--- OA_place: publisher _id: '19271' abstract: - lang: eng text: "The medial habenula (MHb) is implicated in regulating emotional responses\r\nto aversive events. Studies in zebrafish have identified a remarkable morphological\r\nleft-right asymmetry in the dorsal habenula (zebrafish equivalent of mammalian\r\nMHb)-to-interpeduncular nucleus (IPN) pathway and its left-side specific role in\r\nmodulating fear responses. However, there is little evidence for structural or\r\nfunctional lateralization in the mammalian MHb-IPN pathway.\r\nHere, I investigated the synaptic properties of the left and right MHb\r\nafferents to the IPN in mice and addressed whether these synaptic connections\r\nselectively influence the expression of conditioned fear in mice. My findings reveal\r\nthat each individual IPN neuron receives inputs from both left and right MHb.\r\nElectrophysiological recordings from the same postsynaptic IPN neurons\r\ndemonstrate that the left MHb-originating synapses exhibit lower release\r\nprobability and higher \U0001D6FE-aminobutyric acid type B receptor (GABABR)-mediated\r\npotentiation compared to the right MHb-originating synapses. Interestingly,\r\nchemogenetic inhibition of cholinergic neurons in the left but not the right MHb\r\nsignificantly attenuated cue-dependent fear recall. Furthermore, conditional\r\ndeletion of GABABR in the left MHb interfered with the recall of cued fear memory,\r\nwhereas that in the right MHb neurons spared fear memory expression.\r\nCollectively, I demonstrate a functional asymmetry of the MHb in mice,\r\nrevealing a predominant role for GABABR-mediated signaling in the left MHb-IPN\r\npathway in the modulation of fear memories. These findings suggest that\r\nlateralized pathways could represent a fundamental principle in the neural\r\nregulation of emotion across species." acknowledged_ssus: - _id: PreCl - _id: M-Shop acknowledgement: "I would like to thank the European Research Council and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to Ryuichi Shigemoto and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), and the Austrian Neuroscience Association for providing financial support and opportunities, which were important in allowing me to present my work. I also wish to thank the\r\nPreclinical Facility, especially Michael Schunn, for always welcoming me from my earliest days as an intern. My gratitude goes as well to the Miba Machine Shop, in particular Todor Asenov, Astrit Arslani, and Thomas Menner, whose technical expertise often saved the day." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hüseyin C full_name: Önal, Hüseyin C id: 4659D740-F248-11E8-B48F-1D18A9856A87 last_name: Önal orcid: 0000-0002-2771-2011 citation: ama: Önal C. Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. 2025. doi:10.15479/AT-ISTA-19271 apa: Önal, C. (2025). Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19271 chicago: Önal, Cihan. “Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19271. ieee: C. Önal, “Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula,” Institute of Science and Technology Austria, 2025. ista: Önal C. 2025. Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula. Institute of Science and Technology Austria. mla: Önal, Cihan. Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19271. short: C. Önal, Asymmetrical Modulation of Fear Expression via GABAB Receptors in the Mouse Medial Habenula, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-02-28T14:15:53Z date_published: 2025-03-04T00:00:00Z date_updated: 2026-10-21T08:33:44Z day: '04' ddc: - '570' - '571' - '573' - '599' degree_awarded: PhD department: - _id: GradSch - _id: RySh doi: 10.15479/AT-ISTA-19271 ec_funded: 1 file: - access_level: closed checksum: c1a4d75a7471de9f954697b06cd18d28 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: hoenal date_created: 2025-02-28T13:57:01Z date_updated: 2026-02-01T23:30:02Z embargo_to: open_access file_id: '19272' file_name: Cihan_Onal_Thesis_Final.docx file_size: 25869143 relation: source_file - access_level: open_access checksum: de4e62147ab9f04098dc8cd898c630da content_type: application/pdf creator: hoenal date_created: 2025-02-28T13:57:04Z date_updated: 2026-02-01T23:30:02Z embargo: 2026-02-01 file_id: '19273' file_name: Cihan_Onal_Thesis_Final_pdfa.pdf file_size: 12077596 relation: main_file file_date_updated: 2026-02-01T23:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19271 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '03' oa: 1 oa_version: Published Version project: - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9437' relation: part_of_dissertation status: public - id: '15084' relation: part_of_dissertation status: public status: public supervisor: - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 title: Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '19478' abstract: - lang: eng text: "Auxin is one of the most important phytohormones, playing a crucial role in plant growth and \r\ndevelopment. Genetic studies in Arabidopsis have identified core components of auxin \r\nsignalling and established the classical transcriptional regulation mechanism. This classical \r\nparadigm recognizes TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN \r\nSIGNALLING F-BOX (AFB) proteins as auxin receptors possessing E3 ubiquitin ligase \r\nactivity. Auxin functions as a \"molecular glue\" enhancing TIR1/AFB-Aux/IAA \r\n(AUXIN/INDOLE-3-ACETIC ACID) inhibitor interactions, leading to Aux/IAAs’ \r\nubiquitination and degradation. This process releases AUXIN RESPONSE FACTORs (ARFs) \r\nfrom repression, enabling transcriptional activation of auxin-responsive genes. Notably, the \r\ndiscovery of adenylate cyclase (AC) activity in TIR1/AFBs, catalysing cAMP production from \r\nATP, presents novel transcriptional regulatory possibilities, though cAMP's mechanistic role \r\nin auxin signalling remains unclear. Beyond transcriptional regulation (slow response) a non\r\ntranscriptional pathway (rapid response) mediated by AFB1 also exists, as auxin triggers rapid \r\nroot growth inhibition within 30 seconds. How TIR1 and AFB1, with their distinct subcellular \r\nlocalizations, differentially regulate transcriptional and non-transcriptional processes remains \r\nunclear. To address these two key questions, this study conducted the following investigations. \r\nTIR1 and AFB1 display distinct subcellular localization patterns, with AFB1 specifically \r\nmediating auxin-induced rapid root growth inhibition. To examine whether subcellular \r\nlocalization differences contribute to functional divergence between TIR1 and AFB1, we \r\nutilized microfluidic systems combined with genetic complementation assays. Nuclear export \r\nsignal-fused TIR1 failed to rescue the rapid response defects observed in afb1 mutants. In \r\ncontrast, nuclear localization signal-fused AFB1 exhibited dual functional deficiencies: it \r\nneither restored the rapid response impairment in afb1 mutants nor compensated for \r\ntranscriptional regulation defects in tir1 mutants which limitation stemmed from AFB1's \r\nintrinsic incapacity to assemble functional SCF complexes. These results collectively establish \r\nthat the functional specialization of TIR1 and AFB1 is governed by both their subcellular \r\ncompartmentalization and inherent biochemical characteristics. \r\nThe mechanism by which cAMP derived from the auxin receptor TIR1/AFB modulates \r\ntranscriptional regulation remains undefined. To address this, we genetically dissociated TIR1 \r\nAC activity from its E3 ubiquitin ligase function to investigate cAMP's signalling role. AC\r\ninactivating mutations preserved TIR1-mediated Aux/IAAs’ degradation but abolished ARF\r\ni \r\ndependent transcriptional activation. tir1afb2 mutants expressing AC-deficient TIR1 variants \r\nfailed to restore transcriptional responses. Crucially, compartmentalized cAMP accumulation \r\nwithin Aux/IAA - ARF complexes vicinity triggered auxin signalling independently of both \r\nauxin perception and Aux/IAAs’ degradation, confirming its secondary messenger identity. \r\nFurther mechanistic analysis demonstrated cAMP directly interact with ARF. cAMP \r\ndirectly promotes ARF dissociation from Aux/IAA repressors and enhances ARF \r\nhomodimerization. Genetic complementation assays revealed that ARF mutants lacking \r\nconserved cAMP-binding motifs exhibited partial functional recovery, providing direct \r\nevidence for cAMP-ARF physical interaction during signal propagation. \r\nThese findings collectively challenge the established model of auxin signalling and define \r\na novel TIR1-cAMP-ARF regulatory axis, substantially advancing our comprehension of \r\nauxin-mediated physiological regulation. " acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: "This project was funded by the European Research Council Advanced Grant (ETAP-742985),\r\nEuropean Research Council (ERC; 101142681 CYNIPS), Austrian Science Fund (FWF; P\r\n37051-B)." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Huihuang full_name: Chen, Huihuang id: 83c96512-15b2-11ec-abd3-b7eede36184f last_name: Chen citation: ama: Chen H. The cAMP second messenger in auxin signalling. 2025. doi:10.15479/AT-ISTA-19478 apa: Chen, H. (2025). The cAMP second messenger in auxin signalling. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19478 chicago: Chen, Huihuang. “The CAMP Second Messenger in Auxin Signalling.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19478. ieee: H. Chen, “The cAMP second messenger in auxin signalling,” Institute of Science and Technology Austria, 2025. ista: Chen H. 2025. The cAMP second messenger in auxin signalling. Institute of Science and Technology Austria. mla: Chen, Huihuang. The CAMP Second Messenger in Auxin Signalling. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19478. short: H. Chen, The CAMP Second Messenger in Auxin Signalling, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-04-04T07:48:24Z date_published: 2025-04-04T00:00:00Z date_updated: 2026-10-23T07:25:54Z day: '04' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/AT-ISTA-19478 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: b154973663a1bba505683faab7ae5ead content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: hchen date_created: 2025-04-08T08:00:07Z date_updated: 2026-10-08T22:30:02Z embargo_to: open_access file_id: '19526' file_name: Thesis_0403_Huihuang.docx file_size: 16344814 relation: source_file - access_level: open_access checksum: 0099565f024388830c125ec17375c1a0 content_type: application/pdf creator: hchen date_created: 2025-04-08T08:00:06Z date_updated: 2026-10-09T22:30:03Z embargo: 2026-10-08 file_id: '19527' file_name: Thesis_0406_PDFA_Huihuang_1.pdf file_size: 8482147 relation: main_file file_date_updated: 2026-10-09T22:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-19478 has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '118' project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19421' relation: part_of_dissertation status: public - id: '13212' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: The cAMP second messenger in auxin signalling type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20467' abstract: - lang: eng text: "Prostaglandins play a central role in the inflammatory response. Prostaglandins are synthesized \r\nin a rate-limiting manner by the enzyme cyclooxygenase (Cox), which exists in two isoforms: \r\nthe Cox-2 and Cox-1 isoforms. Traditionally, Cox-1 is thought to mediate homeostatic \r\nfunctions due to its constitutive expression due to its constitutive expression, whereas Cox-2 is \r\ntemporary induced in response to inflammatory stimuli and is associated with the inflammatory \r\nresponse. Interestingly, in the central nervous system, Cox-1 is predominantly expressed in \r\nmicroglia. As the resident immune cells of the brain, microglia play a key role in inflammation. \r\nCox-1 expressing microglia are increased in neurodegenerative diseases, and both global \r\nknockout of Cox-1 and selective Cox-1 inhibition has been shown to ameliorate inflammatory \r\neffects in neurodegenerative diseases. However, direct evidence elucidating how microglial \r\nCox-1 expression influences their response to insults remains limited and warrants further \r\ninvestigation. \r\nFirst, I utilize the optic nerve crush (ONC) model to study the microglial response to injury and \r\ninflammation, confirming a reactive microglial response in both the crushed and uninjured \r\ncontralateral retina using CD68 expression and morphological analysis. While previous studies \r\nreported retinal ganglion cell (RGC) loss in the contralateral eye, I did not observe this, \r\nsuggesting that unilateral ONC induces microglial activation in the contralateral eye without \r\nRGC degeneration. To explore the role of Cox-1 in this response, I generated a mouse model \r\nwith microglia-specific deletion of Cox-1. After ONC, these mice exhibited an attenuated \r\nmicroglial response in both the ipsilateral and contralateral retinas, as well as in visual \r\nprocessing areas of the brain. Notably, Cox-2 does not show any expression after ONC in both \r\nwild-type and Cox-1 knockout mice Additionally, Cox-1KO mice show a reduction in \r\nphagocytic cups and a reduction in microglia proliferation after ONC. However, due to \r\nreproducibility problems of the observed phenotype, even after the generation of two new \r\nmouse models, I cannot draw any definitive conclusions based on the data. \r\nNext, due to the ambiguity of the mouse model, I explored an alternative route to investigate \r\nfunctional consequences of Cox-1 in microglia. I generated a COX1 knock-out human induced \r\npluripotent cell (hIPSC) line using CRISPR/Cas9. These cells are were differentiated in \r\nmicroglia-like cells and integrated in dissociated retinal organoids according to protocols \r\ndeveloped in our lab. In response to LPS and POLY(I:C) stimulation, the release and expression \r\nof cytokines and chemokines was decreased in COX1 knockout cells. However, the \r\nprostaglandin PGE2 was not increased in microglia-like cells in both control and COX1 \r\nknockout cells. \r\nOverall, the results from the COX1 knock-out microglia-like cells suggests that COX1 \r\nexpression in microglia play a role in neuroinflammation by affecting the release of \r\ninflammatory cytokines and chemokines. Hereby further challenging that the dogma of the \r\nCox-1 isoform involved in housekeeping functions and the Cox-2 isoform involved in \r\ninflammation applies for the central nervous system. " acknowledged_ssus: - _id: Bio - _id: SSU - _id: PreCl - _id: LifeSc acknowledgement: "The work presented in this Thesis was carried out at the Institute of Science and Technology\r\nAustria (ISTA), and was supported by the Austrian Science Fund (FWF) [10.55776/P37131].\r\nI would like to thank the Scientific Service Units (SSU) of ISTA for the provided resources,\r\nspecifically the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the\r\nPre-Clinical Facility (PCF) team, specifically Sonja Haslinger, Claudia Gold, and Michael\r\nSchunn, for mouse colony management and support. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Florianne E full_name: Miteva, Florianne E id: 3526230C-F248-11E8-B48F-1D18A9856A87 last_name: Miteva citation: ama: Miteva FE. The role of cyclooxygenase 1 on microglial response to inflammatory stressors. 2025. doi:10.15479/AT-ISTA-20467 apa: Miteva, F. E. (2025). The role of cyclooxygenase 1 on microglial response to inflammatory stressors. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20467 chicago: Miteva, Florianne E. “The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory Stressors.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20467. ieee: F. E. Miteva, “The role of cyclooxygenase 1 on microglial response to inflammatory stressors,” Institute of Science and Technology Austria, 2025. ista: Miteva FE. 2025. The role of cyclooxygenase 1 on microglial response to inflammatory stressors. Institute of Science and Technology Austria. mla: Miteva, Florianne E. The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory Stressors. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20467. short: F.E. Miteva, The Role of Cyclooxygenase 1 on Microglial Response to Inflammatory Stressors, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-14T10:24:41Z date_published: 2025-10-14T00:00:00Z date_updated: 2026-10-23T08:01:12Z day: '14' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SaSi doi: 10.15479/AT-ISTA-20467 doi_confirm: '1' file: - access_level: open_access checksum: 03537697be8c688d3a05cf948288e48f content_type: application/pdf creator: fschootu date_created: 2025-10-17T11:09:11Z date_updated: 2026-10-14T22:30:02Z embargo: 2026-10-14 file_id: '20484' file_name: 2025_Miteva_Florianne_thesis.pdf file_size: 13668588 relation: main_file - access_level: closed checksum: df4930d7211cf9cfe1254b77204dc1d3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: fschootu date_created: 2025-10-23T11:33:06Z date_updated: 2026-10-14T22:30:02Z embargo_to: open_access file_id: '20525' file_name: 2025_Miteva_florianne_thesis.docx file_size: 28991918 relation: source_file file_date_updated: 2026-10-14T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20467 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '99' project: - _id: 7be82147-9f16-11ee-852c-f44682d73140 grant_number: P37131 name: Dissecting the morpho-functional relationship of microglia publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19566' relation: part_of_dissertation status: public status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: The role of cyclooxygenase 1 on microglial response to inflammatory stressors tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- APC_amount: 2236,02 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19566' abstract: - lang: eng text: "Purpose: Optic nerve crush (ONC) is a model for studying optic nerve trauma. Unilateral ONC induces massive retinal ganglion cell (RGC) degeneration in the affected eye, leading to vision loss within a month. A common assumption has been that the non-injured contralateral eye is unaffected due to the minimal retino-retinal projections of the RGCs at the chiasm. Yet, recently, microglia, the brain-resident macrophages, have shown a responsive phenotype in the contralateral eye after ONC. Whether RGC loss accompanies this phenotype is still controversial.\r\n\r\nMethods: Using the available RGCode algorithm and developing our own RGC-Quant deep-learning-based tool, we quantify RGC's total number and density across the entire retina after ONC.\r\n\r\nResults: We confirm a short-term microglia response in the contralateral eye after ONC, but this did not affect the microglia number. Furthermore, we cannot confirm the previously reported RGC loss between naïve and contralateral retinas 5 weeks after ONC induction across the commonly used Cx3cr1creERT2 and C57BL6/J mouse models. Neither sex nor the direct comparison of the RGC markers Brn3a and RBPMS, with Brn3a co-labeling, on average, 89% of the RBPMS+-cells, explained this discrepancy, suggesting that the early microglia-responsive phenotype does not have immediate consequences on the RGC number.\r\n\r\nConclusions: Our results corroborate that unilateral optic nerve injury elicits a microglial response in the uninjured contralateral eye but without RGC loss. Therefore, the contralateral eye should be treated separately and not as an ONC control." acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl acknowledgement: "The authors thank the Scientific Service Units (SSU) of ISTA for the provided resources, specifically the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger, Claudia Gold, and Michael Schunn, for mouse colony management and support. We thank all members of the Siegert group for constant feedback on the project and the manuscript. \r\nSupported in whole or in part by the Austrian Science Fund (FWF) [10.55776/P37131]. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. " article_number: '49' article_processing_charge: Yes article_type: original author: - first_name: Florianne E full_name: Schoot Uiterkamp, Florianne E id: 3526230C-F248-11E8-B48F-1D18A9856A87 last_name: Schoot Uiterkamp - first_name: Margaret E full_name: Maes, Margaret E id: 3838F452-F248-11E8-B48F-1D18A9856A87 last_name: Maes orcid: 0000-0001-9642-1085 - first_name: Mohammad full_name: Alamalhoda, Mohammad last_name: Alamalhoda - first_name: Arsalan full_name: Firoozi, Arsalan last_name: Firoozi - first_name: Gloria full_name: Colombo, Gloria id: 3483CF6C-F248-11E8-B48F-1D18A9856A87 last_name: Colombo orcid: 0000-0001-9434-8902 - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 citation: ama: Miteva FE, Maes ME, Alamalhoda M, Firoozi A, Colombo G, Siegert S. Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye. Investigative Ophthalmology & Visual Science. 2025;66(3). doi:10.1167/iovs.66.3.49 apa: Miteva, F. E., Maes, M. E., Alamalhoda, M., Firoozi, A., Colombo, G., & Siegert, S. (2025). Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye. Investigative Ophthalmology & Visual Science. Association for Research in Vision and Ophthalmology. https://doi.org/10.1167/iovs.66.3.49 chicago: Miteva, Florianne E, Margaret E Maes, Mohammad Alamalhoda, Arsalan Firoozi, Gloria Colombo, and Sandra Siegert. “Optic Nerve Crush Does Not Induce Retinal Ganglion Cell Loss in the Contralateral Eye.” Investigative Ophthalmology & Visual Science. Association for Research in Vision and Ophthalmology, 2025. https://doi.org/10.1167/iovs.66.3.49. ieee: F. E. Miteva, M. E. Maes, M. Alamalhoda, A. Firoozi, G. Colombo, and S. Siegert, “Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye,” Investigative Ophthalmology & Visual Science, vol. 66, no. 3. Association for Research in Vision and Ophthalmology, 2025. ista: Miteva FE, Maes ME, Alamalhoda M, Firoozi A, Colombo G, Siegert S. 2025. Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye. Investigative Ophthalmology & Visual Science. 