--- OA_place: repository OA_type: green _id: '19520' abstract: - lang: eng text: Vertebrates exhibit a wide range of motor behaviors, ranging from swimming to complex limb-based movements. Here we take advantage of frog metamorphosis, which captures a swim-to-limb-based movement transformation during the development of a single organism, to explore changes in the underlying spinal circuits. We find that the tadpole spinal cord contains small and largely homogeneous populations of motor neurons (MNs) and V1 interneurons (V1s) at early escape swimming stages. These neuronal populations only modestly increase in number and subtype heterogeneity with the emergence of free swimming. In contrast, during frog metamorphosis and the emergence of limb movement, there is a dramatic expansion of MN and V1 interneuron number and transcriptional heterogeneity, culminating in cohorts of neurons that exhibit striking molecular similarity to mammalian motor circuits. CRISPR/Cas9-mediated gene disruption of the limb MN and V1 determinants FoxP1 and Engrailed-1, respectively, results in severe but selective deficits in tail and limb function. Our work thus demonstrates that neural diversity scales exponentially with increasing behavioral complexity and illustrates striking evolutionary conservation in the molecular organization and function of motor circuits across species. acknowledged_ssus: - _id: Bio acknowledgement: "We would like to thank the members of the Sweeney Lab (especially Stavros Papadopoulos and\r\nSophie Gobeil) for their contributions to this project and, in addition to the lab, Graziana Gatto\r\nand Mario de Bono, for discussion, and support. We are also grateful to Tom Jessell and Chris\r\nKintner for their scientific insight and mentorship during the conception of this project. This\r\nproject would also not have been possible with the technical support of the Matthias Nowak,\r\nVerena Mayer and the Aquatics as well as the Imaging and Optics Facility support teams\r\n(ISTA). In addition, we thank our funding sources for providing the resources to do these\r\nexperiments: FTI Strategy Lower Austria Dissertation Grant Number FT121-D-046 (D.V.);\r\nHorizon Europe ERC Starting Grant Number 101041551 (L.B.S., F.A.T. and D.V); Special\r\nResearch Program (SFB) of the Austrian Science Fund (FWF) Project number F7814-B (L.B.S);\r\nNINDS 5R35NS116858 (J.S.D); CZI grant DAF2020-225401 (DOI): 10.37921/120055ratwvi\r\n(R.H.); NIH grant number R01NS123116 (J.B.B); American Lebanese Syrian Associated\r\nCharities (ALSAC) (J.B.B.); German Academic Exchange Service (DAAD) IFI Grant Number\r\n57515251-91853472 (Z.H.); and Project A.L.S. (S.B-M.). " article_processing_charge: No author: - first_name: David full_name: Vijatovic, David id: cf391e77-ec3c-11ea-a124-d69323410b58 last_name: Vijatovic - first_name: 'Florina Alexandra ' full_name: 'Toma, Florina Alexandra ' id: 2f73f876-f128-11eb-9611-b96b5a30cb0e last_name: Toma - first_name: Zoe P full_name: Harrington, Zoe P id: a8144562-32c9-11ee-b5ce-d9800628bda2 last_name: Harrington orcid: 0009-0008-0158-4032 - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Alexandra J. full_name: Trevisan, Alexandra J. last_name: Trevisan - first_name: Phillip full_name: Chapman, Phillip last_name: Chapman - first_name: Mara full_name: Julseth, Mara id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1 last_name: Julseth - first_name: Susan full_name: Brenner-Morton, Susan last_name: Brenner-Morton - first_name: Mariano I. full_name: Gabitto, Mariano I. last_name: Gabitto - first_name: Jeremy S. full_name: Dasen, Jeremy S. last_name: Dasen - first_name: Jay B. full_name: Bikoff, Jay B. last_name: Bikoff - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 citation: ama: Vijatovic D, Toma FA, Harrington ZP, et al. Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. bioRxiv. doi:10.1101/2024.09.20.614050 apa: Vijatovic, D., Toma, F. A., Harrington, Z. P., Sommer, C. M., Hauschild, R., Trevisan, A. J., … Sweeney, L. B. (n.d.). Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. bioRxiv. https://doi.org/10.1101/2024.09.20.614050 chicago: Vijatovic, David, Florina Alexandra Toma, Zoe P Harrington, Christoph M Sommer, Robert Hauschild, Alexandra J. Trevisan, Phillip Chapman, et al. “Spinal Neuron Diversity Scales Exponentially with Swim-to-Limb Transformation during Frog Metamorphosis.” BioRxiv, n.d. https://doi.org/10.1101/2024.09.20.614050. ieee: D. Vijatovic et al., “Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis,” bioRxiv. . ista: Vijatovic D, Toma FA, Harrington ZP, Sommer CM, Hauschild R, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney LB. Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis. bioRxiv, 10.1101/2024.09.20.614050. mla: Vijatovic, David, et al. “Spinal Neuron Diversity Scales Exponentially with Swim-to-Limb Transformation during Frog Metamorphosis.” BioRxiv, doi:10.1101/2024.09.20.614050. short: D. Vijatovic, F.A. Toma, Z.P. Harrington, C.M. Sommer, R. Hauschild, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton, M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, BioRxiv (n.d.). corr_author: '1' date_created: 2025-04-07T08:48:28Z date_published: 2024-09-27T00:00:00Z date_updated: 2025-05-14T11:40:13Z day: '27' department: - _id: LoSw - _id: TiVo - _id: Bio - _id: NiBa doi: 10.1101/2024.09.20.614050 fulldoi: https://doi.org/10.1101/2024.09.20.614050 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.09.20.614050 month: '09' oa: 1 oa_version: Preprint project: - _id: bd73af52-d553-11ed-ba76-912049f0ac7a grant_number: FTI21-D-046 name: Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis - _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae grant_number: '101041551' name: Development and Evolution of Tetrapod Motor Circuits - _id: c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473 grant_number: CZI01 name: Tools for automation and feedback microscopy publication: bioRxiv publication_status: submitted status: public title: Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '19800' abstract: - lang: eng text: "This archive contains all the code and data necessary to reproduce the results presented in the \r\n\"Mapping the attractor landscape of Boolean networks\" paper." article_processing_charge: No author: - first_name: Van Giang full_name: trinh, Van Giang last_name: trinh - first_name: Kyu Hyong full_name: Park, Kyu Hyong last_name: Park - first_name: Samuel full_name: Pastva, Samuel id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b last_name: Pastva orcid: 0000-0003-1993-0331 - first_name: Jordan full_name: Rozum, Jordan last_name: Rozum citation: ama: trinh VG, Park KH, Pastva S, Rozum J. Mapping the attractor landscape of Boolean networks. 2024. doi:10.5281/ZENODO.13854759 apa: trinh, V. G., Park, K. H., Pastva, S., & Rozum, J. (2024). Mapping the attractor landscape of Boolean networks. Zenodo. https://doi.org/10.5281/ZENODO.13854759 chicago: trinh, Van Giang, Kyu Hyong Park, Samuel Pastva, and Jordan Rozum. “Mapping the Attractor Landscape of Boolean Networks.” Zenodo, 2024. https://doi.org/10.5281/ZENODO.13854759. ieee: V. G. trinh, K. H. Park, S. Pastva, and J. Rozum, “Mapping the attractor landscape of Boolean networks.” Zenodo, 2024. ista: trinh VG, Park KH, Pastva S, Rozum J. 2024. Mapping the attractor landscape of Boolean networks, Zenodo, 10.5281/ZENODO.13854759. mla: trinh, Van Giang, et al. Mapping the Attractor Landscape of Boolean Networks. Zenodo, 2024, doi:10.5281/ZENODO.13854759. short: V.G. trinh, K.H. Park, S. Pastva, J. Rozum, (2024). date_created: 2025-06-10T07:10:01Z date_published: 2024-09-28T00:00:00Z date_updated: 2025-09-30T12:46:33Z day: '28' ddc: - '000' department: - _id: ToHe doi: 10.5281/ZENODO.13854759 fulldoi: https://doi.org/10.5281/ZENODO.13854759 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.13854760 month: '09' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '19796' relation: used_in_publication status: public status: public title: Mapping the attractor landscape of Boolean networks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '19809' abstract: - lang: eng text: In many physical situations in which many-body assemblies exist at temperature T, a characteristic quantum-mechanical time scale of approximately h/kbT can be identified in both theory and experiment, leading to speculation that it may be the shortest meaningful time in such circumstances. This behavior can be investigated by probing the scattering rate of electrons in a broad class of materials often referred to as “strongly correlated metals”. It is clear that in some cases only electron–electron scattering can be its cause, while in others it arises from high-temperature scattering of electrons from quantized lattice vibrations, i.e., phonons. In metallic oxides, which are among the most studied materials, analysis of electrical transport does not satisfactorily identify the relevant scattering mechanism at “high” temperatures near room temperature. We therefore employ a contactless optical method to measure thermal diffusivity in two Ru-based layered perovskites, Sr3Ru2O7 and Sr2RuO4, and use the measurements to extract the dimensionless Lorenz ratio. By comparing our results to the literature data on both conventional and unconventional metals, we show how the analysis of high-temperature thermal transport can both give important insight into dominant scattering mechanisms and be offered as a stringent test of theories attempting to explain anomalous scattering. article_processing_charge: No article_type: original author: - first_name: Fei full_name: Sun, Fei last_name: Sun - first_name: Simli full_name: Mishra, Simli last_name: Mishra - first_name: Ulrike full_name: Stockert, Ulrike last_name: Stockert - first_name: Ramzy full_name: Daou, Ramzy last_name: Daou - first_name: Naoki full_name: Kikugawa, Naoki last_name: Kikugawa - first_name: Robin S. full_name: Perry, Robin S. last_name: Perry - first_name: Elena full_name: Hassinger, Elena last_name: Hassinger - first_name: Sean A. full_name: Hartnoll, Sean A. last_name: Hartnoll - first_name: Andrew P. full_name: Mackenzie, Andrew P. last_name: Mackenzie - first_name: Veronika full_name: Sunko, Veronika id: 23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3 last_name: Sunko orcid: 0000-0003-2724-3523 citation: ama: Sun F, Mishra S, Stockert U, et al. The Lorenz ratio as a guide to scattering contributions to transport in strongly correlated metals. Proceedings of the National Academy of Sciences. 