[{"citation":{"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.","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","ieee":"D. Vijatovic et al., “Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis,” bioRxiv. .","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.).","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."},"OA_place":"repository","_id":"19520","publication":"bioRxiv","abstract":[{"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.","lang":"eng"}],"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.). ","year":"2024","day":"27","doi":"10.1101/2024.09.20.614050","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"},{"name":"Development and Evolution of Tetrapod Motor Circuits","grant_number":"101041551","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae"},{"grant_number":"CZI01","_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","name":"Tools for automation and feedback microscopy"}],"department":[{"_id":"LoSw"},{"_id":"TiVo"},{"_id":"Bio"},{"_id":"NiBa"}],"publication_status":"submitted","OA_type":"green","date_published":"2024-09-27T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.09.20.614050"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_created":"2025-04-07T08:48:28Z","month":"09","oa_version":"Preprint","fulldoi":"https://doi.org/10.1101/2024.09.20.614050","corr_author":"1","type":"preprint","title":"Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis","status":"public","oa":1,"acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"date_updated":"2025-05-14T11:40:13Z","author":[{"last_name":"Vijatovic","id":"cf391e77-ec3c-11ea-a124-d69323410b58","first_name":"David","full_name":"Vijatovic, David"},{"full_name":"Toma, Florina Alexandra ","first_name":"Florina Alexandra ","id":"2f73f876-f128-11eb-9611-b96b5a30cb0e","last_name":"Toma"},{"orcid":"0009-0008-0158-4032","full_name":"Harrington, Zoe P","id":"a8144562-32c9-11ee-b5ce-d9800628bda2","last_name":"Harrington","first_name":"Zoe P"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"},{"full_name":"Trevisan, Alexandra J.","first_name":"Alexandra J.","last_name":"Trevisan"},{"full_name":"Chapman, Phillip","last_name":"Chapman","first_name":"Phillip"},{"full_name":"Julseth, Mara","last_name":"Julseth","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","first_name":"Mara"},{"last_name":"Brenner-Morton","first_name":"Susan","full_name":"Brenner-Morton, Susan"},{"full_name":"Gabitto, Mariano I.","first_name":"Mariano I.","last_name":"Gabitto"},{"full_name":"Dasen, Jeremy S.","first_name":"Jeremy S.","last_name":"Dasen"},{"full_name":"Bikoff, Jay B.","last_name":"Bikoff","first_name":"Jay B."},{"last_name":"Sweeney","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601","full_name":"Sweeney, Lora Beatrice Jaeger"}]},{"department":[{"_id":"ToHe"}],"publisher":"Zenodo","date_created":"2025-06-10T07:10:01Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-09-28T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.13854760"}],"OA_type":"green","_id":"19800","citation":{"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","ista":"trinh VG, Park KH, Pastva S, Rozum J. 2024. Mapping the attractor landscape of Boolean networks, Zenodo, 10.5281/ZENODO.13854759.","ama":"trinh VG, Park KH, Pastva S, Rozum J. Mapping the attractor landscape of Boolean networks. 2024. doi: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.","short":"V.G. trinh, K.H. Park, S. Pastva, J. Rozum, (2024).","mla":"trinh, Van Giang, et al. Mapping the Attractor Landscape of Boolean Networks. Zenodo, 2024, doi: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."},"OA_place":"repository","day":"28","doi":"10.5281/ZENODO.13854759","ddc":["000"],"related_material":{"record":[{"relation":"used_in_publication","id":"19796","status":"public"}]},"abstract":[{"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.","lang":"eng"}],"year":"2024","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"trinh, Van Giang","first_name":"Van Giang","last_name":"trinh"},{"full_name":"Park, Kyu Hyong","first_name":"Kyu Hyong","last_name":"Park"},{"first_name":"Samuel","last_name":"Pastva","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","full_name":"Pastva, Samuel","orcid":"0000-0003-1993-0331"},{"first_name":"Jordan","last_name":"Rozum","full_name":"Rozum, Jordan"}],"date_updated":"2025-09-30T12:46:33Z","has_accepted_license":"1","oa_version":"Published Version","fulldoi":"https://doi.org/10.5281/ZENODO.13854759","month":"09","status":"public","title":"Mapping the attractor landscape of Boolean networks","type":"research_data_reference"},{"OA_type":"hybrid","date_created":"2025-06-10T09:12:41Z","date_published":"2024-08-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"National Academy of Sciences","day":"27","OA_place":"publisher","publication":"Proceedings of the National Academy of Sciences","_id":"19809","has_accepted_license":"1","external_id":{"pmid":["39172781"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 121","title":"The Lorenz ratio as a guide to scattering contributions to transport in strongly correlated metals","type":"journal_article","status":"public","quality_controlled":"1","month":"08","issue":"35","extern":"1","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2318159121","open_access":"1"}],"volume":121,"article_type":"original","scopus_import":"1","year":"2024","abstract":[{"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.","lang":"eng"}],"doi":"10.1073/pnas.2318159121","citation":{"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.","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).","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.","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.","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","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).","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"},"language":[{"iso":"eng"}],"date_updated":"2025-06-10T11:50:48Z","author":[{"first_name":"Fei","last_name":"Sun","full_name":"Sun, Fei"},{"last_name":"Mishra","first_name":"Simli","full_name":"Mishra, Simli"},{"last_name":"Stockert","first_name":"Ulrike","full_name":"Stockert, Ulrike"},{"full_name":"Daou, Ramzy","last_name":"Daou","first_name":"Ramzy"},{"full_name":"Kikugawa, Naoki","last_name":"Kikugawa","first_name":"Naoki"},{"full_name":"Perry, Robin S.","first_name":"Robin S.","last_name":"Perry"},{"full_name":"Hassinger, Elena","last_name":"Hassinger","first_name":"Elena"},{"first_name":"Sean A.","last_name":"Hartnoll","full_name":"Hartnoll, Sean A."