--- OA_place: publisher _id: '20339' abstract: - lang: eng text: "This thesis investigates the interplay between algebraic and topological methods and combinatorial problems, focusing on approximate graph colourings and mass partitioning. The unifying theme throughout the dissertation is the use of continuous maps and symmetry constraints to extract combinatorial insights.\r\n\r\nWe first explore approximate graph colouring problems and more generally promise constraint satisfaction problems. Using tools from equivariant topology in combination with the general theory of polymorphism of a promise constraint satisfaction problem, we establish hardness for specific types of approximations.\r\n\r\nIn the second part, we address mass partitioning problems, where one seeks to divide geometric objects or measures in Euclidean space into parts of equal size using hyperplanes. Employing techniques from topological combinatorics (configuration space/test map setup and Borsuk–Ulam type theorems), we both obtain a new equipartitioning result in the and provide a fast algorithm for computing equipartitioning of point sets in 3D.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Gianluca full_name: Tasinato, Gianluca id: 0433290C-AF8F-11E9-A4C7-F729E6697425 last_name: Tasinato citation: ama: 'Tasinato G. Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems. 2025. doi:10.15479/AT-ISTA-20339' apa: 'Tasinato, G. (2025). Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20339' chicago: 'Tasinato, Gianluca. “Topological Methods in Discrete Geometry and Theoretical Computer Science: Measure Partitioning and Constraint Satisfaction Problems.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20339.' ieee: 'G. Tasinato, “Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems,” Institute of Science and Technology Austria, 2025.' ista: 'Tasinato G. 2025. Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems. Institute of Science and Technology Austria.' mla: 'Tasinato, Gianluca. Topological Methods in Discrete Geometry and Theoretical Computer Science: Measure Partitioning and Constraint Satisfaction Problems. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20339.' short: 'G. Tasinato, Topological Methods in Discrete Geometry and Theoretical Computer Science: Measure Partitioning and Constraint Satisfaction Problems, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-09-10T12:17:55Z date_published: 2025-09-10T00:00:00Z date_updated: 2026-10-21T13:23:55Z day: '10' ddc: - '516' degree_awarded: PhD department: - _id: GradSch - _id: UlWa doi: 10.15479/AT-ISTA-20339 doi_confirm: '1' file: - access_level: closed checksum: ae097a515b9bb4d4b025ca854ae2ed76 content_type: application/x-zip-compressed creator: gtasinat date_created: 2025-09-11T12:24:12Z date_updated: 2025-09-11T12:24:12Z file_id: '20344' file_name: thesis-source.zip file_size: 2218562 relation: source_file - access_level: open_access checksum: 04b2e016409e52167ce42b0eef839fbf content_type: application/pdf creator: gtasinat date_created: 2025-09-11T12:26:14Z date_updated: 2025-09-11T12:26:14Z file_id: '20345' file_name: 2025_Tasinato_Gianluca_Thesis.pdf file_size: 10071982 relation: main_file success: 1 file_date_updated: 2025-09-11T12:26:14Z fulldoi: https://doi.org/10.15479/AT-ISTA-20339 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '09' oa: 1 oa_version: Published Version page: '106' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20008' relation: part_of_dissertation status: public - id: '19860' relation: part_of_dissertation status: public - id: '15168' relation: part_of_dissertation status: public status: public supervisor: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 title: 'Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems' 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: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18157' abstract: - lang: eng text: "Interest in sliding block puzzles dates back to the 15-puzzle, seemingly invented by Noyes Chapman in 1874 (see [23] for an account of the fascinating history of the puzzle). The game consists of fifteen movable square blocks numbered \r\n and arranged within a \r\n square box, leaving one empty space (see Figure 1). The task at hand is to start from a given configuration of the numbered blocks and reach the desired target configuration, where the only allowed move is to slide a numbered block into an adjacent empty space. This task seemed to be unpredictably either very easy to accomplish, or completely impossible, and the puzzle turned into a worldwide sensation in the spring of 1880. A particularly challenging instance, known as the 13-15-14 puzzle, consisted of initial and target configurations that differed by a single swap (historically this swap involved the blocks labeled 14 and 15). The craze of this puzzle was such that it consistently made newspaper headlines in 1880, with an article in the New York Times lamenting that it was “threatening our free institutions” [23, p. 9]. Various prizes were offered for anyone who could solve this challenge, beginning with a $25 set of teeth and culminating with Sam Loyd’s famous $1,000 cash prize." acknowledgement: Open access funding provided by Copenhagen University. article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Florestan R full_name: Brunck, Florestan R id: 6ab6e556-f394-11eb-9cf6-9dfb78f00d8d last_name: Brunck - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 citation: ama: 'Brunck FR, Kwan MA. Books, Hallways, and social butterflies: A note on sliding block puzzles. Mathematical Intelligencer. 2025;47:52-65. doi:10.1007/s00283-024-10358-x' apa: 'Brunck, F. R., & Kwan, M. A. (2025). Books, Hallways, and social butterflies: A note on sliding block puzzles. Mathematical Intelligencer. Springer Nature. https://doi.org/10.1007/s00283-024-10358-x' chicago: 'Brunck, Florestan R, and Matthew Alan Kwan. “Books, Hallways, and Social Butterflies: A Note on Sliding Block Puzzles.” Mathematical Intelligencer. Springer Nature, 2025. https://doi.org/10.1007/s00283-024-10358-x.' ieee: 'F. R. Brunck and M. A. Kwan, “Books, Hallways, and social butterflies: A note on sliding block puzzles,” Mathematical Intelligencer, vol. 47. Springer Nature, pp. 52–65, 2025.' ista: 'Brunck FR, Kwan MA. 2025. Books, Hallways, and social butterflies: A note on sliding block puzzles. Mathematical Intelligencer. 47, 52–65.' mla: 'Brunck, Florestan R., and Matthew Alan Kwan. “Books, Hallways, and Social Butterflies: A Note on Sliding Block Puzzles.” Mathematical Intelligencer, vol. 47, Springer Nature, 2025, pp. 52–65, doi:10.1007/s00283-024-10358-x.' short: F.R. Brunck, M.A. Kwan, Mathematical Intelligencer 47 (2025) 52–65. das_tickbox: '0' date_created: 2024-09-29T22:01:38Z date_published: 2025-03-01T00:00:00Z date_updated: 2026-10-21T13:42:19Z day: '01' ddc: - '510' department: - _id: UlWa - _id: MaKw doi: 10.1007/s00283-024-10358-x external_id: arxiv: - '2303.09459' isi: - '001318056000001' file: - access_level: open_access checksum: c932ebe45c460d4a73f5b2dcca643db1 content_type: application/pdf creator: dernst date_created: 2025-04-08T11:17:45Z date_updated: 2025-04-08T11:17:45Z file_id: '19530' file_name: 2025_MathIntelligencer_Brunck.pdf file_size: 1760643 relation: main_file success: 1 file_date_updated: 2025-04-08T11:17:45Z fulldoi: https://doi.org/10.1007/s00283-024-10358-x has_accepted_license: '1' intvolume: ' 47' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 52-65 publication: Mathematical Intelligencer publication_identifier: issn: - 0343-6993 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: 'Books, Hallways, and social butterflies: A note on sliding block puzzles' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 47 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21007' abstract: - lang: eng text: 'Currently, the best known tradeoff between approximation ratio and complexity for the Sparsest Cut problem is achieved by the algorithm in [Sherman, FOCS 2009]: it computes O(√(log n)/ε)-approximation using O(nε logO(1) n) maxflows for any ε∈[Θ(1/log n),Θ(1)]. It works by solving the SDP relaxation of [Arora-Rao-Vazirani, STOC 2004] using the Multiplicative Weights Update algorithm (MW) of [Arora-Kale, JACM 2016]. To implement one MW step, Sherman approximately solves a multicommodity flow problem using another application of MW. Nested MW steps are solved via a certain "chaining" algorithm that combines results of multiple calls to the maxflow algorithm. We present an alternative approach that avoids solving the multicommodity flow problem and instead computes "violating paths". This simplifies Sherman''s algorithm by removing a need for a nested application of MW, and also allows parallelization: we show how to compute O(√(log n)/ε)-approximation via O(logO(1) n) maxflows using O(nε) processors. We also revisit Sherman''s chaining algorithm, and present a simpler version together with a new analysis.' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Kolmogorov V. A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT. ACM Transactions on Algorithms. 2025;21(4):1-22. doi:10.1145/3748723 apa: Kolmogorov, V. (2025). A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT. ACM Transactions on Algorithms. Association for Computing Machinery. https://doi.org/10.1145/3748723 chicago: Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for SPARSEST CUT.” ACM Transactions on Algorithms. Association for Computing Machinery, 2025. https://doi.org/10.1145/3748723. ieee: V. Kolmogorov, “A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT,” ACM Transactions on Algorithms, vol. 21, no. 4. Association for Computing Machinery, pp. 1–22, 2025. ista: Kolmogorov V. 2025. A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT. ACM Transactions on Algorithms. 21(4), 1–22. mla: Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for SPARSEST CUT.” ACM Transactions on Algorithms, vol. 21, no. 4, Association for Computing Machinery, 2025, pp. 1–22, doi:10.1145/3748723. short: V. Kolmogorov, ACM Transactions on Algorithms 21 (2025) 1–22. corr_author: '1' date_created: 2026-01-20T10:04:02Z date_published: 2025-10-01T00:00:00Z date_updated: 2026-10-21T13:45:27Z day: '01' ddc: - '510' department: - _id: VlKo doi: 10.1145/3748723 external_id: arxiv: - '2307.00115' file: - access_level: open_access checksum: 4a80fdb1e3711b9a2768d2bb8f6d3b4e content_type: application/pdf creator: dernst date_created: 2026-01-21T09:38:09Z date_updated: 2026-01-21T09:38:09Z file_id: '21031' file_name: 2025_ACMToA_Kolmogorov.pdf file_size: 2208302 relation: main_file success: 1 file_date_updated: 2026-01-21T09:38:09Z fulldoi: https://doi.org/10.1145/3748723 has_accepted_license: '1' intvolume: ' 21' issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1-22 publication: ACM Transactions on Algorithms publication_identifier: eissn: - 1549-6333 issn: - 1549-6325 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '17236' relation: shorter_version status: public scopus_import: '1' status: public title: A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT 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: 21 year: '2025' ... --- OA_place: repository OA_type: green _id: '19026' abstract: - lang: eng text: The back-action damping of mechanical motion by electromagnetic radiation is typically overwhelmed by internal loss channels unless demanding experimental ingredients such as superconducting resonators, high-quality optical cavities, or large magnetic fields are employed. Here we demonstrate the first room temperature, cavity-free, all-electric device where back-action damping exceeds internal loss, enabled by a mechanically compliant parallel-plate capacitor with a nanoscale plate separation and an aspect ratio exceeding 1,000. The device has 4 orders of magnitude lower insertion loss than a comparable commercial quartz crystal and achieves a position imprecision rivaling optical interferometers. With the help of a back-action isolation scheme, we observe radiative cooling of mechanical motion by a remote cryogenic load. This work provides a technologically accessible route to high-precision sensing, transduction, and signal processing. acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: We thank Carissa Kumar and Vibha Padmanabhan for assistance in comparing performance with devices across the literature. We thank Andrew Cleland for helpful comments on this work. We are grateful for support from the Miba Machine Shop and Nanofabrication facility at IST Austria. This work was supported by the Austrian FWF grant P33692–N and includes a recipient of a DOC Fellowship of the Austrian Academy of Sciences (DOC – No. 26088) at the Institute of Science and Technology, Austria. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Denise full_name: Puglia, Denise id: 4D495994-AE37-11E9-AC72-31CAE5697425 last_name: Puglia orcid: 0000-0003-1144-2763 - first_name: Rachel H full_name: Odessey, Rachel H id: 9a7a5123-8972-11ed-ae7b-dd1f2af457bd last_name: Odessey - first_name: Peter full_name: Burns, Peter last_name: Burns - first_name: Niklas full_name: Luhmann, Niklas last_name: Luhmann - first_name: Silvan full_name: Schmid, Silvan last_name: Schmid - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 citation: ama: Puglia D, Odessey RH, Burns P, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical motion. Nano Letters. 2025;25(7):2749-2755. doi:10.1021/acs.nanolett.4c05796 apa: Puglia, D., Odessey, R. H., Burns, P., Luhmann, N., Schmid, S., & Higginbotham, A. P. (2025). Room temperature, cavity-free capacitive strong coupling to mechanical motion. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.4c05796 chicago: Puglia, Denise, Rachel H Odessey, Peter Burns, Niklas Luhmann, Silvan Schmid, and Andrew P Higginbotham. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical Motion.” Nano Letters. American Chemical Society, 2025. https://doi.org/10.1021/acs.nanolett.4c05796. ieee: D. Puglia, R. H. Odessey, P. Burns, N. Luhmann, S. Schmid, and A. P. Higginbotham, “Room temperature, cavity-free capacitive strong coupling to mechanical motion,” Nano Letters, vol. 25, no. 7. American Chemical Society, pp. 2749–2755, 2025. ista: Puglia D, Odessey RH, Burns P, Luhmann N, Schmid S, Higginbotham AP. 2025. Room temperature, cavity-free capacitive strong coupling to mechanical motion. Nano Letters. 25(7), 2749–2755. mla: Puglia, Denise, et al. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical Motion.” Nano Letters, vol. 25, no. 7, American Chemical Society, 2025, pp. 2749–55, doi:10.1021/acs.nanolett.4c05796. short: D. Puglia, R.H. Odessey, P. Burns, N. Luhmann, S. Schmid, A.P. Higginbotham, Nano Letters 25 (2025) 2749–2755. corr_author: '1' date_created: 2025-02-16T23:02:34Z date_published: 2025-02-06T00:00:00Z date_updated: 2026-10-21T14:08:09Z day: '06' department: - _id: AnHi doi: 10.1021/acs.nanolett.4c05796 external_id: arxiv: - '2407.15314' isi: - '001415246000001' fulldoi: https://doi.org/10.1021/acs.nanolett.4c05796 intvolume: ' 25' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2407.15314 month: '02' oa: 1 oa_version: Preprint page: 2749-2755 project: - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition - _id: 62843413-2b32-11ec-9570-c4ec6eabfae7 grant_number: '26088' name: Surface Charge and Tunneling Multi-Mode Imaging publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: record: - id: '18143' relation: earlier_version status: public scopus_import: '1' status: public title: Room temperature, cavity-free capacitive strong coupling to mechanical motion type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 25 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20656' abstract: - lang: eng text: Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a prerequisite for (1) self-organizing processes, including vascular tissue formation, and (2) directional growth responses such as gravitropism. Here, we identify a mechanism by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface AUXIN-BINDING PROTEIN1 (ABP1)-TRANSMEMBRANE KINASE 1 (TMK1) receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE 3 (ABL3) auxin receptor. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably for other self-organizing developmental phenomena. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We gratefully acknowledge Tongda Xu for experimental, material, and conceptual support. We thank William Gray for providing material, Nataliia Gnyliukh and Ema Cervenova for help with manuscript preparation, and Julia Schmid for help with cloning. We thank Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions and support with phospho-proteomic analyses. We thank the Bioimaging and Life Science facilities at the Institute of Science and Technology Austria (ISTA) for their excellent service and assistance. The research leading to these results has received funding from the European Union (ERC, CYNIPS, 101142681) and Austrian Science Fund (FWF; I 6123-B) to J.F., and Y.J. was funded by ERC no. 3363360-APPL under FP/2007-2013. L.R. was supported by the FP7-PEOPLE-2011-COFUND ISTFELLOW program (IC1023FELL01) and the European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 985-2016). S.T. was supported by the National Natural Science Foundation of China (32321001, 32570366). The work of J.H. was supported by the project JG_2024_003 implemented within the Palacký University Young Researcher Grant. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Lukas full_name: Fiedler, Lukas id: 7c417475-8972-11ed-ae7b-8b674ca26986 last_name: Fiedler - first_name: Minxia full_name: Zou, Minxia id: 5c243f41-03f3-11ec-841c-96faf48a7ef9 last_name: Zou - first_name: Caterina full_name: Giannini, Caterina id: e3fdddd5-f6e0-11ea-865d-ca99ee6367f4 last_name: Giannini - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: Dmitrii full_name: Vladimirtsev, Dmitrii id: 60466724-5355-11ee-ae5a-fa55e8f99c3d last_name: Vladimirtsev - first_name: Marek full_name: Randuch, Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch - first_name: Yongfan full_name: Yu, Yongfan last_name: Yu - first_name: Zuzana full_name: Gelová, Zuzana id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425 last_name: Gelová orcid: 0000-0003-4783-1752 - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Jakub full_name: Hajny, Jakub id: 4800CC20-F248-11E8-B48F-1D18A9856A87 last_name: Hajny orcid: 0000-0003-2140-7195 - first_name: Meng full_name: Chen, Meng last_name: Chen - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Maria Mar full_name: Marques-Bueno, Maria Mar last_name: Marques-Bueno - first_name: Zainab full_name: Quddoos, Zainab id: 32ff3c64-04a0-11f0-a50f-d0c45bfac466 last_name: Quddoos - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: Ivan full_name: Kulich, Ivan id: 57a1567c-8314-11eb-9063-c9ddc3451a54 last_name: Kulich - first_name: Yvon full_name: Jaillais, Yvon last_name: Jaillais - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism. Cell. 2025;188(22):6138-6150.e17. doi:10.1016/j.cell.2025.08.026 apa: Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev, D., … Friml, J. (2025). ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism. Cell. Cell Press. https://doi.org/10.1016/j.cell.2025.08.026 chicago: Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini, Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” Cell. Cell Press, 2025. https://doi.org/10.1016/j.cell.2025.08.026. ieee: L. Rodriguez Solovey et al., “ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism,” Cell, vol. 188, no. 22. Cell Press, p. 6138–6150.e17, 2025. ista: Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Kulich I, Jaillais Y, Friml J. 2025. ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism. Cell. 188(22), 6138–6150.e17. mla: Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” Cell, vol. 188, no. 22, Cell Press, 2025, p. 6138–6150.e17, doi:10.1016/j.cell.2025.08.026. short: L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev, M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer, L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, I. Kulich, Y. Jaillais, J. Friml, Cell 188 (2025) 6138–6150.e17. corr_author: '1' date_created: 2025-11-19T09:44:31Z date_published: 2025-10-30T00:00:00Z date_updated: 2026-10-22T09:15:44Z day: '30' ddc: - '580' department: - _id: JiFr - _id: XiFe doi: 10.1016/j.cell.2025.08.026 ec_funded: 1 external_id: isi: - '001616077900005' pmid: - '41043433' file: - access_level: open_access checksum: 8ac396a0806ad7f2e4e7a0c1eed712ce content_type: application/pdf creator: dernst date_created: 2025-11-24T10:55:18Z date_updated: 2025-11-24T10:55:18Z file_id: '20679' file_name: 2025_Cell_Rodriguez.pdf file_size: 17825465 relation: main_file success: 1 file_date_updated: 2025-11-24T10:55:18Z fulldoi: https://doi.org/10.1016/j.cell.2025.08.026 has_accepted_license: '1' intvolume: ' 188' isi: 1 issue: '22' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 6138-6150.e17 pmid: 1 project: - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptors for auxin canalization in Arabidopsis - _id: 26060676-B435-11E9-9278-68D0E5697425 grant_number: ALTF 985-2016 name: Cell surface receptor complexes for auxin signaling in plants - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: record: - id: '19399' relation: earlier_version status: public - id: '23145' relation: dissertation_contains status: public status: public title: ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism 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: 188 year: '2025' ... --- OA_place: repository OA_type: green _id: '23174' abstract: - lang: eng text: Roots must continuously adapt their growth and have evolved the ability to rapidly respond to diverse environmental and hormonal cues, including the phytohormone auxin. Auxin-induced cellular responses involve membrane depolarization, cytosolic calcium (Ca²⁺) elevation, and extracellular pH increase, but how these processes lead to rapid growth regulation remains unclear. Here, we show that cytosolic Ca²⁺ acts as a universal signal integrating diverse cues for rapid regulation of root growth. Using live imaging, microfluidics, and optogenetics in Arabidopsis, we demonstrate that a swift rise in cytosolic Ca²⁺ is the primary target of auxin signaling affecting growth inhibition. Disruption of Ca²⁺ influx abolishes these responses, whereas light-gated Ca²⁺ influx from the apoplast or endoplasmic reticulum stores inhibits growth. Multiple unrelated stimuli—including auxin, extracellular ATP, RALF peptides, and hydrogen peroxide—converge on this Ca²⁺-dependent mechanism. Cytosolic Ca²⁺ elevation thus represents a necessary and sufficient step for rapid growth inhibition, revealing a unifying principle of root signaling. acknowledgement: "We gratefully acknowledge Dr. Andrea Bleckmann, creator of pBLAX000 vector and Dr. Shiqiang Gao for donation of template used in XXM-ER cloning. This research was supported by the Laboratory Support Facility, the Plant Facility, the IT Facility and the Imaging and Optical Facility of the Institute of Science and Technology Austria. The graphical elements used in Fig. 5 were adapted and modified from Servier, https://smart.servier.com, and are used under CC BY 3.0 licence. The authors acknowledge the use of AI-tools (Microsoft Copilot, Gemini) for language refinement. All content was critically reviewed by authors.