2024;121(35). doi:10.1073/pnas.2318159121 apa: Sun, F., Mishra, S., Stockert, U., Daou, R., Kikugawa, N., Perry, R. S., … Sunko, V. (2024). The Lorenz ratio as a guide to scattering contributions to transport in strongly correlated metals. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2318159121 chicago: Sun, Fei, Simli Mishra, Ulrike Stockert, Ramzy Daou, Naoki Kikugawa, Robin S. Perry, Elena Hassinger, Sean A. Hartnoll, Andrew P. Mackenzie, and Veronika Sunko. “The Lorenz Ratio as a Guide to Scattering Contributions to Transport in Strongly Correlated Metals.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2318159121. ieee: F. Sun et al., “The Lorenz ratio as a guide to scattering contributions to transport in strongly correlated metals,” Proceedings of the National Academy of Sciences, vol. 121, no. 35. National Academy of Sciences, 2024. ista: Sun F, Mishra S, Stockert U, Daou R, Kikugawa N, Perry RS, Hassinger E, Hartnoll SA, Mackenzie AP, Sunko V. 2024. The Lorenz ratio as a guide to scattering contributions to transport in strongly correlated metals. Proceedings of the National Academy of Sciences. 121(35). mla: Sun, Fei, et al. “The Lorenz Ratio as a Guide to Scattering Contributions to Transport in Strongly Correlated Metals.” Proceedings of the National Academy of Sciences, vol. 121, no. 35, National Academy of Sciences, 2024, doi:10.1073/pnas.2318159121. short: F. Sun, S. Mishra, U. Stockert, R. Daou, N. Kikugawa, R.S. Perry, E. Hassinger, S.A. Hartnoll, A.P. Mackenzie, V. Sunko, Proceedings of the National Academy of Sciences 121 (2024). date_created: 2025-06-10T09:12:41Z date_published: 2024-08-27T00:00:00Z date_updated: 2025-06-10T11:50:48Z day: '27' doi: 10.1073/pnas.2318159121 extern: '1' external_id: pmid: - '39172781' fulldoi: https://doi.org/10.1073/pnas.2318159121 has_accepted_license: '1' intvolume: ' 121' issue: '35' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.2318159121 month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: The Lorenz ratio as a guide to scattering contributions to transport in strongly correlated metals 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: 121 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19816' abstract: - lang: eng text: 'Understanding and manipulating emergent phases, which are themes at the forefront of quantum-materials research, rely on identifying their underlying symmetries. This general principle has been particularly prominent in materials with coupled electronic and magnetic degrees of freedom, in which magnetic order influences the electronic band structure and can lead to exotic topological effects. However, identifying symmetry of a magnetically ordered phase can pose a challenge, particularly in the presence of small domains. Here we introduce a multimodal approach for determining magnetic structures, which combines symmetry-sensitive optical probes, scattering, and group-theoretical analysis. We apply it to EuIn2⁢As2, a material that has received attention as a candidate axion insulator. While first-principles calculations predict this state on the assumption of a simple collinear antiferromagnetic structure, subsequent neutron-scattering measurements reveal a much more intricate magnetic ground state characterized by two coexisting magnetic wave vectors reached by successive thermal phase transitions. The proposed high- and low-temperature phases are a spin helix and a state with interpenetrating helical and Néel antiferromagnetic order termed a “broken helix,” respectively. Employing a multimodal approach, we identify the magnetic structure associated with these two phases of EuIn2⁢As2. We find that the higher-temperature phase is characterized by a variation of the magnetic moment amplitude from layer to layer, with the moment vanishing entirely in every third Eu layer. The lower-temperature structure is similar to the broken helix, with one important difference: Because of local strain, the relative orientation of the magnetic structure and the lattice is not fixed. Consequently, the symmetry required to protect the axion phase is not generically protected in EuIn2⁢As2, but we show that it can be restored if the magnetic structure is tuned with uniaxial strain. Finally, we present a spin Hamiltonian that identifies the spin interactions that account for the complex magnetic order in EuIn2⁢As2. Our work highlights the importance of a multimodal approach in determining the symmetry of complex order parameters.' article_number: '031013' article_processing_charge: No article_type: original author: - first_name: E. full_name: Donoway, E. last_name: Donoway - first_name: T. V. full_name: Trevisan, T. V. last_name: Trevisan - first_name: A. full_name: Liebman-Peláez, A. last_name: Liebman-Peláez - first_name: R. P. full_name: Day, R. P. last_name: Day - first_name: K. full_name: Yamakawa, K. last_name: Yamakawa - first_name: Y. full_name: Sun, Y. last_name: Sun - first_name: J. R. full_name: Soh, J. R. last_name: Soh - first_name: D. full_name: Prabhakaran, D. last_name: Prabhakaran - first_name: A. T. full_name: Boothroyd, A. T. last_name: Boothroyd - first_name: R. M. full_name: Fernandes, R. M. last_name: Fernandes - first_name: J. G. full_name: Analytis, J. G. last_name: Analytis - first_name: J. E. full_name: Moore, J. E. last_name: Moore - first_name: J. full_name: Orenstein, J. last_name: Orenstein - first_name: Veronika full_name: Sunko, Veronika id: 23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3 last_name: Sunko orcid: 0000-0003-2724-3523 citation: ama: Donoway E, Trevisan TV, Liebman-Peláez A, et al. Multimodal approach reveals the symmetry-breaking pathway to the broken helix in EuIn2As2. Physical Review X. 2024;14(3). doi:10.1103/physrevx.14.031013 apa: Donoway, E., Trevisan, T. V., Liebman-Peláez, A., Day, R. P., Yamakawa, K., Sun, Y., … Sunko, V. (2024). Multimodal approach reveals the symmetry-breaking pathway to the broken helix in EuIn2As2. Physical Review X. American Physical Society. https://doi.org/10.1103/physrevx.14.031013 chicago: Donoway, E., T. V. Trevisan, A. Liebman-Peláez, R. P. Day, K. Yamakawa, Y. Sun, J. R. Soh, et al. “Multimodal Approach Reveals the Symmetry-Breaking Pathway to the Broken Helix in EuIn2As2.” Physical Review X. American Physical Society, 2024. https://doi.org/10.1103/physrevx.14.031013. ieee: E. Donoway et al., “Multimodal approach reveals the symmetry-breaking pathway to the broken helix in EuIn2As2,” Physical Review X, vol. 14, no. 3. American Physical Society, 2024. ista: Donoway E, Trevisan TV, Liebman-Peláez A, Day RP, Yamakawa K, Sun Y, Soh JR, Prabhakaran D, Boothroyd AT, Fernandes RM, Analytis JG, Moore JE, Orenstein J, Sunko V. 2024. Multimodal approach reveals the symmetry-breaking pathway to the broken helix in EuIn2As2. Physical Review X. 14(3), 031013. mla: Donoway, E., et al. “Multimodal Approach Reveals the Symmetry-Breaking Pathway to the Broken Helix in EuIn2As2.” Physical Review X, vol. 14, no. 3, 031013, American Physical Society, 2024, doi:10.1103/physrevx.14.031013. short: E. Donoway, T.V. Trevisan, A. Liebman-Peláez, R.P. Day, K. Yamakawa, Y. Sun, J.R. Soh, D. Prabhakaran, A.T. Boothroyd, R.M. Fernandes, J.G. Analytis, J.E. Moore, J. Orenstein, V. Sunko, Physical Review X 14 (2024). date_created: 2025-06-10T09:17:30Z date_published: 2024-07-22T00:00:00Z date_updated: 2025-06-10T13:14:20Z day: '22' doi: 10.1103/physrevx.14.031013 extern: '1' fulldoi: https://doi.org/10.1103/physrevx.14.031013 intvolume: ' 14' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1103/physrevx.14.031013 month: '07' oa: 1 oa_version: Published Version publication: Physical Review X publication_identifier: eissn: - 2160-3308 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Multimodal approach reveals the symmetry-breaking pathway to the broken helix in EuIn2As2 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2024' ... --- OA_place: repository _id: '19884' abstract: - lang: eng text: "This is Marlin, a Mixed Auto-Regressive Linear kernel (and the name of one of the planet's fastest fish), an extremely optimized FP16xINT4 matmul kernel aimed at LLM inference that can deliver close to ideal (4x) speedups up to batchsizes of 16-32 tokens (in contrast to the 1-2 tokens of prior work with comparable speedup).\r\n\r\nAdditionally, it includes Sparse-Marlin, an extension of the MARLIN kernels adding support to 2:4 weight sparsity, achieving 5.3x speedups on NVIDIA GPUs (Ampere/Ada)." article_processing_charge: No author: - first_name: Elias full_name: Frantar, Elias id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f last_name: Frantar - first_name: Roberto full_name: Castro, Roberto last_name: Castro - first_name: Jiale full_name: Chen, Jiale id: 4d0a9064-1ff6-11ee-9fa6-ec046c604785 last_name: Chen orcid: 0000-0001-5337-5875 - first_name: Torsten full_name: Hoefler, Torsten last_name: Hoefler - 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: 'Frantar E, Castro R, Chen J, Hoefler T, Alistarh D-A. MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models. 2024. doi:10.5281/ZENODO.14213091' apa: 'Frantar, E., Castro, R., Chen, J., Hoefler, T., & Alistarh, D.-A. (2024). MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models. Zenodo. https://doi.org/10.5281/ZENODO.14213091' chicago: 'Frantar, Elias, Roberto Castro, Jiale Chen, Torsten Hoefler, and Dan-Adrian Alistarh. “MARLIN: Mixed-Precision Auto-Regressive Parallel Inference on Large Language Models.” Zenodo, 2024. https://doi.org/10.5281/ZENODO.14213091.' ieee: 'E. Frantar, R. Castro, J. Chen, T. Hoefler, and D.-A. Alistarh, “MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models.” Zenodo, 2024.' ista: 'Frantar E, Castro R, Chen J, Hoefler T, Alistarh D-A. 2024. MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models, Zenodo, 10.5281/ZENODO.14213091.' mla: 'Frantar, Elias, et al. MARLIN: Mixed-Precision Auto-Regressive Parallel Inference on Large Language Models. Zenodo, 2024, doi:10.5281/ZENODO.14213091.' short: E. Frantar, R. Castro, J. Chen, T. Hoefler, D.