},{"last_name":"Mackenzie","first_name":"Andrew P.","full_name":"Mackenzie, Andrew P."},{"last_name":"Sunko","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","first_name":"Veronika","orcid":"0000-0003-2724-3523","full_name":"Sunko, Veronika"}],"pmid":1,"oa":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"fulldoi":"https://doi.org/10.1073/pnas.2318159121","oa_version":"Published Version"},{"intvolume":" 14","quality_controlled":"1","month":"07","type":"journal_article","title":"Multimodal approach reveals the symmetry-breaking pathway to the broken helix in EuIn2As2","status":"public","publisher":"American Physical Society","publication_status":"published","OA_type":"gold","date_published":"2024-07-22T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-06-10T09:17:30Z","OA_place":"publisher","_id":"19816","publication":"Physical Review X","day":"22","oa":1,"DOAJ_listed":"1","language":[{"iso":"eng"}],"date_updated":"2025-06-10T13:14:20Z","author":[{"full_name":"Donoway, E.","last_name":"Donoway","first_name":"E."},{"full_name":"Trevisan, T. V.","last_name":"Trevisan","first_name":"T. V."},{"full_name":"Liebman-Peláez, A.","first_name":"A.","last_name":"Liebman-Peláez"},{"last_name":"Day","first_name":"R. P.","full_name":"Day, R. P."},{"first_name":"K.","last_name":"Yamakawa","full_name":"Yamakawa, K."},{"first_name":"Y.","last_name":"Sun","full_name":"Sun, Y."},{"full_name":"Soh, J. R.","last_name":"Soh","first_name":"J. R."},{"full_name":"Prabhakaran, D.","last_name":"Prabhakaran","first_name":"D."},{"full_name":"Boothroyd, A. T.","last_name":"Boothroyd","first_name":"A. T."},{"last_name":"Fernandes","first_name":"R. M.","full_name":"Fernandes, R. M."},{"first_name":"J. G.","last_name":"Analytis","full_name":"Analytis, J. G."},{"full_name":"Moore, J. E.","first_name":"J. E.","last_name":"Moore"},{"last_name":"Orenstein","first_name":"J.","full_name":"Orenstein, J."},{"full_name":"Sunko, Veronika","orcid":"0000-0003-2724-3523","first_name":"Veronika","last_name":"Sunko","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3"}],"fulldoi":"https://doi.org/10.1103/physrevx.14.031013","oa_version":"Published Version","article_number":"031013","publication_identifier":{"eissn":["2160-3308"]},"volume":14,"article_type":"original","issue":"3","extern":"1","main_file_link":[{"url":"https://doi.org/10.1103/physrevx.14.031013","open_access":"1"}],"article_processing_charge":"No","citation":{"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.","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","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.","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.","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)."},"abstract":[{"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.","lang":"eng"}],"year":"2024","scopus_import":"1","doi":"10.1103/physrevx.14.031013"},{"doi":"10.5281/ZENODO.14213091","day":"24","ddc":["000"],"related_material":{"record":[{"relation":"used_for_analysis_in","status":"public","id":"19877"}]},"abstract":[{"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).","lang":"eng"}],"year":"2024","_id":"19884","OA_place":"repository","citation":{"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.","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","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.","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.","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)."},"date_created":"2025-06-24T06:09:18Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-11-24T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.14213091","open_access":"1"}],"department":[{"_id":"DaAl"}],"publisher":"Zenodo","status":"public","title":"MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models","type":"research_data_reference","fulldoi":"https://doi.org/10.5281/ZENODO.14213091","corr_author":"1","oa_version":"Published Version","month":"11","date_updated":"2025-09-30T13:41:56Z","author":[{"full_name":"Frantar, Elias","first_name":"Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","last_name":"Frantar"},{"full_name":"Castro, Roberto","last_name":"Castro","first_name":"Roberto"},{"last_name":"Chen","id":"4d0a9064-1ff6-11ee-9fa6-ec046c604785","first_name":"Jiale","orcid":"0000-0001-5337-5875","full_name":"Chen, Jiale"},{"full_name":"Hoefler, Torsten","first_name":"Torsten","last_name":"Hoefler"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"fulldoi":"https://doi.org/10.1002/adma.202470004","oa_version":"Published Version","article_number":"2470004","publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"oa":1,"author":[{"last_name":"Zeng","first_name":"Guifang","full_name":"Zeng, Guifang"},{"last_name":"Sun","first_name":"Qing","full_name":"Sun, Qing"},{"full_name":"Horta, Sharona","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta"},{"last_name":"Wang","first_name":"Shang","full_name":"Wang, Shang"},{"full_name":"Lu, Xuan","first_name":"Xuan","last_name":"Lu"},{"first_name":"Chao Yue","last_name":"Zhang","full_name":"Zhang, Chao Yue"},{"first_name":"Jing","last_name":"Li","full_name":"Li, Jing"},{"full_name":"Li, Junshan","first_name":"Junshan","last_name":"Li"},{"full_name":"Ci, Lijie","last_name":"Ci","first_name":"Lijie"},{"full_name":"Tian, Yanhong","last_name":"Tian","first_name":"Yanhong"},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"date_updated":"2026-06-18T18:19:28Z","language":[{"iso":"eng"}],"citation":{"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.","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.","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.","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","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.","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","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."