[{"author":[{"first_name":"Matthew T","last_name":"Scoggins","full_name":"Scoggins, Matthew T"},{"id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","first_name":"Zoltán","last_name":"Haiman","full_name":"Haiman, Zoltán"}],"oa_version":"Published Version","date_updated":"2024-09-12T09:08:08Z","intvolume":" 531","abstract":[{"text":"Supermassive black holes (SMBHs) with masses of ∼109 M⊙ within the first billion year of the universe challenge our conventional understanding of black hole formation and growth. One pathway to these SMBHs proposes that supermassive stars born in pristine atomic cooling haloes yield massive seed BHs evolving to these early SMBHs. This scenario leads to an overly massive BH galaxy (OMBG), in which the BH to stellar mass ratio is initially Mbh/M* ≥ 1, well in excess of the typical values of ∼10−3 at low redshifts. Previously, we have investigated two massive seed BH candidates from the Renaissance simulation and found that they remain outliers on the Mbh–M* relation until the OMBG merges with a much more massive halo at z = 8. In this work, we use Monte-Carlo merger trees to investigate the evolution of the Mbh–M* relation for 50 000 protogalaxies hosting massive BH seeds, across 10 000 trees that merge into a 1012 M⊙ halo at z = 6. We find that up to 60 per cent (depending on growth parameters) of these OMBGs remain strong outliers for several 100 Myr, down to redshifts detectable with JWST and with sensitive X-ray telescopes. This represents a way to diagnose the massive-seed formation pathway for early SMBHs. We expect to find ∼0.1–1 of these objects per JWST Near Infrared Camera (NIRCam) field per unit redshift at z ≳ 6. Recently detected SMBHs with masses of ∼107 M⊙ and low-inferred stellar-mass hosts may be examples of this population.","lang":"eng"}],"title":"Diagnosing the massive-seed pathway to high-redshift black holes: statistics of the evolving black hole to host galaxy mass ratio","day":"13","publication_identifier":{"issn":["0035-8711","1365-2966"]},"publication":"Monthly Notices of the Royal Astronomical Society","date_created":"2024-09-05T09:43:52Z","main_file_link":[{"open_access":"1","url":"https://doi.org/https://doi.org/10.1093/mnras/stae1449"}],"status":"public","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","citation":{"apa":"Scoggins, M. T., & Haiman, Z. (2024). Diagnosing the massive-seed pathway to high-redshift black holes: statistics of the evolving black hole to host galaxy mass ratio. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stae1449","ama":"Scoggins MT, Haiman Z. Diagnosing the massive-seed pathway to high-redshift black holes: statistics of the evolving black hole to host galaxy mass ratio. Monthly Notices of the Royal Astronomical Society. 2024;531(4):4584-4597. doi:10.1093/mnras/stae1449","ieee":"M. T. Scoggins and Z. Haiman, “Diagnosing the massive-seed pathway to high-redshift black holes: statistics of the evolving black hole to host galaxy mass ratio,” Monthly Notices of the Royal Astronomical Society, vol. 531, no. 4. Oxford University Press, pp. 4584–4597, 2024.","short":"M.T. Scoggins, Z. Haiman, Monthly Notices of the Royal Astronomical Society 531 (2024) 4584–4597.","chicago":"Scoggins, Matthew T, and Zoltán Haiman. “Diagnosing the Massive-Seed Pathway to High-Redshift Black Holes: Statistics of the Evolving Black Hole to Host Galaxy Mass Ratio.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2024. https://doi.org/10.1093/mnras/stae1449.","ista":"Scoggins MT, Haiman Z. 2024. Diagnosing the massive-seed pathway to high-redshift black holes: statistics of the evolving black hole to host galaxy mass ratio. Monthly Notices of the Royal Astronomical Society. 531(4), 4584–4597.","mla":"Scoggins, Matthew T., and Zoltán Haiman. “Diagnosing the Massive-Seed Pathway to High-Redshift Black Holes: Statistics of the Evolving Black Hole to Host Galaxy Mass Ratio.” Monthly Notices of the Royal Astronomical Society, vol. 531, no. 4, Oxford University Press, 2024, pp. 4584–97, doi:10.1093/mnras/stae1449."},"type":"journal_article","volume":531,"month":"06","scopus_import":"1","_id":"17535","page":"4584-4597","quality_controlled":"1","year":"2024","oa":1,"doi":"10.1093/mnras/stae1449","publisher":"Oxford University Press","date_published":"2024-06-13T00:00:00Z","language":[{"iso":"eng"}],"issue":"4","article_type":"original","extern":"1"},{"type":"journal_article","volume":109,"publication_status":"published","citation":{"ieee":"L. M. Krauth, J. Davelaar, Z. Haiman, J. R. Westernacher-Schneider, J. Zrake, and A. MacFadyen, “Self-lensing flares from black hole binaries: General-relativistic ray tracing of circumbinary accretion simulations,” Physical Review D, vol. 109, no. 10. American Physical Society (APS), 2024.","apa":"Krauth, L. M., Davelaar, J., Haiman, Z., Westernacher-Schneider, J. R., Zrake, J., & MacFadyen, A. (2024). Self-lensing flares from black hole binaries: General-relativistic ray tracing of circumbinary accretion simulations. Physical Review D. American Physical Society (APS). https://doi.org/10.1103/physrevd.109.103014","ama":"Krauth LM, Davelaar J, Haiman Z, Westernacher-Schneider JR, Zrake J, MacFadyen A. Self-lensing flares from black hole binaries: General-relativistic ray tracing of circumbinary accretion simulations. Physical Review D. 2024;109(10). doi:10.1103/physrevd.109.103014","ista":"Krauth LM, Davelaar J, Haiman Z, Westernacher-Schneider JR, Zrake J, MacFadyen A. 2024. Self-lensing flares from black hole binaries: General-relativistic ray tracing of circumbinary accretion simulations. Physical Review D. 109(10), 103014.","chicago":"Krauth, Luke Major, Jordy Davelaar, Zoltán Haiman, John Ryan Westernacher-Schneider, Jonathan Zrake, and Andrew MacFadyen. “Self-Lensing Flares from Black Hole Binaries: General-Relativistic Ray Tracing of Circumbinary Accretion Simulations.” Physical Review D. American Physical Society (APS), 2024. https://doi.org/10.1103/physrevd.109.103014.","mla":"Krauth, Luke Major, et al. “Self-Lensing Flares from Black Hole Binaries: General-Relativistic Ray Tracing of Circumbinary Accretion Simulations.” Physical Review D, vol. 109, no. 10, 103014, American Physical Society (APS), 2024, doi:10.1103/physrevd.109.103014.","short":"L.M. Krauth, J. Davelaar, Z. Haiman, J.R. Westernacher-Schneider, J. Zrake, A. MacFadyen, Physical Review D 109 (2024)."