--- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19548' abstract: - lang: eng text: "We consider the BCS energy gap „.T / (essentially given by „.T / \x19 \x81.T; p\x16/,\r\nthe BCS order parameter) at all temperatures 0 \x14 T \x14 Tc up to the critical one, Tc, and show\r\nthat, in the limit of weak coupling, the ratio „.T /=Tc is given by a universal function of the relative temperature T =Tc. On the one hand, this recovers a recent result by Langmann and Triola\r\n[Phys. Rev. B 108 (2023), no. 10, article no. 104503] on three-dimensional s-wave superconductors for temperatures bounded uniformly away from Tc. On the other hand, our result lifts these\r\nrestrictions, as we consider arbitrary spatial dimensions d 2 ¹1; 2; 3º, discuss superconductors\r\nwith non-zero angular momentum (primarily in two dimensions), and treat the perhaps physically most interesting (due to the occurrence of the superconducting phase transition) regime of\r\ntemperatures close to Tc.\r\n\r\n​\r\n ." acknowledgement: "We thank Andreas Deuchert, Christian Hainzl, Edwin Langmann, Marius Lemm, Robert Seiringer, and Jan Philip Solovej for helpful discussions,\r\nand Edwin Langmann and Robert Seiringer for valuable comments on an earlier version of the manuscript.\r\nFunding. Joscha Henheik gratefully acknowledges partial financial support by the\r\nERC Advanced Grant “RMTBeyond” No. 101020331. Asbjørn Bækgaard Lauritsen\r\ngratefully acknowledges partial financial support by the Austrian Science Fund (FWF)\r\nthrough grant DOI 10.55776/I6427 (as part of the SFB/TRR 352).\r\n" article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Sven Joscha full_name: Henheik, Sven Joscha id: 31d731d7-d235-11ea-ad11-b50331c8d7fb last_name: Henheik orcid: 0000-0003-1106-327X - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 citation: ama: Henheik SJ, Lauritsen AB. Universal behavior of the BCS energy gap. Journal of Spectral Theory. 2025;15(1):305–352. doi:10.4171/JST/540 apa: Henheik, S. J., & Lauritsen, A. B. (2025). Universal behavior of the BCS energy gap. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/540 chicago: Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “Universal Behavior of the BCS Energy Gap.” Journal of Spectral Theory. EMS Press, 2025. https://doi.org/10.4171/JST/540. ieee: S. J. Henheik and A. B. Lauritsen, “Universal behavior of the BCS energy gap,” Journal of Spectral Theory, vol. 15, no. 1. EMS Press, pp. 305–352, 2025. ista: Henheik SJ, Lauritsen AB. 2025. Universal behavior of the BCS energy gap. Journal of Spectral Theory. 15(1), 305–352. mla: Henheik, Sven Joscha, and Asbjørn Bækgaard Lauritsen. “Universal Behavior of the BCS Energy Gap.” Journal of Spectral Theory, vol. 15, no. 1, EMS Press, 2025, pp. 305–352, doi:10.4171/JST/540. short: S.J. Henheik, A.B. Lauritsen, Journal of Spectral Theory 15 (2025) 305–352. corr_author: '1' date_created: 2025-04-11T09:19:28Z date_published: 2025-01-09T00:00:00Z date_updated: 2026-07-29T13:18:17Z day: '09' ddc: - '500' department: - _id: LaEr - _id: RoSe doi: 10.4171/JST/540 ec_funded: 1 external_id: arxiv: - '2312.11310' isi: - '001438931600009' file: - access_level: open_access checksum: f49e06e8dba819f7ad52a202e287ebca content_type: application/pdf creator: cchlebak date_created: 2025-04-11T09:13:31Z date_updated: 2025-04-11T09:13:31Z file_id: '19549' file_name: Henheik_JSpectralTheory_2025.pdf file_size: 779158 relation: main_file success: 1 file_date_updated: 2025-04-11T09:13:31Z fulldoi: https://doi.org/10.4171/JST/540 has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '01' oa: 1 oa_version: Published Version page: 305–352 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta - _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b grant_number: I06427 name: Mathematical Challenges in BCS Theory of Superconductivity publication: Journal of Spectral Theory publication_identifier: eissn: - 1664-0403 publication_status: published publisher: EMS Press quality_controlled: '1' related_material: record: - id: '19540' relation: dissertation_contains status: public scopus_import: '1' status: public title: Universal behavior of the BCS energy gap 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: 15 year: '2025' ... --- OA_place: repository _id: '19552' abstract: - lang: eng text: "Particle creation terms in quantum Hamiltonians are usually ultraviolet\r\ndivergent and thus mathematically ill defined. A rather novel way of solving\r\nthis problem is based on imposing so-called interior-boundary conditions on the\r\nwave function. Previous papers showed that this approach works in the\r\nnon-relativistic regime, but particle creation is mostly relevant in the\r\nrelativistic case after all. In flat relativistic space-time (that is,\r\nneglecting gravity), the approach was previously found to work only for certain\r\nsomewhat artificial cases. Here, as a way of taking gravity into account, we\r\nconsider curved space-time, specifically the super-critical\r\nReissner-Nordstr\\\"om space-time, which features a naked timelike singularity.\r\nWe find that the interior-boundary approach works fully in this setting; in\r\nparticular, we prove rigorously the existence of well-defined, self-adjoint\r\nHamiltonians with particle creation at the singularity, based on\r\ninterior-boundary conditions. We also non-rigorously analyze the asymptotic\r\nbehavior of the Bohmian trajectories and construct the corresponding Bohm-Bell\r\nprocess of particle creation, motion, and annihilation. The upshot is that in\r\nquantum physics, a naked space-time singularity need not lead to a breakdown of\r\nphysical laws, but on the contrary allows for boundary conditions governing\r\nwhat comes out of the singularity and thereby removing the ultraviolet\r\ndivergence." acknowledgement: "JH gratefully acknowledges partial financial support by the ERC Advanced\r\nGrant “RMTBeyond” No. 101020331." article_processing_charge: No arxiv: 1 author: - first_name: Sven Joscha full_name: Henheik, Sven Joscha id: 31d731d7-d235-11ea-ad11-b50331c8d7fb last_name: Henheik orcid: 0000-0003-1106-327X - first_name: Bipul full_name: Poudyal, Bipul last_name: Poudyal - first_name: Roderich full_name: Tumulka, Roderich last_name: Tumulka citation: ama: Henheik SJ, Poudyal B, Tumulka R. How a space-time singularity helps remove the ultraviolet divergence problem. arXiv. doi:10.48550/arXiv.2409.00677 apa: Henheik, S. J., Poudyal, B., & Tumulka, R. (n.d.). How a space-time singularity helps remove the ultraviolet divergence problem. arXiv. https://doi.org/10.48550/arXiv.2409.00677 chicago: Henheik, Sven Joscha, Bipul Poudyal, and Roderich Tumulka. “How a Space-Time Singularity Helps Remove the Ultraviolet Divergence Problem.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2409.00677. ieee: S. J. Henheik, B. Poudyal, and R. Tumulka, “How a space-time singularity helps remove the ultraviolet divergence problem,” arXiv. . ista: Henheik SJ, Poudyal B, Tumulka R. How a space-time singularity helps remove the ultraviolet divergence problem. arXiv, 10.48550/arXiv.2409.00677. mla: Henheik, Sven Joscha, et al. “How a Space-Time Singularity Helps Remove the Ultraviolet Divergence Problem.” ArXiv, doi:10.48550/arXiv.2409.00677. short: S.J. Henheik, B. Poudyal, R. Tumulka, ArXiv (n.d.). corr_author: '1' date_created: 2025-04-11T12:07:25Z date_published: 2025-02-28T00:00:00Z date_updated: 2026-07-29T13:18:16Z day: '28' department: - _id: LaEr doi: 10.48550/arXiv.2409.00677 ec_funded: 1 external_id: arxiv: - '2409.00677' fulldoi: https://doi.org/10.48550/arXiv.2409.00677 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2409.00677 month: '02' oa: 1 oa_version: Preprint project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: arXiv publication_status: draft related_material: record: - id: '19540' relation: dissertation_contains status: public status: public title: How a space-time singularity helps remove the ultraviolet divergence problem type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '19785' abstract: - lang: eng text: 'We consider a family of totally asymmetric simple exclusion processes (TASEPs), consisting of particles on a lattice that require binding by a “token” in various physical configurations to advance over the lattice. Using a combination of theory and simulations, we address the following questions: (i) How does token binding kinetics affect the current-density relation on the lattice? (ii) How does this current-density relation depend on the scarcity of tokens? (iii) How do tokens propagate the effects of the locally imposed disorder (such as a slow site) over the entire lattice? (iv) How does a shared pool of tokens couple concurrent TASEPs running on multiple lattices? and (v) How do our results translate to TASEPs with open boundaries that exchange particles with the reservoir? Since real particle motion (including in biological systems that inspired the standard TASEP model, e.g., protein synthesis or movement of molecular motors) is often catalyzed, regulated, actuated, or otherwise mediated, the token-driven TASEP dynamics analyzed in this paper should allow for a better understanding of real systems and enable a closer match between TASEP theory and experimental observations.' acknowledgement: B.K. thanks Stefano Elefante, Simon Rella, and Michal Hledík for their help with the usage of the cluster. B.K. additionally thanks Călin Guet and his group for help and advice. We thank M. Hennessey-Wesen and Luca Ciandrini for constructive comments on the paper. We thank Ankita Gupta (Indian Institute of Technology) for spotting a typographical error in Eq. (50) in the preprint version of this paper. article_number: '054122' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Bor full_name: Kavcic, Bor id: 350F91D2-F248-11E8-B48F-1D18A9856A87 last_name: Kavcic orcid: 0000-0001-6041-254X - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion processes. Physical Review E. 2025;111(5). doi:10.1103/physreve.111.054122 apa: Kavcic, B., & Tkačik, G. (2025). Token-driven totally asymmetric simple exclusion processes. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.111.054122 chicago: Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Processes.” Physical Review E. American Physical Society, 2025. https://doi.org/10.1103/physreve.111.054122. ieee: B. Kavcic and G. Tkačik, “Token-driven totally asymmetric simple exclusion processes,” Physical Review E, vol. 111, no. 5. American Physical Society, 2025. ista: Kavcic B, Tkačik G. 2025. Token-driven totally asymmetric simple exclusion processes. Physical Review E. 111(5), 054122. mla: Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Processes.” Physical Review E, vol. 111, no. 5, 054122, American Physical Society, 2025, doi:10.1103/physreve.111.054122. short: B. Kavcic, G. Tkačik, Physical Review E 111 (2025). corr_author: '1' date_created: 2025-06-03T09:01:55Z date_published: 2025-05-19T00:00:00Z date_updated: 2026-08-04T08:34:22Z day: '19' ddc: - '570' department: - _id: GaTk doi: 10.1103/physreve.111.054122 external_id: isi: - '001496415600007' file: - access_level: open_access checksum: e8851ccd7cd0525c08c7308710413e74 content_type: application/pdf creator: dernst date_created: 2025-06-03T09:18:20Z date_updated: 2025-06-03T09:18:20Z file_id: '19787' file_name: 2025_PhysRevE_Kavcic.pdf file_size: 2766143 relation: main_file success: 1 file_date_updated: 2025-06-03T09:18:20Z fulldoi: https://doi.org/10.1103/physreve.111.054122 has_accepted_license: '1' intvolume: ' 111' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '19658' relation: research_data status: public - id: '10579' relation: earlier_version status: public scopus_import: '1' status: public title: Token-driven totally asymmetric simple exclusion processes 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 111 year: '2025' ... --- _id: '20641' abstract: - lang: eng text: 'Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions. ' acknowledged_ssus: - _id: NMR - _id: LifeSc acknowledgement: "We thank Nikolai R. Skrynnikov and Olga O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to Tobias Schubeis (Lyon) for advice with GB1 crystallization, and Rebecca Schmid for initial crystallization trials.\r\nWe thank Sebastian Falkner for assistance with constructing the structural model of the IgG:GB1 complex.\r\nThis research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank Petra Rovó and Margarita Valhondo Falcón for excellent support of the NMR facility.\r\nLea M. Becker is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01). Christophe Chipot acknowledges the European Research Council (grant project 101097272 ``MilliInMicro'') and the Métropole du Grand Nancy (grant project ``ARC''). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011." article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Becker LM, Schanda P. Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” 2025. doi:10.15479/AT-ISTA-20641 apa: Becker, L. M., & Schanda, P. (2025). Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20641 chicago: Becker, Lea Marie, and Paul Schanda. “Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20641. ieee: L. M. Becker and P. Schanda, “Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2025. ista: Becker LM, Schanda P. 2025. Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-20641. mla: Becker, Lea Marie, and Paul Schanda. Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20641. short: L.M. Becker, P. Schanda, (2025). contributor: - contributor_type: researcher first_name: 'Haohao ' last_name: Fu - contributor_type: researcher first_name: Benjamin id: 71cda2f3-e604-11ee-a1df-da10587eda3f last_name: Tatman - contributor_type: researcher first_name: Matthias last_name: Dreydoppel - contributor_type: researcher first_name: Anna id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471 last_name: Kapitonova - contributor_type: researcher first_name: Daniel id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E last_name: Balazs orcid: 0000-0001-7597-043X - contributor_type: researcher first_name: Ulrich last_name: Weininger - contributor_type: researcher first_name: Sylvain last_name: Engilberge - contributor_type: researcher first_name: Christophe last_name: Chipot corr_author: '1' date_created: 2025-11-13T09:29:58Z date_published: 2025-11-18T00:00:00Z date_updated: 2026-08-04T09:32:44Z day: '18' ddc: - '572' department: - _id: GradSch - _id: PaSc doi: 10.15479/AT-ISTA-20641 file: - access_level: open_access checksum: a73a0550c644957e7f62241e239d3a1d content_type: application/zip creator: lbecker date_created: 2025-11-13T09:38:35Z date_updated: 2026-02-17T10:16:57Z file_id: '20643' file_name: Research_Data.zip file_size: 1806589513 relation: main_file - access_level: open_access checksum: 7176b257f753c213a0460ee06f802363 content_type: application/pdf creator: lbecker date_created: 2025-11-17T11:54:17Z date_updated: 2026-02-17T10:16:57Z file_id: '20652' file_name: README.pdf file_size: 191376 relation: table_of_contents file_date_updated: 2026-02-17T10:16:57Z fulldoi: https://doi.org/10.15479/AT-ISTA-20641 has_accepted_license: '1' license: https://creativecommons.org/licenses/by-nc/4.0/ month: '11' oa: 1 oa_version: Published Version project: - _id: 7be609c4-9f16-11ee-852c-85015ce2b9b0 grant_number: '26777' name: Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches publisher: Institute of Science and Technology Austria related_material: record: - id: '21145' relation: later_version status: public - id: '22105' relation: used_in_publication status: public status: public title: Data for "Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes" tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18820' abstract: - lang: eng text: 'Feature selection is essential in the analysis of molecular systems and many other fields, but several uncertainties remain: What is the optimal number of features for a simplified, interpretable model that retains essential information? How should features with different units be aligned, and how should their relative importance be weighted? Here, we introduce the Differentiable Information Imbalance (DII), an automated method to rank information content between sets of features. Using distances in a ground truth feature space, DII identifies a low-dimensional subset of features that best preserves these relationships. Each feature is scaled by a weight, which is optimized by minimizing the DII through gradient descent. This allows simultaneously performing unit alignment and relative importance scaling, while preserving interpretability. DII can also produce sparse solutions and determine the optimal size of the reduced feature space. We demonstrate the usefulness of this approach on two benchmark molecular problems: (1) identifying collective variables that describe conformations of a biomolecule, and (2) selecting features for training a machine-learning force field. These results show the potential of DII in addressing feature selection challenges and optimizing dimensionality in various applications. The method is available in the Python library DADApy.' acknowledgement: The authors thank Dr. Matteo Carli for providing the CLN025 replica exchange MD trajectory and Matteo Allione for the fruitful discussions connected with the idea of the linear scaling estimator. This work was partially funded by NextGenerationEU through the Italian National Centre for HPC, Big Data, and Quantum Computing (Grant No. CN00000013 received by A.L.). A.L. also acknowledges financial support by the region Friuli Venezia Giulia (project F53C22001770002 received by A.L.). article_number: '270' article_processing_charge: Yes article_type: original author: - first_name: Romina full_name: Wild, Romina last_name: Wild - first_name: Felix full_name: Wodaczek, Felix id: 8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e last_name: Wodaczek orcid: 0009-0000-1457-795X - first_name: Vittorio full_name: Del Tatto, Vittorio last_name: Del Tatto - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Alessandro full_name: Laio, Alessandro last_name: Laio citation: ama: Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. Nature Communications. 2025;16. doi:10.1038/s41467-024-55449-7 apa: Wild, R., Wodaczek, F., Del Tatto, V., Cheng, B., & Laio, A. (2025). Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-55449-7 chicago: Wild, Romina, Felix Wodaczek, Vittorio Del Tatto, Bingqing Cheng, and Alessandro Laio. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-024-55449-7. ieee: R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, and A. Laio, “Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance,” Nature Communications, vol. 16. Springer Nature, 2025. ista: Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. 2025. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. Nature Communications. 16, 270. mla: Wild, Romina, et al. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” Nature Communications, vol. 16, 270, Springer Nature, 2025, doi:10.1038/s41467-024-55449-7. short: R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, A. Laio, Nature Communications 16 (2025). das_tickbox: '1' dataavailabilitystatement: 'The data generated by feature selection in this study have been deposited on OSF at the following URL: https://osf.io/swtg5. The processed molecular dynamics and H2O structure data are also available at OSF. The data files necessary for carrying out all analyses and source data are available at the same OSF URL. Source data are provided with this paper.' date_created: 2025-01-12T23:04:00Z date_published: 2025-01-02T00:00:00Z date_updated: 2026-08-07T09:43:12Z day: '02' ddc: - '570' department: - _id: AnSa - _id: BiCh doi: 10.1038/s41467-024-55449-7 external_id: isi: - '001389959100009' pmid: - '39747013' file: - access_level: open_access checksum: b3d0f3568d9a87c494cf231a5324029a content_type: application/pdf creator: dernst date_created: 2025-01-14T06:59:25Z date_updated: 2025-01-14T06:59:25Z file_id: '18846' file_name: 2025_NatureComm_Wild.pdf file_size: 1216738 relation: main_file success: 1 file_date_updated: 2025-01-14T06:59:25Z fulldoi: https://doi.org/10.1038/s41467-024-55449-7 has_accepted_license: '1' intvolume: ' 16' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: no title: Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 16 year: '2025' ... --- OA_place: repository OA_type: green _id: '20926' abstract: - lang: eng text: Most current machine learning interatomic potentials (MLIPs) rely on short-range approximations, without explicit treatment of long-range electrostatics. To address this, we recently developed the Latent Ewald Summation (LES) method, which infers electrostatic interactions, polarization, and Born effective charges (BECs), just by learning from energy and force training data. Here, we present LES as a standalone library, compatible with any short-range MLIP, and demonstrate its integration with methods such as MACE, NequIP, Allegro, CACE, CHGNet, and UMA. We benchmark LES-enhanced models on distinct systems, including bulk water, polar dipeptides, and gold dimer adsorption on defective substrates, and show that LES not only captures correct electrostatics but also improves accuracy. Additionally, we scale LES to large and chemically diverse data by training MACELES-OFF on the SPICE set containing molecules and clusters, making a universal MLIP with electrostatics for organic systems, including biomolecules. MACELES-OFF is more accurate than its short-range counterpart (MACE-OFF) trained on the same data set, predicts dipoles and BECs reliably, and has better descriptions of bulk liquids. By enabling efficient long-range electrostatics without directly training on electrical properties, LES paves the way for electrostatic foundation MLIPs. acknowledgement: Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Number R35GM159986. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. D.K. and B.C. acknowledge funding from Toyota Research Institute Synthesis Advanced Research Challenge. T.J.I., D.S.K. and P.Z. acknowledge funding from BIDMaP Postdoctoral Fellowship. T.J.I. used resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy Office of Science User Facility using NERSC award DOEERCAP0031751 ′GenAI@NERSC’. The authors thank Bowen Deng for valuable discussions on MatGL implementation, and thank Gabor Csanyi for stimulating discussions. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Dongjin full_name: Kim, Dongjin last_name: Kim - first_name: Xiaoyu full_name: Wang, Xiaoyu id: 8dff9c62-32b0-11ee-9fa8-fc73025e10f3 last_name: Wang - first_name: Santiago full_name: Vargas, Santiago last_name: Vargas - first_name: Peichen full_name: Zhong, Peichen last_name: Zhong - first_name: Daniel S. full_name: King, Daniel S. last_name: King - first_name: Theo Jaffrelot full_name: Inizan, Theo Jaffrelot last_name: Inizan - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Kim D, Wang X, Vargas S, et al. A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. 2025;21(24):12709-12724. doi:10.1021/acs.jctc.5c01400 apa: Kim, D., Wang, X., Vargas, S., Zhong, P., King, D. S., Inizan, T. J., & Cheng, B. (2025). A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01400 chicago: Kim, Dongjin, Xiaoyu Wang, Santiago Vargas, Peichen Zhong, Daniel S. King, Theo Jaffrelot Inizan, and Bingqing Cheng. “A Universal Augmentation Framework for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” Journal of Chemical Theory and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01400. ieee: D. Kim et al., “A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials,” Journal of Chemical Theory and Computation, vol. 21, no. 24. American Chemical Society, pp. 12709–12724, 2025. ista: Kim D, Wang X, Vargas S, Zhong P, King DS, Inizan TJ, Cheng B. 2025. A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. 21(24), 12709–12724. mla: Kim, Dongjin, et al. “A Universal Augmentation Framework for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” Journal of Chemical Theory and Computation, vol. 21, no. 24, American Chemical Society, 2025, pp. 12709–24, doi:10.1021/acs.jctc.5c01400. short: D. Kim, X. Wang, S. Vargas, P. Zhong, D.S. King, T.J. Inizan, B. Cheng, Journal of Chemical Theory and Computation 21 (2025) 12709–12724. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The training sets, training scripts, and trained potentials are available at https://github.com/ChengUCB/les_fit. The LES library is publicly available at https://github.com/ChengUCB/les. The CACE package with the LES implementation is available at https://github.com/BingqingCheng/cace. The MACE package with the LES implementation is available at https://github.com/ACEsuit/mace. The NequIP and Allegro LES extension package is available at https://github.com/ChengUCB/NequIP-LES. The MatGL package with the LES implementation is available at https://github.com/ChengUCB/matgl. The UMA package with the LES implementation is available at https://github.com/santi921/fairchem/tree/les_branch. date_created: 2026-01-04T23:01:33Z date_published: 2025-12-10T00:00:00Z date_updated: 2026-08-07T09:35:25Z day: '10' department: - _id: GradSch - _id: BiCh doi: 10.1021/acs.jctc.5c01400 external_id: arxiv: - '2507.14302' pmid: - '41368735 ' fulldoi: https://doi.org/10.1021/acs.jctc.5c01400 intvolume: ' 21' issue: '24' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2507.14302 month: '12' oa: 1 oa_version: Preprint page: 12709-12724 pmid: 1 publication: Journal of Chemical Theory and Computation publication_identifier: eissn: - 1549-9626 issn: - 1549-9618 publication_status: published publisher: American Chemical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 21 year: '2025' ... --- OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20990' abstract: - lang: eng text: Modeling the response of material and chemical systems to electric fields remains a longstanding challenge. Machine learning interatomic potentials (MLIPs) offer an efficient and scalable alternative to quantum mechanical methods, but do not by themselves incorporate electrical response. Here, we show that polarization and Born effective charge (BEC) tensors can be directly extracted from long-range MLIPs within the Latent Ewald Summation (LES) framework, solely by learning from energy and force data. Using this approach, we predict the infrared spectra of bulk water under zero or finite external electric fields, ionic conductivities of high-pressure superionic ice, and the phase transition and hysteresis in ferroelectric PbTiO3 perovskite. This work thus extends the capability of MLIPs to predict electrical response –without training on charges or polarization or BECs– and enables accurate modeling of electric-field-driven processes in diverse systems at scale. acknowledgement: The authors thank for valuable discussions with Pinchen Xie, David Limmer, Jeff Neaton, and Greg Voth. The authors thank Sebastien Hamel for providing the DFT MD trajectories for superionic water, and help clarifying questions related to the pseudopotentials. The authors thank Federico Grasselli and Stefano Baroni for providing data and notebooks for computing the conductivity of a molten salt. This research used the Savio computational cluster resource provided by the Berkeley Research Computing program at the University of California, Berkeley (supported by the UC Berkeley Chancellor, Vice Chancellor for Research, and Chief Information Officer). D.S.K. and P.Z. acknowledge funding from the BIDMaP Postdoctoral Fellowship. article_number: '384' article_processing_charge: Yes article_type: original author: - first_name: Peichen full_name: Zhong, Peichen last_name: Zhong - first_name: Dongjin full_name: Kim, Dongjin last_name: Kim - first_name: Daniel S. full_name: King, Daniel S. last_name: King - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Zhong P, Kim D, King DS, Cheng B. Machine learning interatomic potential can infer electrical response. npj Computational Materials. 2025;11. doi:10.1038/s41524-025-01911-z apa: Zhong, P., Kim, D., King, D. S., & Cheng, B. (2025). Machine learning interatomic potential can infer electrical response. Npj Computational Materials. Springer Nature. https://doi.org/10.1038/s41524-025-01911-z chicago: Zhong, Peichen, Dongjin Kim, Daniel S. King, and Bingqing Cheng. “Machine Learning Interatomic Potential Can Infer Electrical Response.” Npj Computational Materials. Springer Nature, 2025. https://doi.org/10.1038/s41524-025-01911-z. ieee: P. Zhong, D. Kim, D. S. King, and B. Cheng, “Machine learning interatomic potential can infer electrical response,” npj Computational Materials, vol. 11. Springer Nature, 2025. ista: Zhong P, Kim D, King DS, Cheng B. 2025. Machine learning interatomic potential can infer electrical response. npj Computational Materials. 