},"ddc":["530"],"doi":"10.1002/adma.202470004","abstract":[{"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.","lang":"eng"}],"year":"2024","department":[{"_id":"MaIb"}],"volume":36,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/adma.202470004"}],"article_processing_charge":"No","issue":"1","month":"01","quality_controlled":"1","status":"public","type":"other_academic_publication","title":"A layered Bi2Te3@PPy cathode for aqueous Zinc‐Ion batteries: Mechanism and application in printed flexible batteries","intvolume":" 36","_id":"20057","publication":"Advanced Materials","OA_place":"publisher","day":"04","publisher":"Wiley","publication_status":"published","date_published":"2024-01-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-07-21T08:53:06Z","OA_type":"free access"},{"article_processing_charge":"Yes","issue":"45","article_type":"original","ddc":["570"],"doi":"10.62876/lr.vi45.6481","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”.","year":"2024","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)."},{"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","lang":"eng"}],"citation":{"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","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","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.","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.","short":"S. Carls-Diamante, A. Laciny, Lógoi. Revista de Filosofía (2024) 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.","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."},"date_updated":"2025-09-09T08:51:00Z","author":[{"full_name":"Carls-Diamante, Sidney","last_name":"Carls-Diamante","first_name":"Sidney"},{"full_name":"Laciny, Alice","orcid":"0000-0002-5485-1391","last_name":"Laciny","id":"accace3f-3f77-11eb-b1df-f1221b04cb95","first_name":"Alice"}],"language":[{"iso":"eng"}],"DOAJ_listed":"1","PlanS_conform":"1","oa":1,"publication_identifier":{"eissn":["1316-693X"],"issn":["2790-5144"]},"file":[{"relation":"main_file","success":1,"file_name":"2025_Logoi_CarlsDiamante.pdf","file_id":"20317","content_type":"application/pdf","date_created":"2025-09-09T08:48:53Z","file_size":354124,"checksum":"04c950f26ad68455c3a303c87ccf2349","access_level":"open_access","date_updated":"2025-09-09T08:48:53Z","creator":"dernst"}],"fulldoi":"https://doi.org/10.62876/lr.vi45.6481","oa_version":"Published Version","corr_author":"1","date_created":"2025-07-21T10:35:39Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-03-19T00:00:00Z","OA_type":"gold","publication_status":"published","publisher":"Universidad Católica Andrés Bello","day":"19","page":"88-114","publication":"Lógoi. Revista de Filosofía","_id":"20060","OA_place":"publisher","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"status":"public","title":"Stuck in uncertainty: A predictive processing/ active inference account of procrastination-like behaviour in autism","type":"journal_article","file_date_updated":"2025-09-09T08:48:53Z","quality_controlled":"1","month":"03"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"has_accepted_license":"1","author":[{"last_name":"Nabeel","first_name":"Arshed","full_name":"Nabeel, Arshed"},{"last_name":"Karichannavar","first_name":"Ashwin","full_name":"Karichannavar, Ashwin"},{"full_name":"Palathingal, Shuaib","last_name":"Palathingal","first_name":"Shuaib"},{"full_name":"Jhawar, Jitesh","first_name":"Jitesh","last_name":"Jhawar"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","first_name":"David","full_name":"Brückner, David","orcid":"0000-0001-7205-2975"},{"first_name":"Masila","last_name":"Danny Raj","full_name":"Danny Raj, Masila"},{"full_name":"Guttal, Vishwesha","last_name":"Guttal","first_name":"Vishwesha"}],"date_updated":"2025-09-30T14:14:42Z","month":"09","oa_version":"Published Version","fulldoi":"https://doi.org/10.5281/ZENODO.7137151","type":"research_data_reference","title":"PyDaddy: A Python Package for Discovering SDEs from Time Series Data","status":"public","publisher":"Zenodo","department":[{"_id":"EdHa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7137151"}],"date_published":"2024-09-18T00:00:00Z","date_created":"2025-08-05T06:49:59Z","article_processing_charge":"No","citation":{"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","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.","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","ieee":"A. Nabeel et al., “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024.","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, M. Danny Raj, V. Guttal, (2024).","mla":"Nabeel, Arshed, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo, 2024, doi: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."},"_id":"20121","acknowledgement":"This study was partially funded by Science and Engineering Research Board, Department of Science and Technology, Government of India to Vishwesha Guttal.","year":"2024","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."