\r\n\r\nFunder Information Declared\r\nEuropean Research Council, 101142681 CYNIPS\r\nAustrian Science Fund, P 37051-B" article_processing_charge: No author: - first_name: Marek full_name: Randuch, Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch - first_name: Ivan full_name: Kulich, Ivan id: 57a1567c-8314-11eb-9063-c9ddc3451a54 last_name: Kulich - first_name: Dmitrii full_name: Vladimirtsev, Dmitrii id: 60466724-5355-11ee-ae5a-fa55e8f99c3d last_name: Vladimirtsev - first_name: Shouguang full_name: Huang, Shouguang last_name: Huang - first_name: Rainer full_name: Hedrich, Rainer last_name: Hedrich - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 biorxivid: 1 citation: ama: Randuch M, Kulich I, Vladimirtsev D, Huang S, Hedrich R, Friml J. Cytosolic Ca2+ as a universal signal for rapid root growth regulation. bioRxiv. doi:10.1101/2025.10.17.683082 apa: Randuch, M., Kulich, I., Vladimirtsev, D., Huang, S., Hedrich, R., & Friml, J. (n.d.). Cytosolic Ca2+ as a universal signal for rapid root growth regulation. bioRxiv. https://doi.org/10.1101/2025.10.17.683082 chicago: Randuch, Marek, Ivan Kulich, Dmitrii Vladimirtsev, Shouguang Huang, Rainer Hedrich, and Jiří Friml. “Cytosolic Ca2+ as a Universal Signal for Rapid Root Growth Regulation.” BioRxiv, n.d. https://doi.org/10.1101/2025.10.17.683082. ieee: M. Randuch, I. Kulich, D. Vladimirtsev, S. Huang, R. Hedrich, and J. Friml, “Cytosolic Ca2+ as a universal signal for rapid root growth regulation,” bioRxiv. . ista: Randuch M, Kulich I, Vladimirtsev D, Huang S, Hedrich R, Friml J. Cytosolic Ca2+ as a universal signal for rapid root growth regulation. bioRxiv, 10.1101/2025.10.17.683082. mla: Randuch, Marek, et al. “Cytosolic Ca2+ as a Universal Signal for Rapid Root Growth Regulation.” BioRxiv, doi:10.1101/2025.10.17.683082. short: M. Randuch, I. Kulich, D. Vladimirtsev, S. Huang, R. Hedrich, J. Friml, BioRxiv (n.d.). corr_author: '1' date_created: 2026-10-19T11:44:48Z date_published: 2025-10-17T00:00:00Z date_updated: 2026-10-22T09:15:44Z day: '17' department: - _id: JiFr doi: 10.1101/2025.10.17.683082 external_id: biorxivid: - 10.1101/2025.10.17.683082 fulldoi: https://doi.org/10.1101/2025.10.17.683082 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.10.17.683082 month: '10' oa: 1 oa_version: Preprint project: - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors publication: bioRxiv publication_status: draft related_material: record: - id: '23145' relation: dissertation_contains status: public status: public title: Cytosolic Ca2+ as a universal signal for rapid root growth regulation 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '20485' acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: "I would also like to acknowledge the funding that I received from the European Union’s\r\nHorizon 2020 research and Innovation programme under the Marie Sklodowska-Curie\r\nGrant Agreement No. 665385. This work would not have been possible without the contribution and support of people\r\nbehind the scientific service units at ISTA: the Life Science Facility (LSF), Imaging and\r\nOptics Facility (IOF), the Bioinformatics Unit, Protein Services Unit and\r\nElectrophysiology Unit. I would also like to recognize the work of people at the Vienna\r\nBiocenter (VBC) Mass Spectrometry Facility, particularly Markus Hartl and WeiQiang\r\nChen. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michaela full_name: Misova, Michaela id: 495A3C32-F248-11E8-B48F-1D18A9856A87 last_name: Misova orcid: 0000-0003-2427-6856 citation: ama: Misova M. Dissecting gap junction biology using the C. elegans nervous system. 2025. doi:10.15479/AT-ISTA-20485 apa: Misova, M. (2025). Dissecting gap junction biology using the C. elegans nervous system. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20485 chicago: Misova, Michaela. “Dissecting Gap Junction Biology Using the C. Elegans Nervous System.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20485. ieee: M. Misova, “Dissecting gap junction biology using the C. elegans nervous system,” Institute of Science and Technology Austria, 2025. ista: Misova M. 2025. Dissecting gap junction biology using the C. elegans nervous system. Institute of Science and Technology Austria. mla: Misova, Michaela. Dissecting Gap Junction Biology Using the C. Elegans Nervous System. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20485. short: M. Misova, Dissecting Gap Junction Biology Using the C. Elegans Nervous System, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-17T16:15:09Z date_published: 2025-10-23T00:00:00Z date_updated: 2026-10-23T22:30:03Z day: '23' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: MaDe doi: 10.15479/AT-ISTA-20485 ec_funded: 1 file: - access_level: closed checksum: e042ea314e7e13fce76c6c95e126779a content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mmisova date_created: 2025-10-23T08:22:35Z date_updated: 2026-10-23T22:30:02Z embargo_to: open_access file_id: '20518' file_name: 2025-Misova-Michaela-Thesis.docx file_size: 75070995 relation: source_file - access_level: open_access checksum: fcd8973d6a025256eb0eb1a82c02172c content_type: application/pdf creator: mmisova date_created: 2025-10-23T08:21:21Z date_updated: 2026-10-23T22:30:02Z embargo: 2026-10-23 file_id: '20519' file_name: 2025-Misova-Michaela-Thesis.pdf file_size: 10974630 relation: main_file file_date_updated: 2026-10-23T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20485 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '155' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-068-8 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 title: Dissecting gap junction biology using the C. elegans nervous system 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '19557' acknowledged_ssus: - _id: Bio - _id: PreCl - _id: ScienComp acknowledgement: "The work presented in this doctoral thesis was performed at the Institute of Science\r\nand Technology (ISTA) and financially supported by a European Research Council\r\n(ERC) Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the\r\nAustrian Science Fund (FWF) to Gaia Novarino (PE1028W1232). I am very thankful\r\nto the Doctoral Program “Molecular Drug Targets” (MolTag) for offering me financial\r\nsupport to perform essential experiments during my PhD studies and to participate in\r\ninternational conferences and courses." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lena A full_name: Schwarz, Lena A id: 29A8453C-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz citation: ama: Schwarz LA. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. 2025. doi:10.15479/AT-ISTA-19557 apa: Schwarz, L. A. (2025). Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19557 chicago: Schwarz, Lena A. “Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19557. ieee: L. A. Schwarz, “Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution,” Institute of Science and Technology Austria, 2025. ista: Schwarz LA. 2025. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. Institute of Science and Technology Austria. mla: Schwarz, Lena A. Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19557. short: L.A. Schwarz, Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-04-14T06:59:06Z date_published: 2025-04-14T00:00:00Z date_updated: 2026-10-15T22:30:03Z day: '14' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: GaNo doi: 10.15479/AT-ISTA-19557 file: - access_level: closed checksum: 50290a8604edb0a720387f01e9d59fe4 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lschwarz date_created: 2025-04-15T08:43:36Z date_updated: 2026-10-15T22:30:02Z embargo_to: open_access file_id: '19561' file_name: Schwarz_Thesis_2025_FINAL.docx file_size: 21783427 relation: source_file - access_level: open_access checksum: ed028488180ac4901e018ef1c330cf01 content_type: application/pdf creator: lschwarz date_created: 2025-04-15T08:43:42Z date_updated: 2026-10-15T22:30:02Z embargo: 2026-10-15 file_id: '19562' file_name: Schwarz_Thesis_2025_FINALpdfa.pdf file_size: 11432175 relation: main_file file_date_updated: 2026-10-15T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19557 has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '124' project: - _id: 9B91375C-BA93-11EA-9121-9846C619BF3A grant_number: '707964' name: Critical windows and reversibility of ASD associated with mutations in chromatin remodelers - _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6 grant_number: '101044865' name: Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12802' relation: part_of_dissertation status: public - id: '9429' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 title: Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_embargo: '6' OA_place: publisher _id: '20798' abstract: - lang: eng text: "Atom interferometers measure the relative phase shifts between coherent matter-wave paths\r\nthat arise from interactions with external fields or inertial forces. Due to their exceptional\r\nphase sensitivity, atom interferometers became an essential tool for precision measurements\r\nand fundamental physics experiments, finding applications in geodesy, gravimetry, and inertial\r\nnavigation. However, their measurement precision is limited by quantum projection noise,\r\nwhich arises from the Heisenberg uncertainty principle, preventing the measurement of atomic\r\nstates with absolute precision. The generation of entanglement between the atoms offers a\r\npath to surpass this so-called standard quantum limit, thereby enhancing the interferometer’s\r\nphase sensitivity beyond classical measurement bounds.\r\nThis thesis reports on the development of an atom interferometer experiment designed to\r\nrealize cavity-mediated, squeezed Mach-Zehnder-type interferometry with ultra-cold 87Rb atoms.\r\nThe experiment combines cavity-aided spin-squeezing with cavity-mediated Mach-Zehnder\r\ninterferometry to demonstrate entanglement-enhanced phase sensitivity. The experiment is\r\ncentered on a triangular optical cavity that mediates all relevant atom-light interactions. The\r\ncavity provides optical trapping, spin-squeezing, and Raman beam-splitter operations, enabling\r\nto perform interferometry on a continuously trapped atomic ensemble.\r\nThe thesis elaborates on the fundamental theoretical framework, the cavity design, and the full\r\noptical setup, including the detailed configuration of the developed laser stabilization methods.\r\nExperimentally, continuous loading methods were explored, resulting in an accumulation of\r\nup to 4 × 106\r\natoms in the dipole trap within a cycle time of 500 ms. The AC Stark shift\r\ncompensation method developed for continuous loading was further applied for in-trap cooling\r\nto 10 µK, and optical pumping for efficient atomic state preparation. Coherent state control\r\nwas verified via observation of microwave-driven Rabi oscillations, and used to characterize\r\natom-cavity coupling.\r\nThese presented results establish the experimental groundwork for the future development of\r\ncavity-mediated, entanglement-enhanced Mach-Zehnder-type atom interferometry." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sebastian full_name: Wald, Sebastian id: 133F200A-B015-11E9-AD41-0EDAE5697425 last_name: Wald orcid: 0000-0002-5869-1604 citation: ama: Wald S. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. 2025. doi:10.15479/AT-ISTA-20798 apa: Wald, S. (2025). Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20798 chicago: Wald, Sebastian. “Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20798. ieee: S. Wald, “Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry,” Institute of Science and Technology Austria, 2025. ista: Wald S. 2025. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. Institute of Science and Technology Austria. mla: Wald, Sebastian. Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20798. short: S. Wald, Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry, Institute of Science and Technology Austria, 2025. corr_author: '1' das_tickbox: '1' date_created: 2025-12-11T11:48:11Z date_published: 2025-12-11T00:00:00Z date_updated: 2026-07-24T08:07:28Z day: '11' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: OnHo doi: 10.15479/AT-ISTA-20798 doi_confirm: '1' file: - access_level: open_access checksum: 1be72faf529a5e8a2d03cb3d5f808b77 content_type: application/pdf creator: swald date_created: 2025-12-12T11:53:42Z date_updated: 2026-06-15T22:30:03Z embargo: 2026-06-15 file_id: '20809' file_name: 2025_Wald_Sebastian_Thesis.pdf file_size: 47536855 relation: main_file - access_level: closed checksum: 8c3a1904dceb4bcd04bc9f14b2594bab content_type: application/x-zip-compressed creator: swald date_created: 2025-12-12T11:54:55Z date_updated: 2026-06-15T22:30:03Z embargo_to: open_access file_id: '20810' file_name: 2025_Wald_Sebastian_Thesis.zip file_size: 40127601 relation: source_file file_date_updated: 2026-06-15T22:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-20798 has_accepted_license: '1' keyword: - entanglement-enhanced atom interferometry - cavity QED - spin-squeezing - dipole trap - quantum optics language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '12' oa: 1 oa_version: Published Version page: '152' publication_identifier: isbn: - 978-3-99078-075-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14759' relation: part_of_dissertation status: public status: public supervisor: - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X title: Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_embargo: 6 months OA_place: publisher OA_type: hybrid _id: '19498' abstract: - lang: eng text: A dynamic interplay between fast synaptic signals and slower neuromodulatory signals controls the excitatory/inhibitory (E/I) balance within neuronal circuits. The mechanisms by which neuropeptide signaling is regulated to maintain E/I balance remain uncertain. We designed a genetic screen to isolate genes involved in the peptidergic maintenance of the E/I balance in the C. elegans motor circuit. This screen identified the C. elegans orthologs of the presynaptic phosphoprotein synapsin (snn-1) and the protein phosphatase 1 (PP1) regulatory subunit PHACTR1 (phac-1). We demonstrate that both phac-1 and snn-1 alter the motor behavior of C. elegans, and genetic interactions suggest that SNN-1 contributes to PP1-PHAC-1 holoenzyme signaling. De novo variants of human PHACTR1, associated with early-onset epilepsies [developmental and epileptic encephalopathy 70 (DEE70)], when expressed in C. elegans resulted in constitutive PP1-PHAC-1 holoenzyme activity. Unregulated PP1-PHAC-1 signaling alters the synapsin and actin cytoskeleton and increases neuropeptide release by cholinergic motor neurons, which secondarily affects the presynaptic vesicle cycle. Together, these results clarify the dominant mechanisms of action of the DEE70 alleles and suggest that altered neuropeptide release may alter E/I balance in DEE70. acknowledgement: P.L. is a research associate of the Belgian National Fund for Scientific Research (FRS-FNRS). K.S., M.S.-G., S.S., and P.L. are supported by grants from the FRS-FNRS. This work was supported by an Advanced ERC Grant (269058 ACMO) to M.D.B. We thank the team of Alexander Gottschalk for the snn-1(S9A) strain. We thank the Imaging Facility of the Faculty of Medicine (LiMiF) of the Universite Libre de Bruxelles, supported by FRS-FNRS. This work made use of instruments in the Electron Microscopy Core of the University of Illinois Chicago Research Resources Center as well as the BioCryo facility of Northwestern University's NUANCE Center, which has received support from the SHyNE Resource (NSF ECCS-2025633), the IIN, and Northwestern's MRSEC program (NSF DMR-2308691). Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). article_number: e1767232024 article_processing_charge: No article_type: original author: - first_name: Aikaterini full_name: Stratigi, Aikaterini last_name: Stratigi - first_name: Miguel full_name: Soler-García, Miguel last_name: Soler-García - first_name: Mia full_name: Krout, Mia last_name: Krout - first_name: Shikha full_name: Shukla, Shikha last_name: Shukla - first_name: Mario full_name: De Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: De Bono orcid: 0000-0001-8347-0443 - first_name: Janet E. full_name: Richmond, Janet E. last_name: Richmond - first_name: Patrick full_name: Laurent, Patrick last_name: Laurent citation: ama: Stratigi A, Soler-García M, Krout M, et al. Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. Journal of Neuroscience. 2025;45(13). doi:10.1523/JNEUROSCI.1767-23.2024 apa: Stratigi, A., Soler-García, M., Krout, M., Shukla, S., de Bono, M., Richmond, J. E., & Laurent, P. (2025). Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1767-23.2024 chicago: Stratigi, Aikaterini, Miguel Soler-García, Mia Krout, Shikha Shukla, Mario de Bono, Janet E. Richmond, and Patrick Laurent. “Neuroendocrine Control of Synaptic Transmission by PHAC-1 in C. Elegans.” Journal of Neuroscience. Society for Neuroscience, 2025. https://doi.org/10.1523/JNEUROSCI.1767-23.2024. ieee: A. Stratigi et al., “Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans,” Journal of Neuroscience, vol. 45, no. 13. Society for Neuroscience, 2025. ista: Stratigi A, Soler-García M, Krout M, Shukla S, de Bono M, Richmond JE, Laurent P. 2025. Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans. Journal of Neuroscience. 45(13), e1767232024. mla: Stratigi, Aikaterini, et al. “Neuroendocrine Control of Synaptic Transmission by PHAC-1 in C. Elegans.” Journal of Neuroscience, vol. 45, no. 13, e1767232024, Society for Neuroscience, 2025, doi:10.1523/JNEUROSCI.1767-23.2024. short: A. Stratigi, M. Soler-García, M. Krout, S. Shukla, M. de Bono, J.E. Richmond, P. Laurent, Journal of Neuroscience 45 (2025). date_created: 2025-04-06T22:01:32Z date_published: 2025-03-26T00:00:00Z date_updated: 2026-07-28T11:30:41Z day: '26' ddc: - '570' department: - _id: MaDe doi: 10.1523/JNEUROSCI.1767-23.2024 external_id: isi: - '001460952700001' pmid: - '39919830' file: - access_level: open_access checksum: 7befc0168f4cd5bd2b0fcff9e2a94784 content_type: application/pdf creator: dernst date_created: 2025-04-07T11:57:19Z date_updated: 2025-09-27T22:30:02Z embargo: 2025-09-27 file_id: '19525' file_name: 2025_JourNeuroscience_Stratigi.pdf file_size: 3111735 relation: main_file file_date_updated: 2025-09-27T22:30:02Z fulldoi: https://doi.org/10.1523/JNEUROSCI.1767-23.2024 has_accepted_license: '1' intvolume: ' 45' isi: 1 issue: '13' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Journal of Neuroscience publication_identifier: eissn: - 1529-2401 issn: - 0270-6474 publication_status: published publisher: Society for Neuroscience quality_controlled: '1' scopus_import: '1' status: public title: Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans 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: '2025' ... --- OA_place: publisher _id: '18871' abstract: - lang: eng text: "\"Can we do this with a new type of computer - a quantum computer?\". This famous\r\nquotation of the brilliant Richard Feynman within a conference talk on \"Simulating physics\r\nwith computers.” is often reverently praised as the origin of the field of quantum computing.\r\nThe idea was to use quantum mechanical systems itself to simulate \"Nature\", which is\r\ninherently quantum mechanical. Now, 43 years later, the theoretical framework of how such\r\na computer can operate has been developed. Two main important concepts for a potential\r\nquantum supremacy, superposition and entanglement, have been exploited to design quantum\r\nalgorithms to significantly speed up certain tasks. Yet, the specific hardware implementation\r\nis still far from being certain, in fact the race between the most promising platforms such as\r\nsuperconducting qubits, bosonic codes, cold atoms, trapped ions, optical computing as well\r\nas spin qubits has recently intensified. If one also includes the most mature applications of\r\nquantum communication technologies, secure quantum key distribution and quantum random\r\nnumber generators, as part of a quantum information technology ecosystem, we are confronted\r\nwith a plethora of different materials, concepts, and also operation frequencies. While\r\nsuperconducting qubits, bosonic codes and spin qubits work in the regime of approximately 5\r\nGHz and are controlled by electrical fields, trapped ions, cold atoms, and optical quantum\r\ncomputing operate with light in the infrared or visible range.\r\nConsequently, a quantum frequency converter or microwave-optic transducer is required\r\nto interface the different frequency domains or establish a long-range network connection\r\nwith suitable telecom fibers. In fact, the combination of different frequency regimes is also\r\nan essential part in our classical modern communication network, where computations are\r\nperformed in electrical circuits and the information exchange over longer distances happens\r\nvia optical fibers. However, the specific challenges specific to building a quantum computer,\r\nalso apply to the development of such a quantum frequency transducer: 1) As we deal with\r\nsingle excitations as the carrier of information, i.e. the smallest possible quantity, the signal\r\ncan easily be corrupted by other noise sources which needs to be avoided by all means. This\r\nis also the reason why microwave quantum computers operate at temperature environments\r\nclose to zero temperature (< 0.1 Kelvin) to avoid corruption by thermal noise. 2) The\r\nfrequency interface generally needs to preserve the phase of the signal as an essential part\r\nof the quantum state. And 3) Quantum signals cannot be copied which would be a typical\r\nstrategy to account for errors in classical computers. And finally, there is a challenge specific to\r\nmicrowave-optic transducers: While quantum computers are operating in one specific frequency\r\ndomain, microwave-optic transducers combine microwave and optical fields in one device.\r\nThis results in the particular challenge that high-energy optical radiation, which is usually\r\nwell-shielded from superconducting microwave quantum processors, are now an essential part\r\nof the device. The concomitant optical radiation in the operating transducer will inevitably\r\nhave a detrimental effect on the superconducting microwave components. Together with the\r\nrequirement of minimal background noise for quantum-limited operation as described above,\r\nv\r\nheating from the absorption of optical photons within the same device where single microwave\r\nexcitations are processed forms a formidable challenge.\r\nThis thesis aims to address this challenge by developing microwave-optic transducers where\r\nthe impact of optical absorption on superconducting circuits in general and superconducting\r\nqubits specifically can be mitigated. In our first approach, we developed a compact device\r\nwith optimized interaction strengths between the different frequency domains. This minimizes\r\nthe optical powers used for transducer operation and thus the optical absorption heating. This\r\nwork was - to the best of our knowledge - the first comprehensive noise study, in an integrated\r\nmicrowave-optic transducer. Unfortunately, we saw that the optical absorption heating added\r\nnoise way above a single excitation. Consequently, a potential quantum signal would have\r\nbeen buried in the noise, added by the transduction.\r\nBuilding on this insight, we utilized a three-dimensional microwave-optic transducer instead\r\nof an integrated device. The larger heat capacity of the macroscopic device with a size\r\nof a few millimeters can absorb a larger fraction of the optical heating before it increases\r\nthe temperature of the device. This allowed us to interface the transducer directly with a\r\nsuperconducting qubit to readout the qubit state in a novel all-optical manner. We showed\r\nthat the microwave-optic transducer can be operated in a regime in which optical fields don’t\r\nharm the sensitive qubit. This is an important prerequisite for the operation of microwave-optic\r\ntransducers in conjunction with microwave quantum processors and brings the integration and\r\nseamless orchestration of different frequency components in a quantum network a step closer.