[{"oa_version":"None","type":"journal_article","month":"01","article_processing_charge":"No","scopus_import":"1","ddc":["540"],"article_number":"e202214339","article_type":"original","_id":"21813","volume":62,"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"day":"02","doi":"10.1002/anie.202214339","pmid":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-05-12T06:46:11Z","date_created":"2026-05-06T10:51:36Z","title":"Controlled Diels–Alder “Click” strategy to access mechanically aligned main‐chain liquid crystal networks","publication":"Angewandte Chemie International Edition","publisher":"Wiley","abstract":[{"lang":"eng","text":"Aligned liquid crystal polymers are materials of interest for electronic, optic, biological and soft robotic applications. The manufacturing and processing of these materials have been widely explored with mechanical alignment establishing itself as a preferred method due to its ease of use and widespread applicability. However, the fundamental chemistry behind the required two‐step polymerization for mechanical alignment has limitations in both fabrication and substrate compatibility. In this work we introduce a new protection‐deprotection approach utilizing a two‐stage Diels–Alder cyclopentadiene‐maleimide step‐growth polymerization to enable mild yet efficient, fast, controlled, reproducible and user‐friendly polymerizations, broadening the scope of liquid crystal systems. Thorough characterization of the films by DSC, DMA, POM and WAXD show the successful synthesis of a uniaxially aligned liquid crystal network with thermomechanical actuation abilities."}],"intvolume":" 62","issue":"1","author":[{"first_name":"Jesus","full_name":"Guillen Campos, Jesus","last_name":"Guillen Campos"},{"id":"7aca2cfc-46cf-11f0-abd3-8c96b5186745","full_name":"Stricker, Friedrich J","first_name":"Friedrich J","last_name":"Stricker"},{"last_name":"Clark","first_name":"Kyle D.","full_name":"Clark, Kyle D."},{"full_name":"Park, Minwook","first_name":"Minwook","last_name":"Park"},{"last_name":"Bailey","first_name":"Sophia J.","full_name":"Bailey, Sophia J."},{"last_name":"Kuenstler","first_name":"Alexa S.","full_name":"Kuenstler, Alexa S."},{"first_name":"Ryan C.","full_name":"Hayward, Ryan C.","last_name":"Hayward"},{"last_name":"Read de Alaniz","first_name":"Javier","full_name":"Read de Alaniz, Javier"}],"date_published":"2023-01-02T00:00:00Z","year":"2023","status":"public","extern":"1","publication_status":"published","citation":{"apa":"Guillen Campos, J., Stricker, F. J., Clark, K. D., Park, M., Bailey, S. J., Kuenstler, A. S., … Read de Alaniz, J. (2023). Controlled Diels–Alder “Click” strategy to access mechanically aligned main‐chain liquid crystal networks. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202214339","ieee":"J. Guillen Campos et al., “Controlled Diels–Alder ‘Click’ strategy to access mechanically aligned main‐chain liquid crystal networks,” Angewandte Chemie International Edition, vol. 62, no. 1. Wiley, 2023.","ama":"Guillen Campos J, Stricker FJ, Clark KD, et al. Controlled Diels–Alder “Click” strategy to access mechanically aligned main‐chain liquid crystal networks. Angewandte Chemie International Edition. 2023;62(1). doi:10.1002/anie.202214339","ista":"Guillen Campos J, Stricker FJ, Clark KD, Park M, Bailey SJ, Kuenstler AS, Hayward RC, Read de Alaniz J. 2023. Controlled Diels–Alder “Click” strategy to access mechanically aligned main‐chain liquid crystal networks. Angewandte Chemie International Edition. 62(1), e202214339.","mla":"Guillen Campos, Jesus, et al. “Controlled Diels–Alder ‘Click’ Strategy to Access Mechanically Aligned Main‐chain Liquid Crystal Networks.” Angewandte Chemie International Edition, vol. 62, no. 1, e202214339, Wiley, 2023, doi:10.1002/anie.202214339.","short":"J. Guillen Campos, F.J. Stricker, K.D. Clark, M. Park, S.J. Bailey, A.S. Kuenstler, R.C. Hayward, J. Read de Alaniz, Angewandte Chemie International Edition 62 (2023).","chicago":"Guillen Campos, Jesus, Friedrich J Stricker, Kyle D. Clark, Minwook Park, Sophia J. Bailey, Alexa S. Kuenstler, Ryan C. Hayward, and Javier Read de Alaniz. “Controlled Diels–Alder ‘Click’ Strategy to Access Mechanically Aligned Main‐chain Liquid Crystal Networks.” Angewandte Chemie International Edition. Wiley, 2023. https://doi.org/10.1002/anie.202214339."},"OA_type":"closed access","quality_controlled":"1","external_id":{"pmid":["36315038"]},"language":[{"iso":"eng"}]},{"oa_version":"Published Version","month":"07","type":"journal_article","article_processing_charge":"No","ddc":["540"],"scopus_import":"1","page":"1994-2005","article_type":"original","volume":9,"_id":"21807","publication_identifier":{"issn":["2451-9308"],"eissn":["2451-9294"]},"doi":"10.1016/j.chempr.2023.05.011","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"13","date_updated":"2026-05-12T06:49:20Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chempr.2023.05.011"}],"date_created":"2026-05-06T10:44:09Z","publication":"Chem","title":"Selective control of donor-acceptor Stenhouse adduct populations with non-selective stimuli","publisher":"Elsevier","oa":1,"abstract":[{"lang":"eng","text":"Multifaceted material responses upon exposure to stimuli are key for developing life-like materials. Developing such synthetic systems, though not trivial, typically relies on orthogonal stimuli to enable control of molecular systems that enable multi-responsive behavior. Access to complex tunable reaction mechanisms with diverse energy landscapes offers an alternative strategy for controlling out-of-equilibrium processes without requiring orthogonal stimuli for each responsive unit. Donor-acceptor Stenhouse adducts (DASAs) are a class of photoswitches that have complex, tunable, and environmentally sensitive reaction pathways. We present the control of donor-acceptor Stenhouse adduct equilibrium and photoswitching kinetics through changes in the polarity of their environment. Polarity and light can be used to selectively control the pathway outcomes of three DASA derivatives where the orthogonal response comes from changes in the energy landscape and is not driven by their orthogonal response to the given stimuli. This work paves the way to designing multi-responsive and self-regulating life-like materials."}],"OA_place":"publisher","issue":"7","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","intvolume":" 9","author":[{"id":"7aca2cfc-46cf-11f0-abd3-8c96b5186745","full_name":"Stricker, Friedrich J","first_name":"Friedrich J","last_name":"Stricker"},{"last_name":"Peterson","first_name":"Julie","full_name":"Peterson, Julie"},{"full_name":"Sandlass, Sara K.","first_name":"Sara K.","last_name":"Sandlass"},{"last_name":"de Tagyos","full_name":"de Tagyos, Aurora","first_name":"Aurora"},{"first_name":"Miranda","full_name":"Sroda, Miranda","last_name":"Sroda"},{"last_name":"Seshadri","full_name":"Seshadri, Serena","first_name":"Serena"},{"last_name":"Gordon","full_name":"Gordon, Michael J.","first_name":"Michael J."},{"full_name":"Read de Alaniz, Javier","first_name":"Javier","last_name":"Read de Alaniz"}],"publication_status":"published","status":"public","extern":"1","date_published":"2023-07-13T00:00:00Z","year":"2023","OA_type":"hybrid","citation":{"mla":"Stricker, Friedrich J., et al. “Selective Control of Donor-Acceptor Stenhouse Adduct Populations with Non-Selective Stimuli.” Chem, vol. 9, no. 7, Elsevier, 2023, pp. 1994–2005, doi:10.1016/j.chempr.2023.05.011.","apa":"Stricker, F. J., Peterson, J., Sandlass, S. K., de Tagyos, A., Sroda, M., Seshadri, S., … Read de Alaniz, J. (2023). Selective control of donor-acceptor Stenhouse adduct populations with non-selective stimuli. Chem. Elsevier. https://doi.org/10.1016/j.chempr.2023.05.011","ieee":"F. J. Stricker et al., “Selective control of donor-acceptor Stenhouse adduct populations with non-selective stimuli,” Chem, vol. 9, no. 7. Elsevier, pp. 1994–2005, 2023.","ama":"Stricker FJ, Peterson J, Sandlass SK, et al. Selective control of donor-acceptor Stenhouse adduct populations with non-selective stimuli. Chem. 2023;9(7):1994-2005. doi:10.1016/j.chempr.2023.05.011","ista":"Stricker FJ, Peterson J, Sandlass SK, de Tagyos A, Sroda M, Seshadri S, Gordon MJ, Read de Alaniz J. 2023. Selective control of donor-acceptor Stenhouse adduct populations with non-selective stimuli. Chem. 9(7), 1994–2005.","chicago":"Stricker, Friedrich J, Julie Peterson, Sara K. Sandlass, Aurora de Tagyos, Miranda Sroda, Serena Seshadri, Michael J. Gordon, and Javier Read de Alaniz. “Selective Control of Donor-Acceptor Stenhouse Adduct Populations with Non-Selective Stimuli.” Chem. Elsevier, 2023. https://doi.org/10.1016/j.chempr.2023.05.011.","short":"F.J. Stricker, J. Peterson, S.K. Sandlass, A. de Tagyos, M. Sroda, S. Seshadri, M.J. Gordon, J. Read de Alaniz, Chem 9 (2023) 1994–2005."