66(3), 49. mla: Miteva, Florianne E., et al. “Optic Nerve Crush Does Not Induce Retinal Ganglion Cell Loss in the Contralateral Eye.” Investigative Ophthalmology & Visual Science, vol. 66, no. 3, 49, Association for Research in Vision and Ophthalmology, 2025, doi:10.1167/iovs.66.3.49. short: F.E. Miteva, M.E. Maes, M. Alamalhoda, A. Firoozi, G. Colombo, S. Siegert, Investigative Ophthalmology & Visual Science 66 (2025). corr_author: '1' date_created: 2025-04-15T13:40:35Z date_published: 2025-03-01T00:00:00Z date_updated: 2026-11-04T23:31:20Z day: '01' ddc: - '570' department: - _id: SaSi doi: 10.1167/iovs.66.3.49 external_id: pmid: - '40126507' file: - access_level: open_access checksum: e8722ce5792f6c08fe1e191f7de6f147 content_type: application/pdf creator: dernst date_created: 2025-04-15T13:49:10Z date_updated: 2025-04-15T13:49:10Z file_id: '19567' file_name: 2025_IOVS_SchootUiterkamp.pdf file_size: 2721477 relation: main_file success: 1 file_date_updated: 2025-04-15T13:49:10Z fulldoi: https://doi.org/10.1167/iovs.66.3.49 has_accepted_license: '1' intvolume: ' 66' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 7be82147-9f16-11ee-852c-f44682d73140 grant_number: P37131 name: Dissecting the morpho-functional relationship of microglia - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: Investigative Ophthalmology & Visual Science publication_identifier: issn: - 1552-5783 publication_status: published publisher: Association for Research in Vision and Ophthalmology quality_controlled: '1' related_material: link: - relation: software url: https://github.com/siegert-lab/RGC-Quant record: - id: '20467' relation: dissertation_contains status: public scopus_import: '1' status: public title: Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '19421' abstract: - lang: eng text: The phytohormone auxin (Aux) is a principal endogenous developmental signal in plants. It mediates transcriptional reprogramming by a well-established canonical signalling mechanism. TIR1/AFB auxin receptors are F-box subunits of an ubiquitin ligase complex; after auxin perception, they associate with Aux/IAA transcriptional repressors and ubiquitinate them for degradation, thus enabling the activation of auxin response factor (ARF) transcription factors1,2,3. Here we revise this paradigm by showing that without TIR1 adenylate cyclase (AC) activity4, auxin-induced degradation of Aux/IAAs is not sufficient to mediate the transcriptional auxin response. Abolishing the TIR1 AC activity does not affect auxin-induced degradation of Aux/IAAs but renders TIR1 non-functional in mediating transcriptional reprogramming and auxin-regulated development, including shoot, root, root hair growth and lateral root formation. Transgenic plants show that local cAMP production in the vicinity of the Aux/IAA–ARF complex by unrelated AC enzymes bypasses the need for auxin perception and is sufficient to induce ARF-mediated transcription. These discoveries revise the canonical model of auxin signalling and establish TIR1/AFB-produced cAMP as a second messenger essential for transcriptional reprograming. acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: We are grateful to J. Callis and H.-Q. Yang for sharing materials and to M. Estelle and S. Kepinski for inspiring discussions. This research was supported by the Laboratory Support Facility, the Plant Facility and the Imaging and Optics Facility of the Institute of Science and Technology Austria. This project has received funding from the European Research Council (101142681 CYNIPS) and Austrian Science Fund (P 37051-B). L.Q. was supported by the National Natural Science Foundation of China (grant no. 32470327). M.Z. was supported by the Interdisciplinary Project Committee of the Institute of Science and Technology Austria, and Y.P. was supported by an EMBO Postdoctoral Fellowship (ALTF 38-2023). Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Huihuang full_name: Chen, Huihuang id: 83c96512-15b2-11ec-abd3-b7eede36184f last_name: Chen - first_name: Linlin full_name: Qi, Linlin id: 44B04502-A9ED-11E9-B6FC-583AE6697425 last_name: Qi orcid: 0000-0001-5187-8401 - first_name: Minxia full_name: Zou, Minxia id: 5c243f41-03f3-11ec-841c-96faf48a7ef9 last_name: Zou - first_name: Mengting full_name: Lu, Mengting id: a8198a14-1ffe-11ee-8b67-d2bdff9d9178 last_name: Lu - first_name: M full_name: Kwiatkowski, M last_name: Kwiatkowski - first_name: Yuanrong full_name: Pei, Yuanrong id: 98605edc-6ce7-11ee-95f3-cc16b866efcd last_name: Pei - first_name: K full_name: Jaworski, K last_name: Jaworski - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Chen H, Qi L, Zou M, et al. TIR1-produced cAMP as a second messenger in transcriptional auxin signalling. Nature. 2025;640:1011-1016. doi:10.1038/s41586-025-08669-w apa: Chen, H., Qi, L., Zou, M., Lu, M., Kwiatkowski, M., Pei, Y., … Friml, J. (2025). TIR1-produced cAMP as a second messenger in transcriptional auxin signalling. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-08669-w chicago: Chen, Huihuang, Linlin Qi, Minxia Zou, Mengting Lu, M Kwiatkowski, Yuanrong Pei, K Jaworski, and Jiří Friml. “TIR1-Produced CAMP as a Second Messenger in Transcriptional Auxin Signalling.” Nature. Springer Nature, 2025. https://doi.org/10.1038/s41586-025-08669-w. ieee: H. Chen et al., “TIR1-produced cAMP as a second messenger in transcriptional auxin signalling,” Nature, vol. 640. Springer Nature, pp. 1011–1016, 2025. ista: Chen H, Qi L, Zou M, Lu M, Kwiatkowski M, Pei Y, Jaworski K, Friml J. 2025. TIR1-produced cAMP as a second messenger in transcriptional auxin signalling. Nature. 640, 1011–1016. mla: Chen, Huihuang, et al. “TIR1-Produced CAMP as a Second Messenger in Transcriptional Auxin Signalling.” Nature, vol. 640, Springer Nature, 2025, pp. 1011–16, doi:10.1038/s41586-025-08669-w. short: H. Chen, L. Qi, M. Zou, M. Lu, M. Kwiatkowski, Y. Pei, K. Jaworski, J. Friml, Nature 640 (2025) 1011–1016. corr_author: '1' date_created: 2025-03-19T09:44:39Z date_published: 2025-04-24T00:00:00Z date_updated: 2026-11-04T23:31:20Z day: '24' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41586-025-08669-w external_id: isi: - '001437493900001' pmid: - '40044868' file: - access_level: open_access checksum: f5f18081003e7a1b8e372ecb7da82e7d content_type: application/pdf creator: dernst date_created: 2025-08-05T12:29:35Z date_updated: 2025-08-05T12:29:35Z file_id: '20132' file_name: 2025_Nature_Chen.pdf file_size: 13549245 relation: main_file success: 1 file_date_updated: 2025-08-05T12:29:35Z fulldoi: https://doi.org/10.1038/s41586-025-08669-w has_accepted_license: '1' intvolume: ' 640' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1011-1016 pmid: 1 project: - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/updating-the-textbook/ record: - id: '19478' relation: dissertation_contains status: public status: public title: TIR1-produced cAMP as a second messenger in transcriptional auxin signalling tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 640 year: '2025' ... --- OA_place: publisher _id: '20415' abstract: - lang: eng text: "Well-defined powder precursors are important for the rational design of crystalline inorganic \r\nmaterials with controlled defects and functional properties. Such powders can be prepared from \r\ndried nanoparticles synthesized using a surfactant-assisted/colloidal method that provides \r\nprecise control over size, shape, composition, and surface chemistry of nanoparticles. These \r\ntailored nanoparticles further act as building blocks for three-dimensional assemblies, \r\nexhibiting collective nanoscale properties and enabling tailored microstructures of crystalline \r\ninorganic materials. However, the programmable engineering of such materials using \r\nnanoparticle-based precursors remains limited, due to a lack of fundamental understanding of \r\nboth the synthesis of nanoparticles and their conversion into macroscopic solids. Furthermore, \r\nthe formation of three-dimensional assemblies often requires multi-step post-synthetic \r\ntreatments, which can limit reproducibility and the production of the bulk inorganic materials. \r\nIn this thesis, I demonstrate a key synthetic parameter governing the formation of desired \r\nnanostructures, especially metal/semiconductor core–shell nanoparticles which are potential \r\nprecursors for engineering composition, crystal structure, and defects of final materials. Then, \r\nI investigate their transformative pathways to unveil structural and chemical changes that occur \r\nduring heat treatment of the nanoparticle-based precursors. Building on understanding of \r\natomic-scale interactions during nanoparticle-based precursor formation, I further demonstrate \r\nthe possibility of synthesizing the nanoparticle assembly directly in the nanoparticle synthesis \r\nreaction and rationalize the process of in situ self-assembly of nanoparticles. Finally, the impact \r\nof NP-based precursors on the formation and properties of crystalline inorganic materials is \r\nevaluated, demonstrating the potential of employing NP-based precursors for the rational \r\ndesign of functional inorganic materials. " acknowledged_ssus: - _id: LifeSc - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Seungho full_name: Lee, Seungho id: BB243B88-D767-11E9-B658-BC13E6697425 last_name: Lee orcid: 0000-0002-6962-8598 citation: ama: Lee S. Nanoparticle-based precursors toward advanced crystalline inorganic solids. 2025. doi:10.15479/AT-ISTA-20415 apa: Lee, S. (2025). Nanoparticle-based precursors toward advanced crystalline inorganic solids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20415 chicago: Lee, Seungho. “Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20415. ieee: S. Lee, “Nanoparticle-based precursors toward advanced crystalline inorganic solids,” Institute of Science and Technology Austria, 2025. ista: Lee S. 2025. Nanoparticle-based precursors toward advanced crystalline inorganic solids. Institute of Science and Technology Austria. mla: Lee, Seungho. Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20415. short: S. Lee, Nanoparticle-Based Precursors toward Advanced Crystalline Inorganic Solids, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-01T09:04:00Z date_published: 2025-10-01T00:00:00Z date_updated: 2026-10-23T08:16:15Z day: '01' ddc: - '540' degree_awarded: PhD department: - _id: GradSch - _id: MaIb doi: 10.15479/AT-ISTA-20415 doi_confirm: '1' file: - access_level: closed checksum: fa6d5946feb37b678ee1c6dffb4fa167 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: slee date_created: 2025-10-03T12:29:43Z date_updated: 2026-10-03T22:30:02Z embargo_to: open_access file_id: '20420' file_name: 2025_Lee_Seungho_Thesis.docx file_size: 88706648 relation: source_file - access_level: open_access checksum: c5ba6d464113ad0c5812a9d24b539b86 content_type: application/pdf creator: slee date_created: 2025-10-03T12:29:25Z date_updated: 2026-10-03T22:30:02Z embargo: 2026-10-03 file_id: '20421' file_name: 2025_Lee_Seungho_Thesis__.pdf file_size: 14587276 relation: main_file file_date_updated: 2026-10-03T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20415 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '144' project: - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12237' relation: part_of_dissertation status: public - id: '15357' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Loredana full_name: Protesescu, Loredana last_name: Protesescu - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 title: Nanoparticle-based precursors toward advanced crystalline inorganic solids type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: repository OA_type: green _id: '22026' abstract: - lang: eng text: We address two pressing questions in the theory of the Korteweg–de Vries (KdV) equation. First, we show the uniqueness of solutions to KdV that are merely bounded, without any further decay, regularity, periodicity, or almost periodicity assumptions. The second question, emphasized by Deift, regards whether almost periodic initial data leads to almost periodic solutions to KdV. Building on the new observation that this is false for the Airy equation, we construct an example of almost periodic initial data whose KdV evolution remains bounded, but fails to be almost periodic at a later time. Our uniqueness result ensures that the solution constructed is the unique development of this initial data. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Andreia full_name: Chapouto, Andreia last_name: Chapouto - first_name: Rowan full_name: Killip, Rowan last_name: Killip - first_name: Monica full_name: Visan, Monica id: 056daca0-b8d1-11f0-964f-f91054abf8ca last_name: Visan citation: ama: 'Chapouto A, Killip R, Vişan M. Bounded solutions of KdV: Uniqueness and the loss of almost periodicity. Duke Mathematical Journal. 2024;173(7):1227-1267. doi:10.1215/00127094-2023-0035' apa: 'Chapouto, A., Killip, R., & Vişan, M. (2024). Bounded solutions of KdV: Uniqueness and the loss of almost periodicity. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2023-0035' chicago: 'Chapouto, Andreia, Rowan Killip, and Monica Vişan. “Bounded Solutions of KdV: Uniqueness and the Loss of Almost Periodicity.” Duke Mathematical Journal. Duke University Press, 2024. https://doi.org/10.1215/00127094-2023-0035.' ieee: 'A. Chapouto, R. Killip, and M. Vişan, “Bounded solutions of KdV: Uniqueness and the loss of almost periodicity,” Duke Mathematical Journal, vol. 173, no. 7. Duke University Press, pp. 1227–1267, 2024.' ista: 'Chapouto A, Killip R, Vişan M. 2024. Bounded solutions of KdV: Uniqueness and the loss of almost periodicity. Duke Mathematical Journal. 173(7), 1227–1267.' mla: 'Chapouto, Andreia, et al. “Bounded Solutions of KdV: Uniqueness and the Loss of Almost Periodicity.” Duke Mathematical Journal, vol. 173, no. 7, Duke University Press, 2024, pp. 1227–67, doi:10.1215/00127094-2023-0035.' short: A. Chapouto, R. Killip, M. Vişan, Duke Mathematical Journal 173 (2024) 1227–1267. das_tickbox: '1' date_created: 2026-06-19T07:34:05Z date_published: 2024-05-15T00:00:00Z date_updated: 2026-06-22T10:32:25Z day: '15' doi: 10.1215/00127094-2023-0035 extern: '1' external_id: arxiv: - '2209.07501' fulldoi: https://doi.org/10.1215/00127094-2023-0035 intvolume: ' 173' issue: '7' keyword: - Almost-periodic solutions - Korteweg–de Vries - unconditional uniqueness language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2209.07501 month: '05' oa: 1 oa_version: Preprint page: 1227-1267 publication: Duke Mathematical Journal publication_identifier: issn: - 0012-7094 publication_status: published publisher: Duke University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Bounded solutions of KdV: Uniqueness and the loss of almost periodicity' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 173 year: '2024' ... --- OA_place: repository OA_type: green _id: '20838' abstract: - lang: eng text: "For any 1 ≤ r ≤ ∞, we show that every diffeomorphism of a manifold of the form\r\nR/Z × M is a total renormalization of a Cr-close to identity map. In other words, for\r\nevery diffeomorphism f of R/Z×M, there exists a map g arbitrarily close to identity\r\nsuch that the first return map of g to a domain is conjugate to f and moreover the\r\norbit of this domain is equal to R/Z×M. This enables us to localize near the identity\r\nthe existence of many properties in dynamical systems, such as being Bernoulli for a\r\nsmooth volume form." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Pierre full_name: Berger, Pierre last_name: Berger - first_name: Nicolaz full_name: Gourmelon, Nicolaz last_name: Gourmelon - first_name: Mathieu full_name: Helfter, Mathieu id: 7d296fbe-e2c6-11ee-84d3-d5c2945f9a57 last_name: Helfter citation: ama: Berger P, Gourmelon N, Helfter M. Every diffeomorphism is a total renormalization of a close to identity map. Inventiones mathematicae. 2024;239(2):431-468. doi:10.1007/s00222-024-01305-w apa: Berger, P., Gourmelon, N., & Helfter, M. (2024). Every diffeomorphism is a total renormalization of a close to identity map. Inventiones Mathematicae. Springer Nature. https://doi.org/10.1007/s00222-024-01305-w chicago: Berger, Pierre, Nicolaz Gourmelon, and Mathieu Helfter. “Every Diffeomorphism Is a Total Renormalization of a Close to Identity Map.” Inventiones Mathematicae. Springer Nature, 2024. https://doi.org/10.1007/s00222-024-01305-w. ieee: P. Berger, N. Gourmelon, and M. Helfter, “Every diffeomorphism is a total renormalization of a close to identity map,” Inventiones mathematicae, vol. 239, no. 2. Springer Nature, pp. 431–468, 2024. ista: Berger P, Gourmelon N, Helfter M. 2024. Every diffeomorphism is a total renormalization of a close to identity map. Inventiones mathematicae. 239(2), 431–468. mla: Berger, Pierre, et al. “Every Diffeomorphism Is a Total Renormalization of a Close to Identity Map.” Inventiones Mathematicae, vol. 239, no. 2, Springer Nature, 2024, pp. 431–68, doi:10.1007/s00222-024-01305-w. short: P. Berger, N. Gourmelon, M. Helfter, Inventiones Mathematicae 239 (2024) 431–468. date_created: 2025-12-19T10:15:13Z date_published: 2024-12-19T00:00:00Z date_updated: 2025-12-29T12:03:10Z day: '19' doi: 10.1007/s00222-024-01305-w extern: '1' external_id: arxiv: - '2210.09064' fulldoi: https://doi.org/10.1007/s00222-024-01305-w intvolume: ' 239' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2210.09064 month: '12' oa: 1 oa_version: Preprint page: 431-468 publication: Inventiones mathematicae publication_identifier: eissn: - 1432-1297 issn: - 0020-9910 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Every diffeomorphism is a total renormalization of a close to identity map type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 239 year: '2024' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20961' abstract: - lang: eng text: Self-replicating molecules and well-defined folded macromolecules are of great significance in the emergence and evolution of life. How they may interconnect and affect each other remains largely elusive. Here, we demonstrate an abiotic system where a single building block can oligomerize to yield either a self-replicating molecule or a foldamer. Specifically, agitation of a disulfide-based dynamic combinatorial library at moderately elevated pH channels it selectively into a self-replicating hexamer assembled into fibers, after passing through a period where a 15-subunit macrocyclic foldamer existed transiently. Without mechanoagitation or at lower pH, the formation of hexamer fiber is suppressed, resulting in the accumulation of the 15mer foldamer. Foldamer and self-replicator can be interconverted in response to external stimuli, including agitation and a change in pH. Furthermore, upon the addition of a photoacid, the pH of the medium can be controlled by irradiation, driving the switching between replicator and foldamer and allowing a dissipative out-of-equilibrium state to be accessed, using light as a source of energy. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Yulong full_name: Jin, Yulong last_name: Jin - first_name: Pradeep K full_name: Mandal, Pradeep K id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3 last_name: Mandal orcid: 0000-0001-5996-956X - first_name: Juntian full_name: Wu, Juntian last_name: Wu - first_name: Armin full_name: Kiani, Armin last_name: Kiani - first_name: Rui full_name: Zhao, Rui last_name: Zhao - first_name: Ivan full_name: Huc, Ivan last_name: Huc - first_name: Sijbren full_name: Otto, Sijbren last_name: Otto citation: ama: Jin Y, Mandal PK, Wu J, et al. Light-mediated interconversion between a foldamer and a self-replicator. Journal of the American Chemical Society. 2024;146(49):33395-33402. doi:10.1021/jacs.4c09114 apa: Jin, Y., Mandal, P. K., Wu, J., Kiani, A., Zhao, R., Huc, I., & Otto, S. (2024). Light-mediated interconversion between a foldamer and a self-replicator. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.4c09114 chicago: Jin, Yulong, Pradeep K Mandal, Juntian Wu, Armin Kiani, Rui Zhao, Ivan Huc, and Sijbren Otto. “Light-Mediated Interconversion between a Foldamer and a Self-Replicator.” Journal of the American Chemical Society. American Chemical Society, 2024. https://doi.org/10.1021/jacs.4c09114. ieee: Y. Jin et al., “Light-mediated interconversion between a foldamer and a self-replicator,” Journal of the American Chemical Society, vol. 146, no. 49. American Chemical Society, pp. 33395–33402, 2024. ista: Jin Y, Mandal PK, Wu J, Kiani A, Zhao R, Huc I, Otto S. 2024. Light-mediated interconversion between a foldamer and a self-replicator. Journal of the American Chemical Society. 146(49), 33395–33402. mla: Jin, Yulong, et al. “Light-Mediated Interconversion between a Foldamer and a Self-Replicator.” Journal of the American Chemical Society, vol. 146, no. 49, American Chemical Society, 2024, pp. 33395–402, doi:10.1021/jacs.4c09114. short: Y. Jin, P.K. Mandal, J. Wu, A. Kiani, R. Zhao, I. Huc, S. Otto, Journal of the American Chemical Society 146 (2024) 33395–33402. date_created: 2026-01-08T07:05:57Z date_published: 2024-11-26T00:00:00Z date_updated: 2026-01-19T11:03:31Z day: '26' ddc: - '540' doi: 10.1021/jacs.4c09114 extern: '1' external_id: pmid: - '39590511' fulldoi: https://doi.org/10.1021/jacs.4c09114 has_accepted_license: '1' intvolume: ' 146' issue: '49' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/jacs.4c09114 month: '11' oa: 1 oa_version: Published Version page: 33395-33402 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Light-mediated interconversion between a foldamer and a self-replicator tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 146 year: '2024' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20962' abstract: - lang: eng text: Systems chemistry has emerged as a useful paradigm to access structures and phenomena typically exhibited by living systems, including complex molecular systems such as self-replicators and foldamers. As we progress further toward the noncovalent synthesis of life-like systems, and eventually life itself, it is necessary to gain control over assembly pathways. Dissipative chemical fueling has enabled access to stable populations of (self-assembled) structures that would normally form only transiently. Here, we report a synthetic dynamic combinatorial library, made from a single structurally simple building block, from which a self-replicator and a foldamer can emerge along two distinct and competing pathways through an inter- or intramolecular assembly process, respectively. A fueled chemical reaction cycle is then set up to generate the foldamer transiently, in the presence of the self-replicator. The partitioning of the building block between the folding and self-replication pathways and the duration of the fueled reaction cycles are controlled by adjusting the amount of the chemical fuel. An out-of-equilibrium steady state involving the two assemblies could also be achieved by using a continuous stirred tank reactor with inflow and outflow of material. This work connects the domains of folding and self-replication in synthetic systems through dissipative out-of-equilibrium chemistry. It demonstrates that foldamers and self-replicators, formed from the same building block, can stably coexist if the system is continuously supplied with energy, while at equilibrium, the Gibbs phase rule prohibits such coexistence. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Ankush full_name: Sood, Ankush last_name: Sood - first_name: Pradeep K full_name: Mandal, Pradeep K id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3 last_name: Mandal orcid: 0000-0001-5996-956X - first_name: Jim full_name: Ottelé, Jim last_name: Ottelé - first_name: Juntian full_name: Wu, Juntian last_name: Wu - first_name: Marcel full_name: Eleveld, Marcel last_name: Eleveld - first_name: Joydev full_name: Hatai, Joydev last_name: Hatai - first_name: Charalampos G. full_name: Pappas, Charalampos G. last_name: Pappas - first_name: Ivan full_name: Huc, Ivan last_name: Huc - first_name: Sijbren full_name: Otto, Sijbren last_name: Otto citation: ama: Sood A, Mandal PK, Ottelé J, et al. Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry. Journal of the American Chemical Society. 2024;146(49):33386-33394. doi:10.1021/jacs.4c09111 apa: Sood, A., Mandal, P. K., Ottelé, J., Wu, J., Eleveld, M., Hatai, J., … Otto, S. (2024). Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.4c09111 chicago: Sood, Ankush, Pradeep K Mandal, Jim Ottelé, Juntian Wu, Marcel Eleveld, Joydev Hatai, Charalampos G. Pappas, Ivan Huc, and Sijbren Otto. “Simultaneous Formation of a Foldamer and a Self-Replicator by out-of-Equilibrium Dynamic Covalent Chemistry.” Journal of the American Chemical Society. American Chemical Society, 2024. https://doi.org/10.1021/jacs.4c09111. ieee: A. Sood et al., “Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry,” Journal of the American Chemical Society, vol. 146, no. 49. American Chemical Society, pp. 33386–33394, 2024. ista: Sood A, Mandal PK, Ottelé J, Wu J, Eleveld M, Hatai J, Pappas CG, Huc I, Otto S. 2024. Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry. Journal of the American Chemical Society. 146(49), 33386–33394. mla: Sood, Ankush, et al. “Simultaneous Formation of a Foldamer and a Self-Replicator by out-of-Equilibrium Dynamic Covalent Chemistry.” Journal of the American Chemical Society, vol. 146, no. 49, American Chemical Society, 2024, pp. 33386–94, doi:10.1021/jacs.4c09111. short: A. Sood, P.K. Mandal, J. Ottelé, J. Wu, M. Eleveld, J. Hatai, C.G. Pappas, I. Huc, S. Otto, Journal of the American Chemical Society 146 (2024) 33386–33394. date_created: 2026-01-08T07:06:27Z date_published: 2024-11-26T00:00:00Z date_updated: 2026-01-19T10:57:53Z day: '26' doi: 10.1021/jacs.4c09111 extern: '1' external_id: pmid: - '39590110' fulldoi: https://doi.org/10.1021/jacs.4c09111 has_accepted_license: '1' intvolume: ' 146' issue: '49' keyword: - Fibers - Foldamers - Macrocycles - Monomers - Peptides - Proteins language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/jacs.4c09111 month: '11' oa: 1 oa_version: Published Version page: 33386-33394 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Simultaneous formation of a foldamer and a self-replicator by out-of-equilibrium dynamic covalent chemistry tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 146 year: '2024' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20967' abstract: - lang: eng text: A biotinylated helical aromatic oligoamide foldamer equivalent in size to a 24mer peptide was designed without any prejudice other than to display various polar and hydrophobic side chains at its surface. It was synthesized on solid phase, its P- and M-helical conformers were separated by HPLC on a chiral stationary phase, and the solid state structure of a non-biotinylated analogue was elucidated by X-ray crystallography. Pull-down experiments from a yeast cell lysate using the foldamer as a bait followed by proteomic analysis revealed potential protein binding partners. Three of these proteins were recombinantly expressed. Biolayer interferometry showed submicromolar binding demonstrating the potential of a given foldamer to have affinity for certain proteins in the absence of design considerations. Yet, binding selectivity was low in all three cases since both P- and M-conformers bound to the proteins with similar affinities. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Sunbum full_name: Kwon, Sunbum last_name: Kwon - first_name: Vasily full_name: Morozov, Vasily last_name: Morozov - first_name: Lingfei full_name: Wang, Lingfei last_name: Wang - first_name: Pradeep K full_name: Mandal, Pradeep K id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3 last_name: Mandal orcid: 0000-0001-5996-956X - first_name: Stéphane full_name: Chaignepain, Stéphane last_name: Chaignepain - first_name: Céline full_name: Douat, Céline last_name: Douat - first_name: Ivan full_name: Huc, Ivan last_name: Huc citation: ama: Kwon S, Morozov V, Wang L, et al. Interrogating the potential of helical aromatic foldamers for protein recognition. Organic & Biomolecular Chemistry. 2024;22(48):9342-9347. doi:10.1039/d4ob01436g apa: Kwon, S., Morozov, V., Wang, L., Mandal, P. K., Chaignepain, S., Douat, C., & Huc, I. (2024). Interrogating the potential of helical aromatic foldamers for protein recognition. Organic & Biomolecular Chemistry. Royal Society of Chemistry. https://doi.org/10.1039/d4ob01436g chicago: Kwon, Sunbum, Vasily Morozov, Lingfei Wang, Pradeep K Mandal, Stéphane Chaignepain, Céline Douat, and Ivan Huc. “Interrogating the Potential of Helical Aromatic Foldamers for Protein Recognition.” Organic & Biomolecular Chemistry. Royal Society of Chemistry, 2024. https://doi.org/10.1039/d4ob01436g. ieee: S. Kwon et al., “Interrogating the potential of helical aromatic foldamers for protein recognition,” Organic & Biomolecular Chemistry, vol. 22, no. 48. Royal Society of Chemistry, pp. 9342–9347, 2024. ista: Kwon S, Morozov V, Wang L, Mandal PK, Chaignepain S, Douat C, Huc I. 2024. Interrogating the potential of helical aromatic foldamers for protein recognition. Organic & Biomolecular Chemistry. 22(48), 9342–9347. mla: Kwon, Sunbum, et al. “Interrogating the Potential of Helical Aromatic Foldamers for Protein Recognition.” Organic & Biomolecular Chemistry, vol. 22, no. 48, Royal Society of Chemistry, 2024, pp. 9342–47, doi:10.1039/d4ob01436g. short: S. Kwon, V. Morozov, L. Wang, P.K. Mandal, S. Chaignepain, C. Douat, I. Huc, Organic & Biomolecular Chemistry 22 (2024) 9342–9347. date_created: 2026-01-11T14:32:23Z date_published: 2024-10-30T00:00:00Z date_updated: 2026-01-20T06:56:44Z day: '30' doi: 10.1039/d4ob01436g extern: '1' external_id: pmid: - '39501876' fulldoi: https://doi.org/10.1039/d4ob01436g has_accepted_license: '1' intvolume: ' 22' issue: '48' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1039/D4OB01436G month: '10' oa: 1 oa_version: Published Version page: 9342-9347 pmid: 1 publication: Organic & Biomolecular Chemistry publication_identifier: eissn: - 1477-0539 issn: - 1477-0520 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Interrogating the potential of helical aromatic foldamers for protein recognition tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21064' abstract: - lang: eng text: The James Webb Space Telescope (JWST) is revolutionizing our knowledge of z > 5 galaxies and their actively accreting black holes. Using the JWST Cycle 1 Treasury program Ultradeep NIRSpec and NIRCam Observations before the Epoch of Reionization (UNCOVER) in the lensing field A2744, we report the identification of a sample of little red dots at 3 < zphot < 7 that likely contain highly reddened accreting supermassive black holes. Using a NIRCam-only selection to F444W < 27.7 mag, we find 26 sources over the ∼45 arcmin^2 field that are blue in F115W − F200W ∼ 0 (or βUV ∼ –2.0 for fλ ∝ λ^β), red in F200W − F444W = 1−4 (βopt ∼ +2.0), and are dominated by a point-source-like central component. Of the 20 sources with deep Atacama Large Millimeter/submillimeter Array (ALMA) 1.2 mm coverage, none are detected individually or in a stack. For the majority of the sample, spectral energy distribution fits to the JWST+ALMA observations prefer models with hot dust rather than obscured star formation to reproduce the red NIRCam colors and ALMA 1.2 mm nondetections. While compact dusty star formation cannot be ruled out, the combination of extremely small sizes (〈re〉 ≈ 50 pc after correction for magnification), red rest-frame optical slopes, and hot dust can be explained by reddened broad-line active galactic nuclei (AGNs). Our targets have faint M1450 ≈ −14 to −18 mag but inferred bolometric luminosities of Lbol = 10^43–10^46 erg s^−1, reflecting their obscured nature. If the candidates are confirmed as AGNs with upcoming UNCOVER spectroscopy, then we have found an abundant population of reddened luminous AGNs that are at least ten times more numerous than UV-luminous AGNs at the same intrinsic bolometric luminosity. acknowledgement: 'I.L. acknowledges support from Australian Research Council Future Fellowship FT220100798. J.E.G. and A.D.G acknowledge support from NSF/AAG grant #1007094, and J.E.G. also acknowledges support from NSF/AAG grant #1007052. L.J.F. and A.Z. acknowledge support by Grant No. 2020750 from the United States–Israel Binational Science Foundation (BSF) and grant No. 2109066 from the United States National Science Foundation (NSF), and by the Ministry of Science & Technology of Israel. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant #140. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. P.D. acknowledges support from the NWO grant 016.VIDI.189.162 (“ODIN”) and from the European Commission’s and University of Groningen’s CO-FUND Rosalind Franklin program. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. This paper makes use of the ALMA data: ADS/JAO. ALMA #2022.1.00073.S, 2018.1.00035.L, and 2013.1.00999.S. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada), MOST and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO and NAOJ. The research of C.C.W. is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation.' article_number: '92' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Ivo full_name: Labbe, Ivo last_name: Labbe - first_name: Jenny E. full_name: Greene, Jenny E. last_name: Greene - first_name: Rachel full_name: Bezanson, Rachel last_name: Bezanson - first_name: Seiji full_name: Fujimoto, Seiji last_name: Fujimoto - first_name: Lukas J. full_name: Furtak, Lukas J. last_name: Furtak - first_name: Andy D. full_name: Goulding, Andy D. last_name: Goulding - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Rohan P. full_name: Naidu, Rohan P. last_name: Naidu - first_name: Pascal A. full_name: Oesch, Pascal A. last_name: Oesch - first_name: Hakim full_name: Atek, Hakim last_name: Atek - first_name: Gabriel full_name: Brammer, Gabriel last_name: Brammer - first_name: Iryna full_name: Chemerynska, Iryna last_name: Chemerynska - first_name: Dan full_name: Coe, Dan last_name: Coe - first_name: Sam E. full_name: Cutler, Sam E. last_name: Cutler - first_name: Pratika full_name: Dayal, Pratika last_name: Dayal - first_name: Robert full_name: Feldmann, Robert last_name: Feldmann - first_name: Marijn full_name: Franx, Marijn last_name: Franx - first_name: Karl full_name: Glazebrook, Karl last_name: Glazebrook - first_name: Joel full_name: Leja, Joel last_name: Leja - first_name: Michael full_name: Maseda, Michael last_name: Maseda - first_name: Danilo full_name: Marchesini, Danilo last_name: Marchesini - first_name: Themiya full_name: Nanayakkara, Themiya last_name: Nanayakkara - first_name: Erica J. full_name: Nelson, Erica J. last_name: Nelson - first_name: Richard full_name: Pan, Richard last_name: Pan - first_name: Casey full_name: Papovich, Casey last_name: Papovich - first_name: Sedona H. full_name: Price, Sedona H. last_name: Price - first_name: Katherine A. full_name: Suess, Katherine A. last_name: Suess - first_name: Bingjie 冰洁 full_name: Wang, Bingjie 冰洁 last_name: Wang - first_name: John R. full_name: Weaver, John R. last_name: Weaver - first_name: Katherine E. full_name: Whitaker, Katherine E. last_name: Whitaker - first_name: Christina C. full_name: Williams, Christina C. last_name: Williams - first_name: Adi full_name: Zitrin, Adi last_name: Zitrin citation: ama: 'Labbe I, Greene JE, Bezanson R, et al. UNCOVER: Candidate red active galactic nuclei at 3 < z < 7 with JWST and ALMA. The Astrophysical Journal. 