--- _id: '14703' abstract: - lang: eng text: We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation. acknowledgement: "The authors would like to thank Chris Wojtan for his continuous support and several interesting discussions. Part of this research was performed during two visits: one of SI to the BIDSA research center at Bocconi University, and one of HL to the Institute of Science and Technology Austria. Both host institutions are warmly acknowledged for the hospital-\r\nity. HL is partially supported by the MUR-Prin 2022-202244A7YL “Gradient Flows and Non-Smooth Geometric Structures with Applications to Optimization and Machine Learning”, funded by the European Union - Next Generation EU. SI is supported in part by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council." article_number: '2312.12213' article_processing_charge: No arxiv: 1 author: - first_name: Sadashige full_name: Ishida, Sadashige id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425 last_name: Ishida - first_name: Hugo full_name: Lavenant, Hugo last_name: Lavenant citation: ama: Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. doi:10.48550/arXiv.2312.12213 apa: Ishida, S., & Lavenant, H. (n.d.). Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. https://doi.org/10.48550/arXiv.2312.12213 chicago: Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2312.12213. ieee: S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” arXiv. . ista: Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv, 2312.12213. mla: Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, 2312.12213, doi:10.48550/arXiv.2312.12213. short: S. Ishida, H. Lavenant, ArXiv (n.d.). date_created: 2023-12-21T10:14:37Z date_published: 2023-12-19T00:00:00Z date_updated: 2023-12-27T13:44:33Z day: '19' department: - _id: GradSch - _id: ChWo doi: 10.48550/arXiv.2312.12213 external_id: arxiv: - '2312.12213' keyword: - Optimal transport - Hamilton-Jacobi equation - convex optimization language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2312.12213 month: '12' oa: 1 oa_version: Preprint project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: arXiv publication_status: submitted status: public title: Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation type: preprint user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14709' abstract: - lang: eng text: Amid the delays due to the global pandemic, in early October 2022, the auxin community gathered in the idyllic peninsula of Cavtat, Croatia. More than 170 scientists from across the world converged to discuss the latest advancements in fundamental and applied research in the field. The topics, from signalling and transport to plant architecture and response to the environment, show how auxin research must bridge from the molecular realm to macroscopic developmental responses. This is mirrored in this collection of reviews, contributed by participants of the Auxin 2022 meeting. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Marta full_name: Del Bianco, Marta last_name: Del Bianco - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Lucia full_name: Strader, Lucia last_name: Strader - first_name: Stefan full_name: Kepinski, Stefan last_name: Kepinski citation: ama: 'Del Bianco M, Friml J, Strader L, Kepinski S. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 2023;74(22):6889-6892. doi:10.1093/jxb/erad420' apa: 'Del Bianco, M., Friml, J., Strader, L., & Kepinski, S. (2023). Auxin research: Creating tools for a greener future. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erad420' chicago: 'Del Bianco, Marta, Jiří Friml, Lucia Strader, and Stefan Kepinski. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany. Oxford University Press, 2023. https://doi.org/10.1093/jxb/erad420.' ieee: 'M. Del Bianco, J. Friml, L. Strader, and S. Kepinski, “Auxin research: Creating tools for a greener future,” Journal of Experimental Botany, vol. 74, no. 22. Oxford University Press, pp. 6889–6892, 2023.' ista: 'Del Bianco M, Friml J, Strader L, Kepinski S. 2023. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 74(22), 6889–6892.' mla: 'Del Bianco, Marta, et al. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany, vol. 74, no. 22, Oxford University Press, 2023, pp. 6889–92, doi:10.1093/jxb/erad420.' short: M. Del Bianco, J. Friml, L. Strader, S. Kepinski, Journal of Experimental Botany 74 (2023) 6889–6892. date_created: 2023-12-24T23:00:53Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T09:29:24Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1093/jxb/erad420 external_id: pmid: - '38038239' file: - access_level: open_access checksum: f66fb960fd791dea53fd0e087f2fbbe8 content_type: application/pdf creator: dernst date_created: 2024-01-02T09:23:57Z date_updated: 2024-01-02T09:23:57Z file_id: '14724' file_name: 2023_JourExperimentalBotany_DelBianco.pdf file_size: 425194 relation: main_file success: 1 file_date_updated: 2024-01-02T09:23:57Z has_accepted_license: '1' intvolume: ' 74' issue: '22' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '12' oa: 1 oa_version: Published Version page: 6889-6892 pmid: 1 publication: Journal of Experimental Botany publication_identifier: eissn: - 1460-2431 issn: - 0022-0957 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Auxin research: Creating tools for a greener future' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 74 year: '2023' ... --- _id: '14710' abstract: - lang: eng text: The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells. acknowledgement: 'We thank Lucy Colwell for suggesting that we use covariance based methods to predict contacts and Yang Hsia, Scott Boyken, Zibo Chen, and David Baker for collaborations on designed protein complexes. We also thank Ned Wingreen for suggesting the alternative derivation of (11). This research was supported by the Office of Naval Research through ONR N00014-17-1-3029, the Simons Foundation the NSF-Simons Center for Mathematical and Statistical Analysis of Biology at Harvard (award number #1764269), the Peter B. Lewis ’55 Lewis-Sigler Institute/Genomics Fund through the Lewis-Sigler Institute of Integrative Genomics at Princeton University, and the National Science Foundation through the Center for the Physics of Biological Function (PHY-1734030).' article_number: '8328' article_processing_charge: Yes article_type: original author: - first_name: Agnese I. full_name: Curatolo, Agnese I. last_name: Curatolo - first_name: Ofer full_name: Kimchi, Ofer last_name: Kimchi - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Ryan K. full_name: Krueger, Ryan K. last_name: Krueger - first_name: Michael P. full_name: Brenner, Michael P. last_name: Brenner citation: ama: Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 2023;14. doi:10.1038/s41467-023-43168-4 apa: Curatolo, A. I., Kimchi, O., Goodrich, C. P., Krueger, R. K., & Brenner, M. P. (2023). A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-43168-4 chicago: Curatolo, Agnese I., Ofer Kimchi, Carl Peter Goodrich, Ryan K. Krueger, and Michael P. Brenner. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-43168-4. ieee: A. I. Curatolo, O. Kimchi, C. P. Goodrich, R. K. Krueger, and M. P. Brenner, “A computational toolbox for the assembly yield of complex and heterogeneous structures,” Nature Communications, vol. 14. Springer Nature, 2023. ista: Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. 2023. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 14, 8328. mla: Curatolo, Agnese I., et al. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications, vol. 14, 8328, Springer Nature, 2023, doi:10.1038/s41467-023-43168-4. short: A.I. Curatolo, O. Kimchi, C.P. Goodrich, R.K. Krueger, M.P. Brenner, Nature Communications 14 (2023). date_created: 2023-12-24T23:00:53Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T11:36:46Z day: '01' ddc: - '530' department: - _id: CaGo doi: 10.1038/s41467-023-43168-4 file: - access_level: open_access checksum: fd9e9d527c2691f03fbc24031a75a3b3 content_type: application/pdf creator: kschuh date_created: 2023-12-27T08:40:43Z date_updated: 2023-12-27T08:40:43Z file_id: '14714' file_name: 2023_NatureComm_Curatolo.pdf file_size: 1342319 relation: main_file success: 1 file_date_updated: 2023-12-27T08:40:43Z has_accepted_license: '1' intvolume: ' 14' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A computational toolbox for the assembly yield of complex and heterogeneous structures tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '14715' abstract: - lang: eng text: We consider N trapped bosons in the mean-field limit with coupling constant λN = 1/(N − 1). The ground state of such systems exhibits Bose–Einstein condensation. We prove that the probability of finding ℓ particles outside the condensate wave function decays exponentially in ℓ. acknowledgement: We thank Lea Boßmann, Phan Thành Nam and Simone Rademacher for helpful remarks. P.P. acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Grant No. SFB/TRR 352 “Mathematics of Many-Body Quantum Systems and Their Collective Phenomena.” article_number: '121901' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas - first_name: Peter full_name: Pickl, Peter last_name: Pickl citation: ama: Mitrouskas DJ, Pickl P. Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. 2023;64(12). doi:10.1063/5.0172199 apa: Mitrouskas, D. J., & Pickl, P. (2023). Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0172199 chicago: Mitrouskas, David Johannes, and Peter Pickl. “Exponential Decay of the Number of Excitations in the Weakly Interacting Bose Gas.” Journal of Mathematical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0172199. ieee: D. J. Mitrouskas and P. Pickl, “Exponential decay of the number of excitations in the weakly interacting Bose gas,” Journal of Mathematical Physics, vol. 64, no. 12. AIP Publishing, 2023. ista: Mitrouskas DJ, Pickl P. 2023. Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. 64(12), 121901. mla: Mitrouskas, David Johannes, and Peter Pickl. “Exponential Decay of the Number of Excitations in the Weakly Interacting Bose Gas.” Journal of Mathematical Physics, vol. 64, no. 12, 121901, AIP Publishing, 2023, doi:10.1063/5.0172199. short: D.J. Mitrouskas, P. Pickl, Journal of Mathematical Physics 64 (2023). date_created: 2023-12-31T23:01:02Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T08:51:28Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1063/5.0172199 external_id: arxiv: - '2307.11062' file: - access_level: open_access checksum: 66572f718a36465576cf0d6b3f7e01fc content_type: application/pdf creator: dernst date_created: 2024-01-02T08:45:07Z date_updated: 2024-01-02T08:45:07Z file_id: '14722' file_name: 2023_JourMathPhysics_Mitrouskas.pdf file_size: 4346922 relation: main_file success: 1 file_date_updated: 2024-01-02T08:45:07Z has_accepted_license: '1' intvolume: ' 64' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Journal of Mathematical Physics publication_identifier: eissn: - 1089-7658 issn: - 0022-2488 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Exponential decay of the number of excitations in the weakly interacting Bose gas tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 64 year: '2023' ... --- _id: '14716' abstract: - lang: eng text: "Background: Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature.\r\n\r\nResults: In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models’ performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics.\r\n\r\nConclusions: Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers." acknowledgement: Open Access funding enabled and organized by Projekt DEAL. A.Y. and O.V.K. acknowledge financial support from the Klaus Faber Foundation. A.A.A. was funded by the Helmholtz AI project AMR-XAI. The work of O.O.B. is funded by Fonds zur Förderung der Wissenschaftlichen Forschung (FWF), Grant ESP 253-B. article_number: '404' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Alper full_name: Yurtseven, Alper last_name: Yurtseven - first_name: Sofia full_name: Buyanova, Sofia id: 2F54A7BC-3902-11EA-AC87-BC9F3DDC885E last_name: Buyanova - first_name: Amay Ajaykumar A. full_name: Agrawal, Amay Ajaykumar A. last_name: Agrawal - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Olga V V. full_name: Kalinina, Olga V V. last_name: Kalinina citation: ama: Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 2023;23(1). doi:10.1186/s12866-023-03147-7 apa: Yurtseven, A., Buyanova, S., Agrawal, A. A. A., Bochkareva, O., & Kalinina, O. V. V. (2023). Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. Springer Nature. https://doi.org/10.1186/s12866-023-03147-7 chicago: Yurtseven, Alper, Sofia Buyanova, Amay Ajaykumar A. Agrawal, Olga Bochkareva, and Olga V V. Kalinina. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.” BMC Microbiology. Springer Nature, 2023. https://doi.org/10.1186/s12866-023-03147-7. ieee: A. Yurtseven, S. Buyanova, A. A. A. Agrawal, O. Bochkareva, and O. V. V. Kalinina, “Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis,” BMC Microbiology, vol. 23, no. 1. Springer Nature, 2023. ista: Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. 2023. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 23(1), 404. mla: Yurtseven, Alper, et al. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.” BMC Microbiology, vol. 23, no. 1, 404, Springer Nature, 2023, doi:10.1186/s12866-023-03147-7. short: A. Yurtseven, S. Buyanova, A.A.A. Agrawal, O. Bochkareva, O.V.V. Kalinina, BMC Microbiology 23 (2023). date_created: 2023-12-31T23:01:02Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T09:20:57Z day: '01' ddc: - '570' department: - _id: FyKo doi: 10.1186/s12866-023-03147-7 external_id: pmid: - '38124060' file: - access_level: open_access checksum: 7ff5e95f3496ff663301eb4a13a316d5 content_type: application/pdf creator: dernst date_created: 2024-01-02T09:09:32Z date_updated: 2024-01-02T09:09:32Z file_id: '14723' file_name: 2023_BMCMicrobiology_Yurtseven.pdf file_size: 1979922 relation: main_file success: 1 file_date_updated: 2024-01-02T09:09:32Z has_accepted_license: '1' intvolume: ' 23' issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: BMC Microbiology publication_identifier: eissn: - 1471-2180 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2023' ... --- _id: '14717' abstract: - lang: eng text: We count primitive lattices of rank d inside Zn as their covolume tends to infinity, with respect to certain parameters of such lattices. These parameters include, for example, the subspace that a lattice spans, namely its projection to the Grassmannian; its homothety class and its equivalence class modulo rescaling and rotation, often referred to as a shape. We add to a prior work of Schmidt by allowing sets in the spaces of parameters that are general enough to conclude the joint equidistribution of these parameters. In addition to the primitive d-lattices Λ themselves, we also consider their orthogonal complements in Zn⁠, A1⁠, and show that the equidistribution occurs jointly for Λ and A1⁠. Finally, our asymptotic formulas for the number of primitive lattices include an explicit bound on the error term. acknowledgement: This work was done when both authors were visiting Institute of Science and Technology (IST) Austria. T.H. was being supported by Engineering and Physical Sciences Research Council grant EP/P026710/1. Y.K. had a great time there and is grateful for the hospitality. The appendix to this paper is largely based on a mini course T.H. had given at IST in February 2020. article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Tal full_name: Horesh, Tal id: C8B7BF48-8D81-11E9-BCA9-F536E6697425 last_name: Horesh - first_name: Yakov full_name: Karasik, Yakov last_name: Karasik citation: ama: Horesh T, Karasik Y. Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. 2023;74(4):1253-1294. doi:10.1093/qmath/haad008 apa: Horesh, T., & Karasik, Y. (2023). Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haad008 chicago: Horesh, Tal, and Yakov Karasik. “Equidistribution of Primitive Lattices in ℝn.” Quarterly Journal of Mathematics. Oxford University Press, 2023. https://doi.org/10.1093/qmath/haad008. ieee: T. Horesh and Y. Karasik, “Equidistribution of primitive lattices in ℝn,” Quarterly Journal of Mathematics, vol. 74, no. 4. Oxford University Press, pp. 1253–1294, 2023. ista: Horesh T, Karasik Y. 2023. Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. 74(4), 1253–1294. mla: Horesh, Tal, and Yakov Karasik. “Equidistribution of Primitive Lattices in ℝn.” Quarterly Journal of Mathematics, vol. 74, no. 4, Oxford University Press, 2023, pp. 1253–94, doi:10.1093/qmath/haad008. short: T. Horesh, Y. Karasik, Quarterly Journal of Mathematics 74 (2023) 1253–1294. date_created: 2023-12-31T23:01:03Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T07:39:55Z day: '01' ddc: - '510' department: - _id: TiBr doi: 10.1093/qmath/haad008 external_id: arxiv: - '2012.04508' file: - access_level: open_access checksum: bf29baa9eae8500f3374dbcb80712687 content_type: application/pdf creator: dernst date_created: 2024-01-02T07:37:09Z date_updated: 2024-01-02T07:37:09Z file_id: '14720' file_name: 2023_QuarterlyJourMath_Horesh.pdf file_size: 724748 relation: main_file success: 1 file_date_updated: 2024-01-02T07:37:09Z has_accepted_license: '1' intvolume: ' 74' issue: '4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 1253-1294 project: - _id: 26A8D266-B435-11E9-9278-68D0E5697425 grant_number: EP-P026710-2 name: Between rational and integral points publication: Quarterly Journal of Mathematics publication_identifier: eissn: - 1464-3847 issn: - 0033-5606 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Equidistribution of primitive lattices in ℝn tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 74 year: '2023' ... --- _id: '14718' abstract: - lang: eng text: 'Binary decision diagrams (BDDs) are one of the fundamental data structures in formal methods and computer science in general. However, the performance of BDD-based algorithms greatly depends on memory latency due to the reliance on large hash tables and thus, by extension, on the speed of random memory access. This hinders the full utilisation of resources available on modern CPUs, since the absolute memory latency has not improved significantly for at least a decade. In this paper, we explore several implementation techniques that improve the performance of BDD manipulation either through enhanced memory locality or by partially eliminating random memory access. On