},"quality_controlled":"1","language":[{"iso":"eng"}]},{"oa_version":"None","type":"journal_article","month":"01","article_processing_charge":"No","scopus_import":"1","page":"33-39","article_type":"letter_note","_id":"21818","volume":12,"publication_identifier":{"eissn":["2161-1653"]},"day":"17","doi":"10.1021/acsmacrolett.2c00616","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-05-12T10:03:44Z","pmid":1,"date_created":"2026-05-06T10:55:24Z","title":"Design of surface-aligned main-chain liquid-crystal networks prepared under ambient, light-free conditions using the Diels–Alder cycloaddition","publication":"ACS Macro Letters","publisher":"American Chemical Society","abstract":[{"text":"Surface-aligned liquid-crystal networks (LCNs) offer a solution for developing functional materials capable of performing a range of tasks, including actuation, shape memory, and surfaces patterning. Here we show that Diels–Alder cycloaddition can be used to prepare the backbone of planar aligned LCNs under mild ambient conditions without the addition of additives or UV irradiation. The mechanical properties of the networks have robust viscoelastic modulus and stiffness with a reversible local free volume change upon physical aging. This study shows new opportunities to design surface-aligned LCNs based on additive free step-growth Diels–Alder polymerization and enables the potential to incorporate a wider range of photochromic materials into LCNs.","lang":"eng"}],"intvolume":" 12","issue":"1","author":[{"last_name":"Park","full_name":"Park, Minwook","first_name":"Minwook"},{"last_name":"Stricker","first_name":"Friedrich J","full_name":"Stricker, Friedrich J","id":"7aca2cfc-46cf-11f0-abd3-8c96b5186745"},{"last_name":"Campos","first_name":"Jesus Guillen","full_name":"Campos, Jesus Guillen"},{"last_name":"Clark","first_name":"Kyle D.","full_name":"Clark, Kyle D."},{"last_name":"Lee","first_name":"Jaejun","full_name":"Lee, Jaejun"},{"last_name":"Kwon","first_name":"Younghoon","full_name":"Kwon, Younghoon"},{"last_name":"Valentine","full_name":"Valentine, Megan T.","first_name":"Megan T."},{"last_name":"Read de Alaniz","full_name":"Read de Alaniz, Javier","first_name":"Javier"}],"year":"2023","date_published":"2023-01-17T00:00:00Z","extern":"1","publication_status":"published","status":"public","OA_type":"closed access","citation":{"chicago":"Park, Minwook, Friedrich J Stricker, Jesus Guillen Campos, Kyle D. Clark, Jaejun Lee, Younghoon Kwon, Megan T. Valentine, and Javier Read de Alaniz. “Design of Surface-Aligned Main-Chain Liquid-Crystal Networks Prepared under Ambient, Light-Free Conditions Using the Diels–Alder Cycloaddition.” ACS Macro Letters. American Chemical Society, 2023. https://doi.org/10.1021/acsmacrolett.2c00616.","short":"M. Park, F.J. Stricker, J.G. Campos, K.D. Clark, J. Lee, Y. Kwon, M.T. Valentine, J. Read de Alaniz, ACS Macro Letters 12 (2023) 33–39.","mla":"Park, Minwook, et al. “Design of Surface-Aligned Main-Chain Liquid-Crystal Networks Prepared under Ambient, Light-Free Conditions Using the Diels–Alder Cycloaddition.” ACS Macro Letters, vol. 12, no. 1, American Chemical Society, 2023, pp. 33–39, doi:10.1021/acsmacrolett.2c00616.","ista":"Park M, Stricker FJ, Campos JG, Clark KD, Lee J, Kwon Y, Valentine MT, Read de Alaniz J. 2023. Design of surface-aligned main-chain liquid-crystal networks prepared under ambient, light-free conditions using the Diels–Alder cycloaddition. ACS Macro Letters. 12(1), 33–39.","ama":"Park M, Stricker FJ, Campos JG, et al. Design of surface-aligned main-chain liquid-crystal networks prepared under ambient, light-free conditions using the Diels–Alder cycloaddition. ACS Macro Letters. 2023;12(1):33-39. doi:10.1021/acsmacrolett.2c00616","apa":"Park, M., Stricker, F. J., Campos, J. G., Clark, K. D., Lee, J., Kwon, Y., … Read de Alaniz, J. (2023). Design of surface-aligned main-chain liquid-crystal networks prepared under ambient, light-free conditions using the Diels–Alder cycloaddition. ACS Macro Letters. American Chemical Society. https://doi.org/10.1021/acsmacrolett.2c00616","ieee":"M. Park et al., “Design of surface-aligned main-chain liquid-crystal networks prepared under ambient, light-free conditions using the Diels–Alder cycloaddition,” ACS Macro Letters, vol. 12, no. 1. American Chemical Society, pp. 33–39, 2023."},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["36541858"]}},{"citation":{"ista":"Sandlass S, Stricker FJ, Fragoso D, de Alaniz JR, Gordon MJ. 2023. Effect of polymer host matrix on multi-stage isomerization kinetics of DASA photochromes. Journal of Photochemistry and Photobiology A: Chemistry. 444, 114964.","ama":"Sandlass S, Stricker FJ, Fragoso D, de Alaniz JR, Gordon MJ. Effect of polymer host matrix on multi-stage isomerization kinetics of DASA photochromes. Journal of Photochemistry and Photobiology A: Chemistry. 2023;444. doi:10.1016/j.jphotochem.2023.114964","apa":"Sandlass, S., Stricker, F. J., Fragoso, D., de Alaniz, J. R., & Gordon, M. J. (2023). Effect of polymer host matrix on multi-stage isomerization kinetics of DASA photochromes. Journal of Photochemistry and Photobiology A: Chemistry. Elsevier. https://doi.org/10.1016/j.jphotochem.2023.114964","ieee":"S. Sandlass, F. J. Stricker, D. Fragoso, J. R. de Alaniz, and M. J. Gordon, “Effect of polymer host matrix on multi-stage isomerization kinetics of DASA photochromes,” Journal of Photochemistry and Photobiology A: Chemistry, vol. 444. Elsevier, 2023.","mla":"Sandlass, Sara, et al. “Effect of Polymer Host Matrix on Multi-Stage Isomerization Kinetics of DASA Photochromes.” Journal of Photochemistry and Photobiology A: Chemistry, vol. 444, 114964, Elsevier, 2023, doi:10.1016/j.jphotochem.2023.114964.","short":"S. Sandlass, F.J. Stricker, D. Fragoso, J.R. de Alaniz, M.J. Gordon, Journal of Photochemistry and Photobiology A: Chemistry 444 (2023).","chicago":"Sandlass, Sara, Friedrich J Stricker, Daniel Fragoso, Javier Read de Alaniz, and Michael J. Gordon. “Effect of Polymer Host Matrix on Multi-Stage Isomerization Kinetics of DASA Photochromes.” Journal of Photochemistry and Photobiology A: Chemistry. Elsevier, 2023. https://doi.org/10.1016/j.jphotochem.2023.114964."},"OA_type":"free access","status":"public","extern":"1","publication_status":"published","date_published":"2023-10-01T00:00:00Z","year":"2023","language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"full_name":"Sandlass, Sara","first_name":"Sara","last_name":"Sandlass"},{"last_name":"Stricker","full_name":"Stricker, Friedrich J","id":"7aca2cfc-46cf-11f0-abd3-8c96b5186745","first_name":"Friedrich J"},{"last_name":"Fragoso","full_name":"Fragoso, Daniel","first_name":"Daniel"},{"full_name":"de Alaniz, Javier Read","first_name":"Javier Read","last_name":"de Alaniz"},{"last_name":"Gordon","full_name":"Gordon, Michael J.","first_name":"Michael J."}],"intvolume":" 444","publisher":"Elsevier","OA_place":"publisher","abstract":[{"lang":"eng","text":"Molecular photoswitches provide a means for imparting synthetic structures with intrinsically logical and highly\r\ntunable photoresponsive properties. One variety of organic photoswitches known as Donor-Acceptor Stenhouse\r\nAdducts, or DASAs, are promising candidates for next generation light responsive materials because of their\r\nunique ability to stabilize three photochemically distinct isomeric states in solution, while their counterparts are\r\nstrictly limited to binary state behavior. In this work, we show how polymethacrylate host matrices shift the\r\nenergetic landscape of DASA relative to solution, prohibiting accumulation of an intermediate third isomeric\r\nstate by decelerating critical steps in the photoswitching mechanism. Specifically, we employ a dual-wavelength,\r\nphase locked detection scheme to probe thermal isomerizations in the switching process that occur at fast (~ms)\r\ntime scales that are inaccessible by standard UV–Vis spectroscopic techniques. The results of this study provide\r\nvaluable insight into the mechanism of multistate DASA reactivity and establish the foundation necessary to\r\nguide future efforts in offsetting kinetic matrix effects to enable dynamic, three state photoswitching in polymeric\r\nhosts. "}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-05-18T09:19:40Z","main_file_link":[{"url":"https://doi.org/10.1016/j.jphotochem.2023.114964","open_access":"1"}],"publication":"Journal of Photochemistry and Photobiology A: Chemistry","title":"Effect of polymer host matrix on multi-stage isomerization kinetics of DASA photochromes","date_created":"2026-05-06T10:57:28Z","volume":444,"_id":"21821","day":"01","doi":"10.1016/j.jphotochem.2023.114964","publication_identifier":{"issn":["1010-6030"],"eissn":["1873-2666"]},"article_number":"114964","article_type":"original","article_processing_charge":"No","ddc":["540"],"scopus_import":"1","month":"10","type":"journal_article","oa_version":"Published Version"},{"author":[{"last_name":"Iofinova","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","orcid":"0000-0002-7778-3221","full_name":"Iofinova, Eugenia B","first_name":"Eugenia B"},{"last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra","first_name":"Elena-Alexandra"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"}],"citation":{"short":"E.B. Iofinova, A. Krumes, D.