2024;978. doi:10.3847/1538-4357/ad3551' apa: 'Labbe, I., Greene, J. E., Bezanson, R., Fujimoto, S., Furtak, L. J., Goulding, A. D., … Zitrin, A. (2024). UNCOVER: Candidate red active galactic nuclei at 3 < z < 7 with JWST and ALMA. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad3551' chicago: 'Labbe, Ivo, Jenny E. Greene, Rachel Bezanson, Seiji Fujimoto, Lukas J. Furtak, Andy D. Goulding, Jorryt J Matthee, et al. “UNCOVER: Candidate Red Active Galactic Nuclei at 3 < z < 7 with JWST and ALMA.” The Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad3551.' ieee: 'I. Labbe et al., “UNCOVER: Candidate red active galactic nuclei at 3 < z < 7 with JWST and ALMA,” The Astrophysical Journal, vol. 978. IOP Publishing, 2024.' ista: 'Labbe I, Greene JE, Bezanson R, Fujimoto S, Furtak LJ, Goulding AD, Matthee JJ, Naidu RP, Oesch PA, Atek H, Brammer G, Chemerynska I, Coe D, Cutler SE, Dayal P, Feldmann R, Franx M, Glazebrook K, Leja J, Maseda M, Marchesini D, Nanayakkara T, Nelson EJ, Pan R, Papovich C, Price SH, Suess KA, Wang B冰洁, Weaver JR, Whitaker KE, Williams CC, Zitrin A. 2024. UNCOVER: Candidate red active galactic nuclei at 3 < z < 7 with JWST and ALMA. The Astrophysical Journal. 978, 92.' mla: 'Labbe, Ivo, et al. “UNCOVER: Candidate Red Active Galactic Nuclei at 3 < z < 7 with JWST and ALMA.” The Astrophysical Journal, vol. 978, 92, IOP Publishing, 2024, doi:10.3847/1538-4357/ad3551.' short: I. Labbe, J.E. Greene, R. Bezanson, S. Fujimoto, L.J. Furtak, A.D. Goulding, J.J. Matthee, R.P. Naidu, P.A. Oesch, H. Atek, G. Brammer, I. Chemerynska, D. Coe, S.E. Cutler, P. Dayal, R. Feldmann, M. Franx, K. Glazebrook, J. Leja, M. Maseda, D. Marchesini, T. Nanayakkara, E.J. Nelson, R. Pan, C. Papovich, S.H. Price, K.A. Suess, B.冰洁 Wang, J.R. Weaver, K.E. Whitaker, C.C. Williams, A. Zitrin, The Astrophysical Journal 978 (2024). date_created: 2026-01-28T15:26:12Z date_published: 2024-12-26T00:00:00Z date_updated: 2026-02-10T06:49:49Z day: '26' ddc: - '520' department: - _id: JoMa doi: 10.3847/1538-4357/ad3551 external_id: arxiv: - '2306.07320' file: - access_level: open_access checksum: 825c35ebd26e292c8a5c2bffac327854 content_type: application/pdf creator: dernst date_created: 2026-02-10T06:44:24Z date_updated: 2026-02-10T06:44:24Z file_id: '21201' file_name: 2024_AstrophysicalJourn_Labbe.pdf file_size: 5041924 relation: main_file success: 1 file_date_updated: 2026-02-10T06:44:24Z fulldoi: https://doi.org/10.3847/1538-4357/ad3551 has_accepted_license: '1' intvolume: ' 978' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: The Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'UNCOVER: Candidate red active galactic nuclei at 3 < z < 7 with JWST and ALMA' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 978 year: '2024' ... --- OA_place: repository OA_type: green _id: '21304' abstract: - lang: eng text: No description provided. article_processing_charge: No author: - first_name: Miguel full_name: Santana de Freitas Amaral, Miguel id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501 last_name: Santana de Freitas Amaral citation: ama: 'Santana de Freitas Amaral M. archaeal_membranes : code and examples. 2024. doi:10.5281/ZENODO.13934991' apa: 'Santana de Freitas Amaral, M. (2024). archaeal_membranes : code and examples. Zenodo. https://doi.org/10.5281/ZENODO.13934991' chicago: 'Santana de Freitas Amaral, Miguel. “Archaeal_membranes : Code and Examples.” Zenodo, 2024. https://doi.org/10.5281/ZENODO.13934991.' ieee: 'M. Santana de Freitas Amaral, “archaeal_membranes : code and examples.” Zenodo, 2024.' ista: 'Santana de Freitas Amaral M. 2024. archaeal_membranes : code and examples, Zenodo, 10.5281/ZENODO.13934991.' mla: 'Santana de Freitas Amaral, Miguel. Archaeal_membranes : Code and Examples. Zenodo, 2024, doi:10.5281/ZENODO.13934991.' short: M. Santana de Freitas Amaral, (2024). corr_author: '1' date_created: 2026-02-17T12:52:26Z date_published: 2024-10-15T00:00:00Z date_updated: 2026-02-23T11:49:05Z day: '15' department: - _id: AnSa doi: 10.5281/ZENODO.13934991 fulldoi: https://doi.org/10.5281/ZENODO.13934991 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.13934991 month: '10' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '21251' relation: used_for_analysis_in status: public status: public title: 'archaeal_membranes : code and examples' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21528' abstract: - lang: eng text: We present a framework for the end-to-end optimization of metasurface imaging systems that reconstruct targets using compressed sensing, a technique for solving underdetermined imaging problems when the target object exhibits sparsity (e.g., the object can be described by a small number of nonzero values, but the positions of these values are unknown). We nest an iterative, unapproximated compressed sensing reconstruction algorithm into our end-to-end optimization pipeline, resulting in an interpretable, data-efficient method for maximally leveraging metaoptics to exploit object sparsity. We apply our framework to super-resolution imaging and high-resolution depth imaging with a phase-change material. In both situations, our end-to-end framework effectively optimizes metasurface structures for compressed sensing recovery, automatically balancing a number of complicated design considerations to select an imaging measurement matrix from a complex, physically constrained manifold with millions of dimensions. The optimized metasurface imaging systems are robust to noise, significantly improving over random scattering surfaces and approaching the ideal compressed sensing performance of a Gaussian matrix, showing how a physical metasurface system can demonstrably approach the mathematical limits of compressed sensing. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Gaurav full_name: Arya, Gaurav last_name: Arya - first_name: William F. full_name: Li, William F. last_name: Li - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Marin full_name: Soljačić, Marin last_name: Soljačić - first_name: Steven G. full_name: Johnson, Steven G. last_name: Johnson - first_name: Zin full_name: Lin, Zin last_name: Lin citation: ama: Arya G, Li WF, Roques-Carmes C, Soljačić M, Johnson SG, Lin Z. End-to-end optimization of metasurfaces for imaging with compressed sensing. ACS Photonics. 2024;11(5):2077-2087. doi:10.1021/acsphotonics.4c00259 apa: Arya, G., Li, W. F., Roques-Carmes, C., Soljačić, M., Johnson, S. G., & Lin, Z. (2024). End-to-end optimization of metasurfaces for imaging with compressed sensing. ACS Photonics. American Chemical Society. https://doi.org/10.1021/acsphotonics.4c00259 chicago: Arya, Gaurav, William F. Li, Charles Roques-Carmes, Marin Soljačić, Steven G. Johnson, and Zin Lin. “End-to-End Optimization of Metasurfaces for Imaging with Compressed Sensing.” ACS Photonics. American Chemical Society, 2024. https://doi.org/10.1021/acsphotonics.4c00259. ieee: G. Arya, W. F. Li, C. Roques-Carmes, M. Soljačić, S. G. Johnson, and Z. Lin, “End-to-end optimization of metasurfaces for imaging with compressed sensing,” ACS Photonics, vol. 11, no. 5. American Chemical Society, pp. 2077–2087, 2024. ista: Arya G, Li WF, Roques-Carmes C, Soljačić M, Johnson SG, Lin Z. 2024. End-to-end optimization of metasurfaces for imaging with compressed sensing. ACS Photonics. 11(5), 2077–2087. mla: Arya, Gaurav, et al. “End-to-End Optimization of Metasurfaces for Imaging with Compressed Sensing.” ACS Photonics, vol. 11, no. 5, American Chemical Society, 2024, pp. 2077–87, doi:10.1021/acsphotonics.4c00259. short: G. Arya, W.F. Li, C. Roques-Carmes, M. Soljačić, S.G. Johnson, Z. Lin, ACS Photonics 11 (2024) 2077–2087. date_created: 2026-03-30T12:22:47Z date_published: 2024-04-23T00:00:00Z date_updated: 2026-04-27T09:03:21Z day: '23' ddc: - '530' doi: 10.1021/acsphotonics.4c00259 extern: '1' external_id: arxiv: - '2201.12348' fulldoi: https://doi.org/10.1021/acsphotonics.4c00259 intvolume: ' 11' issue: '5' keyword: - end-to-end - optimization - metasurface - imaging - compressed sensing language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2201.12348 month: '04' oa: 1 oa_version: Preprint page: 2077-2087 publication: ACS Photonics publication_identifier: eissn: - 2330-4022 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: End-to-end optimization of metasurfaces for imaging with compressed sensing type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 11 year: '2024' ... --- OA_place: repository OA_type: green _id: '21529' abstract: - lang: eng text: 'A central challenge in the emerging field of free-electron quantum optics is to achieve strong quantum interaction and single-photon nonlinearity between a flying free electron and a photonic mode. Existing schemes are intrinsically limited by electron diffraction, which puts an upper bound on the interaction length and, therefore, on the strength of quantum coupling and nonlinearity. Here, we propose “free-electron fibers”: effectively one-dimensional photonic systems where free electrons copropagate with two guided modes. The first mode applies a ponderomotive trap to the free electron, removing the limitations due to electron diffraction. The second mode strongly couples to the guided free electron with an enhanced coupling that is orders of magnitude larger than previous designs. The extended interaction lengths enabled by our scheme allow for strong single-photon nonlinearities mediated by free electrons. We predict novel quantum effects in our system such as deterministic single-photon emission and nonlinear multimode dynamics. Our proposal paves the way toward the realization of heralded macroscopic nonclassical light generation, deterministic single-photon sources, and quantum gates controlled by free-electron–photon interactions.' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Aviv full_name: Karnieli, Aviv last_name: Karnieli - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Nicholas full_name: Rivera, Nicholas last_name: Rivera - first_name: Shanhui full_name: Fan, Shanhui last_name: Fan citation: ama: Karnieli A, Roques-Carmes C, Rivera N, Fan S. Strong coupling and single-photon nonlinearity in free-electron quantum optics. ACS Photonics. 