a benchmark suite of 600+ BDDs derived from real-world applications, we demonstrate runtime that is comparable or better than parallelising the same operations on eight CPU cores. ' acknowledgement: "This work was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413 and the\r\n“VAMOS” grant ERC-2020-AdG 101020093." article_processing_charge: No author: - first_name: Samuel full_name: Pastva, Samuel id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b last_name: Pastva orcid: 0000-0003-1993-0331 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: 'Pastva S, Henzinger TA. Binary decision diagrams on modern hardware. In: Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design. TU Vienna Academic Press; 2023:122-131. doi:10.34727/2023/isbn.978-3-85448-060-0_20' apa: 'Pastva, S., & Henzinger, T. A. (2023). Binary decision diagrams on modern hardware. In Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design (pp. 122–131). Ames, IA, United States: TU Vienna Academic Press. https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20' chicago: Pastva, Samuel, and Thomas A Henzinger. “Binary Decision Diagrams on Modern Hardware.” In Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, 122–31. TU Vienna Academic Press, 2023. https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20. ieee: S. Pastva and T. A. Henzinger, “Binary decision diagrams on modern hardware,” in Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, Ames, IA, United States, 2023, pp. 122–131. ista: 'Pastva S, Henzinger TA. 2023. Binary decision diagrams on modern hardware. Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design. FMCAD: Conference on Formal Methods in Computer-aided design, 122–131.' mla: Pastva, Samuel, and Thomas A. Henzinger. “Binary Decision Diagrams on Modern Hardware.” Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, TU Vienna Academic Press, 2023, pp. 122–31, doi:10.34727/2023/isbn.978-3-85448-060-0_20. short: S. Pastva, T.A. Henzinger, in:, Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, TU Vienna Academic Press, 2023, pp. 122–131. conference: end_date: 2023-10-27 location: Ames, IA, United States name: 'FMCAD: Conference on Formal Methods in Computer-aided design' start_date: 2023-10-25 date_created: 2023-12-31T23:01:03Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-02T08:16:28Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.34727/2023/isbn.978-3-85448-060-0_20 ec_funded: 1 file: - access_level: open_access checksum: 818d6e13dd508f3a04f0941081022e5d content_type: application/pdf creator: dernst date_created: 2024-01-02T08:14:23Z date_updated: 2024-01-02T08:14:23Z file_id: '14721' file_name: 2023_FMCAD_Pastva.pdf file_size: 524321 relation: main_file success: 1 file_date_updated: 2024-01-02T08:14:23Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 122-131 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design publication_identifier: isbn: - '9783854480600' publication_status: published publisher: TU Vienna Academic Press quality_controlled: '1' scopus_import: '1' status: public title: Binary decision diagrams on modern hardware tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14719' abstract: - lang: eng text: Lithium–sulfur batteries are regarded as an advantageous option for meeting the growing demand for high-energy-density storage, but their commercialization relies on solving the current limitations of both sulfur cathodes and lithium metal anodes. In this scenario, the implementation of lithium sulfide (Li2S) cathodes compatible with alternative anode materials such as silicon has the potential to alleviate the safety concerns associated with lithium metal. In this direction, here, we report a sulfur cathode based on Li2S nanocrystals grown on a catalytic host consisting of CoFeP nanoparticles supported on tubular carbon nitride. Nanosized Li2S is incorporated into the host by a scalable liquid infiltration–evaporation method. Theoretical calculations and experimental results demonstrate that the CoFeP–CN composite can boost the polysulfide adsorption/conversion reaction kinetics and strongly reduce the initial overpotential activation barrier by stretching the Li–S bonds of Li2S. Besides, the ultrasmall size of the Li2S particles in the Li2S–CoFeP–CN composite cathode facilitates the initial activation. Overall, the Li2S–CoFeP–CN electrodes exhibit a low activation barrier of 2.56 V, a high initial capacity of 991 mA h gLi2S–1, and outstanding cyclability with a small fading rate of 0.029% per cycle over 800 cycles. Moreover, Si/Li2S full cells are assembled using the nanostructured Li2S–CoFeP–CN cathode and a prelithiated anode based on graphite-supported silicon nanowires. These Si/Li2S cells demonstrate high initial discharge capacities above 900 mA h gLi2S–1 and good cyclability with a capacity fading rate of 0.28% per cycle over 150 cycles. acknowledged_ssus: - _id: EM-Fac - _id: NanoFab acknowledgement: The authors acknowledge the support from the 2BoSS project of the ERA-MIN3 program with the Spanish grant number PCI2022-132985/AEI/10.13039/501100011033 and the French grant number ANR-22-MIN3-0003-01. J.L. acknowledges the support from the Natural Science Foundation of Sichuan Province 2022NSFSC1229. The authors acknowledge the funding from Generalitat de Catalunya 2021 SGR 01581 and European Union NextGenerationEU/PRTR. This research was supported by the Scientific Service Units (SSU) of ISTA Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). article_processing_charge: No article_type: original author: - first_name: Hamid full_name: Mollania, Hamid last_name: Mollania - first_name: Chaoqi full_name: Zhang, Chaoqi last_name: Zhang - first_name: Ruifeng full_name: Du, Ruifeng last_name: Du - first_name: Xueqiang full_name: Qi, Xueqiang last_name: Qi - first_name: Junshan full_name: Li, Junshan last_name: Li - first_name: Sharona full_name: Horta, Sharona id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc last_name: Horta - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Caroline full_name: Keller, Caroline last_name: Keller - first_name: Pascale full_name: Chenevier, Pascale last_name: Chenevier - first_name: Majid full_name: Oloomi-Buygi, Majid last_name: Oloomi-Buygi - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Mollania H, Zhang C, Du R, et al. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 2023;15(50):58462–58475. doi:10.1021/acsami.3c14072 apa: Mollania, H., Zhang, C., Du, R., Qi, X., Li, J., Horta, S., … Cabot, A. (2023). Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c14072 chicago: Mollania, Hamid, Chaoqi Zhang, Ruifeng Du, Xueqiang Qi, Junshan Li, Sharona Horta, Maria Ibáñez, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” ACS Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c14072. ieee: H. Mollania et al., “Nanostructured Li₂S cathodes for silicon-sulfur batteries,” ACS Applied Materials and Interfaces, vol. 15, no. 50. American Chemical Society, pp. 58462–58475, 2023. ista: Mollania H, Zhang C, Du R, Qi X, Li J, Horta S, Ibáñez M, Keller C, Chenevier P, Oloomi-Buygi M, Cabot A. 2023. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 15(50), 58462–58475. mla: Mollania, Hamid, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” ACS Applied Materials and Interfaces, vol. 15, no. 50, American Chemical Society, 2023, pp. 58462–58475, doi:10.1021/acsami.3c14072. short: H. Mollania, C. Zhang, R. Du, X. Qi, J. Li, S. Horta, M. Ibáñez, C. Keller, P. Chenevier, M. Oloomi-Buygi, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 58462–58475. date_created: 2023-12-31T23:01:03Z date_published: 2023-12-05T00:00:00Z date_updated: 2024-01-02T08:35:06Z day: '05' department: - _id: MaIb doi: 10.1021/acsami.3c14072 intvolume: ' 15' issue: '50' language: - iso: eng month: '12' oa_version: None page: 58462–58475 publication: ACS Applied Materials and Interfaces publication_identifier: eissn: - 1944-8252 issn: - 1944-8244 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Nanostructured Li₂S cathodes for silicon-sulfur batteries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2023' ... --- _id: '14732' abstract: - lang: eng text: 'Fragmented landscapes pose a significant threat to the persistence of species as they are highly susceptible to heightened risk of extinction due to the combined effects of genetic and demographic factors such as genetic drift and demographic stochasticity. This paper explores the intricate interplay between genetic load and extinction risk within metapopulations with a focus on understanding the impact of eco-evolutionary feedback mechanisms. We distinguish between two models of selection: soft selection, characterised by subpopulations maintaining carrying capacity despite load, and hard selection, where load can significantly affect population size. Within the soft selection framework, we investigate the impact of gene flow on genetic load at a single locus, while also considering the effect of selection strength and dominance coefficient. We subsequently build on this to examine how gene flow influences both population size and load under hard selection as well as identify critical thresholds for metapopulation persistence. Our analysis employs the diffusion, semi-deterministic and effective migration approximations. Our findings reveal that under soft selection, even modest levels of migration can significantly alleviate the burden of load. In sharp contrast, with hard selection, a much higher degree of gene flow is required to mitigate load and prevent the collapse of the metapopulation. Overall, this study sheds light into the crucial role migration plays in shaping the dynamics of genetic load and extinction risk in fragmented landscapes, offering valuable insights for conservation strategies and the preservation of diversity in a changing world.' article_processing_charge: No author: - first_name: Oluwafunmilola O full_name: Olusanya, Oluwafunmilola O id: 41AD96DC-F248-11E8-B48F-1D18A9856A87 last_name: Olusanya orcid: 0000-0003-1971-8314 - first_name: Kseniia full_name: Khudiakova, Kseniia id: 4E6DC800-AE37-11E9-AC72-31CAE5697425 last_name: Khudiakova orcid: 0000-0002-6246-1465 - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva citation: ama: Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv. doi:10.1101/2023.12.02.569702 apa: Olusanya, O. O., Khudiakova, K., & Sachdeva, H. (n.d.). Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv. https://doi.org/10.1101/2023.12.02.569702 chicago: Olusanya, Oluwafunmilola O, Kseniia Khudiakova, and Himani Sachdeva. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, n.d. https://doi.org/10.1101/2023.12.02.569702. ieee: O. O. Olusanya, K. Khudiakova, and H. Sachdeva, “Genetic load, eco-evolutionary feedback and extinction in a metapopulation,” bioRxiv. . ista: Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv, 10.1101/2023.12.02.569702. mla: Olusanya, Oluwafunmilola O., et al. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, doi:10.1101/2023.12.02.569702. short: O.O. Olusanya, K. Khudiakova, H. Sachdeva, BioRxiv (n.d.). date_created: 2024-01-04T09:35:54Z date_published: 2023-12-04T00:00:00Z date_updated: 2025-05-26T09:05:10Z day: '04' department: - _id: NiBa - _id: JaMa doi: 10.1101/2023.12.02.569702 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2023.12.02.569702v1 month: '12' oa: 1 oa_version: Preprint project: - _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8 grant_number: P32896 name: Causes and consequences of population fragmentation - _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8 grant_number: '26293' name: The impact of deleterious mutations on small populations - _id: 34c872fe-11ca-11ed-8bc3-8534b82131e6 grant_number: '26380' name: Polygenic Adaptation in a Metapopulation publication: bioRxiv publication_status: submitted related_material: record: - id: '14711' relation: dissertation_contains status: public status: public title: Genetic load, eco-evolutionary feedback and extinction in a metapopulation tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14733' abstract: - lang: eng text: Redox flow batteries (RFBs) rely on the development of cheap, highly soluble, and high-energy-density electrolytes. Several candidate quinones have already been investigated in the literature as two-electron anolytes or catholytes, benefiting from fast kinetics, high tunability, and low cost. Here, an investigation of nitrogen-rich fused heteroaromatic quinones was carried out to explore avenues for electrolyte development. These quinones were synthesized and screened by using electrochemical techniques. The most promising candidate, 4,8-dioxo-4,8-dihydrobenzo[1,2-d:4,5-d′]bis([1,2,3]triazole)-1,5-diide (−0.68 V(SHE)), was tested in both an asymmetric and symmetric full-cell setup resulting in capacity fade rates of 0.35% per cycle and 0.0124% per cycle, respectively. In situ ultraviolet-visible spectroscopy (UV–Vis), nuclear magnetic resonance (NMR), and electron paramagnetic resonance (EPR) spectroscopies were used to investigate the electrochemical stability of the charged species during operation. UV–Vis spectroscopy, supported by density functional theory (DFT) modeling, reaffirmed that the two-step charging mechanism observed during battery operation consisted of two, single-electron transfers. The radical concentration during battery operation and the degree of delocalization of the unpaired electron were quantified with NMR and EPR spectroscopy. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Rajesh B full_name: Jethwa, Rajesh B id: 4cc538d5-803f-11ed-ab7e-8139573aad8f last_name: Jethwa orcid: 0000-0002-0404-4356 - first_name: Dominic full_name: Hey, Dominic last_name: Hey - first_name: Rachel N. full_name: Kerber, Rachel N. last_name: Kerber - first_name: Andrew D. full_name: Bond, Andrew D. last_name: Bond - first_name: Dominic S. full_name: Wright, Dominic S. last_name: Wright - first_name: Clare P. full_name: Grey, Clare P. last_name: Grey citation: ama: Jethwa RB, Hey D, Kerber RN, Bond AD, Wright DS, Grey CP. Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. 2023. doi:10.1021/acsaem.3c02223 apa: Jethwa, R. B., Hey, D., Kerber, R. N., Bond, A. D., Wright, D. S., & Grey, C. P. (2023). Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. American Chemical Society. https://doi.org/10.1021/acsaem.3c02223 chicago: Jethwa, Rajesh B, Dominic Hey, Rachel N. Kerber, Andrew D. Bond, Dominic S. Wright, and Clare P. Grey. “Exploring the Landscape of Heterocyclic Quinones for Redox Flow Batteries.” ACS Applied Energy Materials. American Chemical Society, 2023. https://doi.org/10.1021/acsaem.3c02223. ieee: R. B. Jethwa, D. Hey, R. N. Kerber, A. D. Bond, D. S. Wright, and C. P. Grey, “Exploring the landscape of heterocyclic quinones for redox flow batteries,” ACS Applied Energy Materials. American Chemical Society, 2023. ista: Jethwa RB, Hey D, Kerber RN, Bond AD, Wright DS, Grey CP. 2023. Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. mla: Jethwa, Rajesh B., et al. “Exploring the Landscape of Heterocyclic Quinones for Redox Flow Batteries.” ACS Applied Energy Materials, American Chemical Society, 2023, doi:10.1021/acsaem.3c02223. short: R.B. Jethwa, D. Hey, R.N. Kerber, A.D. Bond, D.S. Wright, C.P. Grey, ACS Applied Energy Materials (2023). date_created: 2024-01-05T09:20:48Z date_published: 2023-12-28T00:00:00Z date_updated: 2024-01-08T09:03:01Z day: '28' ddc: - '540' department: - _id: StFr doi: 10.1021/acsaem.3c02223 ec_funded: 1 has_accepted_license: '1' keyword: - Electrical and Electronic Engineering - Materials Chemistry - Electrochemistry - Energy Engineering and Power Technology - Chemical Engineering (miscellaneous) language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/acsaem.3c02223 month: '12' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: ACS Applied Energy Materials publication_identifier: eissn: - 2574-0962 publication_status: epub_ahead publisher: American Chemical Society quality_controlled: '1' status: public title: Exploring the landscape of heterocyclic quinones for redox flow batteries tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14734' abstract: - lang: eng text: Developing cost-effective and high-performance thermoelectric (TE) materials to assemble efficient TE devices presents a multitude of challenges and opportunities. Cu3SbSe4 is a promising p-type TE material based on relatively earth abundant elements. However, the challenge lies in its poor electrical conductivity. Herein, an efficient and scalable solution-based approach is developed to synthesize high-quality Cu3SbSe4 nanocrystals doped with Pb at the Sb site. After ligand displacement and annealing treatments, the dried powders are consolidated into dense pellets, and their TE properties are investigated. Pb doping effectively increases the charge carrier concentration, resulting in a significant increase in electrical conductivity, while the Seebeck coefficients remain consistently high. The calculated band structure shows that Pb doping induces band convergence, thereby increasing the effective mass. Furthermore, the large ionic radius of Pb2+ results in the generation of additional point and plane defects and interphases, dramatically enhancing phonon scattering, which significantly decreases the lattice thermal conductivity at high temperatures. Overall, a maximum figure of merit (zTmax) ≈ 0.85 at 653 K is obtained in Cu3Sb0.97Pb0.03Se4. This represents a 1.6-fold increase compared to the undoped sample and exceeds most doped Cu3SbSe4-based materials produced by solid-state, demonstrating advantages of versatility and cost-effectiveness using a solution-based technology. acknowledgement: Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges financial support from the National Natural Science Foundation of China (NSFC) (Grant No. 22208293). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation. article_processing_charge: No article_type: original author: - first_name: Shanhong full_name: Wan, Shanhong last_name: Wan - first_name: Shanshan full_name: Xiao, Shanshan last_name: Xiao - first_name: Mingquan full_name: Li, Mingquan last_name: Li - first_name: Xin full_name: Wang, Xin last_name: Wang - first_name: Khak Ho full_name: Lim, Khak Ho last_name: Lim - first_name: Min full_name: Hong, Min last_name: Hong - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 citation: ama: Wan S, Xiao S, Li M, et al. Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods. 2023. doi:10.1002/smtd.202301377 apa: Wan, S., Xiao, S., Li, M., Wang, X., Lim, K. H., Hong, M., … Liu, Y. (2023). Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods. Wiley. https://doi.org/10.1002/smtd.202301377 chicago: Wan, Shanhong, Shanshan Xiao, Mingquan Li, Xin Wang, Khak Ho Lim, Min Hong, Maria Ibáñez, Andreu Cabot, and Yu Liu. “Band Engineering through Pb-Doping of Nanocrystal Building Blocks to Enhance Thermoelectric Performance in Cu3SbSe4.” Small Methods. Wiley, 2023. https://doi.org/10.1002/smtd.202301377. ieee: S. Wan et al., “Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4,” Small Methods. Wiley, 2023. ista: Wan S, Xiao S, Li M, Wang X, Lim KH, Hong M, Ibáñez M, Cabot A, Liu Y. 2023. Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods. mla: Wan, Shanhong, et al. “Band Engineering through Pb-Doping of Nanocrystal Building Blocks to Enhance Thermoelectric Performance in Cu3SbSe4.” Small Methods, Wiley, 2023, doi:10.1002/smtd.202301377. short: S. Wan, S. Xiao, M. Li, X. Wang, K.H. Lim, M. Hong, M. Ibáñez, A. Cabot, Y. Liu, Small Methods (2023). date_created: 2024-01-07T23:00:51Z date_published: 2023-12-28T00:00:00Z date_updated: 2024-01-08T09:17:04Z day: '28' department: - _id: MaIb doi: 10.1002/smtd.202301377 external_id: pmid: - '38152986' language: - iso: eng month: '12' oa_version: None pmid: 1 project: - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication: Small Methods publication_identifier: eissn: - 2366-9608 publication_status: epub_ahead publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14735' abstract: - lang: eng text: "Scaling blockchain protocols to perform on par with the expected needs of Web3.0 has been proven to be a challenging task with almost a decade of research. In the forefront of the current solution is the idea of separating the execution of the updates encoded in a block from the ordering of blocks. In order to achieve this, a new class of protocols called rollups has emerged. Rollups have as input a total ordering of valid and invalid transactions and as output a new valid state-transition.\r\nIf we study rollups from a distributed computing perspective, we uncover that rollups take as input the output of a Byzantine Atomic Broadcast (BAB) protocol and convert it to a State Machine Replication (SMR) protocol. BAB and SMR, however, are considered equivalent as far as distributed computing is concerned and a solution to one can easily be retrofitted to solve the other simply by adding/removing an execution step before the validation of the input.\r\nThis “easy” step of retrofitting an atomic broadcast solution to implement an SMR has, however, been overlooked in practice. In this paper, we formalize the problem and show that after BAB is solved, traditional impossibility results for consensus no longer apply towards an SMR. Leveraging this we propose a distributed execution protocol that allows reduced execution and storage cost per executor (O(log2n/n)) without relaxing the network assumptions of the underlying BAB protocol and providing censorship-resistance. Finally, we propose efficient non-interactive light client constructions that leverage our efficient execution protocols and do not require any synchrony assumptions or expensive ZK-proofs." acknowledgement: 'Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Christos full_name: Stefo, Christos id: a20e8902-32b0-11ee-9fa8-b23fa638b793 last_name: Stefo - first_name: Zhuolun full_name: Xiang, Zhuolun last_name: Xiang - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias citation: ama: 'Stefo C, Xiang Z, Kokoris Kogias E. Executing and proving over dirty ledgers. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:3-20. doi:10.1007/978-3-031-47754-6_1' apa: 'Stefo, C., Xiang, Z., & Kokoris Kogias, E. (2023). Executing and proving over dirty ledgers. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 3–20). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_1' chicago: Stefo, Christos, Zhuolun Xiang, and Eleftherios Kokoris Kogias. “Executing and Proving over Dirty Ledgers.” In 27th International Conference on Financial Cryptography and Data Security, 13950:3–20. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_1. ieee: C. Stefo, Z. Xiang, and E. Kokoris Kogias, “Executing and proving over dirty ledgers,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 3–20. ista: 'Stefo C, Xiang Z, Kokoris Kogias E. 2023. Executing and proving over dirty ledgers. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 3–20.' mla: Stefo, Christos, et al. “Executing and Proving over Dirty Ledgers.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 3–20, doi:10.1007/978-3-031-47754-6_1. short: C. Stefo, Z. Xiang, E. Kokoris Kogias, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 3–20. conference: end_date: 2023-05-05 location: Bol, Brac, Croatia name: 'FC: Financial Cryptography and Data Security' start_date: 2023-05-01 date_created: 2024-01-08T09:17:38Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T09:28:14Z day: '01' department: - _id: ElKo - _id: GradSch doi: 10.1007/978-3-031-47754-6_1 intvolume: ' 13950' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2022/1554 month: '12' oa: 1 oa_version: Preprint page: 3-20 project: - _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f grant_number: F8512 name: Secure Network and Hardware for Efficient Blockchains publication: 27th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - '9783031477546' eissn: - 0302-9743 isbn: - '9783031477539' issn: - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Executing and proving over dirty ledgers type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13950 year: '2023' ... --- _id: '14736' abstract: - lang: eng text: Payment channel networks (PCNs) are a promising technology to improve the scalability of cryptocurrencies. PCNs, however, face the challenge that the frequent usage of certain routes may deplete channels in one direction, and hence prevent further transactions. In order to reap the full potential of PCNs, recharging and rebalancing mechanisms are required to provision channels, as well as an admission control logic to decide which transactions to reject in case capacity is insufficient. This paper presents a formal model of this optimisation problem. In particular, we consider an online algorithms perspective, where transactions arrive over time in an unpredictable manner. Our main contributions are competitive online algorithms which come with provable guarantees over time. We empirically evaluate our algorithms on randomly generated transactions to compare the average performance of our algorithms to our theoretical bounds. We also show how this model and approach differs from related problems in classic communication networks. acknowledgement: Supported by the German Federal Ministry of Education and Research (BMBF), grant 16KISK020K (6G-RIC), 2021–2025, and ERC CoG 863818 (ForM-SMArt). alternative_title: - LNCS article_processing_charge: No author: - first_name: Mahsa full_name: Bastankhah, Mahsa last_name: Bastankhah - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Mohammad Ali full_name: Maddah-Ali, Mohammad Ali last_name: Maddah-Ali - first_name: Stefan full_name: Schmid, Stefan last_name: Schmid - first_name: Jakub full_name: Svoboda, Jakub id: 130759D2-D7DD-11E9-87D2-DE0DE6697425 last_name: Svoboda orcid: 0000-0002-1419-3267 - first_name: Michelle X full_name: Yeo, Michelle X id: 2D82B818-F248-11E8-B48F-1D18A9856A87 last_name: Yeo orcid: 0009-0001-3676-4809 citation: ama: 'Bastankhah M, Chatterjee K, Maddah-Ali MA, Schmid S, Svoboda J, Yeo MX. R2: Boosting liquidity in payment channel networks with online admission control. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:309-325. doi:10.1007/978-3-031-47754-6_18' apa: 'Bastankhah, M., Chatterjee, K., Maddah-Ali, M. A., Schmid, S., Svoboda, J., & Yeo, M. X. (2023). R2: Boosting liquidity in payment channel networks with online admission control. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 309–325). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_18' chicago: 'Bastankhah, Mahsa, Krishnendu Chatterjee, Mohammad Ali Maddah-Ali, Stefan Schmid, Jakub Svoboda, and Michelle X Yeo. “R2: Boosting Liquidity in Payment Channel Networks with Online Admission Control.” In 27th International Conference on Financial Cryptography and Data Security, 13950:309–25. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_18.' ieee: 'M. Bastankhah, K. Chatterjee, M. A. Maddah-Ali, S. Schmid, J. Svoboda, and M. X. Yeo, “R2: Boosting liquidity in payment channel networks with online admission control,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 309–325.' ista: 'Bastankhah M, Chatterjee K, Maddah-Ali MA, Schmid S, Svoboda J, Yeo MX. 2023. R2: Boosting liquidity in payment channel networks with online admission control. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 309–325.' mla: 'Bastankhah, Mahsa, et al. “R2: Boosting Liquidity in Payment Channel Networks with Online Admission Control.