--- _id: '14628' abstract: - lang: eng text: We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration. acknowledgement: "The authors thank Mina Konaković Luković and Michael Foshey for their early contributions to this project, David Palmer and Paul Zhang for their insightful discussions about minimal surfaces and the CSCM, Julian Panetta for providing the Elastic Textures code, and Hannes Hergeth for his feedback and support. We also thank our user study participants and anonymous reviewers.\r\nThis material is based upon work supported by the National Science Foundation\r\n(NSF) Graduate Research Fellowship under Grant No. 2141064; the MIT Morningside\r\nAcademy for Design Fellowship; the Defense Advanced Research Projects Agency\r\n(DARPA) Grant No. FA8750-20-C-0075; the ERC Consolidator Grant No. 101045083,\r\n“CoDiNA: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena”; and the NewSat project, which is co-funded by the Operational Program for Competitiveness and Internationalisation (COMPETE2020), Portugal 2020, the European Regional Development Fund (ERDF), and the Portuguese Foundation for Science and Technology (FTC) under the MIT Portugal program." article_number: '168' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Liane full_name: Makatura, Liane last_name: Makatura - first_name: Bohan full_name: Wang, Bohan last_name: Wang - first_name: Yi-Lu full_name: Chen, Yi-Lu id: 0b467602-dbcd-11ea-9d1d-ed480aa46b70 last_name: Chen - first_name: Bolei full_name: Deng, Bolei last_name: Deng - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik citation: ama: 'Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 2023;42(5). doi:10.1145/3605389' apa: 'Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., & Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3605389' chicago: 'Makatura, Liane, Bohan Wang, Yi-Lu Chen, Bolei Deng, Chris Wojtan, Bernd Bickel, and Wojciech Matusik. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3605389.' ieee: 'L. Makatura et al., “Procedural metamaterials: A unified procedural graph for metamaterial design,” ACM Transactions on Graphics, vol. 42, no. 5. Association for Computing Machinery, 2023.' ista: 'Makatura L, Wang B, Chen Y-L, Deng B, Wojtan C, Bickel B, Matusik W. 2023. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 42(5), 168.' mla: 'Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics, vol. 42, no. 5, 168, Association for Computing Machinery, 2023, doi:10.1145/3605389.' short: L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023). date_created: 2023-11-29T15:02:03Z date_published: 2023-10-01T00:00:00Z date_updated: 2025-09-09T13:33:58Z day: '01' ddc: - '531' - '006' department: - _id: GradSch - _id: ChWo - _id: BeBi doi: 10.1145/3605389 external_id: isi: - '001086833300007' file: - access_level: open_access checksum: 0192f597d7a2ceaf89baddfd6190d4c8 content_type: application/zip creator: yichen date_created: 2023-11-29T15:16:01Z date_updated: 2023-11-29T15:16:01Z file_id: '14630' file_name: tog-22-0089-File004.zip file_size: 95467870 relation: main_file success: 1 - access_level: open_access checksum: 7fb024963be81933494f38de191e4710 content_type: application/zip creator: yichen date_created: 2023-11-29T15:16:01Z date_updated: 2023-11-29T15:16:01Z file_id: '14631' file_name: tog-22-0089-File005.zip file_size: 103731880 relation: main_file success: 1 - access_level: open_access checksum: b7d6829ce396e21cac9fae0ec7130a6b content_type: application/pdf creator: dernst date_created: 2023-12-04T08:04:14Z date_updated: 2023-12-04T08:04:14Z file_id: '14638' file_name: 2023_ACMToG_Makatura.pdf file_size: 57067476 relation: main_file success: 1 file_date_updated: 2023-12-04T08:04:14Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '5' keyword: - Computer Graphics and Computer-Aided Design language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: ACM Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'Procedural metamaterials: A unified procedural graph for metamaterial design' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 42 year: '2023' ... --- OA_place: publisher _id: '14651' abstract: - lang: eng text: 'For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.' acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X citation: ama: Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651 apa: Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651 chicago: Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14651. ieee: L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023. ista: Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. mla: Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14651. short: L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023. corr_author: '1' date_created: 2023-12-11T19:30:37Z date_published: 2023-12-12T00:00:00Z date_updated: 2026-04-07T13:28:30Z day: '12' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:14651 ec_funded: 1 file: - access_level: open_access checksum: 520bdb61e95e66070e02824947d2c5fa content_type: application/pdf creator: larathoo date_created: 2023-12-13T15:37:55Z date_updated: 2023-12-13T15:37:55Z file_id: '14684' file_name: Phd_Thesis_LA.pdf file_size: 34101468 relation: main_file success: 1 - access_level: closed checksum: d8e59afd0817c98fba2564a264508e5c content_type: application/zip creator: larathoo date_created: 2023-12-13T15:42:23Z date_updated: 2023-12-14T08:58:18Z file_id: '14685' file_name: Phd_Thesis_LA.zip file_size: 31052872 relation: source_file - access_level: closed checksum: 9a778c949932286f4519e1f1fca2820d content_type: application/zip creator: larathoo date_created: 2023-12-11T19:24:59Z date_updated: 2023-12-14T08:58:18Z file_id: '14681' file_name: Supplementary_Materials.zip file_size: 10713896 relation: supplementary_material file_date_updated: 2023-12-14T08:58:18Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '96' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11411' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2023' ... --- _id: '14735' abstract: - lang: eng text: "Scaling blockchain protocols to perform on par with the expected needs of Web3.0 has been proven to be a challenging task with almost a decade of research. In the forefront of the current solution is the idea of separating the execution of the updates encoded in a block from the ordering of blocks. In order to achieve this, a new class of protocols called rollups has emerged. Rollups have as input a total ordering of valid and invalid transactions and as output a new valid state-transition.\r\nIf we study rollups from a distributed computing perspective, we uncover that rollups take as input the output of a Byzantine Atomic Broadcast (BAB) protocol and convert it to a State Machine Replication (SMR) protocol. BAB and SMR, however, are considered equivalent as far as distributed computing is concerned and a solution to one can easily be retrofitted to solve the other simply by adding/removing an execution step before the validation of the input.\r\nThis “easy” step of retrofitting an atomic broadcast solution to implement an SMR has, however, been overlooked in practice. In this paper, we formalize the problem and show that after BAB is solved, traditional impossibility results for consensus no longer apply towards an SMR. Leveraging this we propose a distributed execution protocol that allows reduced execution and storage cost per executor (O(log2n/n)) without relaxing the network assumptions of the underlying BAB protocol and providing censorship-resistance. Finally, we propose efficient non-interactive light client constructions that leverage our efficient execution protocols and do not require any synchrony assumptions or expensive ZK-proofs." acknowledgement: 'Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Christos full_name: Stefo, Christos id: a20e8902-32b0-11ee-9fa8-b23fa638b793 last_name: Stefo - first_name: Zhuolun full_name: Xiang, Zhuolun last_name: Xiang - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias citation: ama: 'Stefo C, Xiang Z, Kokoris Kogias E. Executing and proving over dirty ledgers. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:3-20. doi:10.1007/978-3-031-47754-6_1' apa: 'Stefo, C., Xiang, Z., & Kokoris Kogias, E. (2023). Executing and proving over dirty ledgers. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 3–20). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_1' chicago: Stefo, Christos, Zhuolun Xiang, and Eleftherios Kokoris Kogias. “Executing and Proving over Dirty Ledgers.” In 27th International Conference on Financial Cryptography and Data Security, 13950:3–20. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_1. ieee: C. Stefo, Z. Xiang, and E. Kokoris Kogias, “Executing and proving over dirty ledgers,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 3–20. ista: 'Stefo C, Xiang Z, Kokoris Kogias E. 2023. Executing and proving over dirty ledgers. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 3–20.' mla: Stefo, Christos, et al. “Executing and Proving over Dirty Ledgers.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 3–20, doi:10.1007/978-3-031-47754-6_1. short: C. Stefo, Z. Xiang, E. Kokoris Kogias, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 3–20. conference: end_date: 2023-05-05 location: Bol, Brac, Croatia name: 'FC: Financial Cryptography and Data Security' start_date: 2023-05-01 corr_author: '1' date_created: 2024-01-08T09:17:38Z date_published: 2023-12-01T00:00:00Z date_updated: 2025-09-09T14:07:16Z day: '01' department: - _id: ElKo - _id: GradSch doi: 10.1007/978-3-031-47754-6_1 external_id: isi: - '001150222600001' intvolume: ' 13950' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2022/1554 month: '12' oa: 1 oa_version: Preprint page: 3-20 project: - _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f grant_number: F8512 name: Security and Privacy by Design for Complex Systems publication: 27th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - '9783031477546' eissn: - 0302-9743 isbn: - '9783031477539' issn: - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Executing and proving over dirty ledgers type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 13950 year: '2023' ... --- _id: '15292' abstract: - lang: eng text: We present a rigid body animation technique which prevents solids from interpenetrating, dissipates energy through friction, and propagates shocks through contacts. We employ the Alternating Direction Method of Multipliers (ADMM) to couple non-smooth Coulomb friction with impact propagation, allowing efficient and accurate non-smooth dynamics along with a correct transmission of impacts through assemblies of rigid bodies. We further extend our method to model adhesion, dynamic friction and lubricated contact. acknowledgement: We thank the anonymous reviewers and the members of the Visual Computing Group at ISTA for their helpful comments. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing, and was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA) article_processing_charge: No author: - first_name: Yi-Lu full_name: Chen, Yi-Lu id: 0b467602-dbcd-11ea-9d1d-ed480aa46b70 last_name: Chen - first_name: Mickaël full_name: Ly, Mickaël id: 6340d7f0-b48d-11eb-b10d-b7487e71d9f1 last_name: Ly - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Chen Y-L, Ly M, Wojtan C. Unified Treatment of Contact, Friction and Shock-Propagation in Rigid Body Animation. ACM; 2023. doi:10.1145/3606037.3606836 apa: 'Chen, Y.-L., Ly, M., & Wojtan, C. (2023). Unified treatment of contact, friction and shock-propagation in rigid body animation. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. Los Angeles, CA, United States: ACM. https://doi.org/10.1145/3606037.3606836' chicago: Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. Unified Treatment of Contact, Friction and Shock-Propagation in Rigid Body Animation. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. ACM, 2023. https://doi.org/10.1145/3606037.3606836. ieee: Y.-L. Chen, M. Ly, and C. Wojtan, Unified treatment of contact, friction and shock-propagation in rigid body animation. ACM, 2023. ista: Chen Y-L, Ly M, Wojtan C. 2023. Unified treatment of contact, friction and shock-propagation in rigid body animation, ACM,p. mla: Chen, Yi-Lu, et al. “Unified Treatment of Contact, Friction and Shock-Propagation in Rigid Body Animation.” Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2023, doi:10.1145/3606037.3606836. short: Y.-L. Chen, M. Ly, C. Wojtan, Unified Treatment of Contact, Friction and Shock-Propagation in Rigid Body Animation, ACM, 2023. conference: end_date: 2023-08-06 location: Los Angeles, CA, United States name: 'SCA: Symposium on Computer Animation' start_date: 2023-08-04 corr_author: '1' date_created: 2024-04-03T14:57:23Z date_published: 2023-08-01T00:00:00Z date_updated: 2025-04-14T12:58:27Z day: '01' ddc: - '005' - '531' department: - _id: GradSch - _id: ChWo doi: 10.1145/3606037.3606836 file: - access_level: open_access checksum: 88bdef929ca262ee0eefae0bbc649139 content_type: video/mp4 creator: yichen date_created: 2024-04-03T14:58:24Z date_updated: 2024-04-03T14:58:24Z file_id: '15293' file_name: video.mp4 file_size: 58770929 relation: main_file success: 1 - access_level: open_access checksum: c06881ba847da365a74ac09c953eaffd content_type: application/pdf creator: yichen date_created: 2024-04-03T14:58:23Z date_updated: 2024-04-03T14:58:23Z file_id: '15294' file_name: frictionPoster_clean.pdf file_size: 3951968 relation: main_file success: 1 file_date_updated: 2024-04-03T14:58:24Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: None project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation publication_status: published publisher: ACM related_material: record: - id: '14748' relation: other status: public status: public title: Unified treatment of contact, friction and shock-propagation in rigid body animation type: conference_poster user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- OA_place: repository OA_type: green _id: '20572' abstract: - lang: eng text: "We present an elementary non-recursive formula for the multivariate moments\r\nof the Dirichlet distribution on the standard simplex, in terms of the pattern\r\ninventory of the moments' exponents. We obtain analog formulas for the\r\nmultivariate moments of the Dirichlet-Ferguson and Gamma measures. We further\r\nintroduce a polychromatic analogue of Ewens sampling formula on colored integer\r\npartitions, discuss its relation with suitable extensions of Hoppe's urn model\r\nand of the Chinese restaurant process, and prove that it satisfies an adapted\r\nnotion of consistency in the sense of Kingman." acknowledgement: This research was funded by the Austrian Science Fund (FWF) ESPRIT 208. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. F.Q. gratefully acknowledges support by the Austrian Science Fund (FWF), Project SFB F65. The authors are grateful to Professor Nathanaël Berestycki for several helpful suggestions, and to Nicola Battisti and Dr. Elizabeth Hollwey for enlightening discussions on DNA-methylation. article_number: '2309.11292' article_processing_charge: No arxiv: 1 author: - first_name: Lorenzo full_name: Dello Schiavo, Lorenzo id: ECEBF480-9E4F-11EA-B557-B0823DDC885E last_name: Dello Schiavo orcid: 0000-0002-9881-6870 - first_name: Filippo full_name: Quattrocchi, Filippo id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308 last_name: Quattrocchi orcid: 0009-0000-9773-1931 citation: ama: Dello Schiavo L, Quattrocchi F. Multivariate Dirichlet moments and a polychromatic Ewens sampling formula. arXiv. doi:10.48550/arXiv.2309.11292 apa: Dello Schiavo, L., & Quattrocchi, F. (n.d.). Multivariate Dirichlet moments and a polychromatic Ewens sampling formula. arXiv. https://doi.org/10.48550/arXiv.2309.11292 chicago: Dello Schiavo, Lorenzo, and Filippo Quattrocchi. “Multivariate Dirichlet Moments and a Polychromatic Ewens Sampling Formula.