[{"intvolume":"        15","date_updated":"2025-09-09T14:09:32Z","status":"public","type":"journal_article","keyword":["General Biochemistry","Genetics and Molecular Biology"],"publisher":"Cold Spring Harbor Laboratory Press","doi":"10.1101/cshperspect.a041447","acknowledgement":"K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper.","year":"2023","pmid":1,"_id":"14742","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"article_type":"original","date_created":"2024-01-08T12:43:48Z","quality_controlled":"1","publication_identifier":{"issn":["1943-0264"]},"language":[{"iso":"eng"}],"date_published":"2023-11-01T00:00:00Z","citation":{"ama":"Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. <i>Cold Spring Harbor Perspectives in Biology</i>. 2023;15(11). doi:<a href=\"https://doi.org/10.1101/cshperspect.a041447\">10.1101/cshperspect.a041447</a>","chicago":"Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2023. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>.","ieee":"K. Lucek <i>et al.</i>, “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 15, no. 11. Cold Spring Harbor Laboratory Press, 2023.","mla":"Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory Press, 2023, doi:<a href=\"https://doi.org/10.1101/cshperspect.a041447\">10.1101/cshperspect.a041447</a>.","apa":"Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>","short":"K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden, A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023).","ista":"Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447."},"oa":1,"month":"11","volume":15,"article_processing_charge":"No","scopus_import":"1","publication_status":"published","article_number":"a041447","oa_version":"Published Version","abstract":[{"text":"Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.","lang":"eng"}],"day":"01","publication":"Cold Spring Harbor Perspectives in Biology","issue":"11","external_id":{"isi":["001096272600001"],"pmid":["37604585"]},"author":[{"first_name":"Kay","full_name":"Lucek, Kay","last_name":"Lucek"},{"full_name":"Giménez, Mabel D.","last_name":"Giménez","first_name":"Mabel D."},{"first_name":"Mathieu","full_name":"Joron, Mathieu","last_name":"Joron"},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"last_name":"Searle","first_name":"Jeremy B.","full_name":"Searle, Jeremy B."},{"full_name":"Walden, Nora","last_name":"Walden","first_name":"Nora"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"}],"title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a041447"}]},{"scopus_import":"1","publication_status":"published","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Leader-based consensus algorithms are fast and efficient under normal conditions, but lack robustness to adverse conditions due to their reliance on timeouts for liveness. We present QuePaxa, the first protocol offering state-of-the-art normal-case efficiency without depending on timeouts. QuePaxa uses a novel randomized asynchronous consensus core to tolerate adverse conditions such as denial-of-service (DoS) attacks, while a one-round-trip fast path preserves the normal-case efficiency of Multi-Paxos or Raft. By allowing simultaneous proposers without destructive interference, and using short hedging delays instead of conservative timeouts to limit redundant effort, QuePaxa permits rapid recovery after leader failure without risking costly view changes due to false timeouts. By treating leader choice and hedging delay as a multi-armed-bandit optimization, QuePaxa achieves responsiveness to prevalent conditions, and can choose the best leader even if the current one has not failed. Experiments with a prototype confirm that QuePaxa achieves normal-case LAN and WAN performance of 584k and 250k cmd/sec in throughput, respectively, comparable to Multi-Paxos. Under conditions such as DoS attacks, misconfigurations, or slow leaders that severely impact existing protocols, we find that QuePaxa remains live with median latency under 380ms in WAN experiments."}],"day":"01","publication":"Proceedings of the 29th Symposium on Operating Systems Principles","external_id":{"isi":["001135072900018"]},"author":[{"last_name":"Tennage","full_name":"Tennage, Pasindu","first_name":"Pasindu"},{"full_name":"Basescu, Cristina","first_name":"Cristina","last_name":"Basescu"},{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"full_name":"Syta, Ewa","last_name":"Syta","first_name":"Ewa"},{"full_name":"Jovanovic, Philipp","first_name":"Philipp","last_name":"Jovanovic"},{"last_name":"Estrada-Galinanes","full_name":"Estrada-Galinanes, Vero","first_name":"Vero"},{"last_name":"Ford","full_name":"Ford, Bryan","first_name":"Bryan"}],"title":"QuePaxa: Escaping the tyranny of timeouts in consensus","department":[{"_id":"ElKo"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3600006.3613150"}],"date_updated":"2025-09-09T14:10:09Z","type":"conference","status":"public","publisher":"Association for Computing Machinery","acknowledgement":"The authors would like to thank Marcos K. Aguilera, Pierluca Borsò, Aleksey Charapko, Rachid Guerraoui, Jovan Komatovic, Derek Leung, Louis-Henri Merino, Shailesh Mishra, Haochen Pan, Rodrigo Rodrigues, Lewis Tseng, and Haoqian Zhang for their helpful feedback on early drafts of this paper.","doi":"10.1145/3600006.3613150","year":"2023","_id":"14743","page":"281-297","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"conference":{"start_date":"2023-10-23","location":"Koblenz, Germany","name":"SOSP: Symposium on Operating Systems Principles","end_date":"2023-10-26"},"date_created":"2024-01-08T12:54:35Z","publication_identifier":{"isbn":["9798400702297"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2023-10-01T00:00:00Z","citation":{"mla":"Tennage, Pasindu, et al. “QuePaxa: Escaping the Tyranny of Timeouts in Consensus.” <i>Proceedings of the 29th Symposium on Operating Systems Principles</i>, Association for Computing Machinery, 2023, pp. 281–97, doi:<a href=\"https://doi.org/10.1145/3600006.3613150\">10.1145/3600006.3613150</a>.","ieee":"P. Tennage <i>et al.</i>, “QuePaxa: Escaping the tyranny of timeouts in consensus,” in <i>Proceedings of the 29th Symposium on Operating Systems Principles</i>, Koblenz, Germany, 2023, pp. 281–297.","apa":"Tennage, P., Basescu, C., Kokoris Kogias, E., Syta, E., Jovanovic, P., Estrada-Galinanes, V., &#38; Ford, B. (2023). QuePaxa: Escaping the tyranny of timeouts in consensus. In <i>Proceedings of the 29th Symposium on Operating Systems Principles</i> (pp. 281–297). Koblenz, Germany: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3600006.3613150\">https://doi.org/10.1145/3600006.3613150</a>","chicago":"Tennage, Pasindu, Cristina Basescu, Eleftherios Kokoris Kogias, Ewa Syta, Philipp Jovanovic, Vero Estrada-Galinanes, and Bryan Ford. “QuePaxa: Escaping the Tyranny of Timeouts in Consensus.” In <i>Proceedings of the 29th Symposium on Operating Systems Principles</i>, 281–97. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3600006.3613150\">https://doi.org/10.1145/3600006.3613150</a>.","ama":"Tennage P, Basescu C, Kokoris Kogias E, et al. QuePaxa: Escaping the tyranny of timeouts in consensus. In: <i>Proceedings of the 29th Symposium on Operating Systems Principles</i>. Association for Computing Machinery; 2023:281-297. doi:<a href=\"https://doi.org/10.1145/3600006.3613150\">10.1145/3600006.3613150</a>","short":"P. Tennage, C. Basescu, E. Kokoris Kogias, E. Syta, P. Jovanovic, V. Estrada-Galinanes, B. Ford, in:, Proceedings of the 29th Symposium on Operating Systems Principles, Association for Computing Machinery, 2023, pp. 281–297.","ista":"Tennage P, Basescu C, Kokoris Kogias E, Syta E, Jovanovic P, Estrada-Galinanes V, Ford B. 2023. QuePaxa: Escaping the tyranny of timeouts in consensus. Proceedings of the 29th Symposium on Operating Systems Principles. SOSP: Symposium on Operating Systems Principles, 281–297."},"oa":1,"article_processing_charge":"No","month":"10"},{"intvolume":"       145","status":"public","publisher":"American Chemical Society","type":"journal_article","date_updated":"2025-12-10T12:29:11Z","doi":"10.1021/jacs.3c04487","pmid":1,"year":"2023","page":"18182-18204","_id":"17860","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"closed access","article_type":"original","date_created":"2024-09-06T12:49:27Z","quality_controlled":"1","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"language":[{"iso":"eng"}],"date_published":"2023-09-23T00:00:00Z","citation":{"ama":"Li L, Prindle CR, Shi W, Nuckolls C, Venkataraman L. Radical single-molecule junctions. <i>Journal of the American Chemical Society</i>. 2023;145(33):18182-18204. doi:<a href=\"https://doi.org/10.1021/jacs.3c04487\">10.1021/jacs.3c04487</a>","chicago":"Li, Liang, Claudia R. Prindle, Wanzhuo Shi, Colin Nuckolls, and Latha Venkataraman. “Radical Single-Molecule Junctions.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/jacs.3c04487\">https://doi.org/10.1021/jacs.3c04487</a>.","mla":"Li, Liang, et al. “Radical Single-Molecule Junctions.” <i>Journal of the American Chemical Society</i>, vol. 145, no. 33, American Chemical Society, 2023, pp. 18182–204, doi:<a href=\"https://doi.org/10.1021/jacs.3c04487\">10.1021/jacs.3c04487</a>.","ieee":"L. Li, C. R. Prindle, W. Shi, C. Nuckolls, and L. Venkataraman, “Radical single-molecule junctions,” <i>Journal of the American Chemical Society</i>, vol. 145, no. 33. American Chemical Society, pp. 18182–18204, 2023.","apa":"Li, L., Prindle, C. R., Shi, W., Nuckolls, C., &#38; Venkataraman, L. (2023). Radical single-molecule junctions. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.3c04487\">https://doi.org/10.1021/jacs.3c04487</a>","short":"L. Li, C.R. Prindle, W. Shi, C. Nuckolls, L. Venkataraman, Journal of the American Chemical Society 145 (2023) 18182–18204.","ista":"Li L, Prindle CR, Shi W, Nuckolls C, Venkataraman L. 2023. Radical single-molecule junctions. Journal of the American Chemical Society. 145(33), 18182–18204."},"article_processing_charge":"No","volume":145,"month":"09","scopus_import":"1","publication_status":"published","extern":"1","oa_version":"None","abstract":[{"text":"Radicals are unique molecular systems for applications in electronic devices due to their open-shell electronic structures. Radicals can function as good electrical conductors and switches in molecular circuits while also holding great promise in the field of molecular spintronics. However, it is both challenging to create stable, persistent radicals and to understand their properties in molecular junctions. The goal of this Perspective is to address this dual challenge by providing design principles for the synthesis of stable radicals relevant to molecular junctions, as well as offering current insight into the electronic properties of radicals in single-molecule devices. By exploring both the chemical and physical properties of established radical systems, we will facilitate increased exploration and development of radical-based molecular systems.","lang":"eng"}],"day":"23","issue":"33","publication":"Journal of the American Chemical Society","external_id":{"pmid":["37555594"]},"author":[{"first_name":"Liang","full_name":"Li, Liang","last_name":"Li"},{"full_name":"Prindle, Claudia R.","last_name":"Prindle","first_name":"Claudia R."