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 309–25, doi:10.1007/978-3-031-47754-6_18.' short: M. Bastankhah, K. Chatterjee, M.A. Maddah-Ali, S. Schmid, J. Svoboda, M.X. Yeo, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 309–325. conference: end_date: 2023-05-05 location: Bol, Brac, Croatia name: 'FC: Financial Cryptography and Data Security' start_date: 2023-05-01 date_created: 2024-01-08T09:30:22Z date_published: 2023-12-01T00:00:00Z date_updated: 2025-07-14T09:10:01Z day: '01' department: - _id: KrCh - _id: KrPi doi: 10.1007/978-3-031-47754-6_18 ec_funded: 1 intvolume: ' 13950' language: - iso: eng month: '12' oa_version: None page: 309-325 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: 27th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - '9783031477546' eissn: - 1611-3349 isbn: - '9783031477539' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'R2: Boosting liquidity in payment channel networks with online admission control' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13950 year: '2023' ... --- _id: '14737' abstract: - lang: eng text: 'John’s fundamental theorem characterizing the largest volume ellipsoid contained in a convex body $K$ in $\mathbb{R}^{d}$ has seen several generalizations and extensions. One direction, initiated by V. Milman is to replace ellipsoids by positions (affine images) of another body $L$. Another, more recent direction is to consider logarithmically concave functions on $\mathbb{R}^{d}$ instead of convex bodies: we designate some special, radially symmetric log-concave function $g$ as the analogue of the Euclidean ball, and want to find its largest integral position under the constraint that it is pointwise below some given log-concave function $f$. We follow both directions simultaneously: we consider the functional question, and allow essentially any meaningful function to play the role of $g$ above. Our general theorems jointly extend known results in both directions. The dual problem in the setting of convex bodies asks for the smallest volume ellipsoid, called Löwner’s ellipsoid, containing $K$. We consider the analogous problem for functions: we characterize the solutions of the optimization problem of finding a smallest integral position of some log-concave function $g$ under the constraint that it is pointwise above $f$. It turns out that in the functional setting, the relationship between the John and the Löwner problems is more intricate than it is in the setting of convex bodies.' acknowledgement: "We thank Alexander Litvak for the many discussions on Theorem 1.1. Igor Tsiutsiurupa participated in the early stage of this project. To our deep regret, Igor chose another road for his life and stopped working with us.\r\nThis work was supported by the János Bolyai Scholarship of the Hungarian Academy of Sciences [to M.N.]; the National Research, Development, and Innovation Fund (NRDI) [K119670 and K131529 to M.N.]; and the ÚNKP-22-5 New National Excellence Program of the Ministry for Innovation and Technology from the source of the NRDI [to M.N.]." article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Grigory full_name: Ivanov, Grigory id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E last_name: Ivanov - first_name: Márton full_name: Naszódi, Márton last_name: Naszódi citation: ama: Ivanov G, Naszódi M. Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. 2023;2023(23):20613-20669. doi:10.1093/imrn/rnad210 apa: Ivanov, G., & Naszódi, M. (2023). Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnad210 chicago: Ivanov, Grigory, and Márton Naszódi. “Functional John and Löwner Conditions for Pairs of Log-Concave Functions.” International Mathematics Research Notices. Oxford University Press, 2023. https://doi.org/10.1093/imrn/rnad210. ieee: G. Ivanov and M. Naszódi, “Functional John and Löwner conditions for pairs of log-concave functions,” International Mathematics Research Notices, vol. 2023, no. 23. Oxford University Press, pp. 20613–20669, 2023. ista: Ivanov G, Naszódi M. 2023. Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. 2023(23), 20613–20669. mla: Ivanov, Grigory, and Márton Naszódi. “Functional John and Löwner Conditions for Pairs of Log-Concave Functions.” International Mathematics Research Notices, vol. 2023, no. 23, Oxford University Press, 2023, pp. 20613–69, doi:10.1093/imrn/rnad210. short: G. Ivanov, M. Naszódi, International Mathematics Research Notices 2023 (2023) 20613–20669. date_created: 2024-01-08T09:48:56Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T09:57:25Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.1093/imrn/rnad210 external_id: arxiv: - '2212.11781' file: - access_level: open_access checksum: 353666cea80633beb0f1ffd342dff6d4 content_type: application/pdf creator: dernst date_created: 2024-01-08T09:53:09Z date_updated: 2024-01-08T09:53:09Z file_id: '14738' file_name: 2023_IMRN_Ivanov.pdf file_size: 815777 relation: main_file success: 1 file_date_updated: 2024-01-08T09:53:09Z has_accepted_license: '1' intvolume: ' 2023' issue: '23' keyword: - General Mathematics language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 20613-20669 publication: International Mathematics Research Notices publication_identifier: eissn: - 1687-0247 issn: - 1073-7928 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Functional John and Löwner conditions for pairs of log-concave functions tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2023 year: '2023' ... --- _id: '14739' abstract: - lang: eng text: Attempts to incorporate topological information in supervised learning tasks have resulted in the creation of several techniques for vectorizing persistent homology barcodes. In this paper, we study thirteen such methods. Besides describing an organizational framework for these methods, we comprehensively benchmark them against three well-known classification tasks. Surprisingly, we discover that the best-performing method is a simple vectorization, which consists only of a few elementary summary statistics. Finally, we provide a convenient web application which has been designed to facilitate exploration and experimentation with various vectorization methods. acknowledgement: "The work of Maria-Jose Jimenez, Eduardo Paluzo-Hidalgo and Manuel Soriano-Trigueros was supported in part by the Spanish grant Ministerio de Ciencia e Innovacion under Grants TED2021-129438B-I00 and PID2019-107339GB-I00, and in part by REXASI-PRO H-EU project, call HORIZON-CL4-2021-HUMAN-01-01 under Grant 101070028. The work of\r\nMaria-Jose Jimenez was supported by a grant of Convocatoria de la Universidad de Sevilla para la recualificacion del sistema universitario español, 2021-23, funded by the European Union, NextGenerationEU. The work of Vidit Nanda was supported in part by EPSRC under Grant EP/R018472/1 and in part by US AFOSR under Grant FA9550-22-1-0462. \r\nWe are grateful to the team of GUDHI and TEASPOON developers, for their work and their support. We are also grateful to Streamlit for providing extra resources to deploy the web app\r\nonline on Streamlit community cloud. We thank the anonymous referees for their helpful suggestions." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Dashti full_name: Ali, Dashti last_name: Ali - first_name: Aras full_name: Asaad, Aras last_name: Asaad - first_name: Maria-Jose full_name: Jimenez, Maria-Jose last_name: Jimenez - first_name: Vidit full_name: Nanda, Vidit last_name: Nanda - first_name: Eduardo full_name: Paluzo-Hidalgo, Eduardo last_name: Paluzo-Hidalgo - first_name: Manuel full_name: Soriano Trigueros, Manuel id: 15ebd7cf-15bf-11ee-aebd-bb4bb5121ea8 last_name: Soriano Trigueros orcid: 0000-0003-2449-1433 citation: ama: Ali D, Asaad A, Jimenez M-J, Nanda V, Paluzo-Hidalgo E, Soriano Trigueros M. A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2023;45(12):14069-14080. doi:10.1109/tpami.2023.3308391 apa: Ali, D., Asaad, A., Jimenez, M.-J., Nanda, V., Paluzo-Hidalgo, E., & Soriano Trigueros, M. (2023). A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/tpami.2023.3308391 chicago: Ali, Dashti, Aras Asaad, Maria-Jose Jimenez, Vidit Nanda, Eduardo Paluzo-Hidalgo, and Manuel Soriano Trigueros. “A Survey of Vectorization Methods in Topological Data Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2023. https://doi.org/10.1109/tpami.2023.3308391. ieee: D. Ali, A. Asaad, M.-J. Jimenez, V. Nanda, E. Paluzo-Hidalgo, and M. Soriano Trigueros, “A survey of vectorization methods in topological data analysis,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 45, no. 12. IEEE, pp. 14069–14080, 2023. ista: Ali D, Asaad A, Jimenez M-J, Nanda V, Paluzo-Hidalgo E, Soriano Trigueros M. 2023. A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 45(12), 14069–14080. mla: Ali, Dashti, et al. “A Survey of Vectorization Methods in Topological Data Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 45, no. 12, IEEE, 2023, pp. 14069–80, doi:10.1109/tpami.2023.3308391. short: D. Ali, A. Asaad, M.