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2309.11292. ieee: L. Dello Schiavo and F. Quattrocchi, “Multivariate Dirichlet moments and a polychromatic Ewens sampling formula,” arXiv. . ista: Dello Schiavo L, Quattrocchi F. Multivariate Dirichlet moments and a polychromatic Ewens sampling formula. arXiv, 2309.11292. mla: Dello Schiavo, Lorenzo, and Filippo Quattrocchi. “Multivariate Dirichlet Moments and a Polychromatic Ewens Sampling Formula.” ArXiv, 2309.11292, doi:10.48550/arXiv.2309.11292. short: L. Dello Schiavo, F. Quattrocchi, ArXiv (n.d.). corr_author: '1' date_created: 2025-10-28T13:13:08Z date_published: 2023-09-20T00:00:00Z date_updated: 2025-11-24T13:53:48Z day: '20' department: - _id: GradSch - _id: JaMa doi: 10.48550/arXiv.2309.11292 external_id: arxiv: - '2309.11292' keyword: - Dirichlet distribution - Ewens sampling formula - Hoppe urn model - colored partitions language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2309.11292 month: '09' oa: 1 oa_version: Preprint project: - _id: 34dbf174-11ca-11ed-8bc3-afe9d43d4b9c grant_number: E208 name: Configuration Spaces over Non-Smooth Spaces - _id: 260482E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F06504 name: Taming Complexity in Partial Differential Systems publication: arXiv publication_status: draft status: public title: Multivariate Dirichlet moments and a polychromatic Ewens sampling formula type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14863' article_number: EGU23-6157 article_processing_charge: No author: - first_name: Andrea full_name: Polesello, Andrea id: 74c777f4-32da-11ee-b498-874db0835561 last_name: Polesello - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Claudia full_name: Pasquero, Claudia last_name: Pasquero - first_name: Agostino N. full_name: Meroni, Agostino N. last_name: Meroni citation: ama: 'Polesello A, Muller CJ, Pasquero C, Meroni AN. Intensification mechanisms of tropical cyclones. In: EGU General Assembly 2023. European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-6157' apa: 'Polesello, A., Muller, C. J., Pasquero, C., & Meroni, A. N. (2023). Intensification mechanisms of tropical cyclones. In EGU General Assembly 2023. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-6157' chicago: Polesello, Andrea, Caroline J Muller, Claudia Pasquero, and Agostino N. Meroni. “Intensification Mechanisms of Tropical Cyclones.” In EGU General Assembly 2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-6157. ieee: A. Polesello, C. J. Muller, C. Pasquero, and A. N. Meroni, “Intensification mechanisms of tropical cyclones,” in EGU General Assembly 2023, Vienna, Austria & Virtual, 2023. ista: Polesello A, Muller CJ, Pasquero C, Meroni AN. 2023. Intensification mechanisms of tropical cyclones. EGU General Assembly 2023. EGU General Assembly, EGU23-6157. mla: Polesello, Andrea, et al. “Intensification Mechanisms of Tropical Cyclones.” EGU General Assembly 2023, EGU23-6157, European Geosciences Union, 2023, doi:10.5194/egusphere-egu23-6157. short: A. Polesello, C.J. Muller, C. Pasquero, A.N. Meroni, in:, EGU General Assembly 2023, European Geosciences Union, 2023. conference: end_date: 2023-04-28 location: Vienna, Austria & Virtual name: EGU General Assembly start_date: 2023-04-23 corr_author: '1' date_created: 2024-01-22T12:08:12Z date_published: 2023-04-13T00:00:00Z date_updated: 2026-07-02T06:42:45Z day: '13' ddc: - '550' department: - _id: CaMu - _id: GradSch doi: 10.5194/egusphere-egu23-6157 file: - access_level: open_access checksum: 8cb88c1bc80ccee328478a62064d98f7 content_type: application/pdf creator: dernst date_created: 2024-01-24T11:19:54Z date_updated: 2024-01-24T11:19:54Z file_id: '14883' file_name: 2023_EGU_Polesello.pdf file_size: 296769 relation: main_file success: 1 file_date_updated: 2024-01-24T11:19:54Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: EGU General Assembly 2023 publication_status: published publisher: European Geosciences Union status: public title: Intensification mechanisms of tropical cyclones tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- OA_place: publisher _id: '12885' abstract: - lang: eng text: 'High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. ' acknowledged_ssus: - _id: EM-Fac - _id: NanoFab alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mariano full_name: Calcabrini, Mariano id: 45D7531A-F248-11E8-B48F-1D18A9856A87 last_name: Calcabrini orcid: 0000-0003-4566-5877 citation: ama: 'Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:10.15479/at:ista:12885' apa: 'Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885' chicago: 'Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.' ieee: 'M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.' ista: 'Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.' mla: 'Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.' short: 'M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.' corr_author: '1' date_created: 2023-05-02T07:58:57Z date_published: 2023-04-28T00:00:00Z date_updated: 2026-07-06T12:16:05Z day: '28' ddc: - '546' - '541' degree_awarded: PhD department: - _id: GradSch - _id: MaIb doi: 10.15479/at:ista:12885 ec_funded: 1 file: - access_level: closed checksum: 9347b0e09425f56fdcede5d3528404dc content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mcalcabr date_created: 2023-05-02T07:43:18Z date_updated: 2023-05-02T07:43:18Z file_id: '12887' file_name: Thesis_Calcabrini.docx file_size: 99627036 relation: source_file - access_level: open_access checksum: 2d188b76621086cd384f0b9264b0a576 content_type: application/pdf creator: mcalcabr date_created: 2023-05-02T07:42:45Z date_updated: 2023-05-02T07:42:45Z file_id: '12888' file_name: Thesis_Calcabrini_pdfa.pdf file_size: 8742220 relation: main_file success: 1 file_date_updated: 2023-05-02T07:43:18Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '82' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-028-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12237' relation: part_of_dissertation status: public - id: '10806' relation: part_of_dissertation status: public - id: '10123' relation: part_of_dissertation status: public - id: '9118' relation: part_of_dissertation status: public - id: '10042' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 title: 'Nanoparticle-based semiconductor solids: From synthesis to consolidation' type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2023' ... --- _id: '14260' abstract: - lang: eng text: "This paper presents Lincheck, a new practical and user-friendly framework for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck provides a simple and declarative way to write concurrent tests: instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. The framework automatically generates a set of concurrent scenarios, examines them using stress-testing or bounded model checking, and verifies that the results of each invocation are correct. Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo the best of our knowledge, Lincheck is the first production-ready tool on the JVM that offers such a simple way of writing concurrent tests, without requiring special skills or expertise. We successfully integrated Lincheck in the development process of several large projects, such as Kotlin Coroutines, and identified new bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is used in most of the synchronization primitives. We believe that Lincheck can significantly improve the quality and productivity of concurrent algorithms research and development and become the state-of-the-art tool for checking their correctness." alternative_title: - LNCS article_processing_charge: Yes (in subscription journal) author: - first_name: Nikita full_name: Koval, Nikita id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87 last_name: Koval - first_name: Alexander full_name: Fedorov, Alexander id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6 last_name: Fedorov - first_name: Maria full_name: Sokolova, Maria last_name: Sokolova - first_name: Dmitry full_name: Tsitelov, Dmitry last_name: Tsitelov - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. In: 35th International Conference on Computer Aided Verification. Vol 13964. Springer Nature; 2023:156-169. doi:10.1007/978-3-031-37706-8_8' apa: 'Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. In 35th International Conference on Computer Aided Verification (Vol. 13964, pp. 156–169). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_8' chicago: 'Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” In 35th International Conference on Computer Aided Verification, 13964:156–69. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_8.' ieee: 'N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM,” in 35th International Conference on Computer Aided Verification, Paris, France, 2023, vol. 13964, pp. 156–169.' ista: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM. 35th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13964, 156–169.' mla: 'Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” 35th International Conference on Computer Aided Verification, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:10.1007/978-3-031-37706-8_8.' short: N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 156–169. conference: end_date: 2023-07-22 location: Paris, France name: 'CAV: Computer Aided Verification' start_date: 2023-07-17 das_tickbox: '1' date_created: 2023-09-03T22:01:16Z date_published: 2023-07-17T00:00:00Z date_updated: 2026-07-07T13:39:36Z day: '17' ddc: - '000' department: - _id: DaAl - _id: GradSch doi: 10.1007/978-3-031-37706-8_8 external_id: isi: - '001310786500008' file: - access_level: open_access checksum: c346016393123a0a2338ad4d976f61bc content_type: application/pdf creator: dernst date_created: 2023-09-06T08:16:25Z date_updated: 2023-09-06T08:16:25Z file_id: '14275' file_name: 2023_LNCS_Koval.pdf file_size: 421408 relation: main_file success: 1 file_date_updated: 2023-09-06T08:16:25Z has_accepted_license: '1' intvolume: ' 13964' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 156-169 publication: 35th International Conference on Computer Aided Verification publication_identifier: eissn: - 1611-3349 isbn: - '9783031377051' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '14995' relation: research_data status: public scopus_import: '1' status: public title: 'Lincheck: A practical framework for testing concurrent data structures on JVM' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13964 year: '2023' ... --- OA_place: publisher _id: '14547' abstract: - lang: eng text: "Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier." acknowledged_ssus: - _id: NanoFab - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Duc T full_name: Phan, Duc T id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87 last_name: Phan citation: ama: Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:10.15479/14547 apa: Phan, D. T. (2023). Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. https://doi.org/10.15479/14547 chicago: Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14547. ieee: D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023. ista: Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. mla: Phan, Duc T. Resonant Microwave Spectroscopy of Al-InAs. Institute of Science and Technology Austria, 2023, doi:10.15479/14547. short: D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023. corr_author: '1' date_created: 2023-11-17T13:45:26Z date_published: 2023-11-16T00:00:00Z date_updated: 2026-07-08T08:38:43Z day: '16' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: AnHi doi: 10.15479/14547 file: - access_level: open_access checksum: db0c37d213bc002125bd59690e9db246 content_type: application/pdf creator: pduc date_created: 2023-11-17T13:36:44Z date_updated: 2023-11-22T09:46:06Z file_id: '14548' file_name: Phan_Thesis_pdfa.pdf file_size: 34828019 relation: main_file - access_level: closed checksum: 8d3bd6afa279a0078ffd13e06bb6d56d content_type: application/zip creator: pduc date_created: 2023-11-17T13:44:53Z date_updated: 2023-11-17T13:47:54Z file_id: '14549' file_name: dissertation_src.zip file_size: 279319709 relation: source_file file_date_updated: 2023-11-22T09:46:06Z has_accepted_license: '1' keyword: - superconductor-semiconductor - superconductivity - Al - InAs - p-wave - superconductivity - JPA - microwave language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '11' oa: 1 oa_version: Published Version page: '80' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10851' relation: part_of_dissertation status: public - id: '13264' relation: part_of_dissertation status: public status: public supervisor: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 title: Resonant microwave spectroscopy of Al-InAs tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2023' ... --- OA_place: publisher _id: '14641' abstract: - lang: eng text: "Mutation rates represent the net result of complex interactions among various\r\ncellular processes and can dramatically influence the evolutionary fate of\r\nmicrobial populations. However, many popular techniques used to study\r\nmutations are subject to the confounding effects of heredity and the subtleties\r\nof adaptation to selection, all of which make it difficult to observe any dynamic\r\nresponses of mutation rates to fitness challenges. Furthermore, in spite of the\r\nubiquity of quorum sensing systems across the bacterial domain and relevance\r\nfor many physiological behaviors, the effects of such mechanisms on mutation\r\nrate and adaptation remain poorly understood. In the following work, I\r\npresent the development of a microfluidic droplet-based method to measure\r\nsingle base-pair mutation rates in growing populations of the bacterium\r\nEscherichia coli. I use this method to observe a stress-induced increase in\r\nmutation rate that is mediated by luxS, a highly conserved bacterial quorum\r\nsensing component. I also show that the aforementioned increase in mutation\r\nrate, and its associated control by luxS, corresponds to a higher degree of\r\nadaptability under competitive environments." acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: CampIT alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mike full_name: Hennessey-Wesen, Mike id: 3F338C72-F248-11E8-B48F-1D18A9856A87 last_name: Hennessey-Wesen citation: ama: Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:10.15479/at:ista:14641 apa: Hennessey-Wesen, M. (2023). Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14641 chicago: Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14641. ieee: M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023. ista: Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. mla: Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641. short: M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023. corr_author: '1' das_tickbox: '1' date_created: 2023-12-04T13:17:37Z date_published: 2023-11-30T00:00:00Z date_updated: 2026-07-13T10:55:56Z day: '30' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/at:ista:14641 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: 4127c285b34f4bf7fb31ef24f9d14c25 content_type: application/vnd.oasis.opendocument.text creator: mhenness date_created: 2023-12-06T13:13:26Z date_updated: 2024-11-30T23:30:05Z embargo_to: open_access file_id: '14648' file_name: mike_thesis_v06-12-2023.odt file_size: 46405919 relation: source_file - access_level: closed checksum: f5203a61eddaf35235bbc51904d73982 content_type: application/pdf creator: mhenness date_created: 2023-12-06T13:14:15Z date_updated: 2026-07-13T10:55:56Z embargo: 2026-11-18 embargo_to: open_access file_id: '14649' file_name: mike_thesis_v06-12-2023.pdf file_size: 21282155 relation: main_file - access_level: closed checksum: 902102d26d30e74dbd6cdd70a65820c3 content_type: application/pdf creator: cchlebak date_created: 2025-05-20T12:59:12Z date_updated: 2025-05-20T22:31:34Z description: for printing purposes only embargo_to: open_access file_id: '19720' file_name: 2023_Hennessey_Michael_Thesis_print.pdf file_size: 45847968 relation: other title: Print version file_date_updated: 2026-07-13T10:55:56Z has_accepted_license: '1' keyword: - microfluidics - miceobiology - mutations - quorum sensing language: - iso: eng month: '11' oa_version: Published Version page: '104' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: Adaptive mutation in E. coli modulated by luxS type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12675' abstract: - lang: eng text: Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein--protein interactions. By studying a pair of structurally homologous cross-β amyloid fibrils, HET-s and HELLF, with a specific isotope-labeling approach and magic-angle-spinning (MAS) NMR, we have characterized the dynamic behavior of Phe and Tyr aromatic rings to show that the hydrophobic amyloid core is rigid, without any sign of "breathing motions" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips, on a variety of time scales from ns to µs. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from a NMR structural ensemble of such amyloid cross-β architecture. acknowledgement: We thank AlbertA. Smith (Leipzig)for insightful discussions. This work was supported by funding from the European Research Council (StG-2012-311318 to P.S.) and used the platforms of the Grenoble Instruct-ERIC center (ISBG;UMS 3518 CNRS-CEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology(PSB) and facilities and expertiseof the Biophysical and Structural Chemistry platform (BPCS) at IECB,CNRSUAR3033,INSERMUS001 and Bordeaux University. article_number: e202219314 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Mélanie full_name: Berbon, Mélanie last_name: Berbon - first_name: Alicia full_name: Vallet, Alicia last_name: Vallet - first_name: Axelle full_name: Grelard, Axelle last_name: Grelard - first_name: Estelle full_name: Morvan, Estelle last_name: Morvan - first_name: Benjamin full_name: Bardiaux, Benjamin last_name: Bardiaux - first_name: Roman full_name: Lichtenecker, Roman last_name: Lichtenecker - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Antoine full_name: Loquet, Antoine last_name: Loquet - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Becker LM, Berbon M, Vallet A, et al. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 2023;62(19). doi:10.1002/anie.202219314 apa: Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202219314 chicago: Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” Angewandte Chemie International Edition. Wiley, 2023. https://doi.org/10.1002/anie.202219314. ieee: L. M. Becker et al., “The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues,” Angewandte Chemie International Edition, vol. 62, no. 19. Wiley, 2023. ista: Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 62(19), e202219314. mla: Becker, Lea Marie, et al. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” Angewandte Chemie International Edition, vol. 62, no. 19, e202219314, Wiley, 2023, doi:10.1002/anie.202219314. short: L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie International Edition 62 (2023). corr_author: '1' date_created: 2023-02-24T10:45:01Z date_published: 2023-05-01T00:00:00Z date_updated: 2026-07-20T09:49:12Z day: '01' ddc: - '540' department: - _id: GradSch - _id: PaSc doi: 10.1002/anie.202219314 external_id: isi: - '000956919900001' pmid: - '36738230' file: - access_level: open_access checksum: 7dd083ed8850faa55c34e411ed390de9 content_type: application/pdf creator: dernst date_created: 2023-08-16T12:33:31Z date_updated: 2023-08-16T12:33:31Z file_id: '14072' file_name: 2023_AngewChemInt_Becker.pdf file_size: 1422445 relation: main_file success: 1 file_date_updated: 2023-08-16T12:33:31Z has_accepted_license: '1' intvolume: ' 62' isi: 1 issue: '19' keyword: - General Chemistry - Catalysis language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/dancing-styles-of-atoms/ record: - id: '12497' relation: research_data status: public - id: '14861' relation: other status: public - id: '22334' relation: dissertation_contains status: public scopus_import: '1' status: public title: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues 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: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2023' ... --- OA_place: repository _id: '15039' abstract: - lang: eng text: 'A crucial property for achieving secure, trustworthy and interpretable deep learning systems is their robustness: small changes to a system''s inputs should not result in large changes to its outputs. Mathematically, this means one strives for networks with a small Lipschitz constant. Several recent works have focused on how to construct such Lipschitz networks, typically by imposing constraints on the weight matrices. In this work, we study an orthogonal aspect, namely the role of the activation function. We show that commonly used activation functions, such as MaxMin, as well as all piece-wise linear ones with two segments unnecessarily restrict the class of representable functions, even in the simplest one-dimensional setting. We furthermore introduce the new N-activation function that is provably more expressive than currently popular activation functions. We provide code at this https URL.' article_number: '2311.06103' article_processing_charge: No arxiv: 1 author: - first_name: Bernd full_name: Prach, Bernd id: 2D561D42-C427-11E9-89B4-9C1AE6697425 last_name: Prach - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations. arXiv. doi:10.48550/ARXIV.2311.06103 apa: Prach, B., & Lampert, C. (n.d.). 1-Lipschitz neural networks are more expressive with N-activations. arXiv. https://doi.org/10.48550/ARXIV.2311.06103 chicago: Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More Expressive with N-Activations.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2311.06103. ieee: B. Prach and C. Lampert, “1-Lipschitz neural networks are more expressive with N-activations,” arXiv. . ista: Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations. arXiv, 2311.06103. mla: Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More Expressive with N-Activations.” ArXiv, 2311.06103, doi:10.48550/ARXIV.2311.06103. short: B. Prach, C. Lampert, ArXiv (n.d.). corr_author: '1' date_created: 2024-02-28T17:59:32Z date_published: 2023-11-10T00:00:00Z date_updated: 2026-07-27T12:47:43Z day: '10' department: - _id: GradSch - _id: ChLa doi: 10.48550/ARXIV.2311.06103 external_id: arxiv: - '2311.06103' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2311.06103 month: '11' oa: 1 oa_version: Preprint publication: arXiv publication_status: draft related_material: record: - id: '19759' relation: dissertation_contains status: public status: public title: 1-Lipschitz neural networks are more expressive with N-activations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13221' abstract: - lang: eng text: The safety-liveness dichotomy is a fundamental concept in formal languages which plays a key role in verification. Recently, this dichotomy has been lifted to quantitative properties, which are arbitrary functions from infinite words to partially-ordered domains. We look into harnessing the dichotomy for the specific classes of quantitative properties expressed by quantitative automata. These automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totallyordered domain of real numbers. In this automata-theoretic setting, we establish a connection between quantitative safety and topological continuity and provide an alternative characterization of quantitative safety and liveness in terms of their boolean counterparts. For all common value functions, we show how the safety closure of a quantitative automaton can be constructed in PTime, and we provide PSpace-complete checks of whether a given quantitative automaton is safe or live, with the exception of LimInfAvg and LimSupAvg automata, for which the safety check is in ExpSpace. Moreover, for deterministic Sup, LimInf, and LimSup automata, we give PTime decompositions into safe and live automata. These decompositions enable the separation of techniques for safety and liveness verification for quantitative specifications. acknowledgement: We thank Christof Löding for pointing us to some results on PSpace-hardess of universality problems and the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22. alternative_title: - LIPIcs article_number: '17' article_processing_charge: No arxiv: 1 author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Nicolas Adrien full_name: Mazzocchi, Nicolas Adrien id: b26baa86-3308-11ec-87b0-8990f34baa85 last_name: Mazzocchi - first_name: Naci E full_name: Sarac, Naci E id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425 last_name: Sarac citation: ama: 'Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative automata. In: 34th International Conference on Concurrency Theory. Vol 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.CONCUR.2023.17' apa: 'Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Safety and liveness of quantitative automata. In 34th International Conference on Concurrency Theory (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17' chicago: Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Automata.” In 34th International Conference on Concurrency Theory, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17. ieee: U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative automata,” in 34th International Conference on Concurrency Theory, Antwerp, Belgium, 2023, vol. 279. ista: 'Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Safety and liveness of quantitative automata. 34th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 17.' mla: Boker, Udi, et al. “Safety and Liveness of Quantitative Automata.” 