[{"publisher":"Elsevier","intvolume":" 807","isi":1,"related_material":{"record":[{"relation":"earlier_version","id":"1341","status":"public"}]},"project":[{"call_identifier":"FWF","grant_number":"S11402-N23","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","call_identifier":"FWF"}],"publication_identifier":{"issn":["0304-3975"]},"volume":807,"day":"06","language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000512219400004"]},"publication":"Theoretical Computer Science","doi":"10.1016/j.tcs.2019.06.031","month":"02","ddc":["000"],"quality_controlled":"1","date_updated":"2026-04-16T09:35:15Z","_id":"6761","type":"journal_article","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2020-02-06T00:00:00Z","article_processing_charge":"No","page":"42-55","department":[{"_id":"ToHe"}],"date_created":"2019-08-04T21:59:20Z","file_date_updated":"2020-10-09T06:31:22Z","abstract":[{"lang":"eng","text":"In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability."}],"file":[{"content_type":"application/pdf","file_id":"8639","creator":"dernst","success":1,"file_size":1413001,"access_level":"open_access","date_created":"2020-10-09T06:31:22Z","checksum":"e86635417f45eb2cd75778f91382f737","date_updated":"2020-10-09T06:31:22Z","relation":"main_file","file_name":"2020_TheoreticalCS_Avni.pdf"}],"article_type":"original","title":"Dynamic resource allocation games","citation":{"apa":"Avni, G., Henzinger, T. A., & Kupferman, O. (2020). Dynamic resource allocation games. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2019.06.031","ieee":"G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation games,” Theoretical Computer Science, vol. 807. Elsevier, pp. 42–55, 2020.","ista":"Avni G, Henzinger TA, Kupferman O. 2020. Dynamic resource allocation games. Theoretical Computer Science. 807, 42–55.","short":"G. Avni, T.A. Henzinger, O. Kupferman, Theoretical Computer Science 807 (2020) 42–55.","ama":"Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. Theoretical Computer Science. 2020;807:42-55. doi:10.1016/j.tcs.2019.06.031","chicago":"Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation Games.” Theoretical Computer Science. Elsevier, 2020. https://doi.org/10.1016/j.tcs.2019.06.031.","mla":"Avni, Guy, et al. “Dynamic Resource Allocation Games.” Theoretical Computer Science, vol. 807, Elsevier, 2020, pp. 42–55, doi:10.1016/j.tcs.2019.06.031."},"author":[{"last_name":"Avni","full_name":"Avni, Guy","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"oa":1,"scopus_import":"1","oa_version":"Submitted Version","year":"2020","has_accepted_license":"1"},{"article_type":"original","author":[{"last_name":"Jankowiak","full_name":"Jankowiak, Gaspard","first_name":"Gaspard"},{"first_name":"Diane","full_name":"Peurichard, Diane","last_name":"Peurichard"},{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","orcid":"0000-0003-0666-8928","last_name":"Reversat","full_name":"Reversat, Anne"},{"full_name":"Schmeiser, Christian","last_name":"Schmeiser","first_name":"Christian"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K"}],"citation":{"ama":"Jankowiak G, Peurichard D, Reversat A, Schmeiser C, Sixt MK. Modeling adhesion-independent cell migration. Mathematical Models and Methods in Applied Sciences. 2020;30(3):513-537. doi:10.1142/S021820252050013X","chicago":"Jankowiak, Gaspard, Diane Peurichard, Anne Reversat, Christian Schmeiser, and Michael K Sixt. “Modeling Adhesion-Independent Cell Migration.” Mathematical Models and Methods in Applied Sciences. World Scientific Publishing, 2020. https://doi.org/10.1142/S021820252050013X.","short":"G. Jankowiak, D. Peurichard, A. Reversat, C. Schmeiser, M.K. Sixt, Mathematical Models and Methods in Applied Sciences 30 (2020) 513–537.","ista":"Jankowiak G, Peurichard D, Reversat A, Schmeiser C, Sixt MK. 2020. Modeling adhesion-independent cell migration. Mathematical Models and Methods in Applied Sciences. 30(3), 513–537.","mla":"Jankowiak, Gaspard, et al. “Modeling Adhesion-Independent Cell Migration.” Mathematical Models and Methods in Applied Sciences, vol. 30, no. 3, World Scientific Publishing, 2020, pp. 513–37, doi:10.1142/S021820252050013X.","apa":"Jankowiak, G., Peurichard, D., Reversat, A., Schmeiser, C., & Sixt, M. K. (2020). Modeling adhesion-independent cell migration. Mathematical Models and Methods in Applied Sciences. World Scientific Publishing. https://doi.org/10.1142/S021820252050013X","ieee":"G. Jankowiak, D. Peurichard, A. Reversat, C. Schmeiser, and M. K. Sixt, “Modeling adhesion-independent cell migration,” Mathematical Models and Methods in Applied Sciences, vol. 30, no. 3. World Scientific Publishing, pp. 513–537, 2020."},"title":"Modeling adhesion-independent cell migration","department":[{"_id":"MiSi"}],"acknowledgement":"This work has been supported by the Vienna Science and Technology Fund, Grant no. LS13-029. G.J. and C.S. also acknowledge support by the Austrian Science Fund, Grants no. W1245, F 65, and W1261, as well as by the Fondation Sciences Mathématiques de Paris, and by Paris-Sciences-et-Lettres.","page":"513-537","abstract":[{"text":"A two-dimensional mathematical model for cells migrating without adhesion capabilities is presented and analyzed. Cells are represented by their cortex, which is modeled as an elastic curve, subject to an internal pressure force. Net polymerization or depolymerization in the cortex is modeled via local addition or removal of material, driving a cortical flow. The model takes the form of a fully nonlinear degenerate parabolic system. An existence analysis is carried out by adapting ideas from the theory of gradient flows. Numerical simulations show that these simple rules can account for the behavior observed in experiments, suggesting a possible mechanical mechanism for adhesion-independent motility.","lang":"eng"}],"date_created":"2020-03-31T11:25:05Z","year":"2020","oa":1,"oa_version":"Preprint","scopus_import":"1","language":[{"iso":"eng"}],"day":"18","publication":"Mathematical Models and Methods in Applied Sciences","external_id":{"isi":["000525349900003"],"arxiv":["1903.09426"]},"publication_status":"published","isi":1,"intvolume":" 30","publisher":"World Scientific Publishing","volume":30,"publication_identifier":{"issn":["0218-2025"]},"project":[{"grant_number":"LS13-029","name":"Modeling of Polarization and Motility of Leukocytes in Three-Dimensional Environments","_id":"25AD6156-B435-11E9-9278-68D0E5697425"}],"date_published":"2020-03-18T00:00:00Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.09426"}],"type":"journal_article","article_processing_charge":"No","issue":"3","arxiv":1,"doi":"10.1142/S021820252050013X","month":"03","_id":"7623","date_updated":"2026-04-16T09:35:31Z","quality_controlled":"1"},{"date_published":"2020-09-14T00:00:00Z","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","ddc":["003"],"doi":"10.15479/AT:ISTA:8386","month":"09","date_updated":"2026-04-16T10:06:31Z","_id":"8386","language":[{"iso":"eng"}],"day":"14","degree_awarded":"PhD","corr_author":"1","acknowledged_ssus":[{"_id":"SSU"}],"publication_status":"published","ec_funded":1,"publisher":"Institute of Science and Technology Austria","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","name":"Distributed 3D Object Design","grant_number":"642841","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","full_name":"Bickel, Bernd"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"486"},{"status":"public","id":"1002","relation":"part_of_dissertation"}]},"year":"2020","OA_place":"publisher","has_accepted_license":"1","oa":1,"oa_version":"Published Version","file":[{"file_name":"Thesis_Ran.zip","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba","date_created":"2020-09-14T01:02:59Z","access_level":"closed","file_size":1245800191,"relation":"source_file","date_updated":"2020-09-14T12:18:43Z","file_id":"8388","creator":"rzhang","content_type":"application/x-zip-compressed"},{"creator":"rzhang","file_id":"8396","success":1,"content_type":"application/pdf","file_name":"PhD_thesis_Ran Zhang_20200915.pdf","file_size":161385316,"checksum":"817e20c33be9247f906925517c56a40d","access_level":"open_access","date_created":"2020-09-15T12:51:53Z","date_updated":"2020-09-15T12:51:53Z","relation":"main_file"}],"author":[{"last_name":"Zhang","full_name":"Zhang, Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran","orcid":"0000-0002-3808-281X"}],"citation":{"ieee":"R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020.","apa":"Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386","mla":"Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386.","short":"R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020.","ista":"Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria.","chicago":"Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386.","ama":"Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386"},"title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","acknowledgement":"The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria.","department":[{"_id":"BeBi"}],"page":"148","date_created":"2020-09-14T01:04:53Z","abstract":[{"lang":"eng","text":"Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting."}],"file_date_updated":"2020-09-15T12:51:53Z"},{"date_published":"2020-05-01T00:00:00Z","type":"conference","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/364"}],"article_processing_charge":"No","alternative_title":["LNCS"],"month":"05","doi":"10.1007/978-3-030-45727-3_16","quality_controlled":"1","date_updated":"2026-04-16T10:21:02Z","_id":"7966","language":[{"iso":"eng"}],"day":"01","publication":"Advances in Cryptology – EUROCRYPT 2020","external_id":{"isi":["000828688000016"]},"publication_status":"published","isi":1,"ec_funded":1,"publisher":"Springer Nature","intvolume":" 12107","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"volume":12107,"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030457266"],"eisbn":["9783030457273"]},"year":"2020","conference":{"start_date":"2020-05-11","end_date":"2020-05-15","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"oa":1,"oa_version":"Submitted Version","scopus_import":"1","author":[{"full_name":"Auerbach, Benedikt","last_name":"Auerbach","orcid":"0000-0002-7553-6606","first_name":"Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425"},{"first_name":"Federico","full_name":"Giacon, Federico","last_name":"Giacon"},{"last_name":"Kiltz","full_name":"Kiltz, Eike","first_name":"Eike"}],"citation":{"apa":"Auerbach, B., Giacon, F., & Kiltz, E. (2020). Everybody’s a target: Scalability in public-key encryption. In Advances in Cryptology – EUROCRYPT 2020 (Vol. 12107, pp. 475–506). Springer Nature. https://doi.org/10.1007/978-3-030-45727-3_16","ieee":"B. Auerbach, F. Giacon, and E. Kiltz, “Everybody’s a target: Scalability in public-key encryption,” in Advances in Cryptology – EUROCRYPT 2020, 2020, vol. 12107, pp. 475–506.","ama":"Auerbach B, Giacon F, Kiltz E. Everybody’s a target: Scalability in public-key encryption. In: Advances in Cryptology – EUROCRYPT 2020. Vol 12107. Springer Nature; 2020:475-506. doi:10.1007/978-3-030-45727-3_16","chicago":"Auerbach, Benedikt, Federico Giacon, and Eike Kiltz. “Everybody’s a Target: Scalability in Public-Key Encryption.” In Advances in Cryptology – EUROCRYPT 2020, 12107:475–506. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45727-3_16.","short":"B. Auerbach, F. Giacon, E. Kiltz, in:, Advances in Cryptology – EUROCRYPT 2020, Springer Nature, 2020, pp. 475–506.","ista":"Auerbach B, Giacon F, Kiltz E. 2020. Everybody’s a target: Scalability in public-key encryption. Advances in Cryptology – EUROCRYPT 2020. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 12107, 475–506.","mla":"Auerbach, Benedikt, et al. “Everybody’s a Target: Scalability in Public-Key Encryption.” Advances in Cryptology – EUROCRYPT 2020, vol. 12107, Springer Nature, 2020, pp. 475–506, doi:10.1007/978-3-030-45727-3_16."},"title":"Everybody’s a target: Scalability in public-key encryption","department":[{"_id":"KrPi"}],"page":"475-506","date_created":"2020-06-15T07:13:37Z","abstract":[{"lang":"eng","text":"For 1≤m≤n, we consider a natural m-out-of-n multi-instance scenario for a public-key encryption (PKE) scheme. An adversary, given n independent instances of PKE, wins if he breaks at least m out of the n instances. In this work, we are interested in the scaling factor of PKE schemes, SF, which measures how well the difficulty of breaking m out of the n instances scales in m. That is, a scaling factor SF=ℓ indicates that breaking m out of n instances is at least ℓ times more difficult than breaking one single instance. A PKE scheme with small scaling factor hence provides an ideal target for mass surveillance. In fact, the Logjam attack (CCS 2015) implicitly exploited, among other things, an almost constant scaling factor of ElGamal over finite fields (with shared group parameters).\r\n\r\nFor Hashed ElGamal over elliptic curves, we use the generic group model to argue that the scaling factor depends on the scheme's granularity. In low granularity, meaning each public key contains its independent group parameter, the scheme has optimal scaling factor SF=m; In medium and high granularity, meaning all public keys share the same group parameter, the scheme still has a reasonable scaling factor SF=√m. Our findings underline that instantiating ElGamal over elliptic curves should be preferred to finite fields in a multi-instance scenario.\r\n\r\nAs our main technical contribution, we derive new generic-group lower bounds of Ω(√(mp)) on the difficulty of solving both the m-out-of-n Gap Discrete Logarithm and the m-out-of-n Gap Computational Diffie-Hellman problem over groups of prime order p, extending a recent result by Yun (EUROCRYPT 2015). We establish the lower bound by studying the hardness of a related computational problem which we call the search-by-hypersurface problem."}]},{"citation":{"short":"T.A. Henzinger, N.E. Sarac, in:, Runtime Verification, Springer Nature, 2020, pp. 3–18.","ista":"Henzinger TA, Sarac NE. 2020. Monitorability under assumptions. Runtime Verification. RV: Runtime Verification, LNCS, vol. 12399, 3–18.","chicago":"Henzinger, Thomas A, and Naci E Sarac. “Monitorability under Assumptions.” In Runtime Verification, 12399:3–18. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-60508-7_1.","ama":"Henzinger TA, Sarac NE. Monitorability under assumptions. In: Runtime Verification. Vol 12399. Springer Nature; 2020:3-18. doi:10.1007/978-3-030-60508-7_1","mla":"Henzinger, Thomas A., and Naci E. Sarac. “Monitorability under Assumptions.” Runtime Verification, vol. 12399, Springer Nature, 2020, pp. 3–18, doi:10.1007/978-3-030-60508-7_1.","apa":"Henzinger, T. A., & Sarac, N. E. (2020). Monitorability under assumptions. In Runtime Verification (Vol. 12399, pp. 3–18). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-030-60508-7_1","ieee":"T. A. Henzinger and N. E. Sarac, “Monitorability under assumptions,” in Runtime Verification, Los Angeles, CA, United States, 2020, vol. 12399, pp. 3–18."},"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac","full_name":"Sarac, Naci E"}],"title":"Monitorability under assumptions","file":[{"file_name":"monitorability.pdf","file_size":478148,"date_created":"2020-10-15T14:28:06Z","checksum":"00661f9b7034f52e18bf24fa552b8194","access_level":"open_access","relation":"main_file","date_updated":"2020-10-15T14:28:06Z","creator":"esarac","file_id":"8665","success":1,"content_type":"application/pdf"}],"file_date_updated":"2020-10-15T14:28:06Z","abstract":[{"lang":"eng","text":"We introduce the monitoring of trace properties under assumptions. An assumption limits the space of possible traces that the monitor may encounter. An assumption may result from knowledge about the system that is being monitored, about the environment, or about another, connected monitor. We define monitorability under assumptions and study its theoretical properties. In particular, we show that for every assumption A, the boolean combinations of properties that are safe or co-safe relative to A are monitorable under A. We give several examples and constructions on how an assumption can make a non-monitorable property monitorable, and how an assumption can make a monitorable property monitorable with fewer resources, such as integer registers."}],"date_created":"2020-10-07T15:05:37Z","department":[{"_id":"ToHe"}],"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","page":"3-18","has_accepted_license":"1","year":"2020","conference":{"end_date":"2020-10-09","name":"RV: Runtime Verification","start_date":"2020-10-06","location":"Los Angeles, CA, United States"},"oa_version":"Submitted Version","scopus_import":"1","oa":1,"publication":"Runtime Verification","external_id":{"isi":["000728160600001"]},"publication_status":"published","language":[{"iso":"eng"}],"day":"02","volume":12399,"publication_identifier":{"isbn":["9783030605070"],"eissn":["1611-3349"],"eisbn":["9783030605087"],"issn":["0302-9743"]},"project":[{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"isi":1,"intvolume":" 12399","publisher":"Springer Nature","alternative_title":["LNCS"],"article_processing_charge":"No","date_published":"2020-10-02T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","type":"conference","_id":"8623","date_updated":"2026-04-16T10:22:01Z","quality_controlled":"1","ddc":["000"],"doi":"10.1007/978-3-030-60508-7_1","month":"10"},{"date_updated":"2026-04-16T10:21:31Z","quality_controlled":"1","_id":"10865","doi":"10.1007/978-3-030-45374-9_8","month":"04","article_processing_charge":"No","type":"book_chapter","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2020/090"}],"date_published":"2020-04-29T00:00:00Z","volume":12110,"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030453732"],"eisbn":["9783030453749"]},"editor":[{"full_name":"Kiayias, A","last_name":"Kiayias","first_name":"A"}],"intvolume":" 12110","publisher":"Springer Nature","isi":1,"publication_status":"published","corr_author":"1","publication":"Public-Key Cryptography","external_id":{"isi":["001299210200008"]},"day":"29","language":[{"iso":"eng"}],"scopus_import":"1","place":"Cham","oa_version":"Preprint","oa":1,"year":"2020","date_created":"2022-03-18T11:35:51Z","abstract":[{"lang":"eng","text":"We introduce the notion of Witness Maps as a cryptographic notion of a proof system. A Unique Witness Map (UWM) deterministically maps all witnesses for an NP statement to a single representative witness, resulting in a computationally sound, deterministic-prover, non-interactive witness independent proof system. A relaxation of UWM, called Compact Witness Map (CWM), maps all the witnesses to a small number of witnesses, resulting in a “lossy” deterministic-prover, non-interactive proof-system. We also define a Dual Mode Witness Map (DMWM) which adds an “extractable” mode to a CWM.\r\nOur main construction is a DMWM for all NP relations, assuming sub-exponentially secure indistinguishability obfuscation ( iO ), along with standard cryptographic assumptions. The DMWM construction relies on a CWM and a new primitive called Cumulative All-Lossy-But-One Trapdoor Functions (C-ALBO-TDF), both of which are in turn instantiated based on iO and other primitives. Our instantiation of a CWM is in fact a UWM; in turn, we show that a UWM implies Witness Encryption. Along the way to constructing UWM and C-ALBO-TDF, we also construct, from standard assumptions, Puncturable Digital Signatures and a new primitive called Cumulative Lossy Trapdoor Functions (C-LTDF). The former improves up on a construction of Bellare et al. (Eurocrypt 2016), who relied on sub-exponentially secure iO and sub-exponentially secure OWF.\r\nAs an application of our constructions, we show how to use a DMWM to construct the first leakage and tamper-resilient signatures with a deterministic signer, thereby solving a decade old open problem posed by Katz and Vaikunthanathan (Asiacrypt 2009), by Boyle, Segev and Wichs (Eurocrypt 2011), as well as by Faonio and Venturi (Asiacrypt 2016). Our construction achieves the optimal leakage rate of 1−o(1) ."}],"page":"220-246","acknowledgement":"We would like to thank the anonymous reviewers of PKC 2019 for their useful comments and suggestions. We thank Omer Paneth for pointing out to us the connection between Unique Witness Maps (UWM) and Witness encryption (WE). The first author would like to acknowledge Pandu Rangan for his involvement during the initial discussion phase of the project.","series_title":"LNCS","title":"Witness maps and applications","citation":{"apa":"Chakraborty, S., Prabhakaran, M., & Wichs, D. (2020). Witness maps and applications. In A. Kiayias (Ed.), Public-Key Cryptography (Vol. 12110, pp. 220–246). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-45374-9_8","ieee":"S. Chakraborty, M. Prabhakaran, and D. Wichs, “Witness maps and applications,” in Public-Key Cryptography, vol. 12110, A. Kiayias, Ed. Cham: Springer Nature, 2020, pp. 220–246.","short":"S. Chakraborty, M. Prabhakaran, D. Wichs, in:, A. Kiayias (Ed.), Public-Key Cryptography, Springer Nature, Cham, 2020, pp. 220–246.","ista":"Chakraborty S, Prabhakaran M, Wichs D. 2020.Witness maps and applications. In: Public-Key Cryptography. vol. 12110, 220–246.","ama":"Chakraborty S, Prabhakaran M, Wichs D. Witness maps and applications. In: Kiayias A, ed. Public-Key Cryptography. Vol 12110. LNCS. Cham: Springer Nature; 2020:220-246. doi:10.1007/978-3-030-45374-9_8","chicago":"Chakraborty, Suvradip, Manoj Prabhakaran, and Daniel Wichs. “Witness Maps and Applications.” In Public-Key Cryptography, edited by A Kiayias, 12110:220–46. LNCS. Cham: Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45374-9_8.","mla":"Chakraborty, Suvradip, et al. “Witness Maps and Applications.” Public-Key Cryptography, edited by A Kiayias, vol. 12110, Springer Nature, 2020, pp. 220–46, doi:10.1007/978-3-030-45374-9_8."},"author":[{"full_name":"Chakraborty, Suvradip","last_name":"Chakraborty","first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425"},{"last_name":"Prabhakaran","full_name":"Prabhakaran, Manoj","first_name":"Manoj"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}]},{"day":"01","language":[{"iso":"eng"}],"publication_status":"published","corr_author":"1","publication":"Communications in Mathematical Physics","external_id":{"isi":["000527910700019"],"arxiv":["1809.01902"]},"ec_funded":1,"publisher":"Springer Nature","intvolume":" 374","isi":1,"project":[{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","grant_number":"P27533_N27"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227"}],"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"volume":374,"type":"journal_article","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-03-01T00:00:00Z","article_processing_charge":"No","month":"03","doi":"10.1007/s00220-019-03505-5","arxiv":1,"ddc":["530"],"date_updated":"2025-04-14T07:27:00Z","quality_controlled":"1","_id":"6649","file":[{"content_type":"application/pdf","file_id":"6668","creator":"dernst","access_level":"open_access","checksum":"f9dd6dd615a698f1d3636c4a092fed23","date_created":"2019-07-24T07:19:10Z","file_size":853289,"relation":"main_file","date_updated":"2020-07-14T12:47:35Z","file_name":"2019_CommMathPhysics_Benedikter.pdf"}],"article_type":"original","title":"Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime","author":[{"last_name":"Benedikter","full_name":"Benedikter, Niels P","first_name":"Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1071-6091"},{"first_name":"Phan Thành","full_name":"Nam, Phan Thành","last_name":"Nam"},{"first_name":"Marcello","full_name":"Porta, Marcello","last_name":"Porta"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"citation":{"ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime,” Communications in Mathematical Physics, vol. 374. Springer Nature, pp. 2097–2150, 2020.","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., & Seiringer, R. (2020). Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03505-5","mla":"Benedikter, Niels P., et al. “Optimal Upper Bound for the Correlation Energy of a Fermi Gas in the Mean-Field Regime.” Communications in Mathematical Physics, vol. 374, Springer Nature, 2020, pp. 2097–2150, doi:10.1007/s00220-019-03505-5.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Communications in Mathematical Physics 374 (2020) 2097–2150.","ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2020. Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime. Communications in Mathematical Physics. 374, 2097–2150.","chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Optimal Upper Bound for the Correlation Energy of a Fermi Gas in the Mean-Field Regime.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-019-03505-5.","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime. Communications in Mathematical Physics. 2020;374:2097–2150. doi:10.1007/s00220-019-03505-5"},"page":"2097–2150","department":[{"_id":"RoSe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2019-07-18T13:30:04Z","file_date_updated":"2020-07-14T12:47:35Z","abstract":[{"lang":"eng","text":"While Hartree–Fock theory is well established as a fundamental approximation for interacting fermions, it has been unclear how to describe corrections to it due to many-body correlations. In this paper we start from the Hartree–Fock state given by plane waves and introduce collective particle–hole pair excitations. These pairs can be approximately described by a bosonic quadratic Hamiltonian. We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type upper bound to the ground state energy. Our result justifies the random-phase approximation in the mean-field scaling regime, for repulsive, regular interaction potentials.\r\n"}],"year":"2020","has_accepted_license":"1","oa":1,"scopus_import":"1","oa_version":"Published Version"},{"publication_identifier":{"eissn":["2296-9039"],"issn":["2296-9020"]},"volume":6,"project":[{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"publisher":"Springer Nature","intvolume":" 6","external_id":{"pmid":["33195442"]},"publication":"Journal of Elliptic and Parabolic Equations","corr_author":"1","publication_status":"published","language":[{"iso":"eng"}],"day":"01","_id":"7866","quality_controlled":"1","date_updated":"2025-07-17T08:12:24Z","ddc":["510"],"doi":"10.1007/s41808-020-00068-8","month":"12","article_processing_charge":"No","date_published":"2020-12-01T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","abstract":[{"lang":"eng","text":"In this paper, we establish convergence to equilibrium for a drift–diffusion–recombination system modelling the charge transport within certain semiconductor devices. More precisely, we consider a two-level system for electrons and holes which is augmented by an intermediate energy level for electrons in so-called trapped states. The recombination dynamics use the mass action principle by taking into account this additional trap level. The main part of the paper is concerned with the derivation of an entropy–entropy production inequality, which entails exponential convergence to the equilibrium via the so-called entropy method. The novelty of our approach lies in the fact that the entropy method is applied uniformly in a fast-reaction parameter which governs the lifetime of electrons on the trap level. Thus, the resulting decay estimate for the densities of electrons and holes extends to the corresponding quasi-steady-state approximation."}],"file_date_updated":"2020-11-25T08:59:59Z","date_created":"2020-05-17T22:00:45Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"JuFi"}],"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). The second author has been supported by the International Research Training Group IGDK 1754 “Optimization and Numerical Analysis for Partial Differential Equations with Nonsmooth Structures”, funded by the German Research Council (DFG) and the Austrian Science Fund (FWF) under grant number [W 1244-N18].","page":"529-598","author":[{"first_name":"Klemens","full_name":"Fellner, Klemens","last_name":"Fellner"},{"last_name":"Kniely","full_name":"Kniely, Michael","first_name":"Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333"}],"citation":{"ama":"Fellner K, Kniely M. Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model. Journal of Elliptic and Parabolic Equations. 2020;6:529-598. doi:10.1007/s41808-020-00068-8","chicago":"Fellner, Klemens, and Michael Kniely. “Uniform Convergence to Equilibrium for a Family of Drift–Diffusion Models with Trap-Assisted Recombination and the Limiting Shockley–Read–Hall Model.” Journal of Elliptic and Parabolic Equations. Springer Nature, 2020. https://doi.org/10.1007/s41808-020-00068-8.","ista":"Fellner K, Kniely M. 2020. Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model. Journal of Elliptic and Parabolic Equations. 6, 529–598.","short":"K. Fellner, M. Kniely, Journal of Elliptic and Parabolic Equations 6 (2020) 529–598.","mla":"Fellner, Klemens, and Michael Kniely. “Uniform Convergence to Equilibrium for a Family of Drift–Diffusion Models with Trap-Assisted Recombination and the Limiting Shockley–Read–Hall Model.” Journal of Elliptic and Parabolic Equations, vol. 6, Springer Nature, 2020, pp. 529–98, doi:10.1007/s41808-020-00068-8.","apa":"Fellner, K., & Kniely, M. (2020). Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model. Journal of Elliptic and Parabolic Equations. Springer Nature. https://doi.org/10.1007/s41808-020-00068-8","ieee":"K. Fellner and M. Kniely, “Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model,” Journal of Elliptic and Parabolic Equations, vol. 6. Springer Nature, pp. 529–598, 2020."},"title":"Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model","pmid":1,"article_type":"original","file":[{"file_name":"2020_JourEllipticParabEquat_Fellner.pdf","file_size":8408694,"checksum":"6bc6832caacddceee1471291e93dcf1d","date_created":"2020-11-25T08:59:59Z","access_level":"open_access","relation":"main_file","date_updated":"2020-11-25T08:59:59Z","creator":"dernst","file_id":"8802","success":1,"content_type":"application/pdf"}],"oa_version":"Published Version","scopus_import":"1","oa":1,"has_accepted_license":"1","year":"2020"},{"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1364/OPTICA.386613","open_access":"1"}],"type":"journal_article","date_published":"2020-05-18T00:00:00Z","OA_type":"gold","article_processing_charge":"No","doi":"10.1364/optica.386613","month":"05","ddc":["530"],"issue":"5","_id":"21640","date_updated":"2026-04-27T07:06:04Z","quality_controlled":"1","day":"18","language":[{"iso":"eng"}],"publication_status":"published","publication":"Optica","publisher":"Optica Publishing Group","intvolume":" 7","volume":7,"publication_identifier":{"eissn":["2334-2536"]},"OA_place":"publisher","year":"2020","oa":1,"scopus_import":"1","oa_version":"Published Version","extern":"1","article_type":"original","title":"Accelerating recurrent Ising machines in photonic integrated circuits","DOAJ_listed":"1","citation":{"apa":"Prabhu, M., Roques-Carmes, C., Shen, Y., Harris, N., Jing, L., Carolan, J., … Soljačić, M. (2020). Accelerating recurrent Ising machines in photonic integrated circuits. Optica. Optica Publishing Group. https://doi.org/10.1364/optica.386613","ieee":"M. Prabhu et al., “Accelerating recurrent Ising machines in photonic integrated circuits,” Optica, vol. 7, no. 5. Optica Publishing Group, pp. 551–558, 2020.","ista":"Prabhu M, Roques-Carmes C, Shen Y, Harris N, Jing L, Carolan J, Hamerly R, Baehr-Jones T, Hochberg M, Čeperić V, Joannopoulos JD, Englund DR, Soljačić M. 2020. Accelerating recurrent Ising machines in photonic integrated circuits. Optica. 7(5), 551–558.","short":"M. Prabhu, C. Roques-Carmes, Y. Shen, N. Harris, L. Jing, J. Carolan, R. Hamerly, T. Baehr-Jones, M. Hochberg, V. Čeperić, J.D. Joannopoulos, D.R. Englund, M. Soljačić, Optica 7 (2020) 551–558.","ama":"Prabhu M, Roques-Carmes C, Shen Y, et al. Accelerating recurrent Ising machines in photonic integrated circuits. Optica. 2020;7(5):551-558. doi:10.1364/optica.386613","chicago":"Prabhu, Mihika, Charles Roques-Carmes, Yichen Shen, Nicholas Harris, Li Jing, Jacques Carolan, Ryan Hamerly, et al. “Accelerating Recurrent Ising Machines in Photonic Integrated Circuits.” Optica. Optica Publishing Group, 2020. https://doi.org/10.1364/optica.386613.","mla":"Prabhu, Mihika, et al. “Accelerating Recurrent Ising Machines in Photonic Integrated Circuits.” Optica, vol. 7, no. 5, Optica Publishing Group, 2020, pp. 551–58, doi:10.1364/optica.386613."},"author":[{"first_name":"Mihika","full_name":"Prabhu, Mihika","last_name":"Prabhu"},{"first_name":"Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles","last_name":"Roques-Carmes"},{"first_name":"Yichen","last_name":"Shen","full_name":"Shen, Yichen"},{"first_name":"Nicholas","last_name":"Harris","full_name":"Harris, Nicholas"},{"full_name":"Jing, Li","last_name":"Jing","first_name":"Li"},{"full_name":"Carolan, Jacques","last_name":"Carolan","first_name":"Jacques"},{"full_name":"Hamerly, Ryan","last_name":"Hamerly","first_name":"Ryan"},{"full_name":"Baehr-Jones, Tom","last_name":"Baehr-Jones","first_name":"Tom"},{"full_name":"Hochberg, Michael","last_name":"Hochberg","first_name":"Michael"},{"first_name":"Vladimir","last_name":"Čeperić","full_name":"Čeperić, Vladimir"},{"first_name":"John D.","last_name":"Joannopoulos","full_name":"Joannopoulos, John D."},{"first_name":"Dirk R.","last_name":"Englund","full_name":"Englund, Dirk R."},{"full_name":"Soljačić, Marin","last_name":"Soljačić","first_name":"Marin"}],"page":"551-558","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"abstract":[{"lang":"eng","text":"Conventional computing architectures have no known efficient algorithms for combinatorial optimization tasks such\r\nas the Ising problem, which requires finding the ground state spin configuration of an arbitrary Ising graph. Physical\r\nIsing machines have recently been developed as an alternative to conventional exact and heuristic solvers; however,\r\nthese machines typically suffer from decreased ground state convergence probability or universality for high edge-\r\ndensity graphs or arbitrary graph weights, respectively. We experimentally demonstrate a proof-of-principle integrated\r\nnanophotonic recurrent Ising sampler (INPRIS), using a hybrid scheme combining electronics and silicon-on-insulator\r\nphotonics, that is capable of converging to the ground state of various four-spin graphs with high probability. The\r\nINPRIS results indicate that noise may be used as a resource to speed up the ground state search and to explore larger\r\nregions of the phase space, thus allowing one to probe noise-dependent physical observables. Since the recurrent pho-\r\ntonic transformation that our machine imparts is a fixed function of the graph problem and therefore compatible with\r\noptoelectronic architectures that support GHz clock rates (such as passive or non-volatile photonic circuits that do not\r\nrequire reprogramming at each iteration), this work suggests the potential for future systems that could achieve orders-\r\nof-magnitude speedups in exploring the solution space of combinatorially hard problems. "}],"date_created":"2026-03-30T12:22:48Z"},{"intvolume":" 28","publisher":"Optica Publishing Group","publication_identifier":{"issn":["1094-4087"]},"volume":28,"day":"26","language":[{"iso":"eng"}],"publication_status":"published","publication":"Optics Express","external_id":{"arxiv":["2007.11661"],"pmid":["33182865"]},"doi":"10.1364/oe.403192","month":"10","arxiv":1,"ddc":["530"],"issue":"23","quality_controlled":"1","date_updated":"2026-04-27T07:08:18Z","_id":"21637","type":"journal_article","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1364/OE.403192"}],"OA_type":"gold","date_published":"2020-10-26T00:00:00Z","article_processing_charge":"No","page":"33854-33868","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2026-03-30T12:22:48Z","abstract":[{"text":"We demonstrate new axisymmetric inverse-design techniques that can solve problems radically different from traditional lenses, including reconfigurable lenses (that shift a multi-frequency focal spot in response to refractive-index changes) and widely separated multi-wavelength lenses (λ = 1 µm and 10 µm). We also present experimental validation for an axisymmetric inverse-designed monochrome lens in the near-infrared fabricated via two-photon polymerization. Axisymmetry allows fullwave Maxwell solvers to be scaled up to structures hundreds or even thousands of wavelengths in diameter before requiring domain-decomposition approximations, while multilayer topology optimization with ∼105 degrees of freedom can tackle challenging design problems even when restricted to axisymmetric structures.","lang":"eng"}],"extern":"1","article_type":"original","pmid":1,"title":"Fullwave Maxwell inverse design of axisymmetric, tunable, and multi-scale multi-wavelength metalenses","DOAJ_listed":"1","author":[{"first_name":"Rasmus E.","full_name":"Christiansen, Rasmus E.","last_name":"Christiansen"},{"full_name":"Lin, Zin","last_name":"Lin","first_name":"Zin"},{"first_name":"Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles","last_name":"Roques-Carmes"},{"first_name":"Yannick","last_name":"Salamin","full_name":"Salamin, Yannick"},{"first_name":"Steven E.","full_name":"Kooi, Steven E.","last_name":"Kooi"},{"first_name":"John D.","last_name":"Joannopoulos","full_name":"Joannopoulos, John D."},{"full_name":"Soljačić, Marin","last_name":"Soljačić","first_name":"Marin"},{"last_name":"Johnson","full_name":"Johnson, Steven G.","first_name":"Steven G."}],"citation":{"mla":"Christiansen, Rasmus E., et al. “Fullwave Maxwell Inverse Design of Axisymmetric, Tunable, and Multi-Scale Multi-Wavelength Metalenses.” Optics Express, vol. 28, no. 23, Optica Publishing Group, 2020, pp. 33854–68, doi:10.1364/oe.403192.","short":"R.E. Christiansen, Z. Lin, C. Roques-Carmes, Y. Salamin, S.E. Kooi, J.D. Joannopoulos, M. Soljačić, S.G. Johnson, Optics Express 28 (2020) 33854–33868.","ista":"Christiansen RE, Lin Z, Roques-Carmes C, Salamin Y, Kooi SE, Joannopoulos JD, Soljačić M, Johnson SG. 2020. Fullwave Maxwell inverse design of axisymmetric, tunable, and multi-scale multi-wavelength metalenses. Optics Express. 28(23), 33854–33868.","ama":"Christiansen RE, Lin Z, Roques-Carmes C, et al. Fullwave Maxwell inverse design of axisymmetric, tunable, and multi-scale multi-wavelength metalenses. Optics Express. 2020;28(23):33854-33868. doi:10.1364/oe.403192","chicago":"Christiansen, Rasmus E., Zin Lin, Charles Roques-Carmes, Yannick Salamin, Steven E. Kooi, John D. Joannopoulos, Marin Soljačić, and Steven G. Johnson. “Fullwave Maxwell Inverse Design of Axisymmetric, Tunable, and Multi-Scale Multi-Wavelength Metalenses.” Optics Express. Optica Publishing Group, 2020. https://doi.org/10.1364/oe.403192.","ieee":"R. E. Christiansen et al., “Fullwave Maxwell inverse design of axisymmetric, tunable, and multi-scale multi-wavelength metalenses,” Optics Express, vol. 28, no. 23. Optica Publishing Group, pp. 33854–33868, 2020.","apa":"Christiansen, R. E., Lin, Z., Roques-Carmes, C., Salamin, Y., Kooi, S. E., Joannopoulos, J. D., … Johnson, S. G. (2020). Fullwave Maxwell inverse design of axisymmetric, tunable, and multi-scale multi-wavelength metalenses. Optics Express. Optica Publishing Group. https://doi.org/10.1364/oe.403192"},"oa":1,"scopus_import":"1","oa_version":"Published Version","OA_place":"publisher","year":"2020"},{"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1515/nanoph-2020-0579"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","type":"journal_article","date_published":"2020-12-23T00:00:00Z","OA_type":"gold","_id":"21642","quality_controlled":"1","date_updated":"2026-04-27T09:29:25Z","doi":"10.1515/nanoph-2020-0579","month":"12","ddc":["530"],"issue":"3","arxiv":1,"publication_status":"published","publication":"Nanophotonics","external_id":{"arxiv":["2006.09145"]},"day":"23","language":[{"iso":"eng"}],"volume":10,"publication_identifier":{"eissn":["2192-8614"],"issn":["2192-8614"]},"publisher":"Wiley","intvolume":" 10","keyword":["computational imaging","end-to-end photonic inverse design","inverse scattering","meta-optics","polarimetry"],"OA_place":"publisher","year":"2020","scopus_import":"1","oa_version":"Published Version","oa":1,"DOAJ_listed":"1","title":"End‐to‐end nanophotonic inverse design for imaging and polarimetry","author":[{"last_name":"Lin","full_name":"Lin, Zin","first_name":"Zin"},{"full_name":"Roques-Carmes, Charles","last_name":"Roques-Carmes","first_name":"Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82"},{"first_name":"Raphaël","last_name":"Pestourie","full_name":"Pestourie, Raphaël"},{"first_name":"Marin","last_name":"Soljačić","full_name":"Soljačić, Marin"},{"first_name":"Arka","full_name":"Majumdar, Arka","last_name":"Majumdar"},{"first_name":"Steven G.","full_name":"Johnson, Steven G.","last_name":"Johnson"}],"citation":{"ieee":"Z. Lin, C. Roques-Carmes, R. Pestourie, M. Soljačić, A. Majumdar, and S. G. Johnson, “End‐to‐end nanophotonic inverse design for imaging and polarimetry,” Nanophotonics, vol. 10, no. 3. Wiley, pp. 1177–1187, 2020.","apa":"Lin, Z., Roques-Carmes, C., Pestourie, R., Soljačić, M., Majumdar, A., & Johnson, S. G. (2020). End‐to‐end nanophotonic inverse design for imaging and polarimetry. Nanophotonics. Wiley. https://doi.org/10.1515/nanoph-2020-0579","mla":"Lin, Zin, et al. “End‐to‐end Nanophotonic Inverse Design for Imaging and Polarimetry.” Nanophotonics, vol. 10, no. 3, Wiley, 2020, pp. 1177–87, doi:10.1515/nanoph-2020-0579.","ama":"Lin Z, Roques-Carmes C, Pestourie R, Soljačić M, Majumdar A, Johnson SG. End‐to‐end nanophotonic inverse design for imaging and polarimetry. Nanophotonics. 2020;10(3):1177-1187. doi:10.1515/nanoph-2020-0579","chicago":"Lin, Zin, Charles Roques-Carmes, Raphaël Pestourie, Marin Soljačić, Arka Majumdar, and Steven G. Johnson. “End‐to‐end Nanophotonic Inverse Design for Imaging and Polarimetry.” Nanophotonics. Wiley, 2020. https://doi.org/10.1515/nanoph-2020-0579.","ista":"Lin Z, Roques-Carmes C, Pestourie R, Soljačić M, Majumdar A, Johnson SG. 2020. End‐to‐end nanophotonic inverse design for imaging and polarimetry. Nanophotonics. 10(3), 1177–1187.","short":"Z. Lin, C. Roques-Carmes, R. Pestourie, M. Soljačić, A. Majumdar, S.G. Johnson, Nanophotonics 10 (2020) 1177–1187."},"extern":"1","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"abstract":[{"lang":"eng","text":"By codesigning a metaoptical front end in conjunction with an image‐processing back end, we demonstrate noise sensitivity and compactness substantially superior to either an optics‐only or a computation‐only approach, illustrated by two examples: subwavelength imaging and reconstruction of the full polarization coherence matrices of multiple light sources. Our end‐to‐end inverse designs couple the solution of the full Maxwell equations—exploiting all aspects of wave physics arising in subwavelength scatterers—with inverse‐scattering algorithms in a single large‐scale optimization involving degrees of freedom. The resulting structures scatter light in a way that is radically different from either a conventional lens or a random microstructure, and suppress the noise sensitivity of the inverse‐scattering computation by several orders of magnitude. Incorporating the full wave physics is especially crucial for detecting spectral and polarization information that is discarded by geometric optics and scalar diffraction theory."}],"date_created":"2026-03-30T12:22:48Z","page":"1177-1187"},{"day":"13","language":[{"iso":"eng"}],"publication_status":"published","publication":"Proceedings of the 37th International Conference on Machine Learning","external_id":{"arxiv":["1912.10095"]},"intvolume":" 119","publisher":"ML Research Press","related_material":{"record":[{"status":"public","id":"17465","relation":"dissertation_contains"}]},"volume":119,"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","type":"conference","date_published":"2020-07-13T00:00:00Z","article_processing_charge":"No","month":"07","ddc":["000"],"arxiv":1,"_id":"9198","date_updated":"2026-05-19T22:30:05Z","quality_controlled":"1","file":[{"file_id":"9217","creator":"dernst","success":1,"content_type":"application/pdf","file_name":"2020_PMLR_Shevchenko.pdf","file_size":5336380,"checksum":"f042c8d4316bd87c6361aa76f1fbdbbe","date_created":"2021-03-02T15:38:14Z","access_level":"open_access","date_updated":"2021-03-02T15:38:14Z","relation":"main_file"}],"title":"Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks","citation":{"short":"A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 8773–8784.","ista":"Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. Proceedings of the 37th International Conference on Machine Learning. vol. 119, 8773–8784.","ama":"Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:8773-8784.","chicago":"Shevchenko, Aleksandr, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In Proceedings of the 37th International Conference on Machine Learning, 119:8773–84. ML Research Press, 2020.","mla":"Shevchenko, Aleksandr, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 8773–84.","apa":"Shevchenko, A., & Mondelli, M. (2020). Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 8773–8784). ML Research Press.","ieee":"A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks,” in Proceedings of the 37th International Conference on Machine Learning, 2020, vol. 119, pp. 8773–8784."},"author":[{"full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko","first_name":"Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425"},{"full_name":"Mondelli, Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"page":"8773-8784","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"acknowledgement":"M. Mondelli was partially supported by the 2019 LopezLoreta Prize. The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed Algorithms and Systems Lab for providing computational resources.","abstract":[{"lang":"eng","text":"The optimization of multilayer neural networks typically leads to a solution\r\nwith zero training error, yet the landscape can exhibit spurious local minima\r\nand the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon: we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization makes the landscape of multilayer neural networks\r\napproximately connected and thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions are connected via a piecewise linear\r\npath, and the increase in loss along this path vanishes as the number of\r\nneurons grows large. This result is a consequence of the fact that the\r\nparameters found by SGD are increasingly dropout stable as the network becomes\r\nwider. We show that, if we remove part of the neurons (and suitably rescale the\r\nremaining ones), the change in loss is independent of the total number of\r\nneurons, and it depends only on how many neurons are left. Our results exhibit\r\na mild dependence on the input dimension: they are dimension-free for two-layer\r\nnetworks and depend linearly on the dimension for multilayer networks. We\r\nvalidate our theoretical findings with numerical experiments for different\r\narchitectures and classification tasks."}],"file_date_updated":"2021-03-02T15:38:14Z","date_created":"2021-02-25T09:36:22Z","year":"2020","has_accepted_license":"1","oa":1,"oa_version":"Published Version"},{"_id":"8350","date_updated":"2025-09-11T07:08:52Z","ddc":["570"],"doi":"10.15479/AT:ISTA:8350","month":"09","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"date_published":"2020-09-09T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"7001","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6508"},{"relation":"part_of_dissertation","id":"735","status":"public"},{"status":"public","id":"661","relation":"part_of_dissertation"}]},"supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn"}],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"corr_author":"1","degree_awarded":"PhD","publication_status":"published","language":[{"iso":"eng"}],"day":"09","oa_version":"None","oa":1,"has_accepted_license":"1","year":"2020","file_date_updated":"2021-09-11T22:30:05Z","abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions.","lang":"eng"}],"date_created":"2020-09-09T11:12:10Z","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts.","page":"107","citation":{"chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350.","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:10.15479/AT:ISTA:8350","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","mla":"Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350.","apa":"Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020."},"author":[{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","full_name":"Shamipour, Shayan","last_name":"Shamipour"}],"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","file":[{"file_id":"8351","creator":"sshamip","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Shayan-Thesis-Final.docx","file_size":65194814,"date_created":"2020-09-09T11:06:27Z","access_level":"closed","checksum":"6e47871c74f85008b9876112eb3fcfa1","embargo_to":"open_access","date_updated":"2021-09-11T22:30:05Z","relation":"source_file"},{"content_type":"application/pdf","creator":"sshamip","file_id":"8352","date_updated":"2021-09-11T22:30:05Z","relation":"main_file","access_level":"open_access","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","date_created":"2020-09-09T11:06:13Z","file_size":23729605,"file_name":"Shayan-Thesis-Final.pdf","embargo":"2021-09-10"}]},{"oa_version":"None","oa":1,"has_accepted_license":"1","year":"2020","abstract":[{"lang":"eng","text":"Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry.\r\nThis work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo."}],"file_date_updated":"2021-10-31T23:30:05Z","date_created":"2020-04-24T16:00:51Z","department":[{"_id":"CaGu"}],"page":"98","author":[{"first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6709-2195","last_name":"Kainrath","full_name":"Kainrath, Stephanie"}],"citation":{"ista":"Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria.","short":"S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020.","chicago":"Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7680.","ama":"Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:10.15479/AT:ISTA:7680","mla":"Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680.","apa":"Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680","ieee":"S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020."},"title":"Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals","file":[{"file_size":3268017,"access_level":"open_access","checksum":"fb9a4468eb27be92690728e35c823796","date_created":"2020-04-28T11:19:21Z","relation":"main_file","date_updated":"2021-10-31T23:30:05Z","embargo":"2021-10-30","file_name":"Thesis_without-signatures_PDFA.pdf","content_type":"application/pdf","creator":"stgingl","file_id":"7692"},{"content_type":"application/octet-stream","file_id":"7693","creator":"stgingl","embargo_to":"open_access","relation":"source_file","date_updated":"2021-10-31T23:30:05Z","file_size":5167703,"date_created":"2020-04-28T11:19:24Z","checksum":"f6c80ca97104a631a328cb79a2c53493","access_level":"closed","file_name":"Thesis_without signatures.docx"}],"_id":"7680","date_updated":"2025-11-03T23:30:47Z","ddc":["570"],"doi":"10.15479/AT:ISTA:7680","month":"04","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"date_published":"2020-04-24T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"dissertation","publication_identifier":{"eissn":["2663-337X"]},"related_material":{"record":[{"relation":"dissertation_contains","id":"1028","status":"public"}]},"supervisor":[{"last_name":"Janovjak","full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"}],"publisher":"Institute of Science and Technology Austria","corr_author":"1","degree_awarded":"PhD","publication_status":"published","language":[{"iso":"eng"}],"day":"24"},{"publisher":"Elsevier","intvolume":" 212","isi":1,"keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"related_material":{"record":[{"status":"public","id":"14592","relation":"used_in_publication"},{"relation":"dissertation_contains","id":"12491","status":"public"}]},"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"publication_identifier":{"issn":["1047-8477"]},"volume":212,"day":"01","language":[{"iso":"eng"}],"publication_status":"published","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"corr_author":"1","external_id":{"pmid":["32987119"],"isi":["000600997800008"]},"publication":"Journal of Structural Biology","doi":"10.1016/j.jsb.2020.107633","month":"12","ddc":["570"],"issue":"3","quality_controlled":"1","date_updated":"2026-05-19T22:30:09Z","_id":"8586","type":"journal_article","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-12-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","acknowledgement":"This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract.","department":[{"_id":"FlSc"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2020-09-29T13:24:06Z","file_date_updated":"2020-12-10T14:01:10Z","abstract":[{"lang":"eng","text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications."}],"file":[{"date_updated":"2020-12-10T14:01:10Z","relation":"main_file","file_size":7076870,"access_level":"open_access","date_created":"2020-12-10T14:01:10Z","checksum":"c48cbf594e84fc2f91966ffaafc0918c","file_name":"2020_JourStrucBiology_Faessler.pdf","content_type":"application/pdf","success":1,"file_id":"8937","creator":"dernst"}],"pmid":1,"article_type":"original","title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","citation":{"chicago":"Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural Biology. Elsevier, 2020. https://doi.org/10.1016/j.jsb.2020.107633.","ama":"Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 2020;212(3). doi:10.1016/j.jsb.2020.107633","ista":"Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633.","short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020).","mla":"Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural Biology, vol. 212, no. 3, 107633, Elsevier, 2020, doi:10.1016/j.jsb.2020.107633.","apa":"Fäßler, F., Zens, B., Hauschild, R., & Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2020.107633","ieee":"F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” Journal of Structural Biology, vol. 212, no. 3. Elsevier, 2020."},"author":[{"first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","last_name":"Fäßler","full_name":"Fäßler, Florian"},{"orcid":"0000-0002-9561-1239","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","full_name":"Zens, Bettina","last_name":"Zens"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian KM"}],"oa":1,"scopus_import":"1","oa_version":"Published Version","article_number":"107633","year":"2020","has_accepted_license":"1"},{"oa":1,"scopus_import":"1","oa_version":"Published Version","article_number":"jcs239020","year":"2020","has_accepted_license":"1","acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months.","department":[{"_id":"FlSc"}],"date_created":"2020-09-17T14:00:33Z","file_date_updated":"2020-10-11T22:30:02Z","abstract":[{"text":"Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. ","lang":"eng"}],"file":[{"content_type":"application/pdf","creator":"dernst","file_id":"8435","access_level":"open_access","checksum":"ba917e551acc4ece2884b751434df9ae","date_created":"2020-09-17T14:07:51Z","file_size":13493302,"date_updated":"2020-10-11T22:30:02Z","relation":"main_file","file_name":"2020_JournalCellScience_Dimchev.pdf","embargo":"2020-10-10"}],"pmid":1,"article_type":"original","title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","citation":{"ama":"Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 2020;133(7). doi:10.1242/jcs.239020","chicago":"Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.239020.","short":"G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020).","ista":"Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020.","mla":"Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal of Cell Science, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:10.1242/jcs.239020.","apa":"Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.239020","ieee":"G. A. Dimchev et al., “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” Journal of Cell Science, vol. 133, no. 7. The Company of Biologists, 2020."},"author":[{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","first_name":"Georgi A"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"first_name":"Ashley C.","full_name":"Humphries, Ashley C.","last_name":"Humphries"},{"full_name":"Schaks, Matthias","last_name":"Schaks","first_name":"Matthias"},{"full_name":"Dimchev, Vanessa","last_name":"Dimchev","first_name":"Vanessa"},{"full_name":"Stradal, Theresia E. B.","last_name":"Stradal","first_name":"Theresia E. B."},{"first_name":"Jan","full_name":"Faix, Jan","last_name":"Faix"},{"last_name":"Krause","full_name":"Krause, Matthias","first_name":"Matthias"},{"first_name":"Michael","last_name":"Way","full_name":"Way, Michael"},{"full_name":"Falcke, Martin","last_name":"Falcke","first_name":"Martin"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"}],"doi":"10.1242/jcs.239020","month":"04","ddc":["570"],"issue":"7","quality_controlled":"1","date_updated":"2025-04-15T07:52:13Z","_id":"8434","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","date_published":"2020-04-09T00:00:00Z","article_processing_charge":"No","publisher":"The Company of Biologists","intvolume":" 133","isi":1,"keyword":["Cell Biology"],"project":[{"grant_number":"M02495","call_identifier":"FWF","name":"Protein structure and function in filopodia across scales","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"volume":133,"day":"09","language":[{"iso":"eng"}],"publication_status":"published","external_id":{"pmid":[" 32094266"],"isi":["000534387800005"]},"publication":"Journal of Cell Science"},{"isi":1,"publisher":"Springer Nature","ec_funded":1,"intvolume":" 38","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"volume":38,"project":[{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41587-020-0578-0"}]},"language":[{"iso":"eng"}],"day":"27","external_id":{"isi":["000529298800003"],"pmid":["32341562"]},"publication":"Nature Biotechnology","publication_status":"published","ddc":["570"],"doi":"10.1038/s41587-020-0500-9","month":"04","_id":"7889","date_updated":"2025-04-14T07:49:47Z","quality_controlled":"1","date_published":"2020-04-27T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","type":"journal_article","article_processing_charge":"No","department":[{"_id":"FyKo"}],"acknowledgement":"This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL. This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S. acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which performed the sequencing and bioinformatic analysis.","page":"944-946","file_date_updated":"2021-03-02T23:30:03Z","abstract":[{"text":"Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants.","lang":"eng"}],"date_created":"2020-05-25T15:02:00Z","pmid":1,"article_type":"original","file":[{"embargo":"2021-03-01","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","file_size":1180086,"access_level":"open_access","date_created":"2020-08-28T08:57:07Z","checksum":"1b30467500ec6277229a875b06e196d0","date_updated":"2021-03-02T23:30:03Z","relation":"main_file","file_id":"8316","creator":"dernst","content_type":"application/pdf"}],"citation":{"chicago":"Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology. Springer Nature, 2020. https://doi.org/10.1038/s41587-020-0500-9.","ama":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically encoded autoluminescence. Nature Biotechnology. 2020;38:944-946. doi:10.1038/s41587-020-0500-9","ista":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.","short":"T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V. Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova, S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V. Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S. Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan, Nature Biotechnology 38 (2020) 944–946.","mla":"Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology, vol. 38, Springer Nature, 2020, pp. 944–46, doi:10.1038/s41587-020-0500-9.","apa":"Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-020-0500-9","ieee":"T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,” Nature Biotechnology, vol. 38. Springer Nature, pp. 944–946, 2020."},"author":[{"last_name":"Mitiouchkina","full_name":"Mitiouchkina, Tatiana","first_name":"Tatiana"},{"last_name":"Mishin","full_name":"Mishin, Alexander S.","first_name":"Alexander S."},{"orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa","last_name":"Gonzalez Somermeyer"},{"first_name":"Nadezhda M.","last_name":"Markina","full_name":"Markina, Nadezhda M."},{"last_name":"Chepurnyh","full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V."},{"first_name":"Elena B.","last_name":"Guglya","full_name":"Guglya, Elena B."},{"full_name":"Karataeva, Tatiana A.","last_name":"Karataeva","first_name":"Tatiana A."},{"last_name":"Palkina","full_name":"Palkina, Kseniia A.","first_name":"Kseniia A."},{"full_name":"Shakhova, Ekaterina S.","last_name":"Shakhova","first_name":"Ekaterina S."},{"full_name":"Fakhranurova, Liliia I.","last_name":"Fakhranurova","first_name":"Liliia I."},{"last_name":"Chekova","full_name":"Chekova, Sofia V.","first_name":"Sofia V."},{"full_name":"Tsarkova, Aleksandra S.","last_name":"Tsarkova","first_name":"Aleksandra S."},{"full_name":"Golubev, Yaroslav V.","last_name":"Golubev","first_name":"Yaroslav V."},{"first_name":"Vadim V.","full_name":"Negrebetsky, Vadim V.","last_name":"Negrebetsky"},{"first_name":"Sergey A.","full_name":"Dolgushin, Sergey A.","last_name":"Dolgushin"},{"first_name":"Pavel V.","full_name":"Shalaev, Pavel V.","last_name":"Shalaev"},{"full_name":"Shlykov, Dmitry","last_name":"Shlykov","first_name":"Dmitry"},{"first_name":"Olesya A.","last_name":"Melnik","full_name":"Melnik, Olesya A."},{"full_name":"Shipunova, Victoria O.","last_name":"Shipunova","first_name":"Victoria O."},{"full_name":"Deyev, Sergey M.","last_name":"Deyev","first_name":"Sergey M."},{"full_name":"Bubyrev, Andrey I.","last_name":"Bubyrev","first_name":"Andrey I."},{"first_name":"Alexander S.","full_name":"Pushin, Alexander S.","last_name":"Pushin"},{"last_name":"Choob","full_name":"Choob, Vladimir V.","first_name":"Vladimir V."},{"first_name":"Sergey V.","last_name":"Dolgov","full_name":"Dolgov, Sergey V."},{"full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."},{"last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S.","first_name":"Karen S."}],"title":"Plants with genetically encoded autoluminescence","oa":1,"oa_version":"Submitted Version","scopus_import":"1","year":"2020","has_accepted_license":"1"},{"article_processing_charge":"No","type":"journal_article","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-04-06T00:00:00Z","quality_controlled":"1","date_updated":"2026-05-19T22:30:13Z","_id":"7888","month":"04","doi":"10.7554/elife.55190","ddc":["570"],"publication_status":"published","corr_author":"1","publication":"eLife","external_id":{"pmid":["32250246"],"isi":["000531544400001"]},"day":"06","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"12891","status":"public","relation":"dissertation_contains"}]},"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425"},{"_id":"266BC5CE-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429"}],"publication_identifier":{"issn":["2050-084X"]},"volume":9,"intvolume":" 9","ec_funded":1,"publisher":"eLife Sciences Publications","isi":1,"has_accepted_license":"1","article_number":"e55190","year":"2020","scopus_import":"1","oa_version":"Published Version","oa":1,"title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","citation":{"mla":"Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife, vol. 9, e55190, eLife Sciences Publications, 2020, doi:10.7554/elife.55190.","ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020).","chicago":"Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55190.","ama":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 2020;9. doi:10.7554/elife.55190","ieee":"A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” eLife, vol. 9. eLife Sciences Publications, 2020.","apa":"Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., & Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55190"},"author":[{"full_name":"Schauer, Alexandra","last_name":"Schauer","orcid":"0000-0001-7659-9142","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nunes Pinheiro, Diana C","last_name":"Nunes Pinheiro","orcid":"0000-0003-4333-7503","first_name":"Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"file":[{"file_name":"2020_eLife_Schauer.pdf","relation":"main_file","date_updated":"2020-07-14T12:48:04Z","access_level":"open_access","date_created":"2020-05-25T15:15:43Z","checksum":"f6aad884cf706846ae9357fcd728f8b5","file_size":7744848,"creator":"dernst","file_id":"7890","content_type":"application/pdf"}],"article_type":"original","pmid":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2020-05-25T15:01:40Z","file_date_updated":"2020-07-14T12:48:04Z","abstract":[{"text":"Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order.","lang":"eng"}],"department":[{"_id":"CaHe"},{"_id":"Bio"}]},{"year":"2020","conference":{"name":"NeurIPS: Conference on Neural Information Processing Systems","end_date":"2020-12-12","start_date":"2020-12-06","location":"Vancouver, Canada"},"oa_version":"Published Version","scopus_import":"1","oa":1,"author":[{"last_name":"Confavreux","full_name":"Confavreux, Basile J","first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E"},{"last_name":"Zenke","full_name":"Zenke, Friedemann","first_name":"Friedemann"},{"last_name":"Agnes","full_name":"Agnes, Everton J.","first_name":"Everton J."},{"last_name":"Lillicrap","full_name":"Lillicrap, Timothy","first_name":"Timothy"},{"last_name":"Vogels","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181"}],"citation":{"ieee":"B. J. Confavreux, F. Zenke, E. J. Agnes, T. Lillicrap, and T. P. Vogels, “A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 16398–16408.","apa":"Confavreux, B. J., Zenke, F., Agnes, E. J., Lillicrap, T., & Vogels, T. P. (2020). A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In Advances in Neural Information Processing Systems (Vol. 33, pp. 16398–16408). Vancouver, Canada.","mla":"Confavreux, Basile J., et al. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” Advances in Neural Information Processing Systems, vol. 33, 2020, pp. 16398–408.","ista":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. 2020. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 33, 16398–16408.","short":"B.J. Confavreux, F. Zenke, E.J. Agnes, T. Lillicrap, T.P. Vogels, in:, Advances in Neural Information Processing Systems, 2020, pp. 16398–16408.","ama":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In: Advances in Neural Information Processing Systems. Vol 33. ; 2020:16398-16408.","chicago":"Confavreux, Basile J, Friedemann Zenke, Everton J. Agnes, Timothy Lillicrap, and Tim P Vogels. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” In Advances in Neural Information Processing Systems, 33:16398–408, 2020."},"title":"A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network","date_created":"2021-07-04T22:01:27Z","abstract":[{"lang":"eng","text":"The search for biologically faithful synaptic plasticity rules has resulted in a large body of models. They are usually inspired by – and fitted to – experimental data, but they rarely produce neural dynamics that serve complex functions. These failures suggest that current plasticity models are still under-constrained by existing data. Here, we present an alternative approach that uses meta-learning to discover plausible synaptic plasticity rules. Instead of experimental data, the rules are constrained by the functions they implement and the structure they are meant to produce. Briefly, we parameterize synaptic plasticity rules by a Volterra expansion and then use supervised learning methods (gradient descent or evolutionary strategies) to minimize a problem-dependent loss function that quantifies how effectively a candidate plasticity rule transforms an initially random network into one with the desired function. We first validate our approach by re-discovering previously described plasticity rules, starting at the single-neuron level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction of most variability of inputs to a neuron (i.e., the first principal component). We expand the problem to the network level and ask the framework to find Oja’s rule together with an anti-Hebbian rule such that an initially random two-layer firing-rate network will recover several principal components of the input space after learning. Next, we move to networks of integrate-and-fire neurons with plastic inhibitory afferents. We train for rules that achieve a target firing rate by countering tuned excitation. Our algorithm discovers a specific subset of the manifold of rules that can solve this task. Our work is a proof of principle of an automated and unbiased approach to unveil synaptic plasticity rules that obey biological constraints and can solve complex functions."}],"acknowledgement":"We would like to thank Chaitanya Chintaluri, Georgia Christodoulou, Bill Podlaski and Merima Šabanovic for useful discussions and comments. This work was supported by a Wellcome Trust ´ Senior Research Fellowship (214316/Z/18/Z), a BBSRC grant (BB/N019512/1), an ERC consolidator Grant (SYNAPSEEK), a Leverhulme Trust Project Grant (RPG-2016-446), and funding from École Polytechnique, Paris.","department":[{"_id":"TiVo"}],"page":"16398-16408","article_processing_charge":"No","date_published":"2020-12-06T00:00:00Z","type":"conference","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html","open_access":"1"}],"date_updated":"2026-05-19T22:30:15Z","quality_controlled":"1","_id":"9633","month":"12","publication":"Advances in Neural Information Processing Systems","publication_status":"published","language":[{"iso":"eng"}],"day":"06","project":[{"_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020","grant_number":"819603"},{"grant_number":"214316/Z/18/Z","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87"}],"publication_identifier":{"issn":["1049-5258"]},"volume":33,"related_material":{"record":[{"id":"14422","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://doi.org/10.1101/2020.10.24.353409","relation":"is_continued_by"}]},"intvolume":" 33","ec_funded":1},{"oa_version":"Submitted Version","scopus_import":"1","oa":1,"has_accepted_license":"1","year":"2020","article_number":"100856","file_date_updated":"2022-05-16T22:30:04Z","abstract":[{"lang":"eng","text":"This paper presents a novel abstraction technique for analyzing Lyapunov and asymptotic stability of polyhedral switched systems. A polyhedral switched system is a hybrid system in which the continuous dynamics is specified by polyhedral differential inclusions, the invariants and guards are specified by polyhedral sets and the switching between the modes do not involve reset of variables. A finite state weighted graph abstracting the polyhedral switched system is constructed from a finite partition of the state–space, such that the satisfaction of certain graph conditions, such as the absence of cycles with product of weights on the edges greater than (or equal) to 1, implies the stability of the system. However, the graph is in general conservative and hence, the violation of the graph conditions does not imply instability. If the analysis fails to establish stability due to the conservativeness in the approximation, a counterexample (cycle with product of edge weights greater than or equal to 1) indicating a potential reason for the failure is returned. Further, a more precise approximation of the switched system can be constructed by considering a finer partition of the state–space in the construction of the finite weighted graph. We present experimental results on analyzing stability of switched systems using the above method."}],"date_created":"2020-02-02T23:00:59Z","tmp":{"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","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"department":[{"_id":"ToHe"}],"author":[{"first_name":"Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0003−2936−5719","last_name":"Garcia Soto","full_name":"Garcia Soto, Miriam"},{"last_name":"Prabhakar","full_name":"Prabhakar, Pavithra","first_name":"Pavithra"}],"citation":{"apa":"Garcia Soto, M., & Prabhakar, P. (2020). Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2020.100856","ieee":"M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability of polyhedral switched systems,” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5. Elsevier, 2020.","ista":"Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.","short":"M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020).","ama":"Garcia Soto M, Prabhakar P. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 2020;36(5). doi:10.1016/j.nahs.2020.100856","chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2020. https://doi.org/10.1016/j.nahs.2020.100856.","mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5, 100856, Elsevier, 2020, doi:10.1016/j.nahs.2020.100856."},"title":"Abstraction based verification of stability of polyhedral switched systems","article_type":"original","file":[{"creator":"dernst","file_id":"8688","content_type":"application/pdf","file_name":"2020_NAHS_GarciaSoto.pdf","embargo":"2022-05-15","access_level":"open_access","date_created":"2020-10-21T13:16:45Z","checksum":"560abfddb53f9fe921b6744f59f2cfaa","file_size":818774,"date_updated":"2022-05-16T22:30:04Z","relation":"main_file"}],"_id":"7426","quality_controlled":"1","date_updated":"2025-04-15T06:26:15Z","ddc":["000"],"issue":"5","doi":"10.1016/j.nahs.2020.100856","month":"05","article_processing_charge":"No","date_published":"2020-05-01T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","publication_identifier":{"issn":["1751-570X"]},"volume":36,"project":[{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"}],"isi":1,"intvolume":" 36","publisher":"Elsevier","publication":"Nonlinear Analysis: Hybrid Systems","external_id":{"isi":["000528828600003"]},"corr_author":"1","publication_status":"published","language":[{"iso":"eng"}],"day":"01"}]