\r\n" acknowledged_ssus: - _id: SSU - _id: M-Shop - _id: NanoFab acknowledgement: "This work was supported by the European Research Council under grant agreement no. 758053\r\n(ERC StG QUNNECT) and the European Union’s Horizon 2020 research, innovation program\r\nunder grant agreement no. 899354 (FETopen SuperQuLAN) and the Austrian Science Fund\r\n(FWF) through BeyondC (F7105). I want to acknowledge generous support from the Austrian\r\nAcademy of Sciences from a DOC [Doctoral program of the Austrian Academy of Sciences]\r\nfellowship (no. 25129).\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 citation: ama: Arnold GM. Microwave-optic interconnects for superconducting circuits. 2025. doi:10.15479/at:ista:18871 apa: Arnold, G. M. (2025). Microwave-optic interconnects for superconducting circuits. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18871 chicago: Arnold, Georg M. “Microwave-Optic Interconnects for Superconducting Circuits.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/at:ista:18871. ieee: G. M. Arnold, “Microwave-optic interconnects for superconducting circuits,” Institute of Science and Technology Austria, 2025. ista: Arnold GM. 2025. Microwave-optic interconnects for superconducting circuits. Institute of Science and Technology Austria. mla: Arnold, Georg M. Microwave-Optic Interconnects for Superconducting Circuits. Institute of Science and Technology Austria, 2025, doi:10.15479/at:ista:18871. short: G.M. Arnold, Microwave-Optic Interconnects for Superconducting Circuits, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-01-24T10:28:39Z date_published: 2025-01-24T00:00:00Z date_updated: 2026-04-16T12:20:43Z day: '24' ddc: - '530' degree_awarded: PhD department: - _id: JoFi - _id: GradSch doi: 10.15479/at:ista:18871 ec_funded: 1 file: - access_level: closed checksum: 71872702e8f46c275eaea44efc4d304f content_type: application/x-zip-compressed creator: cchlebak date_created: 2025-01-29T08:38:08Z date_updated: 2026-01-29T23:30:03Z embargo_to: open_access file_id: '18946' file_name: tex for upload.zip file_size: 18856130 relation: source_file - access_level: open_access checksum: dfaa06591970f4bff163705802fad56d content_type: application/pdf creator: cchlebak date_created: 2025-01-29T08:38:34Z date_updated: 2026-01-29T23:30:03Z embargo: 2026-01-29 file_id: '18947' file_name: ISTThesisGA2022_final.pdf file_size: 17344760 relation: main_file file_date_updated: 2026-01-29T23:30:03Z fulldoi: https://doi.org/10.15479/at:ista:18871 has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '135' project: - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 9B868D20-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '899354' name: Quantum Local Area Networks with Superconducting Qubits - _id: 2671EB66-B435-11E9-9278-68D0E5697425 name: Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6609' relation: part_of_dissertation status: public - id: '8529' relation: part_of_dissertation status: public - id: '18953' relation: part_of_dissertation status: public - id: '10924' relation: part_of_dissertation status: public - id: '9114' relation: part_of_dissertation status: public - id: '13200' 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: Microwave-optic interconnects for superconducting circuits 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_embargo: '6' OA_place: publisher _id: '19745' abstract: - lang: eng text: "Cell migration is a crucial process in animal development and maintenance. It is incredibly\r\nheterogeneous, with different cell types utilizing fundamentally distinct migration strategies.\r\nThe strategies also depend on the cellular microenvironment, where cells can switch between\r\nmigration modes as they encounter new environmental cues. In this thesis, we investigated\r\nhow dendritic cells adapt their migration strategy when encountering geometrically,\r\nmechanically and chemically distinct environments.\r\nWhen dendritic cells are embedded in a homogeneous fibrous network, they migrate in a fast\r\nand directional amoeboid manner. In this migration strategy, extracellular proteolysis and\r\nintegrin-mediated adhesions are dispensable. Instead, the cells use topography of the\r\nenvironment to propel their cell body forward. To migrate efficiently in the maze of different\r\npore sizes, they position the nucleus ahead of the microtubule organizing center (MTOC) and\r\nuse it to gauge the pores to identify the path of least resistance. Our aim was to identify\r\nwhether dendritic cells adapt their migration strategy when encountering asymmetrical\r\ntransitions into much denser environments with limited choice of large pores. In such invasive\r\ntransitions it is unclear if the cells can cross tight pores without the use of adhesions and\r\nextracellular proteolysis and whether they maintain the nucleus in the cell front.\r\nUsing various cell migration assays such as fibrous 3D collagen gels, geometrically defined\r\nmicrochannels with constrictions and simplistic under agarose migration assay, we provide\r\na comprehensive characterization of invasive migration of dendritic cells. We show that\r\nduring invasion the cells stall and stretch, reflecting the difficulty to translocate the bulky cell\r\nbody into the dense environment. In collagen gels, we show that dendritic cells can invade\r\nwithout proteolysis and adhesions. Instead, they utilize contractility, which can lead to largescale collagen compressions. During invasion, the nucleus stalls at tight constrictions, leading\r\nto a transient organelle reorientation. To resolve the stalling, upregulated rear contractility is\r\nrequired. This contractile force is simultaneously necessary for reverting the nucleus back to\r\nthe cell front after invasion and maintaining this positioning during permissive migration.\r\nA functional role of the reorientation was uncovered in the first collaboration project.\r\nA prominent central actin pool was identified around the MTOC, especially pronounced in\r\ndense and compressive environments. The actin pool was shown to generate pushing forces\r\nto dilate the space for cell translocation. These forces are only necessary in non-permissive\r\nenvironments, where the nucleus reorients to the cell rear, allowing the actin pool to\r\ngenerate space. In permissive environments where space generation is dispensable, the\r\nMTOC is located behind the nucleus and the actin cloud has reduced intensity, allowing more\r\nactin to be incorporated into the lamellipodium, speeding up migration.\r\nIn the second collaboration project, we investigated the effects of distinct chemical\r\nenvironments on dendritic cell migration. The strikingly persistent migration of these cells\r\nwas explained by their ability to modulate and even self-generate chemokine gradients. This\r\nallows the cells to migrate faster and more persistent in uniform chemokine fields compared\r\nto imposed chemokine gradients. The chemokine receptor CCR7 was identified as a crucial\r\nplayer in this process, both sensing the signal and internalizing the chemokine to create a sink." acknowledgement: "This project has received funding from the Austrian Science Fund (FWF) via the doctorate\r\ncollege DK NanoCell and from the European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Nikola full_name: Canigova, Nikola id: 3795523E-F248-11E8-B48F-1D18A9856A87 last_name: Canigova orcid: 0000-0002-8518-5926 citation: ama: Canigova N. Adaptive strategies of dendritic cell migration in response to environmental cues. 2025. doi:10.15479/AT-ISTA-19745 apa: Canigova, N. (2025). Adaptive strategies of dendritic cell migration in response to environmental cues. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19745 chicago: Canigova, Nikola. “Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19745. ieee: N. Canigova, “Adaptive strategies of dendritic cell migration in response to environmental cues,” Institute of Science and Technology Austria, 2025. ista: Canigova N. 2025. Adaptive strategies of dendritic cell migration in response to environmental cues. Institute of Science and Technology Austria. mla: Canigova, Nikola. Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19745. short: N. Canigova, Adaptive Strategies of Dendritic Cell Migration in Response to Environmental Cues, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-05-26T08:49:00Z date_published: 2025-05-27T00:00:00Z date_updated: 2026-06-18T17:34:48Z day: '27' ddc: - '570' degree_awarded: PhD department: - _id: MiSi - _id: GradSch doi: 10.15479/AT-ISTA-19745 ec_funded: 1 file: - access_level: closed checksum: 1a2d1525d19347fbb879ef57c02951bf content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2025-05-28T07:38:17Z date_updated: 2025-11-27T23:30:02Z embargo_to: open_access file_id: '19748' file_name: NikolaCanigova_Thesis_final.docx file_size: 103879193 relation: source_file - access_level: open_access checksum: c1d8f9a40a8e19fcf895373f4b773a46 content_type: application/pdf creator: cchlebak date_created: 2025-05-28T07:39:53Z date_updated: 2025-11-27T23:30:02Z embargo: 2025-11-27 file_id: '19749' file_name: NikolaCanigova_Thesis_final_PDFA2a_fixed.pdf file_size: 194530600 relation: main_file file_date_updated: 2025-11-27T23:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19745 has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '133' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 265E2996-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W01250-B20 name: Nano-Analytics of Cellular Systems publication_identifier: isbn: - 978-3-99078-058-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14274' relation: part_of_dissertation status: public status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 title: Adaptive strategies of dendritic cell migration in response to environmental cues type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '19431' abstract: - lang: eng text: "Gene expression is crucial for cell differentiation, development and survival of\r\norganisms. It consists of several steps, starting with transcription that is mediated by\r\nRNA polymerases. These are protein machineries transcribing and producing different\r\ntypes of RNAs. Although, the individual steps of transcription by RNA polymerase II\r\n(Pol II) as well as the structure of Pol II has been extensively studied, surprisingly,\r\nthere is still little known about its regulation and assembly in cytoplasm. Among the\r\nproteins that are important in biogenesis of Pol II are RNA polymerase II associating\r\nproteins (RPAP) and small GPN-loop GTPases (GPN). Both of these protein groups\r\nwere shown to take essential part in assembly of Pol II.\r\nThe aim of this project was to deepen our knowledge in regulation of Pol II in\r\nthe cytoplasm as well as the proteins involved in this process. Techniques of structural\r\nbiology, biochemistry and cell biology were employed to study and characterize cytoplasmic Pol II and its interacting partners.\r\nThis study shows for the first time the structure of cytoplasmic Pol II at high\r\nresolution. The structure also reveals proteins interacting with Pol II in cytoplasm,\r\nnamely GDOWN1, RPAP2. Comparing the structure of cytoplasmic Pol II with transcribing Pol II revealed striking difference in clamp region that is not in closed state.\r\nFurthermore, GDOWN1 and RPAP2 make steric clashes with various transcription\r\nfactors bound to Pol II during different stages of transcription. Even though GPN1 and\r\nGPN3 proteins were not resolved in the cytoplasmic Pol II structure, they are part of\r\nthe complex and their interaction with Pol II was confirmed in vitro. RPAP2 stabilizes\r\nthese proteins on Pol II and several experiments suggest that they interact with the\r\nclamp region. In addition, GDOWN1, RPAP2 and GPNs might keep clamp in open or\r\npartially open state. Based on these results I propose a novel model of regulation of\r\nPol II in cytoplasm. GDOWN1, RPAP2, GPN1 and GPN3 bind to Pol II in cytoplasm\r\nand doing so they can prevent pre-mature binding of DNA or RNA and different transcription factors to Pol II in cytoplasm or before engaging in transcription nucleus.