--- OA_place: publisher _id: '17490' abstract: - lang: eng text: "Deep learning is essential in numerous applications nowadays, with many recent advancements made possible by training very large models. Despite their broad applicability, training neural networks is often time-intensive, and it is usually impractical to manage large models and datasets on a single machine. To address these issues, distributed deep learning training has become increasingly important. However, distributed training requires synchronization among nodes, and the mini-batch stochastic gradient descent algorithm places a significant load on network connections. A possible solution to tackle the synchronization bottleneck is to reduce a message size by lossy compression.\r\n\r\nIn this thesis, we investigate systems and algorithmic approaches to communication compression during training. From the systems perspective, we demonstrate that a common approach of expensive hardware overprovisioning can be replaced through a thorough system design. We introduce a framework that introduces efficient software support for compressed communication in machine learning applications, applicable to both multi-GPU single-node training and larger-scale multi-node training. Our framework integrates with popular ML frameworks, providing up to 3x speedups for multi-GPU nodes based on commodity hardware and order-of-magnitude improvements in the multi-node setting, with negligible impact on accuracy.\r\n\r\nAlso, we consider an application of our framework to different communication schemes, such as Fully Sharded Data Parallel. We provide strong convergence guarantees for the compression in such a setup. Empirical validation shows that our method preserves model accuracy for GPT-family models with up to 1.3 billion parameters, while completely removing the communication bottlenecks of non-compressed alternatives, providing up to 2.2x speedups end-to-end.\r\n\r\nFrom the algorithmic side, we propose a general framework that dynamically adjusts the degree of compression across a model's layers during training. This approach enhances overall compression and results in significant speedups without compromising accuracy. Our algorithm utilizes an adaptive algorithm that automatically selects the optimal compression parameters for model layers, ensuring the best compression ratio while adhering to an error constraint. Our method is effective across all existing families of compression methods. It achieves up to 2.5x faster training and up to a 5x improvement in compression compared to efficient implementations of current approaches. Additionally, LGreCo can complement existing adaptive algorithms.\r\n" acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Ilia full_name: Markov, Ilia id: D0CF4148-C985-11E9-8066-0BDEE5697425 last_name: Markov citation: ama: 'Markov I. Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective. 2024. doi:10.15479/at:ista:17490' apa: 'Markov, I. (2024). Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17490' chicago: 'Markov, Ilia. “Communication-Efficient Distributed Training of Deep Neural Networks : An Algorithms and Systems Perspective.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17490.' ieee: 'I. Markov, “Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective,” Institute of Science and Technology Austria, 2024.' ista: 'Markov I. 2024. Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective. Institute of Science and Technology Austria.' mla: 'Markov, Ilia. Communication-Efficient Distributed Training of Deep Neural Networks : An Algorithms and Systems Perspective. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17490.' short: 'I. Markov, Communication-Efficient Distributed Training of Deep Neural Networks : An Algorithms and Systems Perspective, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-09-04T08:51:11Z date_published: 2024-09-04T00:00:00Z date_updated: 2026-06-18T17:55:23Z day: '04' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: DaAl doi: 10.15479/at:ista:17490 ec_funded: 1 file: - access_level: closed checksum: 77609f4835d2730e46fa0d42d9134ed9 content_type: application/x-zip-compressed creator: imarkov date_created: 2024-09-04T08:35:35Z date_updated: 2024-09-04T08:35:35Z file_id: '17491' file_name: Thesis.zip file_size: 43327753 relation: source_file - access_level: open_access checksum: 9e68f7217570f756ceb8f70b980938cd content_type: application/pdf creator: imarkov date_created: 2024-09-04T08:36:06Z date_updated: 2024-09-04T08:36:06Z file_id: '17492' file_name: Thesis_final_version_pdfa2.pdf file_size: 2756082 relation: main_file success: 1 file_date_updated: 2024-09-04T08:36:06Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '09' oa: 1 oa_version: Published Version page: '102' project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14461' relation: part_of_dissertation status: public - id: '12780' relation: part_of_dissertation status: public - id: '17456' relation: part_of_dissertation status: public status: public supervisor: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: 'Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- APC_amount: 4863,6 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17493' abstract: - lang: eng text: Estimating global properties of many-body quantum systems such as entropy or bipartite entanglement is a notoriously difficult task, typically requiring a number of measurements or classical postprocessing resources growing exponentially in the system size. In this work, we address the problem of estimating global entropies and mixed-state entanglement via partial-transposed (PT) moments and show that efficient estimation strategies exist under the assumption that all the spatial correlation lengths are finite. Focusing on one-dimensional systems, we identify a set of approximate factorization conditions (AFCs) on the system density matrix, which allow us to reconstruct entropies and PT moments from information on local subsystems. This identification yields a simple and efficient strategy for entropy and entanglement estimation. Our method could be implemented in different ways, depending on how information on local subsystems is extracted. Focusing on randomized measurements providing a practical and common measurement scheme, we prove that our protocol requires only polynomially many measurements and postprocessing operations, assuming that the