--- OA_place: publisher OA_type: green _id: '21857' abstract: - lang: eng text: "The availability of powerful open-source large language models (LLMs) opens exciting use cases, such as using personal data to fine-tune these models to imitate a user’s unique writing style. Two key requirements for this functionality are personalization–in the sense that the output should recognizably reflect the user’s own writing style—and privacy–users may justifiably be wary of uploading extremely personal data, such as their email archive, to a third-party service. In this paper, we demonstrate the feasibility of training and running such an assistant, which we call Panza, on commodity hardware, for the specific use case of email generation. Panza’s personalization features are based on a combination of parameter-efficient fine-tuning using a variant of the Reverse Instructions technique [1] and Retrieval-Augmented Generation (RAG) [2]. We demonstrate that this combination allows us to fine-tune an LLM to reflect a user’s writing style using limited data, while executing on extremely limited resources, e.g. on a free Google Colab instance. Our key methodological contribution is the first detailed study of evaluation metrics for this task, and\r\nof how different choices of system components–the use of RAG and of different fine-tuning approaches–impact the system’s performance. Additionally, we demonstrate that very little data - under 100 email samples - are sufficient to create models that convincingly imitate humans, showcasing a previously unknown attack vector in language models. We are releasing the full Panza code as well as three new email datasets licensed for research use." article_number: '81' article_processing_charge: No author: - first_name: Armand full_name: Nicolicioiu, Armand last_name: Nicolicioiu - first_name: Eugenia B full_name: Iofinova, Eugenia B id: f9a17499-f6e0-11ea-865d-fdf9a3f77117 last_name: Iofinova orcid: 0000-0002-7778-3221 - first_name: Andrej full_name: Jovanovic, Andrej last_name: Jovanovic - first_name: Eldar full_name: Kurtic, Eldar id: 47beb3a5-07b5-11eb-9b87-b108ec578218 last_name: Kurtic - first_name: Mahdi full_name: Nikdan, Mahdi id: 66374281-f394-11eb-9cf6-869147deecc0 last_name: Nikdan - first_name: Andrei full_name: Panferov, Andrei id: 2c18daae-4dbe-11ef-8491-98ce2d960f09 last_name: Panferov - first_name: Ilia full_name: Markov, Ilia id: D0CF4148-C985-11E9-8066-0BDEE5697425 last_name: Markov - first_name: Nir full_name: Shavit, Nir last_name: Shavit - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Nicolicioiu A, Iofinova EB, Jovanovic A, et al. Panza: Investigating the Feasibility of Fully-Local Personalized Text Generation. OpenReview; 2026.' apa: 'Nicolicioiu, A., Iofinova, E. B., Jovanovic, A., Kurtic, E., Nikdan, M., Panferov, A., … Alistarh, D.-A. (2026). Panza: Investigating the feasibility of fully-local personalized text generation. Third Conference on Parsimony and Learning (Proceedings Track). Tübíngen, Germany: OpenReview.' chicago: 'Nicolicioiu, Armand, Eugenia B Iofinova, Andrej Jovanovic, Eldar Kurtic, Mahdi Nikdan, Andrei Panferov, Ilia Markov, Nir Shavit, and Dan-Adrian Alistarh. Panza: Investigating the Feasibility of Fully-Local Personalized Text Generation. Third Conference on Parsimony and Learning (Proceedings Track). OpenReview, 2026.' ieee: 'A. Nicolicioiu et al., Panza: Investigating the feasibility of fully-local personalized text generation. OpenReview, 2026.' ista: 'Nicolicioiu A, Iofinova EB, Jovanovic A, Kurtic E, Nikdan M, Panferov A, Markov I, Shavit N, Alistarh D-A. 2026. Panza: Investigating the feasibility of fully-local personalized text generation, OpenReview,p.' mla: 'Nicolicioiu, Armand, et al. “Panza: Investigating the Feasibility of Fully-Local Personalized Text Generation.” Third Conference on Parsimony and Learning (Proceedings Track), 81, OpenReview, 2026.' short: 'A. Nicolicioiu, E.B. Iofinova, A. Jovanovic, E. Kurtic, M. Nikdan, A. Panferov, I. Markov, N. Shavit, D.-A. Alistarh, Panza: Investigating the Feasibility of Fully-Local Personalized Text Generation, OpenReview, 2026.' conference: end_date: 2026-03-26 location: Tübíngen, Germany name: 'CPAL: Conference on Parsimony and Learning' start_date: 2026-03-23 corr_author: '1' date_created: 2026-05-11T08:50:28Z date_published: 2026-03-06T00:00:00Z date_updated: 2026-05-19T11:20:27Z day: '06' department: - _id: GradSch - _id: DaAl keyword: - LLMs - PEFT - LoRA - personalization - efficient ML language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ main_file_link: - open_access: '1' url: https://openreview.net/pdf?id=soFWnTqd23 month: '03' oa: 1 oa_version: Accepted Version publication: Third Conference on Parsimony and Learning (Proceedings Track) publication_status: published publisher: OpenReview quality_controlled: '1' related_material: record: - id: '21854' relation: dissertation_contains status: public status: public title: 'Panza: Investigating the feasibility of fully-local personalized text generation' 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: conference_poster user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository OA_type: green _id: '21859' abstract: - lang: eng text: As artificial neural networks, and specifically large language models, have improved rapidly in capabilities and quality, they have increasingly been deployed in real-world applications, from customer service to Google search, despite the fact that they frequently make factually incorrect or undesirable statements. This trend has inspired practical and academic interest in model editing, that is, in adjusting the weights of the model to modify its likely outputs for queries relating to a specific fact or set of facts. This may be done either to amend a fact or set of facts, for instance, to fix a frequent error in the training data, or to suppress a fact or set of facts entirely, for instance, in case of dangerous knowledge. Multiple methods have been proposed to do such edits. However, at the same time, it has been shown that such model editing can be brittle and incomplete. Moreover the effectiveness of any model editing method necessarily depends on the data on which the model is trained, and, therefore, a good understanding of the interaction of the training data distribution and the way it is stored in the network is necessary and helpful to reliably perform model editing. However, working with large language models trained on real-world data does not allow us to understand this relationship or fully measure the effects of model editing. We therefore propose Behemoth, a fully synthetic data generation framework. To demonstrate the practical insights from the framework, we explore model editing in the context of simple tabular data, demonstrating surprising findings that, in some cases, echo real-world results, for instance, that in some cases restricting the update rank results in a more effective update. acknowledged_ssus: - _id: ScienComp acknowledgement: "EI thanks Weiwei Yang, Janardhan Kulkani, and Kate Lytvynets for their advice and support in\r\ndeveloping an earlier version of the Behemoth library. This research was supported by the Scientific\r\nService Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).\r\nEI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35.\r\n" article_processing_charge: No arxiv: 1 author: - first_name: Eugenia B full_name: Iofinova, Eugenia B id: f9a17499-f6e0-11ea-865d-fdf9a3f77117 last_name: Iofinova orcid: 0000-0002-7778-3221 - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Iofinova EB, Alistarh D-A. Behemoth: Benchmarking unlearning in LLMs using fully synthetic data. arXiv. doi:10.48550/arXiv.2601.23153' apa: 'Iofinova, E. B., & Alistarh, D.-A. (n.d.). Behemoth: Benchmarking unlearning in LLMs using fully synthetic data. arXiv. https://doi.org/10.48550/arXiv.2601.23153' chicago: 'Iofinova, Eugenia B, and Dan-Adrian Alistarh. “Behemoth: Benchmarking Unlearning in LLMs Using Fully Synthetic Data.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2601.23153.' ieee: 'E. B. Iofinova and D.-A. Alistarh, “Behemoth: Benchmarking unlearning in LLMs using fully synthetic data,” arXiv. .' ista: 'Iofinova EB, Alistarh D-A. Behemoth: Benchmarking unlearning in LLMs using fully synthetic data. arXiv, 10.48550/arXiv.2601.23153.' mla: 'Iofinova, Eugenia B., and Dan-Adrian Alistarh. “Behemoth: Benchmarking Unlearning in LLMs Using Fully Synthetic Data.” ArXiv, doi:10.48550/arXiv.2601.23153.' short: E.B. Iofinova, D.-A. Alistarh, ArXiv (n.d.). corr_author: '1' date_created: 2026-05-11T08:58:07Z date_published: 2026-01-30T00:00:00Z date_updated: 2026-05-19T11:20:27Z day: '30' department: - _id: GradSch - _id: DaAl doi: 10.48550/arXiv.2601.23153 external_id: arxiv: - '2601.23153' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2601.23153 month: '01' oa: 1 oa_version: Preprint project: - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: W1260-N35 name: Vienna Graduate School on Computational Optimization publication: arXiv publication_status: draft related_material: record: - id: '21854' relation: dissertation_contains status: public status: public title: 'Behemoth: Benchmarking unlearning in LLMs using fully synthetic data' type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '21863' abstract: - lang: eng text: "Atoms and photons, two things so different but yet so alike. The former, the building block of matter, something we learn about in school and imagine it as some tiny marbles encircled by other tinier marbles. The latter, an electromagnetic wave, a light particle or an excitation of the electromagnetic field. Quantum mechanics tells us about the properties of these two entities. And even if it sounds, looks and writes counter-intuitive, it has proven right for over a century now.\r\n\r\nIn this work, I elaborate on how we tested the laws of quantum mechanics and how we used them learn more about the tiny building blocks of nature and the fields they use to talk to each other. The atoms we use, are artificial. Superconducting qubits, small electrical circuits with quantized energy levels behave like electrons that transition between different orbitals in an atom. One of the qubits' advantages, is also a big disadvantage. We design the circuits' energy levels and fabricate them in a cleanroom. This allows for arbitrary spaced energy levels but in contrast to real atoms, prevents two superconducting qubits from being alike. Still, this qubit platform is one of the frontrunners for future quantum computing technology and testing fundamental physics due to their scalability.\r\n\r\nWe interface superconducting qubits, which operate in the GHz regime, with microwave photons. We use 3D aluminum cavities as mediators between qubits and photons. The cavities allow for non-destructive readout of the qubit state, they shield the qubits from noise at the qubit frequency and they give us an easy way to frequency-tune these joint systems.\r\n\r\nWe need to operate superconducting qubits and their cavities at millikelvin temperatures in dilution refrigerators. At higher temperatures, superconductivity suffers and even worse, the environment is filled with thermal noise photons. This poses a fundamental limitation on the scalability of superconducting qubit devices. Also connecting multiple devices in different fridges does not work over room temperature links because the microwave photons used for this purpose will be covered in noise and the quantum information they carry, will be unusable.