[{"oa":1,"type":"journal_article","article_number":"149","date_published":"2024-01-22T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","article_processing_charge":"No","year":"2024","intvolume":" 961","language":[{"iso":"eng"}],"publisher":"American Astronomical Society","abstract":[{"text":"Close encounters between stellar-mass black holes (BHs) and stars occur frequently in dense star clusters and in the disks of active galactic nuclei. Recent studies have shown that in highly eccentric close encounters, the star can be tidally disrupted by the BH in a microtidal disruption event (microTDE), resulting in rapid mass accretion and possibly bright electromagnetic signatures. Here we consider a scenario in which the star might approach the stellar-mass BH in a gradual, nearly circular inspiral, under the influence of dynamical friction in a circum-binary gas disk or three-body interactions in a star cluster. We perform hydrodynamics simulations of this scenario using the smoothed particle hydrodynamics code PHANTOM. We find that under certain circumstances (for initial eccentricity e0 ≳ 0.4 and penetration factor β = 1, or e0 < 0.4 and β ≲ 0.67), the mass of the star is slowly stripped away by the BH. We call this gradual tidal disruption a \"tidal-peeling event.\" Additionally, we discover that some low-eccentricity microTDEs (e0 < 0.4 and β = 1) are a new form of fast luminous transients similar to parabolic microTDEs. Depending on the initial distance and eccentricity of the encounter, these low-eccentricity microTDEs might exhibit significant accretion rates and orbital evolution distinct from those of a typical (eccentric) microTDE.","lang":"eng"}],"date_created":"2024-09-05T12:36:41Z","publication":"The Astrophysical Journal","status":"public","month":"01","issue":"2","day":"22","publication_identifier":{"issn":["0004-637X","1538-4357"]},"article_type":"original","title":"“Tidal Peeling Events”: Low-eccentricity tidal disruption of a star by a stellar-mass black hole","date_updated":"2024-09-19T12:21:53Z","author":[{"first_name":"Chengcheng","last_name":"Xin","full_name":"Xin, Chengcheng"},{"id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán","first_name":"Zoltán","last_name":"Haiman"},{"full_name":"Perna, Rosalba","first_name":"Rosalba","last_name":"Perna"},{"first_name":"Yihan","last_name":"Wang","full_name":"Wang, Yihan"},{"full_name":"Ryu, Taeho","first_name":"Taeho","last_name":"Ryu"}],"doi":"10.3847/1538-4357/ad11d3","citation":{"short":"C. Xin, Z. Haiman, R. Perna, Y. Wang, T. Ryu, The Astrophysical Journal 961 (2024).","chicago":"Xin, Chengcheng, Zoltán Haiman, Rosalba Perna, Yihan Wang, and Taeho Ryu. “‘Tidal Peeling Events’: Low-Eccentricity Tidal Disruption of a Star by a Stellar-Mass Black Hole.” The Astrophysical Journal. American Astronomical Society, 2024. https://doi.org/10.3847/1538-4357/ad11d3.","ista":"Xin C, Haiman Z, Perna R, Wang Y, Ryu T. 2024. “Tidal Peeling Events”: Low-eccentricity tidal disruption of a star by a stellar-mass black hole. The Astrophysical Journal. 961(2), 149.","ama":"Xin C, Haiman Z, Perna R, Wang Y, Ryu T. “Tidal Peeling Events”: Low-eccentricity tidal disruption of a star by a stellar-mass black hole. The Astrophysical Journal. 2024;961(2). doi:10.3847/1538-4357/ad11d3","apa":"Xin, C., Haiman, Z., Perna, R., Wang, Y., & Ryu, T. (2024). “Tidal Peeling Events”: Low-eccentricity tidal disruption of a star by a stellar-mass black hole. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ad11d3","mla":"Xin, Chengcheng, et al. “‘Tidal Peeling Events’: Low-Eccentricity Tidal Disruption of a Star by a Stellar-Mass Black Hole.” The Astrophysical Journal, vol. 961, no. 2, 149, American Astronomical Society, 2024, doi:10.3847/1538-4357/ad11d3.","ieee":"C. Xin, Z. Haiman, R. Perna, Y. Wang, and T. Ryu, “‘Tidal Peeling Events’: Low-eccentricity tidal disruption of a star by a stellar-mass black hole,” The Astrophysical Journal, vol. 961, no. 2. American Astronomical Society, 2024."},"volume":961,"scopus_import":"1","oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.3847/1538-4357/ad11d3","open_access":"1"}],"_id":"17590","extern":"1"},{"status":"public","ddc":["570"],"month":"09","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","abstract":[{"text":"Understanding the relationship between a given phenotype and its underlying genotype or genotypes is one of the most pressing challenges of biology, as it lies at the heart of not only basic understanding of evolutionary theory, but also of practical applications in medicine and bioengineering. Understanding this relationship is complicated by the ubiquitous phenomenon of epistasis, wherein mutation effects are dependent on their genetic context. Fitness landscapes — representations of phenotype as a function of genotype — are being increasingly used as a tool to study the effects and interactions of thousands of mutations, but are experimentally limited to exploring a small fraction of a protein’s theoretical sequence space. Furthermore, not all regions of said sequence space are necessarily equally informative. Thus, gene selection for landscape surveys should be carefully considered in order to maximize the usable output of necessarily limited data.\r\n\r\nIn this work, we analyzed the fitness landscapes of orthologous green fluorescent proteins from four different species, by systematically measuring the phenotype, fluorescence, of tens of thousands of mutant genotypes from each protein. These landscapes were highly heterogeneous, with some genes being mutationally robust and displaying epistasis only rarely, and others being highly epistatic and mutationally fragile. We used this data to train machine learning models to predict fluorescence from genotype. Although the training data contained almost exclusively genotypes with less than 3% sequence divergence from the original wild-type sequences, we were able to create novel, functional genotypes with up to 20% sequence divergence. Counterintuitively however, genes with high mutational robustness and rare epistasis were more difficult to introduce large numbers of mutations into, not less. This represents the first study of large-scale fitness landscapes of a protein family, and provides insights into how to approach future landscape surveys and their applications in novel protein design.","lang":"eng"}],"date_created":"2024-09-06T12:57:44Z","alternative_title":["ISTA Thesis"],"date_published":"2024-09-06T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"relation":"main_file","date_created":"2024-09-27T10:32:33Z","checksum":"d3303724e8d3c91321d71bbad4062048","file_name":"louisa_thesis_draft__240904b.pdf","creator":"lgonzale","file_size":11219837,"content_type":"application/pdf","access_level":"open_access","file_id":"18151","date_updated":"2024-09-27T10:32:33Z"},{"file_id":"18152","date_updated":"2024-09-27T10:34:34Z","relation":"source_file","date_created":"2024-09-27T10:34:34Z","creator":"lgonzale","checksum":"22e63f7f9014dffde2af7a47e7d1d014","file_name":"louisa_thesis_draft__240904b.docx","file_size":43338677,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"}],"publication_status":"published","year":"2024","article_processing_charge":"No","oa":1,"type":"dissertation","ec_funded":1,"page":"89","oa_version":"Published Version","_id":"17850","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"chicago":"Gonzalez Somermeyer, Louisa. “Fitness Landscapes of Orthologous Green Fluorescent Proteins.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17850.","short":"L. Gonzalez Somermeyer, Fitness Landscapes of Orthologous Green Fluorescent Proteins, Institute of Science and Technology Austria, 2024.","ieee":"L. Gonzalez Somermeyer, “Fitness landscapes of orthologous green fluorescent proteins,” Institute of Science and Technology Austria, 2024.","mla":"Gonzalez Somermeyer, Louisa. Fitness Landscapes of Orthologous Green Fluorescent Proteins. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17850.","apa":"Gonzalez Somermeyer, L. (2024). Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17850","ama":"Gonzalez Somermeyer L. Fitness landscapes of orthologous green fluorescent proteins. 2024. doi:10.15479/at:ista:17850","ista":"Gonzalez Somermeyer L. 2024. Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria."},"doi":"10.15479/at:ista:17850","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"department":[{"_id":"GradSch"},{"_id":"FyKo"}],"title":"Fitness landscapes of orthologous green fluorescent proteins","date_updated":"2026-04-07T13:25:01Z","author":[{"last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"06","publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2024-09-27T10:34:34Z","related_material":{"link":[{"url":"https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks","relation":"software"}],"record":[{"relation":"part_of_dissertation","id":"11448","status":"public"}]}},{"month":"02","status":"public","publication":"Nature Communications","pmid":1,"abstract":[{"lang":"eng","text":"Metal-metal contacts, though not yet widely realized, may provide exciting opportunities to serve as tunable and functional interfaces in single-molecule devices. One of the simplest components which might facilitate such binding interactions is the ferrocene group. Notably, direct bonds between the ferrocene iron center and metals such as Pd or Co have been demonstrated in molecular complexes comprising coordinating ligands attached to the cyclopentadienyl rings. Here, we demonstrate that ferrocene-based single-molecule devices with Fe-Au interfacial contact geometries form at room temperature in the absence of supporting coordinating ligands. Applying a photoredox reaction, we propose that ferrocene only functions effectively as a contact group when oxidized, binding to gold through a formal Fe3+ center. This observation is further supported by a series of control measurements and density functional theory calculations. Our findings extend the scope of junction contact chemistries beyond those involving main group elements, lay the foundation for light switchable ferrocene-based single-molecule devices, and highlight new potential mechanistic function(s) of unsubstituted ferrocenium groups in synthetic processes."}],"date_created":"2024-09-06T12:38:44Z","publisher":"Springer Nature","OA_type":"gold","language":[{"iso":"eng"}],"intvolume":" 15","year":"2024","article_processing_charge":"Yes","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-02-16T00:00:00Z","article_number":"1439","type":"journal_article","oa":1,"extern":"1","_id":"17852","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-024-45707-z"}],"oa_version":"Published Version","quality_controlled":"1","scopus_import":"1","volume":15,"citation":{"apa":"Lee, W., Li, L., Camarasa-Gómez, M., Hernangómez-Pérez, D., Roy, X., Evers, F., … Venkataraman, L. (2024). Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-45707-z","ama":"Lee W, Li L, Camarasa-Gómez M, et al. Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions. Nature Communications. 2024;15. doi:10.1038/s41467-024-45707-z","ista":"Lee W, Li L, Camarasa-Gómez M, Hernangómez-Pérez D, Roy X, Evers F, Inkpen MS, Venkataraman L. 2024. Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions. Nature Communications. 