state to be measured satisfies the AFCs. We prove that the AFCs hold for finite-depth quantum-circuit states and translation-invariant matrix-product density operators and provide numerical evidence that they are satisfied in more general, physically interesting cases, including thermal states of local Hamiltonians. We argue that our method could be practically useful to detect bipartite mixed-state entanglement for large numbers of qubits available in today’s quantum platforms. acknowledgement: B. V. acknowledges funding from the Austrian Science Foundation (Grant No. FWF, P 32597 N), from the French National Research Agency via the JCJC project QRand (Grant No. ANR-20-CE47-0005), and via the research programs Plan France 2030 EPIQ (Grant No. ANR-22-PETQ-0007), QUBITAF (Grant No. ANR-22-PETQ-0004), and HQI (Grant No. ANR-22-PNCQ-0002). M. L. and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). M. S. acknowledges the hospitality of KITP supported in part by the National Science Foundation under Grants No. NSF PHY-1748958 and No. NSF PHY-2309135. J. I. C. is supported by the Hightech Agenda Bayern Plus through the Munich Quantum Valley and the German Federal Ministry of Education and Research through EQUAHUMO (Grant No. 13N16066). P. Z. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 101113690 (PASQuanS2.1). article_number: '031035' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Benoît full_name: Vermersch, Benoît last_name: Vermersch - first_name: Marko full_name: Ljubotina, Marko id: F75EE9BE-5C90-11EA-905D-16643DDC885E last_name: Ljubotina orcid: 0000-0003-0038-7068 - first_name: J. Ignacio full_name: Cirac, J. Ignacio last_name: Cirac - first_name: Peter full_name: Zoller, Peter last_name: Zoller - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Lorenzo full_name: Piroli, Lorenzo last_name: Piroli citation: ama: Vermersch B, Ljubotina M, Cirac JI, Zoller P, Serbyn M, Piroli L. Many-body entropies and entanglement from polynomially many local measurements. Physical Review X. 2024;14(3). doi:10.1103/physrevx.14.031035 apa: Vermersch, B., Ljubotina, M., Cirac, J. I., Zoller, P., Serbyn, M., & Piroli, L. (2024). Many-body entropies and entanglement from polynomially many local measurements. Physical Review X. American Physical Society. https://doi.org/10.1103/physrevx.14.031035 chicago: Vermersch, Benoît, Marko Ljubotina, J. Ignacio Cirac, Peter Zoller, Maksym Serbyn, and Lorenzo Piroli. “Many-Body Entropies and Entanglement from Polynomially Many Local Measurements.” Physical Review X. American Physical Society, 2024. https://doi.org/10.1103/physrevx.14.031035. ieee: B. Vermersch, M. Ljubotina, J. I. Cirac, P. Zoller, M. Serbyn, and L. Piroli, “Many-body entropies and entanglement from polynomially many local measurements,” Physical Review X, vol. 14, no. 3. American Physical Society, 2024. ista: Vermersch B, Ljubotina M, Cirac JI, Zoller P, Serbyn M, Piroli L. 2024. Many-body entropies and entanglement from polynomially many local measurements. Physical Review X. 14(3), 031035. mla: Vermersch, Benoît, et al. “Many-Body Entropies and Entanglement from Polynomially Many Local Measurements.” Physical Review X, vol. 14, no. 3, 031035, American Physical Society, 2024, doi:10.1103/physrevx.14.031035. short: B. Vermersch, M. Ljubotina, J.I. Cirac, P. Zoller, M. Serbyn, L. Piroli, Physical Review X 14 (2024). date_created: 2024-09-04T18:57:11Z date_published: 2024-08-26T00:00:00Z date_updated: 2025-09-08T09:04:14Z day: '26' ddc: - '530' department: - _id: MaSe doi: 10.1103/physrevx.14.031035 ec_funded: 1 external_id: arxiv: - '2311.08108' isi: - '001299667100002' file: - access_level: open_access checksum: 1b114acc89025120727200681e4e9074 content_type: application/pdf creator: cchlebak date_created: 2024-09-05T09:39:00Z date_updated: 2024-09-05T09:39:00Z file_id: '17532' file_name: 2024_PhysRevX_Vermersch.pdf file_size: 1408836 relation: main_file success: 1 file_date_updated: 2024-09-05T09:39:00Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '3' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Physical Review X publication_identifier: issn: - 2160-3308 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Many-body entropies and entanglement from polynomially many local measurements tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 14 year: '2024' ... --- OA_place: publisher OA_type: free access _id: '17494' acknowledgement: I would like to thank K Kiernan for insightful comments and feedback. J P K Bravo is supported by IST Austria. article_processing_charge: No article_type: letter_note author: - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 citation: ama: 'Bravo JPK. Anti-plasmid immunity: A key to pathogen success? Future Microbiology. 2024;19(15):1269-1272. doi:10.1080/17460913.2024.2389720' apa: 'Bravo, J. P. K. (2024). Anti-plasmid immunity: A key to pathogen success? Future Microbiology. Taylor & Francis. https://doi.org/10.1080/17460913.2024.2389720' chicago: 'Bravo, Jack Peter Kelly. “Anti-Plasmid Immunity: A Key to Pathogen Success?” Future Microbiology. Taylor & Francis, 2024. https://doi.org/10.1080/17460913.2024.2389720.' ieee: 'J. P. K. Bravo, “Anti-plasmid immunity: A key to pathogen success?,” Future Microbiology, vol. 19, no. 15. Taylor & Francis, pp. 1269–1272, 2024.' ista: 'Bravo JPK. 2024. Anti-plasmid immunity: A key to pathogen success? Future Microbiology. 19(15), 1269–1272.' mla: 'Bravo, Jack Peter Kelly. “Anti-Plasmid Immunity: A Key to Pathogen Success?” Future Microbiology, vol. 19, no. 15, Taylor & Francis, 2024, pp. 1269–72, doi:10.1080/17460913.2024.2389720.' short: J.P.K. Bravo, Future Microbiology 19 (2024) 1269–1272. corr_author: '1' date_created: 2024-09-05T07:32:00Z date_published: 2024-10-01T00:00:00Z date_updated: 2026-06-18T17:56:59Z day: '01' ddc: - '570' department: - _id: JaBr doi: 10.1080/17460913.2024.2389720 external_id: isi: - '001306115400001' pmid: - '39230568' has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '15' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1080/17460913.2024.2389720 month: '10' oa: 1 oa_version: Published Version page: 1269-1272 pmid: 1 publication: Future Microbiology publication_identifier: eissn: - 1746-0921 issn: - 1746-0913 publication_status: published publisher: Taylor & Francis quality_controlled: '1' scopus_import: '1' status: public title: 'Anti-plasmid immunity: A key to pathogen success?' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2024' ... --- _id: '17495' abstract: - lang: eng text: Rust is a modern systems programming language whose ownership-based type system statically guarantees memory safety, making it particularly well-suited to the domain of safety-critical systems. In recent years, a wellspring of automated deductive verification tools have emerged for establishing functional correctness of Rust code. However, none of the previous tools produce foundational proofs (machine-checkable in a general-purpose proof assistant), and all of them are restricted to the safe fragment of Rust. This is a problem because the vast majority of Rust programs make use of unsafe code at critical points, such as in the implementation of widely-used APIs. We propose RefinedRust, a refinement type system—proven sound in the Coq proof assistant—with the goal of establishing foundational semi-automated functional correctness verification of both safe and unsafe Rust code. We have developed a prototype verification tool implementing RefinedRust. Our tool translates Rust code (with user annotations) into a model of Rust embedded in Coq, and then checks its adherence to the RefinedRust type system using separation logic automation in Coq. All proofs generated by RefinedRust are checked by the Coq proof assistant, so the automation and type system do not have to be trusted. We evaluate the effectiveness of RefinedRust by verifying a variant of Rust’s Vec implementation that involves intricate reasoning about unsafe pointer-manipulating code. article_processing_charge: No article_type: original author: - first_name: Lennard full_name: Gäher, Lennard last_name: Gäher - first_name: Michael Joachim full_name: Sammler, Michael Joachim id: 510d3901-2a03-11ee-914d-d9ae9011f0a7 last_name: Sammler - first_name: Ralf full_name: Jung, Ralf last_name: Jung - first_name: Robbert full_name: Krebbers, Robbert last_name: Krebbers - first_name: Derek full_name: Dreyer, Derek last_name: Dreyer citation: ama: 'Gäher L, Sammler MJ, Jung R, Krebbers R, Dreyer D. RefinedRust: A type system for high-assurance verification of rust programs. Proceedings of the ACM on Programming Languages. 2024;8(PLDI):1115-1139. doi:10.1145/3656422' apa: 'Gäher, L., Sammler, M. J., Jung, R., Krebbers, R., & Dreyer, D. (2024). RefinedRust: A type system for high-assurance verification of rust programs. Proceedings of the ACM on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3656422' chicago: 'Gäher, Lennard, Michael Joachim Sammler, Ralf Jung, Robbert Krebbers, and Derek Dreyer. “RefinedRust: A Type System for High-Assurance Verification of Rust Programs.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2024. https://doi.org/10.1145/3656422.' ieee: 'L. Gäher, M. J. Sammler, R. Jung, R. Krebbers, and D. Dreyer, “RefinedRust: A type system for high-assurance verification of rust programs,” Proceedings of the ACM on Programming Languages, vol. 8, no. PLDI. Association for Computing Machinery, pp. 1115–1139, 2024.' ista: 'Gäher L, Sammler MJ, Jung R, Krebbers R, Dreyer D. 2024. RefinedRust: A type system for high-assurance verification of rust programs. Proceedings of the ACM on Programming Languages. 8(PLDI), 1115–1139.' mla: 'Gäher, Lennard, et al. “RefinedRust: A Type System for High-Assurance Verification of Rust Programs.” Proceedings of the ACM on Programming Languages, vol. 8, no. PLDI, Association for Computing Machinery, 2024, pp. 1115–39, doi:10.1145/3656422.' short: L. Gäher, M.J. Sammler, R. Jung, R. Krebbers, D. Dreyer, Proceedings of the ACM on Programming Languages 8 (2024) 1115–1139. date_created: 2024-09-05T07:52:27Z date_published: 2024-06-20T00:00:00Z date_updated: 2024-09-10T07:16:49Z day: '20' doi: 10.1145/3656422 extern: '1' intvolume: ' 8' issue: PLDI language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/3656422 month: '06' oa: 1 oa_version: Published Version page: 1115-1139 publication: Proceedings of the ACM on Programming Languages publication_identifier: issn: - 2475-1421 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'RefinedRust: A type system for high-assurance verification of rust programs' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 8 year: '2024' ... --- _id: '17497' abstract: - lang: eng text: 'Over the past two decades, there has been a great deal of progress on verification of full functional correctness of programs using separation logic, sometimes even producing “foundational” proofs in proof assistants like Coq. Unfortunately, even though existing approaches to this problem provide significant support for automated verification, they still incur a significant specification overhead: the user must supply the specification against which the program is verified, and the specification may be long, complex, or tedious to formulate. In this paper, we introduce Quiver, the first technique for inferring functional correctness specifications in separation logic while simultaneously verifying foundationally that they are correct. To guide Quiver towards the final specification, we take hints from the user in the form of a specification sketch, and then complete the sketch using inference. To do so, Quiver introduces a new abductive deductive verification technique, which integrates ideas from abductive inference (for specification inference) together with deductive separation logic automation (for foundational verification). The result is that users have to provide some guidance, but significantly less than with traditional deductive verification techniques based on separation logic. We have evaluated Quiver on a range of case studies, including code from popular open-source libraries.' article_processing_charge: No article_type: original author: - first_name: Simon full_name: Spies, Simon last_name: Spies - first_name: Lennard full_name: Gäher, Lennard last_name: Gäher - first_name: Michael Joachim full_name: Sammler, Michael Joachim id: 510d3901-2a03-11ee-914d-d9ae9011f0a7 last_name: Sammler - first_name: Derek full_name: Dreyer, Derek last_name: Dreyer citation: ama: 'Spies S, Gäher L, Sammler MJ, Dreyer D. Quiver: Guided abductive inference of separation logic specifications in coq. Proceedings of the ACM on Programming Languages. 