11, 384. mla: Zhong, Peichen, et al. “Machine Learning Interatomic Potential Can Infer Electrical Response.” Npj Computational Materials, vol. 11, 384, Springer Nature, 2025, doi:10.1038/s41524-025-01911-z. short: P. Zhong, D. Kim, D.S. King, B. Cheng, Npj Computational Materials 11 (2025). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The training sets, training scripts, BEC inference scripts, and trained CACE potentials are available at https://github.com/BingqingCheng/LES-BEC. date_created: 2026-01-15T12:17:07Z date_published: 2025-12-29T00:00:00Z date_updated: 2026-08-07T09:38:09Z day: '29' ddc: - '540' department: - _id: BiCh doi: 10.1038/s41524-025-01911-z file: - access_level: open_access checksum: cc999804ba3bfed809ae46c73869e4e3 content_type: application/pdf creator: dernst date_created: 2026-01-20T07:22:04Z date_updated: 2026-01-20T07:22:04Z file_id: '21005' file_name: 2025_npj_Zhong.pdf file_size: 2686255 relation: main_file success: 1 file_date_updated: 2026-01-20T07:22:04Z fulldoi: https://doi.org/10.1038/s41524-025-01911-z has_accepted_license: '1' intvolume: ' 11' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: npj Computational Materials publication_identifier: eissn: - 2057-3960 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: no title: Machine learning interatomic potential can infer electrical response 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 11 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20492' abstract: - lang: eng text: The glassy thermal conductivities observed in crystalline inorganic perovskites such as Cs3Bi2I6Cl3 are perplexing and lacking theoretical explanations. Here, we first experimentally measure its thermal transport behavior from 20 to 300 K, after synthesizing Cs3Bi2I6Cl3 single crystals. Using path-integral molecular dynamics simulations driven by machine learning potentials, we reveal that Cs3Bi2I6Cl3 has large lattice distortions at low temperatures, which may be related to the large atomic size mismatch. Employing the Wigner formulation of thermal transport, we reproduce theexperimental thermal conductivities based on lattice-distorted structures. This studythus provides a framework for predicting and understanding glassy thermal transportin materials with strong lattice disorder. acknowledged_ssus: - _id: ScienComp acknowledgement: Z.Z. acknowledges the European Union’s Horizon2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. We acknowledge the high-performance computing facilities offered by Institute of Science and Technology Austria and The University of Hong Kong. article_processing_charge: No article_type: original author: - first_name: Zezhu full_name: Zeng, Zezhu id: 54a2c730-803f-11ed-ab7e-95b29d2680e7 last_name: Zeng orcid: 0000-0001-5126-4928 - first_name: Zheyong full_name: Fan, Zheyong last_name: Fan - first_name: Michele full_name: Simoncelli, Michele last_name: Simoncelli - first_name: Chen full_name: Chen, Chen last_name: Chen - first_name: Ting full_name: Liang, Ting last_name: Liang - first_name: Yue full_name: Chen, Yue last_name: Chen - first_name: Geoff full_name: Thornton, Geoff last_name: Thornton - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Zeng Z, Fan Z, Simoncelli M, et al. Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3. Proceedings of the National Academy of Sciences. 2025;122(41):e2415664122. doi:10.1073/pnas.2415664122 apa: Zeng, Z., Fan, Z., Simoncelli, M., Chen, C., Liang, T., Chen, Y., … Cheng, B. (2025). Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2415664122 chicago: Zeng, Zezhu, Zheyong Fan, Michele Simoncelli, Chen Chen, Ting Liang, Yue Chen, Geoff Thornton, and Bingqing Cheng. “Lattice Distortion Leads to Glassy Thermal Transport in Crystalline Cs3Bi2I6Cl3.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2415664122. ieee: Z. Zeng et al., “Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3,” Proceedings of the National Academy of Sciences, vol. 122, no. 41. National Academy of Sciences, p. e2415664122, 2025. ista: Zeng Z, Fan Z, Simoncelli M, Chen C, Liang T, Chen Y, Thornton G, Cheng B. 2025. Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3. Proceedings of the National Academy of Sciences. 122(41), e2415664122. mla: Zeng, Zezhu, et al. “Lattice Distortion Leads to Glassy Thermal Transport in Crystalline Cs3Bi2I6Cl3.” Proceedings of the National Academy of Sciences, vol. 122, no. 41, National Academy of Sciences, 2025, p. e2415664122, doi:10.1073/pnas.2415664122. short: Z. Zeng, Z. Fan, M. Simoncelli, C. Chen, T. Liang, Y. Chen, G. Thornton, B. Cheng, Proceedings of the National Academy of Sciences 122 (2025) e2415664122. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: Primitive Data Types have been deposited in GitHub (Cs3Bi2I6Cl3_heat_conductivity) (https://github.com/ZengZezhu/Cs3Bi2I6Cl3_heat_conductivity) (74). date_created: 2025-10-19T22:01:31Z date_published: 2025-10-14T00:00:00Z date_updated: 2026-08-07T10:11:03Z day: '14' ddc: - '540' department: - _id: BiCh doi: 10.1073/pnas.2415664122 ec_funded: 1 external_id: isi: - '001600415200001' pmid: - '41052324' file: - access_level: open_access checksum: 3f9cd0d67ffe9110fb238407671584b7 content_type: application/pdf creator: dernst date_created: 2025-10-21T10:02:15Z date_updated: 2025-10-21T10:02:15Z file_id: '20513' file_name: 2025_PNAS_Zeng.pdf file_size: 12244843 relation: main_file success: 1 file_date_updated: 2025-10-21T10:02:15Z fulldoi: https://doi.org/10.1073/pnas.2415664122 has_accepted_license: '1' intvolume: ' 122' isi: 1 issue: '41' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: e2415664122 pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: software url: https://github.com/ZengZezhu/Cs3Bi2I6Cl3_heat_conductivity researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 122 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '20011' abstract: - lang: eng text: Heat transport in glasses over a wide temperature range is critical for applications in gate dielectrics and thermal insulators but remains poorly understood due to the challenges in modeling vibrational anharmonicity and configurational dynamics across the glass transition. Recent predictions show an unusual decrease in thermal conductivity (κ) with temperature in amorphous hafnia (a-HfO2), contrasting with the typical trend in glasses. Using molecular dynamics with a machine-learning-based neuroevolution potential, we compute κ of a-HfO2 from 50 K to 2000 K. At low temperatures, the Wigner transport equation captures both anharmonicity and quantum statistics. Above 1200 K, atomic diffusion invalidates the quasiparticle picture, and we resort to the Green–Kubo method to capture convective transport. We further extend the Wigner transport equation to supercooled a-HfO2, revealing the crucial role of low-frequency modes in facilitating heat transport. The computed κ, based on both Green–Kubo and Wigner transport theories, increases continuously with temperature up to 2000 K. acknowledged_ssus: - _id: ScienComp acknowledgement: We thank Ludovic Berthier for fruitful discussions and Ting Liang for providing the initial structures of a-SiO2. Z.Z. acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Programme, under Marie Skłodowska-Curie grant agreement No. 101034413. The authors also acknowledge the research computing facilities provided by HPC ISTA and ITS HKU. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Zezhu full_name: Zeng, Zezhu id: 54a2c730-803f-11ed-ab7e-95b29d2680e7 last_name: Zeng orcid: 0000-0001-5126-4928 - first_name: Xia full_name: Liang, Xia last_name: Liang - first_name: Zheyong full_name: Fan, Zheyong last_name: Fan - first_name: Yue full_name: Chen, Yue last_name: Chen - first_name: Michele full_name: Simoncelli, Michele last_name: Simoncelli - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Zeng Z, Liang X, Fan Z, Chen Y, Simoncelli M, Cheng B. Thermal transport of amorphous hafnia across the glass transition. ACS Materials Letters. 2025:2695-2701. doi:10.1021/acsmaterialslett.5c00263 apa: Zeng, Z., Liang, X., Fan, Z., Chen, Y., Simoncelli, M., & Cheng, B. (2025). Thermal transport of amorphous hafnia across the glass transition. ACS Materials Letters. American Chemical Society. https://doi.org/10.1021/acsmaterialslett.5c00263 chicago: Zeng, Zezhu, Xia Liang, Zheyong Fan, Yue Chen, Michele Simoncelli, and Bingqing Cheng. “Thermal Transport of Amorphous Hafnia across the Glass Transition.” ACS Materials Letters. American Chemical Society, 2025. https://doi.org/10.1021/acsmaterialslett.5c00263. ieee: Z. Zeng, X. Liang, Z. Fan, Y. Chen, M. Simoncelli, and B. Cheng, “Thermal transport of amorphous hafnia across the glass transition,” ACS Materials Letters. American Chemical Society, pp. 2695–2701, 2025. ista: Zeng Z, Liang X, Fan Z, Chen Y, Simoncelli M, Cheng B. 2025. Thermal transport of amorphous hafnia across the glass transition. ACS Materials Letters., 2695–2701. mla: Zeng, Zezhu, et al. “Thermal Transport of Amorphous Hafnia across the Glass Transition.” ACS Materials Letters, American Chemical Society, 2025, pp. 2695–701, doi:10.1021/acsmaterialslett.5c00263. short: Z. Zeng, X. Liang, Z. Fan, Y. Chen, M. Simoncelli, B. Cheng, ACS Materials Letters (2025) 2695–2701. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: All necessary source data files generated for this study are available in the GitHub repository https://github.com/ZengZezhu/heat-conductivity-a-HfO2. date_created: 2025-07-13T22:01:24Z date_published: 2025-06-30T00:00:00Z date_updated: 2026-08-07T10:06:48Z day: '30' ddc: - '530' department: - _id: BiCh doi: 10.1021/acsmaterialslett.5c00263 ec_funded: 1 external_id: isi: - '001520226300001' file: - access_level: open_access checksum: d61e63439ddeaef29e9a2ee0f65c4ec1 content_type: application/pdf creator: dernst date_created: 2025-12-30T09:13:06Z date_updated: 2025-12-30T09:13:06Z file_id: '20903' file_name: 2025_ACSMaterialsLetters_Zeng.pdf file_size: 2402059 relation: main_file success: 1 file_date_updated: 2025-12-30T09:13:06Z fulldoi: https://doi.org/10.1021/acsmaterialslett.5c00263 has_accepted_license: '1' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 2695-2701 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: ACS Materials Letters publication_identifier: eissn: - 2639-4979 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: link: - relation: software url: https://github.com/ZengZezhu/heat-conductivity-a-HfO2 researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Thermal transport of amorphous hafnia across the glass transition 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19495' abstract: - lang: eng text: Machine learning interatomic potentials (MLIPs) often neglect long-range interactions, such as electrostatic and dispersion forces. In this work, we introduce a straightforward and efficient method to account for long-range interactions by learning a hidden variable from local atomic descriptors and applying an Ewald summation to this variable. We demonstrate that in systems including charged and polar molecular dimers, bulk water, and water-vapor interface, standard short-ranged MLIPs can lead to unphysical predictions even when employing message passing. The long-range models effectively eliminate these artifacts, with only about twice the computational cost of short-range MLIPs. acknowledgement: B. C. thanks David Limmer for providing the water slab dataset, and Carolin Faller for the NaCl dataset. article_number: '80' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Cheng B. Latent Ewald summation for machine learning of long-range interactions. npj Computational Materials. 2025;11. doi:10.1038/s41524-025-01577-7 apa: Cheng, B. (2025). Latent Ewald summation for machine learning of long-range interactions. Npj Computational Materials. Springer Nature. https://doi.org/10.1038/s41524-025-01577-7 chicago: Cheng, Bingqing. “Latent Ewald Summation for Machine Learning of Long-Range Interactions.” Npj Computational Materials. Springer Nature, 2025. https://doi.org/10.1038/s41524-025-01577-7. ieee: B. Cheng, “Latent Ewald summation for machine learning of long-range interactions,” npj Computational Materials, vol. 11. Springer Nature, 2025. ista: Cheng B. 2025. Latent Ewald summation for machine learning of long-range interactions. npj Computational Materials. 11, 80. mla: Cheng, Bingqing. “Latent Ewald Summation for Machine Learning of Long-Range Interactions.” Npj Computational Materials, vol. 11, 80, Springer Nature, 2025, doi:10.1038/s41524-025-01577-7. short: B. Cheng, Npj Computational Materials 11 (2025). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The training scripts, trained CACE potentials, and MD input files are available at https://github.com/BingqingCheng/cace-lr-fit. date_created: 2025-04-06T22:01:32Z date_published: 2025-03-26T00:00:00Z date_updated: 2026-08-07T10:04:17Z day: '26' ddc: - '000' department: - _id: BiCh doi: 10.1038/s41524-025-01577-7 external_id: arxiv: - '2408.15165' isi: - '001453622900002' file: - access_level: open_access checksum: cc99b7407a12139d9b2d8457961935ae content_type: application/pdf creator: dernst date_created: 2025-04-08T09:34:58Z date_updated: 2025-04-08T09:34:58Z file_id: '19528' file_name: 2025_npjCompMaterials_Cheng.pdf file_size: 1608315 relation: main_file success: 1 file_date_updated: 2025-04-08T09:34:58Z fulldoi: https://doi.org/10.1038/s41524-025-01577-7 has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: npj Computational Materials publication_identifier: eissn: - 2057-3960 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: unclear scopus_import: '1' status: public supplementarymaterial: no title: Latent Ewald summation for machine learning of long-range interactions 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 11 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '20702' abstract: - lang: eng text: Qualitative and quantitative orbital properties such as bonding/antibonding character, localization, and orbital energies are critical to how chemists understand reactivity, catalysis, and excited-state behavior. Despite this, representations of orbitals in deep learning models have been very underdeveloped relative to representations of molecular geometries and Hamiltonians. Here, we apply state-of-the-art equivariant deep learning architectures to the task of assigning global labels to orbitals, namely energies characterizations, given the molecular coefficients from Hartree–Fock or density functional theory. The architecture we have developed, the Cartesian Equivariant Orbital Network (CEONET), shows how molecular orbital coefficients are readily featurized as equivariant node features common to all graph-based machine-learned potentials. We find that CEONET performs well at predicting difficult quantitative labels such as the orbital energy and orbital entropy. Furthermore, we find that the CEONET representation provides an intuitive latent space for differentiating orbital character for the qualitative assignment of e.g. bonding or antibonding character. In addition to providing a useful representation for further integrating deep learning with electronic structure theory, we expect CEONET to be useful for automatizing and interpreting the results of advanced electronic structure methods such as complete active space self-consistent field theory. In particular, the ability of CEONET to infer multireference character via the orbital entropy paves the way toward the machine-learned selection of active spaces. acknowledgement: This work is supported as part of the Catalyst Design for Decarbonization Center, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under award no. DE-SC0023383. We thank the Research Computing Center at the University of Chicago and for access to computational resources. Additionally, this research used the Savio computational cluster resource provided by the Berkeley Research Computing program at the University of California (UC), Berkeley (supported by the UC Berkeley Chancellor, Vice Chancellor for Research, and Chief Information Officer). Furthermore, we thank Matthew Hennefarth and Matt Hermes for useful discussions. article_number: e2510235122 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Daniel S. full_name: King, Daniel S. last_name: King - first_name: Daniel full_name: Grzenda, Daniel last_name: Grzenda - first_name: Ray full_name: Zhu, Ray last_name: Zhu - first_name: Nathaniel full_name: Hudson, Nathaniel last_name: Hudson - first_name: Ian full_name: Foster, Ian last_name: Foster - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Laura full_name: Gagliardi, Laura last_name: Gagliardi citation: ama: King DS, Grzenda D, Zhu R, et al. Cartesian equivariant representations for learning and understanding molecular orbitals. Proceedings of the National Academy of Sciences. 2025;122(48). doi:10.1073/pnas.2510235122 apa: King, D. S., Grzenda, D., Zhu, R., Hudson, N., Foster, I., Cheng, B., & Gagliardi, L. (2025). Cartesian equivariant representations for learning and understanding molecular orbitals. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2510235122 chicago: King, Daniel S., Daniel Grzenda, Ray Zhu, Nathaniel Hudson, Ian Foster, Bingqing Cheng, and Laura Gagliardi. “Cartesian Equivariant Representations for Learning and Understanding Molecular Orbitals.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2510235122. ieee: D. S. King et al., “Cartesian equivariant representations for learning and understanding molecular orbitals,” Proceedings of the National Academy of Sciences, vol. 122, no. 48. National Academy of Sciences, 2025. ista: King DS, Grzenda D, Zhu R, Hudson N, Foster I, Cheng B, Gagliardi L. 2025. Cartesian equivariant representations for learning and understanding molecular orbitals. Proceedings of the National Academy of Sciences. 122(48), e2510235122. mla: King, Daniel S., et al. “Cartesian Equivariant Representations for Learning and Understanding Molecular Orbitals.” Proceedings of the National Academy of Sciences, vol. 122, no. 48, e2510235122, National Academy of Sciences, 2025, doi:10.1073/pnas.2510235122. short: D.S. King, D. Grzenda, R. Zhu, N. Hudson, I. Foster, B. Cheng, L. Gagliardi, Proceedings of the National Academy of Sciences 122 (2025). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: Code has been deposited to https://github.com/GagliardiGroup/CEONet (83). Data has been deposited to https://doi.org/10.5281/zenodo.16934624 (84). date_created: 2025-11-30T23:02:06Z date_published: 2025-12-02T00:00:00Z date_updated: 2026-08-07T10:27:53Z day: '02' ddc: - '540' department: - _id: BiCh doi: 10.1073/pnas.2510235122 external_id: pmid: - '41269783' file: - access_level: open_access checksum: 58051539a884c7a97306fd3afdb539ac content_type: application/pdf creator: dernst date_created: 2025-12-01T08:41:32Z date_updated: 2025-12-01T08:41:32Z file_id: '20719' file_name: 2025_PNAS_King.pdf file_size: 27607870 relation: main_file success: 1 file_date_updated: 2025-12-01T08:41:32Z fulldoi: https://doi.org/10.1073/pnas.2510235122 has_accepted_license: '1' intvolume: ' 122' issue: '48' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: software url: 'https://github.com/GagliardiGroup/CEONet ' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Cartesian equivariant representations for learning and understanding molecular orbitals 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 122 year: '2025' ... --- OA_type: closed access _id: '20704' abstract: - lang: eng text: Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In this work, we introduce a discrete flow matching model, tailored for systems with discrete phase-space coordinates (e.g., the Ising model or a multicomponent system on a lattice). This approach enables a single model to sample free energy surfaces over a wide temperature range with minimal training overhead, and the model generation is scalable to larger lattice sizes than those in the training set. We demonstrate our approach on the 2D Ising model, showing efficient and reliable free energy sampling. These results highlight the potential of flow matching for low-cost, scalable free energy sampling in discrete systems and suggest promising extensions to alchemical degrees of freedom in crystalline materials. The codebase developed for this work is openly available at https://github.com/tuoping/alchemicalFES. acknowledged_ssus: - _id: ScienComp acknowledgement: P.T. acknowledges funding from FFG MAGNIFICO and the BIDMaP Postdoctoral Fellowship. Z.Z. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. The authors acknowledge the research computing facilities provided by the Institute of Science and Technology Austria (ISTA), and resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy Office of Science User Facility using NERSC award DOEERCAP0031751 ’GenAI@NERSC’. P.T. acknowledges valued discussions with Dr. Daniel King, Dr. Lei Wang, and Dr. Fuzhi Dai. article_processing_charge: No article_type: original author: - first_name: Ping full_name: Tuo, Ping id: 6e5644c0-c180-11ed-a2da-facc4c9f4f09 last_name: Tuo - first_name: Zezhu full_name: Zeng, Zezhu id: 54a2c730-803f-11ed-ab7e-95b29d2680e7 last_name: Zeng orcid: 0000-0001-5126-4928 - first_name: Jiale full_name: Chen, Jiale id: 4d0a9064-1ff6-11ee-9fa6-ec046c604785 last_name: Chen orcid: 0000-0001-5337-5875 - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Tuo P, Zeng Z, Chen J, Cheng B. Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. 2025;21(22):11427-11435. doi:10.1021/acs.jctc.5c01248 apa: Tuo, P., Zeng, Z., Chen, J., & Cheng, B. (2025). Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01248 chicago: Tuo, Ping, Zezhu Zeng, Jiale Chen, and Bingqing Cheng. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” Journal of Chemical Theory and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01248. ieee: P. Tuo, Z. Zeng, J. Chen, and B. Cheng, “Scalable multitemperature free energy sampling of classical Ising spin states,” Journal of Chemical Theory and Computation, vol. 21, no. 22. American Chemical Society, pp. 11427–11435, 2025. ista: Tuo P, Zeng Z, Chen J, Cheng B. 2025. Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. 21(22), 11427–11435. mla: Tuo, Ping, et al. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” Journal of Chemical Theory and Computation, vol. 21, no. 22, American Chemical Society, 2025, pp. 11427–35, doi:10.1021/acs.jctc.5c01248. short: P. Tuo, Z. Zeng, J. Chen, B. Cheng, Journal of Chemical Theory and Computation 21 (2025) 11427–11435. corr_author: '1' das_tickbox: '0' date_created: 2025-11-30T23:02:06Z date_published: 2025-10-31T00:00:00Z date_updated: 2026-08-07T10:29:06Z day: '31' department: - _id: BiCh - _id: DaAl doi: 10.1021/acs.jctc.5c01248 ec_funded: 1 external_id: isi: - '001605927900001' pmid: - '41172130' fulldoi: https://doi.org/10.1021/acs.jctc.5c01248 intvolume: ' 21' isi: 1 issue: '22' language: - iso: eng month: '10' oa_version: None page: 11427-11435 pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Journal of Chemical Theory and Computation publication_identifier: eissn: - 1549-9626 issn: - 1549-9618 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: link: - relation: software url: https://github.com/tuoping/alchemicalFES researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Scalable multitemperature free energy sampling of classical Ising spin states type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 21 year: '2025' ... --- APC_amount: 3948 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '19593' abstract: - lang: eng text: Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, our knowledge about the safe usage of anti-inflammatory drugs during pregnancy is still limited. While human induced pluripotent stem cells (hIPSC)-derived brain organoid models have started to explore functional consequences upon viral stimulation, these models commonly lack microglia, which are susceptible to and promote inflammation. Furthermore, microglia are actively involved in neuronal development. Here, we generate hIPSC-derived microglia precursor cells and assemble them into retinal organoids. Once the outer plexiform layer forms, these hIPSC-derived microglia (iMG) fully integrate into the retinal organoids. Since the ganglion cell survival declines by this time in 3D-retinal organoids, we adapted the model into 2D and identify that the improved ganglion cell number significantly decreases only with iMG presence. In parallel, we applied the immunostimulant POLY(I:C) to mimic a fetal viral infection. While POLY(I:C) exposure alters the iMG phenotype, it does not hinder their interaction with ganglion cells. Furthermore, iMG significantly enhance the supernatant’s inflammatory secretome and increase retinal cell proliferation. Simultaneous exposure with the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated changes of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG, ibuprofen rescues this effect only if iMG are present. Mechanistically, ibuprofen targets the enzymes cyclooxygenase 1 and 2 (COX1/PTGS1 and COX2/PTGS2) simultaneously, from which iMG mainly express COX1. Selective COX1 blockage fails to restore the calcium peak amplitude upon POLY(I:C) stimulation, suggesting ibuprofen’s beneficial effect depends on the presence and interplay of COX1 and COX2. These findings underscore the importance of microglia in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development. acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: We thank the scientific service units at ISTA, specifically the Lab Support Facility (LSF), the Molecular Biology Services/Virus Services Team, specifically Flavia Gama Gomes Leite and Mark Andrew Smyth, for the virus production, and the Imaging and Optics Facility (IOF). We thank all members of the Siegert group and Marco Benevento for their constant feedback on the project and comments on the manuscript. A special thanks to Rouven Schulz for input on statistical analysis and sharing R-scripts, Gloria Colombo for the introduction to cell sorting, Negar Vehdani and Florianne Schoot Uiterkamp for their support in cell culture. This research was supported by the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.). article_number: '98' article_processing_charge: Yes article_type: original author: - first_name: Verena full_name: Hübschmann, Verena id: 32B7C918-F248-11E8-B48F-1D18A9856A87 last_name: Hübschmann - first_name: Medina full_name: Korkut, Medina id: 4B51CE74-F248-11E8-B48F-1D18A9856A87 last_name: Korkut orcid: 0000-0003-4309-2251 - first_name: Alessandro full_name: Venturino, Alessandro id: 41CB84B2-F248-11E8-B48F-1D18A9856A87 last_name: Venturino orcid: 0000-0003-2356-9403 - first_name: Juan Pablo full_name: Maya-Arteaga, Juan Pablo id: c815d433-1f5d-11f0-a875-dad18b1e5924 last_name: Maya-Arteaga - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 citation: ama: Schmied V, Korkut M, Venturino A, Maya-Arteaga JP, Siegert S. Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. Journal of Neuroinflammation. 2025;22(1). doi:10.1186/s12974-025-03366-x apa: Schmied, V., Korkut, M., Venturino, A., Maya-Arteaga, J. P., & Siegert, S. (2025). Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. Journal of Neuroinflammation. Springer Nature. https://doi.org/10.1186/s12974-025-03366-x chicago: Schmied, Verena, Medina Korkut, Alessandro Venturino, Juan Pablo Maya-Arteaga, and Sandra Siegert. “Microglia Determine an Immune-Challenged Environment and Facilitate Ibuprofen Action in Human Retinal Organoids.” Journal of Neuroinflammation. Springer Nature, 2025. https://doi.org/10.1186/s12974-025-03366-x. ieee: V. Schmied, M. Korkut, A. Venturino, J. P. Maya-Arteaga, and S. Siegert, “Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids,” Journal of Neuroinflammation, vol. 22, no. 1. Springer Nature, 2025. ista: Schmied V, Korkut M, Venturino A, Maya-Arteaga JP, Siegert S. 2025. Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. Journal of Neuroinflammation. 