}],"related_material":{"record":[{"relation":"used_for_analysis_in","status":"public","id":"20056"}]},"day":"18","doi":"10.5281/ZENODO.7137151","ddc":["570"]},{"publisher":"Elsevier","publication_status":"published","OA_type":"green","date_published":"2024-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-12-09T14:22:40Z","OA_place":"repository","_id":"20756","publication":"Current Opinion in Chemical Biology","day":"01","intvolume":" 83","external_id":{"pmid":["39369557"]},"month":"12","quality_controlled":"1","type":"journal_article","title":"Catalyzing the future: Recent advances in chemical synthesis using enzymes","status":"public","article_type":"original","volume":83,"extern":"1","main_file_link":[{"open_access":"1","url":"https://europepmc.org/article/med/39369557#free-full-text"}],"article_processing_charge":"No","citation":{"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.","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).","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.","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"},"abstract":[{"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.","lang":"eng"}],"year":"2024","scopus_import":"1","doi":"10.1016/j.cbpa.2024.102536","pmid":1,"oa":1,"language":[{"iso":"eng"}],"author":[{"full_name":"Reisenbauer, Julia","first_name":"Julia","last_name":"Reisenbauer","id":"51d862e9-36ee-11f0-86d3-8534c85a5496"},{"last_name":"Sicinski","first_name":"Kathleen M.","full_name":"Sicinski, Kathleen M."},{"last_name":"Arnold","first_name":"Frances H.","full_name":"Arnold, Frances H."}],"date_updated":"2025-12-16T13:03:48Z","oa_version":"Submitted Version","fulldoi":"https://doi.org/10.1016/j.cbpa.2024.102536","article_number":"102536","publication_identifier":{"eissn":["1879-0402"],"issn":["1367-5931"]}},{"OA_place":"publisher","_id":"20757","publication":"Chemical Communications","page":"9254-9257","day":"02","publisher":"Royal Society of Chemistry","publication_status":"published","OA_type":"hybrid","date_published":"2024-08-02T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-12-09T14:23:00Z","quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc/3.0/","month":"08","type":"journal_article","title":"Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","short":"CC BY-NC (3.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode"},"intvolume":" 60","external_id":{"pmid":["39118590"]},"has_accepted_license":"1","citation":{"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.","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","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.","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.","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."},"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."}],"year":"2024","scopus_import":"1","doi":"10.1039/d4cc02609h","volume":60,"article_type":"original","extern":"1","issue":"69","main_file_link":[{"url":"https://doi.org/10.1039/D4CC02609H","open_access":"1"}],"article_processing_charge":"No","oa_version":"Published Version","fulldoi":"https://doi.org/10.1039/d4cc02609h","publication_identifier":{"issn":["1359-7345"],"eissn":["1364-548X"]},"pmid":1,"oa":1,"language":[{"iso":"eng"}],"author":[{"full_name":"Botlik, Bence B.","last_name":"Botlik","first_name":"Bence B."},{"first_name":"Patrick","last_name":"Finkelstein","full_name":"Finkelstein, Patrick"},{"first_name":"Ann-Sophie K.","last_name":"Paschke","full_name":"Paschke, Ann-Sophie K."},{"full_name":"Reisenbauer, Julia","first_name":"Julia","id":"51d862e9-36ee-11f0-86d3-8534c85a5496","last_name":"Reisenbauer"},{"last_name":"Morandi","first_name":"Bill","full_name":"Morandi, Bill"}],"date_updated":"2025-12-16T11:19:43Z"},{"fulldoi":"https://doi.org/10.1042/bsr20230502","oa_version":"Published Version","article_number":"BSR20230502","publication_identifier":{"eissn":["1573-4935"],"issn":["0144-8463"]},"pmid":1,"oa":1,"language":[{"iso":"eng"}],"date_updated":"2025-12-15T10:21:56Z","author":[{"last_name":"Panska","first_name":"Lucie","full_name":"Panska, Lucie"},{"full_name":"Nedvedova, Stepanka","last_name":"Nedvedova","first_name":"Stepanka"},{"last_name":"Vacek","first_name":"Vojtech","full_name":"Vacek, Vojtech"},{"first_name":"Daniela","last_name":"Krivska","full_name":"Krivska, Daniela"},{"full_name":"Konecny, Lukas","first_name":"Lukas","last_name":"Konecny"},{"orcid":"0000-0002-3845-3465","full_name":"Knop, Filip","first_name":"Filip","id":"25f3131f-6e7c-11ef-8296-b64ccd4a1b69","last_name":"Knop"},{"full_name":"Kutil, Zsofia","last_name":"Kutil","first_name":"Zsofia"},{"first_name":"Lubica","last_name":"Skultetyova","full_name":"Skultetyova, Lubica"},{"full_name":"Leontovyc, Adrian","last_name":"Leontovyc","first_name":"Adrian"},{"last_name":"Ulrychova","first_name":"Lenka","full_name":"Ulrychova, Lenka"},{"full_name":"Sakanari, Judy","first_name":"Judy","last_name":"Sakanari"},{"last_name":"Asahina","first_name":"Masako","full_name":"Asahina, Masako"},{"full_name":"Barinka, Cyril","first_name":"Cyril","last_name":"Barinka"},{"last_name":"Macurkova","first_name":"Marie","full_name":"Macurkova, Marie"},{"first_name":"Jan","last_name":"Dvorak","full_name":"Dvorak, Jan"}],"citation":{"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.","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).","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.","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"},"abstract":[{"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.","lang":"eng"}],"year":"2024","scopus_import":"1","ddc":["570"],"doi":"10.1042/bsr20230502","article_type":"original","volume":44,"extern":"1","issue":"1","main_file_link":[{"url":"https://doi.org/10.1042/BSR20230502","open_access":"1"}],"article_processing_charge":"Yes (in subscription journal)","month":"01","quality_controlled":"1","type":"journal_article","title":"Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 44","has_accepted_license":"1","external_id":{"pmid":["38108122 "]},"OA_place":"publisher","_id":"20807","publication":"Bioscience Reports","day":"12","publisher":"Portland Press","publication_status":"published","OA_type":"hybrid","date_published":"2024-01-12T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-12-12T09:03:54Z"},{"status":"public","type":"journal_article","title":"Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity","month":"07","quality_controlled":"1","external_id":{"pmid":["39028260"]},"intvolume":" 