-A. Alistarh, in:, 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 24364–24373.","chicago":"Iofinova, Eugenia B, Alexandra Krumes, and Dan-Adrian Alistarh. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” In 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 24364–73. IEEE, 2023. https://doi.org/10.1109/cvpr52729.2023.02334.","ama":"Iofinova EB, Krumes A, Alistarh D-A. Bias in pruned vision models: In-depth analysis and countermeasures. In: 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2023:24364-24373. doi:10.1109/cvpr52729.2023.02334","ieee":"E. B. Iofinova, A. Krumes, and D.-A. Alistarh, “Bias in pruned vision models: In-depth analysis and countermeasures,” in 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Vancouver, BC, Canada, 2023, pp. 24364–24373.","apa":"Iofinova, E. B., Krumes, A., & Alistarh, D.-A. (2023). Bias in pruned vision models: In-depth analysis and countermeasures. In 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 24364–24373). Vancouver, BC, Canada: IEEE. https://doi.org/10.1109/cvpr52729.2023.02334","ista":"Iofinova EB, Krumes A, Alistarh D-A. 2023. Bias in pruned vision models: In-depth analysis and countermeasures. 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 24364–24373.","mla":"Iofinova, Eugenia B., et al. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 24364–73, doi:10.1109/cvpr52729.2023.02334."},"corr_author":"1","publication_status":"published","status":"public","date_published":"2023-08-22T00:00:00Z","year":"2023","external_id":{"isi":["001062531308068"],"arxiv":["2304.12622"]},"language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2304.12622","open_access":"1"}],"arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-05-19T11:20:27Z","related_material":{"record":[{"relation":"dissertation_contains","id":"21854","status":"public"}],"link":[{"url":"https://github.com/IST-DASLab/pruned-vision-model-bias","relation":"software"}]},"publication":"2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition","title":"Bias in pruned vision models: In-depth analysis and countermeasures","acknowledgement":"The authors would like to sincerely thank Sara Hooker for her feedback during the development of this work. EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35. AP and DA acknowledge generous ERC support, via Starting Grant 805223 ScaleML.","date_created":"2024-01-10T08:42:40Z","publisher":"IEEE","ec_funded":1,"abstract":[{"text":"Pruning—that is, setting a significant subset of the parameters of a neural network to zero—is one of the most popular methods of model compression. Yet, several recent works have raised the issue that pruning may induce or exacerbate bias in the output of the compressed model. Despite existing evidence for this phenomenon, the relationship between neural network pruning and induced bias is not well-understood. In this work, we systematically investigate and characterize this phenomenon in Convolutional Neural Networks for computer vision. First, we show that it is in fact possible to obtain highly-sparse models, e.g. with less than 10% remaining weights, which do not decrease in accuracy nor substantially increase in bias when compared to dense models. At the same time, we also find that, at higher sparsities, pruned models exhibit higher uncertainty in their outputs, as well as increased correlations, which we directly link to increased bias. We propose easy-to-use criteria which, based only on the uncompressed model, establish whether bias will increase with pruning, and identify the samples most susceptible to biased predictions post-compression. Our code can be found at https://github.com/IST-DASLab/pruned-vision-model-bias.","lang":"eng"}],"oa":1,"conference":{"end_date":"2023-06-24","name":"CVPR: Conference on Computer Vision and Pattern Recognition","location":"Vancouver, BC, Canada","start_date":"2023-06-17"},"project":[{"name":"Vienna Graduate School on Computational Optimization","grant_number":"W1260-N35","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A"},{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}],"_id":"14771","doi":"10.1109/cvpr52729.2023.02334","day":"22","publication_identifier":{"eisbn":["9798350301298"],"eissn":["2575-7075"]},"month":"08","type":"conference","oa_version":"Preprint","article_processing_charge":"No","page":"24364-24373","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"isi":1},{"oa_version":"Published Version","month":"07","type":"dissertation","article_processing_charge":"No","ddc":["530"],"page":"184","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors","grant_number":"F8606","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"}],"_id":"13286","publication_identifier":{"issn":["2663-337X"]},"day":"21","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (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"},"doi":"10.15479/at:ista:13286","date_updated":"2026-06-03T07:16:01Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2023-07-24T14:10:45Z","related_material":{"record":[{"status":"public","id":"12522","relation":"research_data"},{"status":"public","id":"12118","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8910","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"13312"}]},"title":"Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium","ec_funded":1,"publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"date_updated":"2023-08-11T10:01:34Z","access_level":"closed","date_created":"2023-08-11T09:27:39Z","file_id":"14033","creator":"mvalenti","file_name":"PhD_thesis_Valentini_final.zip","file_size":56121429,"relation":"source_file","content_type":"application/x-zip-compressed","checksum":"666ee31c7eade89679806287c062fa14"},{"file_id":"14035","date_created":"2023-08-11T14:39:17Z","date_updated":"2023-08-11T14:39:17Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"0992f2ebef152dee8e70055350ebbb55","creator":"mvalenti","file_size":38199711,"file_name":"PhD_thesis_Valentini_final_validated.pdf"}],"abstract":[{"text":"Semiconductor-superconductor hybrid systems are the harbour of many intriguing mesoscopic phenomena. This material combination leads to spatial variations of the superconducting properties, which gives rise to Andreev bound states (ABSs). Some of these states might exhibit remarkable properties that render them highly desirable for topological quantum computing. The most prominent and hunted of such states are Majorana zero modes (MZMs), quasiparticles equals to their own quasiparticles that they follow non-abelian statistics. In this thesis, we first introduce the general framework of such hybrid systems and, then, we unveil a series of mesoscopic phenomena that we discovered. Firstly, we show tunneling spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures. Then, we introduce a novel protocol which allowed the integration of tunneling spectroscopy with Coulomb spectroscopy within the same device. Employing this approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally confined states reveal charge transport phenomenology similar to the one expected for MZMs. These findings shed light on the intricate interplay between superconductivity and quantum confinement, which brought us to explore another material platform, i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce superconductivity in such system, we showed how to engineer the proximity effect and we revealed a superconducting hard gap. Finally, we created a superconducting radio frequency driven ideal diode and a generator of non-sinusoidal current-phase relations. Our results open the path for the exploration of protected superconducting qubits and more complex hybrid devices in planar Germanium, like Kitaev chains and hybrid qubit devices.","lang":"eng"}],"OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","author":[{"last_name":"Valentini","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco"}],"has_accepted_license":"1","publication_status":"published","status":"public","date_published":"2023-07-21T00:00:00Z","year":"2023","file_date_updated":"2023-08-11T14:39:17Z","corr_author":"1","alternative_title":["ISTA Thesis"],"citation":{"short":"M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium, Institute of Science and Technology Austria, 2023.","chicago":"Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13286.","apa":"Valentini, M. (2023). Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13286","ieee":"M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,” Institute of Science and Technology Austria, 2023.","ama":"Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:10.15479/at:ista:13286","ista":"Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria.","mla":"Valentini, Marco. Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13286."},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}]},{"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001095315600001"],"arxiv":["2206.14104"]},"acknowledged_ssus":[{"_id":"NanoFab"}],"date_published":"2023-10-20T00:00:00Z","year":"2023","publication_status":"published","status":"public","citation":{"short":"M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, Physical Review Applied 20 (2023).","chicago":"Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Physical Review Applied. American Physical Society, 2023. https://doi.org/10.1103/PhysRevApplied.20.044054.","ista":"Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2023. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. 20(4), 044054.","apa":"Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., & Fink, J. M. (2023). Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.20.044054","ama":"Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. 2023;20(4). doi:10.1103/PhysRevApplied.20.044054","ieee":"M. Zemlicka et al., “Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses,” Physical Review Applied, vol. 20, no. 4. American Physical Society, 2023.","mla":"Zemlicka, Martin, et al. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Physical Review Applied, vol. 20, no. 4, 044054, American Physical Society, 2023, doi:10.1103/PhysRevApplied.20.044054."},"corr_author":"1","intvolume":" 20","issue":"4","author":[{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin","orcid":"0009-0005-0878-3032","first_name":"Martin","last_name":"Zemlicka"},{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko"},{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","first_name":"Matilda","last_name":"Peruzzo"},{"last_name":"Hassani","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","full_name":"Trioni, Andrea","first_name":"Andrea","last_name":"Trioni"},{"first_name":"Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink"}],"oa":1,"abstract":[{"lang":"eng","text":"State-of-the-art transmon qubits rely on large capacitors, which systematically improve their coherence due to reduced surface-loss participation. However, this approach increases both the footprint and the parasitic cross-coupling and is ultimately limited by radiation losses—a potential roadblock for scaling up quantum processors to millions of qubits. In this work we present transmon qubits with sizes as low as 36 × 39 µm2 with 100-nm-wide vacuum-gap capacitors that are micromachined from commercial silicon-on-insulator wafers and shadow evaporated with aluminum. We achieve a vacuum participation ratio up to 99.6% in an in-plane design that is compatible with standard coplanar circuits. Qubit relaxationtime measurements for small gaps with high zero-point electric field variance of up to 22 V/m reveal a double exponential decay indicating comparably strong qubit interaction with long-lived two-level systems. The exceptionally high selectivity of up to 20 dB to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon dielectric loss tangent of aluminum oxide previously exposed to ambient conditions. In terms of future scaling potential, we achieve a ratio of qubit quality factor to a footprint area equal to 20 µm−2, which is comparable with the highest T1 devices relying on larger geometries, a value that could improve substantially for lower surface-loss superconductors. "}],"ec_funded":1,"publisher":"American Physical Society","date_created":"2023-11-12T23:00:55Z","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105), the European Research Council under Grant Agreement No. 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. M.Z. was the recipient of a SAIA scholarship, E.R. of\r\na DOC fellowship of the Austrian Academy of Sciences, and M.P. of a Pöttinger scholarship at IST Austria. S.B. acknowledges support from Marie Skłodowska Curie Program No. 707438 (MSC-IF SUPEREOM). J.M.F. acknowledges support from the Horizon Europe Program HORIZON-CL4-2022-QUANTUM-01-SGA via Project No. 101113946 OpenSuperQPlus100 and the ISTA Nanofabrication Facility.","title":"Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses","publication":"Physical Review Applied","related_material":{"record":[{"id":"14520","relation":"research_data","status":"public"}]},"main_file_link":[{"url":"https://arxiv.org/abs/2206.14104","open_access":"1"}],"arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-03T07:16:02Z","publication_identifier":{"eissn":["2331-7019"]},"doi":"10.1103/PhysRevApplied.20.044054","day":"20","_id":"14517","project":[{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"},{"grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"101080139","name":"Open Superconducting Quantum Computers (OpenSuperQPlus)","_id":"bdb7cfc1-d553-11ed-ba76-d2eaab167738"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"volume":20,"article_type":"original","article_number":"044054","scopus_import":"1","isi":1,"department":[{"_id":"JoFi"}],"article_processing_charge":"No","oa_version":"Preprint","type":"journal_article","month":"10"},{"month":"06","type":"preprint","oa_version":"Preprint","article_processing_charge":"No","department":[{"_id":"GeKa"},{"_id":"M-Shop"}],"ddc":["530"],"article_number":"2306.07109","project":[{"grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"name":"Towards scalable hut wire quantum devices","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"grant_number":"F8606","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"_id":"13312","day":"13","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.48550/arXiv.2306.07109","date_updated":"2026-04-07T13:27:22Z","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.07109","open_access":"1"}],"related_material":{"record":[{"status":"public","id":"13286","relation":"dissertation_contains"}]},"publication":"arXiv","keyword":["Mesoscale and Nanoscale Physics"],"title":"Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas","acknowledgement":"The authors acknowledge Alexander Brinkmann, Alessandro Crippa, Andrew Higginbotham, Andrea Iorio, Giordano\r\nScappucci and Christian Schonenberger for helpful discussions. We thank Marcel Verheijen for the support in the\r\nTEM analysis. This research and related results were made\r\npossible with the support of the NOMIS Foundation. It was\r\nsupported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the\r\nnanofabrication facility, the European Union’s Horizon 2020\r\nresearch and innovation programme under Grant Agreement\r\nNo 862046, the HORIZON-RIA 101069515 project and the\r\nFWF Projects #P-32235, #P-36507 and #F-8606. R.S.S.\r\nacknowledges Spanish CM “Talento Program” Project No.\r\n2022-T1/IND-24070.","date_created":"2023-07-26T11:17:20Z","ec_funded":1,"abstract":[{"text":"Superconductor/semiconductor hybrid devices have attracted increasing\r\ninterest in the past years. Superconducting electronics aims to complement\r\nsemiconductor technology, while hybrid architectures are at the forefront of\r\nnew ideas such as topological superconductivity and protected qubits. In this\r\nwork, we engineer the induced superconductivity in two-dimensional germanium\r\nhole gas by varying the distance between the quantum well and the aluminum. We\r\ndemonstrate a hard superconducting gap and realize an electrically and flux\r\ntunable superconducting diode using a superconducting quantum interference\r\ndevice (SQUID). This allows to tune the current phase relation (CPR), to a\r\nregime where single Cooper pair tunneling is suppressed, creating a $ \\sin\r\n\\left( 2 \\varphi \\right)$ CPR. Shapiro experiments complement this\r\ninterpretation and the microwave drive allows to create a diode with $ \\approx\r\n100 \\%$ efficiency. The reported results open up the path towards monolithic\r\nintegration of spin qubit devices, microwave resonators and (protected)\r\nsuperconducting qubits on a silicon technology compatible platform.","lang":"eng"}],"OA_place":"repository","oa":1,"author":[{"last_name":"Valentini","full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco"},{"first_name":"Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver","last_name":"Sagi"},{"last_name":"Baghumyan","full_name":"Baghumyan, Levon","first_name":"Levon"},{"first_name":"Thijs de","full_name":"Gijsel, Thijs de","last_name":"Gijsel"},{"last_name":"Jung","first_name":"Jason","full_name":"Jung, Jason","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Calcaterra","first_name":"Stefano","full_name":"Calcaterra, Stefano"},{"first_name":"Andrea","full_name":"Ballabio, Andrea","last_name":"Ballabio"},{"full_name":"Servin, Juan Aguilera","first_name":"Juan Aguilera","last_name":"Servin"},{"last_name":"Aggarwal","first_name":"Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","full_name":"Aggarwal, Kushagra","orcid":"0000-0001-9985-9293"},{"orcid":"0009-0003-9037-8831","full_name":"Janik, Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian","last_name":"Janik"},{"last_name":"Adletzberger","full_name":"Adletzberger, Thomas","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"last_name":"Souto","full_name":"Souto, Rubén Seoane","first_name":"Rubén Seoane"},{"first_name":"Martin","full_name":"Leijnse, Martin","last_name":"Leijnse"},{"last_name":"Danon","full_name":"Danon, Jeroen","first_name":"Jeroen"},{"last_name":"Schrade","full_name":"Schrade, Constantin","first_name":"Constantin"},{"last_name":"Bakkers","full_name":"Bakkers, Erik","first_name":"Erik"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"first_name":"Giovanni","full_name":"Isella, Giovanni","last_name":"Isella"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"}],"citation":{"apa":"Valentini, M., Sagi, O., Baghumyan, L., Gijsel, T. de, Jung, J., Calcaterra, S., … Katsaros, G. (n.d.). Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. https://doi.org/10.48550/arXiv.2306.07109","ieee":"M. Valentini et al., “Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas,” arXiv. .","ama":"Valentini M, Sagi O, Baghumyan L, et al. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. doi:10.48550/arXiv.2306.07109","ista":"Valentini M, Sagi O, Baghumyan L, Gijsel T de, Jung J, Calcaterra S, Ballabio A, Servin JA, Aggarwal K, Janik M, Adletzberger T, Souto RS, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv, 2306.07109.","mla":"Valentini, Marco, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, 2306.07109, doi:10.48550/arXiv.2306.07109.","short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.A. Servin, K. Aggarwal, M. Janik, T. Adletzberger, R.S. Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2306.07109."},"corr_author":"1","publication_status":"draft","status":"public","date_published":"2023-06-13T00:00:00Z","year":"2023","language":[{"iso":"eng"}],"external_id":{"arxiv":["2306.07109"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}]},{"ddc":["530"],"oa":1,"department":[{"_id":"JoFi"}],"abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Tunable directional photon scattering from a pair of superconducting qubits\" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"article_processing_charge":"No","publisher":"Zenodo","oa_version":"Published Version","date_created":"2023-06-06T07:36:50Z","related_material":{"record":[{"id":"13117","relation":"used_in_publication","status":"public"}]},"month":"04","type":"research_data_reference","title":"Tunable directional photon scattering from a pair of superconducting qubits","date_updated":"2026-06-03T07:16:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7858567"}],"doi":"10.5281/ZENODO.7858567","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"28","status":"public","year":"2023","_id":"13124","date_published":"2023-04-28T00:00:00Z","corr_author":"1","citation":{"chicago":"Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7858567.","short":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023).","mla":"Redchenko, Elena, et al. Tunable Directional Photon Scattering from a Pair of Superconducting Qubits. Zenodo, 2023, doi:10.5281/ZENODO.7858567.","ista":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, 10.5281/ZENODO.7858567.","apa":"Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. https://doi.org/10.5281/ZENODO.7858567","ieee":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023.","ama":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:10.5281/ZENODO.7858567"},"author":[{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko"},{"full_name":"Poshakinskiy, Alexander","first_name":"Alexander","last_name":"Poshakinskiy"},{"last_name":"Sett","first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya","orcid":"0000-0001-7641-8348"},{"last_name":"Zemlicka","first_name":"Martin","orcid":"0009-0005-0878-3032","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Poddubny, Alexander","first_name":"Alexander","last_name":"Poddubny"},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}]},{"month":"12","type":"journal_article","oa_version":"Published Version","page":"1916-1926","department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}],"isi":1,"ddc":["530"],"scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","article_type":"original","doi":"10.1038/s41567-023-02218-w","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"01","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"volume":19,"project":[{"call_identifier":"H2020","grant_number":"679239","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607"},{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360"}],"_id":"13314","publication":"Nature Physics","related_material":{"record":[{"status":"public","relation":"research_data","id":"13116"},{"status":"public","id":"21423","relation":"dissertation_contains"},{"relation":"research_data","id":"21439","status":"public"}]},"title":"Chiral and nematic phases of flexible active filaments","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).","date_created":"2023-07-27T14:44:45Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-06-10T09:41:11Z","pmid":1,"abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division."}],"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"bc7673ca07d37309013a86166577b2f7","creator":"dernst","file_name":"2023_NaturePhysics_Dunajova.pdf","file_size":22471673,"file_id":"14916","success":1,"date_created":"2024-01-30T14:28:30Z","access_level":"open_access","date_updated":"2024-01-30T14:28:30Z"}],"oa":1,"publisher":"Springer Nature","ec_funded":1,"has_accepted_license":"1","author":[{"id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana","first_name":"Zuzana","last_name":"Dunajova"},{"last_name":"Prats Mateu","id":"299FE892-F248-11E8-B48F-1D18A9856A87","full_name":"Prats Mateu, Batirtze","first_name":"Batirtze"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","first_name":"Philipp","last_name":"Radler"},{"first_name":"Keesiang","full_name":"Lim, Keesiang","last_name":"Lim"},{"last_name":"Brandis","full_name":"Brandis, Dörte","id":"21d64d35-f128-11eb-9611-b8bcca7a12fd","first_name":"Dörte"},{"full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Velicky"},{"first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"},{"last_name":"Wong","full_name":"Wong, Richard W.","first_name":"Richard W."},{"last_name":"Elgeti","first_name":"Jens","full_name":"Elgeti, Jens"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo"},{"first_name":"Martin","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"}],"intvolume":" 19","external_id":{"isi":["001178645300041"],"pmid":["38075437"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"quality_controlled":"1","file_date_updated":"2024-01-30T14:28:30Z","citation":{"mla":"Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:10.1038/s41567-023-02218-w.","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. Nature Physics. 2023;19:1916-1926. doi:10.1038/s41567-023-02218-w","ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments,” Nature Physics, vol. 19. Springer Nature, pp. 1916–1926, 2023.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02218-w","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments. Nature Physics. 19, 1916–1926.","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02218-w.","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023) 1916–1926."},"corr_author":"1","publication_status":"published","status":"public","year":"2023","date_published":"2023-12-01T00:00:00Z"},{"publication_identifier":{"eissn":["2640-3498"]},"day":"30","volume":202,"_id":"14459","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2023-07-29","location":"Honolulu, Hawaii, HI, United States","start_date":"2023-07-23"},"scopus_import":"1","page":"31151-31209","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"article_processing_charge":"No","oa_version":"Preprint","month":"07","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["2212.13468"]},"publication_status":"published","status":"public","date_published":"2023-07-30T00:00:00Z","year":"2023","alternative_title":["PMLR"],"citation":{"short":"A. Shevchenko, K. Kögler, H. Hassani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 31151–31209.","chicago":"Shevchenko, Alexander, Kevin Kögler, Hamed Hassani, and Marco Mondelli. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” In Proceedings of the 40th International Conference on Machine Learning, 202:31151–209. ML Research Press, 2023.","ista":"Shevchenko A, Kögler K, Hassani H, Mondelli M. 2023. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 31151–31209.","apa":"Shevchenko, A., Kögler, K., Hassani, H., & Mondelli, M. (2023). Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press.","ieee":"A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits of two-layer autoencoders, and achieving them with gradient methods,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 31151–31209.","ama":"Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:31151-31209.","mla":"Shevchenko, Alexander, et al. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 31151–209."},"corr_author":"1","intvolume":" 202","author":[{"first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","last_name":"Shevchenko"},{"last_name":"Kögler","full_name":"Kögler, Kevin","id":"94ec913c-dc85-11ea-9058-e5051ab2428b","first_name":"Kevin"},{"first_name":"Hamed","full_name":"Hassani, Hamed","last_name":"Hassani"},{"last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"oa":1,"abstract":[{"text":"Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions.","lang":"eng"}],"publisher":"ML Research Press","acknowledgement":"Aleksandr Shevchenko, Kevin Kogler and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed Hassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","date_created":"2023-10-29T23:01:17Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17465"}]},"publication":"Proceedings of the 40th International Conference on Machine Learning","title":"Fundamental limits of two-layer autoencoders, and achieving them with gradient methods","date_updated":"2026-06-14T22:30:04Z","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.13468"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"file_date_updated":"2023-12-08T23:30:04Z","corr_author":"1","citation":{"short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12897.","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","apa":"Hafner, C. (2023). Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12897","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","mla":"Hafner, Christian. Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12897."},"alternative_title":["ISTA Thesis"],"year":"2023","date_published":"2023-05-05T00:00:00Z","publication_status":"published","status":"public","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"author":[{"last_name":"Hafner","full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","ec_funded":1,"abstract":[{"lang":"eng","text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will."}],"file":[{"embargo":"2023-12-07","access_level":"open_access","date_updated":"2023-12-08T23:30:04Z","file_id":"12942","date_created":"2023-05-11T10:43:20Z","creator":"chafner","file_name":"thesis-hafner-2023may11-a2b.pdf","file_size":50714445,"content_type":"application/pdf","relation":"main_file","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a"},{"date_updated":"2023-12-08T23:30:04Z","access_level":"closed","file_id":"12943","date_created":"2023-05-11T10:43:44Z","file_name":"thesis-release-form.pdf","file_size":265319,"creator":"chafner","embargo_to":"open_access","checksum":"a6b51334be2b81672357b1549afab40c","content_type":"application/pdf","relation":"source_file"}],"oa":1,"date_updated":"2025-04-15T07:16:15Z","user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","related_material":{"record":[{"relation":"part_of_dissertation","id":"9817","status":"public"},{"relation":"dissertation_contains","id":"13188","status":"public"},{"id":"7117","relation":"part_of_dissertation","status":"public"}]},"date_created":"2023-05-05T10:40:14Z","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"_id":"12897","supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"}],"doi":"10.15479/at:ista:12897","day":"05","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-031-2"]},"degree_awarded":"PhD","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"page":"180","ddc":["516","004","518","531"],"type":"dissertation","month":"05","oa_version":"Published Version"},{"acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Julian Fischer for his help in proving Proposition 1. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 715767).","date_created":"2023-07-04T07:41:30Z","keyword":["Computer Graphics","Computational Design","Computational Geometry","Shape Modeling"],"publication":"ACM Transactions on Graphics","related_material":{"record":[{"id":"12897","relation":"part_of_dissertation","status":"public"}]},"title":"The design space of Kirchhoff rods","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-14T22:30:06Z","oa":1,"file":[{"file_size":19635168,"file_name":"kirchhoff-rods.pdf","creator":"chafner","checksum":"4954c1cfa487725bc156dcfec872478a","content_type":"application/pdf","relation":"main_file","date_updated":"2023-07-04T08:11:28Z","access_level":"open_access","file_id":"13194","date_created":"2023-07-04T08:11:28Z","success":1},{"title":"Supplemental Material with Proofs","file_id":"13190","date_created":"2023-07-04T07:46:28Z","date_updated":"2023-07-04T07:46:28Z","access_level":"open_access","content_type":"application/pdf","relation":"supplementary_material","checksum":"79c9975fbc82ff71f1767331d2204cca","creator":"chafner","file_size":420909,"file_name":"supp-main.pdf"},{"date_created":"2023-07-04T07:46:30Z","file_id":"13191","title":"Cheat Sheet for Notation","date_updated":"2023-07-04T07:46:30Z","access_level":"open_access","checksum":"4ab647e4f03c711e1e6a5fc1eb8684db","content_type":"application/pdf","relation":"supplementary_material","file_name":"supp-cheat.pdf","file_size":430086,"creator":"chafner"},{"checksum":"c0fd9a57d012046de90c185ffa904b76","content_type":"video/mp4","relation":"supplementary_material","file_size":268088064,"file_name":"kirchhoff-video-final.mp4","creator":"chafner","date_created":"2023-07-04T07:46:39Z","file_id":"13192","title":"Supplemental Video","date_updated":"2023-07-04T07:46:39Z","access_level":"open_access"},{"file_size":25790,"file_name":"matlab-submission.zip","creator":"chafner","checksum":"71b00712b489ada2cd9815910ee180a9","relation":"supplementary_material","content_type":"application/x-zip-compressed","access_level":"open_access","date_updated":"2023-07-04T07:47:10Z","date_created":"2023-07-04T07:47:10Z","file_id":"13193","title":"Matlab Source Code with Example"}],"abstract":[{"lang":"eng","text":"The Kirchhoff rod model describes the bending and twisting of slender elastic rods in three dimensions, and has been widely studied to enable the prediction of how a rod will deform, given its geometry and boundary conditions. In this work, we study a number of inverse problems with the goal of computing the geometry of a straight rod that will automatically deform to match a curved target shape after attaching its endpoints to a support structure. Our solution lets us finely control the static equilibrium state of a rod by varying the cross-sectional profiles along its length.\r\nWe also show that the set of physically realizable equilibrium states admits a concise geometric description in terms of linear line complexes, which leads to very efficient computational design algorithms. Implemented in an interactive software tool, they allow us to convert three-dimensional hand-drawn spline curves to elastic rods, and give feedback about the feasibility and practicality of a design in real time. We demonstrate the efficacy of our method by designing and manufacturing several physical prototypes with applications to interior design and soft robotics."}],"ec_funded":1,"publisher":"Association for Computing Machinery","has_accepted_license":"1","issue":"5","intvolume":" 42","author":[{"last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"quality_controlled":"1","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"external_id":{"isi":["001086833300010"]},"status":"public","publication_status":"published","year":"2023","date_published":"2023-09-20T00:00:00Z","corr_author":"1","citation":{"chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3606033.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 42 (2023).","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.” ACM Transactions on Graphics, vol. 42, no. 5, 171, Association for Computing Machinery, 2023, doi:10.1145/3606033.","ista":"Hafner C, Bickel B. 2023. The design space of Kirchhoff rods. ACM Transactions on Graphics. 42(5), 171.","ieee":"C. Hafner and B. Bickel, “The design space of Kirchhoff rods,” ACM Transactions on Graphics, vol. 42, no. 5. Association for Computing Machinery, 2023.","ama":"Hafner C, Bickel B. The design space of Kirchhoff rods. ACM Transactions on Graphics. 2023;42(5). doi:10.1145/3606033","apa":"Hafner, C., & Bickel, B. (2023). The design space of Kirchhoff rods. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3606033"},"file_date_updated":"2023-07-04T08:11:28Z","oa_version":"Submitted Version","month":"09","type":"journal_article","isi":1,"ddc":["516"],"scopus_import":"1","department":[{"_id":"BeBi"}],"article_processing_charge":"No","article_type":"original","article_number":"171","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"doi":"10.1145/3606033","day":"20","volume":42,"project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"_id":"13188"},{"status":"public","publication_status":"published","year":"2023","date_published":"2023-02-02T00:00:00Z","file_date_updated":"2024-02-08T23:30:04Z","corr_author":"1","alternative_title":["ISTA Thesis"],"citation":{"short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491","mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491."