34th International Conference on Concurrency Theory, vol. 279, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.CONCUR.2023.17. short: U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 34th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. conference: end_date: 2023-09-23 location: Antwerp, Belgium name: 'CONCUR: Conference on Concurrency Theory' start_date: 2023-09-18 corr_author: '1' date_created: 2023-07-14T10:00:15Z date_published: 2023-09-01T00:00:00Z date_updated: 2026-07-27T12:48:18Z day: '01' ddc: - '000' department: - _id: GradSch - _id: ToHe doi: 10.4230/LIPIcs.CONCUR.2023.17 ec_funded: 1 external_id: arxiv: - '2307.06016' isi: - '001570542500017' file: - access_level: open_access checksum: d40e57a04448ea5c77d7e1cfb9590a81 content_type: application/pdf creator: esarac date_created: 2023-07-14T12:03:48Z date_updated: 2023-07-14T12:03:48Z file_id: '13224' file_name: CONCUR23.pdf file_size: 755529 relation: main_file success: 1 file_date_updated: 2023-07-14T12:03:48Z has_accepted_license: '1' intvolume: ' 279' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 34th International Conference on Concurrency Theory publication_identifier: eissn: - 1868-8969 isbn: - '9783959772990' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '20342' relation: later_version status: public - id: '20147' relation: dissertation_contains status: public scopus_import: '1' status: public title: Safety and liveness of quantitative automata tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 279 year: '2023' ... --- _id: '12762' abstract: - lang: eng text: Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations. acknowledgement: This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie action (grant agreement No. 754411 to F.L.). article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Fabrizio full_name: Lombardi, Fabrizio id: A057D288-3E88-11E9-986D-0CF4E5697425 last_name: Lombardi orcid: 0000-0003-2623-5249 - first_name: Selver full_name: Pepic, Selver id: F93245C4-C3CA-11E9-B4F0-C6F4E5697425 last_name: Pepic - first_name: Oren full_name: Shriki, Oren last_name: Shriki - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 citation: ama: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9 apa: Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-023-00410-9 chicago: Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9. ieee: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” Nature Computational Science, vol. 3. Springer Nature, pp. 254–263, 2023. ista: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263. mla: Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63, doi:10.1038/s43588-023-00410-9. short: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263. corr_author: '1' date_created: 2023-03-26T22:01:08Z date_published: 2023-03-20T00:00:00Z date_updated: 2026-07-29T06:53:41Z day: '20' ddc: - '570' department: - _id: GaTk - _id: GradSch doi: 10.1038/s43588-023-00410-9 ec_funded: 1 external_id: arxiv: - '2108.06686' isi: - '000968161800002' pmid: - '38177880' file: - access_level: open_access checksum: 7c63b2b2edfd68aaffe96d70ca6a865a content_type: application/pdf creator: dernst date_created: 2023-08-16T12:39:57Z date_updated: 2023-08-16T12:39:57Z file_id: '14073' file_name: 2023_NatureCompScience_Lombardi.pdf file_size: 4474284 relation: main_file success: 1 file_date_updated: 2023-08-16T12:39:57Z has_accepted_license: '1' intvolume: ' 3' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 254-263 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: eb943429-77a9-11ec-83b8-9f471cdf5c67 grant_number: M03318 name: Functional Advantages of Critical Brain Dynamics - _id: 626c45b5-2b32-11ec-9570-e509828c1ba6 grant_number: P34015 name: Efficient coding with biophysical realism publication: Nature Computational Science publication_identifier: eissn: - 2662-8457 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '10912' relation: earlier_version status: public scopus_import: '1' status: public title: Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain 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: 3 year: '2023' ... --- _id: '13120' abstract: - lang: eng text: 'We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant. We defined basic notions of rewrite rules and of words derived by a grammar, and used grammars to show closure of the class of type-0 languages under four operations: union, reversal, concatenation, and the Kleene star. The literature mostly focuses on Turing machine arguments, which are possibly more difficult to formalize. For the Kleene star, we could not follow the literature and came up with our own grammar-based construction.' acknowledgement: "Jasmin Blanchette: This research has received funding from the Netherlands Organization\r\nfor Scientific Research (NWO) under the Vidi program (project No. 016.Vidi.189.037, Lean Forward).\r\n__\r\nWe thank Vladimir Kolmogorov for making this collaboration possible. We\r\nthank Václav Končický for discussing ideas about the Kleene star construction. We thank Patrick Johnson, Floris van Doorn, and Damiano Testa for their small yet very valuable contributions to our code. We thank Eric Wieser for simplifying one of our proofs. We thank Mark Summerfield for suggesting textual improvements. We thank the anonymous reviewers for very helpful comments. Finally, we thank the Lean community for helping us with various technical issues and answering many questions. " alternative_title: - LIPIcs article_number: '15' article_processing_charge: No arxiv: 1 author: - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X - first_name: Jasmin full_name: Blanchette, Jasmin last_name: Blanchette citation: ama: 'Dvorak M, Blanchette J. Closure properties of general grammars - formally verified. In: 14th International Conference on Interactive Theorem Proving. Vol 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ITP.2023.15' apa: 'Dvorak, M., & Blanchette, J. (2023). Closure properties of general grammars - formally verified. In 14th International Conference on Interactive Theorem Proving (Vol. 268). Bialystok, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITP.2023.15' chicago: Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” In 14th International Conference on Interactive Theorem Proving, Vol. 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ITP.2023.15. ieee: M. Dvorak and J. Blanchette, “Closure properties of general grammars - formally verified,” in 14th International Conference on Interactive Theorem Proving, Bialystok, Poland, 2023, vol. 268. ista: 'Dvorak M, Blanchette J. 2023. Closure properties of general grammars - formally verified. 14th International Conference on Interactive Theorem Proving. ITP: Interactive Theorem Proving, LIPIcs, vol. 268, 15.' mla: Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” 14th International Conference on Interactive Theorem Proving, vol. 268, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ITP.2023.15. short: M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. conference: end_date: 2023-08-04 location: Bialystok, Poland name: 'ITP: Interactive Theorem Proving' start_date: 2023-07-31 corr_author: '1' date_created: 2023-06-05T07:29:05Z date_published: 2023-07-27T00:00:00Z date_updated: 2026-07-29T12:56:51Z day: '27' ddc: - '000' department: - _id: GradSch - _id: VlKo doi: 10.4230/LIPIcs.ITP.2023.15 external_id: arxiv: - '2302.06420' isi: - '001515590500015' file: - access_level: open_access checksum: 773a0197f05b67feaa6cb1e17ec3642d content_type: application/pdf creator: dernst date_created: 2023-08-07T11:55:43Z date_updated: 2023-08-07T11:55:43Z file_id: '13982' file_name: 2023_LIPIcS_Dvorak.pdf file_size: 715976 relation: main_file success: 1 file_date_updated: 2023-08-07T11:55:43Z has_accepted_license: '1' intvolume: ' 268' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: 14th International Conference on Interactive Theorem Proving publication_identifier: eissn: - 1868-8969 isbn: - '9783959772846' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: link: - relation: software url: https://github.com/madvorak/grammars/tree/publish record: - id: '21393' relation: dissertation_contains status: public scopus_import: '1' status: public title: Closure properties of general grammars - formally verified tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 268 year: '2023' ... --- _id: '13049' abstract: - lang: eng text: "We propose a computational design approach for covering a surface with individually addressable RGB LEDs, effectively forming a low-resolution surface screen. To achieve a low-cost and scalable approach, we propose creating designs from flat PCB panels bent in-place along the surface of a 3D printed core. Working with standard rigid PCBs enables the use of\r\nestablished PCB manufacturing services, allowing the fabrication of designs with several hundred LEDs. \r\nOur approach optimizes the PCB geometry for folding, and then jointly optimizes the LED packing, circuit and routing, solving a challenging layout problem under strict manufacturing requirements. Unlike paper, PCBs cannot bend beyond a certain point without breaking. Therefore, we introduce parametric cut patterns acting as hinges, designed to allow bending while remaining compact. To tackle the joint optimization of placement, circuit and routing, we propose a specialized algorithm that splits the global problem into one sub-problem per triangle, which is then individually solved.