-J. Jimenez, V. Nanda, E. Paluzo-Hidalgo, M. Soriano Trigueros, IEEE Transactions on Pattern Analysis and Machine Intelligence 45 (2023) 14069–14080. date_created: 2024-01-08T09:59:46Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T10:11:46Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1109/tpami.2023.3308391 file: - access_level: open_access checksum: 465c28ef0b151b4b1fb47977ed5581ab content_type: application/pdf creator: dernst date_created: 2024-01-08T10:09:14Z date_updated: 2024-01-08T10:09:14Z file_id: '14740' file_name: 2023_IEEEToP_Ali.pdf file_size: 2370988 relation: main_file success: 1 file_date_updated: 2024-01-08T10:09:14Z has_accepted_license: '1' intvolume: ' 45' issue: '12' keyword: - Applied Mathematics - Artificial Intelligence - Computational Theory and Mathematics - Computer Vision and Pattern Recognition - Software language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 14069-14080 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_identifier: eissn: - 1939-3539 issn: - 0162-8828 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: A survey of vectorization methods in topological data analysis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2023' ... --- _id: '14742' abstract: - lang: eng text: "Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life." acknowledgement: "K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper." article_number: a041447 article_processing_charge: No article_type: original author: - first_name: Kay full_name: Lucek, Kay last_name: Lucek - first_name: Mabel D. full_name: Giménez, Mabel D. last_name: Giménez - first_name: Mathieu full_name: Joron, Mathieu last_name: Joron - first_name: Marina full_name: Rafajlović, Marina last_name: Rafajlović - first_name: Jeremy B. full_name: Searle, Jeremy B. last_name: Searle - first_name: Nora full_name: Walden, Nora last_name: Walden - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria citation: ama: 'Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 2023;15(11). doi:10.1101/cshperspect.a041447' apa: 'Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory. https://doi.org/10.1101/cshperspect.a041447' chicago: 'Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory, 2023. https://doi.org/10.1101/cshperspect.a041447.' ieee: 'K. Lucek et al., “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.' ista: 'Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447.' mla: 'Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:10.1101/cshperspect.a041447.' short: K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden, A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023). date_created: 2024-01-08T12:43:48Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-08T12:52:29Z day: '01' department: - _id: NiBa - _id: BeVi doi: 10.1101/cshperspect.a041447 external_id: pmid: - '37604585' intvolume: ' 15' issue: '11' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/cshperspect.a041447 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Cold Spring Harbor Perspectives in Biology publication_identifier: issn: - 1943-0264 publication_status: published publisher: Cold Spring Harbor Laboratory quality_controlled: '1' scopus_import: '1' status: public title: 'The impact of chromosomal rearrangements in speciation: From micro- to macroevolution' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2023' ... --- _id: '14743' abstract: - lang: eng text: Leader-based consensus algorithms are fast and efficient under normal conditions, but lack robustness to adverse conditions due to their reliance on timeouts for liveness. We present QuePaxa, the first protocol offering state-of-the-art normal-case efficiency without depending on timeouts. QuePaxa uses a novel randomized asynchronous consensus core to tolerate adverse conditions such as denial-of-service (DoS) attacks, while a one-round-trip fast path preserves the normal-case efficiency of Multi-Paxos or Raft. By allowing simultaneous proposers without destructive interference, and using short hedging delays instead of conservative timeouts to limit redundant effort, QuePaxa permits rapid recovery after leader failure without risking costly view changes due to false timeouts. By treating leader choice and hedging delay as a multi-armed-bandit optimization, QuePaxa achieves responsiveness to prevalent conditions, and can choose the best leader even if the current one has not failed. Experiments with a prototype confirm that QuePaxa achieves normal-case LAN and WAN performance of 584k and 250k cmd/sec in throughput, respectively, comparable to Multi-Paxos. Under conditions such as DoS attacks, misconfigurations, or slow leaders that severely impact existing protocols, we find that QuePaxa remains live with median latency under 380ms in WAN experiments. acknowledgement: The authors would like to thank Marcos K. Aguilera, Pierluca Borsò, Aleksey Charapko, Rachid Guerraoui, Jovan Komatovic, Derek Leung, Louis-Henri Merino, Shailesh Mishra, Haochen Pan, Rodrigo Rodrigues, Lewis Tseng, and Haoqian Zhang for their helpful feedback on early drafts of this paper. article_processing_charge: No author: - first_name: Pasindu full_name: Tennage, Pasindu last_name: Tennage - first_name: Cristina full_name: Basescu, Cristina last_name: Basescu - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Ewa full_name: Syta, Ewa last_name: Syta - first_name: Philipp full_name: Jovanovic, Philipp last_name: Jovanovic - first_name: Vero full_name: Estrada-Galinanes, Vero last_name: Estrada-Galinanes - first_name: Bryan full_name: Ford, Bryan last_name: Ford citation: ama: 'Tennage P, Basescu C, Kokoris Kogias E, et al. QuePaxa: Escaping the tyranny of timeouts in consensus. In: Proceedings of the 29th Symposium on Operating Systems Principles. Association for Computing Machinery; 2023:281-297. doi:10.1145/3600006.3613150' apa: 'Tennage, P., Basescu, C., Kokoris Kogias, E., Syta, E., Jovanovic, P., Estrada-Galinanes, V., & Ford, B. (2023). QuePaxa: Escaping the tyranny of timeouts in consensus. In Proceedings of the 29th Symposium on Operating Systems Principles (pp. 281–297). Koblenz, Germany: Association for Computing Machinery. https://doi.org/10.1145/3600006.3613150' chicago: 'Tennage, Pasindu, Cristina Basescu, Eleftherios Kokoris Kogias, Ewa Syta, Philipp Jovanovic, Vero Estrada-Galinanes, and Bryan Ford. “QuePaxa: Escaping the Tyranny of Timeouts in Consensus.” In Proceedings of the 29th Symposium on Operating Systems Principles, 281–97. Association for Computing Machinery, 2023. https://doi.org/10.1145/3600006.3613150.' ieee: 'P. Tennage et al., “QuePaxa: Escaping the tyranny of timeouts in consensus,” in Proceedings of the 29th Symposium on Operating Systems Principles, Koblenz, Germany, 2023, pp. 281–297.' ista: 'Tennage P, Basescu C, Kokoris Kogias E, Syta E, Jovanovic P, Estrada-Galinanes V, Ford B. 2023. QuePaxa: Escaping the tyranny of timeouts in consensus. Proceedings of the 29th Symposium on Operating Systems Principles. SOSP: Symposium on Operating Systems Principles, 281–297.' mla: 'Tennage, Pasindu, et al. “QuePaxa: Escaping the Tyranny of Timeouts in Consensus.” Proceedings of the 29th Symposium on Operating Systems Principles, Association for Computing Machinery, 2023, pp. 281–97, doi:10.1145/3600006.3613150.' short: P. Tennage, C. Basescu, E. Kokoris Kogias, E. Syta, P. Jovanovic, V. Estrada-Galinanes, B. Ford, in:, Proceedings of the 29th Symposium on Operating Systems Principles, Association for Computing Machinery, 2023, pp. 281–297. conference: end_date: 2023-10-26 location: Koblenz, Germany name: 'SOSP: Symposium on Operating Systems Principles' start_date: 2023-10-23 date_created: 2024-01-08T12:54:35Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-02-28T12:51:24Z day: '01' department: - _id: ElKo doi: 10.1145/3600006.3613150 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/3600006.3613150 month: '10' oa: 1 oa_version: Published Version page: 281-297 publication: Proceedings of the 29th Symposium on Operating Systems Principles publication_identifier: isbn: - '9798400702297' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'QuePaxa: Escaping the tyranny of timeouts in consensus' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14744' abstract: - lang: eng text: "Sharding distributed ledgers is a promising on-chain solution for scaling blockchains but lacks formal grounds, nurturing skepticism on whether such complex systems can scale blockchains securely. We fill this gap by introducing the first formal framework as well as a roadmap to robust sharding. In particular, we first define the properties sharded distributed ledgers should fulfill. We build upon and extend the Bitcoin backbone protocol by defining consistency and scalability. Consistency encompasses the need for atomic execution of cross-shard transactions to preserve safety, whereas scalability encapsulates the speedup a sharded system can gain in comparison to a non-sharded system.