-A. Alistarh, (2024). corr_author: '1' date_created: 2025-06-24T06:09:18Z date_published: 2024-11-24T00:00:00Z date_updated: 2025-09-30T13:41:56Z day: '24' ddc: - '000' department: - _id: DaAl doi: 10.5281/ZENODO.14213091 fulldoi: https://doi.org/10.5281/ZENODO.14213091 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.14213091 month: '11' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '19877' relation: used_for_analysis_in status: public status: public title: 'MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher OA_type: free access _id: '20057' abstract: - lang: eng text: In article number 2305128, Qing Sun, Shang Wang, Yanhong Tian, Andreu Cabot, and co-workers report an investigation of the energy-storage mechanism of a layered Bi2Te3-based cathode for aqueous zinc-ion batteries (ZIBs). They demonstrate that the zinc ion is not inserted into the cathode as previously assumed; in contrast, proton charge-storage dominates the process. They also demonstrate the great application prospects of aqueous ZIBs in flexible electronics via jet printing technology. article_number: '2470004' article_processing_charge: No author: - first_name: Guifang full_name: Zeng, Guifang last_name: Zeng - first_name: Qing full_name: Sun, Qing last_name: Sun - first_name: Sharona full_name: Horta, Sharona id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc last_name: Horta - first_name: Shang full_name: Wang, Shang last_name: Wang - first_name: Xuan full_name: Lu, Xuan last_name: Lu - first_name: Chao Yue full_name: Zhang, Chao Yue last_name: Zhang - first_name: Jing full_name: Li, Jing last_name: Li - first_name: Junshan full_name: Li, Junshan last_name: Li - first_name: Lijie full_name: Ci, Lijie last_name: Ci - first_name: Yanhong full_name: Tian, Yanhong last_name: Tian - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Zeng G, Sun Q, Horta S, et al. A Layered Bi2Te3@PPy Cathode for Aqueous Zinc‐Ion Batteries: Mechanism and Application in Printed Flexible Batteries. Vol 36. Wiley; 2024. doi:10.1002/adma.202470004' apa: 'Zeng, G., Sun, Q., Horta, S., Wang, S., Lu, X., Zhang, C. Y., … Cabot, A. (2024). A layered Bi2Te3@PPy cathode for aqueous Zinc‐Ion batteries: Mechanism and application in printed flexible batteries. Advanced Materials (Vol. 36). Wiley. https://doi.org/10.1002/adma.202470004' chicago: 'Zeng, Guifang, Qing Sun, Sharona Horta, Shang Wang, Xuan Lu, Chao Yue Zhang, Jing Li, et al. A Layered Bi2Te3@PPy Cathode for Aqueous Zinc‐Ion Batteries: Mechanism and Application in Printed Flexible Batteries. Advanced Materials. Vol. 36. Wiley, 2024. https://doi.org/10.1002/adma.202470004.' ieee: 'G. Zeng et al., A layered Bi2Te3@PPy cathode for aqueous Zinc‐Ion batteries: Mechanism and application in printed flexible batteries, vol. 36, no. 1. Wiley, 2024.' ista: 'Zeng G, Sun Q, Horta S, Wang S, Lu X, Zhang CY, Li J, Li J, Ci L, Tian Y, Ibáñez M, Cabot A. 2024. A layered Bi2Te3@PPy cathode for aqueous Zinc‐Ion batteries: Mechanism and application in printed flexible batteries, Wiley,p.' mla: 'Zeng, Guifang, et al. “A Layered Bi2Te3@PPy Cathode for Aqueous Zinc‐Ion Batteries: Mechanism and Application in Printed Flexible Batteries.” Advanced Materials, vol. 36, no. 1, 2470004, Wiley, 2024, doi:10.1002/adma.202470004.' short: 'G. Zeng, Q. Sun, S. Horta, S. Wang, X. Lu, C.Y. Zhang, J. Li, J. Li, L. Ci, Y. Tian, M. Ibáñez, A. Cabot, A Layered Bi2Te3@PPy Cathode for Aqueous Zinc‐Ion Batteries: Mechanism and Application in Printed Flexible Batteries, Wiley, 2024.' date_created: 2025-07-21T08:53:06Z date_published: 2024-01-04T00:00:00Z date_updated: 2026-06-18T18:19:28Z day: '04' ddc: - '530' department: - _id: MaIb doi: 10.1002/adma.202470004 fulldoi: https://doi.org/10.1002/adma.202470004 intvolume: ' 36' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/adma.202470004 month: '01' oa: 1 oa_version: Published Version publication: Advanced Materials publication_identifier: eissn: - 1521-4095 issn: - 0935-9648 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: 'A layered Bi2Te3@PPy cathode for aqueous Zinc‐Ion batteries: Mechanism and application in printed flexible batteries' type: other_academic_publication user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20060' abstract: - lang: spa text: "Un fenómeno a menudo asociado con el autismo es un modo atípico de función ejecutiva, cuyas manifestaciones incluyen dificultad para iniciar tareas. En algunos casos, esto va acompañado de sentimientos de inercia y sensaciones que pueden describirse como inquietud y parálisis simultáneas. En consecuencia, la dificultad para iniciar las tareas puede dar lugar a la procrastinación, ya sea simplemente posponiendo el trabajo en la tarea objetivo o realizando otras tareas no relacionadas antes de dedicarse a la tarea objetivo. Curiosamente, sin embargo, también está documentado que, una vez iniciada una tarea, los autistas pueden centrarse en ella intensamente y durante periodos prolongados de tiempo, especialmente cuando les resulta interesante. \r\nEste trabajo utiliza el procesamiento predictivo y la inferencia activa para modelar la relación entre la función ejecutiva, la procrastinación y la hiperfocalización en el autismo. Este modelo integra las causas conocidas y propuestas de los déficits en la función ejecutiva y el papel que desempeña el interés en la regulación de la atención y la motivación. El modelo propone que la procrastinación es el resultado de procesos diferenciales de minimización de errores de predicción, como la ponderación de estímulos sensoriales. Se discuten los vínculos con modelos propuestos previamente, como la coherencia central débil (CCC), y la teoría de los priores altos e inflexibles de los errores de predicción en el autismo (HIPPEA)." - lang: eng text: A phenomenon often associated with autism is an atypical mode of executive function, manifestations of which include difficulty in initiating tasks. In some cases, this is accompanied by feelings of inertia and sensations that can be described as simultaneous restlessness and paralysis. Consequently, difficulty in getting started on tasks can result in procrastination, either by simply postponing working on the target task or by performing other unrelated tasks before engaging in the target task. Interestingly, however, it is also documented that once a task has been started, autistic persons may focus on it intensely and for prolonged periods of time, especially when it is interesting to them.This paper uses predictive processing and active inference to model therelationship between executive function, procrastination, and hyperfocus in autism. This model integrates the known and proposed causes of deficits in executive function and the role played by interest in attention regulation and motivation. The model proposes that procrastination is the outcome of differential prediction-error minimizing processes, such as weighting of sensory stimuli. Links to previously proposed models such as weak central coherence (WCC), and the theory of high, inflexible priors of prediction errors in autism (HIPPEA) are discussed acknowledgement: Sidney Carls-Diamante was supported by the Federal Ministry of Education and Research (BMBF) and the Baden-Württemberg Ministry of Science as part of the Excellence Strategy of the German Federal and State Governments. Alice Laciny was supported by the 2021 UNESCO L’Oréal grant for women in science, awarded for the project “Neurodiversity and anthropomorphism in social insect research”. article_processing_charge: Yes article_type: original author: - first_name: Sidney full_name: Carls-Diamante, Sidney last_name: Carls-Diamante - first_name: Alice full_name: Laciny, Alice id: accace3f-3f77-11eb-b1df-f1221b04cb95 last_name: Laciny orcid: 0000-0002-5485-1391 citation: ama: 'Carls-Diamante S, Laciny A. Stuck in uncertainty: A predictive processing/ active inference account of procrastination-like behaviour in autism. Lógoi Revista de Filosofía. 2024;(45):88-114. doi:10.62876/lr.vi45.6481' apa: 'Carls-Diamante, S., & Laciny, A. (2024). Stuck in uncertainty: A predictive processing/ active inference account of procrastination-like behaviour in autism. Lógoi. Revista de Filosofía. Universidad Católica Andrés Bello. https://doi.org/10.62876/lr.vi45.6481' chicago: 'Carls-Diamante, Sidney, and Alice Laciny. “Stuck in Uncertainty: A Predictive Processing/ Active Inference Account of Procrastination-like Behaviour in Autism.” Lógoi. Revista de Filosofía. Universidad Católica Andrés Bello, 2024. https://doi.org/10.62876/lr.vi45.6481.' ieee: 'S. Carls-Diamante and A. Laciny, “Stuck in uncertainty: A predictive processing/ active inference account of procrastination-like behaviour in autism,” Lógoi. Revista de Filosofía, no. 45. Universidad Católica Andrés Bello, pp. 88–114, 2024.' ista: 'Carls-Diamante S, Laciny A. 2024. Stuck in uncertainty: A predictive processing/ active inference account of procrastination-like behaviour in autism. Lógoi. Revista de Filosofía. (45), 88–114.' mla: 'Carls-Diamante, Sidney, and Alice Laciny. “Stuck in Uncertainty: A Predictive Processing/ Active Inference Account of Procrastination-like Behaviour in Autism.” Lógoi. Revista de Filosofía, no. 45, Universidad Católica Andrés Bello, 2024, pp. 88–114, doi:10.62876/lr.vi45.6481.' short: S. Carls-Diamante, A. Laciny, Lógoi. Revista de Filosofía (2024) 88–114. corr_author: '1' date_created: 2025-07-21T10:35:39Z date_published: 2024-03-19T00:00:00Z date_updated: 2025-09-09T08:51:00Z day: '19' ddc: - '570' doi: 10.62876/lr.vi45.6481 file: - access_level: open_access checksum: 04c950f26ad68455c3a303c87ccf2349 content_type: application/pdf creator: dernst date_created: 2025-09-09T08:48:53Z date_updated: 2025-09-09T08:48:53Z file_id: '20317' file_name: 2025_Logoi_CarlsDiamante.pdf file_size: 354124 relation: main_file success: 1 file_date_updated: 2025-09-09T08:48:53Z fulldoi: https://doi.org/10.62876/lr.vi45.6481 has_accepted_license: '1' issue: '45' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '03' oa: 1 oa_version: Published Version page: 88-114 publication: Lógoi. Revista de Filosofía publication_identifier: eissn: - 1316-693X issn: - 2790-5144 publication_status: published publisher: Universidad Católica Andrés Bello quality_controlled: '1' status: public title: 'Stuck in uncertainty: A predictive processing/ active inference account of procrastination-like behaviour in autism' 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: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- _id: '20121' abstract: - lang: eng text: PyDaddy is an open source package which is a key contribution of the manuscript Nabeel et al, arXiv:2205.02645. The basic scientific premise for this package is to discover the nature of stochasticity in ecological time series datasets. It is well known that the stochasticity can affect the dynamics of ecological systems in counter-intuitive ways. Without understanding the equations (typically, in the form of stochastic differential equations or SDEs, in short) that govern the dynamics of populations or ecosystems, it's challenging to determine the impact of randomness on real datasets. In this manuscript and accompanying package, we introduce a methodology for discovering equations (SDEs) that transforms time series data of state variables into stochastic differential equations. This approach merges traditional stochastic calculus with modern equation-discovery techniques. We showcase the generality of our method through various applications and discuss its limitations and potential pitfalls, offering diagnostic measures to address these challenges. acknowledgement: This study was partially funded by Science and Engineering Research Board, Department of Science and Technology, Government of India to Vishwesha Guttal. article_processing_charge: No author: - first_name: Arshed full_name: Nabeel, Arshed last_name: Nabeel - first_name: Ashwin full_name: Karichannavar, Ashwin last_name: Karichannavar - first_name: Shuaib full_name: Palathingal, Shuaib last_name: Palathingal - first_name: Jitesh full_name: Jhawar, Jitesh last_name: Jhawar - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Masila full_name: Danny Raj, Masila last_name: Danny Raj - first_name: Vishwesha full_name: Guttal, Vishwesha last_name: Guttal citation: ama: 'Nabeel A, Karichannavar A, Palathingal S, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. 2024. doi:10.5281/ZENODO.7137151' apa: 'Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Danny Raj, M., & Guttal, V. (2024). PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo. https://doi.org/10.5281/ZENODO.7137151' chicago: 'Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Masila Danny Raj, and Vishwesha Guttal. “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024. https://doi.org/10.5281/ZENODO.7137151.' ieee: 'A. Nabeel et al., “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024.' ista: 'Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Danny Raj M, Guttal V. 2024. PyDaddy: A Python Package for Discovering SDEs from Time Series Data, Zenodo, 10.5281/ZENODO.7137151.' mla: 'Nabeel, Arshed, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo, 2024, doi:10.5281/ZENODO.7137151.' short: A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, M. Danny Raj, V. Guttal, (2024). date_created: 2025-08-05T06:49:59Z date_published: 2024-09-18T00:00:00Z date_updated: 2025-09-30T14:14:42Z day: '18' ddc: - '570' department: - _id: EdHa doi: 10.5281/ZENODO.7137151 fulldoi: https://doi.org/10.5281/ZENODO.7137151 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7137151 month: '09' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '20056' relation: used_for_analysis_in status: public status: public title: 'PyDaddy: A Python Package for Discovering SDEs from Time Series Data' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '20756' abstract: - lang: eng text: Biocatalysis has the potential to address the need for more sustainable organic synthesis routes. Protein engineering can tune enzymes to perform in cascade reactions and for efficient synthesis of enantiomerically enriched compounds, using both natural and new-to-nature reaction pathways. This review highlights recent achievements in biocatalysis, especially the development of novel enzymatic syntheses to access versatile small molecule intermediates and complex biomolecules. Biocatalytic strategies for the degradation of persistent pollutants and approaches for biomass valorization are also discussed. The transition of chemical synthesis to a greener future will be accelerated by implementing enzymes and engineering them for high performance and new activities. article_number: '102536' article_processing_charge: No article_type: original author: - first_name: Julia full_name: Reisenbauer, Julia id: 51d862e9-36ee-11f0-86d3-8534c85a5496 last_name: Reisenbauer - first_name: Kathleen M. full_name: Sicinski, Kathleen M. last_name: Sicinski - first_name: Frances H. full_name: Arnold, Frances H. last_name: Arnold citation: ama: 'Reisenbauer J, Sicinski KM, Arnold FH. Catalyzing the future: Recent advances in chemical synthesis using enzymes. Current Opinion in Chemical Biology. 2024;83. doi:10.1016/j.cbpa.2024.102536' apa: 'Reisenbauer, J., Sicinski, K. M., & Arnold, F. H. (2024). Catalyzing the future: Recent advances in chemical synthesis using enzymes. Current Opinion in Chemical Biology. Elsevier. https://doi.org/10.1016/j.cbpa.2024.102536' chicago: 'Reisenbauer, Julia, Kathleen M. Sicinski, and Frances H. Arnold. “Catalyzing the Future: Recent Advances in Chemical Synthesis Using Enzymes.” Current Opinion in Chemical Biology. Elsevier, 2024. https://doi.org/10.1016/j.cbpa.2024.102536.' ieee: 'J. Reisenbauer, K. M. Sicinski, and F. H. Arnold, “Catalyzing the future: Recent advances in chemical synthesis using enzymes,” Current Opinion in Chemical Biology, vol. 83. Elsevier, 2024.' ista: 'Reisenbauer J, Sicinski KM, Arnold FH. 2024. Catalyzing the future: Recent advances in chemical synthesis using enzymes. Current Opinion in Chemical Biology. 83, 102536.' mla: 'Reisenbauer, Julia, et al. “Catalyzing the Future: Recent Advances in Chemical Synthesis Using Enzymes.” Current Opinion in Chemical Biology, vol. 83, 102536, Elsevier, 2024, doi:10.1016/j.cbpa.2024.102536.' short: J. Reisenbauer, K.M. Sicinski, F.H. Arnold, Current Opinion in Chemical Biology 83 (2024). date_created: 2025-12-09T14:22:40Z date_published: 2024-12-01T00:00:00Z date_updated: 2025-12-16T13:03:48Z day: '01' doi: 10.1016/j.cbpa.2024.102536 extern: '1' external_id: pmid: - '39369557' fulldoi: https://doi.org/10.1016/j.cbpa.2024.102536 intvolume: ' 83' language: - iso: eng main_file_link: - open_access: '1' url: https://europepmc.org/article/med/39369557#free-full-text month: '12' oa: 1 oa_version: Submitted Version pmid: 1 publication: Current Opinion in Chemical Biology publication_identifier: eissn: - 1879-0402 issn: - 1367-5931 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Catalyzing the future: Recent advances in chemical synthesis using enzymes' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 83 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '20757' abstract: - lang: eng text: We report the utilisation of an iodine(III) reagent to access α,β-unsaturated carbonyls from the corresponding silyl enol ethers and enol phosphates. The transformation can also be carried out in one pot, directly dehydrogenating carbonyls. article_processing_charge: No article_type: original author: - first_name: Bence B. full_name: Botlik, Bence B. last_name: Botlik - first_name: Patrick full_name: Finkelstein, Patrick last_name: Finkelstein - first_name: Ann-Sophie K. full_name: Paschke, Ann-Sophie K. last_name: Paschke - first_name: Julia full_name: Reisenbauer, Julia id: 51d862e9-36ee-11f0-86d3-8534c85a5496 last_name: Reisenbauer - first_name: Bill full_name: Morandi, Bill last_name: Morandi citation: ama: Botlik BB, Finkelstein P, Paschke A-SK, Reisenbauer J, Morandi B. Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. Chemical Communications. 2024;60(69):9254-9257. doi:10.1039/d4cc02609h apa: Botlik, B. B., Finkelstein, P., Paschke, A.-S. K., Reisenbauer, J., & Morandi, B. (2024). Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/d4cc02609h chicago: Botlik, Bence B., Patrick Finkelstein, Ann-Sophie K. Paschke, Julia Reisenbauer, and Bill Morandi. “Versatile Dehydrogenation of Carbonyls Enabled by an Iodine(III) Reagent.” Chemical Communications. Royal Society of Chemistry, 2024. https://doi.org/10.1039/d4cc02609h. ieee: B. B. Botlik, P. Finkelstein, A.-S. K. Paschke, J. Reisenbauer, and B. Morandi, “Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent,” Chemical Communications, vol. 60, no. 69. Royal Society of Chemistry, pp. 9254–9257, 2024. ista: Botlik BB, Finkelstein P, Paschke A-SK, Reisenbauer J, Morandi B. 2024. Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. Chemical Communications. 60(69), 9254–9257. mla: Botlik, Bence B., et al. “Versatile Dehydrogenation of Carbonyls Enabled by an Iodine(III) Reagent.” Chemical Communications, vol. 60, no. 69, Royal Society of Chemistry, 2024, pp. 9254–57, doi:10.1039/d4cc02609h. short: B.B. Botlik, P. Finkelstein, A.-S.K. Paschke, J. Reisenbauer, B. Morandi, Chemical Communications 60 (2024) 9254–9257. date_created: 2025-12-09T14:23:00Z date_published: 2024-08-02T00:00:00Z date_updated: 2025-12-16T11:19:43Z day: '02' doi: 10.1039/d4cc02609h extern: '1' external_id: pmid: - '39118590' fulldoi: https://doi.org/10.1039/d4cc02609h has_accepted_license: '1' intvolume: ' 60' issue: '69' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/3.