\r\nThis research contributes to the current knowledge of molecular mechanisms\r\nof Pol II regulation in cytoplasm." acknowledged_ssus: - _id: LifeSc - _id: EM-Fac - _id: ScienComp acknowledgement: 'I would also like to acknowledge the ISTA Facilities: Lab Support Facility, Protein Services and Electron Microscopy Facility (EMF) and Scientific Computing. EMF for their support during data collections and troubleshooting, especially Valentin. Scientific Computing for solving quickly any issues related with cluster.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Annamaria full_name: Hlavata, Annamaria id: 36062FEC-F248-11E8-B48F-1D18A9856A87 last_name: Hlavata citation: ama: Hlavata A. Regulation of Cytoplasmic RNA Polymerase II. 2025. doi:10.15479/10.15479/AT-ISTA-19431 apa: Hlavata, A. (2025). Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria. https://doi.org/10.15479/10.15479/AT-ISTA-19431 chicago: Hlavata, Annamaria. “Regulation of Cytoplasmic RNA Polymerase II.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/10.15479/AT-ISTA-19431. ieee: A. Hlavata, “Regulation of Cytoplasmic RNA Polymerase II,” Institute of Science and Technology Austria, 2025. ista: Hlavata A. 2025. Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria. mla: Hlavata, Annamaria. Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria, 2025, doi:10.15479/10.15479/AT-ISTA-19431. short: A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-03-20T12:52:47Z date_published: 2025-03-20T00:00:00Z date_updated: 2026-04-07T11:46:32Z day: '20' ddc: - '572' degree_awarded: PhD department: - _id: GradSch - _id: CaBe doi: 10.15479/10.15479/AT-ISTA-19431 file: - access_level: closed checksum: b7ddf424ffe95f8c767c53c8bb62d4f3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ahlavata date_created: 2025-03-24T12:48:36Z date_updated: 2026-03-20T23:30:04Z embargo_to: open_access file_id: '19448' file_name: PhD_Thesis_Hlavata_final_submission.docx file_size: 23506747 relation: source_file - access_level: open_access checksum: 6c5a59c9bac467c3d0b3ffb8ea6d9fd4 content_type: application/pdf creator: ahlavata date_created: 2025-03-24T12:51:10Z date_updated: 2026-03-20T23:30:04Z embargo: 2026-03-20 file_id: '19449' file_name: PhD_Thesis_Hlavata_final_submission_update.pdf file_size: 9478591 relation: main_file file_date_updated: 2026-03-20T23:30:04Z fulldoi: https://doi.org/10.15479/10.15479/AT-ISTA-19431 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '83' publication_identifier: eissn: - 2663-337X isbn: - 978-3-99078-055-8 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 title: Regulation of Cytoplasmic RNA Polymerase II type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_type: closed access _id: '19302' abstract: - lang: eng text: "Social interaction networks of insect colonies facilitate efficient information exchange and\r\ndemonstrate adaptive changes to mitigate disease transmission. While circadian rhythms\r\ninfluence individual behaviour, their role in shaping colony-level defences against pathogens\r\nremains unexplored. Here, we investigate whether social networks of the black garden ant,\r\nLasius niger, exhibit circadian rhythms and how these rhythms influence disease vulnerability\r\nwhen colonies are exposed to a pathogen during the day or the night.\r\nWe first establish baseline daily variations in activity and network dynamics in pathogen-free\r\ncolonies, revealing constitutive daily fluctuations in disease susceptibility. Subsequently, we\r\nexamine pathogen-induced changes in sanitary care and network dynamics by exposing\r\nforagers to a natural pathogen (Metarhizium brunneum) during either the day or the night.\r\nIndividual pathogen loads were measured after a nine-hour post-exposure period to evaluate\r\ntransmission outcomes.\r\nOur results demonstrate that diurnal ant colonies maintain robust circadian patterns in network\r\nproperties while flexibly adapting to pathogen exposure. Ants upregulate sanitary care\r\nirrespective of exposure timing, prioritising the protection of the valuable colony centre\r\nconsisting of nurses and the queen. These findings underscore the robustness and adaptability\r\nof ant colonies in balancing circadian rhythms with effective social immune responses." acknowledged_ssus: - _id: LifeSc acknowledgement: Thank you to the Lab Support Facility at ISTA. Thank you to the European Research Council (ERC) for their funding under the European Union’s Horizon 2020 research and innovation program (ERC Consolidator Grant EPIDEMICSonCHIP, No. 771402, to Sylvia Cremer, and ERC Starting Grant DISEASE, No. 802628, to Nathalie Stroeymeyt). alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Linda full_name: Sartoris, Linda id: 2B9284CA-F248-11E8-B48F-1D18A9856A87 last_name: Sartoris citation: ama: Sartoris L. The effect of circadian rhythm on organisational immunity of ant colonies. 2025. doi:10.15479/AT-ISTA-19302 apa: Sartoris, L. (2025). The effect of circadian rhythm on organisational immunity of ant colonies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19302 chicago: Sartoris, Linda. “The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19302. ieee: L. Sartoris, “The effect of circadian rhythm on organisational immunity of ant colonies,” Institute of Science and Technology Austria, 2025. ista: Sartoris L. 2025. The effect of circadian rhythm on organisational immunity of ant colonies. Institute of Science and Technology Austria. mla: Sartoris, Linda. The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19302. short: L. Sartoris, The Effect of Circadian Rhythm on Organisational Immunity of Ant Colonies, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-03-06T12:16:54Z date_published: 2025-02-24T00:00:00Z date_updated: 2026-03-02T23:31:14Z day: '24' ddc: - '577' degree_awarded: PhD department: - _id: GradSch - _id: SyCr doi: 10.15479/AT-ISTA-19302 ec_funded: 1 file: - access_level: closed checksum: 7e9466dcf3681454211b74b5107e9f7b content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lsartori date_created: 2025-03-07T10:16:11Z date_updated: 2026-02-23T23:30:03Z embargo_to: open_access file_id: '19310' file_name: Thesis_Linda_Sartoris.docx file_size: 7129583 relation: source_file - access_level: closed checksum: 2ccfcf32f0590bb0ec1a488e606a73f5 content_type: application/pdf creator: lsartori date_created: 2025-03-11T10:42:20Z date_updated: 2026-03-02T23:31:13Z description: for printing purposes only embargo_to: open_access file_id: '19384' file_name: thesis_Sartoris_for_print.pdf file_size: 3199703 relation: other - access_level: open_access checksum: 1d1f3c1279065b1a7f407ff6d1ee1503 content_type: application/pdf creator: lsartori date_created: 2025-03-11T10:52:00Z date_updated: 2026-02-23T23:30:03Z embargo: 2026-02-23 file_id: '19385' file_name: Thesis_Linda_Sartoris.pdf file_size: 3183186 relation: main_file file_date_updated: 2026-03-02T23:31:13Z fulldoi: https://doi.org/10.15479/AT-ISTA-19302 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '02' oa: 1 oa_version: Published Version page: '85' project: - _id: 2649B4DE-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771402' name: Epidemics in ant societies on a chip publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 title: The effect of circadian rhythm on organisational immunity of ant colonies 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: '2025' ... --- OA_embargo: 6 months OA_place: publisher _id: '19456' abstract: - lang: eng text: "Making decisions requires flexibly adapting to changing environments, a process that\r\ndepends on accurately interpreting current contingencies and integrating them with\r\npast experience. Two brain regions are particularly critical for this process, the medial\r\nprefrontal cortex (mPFC) and the hippocampus. Using contextual information from the\r\nhippocampus, the mPFC selects relevant cognitive frameworks and suppresses\r\nirrelevant ones to guide appropriate actions. Several studies have shown that some\r\nmPFC pyramidal neurons become spatially tuned when spatial information is required\r\nto guide goal-directed behavior. However, the role of prefrontal spatial representations\r\nin learning and decision making is not well understood. This work aims to characterize\r\nthe role of mPFC spatial tuning in supporting a contextual association task. Rats were\r\ntrained to learn two cue–location associations on a radial arm maze over multiple days,\r\nwhile we simultaneously recorded from dorsal CA1 of the hippocampus and the\r\nprelimbic area of the mPFC. We describe a subset of spatially tuned hippocampal and\r\nprefrontal pyramidal neurons that “flicker” between multiple spatial representations on\r\ndifferent trials, suggesting dynamic, context-dependent coding. This flickering may\r\nprovide a substrate for how the network reorganizes in response to task demands,\r\nlikely by enabling the flexible evaluation of competing representations. " acknowledged_ssus: - _id: PreCl - _id: Bio - _id: LifeSc - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andrea D full_name: Cumpelik, Andrea D id: 3F158B32-F248-11E8-B48F-1D18A9856A87 last_name: Cumpelik orcid: 0000-0003-1727-6612 citation: ama: Cumpelik AD. The role of prefrontal spatial coding in supporting a contextual association task. 2025. doi:10.15479/AT-ISTA-19456 apa: Cumpelik, A. D. (2025). The role of prefrontal spatial coding in supporting a contextual association task. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19456 chicago: Cumpelik, Andrea D. “The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19456. ieee: A. D. Cumpelik, “The role of prefrontal spatial coding in supporting a contextual association task,” Institute of Science and Technology Austria, 2025. ista: Cumpelik AD. 2025. The role of prefrontal spatial coding in supporting a contextual association task. Institute of Science and Technology Austria. mla: Cumpelik, Andrea D. The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19456. short: A.D. Cumpelik, The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-03-25T11:22:38Z date_published: 2025-02-18T00:00:00Z date_updated: 2026-04-07T12:37:58Z day: '18' ddc: - '612' degree_awarded: PhD department: - _id: GradSch - _id: JoCs doi: 10.15479/AT-ISTA-19456 file: - access_level: open_access checksum: 1c7573303d8e5f6da3eb03d59055390f content_type: application/pdf creator: acumpeli date_created: 2025-03-25T11:07:55Z date_updated: 2025-09-30T22:30:02Z embargo: 2025-09-30 file_id: '19457' file_name: 2025_Thesis_Cumpelik_corrections_PDFA.pdf file_size: 11869040 relation: main_file - access_level: closed checksum: b93265ebd9a53f7a14100d0d48b4ff5b content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: acumpeli date_created: 2025-03-25T11:08:05Z date_updated: 2025-09-30T22:30:02Z embargo_to: open_access file_id: '19458' file_name: 2025_Thesis_Cumpelik_corrections.docx file_size: 20436467 relation: source_file file_date_updated: 2025-09-30T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19456 has_accepted_license: '1' keyword: - neuroscience - decision making - learning - cognitive flexibility - medial prefrontal cortex - hippocampus - electrophysiology language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '96' publication_identifier: isbn: - 978-3-99078-056-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: The role of prefrontal spatial coding in supporting a contextual association task type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '19993' abstract: - lang: eng text: "Ants are frequently challenged by different pathogens, which they counter with\r\nindividual and collective responses. Usually, the pathogens like fungi or viruses are\r\nsolitary and passive pathogens transmitted from host to host. Here, we use a nematobacterial pathogen complex to study worm-borne disease in black garden ants. These\r\nentomopathogenic nematodes are active parasites with an own behavior and chasing\r\npray.\r\nIn the first chapter, we investigated the basic biology of the host-pathogen relationship.\r\nWe tested different ant life stages and found that adult ants display defense behaviors\r\nand are generally resistant to nematode infection, whereas brood is highly susceptible.\r\nIn the case of worker pupae, we found a slight protective effect of the cocoon. When\r\nlarvae are accompanied by adults, meaning a queen or a group of workers, survival is\r\nsignificantly enhanced. Moreover, we found that nematodes can transmit from infected\r\ncadavers to healthy worker larvae, confirming a transmissible disease in ants. Again,\r\nworker presence significantly reduces transmission risk. In the end, we were also able\r\nto disentangle the pathogen system and investigate the pathogenic effect of the\r\nbacterial and nematode components.\r\nIn the second chapter, we studied the effect of multiple infections in adult queens and\r\nqueen larvae. By multiple exposures in the mode of coinfection and superinfections,\r\nwe wanted to assess the detrimental effect of combined fungal and nematode\r\nexposure to better understand how the pathogens interact with each other in an ant\r\nhost. We found instances where combined exposure lead to higher mortality in a given\r\ntime frame in both, adult queens and queen larvae.\r\nOverall entomopathogenic nematodes are a promising model to study worm infections\r\nin ants which extend our knowledge on collective disease defense." acknowledged_ssus: - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Florian full_name: Strahodinsky, Florian id: 979E35EE-C996-11E9-8C7C-CF13E6697425 last_name: Strahodinsky citation: ama: Strahodinsky F. Social immunity in a tri-partite host-pathogen relationship. 2025. doi:10.15479/AT-ISTA-19993 apa: Strahodinsky, F. (2025). Social immunity in a tri-partite host-pathogen relationship. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19993 chicago: Strahodinsky, Florian. “Social Immunity in a Tri-Partite Host-Pathogen Relationship.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19993. ieee: F. Strahodinsky, “Social immunity in a tri-partite host-pathogen relationship,” Institute of Science and Technology Austria, 2025. ista: Strahodinsky F. 2025. Social immunity in a tri-partite host-pathogen relationship. Institute of Science and Technology Austria. mla: Strahodinsky, Florian. Social Immunity in a Tri-Partite Host-Pathogen Relationship. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19993. short: F. Strahodinsky, Social Immunity in a Tri-Partite Host-Pathogen Relationship, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-07-10T14:12:20Z date_published: 2025-07-11T00:00:00Z date_updated: 2026-04-07T12:39:58Z day: '11' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SyCr doi: 10.15479/AT-ISTA-19993 file: - access_level: closed checksum: df3a02f0d937ea9a3d79d5fb94fff097 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: fstrahod date_created: 2025-07-14T13:18:37Z date_updated: 2026-01-15T23:30:03Z embargo_to: open_access file_id: '20021' file_name: Thesis_Florian_Strahodinsky_DOCX.docx file_size: 9857392 relation: source_file - access_level: open_access checksum: 7164c21fe1946e839f7b8acd255ce803 content_type: application/pdf creator: fstrahod date_created: 2025-07-14T13:18:38Z date_updated: 2026-01-15T23:30:03Z embargo: 2026-01-15 file_id: '20022' file_name: Thesis_Florian_Strahodinsky_PDF.pdf file_size: 6439602 relation: main_file file_date_updated: 2026-01-15T23:30:03Z fulldoi: https://doi.org/10.15479/AT-ISTA-19993 has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '138' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 title: Social immunity in a tri-partite host-pathogen relationship tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_embargo: '12' OA_place: publisher _id: '19722' abstract: - lang: eng text: "As root epidermal cells progress from a phase of elongation to differentiation, their\r\ncortical microtubule (MT) arrays exhibit a transversal-to-longitudinal reorientation. The\r\nhormone cytokinin, a key regulator of root development, facilitates these cytoskeletal\r\nchanges. However, the molecular mechanisms underlying hormone-mediated MT\r\nreorientation during root development are still unknown. Here, we find that MT reorientation\r\nin root cells differs from the existing model in hypocotyl cells, as it does not rely on MT plusend rescue. We show that cytokinin facilitates MT array reorganization during cell\r\ndifferentiation by promoting katanin’s (KTN1) severing activity, and by modulating KTN1’s\r\nassociation with microtubules. Cytokinin regulates SPIRAL2 (SPR2) in a phosphorylationdependent manner, directing its localization to, and stabilization of, the new MT minus-end\r\ncreated by katanin-mediated severing at crossovers. Notably, our findings suggest that\r\ndynamic and reversible phosphorylation at S579 of SPR2 is crucial for the proper functioning\r\nof the MT severing machinery. Finally, we identify MAP65-1 and CLASP as additional targets\r\nof cytokinin-dependent phosphoregulation. Cytokinin treatment decreases MT-MAP65-1\r\nassociation in elongating cells, likely to expose MTs to KTN1-mediated severing, whereas it\r\nincreases MT-CLASP association to stabilize the growing plus-end. In this way, cytokinin drives\r\nMT reorganization during cell development by simultaneously modulating several\r\nmicrotubule-associated proteins. These results reveal key molecular players in hormonemediated cytoskeletal regulation, and highlight protein phosphorylation as a powerful tool\r\nduring this process." acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: Special thanks to the Plant Facility. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Syamala full_name: Inumella, Syamala id: F8660870-D756-11E9-98C5-34DFE5697425 last_name: Inumella orcid: 0009-0002-5890-120X citation: ama: Inumella S. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. 2025. doi:10.15479/AT-ISTA-19722 apa: Inumella, S. (2025). Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19722 chicago: Inumella, Syamala. “Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19722. ieee: S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025. ista: Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria. mla: Inumella, Syamala. Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19722. short: S. Inumella, Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-05-23T15:21:29Z date_published: 2025-05-23T00:00:00Z date_updated: 2026-06-12T08:34:29Z day: '23' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-19722 file: - access_level: open_access checksum: 847ec70b2e40f50e0ddc7b8da201d52c content_type: application/pdf creator: sinumell date_created: 2025-05-28T11:59:11Z date_updated: 2026-05-23T22:30:02Z embargo: 2026-05-23 file_id: '19757' file_name: Final Thesis_Syamala Inumella.pdf file_size: 8292363 relation: main_file - access_level: closed checksum: 17cdffdae13a5f65bdad9c84e9e0e3bd content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: sinumell date_created: 2025-05-28T11:59:11Z date_updated: 2026-05-23T22:30:02Z embargo_to: open_access file_id: '19758' file_name: Final Thesis_Syamala Inumella.docx file_size: 7145703 relation: source_file file_date_updated: 2026-05-23T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-19722 has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '113' publication_identifier: isbn: - 978-3-99078-059-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria 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: Molecular mechanisms of microtubule reorganization in elongating root epidermal cells type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20470' abstract: - lang: eng text: "Systems design has classically relied on composable systems, in which individual subsystems\r\nhave defined inputs, outputs, and interactions with each other; however, attempts at\r\ndesigning complex systems in synthetic biology has often run in to issues of crosstalk and\r\ninterference, given that these systems must function within the context of the host. In nature,\r\nmobile genetic elements are systems that have evolved to travel between hosts, and thus\r\nappear to be a good candidate with which to evaluate composability. Selecting temperate\r\nphages as a model system, I used mathematical modelling to identify sources of information\r\nthat temperate phages should respond to. I found that essential proteins of temperate phages\r\ncan interfere with potential hosts, indicating limitations to composability. I also designed a\r\nlysogeny reporter construct and characterize its behavior across various laboratory and\r\nenvironmental strains, finding differences in phage lambda lysogens, and potential\r\ninterference from prophages that already exist within the environmental strains. Although\r\nthe information gathered is not conclusive, it suggests that composability is not a key property\r\nof temperate phages, implying that biological systems may not be composable, and that other\r\nsystem design principles should be considered when designing synthetic systems." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bryan full_name: Wu, Bryan id: 3C521EBA-F248-11E8-B48F-1D18A9856A87 last_name: Wu citation: ama: Wu B. An examination on phages as a naturally composable system. 2025. doi:10.15479/AT-ISTA-20470 apa: Wu, B. (2025). An examination on phages as a naturally composable system. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20470 chicago: Wu, Bryan. “An Examination on Phages as a Naturally Composable System.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20470. ieee: B. Wu, “An examination on phages as a naturally composable system,” Institute of Science and Technology Austria, 2025. ista: Wu B. 2025. An examination on phages as a naturally composable system. Institute of Science and Technology Austria. mla: Wu, Bryan. An Examination on Phages as a Naturally Composable System. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20470. short: B. Wu, An Examination on Phages as a Naturally Composable System, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-15T13:30:21Z date_published: 2025-10-30T00:00:00Z date_updated: 2026-05-06T08:01:28Z day: '30' ddc: - '579' degree_awarded: PhD department: - _id: GradSch - _id: CaGu doi: 10.15479/AT-ISTA-20470 file: - access_level: closed checksum: d32ea83f259f6b0506325cd57b1d44c3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: brwu date_created: 2025-10-21T17:33:27Z date_updated: 2026-04-30T22:30:02Z embargo_to: open_access file_id: '20516' file_name: 2025_Wu_Bryan_Thesis.docx file_size: 10603235 relation: source_file - access_level: open_access checksum: 53590046fd3244c5550b4022282449d2 content_type: application/pdf creator: brwu date_created: 2025-10-21T17:33:26Z date_updated: 2026-04-30T22:30:02Z embargo: 2026-04-30 file_id: '20517' file_name: 2025_Wu_Bryan_Thesis.pdf file_size: 6251936 relation: main_file file_date_updated: 2026-04-30T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20470 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '102' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: An examination on phages as a naturally composable system type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20777' abstract: - lang: eng text: "A major challenge in neuroscience is deciphering how the brain orchestrates behavior in\r\nresponse to changes in environmental conditions. This process is characterized by several\r\nprocessing stages, from perception to the storage of important information. Information\r\nstorage is performed by a memory system implemented through complex networks of highly\r\ninterconnected neurons. The collective operational principles of neuronal networks that support\r\nformation and storage are the main topics of this thesis.\r\nTo investigate the collective dynamics of the hippocampus from the perspective of the brain\r\ncriticality hypothesis, I started by analyzing cascades of neural activity ¯ neuronal avalanches\r\n¯ that have been characterized by the absence of a typical spatial or temporal scale. Measures\r\nderived from neuronal avalanches suggested that during wakefulness the hippocampus operated\r\nfurther away from criticality than during sleep/rest. In addition, neural activity propagated\r\ndifferently in these two brain states, as indicated by different collapses of the avalanche shapes.\r\nNext, the Phenomenological Renormalization Group approach also indicated conceptually\r\nsimilar differences, through the scaling exponent of activity variance α, which was higher during\r\nsleep/rest than during awake. These results confirmed that the activity of the hippocampus\r\nexhibits signatures of criticality and that these signatures change with the state of the brain.\r\nNext, I found that memory retention was predicted by the scaling exponent of activity variance\r\nα. The exponent α measured during the sleep/rest session that followed learning correlated\r\nwith memory retention during the subsequent unrewarded testing session. Moreover, α\r\npredicted performance even when controlled for reactivation that occurs in parallel. Second, α\r\nmeasured in the sleep/rest phase that preceded learning was correlated with the learning speed.\r\nI analyzed distributions of the cells’ characteristic timescale and burstiness. The day-to-day\r\nvariability of these distributions, during sleep/rest that followed learning, correlated with the\r\nscaling exponent of activity variance α, as well as with memory retention. These findings\r\nconfirmed that variance scaling and functional heterogeneity provide behaviorally meaningful\r\nperspectives on hippocampal activity, as they are directly related to memory consolidation.\r\nI further investigated the process of memory acquisition and consolidation between the\r\nhippocampus CA1 and the mEC. During learning, CA1 cells shifted their firing field towards\r\nthe goals, while mEC cells remained mostly stable, shifting their firing fields towards the goals\r\nduring sleep/rest that followed learning. This shift during sleep/rest was supported by the\r\nreactivation process, which occurred in two ways, synchronously with CA1 (during SWRs) and\r\nindependently of the hippocampal SWRs. Both types of reactivation predicted subsequent\r\nmemory retention, as well as the amount of goal-related remapping. Again, the day-to-day\r\nvariability of the distribution of the cell timescales correlated with the goal-related remapping,\r\nin CA1 during the learning session and in mEC during sleep/rest. These results suggest that\r\nin spatial navigation tasks, the functional responsibilities of CA1 and mEC change between\r\nlearning and sleep/rest and that their function benefits from increased functional heterogeneity\r\namong cells.\r\n" acknowledgement: "My work has been funded through the project \"Functional Advantages of Critical Brain\r\nDynamics\" of the ISTA interdisciplinary fund and through the FWF.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Predrag full_name: Zivadinovic, Predrag id: 68AA0E5A-AFDA-11E9-9994-141DE6697425 last_name: Zivadinovic citation: ama: Zivadinovic P. Scale-free activity as a basis for spatial learning and memory in the brain. 2025. doi:10.15479/AT-ISTA-20777 apa: Zivadinovic, P. (2025). Scale-free activity as a basis for spatial learning and memory in the brain. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20777 chicago: Zivadinovic, Predrag. “Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20777. ieee: P. Zivadinovic, “Scale-free activity as a basis for spatial learning and memory in the brain,” Institute of Science and Technology Austria, 2025. ista: Zivadinovic P. 2025. Scale-free activity as a basis for spatial learning and memory in the brain. Institute of Science and Technology Austria. mla: Zivadinovic, Predrag. Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20777. short: P. Zivadinovic, Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain, Institute of Science and Technology Austria, 2025. corr_author: '1' das_tickbox: '1' date_created: 2025-12-10T19:37:41Z date_published: 2025-12-11T00:00:00Z date_updated: 2026-07-24T08:14:37Z day: '11' ddc: - '570' - '539' - '571' degree_awarded: PhD department: - _id: GradSch - _id: JoCs doi: 10.15479/AT-ISTA-20777 doi_confirm: '1' file: - access_level: open_access checksum: aae9d1ed53f7b67f75e289c26a02b72f content_type: application/pdf creator: pzivadin date_created: 2025-12-10T19:28:20Z date_updated: 2026-06-11T22:30:02Z embargo: 2026-06-11 file_id: '20778' file_name: 2025_Zivadinovic_Predrag_PhD_thesis.pdf file_size: 8105379 relation: main_file - access_level: closed checksum: 8a08a3804ce7d9d625fdf1631113da8c content_type: application/zip creator: pzivadin date_created: 2025-12-10T19:28:10Z date_updated: 2026-06-11T22:30:02Z embargo_to: open_access file_id: '20779' file_name: 2025_Zivadinovic_Predrag_PhD_thesis_source.zip file_size: 8512240 relation: source_file file_date_updated: 2026-06-11T22:30:02Z fulldoi: https://doi.org/10.15479/AT-ISTA-20777 has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '104' project: - _id: eb943429-77a9-11ec-83b8-9f471cdf5c67 grant_number: M03318 name: Functional Advantages of Critical Brain Dynamics publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: Scale-free activity as a basis for spatial learning and memory in the brain type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- APC_amount: 7068 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19424' abstract: - lang: eng text: "Hole spin qubits are rapidly emerging as the workhorse of semiconducting quantum processors because of their large spin-orbit interaction, enabling fast all-electric operations at low power. However, spin-orbit interaction also causes non-uniformities in devices, resulting in locally varying qubit energies and site-dependent anisotropies. While these anisotropies can be used to drive single-spins, if not properly harnessed, they can hinder the path toward large-scale quantum processors. Here, we report on microwave-driven singlet-triplet qubits in planar germanium and use them to investigate the anisotropy of two spins in a double quantum dot. We show two distinct operating regimes depending on the magnetic field direction. For in-plane fields, the two spins are largely anisotropic, and electrically tunable, which enables to measure all the available transitions; coherence times exceeding 3 $\\mu$s are extracted. For out-of-plane fields, they have an isotropic response but preserve the substantial energy difference required to address the singlet-triplet qubit. Even in this field direction, where the qubit lifetime\r\nis strongly affected by nuclear spins, we find 400 ns coherence times. Our work adds a valuable tool to investigate and harness the anisotropy of spin qubits and can be implemented in any large-scale NxN device, facilitating the path towards scalable quantum processors." acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: "We thank A. Crippa for helpful discussions. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation, the HORIZON-RIA 101069515 project and the FWF Projects with DOI:10.55776/F86 and DOI:10.55776/I5060. M.R.-R. acknowledges support from the Netherlands Organization of Scientific Research (NWO) under Veni grant VI.Veni.212.223. The\r\nResearch of S.B. and M.R.-R. was sponsored in part by the Army Research Office and was accomplished under Award Number: W911NF-23-1-0110. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein." article_number: '3862' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Jaime full_name: Saez Mollejo, Jaime id: e0390f72-f6e0-11ea-865d-862393336714 last_name: Saez Mollejo - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 - first_name: Yona A full_name: Schell, Yona A id: fe39122d-06bb-11ec-a33b-9e22b40e40a5 last_name: Schell - first_name: Josip full_name: Kukucka, Josip id: 3F5D8856-F248-11E8-B48F-1D18A9856A87 last_name: Kukucka - first_name: Stefano full_name: Calcaterra, Stefano last_name: Calcaterra - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Maximilian full_name: Rimbach-Russ, Maximilian last_name: Rimbach-Russ - first_name: Stefano full_name: Bosco, Stefano last_name: Bosco - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Saez Mollejo J, Jirovec D, Schell YA, et al. Exchange anisotropies in microwave-driven singlet-triplet qubits. Nature Communications. 2025;16. doi:10.1038/s41467-025-58969-y apa: Saez Mollejo, J., Jirovec, D., Schell, Y. A., Kukucka, J., Calcaterra, S., Chrastina, D., … Katsaros, G. (2025). Exchange anisotropies in microwave-driven singlet-triplet qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-58969-y chicago: Saez Mollejo, Jaime, Daniel Jirovec, Yona A Schell, Josip Kukucka, Stefano Calcaterra, Daniel Chrastina, Giovanni Isella, Maximilian Rimbach-Russ, Stefano Bosco, and Georgios Katsaros. “Exchange Anisotropies in Microwave-Driven Singlet-Triplet Qubits.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-58969-y. ieee: J. Saez Mollejo et al., “Exchange anisotropies in microwave-driven singlet-triplet qubits,” Nature Communications, vol. 16. Springer Nature, 2025. ista: Saez Mollejo J, Jirovec D, Schell YA, Kukucka J, Calcaterra S, Chrastina D, Isella G, Rimbach-Russ M, Bosco S, Katsaros G. 2025. Exchange anisotropies in microwave-driven singlet-triplet qubits. Nature Communications. 16, 3862. mla: Saez Mollejo, Jaime, et al. “Exchange Anisotropies in Microwave-Driven Singlet-Triplet Qubits.” Nature Communications, vol. 16, 3862, Springer Nature, 2025, doi:10.1038/s41467-025-58969-y. short: J. Saez Mollejo, D. Jirovec, Y.A. Schell, J. Kukucka, S. Calcaterra, D. Chrastina, G. Isella, M. Rimbach-Russ, S. Bosco, G. Katsaros, Nature Communications 16 (2025). corr_author: '1' date_created: 2025-03-19T13:28:12Z date_published: 2025-04-24T00:00:00Z date_updated: 2026-10-29T23:30:46Z day: '24' ddc: - '530' department: - _id: GeKa doi: 10.1038/s41467-025-58969-y external_id: arxiv: - '2408.03224' isi: - '001475587400022' pmid: - '40274808' file: - access_level: open_access checksum: 13fe84cddc9d4e47213bf17acdac70d7 content_type: application/pdf creator: dernst date_created: 2025-05-05T07:08:23Z date_updated: 2025-05-05T07:08:23Z file_id: '19645' file_name: 2025_NatureComm_SaezMollejo.pdf file_size: 1548756 relation: main_file success: 1 file_date_updated: 2025-05-05T07:08:23Z fulldoi: https://doi.org/10.1038/s41467-025-58969-y has_accepted_license: '1' intvolume: ' 16' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452 grant_number: '101069515' name: Integrated Germanium Quantum Technology - _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e grant_number: F8606 name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors' - _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1 grant_number: I05060 name: High impedance circuit quantum electrodynamics with hole spins - _id: 262116AA-B435-11E9-9278-68D0E5697425 name: Hybrid Semiconductor - Superconductor Quantum Devices - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: research_data url: https://ista.ac.at/en/news/the-shadow-of-an-electron/ record: - id: '19409' relation: research_data status: public - id: '19836' relation: dissertation_contains status: public scopus_import: '1' status: public title: Exchange anisotropies in microwave-driven singlet-triplet qubits 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: 16 year: '2025' ...