2024;8(PLDI):889-913. doi:10.1145/3656413' apa: 'Spies, S., Gäher, L., Sammler, M. J., & Dreyer, D. (2024). Quiver: Guided abductive inference of separation logic specifications in coq. Proceedings of the ACM on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3656413' chicago: 'Spies, Simon, Lennard Gäher, Michael Joachim Sammler, and Derek Dreyer. “Quiver: Guided Abductive Inference of Separation Logic Specifications in Coq.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2024. https://doi.org/10.1145/3656413.' ieee: 'S. Spies, L. Gäher, M. J. Sammler, and D. Dreyer, “Quiver: Guided abductive inference of separation logic specifications in coq,” Proceedings of the ACM on Programming Languages, vol. 8, no. PLDI. Association for Computing Machinery, pp. 889–913, 2024.' ista: 'Spies S, Gäher L, Sammler MJ, Dreyer D. 2024. Quiver: Guided abductive inference of separation logic specifications in coq. Proceedings of the ACM on Programming Languages. 8(PLDI), 889–913.' mla: 'Spies, Simon, et al. “Quiver: Guided Abductive Inference of Separation Logic Specifications in Coq.” Proceedings of the ACM on Programming Languages, vol. 8, no. PLDI, Association for Computing Machinery, 2024, pp. 889–913, doi:10.1145/3656413.' short: S. Spies, L. Gäher, M.J. Sammler, D. Dreyer, Proceedings of the ACM on Programming Languages 8 (2024) 889–913. date_created: 2024-09-05T08:10:41Z date_published: 2024-06-20T00:00:00Z date_updated: 2024-09-10T12:00:57Z day: '20' doi: 10.1145/3656413 extern: '1' intvolume: ' 8' issue: PLDI language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/3656413 month: '06' oa: 1 oa_version: Published Version page: 889-913 publication: Proceedings of the ACM on Programming Languages publication_identifier: issn: - 2475-1421 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'Quiver: Guided abductive inference of separation logic specifications in coq' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 8 year: '2024' ... --- _id: '17517' abstract: - lang: eng text: We present an analysis of NuSTAR X-ray observations of three active galactic nuclei (AGN) that were identified as candidate subparsec binary supermassive black hole (SMBH) systems in the Catalina Real-Time Transient Survey based on apparent periodicity in their optical light curves. Simulations predict that close-separation accreting SMBH binaries will have different X-ray spectra than single accreting SMBHs. We previously observed these AGN with Chandra and found no differences between their low-energy X-ray properties and the larger AGN population. However, some models predict differences to be more prominent at energies higher than probed by Chandra. We find that even at the higher energies probed by NuSTAR, the spectra of these AGN are indistinguishable from the larger AGN population. This could rule out models predicting large differences in the X-ray spectra in the NuSTAR bands. Alternatively, it might mean that these three AGN are not binary SMBHs. article_number: '104' article_processing_charge: No article_type: original author: - first_name: M. Lynne full_name: Saade, M. Lynne last_name: Saade - first_name: Murray full_name: Brightman, Murray last_name: Brightman - first_name: Daniel full_name: Stern, Daniel last_name: Stern - first_name: Thomas full_name: Connor, Thomas last_name: Connor - first_name: S. G. full_name: Djorgovski, S. G. last_name: Djorgovski - first_name: Daniel J. full_name: D’Orazio, Daniel J. last_name: D’Orazio - first_name: K. E. S. full_name: Ford, K. E. S. last_name: Ford - first_name: Matthew J. full_name: Graham, Matthew J. last_name: Graham - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: Hyunsung D. full_name: Jun, Hyunsung D. last_name: Jun - first_name: Elias full_name: Kammoun, Elias last_name: Kammoun - first_name: Ralph P. full_name: Kraft, Ralph P. last_name: Kraft - first_name: Barry full_name: McKernan, Barry last_name: McKernan - first_name: Alexei full_name: Vikhlinin, Alexei last_name: Vikhlinin - first_name: Dominic J. full_name: Walton, Dominic J. last_name: Walton citation: ama: Saade ML, Brightman M, Stern D, et al. NuSTAR observations of candidate subparsec binary supermassive black holes. The Astrophysical Journal. 2024;966(1). doi:10.3847/1538-4357/ad372e apa: Saade, M. L., Brightman, M., Stern, D., Connor, T., Djorgovski, S. G., D’Orazio, D. J., … Walton, D. J. (2024). NuSTAR observations of candidate subparsec binary supermassive black holes. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ad372e chicago: Saade, M. Lynne, Murray Brightman, Daniel Stern, Thomas Connor, S. G. Djorgovski, Daniel J. D’Orazio, K. E. S. Ford, et al. “NuSTAR Observations of Candidate Subparsec Binary Supermassive Black Holes.” The Astrophysical Journal. American Astronomical Society, 2024. https://doi.org/10.3847/1538-4357/ad372e. ieee: M. L. Saade et al., “NuSTAR observations of candidate subparsec binary supermassive black holes,” The Astrophysical Journal, vol. 966, no. 1. American Astronomical Society, 2024. ista: Saade ML, Brightman M, Stern D, Connor T, Djorgovski SG, D’Orazio DJ, Ford KES, Graham MJ, Haiman Z, Jun HD, Kammoun E, Kraft RP, McKernan B, Vikhlinin A, Walton DJ. 2024. NuSTAR observations of candidate subparsec binary supermassive black holes. The Astrophysical Journal. 966(1), 104. mla: Saade, M. Lynne, et al. “NuSTAR Observations of Candidate Subparsec Binary Supermassive Black Holes.” The Astrophysical Journal, vol. 966, no. 1, 104, American Astronomical Society, 2024, doi:10.3847/1538-4357/ad372e. short: M.L. Saade, M. Brightman, D. Stern, T. Connor, S.G. Djorgovski, D.J. D’Orazio, K.E.S. Ford, M.J. Graham, Z. Haiman, H.D. Jun, E. Kammoun, R.P. Kraft, B. McKernan, A. Vikhlinin, D.J. Walton, The Astrophysical Journal 966 (2024). date_created: 2024-09-05T08:57:37Z date_published: 2024-04-29T00:00:00Z date_updated: 2024-09-10T14:31:31Z day: '29' doi: 10.3847/1538-4357/ad372e extern: '1' intvolume: ' 966' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3847/1538-4357/ad372e month: '04' oa: 1 oa_version: Published Version publication: The Astrophysical Journal publication_identifier: issn: - 0004-637X - 1538-4357 publication_status: published publisher: American Astronomical Society quality_controlled: '1' scopus_import: '1' status: public title: NuSTAR observations of candidate subparsec binary supermassive black holes type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 966 year: '2024' ... --- _id: '17531' abstract: - lang: eng text: The astrophysical origin of stellar-mass black hole (BH) mergers discovered through gravitational waves (GWs) is widely debated. Mergers in the disks of active galactic nuclei (AGNs) represent promising environments for at least a fraction of these events, with possible observational clues in the GW data. An additional clue to unveil AGN merger environments is provided by possible electromagnetic emission from postmerger accreting BHs. Associated with BH mergers in AGN disks, emission from shocks emerging around jets launched by accreting merger remnants is expected. Here we compute the properties of the emission produced during breakout and the subsequent adiabatic expansion phase of the shocks, and we then apply this model to optical flares suggested to be possibly associated with GW events. We find that the majority of the reported flares can be explained by breakout and shock cooling emission. If the optical flares are produced by shock cooling emission, they would display moderate color evolution, possibly color variations among different events, and a positive correlation between delay time and flare duration and would be preceded by breakout emission in X-rays. If the breakout emission dominates the observed lightcurve, we predict the color to be distributed in a narrow range in the optical band and the delay time from GW to electromagnetic emission to be longer than ∼2 days. Hence, further explorations of delay time distributions, flare color evolution, and associated X-ray emission will be useful to test the proposed emission model for the observed flares. article_number: '21' article_processing_charge: No article_type: original author: - first_name: Hiromichi full_name: Tagawa, Hiromichi last_name: Tagawa - first_name: Shigeo S full_name: Kimura, Shigeo S last_name: Kimura - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: Rosalba full_name: Perna, Rosalba last_name: Perna - first_name: Imre full_name: Bartos, Imre last_name: Bartos citation: ama: Tagawa H, Kimura SS, Haiman Z, Perna R, Bartos I. Shock cooling and breakout emission for optical flares associated with gravitational-wave events. The Astrophysical Journal. 2024;966(1). doi:10.3847/1538-4357/ad2e0b apa: Tagawa, H., Kimura, S. S., Haiman, Z., Perna, R., & Bartos, I. (2024). Shock cooling and breakout emission for optical flares associated with gravitational-wave events. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ad2e0b chicago: Tagawa, Hiromichi, Shigeo S Kimura, Zoltán Haiman, Rosalba Perna, and Imre Bartos. “Shock Cooling and Breakout Emission for Optical Flares Associated with Gravitational-Wave Events.” The Astrophysical Journal. American Astronomical Society, 2024. https://doi.org/10.3847/1538-4357/ad2e0b. ieee: H. Tagawa, S. S. Kimura, Z. Haiman, R. Perna, and I. Bartos, “Shock cooling and breakout emission for optical flares associated with gravitational-wave events,” The Astrophysical Journal, vol. 966, no. 1. American Astronomical Society, 2024. ista: Tagawa H, Kimura SS, Haiman Z, Perna R, Bartos I. 2024. Shock cooling and breakout emission for optical flares associated with gravitational-wave events. The Astrophysical Journal. 966(1), 21. mla: Tagawa, Hiromichi, et al. “Shock Cooling and Breakout Emission for Optical Flares Associated with Gravitational-Wave Events.” The Astrophysical Journal, vol. 966, no. 1, 21, American Astronomical Society, 2024, doi:10.3847/1538-4357/ad2e0b. short: H. Tagawa, S.S. Kimura, Z. Haiman, R. Perna, I. Bartos, The Astrophysical Journal 966 (2024). date_created: 2024-09-05T09:38:53Z date_published: 2024-04-23T00:00:00Z date_updated: 2024-09-11T09:15:47Z day: '23' doi: 10.3847/1538-4357/ad2e0b extern: '1' intvolume: ' 966' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3847/1538-4357/ad2e0b month: '04' oa: 1 oa_version: Published Version publication: The Astrophysical Journal publication_identifier: issn: - 0004-637X - 1538-4357 publication_status: published publisher: American Astronomical Society quality_controlled: '1' scopus_import: '1' status: public title: Shock cooling and breakout emission for optical flares associated with gravitational-wave events type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 966 year: '2024' ... --- _id: '17535' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Matthew T full_name: Scoggins, Matthew T last_name: Scoggins - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman citation: 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' 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' 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.' 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.' 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.' short: M.T. Scoggins, Z. Haiman, Monthly Notices of the Royal Astronomical Society 531 (2024) 4584–4597. date_created: 2024-09-05T09:43:52Z date_published: 2024-06-13T00:00:00Z date_updated: 2024-09-12T09:08:08Z day: '13' doi: 10.1093/mnras/stae1449 extern: '1' intvolume: ' 531' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/https://doi.org/10.1093/mnras/stae1449 month: '06' oa: 1 oa_version: Published Version page: 4584-4597 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Diagnosing the massive-seed pathway to high-redshift black holes: statistics of the evolving black hole to host galaxy mass ratio' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 531 year: '2024' ... --- _id: '17545' abstract: - lang: eng 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. article_number: '103014' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Luke Major full_name: Krauth, Luke Major last_name: Krauth - first_name: Jordy full_name: Davelaar, Jordy last_name: Davelaar - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: John Ryan full_name: Westernacher-Schneider, John Ryan last_name: Westernacher-Schneider - first_name: Jonathan full_name: Zrake, Jonathan last_name: Zrake - first_name: Andrew full_name: MacFadyen, Andrew last_name: MacFadyen citation: 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' 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' 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.' 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.' 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.' 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). date_created: 2024-09-05T10:04:45Z date_published: 2024-05-10T00:00:00Z date_updated: 2024-09-18T09:01:52Z day: '10' doi: 10.1103/physrevd.109.103014 extern: '1' external_id: arxiv: - '2310.19766' intvolume: ' 109' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2310.19766' month: '05' oa: 1 oa_version: Preprint publication: Physical Review D publication_identifier: issn: - 2470-0010 - 2470-0029 publication_status: published publisher: American Physical Society (APS) quality_controlled: '1' scopus_import: '1' status: public title: 'Self-lensing flares from black hole binaries: General-relativistic ray tracing of circumbinary accretion simulations' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 109 year: '2024' ... --- _id: '17546' 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. article_number: '76' article_processing_charge: No article_type: original author: - first_name: John Ryan full_name: Westernacher-Schneider, John Ryan last_name: Westernacher-Schneider - first_name: Jonathan full_name: Zrake, Jonathan last_name: Zrake - first_name: Andrew full_name: MacFadyen, Andrew last_name: MacFadyen - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman citation: 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 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. 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. ista: Westernacher-Schneider JR, Zrake J, MacFadyen A, Haiman Z. 2024. Eccentric minidisks in accreting binaries. The Astrophysical Journal. 962(1), 76. 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. short: J.R. Westernacher-Schneider, J. Zrake, A. MacFadyen, Z. Haiman, The Astrophysical Journal 962 (2024). date_created: 2024-09-05T10:06:09Z date_published: 2024-02-08T00:00:00Z date_updated: 2024-09-18T09:16:14Z day: '08' doi: 10.3847/1538-4357/ad1a17 extern: '1' intvolume: ' 962' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3847/1538-4357/ad1a17 month: '02' oa: 1 oa_version: Published Version publication: The Astrophysical Journal publication_identifier: issn: - 0004-637X - 1538-4357 publication_status: published publisher: American Astronomical Society quality_controlled: '1' scopus_import: '1' status: public title: Eccentric minidisks in accreting binaries type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 962 year: '2024' ... --- _id: '17590' 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. article_number: '149' article_processing_charge: No article_type: original author: - first_name: Chengcheng full_name: Xin, Chengcheng last_name: Xin - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: Rosalba full_name: Perna, Rosalba last_name: Perna - first_name: Yihan full_name: Wang, Yihan last_name: Wang - first_name: Taeho full_name: Ryu, Taeho last_name: Ryu citation: 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' 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.' 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.' 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.' 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.' short: C. Xin, Z. Haiman, R. Perna, Y. Wang, T. Ryu, The Astrophysical Journal 961 (2024). date_created: 2024-09-05T12:36:41Z date_published: 2024-01-22T00:00:00Z date_updated: 2024-09-19T12:21:53Z day: '22' doi: 10.3847/1538-4357/ad11d3 extern: '1' intvolume: ' 961' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3847/1538-4357/ad11d3 month: '01' oa: 1 oa_version: Published Version publication: The Astrophysical Journal publication_identifier: issn: - 0004-637X - 1538-4357 publication_status: published publisher: American Astronomical Society quality_controlled: '1' scopus_import: '1' status: public title: '“Tidal Peeling Events”: Low-eccentricity tidal disruption of a star by a stellar-mass black hole' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 961 year: '2024' ... --- OA_place: publisher _id: '17850' abstract: - lang: eng 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." acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Louisa full_name: Gonzalez Somermeyer, Louisa id: 4720D23C-F248-11E8-B48F-1D18A9856A87 last_name: Gonzalez Somermeyer orcid: 0000-0001-9139-5383 citation: 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 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. ieee: L. Gonzalez Somermeyer, “Fitness landscapes of orthologous green fluorescent proteins,” Institute of Science and Technology Austria, 2024. ista: Gonzalez Somermeyer L. 2024. Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria. mla: Gonzalez Somermeyer, Louisa. Fitness Landscapes of Orthologous Green Fluorescent Proteins. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17850. short: L. Gonzalez Somermeyer, Fitness Landscapes of Orthologous Green Fluorescent Proteins, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-06T12:57:44Z date_published: 2024-09-06T00:00:00Z date_updated: 2026-04-07T13:25:01Z day: '06' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: FyKo doi: 10.15479/at:ista:17850 ec_funded: 1 file: - access_level: open_access checksum: d3303724e8d3c91321d71bbad4062048 content_type: application/pdf creator: lgonzale date_created: 2024-09-27T10:32:33Z date_updated: 2024-09-27T10:32:33Z file_id: '18151' file_name: louisa_thesis_draft__240904b.pdf file_size: 11219837 relation: main_file - access_level: closed checksum: 22e63f7f9014dffde2af7a47e7d1d014 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lgonzale date_created: 2024-09-27T10:34:34Z date_updated: 2024-09-27T10:34:34Z file_id: '18152' file_name: louisa_thesis_draft__240904b.docx file_size: 43338677 relation: source_file file_date_updated: 2024-09-27T10:34:34Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '09' oa: 1 oa_version: Published Version page: '89' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: link: - relation: software url: https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks record: - id: '11448' relation: part_of_dissertation status: public status: public supervisor: - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 title: Fitness landscapes of orthologous green fluorescent proteins tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17852' 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. article_number: '1439' article_processing_charge: Yes article_type: original author: - first_name: Woojung full_name: Lee, Woojung last_name: Lee - first_name: Liang full_name: Li, Liang last_name: Li - first_name: María full_name: Camarasa-Gómez, María last_name: Camarasa-Gómez - first_name: Daniel full_name: Hernangómez-Pérez, Daniel last_name: Hernangómez-Pérez - first_name: Xavier full_name: Roy, Xavier last_name: Roy - first_name: Ferdinand full_name: Evers, Ferdinand last_name: Evers - first_name: Michael S. full_name: Inkpen, Michael S. last_name: Inkpen - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: 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 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 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. ieee: W. Lee et al., “Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions,” Nature Communications, vol. 15. Springer Nature, 2024. 