 2020, pp. 663–71, doi:10.24033/asens.2431. short: C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 663–671. date_created: 2020-09-20T22:01:38Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-08-22T09:27:57Z day: '01' department: - _id: TaHa doi: 10.24033/asens.2431 external_id: arxiv: - '1708.08013' isi: - '000592182600004' intvolume: ' 53' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.08013 month: '06' oa: 1 oa_version: Preprint page: 663-671 publication: Annales Scientifiques de l'Ecole Normale Superieure publication_identifier: issn: - 0012-9593 publication_status: published publisher: Société Mathématique de France quality_controlled: '1' scopus_import: '1' status: public title: On the K-theory stable bases of the springer resolution type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 53 year: '2020' ... --- _id: '14000' abstract: - lang: eng text: This chapter presents an overview of the state of the art in attosecond time-resolved spectroscopy. The theoretical foundations of strong-field light–matter interaction and attosecond pulse generation are described. The enabling laser technologies are reviewed from chirped-pulse amplification and carrier-envelope-phase stabilization to the generation and characterization of attosecond pulses. The applications of attosecond pulses and pulse trains in electron- or ion-imaging experiments are presented, followed by attosecond electron spectroscopy in larger molecules. After this, high-harmonic spectroscopy and its applications to probing charge migration on attosecond time scales is reviewed. The rapidly evolving field of molecular photoionization delays is discussed. Finally, the applications of attosecond transient absorption to probing molecular dynamics are presented. article_processing_charge: No author: - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: 'Baykusheva DR, Wörner HJ. Attosecond Molecular Dynamics and Spectroscopy. In: Marquardt R, Quack M, eds. Molecular Spectroscopy and Quantum Dynamics. 1st ed. Elsevier; 2020:113-161. doi:10.1016/b978-0-12-817234-6.00009-x' apa: Baykusheva, D. R., & Wörner, H. J. (2020). Attosecond Molecular Dynamics and Spectroscopy. In R. Marquardt & M. Quack (Eds.), Molecular Spectroscopy and Quantum Dynamics (1st ed., pp. 113–161). Elsevier. https://doi.org/10.1016/b978-0-12-817234-6.00009-x chicago: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular Dynamics and Spectroscopy.” In Molecular Spectroscopy and Quantum Dynamics, edited by Roberto Marquardt and Martin Quack, 1st ed., 113–61. Elsevier, 2020. https://doi.org/10.1016/b978-0-12-817234-6.00009-x. ieee: D. R. Baykusheva and H. J. Wörner, “Attosecond Molecular Dynamics and Spectroscopy,” in Molecular Spectroscopy and Quantum Dynamics, 1st ed., R. Marquardt and M. Quack, Eds. Elsevier, 2020, pp. 113–161. ista: 'Baykusheva DR, Wörner HJ. 2020.Attosecond Molecular Dynamics and Spectroscopy. In: Molecular Spectroscopy and Quantum Dynamics. , 113–161.' mla: Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Attosecond Molecular Dynamics and Spectroscopy.” Molecular Spectroscopy and Quantum Dynamics, edited by Roberto Marquardt and Martin Quack, 1st ed., Elsevier, 2020, pp. 113–61, doi:10.1016/b978-0-12-817234-6.00009-x. short: D.R. Baykusheva, H.J. Wörner, in:, R. Marquardt, M. Quack (Eds.), Molecular Spectroscopy and Quantum Dynamics, 1st ed., Elsevier, 2020, pp. 113–161. date_created: 2023-08-09T13:10:23Z date_published: 2020-09-25T00:00:00Z date_updated: 2023-08-22T09:25:07Z day: '25' doi: 10.1016/b978-0-12-817234-6.00009-x edition: '1' editor: - first_name: Roberto full_name: Marquardt, Roberto last_name: Marquardt - first_name: Martin full_name: Quack, Martin last_name: Quack extern: '1' language: - iso: eng month: '09' oa_version: None page: 113-161 publication: Molecular Spectroscopy and Quantum Dynamics publication_identifier: eisbn: - '0128172355' isbn: - '9780128172353' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Attosecond Molecular Dynamics and Spectroscopy type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '13056' abstract: - lang: eng text: This datasets comprises all data shown in plots of the submitted article "Converting microwave and telecom photons with a silicon photonic nanomechanical interface". Additional raw data are available from the corresponding author on reasonable request. article_processing_charge: No author: - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 - first_name: Matthias full_name: Wulf, Matthias id: 45598606-F248-11E8-B48F-1D18A9856A87 last_name: Wulf orcid: 0000-0001-6613-1378 - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: William J full_name: Hease, William J id: 29705398-F248-11E8-B48F-1D18A9856A87 last_name: Hease orcid: 0000-0001-9868-2166 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561 apa: Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561 chicago: Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561. ieee: G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020. ista: Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561. mla: Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561. short: G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020). date_created: 2023-05-23T13:37:41Z date_published: 2020-07-27T00:00:00Z date_updated: 2023-08-22T09:27:11Z day: '27' ddc: - '530' department: - _id: JoFi doi: 10.5281/ZENODO.3961561 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.3961562 month: '07' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '8529' relation: used_in_publication status: public status: public title: Converting microwave and telecom photons with a silicon photonic nanomechanical interface tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8579' abstract: - lang: eng text: Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells. article_number: '242' article_processing_charge: No article_type: original author: - first_name: Andreea full_name: Andrei, Andreea last_name: Andrei - first_name: Yavuz full_name: Öztürk, Yavuz last_name: Öztürk - first_name: Bahia full_name: Khalfaoui-Hassani, Bahia last_name: Khalfaoui-Hassani - first_name: Juna full_name: Rauch, Juna last_name: Rauch - first_name: Dorian full_name: Marckmann, Dorian last_name: Marckmann - first_name: Petru Iulian full_name: Trasnea, Petru Iulian id: D560034C-10C4-11EA-ABF4-A4B43DDC885E last_name: Trasnea - first_name: Fevzi full_name: Daldal, Fevzi last_name: Daldal - first_name: Hans-Georg full_name: Koch, Hans-Georg last_name: Koch citation: ama: 'Andrei A, Öztürk Y, Khalfaoui-Hassani B, et al. Cu homeostasis in bacteria: The ins and outs. Membranes. 2020;10(9). doi:10.3390/membranes10090242' apa: 'Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea, P. I., … Koch, H.-G. (2020). Cu homeostasis in bacteria: The ins and outs. Membranes. MDPI. https://doi.org/10.3390/membranes10090242' chicago: 'Andrei, Andreea, Yavuz Öztürk, Bahia Khalfaoui-Hassani, Juna Rauch, Dorian Marckmann, Petru Iulian Trasnea, Fevzi Daldal, and Hans-Georg Koch. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes. MDPI, 2020. https://doi.org/10.3390/membranes10090242.' ieee: 'A. Andrei et al., “Cu homeostasis in bacteria: The ins and outs,” Membranes, vol. 10, no. 9. MDPI, 2020.' ista: 'Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch H-G. 2020. Cu homeostasis in bacteria: The ins and outs. Membranes. 10(9), 242.' mla: 'Andrei, Andreea, et al. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes, vol. 10, no. 9, 242, MDPI, 2020, doi:10.3390/membranes10090242.' short: A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I. Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020). date_created: 2020-09-28T08:59:26Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-08-22T09:34:06Z day: '01' ddc: - '570' department: - _id: LeSa doi: 10.3390/membranes10090242 external_id: isi: - '000581446000001' file: - access_level: open_access checksum: ceb43d7554e712dea6f36f9287271737 content_type: application/pdf creator: dernst date_created: 2020-09-28T11:36:50Z date_updated: 2020-09-28T11:36:50Z file_id: '8583' file_name: 2020_Membranes_Andrei.pdf file_size: 4612258 relation: main_file success: 1 file_date_updated: 2020-09-28T11:36:50Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Membranes publication_identifier: eissn: - '20770375' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: 'Cu homeostasis in bacteria: The ins and outs' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '8581' abstract: - lang: eng text: The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the ‘proton translocation cluster’ attached to the c-ring and a more distant ‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine. acknowledged_ssus: - _id: EM-Fac - _id: ScienComp acknowledgement: We thank J. Novacek from CEITEC (Brno, Czech Republic) for assistance with collecting the FEI Krios dataset and iNEXT for providing access to CEITEC. We thank the IST Austria EM facility for access and assistance with collecting the FEI Glacios dataset. Data processing was performed at the IST high-performance computing cluster. This work has been supported by iNEXT EM HEDC (proposal 4506), funded by the Horizon 2020 Programme of the European Commission. article_processing_charge: No article_type: original author: - first_name: Gergely full_name: Pinke, Gergely id: 4D5303E6-F248-11E8-B48F-1D18A9856A87 last_name: Pinke - first_name: Long full_name: Zhou, Long id: 3E751364-F248-11E8-B48F-1D18A9856A87 last_name: Zhou orcid: 0000-0002-1864-8951 - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Pinke G, Zhou L, Sazanov LA. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 2020;27(11):1077-1085. doi:10.1038/s41594-020-0503-8 apa: Pinke, G., Zhou, L., & Sazanov, L. A. (2020). Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-020-0503-8 chicago: Pinke, Gergely, Long Zhou, and Leonid A Sazanov. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular Biology. Springer Nature, 2020. https://doi.org/10.1038/s41594-020-0503-8. ieee: G. Pinke, L. Zhou, and L. A. Sazanov, “Cryo-EM structure of the entire mammalian F-type ATP synthase,” Nature Structural and Molecular Biology, vol. 27, no. 11. Springer Nature, pp. 1077–1085, 2020. ista: Pinke G, Zhou L, Sazanov LA. 2020. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 27(11), 1077–1085. mla: Pinke, Gergely, et al. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” Nature Structural and Molecular Biology, vol. 27, no. 11, Springer Nature, 2020, pp. 1077–85, doi:10.1038/s41594-020-0503-8. short: G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology 27 (2020) 1077–1085. date_created: 2020-09-28T08:59:27Z date_published: 2020-11-01T00:00:00Z date_updated: 2023-08-22T09:33:09Z day: '01' department: - _id: LeSa doi: 10.1038/s41594-020-0503-8 external_id: isi: - '000569299400004' pmid: - '32929284' intvolume: ' 27' isi: 1 issue: '11' language: - iso: eng month: '11' oa_version: None page: 1077-1085 pmid: 1 publication: Nature Structural and Molecular Biology publication_identifier: eissn: - '15459985' issn: - '15459993' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/structure-of-atpase-solved/ scopus_import: '1' status: public title: Cryo-EM structure of the entire mammalian F-type ATP synthase type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 27 year: '2020' ...