15, 1439.","mla":"Lee, Woojung, et al. “Photooxidation Driven Formation of Fe-Au Linked Ferrocene-Based Single-Molecule Junctions.” Nature Communications, vol. 15, 1439, Springer Nature, 2024, doi:10.1038/s41467-024-45707-z.","ieee":"W. Lee et al., “Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions,” Nature Communications, vol. 15. Springer Nature, 2024.","short":"W. Lee, L. Li, M. Camarasa-Gómez, D. Hernangómez-Pérez, X. Roy, F. Evers, M.S. Inkpen, L. Venkataraman, Nature Communications 15 (2024).","chicago":"Lee, Woojung, Liang Li, María Camarasa-Gómez, Daniel Hernangómez-Pérez, Xavier Roy, Ferdinand Evers, Michael S. Inkpen, and Latha Venkataraman. “Photooxidation Driven Formation of Fe-Au Linked Ferrocene-Based Single-Molecule Junctions.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-45707-z."},"doi":"10.1038/s41467-024-45707-z","author":[{"full_name":"Lee, Woojung","first_name":"Woojung","last_name":"Lee"},{"full_name":"Li, Liang","first_name":"Liang","last_name":"Li"},{"full_name":"Camarasa-Gómez, María","first_name":"María","last_name":"Camarasa-Gómez"},{"first_name":"Daniel","last_name":"Hernangómez-Pérez","full_name":"Hernangómez-Pérez, Daniel"},{"full_name":"Roy, Xavier","first_name":"Xavier","last_name":"Roy"},{"full_name":"Evers, Ferdinand","last_name":"Evers","first_name":"Ferdinand"},{"full_name":"Inkpen, Michael S.","last_name":"Inkpen","first_name":"Michael S."},{"last_name":"Venkataraman","orcid":"0000-0002-6957-6089","first_name":"Latha","full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"}],"date_updated":"2024-11-18T10:47:10Z","title":"Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions","article_type":"original","publication_identifier":{"issn":["2041-1723"]},"day":"16","DOAJ_listed":"1","OA_place":"publisher","external_id":{"pmid":["38365892"]}},{"extern":"1","_id":"17853","quality_controlled":"1","oa_version":"None","doi":"10.1021/jacs.4c05699","citation":{"ista":"Li L, Louie S, Orchanian NM, Nuckolls C, Venkataraman L. 2024. Long-range gating in single-molecule one-dimensional topological insulators. Journal of the American Chemical Society. 146(24), 16920–16925.","apa":"Li, L., Louie, S., Orchanian, N. M., Nuckolls, C., & Venkataraman, L. (2024). Long-range gating in single-molecule one-dimensional topological insulators. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.4c05699","ama":"Li L, Louie S, Orchanian NM, Nuckolls C, Venkataraman L. Long-range gating in single-molecule one-dimensional topological insulators. Journal of the American Chemical Society. 2024;146(24):16920-16925. doi:10.1021/jacs.4c05699","mla":"Li, Liang, et al. “Long-Range Gating in Single-Molecule One-Dimensional Topological Insulators.” Journal of the American Chemical Society, vol. 146, no. 24, American Chemical Society, 2024, pp. 16920–25, doi:10.1021/jacs.4c05699.","ieee":"L. Li, S. Louie, N. M. Orchanian, C. Nuckolls, and L. Venkataraman, “Long-range gating in single-molecule one-dimensional topological insulators,” Journal of the American Chemical Society, vol. 146, no. 24. American Chemical Society, pp. 16920–16925, 2024.","short":"L. Li, S. Louie, N.M. Orchanian, C. Nuckolls, L. Venkataraman, Journal of the American Chemical Society 146 (2024) 16920–16925.","chicago":"Li, Liang, Shayan Louie, Nicholas M. Orchanian, Colin Nuckolls, and Latha Venkataraman. “Long-Range Gating in Single-Molecule One-Dimensional Topological Insulators.” Journal of the American Chemical Society. American Chemical Society, 2024. https://doi.org/10.1021/jacs.4c05699."},"scopus_import":"1","volume":146,"date_updated":"2024-11-18T10:51:21Z","title":"Long-range gating in single-molecule one-dimensional topological insulators","author":[{"full_name":"Li, Liang","last_name":"Li","first_name":"Liang"},{"full_name":"Louie, Shayan","first_name":"Shayan","last_name":"Louie"},{"last_name":"Orchanian","first_name":"Nicholas M.","full_name":"Orchanian, Nicholas M."},{"full_name":"Nuckolls, Colin","first_name":"Colin","last_name":"Nuckolls"},{"first_name":"Latha","last_name":"Venkataraman","orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"}],"external_id":{"pmid":["38832840"]},"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"article_type":"original","day":"24","status":"public","month":"06","publication":"Journal of the American Chemical Society","issue":"24","language":[{"iso":"eng"}],"OA_type":"closed access","intvolume":" 146","pmid":1,"date_created":"2024-09-06T12:40:17Z","abstract":[{"lang":"eng","text":"Single-molecule one-dimensional topological insulator (1D TI) is a class of molecular wires that exhibit increasing conductance with wire length. This unique trend is due to the coupling between the two low-lying topological edge states of 1D TIs described by the Su–Schrieffer–Heeger model. In principle, this quantum phenomenon within 1D TIs can be utilized to achieve long-range gating in molecular conductors. Here, we study electron transport through a single-edge state of doubly oxidized oligophenylene bis(triarylamine) to understand the effect of the edge state coupling on conductance. We find that conductance is elevated by approximately 1 order of magnitude compared to a control molecule with the same conductance pathway. Density function theory calculations further support that the increase in conductance is due to the interaction between the edge states of 1D TIs. This work demonstrates a new gating paradigm in molecular electronics, while also providing a deeper understanding of how edge states interact and affect electron transport within 1D TIs."}],"publisher":"American Chemical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-06-24T00:00:00Z","year":"2024","article_processing_charge":"No","publication_status":"published","type":"journal_article","page":"16920-16925"},{"date_created":"2024-09-06T12:43:20Z","abstract":[{"text":"As social media platforms continue to grow in popularity, there is an increasing need for science outreach teams to bring STEM content to the virtual landscape. Here, we highlight the use of short-form videos on our TikTok channel─@IvyLeagueScience─as a new way to approach science outreach. Through a combination of content production and data analytics, we were able to build an online platform with >150k followers, 3.6 million likes, and 18 million views. By bringing science to social media, we engage with students across the world, allowing them to experience science-based content. In this case study, we hope to encourage other scientific outreach teams to employ social media as a means of increasing visibility of scientists and STEM careers.","lang":"eng"}],"publisher":"American Chemical Society","language":[{"iso":"eng"}],"OA_type":"closed access","intvolume":" 101","issue":"3","month":"02","status":"public","publication":"Journal of Chemical Education","page":"1319-1324","type":"journal_article","publication_status":"published","year":"2024","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-02-14T00:00:00Z","scopus_import":"1","volume":101,"citation":{"ista":"Prindle CR, Orchanian NM, Venkataraman L, Nuckolls C. 2024. Short-form videos as an emerging social media tool for STEM edutainment. Journal of Chemical Education. 101(3), 1319–1324.","ama":"Prindle CR, Orchanian NM, Venkataraman L, Nuckolls C. Short-form videos as an emerging social media tool for STEM edutainment. Journal of Chemical Education. 2024;101(3):1319-1324. doi:10.1021/acs.jchemed.3c01185","apa":"Prindle, C. R., Orchanian, N. M., Venkataraman, L., & Nuckolls, C. (2024). Short-form videos as an emerging social media tool for STEM edutainment. Journal of Chemical Education. American Chemical Society. https://doi.org/10.1021/acs.jchemed.3c01185","ieee":"C. R. Prindle, N. M. Orchanian, L. Venkataraman, and C. Nuckolls, “Short-form videos as an emerging social media tool for STEM edutainment,” Journal of Chemical Education, vol. 101, no. 3. American Chemical Society, pp. 1319–1324, 2024.","mla":"Prindle, Claudia R., et al. “Short-Form Videos as an Emerging Social Media Tool for STEM Edutainment.” Journal of Chemical Education, vol. 101, no. 3, American Chemical Society, 2024, pp. 1319–24, doi:10.1021/acs.jchemed.3c01185.","short":"C.R. Prindle, N.M. Orchanian, L. Venkataraman, C. Nuckolls, Journal of Chemical Education 101 (2024) 1319–1324.","chicago":"Prindle, Claudia R., Nicholas M. Orchanian, Latha Venkataraman, and Colin Nuckolls. “Short-Form Videos as an Emerging Social Media Tool for STEM Edutainment.” Journal of Chemical Education. American Chemical Society, 2024. https://doi.org/10.1021/acs.jchemed.3c01185."},"doi":"10.1021/acs.jchemed.3c01185","_id":"17854","extern":"1","oa_version":"None","quality_controlled":"1","day":"14","article_type":"original","publication_identifier":{"eissn":["1938-1328"],"issn":["0021-9584"]},"author":[{"full_name":"Prindle, Claudia R.","first_name":"Claudia R.","last_name":"Prindle"},{"last_name":"Orchanian","first_name":"Nicholas M.","full_name":"Orchanian, Nicholas M."},{"last_name":"Venkataraman","orcid":"0000-0002-6957-6089","first_name":"Latha","full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"},{"full_name":"Nuckolls, Colin","last_name":"Nuckolls","first_name":"Colin"}],"title":"Short-form videos as an emerging social media tool for STEM edutainment","date_updated":"2024-11-18T10:55:30Z"},{"day":"05","article_type":"letter_note","publication_identifier":{"issn":["1530-6984","1530-6992"]},"external_id":{"pmid":["38315038"]},"author":[{"full_name":"Paoletta, Angela L.","first_name":"Angela L.","last_name":"Paoletta"},{"first_name":"Latha","last_name":"Venkataraman","orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"}],"title":"Determining transmission characteristics from shot-noise-driven electroluminescence in single-molecule junctions","date_updated":"2024-11-18T10:58:19Z","scopus_import":"1","volume":24,"citation":{"ieee":"A. L. Paoletta and L. Venkataraman, “Determining transmission characteristics from shot-noise-driven electroluminescence in single-molecule junctions,” Nano Letters, vol. 24, no. 6. American Chemical Society, pp. 1931–1935, 2024.","mla":"Paoletta, Angela L., and Latha Venkataraman. “Determining Transmission Characteristics from Shot-Noise-Driven Electroluminescence in Single-Molecule Junctions.” Nano Letters, vol. 24, no. 6, American Chemical Society, 2024, pp. 1931–35, doi:10.1021/acs.nanolett.3c04207.","ista":"Paoletta AL, Venkataraman L. 2024. Determining transmission characteristics from shot-noise-driven electroluminescence in single-molecule junctions. Nano Letters. 24(6), 1931–1935.","apa":"Paoletta, A. L., & Venkataraman, L. (2024). Determining transmission characteristics from shot-noise-driven electroluminescence in single-molecule junctions. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.3c04207","ama":"Paoletta AL, Venkataraman L. Determining transmission characteristics from shot-noise-driven electroluminescence in single-molecule junctions. Nano Letters. 2024;24(6):1931-1935. doi:10.1021/acs.nanolett.3c04207","chicago":"Paoletta, Angela L., and Latha Venkataraman. “Determining Transmission Characteristics from Shot-Noise-Driven Electroluminescence in Single-Molecule Junctions.” Nano Letters. American Chemical Society, 2024. https://doi.org/10.1021/acs.nanolett.3c04207.","short":"A.L. Paoletta, L. Venkataraman, Nano Letters 24 (2024) 1931–1935."