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. short: W. Lee, L. Li, M. Camarasa-Gómez, D. Hernangómez-Pérez, X. Roy, F. Evers, M.S. Inkpen, L. Venkataraman, Nature Communications 15 (2024). date_created: 2024-09-06T12:38:44Z date_published: 2024-02-16T00:00:00Z date_updated: 2024-11-18T10:47:10Z day: '16' doi: 10.1038/s41467-024-45707-z extern: '1' external_id: pmid: - '38365892' intvolume: ' 15' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-024-45707-z month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2024' ... --- OA_type: closed access _id: '17853' 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. article_processing_charge: No article_type: original author: - first_name: Liang full_name: Li, Liang last_name: Li - first_name: Shayan full_name: Louie, Shayan last_name: Louie - first_name: Nicholas M. full_name: Orchanian, Nicholas M. last_name: Orchanian - first_name: Colin full_name: Nuckolls, Colin last_name: Nuckolls - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: 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 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 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. 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. 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. date_created: 2024-09-06T12:40:17Z date_published: 2024-06-24T00:00:00Z date_updated: 2024-11-18T10:51:21Z day: '24' doi: 10.1021/jacs.4c05699 extern: '1' external_id: pmid: - '38832840' intvolume: ' 146' issue: '24' language: - iso: eng month: '06' oa_version: None page: 16920-16925 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Long-range gating in single-molecule one-dimensional topological insulators type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 146 year: '2024' ... --- OA_type: closed access _id: '17854' 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. article_processing_charge: No article_type: original author: - first_name: Claudia R. full_name: Prindle, Claudia R. last_name: Prindle - first_name: Nicholas M. full_name: Orchanian, Nicholas M. last_name: Orchanian - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 - first_name: Colin full_name: Nuckolls, Colin last_name: Nuckolls citation: ama: Prindle CR, Orchanian NM, Venkataraman L, Nuckolls C. Short-form videos as an emerging social media tool for STEM edutainment. Journal of Chemical Education. 2024;101(3):1319-1324. doi:10.1021/acs.jchemed.3c01185 apa: Prindle, C. R., Orchanian, N. M., Venkataraman, L., & Nuckolls, C. (2024). Short-form videos as an emerging social media tool for STEM edutainment. Journal of Chemical Education. American Chemical Society. https://doi.org/10.1021/acs.jchemed.3c01185 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. 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. 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. date_created: 2024-09-06T12:43:20Z date_published: 2024-02-14T00:00:00Z date_updated: 2024-11-18T10:55:30Z day: '14' doi: 10.1021/acs.jchemed.3c01185 extern: '1' intvolume: ' 101' issue: '3' language: - iso: eng month: '02' oa_version: None page: 1319-1324 publication: Journal of Chemical Education publication_identifier: eissn: - 1938-1328 issn: - 0021-9584 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Short-form videos as an emerging social media tool for STEM edutainment type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 101 year: '2024' ... --- _id: '17855' abstract: - lang: eng 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. article_processing_charge: No article_type: letter_note author: - first_name: Angela L. full_name: Paoletta, Angela L. last_name: Paoletta - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: 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 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. 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. ista: Paoletta AL, Venkataraman L. 2024. Determining transmission characteristics from shot-noise-driven electroluminescence in single-molecule junctions. Nano Letters. 24(6), 1931–1935. 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. short: A.L. Paoletta, L. Venkataraman, Nano Letters 24 (2024) 1931–1935. date_created: 2024-09-06T12:44:24Z date_published: 2024-02-05T00:00:00Z date_updated: 2024-11-18T10:58:19Z day: '05' doi: 10.1021/acs.nanolett.3c04207 extern: '1' external_id: pmid: - '38315038' intvolume: ' 24' issue: '6' language: - iso: eng month: '02' oa_version: None page: 1931-1935 pmid: 1 publication: Nano Letters publication_identifier: issn: - 1530-6984 - 1530-6992 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Determining transmission characteristics from shot-noise-driven electroluminescence in single-molecule junctions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2024' ... --- _id: '17856' 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. article_processing_charge: No article_type: letter_note author: - first_name: Claudia R. full_name: Prindle, Claudia R. last_name: Prindle - first_name: Wanzhuo full_name: Shi, Wanzhuo last_name: Shi - first_name: Liang full_name: Li, Liang last_name: Li - first_name: Jesper full_name: Dahl Jensen, Jesper last_name: Dahl Jensen - 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 full_name: Nuckolls, Colin last_name: Nuckolls - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: 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 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 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. 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. 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. 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. 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. date_created: 2024-09-06T12:45:11Z date_published: 2024-01-31T00:00:00Z date_updated: 2024-11-18T11:02:24Z day: '31' doi: 10.1021/jacs.3c14226 extern: '1' external_id: pmid: - '38293735' intvolume: ' 146' issue: '6' language: - iso: eng month: '01' oa_version: None page: 3646-3650 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Effective gating in single-molecule junctions through fano resonances type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 146 year: '2024' ... --- OA_type: closed access _id: '17857' abstract: - lang: eng 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. article_processing_charge: No article_type: letter_note author: - first_name: Johnson full_name: Dalmieda, Johnson last_name: Dalmieda - first_name: Wanzhuo full_name: Shi, Wanzhuo last_name: Shi - first_name: Liang full_name: Li, Liang last_name: Li - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: ama: Dalmieda J, Shi W, Li L, Venkataraman L. Solvent-mediated modulation of the Au–S bond in dithiol molecular junctions. Nano Letters. 2024;24(2):703-707. doi:10.1021/acs.nanolett.3c04058 apa: Dalmieda, J., Shi, W., Li, L., & Venkataraman, L. (2024). Solvent-mediated modulation of the Au–S bond in dithiol molecular junctions. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.3c04058 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. 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. ista: Dalmieda J, Shi W, Li L, Venkataraman L. 2024. Solvent-mediated modulation of the Au–S bond in dithiol molecular junctions. Nano Letters. 24(2), 703–707. mla: Dalmieda, Johnson, et al. “Solvent-Mediated Modulation of the Au–S Bond in Dithiol Molecular Junctions.” Nano Letters, vol. 24, no. 2, American Chemical Society, 2024, pp. 703–07, doi:10.1021/acs.nanolett.3c04058. short: J. Dalmieda, W. Shi, L. Li, L. Venkataraman, Nano Letters 24 (2024) 703–707. date_created: 2024-09-06T12:46:39Z date_published: 2024-01-04T00:00:00Z date_updated: 2024-11-19T12:50:27Z day: '04' doi: 10.1021/acs.nanolett.3c04058 extern: '1' external_id: pmid: - '38175934' intvolume: ' 24' issue: '2' language: - iso: eng month: '01' oa_version: None page: 703-707 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Solvent-mediated modulation of the Au–S bond in dithiol molecular junctions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2024' ... --- OA_type: closed access _id: '17859' 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. article_processing_charge: No article_type: original author: - first_name: Wanzhuo full_name: Shi, Wanzhuo last_name: Shi - first_name: Julia E. full_name: Greenwald, Julia E. last_name: Greenwald - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: 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 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 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. 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. 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. 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. short: W. Shi, J.E. Greenwald, L. Venkataraman, Nano Letters 24 (2024) 9283–9288. date_created: 2024-09-06T12:48:34Z date_published: 2024-07-18T00:00:00Z date_updated: 2024-11-20T15:24:37Z day: '18' doi: 10.1021/acs.nanolett.4c02103 extern: '1' external_id: pmid: - '39023006' intvolume: ' 24' issue: '30' language: - iso: eng month: '07' oa_version: None page: 9283-9288 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Impact of solvent electrostatic environment on molecular junctions probed via electrochemical impedance spectroscopy type: journal_article user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d volume: 24 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17885' abstract: - lang: eng text: 'The formation of new ribosomes is tightly coordinated with cell growth and proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and RNAs follows an intricate scheme of maturation and rearrangement steps across three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate that usnic acid, a lichen secondary metabolite, inhibits the maturation of the large ribosomal subunit in yeast. We combine biochemical characterization of pre-ribosomal particles with a quantitative single-particle cryo-EM approach to monitor changes in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary nucleolar block rapidly rebounds on earlier stages of the pathway which highlights the regulatory linkages between different steps. In summary, we provide an in-depth characterization of the effect of usnic acid on ribosome biogenesis, which may have implications for its reported anti-cancer activities.' acknowledged_ssus: - _id: EM-Fac 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_number: '7511' article_processing_charge: Yes article_type: original author: - first_name: Lisa full_name: Kofler, Lisa last_name: Kofler - first_name: Lorenz full_name: Grundmann, Lorenz last_name: Grundmann - first_name: Magdalena full_name: Gerhalter, Magdalena last_name: Gerhalter - first_name: Michael full_name: Prattes, Michael last_name: Prattes - first_name: Juliane full_name: Merl-Pham, Juliane last_name: Merl-Pham - first_name: Gertrude full_name: Zisser, Gertrude last_name: Zisser - first_name: Irina full_name: Grishkovskaya, Irina last_name: Grishkovskaya - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau orcid: 0000-0003-3904-947X - first_name: Martin full_name: Vareka, Martin last_name: Vareka - first_name: Rolf full_name: Breinbauer, Rolf last_name: Breinbauer - first_name: Stefanie M. full_name: Hauck, Stefanie M. last_name: Hauck - first_name: David full_name: Haselbach, David last_name: Haselbach - first_name: Helmut full_name: Bergler, Helmut last_name: Bergler citation: 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 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. 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. 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). date_created: 2024-09-08T22:01:10Z date_published: 2024-08-29T00:00:00Z date_updated: 2025-09-08T09:13:01Z day: '29' ddc: - '570' department: - _id: EM-Fac doi: 10.1038/s41467-024-51754-3 external_id: isi: - '001457895200001' pmid: - '39209816' file: - access_level: open_access checksum: 7c044538a47182c826d1b526c52958a2 content_type: application/pdf creator: dernst date_created: 2024-09-09T08:56:12Z date_updated: 2024-09-09T08:56:12Z file_id: '17946' file_name: 2024_NatureComm_Kofler.pdf file_size: 3735024 relation: main_file success: 1 file_date_updated: 2024-09-09T08:56:12Z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2024' ...