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1039/D4CC02609H month: '08' oa: 1 oa_version: Published Version page: 9254-9257 pmid: 1 publication: Chemical Communications publication_identifier: eissn: - 1364-548X issn: - 1359-7345 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0) short: CC BY-NC (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '20807' abstract: - lang: eng text: Human glutamate carboxypeptidase 2 (GCP2) from the M28B metalloprotease group is an important target for therapy in neurological disorders and an established tumor marker. However, its physiological functions remain unclear. To better understand general roles, we used the model organism Caenorhabditis elegans to genetically manipulate its three existing orthologous genes and evaluate the impact on worm physiology. The results of gene knockout studies showed that C. elegans GCP2 orthologs affect the pharyngeal physiology, reproduction, and structural integrity of the organism. Promoter-driven GFP expression revealed distinct localization for each of the three gene paralogs, with gcp-2.1 being most abundant in muscles, intestine, and pharyngeal interneurons, gcp-2.2 restricted to the phasmid neurons, and gcp-2.3 located in the excretory cell. The present study provides new insight into the unique phenotypic effects of GCP2 gene knockouts in C. elegans, and the specific tissue localizations. We believe that elucidation of particular roles in a non-mammalian organism can help to explain important questions linked to physiology of this protease group and in extension to human GCP2 involvement in pathophysiological processes. article_number: BSR20230502 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Lucie full_name: Panska, Lucie last_name: Panska - first_name: Stepanka full_name: Nedvedova, Stepanka last_name: Nedvedova - first_name: Vojtech full_name: Vacek, Vojtech last_name: Vacek - first_name: Daniela full_name: Krivska, Daniela last_name: Krivska - first_name: Lukas full_name: Konecny, Lukas last_name: Konecny - first_name: Filip full_name: Knop, Filip id: 25f3131f-6e7c-11ef-8296-b64ccd4a1b69 last_name: Knop orcid: 0000-0002-3845-3465 - first_name: Zsofia full_name: Kutil, Zsofia last_name: Kutil - first_name: Lubica full_name: Skultetyova, Lubica last_name: Skultetyova - first_name: Adrian full_name: Leontovyc, Adrian last_name: Leontovyc - first_name: Lenka full_name: Ulrychova, Lenka last_name: Ulrychova - first_name: Judy full_name: Sakanari, Judy last_name: Sakanari - first_name: Masako full_name: Asahina, Masako last_name: Asahina - first_name: Cyril full_name: Barinka, Cyril last_name: Barinka - first_name: Marie full_name: Macurkova, Marie last_name: Macurkova - first_name: Jan full_name: Dvorak, Jan last_name: Dvorak citation: ama: Panska L, Nedvedova S, Vacek V, et al. Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. Bioscience Reports. 2024;44(1). doi:10.1042/bsr20230502 apa: Panska, L., Nedvedova, S., Vacek, V., Krivska, D., Konecny, L., Knop, F., … Dvorak, J. (2024). Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. Bioscience Reports. Portland Press. https://doi.org/10.1042/bsr20230502 chicago: Panska, Lucie, Stepanka Nedvedova, Vojtech Vacek, Daniela Krivska, Lukas Konecny, Filip Knop, Zsofia Kutil, et al. “Uncovering the Essential Roles of Glutamate Carboxypeptidase 2 Orthologs in Caenorhabditis Elegans.” Bioscience Reports. Portland Press, 2024. https://doi.org/10.1042/bsr20230502. ieee: L. Panska et al., “Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans,” Bioscience Reports, vol. 44, no. 1. Portland Press, 2024. ista: Panska L, Nedvedova S, Vacek V, Krivska D, Konecny L, Knop F, Kutil Z, Skultetyova L, Leontovyc A, Ulrychova L, Sakanari J, Asahina M, Barinka C, Macurkova M, Dvorak J. 2024. Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. Bioscience Reports. 44(1), BSR20230502. mla: Panska, Lucie, et al. “Uncovering the Essential Roles of Glutamate Carboxypeptidase 2 Orthologs in Caenorhabditis Elegans.” Bioscience Reports, vol. 44, no. 1, BSR20230502, Portland Press, 2024, doi:10.1042/bsr20230502. short: L. Panska, S. Nedvedova, V. Vacek, D. Krivska, L. Konecny, F. Knop, Z. Kutil, L. Skultetyova, A. Leontovyc, L. Ulrychova, J. Sakanari, M. Asahina, C. Barinka, M. Macurkova, J. Dvorak, Bioscience Reports 44 (2024). date_created: 2025-12-12T09:03:54Z date_published: 2024-01-12T00:00:00Z date_updated: 2025-12-15T10:21:56Z day: '12' ddc: - '570' doi: 10.1042/bsr20230502 extern: '1' external_id: pmid: - '38108122 ' fulldoi: https://doi.org/10.1042/bsr20230502 has_accepted_license: '1' intvolume: ' 44' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1042/BSR20230502 month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Bioscience Reports publication_identifier: eissn: - 1573-4935 issn: - 0144-8463 publication_status: published publisher: Portland Press quality_controlled: '1' scopus_import: '1' status: public title: Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 44 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '20808' abstract: - lang: eng text: During Caenorhabditis elegans development, multiple cells migrate long distances or extend processes to reach their final position and/or attain proper shape. The Wnt signalling pathway stands out as one of the major coordinators of cell migration or cell outgrowth along the anterior-posterior body axis. The outcome of Wnt signalling is fine-tuned by various mechanisms including endocytosis. In this study, we show that SEL-5, the C. elegans orthologue of mammalian AP2-associated kinase AAK1, acts together with the retromer complex as a positive regulator of EGL-20/Wnt signalling during the migration of QL neuroblast daughter cells. At the same time, SEL-5 in cooperation with the retromer complex is also required during excretory canal cell outgrowth. Importantly, SEL-5 kinase activity is not required for its role in neuronal migration or excretory cell outgrowth, and neither of these processes is dependent on DPY-23/AP2M1 phosphorylation. We further establish that the Wnt proteins CWN-1 and CWN-2, together with the Frizzled receptor CFZ-2, positively regulate excretory cell outgrowth, while LIN-44/Wnt and LIN-17/Frizzled together generate a stop signal inhibiting its extension. article_number: e91054 article_processing_charge: Yes article_type: original author: - first_name: Filip full_name: Knop, Filip id: 25f3131f-6e7c-11ef-8296-b64ccd4a1b69 last_name: Knop orcid: 0000-0002-3845-3465 - first_name: Apolena full_name: Zounarová, Apolena last_name: Zounarová - first_name: Vojtěch full_name: Šabata, Vojtěch last_name: Šabata - first_name: Teije Corneel full_name: Middelkoop, Teije Corneel last_name: Middelkoop - first_name: Marie full_name: Macůrková, Marie last_name: Macůrková citation: ama: Knop F, Zounarová A, Šabata V, Middelkoop TC, Macůrková M. Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. eLife. 2024;13. doi:10.7554/elife.91054 apa: Knop, F., Zounarová, A., Šabata, V., Middelkoop, T. C., & Macůrková, M. (2024). Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.91054 chicago: Knop, Filip, Apolena Zounarová, Vojtěch Šabata, Teije Corneel Middelkoop, and Marie Macůrková. “Caenorhabditis Elegans SEL-5/AAK1 Regulates Cell Migration and Cell Outgrowth Independently of Its Kinase Activity.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.91054. ieee: F. Knop, A. Zounarová, V. Šabata, T. C. Middelkoop, and M. Macůrková, “Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity,” eLife, vol. 13. eLife Sciences Publications, 2024. ista: Knop F, Zounarová A, Šabata V, Middelkoop TC, Macůrková M. 2024. Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. eLife. 13, e91054. mla: Knop, Filip, et al. “Caenorhabditis Elegans SEL-5/AAK1 Regulates Cell Migration and Cell Outgrowth Independently of Its Kinase Activity.” ELife, vol. 13, e91054, eLife Sciences Publications, 2024, doi:10.7554/elife.91054. short: F. Knop, A. Zounarová, V. Šabata, T.C. Middelkoop, M. Macůrková, ELife 13 (2024). date_created: 2025-12-12T09:06:31Z date_published: 2024-07-19T00:00:00Z date_updated: 2025-12-15T10:26:56Z day: '19' doi: 10.7554/elife.91054 extern: '1' external_id: pmid: - '39028260' fulldoi: https://doi.org/10.7554/elife.91054 intvolume: ' 13' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.7554/elife.91054 month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '9651' abstract: - lang: eng text: We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence. acknowledgement: 'Open access funding provided by Institute of Science and Technology (IST Austria). This work was started while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35. It was continued when the first named author was employed at University of Leipzig and the second named author was employed at Institute of Science and Technology of Austria, where he was supported by an IST Fellowship.' article_number: '15' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Michael full_name: Dymond, Michael last_name: Dymond - first_name: Vojtech full_name: Kaluza, Vojtech id: 21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E last_name: Kaluza orcid: 0000-0002-2512-8698 citation: ama: Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 2024;218. doi:10.1007/s10711-023-00862-3 apa: Dymond, M., & Kaluza, V. (2024). Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. Springer Nature. https://doi.org/10.1007/s10711-023-00862-3 chicago: Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata. Springer Nature, 2024. https://doi.org/10.1007/s10711-023-00862-3. ieee: M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” Geometriae Dedicata, vol. 218. Springer Nature, 2024. ista: Dymond M, Kaluza V. 2024. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 218, 15. mla: Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata, vol. 218, 15, Springer Nature, 2024, doi:10.1007/s10711-023-00862-3. short: M. Dymond, V. Kaluza, Geometriae Dedicata 218 (2024). corr_author: '1' date_created: 2021-07-14T07:01:27Z date_published: 2024-02-01T00:00:00Z date_updated: 2025-04-23T07:37:26Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.1007/s10711-023-00862-3 external_id: arxiv: - '2102.13046' isi: - '001105681500001' pmid: - '38021107' file: - access_level: open_access checksum: 9418534ac2f3d6f1f091a8b8ccaed01e content_type: application/pdf creator: dernst date_created: 2024-07-16T10:14:13Z date_updated: 2024-07-16T10:14:13Z file_id: '17257' file_name: 2024_GeometriaeDedicata_Dymond.pdf file_size: 540981 relation: main_file success: 1 file_date_updated: 2024-07-16T10:14:13Z fulldoi: https://doi.org/10.1007/s10711-023-00862-3 has_accepted_license: '1' intvolume: ' 218' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Geometriae Dedicata publication_identifier: eissn: - 1572-9168 issn: - 0046-5755 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Divergence of separated nets with respect to displacement equivalence 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: 218 year: '2024' ... --- APC_amount: 6828 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17202' abstract: - lang: eng text: Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for hybrid quantum circuits. In this study, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material. acknowledged_ssus: - _id: ScienComp - _id: M-Shop - _id: NanoFab acknowledgement: "We acknowledge Lucas Casparis, Jeroen Danon, Valla Fatemi, Morten Kjaergard and Javad Shabani for their valuable insights and comments. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop\r\nand the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the FWF Projects with DOI:10.55776/I5060 and DOI:10.55776/P36507. We also acknowledge the NextGenerationEU PRIN project\r\n2022A8CJP3 (GAMESQUAD) for partial financial support." article_number: '6400' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Oliver full_name: Sagi, Oliver id: 71616374-A8E9-11E9-A7CA-09ECE5697425 last_name: Sagi - first_name: Alessandro full_name: Crippa, Alessandro id: 1F2B21A2-F6E7-11E9-9B82-F7DBE5697425 last_name: Crippa orcid: 0000-0002-2968-611X - first_name: Marco full_name: Valentini, Marco id: C0BB2FAC-D767-11E9-B658-BC13E6697425 last_name: Valentini - first_name: Marian full_name: Janik, Marian id: 396A1950-F248-11E8-B48F-1D18A9856A87 last_name: Janik orcid: 0009-0003-9037-8831 - first_name: Levon full_name: Baghumyan, Levon id: 7aa1f788-b527-11ee-aa9e-e6111a79e0c7 last_name: Baghumyan - first_name: Giorgio full_name: Fabris, Giorgio id: 298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352 last_name: Fabris - first_name: Lucky full_name: Kapoor, Lucky id: 84b9700b-15b2-11ec-abd3-831089e67615 last_name: Kapoor orcid: 0000-0001-8319-2148 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Stefano full_name: Calcaterra, Stefano last_name: Calcaterra - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Sagi O, Crippa A, Valentini M, et al. A gate tunable transmon qubit in planar Ge. Nature Communications. 2024;15. doi:10.1038/s41467-024-50763-6 apa: Sagi, O., Crippa, A., Valentini, M., Janik, M., Baghumyan, L., Fabris, G., … Katsaros, G. (2024). A gate tunable transmon qubit in planar Ge. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-50763-6 chicago: Sagi, Oliver, Alessandro Crippa, Marco Valentini, Marian Janik, Levon Baghumyan, Giorgio Fabris, Lucky Kapoor, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-50763-6. ieee: O. Sagi et al., “A gate tunable transmon qubit in planar Ge,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Sagi O, Crippa A, Valentini M, Janik M, Baghumyan L, Fabris G, Kapoor L, Hassani F, Fink JM, Calcaterra S, Chrastina D, Isella G, Katsaros G. 2024. A gate tunable transmon qubit in planar Ge. Nature Communications. 15, 6400. mla: Sagi, Oliver, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” Nature Communications, vol. 15, 6400, Springer Nature, 2024, doi:10.1038/s41467-024-50763-6. short: O. Sagi, A. Crippa, M. Valentini, M. Janik, L. Baghumyan, G. Fabris, L. Kapoor, F. Hassani, J.M. Fink, S. Calcaterra, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024). corr_author: '1' date_created: 2024-07-04T11:40:45Z date_published: 2024-07-30T00:00:00Z date_updated: 2026-04-07T13:01:55Z day: '30' ddc: - '530' department: - _id: GeKa - _id: JoFi - _id: GradSch doi: 10.1038/s41467-024-50763-6 external_id: arxiv: - '2403.16774' isi: - '001281271000022' pmid: - '39080279' file: - access_level: open_access checksum: ddf5361dcb6c543e2cea818501c09910 content_type: application/pdf creator: dernst date_created: 2024-08-05T08:38:01Z date_updated: 2024-08-05T08:38:01Z file_id: '17388' file_name: 2024_NatureComm_Sagi.pdf file_size: 1928001 relation: main_file success: 1 file_date_updated: 2024-08-05T08:38:01Z fulldoi: https://doi.org/10.1038/s41467-024-50763-6 has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a grant_number: P36507 name: Merging spin and superconducting qubits in planar Ge - _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1 grant_number: I05060 name: High impedance circuit quantum electrodynamics with hole spins - _id: 262116AA-B435-11E9-9278-68D0E5697425 name: Hybrid Semiconductor - Superconductor Quantum Devices - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-024-53910-1 record: - id: '17196' relation: research_data status: public - id: '18076' relation: dissertation_contains status: public scopus_import: '1' status: public title: A gate tunable transmon qubit in planar Ge 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: 15 year: '2024' ... --- _id: '17203' abstract: - lang: eng text: "The behavior of a rigid body primarily depends on its mass moments, which consist of the mass, center of mass, and moments of inertia. It is possible to manipulate these quantities without altering the geometric appearance of an object by introducing cavities in its interior. Algorithms that find cavities of suitable shapes and sizes have enabled the computational design of spinning tops, yo-yos, wheels, buoys, and statically balanced objects. Previous work is based, for example, on topology optimization on voxel grids, which introduces a large number of optimization variables and box constraints, or offset surface computation, which cannot guarantee that solutions to a feasible problem will always be found.\r\n\r\nIn this work, we provide a mathematical analysis of constrained topology optimization problems that depend only on mass moments. This class of problems covers, among others, all applications mentioned above. Our main result is to show that no matter the outer shape of the rigid body to be optimized or the optimization objective and constraints considered, the optimal solution always features a quadric-shaped interface between material and cavities. This proves that optimal interfaces are always ellipsoids, hyperboloids, paraboloids, or one of a few degenerate cases, such as planes.\r\n\r\nThis insight lets us replace a difficult topology optimization problem with a provably equivalent non-linear equation system in a small number (<10) of variables, which represent the coefficients of the quadric. This system can be solved in a few seconds for most examples, provides insights into the geometric structure of many specific applications, and lets us describe their solution properties. Finally, our method integrates seamlessly into modern fabrication workflows because our solutions are analytical surfaces that are native to the CAD domain." acknowledgement: We thank Gianmarco Cherchi for his help in tailoring the Mesh Booleans code for this project, Stefan Jeschke for his help with the photographs, Malina Strugaru and Aleksei Kalinov for their help with the samples, and the anonymous reviewers as well as the members of the ISTA Visual Computing Group for their feedback. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA). article_number: '78' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Christian full_name: Hafner, Christian id: 400429CC-F248-11E8-B48F-1D18A9856A87 last_name: Hafner - 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: 'Hafner C, Ly M, Wojtan C. Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. 2024;43(4). doi:10.1145/3658194' apa: 'Hafner, C., Ly, M., & Wojtan, C. (2024). Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. Denver, Colorado: Association for Computing Machinery. https://doi.org/10.1145/3658194' chicago: 'Hafner, Christian, Mickaël Ly, and Chris Wojtan. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” Transactions on Graphics. Association for Computing Machinery, 2024. https://doi.org/10.1145/3658194.' ieee: 'C. Hafner, M. Ly, and C. Wojtan, “Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments,” Transactions on Graphics, vol. 43, no. 4. Association for Computing Machinery, 2024.' ista: 'Hafner C, Ly M, Wojtan C. 2024. Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. 43(4), 78.' mla: 'Hafner, Christian, et al. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” Transactions on Graphics, vol. 43, no. 4, 78, Association for Computing Machinery, 2024, doi:10.1145/3658194.' short: C. Hafner, M. Ly, C. Wojtan, Transactions on Graphics 43 (2024). conference: end_date: 2024-08-01 location: Denver, Colorado start_date: 2024-07-28 corr_author: '1' date_created: 2024-07-05T12:08:57Z date_published: 2024-07-01T00:00:00Z date_updated: 2025-09-08T08:29:09Z day: '01' ddc: - '516' department: - _id: ChWo doi: 10.1145/3658194 external_id: isi: - '001289270900045' file: - access_level: open_access checksum: 0dc9f5a6422b8a49a79026900f349ee5 content_type: application/pdf creator: chafner date_created: 2024-07-05T12:05:17Z date_updated: 2024-07-05T12:05:17Z file_id: '17204' file_name: sif-final.pdf file_size: 7225150 relation: main_file success: 1 - access_level: open_access checksum: cde433c6a40688d5f1187fb5721f6f94 content_type: application/pdf creator: chafner date_created: 2024-07-05T12:06:03Z date_updated: 2024-07-05T12:06:03Z file_id: '17205' file_name: sif-supp-final.pdf file_size: 397262 relation: supplementary_material - access_level: open_access checksum: c0457a09c2ab9a1c2935c995dcc84907 content_type: video/mp4 creator: chafner date_created: 2024-07-17T09:29:13Z date_updated: 2024-07-17T09:29:13Z file_id: '17276' file_name: sif-video-final.mp4 file_size: 170001305 relation: supplementary_material title: Submission Video file_date_updated: 2024-07-17T09:29:13Z fulldoi: https://doi.org/10.1145/3658194 has_accepted_license: '1' intvolume: ' 43' isi: 1 issue: '4' keyword: - Topology Optimization - Mass Moments - Computational Geometry language: - iso: eng month: '07' 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: 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: 'Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 43 year: '2024' ... --- _id: '17207' acknowledgement: "This research was funded by the Austrian Science Fund (FWF), project doi: 10.55776/P32896, Institutional Identifier: 501100002428, grant number: P32896 and L.F. acknowledges the support of the NOMIS-ISTA Fellowship Program.\r\nWe would like to thank Nick Barton, Roger Butlin, Stuart Baird, Patrik Nosil, and Jason Sexton for their insightful comments on the earlier drafts, and to John Carchrae for his valuable contribution in refining phrasing and enhancing clarity. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission." article_processing_charge: No article_type: letter_note author: - first_name: Louise full_name: Fouqueau, Louise id: 1676e173-8143-11ed-8927-fe165216a93f last_name: Fouqueau orcid: 0000-0003-0371-9339 - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 citation: ama: 'Fouqueau L, Polechova J. Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of evolutionary biology. 2024;37(6):579-587. doi:10.1093/jeb/voae067' apa: 'Fouqueau, L., & Polechova, J. (2024). Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of Evolutionary Biology. Oxford University Press. https://doi.org/10.1093/jeb/voae067' chicago: 'Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” Journal of Evolutionary Biology. Oxford University Press, 2024. https://doi.org/10.1093/jeb/voae067.' ieee: 'L. Fouqueau and J. Polechova, “Eco-evolutionary dynamics in changing environments: Integrating theory with data,” Journal of evolutionary biology, vol. 37, no. 6. Oxford University Press, pp. 579–587, 2024.' ista: 'Fouqueau L, Polechova J. 2024. Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of evolutionary biology. 37(6), 579–587.' mla: 'Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” Journal of Evolutionary Biology, vol. 37, no. 6, Oxford University Press, 2024, pp. 579–87, doi:10.1093/jeb/voae067.' short: L. Fouqueau, J. Polechova, Journal of Evolutionary Biology 37 (2024) 579–587. date_created: 2024-07-07T22:01:04Z date_published: 2024-06-28T00:00:00Z date_updated: 2026-06-18T17:53:35Z day: '28' ddc: - '570' department: - _id: NiBa doi: 10.1093/jeb/voae067 external_id: isi: - '001258359900001' pmid: - '38941551' fulldoi: https://doi.org/10.1093/jeb/voae067 intvolume: ' 37' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/jeb/voae067 month: '06' oa: 1 oa_version: Published Version page: 579-587 pmid: 1 project: - _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8 grant_number: P32896 name: Causes and consequences of population fragmentation - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program publication: Journal of evolutionary biology publication_identifier: eissn: - 1420-9101 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Eco-evolutionary dynamics in changing environments: Integrating theory with data' 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: 37 year: '2024' ... --- OA_place: publisher _id: '17208' abstract: - lang: eng text: "Can current quantum computers provide a speedup over their classical counterparts for some kinds of problems? In this thesis, with a focus on ground state search/preparation, we address some of the challenges that both quantum annealing and variational quantum algorithms suffer from, hindering any possible practical speedup in comparison to the best classical counterparts. \r\n\r\nIn the first part of the thesis, we study the performance of quantum annealing for solving a particular combinatorial optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$. We consider how modifying the initial problem, by adding more interaction terms to the corresponding Hamiltonian, leads to the emergence of a first-order phase transition during the annealing process. This phenomenon causes the total annealing duration, $T$, required to prepare the ground state of $H_C$ with a high probability to increase exponentially with the size of the problem. Our findings indicate that with the growing complexity of problem instances, the likelihood of encountering first-order phase transitions also increases, making quantum annealing an impractical solution for these types of combinatorial optimization problems.\r\n\r\nIn the second part, we focus on the problem of barren plateaus in generic variational quantum algorithms. Barren plateaus correspond to flat regions in the parameter space where the gradient of the cost function is zero in expectation, and with the variance decaying exponentially with the system size, thus obstructing an efficient parameter optimization. We propose an algorithm to circumvent Barren Plateaus by monitoring the entanglement entropy of k-local reduced density matrices, alongside a method for estimating entanglement entropy via classical shadow tomography. We illustrate the approach with the paradigmatic example of the variational quantum eigensolver, and show that our algorithm effectively avoids barren plateaus in the initialization as well as during the optimization stage. \r\n\r\nLastly, in the last two Chapters of this thesis, we focus on the quantum approximate optimization algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial optimization problems in near-term quantum devices. Specifically, we focus on how to develop rigorous initialization strategies with guarantee improvement. Our motivation for this study lies in that for random initialization, the optimization typically leads to local minima with poor performance. Our main result corresponds to the analytical construction of index-1 saddle points or transition states, stationary points with a single direction of descent, as a tool for systematically exploring the QAOA optimization landscape. This leads us to propose a novel greedy parameter initialization strategy that guarantees for the energy to decrease with an increasing number of circuit layers. Furthermore, with precise estimates for the negative Hessian eigenvalue and its eigenvector, we establish a lower bound for energy improvement following a QAOA iteration." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Raimel A full_name: Medina Ramos, Raimel A id: CE680B90-D85A-11E9-B684-C920E6697425 last_name: Medina Ramos orcid: 0000-0002-5383-2869 citation: ama: Medina Ramos RA. Exploring the optimization landscape of variational quantum algorithms. 2024. doi:10.15479/at:ista:17208 apa: Medina Ramos, R. A. (2024). Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17208 chicago: Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational Quantum Algorithms.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17208. ieee: R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum algorithms,” Institute of Science and Technology Austria, 2024. ista: Medina Ramos RA. 2024. Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria. mla: Medina Ramos, Raimel A. Exploring the Optimization Landscape of Variational Quantum Algorithms. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17208. short: R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum Algorithms, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-07-09T09:14:24Z date_published: 2024-07-09T00:00:00Z date_updated: 2026-04-07T12:43:22Z day: '09' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: MaSe doi: 10.15479/at:ista:17208 ec_funded: 1 file: - access_level: closed checksum: 6f45273d04f4418bc2adc018baed0525 content_type: application/zip creator: rmedinar date_created: 2024-07-09T09:21:44Z date_updated: 2024-07-10T11:34:09Z file_id: '17212' file_name: Raimel_Thesis-Final.zip file_size: '14218691' relation: source_file - access_level: open_access checksum: 6724a95bec772dbabc0111b9f08a805e content_type: application/pdf creator: rmedinar date_created: 2024-07-17T09:23:24Z date_updated: 2024-07-17T09:23:24Z file_id: '17275' file_name: Raimel_Thesis-20_pdfa.pdf file_size: 11253627 relation: main_file success: 1 file_date_updated: 2024-07-17T09:23:24Z fulldoi: https://doi.org/10.15479/at:ista:17208 has_accepted_license: '1' keyword: - Quantum computing - Variational Quantum Algorithms - Optimization language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '133' project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10545' relation: part_of_dissertation status: public - id: '10067' relation: part_of_dissertation status: public - id: '17222' relation: part_of_dissertation status: public - id: '13125' relation: part_of_dissertation status: public - id: '11471' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 title: Exploring the optimization landscape of variational quantum algorithms tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- _id: '17214' abstract: - lang: eng text: 'Current numerical algorithms for simulating friction fall in one of two camps: smooth solvers sacrifice the stable treatment of static friction in exchange for fast convergence, and non-smooth solvers accurately compute friction at convergence rates that are often prohibitive for large graphics applications. We introduce a novel bridge between these two ideas that computes static and dynamic friction stably and efficiently. Our key idea is to convert the highly constrained non-smooth problem into an unconstrained smooth problem using logarithmic barriers that converges to the exact solution as accuracy increases. We phrase the problem as an interior point primal-dual problem that can be solved efficiently with Newton iteration. We observe quadratic convergence despite the non-smooth nature of the original problem, and our method is well-suited for large systems of tightly packed objects with many contact points. We demonstrate the efficacy of our method with stable piles of grains and stacks of objects, complex granular flows, and robust interlocking assemblies of rigid bodies.' acknowledgement: We thank Vincent Acary for his help with Siconos, as well as the anonymous reviewers and the members of the Visual Computing Group at ISTA for their helpful comments. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA). article_processing_charge: Yes (via OA deal) 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. Primal-dual non-smooth friction for rigid body animation. In: Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Association for Computing Machinery; 2024. doi:10.1145/3641519.3657485' apa: 'Chen, Y.-L., Ly, M., & Wojtan, C. (2024). Primal-dual non-smooth friction for rigid body animation. In Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Denver, United States: Association for Computing Machinery. https://doi.org/10.1145/3641519.3657485' chicago: Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” In Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Association for Computing Machinery, 2024. https://doi.org/10.1145/3641519.3657485. ieee: Y.-L. Chen, M. Ly, and C. Wojtan, “Primal-dual non-smooth friction for rigid body animation,” in Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Denver, United States, 2024. ista: 'Chen Y-L, Ly M, Wojtan C. 2024. Primal-dual non-smooth friction for rigid body animation. Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. SIGGRAPH: Computer Graphics and Interactive Techniques Conference.' mla: Chen, Yi-Lu, et al. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024, doi:10.1145/3641519.3657485. short: Y.