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"17545","month":"05","scopus_import":"1","arxiv":1,"quality_controlled":"1","year":"2024","external_id":{"arxiv":["2310.19766"]},"article_type":"original","extern":"1","date_published":"2024-05-10T00:00:00Z","publisher":"American Physical Society (APS)","doi":"10.1103/physrevd.109.103014","language":[{"iso":"eng"}],"issue":"10","oa":1,"abstract":[{"text":"Self-lensing flares (SLFs) are expected to be produced once or twice per orbit by an accreting massive black hole binary (MBHB), if the eclipsing MBHBs are observed close to edge-on. SLFs can provide valuable electromagnetic (EM) signatures to accompany the gravitational waves (GWs) detectable by the upcoming Laser Interferometer Space Antenna (LISA). EM follow-ups are crucial for, e.g., sky-localization, and constraining the Hubble constant and the graviton mass. We use high-resolution two-dimensional viscous hydrodynamical simulations of a circumbinary disk (CBD) embedding a MBHB. We then use very high-cadence output of these hydrodynamical simulation inputs for a general-relativistic ray-tracing code to produce synthetic spectra and phase-folded light curves. Our main results show a significant periodic amplification of the flux with the characteristic shape of a sharp flare with a central dip, as the foreground black hole (BH) transits across the minidisk and shadow of the background BH, respectively. These corroborate previous conclusions based on the microlensing approximation and analytical toy models of the emission geometry. We also find that at lower inclinations, without some occlusion of the minidisk emission by the CBD, shocks from quasi-periodic mass-trading between the minidisks can produce bright flares which can mimic SLFs and could hinder their identification.","lang":"eng"}],"oa_version":"Preprint","article_number":"103014","intvolume":" 109","date_updated":"2024-09-18T09:01:52Z","author":[{"first_name":"Luke Major","full_name":"Krauth, Luke Major","last_name":"Krauth"},{"first_name":"Jordy","full_name":"Davelaar, Jordy","last_name":"Davelaar"},{"full_name":"Haiman, Zoltán","last_name":"Haiman","first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36"},{"first_name":"John Ryan","full_name":"Westernacher-Schneider, John Ryan","last_name":"Westernacher-Schneider"},{"full_name":"Zrake, Jonathan","last_name":"Zrake","first_name":"Jonathan"},{"full_name":"MacFadyen, Andrew","last_name":"MacFadyen","first_name":"Andrew"}],"day":"10","title":"Self-lensing flares from black hole binaries: General-relativistic ray tracing of circumbinary accretion simulations","publication":"Physical Review D","publication_identifier":{"issn":["2470-0010","2470-0029"]},"article_processing_charge":"No","date_created":"2024-09-05T10:04:45Z","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2310.19766"}],"status":"public"},{"quality_controlled":"1","year":"2024","oa":1,"publisher":"American Astronomical Society","language":[{"iso":"eng"}],"date_published":"2024-02-08T00:00:00Z","doi":"10.3847/1538-4357/ad1a17","issue":"1","article_type":"original","extern":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","citation":{"ieee":"J. R. Westernacher-Schneider, J. Zrake, A. MacFadyen, and Z. Haiman, “Eccentric minidisks in accreting binaries,” The Astrophysical Journal, vol. 962, no. 1. American Astronomical Society, 2024.","ama":"Westernacher-Schneider JR, Zrake J, MacFadyen A, Haiman Z. Eccentric minidisks in accreting binaries. The Astrophysical Journal. 2024;962(1). doi:10.3847/1538-4357/ad1a17","apa":"Westernacher-Schneider, J. R., Zrake, J., MacFadyen, A., & Haiman, Z. (2024). Eccentric minidisks in accreting binaries. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ad1a17","short":"J.R. Westernacher-Schneider, J. Zrake, A. MacFadyen, Z. Haiman, The Astrophysical Journal 962 (2024).","mla":"Westernacher-Schneider, John Ryan, et al. “Eccentric Minidisks in Accreting Binaries.” The Astrophysical Journal, vol. 962, no. 1, 76, American Astronomical Society, 2024, doi:10.3847/1538-4357/ad1a17.","ista":"Westernacher-Schneider JR, Zrake J, MacFadyen A, Haiman Z. 2024. Eccentric minidisks in accreting binaries. The Astrophysical Journal. 962(1), 76.","chicago":"Westernacher-Schneider, John Ryan, Jonathan Zrake, Andrew MacFadyen, and Zoltán Haiman. “Eccentric Minidisks in Accreting Binaries.” The Astrophysical Journal. American Astronomical Society, 2024. https://doi.org/10.3847/1538-4357/ad1a17."},"type":"journal_article","volume":962,"month":"02","scopus_import":"1","_id":"17546","publication_identifier":{"issn":["0004-637X","1538-4357"]},"publication":"The Astrophysical Journal","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3847/1538-4357/ad1a17"}],"date_created":"2024-09-05T10:06:09Z","status":"public","article_processing_charge":"No","author":[{"full_name":"Westernacher-Schneider, John Ryan","last_name":"Westernacher-Schneider","first_name":"John Ryan"},{"first_name":"Jonathan","full_name":"Zrake, Jonathan","last_name":"Zrake"},{"first_name":"Andrew","last_name":"MacFadyen","full_name":"MacFadyen, Andrew"},{"first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán","last_name":"Haiman"}],"article_number":"76","oa_version":"Published Version","date_updated":"2024-09-18T09:16:14Z","intvolume":" 962","abstract":[{"lang":"eng","text":"We show that gas disks around the components of an orbiting binary system (so-called minidisks) may be susceptible to a resonant instability that causes the minidisks to become significantly eccentric. Eccentricity is injected by, and also induces, regular impacts between the minidisks at roughly the orbital period of the binary. Such eccentric minidisks are seen in vertically integrated, two-dimensional simulations of a circular, equal-mass binary accreting from a circumbinary gas disk with a Γ-law equation of state. Minidisk eccentricity is suppressed by the use of an isothermal equation of state. However, the instability still operates and can be revealed in a minimal disk-binary simulation by removing the circumbinary disk and feeding the minidisks from the component positions. Minidisk eccentricity is also suppressed when the gravitational softening length is large (≳4% of the binary semimajor axis), suggesting that its absence could be an artifact of widely adopted numerical approximations; a follow-up study in three dimensions with well-resolved, geometrically thin minidisks (aspect ratios ≲0.02) may be needed to assess whether eccentric minidisks can occur in real astrophysical environments. If they can, the electromagnetic signature may be important for discriminating between binary and single black hole scenarios for quasiperiodic oscillations in active galactic nuclei; in turn, this might aid in targeted searches with pulsar timing arrays for individual supermassive black hole binary sources of low-frequency gravitational waves."}],"title":"Eccentric minidisks in accreting binaries","day":"08"},{"extern":"1","article_type":"original","oa":1,"issue":"2","language":[{"iso":"eng"}],"doi":"10.3847/1538-4357/ad11d3","date_published":"2024-01-22T00:00:00Z","publisher":"American Astronomical Society","year":"2024","quality_controlled":"1","_id":"17590","scopus_import":"1","month":"01","citation":{"short":"C. Xin, Z. Haiman, R. Perna, Y. Wang, T. Ryu, The Astrophysical Journal 961 (2024).","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.","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.","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.","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","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."