\r\nUsing our model, we explore the limitations of sharding. We show that a sharded ledger with n participants cannot scale under a fully adaptive adversary, but it can scale up to m shards where n=c'm log m, under an epoch-adaptive adversary; the constant c' encompasses the trade-off between security and scalability. This is possible only if the sharded ledgers create succinct proofs of the valid state updates at every epoch. We leverage our results to identify the sufficient components for robust sharding, which we incorporate in a protocol abstraction termed Divide & Scale. To demonstrate the power of our framework, we analyze the most prominent sharded blockchains (Elastico, Monoxide, OmniLedger, RapidChain) and pinpoint where they fail to meet the desired properties." acknowledgement: The work was partially supported by the Austrian Science Fund (FWF) through the project CoRaF (grant agreement 2020388). alternative_title: - LNCS article_processing_charge: No author: - first_name: Zeta full_name: Avarikioti, Zeta last_name: Avarikioti - first_name: Antoine full_name: Desjardins, Antoine id: 06d0c166-aec1-11ee-a7c0-b96e840a602b last_name: Desjardins - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Roger full_name: Wattenhofer, Roger last_name: Wattenhofer citation: ama: 'Avarikioti Z, Desjardins A, Kokoris Kogias E, Wattenhofer R. Divide & Scale: Formalization and roadmap to robust sharding. In: 30th International Colloquium on Structural Information and Communication Complexity. Vol 13892. Springer Nature; 2023:199-245. doi:10.1007/978-3-031-32733-9_10' apa: 'Avarikioti, Z., Desjardins, A., Kokoris Kogias, E., & Wattenhofer, R. (2023). Divide & Scale: Formalization and roadmap to robust sharding. In 30th International Colloquium on Structural Information and Communication Complexity (Vol. 13892, pp. 199–245). Alcalá de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_10' chicago: 'Avarikioti, Zeta, Antoine Desjardins, Eleftherios Kokoris Kogias, and Roger Wattenhofer. “Divide & Scale: Formalization and Roadmap to Robust Sharding.” In 30th International Colloquium on Structural Information and Communication Complexity, 13892:199–245. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_10.' ieee: 'Z. Avarikioti, A. Desjardins, E. Kokoris Kogias, and R. Wattenhofer, “Divide & Scale: Formalization and roadmap to robust sharding,” in 30th International Colloquium on Structural Information and Communication Complexity, Alcalá de Henares, Spain, 2023, vol. 13892, pp. 199–245.' ista: 'Avarikioti Z, Desjardins A, Kokoris Kogias E, Wattenhofer R. 2023. Divide & Scale: Formalization and roadmap to robust sharding. 30th International Colloquium on Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 13892, 199–245.' mla: 'Avarikioti, Zeta, et al. “Divide & Scale: Formalization and Roadmap to Robust Sharding.” 30th International Colloquium on Structural Information and Communication Complexity, vol. 13892, Springer Nature, 2023, pp. 199–245, doi:10.1007/978-3-031-32733-9_10.' short: Z. Avarikioti, A. Desjardins, E. Kokoris Kogias, R. Wattenhofer, in:, 30th International Colloquium on Structural Information and Communication Complexity, Springer Nature, 2023, pp. 199–245. conference: end_date: 2023-06-09 location: Alcalá de Henares, Spain name: 'SIROCCO: Structural Information and Communication Complexity' start_date: 2023-06-06 date_created: 2024-01-08T12:56:46Z date_published: 2023-06-01T00:00:00Z date_updated: 2024-01-09T07:40:57Z day: '01' department: - _id: ElKo doi: 10.1007/978-3-031-32733-9_10 intvolume: ' 13892' language: - iso: eng month: '06' oa_version: None page: 199-245 publication: 30th International Colloquium on Structural Information and Communication Complexity publication_identifier: eisbn: - '9783031327339' eissn: - 1611-3349 isbn: - '9783031327322' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Divide & Scale: Formalization and roadmap to robust sharding' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13892 year: '2023' ... --- _id: '14748' acknowledged_ssus: - _id: ScienComp acknowledgement: We thank the anonymous reviewers and the members of the Visual Computing Group at ISTA for their helpful comments. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing, and was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA). article_number: '5' article_processing_charge: No author: - first_name: Yi-Lu full_name: Chen, Yi-Lu id: 0b467602-dbcd-11ea-9d1d-ed480aa46b70 last_name: Chen - first_name: Mickaël full_name: Ly, Mickaël id: 6340d7f0-b48d-11eb-b10d-b7487e71d9f1 last_name: Ly - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: 'Chen Y-L, Ly M, Wojtan C. Unified treatment of contact, friction and shock-propagation in rigid body animation. In: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. Association for Computing Machinery; 2023. doi:10.1145/3606037.3606836' apa: 'Chen, Y.-L., Ly, M., & Wojtan, C. (2023). Unified treatment of contact, friction and shock-propagation in rigid body animation. In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3606037.3606836' chicago: Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Unified Treatment of Contact, Friction and Shock-Propagation in Rigid Body Animation.” In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. Association for Computing Machinery, 2023. https://doi.org/10.1145/3606037.3606836. ieee: Y.-L. Chen, M. Ly, and C. Wojtan, “Unified treatment of contact, friction and shock-propagation in rigid body animation,” in Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, Los Angeles, CA, United States, 2023. ista: 'Chen Y-L, Ly M, Wojtan C. 2023. Unified treatment of contact, friction and shock-propagation in rigid body animation. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. SCA: Symposium on Computer Animation, 5.' mla: Chen, Yi-Lu, et al. “Unified Treatment of Contact, Friction and Shock-Propagation in Rigid Body Animation.” Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, 5, Association for Computing Machinery, 2023, doi:10.1145/3606037.3606836. short: Y.-L. Chen, M. Ly, C. Wojtan, in:, Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, Association for Computing Machinery, 2023. conference: end_date: 2023-08-06 location: Los Angeles, CA, United States name: 'SCA: Symposium on Computer Animation' start_date: 2023-08-04 date_created: 2024-01-08T13:00:24Z date_published: 2023-08-01T00:00:00Z date_updated: 2024-02-28T12:51:40Z day: '01' department: - _id: ChWo doi: 10.1145/3606037.3606836 language: - iso: eng month: '08' oa_version: None project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation publication_identifier: isbn: - '9798400702686' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: Unified treatment of contact, friction and shock-propagation in rigid body animation type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14749' abstract: - lang: eng text: We unveil a powerful method for the stabilization of laser injection locking based on sensing variations in the output beam ellipticity of an optically seeded laser. The effect arises due to an interference between the seeding beam and the injected laser output. We demonstrate the method for a commercial semiconductor laser without the need for any internal changes to the readily operational injection locked laser system that was used. The method can also be used to increase the mode-hop free tuning range of lasers, and has the potential to fill a void in the low-noise laser industry. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Umang full_name: Mishra, Umang id: 4328fa4c-f128-11eb-9611-c107b0fe4d51 last_name: Mishra - first_name: Vyacheslav full_name: Li, Vyacheslav id: 3A4FAA92-F248-11E8-B48F-1D18A9856A87 last_name: Li - first_name: Sebastian full_name: Wald, Sebastian id: 133F200A-B015-11E9-AD41-0EDAE5697425 last_name: Wald - first_name: Sofya full_name: Agafonova, Sofya id: 09501ff6-dca7-11ea-a8ae-b3e0b9166e80 last_name: Agafonova orcid: 0000-0003-0582-2946 - first_name: Fritz R full_name: Diorico, Fritz R id: 2E054C4C-F248-11E8-B48F-1D18A9856A87 last_name: Diorico - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X citation: ama: Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. 2023;48(15):3973-3976. doi:10.1364/ol.495553 apa: Mishra, U., Li, V., Wald, S., Agafonova, S., Diorico, F. R., & Hosten, O. (2023). Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/ol.495553 chicago: Mishra, Umang, Vyacheslav Li, Sebastian Wald, Sofya Agafonova, Fritz R Diorico, and Onur Hosten. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” Optics Letters. Optica Publishing Group, 2023. https://doi.org/10.1364/ol.495553. ieee: U. Mishra, V. Li, S. Wald, S. Agafonova, F. R. Diorico, and O. Hosten, “Monitoring and active stabilization of laser injection locking using beam ellipticity,” Optics Letters, vol. 48, no. 15. Optica Publishing Group, pp. 3973–3976, 2023. ista: Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. 2023. Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. 48(15), 3973–3976. mla: Mishra, Umang, et al. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” Optics Letters, vol. 48, no. 15, Optica Publishing Group, 2023, pp. 3973–76, doi:10.1364/ol.495553. short: U. Mishra, V. Li, S. Wald, S. Agafonova, F.R. Diorico, O. Hosten, Optics Letters 48 (2023) 3973–3976. date_created: 2024-01-08T13:01:46Z date_published: 2023-07-21T00:00:00Z date_updated: 2024-01-09T08:09:32Z day: '21' department: - _id: OnHo doi: 10.1364/ol.495553 external_id: arxiv: - '2212.01266' intvolume: ' 48' issue: '15' keyword: - Atomic and Molecular Physics - and Optics language: - iso: eng month: '07' oa_version: Preprint page: 3973-3976 publication: Optics Letters publication_identifier: eissn: - 1539-4794 issn: - 0146-9592 publication_status: published publisher: Optica Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Monitoring and active stabilization of laser injection locking using beam ellipticity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2023' ...