2024;11(8):3401-3411. doi:10.1021/acsphotonics.4c00908 apa: Karnieli, A., Roques-Carmes, C., Rivera, N., & Fan, S. (2024). Strong coupling and single-photon nonlinearity in free-electron quantum optics. ACS Photonics. American Chemical Society. https://doi.org/10.1021/acsphotonics.4c00908 chicago: Karnieli, Aviv, Charles Roques-Carmes, Nicholas Rivera, and Shanhui Fan. “Strong Coupling and Single-Photon Nonlinearity in Free-Electron Quantum Optics.” ACS Photonics. American Chemical Society, 2024. https://doi.org/10.1021/acsphotonics.4c00908. ieee: A. Karnieli, C. Roques-Carmes, N. Rivera, and S. Fan, “Strong coupling and single-photon nonlinearity in free-electron quantum optics,” ACS Photonics, vol. 11, no. 8. American Chemical Society, pp. 3401–3411, 2024. ista: Karnieli A, Roques-Carmes C, Rivera N, Fan S. 2024. Strong coupling and single-photon nonlinearity in free-electron quantum optics. ACS Photonics. 11(8), 3401–3411. mla: Karnieli, Aviv, et al. “Strong Coupling and Single-Photon Nonlinearity in Free-Electron Quantum Optics.” ACS Photonics, vol. 11, no. 8, American Chemical Society, 2024, pp. 3401–11, doi:10.1021/acsphotonics.4c00908. short: A. Karnieli, C. Roques-Carmes, N. Rivera, S. Fan, ACS Photonics 11 (2024) 3401–3411. date_created: 2026-03-30T12:22:47Z date_published: 2024-07-29T00:00:00Z date_updated: 2026-04-27T10:30:37Z day: '29' ddc: - '530' doi: 10.1021/acsphotonics.4c00908 extern: '1' external_id: arxiv: - '2403.13071' fulldoi: https://doi.org/10.1021/acsphotonics.4c00908 intvolume: ' 11' issue: '8' keyword: - quantum optics - free electrons - single photon nonlinearity - electron-photon interaction language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2403.13071 month: '07' oa: 1 oa_version: Preprint page: 3401-3411 publication: ACS Photonics publication_identifier: eissn: - 2330-4022 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Strong coupling and single-photon nonlinearity in free-electron quantum optics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21535' abstract: - lang: eng text: Optical phenomena always display some degree of partial coherence between their respective degrees of freedom. Partial coherence is of particular interest in multimodal systems, where classical and quantum correlations between spatial, polarization, and spectral degrees of freedom can lead to fascinating phenomena (e.g., entanglement) and be leveraged for advanced imaging and sensing modalities (e.g., in hyperspectral, polarization, and ghost imaging). Here, we present a universal method to analyze, process, and generate spatially partially coherent light in multimode systems by using self-configuring optical networks. Our method relies on cascaded self-configuring layers whose average power outputs are sequentially optimized. Once optimized, the network separates the input light into its mutually incoherent components, which is formally equivalent to a diagonalization of the input density matrix. We illustrate our method with numerical simulations of Mach-Zehnder interferometer arrays and show how this method can be used to perform partially coherent environmental light sensing, generation of multimode partially coherent light with arbitrary coherency matrices, and unscrambling of quantum optical mixtures. We provide guidelines for the experimental realization of this method, including the influence of losses, paving the way for self-configuring photonic devices that can automatically learn optimal modal representations of partially coherent light fields. article_number: '260' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Shanhui full_name: Fan, Shanhui last_name: Fan - first_name: David A. B. full_name: Miller, David A. B. last_name: Miller citation: ama: 'Roques-Carmes C, Fan S, Miller DAB. Measuring, processing, and generating partially coherent light with self-configuring optics. Light: Science & Applications. 2024;13. doi:10.1038/s41377-024-01622-y' apa: 'Roques-Carmes, C., Fan, S., & Miller, D. A. B. (2024). Measuring, processing, and generating partially coherent light with self-configuring optics. Light: Science & Applications. Springer Nature. https://doi.org/10.1038/s41377-024-01622-y' chicago: 'Roques-Carmes, Charles, Shanhui Fan, and David A. B. Miller. “Measuring, Processing, and Generating Partially Coherent Light with Self-Configuring Optics.” Light: Science & Applications. Springer Nature, 2024. https://doi.org/10.1038/s41377-024-01622-y.' ieee: 'C. Roques-Carmes, S. Fan, and D. A. B. Miller, “Measuring, processing, and generating partially coherent light with self-configuring optics,” Light: Science & Applications, vol. 13. Springer Nature, 2024.' ista: 'Roques-Carmes C, Fan S, Miller DAB. 2024. Measuring, processing, and generating partially coherent light with self-configuring optics. Light: Science & Applications. 13, 260.' mla: 'Roques-Carmes, Charles, et al. “Measuring, Processing, and Generating Partially Coherent Light with Self-Configuring Optics.” Light: Science & Applications, vol. 13, 260, Springer Nature, 2024, doi:10.1038/s41377-024-01622-y.' short: 'C. Roques-Carmes, S. Fan, D.A.B. Miller, Light: Science & Applications 13 (2024).' date_created: 2026-03-30T12:22:47Z date_published: 2024-09-20T00:00:00Z date_updated: 2026-05-05T10:45:37Z day: '20' ddc: - '530' doi: 10.1038/s41377-024-01622-y extern: '1' external_id: arxiv: - '2402.00704' pmid: - '39300058' fulldoi: https://doi.org/10.1038/s41377-024-01622-y intvolume: ' 13' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41377-024-01622-y month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: 'Light: Science & Applications' publication_identifier: eissn: - 2047-7538 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '21634' relation: earlier_version status: public scopus_import: '1' status: public title: Measuring, processing, and generating partially coherent light with self-configuring optics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 13 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21540' abstract: - lang: eng text: Probabilistic machine learning utilizes controllable sources of randomness to encode uncertainty and enable statistical modeling. Harnessing the pure randomness of quantum vacuum noise, which stems from fluctuating electromagnetic fields, has shown promise for high speed and energy-efficient stochastic photonic elements. Nevertheless, photonic computing hardware which can control these stochastic elements to program probabilistic machine learning algorithms has been limited. Here, we implement a photonic probabilistic computer consisting of a controllable stochastic photonic element – a photonic probabilistic neuron (PPN). Our PPN is implemented in a bistable optical parametric oscillator (OPO) with vacuum-level injected bias fields. We then program a measurement-and-feedback loop for time-multiplexed PPNs with electronic processors (FPGA or GPU) to solve certain probabilistic machine learning tasks. We showcase probabilistic inference and image generation of MNIST-handwritten digits, which are representative examples of discriminative and generative models. In both implementations, quantum vacuum noise is used as a random seed to encode classification uncertainty or probabilistic generation of samples. In addition, we propose a path towards an all-optical probabilistic computing platform, with an estimated sampling rate of ~1 Gbps and energy consumption of ~5 fJ/MAC. Our work paves the way for scalable, ultrafast, and energy-efficient probabilistic machine learning hardware. article_number: '7760' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Seou full_name: Choi, Seou last_name: Choi - first_name: Yannick full_name: Salamin, Yannick last_name: Salamin - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Rumen full_name: Dangovski, Rumen last_name: Dangovski - first_name: Di full_name: Luo, Di last_name: Luo - first_name: Zhuo full_name: Chen, Zhuo last_name: Chen - first_name: Michael full_name: Horodynski, Michael last_name: Horodynski - first_name: Jamison full_name: Sloan, Jamison last_name: Sloan - first_name: Shiekh Zia full_name: Uddin, Shiekh Zia last_name: Uddin - first_name: Marin full_name: Soljačić, Marin last_name: Soljačić citation: ama: Choi S, Salamin Y, Roques-Carmes C, et al. Photonic probabilistic machine learning using quantum vacuum noise. Nature Communications. 2024;15. doi:10.1038/s41467-024-51509-0 apa: Choi, S., Salamin, Y., Roques-Carmes, C., Dangovski, R., Luo, D., Chen, Z., … Soljačić, M. (2024). Photonic probabilistic machine learning using quantum vacuum noise. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-51509-0 chicago: Choi, Seou, Yannick Salamin, Charles Roques-Carmes, Rumen Dangovski, Di Luo, Zhuo Chen, Michael Horodynski, Jamison Sloan, Shiekh Zia Uddin, and Marin Soljačić. “Photonic Probabilistic Machine Learning Using Quantum Vacuum Noise.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-51509-0. ieee: S. Choi et al., “Photonic probabilistic machine learning using quantum vacuum noise,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Choi S, Salamin Y, Roques-Carmes C, Dangovski R, Luo D, Chen Z, Horodynski M, Sloan J, Uddin SZ, Soljačić M. 2024. Photonic probabilistic machine learning using quantum vacuum noise. Nature Communications. 15, 7760. mla: Choi, Seou, et al. “Photonic Probabilistic Machine Learning Using Quantum Vacuum Noise.” Nature Communications, vol. 15, 7760, Springer Nature, 2024, doi:10.1038/s41467-024-51509-0. short: S. Choi, Y. Salamin, C. Roques-Carmes, R. Dangovski, D. Luo, Z. Chen, M. Horodynski, J. Sloan, S.Z. Uddin, M. Soljačić, Nature Communications 15 (2024). date_created: 2026-03-30T12:22:47Z date_published: 2024-09-05T00:00:00Z date_updated: 2026-04-27T10:37:35Z day: '05' ddc: - '530' doi: 10.1038/s41467-024-51509-0 extern: '1' external_id: arxiv: - '2403.04731' pmid: - '39237543' fulldoi: https://doi.org/10.1038/s41467-024-51509-0 intvolume: ' 15' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-024-51509-0 month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Photonic probabilistic machine learning using quantum vacuum noise tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2024' ... --- OA_place: repository OA_type: green _id: '21560' abstract: - lang: eng text: Scintillation describes the conversion of high-energy particles into light in transparent media and finds diverse applications such as high-energy particle detection and industrial and medical imaging. This process operates on multiple timescales, with the final radiative step consisting of spontaneous emission, which can be modeled within the framework of quasiequilibrium fluctuational electrodynamics. Scintillation can therefore be controlled and enhanced via nanophotonic effects, which has been proposed and experimentally demonstrated. Such designs have thus far obeyed Lorentz reciprocity, meaning there is a direct equivalence between scintillation emission and absorption by the scintillator. However, scintillators that do not obey Lorentz reciprocity have not been explored, even though they represent an alternative platform for probing emission, which is both nonequilibrium and nonreciprocal in nature. In this work, we propose to harness nonreciprocity to achieve directional control of scintillation emission, granting an additional degree of control over scintillation. Such directionality of light output is useful in improving collection efficiencies along the directions where detectors are located. We present the design of a nonreciprocal scintillator using a one-dimensional magnetophotonic crystal in the Voigt configuration. Our work demonstrates the potential of controlling nonequilibrium such as scintillation by breaking reciprocity and expands the space of nanophotonic design for achieving such control. article_number: '054062' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Olivia Y. full_name: Long, Olivia Y. last_name: Long - first_name: Simo full_name: Pajovic, Simo last_name: Pajovic - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Yoichiro full_name: Tsurimaki, Yoichiro last_name: Tsurimaki - first_name: Nicholas full_name: Rivera, Nicholas last_name: Rivera - first_name: Marin full_name: Soljačić, Marin last_name: Soljačić - first_name: Svetlana V. full_name: Boriskina, Svetlana V. last_name: Boriskina - first_name: Shanhui full_name: Fan, Shanhui last_name: Fan citation: ama: Long OY, Pajovic S, Roques-Carmes C, et al. Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals. Physical Review Applied. 2024;22(5). doi:10.1103/physrevapplied.22.054062 apa: Long, O. Y., Pajovic, S., Roques-Carmes, C., Tsurimaki, Y., Rivera, N., Soljačić, M., … Fan, S. (2024). Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals. Physical Review Applied. American Physical Society. https://doi.org/10.1103/physrevapplied.22.054062 chicago: Long, Olivia Y., Simo Pajovic, Charles Roques-Carmes, Yoichiro Tsurimaki, Nicholas Rivera, Marin Soljačić, Svetlana V. Boriskina, and Shanhui Fan. “Nonreciprocal Scintillation Using One-Dimensional Magneto-Optical Photonic Crystals.” Physical Review Applied. American Physical Society, 2024. https://doi.org/10.1103/physrevapplied.22.054062. ieee: O. Y. Long et al., “Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals,” Physical Review Applied, vol. 22, no. 5. American Physical Society, 2024. ista: Long OY, Pajovic S, Roques-Carmes C, Tsurimaki Y, Rivera N, Soljačić M, Boriskina SV, Fan S. 2024. Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals. Physical Review Applied. 22(5), 054062. mla: Long, Olivia Y., et al. “Nonreciprocal Scintillation Using One-Dimensional Magneto-Optical Photonic Crystals.” Physical Review Applied, vol. 22, no. 5, 054062, American Physical Society, 2024, doi:10.1103/physrevapplied.22.054062. short: O.Y. Long, S. Pajovic, C. Roques-Carmes, Y. Tsurimaki, N. Rivera, M. Soljačić, S.V. Boriskina, S. Fan, Physical Review Applied 22 (2024). date_created: 2026-03-30T12:22:47Z date_published: 2024-11-22T00:00:00Z date_updated: 2026-04-27T10:38:50Z day: '22' doi: 10.1103/physrevapplied.22.054062 extern: '1' external_id: arxiv: - '2409.17002' fulldoi: https://doi.org/10.1103/physrevapplied.22.054062 intvolume: ' 22' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2409.17002 month: '11' oa: 1 oa_version: Preprint publication: Physical Review Applied publication_identifier: issn: - 2331-7019 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21564' abstract: - lang: eng text: Multimode quantum light is enticing for several applications, spanning imaging, spectroscopy, communication, and more. Parametric nonlinear processes have been vital in realizing squeezed and other quantum states of light. However, most work exploiting these processes has focused on generating multimode squeezed vacua and squeezing in mode superpositions (supermodes). Bright squeezing in multiple discrete frequency modes, if realized, could unlock novel applications in quantum-enhanced spectroscopy and optical quantum computing. Here, we show how dissipation engineering of a multimode nonlinear cavity with cascaded three-wave-mixing processes allows us to shape above-threshold frequency combs that feature strong single-mode output amplitude noise squeezing over 10 dB below the shot-noise limit, tunable across the comb. In addition, we demonstrate squeezing for multiple discrete frequency modes above threshold. This bright squeezing arises from enhancement of the (noiseless) nonlinear rate relative to decay rates in the system due to the cascaded generation of photons in a single idler “bath” mode. A natural consequence of the strong nonlinear coupling in our system is the creation of an effective cavity in the synthetic frequency dimension that sustains Bloch oscillations in the modal energy distribution. Bloch mode engineering could provide an opportunity to better control nonlinear energy flow in the synthetic frequency dimension, with exciting applications in quantum random walks and topological photonics. Lastly, we show evidence of long-range correlations in amplitude noise between discrete frequency modes, enabling long-range entanglement in a synthetic frequency dimension and providing a new resource for quantum communication. article_number: '040345' article_processing_charge: No article_type: original author: - first_name: Sahil full_name: Pontula, Sahil last_name: Pontula - first_name: Yannick full_name: Salamin, Yannick last_name: Salamin - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Marin full_name: Soljačić, Marin last_name: Soljačić citation: ama: Pontula S, Salamin Y, Roques-Carmes C, Soljačić M. Shaping quantum noise through cascaded nonlinear processes in a dissipation-engineered multimode cavity. PRX Quantum. 2024;5(4). doi:10.1103/prxquantum.5.040345 apa: Pontula, S., Salamin, Y., Roques-Carmes, C., & Soljačić, M. (2024). Shaping quantum noise through cascaded nonlinear processes in a dissipation-engineered multimode cavity. PRX Quantum. American Physical Society. https://doi.org/10.1103/prxquantum.5.040345 chicago: Pontula, Sahil, Yannick Salamin, Charles Roques-Carmes, and Marin Soljačić. “Shaping Quantum Noise through Cascaded Nonlinear Processes in a Dissipation-Engineered Multimode Cavity.” PRX Quantum. American Physical Society, 2024. https://doi.org/10.1103/prxquantum.5.040345. ieee: S. Pontula, Y. Salamin, C. Roques-Carmes, and M. Soljačić, “Shaping quantum noise through cascaded nonlinear processes in a dissipation-engineered multimode cavity,” PRX Quantum, vol. 5, no. 4. American Physical Society, 2024. ista: Pontula S, Salamin Y, Roques-Carmes C, Soljačić M. 2024. Shaping quantum noise through cascaded nonlinear processes in a dissipation-engineered multimode cavity. PRX Quantum. 5(4), 040345. mla: Pontula, Sahil, et al. “Shaping Quantum Noise through Cascaded Nonlinear Processes in a Dissipation-Engineered Multimode Cavity.” PRX Quantum, vol. 5, no. 4, 040345, American Physical Society, 2024, doi:10.1103/prxquantum.5.040345. short: S. Pontula, Y. Salamin, C. Roques-Carmes, M. Soljačić, PRX Quantum 5 (2024). date_created: 2026-03-30T12:22:47Z date_published: 2024-12-18T00:00:00Z date_updated: 2026-04-27T10:41:06Z day: '18' ddc: - '530' doi: 10.1103/prxquantum.5.040345 extern: '1' fulldoi: https://doi.org/10.1103/prxquantum.5.040345 intvolume: ' 5' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1103/PRXQuantum.5.040345 month: '12' oa: 1 oa_version: Published Version publication: PRX Quantum publication_identifier: issn: - 2691-3399 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Shaping quantum noise through cascaded nonlinear processes in a dissipation-engineered multimode cavity tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21582' abstract: - lang: eng text: 'Scintillation materials convert high-energy radiation to optical light through a complex multistage process. The last stage of the process is spontaneous light emission, which usually governs and limits the scintillator emission rate and light yield. For decades, scintillator research focused on developing faster-emitting materials or external photonic coatings for improving light yields. Here, we experimentally demonstrate a fundamentally different approach: enhancing the scintillation rate and yield via the Purcell effect, utilizing optical environment engineering to boost spontaneous emission. This enhancement is universally applicable to any scintillating material and dopant when the material’s nanoscale geometry is engineered. We design a thin multilayer nanophotonic scintillator, demonstrating Purcell-enhanced scintillation with 50% enhancement in emission rate and 80% enhancement in light yield. The emission is robust to fabrication disorder, further highlighting its potential for x-ray applications. Our results show prospects for bridging nanophotonics and scintillator science toward reduced radiation dosage and increased resolution for high-energy particle detection.' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Yaniv full_name: Kurman, Yaniv last_name: Kurman - first_name: Neta full_name: Lahav, Neta last_name: Lahav - first_name: Roman full_name: Schuetz, Roman last_name: Schuetz - first_name: Avner full_name: Shultzman, Avner last_name: Shultzman - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Alon full_name: Lifshits, Alon last_name: Lifshits - first_name: Segev full_name: Zaken, Segev last_name: Zaken - first_name: Tom full_name: Lenkiewicz, Tom last_name: Lenkiewicz - first_name: Rotem full_name: Strassberg, Rotem last_name: Strassberg - first_name: Orr full_name: Be’er, Orr last_name: Be’er - first_name: Yehonadav full_name: Bekenstein, Yehonadav last_name: Bekenstein - first_name: Ido full_name: Kaminer, Ido last_name: Kaminer citation: ama: Kurman Y, Lahav N, Schuetz R, et al. Purcell-enhanced x-ray scintillation. Science Advances. 2024;10(44). doi:10.1126/sciadv.adq6325 apa: Kurman, Y., Lahav, N., Schuetz, R., Shultzman, A., Roques-Carmes, C., Lifshits, A., … Kaminer, I. (2024). Purcell-enhanced x-ray scintillation. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adq6325 chicago: Kurman, Yaniv, Neta Lahav, Roman Schuetz, Avner Shultzman, Charles Roques-Carmes, Alon Lifshits, Segev Zaken, et al. “Purcell-Enhanced x-Ray Scintillation.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adq6325. ieee: Y. Kurman et al., “Purcell-enhanced x-ray scintillation,” Science Advances, vol. 10, no. 44. American Association for the Advancement of Science, 2024. ista: Kurman Y, Lahav N, Schuetz R, Shultzman A, Roques-Carmes C, Lifshits A, Zaken S, Lenkiewicz T, Strassberg R, Be’er O, Bekenstein Y, Kaminer I. 2024. Purcell-enhanced x-ray scintillation. Science Advances. 10(44). mla: Kurman, Yaniv, et al. “Purcell-Enhanced x-Ray Scintillation.” Science Advances, vol. 10, no. 44, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adq6325. short: Y. Kurman, N. Lahav, R. Schuetz, A. Shultzman, C. Roques-Carmes, A. Lifshits, S. Zaken, T. Lenkiewicz, R. Strassberg, O. Be’er, Y. Bekenstein, I. Kaminer, Science Advances 10 (2024). date_created: 2026-03-30T12:22:48Z date_published: 2024-11-01T00:00:00Z date_updated: 2026-04-27T09:31:51Z day: '01' ddc: - '530' doi: 10.1126/sciadv.adq6325 extern: '1' external_id: arxiv: - '2302.01300' pmid: - '39485836' fulldoi: https://doi.org/10.1126/sciadv.adq6325 intvolume: ' 10' issue: '44' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1126/sciadv.adq6325 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Science Advances publication_identifier: eissn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Purcell-enhanced x-ray scintillation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 10 year: '2024' ...