\r\nOur technique generates PCB blueprints in a completely automated way. After being fabricated by a PCB manufacturing service, the boards are bent and glued by the user onto the 3D printed support. We demonstrate our technique on a range of physical models and virtual examples, creating intricate surface light patterns from hundreds of LEDs." acknowledged_ssus: - _id: M-Shop acknowledgement: We thank the reviewers for the valuable feedback. We also thank the Miba Machine Shop at ISTA, PCBWay, and PragoBoard for helping us with fabrication and assembly. This project was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 715767 – MATERIALIZABLE). article_number: '142' article_processing_charge: No article_type: original author: - first_name: Marco full_name: Freire, Marco last_name: Freire - first_name: Manas full_name: Bhargava, Manas id: FF8FA64C-AA6A-11E9-99AD-50D4E5697425 last_name: Bhargava orcid: 0009-0007-6138-6890 - first_name: Camille full_name: Schreck, Camille id: 2B14B676-F248-11E8-B48F-1D18A9856A87 last_name: Schreck - first_name: Pierre-Alexandre full_name: Hugron, Pierre-Alexandre last_name: Hugron - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Sylvain full_name: Lefebvre, Sylvain last_name: Lefebvre citation: ama: 'Freire M, Bhargava M, Schreck C, Hugron P-A, Bickel B, Lefebvre S. PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. 2023;42(4). doi:10.1145/3592411' apa: 'Freire, M., Bhargava, M., Schreck, C., Hugron, P.-A., Bickel, B., & Lefebvre, S. (2023). PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3592411' chicago: 'Freire, Marco, Manas Bhargava, Camille Schreck, Pierre-Alexandre Hugron, Bernd Bickel, and Sylvain Lefebvre. “PCBend: Light up Your 3D Shapes with Foldable Circuit Boards.” Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3592411.' ieee: 'M. Freire, M. Bhargava, C. Schreck, P.-A. Hugron, B. Bickel, and S. Lefebvre, “PCBend: Light up your 3D shapes with foldable circuit boards,” Transactions on Graphics, vol. 42, no. 4. Association for Computing Machinery, 2023.' ista: 'Freire M, Bhargava M, Schreck C, Hugron P-A, Bickel B, Lefebvre S. 2023. PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. 42(4), 142.' mla: 'Freire, Marco, et al. “PCBend: Light up Your 3D Shapes with Foldable Circuit Boards.” Transactions on Graphics, vol. 42, no. 4, 142, Association for Computing Machinery, 2023, doi:10.1145/3592411.' short: M. Freire, M. Bhargava, C. Schreck, P.-A. Hugron, B. Bickel, S. Lefebvre, Transactions on Graphics 42 (2023). conference: end_date: 2023-08-10 location: Los Angeles, CA, United States name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2023-08-06 corr_author: '1' date_created: 2023-05-22T08:37:04Z date_published: 2023-07-26T00:00:00Z date_updated: 2026-07-29T13:03:30Z day: '26' ddc: - '006' department: - _id: GradSch - _id: BeBi doi: 10.1145/3592411 ec_funded: 1 external_id: isi: - '001044671300108' file: - access_level: open_access checksum: a0b0ba3b36f43a94388e8824613d812a content_type: application/pdf creator: dernst date_created: 2023-06-19T11:02:23Z date_updated: 2023-06-19T11:02:23Z file_id: '13156' file_name: 2023_ACMToG_Freire.pdf file_size: 78940724 relation: main_file success: 1 - access_level: open_access checksum: b9206bbb67af82df49b7e7cdbde3410c content_type: application/pdf creator: dernst date_created: 2023-06-20T12:20:51Z date_updated: 2023-06-20T12:20:51Z file_id: '13157' file_name: 2023_ACMToG_SuppMaterial_Freire.pdf file_size: 34345905 relation: main_file success: 1 file_date_updated: 2023-06-20T12:20:51Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '4' keyword: - PCB design and layout - Mesh geometry models language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '20276' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'PCBend: Light up your 3D shapes with foldable circuit boards' 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 42 year: '2023' ... --- _id: '14343' abstract: - lang: eng text: The total energy of an eigenstate in a composite quantum system tends to be distributed equally among its constituents. We identify the quantum fluctuation around this equipartition principle in the simplest disordered quantum system consisting of linear combinations of Wigner matrices. As our main ingredient, we prove the Eigenstate Thermalisation Hypothesis and Gaussian fluctuation for general quadratic forms of the bulk eigenvectors of Wigner matrices with an arbitrary deformation. acknowledgement: "G.C. and L.E. gratefully acknowledge many discussions with Dominik Schröder at the preliminary stage of this project, especially his essential contribution to identify the correct generalisation of traceless observables to the deformed Wigner ensembles.\r\nL.E. and J.H. acknowledges support by ERC Advanced Grant ‘RMTBeyond’ No. 101020331." article_number: e74 article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Sven Joscha full_name: Henheik, Sven Joscha id: 31d731d7-d235-11ea-ad11-b50331c8d7fb last_name: Henheik orcid: 0000-0003-1106-327X - first_name: Oleksii full_name: Kolupaiev, Oleksii id: 149b70d4-896a-11ed-bdf8-8c63fd44ca61 last_name: Kolupaiev orcid: 0000-0003-1491-4623 citation: ama: Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 2023;11. doi:10.1017/fms.2023.70 apa: Cipolloni, G., Erdös, L., Henheik, S. J., & Kolupaiev, O. (2023). Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2023.70 chicago: Cipolloni, Giorgio, László Erdös, Sven Joscha Henheik, and Oleksii Kolupaiev. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.70. ieee: G. Cipolloni, L. Erdös, S. J. Henheik, and O. Kolupaiev, “Gaussian fluctuations in the equipartition principle for Wigner matrices,” Forum of Mathematics, Sigma, vol. 11. Cambridge University Press, 2023. ista: Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. 2023. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 11, e74. mla: Cipolloni, Giorgio, et al. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma, vol. 11, e74, Cambridge University Press, 2023, doi:10.1017/fms.2023.70. short: G. Cipolloni, L. Erdös, S.J. Henheik, O. Kolupaiev, Forum of Mathematics, Sigma 11 (2023). corr_author: '1' date_created: 2023-09-17T22:01:09Z date_published: 2023-08-23T00:00:00Z date_updated: 2026-07-29T13:18:16Z day: '23' ddc: - '510' department: - _id: LaEr - _id: GradSch doi: 10.1017/fms.2023.70 ec_funded: 1 external_id: arxiv: - '2301.05181' isi: - '001051980200001' file: - access_level: open_access checksum: eb747420e6a88a7796fa934151957676 content_type: application/pdf creator: dernst date_created: 2023-09-20T11:09:35Z date_updated: 2023-09-20T11:09:35Z file_id: '14352' file_name: 2023_ForumMathematics_Cipolloni.pdf file_size: 852652 relation: main_file success: 1 file_date_updated: 2023-09-20T11:09:35Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Forum of Mathematics, Sigma publication_identifier: eissn: - 2050-5094 publication_status: published publisher: Cambridge University Press quality_controlled: '1' related_material: record: - id: '19540' relation: dissertation_contains status: public scopus_import: '1' status: public title: Gaussian fluctuations in the equipartition principle for Wigner matrices 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: 11 year: '2023' ... --- _id: '14421' abstract: - lang: eng text: Only recently has it been possible to construct a self-adjoint Hamiltonian that involves the creation of Dirac particles at a point source in 3d space. Its definition makes use of an interior-boundary condition. Here, we develop for this Hamiltonian a corresponding theory of the Bohmian configuration. That is, we (non-rigorously) construct a Markov jump process $(Q_t)_{t\in\mathbb{R}}$ in the configuration space of a variable number of particles that is $|\psi_t|^2$-distributed at every time t and follows Bohmian trajectories between the jumps. The jumps correspond to particle creation or annihilation events and occur either to or from a configuration with a particle located at the source. The process is the natural analog of Bell's jump process, and a central piece in its construction is the determination of the rate of particle creation. The construction requires an analysis of the asymptotic behavior of the Bohmian trajectories near the source. We find that the particle reaches the source with radial speed 0, but orbits around the source infinitely many times in finite time before absorption (or after emission). acknowledgement: J H gratefully acknowledges partial financial support by the ERC Advanced Grant 'RMTBeyond' No. 101020331. article_number: '445201' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Sven Joscha full_name: Henheik, Sven Joscha id: 31d731d7-d235-11ea-ad11-b50331c8d7fb last_name: Henheik orcid: 0000-0003-1106-327X - first_name: Roderich full_name: Tumulka, Roderich last_name: Tumulka citation: ama: 'Henheik SJ, Tumulka R. Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. 2023;56(44). doi:10.1088/1751-8121/acfe62' apa: 'Henheik, S. J., & Tumulka, R. (2023). Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/acfe62' chicago: 'Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles at a Point Source.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2023. https://doi.org/10.1088/1751-8121/acfe62.' ieee: 'S. J. Henheik and R. Tumulka, “Creation rate of Dirac particles at a point source,” Journal of Physics A: Mathematical and Theoretical, vol. 56, no. 44. IOP Publishing, 2023.' ista: 'Henheik SJ, Tumulka R. 2023. Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. 56(44), 445201.' mla: 'Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles at a Point Source.” Journal of Physics A: Mathematical and Theoretical, vol. 56, no. 44, 445201, IOP Publishing, 2023, doi:10.1088/1751-8121/acfe62.' short: 'S.J. Henheik, R. Tumulka, Journal of Physics A: Mathematical and Theoretical 56 (2023).' corr_author: '1' date_created: 2023-10-12T12:42:53Z date_published: 2023-10-11T00:00:00Z date_updated: 2026-07-29T13:18:16Z day: '11' ddc: - '510' department: - _id: GradSch - _id: LaEr doi: 10.1088/1751-8121/acfe62 ec_funded: 1 external_id: arxiv: - '2211.16606' isi: - '001080908000001' file: - access_level: open_access checksum: 5b68de147dd4c608b71a6e0e844d2ce9 content_type: application/pdf creator: dernst date_created: 2023-10-16T07:07:24Z date_updated: 2023-10-16T07:07:24Z file_id: '14429' file_name: 2023_JourPhysics_Henheik.pdf file_size: 721399 relation: main_file success: 1 file_date_updated: 2023-10-16T07:07:24Z has_accepted_license: '1' intvolume: ' 56' isi: 1 issue: '44' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: 'Journal of Physics A: Mathematical and Theoretical' publication_identifier: eissn: - 1751-8121 issn: - 1751-8113 publication_status: published publisher: IOP Publishing quality_controlled: '1' related_material: record: - id: '19540' relation: dissertation_contains status: public scopus_import: '1' status: public title: Creation rate of Dirac particles at a point source 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: 56 year: '2023' ... --- OA_place: publisher _id: '12491' abstract: - lang: eng text: "The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions." acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bettina full_name: Zens, Bettina id: 45FD126C-F248-11E8-B48F-1D18A9856A87 last_name: Zens orcid: 0000-0002-9561-1239 citation: ama: Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491 apa: Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491 chicago: Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491. ieee: B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023. ista: Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. mla: Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491. short: B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023. corr_author: '1' date_created: 2023-02-02T14:50:20Z date_published: 2023-02-02T00:00:00Z date_updated: 2026-04-07T13:49:23Z day: '02' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: FlSc doi: 10.15479/at:ista:12491 file: - access_level: open_access checksum: 069d87f025e0799bf9e3c375664264f2 content_type: application/pdf creator: bzens date_created: 2023-02-07T13:07:38Z date_updated: 2024-02-08T23:30:04Z embargo: 2024-02-07 file_id: '12527' file_name: PhDThesis_BettinaZens_2023_final.pdf file_size: 23082464 relation: main_file - access_level: closed checksum: 8c66ed203495d6e078ed1002a866520c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: bzens date_created: 2023-02-07T13:09:05Z date_updated: 2024-02-08T23:30:04Z embargo_to: open_access file_id: '12528' file_name: PhDThesis_BettinaZens_2023_final.docx file_size: 106169509 relation: source_file file_date_updated: 2024-02-08T23:30:04Z has_accepted_license: '1' keyword: - cryo-EM - cryo-ET - FIB milling - method development - FIBSEM - extracellular matrix - ECM - cell-derived matrices - CDMs - cell culture - high pressure freezing - HPF - structural biology - tomography - collagen language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '187' project: - _id: eba3b5f6-77a9-11ec-83b8-cf0905748aa3 name: Integrated visual proteomics of reciprocal cell-extracellular matrix interactions - _id: 059B463C-7A3F-11EA-A408-12923DDC885E name: "NÃ\x96-Fonds Preis für die Jungforscherin des Jahres am IST Austria" publication_identifier: isbn: - 978-3-99078-027-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8586' relation: part_of_dissertation status: public status: public supervisor: - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 title: Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2023' ... --- OA_place: publisher _id: '13984' abstract: - lang: eng text: "Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection." acknowledged_ssus: - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Anna full_name: Franschitz, Anna id: 480826C8-F248-11E8-B48F-1D18A9856A87 last_name: Franschitz citation: ama: Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:10.15479/at:ista:13984 apa: Franschitz, A. (2023). Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984 chicago: Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984. ieee: A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023. ista: Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria. mla: Franschitz, Anna. Individual and Social Immunity against Viral Infections in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984. short: A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023. corr_author: '1' date_created: 2023-08-08T15:33:29Z date_published: 2023-08-08T00:00:00Z date_updated: 2026-04-07T13:51:29Z day: '08' ddc: - '570' - '577' degree_awarded: PhD department: - _id: GradSch - _id: SyCr doi: 10.15479/at:ista:13984 file: - access_level: open_access checksum: 55c876b73d49db15228a7f571592ec77 content_type: application/pdf creator: cchlebak date_created: 2024-03-01T08:56:06Z date_updated: 2024-10-29T23:31:04Z embargo_to: open_access file_id: '15044' file_name: Print_Version_Franschitz_Anna_Thesis.pdf file_size: 10416761 relation: main_file title: Combined Version of original Thesis and Addendum - access_level: open_access checksum: 27220243d5d51c3b0d7d61c0879d7a0c content_type: application/pdf creator: afransch date_created: 2023-08-08T18:01:28Z date_updated: 2024-08-09T22:30:03Z embargo: 2024-08-08 file_id: '13986' file_name: Thesis_AnnaFranschitz_202308.pdf file_size: 10797612 relation: main_file - access_level: closed checksum: 40abf7ccca14a3893f72dc7fb88585d6 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: afransch date_created: 2023-08-08T18:02:25Z date_updated: 2024-08-09T22:30:03Z embargo_to: open_access file_id: '13987' file_name: Thesis_AnnaFranschitz_202308.docx file_size: 2619085 relation: source_file - access_level: open_access checksum: 8b991ecc2d59d045cc3cf0d676785ec7 content_type: application/pdf creator: cchlebak date_created: 2024-03-01T08:37:15Z date_updated: 2024-10-29T23:31:04Z description: Minor modifications and clarifications - Feb 2024 embargo: 2024-08-08 file_id: '15042' file_name: Addendum_AnnaFranschitz202402.pdf file_size: 85956 relation: main_file title: Addendum - access_level: closed checksum: 66745aa01f960f17472c024875c049ed content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2024-03-01T08:39:20Z date_updated: 2024-08-09T22:30:03Z embargo_to: open_access file_id: '15043' file_name: Addendum_AnnaFranschitz202402.docx file_size: 11818 relation: source_file title: Addendum - source file file_date_updated: 2024-10-29T23:31:04Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '89' publication_identifier: isbn: - 978-3-99078-034-3 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: Individual and social immunity against viral infections in ants type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2023' ...