},{"last_name":"Shi","full_name":"Shi, Wanzhuo","first_name":"Wanzhuo"},{"full_name":"Nuckolls, Colin","last_name":"Nuckolls","first_name":"Colin"},{"first_name":"Latha","full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","last_name":"Venkataraman","orcid":"0000-0002-6957-6089"}],"title":"Radical single-molecule junctions"},{"author":[{"first_name":"Liang","last_name":"Li","full_name":"Li, Liang"},{"first_name":"Colin","full_name":"Nuckolls, Colin","last_name":"Nuckolls"},{"id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha","last_name":"Venkataraman","full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089"}],"external_id":{"pmid":["37252687"]},"title":"Designing long and highly conducting molecular wires with multiple nontrivial topological states","scopus_import":"1","extern":"1","publication_status":"published","day":"30","abstract":[{"lang":"eng","text":"Molecular one-dimensional topological insulators (1D TIs), described by the Su-Schrieffer-Heeger (SSH) model, are a new class of molecular electronic wires whose low-energy topological edge states endow them with high electrical conductivity. However, when these 1D TIs become long, the high conductance is not sustained because the coupling between the edge states decreases with increasing length. Here, we present a new design where we connect multiple short 1D SSH TI units linearly or in a cycle to create molecular wires with a continuous topological state density. Using a tight-binding method, we show that the linear system gives a length-independent conductance. The cyclic systems show an interesting odd-even effect, with unit transmission in the topological limit, but zero transmission in the trivial limit. Furthermore, based on our calculations, we predict that these systems can support resonant transmission with a quantum of conductance. We can further expand these results to phenylene-based linear and cyclic 1D TI systems and confirm the length-dependent conductance in such systems. "}],"issue":"22","publication":"The Journal of Physical Chemistry Letters","oa_version":"None","publication_identifier":{"eissn":["1948-7185"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2024-09-06T12:50:23Z","citation":{"ista":"Li L, Nuckolls C, Venkataraman L. 2023. Designing long and highly conducting molecular wires with multiple nontrivial topological states. The Journal of Physical Chemistry Letters. 14(22), 5141–5147.","short":"L. Li, C. Nuckolls, L. Venkataraman, The Journal of Physical Chemistry Letters 14 (2023) 5141–5147.","ama":"Li L, Nuckolls C, Venkataraman L. Designing long and highly conducting molecular wires with multiple nontrivial topological states. <i>The Journal of Physical Chemistry Letters</i>. 2023;14(22):5141-5147. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01081\">10.1021/acs.jpclett.3c01081</a>","chicago":"Li, Liang, Colin Nuckolls, and Latha Venkataraman. “Designing Long and Highly Conducting Molecular Wires with Multiple Nontrivial Topological States.” <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01081\">https://doi.org/10.1021/acs.jpclett.3c01081</a>.","apa":"Li, L., Nuckolls, C., &#38; Venkataraman, L. (2023). Designing long and highly conducting molecular wires with multiple nontrivial topological states. <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01081\">https://doi.org/10.1021/acs.jpclett.3c01081</a>","ieee":"L. Li, C. Nuckolls, and L. Venkataraman, “Designing long and highly conducting molecular wires with multiple nontrivial topological states,” <i>The Journal of Physical Chemistry Letters</i>, vol. 14, no. 22. American Chemical Society, pp. 5141–5147, 2023.","mla":"Li, Liang, et al. “Designing Long and Highly Conducting Molecular Wires with Multiple Nontrivial Topological States.” <i>The Journal of Physical Chemistry Letters</i>, vol. 14, no. 22, American Chemical Society, 2023, pp. 5141–47, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01081\">10.1021/acs.jpclett.3c01081</a>."},"volume":14,"article_processing_charge":"No","month":"05","date_published":"2023-05-30T00:00:00Z","doi":"10.1021/acs.jpclett.3c01081","intvolume":"        14","type":"journal_article","status":"public","publisher":"American Chemical Society","date_updated":"2025-01-03T11:36:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"closed access","article_type":"original","year":"2023","pmid":1,"page":"5141-5147","_id":"17861"},{"year":"2023","pmid":1,"_id":"17862","page":"11903-11906","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","article_type":"original","intvolume":"       145","date_updated":"2024-11-25T12:29:49Z","status":"public","type":"journal_article","publisher":"American Chemical Society","doi":"10.1021/jacs.3c02064","date_published":"2023-05-25T00:00:00Z","citation":{"ista":"Wang X, Zhang B, Fowler B, Venkataraman L, Rovis T. 2023. Alkane solvent-derived acylation reaction driven by electric fields. Journal of the American Chemical Society. 145(22), 11903–11906.","short":"X. Wang, B. Zhang, B. Fowler, L. Venkataraman, T. Rovis, Journal of the American Chemical Society 145 (2023) 11903–11906.","apa":"Wang, X., Zhang, B., Fowler, B., Venkataraman, L., &#38; Rovis, T. (2023). Alkane solvent-derived acylation reaction driven by electric fields. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.3c02064\">https://doi.org/10.1021/jacs.3c02064</a>","ieee":"X. Wang, B. Zhang, B. Fowler, L. Venkataraman, and T. Rovis, “Alkane solvent-derived acylation reaction driven by electric fields,” <i>Journal of the American Chemical Society</i>, vol. 145, no. 22. American Chemical Society, pp. 11903–11906, 2023.","mla":"Wang, Xiye, et al. “Alkane Solvent-Derived Acylation Reaction Driven by Electric Fields.” <i>Journal of the American Chemical Society</i>, vol. 145, no. 22, American Chemical Society, 2023, pp. 11903–06, doi:<a href=\"https://doi.org/10.1021/jacs.3c02064\">10.1021/jacs.3c02064</a>.","ama":"Wang X, Zhang B, Fowler B, Venkataraman L, Rovis T. Alkane solvent-derived acylation reaction driven by electric fields. <i>Journal of the American Chemical Society</i>. 2023;145(22):11903-11906. doi:<a href=\"https://doi.org/10.1021/jacs.3c02064\">10.1021/jacs.3c02064</a>","chicago":"Wang, Xiye, Boyuan Zhang, Brandon Fowler, Latha Venkataraman, and Tomislav Rovis. “Alkane Solvent-Derived Acylation Reaction Driven by Electric Fields.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/jacs.3c02064\">https://doi.org/10.1021/jacs.3c02064</a>."},"article_processing_charge":"No","month":"05","volume":145,"date_created":"2024-09-06T12:55:12Z","quality_controlled":"1","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"language":[{"iso":"eng"}],"oa_version":"None","abstract":[{"text":"Electric field acceleration of alkyl hydroperoxide activation to acylate amines in the scanning tunneling microscope-based break-junction is reported. Alkyl hydroperoxide mixtures, generated from hydrocarbon autoxidation in air, were found to be competent reagents for the functionalization of gold surfaces. Intermolecular coupling on the surface in the presence of amines was observed, yielding normal alkylamides. This novel mode of alkyl hydroperoxide activation to generate acylium equivalents was found to be responsive to the magnitude of the bias in the break junction, indicating an electric field influence on this novel reactivity.","lang":"eng"}],"day":"25","issue":"22","publication":"Journal of the American Chemical Society","scopus_import":"1","extern":"1","publication_status":"published","title":"Alkane solvent-derived acylation reaction driven by electric fields","external_id":{"pmid":["37227235"]},"author":[{"first_name":"Xiye","full_name":"Wang, Xiye","last_name":"Wang"},{"first_name":"Boyuan","full_name":"Zhang, Boyuan","last_name":"Zhang"},{"full_name":"Fowler, Brandon","first_name":"Brandon","last_name":"Fowler"},{"orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","last_name":"Venkataraman"},{"first_name":"Tomislav","last_name":"Rovis","full_name":"Rovis, Tomislav"}]},{"date_published":"2023-05-01T00:00:00Z","oa":1,"volume":3,"article_processing_charge":"No","month":"05","citation":{"ista":"Zou Q, Qiu J, Zang Y, Tian H, Venkataraman L. 2023. Modulating single-molecule charge transport through external stimulus. eScience. 3(3), 100115.","short":"Q. Zou, J. Qiu, Y. Zang, H. Tian, L. Venkataraman, EScience 3 (2023).","apa":"Zou, Q., Qiu, J., Zang, Y., Tian, H., &#38; Venkataraman, L. (2023). Modulating single-molecule charge transport through external stimulus. <i>EScience</i>. Elsevier BV. <a href=\"https://doi.org/10.1016/j.esci.2023.100115\">https://doi.org/10.1016/j.esci.2023.100115</a>","ieee":"Q. Zou, J. Qiu, Y. Zang, H. Tian, and L. Venkataraman, “Modulating single-molecule charge transport through external stimulus,” <i>eScience</i>, vol. 3, no. 3. Elsevier BV, 2023.","mla":"Zou, Qi, et al. “Modulating Single-Molecule Charge Transport through External Stimulus.” <i>EScience</i>, vol. 3, no. 3, 100115, Elsevier BV, 2023, doi:<a href=\"https://doi.org/10.1016/j.esci.2023.100115\">10.1016/j.esci.2023.100115</a>.","chicago":"Zou, Qi, Jin Qiu, Yaping Zang, He Tian, and Latha Venkataraman. “Modulating Single-Molecule Charge Transport through External Stimulus.” <i>EScience</i>. Elsevier BV, 2023. <a href=\"https://doi.org/10.1016/j.esci.2023.100115\">https://doi.org/10.1016/j.esci.2023.100115</a>.","ama":"Zou Q, Qiu J, Zang Y, Tian H, Venkataraman L. Modulating single-molecule charge transport through external stimulus. <i>eScience</i>. 