},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"author":[{"last_name":"Zens","orcid":"0000-0002-9561-1239","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","full_name":"Zens, Bettina","first_name":"Bettina"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"date_updated":"2024-02-08T23:30:04Z","access_level":"open_access","embargo":"2024-02-07","date_created":"2023-02-07T13:07:38Z","file_id":"12527","file_size":23082464,"file_name":"PhDThesis_BettinaZens_2023_final.pdf","creator":"bzens","checksum":"069d87f025e0799bf9e3c375664264f2","relation":"main_file","content_type":"application/pdf"},{"file_id":"12528","date_created":"2023-02-07T13:09:05Z","access_level":"closed","date_updated":"2024-02-08T23:30:04Z","embargo_to":"open_access","checksum":"8c66ed203495d6e078ed1002a866520c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_size":106169509,"file_name":"PhDThesis_BettinaZens_2023_final.docx","creator":"bzens"}],"abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions."}],"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-07T13:49:23Z","date_created":"2023-02-02T14:50:20Z","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"related_material":{"record":[{"id":"8586","relation":"part_of_dissertation","status":"public"}]},"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","supervisor":[{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur"}],"project":[{"name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions","_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3"},{"name":"NÃ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"_id":"12491","publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"day":"02","doi":"10.15479/at:ista:12491","degree_awarded":"PhD","article_processing_charge":"No","ddc":["570"],"page":"187","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"oa_version":"Published Version","month":"02","type":"dissertation"},{"author":[{"last_name":"Franschitz","first_name":"Anna","full_name":"Franschitz, Anna","id":"480826C8-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","year":"2023","date_published":"2023-08-08T00:00:00Z","status":"public","publication_status":"published","alternative_title":["ISTA Thesis"],"citation":{"ista":"Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria.","apa":"Franschitz, A. (2023). Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984","ama":"Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:10.15479/at:ista:13984","ieee":"A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023.","mla":"Franschitz, Anna. Individual and Social Immunity against Viral Infections in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984.","short":"A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023.","chicago":"Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984."},"file_date_updated":"2024-10-29T23:31:04Z","corr_author":"1","acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"date_updated":"2026-04-07T13:51:29Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2023-08-08T15:33:29Z","title":"Individual and social immunity against viral infections in ants","publisher":"Institute of Science and Technology Austria","oa":1,"abstract":[{"lang":"eng","text":"Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection."}],"file":[{"embargo_to":"open_access","checksum":"55c876b73d49db15228a7f571592ec77","relation":"main_file","content_type":"application/pdf","file_name":"Print_Version_Franschitz_Anna_Thesis.pdf","file_size":10416761,"creator":"cchlebak","file_id":"15044","date_created":"2024-03-01T08:56:06Z","title":"Combined Version of original Thesis and Addendum","access_level":"open_access","date_updated":"2024-10-29T23:31:04Z"},{"embargo":"2024-08-08","access_level":"open_access","date_updated":"2024-08-09T22:30:03Z","file_id":"13986","date_created":"2023-08-08T18:01:28Z","creator":"afransch","file_name":"Thesis_AnnaFranschitz_202308.pdf","file_size":10797612,"relation":"main_file","content_type":"application/pdf","checksum":"27220243d5d51c3b0d7d61c0879d7a0c"},{"date_created":"2023-08-08T18:02:25Z","file_id":"13987","access_level":"closed","date_updated":"2024-08-09T22:30:03Z","embargo_to":"open_access","checksum":"40abf7ccca14a3893f72dc7fb88585d6","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_AnnaFranschitz_202308.docx","file_size":2619085,"creator":"afransch"},{"title":"Addendum","file_id":"15042","date_created":"2024-03-01T08:37:15Z","embargo":"2024-08-08","date_updated":"2024-10-29T23:31:04Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"8b991ecc2d59d045cc3cf0d676785ec7","description":"Minor modifications and clarifications - Feb 2024","creator":"cchlebak","file_size":85956,"file_name":"Addendum_AnnaFranschitz202402.pdf"},{"creator":"cchlebak","file_size":11818,"file_name":"Addendum_AnnaFranschitz202402.docx","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"66745aa01f960f17472c024875c049ed","embargo_to":"open_access","access_level":"closed","date_updated":"2024-08-09T22:30:03Z","title":"Addendum - source file","file_id":"15043","date_created":"2024-03-01T08:39:20Z"}],"OA_place":"publisher","degree_awarded":"PhD","_id":"13984","supervisor":[{"first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"}],"publication_identifier":{"isbn":["978-3-99078-034-3"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:13984","day":"08","oa_version":"Published Version","type":"dissertation","month":"08","article_processing_charge":"No","ddc":["570","577"],"department":[{"_id":"GradSch"},{"_id":"SyCr"}],"page":"89"},{"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (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"},"doi":"10.15479/at:ista:12964","day":"17","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-032-9"]},"supervisor":[{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"_id":"12964","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"degree_awarded":"PhD","page":"146","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"ddc":["530"],"article_processing_charge":"No","month":"05","type":"dissertation","oa_version":"Published Version","language":[{"iso":"eng"}],"file_date_updated":"2024-05-18T22:30:03Z","corr_author":"1","citation":{"ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","apa":"Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964","mla":"Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964.","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964."},"alternative_title":["ISTA Thesis"],"publication_status":"published","status":"public","date_published":"2023-05-17T00:00:00Z","year":"2023","has_accepted_license":"1","author":[{"first_name":"Daniel R","orcid":"0000-0002-1585-2631","full_name":"Boocock, Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87","last_name":"Boocock"}],"file":[{"file_size":40414730,"file_name":"thesis_boocock.pdf","creator":"dboocock","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","content_type":"application/pdf","relation":"main_file","date_updated":"2024-05-18T22:30:03Z","access_level":"open_access","embargo":"2024-05-17","file_id":"12988","date_created":"2023-05-17T13:39:54Z"},{"creator":"dboocock","file_size":34338567,"file_name":"thesis_boocock.zip","relation":"source_file","content_type":"application/zip","checksum":"581a2313ffeb40fe77e8a122a25a7795","embargo_to":"open_access","access_level":"closed","date_updated":"2024-05-18T22:30:03Z","file_id":"12989","date_created":"2023-05-17T13:39:53Z"}],"OA_place":"publisher","abstract":[{"lang":"eng","text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability."}],"oa":1,"publisher":"Institute of Science and Technology Austria","ec_funded":1,"related_material":{"record":[{"id":"8602","relation":"part_of_dissertation","status":"public"}]},"title":"Mechanochemical pattern formation across biological scales","date_created":"2023-05-15T14:52:36Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-07T13:52:57Z"},{"ddc":["610"],"department":[{"_id":"GradSch"},{"_id":"TiVo"}],"page":"148","article_processing_charge":"No","oa_version":"Published Version","type":"dissertation","month":"10","publication_identifier":{"issn":["2663-337X"]},"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (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"},"day":"12","doi":"10.15479/at:ista:14422","_id":"14422","project":[{"grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020"}],"supervisor":[{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","last_name":"Vogels"}],"degree_awarded":"PhD","oa":1,"OA_place":"publisher","abstract":[{"lang":"eng","text":"Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n"}],"file":[{"date_created":"2023-10-12T14:53:50Z","file_id":"14424","access_level":"open_access","date_updated":"2024-10-13T22:30:04Z","embargo":"2024-10-12","checksum":"7f636555eae7803323df287672fd13ed","content_type":"application/pdf","relation":"main_file","file_name":"Confavreux_Thesis_2A.pdf","file_size":30599717,"creator":"cchlebak"},{"file_name":"Confavreux Thesis.zip","file_size":68406739,"creator":"cchlebak","checksum":"725e85946db92290a4583a0de9779e1b","embargo_to":"open_access","relation":"source_file","content_type":"application/x-zip-compressed","access_level":"closed","date_updated":"2024-10-13T22:30:04Z","date_created":"2023-10-18T07:38:34Z","file_id":"14440"}],"ec_funded":1,"publisher":"Institute of Science and Technology Austria","date_created":"2023-10-12T14:13:25Z","title":"Synapseek: Meta-learning synaptic plasticity rules","related_material":{"record":[{"relation":"part_of_dissertation","id":"9633","status":"public"}]},"date_updated":"2026-04-07T13:53:13Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"date_published":"2023-10-12T00:00:00Z","year":"2023","status":"public","publication_status":"published","corr_author":"1","alternative_title":["ISTA Thesis"],"citation":{"short":"B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023.","chicago":"Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14422.","ista":"Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.","apa":"Confavreux, B. J. (2023). Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14422","ieee":"B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.","ama":"Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:10.15479/at:ista:14422","mla":"Confavreux, Basile J. Synapseek: Meta-Learning Synaptic Plasticity Rules. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14422."},"file_date_updated":"2024-10-13T22:30:04Z","has_accepted_license":"1","author":[{"first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","full_name":"Confavreux, Basile J","last_name":"Confavreux"}]},{"oa_version":"Published Version","month":"04","type":"dissertation","article_processing_charge":"No","ddc":["570"],"page":"115","department":[{"_id":"GradSch"},{"_id":"RySh"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto"}],"project":[{"_id":"267DFB90-B435-11E9-9278-68D0E5697425","name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?"}],"_id":"12809","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:12809","day":"06","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-07T13:53:28Z","date_created":"2023-04-06T07:54:09Z","title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","publisher":"Institute of Science and Technology Austria","oa":1,"OA_place":"publisher","file":[{"checksum":"35b5997d2b0acb461f9d33d073da0df5","content_type":"application/pdf","relation":"main_file","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","file_size":9881969,"creator":"cchlebak","file_id":"12814","date_created":"2023-04-07T06:16:06Z","access_level":"open_access","date_updated":"2024-04-08T22:30:03Z","embargo":"2024-04-07"},{"relation":"source_file","content_type":"application/pdf","embargo_to":"open_access","checksum":"81198f63c294890f6d58e8b29782efdc","creator":"cchlebak","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","file_size":44201583,"date_created":"2023-04-07T06:17:11Z","file_id":"12815","access_level":"closed","date_updated":"2024-04-08T22:30:03Z"},{"checksum":"0317bf7f457bb585f99d453ffa69eb53","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Thesis_CatarinaAlcarva_final.docx","file_size":84731244,"creator":"cchlebak","date_created":"2023-04-07T06:18:05Z","file_id":"12816","access_level":"closed","date_updated":"2024-04-08T22:30:03Z"}],"abstract":[{"text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. ","lang":"eng"}],"author":[{"last_name":"Alcarva","first_name":"Catarina","id":"3A96634C-F248-11E8-B48F-1D18A9856A87","full_name":"Alcarva, Catarina"}],"has_accepted_license":"1","publication_status":"published","status":"public","date_published":"2023-04-06T00:00:00Z","year":"2023","citation":{"ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","apa":"Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809","mla":"Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809."},"alternative_title":["ISTA Thesis"],"corr_author":"1","file_date_updated":"2024-04-08T22:30:03Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}]},{"ddc":["570"],"page":"190","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"article_processing_charge":"No","oa_version":"Published Version","month":"05","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"day":"05","doi":"10.15479/at:ista:12891","supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"_id":"12891","project":[{"call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"degree_awarded":"PhD","oa":1,"file":[{"checksum":"59b0303dc483f40a96a610a90aab7ee9","relation":"main_file","content_type":"application/pdf","file_name":"Thesis_Schauer_final.pdf","file_size":31434230,"creator":"aschauer","date_created":"2023-05-05T13:01:14Z","file_id":"12907","access_level":"open_access","date_updated":"2024-05-06T22:30:03Z","embargo":"2024-05-05"},{"file_id":"12908","date_created":"2023-05-05T13:04:15Z","date_updated":"2024-05-06T22:30:03Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"25f54e12479b6adaabd129a20568e6c1","embargo_to":"open_access","creator":"aschauer","file_name":"Thesis_Schauer_final.docx","file_size":43809109}],"abstract":[{"text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context.","lang":"eng"}],"ec_funded":1,"publisher":"Institute of Science and Technology Austria","date_created":"2023-05-05T08:48:20Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7888"},{"status":"public","id":"8966","relation":"part_of_dissertation"}]},"title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-12T06:56:58Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"status":"public","publication_status":"published","year":"2023","date_published":"2023-05-05T00:00:00Z","file_date_updated":"2024-05-06T22:30:03Z","alternative_title":["ISTA Thesis"],"corr_author":"1","citation":{"mla":"Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12891.","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:10.15479/at:ista:12891","apa":"Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12891","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12891.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023."},"has_accepted_license":"1","author":[{"last_name":"Schauer","first_name":"Alexandra","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"}]},{"oa_version":"Published Version","month":"11","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","isi":1,"ddc":["570"],"scopus_import":"1","page":"8140-8156","department":[{"_id":"JoCs"},{"_id":"GaTk"}],"article_type":"original","volume":43,"_id":"14656","project":[{"call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["1529-2401"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"29","doi":"10.1523/JNEUROSCI.0194-23.2023","pmid":1,"date_updated":"2025-09-09T13:37:51Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.","date_created":"2023-12-10T23:00:58Z","related_material":{"record":[{"relation":"earlier_version","id":"10077","status":"public"}]},"publication":"The Journal of Neuroscience","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","ec_funded":1,"publisher":"Society for Neuroscience","oa":1,"file":[{"file_id":"14674","date_created":"2023-12-11T11:30:37Z","embargo":"2024-06-01","date_updated":"2024-06-02T22:30:03Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"e2503c8f84be1050e28f64320f1d5bd2","creator":"dernst","file_name":"2023_JourNeuroscience_Nardin.pdf","file_size":2280632}],"abstract":[{"lang":"eng","text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain."}],"issue":"48","intvolume":" 43","author":[{"last_name":"Nardin","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele"},{"last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper"},{"last_name":"Savin","full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina"}],"has_accepted_license":"1","status":"public","publication_status":"published","year":"2023","date_published":"2023-11-29T00:00:00Z","citation":{"chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience. Society for Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.0194-23.2023.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43, no. 48, Society for Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” The Journal of Neuroscience, vol. 43, no. 48. Society for Neuroscience, pp. 8140–8156, 2023.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0194-23.2023","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156."},"file_date_updated":"2024-06-02T22:30:03Z","quality_controlled":"1","external_id":{"isi":["001148071000005"],"pmid":["37758476"]},"language":[{"iso":"eng"}]}]