13","day":"19","_id":"20808","publication":"eLife","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-07-19T00:00:00Z","date_created":"2025-12-12T09:06:31Z","OA_type":"gold","publisher":"eLife Sciences Publications","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"article_number":"e91054","fulldoi":"https://doi.org/10.7554/elife.91054","oa_version":"Published Version","author":[{"last_name":"Knop","id":"25f3131f-6e7c-11ef-8296-b64ccd4a1b69","first_name":"Filip","full_name":"Knop, Filip","orcid":"0000-0002-3845-3465"},{"first_name":"Apolena","last_name":"Zounarová","full_name":"Zounarová, Apolena"},{"first_name":"Vojtěch","last_name":"Šabata","full_name":"Šabata, Vojtěch"},{"full_name":"Middelkoop, Teije Corneel","first_name":"Teije Corneel","last_name":"Middelkoop"},{"full_name":"Macůrková, Marie","last_name":"Macůrková","first_name":"Marie"}],"date_updated":"2025-12-15T10:26:56Z","DOAJ_listed":"1","language":[{"iso":"eng"}],"oa":1,"pmid":1,"doi":"10.7554/elife.91054","year":"2024","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","citation":{"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.","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","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.","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.","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)."},"main_file_link":[{"url":"https://doi.org/10.7554/elife.91054","open_access":"1"}],"article_processing_charge":"Yes","extern":"1","article_type":"original","volume":13},{"status":"public","title":"Divergence of separated nets with respect to displacement equivalence","type":"journal_article","file_date_updated":"2024-07-16T10:14:13Z","month":"02","quality_controlled":"1","external_id":{"isi":["001105681500001"],"arxiv":["2102.13046"],"pmid":["38021107"]},"has_accepted_license":"1","intvolume":" 218","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","publication":"Geometriae Dedicata","_id":"9651","OA_place":"publisher","date_created":"2021-07-14T07:01:27Z","date_published":"2024-02-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","publication_status":"published","publisher":"Springer Nature","article_number":"15","isi":1,"publication_identifier":{"issn":["0046-5755"],"eissn":["1572-9168"]},"file":[{"success":1,"relation":"main_file","checksum":"9418534ac2f3d6f1f091a8b8ccaed01e","creator":"dernst","access_level":"open_access","date_updated":"2024-07-16T10:14:13Z","file_size":540981,"date_created":"2024-07-16T10:14:13Z","file_name":"2024_GeometriaeDedicata_Dymond.pdf","file_id":"17257","content_type":"application/pdf"}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.1007/s10711-023-00862-3","corr_author":"1","date_updated":"2025-04-23T07:37:26Z","author":[{"full_name":"Dymond, Michael","last_name":"Dymond","first_name":"Michael"},{"full_name":"Kaluza, Vojtech","orcid":"0000-0002-2512-8698","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","last_name":"Kaluza","first_name":"Vojtech"}],"language":[{"iso":"eng"}],"oa":1,"pmid":1,"ddc":["510"],"doi":"10.1007/s10711-023-00862-3","arxiv":1,"scopus_import":"1","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.","year":"2024","abstract":[{"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.","lang":"eng"}],"citation":{"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).","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.","ista":"Dymond M, Kaluza V. 2024. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 218, 15.","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","ieee":"M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” Geometriae Dedicata, vol. 218. Springer Nature, 2024."},"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"UlWa"}],"volume":218,"article_type":"original"},{"month":"07","quality_controlled":"1","status":"public","type":"journal_article","file_date_updated":"2024-08-05T08:38:01Z","title":"A gate tunable transmon qubit in planar Ge","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"intvolume":" 15","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","external_id":{"pmid":["39080279"],"arxiv":["2403.16774"],"isi":["001281271000022"]},"_id":"17202","publication":"Nature Communications","OA_place":"publisher","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-024-53910-1"}],"record":[{"relation":"research_data","id":"17196","status":"public"},{"relation":"dissertation_contains","status":"public","id":"18076"}]},"day":"30","publisher":"Springer Nature","publication_status":"published","APC_amount":"6828 EUR","date_published":"2024-07-30T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-04T11:40:45Z","OA_type":"gold","fulldoi":"https://doi.org/10.1038/s41467-024-50763-6","corr_author":"1","oa_version":"Published Version","isi":1,"publication_identifier":{"eissn":["2041-1723"]},"article_number":"6400","file":[{"content_type":"application/pdf","file_id":"17388","file_name":"2024_NatureComm_Sagi.pdf","creator":"dernst","access_level":"open_access","date_updated":"2024-08-05T08:38:01Z","checksum":"ddf5361dcb6c543e2cea818501c09910","file_size":1928001,"date_created":"2024-08-05T08:38:01Z","relation":"main_file","success":1}],"oa":1,"pmid":1,"date_updated":"2026-04-07T13:01:55Z","author":[{"full_name":"Sagi, Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","last_name":"Sagi","first_name":"Oliver"},{"orcid":"0000-0002-2968-611X","full_name":"Crippa, Alessandro","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","last_name":"Crippa","first_name":"Alessandro"},{"last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","full_name":"Valentini, Marco"},{"full_name":"Janik, Marian","orcid":"0009-0003-9037-8831","id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik","first_name":"Marian"},{"full_name":"Baghumyan, Levon","first_name":"Levon","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","last_name":"Baghumyan"},{"full_name":"Fabris, Giorgio","first_name":"Giorgio","last_name":"Fabris","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352"},{"full_name":"Kapoor, Lucky","orcid":"0000-0001-8319-2148","last_name":"Kapoor","id":"84b9700b-15b2-11ec-abd3-831089e67615","first_name":"Lucky"},{"full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","first_name":"Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"},{"last_name":"Calcaterra","first_name":"Stefano","full_name":"Calcaterra, Stefano"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"DOAJ_listed":"1","language":[{"iso":"eng"}],"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","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.","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","ieee":"O. Sagi et al., “A gate tunable transmon qubit in planar Ge,” Nature Communications, vol. 15. Springer Nature, 2024.","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).","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."},"ddc":["530"],"doi":"10.1038/s41467-024-50763-6","abstract":[{"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.","lang":"eng"}],"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.","year":"2024","arxiv":1,"scopus_import":"1","department":[{"_id":"GeKa"},{"_id":"JoFi"},{"_id":"GradSch"}],"article_type":"original","volume":15,"project":[{"grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","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"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"article_processing_charge":"Yes"},{"oa":1,"author":[{"first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","last_name":"Hafner","full_name":"Hafner, Christian"},{"full_name":"Ly, Mickaël","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","last_name":"Ly","first_name":"Mickaël"},{"first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"date_updated":"2025-09-08T08:29:09Z","conference":{"location":"Denver, Colorado","start_date":"2024-07-28","end_date":"2024-08-01"},"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1145/3658194","corr_author":"1","oa_version":"Published Version","isi":1,"article_number":"78","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"file":[{"success":1,"relation":"main_file","date_updated":"2024-07-05T12:05:17Z","file_size":7225150,"checksum":"0dc9f5a6422b8a49a79026900f349ee5","date_created":"2024-07-05T12:05:17Z","access_level":"open_access","creator":"chafner","content_type":"application/pdf","file_name":"sif-final.pdf","file_id":"17204"},{"relation":"supplementary_material","content_type":"application/pdf","file_name":"sif-supp-final.pdf","file_id":"17205","creator":"chafner","date_updated":"2024-07-05T12:06:03Z","file_size":397262,"checksum":"cde433c6a40688d5f1187fb5721f6f94","date_created":"2024-07-05T12:06:03Z","access_level":"open_access"},{"relation":"supplementary_material","title":"Submission Video","file_name":"sif-video-final.mp4","file_id":"17276","content_type":"video/mp4","file_size":170001305,"date_updated":"2024-07-17T09:29:13Z","access_level":"open_access","creator":"chafner","checksum":"c0457a09c2ab9a1c2935c995dcc84907","date_created":"2024-07-17T09:29:13Z"}],"department":[{"_id":"ChWo"}],"article_type":"original","project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"volume":43,"article_processing_charge":"Yes (via OA deal)","issue":"4","citation":{"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.","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","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.","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","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.","short":"C. Hafner, M. Ly, C. Wojtan, Transactions on Graphics 43 (2024).","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."},"ddc":["516"],"doi":"10.1145/3658194","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).","year":"2024","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."}],"scopus_import":"1","intvolume":" 43","has_accepted_license":"1","external_id":{"isi":["001289270900045"]},"month":"07","quality_controlled":"1","status":"public","type":"journal_article","file_date_updated":"2024-07-17T09:29:13Z","title":"Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments","publisher":"Association for Computing Machinery","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-07-01T00:00:00Z","date_created":"2024-07-05T12:08:57Z","_id":"17203","publication":"Transactions on Graphics","keyword":["Topology Optimization","Mass Moments","Computational Geometry"],"day":"01"},{"quality_controlled":"1","month":"06","title":"Eco-evolutionary dynamics in changing environments: Integrating theory with data","type":"journal_article","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 37","external_id":{"pmid":["38941551"],"isi":["001258359900001"]},"publication":"Journal of evolutionary biology","_id":"17207","page":"579-587","day":"28","publication_status":"published","publisher":"Oxford University Press","date_created":"2024-07-07T22:01:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-06-28T00:00:00Z","fulldoi":"https://doi.org/10.1093/jeb/voae067","oa_version":"Published Version","publication_identifier":{"eissn":["1420-9101"]},"isi":1,"pmid":1,"oa":1,"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-0371-9339","full_name":"Fouqueau, Louise","id":"1676e173-8143-11ed-8927-fe165216a93f","last_name":"Fouqueau","first_name":"Louise"},{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","first_name":"Jitka","last_name":"Polechova","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-06-18T17:53:35Z","citation":{"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.","short":"L. Fouqueau, J. Polechova, Journal of Evolutionary Biology 37 (2024) 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.","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.","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","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","ista":"Fouqueau L, Polechova J. 2024. Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of evolutionary biology. 37(6), 579–587."},"scopus_import":"1","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.","year":"2024","doi":"10.1093/jeb/voae067","ddc":["570"],"article_type":"letter_note","project":[{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896","name":"Causes and consequences of population fragmentation"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"volume":37,"department":[{"_id":"NiBa"}],"issue":"6","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/jeb/voae067"}]},{"keyword":["Quantum computing","Variational Quantum Algorithms","Optimization"],"related_material":{"record":[{"id":"10545","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10067","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"17222"},{"id":"13125","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"11471"}]},"page":"133","day":"09","_id":"17208","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2024-07-09T00:00:00Z","date_created":"2024-07-09T09:14:24Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","publication_status":"published","supervisor":[{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"}],"status":"public","type":"dissertation","file_date_updated":"2024-07-17T09:23:24Z","title":"Exploring the optimization landscape of variational quantum algorithms","month":"07","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["539"],"doi":"10.15479/at:ista:17208","abstract":[{"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.","lang":"eng"}],"year":"2024","alternative_title":["ISTA Thesis"],"citation":{"short":"R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum Algorithms, Institute of Science and Technology Austria, 2024.","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.","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.","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","ama":"Medina Ramos RA. Exploring the optimization landscape of variational quantum algorithms. 2024. doi:10.15479/at:ista:17208","ista":"Medina Ramos RA. 2024. Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria.","ieee":"R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum algorithms,” Institute of Science and Technology Austria, 2024."},"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"publication_identifier":{"issn":["2663-337X"]},"file":[{"content_type":"application/zip","file_name":"Raimel_Thesis-Final.zip","file_id":"17212","access_level":"closed","date_created":"2024-07-09T09:21:44Z","date_updated":"2024-07-10T11:34:09Z","file_size":"14218691","checksum":"6f45273d04f4418bc2adc018baed0525","creator":"rmedinar","relation":"source_file"},{"success":1,"relation":"main_file","date_created":"2024-07-17T09:23:24Z","checksum":"6724a95bec772dbabc0111b9f08a805e","date_updated":"2024-07-17T09:23:24Z","creator":"rmedinar","access_level":"open_access","file_size":11253627,"content_type":"application/pdf","file_id":"17275","file_name":"Raimel_Thesis-20_pdfa.pdf"}],"ec_funded":1,"fulldoi":"https://doi.org/10.15479/at:ista:17208","oa_version":"Published Version","corr_author":"1","date_updated":"2026-04-07T12:43:22Z","author":[{"id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","first_name":"Raimel A","full_name":"Medina Ramos, Raimel A","orcid":"0000-0002-5383-2869"}],"language":[{"iso":"eng"}],"oa":1},{"quality_controlled":"1","month":"07","type":"conference","file_date_updated":"2024-07-10T11:03:58Z","title":"Primal-dual non-smooth friction for rigid body animation","status":"public","has_accepted_license":"1","external_id":{"isi":["001282218200091"]},"_id":"17214","publication":"Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24","keyword":["physical simulation","frictional contact","rigid body mechanics","non-smooth dynamics"],"day":"01","publisher":"Association for Computing Machinery","publication_status":"published","date_published":"2024-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-10T11:06:20Z","fulldoi":"https://doi.org/10.1145/3641519.3657485","corr_author":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_name":"sig24_friction_authors.pdf","file_id":"17215","creator":"yichen","date_created":"2024-07-10T11:03:14Z","date_updated":"2024-07-10T11:03:14Z","access_level":"open_access","file_size":47309472,"checksum":"b8b203ed09e3995ba0d7e6a76288663a","relation":"main_file","success":1},{"content_type":"application/pdf","file_id":"17216","file_name":"sig24_friction_supplementary.pdf","file_size":10518286,"creator":"yichen","date_created":"2024-07-10T11:03:12Z","checksum":"89d81b397b4b6469d828808a68b70820","access_level":"open_access","date_updated":"2024-07-10T11:03:12Z","relation":"main_file","success":1},{"content_type":"video/mp4","file_id":"17217","file_name":"friction_paper_extra_video_finished.mp4","file_size":71789192,"checksum":"7123deed34a5456810e7b5336a31c657","access_level":"open_access","date_created":"2024-07-10T11:03:51Z","creator":"yichen","date_updated":"2024-07-10T11:03:51Z","relation":"main_file","success":1},{"success":1,"relation":"main_file","date_created":"2024-07-10T11:03:58Z","date_updated":"2024-07-10T11:03:58Z","access_level":"open_access","file_size":280610763,"checksum":"e606fc1ae8f2610ce3b4421566800b45","creator":"yichen","content_type":"video/mp4","file_name":"friction_paper_video_finished.mp4","file_id":"17218"}],"isi":1,"publication_identifier":{"isbn":["9798400705250"]},"oa":1,"conference":{"start_date":"2024-07-28","end_date":"2024-08-01","location":"Denver, United States","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference"},"language":[{"iso":"eng"}],"author":[{"first_name":"Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","last_name":"Chen","full_name":"Chen, Yi-Lu"},{"full_name":"Ly, Mickaël","last_name":"Ly","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","first_name":"Mickaël"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"date_updated":"2025-09-08T08:54:38Z","citation":{"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.","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.","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","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.","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","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."