\r\n\r\nInfrared photons do not suffer from this noise problem since there are close to zero thermal noise photons at their frequencies at room temperature. We cannot simply interface superconducting devices with optical photons due their frequency mismatch and the destructive effect of optical photons on superconductors. Therefore, we use microwave-to-optics transducers that allow to convert microwave photons into optical ones and vice-versa. The transducers that we use are macroscopic electro-optic transducers using the Pockels effect in a disk-shaped Lithium Niobate whispering gallery mode resonator. By using a strong optical pump, photons from the two frequency domains experience a beam-splitter interaction and get converted from one to the other.\r\n\r\nWe measure the generated optical photons using elaborate optical setups, optical heterodyning and single photon detectors to gain knowledge about the qubit state or the converted microwave photons. Bridging the microwave and the optical world allows us to take advantage of both of their strengths but it also requires deep knowledge about both of their working principles.\r\n\r\nIn this work, we describe two experiments that our group conducted to showcase the opportunities that arise from interfacing superconducting qubits with optical photons but also the pitfalls, one may encounter on the way.\r\n\r\nIn the first experiment, we managed to all-optically read out a superconducting qubit. We show that the assignment fidelity, the probability that a measurement of the qubit state matches the prepared state, is close to equal for all-optical, microwave-to-optics and conventional microwave readout. We show T1 and T2 measurements for all three readout types and give an analysis of the noise caused by the optics. Finally, we show that the infrared light does not affect the qubit performance in a negative way but that the heating it causes does. This is an important insight that we used in the next experiment.\r\n\r\nThe second experiment is the upconversion of itinerant single microwave photons to the optical domain. We show that we can generate single microwave photons from a qubit-cavity system. We upconvert these single photons, measure them with a single photon detector and reconstruct their shape. By conducting a single photon Rabi measurement, we show correlations between the microwave and the optical domain. And by thorough signal-to-noise measurements and noise analysis, we find that we can generate single infrared photons with high signal-to-noise ratio 5.1 and low transducer added noise (<0.012 quanta). We show that this measurement creates a path towards entanglement of a superconducting qubit and an optical photon and what parameters need to be improved to achieve it. Additionally, this experiment is a proof of principle for an on-demand infrared single photon source. More generally, it allows to link microwave quantum technology in general to the optical domain." acknowledged_ssus: - _id: M-Shop - _id: NanoFab - _id: LifeSc - _id: SSU acknowledgement: "The author of this work was supported by the European Research Council under grant no.\r\n101089099 (ERC CoG cQEO) and the European Union’s Horizon 2020 research and innovation\r\nprogram under grant no. 899354 (FETopen SuperQuLAN).\r\nThis work was also supported by the European Research Council under grant nos. 758053\r\n(ERC StG QUNNECT), 101248662 (ERC POC CoupledEOT), and the European Innovation\r\nCouncil no. 101187231 (PathfinderOpen CIELO). This research was funded in whole or in part\r\nby the Austrian Science Fund (FWF) [10.55776/F71]. For open access purposes, the author\r\nhas applied a CC BY public copyright license to any author accepted manuscript version arising\r\nfrom this submission.\r\niii\r\nMy co-authors in the works mentioned later acknowledge generous support from the ISTFELLOW program, the NOMIS-ISTA fellowship, the Horizon Europe Program HORIZONCL4-2022-QUANTUM-01-SGA via Project No. 101113946 OpenSuperQPlus100 and a DOC fellowship of the Austrian Academy of Sciences at IST Austria.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Thomas full_name: Werner, Thomas id: 1fcd8497-dba3-11ea-a45e-c6fbd715f7c7 last_name: Werner orcid: 0009-0001-2346-5236 citation: ama: Werner T. Interfacing superconducting qubits with optical photons. 2026. doi:10.15479/AT-ISTA-21863 apa: Werner, T. (2026). Interfacing superconducting qubits with optical photons. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21863 chicago: Werner, Thomas. “Interfacing Superconducting Qubits with Optical Photons.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21863. ieee: T. Werner, “Interfacing superconducting qubits with optical photons,” Institute of Science and Technology Austria, 2026. ista: Werner T. 2026. Interfacing superconducting qubits with optical photons. Institute of Science and Technology Austria. mla: Werner, Thomas. Interfacing Superconducting Qubits with Optical Photons. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21863. short: T. Werner, Interfacing Superconducting Qubits with Optical Photons, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-05-12T09:04:02Z date_published: 2026-05-12T00:00:00Z date_updated: 2026-05-20T13:35:43Z day: '12' ddc: - '530' - '537' - '539' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/AT-ISTA-21863 ec_funded: 1 file: - access_level: open_access checksum: a5b4d8dba83f96e955a3625c0eebee98 content_type: application/pdf creator: twerner date_created: 2026-05-15T15:53:57Z date_updated: 2026-05-15T15:53:57Z file_id: '21879' file_name: 2026_Werner_Thomas_Thesis.pdf file_size: 9330516 relation: main_file - access_level: closed checksum: b41282beaacfb32472769b9e3b1758d8 content_type: application/x-zip-compressed creator: twerner date_created: 2026-05-15T15:54:06Z date_updated: 2026-05-15T15:54:06Z file_id: '21880' file_name: 2026_Werner_Thomas_Thesis.zip file_size: 9370704 relation: source_file file_date_updated: 2026-05-15T15:54:06Z has_accepted_license: '1' keyword: - Superconducting qubits - Quantum optics - Single photons and quantum effects - Nonlinear optics language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '97' project: - _id: bdadfa0d-d553-11ed-ba76-fb85edbd456a grant_number: '101089099' name: 'Cavity Quantum Electro Optics: Microwave photonics with nonclassical states' - _id: 9B868D20-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '899354' name: Quantum Local Area Networks with Superconducting Qubits - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 5b807754-ab3d-11f0-914f-ff8c34502cc9 grant_number: '101248662' name: Integrated optical coupling for low loss electro-optic interconnects - _id: 91aaf765-16d5-11f0-9cad-a8e7e44cccb7 grant_number: '101187231' name: 'Cavity-Integrated Electro-Optics: Measuring, Converting and Manipulating Microwaves with Light' - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits - _id: bdb7cfc1-d553-11ed-ba76-d2eaab167738 grant_number: '101080139' name: Open Superconducting Quantum Computers (OpenSuperQPlus) - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19073' relation: part_of_dissertation status: public - id: '21870' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: Interfacing superconducting qubits with optical photons 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: '2026' ... --- OA_place: repository OA_type: green _id: '21870' abstract: - lang: eng text: Superconducting qubits are a leading candidate for utility-scale quantum computing due to their fast gate speeds and steadily decreasing error rates. The requirement for millikelvin operating temperatures, however, creates a significant scaling bottleneck. Modular architectures using optical fiber links could bridge separate cryogenic nodes, but superconducting circuits do not have coherent optical transitions and microwave-to-optical conversion has not been shown for any non-classical photon state. In this work, we demonstrate the on-demand generation and tomographic reconstruction of itinerant single microwave photons at 8.9 GHz from a superconducting qubit. We upconvert this non-Gaussian state with a transducer added noise below 0.012 quanta and count the converted telecom photons at 193.4 THz with a signal-to-noise ratio of up to 5.1$\pm$1.1. We characterize the trade-offs between throughput and noise, and establish a viable path toward heralded entanglement distribution and gate teleportation. Looking ahead, these results empower existing superconducting devices to take a key role in distributed quantum technologies and heterogeneous quantum systems. acknowledgement: "We thank Fritz Diorico and Onur Hosten who suggested the filter cavity design, and gave important insights about the assembly and the testing of the FabryPerot filter cavities. Ekatrina Fedotova and Diego A.\r\nLancheros Naranjo worked on the filter cavity setup in\r\nthe early stages of this work. Gustavo Wiederhecker and\r\nYiewen Chu provided insights as to the origins of the\r\nobserved optical noise and Nicola Carlon Zambon suggested using telecom filters to mitigate it further. This\r\nwork was supported by the European Research Council under grant agreement no. 101089099 (ERC CoG\r\ncQEO), and 101248662 (ERC POC CoupledEOT), the\r\nEuropean Unions Horizon 2020 research and innovation\r\nprogram under grant agreement no. 899354 (FETopen\r\nSuperQuLAN), the European Innovation Council no.\r\n101187231 (PathfinderOpen CIELO), and the Austrian\r\nScience Fund (FWF) no. F7105 (SFB BeyondC). J.F.\r\nand L.K. acknowledge support from the Horizon Europe\r\nProgram HORIZON-CL4-2022-QUANTUM-01-SGA via\r\nProject No. 101113946 OpenSuperQPlus100. A.M. acknowledges support from the NOMIS-ISTA fellowship." article_processing_charge: No arxiv: 1 author: - first_name: Thomas full_name: Werner, Thomas id: 1fcd8497-dba3-11ea-a45e-c6fbd715f7c7 last_name: Werner orcid: 0009-0001-2346-5236 - first_name: Erfan full_name: Riyazi, Erfan id: 53322f94-5355-11ee-ae5a-ff6f81c87d51 last_name: Riyazi - first_name: Samarth full_name: Hawaldar, Samarth id: 221708e1-1ff6-11ee-9fa6-85146607433e last_name: Hawaldar orcid: 0000-0002-1965-4309 - first_name: Rishabh full_name: Sahu, Rishabh id: 47D26E34-F248-11E8-B48F-1D18A9856A87 last_name: Sahu orcid: 0000-0001-6264-2162 - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 - first_name: Paul Falthansl-Scheinecker full_name: Paul Falthansl-Scheinecker, Paul Falthansl-Scheinecker last_name: Paul Falthansl-Scheinecker - first_name: Jennifer A. Sánchez full_name: Naranjo, Jennifer A. Sánchez last_name: Naranjo - first_name: Dante full_name: Loi, Dante last_name: Loi - first_name: Lucky N. full_name: Kapoor, Lucky N. last_name: Kapoor - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka orcid: 0009-0005-0878-3032 - first_name: Liu full_name: Qiu, Liu id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac last_name: Qiu orcid: 0000-0003-4345-4267 - first_name: Andrei full_name: Militaru, Andrei id: d67706f8-8eb1-11ee-ad1b-9c30dfa19e0b last_name: Militaru - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Werner T, Riyazi E, Hawaldar S, et al. Electro-optic conversion of itinerant Fock states. arXiv. doi:10.48550/arXiv.2602.00928 apa: Werner, T., Riyazi, E., Hawaldar, S., Sahu, R., Arnold, G. M., Paul Falthansl-Scheinecker, P. F.