},"doi":"10.1021/acs.nanolett.3c04207","_id":"17855","extern":"1","oa_version":"None","quality_controlled":"1","page":"1931-1935","type":"journal_article","publication_status":"published","year":"2024","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-02-05T00:00:00Z","pmid":1,"abstract":[{"text":"Biased metal–molecule–metal junctions emit light through electroluminescence, a phenomenon at the intersection of molecular electronics and nanoplasmonics. This can occur when the junction plasmon mode is excited by inelastic electron current fluctuations. Here, we simultaneously measure the conductance and electroluminescence intensity from single-molecule junctions with time resolution in a solution environment at room temperature. We use current versus bias data to determine the molecular junction transport parameters and then relate these to the expected current shot noise. We find that the electroluminescence signal accurately matches the theoretical prediction of shot-noise-driven emission in a large fraction of the molecular junctions studied. This introduces a novel experimental method for qualitatively estimating finite-frequency shot noise in single-molecule junctions under ambient conditions. We further demonstrate that electroluminescence can be used to obtain the level alignment of the frontier orbital dominating transport in the molecular junction.","lang":"eng"}],"date_created":"2024-09-06T12:44:24Z","publisher":"American Chemical Society","language":[{"iso":"eng"}],"intvolume":" 24","issue":"6","month":"02","status":"public","publication":"Nano Letters"},{"author":[{"last_name":"Prindle","first_name":"Claudia R.","full_name":"Prindle, Claudia R."},{"last_name":"Shi","first_name":"Wanzhuo","full_name":"Shi, Wanzhuo"},{"full_name":"Li, Liang","last_name":"Li","first_name":"Liang"},{"first_name":"Jesper","last_name":"Dahl Jensen","full_name":"Dahl Jensen, Jesper"},{"full_name":"Laursen, Bo W.","first_name":"Bo W.","last_name":"Laursen"},{"full_name":"Steigerwald, Michael L.","first_name":"Michael L.","last_name":"Steigerwald"},{"first_name":"Colin","last_name":"Nuckolls","full_name":"Nuckolls, Colin"},{"orcid":"0000-0002-6957-6089","last_name":"Venkataraman","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","full_name":"Venkataraman, Latha"}],"date_updated":"2024-11-18T11:02:24Z","title":"Effective gating in single-molecule junctions through fano resonances","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"article_type":"letter_note","day":"31","external_id":{"pmid":["38293735"]},"extern":"1","_id":"17856","quality_controlled":"1","oa_version":"None","scopus_import":"1","volume":146,"citation":{"chicago":"Prindle, Claudia R., Wanzhuo Shi, Liang Li, Jesper Dahl Jensen, Bo W. Laursen, Michael L. Steigerwald, Colin Nuckolls, and Latha Venkataraman. “Effective Gating in Single-Molecule Junctions through Fano Resonances.” Journal of the American Chemical Society. American Chemical Society, 2024. https://doi.org/10.1021/jacs.3c14226.","short":"C.R. Prindle, W. Shi, L. Li, J. Dahl Jensen, B.W. Laursen, M.L. Steigerwald, C. Nuckolls, L. Venkataraman, Journal of the American Chemical Society 146 (2024) 3646–3650.","mla":"Prindle, Claudia R., et al. “Effective Gating in Single-Molecule Junctions through Fano Resonances.” Journal of the American Chemical Society, vol. 146, no. 6, American Chemical Society, 2024, pp. 3646–50, doi:10.1021/jacs.3c14226.","ieee":"C. R. Prindle et al., “Effective gating in single-molecule junctions through fano resonances,” Journal of the American Chemical Society, vol. 146, no. 6. American Chemical Society, pp. 3646–3650, 2024.","apa":"Prindle, C. R., Shi, W., Li, L., Dahl Jensen, J., Laursen, B. W., Steigerwald, M. L., … Venkataraman, L. (2024). Effective gating in single-molecule junctions through fano resonances. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c14226","ama":"Prindle CR, Shi W, Li L, et al. Effective gating in single-molecule junctions through fano resonances. Journal of the American Chemical Society. 2024;146(6):3646-3650. doi:10.1021/jacs.3c14226","ista":"Prindle CR, Shi W, Li L, Dahl Jensen J, Laursen BW, Steigerwald ML, Nuckolls C, Venkataraman L. 2024. Effective gating in single-molecule junctions through fano resonances. Journal of the American Chemical Society. 146(6), 3646–3650."},"doi":"10.1021/jacs.3c14226","article_processing_charge":"No","year":"2024","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-01-31T00:00:00Z","page":"3646-3650","type":"journal_article","issue":"6","month":"01","status":"public","publication":"Journal of the American Chemical Society","pmid":1,"date_created":"2024-09-06T12:45:11Z","abstract":[{"text":"The successful incorporation of molecules as active circuit elements relies on the ability to tune their electronic properties through chemical design. A synthetic strategy that has been used to manipulate and gate circuit conductance involves attaching a pendant substituent along the molecular conduction pathway. However, such a chemical gate has not yet been shown to significantly modify conductance. Here, we report a novel series of triarylmethylium and triangulenium carbocations gated by different substituents coupled to the delocalized conducting orbitals on the molecular backbone through a Fano resonance. By changing the pendant substituents to modulate the position of the Fano resonance and its coupling to the conducting orbitals, we can regulate the junction conductance by a remarkable factor of 450. This work thus provides a new design principle to enable effective chemical gating of single-molecule devices toward effective molecular transistors.","lang":"eng"}],"publisher":"American Chemical Society","language":[{"iso":"eng"}],"intvolume":" 146"},{"article_type":"letter_note","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"day":"04","external_id":{"pmid":["38175934"]},"author":[{"full_name":"Dalmieda, Johnson","last_name":"Dalmieda","first_name":"Johnson"},{"first_name":"Wanzhuo","last_name":"Shi","full_name":"Shi, Wanzhuo"},{"last_name":"Li","first_name":"Liang","full_name":"Li, Liang"},{"full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","last_name":"Venkataraman","orcid":"0000-0002-6957-6089","first_name":"Latha"}],"date_updated":"2024-11-19T12:50:27Z","title":"Solvent-mediated modulation of the Au–S bond in dithiol molecular junctions","scopus_import":"1","volume":24,"doi":"10.1021/acs.nanolett.3c04058","citation":{"ama":"Dalmieda J, Shi W, Li L, Venkataraman L. Solvent-mediated modulation of the Au–S bond in dithiol molecular junctions. Nano Letters. 2024;24(2):703-707. doi:10.1021/acs.nanolett.3c04058","apa":"Dalmieda, J., Shi, W., Li, L., & Venkataraman, L. (2024). Solvent-mediated modulation of the Au–S bond in dithiol molecular junctions. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.3c04058","ista":"Dalmieda J, Shi W, Li L, Venkataraman L. 2024. Solvent-mediated modulation of the Au–S bond in dithiol molecular junctions. Nano Letters. 24(2), 703–707.","mla":"Dalmieda, Johnson, et al. “Solvent-Mediated Modulation of the Au–S Bond in Dithiol Molecular Junctions.” Nano Letters, vol. 24, no. 2, American Chemical Society, 2024, pp. 703–07, doi:10.1021/acs.nanolett.3c04058.","ieee":"J. Dalmieda, W. Shi, L. Li, and L. Venkataraman, “Solvent-mediated modulation of the Au–S bond in dithiol molecular junctions,” Nano Letters, vol. 24, no. 2. American Chemical Society, pp. 703–707, 2024.","short":"J. Dalmieda, W. Shi, L. Li, L. Venkataraman, Nano Letters 24 (2024) 703–707.","chicago":"Dalmieda, Johnson, Wanzhuo Shi, Liang Li, and Latha Venkataraman. “Solvent-Mediated Modulation of the Au–S Bond in Dithiol Molecular Junctions.” Nano Letters. American Chemical Society, 2024. https://doi.org/10.1021/acs.nanolett.3c04058."},"extern":"1","_id":"17857","quality_controlled":"1","oa_version":"None","page":"703-707","type":"journal_article","article_processing_charge":"No","year":"2024","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-01-04T00:00:00Z","abstract":[{"text":"Gold–dithiol molecular junctions have been studied both experimentally and theoretically. However, the nature of the gold–thiolate bond as it relates to the solvent has seldom been investigated. It is known that solvents can impact the electronic structure of single-molecule junctions, but the correlation between the solvent and dithiol-linked single-molecule junction conductance is not well understood. We study molecular junctions formed with thiol-terminated phenylenes from both 1-chloronaphthalene and 1-bromonaphthalene solutions. We find that the most probable conductance and the distribution of conductances are both affected by the solvent. First-principles calculations show that junction conductance depends on the binding configurations (adatom, atop, and bridge) of the thiolate on the Au surface, as has been shown previously. More importantly, we find that brominated solvents can restrict the binding of thiols to specific Au sites. This mechanism offers new insight into the effects of the solvent environment on covalent bonding in molecular junctions.","lang":"eng"}],"date_created":"2024-09-06T12:46:39Z","pmid":1,"publisher":"American Chemical Society","language":[{"iso":"eng"}],"OA_type":"closed access","intvolume":" 24","issue":"2","status":"public","month":"01","publication":"Nano Letters"},{"author":[{"full_name":"Shi, Wanzhuo","last_name":"Shi","first_name":"Wanzhuo"},{"last_name":"Greenwald","first_name":"Julia E.","full_name":"Greenwald, Julia E."},{"full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha","last_name":"Venkataraman","orcid":"0000-0002-6957-6089"}],"date_updated":"2024-11-20T15:24:37Z","title":"Impact of solvent electrostatic environment on molecular junctions probed via electrochemical impedance spectroscopy","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"article_type":"original","day":"18","external_id":{"pmid":["39023006"]},"extern":"1","_id":"17859","oa_version":"None","quality_controlled":"1","scopus_import":"1","volume":24,"doi":"10.1021/acs.nanolett.4c02103","citation":{"apa":"Shi, W., Greenwald, J. E., & Venkataraman, L. (2024). Impact of solvent electrostatic environment on molecular junctions probed via electrochemical impedance spectroscopy. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.4c02103","ista":"Shi W, Greenwald JE, Venkataraman L. 2024. Impact of solvent electrostatic environment on molecular junctions probed via electrochemical impedance spectroscopy. Nano Letters. 24(30), 9283–9288.","ama":"Shi W, Greenwald JE, Venkataraman L. Impact of solvent electrostatic environment on molecular junctions probed via electrochemical impedance spectroscopy. Nano Letters. 2024;24(30):9283-9288. doi:10.1021/acs.nanolett.4c02103","mla":"Shi, Wanzhuo, et al. “Impact of Solvent Electrostatic Environment on Molecular Junctions Probed via Electrochemical Impedance Spectroscopy.” Nano Letters, vol. 24, no. 30, American Chemical Society, 2024, pp. 9283–88, doi:10.1021/acs.nanolett.4c02103.","ieee":"W. Shi, J. E. Greenwald, and L. Venkataraman, “Impact of solvent electrostatic environment on molecular junctions probed via electrochemical impedance spectroscopy,” Nano Letters, vol. 24, no. 30. American Chemical Society, pp. 9283–9288, 2024.","short":"W. Shi, J.E. Greenwald, L. Venkataraman, Nano Letters 24 (2024) 9283–9288.","chicago":"Shi, Wanzhuo, Julia E. Greenwald, and Latha Venkataraman. “Impact of Solvent Electrostatic Environment on Molecular Junctions Probed via Electrochemical Impedance Spectroscopy.” Nano Letters. American Chemical Society, 2024. https://doi.org/10.1021/acs.nanolett.4c02103."},"article_processing_charge":"No","year":"2024","publication_status":"published","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","date_published":"2024-07-18T00:00:00Z","page":"9283-9288","type":"journal_article","issue":"30","status":"public","publication":"Nano Letters","month":"07","abstract":[{"lang":"eng","text":"The electrostatic environment around nanoscale molecular junctions modulates charge transport; solvents alter this environment. Methods to directly probe solvent effects require correlating measurements of the local electrostatic environment with charge transport across the metal–molecule–metal junction. Here, we measure the conductance and current–voltage characteristics of molecular wires using a scanning tunneling microscope–break junction (STM-BJ) setup in two commonly used solvents. Our results show that the solvent environment induces shifts in molecular conductance, which we quantify, but more importantly we find that the solvent also impacts the magnitude of current rectification in molecular junctions. By incorporating electrochemical impedance spectroscopy into the STM-BJ setup, we measure the capacitance of the dipole layer formed at the metal–solvent interface and show that rectification can be correlated with solvent capacitance. These results provide a method of quantifying the impact of the solvent environment and a path toward improved environmental control of molecular devices."}],"date_created":"2024-09-06T12:48:34Z","pmid":1,"publisher":"American Chemical Society","OA_type":"closed access","language":[{"iso":"eng"}],"intvolume":" 24"},{"date_updated":"2025-09-08T09:13:01Z","title":"The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation","author":[{"first_name":"Lisa","last_name":"Kofler","full_name":"Kofler, Lisa"},{"first_name":"Lorenz","last_name":"Grundmann","full_name":"Grundmann, Lorenz"},{"full_name":"Gerhalter, Magdalena","last_name":"Gerhalter","first_name":"Magdalena"},{"first_name":"Michael","last_name":"Prattes","full_name":"Prattes, Michael"},{"full_name":"Merl-Pham, Juliane","first_name":"Juliane","last_name":"Merl-Pham"},{"full_name":"Zisser, Gertrude","first_name":"Gertrude","last_name":"Zisser"},{"first_name":"Irina","last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Vareka","full_name":"Vareka, Martin"},{"first_name":"Rolf","last_name":"Breinbauer","full_name":"Breinbauer, Rolf"},{"last_name":"Hauck","first_name":"Stefanie M.","full_name":"Hauck, Stefanie M."},{"first_name":"David","last_name":"Haselbach","full_name":"Haselbach, David"},{"full_name":"Bergler, Helmut","last_name":"Bergler","first_name":"Helmut"}],"external_id":{"isi":["001457895200001"],"pmid":["39209816"]},"OA_place":"publisher","DOAJ_listed":"1","article_type":"original","acknowledgement":"We thank Michael A. McAlear, Micheline Fromont-Racin, Philipp Milkereit, Arlen W. Johnson, Sabine Rospert, Ed Hurt, C. Yam, Günter Daum, Wolfgang Zachariae, Katrin Karbstein, Juan P. G. Ballesta, Mercedes Dosil, Miguel Remacha und Jesus de la Cruz for sharing strains or providing antibodies. We thank the members of the Bergler lab and the Haselbach lab for their helpful discussion. We thank Ellen Zhong for helpful discussions about the quantitative cryoDRGN analysis. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility. This research was funded in whole, or in part, by the Austrian Science Foundation grants [https://doi.org/10.55776/P32977], [https://doi.org/10.55776/P29451] and [https://doi.org/10.55776/P32536] (to H.B.). Research at the IMP is generously supported by Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","file_date_updated":"2024-09-09T08:56:12Z","publication_identifier":{"eissn":["2041-1723"]},"day":"29","quality_controlled":"1","oa_version":"Published Version","_id":"17885","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"L. Kofler, L. Grundmann, M. Gerhalter, M. Prattes, J. Merl-Pham, G. Zisser, I. Grishkovskaya, V.-V. Hodirnau, M. Vareka, R. Breinbauer, S.M. Hauck, D. Haselbach, H. Bergler, Nature Communications 15 (2024).","chicago":"Kofler, Lisa, Lorenz Grundmann, Magdalena Gerhalter, Michael Prattes, Juliane Merl-Pham, Gertrude Zisser, Irina Grishkovskaya, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-51754-3.","ama":"Kofler L, Grundmann L, Gerhalter M, et al. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. 2024;15. doi:10.1038/s41467-024-51754-3","ista":"Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau V-V, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. 2024. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. 15, 7511.","apa":"Kofler, L., Grundmann, L., Gerhalter, M., Prattes, M., Merl-Pham, J., Zisser, G., … Bergler, H. (2024). The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-51754-3","ieee":"L. Kofler et al., “The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation,” Nature Communications, vol. 15. Springer Nature, 2024.","mla":"Kofler, Lisa, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” Nature Communications, vol. 15, 7511, Springer Nature, 2024, doi:10.1038/s41467-024-51754-3."},"doi":"10.1038/s41467-024-51754-3","volume":15,"department":[{"_id":"EM-Fac"}],"scopus_import":"1","article_number":"7511","date_published":"2024-08-29T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"creator":"dernst","checksum":"7c044538a47182c826d1b526c52958a2","file_name":"2024_NatureComm_Kofler.pdf","date_created":"2024-09-09T08:56:12Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":3735024,"file_id":"17946","success":1,"date_updated":"2024-09-09T08:56:12Z"}],"year":"2024","article_processing_charge":"Yes","publication_status":"published","oa":1,"type":"journal_article","isi":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"08","publication":"Nature Communications","ddc":["570"],"status":"public","intvolume":" 15","OA_type":"gold","language":[{"iso":"eng"}],"publisher":"Springer Nature","pmid":1,"date_created":"2024-09-08T22:01:10Z","abstract":[{"lang":"eng","text":"The formation of new ribosomes is tightly coordinated with cell growth and proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and RNAs follows an intricate scheme of maturation and rearrangement steps across three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate that usnic acid, a lichen secondary metabolite, inhibits the maturation of the large ribosomal subunit in yeast. We combine biochemical characterization of pre-ribosomal particles with a quantitative single-particle cryo-EM approach to monitor changes in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary nucleolar block rapidly rebounds on earlier stages of the pathway which highlights the regulatory linkages between different steps. In summary, we provide an in-depth characterization of the effect of usnic acid on ribosome biogenesis, which may have implications for its reported anti-cancer activities."}],"has_accepted_license":"1"},{"ddc":["570"],"corr_author":"1","month":"12","status":"public","publication":"Neural Networks","OA_type":"hybrid","language":[{"iso":"eng"}],"intvolume":" 180","has_accepted_license":"1","date_created":"2024-09-08T22:01:10Z","abstract":[{"lang":"eng","text":"Thin pancake-like neuronal networks cultured on top of a planar microelectrode array have been extensively tried out in neuroengineering, as a substrate for the mobile robot’s control unit, i.e., as a cyborg’s brain. Most of these attempts failed due to intricate self-organizing dynamics in the neuronal systems. In particular, the networks may exhibit an emergent spatial map of steady nucleation sites (“n-sites”) of spontaneous population spikes. Being unpredictable and independent of the surface electrode locations, the n-sites drastically change local ability of the network to generate spikes. Here, using a spiking neuronal network model with generative spatially-embedded connectome, we systematically show in simulations that the number, location, and relative activity of spontaneously formed n-sites (“the vitals”) crucially depend on the samplings of three distributions: (1) the network distribution of neuronal excitability, (2) the distribution of connections between neurons of the network, and (3) the distribution of maximal amplitudes of a single synaptic current pulse. Moreover, blocking the dynamics of a small fraction (about 4%) of non-pacemaker neurons having the highest excitability was enough to completely suppress the occurrence of population spikes and their n-sites. This key result is explained theoretically. Remarkably, the n-sites occur taking into account only short-term synaptic plasticity, i.e., without a Hebbian-type plasticity. As the spiking network model used in this study is strictly deterministic, all simulation results can be accurately reproduced. The model, which has already demonstrated a very high richness-to-complexity ratio, can also be directly extended into the three-dimensional case, e.g., for targeting peculiarities of spiking dynamics in cerebral (or brain) organoids. We recommend the model as an excellent illustrative tool for teaching network-level computational neuroscience, complementing a few benchmark models."}],"pmid":1,"publisher":"Elsevier","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-12-01T00:00:00Z","article_number":"106589","publication_status":"published","article_processing_charge":"Yes (via OA deal)","year":"2024","file":[{"file_id":"18825","success":1,"date_updated":"2025-01-13T08:26:08Z","checksum":"6a194323234e01d4ae725f674529cdb1","creator":"dernst","file_name":"2024_NeuralNetworks_Zendrikov.pdf","relation":"main_file","date_created":"2025-01-13T08:26:08Z","content_type":"application/pdf","access_level":"open_access","file_size":6162281}],"isi":1,"ec_funded":1,"type":"journal_article","oa":1,"_id":"17886","quality_controlled":"1","oa_version":"Published Version","project":[{"_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020","grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."}],"doi":"10.1016/j.neunet.2024.106589","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Zendrikov, Dmitrii, and Alexander Paraskevov. “The Vitals for Steady Nucleation Maps of Spontaneous Spiking Coherence in Autonomous Two-Dimensional Neuronal Networks.” Neural Networks. Elsevier, 2024. https://doi.org/10.1016/j.neunet.2024.106589.","short":"D. Zendrikov, A. Paraskevov, Neural Networks 180 (2024).","ieee":"D. Zendrikov and A. Paraskevov, “The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks,” Neural Networks, vol. 180. Elsevier, 2024.","mla":"Zendrikov, Dmitrii, and Alexander Paraskevov. “The Vitals for Steady Nucleation Maps of Spontaneous Spiking Coherence in Autonomous Two-Dimensional Neuronal Networks.” Neural Networks, vol. 180, 106589, Elsevier, 2024, doi:10.1016/j.neunet.2024.106589.","ama":"Zendrikov D, Paraskevov A. The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks. Neural Networks. 2024;180. doi:10.1016/j.neunet.2024.106589","ista":"Zendrikov D, Paraskevov A. 2024. The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks. Neural Networks. 180, 106589.","apa":"Zendrikov, D., & Paraskevov, A. (2024). The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks. Neural Networks. Elsevier. https://doi.org/10.1016/j.neunet.2024.106589"},"scopus_import":"1","department":[{"_id":"TiVo"}],"volume":180,"title":"The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks","date_updated":"2025-09-08T09:12:20Z","author":[{"full_name":"Zendrikov, Dmitrii","last_name":"Zendrikov","first_name":"Dmitrii"},{"id":"d05e3c56-9262-11ed-9231-be692464e5ac","full_name":"Paraskevov, Alexander","first_name":"Alexander","last_name":"Paraskevov"}],"OA_place":"publisher","external_id":{"isi":["001316474600001"],"pmid":["39217864"]},"day":"01","file_date_updated":"2025-01-13T08:26:08Z","article_type":"original","acknowledgement":"A.P. is grateful to Chaitanya Chintaluri, Douglas Feitosa Tomé, and Tim P. Vogels for useful discussions. This work was supported by a European Research Council Consolidator Grant (SYNAPSEEK, 819603, to Tim P. Vogels).","publication_identifier":{"eissn":["1879-2782"],"issn":["0893-6080"]}},{"day":"03","article_type":"original","file_date_updated":"2024-09-09T08:43:32Z","acknowledgement":"J. Fischer and M. Moser have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).\r\nOpen Access funding enabled and organized by Projekt DEAL.","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"arxiv":1,"external_id":{"arxiv":["2311.02997"],"pmid":["39239088"],"isi":["001305530600001"]},"author":[{"full_name":"Abels, Helmut","last_name":"Abels","first_name":"Helmut"},{"orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"},{"first_name":"Maximilian","last_name":"Moser","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c","full_name":"Moser, Maximilian"}],"title":"Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system","date_updated":"2025-09-08T09:11:41Z","scopus_import":"1","department":[{"_id":"JuFi"}],"volume":248,"project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","grant_number":"948819","name":"Bridging Scales in Random Materials"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ieee":"H. Abels, J. L. Fischer, and M. Moser, “Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system,” Archive for Rational Mechanics and Analysis, vol. 248, no. 5. Springer Nature, 2024.","mla":"Abels, Helmut, et al. “Approximation of Classical Two-Phase Flows of Viscous Incompressible Fluids by a Navier–Stokes/Allen–Cahn System.” Archive for Rational Mechanics and Analysis, vol. 248, no. 5, 77, Springer Nature, 2024, doi:10.1007/s00205-024-02020-9.","apa":"Abels, H., Fischer, J. L., & Moser, M. (2024). Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-024-02020-9","ama":"Abels H, Fischer JL, Moser M. Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system. Archive for Rational Mechanics and Analysis. 2024;248(5). doi:10.1007/s00205-024-02020-9","ista":"Abels H, Fischer JL, Moser M. 2024. Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system. Archive for Rational Mechanics and Analysis. 248(5), 77.","chicago":"Abels, Helmut, Julian L Fischer, and Maximilian Moser. “Approximation of Classical Two-Phase Flows of Viscous Incompressible Fluids by a Navier–Stokes/Allen–Cahn System.” Archive for Rational Mechanics and Analysis. Springer Nature, 2024. https://doi.org/10.1007/s00205-024-02020-9.","short":"H. Abels, J.L. Fischer, M. Moser, Archive for Rational Mechanics and Analysis 248 (2024)."},"doi":"10.1007/s00205-024-02020-9","_id":"17887","quality_controlled":"1","oa_version":"Published Version","type":"journal_article","ec_funded":1,"isi":1,"oa":1,"publication_status":"published","year":"2024","article_processing_charge":"Yes (via OA deal)","file":[{"date_updated":"2024-09-09T08:43:32Z","file_id":"17938","success":1,"access_level":"open_access","content_type":"application/pdf","file_size":811131,"creator":"dernst","checksum":"98493a05b84e4513b6394dfad4851ddf","file_name":"2024_ArchiveRatAnalysis_Abels.pdf","date_created":"2024-09-09T08:43:32Z","relation":"main_file"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-09-03T00:00:00Z","article_number":"77","abstract":[{"lang":"eng","text":"We show convergence of the Navier-Stokes/Allen-Cahn system to a classical sharp interface model for the two-phase flow of two viscous incompressible fluids with same viscosities in a smooth bounded domain in two and three space dimensions as long as a smooth solution of the limit system exists. Moreover, we obtain error estimates with the aid of a relative entropy method. Our results hold provided that the mobility mε>0 in the Allen-Cahn equation tends to zero in a subcritical way, i.e., mε=m0εβ for some β∈(0,2) and m0>0 . The proof proceeds by showing via a relative entropy argument that the solution to the Navier-Stokes/Allen-Cahn system remains close to the solution of a perturbed version of the two-phase flow problem, augmented by an extra mean curvature flow term mεHΓt in the interface motion. In a second step, it is easy to see that the solution to the perturbed problem is close to the original two-phase flow."}],"has_accepted_license":"1","date_created":"2024-09-08T22:01:10Z","pmid":1,"publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":" 248","issue":"5","ddc":["510"],"month":"09","status":"public","publication":"Archive for Rational Mechanics and Analysis"},{"article_number":"172","date_published":"2024-09-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"relation":"main_file","date_created":"2024-09-11T07:14:03Z","file_name":"2024_LandscapeEcology_Pocull.pdf","checksum":"2e1cbc320ec1b4447a5a8562a90bcbc3","creator":"dernst","file_size":1494987,"content_type":"application/pdf","access_level":"open_access","file_id":"18054","success":1,"date_updated":"2024-09-11T07:14:03Z"}],"publication_status":"published","year":"2024","article_processing_charge":"Yes (via OA deal)","oa":1,"ec_funded":1,"isi":1,"type":"journal_article","status":"public","corr_author":"1","ddc":["570"],"month":"09","publication":"Landscape Ecology","issue":"9","intvolume":" 39","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","date_created":"2024-09-08T22:01:11Z","abstract":[{"lang":"eng","text":"Context: Biotic resource exploitation is a critical determinant of species’ distributions. However, quantifying resource exploitation patterns through space and time can be difficult, complicating their incorporation in spatial ecology studies. Therefore, understanding the local drivers of spatial patterns of resource exploitation may contribute to better large-scale species distribution models.\r\nObjectives: We investigated (1) how the resource exploitation patterns of two trophic interactions (plant–insect) are explained by insect behaviour, resource aggregation, and potential insect-insect interactions. We also analyzed how (2) resource patch size and (3) resource accessibility in a heterogeneous landscape affected host exploitation patterns.\r\nMethods: We quantified nectar robbing by insects in the genus Bombus (bumblebees) and seed predation by Brachypterolus vestitus larvae (Antirrhinum beetle) on Antirrhinum majus L. (wild snapdragons) in the Pyrenees Mountains, Catalonia, Spain. We tested hypotheses about resource exploitation by integrating spatial analyses at multiple scales.\r\nResults: Both trophic interactions were aggregated, explained by the aggregation of their resource. At some scales, nectar robbing is more aggregated than the resource. Trophic interaction abundance is proportional to resource patch size, following the ideal free distribution model. Landscape features do not explain the locations exploited. Nectar robbing and seed predation occur together more often than expected.\r\nConclusions: Our findings suggest that multiple biotic and ecological spatial factors may simultaneously affect resource exploitation at a local scale. These findings should be considered when developing agricultural projects, management plans and conservation policies."}],"title":"Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects","date_updated":"2025-09-08T09:20:11Z","author":[{"full_name":"Pocull Belles, Guillem","id":"54359172-700c-11ef-a103-c1d91ceac6d6","first_name":"Guillem","last_name":"Pocull Belles"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","full_name":"Baskett, Carina","first_name":"Carina","orcid":"0000-0002-7354-8574","last_name":"Baskett"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001304011900001"]},"day":"01","publication_identifier":{"eissn":["1572-9761"],"issn":["0921-2973"]},"article_type":"original","file_date_updated":"2024-09-11T07:14:03Z","acknowledgement":"For the beetle barcoding, we are very thankful to Brent Emerson’s laboratory at the Consejo Superior de Investigaciones Científicas (CSIC) at the Instituto de Productos Naturales y Agrobiología (IPNA) in La Laguna, Tenerife. Many thanks to numerous field assistants, especially Sandra Cuevas Gallego, Beatriz Pablo Carmona, Luís Santos Cid and Alex Fuster, for their assistance in data collection. Finally, we thank Jesús Muñoz, Virgilio Gómez-Rubio, and two anonymous reviewers for comments that greatly improved the quality of the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). CB received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. NB was funded by the FWF grant “Löwenmaul speciation” P 32166-B32.","oa_version":"Published Version","quality_controlled":"1","_id":"17888","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Pocull Belles, Guillem, Carina Baskett, and Nicholas H Barton. “Multiscale Spatial Analysis of Two Plant–Insect Interactions: Effects of Landscape, Resource Distribution, and Other Insects.” Landscape Ecology. Springer Nature, 2024. https://doi.org/10.1007/s10980-024-01899-9.","short":"G. Pocull Belles, C. Baskett, N.H. Barton, Landscape Ecology 39 (2024).","ieee":"G. Pocull Belles, C. Baskett, and N. H. Barton, “Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects,” Landscape Ecology, vol. 39, no. 9. Springer Nature, 2024.","mla":"Pocull Belles, Guillem, et al. “Multiscale Spatial Analysis of Two Plant–Insect Interactions: Effects of Landscape, Resource Distribution, and Other Insects.” Landscape Ecology, vol. 39, no. 9, 172, Springer Nature, 2024, doi:10.1007/s10980-024-01899-9.","ama":"Pocull Belles G, Baskett C, Barton NH. Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects. Landscape Ecology. 2024;39(9). doi:10.1007/s10980-024-01899-9","ista":"Pocull Belles G, Baskett C, Barton NH. 2024. Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects. Landscape Ecology. 39(9), 172.","apa":"Pocull Belles, G., Baskett, C., & Barton, N. H. (2024). Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects. Landscape Ecology. Springer Nature. https://doi.org/10.1007/s10980-024-01899-9"},"doi":"10.1007/s10980-024-01899-9","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Snapdragon Speciation","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"volume":39,"department":[{"_id":"NiBa"}],"scopus_import":"1"},{"article_number":"637","date_published":"2024-08-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"relation":"main_file","date_created":"2024-09-09T09:01:12Z","file_name":"2024_Entropy_Edelsbrunner.pdf","checksum":"624a9e2c5b49d6c38b88b0f675467ba3","creator":"dernst","file_size":8025139,"content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"17948","date_updated":"2024-09-09T09:01:12Z"}],"year":"2024","article_processing_charge":"Yes","publication_status":"published","oa":1,"type":"journal_article","isi":1,"month":"08","ddc":["510"],"status":"public","publication":"Entropy","issue":"8","intvolume":" 26","language":[{"iso":"eng"}],"publisher":"MDPI","pmid":1,"has_accepted_license":"1","date_created":"2024-09-08T22:01:11Z","abstract":[{"text":"Abstract\r\nMethods used in topological data analysis naturally capture higher-order interactions in point cloud data embedded in a metric space. This methodology was recently extended to data living in an information space, by which we mean a space measured with an information theoretical distance. One such setting is a finite collection of discrete probability distributions embedded in the probability simplex measured with the relative entropy (Kullback–Leibler divergence). More generally, one can work with a Bregman divergence parameterized by a different notion of entropy. While theoretical algorithms exist for this setup, there is a paucity of implementations for exploring and comparing geometric-topological properties of various information spaces. The interest of this work is therefore twofold. First, we propose the first robust algorithms and software for geometric and topological data analysis in information space. Perhaps surprisingly, despite working with Bregman divergences, our design reuses robust libraries for the Euclidean case. Second, using the new software, we take the first steps towards understanding the geometric-topological structure of these spaces. In particular, we compare them with the more familiar spaces equipped with the Euclidean and Fisher metrics.","lang":"eng"}],"date_updated":"2025-09-08T09:13:44Z","title":"Understanding higher-order interactions in information space","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert"},{"full_name":"Ölsböck, Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","first_name":"Katharina","last_name":"Ölsböck","orcid":"0000-0002-4672-8297"},{"first_name":"Hubert","last_name":"Wagner","full_name":"Wagner, Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001305543500001"],"pmid":["39202107"]},"acknowledgement":"We thank Anton Nikitenko for first observing that the Wrap complex can be characterized as stated in Claim (ii) of the Wrap Complex Lemma, and Ondrej Draganov for correcting a critical mistake in one of our formulas in Section 2.","related_material":{"link":[{"relation":"software","url":"https://git.ista.ac.at/katharina.oelsboeck/wrap_2_3-public/"}]},"publication_identifier":{"eissn":["1099-4300"]},"article_type":"original","file_date_updated":"2024-09-09T09:01:12Z","day":"01","oa_version":"Published Version","quality_controlled":"1","_id":"17891","doi":"10.3390/e26080637","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"H. Edelsbrunner, K. Ölsböck, H. Wagner, Entropy 26 (2024).","chicago":"Edelsbrunner, Herbert, Katharina Ölsböck, and Hubert Wagner. “Understanding Higher-Order Interactions in Information Space.” Entropy. MDPI, 2024. https://doi.org/10.3390/e26080637.","apa":"Edelsbrunner, H., Ölsböck, K., & Wagner, H. (2024). Understanding higher-order interactions in information space. Entropy. MDPI. https://doi.org/10.3390/e26080637","ista":"Edelsbrunner H, Ölsböck K, Wagner H. 2024. Understanding higher-order interactions in information space. Entropy. 26(8), 637.","ama":"Edelsbrunner H, Ölsböck K, Wagner H. Understanding higher-order interactions in information space. Entropy. 2024;26(8). doi:10.3390/e26080637","ieee":"H. Edelsbrunner, K. Ölsböck, and H. Wagner, “Understanding higher-order interactions in information space,” Entropy, vol. 26, no. 8. MDPI, 2024.","mla":"Edelsbrunner, Herbert, et al. “Understanding Higher-Order Interactions in Information Space.” Entropy, vol. 26, no. 8, 637, MDPI, 2024, doi:10.3390/e26080637."},"volume":26,"scopus_import":"1","department":[{"_id":"HeEd"}]},{"quality_controlled":"1","oa_version":"Published Version","_id":"17892","volume":110,"scopus_import":"1","department":[{"_id":"EdHa"}],"doi":"10.1103/PhysRevE.110.024404","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E, vol. 110, no. 2, 024404, American Physical Society, 2024, doi:10.1103/PhysRevE.110.024404.","ieee":"F. Olmeda and S. Rulands, “Field theory of enzyme-substrate systems with restricted long-range interactions,” Physical Review E, vol. 110, no. 2. American Physical Society, 2024.","ista":"Olmeda F, Rulands S. 2024. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 110(2), 024404.","apa":"Olmeda, F., & Rulands, S. (2024). Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.110.024404","ama":"Olmeda F, Rulands S. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 2024;110(2). doi:10.1103/PhysRevE.110.024404","chicago":"Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E. American Physical Society, 2024. https://doi.org/10.1103/PhysRevE.110.024404.","short":"F. Olmeda, S. Rulands, Physical Review E 110 (2024)."},"project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"author":[{"last_name":"Olmeda","first_name":"Fabrizio","full_name":"Olmeda, Fabrizio","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689"},{"first_name":"Steffen","last_name":"Rulands","full_name":"Rulands, Steffen"}],"date_updated":"2025-09-08T09:17:18Z","title":"Field theory of enzyme-substrate systems with restricted long-range interactions","article_type":"original","file_date_updated":"2024-09-11T05:59:36Z","acknowledgement":"We thank F. Piazza, M. Henkel, and F. Jülicher for helpful feedback and the entire Rulands group for fruitful discussions. We thank W. Reik, S. Clark, T. Lohoff, and I. Kafetzopoulos for fruitful discussions about the biological aspects of this work. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant No. 950349). This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 101034413.","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"day":"01","external_id":{"isi":["001299670100004"],"pmid":["39294986"]},"issue":"2","publication":"Physical Review E","status":"public","ddc":["530"],"corr_author":"1","month":"08","publisher":"American Physical Society","has_accepted_license":"1","abstract":[{"text":"Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here we study a general model of enzyme-substrate kinetics with restricted long-range interactions described by an exponent −𝛾. We employ a coherent-state path integral and renormalization group approach to calculate the first moment and two-point correlation function of the enzyme-binding profile. We show that starting from an empty substrate the average occupancy follows a power law with an exponent 1/(1−𝛾) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents −𝛾 on short distances and −(2/3)(2−𝛾) on long distances. The crossover between both regimes scales inversely with the average substrate occupancy. Our work allows associating experimental measurements of bound enzyme locations with their binding kinetics and the spatial conformation of the substrate.","lang":"eng"}],"date_created":"2024-09-08T22:01:12Z","pmid":1,"intvolume":" 110","language":[{"iso":"eng"}],"file":[{"file_id":"18053","success":1,"date_updated":"2024-09-11T05:59:36Z","creator":"dernst","checksum":"67fc2cc8eee3155e5c3b7380307d8284","file_name":"2024_PhysReviewE_Olmeda.pdf","relation":"main_file","date_created":"2024-09-11T05:59:36Z","content_type":"application/pdf","access_level":"open_access","file_size":445696}],"article_processing_charge":"Yes (in subscription journal)","year":"2024","publication_status":"published","article_number":"024404","date_published":"2024-08-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"isi":1,"ec_funded":1,"type":"journal_article"},{"quality_controlled":"1","oa_version":"None","_id":"17896","volume":16,"department":[{"_id":"MaIb"}],"scopus_import":"1","citation":{"ama":"Zhou J, Xu S, Shuai Y, et al. Decipher the wavelength and intensity using photothermoelectric detectors. ACS Applied Materials and Interfaces. 2024;16(36):47923-47930. doi:10.1021/acsami.4c10489","ista":"Zhou J, Xu S, Shuai Y, Sun Q, Ma H, Wang C, Wu H, Tan S, Wang Z, Yang L. 2024. Decipher the wavelength and intensity using photothermoelectric detectors. ACS Applied Materials and Interfaces. 16(36), 47923–47930.","apa":"Zhou, J., Xu, S., Shuai, Y., Sun, Q., Ma, H., Wang, C., … Yang, L. (2024). Decipher the wavelength and intensity using photothermoelectric detectors. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.4c10489","ieee":"J. Zhou et al., “Decipher the wavelength and intensity using photothermoelectric detectors,” ACS Applied Materials and Interfaces, vol. 16, no. 36. American Chemical Society, pp. 47923–47930, 2024.","mla":"Zhou, Jiamin, et al. “Decipher the Wavelength and Intensity Using Photothermoelectric Detectors.” ACS Applied Materials and Interfaces, vol. 16, no. 36, American Chemical Society, 2024, pp. 47923–30, doi:10.1021/acsami.4c10489.","short":"J. Zhou, S. Xu, Y. Shuai, Q. Sun, H. Ma, C. Wang, H. Wu, S. Tan, Z. Wang, L. Yang, ACS Applied Materials and Interfaces 16 (2024) 47923–47930.","chicago":"Zhou, Jiamin, Shengduo Xu, Yi Shuai, Qiang Sun, Huangshui Ma, Chao Wang, Haijuan Wu, Shanshan Tan, Zegao Wang, and Lei Yang. “Decipher the Wavelength and Intensity Using Photothermoelectric Detectors.” ACS Applied Materials and Interfaces. American Chemical Society, 2024. https://doi.org/10.1021/acsami.4c10489."},"doi":"10.1021/acsami.4c10489","author":[{"full_name":"Zhou, Jiamin","first_name":"Jiamin","last_name":"Zhou"},{"full_name":"Xu, Shengduo","id":"12ab8624-4c8a-11ec-9e11-e1ac2438f22f","last_name":"Xu","first_name":"Shengduo"},{"last_name":"Shuai","first_name":"Yi","full_name":"Shuai, Yi"},{"full_name":"Sun, Qiang","first_name":"Qiang","last_name":"Sun"},{"first_name":"Huangshui","last_name":"Ma","full_name":"Ma, Huangshui"},{"full_name":"Wang, Chao","last_name":"Wang","first_name":"Chao"},{"full_name":"Wu, Haijuan","last_name":"Wu","first_name":"Haijuan"},{"full_name":"Tan, Shanshan","first_name":"Shanshan","last_name":"Tan"},{"full_name":"Wang, Zegao","last_name":"Wang","first_name":"Zegao"},{"full_name":"Yang, Lei","first_name":"Lei","last_name":"Yang"}],"title":"Decipher the wavelength and intensity using photothermoelectric detectors","date_updated":"2025-09-08T09:15:07Z","day":"11","publication_identifier":{"eissn":["1944-8252"],"issn":["1944-8244"]},"article_type":"original","acknowledgement":"The authors appreciate the Analytical & Testing Center of Sichuan University and Ceshigo Research Service for their supports on material characterization. This study is financial supported by the fund of the State Key Laboratory of Solidification Processing in Northwestern Polytechnical University (NWPU, Grant SKLSP202315), the State Key Laboratory for Mechanical Behavior of Materials (Grant 20232509), and the International Scientific and Technological Innovation Cooperation of Sichuan Province (2024YFHZ0309).","external_id":{"isi":["001300770000001"],"pmid":["39194354"]},"issue":"36","publication":"ACS Applied Materials and Interfaces","status":"public","month":"09","publisher":"American Chemical Society","abstract":[{"text":"Broadband photodetectors that can decipher the wavelength (λ) and intensity (I) of an unknown incident light are urgently demanded. Photothermoelectric (PTE) detectors can achieve ultrabroadband photodetection surpassing the bandgap limitation; however, their practical application is severely hampered by the lack of deciphering strategy. In this work, we report a variable elimination method to decipher λ and I of the incident lights based on an integrated Ag2Se film-based PTE detector. Nanostructured Ag2Se films with controlled thickness are synthesized using an ion sputtering of Ag and a room-temperature selenization method and then assembled into a detector. Under identical illumination, Ag2Se films of different thicknesses produce varying output photothermal voltages, influenced by factors including λ. By establishing a direct relationship between the photothermal voltage and the absorption of Ag2Se films of varied thickness, we successfully eliminate variables independent of λ, thus determining λ. Subsequently, I is determined by the calibrated responsivity relationship using obtained λ. Our PTE detector achieves a broadband spectrum from 400 to 950 nm and high accuracy, with deviations as low as ∼2.63 and ∼0.53% for deciphered λ and I, respectively. This method allows for self-powered broadband decipherable photodetection without a complex device architecture or computational assistance, which could boost the research enthusiasm and promote the commercialization of PTE broadband detectors.","lang":"eng"}],"date_created":"2024-09-08T22:01:13Z","pmid":1,"intvolume":" 16","language":[{"iso":"eng"}],"OA_type":"closed access","publication_status":"published","article_processing_charge":"No","year":"2024","date_published":"2024-09-11T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"47923-47930","type":"journal_article","isi":1},{"article_type":"original","acknowledgement":"This work was financially supported by the SyDEC at project from the Spanish MCIN/AEI/FEDER (PID2022-136883OB-C22) and Generalitat de Catalunya 2021SGR01581. J. N. H. and P. W. M. acknowledge support from the German Federal Ministry of Education and Research in the framework of the project “Catlab” (03EW0015A/B). L. Yang thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). This work was supported by the European Union Horizon 2020 research and innovation program (No. 857470) and the European Regional Development Fund via the Foundation for Polish Science International Research Agenda PLUS program (No. MAB PLUS/2018/8). The publication was created within the framework of the project of the Minister of Science and Higher Education, Poland “Support for the activities of Centres of Excellence established in Poland under Horizon 2020” under contract no. MEiN/2023/DIR/3795. H. D. and S. M. thank the German Federal Ministry of Education and Research (BMBF) for supporting the Live-XAS project (05K22KE1) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) for support under Germany's Excellence Strategy – EXC 2008/1 – 390540038 – UniSysCat. The authors thank the Helmholtz-Zentrum Berlin (HZB) for beamtime allocation at the KMC-3 synchrotron beamline of the BESSY synchrotron in Berlin-Adlershof and Dr Ivo Zizak as well as Dr Michael Haumann for technical support.","publication_identifier":{"issn":["1754-5692"],"eissn":["1754-5706"]},"day":"22","external_id":{"isi":["001298924700001"]},"author":[{"last_name":"He","first_name":"Ren","full_name":"He, Ren"},{"first_name":"Shiqi","last_name":"Wang","full_name":"Wang, Shiqi"},{"full_name":"Yang, Linlin","first_name":"Linlin","last_name":"Yang"},{"last_name":"Horta","first_name":"Sharona","full_name":"Horta, Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"last_name":"Ding","first_name":"Yang","full_name":"Ding, Yang"},{"full_name":"Di, Chong","last_name":"Di","first_name":"Chong"},{"first_name":"Xuesong","last_name":"Zhang","full_name":"Zhang, Xuesong"},{"full_name":"Xu, Ying","first_name":"Ying","last_name":"Xu"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"last_name":"Zhou","first_name":"Yingtang","full_name":"Zhou, Yingtang"},{"full_name":"Mebs, Stefan","last_name":"Mebs","first_name":"Stefan"},{"full_name":"Dau, Holger","first_name":"Holger","last_name":"Dau"},{"full_name":"Hausmann, Jan Niklas","last_name":"Hausmann","first_name":"Jan Niklas"},{"full_name":"Huo, Wenyi","last_name":"Huo","first_name":"Wenyi"},{"last_name":"Menezes","first_name":"Prashanth W.","full_name":"Menezes, Prashanth W."},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"date_updated":"2025-09-08T09:15:49Z","title":"Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery","volume":17,"department":[{"_id":"MaIb"}],"scopus_import":"1","doi":"10.1039/d4ee01912a","citation":{"short":"R. He, S. Wang, L. Yang, S. Horta, Y. Ding, C. Di, X. Zhang, Y. Xu, M. Ibáñez, Y. Zhou, S. Mebs, H. Dau, J.N. Hausmann, W. Huo, P.W. Menezes, A. Cabot, Energy and Environmental Science 17 (2024) 7193–7208.","chicago":"He, Ren, Shiqi Wang, Linlin Yang, Sharona Horta, Yang Ding, Chong Di, Xuesong Zhang, et al. “Active Site Switching on High Entropy Phosphides as Bifunctional Oxygen Electrocatalysts for Rechargeable/Robust Zn-Air Battery.” Energy and Environmental Science. Royal Society of Chemistry, 2024. https://doi.org/10.1039/d4ee01912a.","ista":"He R, Wang S, Yang L, Horta S, Ding Y, Di C, Zhang X, Xu Y, Ibáñez M, Zhou Y, Mebs S, Dau H, Hausmann JN, Huo W, Menezes PW, Cabot A. 2024. Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery. Energy and Environmental Science. 17(19), 7193–7208.","apa":"He, R., Wang, S., Yang, L., Horta, S., Ding, Y., Di, C., … Cabot, A. (2024). Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery. Energy and Environmental Science. Royal Society of Chemistry. https://doi.org/10.1039/d4ee01912a","ama":"He R, Wang S, Yang L, et al. Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery. Energy and Environmental Science. 2024;17(19):7193-7208. doi:10.1039/d4ee01912a","mla":"He, Ren, et al. “Active Site Switching on High Entropy Phosphides as Bifunctional Oxygen Electrocatalysts for Rechargeable/Robust Zn-Air Battery.” Energy and Environmental Science, vol. 17, no. 19, Royal Society of Chemistry, 2024, pp. 7193–208, doi:10.1039/d4ee01912a.","ieee":"R. He et al., “Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery,” Energy and Environmental Science, vol. 17, no. 19. Royal Society of Chemistry, pp. 7193–7208, 2024."},"quality_controlled":"1","oa_version":"None","_id":"17897","page":"7193-7208","type":"journal_article","isi":1,"article_processing_charge":"No","year":"2024","publication_status":"published","date_published":"2024-08-22T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Royal Society of Chemistry","abstract":[{"lang":"eng","text":"High-entropy materials (HEMs) offer a quasi-continuous spectrum of active sites and have generated great expectations in fields such as electrocatalysis and energy storage. Despite their potential, the complex composition and associated surface phenomena of HEMs pose challenges to their rational design and development. In this context, we have synthesized FeCoNiPdWP high entropy phosphide (HEP) nanoparticles using a low-temperature colloidal method, and explored their application as bifunctional electrocatalysts for the oxygen evolution and reduction reactions (OER/ORR). Our analysis provides a detailed understanding of the individual roles and transformations of each element during OER/ORR operation. Notably, the HEPs exhibit an exceptionally low OER overpotential of 227 mV at 10 mA cm−2, attributed to the reconstructed HEP surface into a FeCoNiPdW high entropy oxyhydroxide with high oxidation states of Fe, Co, and Ni serving as the active sites. Additionally, Pd and W play crucial roles in modulating the electronic structure to optimize the adsorption energy of oxygen intermediates. For the ORR, Pd emerges as the most active component. In the reconstructed catalyst, the strong d–d orbital coupling of especially Pd, Co, and W fine-tunes ORR electron transfer pathways, delivering an ORR half-wave potential of 0.81 V with a pure four-electron reduction mechanism. The practicality of these HEPs catalysts is showcased through the assembly of aqueous zinc–air batteries. These batteries demonstrate a superior specific capacity of 886 mA h gZn−1 and maintain excellent stability over more than 700 hours of continuous operation. Overall, this study not only elucidates the role of each element in HEMs but also establishes a foundational framework for the design and development of next-generation bifunctional oxygen catalysts, broadening the potential applications of these complex materials in advanced energy systems."}],"date_created":"2024-09-08T22:01:13Z","intvolume":" 17","language":[{"iso":"eng"}],"OA_type":"closed access","issue":"19","status":"public","month":"08","publication":"Energy and Environmental Science"},{"type":"book_chapter","ec_funded":1,"page":"123-137","editor":[{"full_name":"Lübke, Joachim H.R. ","last_name":"Lübke","first_name":"Joachim H.R. "},{"last_name":"Rollenhagen","first_name":"Astrid","full_name":"Rollenhagen, Astrid"}],"date_published":"2024-08-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","place":"New York","article_processing_charge":"No","year":"2024","publication_status":"published","language":[{"iso":"eng"}],"publisher":"Springer Nature","alternative_title":["Neuromethods"],"abstract":[{"lang":"eng","text":"Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is an electron microscope (EM) sample preparation technique which allows for high-resolution visualization of membrane proteins with high sensitivity. However, image acquisition of specific replica profiles such as synapses in a large field of EM view needs a valid experience and a long time for manual searching. Here, we describe how to utilize deep learning for automatizing image acquisition of specific profiles of interest in replica samples. This protocol facilitates the labor-intensive collection of EM images, in particular for rare profiles. We provide instructions for using SerialEM image acquisition software in conjunction with object detection by our newly developed deep learning software DarEM, to automatically acquire tilt series of all synapses in a selected region. We then show how to perform a mostly automated analysis of gold particle labeling in the acquired images by utilizing Darea software."}],"date_created":"2024-09-10T12:32:38Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"corr_author":"1","status":"public","month":"08","publication":"New Aspects in Analyzing the Synaptic Organization of the Brain","publication_identifier":{"issn":["0893-2336"],"eisbn":["9781071640197"],"isbn":["9781071640180"],"eissn":["1940-6045"]},"acknowledgement":"This research was supported by the European Research Council Advanced Grant 694539 to RS and by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility.","day":"27","date_updated":"2025-04-14T07:27:15Z","title":"Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning","author":[{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David","first_name":"David","last_name":"Kleindienst"},{"full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","orcid":"0000-0001-9732-3815","first_name":"Tommaso"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi"}],"doi":"10.1007/978-1-0716-4019-7_8","citation":{"apa":"Kleindienst, D., Costanzo, T., & Shigemoto, R. (2024). Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In J. H. R. Lübke & A. Rollenhagen (Eds.), New Aspects in Analyzing the Synaptic Organization of the Brain (1st ed., pp. 123–137). New York: Springer Nature. https://doi.org/10.1007/978-1-0716-4019-7_8","ista":"Kleindienst D, Costanzo T, Shigemoto R. 2024.Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: New Aspects in Analyzing the Synaptic Organization of the Brain. Neuromethods, , 123–137.","ama":"Kleindienst D, Costanzo T, Shigemoto R. Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning. In: Lübke JHR, Rollenhagen A, eds. New Aspects in Analyzing the Synaptic Organization of the Brain. 1st ed. New York: Springer Nature; 2024:123-137. doi:10.1007/978-1-0716-4019-7_8","ieee":"D. Kleindienst, T. Costanzo, and R. Shigemoto, “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning,” in New Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed., J. H. R. Lübke and A. Rollenhagen, Eds. New York: Springer Nature, 2024, pp. 123–137.","mla":"Kleindienst, David, et al. “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.” New Aspects in Analyzing the Synaptic Organization of the Brain, edited by Joachim H.R. Lübke and Astrid Rollenhagen, 1st ed., Springer Nature, 2024, pp. 123–37, doi:10.1007/978-1-0716-4019-7_8.","short":"D. Kleindienst, T. Costanzo, R. Shigemoto, in:, J.H.R. Lübke, A. Rollenhagen (Eds.), New Aspects in Analyzing the Synaptic Organization of the Brain, 1st ed., Springer Nature, New York, 2024, pp. 123–137.","chicago":"Kleindienst, David, Tommaso Costanzo, and Ryuichi Shigemoto. “Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning.” In New Aspects in Analyzing the Synaptic Organization of the Brain, edited by Joachim H.R. Lübke and Astrid Rollenhagen, 1st ed., 123–37. New York: Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-4019-7_8."},"project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"}],"edition":"1","scopus_import":"1","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"quality_controlled":"1","oa_version":"None","_id":"18052"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","place":"Boca Raton","title":"DNA Cloning","date_published":"2024-09-05T00:00:00Z","date_updated":"2024-09-11T11:16:58Z","publication_status":"published","year":"2024","article_processing_charge":"No","author":[{"last_name":"Watson","orcid":"0000-0002-8698-3823","first_name":"Jake","full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"full_name":"Arroyo-Urea, Sandra","first_name":"Sandra","last_name":"Arroyo-Urea"},{"full_name":"García-Nafría, Javier","first_name":"Javier","last_name":"García-Nafría"}],"type":"book_chapter","day":"05","publication_identifier":{"eisbn":["9781003055211"]},"editor":[{"first_name":"Dongyou","last_name":"Liu","full_name":"Liu, Dongyou"}],"page":"66-72","_id":"18058","publication":"Handbook of Molecular Biotechnology","quality_controlled":"1","month":"09","oa_version":"None","status":"public","language":[{"iso":"eng"}],"citation":{"short":"J. Watson, S. Arroyo-Urea, J. García-Nafría, in:, D. Liu (Ed.), Handbook of Molecular Biotechnology, 1st ed., CRC Press, Boca Raton, 2024, pp. 66–72.","chicago":"Watson, Jake, Sandra Arroyo-Urea, and Javier García-Nafría. “DNA Cloning.” In Handbook of Molecular Biotechnology, edited by Dongyou Liu, 1st ed., 66–72. Boca Raton: CRC Press, 2024. https://doi.org/10.1201/9781003055211-8.","apa":"Watson, J., Arroyo-Urea, S., & García-Nafría, J. (2024). DNA Cloning. In D. Liu (Ed.), Handbook of Molecular Biotechnology (1st ed., pp. 66–72). Boca Raton: CRC Press. https://doi.org/10.1201/9781003055211-8","ista":"Watson J, Arroyo-Urea S, García-Nafría J. 2024.DNA Cloning. In: Handbook of Molecular Biotechnology. , 66–72.","ama":"Watson J, Arroyo-Urea S, García-Nafría J. DNA Cloning. In: Liu D, ed. Handbook of Molecular Biotechnology. 1st ed. Boca Raton: CRC Press; 2024:66-72. doi:10.1201/9781003055211-8","mla":"Watson, Jake, et al. “DNA Cloning.” Handbook of Molecular Biotechnology, edited by Dongyou Liu, 1st ed., CRC Press, 2024, pp. 66–72, doi:10.1201/9781003055211-8.","ieee":"J. Watson, S. Arroyo-Urea, and J. García-Nafría, “DNA Cloning,” in Handbook of Molecular Biotechnology, 1st ed., D. Liu, Ed. Boca Raton: CRC Press, 2024, pp. 66–72."},"doi":"10.1201/9781003055211-8","department":[{"_id":"PeJo"}],"date_created":"2024-09-11T10:40:36Z","scopus_import":"1","abstract":[{"text":"DNA cloning is a core technique in biomedical and biotechnological research and is used to assemble and modify DNA fragments at will. While DNA cloning has traditionally relied on restriction enzymes, recent homology-based methods offer improved protocols together with seamless and directional assembly of desired products, overcoming the main disadvantages of restriction enzyme DNA cloning. This chapter provides a historical perspective on DNA cloning, presents a detailed discussion on state-of-the-art in vitro and in vivo homology-based methodologies, covering the basics of how to perform all major plasmid modifications (sub-cloning, site-directed mutagenesis, insertions, and deletions), and gives examples of how to apply these techniques for complex DNA cloning projects.","lang":"eng"}],"edition":"1","publisher":"CRC Press"},{"ddc":["570"],"month":"09","publication":"Communications Biology","status":"public","language":[{"iso":"eng"}],"intvolume":" 7","has_accepted_license":"1","date_created":"2024-09-15T22:01:38Z","pmid":1,"abstract":[{"lang":"eng","text":"The developmental plasticity of the root system plays an essential role in the adaptation of plants to the environment. Among many other signals, auxin and its directional, intercellular transport are critical in regulating root growth and development. In particular, the PIN-FORMED2 (PIN2) auxin exporter acts as a key regulator of root gravitropic growth. Multiple regulators have been reported to be involved in PIN2-mediated root growth; however, our information remains incomplete. Here, we identified ROWY Bro1-domain proteins as important regulators of PIN2 sorting control. Genetic analysis revealed that Arabidopsis rowy1 single mutants and higher-order rowy1 rowy2 rowy3 triple mutants presented a wavy root growth phenotype. Cell biological experiments revealed that ROWY1 and PIN2 colocalized to the apical side of the plasma membrane in the root epidermis and that ROWYs are required for correct PM targeting of PIN2. In addition, ROWYs also affected PIN3 protein abundance in the stele, suggesting the potential involvement of additional PIN transporters as well as other proteins. A global transcriptome analysis revealed that ROWY genes are involved in the Fe2+ availability perception pathway. This work establishes ROWYs as important novel regulators of root gravitropic growth by connecting micronutrient availability to the proper subcellular targeting of PIN auxin transporters."}],"publisher":"Springer Nature","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-09-04T00:00:00Z","article_number":"1085","publication_status":"published","article_processing_charge":"Yes","year":"2024","file":[{"checksum":"7d66af41c90e73d1b8a375eb652a9561","creator":"dernst","file_name":"2024_CommBiology_Peng.pdf","date_created":"2024-09-17T09:44:29Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":7718758,"success":1,"file_id":"18084","date_updated":"2024-09-17T09:44:29Z"}],"isi":1,"type":"journal_article","oa":1,"_id":"18063","oa_version":"Published Version","quality_controlled":"1","project":[{"grant_number":"I06123","name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"},{"grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"}],"citation":{"short":"Y. Peng, K. Ji, Y. Mao, Y. Wang, B. Korbei, C. Luschnig, J. Shen, E. Benková, J. Friml, S. Tan, Communications Biology 7 (2024).","chicago":"Peng, Yakun, Kangkang Ji, Yanbo Mao, Yiqun Wang, Barbara Korbei, Christian Luschnig, Jinbo Shen, Eva Benková, Jiří Friml, and Shutang Tan. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” Communications Biology. Springer Nature, 2024. https://doi.org/10.1038/s42003-024-06747-9.","ama":"Peng Y, Ji K, Mao Y, et al. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. 2024;7. doi:10.1038/s42003-024-06747-9","ista":"Peng Y, Ji K, Mao Y, Wang Y, Korbei B, Luschnig C, Shen J, Benková E, Friml J, Tan S. 2024. Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. 7, 1085.","apa":"Peng, Y., Ji, K., Mao, Y., Wang, Y., Korbei, B., Luschnig, C., … Tan, S. (2024). Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-024-06747-9","ieee":"Y. Peng et al., “Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis,” Communications Biology, vol. 7. Springer Nature, 2024.","mla":"Peng, Yakun, et al. “Polarly Localized Bro1 Domain Proteins Regulate PIN-FORMED Abundance and Root Gravitropic Growth in Arabidopsis.” Communications Biology, vol. 7, 1085, Springer Nature, 2024, doi:10.1038/s42003-024-06747-9."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s42003-024-06747-9","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"scopus_import":"1","volume":7,"title":"Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis","date_updated":"2026-04-07T11:49:33Z","author":[{"full_name":"Peng, Yakun","last_name":"Peng","first_name":"Yakun"},{"full_name":"Ji, Kangkang","first_name":"Kangkang","last_name":"Ji"},{"first_name":"Yanbo","last_name":"Mao","full_name":"Mao, Yanbo"},{"last_name":"Wang","first_name":"Yiqun","id":"82F537F2-B517-11E9-84D7-6433E6697425","full_name":"Wang, Yiqun"},{"full_name":"Korbei, Barbara","first_name":"Barbara","last_name":"Korbei"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"},{"full_name":"Shen, Jinbo","last_name":"Shen","first_name":"Jinbo"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","orcid":"0000-0002-0471-8285","first_name":"Shutang"}],"external_id":{"isi":["001306499600002"],"pmid":["39232040"]},"day":"04","acknowledgement":"We thank Drs. Erika Isono (University of Constance), Grégory Vert (University of Toulouse), and Liwen Jiang (The Chinese University of Hong Kong) for kindly sharing published Arabidopsis lines; Dr. Yuzhou Zhang (ISTA) for help with molecular cloning, and Drs. Melinda Abas (BOKU), Eugenia Russinova (Ghent University), and Zhaojun Ding (Shandong University) for valuable discussions. This work was supported by grants to S.T. from the National Natural Science Foundation of China (32321001), the USTC Research Funds of the Double First-Class Initiative (YD9100002016), the Research Funds from the Center for Advanced Interdisciplinary Science and Biomedicine of IHM, the Division of Life Sciences and Medicine, the University of Science and Technology of China (QYPY20220012), the Fundamental Research Funds for the Central Universities (WK9100000021), and start-up funding from the University of Science and Technology of China and the Chinese Academy of Sciences (GG9100007007, KY9100000026, KY9100000051, and KJ2070000079). J.S. was supported by the National Natural Science Foundation of China (31970181 and 32170342). J.F. was supported by Austrian Science Fund (FWF; projects I6123 and P37051-B).","file_date_updated":"2024-09-17T09:44:29Z","related_material":{"record":[{"id":"20117","relation":"dissertation_contains","status":"public"}]},"article_type":"original","publication_identifier":{"eissn":["2399-3642"]}}]