},"publication_status":"published","volume":961,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","status":"public","main_file_link":[{"url":"https://doi.org/10.3847/1538-4357/ad11d3","open_access":"1"}],"date_created":"2024-09-05T12:36:41Z","publication":"The Astrophysical Journal","publication_identifier":{"issn":["0004-637X","1538-4357"]},"title":"“Tidal Peeling Events”: Low-eccentricity tidal disruption of a star by a stellar-mass black hole","day":"22","intvolume":" 961","date_updated":"2024-09-19T12:21:53Z","article_number":"149","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"author":[{"first_name":"Chengcheng","last_name":"Xin","full_name":"Xin, Chengcheng"},{"full_name":"Haiman, Zoltán","last_name":"Haiman","first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36"},{"last_name":"Perna","full_name":"Perna, Rosalba","first_name":"Rosalba"},{"first_name":"Yihan","last_name":"Wang","full_name":"Wang, Yihan"},{"full_name":"Ryu, Taeho","last_name":"Ryu","first_name":"Taeho"}]},{"APC_amount":"2748 EUR","date_published":"2024-10-26T00:00:00Z","publisher":"Springer Nature","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-75387-9_1","oa":1,"file":[{"creator":"esarac","relation":"main_file","success":1,"date_created":"2024-09-05T14:26:02Z","date_updated":"2024-09-05T14:26:02Z","content_type":"application/pdf","file_size":847422,"file_id":"17635","checksum":"43e432f82be376434b358f3dd7a94b71","access_level":"open_access","file_name":"isola24.pdf"},{"date_created":"2025-01-21T14:39:49Z","relation":"main_file","creator":"dernst","success":1,"file_id":"18865","checksum":"6bc04f07bb5612c0e7ea00ac121a69b6","access_level":"open_access","file_name":"2024_LNCS_Chalupa.pdf","date_updated":"2025-01-21T14:39:49Z","content_type":"application/pdf","file_size":1358706}],"page":"3-20","external_id":{"arxiv":["2409.03569"],"isi":["001419008700001"]},"year":"2024","quality_controlled":"1","scopus_import":"1","month":"10","arxiv":1,"tmp":{"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","image":"/images/cc_by.png"},"_id":"17634","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","corr_author":"1","volume":15222,"type":"conference","citation":{"short":"M. Chalupa, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, Springer Nature, 2024, pp. 3–20.","chicago":"Chalupa, Marek, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “QuAK: Quantitative Automata Kit.” In 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, 15222:3–20. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-75387-9_1.","mla":"Chalupa, Marek, et al. “QuAK: Quantitative Automata Kit.” 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, vol. 15222, Springer Nature, 2024, pp. 3–20, doi:10.1007/978-3-031-75387-9_1.","ista":"Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. 2024. QuAK: Quantitative Automata Kit. 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation. ISoLA: International Symposium on Leveraging Applications, LNCS, vol. 15222, 3–20.","ieee":"M. Chalupa, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “QuAK: Quantitative Automata Kit,” in 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, Crete, Greece, 2024, vol. 15222, pp. 3–20.","apa":"Chalupa, M., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2024). QuAK: Quantitative Automata Kit. In 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation (Vol. 15222, pp. 3–20). Crete, Greece: Springer Nature. https://doi.org/10.1007/978-3-031-75387-9_1","ama":"Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. QuAK: Quantitative Automata Kit. In: 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation. Vol 15222. Springer Nature; 2024:3-20. doi:10.1007/978-3-031-75387-9_1"},"publication_status":"published","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. N. Mazzocchi was affiliated with ISTA when his collaboration started.","status":"public","file_date_updated":"2025-01-21T14:39:49Z","date_created":"2024-09-05T14:27:08Z","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031753862"],"issn":["0302-9743"]},"conference":{"location":"Crete, Greece","start_date":"2024-10-27","name":"ISoLA: International Symposium on Leveraging Applications","end_date":"2024-10-31"},"ec_funded":1,"publication":"12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation","related_material":{"record":[{"status":"public","id":"20147","relation":"dissertation_contains"}]},"day":"26","alternative_title":["LNCS"],"ddc":["000"],"title":"QuAK: Quantitative Automata Kit","project":[{"grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"OA_type":"hybrid","has_accepted_license":"1","isi":1,"author":[{"last_name":"Chalupa","full_name":"Chalupa, Marek","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi"},{"first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac","full_name":"Sarac, Naci E"}],"abstract":[{"text":"System behaviors are traditionally evaluated through binary classifications of correctness, which do not suffice for properties involving quantitative aspects of systems and executions. Quantitative automata offer a more nuanced approach, mapping each execution to a real number by incorporating weighted transitions and value functions generalizing acceptance conditions. In this paper, we introduce QuAK, the first tool designed to automate the analysis of quantitative automata. QuAK currently supports a variety of quantitative automaton types, including Inf, Sup, LimInf, LimSup, LimInfAvg, and LimSupAvg automata, and implements decision procedures for problems such as emptiness, universality, inclusion, equivalence, as well as for checking whether an automaton is safe, live, or constant. Additionally, QuAK is able to compute extremal values when possible, construct safety-liveness decompositions, and monitor system behaviors. We demonstrate the effectiveness of QuAK through experiments focusing on the inclusion, constant-function check, and monitoring problems.","lang":"eng"}],"intvolume":" 15222","date_updated":"2026-04-07T12:02:57Z","oa_version":"Published Version"},{"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:17850","date_published":"2024-09-06T00:00:00Z","publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"file_id":"18151","file_name":"louisa_thesis_draft__240904b.pdf","access_level":"open_access","checksum":"d3303724e8d3c91321d71bbad4062048","content_type":"application/pdf","date_updated":"2024-09-27T10:32:33Z","file_size":11219837,"date_created":"2024-09-27T10:32:33Z","relation":"main_file","creator":"lgonzale"},{"date_created":"2024-09-27T10:34:34Z","creator":"lgonzale","relation":"source_file","access_level":"closed","checksum":"22e63f7f9014dffde2af7a47e7d1d014","file_name":"louisa_thesis_draft__240904b.docx","file_id":"18152","file_size":43338677,"date_updated":"2024-09-27T10:34:34Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"year":"2024","page":"89","_id":"17850","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"month":"09","corr_author":"1","type":"dissertation","degree_awarded":"PhD","citation":{"short":"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.","ista":"Gonzalez Somermeyer L. 2024. Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria.","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.","ama":"Gonzalez Somermeyer L. Fitness landscapes of orthologous green fluorescent proteins. 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","ieee":"L. Gonzalez Somermeyer, “Fitness landscapes of orthologous green fluorescent proteins,” Institute of Science and Technology Austria, 2024."},"supervisor":[{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"}],"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","article_processing_charge":"No","status":"public","file_date_updated":"2024-09-27T10:34:34Z","date_created":"2024-09-06T12:57:44Z","related_material":{"record":[{"id":"11448","relation":"part_of_dissertation","status":"public"}],"link":[{"url":"https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks","relation":"software"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"GradSch"},{"_id":"FyKo"}],"has_accepted_license":"1","day":"06","alternative_title":["ISTA Thesis"],"ddc":["570"],"title":"Fitness landscapes of orthologous green fluorescent proteins","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_updated":"2026-04-07T13:25:01Z","oa_version":"Published Version","author":[{"full_name":"Gonzalez Somermeyer, Louisa","last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa"}]},{"intvolume":" 15","date_updated":"2024-11-18T10:47:10Z","oa_version":"Published Version","article_number":"1439","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."}],"author":[{"last_name":"Lee","full_name":"Lee, Woojung","first_name":"Woojung"},{"first_name":"Liang","last_name":"Li","full_name":"Li, Liang"},{"first_name":"María","last_name":"Camarasa-Gómez","full_name":"Camarasa-Gómez, María"},{"first_name":"Daniel","last_name":"Hernangómez-Pérez","full_name":"Hernangómez-Pérez, Daniel"},{"first_name":"Xavier","full_name":"Roy, Xavier","last_name":"Roy"},{"first_name":"Ferdinand","full_name":"Evers, Ferdinand","last_name":"Evers"},{"full_name":"Inkpen, Michael S.","last_name":"Inkpen","first_name":"Michael S."},{"full_name":"Venkataraman, Latha","last_name":"Venkataraman","orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha"}],"OA_type":"gold","title":"Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions","day":"16","publication":"Nature Communications","DOAJ_listed":"1","publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"Yes","status":"public","date_created":"2024-09-06T12:38:44Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-024-45707-z"}],"citation":{"ieee":"W. Lee et al., “Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions,” Nature Communications, vol. 15. Springer Nature, 2024.","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.","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.","short":"W. Lee, L. Li, M. Camarasa-Gómez, D. Hernangómez-Pérez, X. Roy, F. Evers, M.S. Inkpen, L. Venkataraman, Nature Communications 15 (2024)."},"publication_status":"published","type":"journal_article","volume":15,"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"17852","scopus_import":"1","month":"02","pmid":1,"year":"2024","quality_controlled":"1","external_id":{"pmid":["38365892"]},"extern":"1","article_type":"original","oa":1,"date_published":"2024-02-16T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Springer Nature","doi":"10.1038/s41467-024-45707-z"},{"citation":{"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","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.","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.","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.","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.","short":"L. Li, S. Louie, N.M. Orchanian, C. Nuckolls, L. Venkataraman, Journal of the American Chemical Society 146 (2024) 16920–16925."},"publication_status":"published","volume":146,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"17853","month":"06","scopus_import":"1","pmid":1,"year":"2024","quality_controlled":"1","external_id":{"pmid":["38832840"]},"page":"16920-16925","extern":"1","article_type":"original","issue":"24","publisher":"American Chemical Society","date_published":"2024-06-24T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1021/jacs.4c05699","intvolume":" 146","date_updated":"2024-11-18T10:51:21Z","oa_version":"None","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."}],"author":[{"last_name":"Li","full_name":"Li, Liang","first_name":"Liang"},{"first_name":"Shayan","last_name":"Louie","full_name":"Louie, Shayan"},{"first_name":"Nicholas M.","full_name":"Orchanian, Nicholas M.","last_name":"Orchanian"},{"first_name":"Colin","full_name":"Nuckolls, Colin","last_name":"Nuckolls"},{"full_name":"Venkataraman, Latha","last_name":"Venkataraman","orcid":"0000-0002-6957-6089","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"}],"OA_type":"closed access","title":"Long-range gating in single-molecule one-dimensional topological insulators","day":"24","publication":"Journal of the American Chemical Society","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"article_processing_charge":"No","status":"public","date_created":"2024-09-06T12:40:17Z"},{"extern":"1","article_type":"original","issue":"3","date_published":"2024-02-14T00:00:00Z","doi":"10.1021/acs.jchemed.3c01185","publisher":"American Chemical Society","language":[{"iso":"eng"}],"year":"2024","quality_controlled":"1","page":"1319-1324","_id":"17854","month":"02","scopus_import":"1","citation":{"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.","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.","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.","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","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","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."},"publication_status":"published","type":"journal_article","volume":101,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","status":"public","date_created":"2024-09-06T12:43:20Z","publication":"Journal of Chemical Education","publication_identifier":{"issn":["0021-9584"],"eissn":["1938-1328"]},"OA_type":"closed access","title":"Short-form videos as an emerging social media tool for STEM edutainment","day":"14","date_updated":"2024-11-18T10:55:30Z","intvolume":" 101","oa_version":"None","abstract":[{"lang":"eng","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."}],"author":[{"last_name":"Prindle","full_name":"Prindle, Claudia R.","first_name":"Claudia R."},{"last_name":"Orchanian","full_name":"Orchanian, Nicholas M.","first_name":"Nicholas M."},{"last_name":"Venkataraman","full_name":"Venkataraman, Latha","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","orcid":"0000-0002-6957-6089"},{"last_name":"Nuckolls","full_name":"Nuckolls, Colin","first_name":"Colin"}]},{"external_id":{"pmid":["38315038"]},"page":"1931-1935","year":"2024","quality_controlled":"1","issue":"6","publisher":"American Chemical Society","doi":"10.1021/acs.nanolett.3c04207","date_published":"2024-02-05T00:00:00Z","language":[{"iso":"eng"}],"extern":"1","article_type":"letter_note","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A.L. Paoletta, L. Venkataraman, Nano Letters 24 (2024) 1931–1935.","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.","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.","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","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","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."},"publication_status":"published","volume":24,"type":"journal_article","scopus_import":"1","month":"02","pmid":1,"_id":"17855","publication_identifier":{"issn":["1530-6984","1530-6992"]},"publication":"Nano Letters","status":"public","date_created":"2024-09-06T12:44:24Z","article_processing_charge":"No","author":[{"first_name":"Angela L.","full_name":"Paoletta, Angela L.","last_name":"Paoletta"},{"id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha","orcid":"0000-0002-6957-6089","last_name":"Venkataraman","full_name":"Venkataraman, Latha"}],"intvolume":" 24","date_updated":"2024-11-18T10:58:19Z","oa_version":"None","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"}],"title":"Determining transmission characteristics from shot-noise-driven electroluminescence in single-molecule junctions","day":"05"},{"article_processing_charge":"No","date_created":"2024-09-06T12:45:11Z","status":"public","publication":"Journal of the American Chemical Society","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"day":"31","title":"Effective gating in single-molecule junctions through fano resonances","abstract":[{"lang":"eng","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."}],"oa_version":"None","intvolume":" 146","date_updated":"2024-11-18T11:02:24Z","author":[{"full_name":"Prindle, Claudia R.","last_name":"Prindle","first_name":"Claudia R."},{"first_name":"Wanzhuo","full_name":"Shi, Wanzhuo","last_name":"Shi"},{"full_name":"Li, Liang","last_name":"Li","first_name":"Liang"},{"full_name":"Dahl Jensen, Jesper","last_name":"Dahl Jensen","first_name":"Jesper"},{"first_name":"Bo W.","full_name":"Laursen, Bo W.","last_name":"Laursen"},{"first_name":"Michael L.","full_name":"Steigerwald, Michael L.","last_name":"Steigerwald"},{"first_name":"Colin","last_name":"Nuckolls","full_name":"Nuckolls, Colin"},{"orcid":"0000-0002-6957-6089","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","full_name":"Venkataraman, Latha","last_name":"Venkataraman"}],"article_type":"letter_note","extern":"1","date_published":"2024-01-31T00:00:00Z","publisher":"American Chemical Society","language":[{"iso":"eng"}],"doi":"10.1021/jacs.3c14226","issue":"6","quality_controlled":"1","year":"2024","page":"3646-3650","external_id":{"pmid":["38293735"]},"_id":"17856","pmid":1,"scopus_import":"1","month":"01","type":"journal_article","volume":146,"publication_status":"published","citation":{"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.","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.","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.","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"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"}],"oa_version":"None","intvolume":" 24","date_updated":"2024-11-19T12:50:27Z","author":[{"full_name":"Dalmieda, Johnson","last_name":"Dalmieda","first_name":"Johnson"},{"first_name":"Wanzhuo","full_name":"Shi, Wanzhuo","last_name":"Shi"},{"first_name":"Liang","last_name":"Li","full_name":"Li, Liang"},{"orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha","full_name":"Venkataraman, Latha","last_name":"Venkataraman"}],"OA_type":"closed access","day":"04","title":"Solvent-mediated modulation of the Au–S bond in dithiol molecular junctions","publication":"Nano Letters","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"article_processing_charge":"No","date_created":"2024-09-06T12:46:39Z","status":"public","volume":24,"type":"journal_article","publication_status":"published","citation":{"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.","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","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","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.","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.","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.","short":"J. Dalmieda, W. Shi, L. Li, L. Venkataraman, Nano Letters 24 (2024) 703–707."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"17857","pmid":1,"month":"01","scopus_import":"1","quality_controlled":"1","year":"2024","page":"703-707","external_id":{"pmid":["38175934"]},"article_type":"letter_note","extern":"1","date_published":"2024-01-04T00:00:00Z","publisher":"American Chemical Society","language":[{"iso":"eng"}],"doi":"10.1021/acs.nanolett.3c04058","issue":"2"},{"article_type":"original","extern":"1","date_published":"2024-07-18T00:00:00Z","language":[{"iso":"eng"}],"publisher":"American Chemical Society","doi":"10.1021/acs.nanolett.4c02103","issue":"30","quality_controlled":"1","year":"2024","page":"9283-9288","external_id":{"pmid":["39023006"]},"_id":"17859","pmid":1,"scopus_import":"1","month":"07","type":"journal_article","volume":24,"publication_status":"published","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","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","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.","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.","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.","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."},"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","article_processing_charge":"No","date_created":"2024-09-06T12:48:34Z","status":"public","publication":"Nano Letters","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"OA_type":"closed access","day":"18","title":"Impact of solvent electrostatic environment on molecular junctions probed via electrochemical impedance spectroscopy","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."}],"oa_version":"None","intvolume":" 24","date_updated":"2024-11-20T15:24:37Z","author":[{"first_name":"Wanzhuo","full_name":"Shi, Wanzhuo","last_name":"Shi"},{"first_name":"Julia E.","last_name":"Greenwald","full_name":"Greenwald, Julia E."},{"full_name":"Venkataraman, Latha","last_name":"Venkataraman","orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha"}]},{"author":[{"last_name":"Kofler","full_name":"Kofler, Lisa","first_name":"Lisa"},{"first_name":"Lorenz","last_name":"Grundmann","full_name":"Grundmann, Lorenz"},{"first_name":"Magdalena","last_name":"Gerhalter","full_name":"Gerhalter, Magdalena"},{"first_name":"Michael","full_name":"Prattes, Michael","last_name":"Prattes"},{"first_name":"Juliane","last_name":"Merl-Pham","full_name":"Merl-Pham, Juliane"},{"first_name":"Gertrude","full_name":"Zisser, Gertrude","last_name":"Zisser"},{"last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina","first_name":"Irina"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","orcid":"0000-0003-3904-947X","first_name":"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"},{"first_name":"Stefanie M.","full_name":"Hauck, Stefanie M.","last_name":"Hauck"},{"last_name":"Haselbach","full_name":"Haselbach, David","first_name":"David"},{"last_name":"Bergler","full_name":"Bergler, Helmut","first_name":"Helmut"}],"oa_version":"Published Version","article_number":"7511","date_updated":"2025-09-08T09:13:01Z","intvolume":" 15","abstract":[{"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.","lang":"eng"}],"title":"The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation","ddc":["570"],"day":"29","has_accepted_license":"1","OA_type":"gold","isi":1,"department":[{"_id":"EM-Fac"}],"DOAJ_listed":"1","publication_identifier":{"eissn":["2041-1723"]},"publication":"Nature Communications","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_created":"2024-09-08T22:01:10Z","file_date_updated":"2024-09-09T08:56:12Z","status":"public","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.","article_processing_charge":"Yes","OA_place":"publisher","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","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).","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.","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.","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.","ieee":"L. Kofler et al., “The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation,” Nature Communications, vol. 15. Springer Nature, 2024.","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","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"},"type":"journal_article","volume":15,"pmid":1,"scopus_import":"1","month":"08","_id":"17885","tmp":{"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","image":"/images/cc_by.png"},"external_id":{"isi":["001457895200001"],"pmid":["39209816"]},"quality_controlled":"1","year":"2024","file":[{"file_id":"17946","file_name":"2024_NatureComm_Kofler.pdf","checksum":"7c044538a47182c826d1b526c52958a2","access_level":"open_access","content_type":"application/pdf","date_updated":"2024-09-09T08:56:12Z","file_size":3735024,"date_created":"2024-09-09T08:56:12Z","creator":"dernst","relation":"main_file","success":1}],"oa":1,"doi":"10.1038/s41467-024-51754-3","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_published":"2024-08-29T00:00:00Z","article_type":"original"},{"language":[{"iso":"eng"}],"publisher":"Elsevier","date_published":"2024-12-01T00:00:00Z","doi":"10.1016/j.neunet.2024.106589","oa":1,"file":[{"date_created":"2025-01-13T08:26:08Z","creator":"dernst","relation":"main_file","success":1,"file_id":"18825","file_name":"2024_NeuralNetworks_Zendrikov.pdf","checksum":"6a194323234e01d4ae725f674529cdb1","access_level":"open_access","content_type":"application/pdf","date_updated":"2025-01-13T08:26:08Z","file_size":6162281}],"article_type":"original","external_id":{"isi":["001316474600001"],"pmid":["39217864"]},"year":"2024","quality_controlled":"1","month":"12","scopus_import":"1","pmid":1,"tmp":{"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","image":"/images/cc_by.png"},"_id":"17886","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","type":"journal_article","corr_author":"1","volume":180,"citation":{"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","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","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.","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.","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.","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.","short":"D. Zendrikov, A. Paraskevov, Neural Networks 180 (2024)."},"publication_status":"published","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).","status":"public","file_date_updated":"2025-01-13T08:26:08Z","date_created":"2024-09-08T22:01:10Z","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1879-2782"],"issn":["0893-6080"]},"ec_funded":1,"publication":"Neural Networks","day":"01","ddc":["570"],"title":"The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks","project":[{"name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020","grant_number":"819603"}],"department":[{"_id":"TiVo"}],"OA_type":"hybrid","has_accepted_license":"1","isi":1,"author":[{"first_name":"Dmitrii","last_name":"Zendrikov","full_name":"Zendrikov, Dmitrii"},{"last_name":"Paraskevov","full_name":"Paraskevov, Alexander","id":"d05e3c56-9262-11ed-9231-be692464e5ac","first_name":"Alexander"}],"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."}],"date_updated":"2025-09-08T09:12:20Z","intvolume":" 180","oa_version":"Published Version","article_number":"106589"},{"tmp":{"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","image":"/images/cc_by.png"},"_id":"17887","arxiv":1,"pmid":1,"month":"09","scopus_import":"1","publication_status":"published","citation":{"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","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.","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.","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.","short":"H. Abels, J.L. Fischer, M. Moser, Archive for Rational Mechanics and Analysis 248 (2024)."},"volume":248,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","file":[{"date_created":"2024-09-09T08:43:32Z","creator":"dernst","relation":"main_file","success":1,"file_id":"17938","access_level":"open_access","checksum":"98493a05b84e4513b6394dfad4851ddf","file_name":"2024_ArchiveRatAnalysis_Abels.pdf","date_updated":"2024-09-09T08:43:32Z","content_type":"application/pdf","file_size":811131}],"oa":1,"doi":"10.1007/s00205-024-02020-9","publisher":"Springer Nature","date_published":"2024-09-03T00:00:00Z","language":[{"iso":"eng"}],"issue":"5","quality_controlled":"1","year":"2024","external_id":{"pmid":["39239088"],"arxiv":["2311.02997"],"isi":["001305530600001"]},"has_accepted_license":"1","isi":1,"department":[{"_id":"JuFi"}],"project":[{"name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819","call_identifier":"H2020"}],"title":"Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system","ddc":["510"],"day":"03","oa_version":"Published Version","article_number":"77","date_updated":"2025-09-08T09:11:41Z","intvolume":" 248","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."}],"author":[{"full_name":"Abels, Helmut","last_name":"Abels","first_name":"Helmut"},{"full_name":"Fischer, Julian L","last_name":"Fischer","orcid":"0000-0002-0479-558X","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Moser, Maximilian","last_name":"Moser","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c","first_name":"Maximilian"}],"article_processing_charge":"Yes (via OA deal)","date_created":"2024-09-08T22:01:10Z","file_date_updated":"2024-09-09T08:43:32Z","status":"public","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":"Archive for Rational Mechanics and Analysis","ec_funded":1,"publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]}},{"citation":{"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.","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","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","short":"G. Pocull Belles, C. Baskett, N.H. Barton, Landscape Ecology 39 (2024).","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.","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.","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."