},"year":"2024","abstract":[{"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.","lang":"eng"}],"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).","scopus_import":"1","doi":"10.1145/3641519.3657485","ddc":["621","531","006"],"project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"article_processing_charge":"Yes (via OA deal)"},{"year":"2024","abstract":[{"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.","lang":"eng"}],"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).","scopus_import":"1","doi":"10.1145/3658223","ddc":["004"],"citation":{"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).","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.","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","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.","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","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."},"issue":"4","article_processing_charge":"Yes (via OA deal)","article_type":"original","volume":43,"project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"file":[{"relation":"main_file","success":1,"content_type":"application/pdf","file_name":"2024_ACMToG_HeissSynak.pdf","file_id":"17317","access_level":"open_access","file_size":48763368,"date_created":"2024-07-23T06:35:15Z","checksum":"1917067d4b52d7729019b03560004e43","date_updated":"2024-07-23T06:35:15Z","creator":"dernst"},{"relation":"main_file","success":1,"file_name":"sdtopofixer_final.mp4","file_id":"17221","content_type":"video/mp4","date_updated":"2024-07-10T12:23:44Z","date_created":"2024-07-10T12:23:44Z","checksum":"a4f0e293184bfa034c0c585848806b17","creator":"akalinov","access_level":"open_access","file_size":48021463},{"file_name":"SuperDuperTopoFixer.pdf","file_id":"20633","content_type":"application/pdf","date_created":"2025-11-11T09:50:52Z","creator":"akalinov","file_size":48639581,"date_updated":"2025-11-11T09:50:52Z","access_level":"open_access","checksum":"18fc310a78ec91651148c45a8b89fa44","relation":"preprint","title":"Authors' version of the text"}],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"isi":1,"article_number":"54","fulldoi":"https://doi.org/10.1145/3658223","oa_version":"Published Version","corr_author":"1","language":[{"iso":"eng"}],"date_updated":"2026-04-07T13:02:36Z","author":[{"full_name":"Synak, Peter","last_name":"Synak","id":"331776E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"orcid":"0000-0003-2189-3904","full_name":"Kalinov, Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","last_name":"Kalinov","first_name":"Aleksei"},{"full_name":"Strugaru, Irina-Malina","first_name":"Irina-Malina","last_name":"Strugaru","id":"2afc607f-f128-11eb-9611-8f2a0dfcf074"},{"first_name":"Arian","last_name":"Etemadihaghighi","id":"36cea3aa-f38e-11ec-8ae0-c65ae6f6098f","full_name":"Etemadihaghighi, Arian"},{"first_name":"Huidong","last_name":"Yang","full_name":"Yang, Huidong"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"oa":1,"related_material":{"record":[{"id":"19630","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"18301","status":"public"}]},"keyword":["surface tracking","topology change","non- manifold meshes","multi-material flows","solid modeling"],"day":"01","OA_place":"publisher","_id":"17219","publication":"ACM Transactions on Graphics","OA_type":"hybrid","date_published":"2024-07-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-07-10T12:24:00Z","publisher":"Association for Computing Machinery","publication_status":"published","file_date_updated":"2025-11-11T09:50:52Z","type":"journal_article","title":"Multi-material mesh-based surface tracking with implicit topology changes","status":"public","month":"07","quality_controlled":"1","has_accepted_license":"1","external_id":{"isi":["001289270900021"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"intvolume":" 43"},{"doi":"10.48550/arXiv.2405.10125","arxiv":1,"year":"2024","abstract":[{"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.","lang":"eng"}],"citation":{"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","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","ista":"Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. 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. .","short":"R.A. Medina Ramos, M. Serbyn, ArXiv (n.d.).","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.","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."},"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.10125"}],"department":[{"_id":"MaSe"}],"article_number":"2405.10125","fulldoi":"https://doi.org/10.48550/arXiv.2405.10125","corr_author":"1","oa_version":"Preprint","author":[{"full_name":"Medina Ramos, Raimel A","orcid":"0000-0002-5383-2869","last_name":"Medina Ramos","id":"CE680B90-D85A-11E9-B684-C920E6697425","first_name":"Raimel A"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"}],"date_updated":"2026-04-07T12:43:22Z","language":[{"iso":"eng"}],"oa":1,"day":"16","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"17208"}]},"publication":"arXiv","_id":"17222","OA_place":"repository","date_created":"2024-07-10T13:12:09Z","date_published":"2024-05-16T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"draft","status":"public","title":"A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm","type":"preprint","month":"05","external_id":{"arxiv":["2405.10125"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}}]