-L. Chen, M. Ly, C. Wojtan, in:, Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024. conference: end_date: 2024-08-01 location: Denver, United States name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2024-07-28 corr_author: '1' date_created: 2024-07-10T11:06:20Z date_published: 2024-07-01T00:00:00Z date_updated: 2025-09-08T08:54:38Z day: '01' ddc: - '621' - '531' - '006' department: - _id: GradSch - _id: ChWo doi: 10.1145/3641519.3657485 external_id: isi: - '001282218200091' file: - access_level: open_access checksum: b8b203ed09e3995ba0d7e6a76288663a content_type: application/pdf creator: yichen date_created: 2024-07-10T11:03:14Z date_updated: 2024-07-10T11:03:14Z file_id: '17215' file_name: sig24_friction_authors.pdf file_size: 47309472 relation: main_file success: 1 - access_level: open_access checksum: 89d81b397b4b6469d828808a68b70820 content_type: application/pdf creator: yichen date_created: 2024-07-10T11:03:12Z date_updated: 2024-07-10T11:03:12Z file_id: '17216' file_name: sig24_friction_supplementary.pdf file_size: 10518286 relation: main_file success: 1 - access_level: open_access checksum: 7123deed34a5456810e7b5336a31c657 content_type: video/mp4 creator: yichen date_created: 2024-07-10T11:03:51Z date_updated: 2024-07-10T11:03:51Z file_id: '17217' file_name: friction_paper_extra_video_finished.mp4 file_size: 71789192 relation: main_file success: 1 - access_level: open_access checksum: e606fc1ae8f2610ce3b4421566800b45 content_type: video/mp4 creator: yichen date_created: 2024-07-10T11:03:58Z date_updated: 2024-07-10T11:03:58Z file_id: '17218' file_name: friction_paper_video_finished.mp4 file_size: 280610763 relation: main_file success: 1 file_date_updated: 2024-07-10T11:03:58Z fulldoi: https://doi.org/10.1145/3641519.3657485 has_accepted_license: '1' isi: 1 keyword: - physical simulation - frictional contact - rigid body mechanics - non-smooth dynamics language: - iso: eng month: '07' 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: Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24 publication_identifier: isbn: - '9798400705250' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Primal-dual non-smooth friction for rigid body animation type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '17219' abstract: - lang: eng text: 'We introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts self-intersections into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations with thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting of millions of triangles.' acknowledgement: Peter Heiss-Synak helped conceive the project, helped formulate the algorithm structure, contributed ideas and code to Sections 6 & 8, the mesh data structure, algorithm robustness and benchmarks, helped write the paper, and provided supervision and conceptual solutions throughout the project. Aleksei Kalinov contributed ideas and code to Sections 7, 8.5, and 5, the sparse grid data structure, algorithm robustness and benchmarks, optimized the performance, produced all results, most figures, and the supplementary video, helped write the text, and provided conceptual solutions throughout the project. Malina Strugaru helped implement the mesh data structure and designed re-meshing operations for non-manifold triangle meshes. Arian Etemadi developed early prototypes for ideas in Sections 8.1 and 8.3 and helped write the paper. Huidong Yang developed early prototypes for isosurface extraction and visualization. Chris Wojtan helped conceive the project, helped write the paper, and provided supervision, prototype grid data structure code, and conceptual solutions throughout the project. We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback, Christopher Batty for discussions about LosTopos, and SideFX for the Houdini Education software licenses. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA). article_number: '54' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Peter full_name: Synak, Peter id: 331776E2-F248-11E8-B48F-1D18A9856A87 last_name: Synak - first_name: Aleksei full_name: Kalinov, Aleksei id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02 last_name: Kalinov orcid: 0000-0003-2189-3904 - first_name: Irina-Malina full_name: Strugaru, Irina-Malina id: 2afc607f-f128-11eb-9611-8f2a0dfcf074 last_name: Strugaru - first_name: Arian full_name: Etemadihaghighi, Arian id: 36cea3aa-f38e-11ec-8ae0-c65ae6f6098f last_name: Etemadihaghighi - first_name: Huidong full_name: Yang, Huidong last_name: Yang - 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: Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 2024;43(4). doi:10.1145/3658223 apa: Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., & Wojtan, C. (2024). Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3658223 chicago: Synak, Peter, Aleksei Kalinov, Irina-Malina Strugaru, Arian Etemadi, Huidong Yang, and Chris Wojtan. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” ACM Transactions on Graphics. Association for Computing Machinery, 2024. https://doi.org/10.1145/3658223. ieee: P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, and C. Wojtan, “Multi-material mesh-based surface tracking with implicit topology changes,” ACM Transactions on Graphics, vol. 43, no. 4. Association for Computing Machinery, 2024. ista: Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 2024. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 43(4), 54. mla: Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” ACM Transactions on Graphics, vol. 43, no. 4, 54, Association for Computing Machinery, 2024, doi:10.1145/3658223. short: P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM Transactions on Graphics 43 (2024). corr_author: '1' date_created: 2024-07-10T12:24:00Z date_published: 2024-07-01T00:00:00Z date_updated: 2026-04-07T13:02:36Z day: '01' ddc: - '004' department: - _id: GradSch - _id: ChWo doi: 10.1145/3658223 external_id: isi: - '001289270900021' file: - access_level: open_access checksum: 1917067d4b52d7729019b03560004e43 content_type: application/pdf creator: dernst date_created: 2024-07-23T06:35:15Z date_updated: 2024-07-23T06:35:15Z file_id: '17317' file_name: 2024_ACMToG_HeissSynak.pdf file_size: 48763368 relation: main_file success: 1 - access_level: open_access checksum: a4f0e293184bfa034c0c585848806b17 content_type: video/mp4 creator: akalinov date_created: 2024-07-10T12:23:44Z date_updated: 2024-07-10T12:23:44Z file_id: '17221' file_name: sdtopofixer_final.mp4 file_size: 48021463 relation: main_file success: 1 - access_level: open_access checksum: 18fc310a78ec91651148c45a8b89fa44 content_type: application/pdf creator: akalinov date_created: 2025-11-11T09:50:52Z date_updated: 2025-11-11T09:50:52Z file_id: '20633' file_name: SuperDuperTopoFixer.pdf file_size: 48639581 relation: preprint title: Authors' version of the text file_date_updated: 2025-11-11T09:50:52Z fulldoi: https://doi.org/10.1145/3658223 has_accepted_license: '1' intvolume: ' 43' isi: 1 issue: '4' keyword: - surface tracking - topology change - non- manifold meshes - multi-material flows - solid modeling language: - iso: eng month: '07' 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' related_material: record: - id: '19630' relation: dissertation_contains status: public - id: '18301' relation: dissertation_contains status: public scopus_import: '1' status: public title: Multi-material mesh-based surface tracking with implicit topology changes 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: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2024' ... --- OA_place: repository _id: '17222' abstract: - lang: eng text: "The quantum approximate optimization algorithm (QAOA) uses a quantum computer\r\nto implement a variational method with $2p$ layers of alternating unitary\r\noperators, optimized by a classical computer to minimize a cost function. While\r\nrigorous performance guarantees exist for the QAOA at small depths $p$, the\r\nbehavior at large depths remains less clear, though simulations suggest\r\nexponentially fast convergence for certain problems. In this work, we gain\r\ninsights into the deep QAOA using an analytic expansion of the cost function\r\naround transition states. Transition states are constructed in a recursive\r\nmanner: from the local minima of the QAOA with $p$ layers we obtain transition\r\nstates of the QAOA with $p+1$ layers, which are stationary points characterized\r\nby a unique direction of negative curvature. We construct an analytic estimate\r\nof the negative curvature and the corresponding direction in parameter space at\r\neach transition state. The expansion of the QAOA cost function along the\r\nnegative direction to the quartic order gives a lower bound of the QAOA cost\r\nfunction improvement. We provide physical intuition behind the analytic\r\nexpressions for the local curvature and quartic expansion coefficient. Our\r\nnumerical study confirms the accuracy of our approximations and reveals that\r\nthe obtained bound and the true value of the QAOA cost function gain have a\r\ncharacteristic exponential decrease with the number of layers $p$, with the\r\nbound decreasing more rapidly. Our study establishes an analytical method for\r\nrecursively studying the QAOA that is applicable in the regime of high circuit\r\ndepth." article_number: '2405.10125' article_processing_charge: No arxiv: 1 author: - first_name: Raimel A full_name: Medina Ramos, Raimel A id: CE680B90-D85A-11E9-B684-C920E6697425 last_name: Medina Ramos orcid: 0000-0002-5383-2869 - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. arXiv. doi:10.48550/arXiv.2405.10125 apa: Medina Ramos, R. A., & Serbyn, M. (n.d.). A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. arXiv. https://doi.org/10.48550/arXiv.2405.10125 chicago: Medina Ramos, Raimel A, and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2405.10125. ieee: R. A. Medina Ramos and M. Serbyn, “A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm,” arXiv. . ista: Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. arXiv, 2405.10125. mla: Medina Ramos, Raimel A., and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” ArXiv, 2405.10125, doi:10.48550/arXiv.2405.10125. short: R.A. Medina Ramos, M. Serbyn, ArXiv (n.d.). corr_author: '1' date_created: 2024-07-10T13:12:09Z date_published: 2024-05-16T00:00:00Z date_updated: 2026-04-07T12:43:22Z day: '16' department: - _id: MaSe doi: 10.48550/arXiv.2405.10125 external_id: arxiv: - '2405.10125' fulldoi: https://doi.org/10.48550/arXiv.2405.10125 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2405.10125 month: '05' oa: 1 oa_version: Preprint publication: arXiv publication_status: draft related_material: record: - id: '17208' relation: dissertation_contains status: public status: public title: A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ...