[{"arxiv":1,"date_updated":"2025-04-14T07:27:47Z","ec_funded":1,"publication_status":"published","article_processing_charge":"No","day":"01","publication_identifier":{"issn":["0091-1798"],"eissn":["2168-894X"]},"_id":"11354","year":"2022","abstract":[{"text":"We construct a recurrent diffusion process with values in the space of probability measures over an arbitrary closed Riemannian manifold of dimension d≥2. The process is associated with the Dirichlet form defined by integration of the Wasserstein gradient w.r.t. the Dirichlet–Ferguson measure, and is the counterpart on multidimensional base spaces to the modified massive Arratia flow over the unit interval described in V. Konarovskyi and M.-K. von Renesse (Comm. Pure Appl. Math. 72 (2019) 764–800). Together with two different constructions of the process, we discuss its ergodicity, invariant sets, finite-dimensional approximations, and Varadhan short-time asymptotics.","lang":"eng"}],"page":"591-648","author":[{"orcid":"0000-0002-9881-6870","first_name":"Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","full_name":"Dello Schiavo, Lorenzo"}],"title":"The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold","publication":"Annals of Probability","issue":"2","article_type":"original","citation":{"chicago":"Dello Schiavo, Lorenzo. “The Dirichlet–Ferguson Diffusion on the Space of Probability Measures over a Closed Riemannian Manifold.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AOP1541\">https://doi.org/10.1214/21-AOP1541</a>.","short":"L. Dello Schiavo, Annals of Probability 50 (2022) 591–648.","ama":"Dello Schiavo L. The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold. <i>Annals of Probability</i>. 2022;50(2):591-648. doi:<a href=\"https://doi.org/10.1214/21-AOP1541\">10.1214/21-AOP1541</a>","apa":"Dello Schiavo, L. (2022). The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AOP1541\">https://doi.org/10.1214/21-AOP1541</a>","mla":"Dello Schiavo, Lorenzo. “The Dirichlet–Ferguson Diffusion on the Space of Probability Measures over a Closed Riemannian Manifold.” <i>Annals of Probability</i>, vol. 50, no. 2, Institute of Mathematical Statistics, 2022, pp. 591–648, doi:<a href=\"https://doi.org/10.1214/21-AOP1541\">10.1214/21-AOP1541</a>.","ista":"Dello Schiavo L. 2022. The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold. Annals of Probability. 50(2), 591–648.","ieee":"L. Dello Schiavo, “The Dirichlet–Ferguson diffusion on the space of probability measures over a closed Riemannian manifold,” <i>Annals of Probability</i>, vol. 50, no. 2. Institute of Mathematical Statistics, pp. 591–648, 2022."},"oa":1,"acknowledgement":"Research supported by the Sonderforschungsbereich 1060 and the Hausdorff Center for Mathematics. The author gratefully acknowledges funding of his current position at IST Austria by the Austrian Science Fund (FWF) grant F65 and by the European Research Council (ERC, Grant agreement No. 716117, awarded to Prof. Dr. Jan Maas).","fulldoi":"https://doi.org/10.1214/21-AOP1541","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publisher":"Institute of Mathematical Statistics","date_created":"2022-05-08T22:01:44Z","doi":"10.1214/21-AOP1541","scopus_import":"1","corr_author":"1","status":"public","project":[{"call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"department":[{"_id":"JaMa"}],"volume":50,"external_id":{"arxiv":["1811.11598"],"isi":["000773518500005"]},"language":[{"iso":"eng"}],"oa_version":"Preprint","intvolume":"        50","date_published":"2022-03-01T00:00:00Z","type":"journal_article","quality_controlled":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1811.11598"}],"month":"03"},{"ec_funded":1,"day":"29","article_processing_charge":"No","publication_status":"published","date_updated":"2025-12-30T06:50:51Z","page":"3-22","abstract":[{"text":"Contract-based design is a promising methodology for taming the complexity of developing sophisticated systems. A formal contract distinguishes between assumptions, which are constraints that the designer of a component puts on the environments in which the component can be used safely, and guarantees, which are promises that the designer asks from the team that implements the component. A theory of formal contracts can be formalized as an interface theory, which supports the composition and refinement of both assumptions and guarantees.\r\nAlthough there is a rich landscape of contract-based design methods that address functional and extra-functional properties, we present the first interface theory that is designed for ensuring system-wide security properties. Our framework provides a refinement relation and a composition operation that support both incremental design and independent implementability. We develop our theory for both stateless and stateful interfaces. We illustrate the applicability of our framework with an example inspired from the automotive domain.","lang":"eng"}],"author":[{"last_name":"Bartocci","full_name":"Bartocci, Ezio","first_name":"Ezio"},{"full_name":"Ferrere, Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ana Oliveira","last_name":"Da Costa","full_name":"Da Costa, Ana Oliveira"}],"publication":"Fundamental Approaches to Software Engineering","title":"Information-flow interfaces","publication_identifier":{"isbn":["9783030994280"],"eissn":["1611-3349"],"issn":["0302-9743"]},"alternative_title":["LNCS"],"conference":{"start_date":"2022-04-02","end_date":"2022-04-07","name":"FASE: Fundamental Approaches to Software Engineering","location":"Munich, Germany"},"_id":"11355","year":"2022","file_date_updated":"2022-05-09T06:52:44Z","citation":{"apa":"Bartocci, E., Ferrere, T., Henzinger, T. A., Nickovic, D., &#38; Da Costa, A. O. (2022). Information-flow interfaces. In <i>Fundamental Approaches to Software Engineering</i> (Vol. 13241, pp. 3–22). Munich, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-99429-7_1\">https://doi.org/10.1007/978-3-030-99429-7_1</a>","ama":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. Information-flow interfaces. In: <i>Fundamental Approaches to Software Engineering</i>. Vol 13241. Springer Nature; 2022:3-22. doi:<a href=\"https://doi.org/10.1007/978-3-030-99429-7_1\">10.1007/978-3-030-99429-7_1</a>","mla":"Bartocci, Ezio, et al. “Information-Flow Interfaces.” <i>Fundamental Approaches to Software Engineering</i>, vol. 13241, Springer Nature, 2022, pp. 3–22, doi:<a href=\"https://doi.org/10.1007/978-3-030-99429-7_1\">10.1007/978-3-030-99429-7_1</a>.","ista":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. 2022. Information-flow interfaces. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13241, 3–22.","ieee":"E. Bartocci, T. Ferrere, T. A. Henzinger, D. Nickovic, and A. O. Da Costa, “Information-flow interfaces,” in <i>Fundamental Approaches to Software Engineering</i>, Munich, Germany, 2022, vol. 13241, pp. 3–22.","chicago":"Bartocci, Ezio, Thomas Ferrere, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira Da Costa. “Information-Flow Interfaces.” In <i>Fundamental Approaches to Software Engineering</i>, 13241:3–22. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-99429-7_1\">https://doi.org/10.1007/978-3-030-99429-7_1</a>.","short":"E. Bartocci, T. Ferrere, T.A. Henzinger, D. Nickovic, A.O. Da Costa, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2022, pp. 3–22."},"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2022-05-08T22:01:44Z","isi":1,"publisher":"Springer Nature","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 956123 and was funded in part by the FWF project W1255-N23 and by the ERC-2020-AdG 101020093.","fulldoi":"https://doi.org/10.1007/978-3-030-99429-7_1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","related_material":{"record":[{"status":"public","id":"17094","relation":"extended_version"}]},"doi":"10.1007/978-3-030-99429-7_1","has_accepted_license":"1","status":"public","department":[{"_id":"ToHe"}],"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"oa_version":"Published Version","type":"conference","date_published":"2022-03-29T00:00:00Z","intvolume":"     13241","language":[{"iso":"eng"}],"volume":13241,"external_id":{"isi":["000782393600001"]},"month":"03","file":[{"success":1,"file_id":"11357","access_level":"open_access","date_created":"2022-05-09T06:52:44Z","file_size":479146,"relation":"main_file","content_type":"application/pdf","checksum":"7f6f860b20b8de2a249e9c1b4eee15cf","creator":"dernst","date_updated":"2022-05-09T06:52:44Z","file_name":"2022_LNCS_Bartocci.pdf"}],"ddc":["000"],"quality_controlled":"1"},{"oa_version":"Published Version","type":"journal_article","date_published":"2022-06-15T00:00:00Z","intvolume":"        67","language":[{"iso":"eng"}],"external_id":{"pmid":["36545972"],"isi":["000835291100006"]},"volume":67,"month":"06","ddc":["530"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.scib.2022.04.007"}],"quality_controlled":"1","scopus_import":"1","pmid":1,"doi":"10.1016/j.scib.2022.04.007","status":"public","department":[{"_id":"MaIb"}],"project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"}],"citation":{"chicago":"Chang, Cheng, Bingchao Qin, Lizhong Su, and Li Dong Zhao. “Distinct Electron and Hole Transports in SnSe Crystals.” <i>Science Bulletin</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">https://doi.org/10.1016/j.scib.2022.04.007</a>.","short":"C. Chang, B. Qin, L. Su, L.D. Zhao, Science Bulletin 67 (2022) 1105–1107.","ista":"Chang C, Qin B, Su L, Zhao LD. 2022. Distinct electron and hole transports in SnSe crystals. Science Bulletin. 67(11), 1105–1107.","apa":"Chang, C., Qin, B., Su, L., &#38; Zhao, L. D. (2022). Distinct electron and hole transports in SnSe crystals. <i>Science Bulletin</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">https://doi.org/10.1016/j.scib.2022.04.007</a>","mla":"Chang, Cheng, et al. “Distinct Electron and Hole Transports in SnSe Crystals.” <i>Science Bulletin</i>, vol. 67, no. 11, Elsevier, 2022, pp. 1105–07, doi:<a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">10.1016/j.scib.2022.04.007</a>.","ama":"Chang C, Qin B, Su L, Zhao LD. Distinct electron and hole transports in SnSe crystals. <i>Science Bulletin</i>. 2022;67(11):1105-1107. doi:<a href=\"https://doi.org/10.1016/j.scib.2022.04.007\">10.1016/j.scib.2022.04.007</a>","ieee":"C. Chang, B. Qin, L. Su, and L. D. Zhao, “Distinct electron and hole transports in SnSe crystals,” <i>Science Bulletin</i>, vol. 67, no. 11. Elsevier, pp. 1105–1107, 2022."},"oa":1,"article_type":"letter_note","issue":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-05-08T22:01:44Z","publisher":"Elsevier","isi":1,"fulldoi":"https://doi.org/10.1016/j.scib.2022.04.007","acknowledgement":"This work was supported by the National Science Fund for Distinguished Young Scholars (51925101), National Key Research and Development Program of China (2018YFA0702100), 111 Project (B17002), and Lise Meitner Project (M2889-N).","article_processing_charge":"No","day":"15","publication_status":"published","date_updated":"2026-06-18T10:50:26Z","page":"1105-1107","author":[{"first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","last_name":"Chang"},{"first_name":"Bingchao","full_name":"Qin, Bingchao","last_name":"Qin"},{"first_name":"Lizhong","last_name":"Su","full_name":"Su, Lizhong"},{"full_name":"Zhao, Li Dong","last_name":"Zhao","first_name":"Li Dong"}],"publication":"Science Bulletin","title":"Distinct electron and hole transports in SnSe crystals","publication_identifier":{"issn":["2095-9273"],"eissn":["2095-9281"]},"_id":"11356","year":"2022"},{"doi":"10.1021/acs.nanolett.2c00435","scopus_import":"1","pmid":1,"status":"public","department":[{"_id":"MaSe"}],"external_id":{"pmid":["35405074"],"isi":["000809056900019"],"arxiv":["2109.00556"]},"volume":22,"language":[{"iso":"eng"}],"oa_version":"Preprint","intvolume":"        22","type":"journal_article","date_published":"2022-04-27T00:00:00Z","quality_controlled":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.00556"}],"month":"04","arxiv":1,"date_updated":"2025-06-11T13:47:08Z","publication_status":"published","article_processing_charge":"No","day":"27","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"year":"2022","_id":"11379","abstract":[{"text":"Bernal-stacked multilayer graphene is a versatile platform to explore quantum transport phenomena and interaction physics due to its exceptional tunability via electrostatic gating. For instance, upon applying a perpendicular electric field, its band structure exhibits several off-center Dirac points (so-called Dirac gullies) in each valley. Here, the formation of Dirac gullies and the interaction-induced breakdown of gully coherence is explored via magnetotransport measurements in high-quality Bernal-stacked (ABA) trilayer graphene. At zero magnetic field, multiple Lifshitz transitions indicating the formation of Dirac gullies are identified. In the quantum Hall regime, the emergence of Dirac gullies is evident as an increase in Landau level degeneracy. When tuning both electric and magnetic fields, electron–electron interactions can be controllably enhanced until, beyond critical electric and magnetic fields, the gully degeneracy is eventually lifted. The arising correlated ground state is consistent with a previously predicted nematic phase that spontaneously breaks the rotational gully symmetry.","lang":"eng"}],"page":"3317-3322","author":[{"first_name":"Felix","full_name":"Winterer, Felix","last_name":"Winterer"},{"first_name":"Anna M.","last_name":"Seiler","full_name":"Seiler, Anna M."},{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan"},{"first_name":"Fabian R.","full_name":"Geisenhof, Fabian R.","last_name":"Geisenhof"},{"first_name":"Kenji","full_name":"Watanabe, Kenji","last_name":"Watanabe"},{"last_name":"Taniguchi","full_name":"Taniguchi, Takashi","first_name":"Takashi"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"full_name":"Weitz, R. Thomas","last_name":"Weitz","first_name":"R. Thomas"}],"title":"Spontaneous gully-polarized quantum hall states in ABA trilayer graphene","publication":"Nano Letters","issue":"8","article_type":"original","citation":{"ieee":"F. Winterer <i>et al.</i>, “Spontaneous gully-polarized quantum hall states in ABA trilayer graphene,” <i>Nano Letters</i>, vol. 22, no. 8. American Chemical Society, pp. 3317–3322, 2022.","ama":"Winterer F, Seiler AM, Ghazaryan A, et al. Spontaneous gully-polarized quantum hall states in ABA trilayer graphene. <i>Nano Letters</i>. 2022;22(8):3317-3322. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.2c00435\">10.1021/acs.nanolett.2c00435</a>","apa":"Winterer, F., Seiler, A. M., Ghazaryan, A., Geisenhof, F. R., Watanabe, K., Taniguchi, T., … Weitz, R. T. (2022). Spontaneous gully-polarized quantum hall states in ABA trilayer graphene. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.2c00435\">https://doi.org/10.1021/acs.nanolett.2c00435</a>","mla":"Winterer, Felix, et al. “Spontaneous Gully-Polarized Quantum Hall States in ABA Trilayer Graphene.” <i>Nano Letters</i>, vol. 22, no. 8, American Chemical Society, 2022, pp. 3317–22, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.2c00435\">10.1021/acs.nanolett.2c00435</a>.","ista":"Winterer F, Seiler AM, Ghazaryan A, Geisenhof FR, Watanabe K, Taniguchi T, Serbyn M, Weitz RT. 2022. Spontaneous gully-polarized quantum hall states in ABA trilayer graphene. Nano Letters. 22(8), 3317–3322.","short":"F. Winterer, A.M. Seiler, A. Ghazaryan, F.R. Geisenhof, K. Watanabe, T. Taniguchi, M. Serbyn, R.T. Weitz, Nano Letters 22 (2022) 3317–3322.","chicago":"Winterer, Felix, Anna M. Seiler, Areg Ghazaryan, Fabian R. Geisenhof, Kenji Watanabe, Takashi Taniguchi, Maksym Serbyn, and R. Thomas Weitz. “Spontaneous Gully-Polarized Quantum Hall States in ABA Trilayer Graphene.” <i>Nano Letters</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acs.nanolett.2c00435\">https://doi.org/10.1021/acs.nanolett.2c00435</a>."},"oa":1,"acknowledgement":"We acknowledge funding from the Center for Nanoscience (CeNS) and by the Deutsche\r\nForschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy-EXC-2111-390814868 (MCQST). K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan (Grant Number PMXP0112101001) and JSPS KAKENHI (Grant Numbers 19H05790 and JP20H00354).","fulldoi":"https://doi.org/10.1021/acs.nanolett.2c00435","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Chemical Society","isi":1,"date_created":"2022-05-15T22:01:41Z"},{"month":"05","file":[{"access_level":"open_access","file_id":"11405","success":1,"date_created":"2022-05-23T07:45:33Z","file_size":6387208,"relation":"main_file","content_type":"application/pdf","creator":"dernst","checksum":"7fada58059676a4bb0944b82247af740","date_updated":"2022-05-23T07:45:33Z","file_name":"2022_JourChemPhysics_Palaia.pdf"}],"ddc":["540"],"quality_controlled":"1","oa_version":"Published Version","type":"journal_article","date_published":"2022-05-16T00:00:00Z","intvolume":"       156","language":[{"iso":"eng"}],"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"volume":156,"external_id":{"isi":["000797236000004"],"pmid":["35597653"]},"status":"public","has_accepted_license":"1","department":[{"_id":"AnSa"}],"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020"},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"corr_author":"1","scopus_import":"1","pmid":1,"doi":"10.1063/5.0087769","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-05-22T17:04:48Z","isi":1,"publisher":"AIP Publishing","fulldoi":"https://doi.org/10.1063/5.0087769","acknowledgement":"The authors thank Longhui Zeng and Xiaolei Su (Yale University) for bringing the topic to their attention and for useful comments. This work has received funding from the European Research Council under the European Union’s Horizon\r\n2020 research and innovation program (ERC Grant No. 802960 and Marie Skłodowska-Curie Grant No. 101034413). The authors are grateful to the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by EPSRC (Grant Nos. EP/P020194/1 and EP/T022213/1). The authors acknowledge support from ISTA and from the Royal Society (Grant No. UF160266).","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2022-05-23T07:45:33Z","citation":{"ieee":"I. Palaia and A. Šarić, “Controlling cluster size in 2D phase-separating binary mixtures with specific interactions,” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19. AIP Publishing, 2022.","ama":"Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. 2022;156(19). doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>","mla":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19, 194902, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>.","apa":"Palaia, I., &#38; Šarić, A. (2022). Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>","ista":"Palaia I, Šarić A. 2022. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. The Journal of Chemical Physics. 156(19), 194902.","chicago":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>.","short":"I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022)."},"oa":1,"article_number":"194902","article_type":"original","issue":"19","abstract":[{"text":"By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes.","lang":"eng"}],"publication":"The Journal of Chemical Physics","author":[{"last_name":"Palaia","full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"}],"title":"Controlling cluster size in 2D phase-separating binary mixtures with specific interactions","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"year":"2022","_id":"11400","ec_funded":1,"article_processing_charge":"No","day":"16","publication_status":"published","date_updated":"2025-06-11T14:00:32Z"},{"day":"13","article_processing_charge":"No","publication_status":"published","date_updated":"2023-08-03T07:13:58Z","abstract":[{"lang":"eng","text":"Tin selenide (SnSe) is considered a robust candidate for thermoelectric applications due to its very high thermoelectric figure of merit, ZT, with values of 2.6 in p-type and 2.8 in n-type single crystals. Sn has been replaced with various lower group dopants to achieve successful p-type doping in SnSe with high ZT values. A known, facile, and powerful alternative way to introduce a hole carrier is to use a natural single Sn vacancy, VSn. Through transport and scanning tunneling microscopy studies, we discovered that VSn are dominant in high-quality (slow cooling rate) SnSe single crystals, while multiple vacancies, Vmulti, are dominant in low-quality (high cooling rate) single crystals. Surprisingly, both VSn and Vmulti help to increase the power factors of SnSe, whereas samples with dominant VSn have superior thermoelectric properties in SnSe single crystals. Additionally, the observation that Vmulti are good p-type sources observed in relatively low-quality single crystals is useful in thermoelectric applications because polycrystalline SnSe can be used due to its mechanical strength; this substance is usually fabricated at very high cooling speeds."}],"publication":"NPG Asia Materials","author":[{"first_name":"Van Quang","full_name":"Nguyen, Van Quang","last_name":"Nguyen"},{"first_name":"Thi Ly","full_name":"Trinh, Thi Ly","last_name":"Trinh"},{"last_name":"Chang","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng"},{"first_name":"Li Dong","full_name":"Zhao, Li Dong","last_name":"Zhao"},{"last_name":"Nguyen","full_name":"Nguyen, Thi Huong","first_name":"Thi Huong"},{"last_name":"Duong","full_name":"Duong, Van Thiet","first_name":"Van Thiet"},{"full_name":"Duong, Anh Tuan","last_name":"Duong","first_name":"Anh Tuan"},{"last_name":"Park","full_name":"Park, Jong Ho","first_name":"Jong Ho"},{"full_name":"Park, Sudong","last_name":"Park","first_name":"Sudong"},{"full_name":"Kim, Jungdae","last_name":"Kim","first_name":"Jungdae"},{"first_name":"Sunglae","full_name":"Cho, Sunglae","last_name":"Cho"}],"title":"Unidentified major p-type source in SnSe: Multivacancies","publication_identifier":{"issn":["1884-4049"],"eissn":["1884-4057"]},"year":"2022","_id":"11401","file_date_updated":"2022-05-23T06:47:57Z","citation":{"ista":"Nguyen VQ, Trinh TL, Chang C, Zhao LD, Nguyen TH, Duong VT, Duong AT, Park JH, Park S, Kim J, Cho S. 2022. Unidentified major p-type source in SnSe: Multivacancies. NPG Asia Materials. 14, 42.","apa":"Nguyen, V. Q., Trinh, T. L., Chang, C., Zhao, L. D., Nguyen, T. H., Duong, V. T., … Cho, S. (2022). Unidentified major p-type source in SnSe: Multivacancies. <i>NPG Asia Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41427-022-00393-5\">https://doi.org/10.1038/s41427-022-00393-5</a>","ama":"Nguyen VQ, Trinh TL, Chang C, et al. Unidentified major p-type source in SnSe: Multivacancies. <i>NPG Asia Materials</i>. 2022;14. doi:<a href=\"https://doi.org/10.1038/s41427-022-00393-5\">10.1038/s41427-022-00393-5</a>","mla":"Nguyen, Van Quang, et al. “Unidentified Major P-Type Source in SnSe: Multivacancies.” <i>NPG Asia Materials</i>, vol. 14, 42, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41427-022-00393-5\">10.1038/s41427-022-00393-5</a>.","ieee":"V. Q. Nguyen <i>et al.</i>, “Unidentified major p-type source in SnSe: Multivacancies,” <i>NPG Asia Materials</i>, vol. 14. Springer Nature, 2022.","chicago":"Nguyen, Van Quang, Thi Ly Trinh, Cheng Chang, Li Dong Zhao, Thi Huong Nguyen, Van Thiet Duong, Anh Tuan Duong, et al. “Unidentified Major P-Type Source in SnSe: Multivacancies.” <i>NPG Asia Materials</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41427-022-00393-5\">https://doi.org/10.1038/s41427-022-00393-5</a>.","short":"V.Q. Nguyen, T.L. Trinh, C. Chang, L.D. Zhao, T.H. Nguyen, V.T. Duong, A.T. Duong, J.H. Park, S. Park, J. Kim, S. Cho, NPG Asia Materials 14 (2022)."},"oa":1,"article_number":"42","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2022-05-22T22:01:40Z","isi":1,"publisher":"Springer Nature","fulldoi":"https://doi.org/10.1038/s41427-022-00393-5","acknowledgement":"This work was supported by the National Research Foundation of Korea [NRF-2019R1F1A1058473, NRF-2019R1A6A1A11053838, and NRF-2020K1A4A7A02095438].","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","doi":"10.1038/s41427-022-00393-5","has_accepted_license":"1","status":"public","department":[{"_id":"MaIb"}],"oa_version":"Published Version","type":"journal_article","date_published":"2022-05-13T00:00:00Z","intvolume":"        14","language":[{"iso":"eng"}],"external_id":{"isi":["000794880200001"]},"volume":14,"month":"05","file":[{"file_name":"2022_NPGAsiaMaterials_Nguyen.pdf","date_updated":"2022-05-23T06:47:57Z","checksum":"0579997cc1d28bf66e29357e08e3e39d","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":6202545,"date_created":"2022-05-23T06:47:57Z","file_id":"11404","success":1,"access_level":"open_access"}],"ddc":["540"],"quality_controlled":"1"},{"arxiv":1,"date_updated":"2025-07-10T11:54:34Z","publication_status":"published","day":"01","article_processing_charge":"No","ec_funded":1,"_id":"11402","year":"2022","publication_identifier":{"issn":["0022-0000"],"eissn":["1090-2724"]},"title":"Graph planning with expected finite horizon","publication":"Journal of Computer and System Sciences","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"}],"abstract":[{"text":"Fixed-horizon planning considers a weighted graph and asks to construct a path that maximizes the sum of weights for a given time horizon T. However, in many scenarios, the time horizon is not fixed, but the stopping time is chosen according to some distribution such that the expected stopping time is T. If the stopping-time distribution is not known, then to ensure robustness, the distribution is chosen by an adversary as the worst-case scenario. A stationary plan for every vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution, stationary plans are not sufficient for optimality. Quite surprisingly we show that when an adversary chooses the stopping-time distribution with expected stopping-time T, then stationary plans are sufficient. While computing optimal stationary plans for fixed horizon is NP-complete, we show that computing optimal stationary plans under adversarial stopping-time distribution can be achieved in polynomial time.","lang":"eng"}],"page":"1-21","article_type":"original","oa":1,"citation":{"short":"K. Chatterjee, L. Doyen, Journal of Computer and System Sciences 129 (2022) 1–21.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">https://doi.org/10.1016/j.jcss.2022.04.003</a>.","ieee":"K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,” <i>Journal of Computer and System Sciences</i>, vol. 129. Elsevier, pp. 1–21, 2022.","ama":"Chatterjee K, Doyen L. Graph planning with expected finite horizon. <i>Journal of Computer and System Sciences</i>. 2022;129:1-21. doi:<a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">10.1016/j.jcss.2022.04.003</a>","apa":"Chatterjee, K., &#38; Doyen, L. (2022). Graph planning with expected finite horizon. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">https://doi.org/10.1016/j.jcss.2022.04.003</a>","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” <i>Journal of Computer and System Sciences</i>, vol. 129, Elsevier, 2022, pp. 1–21, doi:<a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">10.1016/j.jcss.2022.04.003</a>.","ista":"Chatterjee K, Doyen L. 2022. Graph planning with expected finite horizon. Journal of Computer and System Sciences. 129, 1–21."},"acknowledgement":"This work was partially supported by Austrian Science Fund (FWF) NFN Grant No RiSE/SHiNE S11407 and by the grant ERC CoG 863818 (ForM-SMArt).","fulldoi":"https://doi.org/10.1016/j.jcss.2022.04.003","publisher":"Elsevier","isi":1,"date_created":"2022-05-22T22:01:40Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.jcss.2022.04.003","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"7402"}]},"scopus_import":"1","project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"department":[{"_id":"KrCh"}],"status":"public","external_id":{"arxiv":["1802.03642"],"isi":["000805002800001"]},"volume":129,"language":[{"iso":"eng"}],"intvolume":"       129","type":"journal_article","date_published":"2022-11-01T00:00:00Z","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1802.03642"}],"month":"11"},{"pmid":1,"scopus_import":"1","doi":"10.1093/genetics/iyac083","related_material":{"record":[{"status":"public","relation":"research_data","id":"9192"},{"status":"public","id":"11321","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"14651"}]},"project":[{"name":"Snapdragon Speciation","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"status":"public","has_accepted_license":"1","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":"       221","type":"journal_article","date_published":"2022-07-01T00:00:00Z","oa_version":"Submitted Version","volume":221,"external_id":{"pmid":["35639938"],"isi":["000803735800001"]},"language":[{"iso":"eng"}],"month":"07","quality_controlled":"1","ddc":["576"],"file":[{"date_created":"2022-05-26T12:48:15Z","file_id":"11412","success":1,"access_level":"open_access","relation":"main_file","file_size":885374,"checksum":"cc2d56deb608bd53c5cc02f03a875107","creator":"larathoo","content_type":"application/pdf","file_name":"Manuscript.pdf","date_updated":"2022-05-26T12:48:15Z"},{"date_updated":"2022-05-26T12:48:21Z","file_name":"SupplementalMaterial.pdf","content_type":"application/pdf","creator":"larathoo","checksum":"693742595b6c7ed809423be01460d083","file_size":1401704,"relation":"main_file","access_level":"open_access","success":1,"file_id":"11413","date_created":"2022-05-26T12:48:21Z"}],"publication_status":"published","article_processing_charge":"No","day":"01","date_updated":"2026-04-07T13:28:29Z","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","publication":"Genetics","author":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","orcid":"0000-0001-6395-386X","full_name":"Surendranadh, Parvathy","last_name":"Surendranadh"},{"orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","full_name":"Arathoon, Louise S","last_name":"Arathoon"},{"last_name":"Baskett","full_name":"Baskett, Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","orcid":"0000-0002-7354-8574"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field"},{"orcid":"0000-0001-6118-0541","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","full_name":"Pickup, Melinda"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"abstract":[{"lang":"eng","text":"Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity."}],"year":"2022","_id":"11411","publication_identifier":{"eissn":["1943-2631"]},"article_number":"iyac083","oa":1,"citation":{"ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. 2022;221(3). doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>","mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>.","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” <i>Genetics</i>, vol. 221, no. 3. Oxford University Press, 2022.","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022)."},"file_date_updated":"2022-05-26T12:48:21Z","issue":"3","article_type":"original","publisher":"Oxford University Press","isi":1,"date_created":"2022-05-26T13:44:50Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","fulldoi":"https://doi.org/10.1093/genetics/iyac083"},{"ddc":["530"],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/5.0097339"}],"month":"05","language":[{"iso":"eng"}],"external_id":{"isi":["000796002100002"]},"volume":120,"oa_version":"Published Version","date_published":"2022-05-12T00:00:00Z","type":"journal_article","intvolume":"       120","status":"public","department":[{"_id":"JoFi"}],"doi":"10.1063/5.0097339","scopus_import":"1","fulldoi":"https://doi.org/10.1063/5.0097339","acknowledgement":"We would like to thank all of the authors who contributed to\r\nthis Special Topic. We would also like to thank the editorial team at\r\nAPL including Jessica Trudeau, Emma Van Burns, Martin Weides,\r\nand Lesley Cohen.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-05-29T22:01:53Z","isi":1,"publisher":"American Institute of Physics","article_type":"letter_note","issue":"19","citation":{"chicago":"Sigillito, Anthony J., Jacob P. Covey, Johannes M Fink, Karl Petersson, and Stefan Preble. “Emerging Qubit Systems: Guest Editorial.” <i>Applied Physics Letters</i>. American Institute of Physics, 2022. <a href=\"https://doi.org/10.1063/5.0097339\">https://doi.org/10.1063/5.0097339</a>.","short":"A.J. Sigillito, J.P. Covey, J.M. Fink, K. Petersson, S. Preble, Applied Physics Letters 120 (2022).","ieee":"A. J. Sigillito, J. P. Covey, J. M. Fink, K. Petersson, and S. Preble, “Emerging qubit systems: Guest editorial,” <i>Applied Physics Letters</i>, vol. 120, no. 19. American Institute of Physics, 2022.","mla":"Sigillito, Anthony J., et al. “Emerging Qubit Systems: Guest Editorial.” <i>Applied Physics Letters</i>, vol. 120, no. 19, 190401, American Institute of Physics, 2022, doi:<a href=\"https://doi.org/10.1063/5.0097339\">10.1063/5.0097339</a>.","apa":"Sigillito, A. J., Covey, J. P., Fink, J. M., Petersson, K., &#38; Preble, S. (2022). Emerging qubit systems: Guest editorial. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/5.0097339\">https://doi.org/10.1063/5.0097339</a>","ama":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. Emerging qubit systems: Guest editorial. <i>Applied Physics Letters</i>. 2022;120(19). doi:<a href=\"https://doi.org/10.1063/5.0097339\">10.1063/5.0097339</a>","ista":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. 2022. Emerging qubit systems: Guest editorial. Applied Physics Letters. 120(19), 190401."},"oa":1,"article_number":"190401","publication_identifier":{"issn":["0003-6951"]},"year":"2022","_id":"11417","abstract":[{"lang":"eng","text":"Over the past few years, the field of quantum information science has seen tremendous progress toward realizing large-scale quantum computers. With demonstrations of quantum computers outperforming classical computers for a select range of problems,1–3 we have finally entered the noisy, intermediate-scale quantum (NISQ) computing era. While the quantum computers of today are technological marvels, they are not yet error corrected, and it is unclear whether any system will scale beyond a few hundred logical qubits without significant changes to architecture and control schemes. Today's quantum systems are analogous to the ENIAC (Electronic Numerical Integrator And Computer) and EDVAC (Electronic Discrete Variable Automatic Computer) systems of the 1940s, which ran on vacuum tubes. These machines were built on a solid, nominally scalable architecture and when they were developed, nobody could have predicted the development of the transistor and the impact of the resulting semiconductor industry. Simply put, the computers of today are nothing like the early computers of the 1940s. We believe that the qubits of future fault-tolerant quantum systems will look quite different from the qubits of the NISQ machines in operation today. This Special Topic issue is devoted to new and emerging quantum systems with a focus on enabling technologies that can eventually lead to the quantum analog to the transistor. We have solicited both research4–18 and perspective articles19–21 to discuss new and emerging qubit systems with a focus on novel materials, encodings, and architectures. We are proud to present a collection that touches on a wide range of technologies including superconductors,7–13,21 semiconductors,15–17,19 and individual atomic qubits.18\r\n"}],"author":[{"last_name":"Sigillito","full_name":"Sigillito, Anthony J.","first_name":"Anthony J."},{"first_name":"Jacob P.","last_name":"Covey","full_name":"Covey, Jacob P."},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","last_name":"Fink"},{"first_name":"Karl","full_name":"Petersson, Karl","last_name":"Petersson"},{"last_name":"Preble","full_name":"Preble, Stefan","first_name":"Stefan"}],"title":"Emerging qubit systems: Guest editorial","publication":"Applied Physics Letters","date_updated":"2026-06-18T17:14:33Z","article_processing_charge":"No","day":"12","publication_status":"published"},{"status":"public","department":[{"_id":"LaEr"}],"doi":"10.1214/21-AOP1552","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.06730"}],"quality_controlled":"1","month":"05","external_id":{"isi":["000793963400005"],"arxiv":["2103.06730"]},"volume":50,"language":[{"iso":"eng"}],"oa_version":"Preprint","intvolume":"        50","date_published":"2022-05-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0091-1798"],"eissn":["2168-894X"]},"year":"2022","_id":"11418","abstract":[{"text":"We consider the quadratic form of a general high-rank deterministic matrix on the eigenvectors of an N×N\r\nWigner matrix and prove that it has Gaussian fluctuation for each bulk eigenvector in the large N limit. The proof is a combination of the energy method for the Dyson Brownian motion inspired by Marcinek and Yau (2021) and our recent multiresolvent local laws (Comm. Math. Phys. 388 (2021) 1005–1048).","lang":"eng"}],"page":"984-1012","title":"Normal fluctuation in quantum ergodicity for Wigner matrices","author":[{"orcid":"0000-0002-4901-7992","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László"},{"first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","last_name":"Schröder","full_name":"Schröder, Dominik J"}],"publication":"Annals of Probability","arxiv":1,"date_updated":"2023-08-03T07:16:53Z","publication_status":"published","article_processing_charge":"No","day":"01","fulldoi":"https://doi.org/10.1214/21-AOP1552","acknowledgement":"L.E. would like to thank Zhigang Bao for many illuminating discussions in an early stage of this research. The authors are also grateful to Paul Bourgade for his comments on the manuscript and the anonymous referee for several useful suggestions.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Institute of Mathematical Statistics","isi":1,"date_created":"2022-05-29T22:01:53Z","issue":"3","article_type":"original","citation":{"ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Normal fluctuation in quantum ergodicity for Wigner matrices. Annals of Probability. 50(3), 984–1012.","mla":"Cipolloni, Giorgio, et al. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>, vol. 50, no. 3, Institute of Mathematical Statistics, 2022, pp. 984–1012, doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>.","ama":"Cipolloni G, Erdös L, Schröder DJ. Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. 2022;50(3):984-1012. doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2022). Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Normal fluctuation in quantum ergodicity for Wigner matrices,” <i>Annals of Probability</i>, vol. 50, no. 3. Institute of Mathematical Statistics, pp. 984–1012, 2022.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Probability 50 (2022) 984–1012."},"oa":1},{"publication":"eLife","author":[{"full_name":"Hori, Tetsuya","last_name":"Hori","first_name":"Tetsuya"},{"orcid":"0000-0002-6170-2546","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku","last_name":"Eguchi","full_name":"Eguchi, Kohgaku"},{"last_name":"Wang","full_name":"Wang, Han Ying","first_name":"Han Ying"},{"full_name":"Miyasaka, Tomohiro","last_name":"Miyasaka","first_name":"Tomohiro"},{"first_name":"Laurent","full_name":"Guillaud, Laurent","last_name":"Guillaud"},{"last_name":"Taoufiq","full_name":"Taoufiq, Zacharie","first_name":"Zacharie"},{"full_name":"Mahapatra, Satyajit","last_name":"Mahapatra","first_name":"Satyajit"},{"first_name":"Hiroshi","last_name":"Yamada","full_name":"Yamada, Hiroshi"},{"first_name":"Kohji","last_name":"Takei","full_name":"Takei, Kohji"},{"first_name":"Tomoyuki","last_name":"Takahashi","full_name":"Takahashi, Tomoyuki"}],"title":"Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer's disease synapse model","abstract":[{"lang":"eng","text":"Elevation of soluble wild-type (WT) tau occurs in synaptic compartments in Alzheimer’s disease. We addressed whether tau elevation affects synaptic transmission at the calyx of Held in slices from mice brainstem. Whole-cell loading of WT human tau (h-tau) in presynaptic terminals at 10–20 µM caused microtubule (MT) assembly and activity-dependent rundown of excitatory neurotransmission. Capacitance measurements revealed that the primary target of WT h-tau is vesicle endocytosis. Blocking MT assembly using nocodazole prevented tau-induced impairments of endocytosis and neurotransmission. Immunofluorescence imaging analyses revealed that MT assembly by WT h-tau loading was associated with an increased MT-bound fraction of the endocytic protein dynamin. A synthetic dodecapeptide corresponding to dynamin 1-pleckstrin-homology domain inhibited MT-dynamin interaction and rescued tau-induced impairments of endocytosis and neurotransmission. We conclude that elevation of presynaptic WT tau induces de novo assembly of MTs, thereby sequestering free dynamins. As a result, endocytosis and subsequent vesicle replenishment are impaired, causing activity-dependent rundown of neurotransmission."}],"_id":"11419","year":"2022","publication_identifier":{"eissn":["2050-084X"]},"day":"05","article_processing_charge":"No","publication_status":"published","date_updated":"2023-08-03T07:15:49Z","date_created":"2022-05-29T22:01:54Z","isi":1,"publisher":"eLife Sciences Publications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank Yasuo Ihara, Nobuyuki Nukina, and Takeshi Sakaba for comments and Patrick Stoney for editing this paper. We also thank Shota Okuda and Mikako Matsubara for their contributions in the early stage of this study, and Satoko Wada-Kakuda for technical assistant with in vitro analysis of tau. This research was supported by funding from Okinawa Institute of Science and Technology and from Technology (OIST) and Core Research for the Evolutional Science and Technology of Japan Science and Technology Agency (CREST) to TT, and by Scientific Research on Innovative Areas to TM (Brain Protein Aging and Dementia Control 26117004).","fulldoi":"https://doi.org/10.7554/eLife.73542","oa":1,"article_number":"e73542","file_date_updated":"2022-05-30T08:09:16Z","citation":{"ieee":"T. Hori <i>et al.</i>, “Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ista":"Hori T, Eguchi K, Wang HY, Miyasaka T, Guillaud L, Taoufiq Z, Mahapatra S, Yamada H, Takei K, Takahashi T. 2022. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. eLife. 11, e73542.","apa":"Hori, T., Eguchi, K., Wang, H. Y., Miyasaka, T., Guillaud, L., Taoufiq, Z., … Takahashi, T. (2022). Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>","mla":"Hori, Tetsuya, et al. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>, vol. 11, e73542, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>.","ama":"Hori T, Eguchi K, Wang HY, et al. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>","chicago":"Hori, Tetsuya, Kohgaku Eguchi, Han Ying Wang, Tomohiro Miyasaka, Laurent Guillaud, Zacharie Taoufiq, Satyajit Mahapatra, Hiroshi Yamada, Kohji Takei, and Tomoyuki Takahashi. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>.","short":"T. Hori, K. Eguchi, H.Y. Wang, T. Miyasaka, L. Guillaud, Z. Taoufiq, S. Mahapatra, H. Yamada, K. Takei, T. Takahashi, ELife 11 (2022)."},"article_type":"original","department":[{"_id":"RySh"}],"status":"public","has_accepted_license":"1","pmid":1,"scopus_import":"1","doi":"10.7554/eLife.73542","month":"05","quality_controlled":"1","file":[{"date_updated":"2022-05-30T08:09:16Z","file_name":"elife-73542-v2.pdf","content_type":"application/pdf","creator":"cchlebak","checksum":"ccddbd167e00ff8375f12998af497152","file_size":2466296,"relation":"main_file","access_level":"open_access","success":1,"file_id":"11421","date_created":"2022-05-30T08:09:16Z"}],"ddc":["616"],"date_published":"2022-05-05T00:00:00Z","type":"journal_article","intvolume":"        11","oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"isi":["000876231600001"],"pmid":["35471147 "]},"volume":11},{"language":[{"iso":"eng"}],"volume":224,"date_published":"2022-06-01T00:00:00Z","type":"conference","intvolume":"       224","oa_version":"Published Version","quality_controlled":"1","file":[{"file_name":"2022_LIPICs_Chambers.pdf","date_updated":"2022-06-07T07:58:30Z","checksum":"b25ce40fade4ebc0bcaae176db4f5f1f","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":17580705,"date_created":"2022-06-07T07:58:30Z","success":1,"file_id":"11437","access_level":"open_access"}],"ddc":["510"],"month":"06","doi":"10.4230/LIPIcs.SoCG.2022.66","editor":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"last_name":"Kerber","full_name":"Kerber, Michael","first_name":"Michael"}],"scopus_import":"1","series_title":"LIPIcs","corr_author":"1","department":[{"_id":"HeEd"}],"project":[{"name":"Learning and triangulating manifolds via collapses","grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"},{"name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"status":"public","has_accepted_license":"1","oa":1,"file_date_updated":"2022-06-07T07:58:30Z","citation":{"short":"E. Chambers, C.D. Fillmore, E.R. Stephenson, M. Wintraecken, in:, X. Goaoc, M. Kerber (Eds.), 38th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, p. 66:1-66:9.","chicago":"Chambers, Erin, Christopher D Fillmore, Elizabeth R Stephenson, and Mathijs Wintraecken. “A Cautionary Tale: Burning the Medial Axis Is Unstable.” In <i>38th International Symposium on Computational Geometry</i>, edited by Xavier Goaoc and Michael Kerber, 224:66:1-66:9. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">https://doi.org/10.4230/LIPIcs.SoCG.2022.66</a>.","ista":"Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. 2022. A cautionary tale: Burning the medial axis is unstable. 38th International Symposium on Computational Geometry. SoCG: Symposium on Computational GeometryLIPIcs vol. 224, 66:1-66:9.","ama":"Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. A cautionary tale: Burning the medial axis is unstable. In: Goaoc X, Kerber M, eds. <i>38th International Symposium on Computational Geometry</i>. Vol 224. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022:66:1-66:9. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">10.4230/LIPIcs.SoCG.2022.66</a>","mla":"Chambers, Erin, et al. “A Cautionary Tale: Burning the Medial Axis Is Unstable.” <i>38th International Symposium on Computational Geometry</i>, edited by Xavier Goaoc and Michael Kerber, vol. 224, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, p. 66:1-66:9, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">10.4230/LIPIcs.SoCG.2022.66</a>.","apa":"Chambers, E., Fillmore, C. D., Stephenson, E. R., &#38; Wintraecken, M. (2022). A cautionary tale: Burning the medial axis is unstable. In X. Goaoc &#38; M. Kerber (Eds.), <i>38th International Symposium on Computational Geometry</i> (Vol. 224, p. 66:1-66:9). Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">https://doi.org/10.4230/LIPIcs.SoCG.2022.66</a>","ieee":"E. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “A cautionary tale: Burning the medial axis is unstable,” in <i>38th International Symposium on Computational Geometry</i>, Berlin, Germany, 2022, vol. 224, p. 66:1-66:9."},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"fulldoi":"https://doi.org/10.4230/LIPIcs.SoCG.2022.66","acknowledgement":"Partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics” and the European Research Council (ERC), grant no. 788183, “Alpha Shape Theory Extended”. Erin Chambers: Supported in part by the National Science Foundation through grants DBI-1759807, CCF-1907612, and CCF-2106672. Mathijs Wintraecken: Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073 Acknowledgements We thank André Lieutier, David Letscher, Ellen Gasparovic, Kathryn Leonard, and Tao Ju for early discussions on this work. We also thank Lu Liu, Yajie Yan and Tao Ju for sharing code to generate the examples.","date_created":"2022-06-01T14:18:04Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-14T07:43:57Z","day":"01","article_processing_charge":"No","publication_status":"published","ec_funded":1,"_id":"11428","year":"2022","conference":{"location":"Berlin, Germany","name":"SoCG: Symposium on Computational Geometry","start_date":"2022-06-07","end_date":"2022-06-10"},"publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-227-3"]},"publication":"38th International Symposium on Computational Geometry","title":"A cautionary tale: Burning the medial axis is unstable","author":[{"last_name":"Chambers","full_name":"Chambers, Erin","first_name":"Erin"},{"id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","first_name":"Christopher D","full_name":"Fillmore, Christopher D","last_name":"Fillmore"},{"orcid":"0000-0002-6862-208X","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","first_name":"Elizabeth R","last_name":"Stephenson","full_name":"Stephenson, Elizabeth R"},{"orcid":"0000-0002-7472-2220","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken"}],"page":"66:1-66:9","abstract":[{"lang":"eng","text":"The medial axis of a set consists of the points in the ambient space without a unique closest point on the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a topologically equivalent skeleton. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities various prunings of the medial axis have been proposed. Here, we examine one type of pruning, called burning. Because of the good experimental results, it was hoped that the burning method of simplifying the medial axis would be stable. In this work we show a simple example that dashes such hopes based on Bing’s house with two rooms, demonstrating an isotopy of a shape where the medial axis goes from collapsible to non-collapsible."}]},{"place":"Cham","doi":"10.1007/978-3-031-06245-2","editor":[{"last_name":"Karimipour","full_name":"Karimipour, Farid","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","first_name":"Farid","orcid":"0000-0001-6746-4174"},{"first_name":"Sabine","full_name":"Storandt, Sabine","last_name":"Storandt"}],"status":"public","department":[{"_id":"HeEd"}],"corr_author":"1","oa_version":"None","intvolume":"     13238","type":"book_editor","date_published":"2022-05-01T00:00:00Z","volume":13238,"language":[{"iso":"eng"}],"month":"05","quality_controlled":"1","publication_status":"published","day":"01","article_processing_charge":"No","date_updated":"2024-10-09T21:02:30Z","abstract":[{"text":"This book constitutes the refereed proceedings of the 18th International Symposium on Web and Wireless Geographical Information Systems, W2GIS 2022, held in Konstanz, Germany, in April 2022.\r\nThe 7 full papers presented together with 6 short papers in the volume were carefully reviewed and selected from 16 submissions.  The papers cover topics that range from mobile GIS and Location-Based Services to Spatial Information Retrieval and Wireless Sensor Networks.","lang":"eng"}],"page":"153","title":"Web and Wireless Geographical Information Systems","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031062445"],"eisbn":["9783031062452"],"issn":["0302-9743"]},"year":"2022","_id":"11429","alternative_title":["LNCS"],"citation":{"short":"F. Karimipour, S. Storandt, eds., Web and Wireless Geographical Information Systems, 1st ed., Springer Nature, Cham, 2022.","chicago":"Karimipour, Farid, and Sabine Storandt, eds. <i>Web and Wireless Geographical Information Systems</i>. 1st ed. Vol. 13238. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>.","ieee":"F. Karimipour and S. Storandt, Eds., <i>Web and Wireless Geographical Information Systems</i>, 1st ed., vol. 13238. Cham: Springer Nature, 2022.","mla":"Karimipour, Farid, and Sabine Storandt, editors. <i>Web and Wireless Geographical Information Systems</i>. 1st ed., vol. 13238, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/978-3-031-06245-2\">10.1007/978-3-031-06245-2</a>.","ama":"Karimipour F, Storandt S, eds. <i>Web and Wireless Geographical Information Systems</i>. Vol 13238. 1st ed. Cham: Springer Nature; 2022. doi:<a href=\"https://doi.org/10.1007/978-3-031-06245-2\">10.1007/978-3-031-06245-2</a>","apa":"Karimipour, F., &#38; Storandt, S. (Eds.). (2022). <i>Web and Wireless Geographical Information Systems</i> (1st ed., Vol. 13238). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>","ista":"Karimipour F, Storandt S eds. 2022. Web and Wireless Geographical Information Systems 1st ed., Cham: Springer Nature, 153p."},"edition":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","date_created":"2022-06-02T05:40:53Z","fulldoi":"https://doi.org/10.1007/978-3-031-06245-2"},{"month":"05","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-03641349/"}],"quality_controlled":"1","oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":"        41","type":"journal_article","date_published":"2022-05-01T00:00:00Z","external_id":{"isi":["000802723900027"]},"volume":41,"language":[{"iso":"eng"}],"status":"public","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020"}],"department":[{"_id":"ChWo"}],"corr_author":"1","scopus_import":"1","doi":"10.1111/cgf.14478","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","isi":1,"date_created":"2022-06-05T22:01:49Z","fulldoi":"https://doi.org/10.1111/cgf.14478","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria and MFX Team at INRIA for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","citation":{"short":"C. Schreck, C. Wojtan, Computer Graphics Forum 41 (2022) 343–353.","chicago":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>.","ieee":"C. Schreck and C. Wojtan, “Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method,” <i>Computer Graphics Forum</i>, vol. 41, no. 2. Wiley, pp. 343–353, 2022.","ista":"Schreck C, Wojtan C. 2022. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. Computer Graphics Forum. 41(2), 343–353.","ama":"Schreck C, Wojtan C. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. 2022;41(2):343-353. doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>","apa":"Schreck, C., &#38; Wojtan, C. (2022). Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>","mla":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>, vol. 41, no. 2, Wiley, 2022, pp. 343–53, doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>."},"oa":1,"issue":"2","article_type":"original","abstract":[{"lang":"eng","text":"This paper proposes a method for simulating liquids in large bodies of water by coupling together a water surface wave simulator with a 3D Navier-Stokes simulator. The surface wave simulation uses the equivalent sources method (ESM) to efficiently animate large bodies of water with precisely controllable wave propagation behavior. The 3D liquid simulator animates complex non-linear fluid behaviors like splashes and breaking waves using off-the-shelf simulators using FLIP or the level set method with semi-Lagrangian advection.\r\nWe combine the two approaches by using the 3D solver to animate localized non-linear behaviors, and the 2D wave solver to animate larger regions with linear surface physics. We use the surface motion from the 3D solver as boundary conditions for 2D surface wave simulator, and we use the velocity and surface heights from the 2D surface wave simulator as boundary conditions for the 3D fluid simulation. We also introduce a novel technique for removing visual artifacts caused by numerical errors in 3D fluid solvers: we use experimental data to estimate the artificial dispersion caused by the 3D solver and we then carefully tune the wave speeds of the 2D solver to match it, effectively eliminating any differences in wave behavior across the boundary. To the best of our knowledge, this is the first time such a empirically driven error compensation approach has been used to remove coupling errors from a physics simulator.\r\nOur coupled simulation approach leverages the strengths of each simulation technique, animating large environments with seamless transitions between 2D and 3D physics."}],"page":"343-353","publication":"Computer Graphics Forum","title":"Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method","author":[{"id":"2B14B676-F248-11E8-B48F-1D18A9856A87","first_name":"Camille","last_name":"Schreck","full_name":"Schreck, Camille"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"_id":"11432","year":"2022","ec_funded":1,"publication_status":"published","day":"01","article_processing_charge":"No","date_updated":"2024-10-22T09:58:19Z"},{"publisher":"Society for Industrial and Applied Mathematics","isi":1,"date_created":"2022-06-05T22:01:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"G.I. acknowledges the financial support from the Ministry of Educational and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926. M.N. was supported by the National Research, Development and Innovation Fund (NRDI) grants K119670 and\r\nKKP-133864 as well as the Bolyai Scholarship of the Hungarian Academy of Sciences and the New National Excellence Programme and the TKP2020-NKA-06 program provided by the NRDI.","fulldoi":"https://doi.org/10.1137/21M1403308","oa":1,"citation":{"ista":"Ivanov G, Naszodi M. 2022. A quantitative Helly-type theorem: Containment in a homothet. SIAM Journal on Discrete Mathematics. 36(2), 951–957.","ama":"Ivanov G, Naszodi M. A quantitative Helly-type theorem: Containment in a homothet. <i>SIAM Journal on Discrete Mathematics</i>. 2022;36(2):951-957. doi:<a href=\"https://doi.org/10.1137/21M1403308\">10.1137/21M1403308</a>","apa":"Ivanov, G., &#38; Naszodi, M. (2022). A quantitative Helly-type theorem: Containment in a homothet. <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1403308\">https://doi.org/10.1137/21M1403308</a>","mla":"Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment in a Homothet.” <i>SIAM Journal on Discrete Mathematics</i>, vol. 36, no. 2, Society for Industrial and Applied Mathematics, 2022, pp. 951–57, doi:<a href=\"https://doi.org/10.1137/21M1403308\">10.1137/21M1403308</a>.","ieee":"G. Ivanov and M. Naszodi, “A quantitative Helly-type theorem: Containment in a homothet,” <i>SIAM Journal on Discrete Mathematics</i>, vol. 36, no. 2. Society for Industrial and Applied Mathematics, pp. 951–957, 2022.","chicago":"Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment in a Homothet.” <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21M1403308\">https://doi.org/10.1137/21M1403308</a>.","short":"G. Ivanov, M. Naszodi, SIAM Journal on Discrete Mathematics 36 (2022) 951–957."},"issue":"2","article_type":"original","author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory","full_name":"Ivanov, Grigory","last_name":"Ivanov"},{"full_name":"Naszodi, Marton","last_name":"Naszodi","first_name":"Marton"}],"title":"A quantitative Helly-type theorem: Containment in a homothet","publication":"SIAM Journal on Discrete Mathematics","abstract":[{"text":"We introduce a new variant of quantitative Helly-type theorems: the minimal homothetic distance of the intersection of a family of convex sets to the intersection of a subfamily of a fixed size. As an application, we establish the following quantitative Helly-type result for the diameter. If $K$ is the intersection of finitely many convex bodies in $\\mathbb{R}^d$, then one can select $2d$ of these bodies whose intersection is of diameter at most $(2d)^3{diam}(K)$. The best previously known estimate, due to Brazitikos [Bull. Hellenic Math. Soc., 62 (2018), pp. 19--25], is $c d^{11/2}$. Moreover, we confirm that the multiplicative factor $c d^{1/2}$ conjectured by Bárány, Katchalski, and Pach [Proc. Amer. Math. Soc., 86 (1982), pp. 109--114] cannot be improved. The bounds above follow from our key result that concerns sparse approximation of a convex polytope by the convex hull of a well-chosen subset of its vertices: Assume that $Q \\subset {\\mathbb R}^d$ is a polytope whose centroid is the origin. Then there exist at most 2d vertices of $Q$ whose convex hull $Q^{\\prime \\prime}$ satisfies $Q \\subset - 8d^3 Q^{\\prime \\prime}.$","lang":"eng"}],"page":"951-957","year":"2022","_id":"11435","publication_identifier":{"issn":["0895-4801"]},"publication_status":"published","day":"11","article_processing_charge":"No","date_updated":"2023-10-18T06:58:03Z","arxiv":1,"month":"04","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2103.04122","open_access":"1"}],"quality_controlled":"1","intvolume":"        36","date_published":"2022-04-11T00:00:00Z","type":"journal_article","oa_version":"Preprint","volume":36,"external_id":{"arxiv":["2103.04122"],"isi":["000793158200002"]},"language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"status":"public","scopus_import":"1","doi":"10.1137/21M1403308"},{"month":"06","file":[{"content_type":"application/pdf","creator":"dernst","checksum":"27f6fe41c6ff84d50445cc9b0176d45b","date_updated":"2022-06-28T08:32:58Z","file_name":"2022_ACM_acceptedversion_Piovarci.pdf","access_level":"open_access","file_id":"11467","success":1,"date_created":"2022-06-28T08:32:58Z","file_size":33994829,"relation":"main_file"}],"ddc":["000"],"OA_type":"hybrid","quality_controlled":"1","oa_version":"Submitted Version","type":"journal_article","date_published":"2022-06-01T00:00:00Z","intvolume":"        41","language":[{"iso":"eng"}],"external_id":{"arxiv":["2201.11819"],"isi":["000830989200091"]},"volume":41,"status":"public","has_accepted_license":"1","department":[{"_id":"BeBi"}],"project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","grant_number":"M03319","name":"Perception-Aware Appearance Fabrication"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020"}],"OA_place":"publisher","corr_author":"1","scopus_import":"1","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/machine-learning-3d-printing-fluids/","relation":"press_release"}]},"doi":"10.1145/3528223.3530144","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2022-06-10T06:41:47Z","publisher":"Association for Computing Machinery","isi":1,"acknowledgement":"This work is graciously supported by the following grant agencies: FWF Lise Meitner (Grant M 3319), SNSF (Grant 200502), ERC Starting Grant (MATERIALIZABLE-715767), NSF (Grant IIS-181507).\r\n","fulldoi":"https://doi.org/10.1145/3528223.3530144","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2022-06-28T08:32:58Z","citation":{"short":"M. Piovarci, M. Foshey, J. Xu, T. Erps, V. Babaei, P. Didyk, S. Rusinkiewicz, W. Matusik, B. Bickel, ACM Transactions on Graphics 41 (2022).","chicago":"Piovarci, Michael, Michael Foshey, Jie Xu, Timothy Erps, Vahid Babaei, Piotr Didyk, Szymon Rusinkiewicz, Wojciech Matusik, and Bernd Bickel. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>.","mla":"Piovarci, Michael, et al. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 112, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>.","ama":"Piovarci M, Foshey M, Xu J, et al. Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>","apa":"Piovarci, M., Foshey, M., Xu, J., Erps, T., Babaei, V., Didyk, P., … Bickel, B. (2022). Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>","ista":"Piovarci M, Foshey M, Xu J, Erps T, Babaei V, Didyk P, Rusinkiewicz S, Matusik W, Bickel B. 2022. Closed-loop control of direct ink writing via reinforcement learning. ACM Transactions on Graphics. 41(4), 112.","ieee":"M. Piovarci <i>et al.</i>, “Closed-loop control of direct ink writing via reinforcement learning,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022."},"oa":1,"article_number":"112","article_type":"original","issue":"4","abstract":[{"text":"Enabling additive manufacturing to employ a wide range of novel, functional materials can be a major boost to this technology. However, making such materials printable requires painstaking trial-and-error by an expert operator,\r\nas they typically tend to exhibit peculiar rheological or hysteresis properties. Even in the case of successfully finding the process parameters, there is no guarantee of print-to-print consistency due to material differences between batches. These challenges make closed-loop feedback an attractive option where the process parameters are adjusted on-the-fly. There are several challenges for designing an efficient controller: the deposition parameters are complex and highly coupled, artifacts occur after long time horizons, simulating the deposition is computationally costly, and learning on hardware is intractable. In this work, we demonstrate the feasibility of learning a closed-loop control policy for additive manufacturing using reinforcement learning. We show that approximate, but efficient, numerical simulation is\r\nsufficient as long as it allows learning the behavioral patterns of deposition that translate to real-world experiences. In combination with reinforcement learning, our model can be used to discover control policies that outperform\r\nbaseline controllers. Furthermore, the recovered policies have a minimal sim-to-real gap. We showcase this by applying our control policy in-vivo on a single-layer, direct ink writing printer. ","lang":"eng"}],"author":[{"full_name":"Piovarci, Michael","last_name":"Piovarci","first_name":"Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","orcid":"0000-0002-5062-4474"},{"first_name":"Michael","last_name":"Foshey","full_name":"Foshey, Michael"},{"first_name":"Jie","last_name":"Xu","full_name":"Xu, Jie"},{"full_name":"Erps, Timothy","last_name":"Erps","first_name":"Timothy"},{"first_name":"Vahid","last_name":"Babaei","full_name":"Babaei, Vahid"},{"first_name":"Piotr","full_name":"Didyk, Piotr","last_name":"Didyk"},{"first_name":"Szymon","full_name":"Rusinkiewicz, Szymon","last_name":"Rusinkiewicz"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"}],"title":"Closed-loop control of direct ink writing via reinforcement learning","publication":"ACM Transactions on Graphics","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"_id":"11442","year":"2022","ec_funded":1,"PlanS_conform":"1","day":"01","article_processing_charge":"No","publication_status":"published","date_updated":"2025-09-10T09:36:45Z","arxiv":1},{"publication":"Transactions of the American Mathematical Society","title":"Extension complexity of low-dimensional polytopes","author":[{"last_name":"Kwan","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sauermann","full_name":"Sauermann, Lisa","first_name":"Lisa"},{"full_name":"Zhao, Yufei","last_name":"Zhao","first_name":"Yufei"}],"abstract":[{"text":"Sometimes, it is possible to represent a complicated polytope as a projection of a much simpler polytope. To quantify this phenomenon, the extension complexity of a polytope P is defined to be the minimum number of facets of a (possibly higher-dimensional) polytope from which P can be obtained as a (linear) projection. This notion is motivated by its relevance to combinatorial optimisation, and has been studied intensively for various specific polytopes associated with important optimisation problems. In this paper we study extension complexity as a parameter of general polytopes, more specifically considering various families of low-dimensional polytopes. First, we prove that for a fixed dimension d, the extension complexity of a random d-dimensional polytope (obtained as the convex hull of random points in a ball or on a sphere) is typically on the order of the square root of its number of vertices. Second, we prove that any cyclic n-vertex polygon (whose vertices lie on a circle) has extension complexity at most 24√n. This bound is tight up to the constant factor 24. Finally, we show that there exists an no(1)-dimensional polytope with at most n vertices and extension complexity n1−o(1). Our theorems are proved with a range of different techniques, which we hope will be of further interest.","lang":"eng"}],"page":"4209-4250","_id":"11443","year":"2022","publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"publication_status":"published","article_processing_charge":"No","day":"01","arxiv":1,"date_updated":"2024-10-09T21:02:31Z","isi":1,"publisher":"American Mathematical Society","date_created":"2022-06-12T22:01:45Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"The research of the first author was supported by SNSF Project 178493 and NSF Award DMS-1953990. The research of the second author supported by NSF Award DMS-1953772.\r\nThe research of the third author was supported by NSF Award DMS-1764176, NSF CAREER Award DMS-2044606, a Sloan Research Fellowship, and the MIT Solomon Buchsbaum Fund. ","fulldoi":"https://doi.org/10.1090/tran/8614","oa":1,"citation":{"ista":"Kwan MA, Sauermann L, Zhao Y. 2022. Extension complexity of low-dimensional polytopes. Transactions of the American Mathematical Society. 375(6), 4209–4250.","ama":"Kwan MA, Sauermann L, Zhao Y. Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. 2022;375(6):4209-4250. doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>","apa":"Kwan, M. A., Sauermann, L., &#38; Zhao, Y. (2022). Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>","mla":"Kwan, Matthew Alan, et al. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6, American Mathematical Society, 2022, pp. 4209–50, doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>.","ieee":"M. A. Kwan, L. Sauermann, and Y. Zhao, “Extension complexity of low-dimensional polytopes,” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6. American Mathematical Society, pp. 4209–4250, 2022.","chicago":"Kwan, Matthew Alan, Lisa Sauermann, and Yufei Zhao. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2022. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>.","short":"M.A. Kwan, L. Sauermann, Y. Zhao, Transactions of the American Mathematical Society 375 (2022) 4209–4250."},"issue":"6","article_type":"original","department":[{"_id":"MaKw"}],"status":"public","corr_author":"1","scopus_import":"1","doi":"10.1090/tran/8614","month":"06","quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2006.08836","open_access":"1"}],"intvolume":"       375","date_published":"2022-06-01T00:00:00Z","type":"journal_article","oa_version":"Preprint","volume":375,"external_id":{"isi":["000798461500001"],"arxiv":["2006.08836"]},"language":[{"iso":"eng"}]},{"corr_author":"1","project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","call_identifier":"H2020"},{"grant_number":"I05127","_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","name":"Evolutionary analysis of gene regulation"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"status":"public","has_accepted_license":"1","doi":"10.1007/s11538-022-01029-z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11538-022-01118-z"}],"record":[{"status":"public","id":"21918","relation":"dissertation_contains"}]},"pmid":1,"scopus_import":"1","quality_controlled":"1","ddc":["510","570"],"file":[{"date_created":"2022-06-20T07:51:32Z","access_level":"open_access","file_id":"11455","success":1,"relation":"main_file","file_size":463025,"creator":"dernst","checksum":"05a1fe7d10914a00c2bca9b447993a65","content_type":"application/pdf","file_name":"2022_BulletinMathBiology_Saona.pdf","date_updated":"2022-06-20T07:51:32Z"}],"month":"06","external_id":{"pmid":["35713756"],"isi":["000812509800001"]},"volume":84,"keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"language":[{"iso":"eng"}],"intvolume":"        84","type":"journal_article","date_published":"2022-06-17T00:00:00Z","oa_version":"Published Version","_id":"11447","year":"2022","publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","author":[{"orcid":"0000-0001-5103-038X","first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia","full_name":"Khudiakova, Kseniia","last_name":"Khudiakova"}],"publication":"Bulletin of Mathematical Biology","abstract":[{"text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.","lang":"eng"}],"date_updated":"2026-06-12T12:43:34Z","publication_status":"published","article_processing_charge":"Yes (via OA deal)","day":"17","ec_funded":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","fulldoi":"https://doi.org/10.1007/s11538-022-01029-z","publisher":"Springer Nature","isi":1,"date_created":"2022-06-17T16:16:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"8","article_type":"original","article_number":"74","oa":1,"citation":{"ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8. Springer Nature, 2022.","apa":"Saona Urmeneta, R. J., Kondrashov, F., &#38; Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. 2022;84(8). doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>.","ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022)."},"file_date_updated":"2022-06-20T07:51:32Z"},{"oa_version":"Published Version","type":"journal_article","date_published":"2022-06-15T00:00:00Z","intvolume":"        13","language":[{"iso":"eng"}],"external_id":{"isi":["000814124400002"],"pmid":["35452605"]},"volume":13,"month":"06","ddc":["570"],"main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2022.03.006","open_access":"1"}],"quality_controlled":"1","scopus_import":"1","pmid":1,"doi":"10.1016/j.cels.2022.03.006","status":"public","department":[{"_id":"SiHi"}],"project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"},{"name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425","grant_number":"LS13-002"}],"citation":{"chicago":"Anderson, Donovan J., Florian Pauler, Aaron Mckenna, Jay Shendure, Simon Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Brain Cell Type and Lineage Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” <i>Cell Systems</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">https://doi.org/10.1016/j.cels.2022.03.006</a>.","short":"D.J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, Cell Systems 13 (2022) 438–453.e5.","apa":"Anderson, D. J., Pauler, F., Mckenna, A., Shendure, J., Hippenmeyer, S., &#38; Horwitz, M. S. (2022). Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. <i>Cell Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">https://doi.org/10.1016/j.cels.2022.03.006</a>","mla":"Anderson, Donovan J., et al. “Simultaneous Brain Cell Type and Lineage Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” <i>Cell Systems</i>, vol. 13, no. 6, Elsevier, 2022, p. 438–453.e5, doi:<a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">10.1016/j.cels.2022.03.006</a>.","ama":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. <i>Cell Systems</i>. 2022;13(6):438-453.e5. doi:<a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">10.1016/j.cels.2022.03.006</a>","ista":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. 2022. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. Cell Systems. 13(6), 438–453.e5.","ieee":"D. J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, and M. S. Horwitz, “Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development,” <i>Cell Systems</i>, vol. 13, no. 6. Elsevier, p. 438–453.e5, 2022."},"oa":1,"article_type":"original","issue":"6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-06-19T22:01:57Z","publisher":"Elsevier","isi":1,"acknowledgement":"D.J.A. thanks Wayne K. Potts, Alan R. Rogers, Kristen Hawkes, Ryk Ward, and Jon Seger for inspiring a young undergraduate to apply evolutionary theory to intraorganism development. Supported by the Paul G. Allen Frontiers Group (University of Washington); NIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program 725780 LinPro to S.H.","fulldoi":"https://doi.org/10.1016/j.cels.2022.03.006","ec_funded":1,"article_processing_charge":"No","day":"15","publication_status":"published","date_updated":"2026-06-18T17:15:22Z","page":"438-453.e5","abstract":[{"text":"Mutations are acquired frequently, such that each cell's genome inscribes its history of cell divisions. Common genomic alterations involve loss of heterozygosity (LOH). LOH accumulates throughout the genome, offering large encoding capacity for inferring cell lineage. Using only single-cell RNA sequencing (scRNA-seq) of mouse brain cells, we found that LOH events spanning multiple genes are revealed as tracts of monoallelically expressed, constitutionally heterozygous single-nucleotide variants (SNVs). We simultaneously inferred cell lineage and marked developmental time points based on X chromosome inactivation and the total number of LOH events while identifying cell types from gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. This type of retrospective analysis could be incorporated into scRNA-seq pipelines and, compared with experimental approaches for determining lineage in model organisms, is applicable where genetic engineering is prohibited, such as humans.","lang":"eng"}],"publication":"Cell Systems","title":"Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development","author":[{"first_name":"Donovan J.","last_name":"Anderson","full_name":"Anderson, Donovan J."},{"orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian"},{"full_name":"Mckenna, Aaron","last_name":"Mckenna","first_name":"Aaron"},{"first_name":"Jay","full_name":"Shendure, Jay","last_name":"Shendure"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"},{"first_name":"Marshall S.","full_name":"Horwitz, Marshall S.","last_name":"Horwitz"}],"publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"_id":"11449","year":"2022"},{"oa_version":"None","intvolume":"       181","date_published":"2022-06-04T00:00:00Z","type":"book_chapter","volume":181,"language":[{"iso":"eng"}],"month":"06","quality_controlled":"1","series_title":"NM","scopus_import":"1","place":"New York","doi":"10.1007/978-1-0716-2321-3_15","editor":[{"last_name":"Yamamoto","full_name":"Yamamoto, Daisuke","first_name":"Daisuke"}],"status":"public","project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"department":[{"_id":"MaDe"}],"corr_author":"1","citation":{"ama":"Artan M, de Bono M. Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Yamamoto D, ed. <i>Behavioral Neurogenetics</i>. Vol 181. NM. New York: Springer Nature; 2022:277-294. doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>","apa":"Artan, M., &#38; de Bono, M. (2022). Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In D. Yamamoto (Ed.), <i>Behavioral Neurogenetics</i> (Vol. 181, pp. 277–294). New York: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>","mla":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, vol. 181, Springer Nature, 2022, pp. 277–94, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>.","ista":"Artan M, de Bono M. 2022.Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Behavioral Neurogenetics. Neuromethods, vol. 181, 277–294.","ieee":"M. Artan and M. de Bono, “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling,” in <i>Behavioral Neurogenetics</i>, vol. 181, D. Yamamoto, Ed. New York: Springer Nature, 2022, pp. 277–294.","chicago":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” In <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, 181:277–94. NM. New York: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>.","short":"M. Artan, M. de Bono, in:, D. Yamamoto (Ed.), Behavioral Neurogenetics, Springer Nature, New York, 2022, pp. 277–294."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","date_created":"2022-06-20T08:10:34Z","acknowledgement":"We thank de Bono lab members for the helpful comments on the manuscript. The biotin-auxotrophic E. coli strain MG1655bioB:kan was a generous gift from J. Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3’UTR entry vector were kindly sent by Dr. Dominique Glauser (University of Fribourg). This work was supported by an Advanced ERC Grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB and an ISTplus Fellowship to MA (Marie Sklodowska-Curie agreement No 754411).","fulldoi":"https://doi.org/10.1007/978-1-0716-2321-3_15","ec_funded":1,"publication_status":"published","article_processing_charge":"No","day":"04","date_updated":"2025-04-14T07:43:58Z","abstract":[{"text":"The proteomes of specialized structures, and the interactomes of proteins of interest, provide entry points to elucidate the functions of molecular machines. Here, we review a proximity-labeling strategy that uses the improved E. coli biotin ligase TurboID to characterize C. elegans protein complexes. Although the focus is on C. elegans neurons, the method is applicable regardless of cell type. We describe detailed extraction procedures that solubilize the bulk of C. elegans proteins and highlight the importance of tagging endogenous genes, to ensure physiological expression levels. We review issues associated with non-specific background noise and the importance of appropriate controls. As proof of principle, we review our analysis of the interactome of a presynaptic active zone protein, ELKS-1. Our aim is to provide a detailed protocol for TurboID-based proximity labeling in C. elegans and to highlight its potential and its limitations to characterize protein complexes and subcellular compartments in this animal.","lang":"eng"}],"page":"277-294","publication":"Behavioral Neurogenetics","title":"Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling","author":[{"id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat","orcid":"0000-0001-8945-6992","last_name":"Artan","full_name":"Artan, Murat"},{"last_name":"de Bono","full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","orcid":"0000-0001-8347-0443"}],"publication_identifier":{"issn":["0893-2336"],"eisbn":["9781071623213"],"isbn":["9781071623206"],"eissn":["1940-6045"]},"_id":"11456","year":"2022","alternative_title":["Neuromethods"]}]