},"publication_status":"published","volume":39,"corr_author":"1","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"17888","tmp":{"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","image":"/images/cc_by.png"},"scopus_import":"1","month":"09","year":"2024","quality_controlled":"1","external_id":{"isi":["001304011900001"]},"article_type":"original","oa":1,"file":[{"access_level":"open_access","checksum":"2e1cbc320ec1b4447a5a8562a90bcbc3","file_name":"2024_LandscapeEcology_Pocull.pdf","file_id":"18054","file_size":1494987,"date_updated":"2024-09-11T07:14:03Z","content_type":"application/pdf","date_created":"2024-09-11T07:14:03Z","success":1,"relation":"main_file","creator":"dernst"}],"issue":"9","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_published":"2024-09-01T00:00:00Z","doi":"10.1007/s10980-024-01899-9","date_updated":"2025-09-08T09:20:11Z","intvolume":" 39","oa_version":"Published Version","article_number":"172","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."}],"author":[{"last_name":"Pocull Belles","full_name":"Pocull Belles, Guillem","id":"54359172-700c-11ef-a103-c1d91ceac6d6","first_name":"Guillem"},{"last_name":"Baskett","full_name":"Baskett, Carina","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"}],"isi":1,"has_accepted_license":"1","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"}],"department":[{"_id":"NiBa"}],"title":"Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects","day":"01","ddc":["570"],"publication":"Landscape Ecology","ec_funded":1,"publication_identifier":{"eissn":["1572-9761"],"issn":["0921-2973"]},"article_processing_charge":"Yes (via OA deal)","file_date_updated":"2024-09-11T07:14:03Z","status":"public","date_created":"2024-09-08T22:01:11Z","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."},{"day":"01","ddc":["520"],"title":"Anatomy of an ionized bubble: NIRCam grism spectroscopy of the z = 6.6 double-peaked Lyman- α emitter COLA1 and its environment","department":[{"_id":"JoMa"}],"isi":1,"has_accepted_license":"1","author":[{"first_name":"Alberto","full_name":"Torralba-Torregrosa, Alberto","last_name":"Torralba-Torregrosa"},{"full_name":"Matthee, Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J"},{"full_name":"Naidu, Rohan P.","last_name":"Naidu","first_name":"Rohan P."},{"first_name":"Ruari","last_name":"Mackenzie","full_name":"Mackenzie, Ruari"},{"first_name":"Gabriele","last_name":"Pezzulli","full_name":"Pezzulli, Gabriele"},{"first_name":"Anne","last_name":"Hutter","full_name":"Hutter, Anne"},{"last_name":"Arnalte-Mur","full_name":"Arnalte-Mur, Pablo","first_name":"Pablo"},{"last_name":"Gurung-López","full_name":"Gurung-López, Siddhartha","first_name":"Siddhartha"},{"first_name":"Sandro","full_name":"Tacchella, Sandro","last_name":"Tacchella"},{"last_name":"Oesch","full_name":"Oesch, Pascal","first_name":"Pascal"},{"first_name":"Daichi","full_name":"Kashino, Daichi","last_name":"Kashino"},{"full_name":"Conroy, Charlie","last_name":"Conroy","first_name":"Charlie"},{"first_name":"David","full_name":"Sobral, David","last_name":"Sobral"}],"abstract":[{"text":"The increasingly neutral intergalactic gas at z > 6 impacts the Lyman-α (Lyα) flux observed from galaxies. One luminous galaxy, COLA1, stands out because of its unique double-peaked Lyα line at z = 6.6, unseen in any simulation of reionization. Here, we present JWST/NIRCam wide-field slitless spectroscopy in a 21 arcmin2 field centered on COLA1. We find 141 galaxies spectroscopically selected through the [O III] doublet at 5.35 < z < 6.95, with 40 of these sources showing Hβ. For COLA1, we additionally detect [O III]4363 as well as Hγ. We measure a systemic redshift of z = 6.5917 for COLA1, confirming the classical double-peak nature of the Lyα profile. This implies that it resides in a highly ionized bubble and that it is leaking ionizing photons with a high escape fraction of fesc(LyC) = 20–50%, making it a prime laboratory to study Lyman continuum escape in the Epoch of Reionization. COLA1 shows all the signs of a prolific ionizer with a Lyα escape fraction of 81 ± 5%, Balmer decrement indicating no dust, a steep UV slope (βUV = −3.2 ± 0.4), and a star-formation surface density ≳10× that of typical galaxies at similar redshift. We detect five galaxies in COLA1’s close environment (Δz < 0.02). Exploiting the high spectroscopic completeness inherent to grism surveys, and using mock simulations that fully mimic the selection function, we show that the number of detected companions is very typical for a normal similarly UV-bright (MUV ∼ −21.3) galaxy – that is, the ionized bubble around COLA1 is unlikely to be due to an excessively large over-density. Instead, the measured ionizing properties suggest that COLA1 by itself might be powering the bubble required to explain its double-peaked Lyα profile (Rion ≈ 0.7 pMpc), with only minor contributions from detected neighbors (−19.5 ≲ MUV ≲ −17.5).","lang":"eng"}],"date_updated":"2025-09-08T09:20:52Z","intvolume":" 689","oa_version":"Published Version","article_number":"A44","acknowledgement":"The authors acknowledge the financial support from the MICIU with funding from the European Union NextGenerationEU and Generalitat Valenciana in the call Programa de Planes Complementarios de I+D+i (PRTR 2022) Project (VAL-JPAS), reference ASFAE/2022/025. This work has been funded by project PID2019-109592GBI00/AEI/10.13039/501100011033 from the Spanish Ministerio de Ciencia e Innovación (MCIN)-Agencia Estatal de Investigación, by the Project of Excellence Prometeo/2020/085 from the Conselleria d’Innovació Universitats, Ciència i Societat Digital de la Generalitat Valenciana. It has also be funded by the Project of Excellence Prometeo/2020/085 from the Conselleria d’Educació, Universitats, i Ocupació de la Generalitat Valenciana. Funded by the European Union (ERC, AGENTS, 101076224). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. ST acknowledges support by the Royal Society Research Grant G125142. AH acknowledges support by the VILLUM FONDEN under grant 37459. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant DNRF140. We acknowledge funding from JWST program GO-1933. Support for this work was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with program # 1933. The specific observations analyzed can be accessed via https://doi.org/10.17909/s9ht-7n34.","status":"public","file_date_updated":"2024-09-11T07:35:00Z","date_created":"2024-09-08T22:01:11Z","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"publication":"Astronomy and Astrophysics","scopus_import":"1","month":"09","arxiv":1,"tmp":{"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","image":"/images/cc_by.png"},"_id":"17889","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","volume":689,"citation":{"ama":"Torralba-Torregrosa A, Matthee JJ, Naidu RP, et al. Anatomy of an ionized bubble: NIRCam grism spectroscopy of the z = 6.6 double-peaked Lyman- α emitter COLA1 and its environment. Astronomy and Astrophysics. 2024;689. doi:10.1051/0004-6361/202450318","apa":"Torralba-Torregrosa, A., Matthee, J. J., Naidu, R. P., Mackenzie, R., Pezzulli, G., Hutter, A., … Sobral, D. (2024). Anatomy of an ionized bubble: NIRCam grism spectroscopy of the z = 6.6 double-peaked Lyman- α emitter COLA1 and its environment. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202450318","ieee":"A. Torralba-Torregrosa et al., “Anatomy of an ionized bubble: NIRCam grism spectroscopy of the z = 6.6 double-peaked Lyman- α emitter COLA1 and its environment,” Astronomy and Astrophysics, vol. 689. EDP Sciences, 2024.","mla":"Torralba-Torregrosa, Alberto, et al. “Anatomy of an Ionized Bubble: NIRCam Grism Spectroscopy of the z = 6.6 Double-Peaked Lyman- α Emitter COLA1 and Its Environment.” Astronomy and Astrophysics, vol. 689, A44, EDP Sciences, 2024, doi:10.1051/0004-6361/202450318.","chicago":"Torralba-Torregrosa, Alberto, Jorryt J Matthee, Rohan P. Naidu, Ruari Mackenzie, Gabriele Pezzulli, Anne Hutter, Pablo Arnalte-Mur, et al. “Anatomy of an Ionized Bubble: NIRCam Grism Spectroscopy of the z = 6.6 Double-Peaked Lyman- α Emitter COLA1 and Its Environment.” Astronomy and Astrophysics. EDP Sciences, 2024. https://doi.org/10.1051/0004-6361/202450318.","ista":"Torralba-Torregrosa A, Matthee JJ, Naidu RP, Mackenzie R, Pezzulli G, Hutter A, Arnalte-Mur P, Gurung-López S, Tacchella S, Oesch P, Kashino D, Conroy C, Sobral D. 2024. Anatomy of an ionized bubble: NIRCam grism spectroscopy of the z = 6.6 double-peaked Lyman- α emitter COLA1 and its environment. Astronomy and Astrophysics. 689, A44.","short":"A. Torralba-Torregrosa, J.J. Matthee, R.P. Naidu, R. Mackenzie, G. Pezzulli, A. Hutter, P. Arnalte-Mur, S. Gurung-López, S. Tacchella, P. Oesch, D. Kashino, C. Conroy, D. Sobral, Astronomy and Astrophysics 689 (2024)."},"publication_status":"published","date_published":"2024-09-01T00:00:00Z","publisher":"EDP Sciences","doi":"10.1051/0004-6361/202450318","language":[{"iso":"eng"}],"oa":1,"file":[{"file_id":"18055","file_name":"2024_AstronomyAstrophysics_TorralbaTorregrosa.pdf","checksum":"a6c0df287c75e8929db9f42badeac859","access_level":"open_access","content_type":"application/pdf","date_updated":"2024-09-11T07:35:00Z","file_size":6225413,"date_created":"2024-09-11T07:35:00Z","creator":"dernst","relation":"main_file","success":1}],"article_type":"original","external_id":{"arxiv":["2404.10040"],"isi":["001303205700016"]},"year":"2024","quality_controlled":"1"},{"article_type":"original","doi":"10.3390/e26080637","date_published":"2024-08-01T00:00:00Z","publisher":"MDPI","language":[{"iso":"eng"}],"issue":"8","file":[{"date_created":"2024-09-09T09:01:12Z","success":1,"relation":"main_file","creator":"dernst","file_name":"2024_Entropy_Edelsbrunner.pdf","checksum":"624a9e2c5b49d6c38b88b0f675467ba3","access_level":"open_access","file_id":"17948","file_size":8025139,"content_type":"application/pdf","date_updated":"2024-09-09T09:01:12Z"}],"oa":1,"quality_controlled":"1","year":"2024","external_id":{"isi":["001305543500001"],"pmid":["39202107"]},"tmp":{"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","image":"/images/cc_by.png"},"_id":"17891","pmid":1,"scopus_import":"1","month":"08","type":"journal_article","volume":26,"publication_status":"published","citation":{"mla":"Edelsbrunner, Herbert, et al. “Understanding Higher-Order Interactions in Information Space.” Entropy, vol. 26, no. 8, 637, MDPI, 2024, doi:10.3390/e26080637.","chicago":"Edelsbrunner, Herbert, Katharina Ölsböck, and Hubert Wagner. “Understanding Higher-Order Interactions in Information Space.” Entropy. MDPI, 2024. 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.","short":"H. Edelsbrunner, K. Ölsböck, H. Wagner, Entropy 26 (2024).","apa":"Edelsbrunner, H., Ölsböck, K., & Wagner, H. (2024). Understanding higher-order interactions in information space. Entropy. MDPI. https://doi.org/10.3390/e26080637","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."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes","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.","date_created":"2024-09-08T22:01:11Z","file_date_updated":"2024-09-09T09:01:12Z","status":"public","related_material":{"link":[{"relation":"software","url":"https://git.ista.ac.at/katharina.oelsboeck/wrap_2_3-public/"}]},"publication":"Entropy","publication_identifier":{"eissn":["1099-4300"]},"department":[{"_id":"HeEd"}],"isi":1,"has_accepted_license":"1","ddc":["510"],"day":"01","title":"Understanding higher-order interactions in information space","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"}],"article_number":"637","oa_version":"Published Version","date_updated":"2025-09-08T09:13:44Z","intvolume":" 26","author":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"orcid":"0000-0002-4672-8297","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","first_name":"Katharina","full_name":"Ölsböck, Katharina","last_name":"Ölsböck"},{"last_name":"Wagner","full_name":"Wagner, Hubert","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}]},{"publication":"Physical Review E","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","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.","date_created":"2024-09-08T22:01:12Z","status":"public","file_date_updated":"2024-09-11T05:59:36Z","abstract":[{"lang":"eng","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."}],"article_number":"024404","oa_version":"Published Version","intvolume":" 110","date_updated":"2025-09-08T09:17:18Z","author":[{"id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","first_name":"Fabrizio","full_name":"Olmeda, Fabrizio","last_name":"Olmeda"},{"first_name":"Steffen","full_name":"Rulands, Steffen","last_name":"Rulands"}],"department":[{"_id":"EdHa"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"isi":1,"has_accepted_license":"1","ddc":["530"],"day":"01","title":"Field theory of enzyme-substrate systems with restricted long-range interactions","quality_controlled":"1","year":"2024","external_id":{"pmid":["39294986"],"isi":["001299670100004"]},"article_type":"original","date_published":"2024-08-01T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.110.024404","publisher":"American Physical Society","issue":"2","file":[{"date_created":"2024-09-11T05:59:36Z","success":1,"creator":"dernst","relation":"main_file","file_name":"2024_PhysReviewE_Olmeda.pdf","checksum":"67fc2cc8eee3155e5c3b7380307d8284","access_level":"open_access","file_id":"18053","file_size":445696,"content_type":"application/pdf","date_updated":"2024-09-11T05:59:36Z"}],"oa":1,"corr_author":"1","volume":110,"type":"journal_article","publication_status":"published","citation":{"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.","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","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","short":"F. Olmeda, S. Rulands, Physical Review E 110 (2024).","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.","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.","ista":"Olmeda F, Rulands S. 2024. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 110(2), 024404."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"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","image":"/images/cc_by.png"},"_id":"17892","pmid":1,"scopus_import":"1","month":"08"}]