-S., … Fink, J. M. (n.d.). Electro-optic conversion of itinerant Fock states. arXiv. https://doi.org/10.48550/arXiv.2602.00928 chicago: Werner, Thomas, Erfan Riyazi, Samarth Hawaldar, Rishabh Sahu, Georg M Arnold, Paul Falthansl-Scheinecker Paul Falthansl-Scheinecker, Jennifer A. Sánchez Naranjo, et al. “Electro-Optic Conversion of Itinerant Fock States.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2602.00928. ieee: T. Werner et al., “Electro-optic conversion of itinerant Fock states,” arXiv. . ista: Werner T, Riyazi E, Hawaldar S, Sahu R, Arnold GM, Paul Falthansl-Scheinecker PF-S, Naranjo JAS, Loi D, Kapoor LN, Zemlicka M, Qiu L, Militaru A, Fink JM. Electro-optic conversion of itinerant Fock states. arXiv, 10.48550/arXiv.2602.00928. mla: Werner, Thomas, et al. “Electro-Optic Conversion of Itinerant Fock States.” ArXiv, doi:10.48550/arXiv.2602.00928. short: T. Werner, E. Riyazi, S. Hawaldar, R. Sahu, G.M. Arnold, P.F.-S. Paul Falthansl-Scheinecker, J.A.S. Naranjo, D. Loi, L.N. Kapoor, M. Zemlicka, L. Qiu, A. Militaru, J.M. Fink, ArXiv (n.d.). corr_author: '1' date_created: 2026-05-12T13:58:18Z date_published: 2026-01-31T00:00:00Z date_updated: 2026-05-20T13:35:42Z day: '31' department: - _id: JoFi - _id: GradSch doi: 10.48550/arXiv.2602.00928 ec_funded: 1 external_id: arxiv: - '2602.00928' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2602.00928 month: '01' oa: 1 oa_version: Preprint project: - _id: bdadfa0d-d553-11ed-ba76-fb85edbd456a grant_number: '101089099' name: 'Cavity Quantum Electro Optics: Microwave photonics with nonclassical states' - _id: 5b807754-ab3d-11f0-914f-ff8c34502cc9 grant_number: '101248662' name: Integrated optical coupling for low loss electro-optic interconnects - _id: 9B868D20-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '899354' name: Quantum Local Area Networks with Superconducting Qubits - _id: 91aaf765-16d5-11f0-9cad-a8e7e44cccb7 grant_number: '101187231' name: 'Cavity-Integrated Electro-Optics: Measuring, Converting and Manipulating Microwaves with Light' - _id: 26927A52-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F07105 name: Integrating superconducting quantum circuits - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program publication: arXiv publication_status: draft related_material: record: - id: '21863' relation: dissertation_contains status: public scopus_import: '1' status: public title: Electro-optic conversion of itinerant Fock states 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: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '21923' abstract: - lang: eng text: "The appearance of simulated natural phenomena heavily depends on the way surfaces are textured. However, applying texture maps to dynamic deformable surfaces presents a significant challenge, due to ever-shifting differences in length scales involved. When these surfaces move and advect the texture along with them, their final appearance degrades as deformed regions dramatically distort their texture map. Modifications to the texture directly at the pixel level in response to the deformation may introduce ghosting artifacts and look unnatural. In the real world, the appearance of surface details on a deforming material changes through the interplay of physical processes such as rupturing, exposure of internal structure, or wrinkling. Motivated by these behaviors, in this work we explore how physical principles can guide the texturing methods based on the measure of surface deformation.\r\nWe present two novel wave-based procedural texturing algorithms which reproduce common physical properties like advection and self-similarity, enabling the plausible animation of deforming objects with extreme texture map distortions. Our algorithms are fully procedural, require no actual physics simulation, and store no state or history of deformation besides the input UV map, making them highly parallelizable on the GPU and efficient enough for real-time applications. We show the versatility of the method by animating physical phenomena with extreme deformations such as flowing lava, stretching putty and outpouring sludge." acknowledged_ssus: - _id: ScienComp acknowledgement: "We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback. We also thank Jonathan Gagnon for their help with running the Lapped Textures codes and SideFX for the Houdini Education software licenses.\r\nImages in Fig. 2 by Kisoulou and Vultured on Unsplash, Michal Jarmoluk and Public Domain Pictures from Pixabay and Hawai‘i Volcanoes NPS on flickr. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing and was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA)." article_number: '154' article_processing_charge: Yes article_type: original author: - first_name: Aleksei full_name: Kalinov, Aleksei id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02 last_name: Kalinov orcid: 0000-0003-2189-3904 - first_name: Mickaël full_name: Ly, Mickaël id: 6340d7f0-b48d-11eb-b10d-b7487e71d9f1 last_name: Ly - first_name: Christian full_name: Hafner, Christian id: 400429CC-F248-11E8-B48F-1D18A9856A87 last_name: Hafner - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Kalinov A, Ly M, Hafner C, Wojtan C. Physics-inspired procedural texturing of extremely deformable surfaces. ACM Transactions on Graphics. 45(4). doi:10.1145/3811353 apa: 'Kalinov, A., Ly, M., Hafner, C., & Wojtan, C. (n.d.). Physics-inspired procedural texturing of extremely deformable surfaces. ACM Transactions on Graphics. Los Angeles, CA, United States: ACM. https://doi.org/10.1145/3811353' chicago: Kalinov, Aleksei, Mickaël Ly, Christian Hafner, and Chris Wojtan. “Physics-Inspired Procedural Texturing of Extremely Deformable Surfaces.” ACM Transactions on Graphics. ACM, n.d. https://doi.org/10.1145/3811353. ieee: A. Kalinov, M. Ly, C. Hafner, and C. Wojtan, “Physics-inspired procedural texturing of extremely deformable surfaces,” ACM Transactions on Graphics, vol. 45, no. 4. ACM. ista: Kalinov A, Ly M, Hafner C, Wojtan C. Physics-inspired procedural texturing of extremely deformable surfaces. ACM Transactions on Graphics. 45(4), 154. mla: Kalinov, Aleksei, et al. “Physics-Inspired Procedural Texturing of Extremely Deformable Surfaces.” ACM Transactions on Graphics, vol. 45, no. 4, 154, ACM, doi:10.1145/3811353. short: A. Kalinov, M. Ly, C. Hafner, C. Wojtan, ACM Transactions on Graphics 45 (n.d.). conference: end_date: 2026-07-23 location: Los Angeles, CA, United States name: 'SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques' start_date: 2026-07-19 corr_author: '1' date_created: 2026-05-29T13:25:16Z date_published: 2026-07-01T00:00:00Z date_updated: 2026-06-02T08:56:50Z day: '01' ddc: - '006' department: - _id: GradSch - _id: ChWo doi: 10.1145/3811353 file: - access_level: open_access checksum: ea165bf731ddd3045f83878dcb833672 content_type: video/mp4 creator: akalinov date_created: 2026-05-29T13:19:33Z date_updated: 2026-05-29T13:19:33Z file_id: '21924' file_name: tog454-article154-supplemental.mp4 file_size: 77337231 relation: main_file success: 1 - access_level: open_access checksum: 6274cfb15ea5ba7324b74afc7b0d9629 content_type: video/mp4 creator: akalinov date_created: 2026-05-29T13:19:37Z date_updated: 2026-05-29T13:19:37Z file_id: '21925' file_name: tog454-article154-video.mp4 file_size: 226633977 relation: main_file success: 1 - access_level: open_access checksum: 9d41b322a7876be9a3311017b9973183 content_type: application/pdf creator: akalinov date_created: 2026-05-29T13:19:33Z date_updated: 2026-05-29T13:19:33Z file_id: '21926' file_name: tog454-article154-supplemental.pdf file_size: 6793867 relation: main_file success: 1 - access_level: open_access checksum: 51bc60d2de867fbfa570652dec7993b4 content_type: application/pdf creator: akalinov date_created: 2026-05-29T13:19:36Z date_updated: 2026-05-29T13:19:36Z file_id: '21927' file_name: tog454-article154-main-1.pdf file_size: 84173392 relation: main_file success: 1 file_date_updated: 2026-05-29T13:19:37Z has_accepted_license: '1' intvolume: ' 45' issue: '4' keyword: - Procedural animation language: - iso: eng month: '07' oa: 1 oa_version: Accepted Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: ACM Transactions on Graphics publication_identifier: issn: - 0730-0301 publication_status: inpress publisher: ACM quality_controlled: '1' status: public title: Physics-inspired procedural texturing of extremely deformable surfaces 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: 45 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21917' abstract: - lang: eng text: A defining feature of quantum many-body systems is the exponential scaling of the Hilbert space with the number of degrees of freedom. This exponential complexity naïvely renders a complete state characterization, for instance via the complete set of bipartite Renyi entropies for all disjoint regions, a challenging task. Recently, a compact way of storing subregions' purities by encoding them as amplitudes of a fictitious quantum wave function, known as entanglement feature, was proposed. Notably, the entanglement feature can be a simple object even for highly entangled quantum states. However the complexity and practical usage of the entanglement feature for general quantum states has not been explored. In this work, we demonstrate that the entanglement feature can be efficiently learned using only a polynomial amount of samples in the number of degrees of freedom through the so-called tensor cross interpolation (TCI) algorithm, assuming it is expressible as a finite bond dimension MPS. We benchmark this learning process on Haar and random MPS states, confirming analytic expectations. Applying the TCI algorithm to quantum eigenstates of various one dimensional quantum systems, we identify cases where eigenstates have entanglement feature learnable with TCI. We conclude with possible applications of the learned entanglement feature, such as quantifying the distance between different entanglement patterns and finding the optimal one-dimensional ordering of physical indices in a given state, highlighting the potential utility of the proposed purity interpolation method. acknowledgement: "We acknowledge useful discussions with Richard Küng\r\non the interpolation methods and error spreading, Ilia\r\nA. Luchnikov, Margarita Davydova, and, in particular, Hiroshi Shinaoka, Marc Ritter, Yuriel Nuñez\r\nfor useful discussions about TCI and the various\r\nworkarounds within the TensorCrossInterpolation.jl\r\nlibrary. We also acknowledge the comments of anonymous Referee B, that encouraged us to expand the\r\nmanuscript with discussion of additional applications\r\nof entanglement feature in Section 4.3. M.S. acknowledges discussions with D. V. Savostyanov at the 2nd\r\nInternational Quantum Tensor Networks (IQTN) plenary meeting at Flatiron Institute’s Center for Computational Quantum Physics (CCQ) for introduction\r\nto the TCI approach. D.K and M.S. acknowledge support by the European Research Council (ERC) under We acknowledge useful discussions with Richard Küng\r\non the interpolation methods and error spreading, Ilia\r\nA. Luchnikov, Margarita Davydova, and, in particular, Hiroshi Shinaoka, Marc Ritter, Yuriel Nuñez\r\nfor useful discussions about TCI and the various\r\nworkarounds within the TensorCrossInterpolation.jl\r\nlibrary. We also acknowledge the comments of anonymous Referee B, that encouraged us to expand the\r\nmanuscript with discussion of additional applications\r\nof entanglement feature in Section 4.3. M.S. acknowledges discussions with D. V. Savostyanov at the 2nd\r\nInternational Quantum Tensor Networks (IQTN) plenary meeting at Flatiron Institute’s Center for Computational Quantum Physics (CCQ) for introduction\r\nto the TCI approach. D.K and M.S. acknowledge support by the European Research Council (ERC) under We acknowledge useful discussions with Richard Küng\r\non the interpolation methods and error spreading, Ilia\r\nA. Luchnikov, Margarita Davydova, and, in particular, Hiroshi Shinaoka, Marc Ritter, Yuriel Nuñez\r\nfor useful discussions about TCI and the various\r\nworkarounds within the TensorCrossInterpolation.jl\r\nlibrary. We also acknowledge the comments of anonymous Referee B, that encouraged us to expand the\r\nmanuscript with discussion of additional applications\r\nof entanglement feature in Section 4.3. M.S. acknowledges discussions with D. V. Savostyanov at the 2nd\r\nInternational Quantum Tensor Networks (IQTN) plenary meeting at Flatiron Institute’s Center for Computational Quantum Physics (CCQ) for introduction\r\nto the TCI approach. D.K and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).\r\nR.V. acknowledges partial support from the US Department of Energy, Office of Science, Basic Energy\r\nSciences, under award No. DE-SC0023999, and the\r\nSwiss National Science Foundation (grant 10008234).\r\nThis research was supported in part by grant NSF\r\nPHY-2309135 to the Kavli Institute for Theoretical\r\nPhysics (KITP)" article_number: '2114' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Dmytro full_name: Kolisnyk, Dmytro id: 530a7320-5355-11ee-ae5a-82a46997aaa7 last_name: Kolisnyk orcid: 0000-0002-8612-8202 - first_name: Raimel A full_name: Medina Ramos, Raimel A id: CE680B90-D85A-11E9-B684-C920E6697425 last_name: Medina Ramos orcid: 0000-0002-5383-2869 - first_name: Romain full_name: Vasseur, Romain last_name: Vasseur - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Kolisnyk D, Medina Ramos RA, Vasseur R, Serbyn M. Tensor cross interpolation of purities in quantum many-body systems. Quantum. 2026;10. doi:10.22331/q-2026-05-22-2114 apa: Kolisnyk, D., Medina Ramos, R. A., Vasseur, R., & Serbyn, M. (2026). Tensor cross interpolation of purities in quantum many-body systems. Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/q-2026-05-22-2114 chicago: Kolisnyk, Dmytro, Raimel A Medina Ramos, Romain Vasseur, and Maksym Serbyn. “Tensor Cross Interpolation of Purities in Quantum Many-Body Systems.” Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2026. https://doi.org/10.22331/q-2026-05-22-2114. ieee: D. Kolisnyk, R. A. Medina Ramos, R. Vasseur, and M. Serbyn, “Tensor cross interpolation of purities in quantum many-body systems,” Quantum, vol. 10. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2026. ista: Kolisnyk D, Medina Ramos RA, Vasseur R, Serbyn M. 2026. Tensor cross interpolation of purities in quantum many-body systems. Quantum. 10, 2114. mla: Kolisnyk, Dmytro, et al. “Tensor Cross Interpolation of Purities in Quantum Many-Body Systems.” Quantum, vol. 10, 2114, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2026, doi:10.22331/q-2026-05-22-2114. short: D. Kolisnyk, R.A. Medina Ramos, R. Vasseur, M. Serbyn, Quantum 10 (2026). corr_author: '1' date_created: 2026-05-26T19:39:12Z date_published: 2026-05-22T00:00:00Z date_updated: 2026-06-02T09:15:13Z day: '22' ddc: - '530' department: - _id: MaSe - _id: GradSch doi: 10.22331/q-2026-05-22-2114 ec_funded: 1 external_id: arxiv: - '2503.17230' file: - access_level: open_access checksum: f8ce78607ad06120cdf894dc8cef55da content_type: application/pdf creator: dernst date_created: 2026-06-02T09:12:11Z date_updated: 2026-06-02T09:12:11Z file_id: '21939' file_name: 2026_Quantum_Kolisnyk.pdf file_size: 3284798 relation: main_file success: 1 file_date_updated: 2026-06-02T09:12:11Z has_accepted_license: '1' intvolume: ' 10' language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: Quantum publication_identifier: eissn: - 2521-327X publication_status: published publisher: Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften quality_controlled: '1' status: public title: Tensor cross interpolation of purities in quantum many-body systems 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: 10 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21929' abstract: - lang: eng text: 'The import of proteins into mitochondria poses fundamental mechanistic challenges: aggregation-prone precursor proteins must be maintained in aqueous compartments and threaded through narrow pores without becoming stuck or mislocalized. Recent evidence from mitochondrial protein import studies and other chaperone systems underscores the critical role of dynamics in balancing sufficiently tight binding, promiscuity, specificity, and release. Dynamic binding of client precursor proteins to import machinery components arises naturally from the avidity of their interactions. Conformational entropy enhances their stability, while the multivalent nature of these interactions ensures that client transfer to downstream insertases occurs without a substantial energy barrier. Here, we discuss this emerging paradigm of dynamic protein handling, using examples where dynamic structures have been resolved and highlight outstanding questions.' acknowledgement: We gratefully acknowledge research funding by the Austrian Science Fund (FWF), projects 10.55776/PAT1647625 and 10.55776/I6223. We thank Prof. Long Li (Peking University) for providing structural models and EM density for the TOM and TIM23 complexes, used to generate part of Figure 3. Open Access funding provided by Institute of Science and Technology Austria. article_number: e70630 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Jakob full_name: Schneider, Jakob id: 64368429-eb97-11eb-a6c2-c980b1f44415 last_name: Schneider - first_name: Undina full_name: Guillerm, Undina id: bb74f472-ae54-11eb-9835-bc9c22fb1183 last_name: Guillerm - first_name: Caroline full_name: Simoes Pereira, Caroline id: 87266c4a-96d2-11ef-be2c-fe5633233ec3 last_name: Simoes Pereira - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Schneider J, Guillerm U, Simoes Pereira C, Schanda P. Dynamic disorder is crucial for mitochondrial protein import. Protein Science. 2026;35(6). doi:10.1002/pro.70630 apa: Schneider, J., Guillerm, U., Simoes Pereira, C., & Schanda, P. (2026). Dynamic disorder is crucial for mitochondrial protein import. Protein Science. Wiley. https://doi.org/10.1002/pro.70630 chicago: Schneider, Jakob, Undina Guillerm, Caroline Simoes Pereira, and Paul Schanda. “Dynamic Disorder Is Crucial for Mitochondrial Protein Import.” Protein Science. Wiley, 2026. https://doi.org/10.1002/pro.70630. ieee: J. Schneider, U. Guillerm, C. Simoes Pereira, and P. Schanda, “Dynamic disorder is crucial for mitochondrial protein import,” Protein Science, vol. 35, no. 6. Wiley, 2026. ista: Schneider J, Guillerm U, Simoes Pereira C, Schanda P. 2026. Dynamic disorder is crucial for mitochondrial protein import. Protein Science. 35(6), e70630. mla: Schneider, Jakob, et al. “Dynamic Disorder Is Crucial for Mitochondrial Protein Import.” Protein Science, vol. 35, no. 6, e70630, Wiley, 2026, doi:10.1002/pro.70630. short: J. Schneider, U. Guillerm, C. Simoes Pereira, P. Schanda, Protein Science 35 (2026). corr_author: '1' date_created: 2026-05-31T22:02:12Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-06-02T07:26:34Z day: '01' ddc: - '572' department: - _id: GradSch - _id: PaSc doi: 10.1002/pro.70630 external_id: pmid: - '42159315' file: - access_level: open_access checksum: e0163459a7238fdcc3fc5e17bedcce9a content_type: application/pdf creator: dernst date_created: 2026-06-02T07:23:12Z date_updated: 2026-06-02T07:23:12Z file_id: '21937' file_name: 2026_ProteinScience_Schneider.pdf file_size: 3897305 relation: main_file success: 1 file_date_updated: 2026-06-02T07:23:12Z has_accepted_license: '1' intvolume: ' 35' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bdb9578d-d553-11ed-ba76-ed5d39fce6f0 grant_number: I06223 name: Structure and mechanism of the mitochondrial MIM insertase publication: Protein Science publication_identifier: eissn: - 1469-896X issn: - 0961-8368 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Dynamic disorder is crucial for mitochondrial protein import 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: 35 year: '2026' ... --- _id: '21145' abstract: - lang: eng text: 'Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions. ' acknowledged_ssus: - _id: NMR - _id: LifeSc acknowledgement: "We thank Nikolai R. Skrynnikov and Olga O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to Tobias Schubeis (Lyon) for advice with GB1 crystallization, and Rebecca Schmid for initial crystallization trials.\r\nWe thank Sebastian Falkner for assistance with constructing the structural model of the IgG:GB1 complex.\r\nThis research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank Petra Rovó and Margarita Valhondo Falcón for excellent support of the NMR facility.\r\nLea M. Becker is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01). Christophe Chipot acknowledges the European Research Council (grant project 101097272 ``MilliInMicro'') and the Métropole du Grand Nancy (grant project ``ARC''). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011." article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot citation: ama: Becker LM, Schanda P, Chipot C. Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” 2026. doi:10.15479/AT-ISTA-21145 apa: Becker, L. M., Schanda, P., & Chipot, C. (2026). Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21145 chicago: Becker, Lea Marie, Paul Schanda, and Christophe Chipot. “Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21145. ieee: L. M. Becker, P. Schanda, and C. Chipot, “Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2026. ista: Becker LM, Schanda P, Chipot C. 2026. Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21145. mla: Becker, Lea Marie, et al. Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21145. short: L.M. Becker, P. Schanda, C. Chipot, (2026). contributor: - contributor_type: researcher first_name: Haohao last_name: Fu - contributor_type: researcher first_name: Benjamin id: 71cda2f3-e604-11ee-a1df-da10587eda3f last_name: Tatman - contributor_type: researcher first_name: Matthias last_name: Dreydoppel - contributor_type: researcher first_name: Anna id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471 last_name: Kapitonova - contributor_type: researcher first_name: Daniel id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E last_name: Balazs orcid: 0000-0001-7597-043X - contributor_type: researcher first_name: Ulrich last_name: Weininger - contributor_type: researcher first_name: Sylvain last_name: Engilberge corr_author: '1' date_created: 2026-02-05T13:54:39Z date_published: 2026-02-09T00:00:00Z date_updated: 2026-06-10T08:25:16Z day: '09' ddc: - '572' department: - _id: GradSch - _id: PaSc doi: 10.15479/AT-ISTA-21145 file: - access_level: open_access checksum: 02a419cce8cea450bc952f35488d2df5 content_type: text/plain creator: lbecker date_created: 2026-02-05T13:52:37Z date_updated: 2026-02-05T13:52:37Z file_id: '21146' file_name: README.txt file_size: 4263 relation: table_of_contents - access_level: open_access checksum: b0b82b1aa73985b0b308a3fa52d21aea content_type: application/zip creator: lbecker date_created: 2026-02-05T13:52:41Z date_updated: 2026-02-05T13:52:41Z file_id: '21147' file_name: Research_Data.zip file_size: 50647107 relation: main_file success: 1 file_date_updated: 2026-02-05T13:52:41Z has_accepted_license: '1' license: https://creativecommons.org/licenses/by-nc/4.0/ month: '02' oa: 1 oa_version: Published Version project: - _id: 7be609c4-9f16-11ee-852c-85015ce2b9b0 grant_number: '26777' name: Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches publisher: Institute of Science and Technology Austria related_material: record: - id: '20641' relation: earlier_version status: public status: public title: Additional Data for "Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes" 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20840' abstract: - lang: eng text: Probing the possibility of entanglement generation through gravity offers a path to tackle the question of whether gravitational fields possess a quantum mechanical nature. A potential realization necessitates systems with low-frequency dynamics at an optimal mass scale, for which the microgram-to-milligram range is a strong contender. Here, after refining a figure-of-merit for the problem, we present a 1-milligram torsional pendulum operating at 18 Hz. We demonstrate laser cooling its motion from room temperature to 240 microkelvins, surpassing by over 20-fold the coldest motions attained for oscillators ranging from micrograms to kilograms. We quantify and contrast the utility of the current approach with other platforms. The achieved performance and large improvement potential highlight milligram-scale torsional pendulums as a powerful platform for precision measurements relevant to future studies at the quantum-gravity interface. acknowledgement: We thank Gerard Higgins, Andrei Militaru, Nikolai Kiesel, and Markus Aspelmeyer for useful discussions on the topic of the figure-of-merit. We thank Teodor Strömberg for helping with the additional characterizations of the optical lever noise. We thank Johannes Fink and Scott Waitukaitis for their helpful feedback on the manuscript. This work was supported by Institute of Science and Technology Austria and the European Research Council under Grant No. 101087907 (ERC CoG QuHAMP). article_number: '80' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Sofya full_name: Agafonova, Sofya id: 09501ff6-dca7-11ea-a8ae-b3e0b9166e80 last_name: Agafonova orcid: 0000-0003-0582-2946 - first_name: Pere full_name: Rosello, Pere last_name: Rosello - first_name: Manuel full_name: Mekonnen, Manuel last_name: Mekonnen - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X citation: ama: Agafonova S, Rosello P, Mekonnen M, Hosten O. One-milligram torsional pendulum toward experiments at the quantum-gravity interface. Communications Physics. 2026;9. doi:10.1038/s42005-026-02514-w apa: Agafonova, S., Rosello, P., Mekonnen, M., & Hosten, O. (2026). One-milligram torsional pendulum toward experiments at the quantum-gravity interface. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-026-02514-w chicago: Agafonova, Sofia, Pere Rosello, Manuel Mekonnen, and Onur Hosten. “One-Milligram Torsional Pendulum toward Experiments at the Quantum-Gravity Interface.” Communications Physics. Springer Nature, 2026. https://doi.org/10.1038/s42005-026-02514-w. ieee: S. Agafonova, P. Rosello, M. Mekonnen, and O. Hosten, “One-milligram torsional pendulum toward experiments at the quantum-gravity interface,” Communications Physics, vol. 9. Springer Nature, 2026. ista: Agafonova S, Rosello P, Mekonnen M, Hosten O. 2026. One-milligram torsional pendulum toward experiments at the quantum-gravity interface. Communications Physics. 9, 80. mla: Agafonova, Sofia, et al. “One-Milligram Torsional Pendulum toward Experiments at the Quantum-Gravity Interface.” Communications Physics, vol. 9, 80, Springer Nature, 2026, doi:10.1038/s42005-026-02514-w. short: S. Agafonova, P. Rosello, M. Mekonnen, O. Hosten, Communications Physics 9 (2026). corr_author: '1' date_created: 2025-12-21T11:39:04Z date_published: 2026-03-04T00:00:00Z date_updated: 2026-06-10T08:36:06Z day: '04' ddc: - '530' department: - _id: GradSch - _id: OnHo doi: 10.1038/s42005-026-02514-w external_id: arxiv: - '2408.09445' file: - access_level: open_access checksum: 62e2175e7e3ad49260ae6a7b4e0860a2 content_type: application/pdf creator: dernst date_created: 2026-03-16T10:07:46Z date_updated: 2026-03-16T10:07:46Z file_id: '21457' file_name: 2026_CommunicationsPhysics_Agafonova.pdf file_size: 1901772 relation: main_file success: 1 file_date_updated: 2026-03-16T10:07:46Z has_accepted_license: '1' intvolume: ' 9' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: bdb2a702-d553-11ed-ba76-f12e3e5a3bc6 grant_number: '101087907' name: 'A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics' publication: Communications Physics publication_identifier: eissn: - 2399-3650 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '20842' relation: research_data status: public scopus_import: '1' status: public title: One-milligram torsional pendulum toward experiments at the quantum-gravity interface 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: 9 year: '2026' ... --- OA_place: repository OA_type: free access _id: '21284' abstract: - lang: eng text: The advantageous characteristics attributed to the 19F nucleus have made it a popular target for NMR once again in recent years. Aside from solution NMR, an increasing number of studies have been conducted applying solid-state magic-angle-spinning NMR to fluorine-labeled samples. Here, the high chemical shift anisotropy and strong dipolar couplings can be utilized to get structural insights into proteins and measure long distances. Despite increasing popularity and promising benefits, the sensitivity of biomolecular 19F MAS NMR often suffers from slow longitudinal T1 relaxation and therefore long recycle delays. In this work, we expand paramagnetic doping, an approach commonly used to reduce proton T1 relaxation times, to 19F-labeled biological samples. We study the effect of Gd(DTPA) and Gd(DTPA-BMA) on 19F and 13C T1 and T2 relaxation in a [5-19F13C]-tryptophan-labeled protein via 19F-detected MAS NMR experiments. The observed paramagnetic relaxation enhancement substantially reduces measurement times of 19F MAS NMR experiments without compromising resolution. Additionally, we report the chemical-shift assignments of all four fluorotryptophan signals in the 12 × 39 kDa large protein using a mutagenesis approach. acknowledged_ssus: - _id: NMR - _id: LifeSc acknowledgement: We thank Ben P. Tatman for insightful discussions. This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility. article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Becker LM, Schanda P. Research data for “Accelerated 19F biomolecular magic-angle spinning NMR with paramagnetic dopants.” 2026. doi:10.15479/AT-ISTA-21284 apa: Becker, L. M., & Schanda, P. (2026). Research data for “Accelerated 19F biomolecular magic-angle spinning NMR with paramagnetic dopants.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21284 chicago: Becker, Lea Marie, and Paul Schanda. “Research Data for ‘Accelerated 19F Biomolecular Magic-Angle Spinning NMR with Paramagnetic Dopants.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21284. ieee: L. M. Becker and P. Schanda, “Research data for ‘Accelerated 19F biomolecular magic-angle spinning NMR with paramagnetic dopants.’” Institute of Science and Technology Austria, 2026. ista: Becker LM, Schanda P. 2026. Research data for ‘Accelerated 19F biomolecular magic-angle spinning NMR with paramagnetic dopants’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21284. mla: Becker, Lea Marie, and Paul Schanda. Research Data for “Accelerated 19F Biomolecular Magic-Angle Spinning NMR with Paramagnetic Dopants.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21284. short: L.M. Becker, P. Schanda, (2026). contributor: - contributor_type: researcher first_name: Giorgia id: 334a5e40-8747-11f0-b671-ba1f5154b4b4 last_name: Toscano - contributor_type: researcher first_name: Anna id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471 last_name: Kapitonova - contributor_type: researcher first_name: Rajkumar id: a3089acd-6806-11ee-bacc-f0c7d500ad20 last_name: Singh - contributor_type: researcher first_name: Undina id: bb74f472-ae54-11eb-9835-bc9c22fb1183 last_name: Guillerm - contributor_type: researcher first_name: Roman last_name: Lichtenecker corr_author: '1' date_created: 2026-02-17T10:17:14Z date_published: 2026-02-18T00:00:00Z date_updated: 2026-06-10T09:28:41Z day: '18' ddc: - '541' department: - _id: GradSch - _id: PaSc doi: 10.15479/AT-ISTA-21284 file: - access_level: open_access checksum: 2d3105f26be578073b88ee1f2ea0bdb1 content_type: application/zip creator: lbecker date_created: 2026-02-17T10:11:14Z date_updated: 2026-02-17T10:11:14Z file_id: '21285' file_name: Research_data.zip file_size: 36996027 relation: main_file success: 1 - access_level: open_access checksum: e24aebcdb8856cb181cbaa02de020ddb content_type: text/plain creator: lbecker date_created: 2026-02-17T10:11:14Z date_updated: 2026-02-17T10:11:14Z file_id: '21286' file_name: README.txt file_size: 1993 relation: table_of_contents file_date_updated: 2026-02-17T10:11:14Z has_accepted_license: '1' month: '2' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria status: public title: Research data for "Accelerated 19F biomolecular magic-angle spinning NMR with paramagnetic dopants" 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: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: repository _id: '21360' acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: "I would like to acknowledge the Austrian Academy of Sciences (ÖAW) and European\r\nResearch Executive Agency (REA) for funding my research (DOC ÖAW Fellowship\r\n26130, Horizon Europe BOLERO Project 101060393). " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stefan full_name: Riegler, Stefan id: FF6018E0-D806-11E9-8E43-0B14E6697425 last_name: Riegler orcid: 0000-0003-3413-1343 citation: ama: 'Riegler S. Root system plasticity under nutrient limitation : Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species. 2026. doi:10.15479/AT-ISTA-21360' apa: 'Riegler, S. (2026). Root system plasticity under nutrient limitation : Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21360' chicago: 'Riegler, Stefan. “Root System Plasticity under Nutrient Limitation : Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21360.' ieee: 'S. Riegler, “Root system plasticity under nutrient limitation : Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species,” Institute of Science and Technology Austria, 2026.' ista: 'Riegler S. 2026. Root system plasticity under nutrient limitation : Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species. Institute of Science and Technology Austria.' mla: 'Riegler, Stefan. Root System Plasticity under Nutrient Limitation : Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21360.' short: 'S. Riegler, Root System Plasticity under Nutrient Limitation : Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species, Institute of Science and Technology Austria, 2026.' corr_author: '1' date_created: 2026-02-27T09:08:14Z date_published: 2026-02-26T00:00:00Z date_updated: 2026-06-10T09:39:12Z day: '26' ddc: - '570' - '575' - '583' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-21360 file: - access_level: closed checksum: 2f1f44e8536c2538f94a440217452c9f content_type: application/x-zip-compressed creator: sriegler date_created: 2026-03-02T10:59:50Z date_updated: 2026-03-02T10:59:50Z file_id: '21386' file_name: 2026_Riegler_Stefan_Thesis.zip file_size: 31430022 relation: source_file - access_level: closed checksum: 2e8dc39640bc26ae5684c944c619719b content_type: application/pdf creator: sriegler date_created: 2026-03-02T10:59:49Z date_updated: 2026-03-02T10:59:49Z embargo: 2027-02-27 embargo_to: open_access file_id: '21387' file_name: 2026_Riegler_Stefan_Thesis.pdf file_size: 11635090 relation: main_file file_date_updated: 2026-03-02T10:59:50Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '02' oa_version: Published Version page: '185' project: - _id: 34afa094-11ca-11ed-8bc3-a375845a59fb grant_number: '101060393' name: Breeding for coffee and cocoa root resilience in low input farming systems based on improved rootstocks publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '21363' relation: research_data status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: 'Root system plasticity under nutrient limitation : Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- _id: '21363' abstract: - lang: eng text: The data contains information on coffee differential gene expression as well as co-expression and trait correlations in two separate experiments. First, contrasting nitrogen supply, second, intra- and interspecific grafting. article_processing_charge: No author: - first_name: Stefan full_name: Riegler, Stefan id: FF6018E0-D806-11E9-8E43-0B14E6697425 last_name: Riegler orcid: 0000-0003-3413-1343 citation: ama: 'Riegler S. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species. 2026. doi:10.15479/AT-ISTA-21363' apa: 'Riegler, S. (2026). Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21363' chicago: 'Riegler, Stefan. “Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21363.' ieee: 'S. Riegler, “Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species.” Institute of Science and Technology Austria, 2026.' ista: 'Riegler S. 2026. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21363.' mla: 'Riegler, Stefan. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21363.' short: S. Riegler, (2026). contributor: - contributor_type: supervisor first_name: Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 corr_author: '1' date_created: 2026-02-27T09:18:41Z date_published: 2026-02-27T00:00:00Z date_updated: 2026-06-10T09:39:13Z day: '27' ddc: - '575' department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-21363 file: - access_level: closed checksum: de9145fa166a28c588b5184a2d3d4fee content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: sriegler date_created: 2026-02-27T09:11:33Z date_updated: 2026-02-27T09:11:33Z embargo: 2027-02-27 embargo_to: open_access file_id: '21364' file_name: SupplementaryTables.xlsx file_size: 63749444 relation: main_file - access_level: closed checksum: ce1f163551c96cee45943a8ea29720b6 content_type: text/plain creator: sriegler date_created: 2026-02-27T09:13:11Z date_updated: 2026-02-27T09:13:11Z embargo: 2027-02-27 embargo_to: open_access file_id: '21365' file_name: ReadMe.txt file_size: 124 relation: main_file file_date_updated: 2026-02-27T09:13:11Z has_accepted_license: '1' month: '02' oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '21360' relation: used_in_publication status: public status: public title: 'Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea species' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: repository _id: '21423' acknowledged_ssus: - _id: ScienComp acknowledgement: "Finally, I gratefully acknowledge funding from the DOC Fellowship of the Austrian Academy\r\nof Sciences (OeAW): grant agreement 26360." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova citation: ama: Dunajova Z. Geometry-driven self-organization of migrating cells and chiral filaments. 2026. doi:10.15479/AT-ISTA-21423 apa: Dunajova, Z. (2026). Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21423 chicago: Dunajova, Zuzana. “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21423. ieee: Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral filaments,” Institute of Science and Technology Austria, 2026. ista: Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria. mla: Dunajova, Zuzana. Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21423. short: Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-03-11T08:30:49Z date_published: 2026-03-11T00:00:00Z date_updated: 2026-06-10T09:41:11Z day: '11' ddc: - '539' - '570' degree_awarded: PhD department: - _id: GradSch - _id: EdHa doi: 10.15479/AT-ISTA-21423 file: - access_level: closed checksum: 47ce6a48a0c63f28eca6e64c9ffd2c84 content_type: application/pdf creator: zdunajov date_created: 2026-03-12T20:38:52Z date_updated: 2026-03-12T20:38:52Z embargo: 2026-09-11 embargo_to: open_access file_id: '21446' file_name: 2026_Dunajova_Zuzana_Thesis_pdfA.pdf file_size: 14662770 relation: main_file - access_level: closed checksum: 5dec5afdffd47c2b0b162d0fe1bed925 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: zdunajov date_created: 2026-03-12T20:40:18Z date_updated: 2026-03-13T11:19:21Z file_id: '21447' file_name: Thesis-Dunajova_source_file.docx file_size: 32961408 relation: source_file file_date_updated: 2026-03-13T11:19:21Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '03' oa_version: Published Version page: '110' project: - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publication_identifier: isbn: - 978-3-99078-076-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13314' relation: part_of_dissertation status: public - id: '13116' relation: research_data status: public - id: '21427' relation: part_of_dissertation status: public - id: '21439' relation: research_data status: public status: public supervisor: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 title: Geometry-driven self-organization of migrating cells and chiral filaments tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository _id: '21137' acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: ScienComp - _id: LifeSc acknowledgement: We thank all members of the Heisenberg, Henkes, and Hannezo groups for their support. We are also grateful to the Imaging and Optics, Scientific Computing, Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their technical assistance and support. Numerical simulations were performed using the computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020 research and innovation programme (grant agreement No. 665385). This work was supported by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to C.-P.H. article_processing_charge: No author: - first_name: Suyash full_name: Naik, Suyash id: 2C0B105C-F248-11E8-B48F-1D18A9856A87 last_name: Naik orcid: 0000-0001-8421-5508 citation: ama: Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:10.15479/AT-ISTA-21137 apa: Naik, S. (2026). Data associated with Keratins coordinate tissue spreading . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21137 chicago: Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading .” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21137. ieee: S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute of Science and Technology Austria, 2026. ista: Naik S. 2026. Data associated with Keratins coordinate tissue spreading , Institute of Science and Technology Austria, 10.15479/AT-ISTA-21137. mla: Naik, Suyash. Data Associated with Keratins Coordinate Tissue Spreading . Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21137. short: S. Naik, (2026). contributor: - contributor_type: researcher first_name: Yann-Edwin last_name: Keta - contributor_type: supervisor first_name: 'Silke ' last_name: Henkes - contributor_type: supervisor first_name: Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - contributor_type: supervisor first_name: Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 corr_author: '1' date_created: 2026-02-04T16:38:02Z date_published: 2026-03-24T00:00:00Z date_updated: 2026-06-10T09:44:10Z day: '24' department: - _id: GradSch - _id: CaHe - _id: EdHa doi: 10.15479/AT-ISTA-21137 ec_funded: 1 file: - access_level: open_access checksum: 5d1fda7e410f24c311fcf6bcf725698f content_type: application/zip creator: snaik date_created: 2026-03-16T11:51:10Z date_updated: 2026-03-16T11:51:10Z description: 'Python3 library written in C++20 to integrate vertex models. Please read the readme at https://github.com/yketa/cells/blob/main/README.md for detailed instructions for installation and usage of the code in this repository. ' file_id: '21461' file_name: cells-main.zip file_size: 725916 relation: main_file title: Cell git repository - access_level: open_access checksum: ee350c8eaed99f3ca348c47c8b190d3c content_type: application/x-zip-compressed creator: snaik date_created: 2026-03-18T14:52:02Z date_updated: 2026-03-18T14:52:02Z file_id: '21464' file_name: DevBranchDataRepo.zip file_size: 282168895 relation: main_file success: 1 - access_level: open_access checksum: 1ecaf2c1a2ce8ff9c75a128cc02d0b8f content_type: text/markdown creator: snaik date_created: 2026-03-18T15:01:32Z date_updated: 2026-03-18T15:01:32Z file_id: '21466' file_name: ReadMe.md file_size: 2231 relation: main_file success: 1 - access_level: open_access checksum: da9a4687e5144b61a64ca341f922046a content_type: image/svg+xml creator: snaik date_created: 2026-03-18T15:12:57Z date_updated: 2026-03-18T15:12:57Z file_id: '21467' file_name: PaperSchematics.svg file_size: 1951210 relation: main_file success: 1 - access_level: open_access checksum: 9ac1054b16c212c6f34d402dce2c80e0 content_type: application/octet-stream creator: snaik date_created: 2026-03-21T03:37:43Z date_updated: 2026-03-21T03:37:43Z file_id: '21468' file_name: maxwell_sketch.tex file_size: 1897 relation: main_file success: 1 - access_level: open_access checksum: 7c9ecf78e2593b3830d96fa94baa08df content_type: application/x-zip-compressed creator: snaik date_created: 2026-03-24T07:21:43Z date_updated: 2026-03-24T07:21:43Z file_id: '21495' file_name: DataRepo.zip file_size: 749368723 relation: main_file success: 1 file_date_updated: 2026-03-24T07:21:43Z has_accepted_license: '1' month: '3' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 8f060199-16d5-11f0-9cad-f3253b266c46 grant_number: PAT 5044023 name: Keratins in epithelial tissue spreading - _id: 252C3B08-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1250-B20 name: Nano-Analytics of Cellular Systems publisher: Institute of Science and Technology Austria status: public title: 'Data associated with Keratins coordinate tissue spreading ' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: repository OA_type: free access _id: '21439' abstract: - lang: eng text: These files contain supplementary movies accompanying the PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments” by Zuzana Dunajova (2026). The videos provide additional visual material supporting the experiments and results described in the thesis. acknowledged_ssus: - _id: Bio - _id: ScienComp article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova citation: ama: Dunajova Z. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” 2026. doi:10.15479/AT-ISTA-21439 apa: Dunajova, Z. (2026). Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21439 chicago: Dunajova, Zuzana. “Supplementary Movies to PhD Thesis ‘Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21439. ieee: Z. Dunajova, “Supplementary movies to PhD thesis ‘Geometry-driven self-organization of migrating cells and chiral filaments.’” Institute of Science and Technology Austria, 2026. ista: Dunajova Z. 2026. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments”, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21439. mla: Dunajova, Zuzana. Supplementary Movies to PhD Thesis “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21439. short: Z. Dunajova, (2026). contributor: - contributor_type: researcher first_name: Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - contributor_type: researcher first_name: Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' corr_author: '1' date_created: 2026-03-11T21:05:20Z date_published: 2026-03-12T00:00:00Z date_updated: 2026-06-10T09:41:12Z day: '12' ddc: - '570' department: - _id: GradSch - _id: EdHa doi: 10.15479/AT-ISTA-21439 file: - access_level: open_access checksum: 47809a9a31b748b16e21e92d11ddc87f content_type: application/zip creator: zdunajov date_created: 2026-03-11T20:41:28Z date_updated: 2026-03-11T20:41:28Z file_id: '21440' file_name: Supplementary_movies_Thesis_Dunajova.zip file_size: 154465214 relation: main_file success: 1 - access_level: open_access checksum: a64a174bc6abf0a5e77631e4fd121f1f content_type: text/plain creator: zdunajov date_created: 2026-03-11T20:52:39Z date_updated: 2026-03-11T20:52:39Z file_id: '21441' file_name: readme.txt file_size: 2289 relation: main_file success: 1 file_date_updated: 2026-03-11T20:52:39Z has_accepted_license: '1' month: '03' oa: 1 oa_version: Published Version project: - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publisher: Institute of Science and Technology Austria related_material: record: - id: '13314' relation: used_in_publication status: public - id: '21427' relation: used_in_publication status: public - id: '21423' relation: used_in_publication status: public status: public title: Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments” tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: publisher _id: '21957' abstract: - lang: eng text: "This thesis investigates algorithmic certification and approximation methods for degenerate semidefinite programs (SDPs) and the singular roots of polynomial systems. In the first part, we present a hybrid symbolic-numeric algorithm for certifying the feasibility of weakly feasible, degenerate SDPs. By reformulating linear matrix inequalities (LMIs) into a structured polynomial system via facial reduction and incidence varieties, we guarantee the existence of an isolated exact solution. This algebraic reduction enables the certification of maximum-rank numerical approximations using methods from algebraic geometry.\r\n\r\nIn the second part, we address the severe ill-conditioning and loss of quadratic convergence that plague standard path-tracking methods near isolated singular roots. To overcome this, we propose tracking algorithms that achieve superlinear convergence without the computational bloat characteristic of classical deflation techniques. By modeling the solution path as a generalized fractional Puiseux series, our approach combines an explicitly derived algebraic predictor with a localized hyperplane desingularization phase during the corrector step. Furthermore, we introduce a continuous path-limit method and an extension of the geometric sequence rule to directly extract exact fractional exponents. This bypasses traditional heuristic trial-and-error methods and explicitly accommodates sparse series expansions. Numerical experiments confirm that our method significantly reduces the cumulative number of matrix inversions while achieving high-accuracy root approximations, even for heavily degenerate systems exhibiting higher coranks." acknowledgement: 'Funding: Vienna Graduate School on Computational Optimization (FWF), grant DOI: 10.55776/W1260.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jeferson full_name: Zapata, Jeferson id: 00223538-AF8F-11E9-A4C7-F729E6697425 last_name: Zapata citation: ama: 'Zapata J. Overcoming degeneracy and singularity : Techniques for semidefinite programs and homotopy continuation endgames. 2026. doi:10.15479/AT-ISTA-21957' apa: 'Zapata, J. (2026). Overcoming degeneracy and singularity : Techniques for semidefinite programs and homotopy continuation endgames. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21957' chicago: 'Zapata, Jeferson. “Overcoming Degeneracy and Singularity : Techniques for Semidefinite Programs and Homotopy Continuation Endgames.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21957.' ieee: 'J. Zapata, “Overcoming degeneracy and singularity : Techniques for semidefinite programs and homotopy continuation endgames,” Institute of Science and Technology Austria, 2026.' ista: 'Zapata J. 2026. Overcoming degeneracy and singularity : Techniques for semidefinite programs and homotopy continuation endgames. Institute of Science and Technology Austria.' mla: 'Zapata, Jeferson. Overcoming Degeneracy and Singularity : Techniques for Semidefinite Programs and Homotopy Continuation Endgames. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21957.' short: 'J. Zapata, Overcoming Degeneracy and Singularity : Techniques for Semidefinite Programs and Homotopy Continuation Endgames, Institute of Science and Technology Austria, 2026.' corr_author: '1' date_created: 2026-06-08T13:29:52Z date_published: 2026-06-09T00:00:00Z date_updated: 2026-06-12T10:37:00Z day: '09' ddc: - '500' degree_awarded: PhD department: - _id: GradSch - _id: VlKo doi: 10.15479/AT-ISTA-21957 file: - access_level: closed checksum: b11a959e99d3dcf61040282b5c837141 content_type: application/zip creator: jzapata date_created: 2026-06-08T13:20:02Z date_updated: 2026-06-08T13:20:02Z file_id: '21958' file_name: istaustriathesis_JZapata.zip file_size: 40811933 relation: source_file - access_level: open_access checksum: edf1e5899b2e31505cd1aa3fe8bd4b7f content_type: application/pdf creator: jzapata date_created: 2026-06-10T13:33:25Z date_updated: 2026-06-10T13:33:25Z file_id: '21992' file_name: 4_Final_Thesis_JZapata_REX.pdf file_size: 2207892 relation: main_file success: 1 file_date_updated: 2026-06-10T13:33:25Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '89' project: - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: W1260-N35 name: Vienna Graduate School on Computational Optimization publication_identifier: isbn: - 978-3-99078-079-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '21144' relation: part_of_dissertation status: public status: public supervisor: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov title: 'Overcoming degeneracy and singularity : Techniques for semidefinite programs and homotopy continuation endgames' 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: '2026' ... --- OA_place: publisher _id: '21918' acknowledged_ssus: - _id: ScienComp acknowledgement: "At different stages of my PhD, my work was supported by several grants: the\r\nDOC fellowship of the Austrian Academy of Sciences (26293, awarded to me),\r\nthe FWF-SFB grant (PT1032F06504 n. F65, awarded to Jan Maas), and the ERC\r\ngrant (PR1032ERC01 n. 716117, awarded to Jan Maas). I also appreciate the help\r\nfrom the Scientific Computing unit for their advice on the cluster usage." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kseniia full_name: Khudiakova, Kseniia id: 4E6DC800-AE37-11E9-AC72-31CAE5697425 last_name: Khudiakova orcid: 0000-0002-6246-1465 citation: ama: Khudiakova K. How epistasis and purifying selection shape genetic diversity. 2026. doi:10.15479/AT-ISTA-21918 apa: Khudiakova, K. (2026). How epistasis and purifying selection shape genetic diversity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21918 chicago: Khudiakova, Kseniia. “How Epistasis and Purifying Selection Shape Genetic Diversity.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21918. ieee: K. Khudiakova, “How epistasis and purifying selection shape genetic diversity,” Institute of Science and Technology Austria, 2026. ista: Khudiakova K. 2026. How epistasis and purifying selection shape genetic diversity. Institute of Science and Technology Austria. mla: Khudiakova, Kseniia. How Epistasis and Purifying Selection Shape Genetic Diversity. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21918. short: K. Khudiakova, How Epistasis and Purifying Selection Shape Genetic Diversity, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-05-27T06:26:08Z date_published: 2026-06-07T00:00:00Z date_updated: 2026-06-12T12:43:35Z day: '07' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: NiBa - _id: JaMa doi: 10.15479/AT-ISTA-21918 ec_funded: 1 file: - access_level: closed checksum: 0cff64ae74f0f9f2d7011700c82f700a content_type: application/x-zip-compressed creator: kkhudiak date_created: 2026-06-09T08:34:38Z date_updated: 2026-06-09T08:40:48Z file_id: '21965' file_name: thesis.zip file_size: 20549813 relation: source_file - access_level: closed checksum: 547ae42de37cc86894af283f1664dbc8 content_type: application/pdf creator: kkhudiak date_created: 2026-06-09T12:28:51Z date_updated: 2026-06-11T12:14:53Z embargo: 2027-06-10 embargo_to: open_access file_id: '21969' file_name: 2026_Khudiakova_Ksenia_Thesis.pdf file_size: 9387029 relation: main_file file_date_updated: 2026-06-11T12:14:53Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '06' oa_version: Published Version page: '89' project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8 grant_number: '26293' name: The impact of deleterious mutations on small populations - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11447' relation: part_of_dissertation status: public - id: '12513' relation: part_of_dissertation status: deleted - id: '21967' relation: part_of_dissertation status: public - id: '21968' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 title: How epistasis and purifying selection shape genetic diversity tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository _id: '21960' abstract: - lang: eng text: "Solitons - localized wave packets that travel without spreading - play a central role in understanding transport and properties of nonlinear systems. In quantum many-body systems, however, such robust excitations are typically destroyed by thermalization. Here, we theoretically demonstrate the existence of solitonic excitations in high-energy states of Rydberg atom chains in the regime of strong nearest-neighbor Rydberg blockade. \r\nThese localized wave packets propagate directionally atop a special class of reviving initial states related to quantum many-body scars and are capable of carrying energy. Exhibiting long coherence times, these states constitute a form of non-ergodic quantum dynamics and can be efficiently implemented on Rydberg atom simulators. In this work, in addition to a phenomenological description of solitons, we identify their counterpart in a classical nonlinear dynamical system, demonstrate their potential use in quantum information transfer, and conjecture their relevance for anomalous energy transport reported in numerical studies of Rydberg atom arrays." article_processing_charge: No author: - first_name: Aron full_name: Kerschbaumer, Aron id: ade85a9c-3200-11ee-973b-91c1eb240410 last_name: Kerschbaumer orcid: 0009-0002-2370-8661 citation: ama: 'Kerschbaumer A. Research Data: “Quasi-solitons in Rydberg atom chains.” 2026. doi:10.15479/AT-ISTA-21960' apa: 'Kerschbaumer, A. (2026). Research Data: “Quasi-solitons in Rydberg atom chains.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21960' chicago: 'Kerschbaumer, Aron. “Research Data: ‘Quasi-Solitons in Rydberg Atom Chains.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21960.' ieee: 'A. Kerschbaumer, “Research Data: ‘Quasi-solitons in Rydberg atom chains.’” Institute of Science and Technology Austria, 2026.' ista: 'Kerschbaumer A. 2026. Research Data: ‘Quasi-solitons in Rydberg atom chains’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21960.' mla: 'Kerschbaumer, Aron. Research Data: “Quasi-Solitons in Rydberg Atom Chains.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21960.' short: A. Kerschbaumer, (2026). contributor: - contributor_type: contact_person first_name: Aron id: ade85a9c-3200-11ee-973b-91c1eb240410 last_name: Kerschbaumer orcid: 0009-0002-2370-8661 - contributor_type: supervisor first_name: Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - contributor_type: researcher first_name: Jean-Yves Marc id: 6c292945-a610-11ed-9eec-c3be1ad62a80 last_name: Desaules orcid: 0000-0002-3749-6375 - contributor_type: researcher first_name: Marko last_name: Ljubotina corr_author: '1' date_created: 2026-06-09T07:17:50Z date_published: 2026-06-16T00:00:00Z date_updated: 2026-06-16T08:00:38Z day: '16' department: - _id: GradSch - _id: MaSe doi: 10.15479/AT-ISTA-21960 ec_funded: 1 file: - access_level: open_access checksum: 133269a105e996c6c44fdd56128259c7 content_type: text/plain creator: akerschb date_created: 2026-06-15T22:01:57Z date_updated: 2026-06-15T22:01:57Z file_id: '22010' file_name: README.txt file_size: 1940 relation: main_file success: 1 - access_level: open_access checksum: 759f9649c3919f4c4ad37a1d104ea32a content_type: application/zip creator: akerschb date_created: 2026-06-15T22:02:07Z date_updated: 2026-06-15T22:02:07Z file_id: '22011' file_name: Soliton_Data.zip file_size: 13259747 relation: main_file success: 1 file_date_updated: 2026-06-15T22:02:07Z has_accepted_license: '1' month: '06' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publisher: Institute of Science and Technology Austria status: public title: 'Research Data: "Quasi-solitons in Rydberg atom chains"' 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: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21980' abstract: - lang: eng text: Despite significant progress in the field of molecular electronics over the last two decades, the quantitative prediction of metal-molecule-metal junction conductance remains a challenge. The standard computational framework combines density functional theory (DFT) with nonequilibrium Green’s functions (NEGF) using low-rung exchange-correlation functionals such as PBE, which overestimate the conductances. More advanced correction methods exist but require complex workflows and high computational cost, limiting their accessibility. Here, we introduce a physically motivated approach that approximates results obtained with high-rung functionals. Our method fits the PBE-calculated transmission to a Breit-Wigner form and subsequently refines the fit parameters using molecular orbital energies and metal densities of states computed for the isolated subsystems with high-rung functionals. This approach is applicable to a broad range of molecular junctions yielding conductance values in quantitative agreement with experiments. Our approach is simple, low-cost, and accurate, making it well-suited for routine and large-scale prediction of single-molecule junction conductance. acknowledgement: This work was supported primarily by the Institute of Science and Technology Austria. L.V. was supported in part by the National Science Foundation (No. NSF-DMR 2241180). Z.-F.L. was supported by an NSF CAREER Award, No. DMR-2044552 and an Alfred P. Sloan Research Fellowship, No. FG-2024-21750. article_processing_charge: Yes (via OA deal) article_type: letter_note author: - first_name: Artem full_name: Gulyaev, Artem id: 83ed7901-7380-11f0-bf20-a0788d5e654d last_name: Gulyaev - first_name: Jyotisman full_name: Hazarika, Jyotisman id: d87714c4-663d-11f0-bd06-caece19833e5 last_name: Hazarika orcid: 0009-0007-2542-7878 - first_name: Zhen-Fei full_name: Liu, Zhen-Fei last_name: Liu - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: ama: Gulyaev A, Hazarika J, Liu Z-F, Venkataraman L. A computationally efficient and accurate method for predicting conductance of single-molecule junctions. Nano Letters. 2026;26(22):7429–7434. doi:10.1021/acs.nanolett.6c01462 apa: Gulyaev, A., Hazarika, J., Liu, Z.-F., & Venkataraman, L. (2026). A computationally efficient and accurate method for predicting conductance of single-molecule junctions. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.6c01462 chicago: Gulyaev, Artem, Jyotisman Hazarika, Zhen-Fei Liu, and Latha Venkataraman. “A Computationally Efficient and Accurate Method for Predicting Conductance of Single-Molecule Junctions.” Nano Letters. American Chemical Society, 2026. https://doi.org/10.1021/acs.nanolett.6c01462. ieee: A. Gulyaev, J. Hazarika, Z.-F. Liu, and L. Venkataraman, “A computationally efficient and accurate method for predicting conductance of single-molecule junctions,” Nano Letters, vol. 26, no. 22. American Chemical Society, pp. 7429–7434, 2026. ista: Gulyaev A, Hazarika J, Liu Z-F, Venkataraman L. 2026. A computationally efficient and accurate method for predicting conductance of single-molecule junctions. Nano Letters. 26(22), 7429–7434. mla: Gulyaev, Artem, et al. “A Computationally Efficient and Accurate Method for Predicting Conductance of Single-Molecule Junctions.” Nano Letters, vol. 26, no. 22, American Chemical Society, 2026, pp. 7429–7434, doi:10.1021/acs.nanolett.6c01462. short: A. Gulyaev, J. Hazarika, Z.-F. Liu, L. Venkataraman, Nano Letters 26 (2026) 7429–7434. corr_author: '1' date_created: 2026-06-10T07:27:19Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-06-16T09:13:30Z day: '01' ddc: - '540' department: - _id: LaVe - _id: GradSch doi: 10.1021/acs.nanolett.6c01462 external_id: pmid: - '42223342' file: - access_level: open_access checksum: 897551374cac28e0db26dcb0b676b8e7 content_type: application/pdf creator: dernst date_created: 2026-06-16T09:11:35Z date_updated: 2026-06-16T09:11:35Z file_id: '22013' file_name: 2026_NanoLetters_Gulyaev.pdf file_size: 3362800 relation: main_file success: 1 file_date_updated: 2026-06-16T09:11:35Z has_accepted_license: '1' intvolume: ' 26' issue: '22' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 7429–7434 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: A computationally efficient and accurate method for predicting conductance of single-molecule junctions 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: 26 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21983' abstract: - lang: eng text: 'Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype–phenotype map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the first of a two-part series, we briefly review the pertinent modeling and simulation efforts for a unique system that enables close, quantitative, and mechanistic links between biophysics, as well as systems, synthetic, and evolutionary biology.' acknowledgement: "We thank Nick Barton and Noa Ottilie Borst for essential contributions to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship, jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science and Technology Austria (ISTA).\r\nThis study was supported by the European Molecular Biology Laboratory (J.C.); the European Molecular Biology Laboratory Interdisciplinary Postdoc Programme (EIPOD) under the Marie Skłodowska-Curie Actions cofund (S.H.A.)." article_number: '102483' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Elia full_name: Mascolo, Elia id: 776a6ed0-a053-11f0-8635-80b95e0e0d53 last_name: Mascolo orcid: 0000-0003-2977-7844 - first_name: Reka E full_name: Körei, Reka E id: 50FDE43E-AA30-11E9-A72B-8A12E6697425 last_name: Körei - first_name: Santiago full_name: Herrera-Álvarez, Santiago last_name: Herrera-Álvarez - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Justin full_name: Crocker, Justin last_name: Crocker - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: 'Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. Current Opinion in Genetics & Development. 2026;99. doi:10.1016/j.gde.2026.102483' apa: 'Mascolo, E., Körei, R. E., Herrera-Álvarez, S., Guet, C. C., Crocker, J., & Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2026.102483' chicago: 'Mascolo, Elia, Reka E Körei, Santiago Herrera-Álvarez, Calin C Guet, Justin Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” Current Opinion in Genetics & Development. Elsevier, 2026. https://doi.org/10.1016/j.gde.2026.102483.' ieee: 'E. Mascolo, R. E. Körei, S. Herrera-Álvarez, C. C. Guet, J. Crocker, and G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps,” Current Opinion in Genetics & Development, vol. 99. Elsevier, 2026.' ista: 'Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. 2026. Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. Current Opinion in Genetics & Development. 99, 102483.' mla: 'Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” Current Opinion in Genetics & Development, vol. 99, 102483, Elsevier, 2026, doi:10.1016/j.gde.2026.102483.' short: E. Mascolo, R.E. Körei, S. Herrera-Álvarez, C.C. Guet, J. Crocker, G. Tkačik, Current Opinion in Genetics & Development 99 (2026). corr_author: '1' date_created: 2026-06-10T07:37:12Z date_published: 2026-05-09T00:00:00Z date_updated: 2026-06-16T12:37:02Z day: '09' ddc: - '570' department: - _id: GradSch - _id: CaGu - _id: GaTk doi: 10.1016/j.gde.2026.102483 external_id: arxiv: - '2601.19681' has_accepted_license: '1' intvolume: ' 99' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.gde.2026.102483 month: '05' oa: 1 oa_version: Published Version publication: Current Opinion in Genetics & Development publication_identifier: eissn: - 1879-0380 issn: - 0959-437X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps' 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: 99 year: '2026' ...