2023;3(3). doi:<a href=\"https://doi.org/10.1016/j.esci.2023.100115\">10.1016/j.esci.2023.100115</a>"},"date_created":"2024-09-06T12:56:54Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2667-1417"]},"quality_controlled":"1","_id":"17863","year":"2023","OA_type":"gold","article_type":"original","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","date_updated":"2024-11-25T12:41:14Z","publisher":"Elsevier BV","status":"public","type":"journal_article","intvolume":"         3","doi":"10.1016/j.esci.2023.100115","title":"Modulating single-molecule charge transport through external stimulus","main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S2667141723000332?via%3Dihub"}],"author":[{"first_name":"Qi","full_name":"Zou, Qi","last_name":"Zou"},{"first_name":"Jin","full_name":"Qiu, Jin","last_name":"Qiu"},{"full_name":"Zang, Yaping","first_name":"Yaping","last_name":"Zang"},{"first_name":"He","full_name":"Tian, He","last_name":"Tian"},{"orcid":"0000-0002-6957-6089","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","full_name":"Venkataraman, Latha","last_name":"Venkataraman"}],"oa_version":"Published Version","issue":"3","publication":"eScience","abstract":[{"lang":"eng","text":"Understanding and tuning charge transport over a single molecule is a fundamental topic in molecular electronics. Single-molecule junctions composed of individual molecules attached to two electrodes are the most common components built for single-molecule charge transport studies. During the past two decades, rapid technical and theoretical advances in single-molecule junctions have increased our understanding of the conductance properties and functions of molecular devices. In this perspective article, we introduce the basic principles of charge transport in single-molecule junctions, then give an overview of recent progress in modulating single-molecule transport through external stimuli such as electric field and potential, light, mechanical force, heat, and chemical environment. Lastly, we discuss challenges and offer views on future developments in molecular electronics."}],"extern":"1","publication_status":"published","scopus_import":"1","article_number":"100115","OA_place":"publisher"},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"quality_controlled":"1","date_created":"2024-09-06T12:57:45Z","volume":145,"month":"01","article_processing_charge":"No","citation":{"ama":"Li L, Louie S, Evans AM, Meirzadeh E, Nuckolls C, Venkataraman L. Topological radical pairs produce ultrahigh conductance in long molecular wires. <i>Journal of the American Chemical Society</i>. 2023;145(4):2492-2498. doi:<a href=\"https://doi.org/10.1021/jacs.2c12059\">10.1021/jacs.2c12059</a>","chicago":"Li, Liang, Shayan Louie, Austin M. Evans, Elena Meirzadeh, Colin Nuckolls, and Latha Venkataraman. “Topological Radical Pairs Produce Ultrahigh Conductance in Long Molecular Wires.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/jacs.2c12059\">https://doi.org/10.1021/jacs.2c12059</a>.","ieee":"L. Li, S. Louie, A. M. Evans, E. Meirzadeh, C. Nuckolls, and L. Venkataraman, “Topological radical pairs produce ultrahigh conductance in long molecular wires,” <i>Journal of the American Chemical Society</i>, vol. 145, no. 4. American Chemical Society, pp. 2492–2498, 2023.","mla":"Li, Liang, et al. “Topological Radical Pairs Produce Ultrahigh Conductance in Long Molecular Wires.” <i>Journal of the American Chemical Society</i>, vol. 145, no. 4, American Chemical Society, 2023, pp. 2492–98, doi:<a href=\"https://doi.org/10.1021/jacs.2c12059\">10.1021/jacs.2c12059</a>.","apa":"Li, L., Louie, S., Evans, A. M., Meirzadeh, E., Nuckolls, C., &#38; Venkataraman, L. (2023). Topological radical pairs produce ultrahigh conductance in long molecular wires. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.2c12059\">https://doi.org/10.1021/jacs.2c12059</a>","short":"L. Li, S. Louie, A.M. Evans, E. Meirzadeh, C. Nuckolls, L. Venkataraman, Journal of the American Chemical Society 145 (2023) 2492–2498.","ista":"Li L, Louie S, Evans AM, Meirzadeh E, Nuckolls C, Venkataraman L. 2023. Topological radical pairs produce ultrahigh conductance in long molecular wires. Journal of the American Chemical Society. 145(4), 2492–2498."},"date_published":"2023-01-23T00:00:00Z","doi":"10.1021/jacs.2c12059","date_updated":"2024-11-25T14:21:10Z","publisher":"American Chemical Society","status":"public","type":"journal_article","intvolume":"       145","OA_type":"closed access","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","_id":"17864","page":"2492-2498","pmid":1,"year":"2023","author":[{"first_name":"Liang","last_name":"Li","full_name":"Li, Liang"},{"full_name":"Louie, Shayan","last_name":"Louie","first_name":"Shayan"},{"last_name":"Evans","full_name":"Evans, Austin M.","first_name":"Austin M."},{"full_name":"Meirzadeh, Elena","last_name":"Meirzadeh","first_name":"Elena"},{"last_name":"Nuckolls","full_name":"Nuckolls, Colin","first_name":"Colin"},{"orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha","last_name":"Venkataraman","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"}],"external_id":{"pmid":["36689781"]},"title":"Topological radical pairs produce ultrahigh conductance in long molecular wires","publication_status":"published","extern":"1","scopus_import":"1","issue":"4","publication":"Journal of the American Chemical Society","day":"23","abstract":[{"lang":"eng","text":"Molecular one-dimensional topological insulators (1D TIs), which conduct through energetically low-lying topological edge states, can be extremely highly conducting and exhibit a reversed conductance decay, affording them great potential as building blocks for nanoelectronic devices. However, these properties can only be observed at the short length limit. To extend the length at which these anomalous effects can be observed, we design topological oligo[n]emeraldine wires using short 1D TIs as building blocks. As the wire length increases, the number of topological states increases, enabling an increased electronic transmission along the wire; specifically, we show that we can drive over a microampere current through a single ∼5 nm molecular wire, appreciably more than what has been observed in other long wires reported to date. Calculations and experiments show that the longest oligo[7]emeraldine with doped topological states has over 106 enhancements in the transmission compared to its pristine form. The discovery of these highly conductive, long organic wires helps overcome a fundamental hurdle to implementing molecules in complex, nanoscale circuitry: their structures become too insulating at lengths that are useful in designing nanoscale circuits."}],"oa_version":"None"},{"year":"2023","pmid":1,"page":"567-572","_id":"17865","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","OA_type":"closed access","article_type":"original","intvolume":"        23","type":"journal_article","publisher":"American Chemical Society","status":"public","date_updated":"2024-11-25T14:49:19Z","doi":"10.1021/acs.nanolett.2c04098","date_published":"2023-01-05T00:00:00Z","citation":{"short":"Y. Wei, L. Li, J.E. Greenwald, L. Venkataraman, Nano Letters 23 (2023) 567–572.","ista":"Wei Y, Li L, Greenwald JE, Venkataraman L. 2023. Voltage-modulated van der waals interaction in single-molecule junctions. Nano Letters. 23(2), 567–572.","mla":"Wei, Yujing, et al. “Voltage-Modulated van Der Waals Interaction in Single-Molecule Junctions.” <i>Nano Letters</i>, vol. 23, no. 2, American Chemical Society, 2023, pp. 567–72, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.2c04098\">10.1021/acs.nanolett.2c04098</a>.","ieee":"Y. Wei, L. Li, J. E. Greenwald, and L. Venkataraman, “Voltage-modulated van der waals interaction in single-molecule junctions,” <i>Nano Letters</i>, vol. 23, no. 2. American Chemical Society, pp. 567–572, 2023.","apa":"Wei, Y., Li, L., Greenwald, J. E., &#38; Venkataraman, L. (2023). Voltage-modulated van der waals interaction in single-molecule junctions. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.2c04098\">https://doi.org/10.1021/acs.nanolett.2c04098</a>","ama":"Wei Y, Li L, Greenwald JE, Venkataraman L. Voltage-modulated van der waals interaction in single-molecule junctions. <i>Nano Letters</i>. 2023;23(2):567-572. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.2c04098\">10.1021/acs.nanolett.2c04098</a>","chicago":"Wei, Yujing, Liang Li, Julia E. Greenwald, and Latha Venkataraman. “Voltage-Modulated van Der Waals Interaction in Single-Molecule Junctions.” <i>Nano Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.nanolett.2c04098\">https://doi.org/10.1021/acs.nanolett.2c04098</a>."},"volume":23,"article_processing_charge":"No","month":"01","date_created":"2024-09-06T12:58:41Z","quality_controlled":"1","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"language":[{"iso":"eng"}],"oa_version":"None","abstract":[{"lang":"eng","text":"Understanding how molecular geometry affects the electronic properties of single-molecule junctions experimentally has been challenging. Typically, metal–molecule–metal junctions are measured using a break-junction method where electrode separation is mechanically evolving during measurement. Here, to probe the impact of the junction geometry on conductance, we apply a sinusoidal modulation to the molecular junction electrode position. Simultaneously, we probe the nonlinearity of the current–voltage characteristics of each junction through a modulation in the applied bias at a different frequency. In turn, we show that junctions formed with molecules that have different molecule–electrode interfaces exhibit statistically distinguishable Fourier-transformed conductances. In particular, we find a marked bias dependence for the modulation of junctions where transmission is mediated thorough the van der Waals (vdW) interaction. We attribute our findings to voltage-modulated vdW interactions at the single-molecule level."}],"day":"05","publication":"Nano Letters","issue":"2","extern":"1","publication_status":"published","title":"Voltage-modulated van der waals interaction in single-molecule junctions","external_id":{"pmid":["36602221"]},"author":[{"first_name":"Yujing","full_name":"Wei, Yujing","last_name":"Wei"},{"first_name":"Liang","full_name":"Li, Liang","last_name":"Li"},{"full_name":"Greenwald, Julia E.","last_name":"Greenwald","first_name":"Julia E."},{"full_name":"Venkataraman, Latha","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha","orcid":"0000-0002-6957-6089"}]},{"title":"Electric fields drive bond homolysis","main_file_link":[{"url":"https://europepmc.org/article/pmc/pmc9931054","open_access":"1"}],"external_id":{"pmid":["36819847"]},"author":[{"last_name":"Zhang","full_name":"Zhang, Boyuan","first_name":"Boyuan"},{"full_name":"Schaack, Cedric","last_name":"Schaack","first_name":"Cedric"},{"last_name":"Prindle","full_name":"Prindle, Claudia R.","first_name":"Claudia R."},{"full_name":"Vo, Ethan A.","first_name":"Ethan A.","last_name":"Vo"},{"last_name":"Aziz","full_name":"Aziz, Miriam","first_name":"Miriam"},{"full_name":"Steigerwald, Michael L.","last_name":"Steigerwald","first_name":"Michael L."},{"full_name":"Berkelbach, Timothy C.","first_name":"Timothy C.","last_name":"Berkelbach"},{"full_name":"Nuckolls, Colin","last_name":"Nuckolls","first_name":"Colin"},{"full_name":"Venkataraman, Latha","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha","orcid":"0000-0002-6957-6089"}],"oa_version":"Published Version","publication":"Chemical Science","issue":"7","abstract":[{"lang":"eng","text":"Electric fields have been used to control and direct chemical reactions in biochemistry and enzymatic catalysis, yet directly applying external electric fields to activate reactions in bulk solution and to characterize them ex situ remains a challenge. Here we utilize the scanning tunneling microscope-based break-junction technique to investigate the electric field driven homolytic cleavage of the radical initiator 4-(methylthio)benzoic peroxyanhydride at ambient temperatures in bulk solution, without the use of co-initiators or photochemical activators. Through time-dependent ex situ quantification by high performance liquid chromatography using a UV-vis detector, we find that the electric field catalyzes the reaction. Importantly, we demonstrate that the reaction rate in a field increases linearly with the solvent dielectric constant. Using density functional theory calculations, we show that the applied electric field decreases the dissociation energy of the O–O bond and stabilizes the product relative to the reactant due to their different dipole moments."}],"day":"16","publication_status":"published","extern":"1","OA_place":"publisher","date_published":"2023-01-16T00:00:00Z","oa":1,"month":"01","volume":14,"article_processing_charge":"Yes","citation":{"ista":"Zhang B, Schaack C, Prindle CR, Vo EA, Aziz M, Steigerwald ML, Berkelbach TC, Nuckolls C, Venkataraman L. 2023. Electric fields drive bond homolysis. Chemical Science. 14(7), 1769–1774.","short":"B. Zhang, C. Schaack, C.R. Prindle, E.A. Vo, M. Aziz, M.L. Steigerwald, T.C. Berkelbach, C. Nuckolls, L. Venkataraman, Chemical Science 14 (2023) 1769–1774.","apa":"Zhang, B., Schaack, C., Prindle, C. R., Vo, E. A., Aziz, M., Steigerwald, M. L., … Venkataraman, L. (2023). Electric fields drive bond homolysis. <i>Chemical Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d2sc06411a\">https://doi.org/10.1039/d2sc06411a</a>","mla":"Zhang, Boyuan, et al. “Electric Fields Drive Bond Homolysis.” <i>Chemical Science</i>, vol. 14, no. 7, Royal Society of Chemistry, 2023, pp. 1769–74, doi:<a href=\"https://doi.org/10.1039/d2sc06411a\">10.1039/d2sc06411a</a>.","ieee":"B. Zhang <i>et al.</i>, “Electric fields drive bond homolysis,” <i>Chemical Science</i>, vol. 14, no. 7. Royal Society of Chemistry, pp. 1769–1774, 2023.","chicago":"Zhang, Boyuan, Cedric Schaack, Claudia R. Prindle, Ethan A. Vo, Miriam Aziz, Michael L. Steigerwald, Timothy C. Berkelbach, Colin Nuckolls, and Latha Venkataraman. “Electric Fields Drive Bond Homolysis.” <i>Chemical Science</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d2sc06411a\">https://doi.org/10.1039/d2sc06411a</a>.","ama":"Zhang B, Schaack C, Prindle CR, et al. Electric fields drive bond homolysis. <i>Chemical Science</i>. 2023;14(7):1769-1774. doi:<a href=\"https://doi.org/10.1039/d2sc06411a\">10.1039/d2sc06411a</a>"},"date_created":"2024-09-06T12:59:45Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-6520"],"eissn":["2041-6539"]},"quality_controlled":"1","_id":"17866","page":"1769-1774","pmid":1,"year":"2023","OA_type":"gold","article_type":"original","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","date_updated":"2024-11-25T15:01:40Z","type":"journal_article","publisher":"Royal Society of Chemistry","status":"public","intvolume":"        14","doi":"10.1039/d2sc06411a"},{"title":"p-adic directions of primitive vectors","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"department":[{"_id":"TiBr"}],"file":[{"content_type":"application/pdf","file_size":1399390,"checksum":"cefc47a2cf55a87f8e4960197f73353b","file_id":"18186","creator":"dernst","date_created":"2024-10-07T11:32:32Z","access_level":"open_access","relation":"main_file","date_updated":"2024-10-07T11:32:32Z","file_name":"2023_MathBesancon_Guilloux.pdf","success":1}],"external_id":{"arxiv":["2103.10889"]},"license":"https://creativecommons.org/licenses/by-nd/4.0/","author":[{"first_name":"Antonin","full_name":"Guilloux, Antonin","last_name":"Guilloux"},{"first_name":"Tal","last_name":"Horesh","full_name":"Horesh, Tal","id":"C8B7BF48-8D81-11E9-BCA9-F536E6697425"}],"oa_version":"Published Version","abstract":[{"text":"Linnik type problems concern the distribution of projections of integral points on the unit sphere as their norm increases, and different generalizations of this phenomenon. Our work addresses a question of this type: we prove the uniform distribution of the projections of primitive Z2 points in the p-adic unit sphere, as their (real) norm tends to infinity. The proof is via counting lattice points in semi-simple S-arithmetic groups.","lang":"eng"},{"text":"Les problèmes de type Linnik concernent la distribution des projections des points entiers sur la sphère unitaire lorsque leur norme augmente et différentes généralisations de ce phénomène. Notre travail s’intéresse à une question de ce type : nous prouvons la distribution uniforme des projections des points primitifs de Z2 sur la sphère unitaire p-adique lorsque leur norme (réelle) tend vers l’infini. La preuve se fait en comptant les points d’un réseau dans des S-groupes arithmétiques semi-simples.","lang":"fre"}],"day":"15","ddc":["510"],"project":[{"name":"Between rational and integral points","_id":"26A8D266-B435-11E9-9278-68D0E5697425","grant_number":"EP-P026710-2"}],"publication":"Publications mathématiques de Besançon - Algèbre et Théorie des nombres","scopus_import":"1","publication_status":"published","corr_author":"1","has_accepted_license":"1","date_published":"2023-06-15T00:00:00Z","file_date_updated":"2024-10-07T11:32:32Z","citation":{"short":"A. Guilloux, T. Horesh, Publications Mathématiques de Besançon - Algèbre et Théorie Des Nombres 2023 (2023) 85–107.","ista":"Guilloux A, Horesh T. 2023. p-adic directions of primitive vectors. Publications mathématiques de Besançon - Algèbre et Théorie des nombres. 2023, 85–107.","ama":"Guilloux A, Horesh T. p-adic directions of primitive vectors. <i>Publications mathématiques de Besançon - Algèbre et Théorie des nombres</i>. 2023;2023:85-107. doi:<a href=\"https://doi.org/10.5802/pmb.50\">10.5802/pmb.50</a>","chicago":"Guilloux, Antonin, and Tal Horesh. “P-Adic Directions of Primitive Vectors.” <i>Publications Mathématiques de Besançon - Algèbre et Théorie Des Nombres</i>. Presses Universitaires de Franche-Comté, 2023. <a href=\"https://doi.org/10.5802/pmb.50\">https://doi.org/10.5802/pmb.50</a>.","ieee":"A. Guilloux and T. Horesh, “p-adic directions of primitive vectors,” <i>Publications mathématiques de Besançon - Algèbre et Théorie des nombres</i>, vol. 2023. Presses Universitaires de Franche-Comté, pp. 85–107, 2023.","mla":"Guilloux, Antonin, and Tal Horesh. “P-Adic Directions of Primitive Vectors.” <i>Publications Mathématiques de Besançon - Algèbre et Théorie Des Nombres</i>, vol. 2023, Presses Universitaires de Franche-Comté, 2023, pp. 85–107, doi:<a href=\"https://doi.org/10.5802/pmb.50\">10.5802/pmb.50</a>.","apa":"Guilloux, A., &#38; Horesh, T. (2023). p-adic directions of primitive vectors. <i>Publications Mathématiques de Besançon - Algèbre et Théorie Des Nombres</i>. Presses Universitaires de Franche-Comté. <a href=\"https://doi.org/10.5802/pmb.50\">https://doi.org/10.5802/pmb.50</a>"},"oa":1,"volume":2023,"month":"06","article_processing_charge":"Yes (in subscription journal)","arxiv":1,"date_created":"2024-10-06T22:01:13Z","quality_controlled":"1","publication_identifier":{"issn":["2804-8504"],"eissn":["2592-6616"]},"language":[{"iso":"eng"}],"year":"2023","_id":"18179","page":"85-107","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","intvolume":"      2023","date_updated":"2025-04-14T09:25:44Z","type":"journal_article","status":"public","publisher":"Presses Universitaires de Franche-Comté","acknowledgement":"The second author is supported by EPRSC grant EP/P026710/1.","doi":"10.5802/pmb.50"},{"scopus_import":"1","extern":"1","publication_status":"published","day":"21","abstract":[{"lang":"eng","text":"Strongly interacting topological matter1 exhibits fundamentally new phenomena with potential applications in quantum information technology2,3. Emblematic instances are fractional quantum Hall (FQH) states4, in which the interplay of a magnetic field and strong interactions gives rise to fractionally charged quasi-particles, long-ranged entanglement and anyonic exchange statistics. Progress in engineering synthetic magnetic fields5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21 has raised the hope to create these exotic states in controlled quantum systems. However, except for a recent Laughlin state of light22, preparing FQH states in engineered systems remains elusive. Here we realize a FQH state with ultracold atoms in an optical lattice. The state is a lattice version of a bosonic ν = 1/2 Laughlin state4,23 with two particles on 16 sites. This minimal system already captures many hallmark features of Laughlin-type FQH states24,25,26,27,28: we observe a suppression of two-body interactions, we find a distinctive vortex structure in the density correlations and we measure a fractional Hall conductivity of σH/σ0 = 0.6(2) by means of the bulk response to a magnetic perturbation. Furthermore, by tuning the magnetic field, we map out the transition point between the normal and the FQH regime through a spectroscopic investigation of the many-body gap. Our work provides a starting point for exploring highly entangled topological matter with ultracold atoms29,30,31,32,33."}],"issue":"7970","publication":"Nature","oa_version":"Preprint","author":[{"id":"b75b3f45-7995-11ef-9bfd-9a9cd02c3577","first_name":"Julian","full_name":"Leonard, Julian","last_name":"Leonard"},{"first_name":"Sooshin","last_name":"Kim","full_name":"Kim, Sooshin"},{"full_name":"Kwan, Joyce","last_name":"Kwan","first_name":"Joyce"},{"first_name":"Perrin","full_name":"Segura, Perrin","last_name":"Segura"},{"full_name":"Grusdt, Fabian","first_name":"Fabian","last_name":"Grusdt"},{"first_name":"Cécile","full_name":"Repellin, Cécile","last_name":"Repellin"},{"last_name":"Goldman","full_name":"Goldman, Nathan","first_name":"Nathan"},{"last_name":"Greiner","full_name":"Greiner, Markus","first_name":"Markus"}],"external_id":{"pmid":["37344594 "],"arxiv":["2210.10919"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.10919","open_access":"1"}],"title":"Realization of a fractional quantum Hall state with ultracold atoms","doi":"10.1038/s41586-023-06122-4","intvolume":"       619","date_updated":"2024-10-08T11:09:24Z","status":"public","publisher":"Springer Nature","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","pmid":1,"year":"2023","_id":"18189","page":"495-499","quality_controlled":"1","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"language":[{"iso":"eng"}],"arxiv":1,"date_created":"2024-10-07T11:46:13Z","citation":{"short":"J. Leonard, S. Kim, J. Kwan, P. Segura, F. Grusdt, C. Repellin, N. Goldman, M. Greiner, Nature 619 (2023) 495–499.","ista":"Leonard J, Kim S, Kwan J, Segura P, Grusdt F, Repellin C, Goldman N, Greiner M. 2023. Realization of a fractional quantum Hall state with ultracold atoms. Nature. 619(7970), 495–499.","ieee":"J. Leonard <i>et al.</i>, “Realization of a fractional quantum Hall state with ultracold atoms,” <i>Nature</i>, vol. 619, no. 7970. Springer Nature, pp. 495–499, 2023.","mla":"Leonard, Julian, et al. “Realization of a Fractional Quantum Hall State with Ultracold Atoms.” <i>Nature</i>, vol. 619, no. 7970, Springer Nature, 2023, pp. 495–99, doi:<a href=\"https://doi.org/10.1038/s41586-023-06122-4\">10.1038/s41586-023-06122-4</a>.","apa":"Leonard, J., Kim, S., Kwan, J., Segura, P., Grusdt, F., Repellin, C., … Greiner, M. (2023). Realization of a fractional quantum Hall state with ultracold atoms. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06122-4\">https://doi.org/10.1038/s41586-023-06122-4</a>","ama":"Leonard J, Kim S, Kwan J, et al. Realization of a fractional quantum Hall state with ultracold atoms. <i>Nature</i>. 2023;619(7970):495-499. doi:<a href=\"https://doi.org/10.1038/s41586-023-06122-4\">10.1038/s41586-023-06122-4</a>","chicago":"Leonard, Julian, Sooshin Kim, Joyce Kwan, Perrin Segura, Fabian Grusdt, Cécile Repellin, Nathan Goldman, and Markus Greiner. “Realization of a Fractional Quantum Hall State with Ultracold Atoms.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06122-4\">https://doi.org/10.1038/s41586-023-06122-4</a>."},"oa":1,"month":"06","article_processing_charge":"No","volume":619,"date_published":"2023-06-21T00:00:00Z"},{"page":"481-485","_id":"18190","year":"2023","article_type":"letter_note","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","status":"public","type":"journal_article","date_updated":"2024-10-08T10:52:08Z","intvolume":"        19","doi":"10.1038/s41567-022-01887-3","date_published":"2023-01-26T00:00:00Z","month":"01","volume":19,"article_processing_charge":"No","oa":1,"citation":{"ama":"Leonard J, Kim S, Rispoli M, et al. Probing the onset of quantum avalanches in a many-body localized system. <i>Nature Physics</i>. 2023;19(4):481-485. doi:<a href=\"https://doi.org/10.1038/s41567-022-01887-3\">10.1038/s41567-022-01887-3</a>","chicago":"Leonard, Julian, Sooshin Kim, Matthew Rispoli, Alexander Lukin, Robert Schittko, Joyce Kwan, Eugene Demler, Dries Sels, and Markus Greiner. “Probing the Onset of Quantum Avalanches in a Many-Body Localized System.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-022-01887-3\">https://doi.org/10.1038/s41567-022-01887-3</a>.","apa":"Leonard, J., Kim, S., Rispoli, M., Lukin, A., Schittko, R., Kwan, J., … Greiner, M. (2023). Probing the onset of quantum avalanches in a many-body localized system. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-022-01887-3\">https://doi.org/10.1038/s41567-022-01887-3</a>","ieee":"J. Leonard <i>et al.</i>, “Probing the onset of quantum avalanches in a many-body localized system,” <i>Nature Physics</i>, vol. 19, no. 4. Springer Nature, pp. 481–485, 2023.","mla":"Leonard, Julian, et al. “Probing the Onset of Quantum Avalanches in a Many-Body Localized System.” <i>Nature Physics</i>, vol. 19, no. 4, Springer Nature, 2023, pp. 481–85, doi:<a href=\"https://doi.org/10.1038/s41567-022-01887-3\">10.1038/s41567-022-01887-3</a>.","ista":"Leonard J, Kim S, Rispoli M, Lukin A, Schittko R, Kwan J, Demler E, Sels D, Greiner M. 2023. Probing the onset of quantum avalanches in a many-body localized system. Nature Physics. 19(4), 481–485.","short":"J. Leonard, S. Kim, M. Rispoli, A. Lukin, R. Schittko, J. Kwan, E. Demler, D. Sels, M. Greiner, Nature Physics 19 (2023) 481–485."},"date_created":"2024-10-07T11:46:33Z","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"oa_version":"Preprint","issue":"4","publication":"Nature Physics","day":"26","abstract":[{"text":"Strongly correlated systems can exhibit unexpected phenomena when brought in a state far from equilibrium. An example is many-body localization, which prevents generic interacting systems from reaching thermal equilibrium even at long times1,2. The stability of the many-body localized phase has been predicted to be hindered by the presence of small thermal inclusions that act as a bath, leading to the delocalization of the entire system through an avalanche propagation mechanism3,4,5,6,7,8. Here we study the dynamics of a thermal inclusion of variable size when it is coupled to a many-body localized system. We find evidence for accelerated transport of thermal inclusion into the localized region. We monitor how the avalanche spreads through the localized system and thermalizes it site by site by measuring the site-resolved entropy over time. Furthermore, we isolate the strongly correlated bath-induced dynamics with multipoint correlations between the bath and the system. Our results have implications on the robustness of many-body localized systems and their critical behaviour.","lang":"eng"}],"publication_status":"published","extern":"1","scopus_import":"1","title":"Probing the onset of quantum avalanches in a many-body localized system","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2012.15270","open_access":"1"}],"external_id":{"arxiv":["2012.15270"]},"author":[{"first_name":"Julian","id":"b75b3f45-7995-11ef-9bfd-9a9cd02c3577","full_name":"Leonard, Julian","last_name":"Leonard"},{"first_name":"Sooshin","full_name":"Kim, Sooshin","last_name":"Kim"},{"last_name":"Rispoli","full_name":"Rispoli, Matthew","first_name":"Matthew"},{"last_name":"Lukin","full_name":"Lukin, Alexander","first_name":"Alexander"},{"full_name":"Schittko, Robert","first_name":"Robert","last_name":"Schittko"},{"first_name":"Joyce","full_name":"Kwan, Joyce","last_name":"Kwan"},{"full_name":"Demler, Eugene","last_name":"Demler","first_name":"Eugene"},{"full_name":"Sels, Dries","first_name":"Dries","last_name":"Sels"},{"first_name":"Markus","last_name":"Greiner","full_name":"Greiner, Markus"}]},{"date_created":"2024-10-08T12:46:41Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["2045-2322"]},"date_published":"2023-04-13T00:00:00Z","oa":1,"article_processing_charge":"No","volume":13,"month":"04","citation":{"short":"A.M. Bronstein, A. Marx, Scientific Reports 13 (2023).","ista":"Bronstein AM, Marx A. 2023. Water stabilizes an alternate turn conformation in horse heart myoglobin. Scientific Reports. 13, 6094.","chicago":"Bronstein, Alex M., and Ailie Marx. “Water Stabilizes an Alternate Turn Conformation in Horse Heart Myoglobin.” <i>Scientific Reports</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41598-023-32821-z\">https://doi.org/10.1038/s41598-023-32821-z</a>.","ama":"Bronstein AM, Marx A. Water stabilizes an alternate turn conformation in horse heart myoglobin. <i>Scientific Reports</i>. 2023;13. doi:<a href=\"https://doi.org/10.1038/s41598-023-32821-z\">10.1038/s41598-023-32821-z</a>","mla":"Bronstein, Alex M., and Ailie Marx. “Water Stabilizes an Alternate Turn Conformation in Horse Heart Myoglobin.” <i>Scientific Reports</i>, vol. 13, 6094, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41598-023-32821-z\">10.1038/s41598-023-32821-z</a>.","ieee":"A. M. Bronstein and A. Marx, “Water stabilizes an alternate turn conformation in horse heart myoglobin,” <i>Scientific Reports</i>, vol. 13. Springer Nature, 2023.","apa":"Bronstein, A. M., &#38; Marx, A. (2023). Water stabilizes an alternate turn conformation in horse heart myoglobin. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-023-32821-z\">https://doi.org/10.1038/s41598-023-32821-z</a>"},"date_updated":"2024-10-09T10:39:26Z","type":"journal_article","status":"public","publisher":"Springer Nature","intvolume":"        13","doi":"10.1038/s41598-023-32821-z","_id":"18207","pmid":1,"year":"2023","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["37055458"]},"author":[{"orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander","first_name":"Alexander","last_name":"Bronstein"},{"last_name":"Marx","first_name":"Ailie","full_name":"Marx, Ailie"}],"title":"Water stabilizes an alternate turn conformation in horse heart myoglobin","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41598-023-32821-z"}],"tmp":{"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)","image":"/images/cc_by.png"},"publication_status":"published","extern":"1","scopus_import":"1","article_number":"6094","has_accepted_license":"1","oa_version":"Published Version","publication":"Scientific Reports","day":"13","abstract":[{"lang":"eng","text":"Comparison of myoglobin structures reveals that protein isolated from horse heart consistently adopts an alternate turn conformation in comparison to its homologues. Analysis of hundreds of high-resolution structures discounts crystallization conditions or the surrounding amino acid protein environment as explaining this difference, that is also not captured by the AlphaFold prediction. Rather, a water molecule is identified as stabilizing the conformation in the horse heart structure, which immediately reverts to the whale conformation in molecular dynamics simulations excluding that structural water."}]},{"oa_version":"Preprint","publication":"Nature Computational Science","issue":"10","day":"05","abstract":[{"lang":"eng","text":"The holy grail of materials science is de novo molecular design, meaning engineering molecules with desired characteristics. The introduction of generative deep learning has greatly advanced efforts in this direction, yet molecular discovery remains challenging and often inefficient. Herein we introduce GaUDI, a guided diffusion model for inverse molecular design that combines an equivariant graph neural net for property prediction and a generative diffusion model. We demonstrate GaUDI’s effectiveness in designing molecules for organic electronic applications by using single- and multiple-objective tasks applied to a generated dataset of 475,000 polycyclic aromatic systems. GaUDI shows improved conditional design, generating molecules with optimal properties and even going beyond the original distribution to suggest better molecules than those in the dataset. In addition to point-wise targets, GaUDI can also be guided toward open-ended targets (for example, a minimum or maximum) and in all cases achieves close to 100% validity of generated molecules."}],"extern":"1","publication_status":"published","scopus_import":"1","title":"Guided diffusion for inverse molecular design","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv-2023-z8ltp"}],"external_id":{"pmid":["38177755"]},"author":[{"full_name":"Weiss, Tomer","last_name":"Weiss","first_name":"Tomer"},{"last_name":"Mayo Yanes","full_name":"Mayo Yanes, Eduardo","first_name":"Eduardo"},{"first_name":"Sabyasachi","full_name":"Chakraborty, Sabyasachi","last_name":"Chakraborty"},{"last_name":"Cosmo","full_name":"Cosmo, Luca","first_name":"Luca"},{"last_name":"Bronstein","full_name":"Bronstein, Alexander","first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","orcid":"0000-0001-9699-8730"},{"full_name":"Gershoni-Poranne, Renana","first_name":"Renana","last_name":"Gershoni-Poranne"}],"_id":"18208","page":"873-882","pmid":1,"year":"2023","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-09T10:44:41Z","status":"public","type":"journal_article","publisher":"Springer Nature","intvolume":"         3","doi":"10.1038/s43588-023-00532-0","date_published":"2023-10-05T00:00:00Z","oa":1,"month":"10","article_processing_charge":"No","volume":3,"citation":{"apa":"Weiss, T., Mayo Yanes, E., Chakraborty, S., Cosmo, L., Bronstein, A. M., &#38; Gershoni-Poranne, R. (2023). Guided diffusion for inverse molecular design. <i>Nature Computational Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43588-023-00532-0\">https://doi.org/10.1038/s43588-023-00532-0</a>","mla":"Weiss, Tomer, et al. “Guided Diffusion for Inverse Molecular Design.” <i>Nature Computational Science</i>, vol. 3, no. 10, Springer Nature, 2023, pp. 873–82, doi:<a href=\"https://doi.org/10.1038/s43588-023-00532-0\">10.1038/s43588-023-00532-0</a>.","ieee":"T. Weiss, E. Mayo Yanes, S. Chakraborty, L. Cosmo, A. M. Bronstein, and R. Gershoni-Poranne, “Guided diffusion for inverse molecular design,” <i>Nature Computational Science</i>, vol. 3, no. 10. Springer Nature, pp. 873–882, 2023.","chicago":"Weiss, Tomer, Eduardo Mayo Yanes, Sabyasachi Chakraborty, Luca Cosmo, Alex M. Bronstein, and Renana Gershoni-Poranne. “Guided Diffusion for Inverse Molecular Design.” <i>Nature Computational Science</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s43588-023-00532-0\">https://doi.org/10.1038/s43588-023-00532-0</a>.","ama":"Weiss T, Mayo Yanes E, Chakraborty S, Cosmo L, Bronstein AM, Gershoni-Poranne R. Guided diffusion for inverse molecular design. <i>Nature Computational Science</i>. 2023;3(10):873-882. doi:<a href=\"https://doi.org/10.1038/s43588-023-00532-0\">10.1038/s43588-023-00532-0</a>","ista":"Weiss T, Mayo Yanes E, Chakraborty S, Cosmo L, Bronstein AM, Gershoni-Poranne R. 2023. Guided diffusion for inverse molecular design. Nature Computational Science. 3(10), 873–882.","short":"T. Weiss, E. Mayo Yanes, S. Chakraborty, L. Cosmo, A.M. Bronstein, R. Gershoni-Poranne, Nature Computational Science 3 (2023) 873–882."},"date_created":"2024-10-08T12:46:58Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["2662-8457"]}},{"title":"Interpretable deep-learning unveils structure–property relationships in polybenzenoid hydrocarbons","main_file_link":[{"url":"10.26434/chemrxiv-2022-krng1","open_access":"1"}],"external_id":{"pmid":["36696660"]},"author":[{"full_name":"Weiss, Tomer","first_name":"Tomer","last_name":"Weiss"},{"full_name":"Wahab, Alexandra","first_name":"Alexandra","last_name":"Wahab"},{"orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander"},{"first_name":"Renana","full_name":"Gershoni-Poranne, Renana","last_name":"Gershoni-Poranne"}],"oa_version":"Preprint","publication":"The Journal of Organic Chemistry","issue":"14","abstract":[{"text":"In this work, interpretable deep learning was used to identify structure–property relationships governing the HOMO–LUMO gap and the relative stability of polybenzenoid hydrocarbons (PBHs) using a ring-based graph representation. This representation was combined with a subunit-based perception of PBHs, allowing chemical insights to be presented in terms of intuitive and simple structural motifs. The resulting insights agree with conventional organic chemistry knowledge and electronic structure-based analyses and also reveal new behaviors and identify influential structural motifs. In particular, we evaluated and compared the effects of linear, angular, and branching motifs on these two molecular properties and explored the role of dispersion in mitigating the torsional strain inherent in nonplanar PBHs. Hence, the observed regularities and the proposed analysis contribute to a deeper understanding of the behavior of PBHs and form the foundation for design strategies for new functional PBHs.","lang":"eng"}],"day":"25","publication_status":"published","extern":"1","scopus_import":"1","date_published":"2023-01-25T00:00:00Z","oa":1,"volume":88,"article_processing_charge":"No","month":"01","citation":{"chicago":"Weiss, Tomer, Alexandra Wahab, Alex M. Bronstein, and Renana Gershoni-Poranne. “Interpretable Deep-Learning Unveils Structure–Property Relationships in Polybenzenoid Hydrocarbons.” <i>The Journal of Organic Chemistry</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.joc.2c02381\">https://doi.org/10.1021/acs.joc.2c02381</a>.","ama":"Weiss T, Wahab A, Bronstein AM, Gershoni-Poranne R. Interpretable deep-learning unveils structure–property relationships in polybenzenoid hydrocarbons. <i>The Journal of Organic Chemistry</i>. 2023;88(14):9645-9656. doi:<a href=\"https://doi.org/10.1021/acs.joc.2c02381\">10.1021/acs.joc.2c02381</a>","apa":"Weiss, T., Wahab, A., Bronstein, A. M., &#38; Gershoni-Poranne, R. (2023). Interpretable deep-learning unveils structure–property relationships in polybenzenoid hydrocarbons. <i>The Journal of Organic Chemistry</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.joc.2c02381\">https://doi.org/10.1021/acs.joc.2c02381</a>","ieee":"T. Weiss, A. Wahab, A. M. Bronstein, and R. Gershoni-Poranne, “Interpretable deep-learning unveils structure–property relationships in polybenzenoid hydrocarbons,” <i>The Journal of Organic Chemistry</i>, vol. 88, no. 14. American Chemical Society, pp. 9645–9656, 2023.","mla":"Weiss, Tomer, et al. “Interpretable Deep-Learning Unveils Structure–Property Relationships in Polybenzenoid Hydrocarbons.” <i>The Journal of Organic Chemistry</i>, vol. 88, no. 14, American Chemical Society, 2023, pp. 9645–56, doi:<a href=\"https://doi.org/10.1021/acs.joc.2c02381\">10.1021/acs.joc.2c02381</a>.","ista":"Weiss T, Wahab A, Bronstein AM, Gershoni-Poranne R. 2023. Interpretable deep-learning unveils structure–property relationships in polybenzenoid hydrocarbons. The Journal of Organic Chemistry. 88(14), 9645–9656.","short":"T. Weiss, A. Wahab, A.M. Bronstein, R. Gershoni-Poranne, The Journal of Organic Chemistry 88 (2023) 9645–9656."},"date_created":"2024-10-08T12:47:17Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1520-6904"],"issn":["0022-3263"]},"_id":"18209","page":"9645-9656","year":"2023","pmid":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-09T10:49:42Z","type":"journal_article","publisher":"American Chemical Society","status":"public","intvolume":"        88","doi":"10.1021/acs.joc.2c02381"},{"date_updated":"2024-10-09T11:21:19Z","type":"conference","status":"public","publisher":"Association for Computing Machinery","extern":"1","publication_status":"published","scopus_import":"1","intvolume":"        11","doi":"10.1145/3582016.3582029","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.7699872"}]},"_id":"18212","page":"282-301","oa_version":"None","year":"2023","publication":"Proceedings of the 28th ACM International Conference on Architectural Support for Programming Languages and Operating Systems","issue":"3","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The high memory bandwidth demand of sparse embedding layers continues to be a critical challenge in scaling the performance of recommendation models. While prior works have exploited heterogeneous memory system designs and partial embedding sum memoization techniques, they offer limited benefits. This is because prior designs either target a very small subset of embeddings to simplify their analysis or incur a high processing cost to account for all embeddings, which does not scale with the large sizes of modern embedding tables. This paper proposes GRACE-a lightweight and scalable graph-based algorithm-system co-design framework to significantly improve the embedding layer performance of recommendation models. GRACE proposes a novel Item Co-occurrence Graph (ICG) that scalably records item co-occurrences. GRACE then presents a new system-aware ICG clustering algorithm to find frequently accessed item combinations of arbitrary lengths to compute and memoize their partial sums. High-frequency partial sums are stored in a software-managed cache space to reduce memory traffic and improve the throughput of computing sparse features. We further present a cache data layout and low-cost address computation logic to efficiently lookup item embeddings and their partial sums. Our evaluation shows that GRACE significantly outperforms the state-of-the-art techniques SPACE and MERCI by 1.5x and 1.4x, respectively.","lang":"eng"}],"date_created":"2024-10-08T12:48:11Z","author":[{"first_name":"Haojie","last_name":"Ye","full_name":"Ye, Haojie"},{"last_name":"Vedula","first_name":"Sanketh","full_name":"Vedula, Sanketh"},{"full_name":"Chen, Yuhan","last_name":"Chen","first_name":"Yuhan"},{"full_name":"Yang, Yichen","first_name":"Yichen","last_name":"Yang"},{"orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein"},{"last_name":"Dreslinski","full_name":"Dreslinski, Ronald","first_name":"Ronald"},{"full_name":"Mudge, Trevor","last_name":"Mudge","first_name":"Trevor"},{"first_name":"Nishil","last_name":"Talati","full_name":"Talati, Nishil"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450399180"]},"quality_controlled":"1","title":"GRACE: A scalable graph-based approach to accelerating recommendation model inference","date_published":"2023-03-01T00:00:00Z","article_processing_charge":"No","month":"03","volume":11,"citation":{"ieee":"H. Ye <i>et al.</i>, “GRACE: A scalable graph-based approach to accelerating recommendation model inference,” in <i>Proceedings of the 28th ACM International Conference on Architectural Support for Programming Languages and Operating Systems</i>, 2023, vol. 11, no. 3, pp. 282–301.","mla":"Ye, Haojie, et al. “GRACE: A Scalable Graph-Based Approach to Accelerating Recommendation Model Inference.” <i>Proceedings of the 28th ACM International Conference on Architectural Support for Programming Languages and Operating Systems</i>, vol. 11, no. 3, Association for Computing Machinery, 2023, pp. 282–301, doi:<a href=\"https://doi.org/10.1145/3582016.3582029\">10.1145/3582016.3582029</a>.","apa":"Ye, H., Vedula, S., Chen, Y., Yang, Y., Bronstein, A. M., Dreslinski, R., … Talati, N. (2023). GRACE: A scalable graph-based approach to accelerating recommendation model inference. In <i>Proceedings of the 28th ACM International Conference on Architectural Support for Programming Languages and Operating Systems</i> (Vol. 11, pp. 282–301). Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3582016.3582029\">https://doi.org/10.1145/3582016.3582029</a>","chicago":"Ye, Haojie, Sanketh Vedula, Yuhan Chen, Yichen Yang, Alex M. Bronstein, Ronald Dreslinski, Trevor Mudge, and Nishil Talati. “GRACE: A Scalable Graph-Based Approach to Accelerating Recommendation Model Inference.” In <i>Proceedings of the 28th ACM International Conference on Architectural Support for Programming Languages and Operating Systems</i>, 11:282–301. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3582016.3582029\">https://doi.org/10.1145/3582016.3582029</a>.","ama":"Ye H, Vedula S, Chen Y, et al. GRACE: A scalable graph-based approach to accelerating recommendation model inference. In: <i>Proceedings of the 28th ACM International Conference on Architectural Support for Programming Languages and Operating Systems</i>. Vol 11. Association for Computing Machinery; 2023:282-301. doi:<a href=\"https://doi.org/10.1145/3582016.3582029\">10.1145/3582016.3582029</a>","short":"H. Ye, S. Vedula, Y. Chen, Y. Yang, A.M. Bronstein, R. Dreslinski, T. Mudge, N. Talati, in:, Proceedings of the 28th ACM International Conference on Architectural Support for Programming Languages and Operating Systems, Association for Computing Machinery, 2023, pp. 282–301.","ista":"Ye H, Vedula S, Chen Y, Yang Y, Bronstein AM, Dreslinski R, Mudge T, Talati N. 2023. GRACE: A scalable graph-based approach to accelerating recommendation model inference. Proceedings of the 28th ACM International Conference on Architectural Support for Programming Languages and Operating Systems. vol. 11, 282–301."}},{"publication_identifier":{"issn":["1556-4681"],"eissn":["1556-472X"]},"quality_controlled":"1","language":[{"iso":"eng"}],"author":[{"full_name":"Hermanns, Judith","last_name":"Hermanns","first_name":"Judith"},{"first_name":"Konstantinos","last_name":"Skitsas","full_name":"Skitsas, Konstantinos"},{"full_name":"Tsitsulin, Anton","last_name":"Tsitsulin","first_name":"Anton"},{"first_name":"Marina","full_name":"Munkhoeva, Marina","last_name":"Munkhoeva"},{"first_name":"Alexander","full_name":"Kyster, Alexander","last_name":"Kyster"},{"full_name":"Nielsen, Simon","first_name":"Simon","last_name":"Nielsen"},{"orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein","first_name":"Alexander","full_name":"Bronstein, Alexander"},{"last_name":"Mottin","full_name":"Mottin, Davide","first_name":"Davide"},{"full_name":"Karras, Panagiotis","last_name":"Karras","first_name":"Panagiotis"}],"date_created":"2024-10-08T12:48:38Z","citation":{"ista":"Hermanns J, Skitsas K, Tsitsulin A, Munkhoeva M, Kyster A, Nielsen S, Bronstein AM, Mottin D, Karras P. 2023. GRASP: Scalable graph alignment by spectral corresponding functions. ACM Transactions on Knowledge Discovery from Data. 17(4), 50.","short":"J. Hermanns, K. Skitsas, A. Tsitsulin, M. Munkhoeva, A. Kyster, S. Nielsen, A.M. Bronstein, D. Mottin, P. Karras, ACM Transactions on Knowledge Discovery from Data 17 (2023).","apa":"Hermanns, J., Skitsas, K., Tsitsulin, A., Munkhoeva, M., Kyster, A., Nielsen, S., … Karras, P. (2023). GRASP: Scalable graph alignment by spectral corresponding functions. <i>ACM Transactions on Knowledge Discovery from Data</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3561058\">https://doi.org/10.1145/3561058</a>","ieee":"J. Hermanns <i>et al.</i>, “GRASP: Scalable graph alignment by spectral corresponding functions,” <i>ACM Transactions on Knowledge Discovery from Data</i>, vol. 17, no. 4. Association for Computing Machinery, 2023.","mla":"Hermanns, Judith, et al. “GRASP: Scalable Graph Alignment by Spectral Corresponding Functions.” <i>ACM Transactions on Knowledge Discovery from Data</i>, vol. 17, no. 4, 50, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3561058\">10.1145/3561058</a>.","ama":"Hermanns J, Skitsas K, Tsitsulin A, et al. GRASP: Scalable graph alignment by spectral corresponding functions. <i>ACM Transactions on Knowledge Discovery from Data</i>. 2023;17(4). doi:<a href=\"https://doi.org/10.1145/3561058\">10.1145/3561058</a>","chicago":"Hermanns, Judith, Konstantinos Skitsas, Anton Tsitsulin, Marina Munkhoeva, Alexander Kyster, Simon Nielsen, Alex M. Bronstein, Davide Mottin, and Panagiotis Karras. “GRASP: Scalable Graph Alignment by Spectral Corresponding Functions.” <i>ACM Transactions on Knowledge Discovery from Data</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3561058\">https://doi.org/10.1145/3561058</a>."},"article_processing_charge":"No","volume":17,"month":"02","date_published":"2023-02-24T00:00:00Z","title":"GRASP: Scalable graph alignment by spectral corresponding functions","doi":"10.1145/3561058","article_number":"50","intvolume":"        17","scopus_import":"1","publisher":"Association for Computing Machinery","extern":"1","type":"journal_article","publication_status":"published","status":"public","date_updated":"2024-10-09T11:24:50Z","day":"24","abstract":[{"text":"What is the best way to match the nodes of two graphs? This graph alignment problem generalizes graph isomorphism and arises in applications from social network analysis to bioinformatics. Some solutions assume that auxiliary information on known matches or node or edge attributes is available, or utilize arbitrary graph features. Such methods fare poorly in the pure form of the problem, in which only graph structures are given. Other proposals translate the problem to one of aligning node embeddings, yet, by doing so, provide only a single-scale view of the graph.\r\nIn this article, we transfer the shape-analysis concept of functional maps from the continuous to the discrete case, and treat the graph alignment problem as a special case of the problem of finding a mapping between functions on graphs. We present GRASP, a method that first establishes a correspondence between functions derived from Laplacian matrix eigenvectors, which capture multiscale structural characteristics, and then exploits this correspondence to align nodes. We enhance the basic form of GRASP by altering two of its components, namely the embedding method and the assignment procedure it employs, leveraging its modular, hence adaptable design. Our experimental study, featuring noise levels higher than anything used in previous studies, shows that the enhanced form of GRASP outperforms scalable state-of-the-art methods for graph alignment across noise levels and graph types, and performs competitively with respect to the best non-scalable ones. We include in our study another modular graph alignment algorithm, CONE, which is also adaptable thanks to its modular nature, and show it can manage graphs with skewed power-law degree distributions.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","publication":"ACM Transactions on Knowledge Discovery from Data","issue":"4","year":"2023","oa_version":"None","_id":"18213"},{"issue":"3","publication":"Proceedings of the VLDB Endowment","day":"01","abstract":[{"lang":"eng","text":"Graph sparsification is a technique that approximates a given graph by a sparse graph with a subset of vertices and/or edges. The goal of an effective sparsification algorithm is to maintain specific graph properties relevant to the downstream task while minimizing the graph's size. Graph algorithms often suffer from long execution time due to the irregularity and the large real-world graph size. Graph sparsification can be applied to greatly reduce the run time of graph algorithms by substituting the full graph with a much smaller sparsified graph, without significantly degrading the output quality. However, the interaction between numerous sparsifiers and graph properties is not widely explored, and the potential of graph sparsification is not fully understood.</jats:p>\r\n          <jats:p>In this work, we cover 16 widely-used graph metrics, 12 representative graph sparsification algorithms, and 14 real-world input graphs spanning various categories, exhibiting diverse characteristics, sizes, and densities. We developed a framework to extensively assess the performance of these sparsification algorithms against graph metrics, and provide insights to the results. Our study shows that there is no one sparsifier that performs the best in preserving all graph properties, e.g. sparsifiers that preserve distance-related graph properties (eccentricity) struggle to perform well on Graph Neural Networks (GNN). This paper presents a comprehensive experimental study evaluating the performance of sparsification algorithms in preserving essential graph metrics. The insights inform future research in incorporating matching graph sparsification to graph algorithms to maximize benefits while minimizing quality degradation. Furthermore, we provide a framework to facilitate the future evaluation of evolving sparsification algorithms, graph metrics, and ever-growing graph data."}],"oa_version":"Preprint","extern":"1","publication_status":"published","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2311.12314","open_access":"1"}],"title":"Demystifying graph sparsification algorithms in graph properties preservation","author":[{"full_name":"Chen, Yuhan","last_name":"Chen","first_name":"Yuhan"},{"full_name":"Ye, Haojie","last_name":"Ye","first_name":"Haojie"},{"first_name":"Sanketh","last_name":"Vedula","full_name":"Vedula, Sanketh"},{"first_name":"Alexander","full_name":"Bronstein, Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein","orcid":"0000-0001-9699-8730"},{"first_name":"Ronald","full_name":"Dreslinski, Ronald","last_name":"Dreslinski"},{"first_name":"Trevor","full_name":"Mudge, Trevor","last_name":"Mudge"},{"last_name":"Talati","full_name":"Talati, Nishil","first_name":"Nishil"}],"external_id":{"arxiv":["2311.12314"]},"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"427-440","_id":"18214","year":"2023","doi":"10.14778/3632093.3632106","status":"public","publisher":"Association for Computing Machinery","type":"journal_article","date_updated":"2024-10-09T11:28:33Z","intvolume":"        17","article_processing_charge":"No","volume":17,"month":"11","oa":1,"citation":{"ista":"Chen Y, Ye H, Vedula S, Bronstein AM, Dreslinski R, Mudge T, Talati N. 2023. Demystifying graph sparsification algorithms in graph properties preservation. Proceedings of the VLDB Endowment. 17(3), 427–440.","short":"Y. Chen, H. Ye, S. Vedula, A.M. Bronstein, R. Dreslinski, T. Mudge, N. Talati, Proceedings of the VLDB Endowment 17 (2023) 427–440.","apa":"Chen, Y., Ye, H., Vedula, S., Bronstein, A. M., Dreslinski, R., Mudge, T., &#38; Talati, N. (2023). Demystifying graph sparsification algorithms in graph properties preservation. <i>Proceedings of the VLDB Endowment</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.14778/3632093.3632106\">https://doi.org/10.14778/3632093.3632106</a>","ieee":"Y. Chen <i>et al.</i>, “Demystifying graph sparsification algorithms in graph properties preservation,” <i>Proceedings of the VLDB Endowment</i>, vol. 17, no. 3. Association for Computing Machinery, pp. 427–440, 2023.","mla":"Chen, Yuhan, et al. “Demystifying Graph Sparsification Algorithms in Graph Properties Preservation.” <i>Proceedings of the VLDB Endowment</i>, vol. 17, no. 3, Association for Computing Machinery, 2023, pp. 427–40, doi:<a href=\"https://doi.org/10.14778/3632093.3632106\">10.14778/3632093.3632106</a>.","chicago":"Chen, Yuhan, Haojie Ye, Sanketh Vedula, Alex M. Bronstein, Ronald Dreslinski, Trevor Mudge, and Nishil Talati. “Demystifying Graph Sparsification Algorithms in Graph Properties Preservation.” <i>Proceedings of the VLDB Endowment</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.14778/3632093.3632106\">https://doi.org/10.14778/3632093.3632106</a>.","ama":"Chen Y, Ye H, Vedula S, et al. Demystifying graph sparsification algorithms in graph properties preservation. <i>Proceedings of the VLDB Endowment</i>. 2023;17(3):427-440. doi:<a href=\"https://doi.org/10.14778/3632093.3632106\">10.14778/3632093.3632106</a>"},"date_published":"2023-11-01T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["2150-8097"]},"date_created":"2024-10-08T12:48:57Z","arxiv":1},{"title":"Using deep reinforcement learning for mmWave real-time scheduling","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2210.01423"}],"external_id":{"arxiv":["2210.01423"]},"author":[{"last_name":"Gahtan","first_name":"Barak","full_name":"Gahtan, Barak"},{"first_name":"Reuven","full_name":"Cohen, Reuven","last_name":"Cohen"},{"orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein","first_name":"Alexander"},{"last_name":"Kedar","full_name":"Kedar, Gil","first_name":"Gil"}],"oa_version":"Preprint","day":"01","abstract":[{"text":"We study the problem of real-time scheduling in a multi-hop millimeter-wave (mmWave) mesh. We develop a model-free deep reinforcement learning algorithm called Adaptive Activator RL (AARL), which determines the subset of mmWave links that should be activated during each time slot and the power level for each link. The most important property of AARL is its ability to make scheduling decisions within the strict time frame constraints of typical 5G mmWave networks. AARL can handle a variety of network topologies, network loads, and interference models, it can also adapt to different workloads. We demonstrate the operation of AARL on several topologies: a small topology with 10 links, a moderately-sized mesh with 48 links, and a large topology with 96 links. We show that for each topology, we compare the throughput obtained by AARL to that of a benchmark algorithm called RPMA (Residual Profit Maximizer Algorithm). The most important advantage of AARL compared to RPMA is that it is much faster and can make the necessary scheduling decisions very rapidly during every time slot, while RPMA cannot. In addition, the quality of the scheduling decisions made by AARL outperforms those made by RPMA.","lang":"eng"}],"publication":"14th International Conference on Network of the Future","scopus_import":"1","extern":"1","publication_status":"published","date_published":"2023-11-01T00:00:00Z","citation":{"ista":"Gahtan B, Cohen R, Bronstein AM, Kedar G. 2023. Using deep reinforcement learning for mmWave real-time scheduling. 14th International Conference on Network of the Future. NoF: Conference on Network of the Future, 71–79.","short":"B. Gahtan, R. Cohen, A.M. Bronstein, G. Kedar, in:, 14th International Conference on Network of the Future, IEEE, 2023, pp. 71–79.","apa":"Gahtan, B., Cohen, R., Bronstein, A. M., &#38; Kedar, G. (2023). Using deep reinforcement learning for mmWave real-time scheduling. In <i>14th International Conference on Network of the Future</i> (pp. 71–79). Izmir, Turkiye: IEEE. <a href=\"https://doi.org/10.1109/nof58724.2023.10302794\">https://doi.org/10.1109/nof58724.2023.10302794</a>","mla":"Gahtan, Barak, et al. “Using Deep Reinforcement Learning for MmWave Real-Time Scheduling.” <i>14th International Conference on Network of the Future</i>, IEEE, 2023, pp. 71–79, doi:<a href=\"https://doi.org/10.1109/nof58724.2023.10302794\">10.1109/nof58724.2023.10302794</a>.","ieee":"B. Gahtan, R. Cohen, A. M. Bronstein, and G. Kedar, “Using deep reinforcement learning for mmWave real-time scheduling,” in <i>14th International Conference on Network of the Future</i>, Izmir, Turkiye, 2023, pp. 71–79.","chicago":"Gahtan, Barak, Reuven Cohen, Alex M. Bronstein, and Gil Kedar. “Using Deep Reinforcement Learning for MmWave Real-Time Scheduling.” In <i>14th International Conference on Network of the Future</i>, 71–79. IEEE, 2023. <a href=\"https://doi.org/10.1109/nof58724.2023.10302794\">https://doi.org/10.1109/nof58724.2023.10302794</a>.","ama":"Gahtan B, Cohen R, Bronstein AM, Kedar G. Using deep reinforcement learning for mmWave real-time scheduling. In: <i>14th International Conference on Network of the Future</i>. IEEE; 2023:71-79. doi:<a href=\"https://doi.org/10.1109/nof58724.2023.10302794\">10.1109/nof58724.2023.10302794</a>"},"month":"11","article_processing_charge":"No","oa":1,"conference":{"location":"Izmir, Turkiye","start_date":"2023-10-04","end_date":"2023-10-06","name":"NoF: Conference on Network of the Future"},"date_created":"2024-10-08T12:50:18Z","arxiv":1,"publication_identifier":{"isbn":["9798350338089"],"eissn":["2833-0072"]},"quality_controlled":"1","language":[{"iso":"eng"}],"year":"2023","page":"71-79","_id":"18215","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","publisher":"IEEE","status":"public","date_updated":"2024-10-09T11:40:45Z","doi":"10.1109/nof58724.2023.10302794"},{"external_id":{"pmid":["37878722"]},"author":[{"full_name":"Rosenberg, Aviv A.","last_name":"Rosenberg","first_name":"Aviv A."},{"full_name":"Yehishalom, Nitsan","first_name":"Nitsan","last_name":"Yehishalom"},{"last_name":"Marx","full_name":"Marx, Ailie","first_name":"Ailie"},{"orcid":"0000-0001-9699-8730","first_name":"Alexander","full_name":"Bronstein, Alexander","last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6"}],"title":"An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2301064120"}],"scopus_import":"1","publication_status":"published","extern":"1","article_number":"e2301064120","oa_version":"Published Version","day":"25","abstract":[{"lang":"eng","text":"Protein structure, both at the global and local level, dictates function. Proteins fold from chains of amino acids, forming secondary structures, α-helices and β-strands, that, at least for globular proteins, subsequently fold into a three-dimensional structure. Here, we show that a Ramachandran-type plot focusing on the two dihedral angles separated by the peptide bond, and entirely contained within an amino acid pair, defines a local structural unit. We further demonstrate the usefulness of this cross-peptide-bond Ramachandran plot by showing that it captures β-turn conformations in coil regions, that traditional Ramachandran plot outliers fall into occupied regions of our plot, and that thermophilic proteins prefer specific amino acid pair conformations. Further, we demonstrate experimentally that the effect of a point mutation on backbone conformation and protein stability depends on the amino acid pair context, i.e., the identity of the adjacent amino acid, in a manner predictable by our method."}],"issue":"44","publication":"Proceedings of the National Academy of Sciences","date_created":"2024-10-08T12:50:36Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2023-10-25T00:00:00Z","citation":{"ista":"Rosenberg AA, Yehishalom N, Marx A, Bronstein AM. 2023. An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units. Proceedings of the National Academy of Sciences. 120(44), e2301064120.","short":"A.A. Rosenberg, N. Yehishalom, A. Marx, A.M. Bronstein, Proceedings of the National Academy of Sciences 120 (2023).","ama":"Rosenberg AA, Yehishalom N, Marx A, Bronstein AM. An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units. <i>Proceedings of the National Academy of Sciences</i>. 2023;120(44). doi:<a href=\"https://doi.org/10.1073/pnas.2301064120\">10.1073/pnas.2301064120</a>","chicago":"Rosenberg, Aviv A., Nitsan Yehishalom, Ailie Marx, and Alex M. Bronstein. “An Amino-Domino Model Described by a Cross-Peptide-Bond Ramachandran Plot Defines Amino Acid Pairs as Local Structural Units.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2301064120\">https://doi.org/10.1073/pnas.2301064120</a>.","apa":"Rosenberg, A. A., Yehishalom, N., Marx, A., &#38; Bronstein, A. M. (2023). An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2301064120\">https://doi.org/10.1073/pnas.2301064120</a>","mla":"Rosenberg, Aviv A., et al. “An Amino-Domino Model Described by a Cross-Peptide-Bond Ramachandran Plot Defines Amino Acid Pairs as Local Structural Units.” <i>Proceedings of the National Academy of Sciences</i>, vol. 120, no. 44, e2301064120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2301064120\">10.1073/pnas.2301064120</a>.","ieee":"A. A. Rosenberg, N. Yehishalom, A. Marx, and A. M. Bronstein, “An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units,” <i>Proceedings of the National Academy of Sciences</i>, vol. 120, no. 44. National Academy of Sciences, 2023."},"month":"10","article_processing_charge":"Yes (in subscription journal)","volume":120,"oa":1,"intvolume":"       120","publisher":"National Academy of Sciences","status":"public","type":"journal_article","date_updated":"2024-10-09T11:55:12Z","doi":"10.1073/pnas.2301064120","year":"2023","pmid":1,"_id":"18216","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original"}]