22(1), 98. mla: Schmied, Verena, et al. “Microglia Determine an Immune-Challenged Environment and Facilitate Ibuprofen Action in Human Retinal Organoids.” Journal of Neuroinflammation, vol. 22, no. 1, 98, Springer Nature, 2025, doi:10.1186/s12974-025-03366-x. short: V. Schmied, M. Korkut, A. Venturino, J.P. Maya-Arteaga, S. Siegert, Journal of Neuroinflammation 22 (2025). corr_author: '1' date_created: 2025-04-20T22:01:28Z date_published: 2025-04-03T00:00:00Z date_updated: 2026-08-12T08:45:16Z day: '03' ddc: - '570' department: - _id: SaSi doi: 10.1186/s12974-025-03366-x external_id: isi: - '001459311800002' pmid: - '40181459' file: - access_level: open_access checksum: dcc355c21ab713e45fda5c61b5fa5299 content_type: application/pdf creator: dernst date_created: 2025-04-22T09:46:27Z date_updated: 2025-04-22T09:46:27Z file_id: '19607' file_name: 2025_JourNeuroinflammation_Schmied.pdf file_size: 4482167 relation: main_file success: 1 file_date_updated: 2025-04-22T09:46:27Z fulldoi: https://doi.org/10.1186/s12974-025-03366-x has_accepted_license: '1' intvolume: ' 22' isi: 1 issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 9B99D380-BA93-11EA-9121-9846C619BF3A grant_number: SC19-017 name: How human microglia shape developing neurons during health and inflammation - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Journal of Neuroinflammation publication_identifier: eissn: - 1742-2094 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/pink-skies/ record: - id: '20074' relation: dissertation_contains status: public scopus_import: '1' status: public title: Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids 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: 22 year: '2025' ... --- OA_place: publisher _id: '20074' abstract: - lang: eng text: "Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. \r\nIn chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. \r\nIn chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. \r\nIn summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Verena full_name: Hübschmann, Verena id: 32B7C918-F248-11E8-B48F-1D18A9856A87 last_name: Hübschmann citation: ama: Schmied V. Human microglia impact neuronal development in retinal organoids. 2025. doi:10.15479/AT-ISTA-20074 apa: Schmied, V. (2025). Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20074 chicago: Schmied, Verena. “Human Microglia Impact Neuronal Development in Retinal Organoids.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20074. ieee: V. Schmied, “Human microglia impact neuronal development in retinal organoids,” Institute of Science and Technology Austria, 2025. ista: Schmied V. 2025. Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria. mla: Schmied, Verena. Human Microglia Impact Neuronal Development in Retinal Organoids. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20074. short: V. Schmied, Human Microglia Impact Neuronal Development in Retinal Organoids, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-07-24T12:37:22Z date_published: 2025-07-24T00:00:00Z date_updated: 2026-08-12T08:45:16Z day: '24' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SaSi doi: 10.15479/AT-ISTA-20074 doi_confirm: '1' file: - access_level: closed checksum: d09f9984002353ad7442358394919bf3 content_type: application/x-zip-compressed creator: vhuebsch date_created: 2025-07-30T08:47:53Z date_updated: 2025-07-30T08:47:53Z file_id: '20086' file_name: PhD_Thesis_Schmied.zip file_size: 43566093 relation: source_file - access_level: open_access checksum: 4833690d7283c587f518ba98eeb2c946 content_type: application/pdf creator: vhuebsch date_created: 2025-07-30T08:47:46Z date_updated: 2025-07-30T09:29:09Z file_id: '20087' file_name: PhD_Thesis_Schmied.pdf file_size: 13120922 relation: main_file file_date_updated: 2025-07-30T09:29:09Z fulldoi: https://doi.org/10.15479/AT-ISTA-20074 has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '151' project: - _id: 9B99D380-BA93-11EA-9121-9846C619BF3A grant_number: SC19-017 name: How human microglia shape developing neurons during health and inflammation publication_identifier: isbn: - 978-3-99078-060-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11478' relation: part_of_dissertation status: public - id: '19593' relation: part_of_dissertation status: public status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: Human microglia impact neuronal development in retinal organoids 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: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: repository OA_type: green _id: '19372' abstract: - lang: eng text: We consider the confined Fröhlich polaron and establish an asymptotic series for the low-energy eigenvalues in negative powers of the coupling constant. The coefficients of the series are derived through a two-fold perturbation approach, involving expansions around the electron Pekar minimizer and the excitations of the quantum field. acknowledgement: M.B. gratefully acknowledges funding from the ERC Advanced Grant ERC-AdG CLaQS, grant agreement n. 83478. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Morris full_name: Brooks, Morris id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425 last_name: Brooks orcid: 0000-0002-6249-0928 - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas citation: ama: Brooks M, Mitrouskas DJ. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. 2025;6(1):281-325. doi:10.2140/pmp.2025.6.281 apa: Brooks, M., & Mitrouskas, D. J. (2025). Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2025.6.281 chicago: Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” Probability and Mathematical Physics. Mathematical Sciences Publishers, 2025. https://doi.org/10.2140/pmp.2025.6.281. ieee: M. Brooks and D. J. Mitrouskas, “Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling,” Probability and Mathematical Physics, vol. 6, no. 1. Mathematical Sciences Publishers, pp. 281–325, 2025. ista: Brooks M, Mitrouskas DJ. 2025. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. 6(1), 281–325. mla: Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” Probability and Mathematical Physics, vol. 6, no. 1, Mathematical Sciences Publishers, 2025, pp. 281–325, doi:10.2140/pmp.2025.6.281. short: M. Brooks, D.J. Mitrouskas, Probability and Mathematical Physics 6 (2025) 281–325. corr_author: '1' date_created: 2025-03-09T23:01:28Z date_published: 2025-02-23T00:00:00Z date_updated: 2026-08-12T08:44:53Z day: '23' department: - _id: RoSe doi: 10.2140/pmp.2025.6.281 external_id: arxiv: - '2306.16373' fulldoi: https://doi.org/10.2140/pmp.2025.6.281 intvolume: ' 6' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2306.16373 month: '02' oa: 1 oa_version: Preprint page: 281-325 publication: Probability and Mathematical Physics publication_identifier: eissn: - 2690-1005 issn: - 2690-0998 publication_status: published publisher: Mathematical Sciences Publishers quality_controlled: '1' scopus_import: '1' status: public title: Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20342' abstract: - lang: eng text: Safety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata. acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22. N. Mazzocchi was affiliated with ISTA when this work was submitted for publication. article_number: '13149' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Nicolas Adrien full_name: Mazzocchi, Nicolas Adrien id: b26baa86-3308-11ec-87b0-8990f34baa85 last_name: Mazzocchi - first_name: Naci E full_name: Sarac, Naci E id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425 last_name: Sarac citation: ama: Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 2025;21(2). doi:10.46298/lmcs-21(2:2)2025 apa: Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2025). Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. EPI Sciences. https://doi.org/10.46298/lmcs-21(2:2)2025 chicago: Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Properties and Automata.” Logical Methods in Computer Science. EPI Sciences, 2025. https://doi.org/10.46298/lmcs-21(2:2)2025. ieee: U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative properties and automata,” Logical Methods in Computer Science, vol. 21, no. 2. EPI Sciences, 2025. ista: Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2025. Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 21(2), 13149. mla: Boker, Udi, et al. “Safety and Liveness of Quantitative Properties and Automata.” Logical Methods in Computer Science, vol. 21, no. 2, 13149, EPI Sciences, 2025, doi:10.46298/lmcs-21(2:2)2025. short: U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, Logical Methods in Computer Science 21 (2025). corr_author: '1' date_created: 2025-09-11T12:17:52Z date_published: 2025-04-08T00:00:00Z date_updated: 2026-08-12T08:46:05Z day: '08' ddc: - '000' department: - _id: GradSch - _id: ToHe doi: 10.46298/lmcs-21(2:2)2025 ec_funded: 1 external_id: arxiv: - '2307.06016' isi: - '001468887900001' file: - access_level: open_access checksum: 0b4d477bd981379724c35a4de2c176e5 content_type: application/pdf creator: esarac date_created: 2025-09-11T12:17:12Z date_updated: 2025-09-11T12:17:12Z file_id: '20343' file_name: 2307.06016.pdf file_size: 709584 relation: main_file success: 1 file_date_updated: 2025-09-11T12:17:12Z fulldoi: https://doi.org/10.46298/lmcs-21(2:2)2025 has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '2' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: Logical Methods in Computer Science publication_identifier: eissn: - 1860-5974 publication_status: published publisher: EPI Sciences quality_controlled: '1' related_material: record: - id: '13221' relation: earlier_version status: public - id: '20147' relation: dissertation_contains status: public scopus_import: '1' status: public title: Safety and liveness of quantitative properties and automata 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: 21 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '19701' abstract: - lang: eng text: 'Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components.' acknowledgement: G.T. acknowledges the support of the Human Frontiers Science Program (HFSP), the Austrian Science Fund (FWF 10.55776/P34015, 10.55776/P28844), and the European Research Council Synergy DYNATRANS (ERC-2023-SyG 101118866) grant. P.R.t.W. performed his work at the research institute AMOLF and acknowledges support from the Dutch Research Council (NWO) and funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 885065). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Pieter Rein Ten full_name: Wolde, Pieter Rein Ten last_name: Wolde citation: ama: Tkačik G, Wolde PRT. Information processing in biochemical networks. Annual Review of Biophysics. 2025;54:249-274. doi:10.1146/annurev-biophys-060524-102720 apa: Tkačik, G., & Wolde, P. R. T. (2025). Information processing in biochemical networks. Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-060524-102720 chicago: Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” Annual Review of Biophysics. Annual Reviews, 2025. https://doi.org/10.1146/annurev-biophys-060524-102720. ieee: G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,” Annual Review of Biophysics, vol. 54. Annual Reviews, pp. 249–274, 2025. ista: Tkačik G, Wolde PRT. 2025. Information processing in biochemical networks. Annual Review of Biophysics. 54, 249–274. mla: Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” Annual Review of Biophysics, vol. 54, Annual Reviews, 2025, pp. 249–74, doi:10.1146/annurev-biophys-060524-102720. short: G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274. corr_author: '1' date_created: 2025-05-18T22:02:50Z date_published: 2025-05-01T00:00:00Z date_updated: 2026-08-12T09:25:42Z day: '01' ddc: - '570' department: - _id: GaTk doi: 10.1146/annurev-biophys-060524-102720 external_id: isi: - '001488641500013' pmid: - '39929539' file: - access_level: open_access checksum: 9ab623b2bc45dcd5fdd2c9577ea8ae9f content_type: application/pdf creator: dernst date_created: 2025-05-19T07:55:51Z date_updated: 2025-05-19T07:55:51Z file_id: '19710' file_name: 2025_AnnualReviewBiophysics_Tkacik.pdf file_size: 317925 relation: main_file success: 1 file_date_updated: 2025-05-19T07:55:51Z fulldoi: https://doi.org/10.1146/annurev-biophys-060524-102720 has_accepted_license: '1' intvolume: ' 54' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 249-274 pmid: 1 project: - _id: 626c45b5-2b32-11ec-9570-e509828c1ba6 grant_number: P34015 name: Efficient coding with biophysical realism - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation - _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9 grant_number: '101118866' name: 'Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos' - _id: 255008E4-B435-11E9-9278-68D0E5697425 grant_number: RGP0065/2012 name: Information processing and computation in fish groups publication: Annual Review of Biophysics publication_identifier: eissn: - 1936-1238 publication_status: published publisher: Annual Reviews quality_controlled: '1' scopus_import: '1' status: public title: Information processing in biochemical networks 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: 54 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20048' abstract: - lang: eng text: 'During embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations.' acknowledgement: We thank all the Heisenberg lab members for discussions and comments on the manuscript, and the Bioimaging and Life Science facilities of ISTA for support with microscopy and fish maintenance, respectively. This study was funded by a Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowship and a Japan Science and Technology Agency PRESTO grant (JPMJPR214B) to Y.M. Open Access funding provided by the Japan Science and Technology Agency. Deposited in PMC for immediate release. article_number: dev204261 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Yuuta full_name: Moriyama, Yuuta id: addc9b8c-67a0-11f0-b374-a2e094825470 last_name: Moriyama orcid: 0000-0002-2853-8051 - first_name: Toshiyuki full_name: Mitsui, Toshiyuki last_name: Mitsui - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Moriyama Y, Mitsui T, Heisenberg C-PJ. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 2025;152(12). doi:10.1242/dev.204261 apa: Moriyama, Y., Mitsui, T., & Heisenberg, C.-P. J. (2025). Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.204261 chicago: Moriyama, Yuuta, Toshiyuki Mitsui, and Carl-Philipp J Heisenberg. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” Development. Company of Biologists, 2025. https://doi.org/10.1242/dev.204261. ieee: Y. Moriyama, T. Mitsui, and C.-P. J. Heisenberg, “Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation,” Development, vol. 152, no. 12. Company of Biologists, 2025. ista: Moriyama Y, Mitsui T, Heisenberg C-PJ. 2025. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 152(12), dev204261. mla: Moriyama, Yuuta, et al. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” Development, vol. 152, no. 12, dev204261, Company of Biologists, 2025, doi:10.1242/dev.204261. short: Y. Moriyama, T. Mitsui, C.-P.J. Heisenberg, Development 152 (2025). corr_author: '1' date_created: 2025-07-21T08:10:32Z date_published: 2025-06-27T00:00:00Z date_updated: 2026-08-12T10:01:31Z day: '27' ddc: - '570' department: - _id: CaHe doi: 10.1242/dev.204261 external_id: isi: - '001525252300001' pmid: - '40576478' file: - access_level: open_access checksum: 808d8aa28df79d23fb661838d1fdc1be content_type: application/pdf creator: dernst date_created: 2025-07-23T08:43:01Z date_updated: 2025-07-23T08:43:01Z file_id: '20070' file_name: 2025_Development_Moriyama.pdf file_size: 25935563 relation: main_file success: 1 file_date_updated: 2025-07-23T08:43:01Z fulldoi: https://doi.org/10.1242/dev.204261 has_accepted_license: '1' intvolume: ' 152' isi: 1 issue: '12' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Development publication_identifier: eissn: - 1477-9129 issn: - 0950-1991 publication_status: published publisher: Company of Biologists quality_controlled: '1' scopus_import: '1' status: public title: Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation 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: 152 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21343' abstract: - lang: eng text: "The large sieve is used to estimate the density of quadratic polynomials Q ∈ Z[x],\r\nsuch that there exists an odd degree polynomial defined over Z which has resultant ±1 with Q.\r\nGiven a monic polynomial R ∈ Z[x] of odd degree, this is used to show that for almost all\r\nquadratic polynomials Q ∈ Z[x], there exists a prime p such that Q and R share a common\r\nroot in Fp. Using recent work of Landesman, an application to the average size of the odd part\r\nof the class group of quadratic number fields is also given" - lang: fre text: ' Le grand crible est utilisé pour estimer la densité des polynômes quadratiques Q ∈ Z[x] tels qu’il existe un polynôme de degré impair défini sur Z dont le résultant avec Q est égal à ±1. Étant donné un polynôme unitaire R ∈ Z[x] de degré impair, on s’en sert pour montrer que, pour presque tous les polynômes quadratiques Q ∈ Z[x], il existe un nombre premier p tel que Q et R aient une racine commune dans Fp. En utilisant des travaux récents de Landesman, on obtient également une application concernant la taille moyenne de la partie impaire du groupe de classe des corps quadratiques.' acknowledgement: While working on this paper, the first author was supported by a FWF grant (DOI 10.55776/P36278). article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Yik Tung full_name: Chan, Yik Tung id: c4c0afc8-9262-11ed-9231-d8b0bc743af1 last_name: Chan orcid: 0000-0001-8467-4106 citation: ama: Browning TD, Chan S. Solubility of a resultant equation and applications. Journal de l’Ecole Polytechnique - Mathematiques. 2025;12:1677-1691. doi:10.5802/jep.320 apa: Browning, T. D., & Chan, S. (2025). Solubility of a resultant equation and applications. Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique. https://doi.org/10.5802/jep.320 chicago: Browning, Timothy D, and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique, 2025. https://doi.org/10.5802/jep.320. ieee: T. D. Browning and S. Chan, “Solubility of a resultant equation and applications,” Journal de l’Ecole Polytechnique - Mathematiques, vol. 12. Ecole Polytechnique, pp. 1677–1691, 2025. ista: Browning TD, Chan S. 2025. Solubility of a resultant equation and applications. Journal de l’Ecole Polytechnique - Mathematiques. 12, 1677–1691. mla: Browning, Timothy D., and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” Journal de l’Ecole Polytechnique - Mathematiques, vol. 12, Ecole Polytechnique, 2025, pp. 1677–91, doi:10.5802/jep.320. short: T.D. Browning, S. Chan, Journal de l’Ecole Polytechnique - Mathematiques 12 (2025) 1677–1691. corr_author: '1' das_tickbox: '0' date_created: 2026-02-22T23:01:36Z date_published: 2025-10-21T00:00:00Z date_updated: 2026-08-12T11:17:50Z day: '21' ddc: - '510' department: - _id: TiBr doi: 10.5802/jep.320 external_id: arxiv: - '2411.09264' file: - access_level: open_access checksum: 828577ea48ac6109d3e9dd1aeddd45c4 content_type: application/pdf creator: dernst date_created: 2026-02-24T07:56:34Z date_updated: 2026-02-24T07:56:34Z file_id: '21356' file_name: 2025_JEP_Browning.pdf file_size: 1003689 relation: main_file success: 1 file_date_updated: 2026-02-24T07:56:34Z fulldoi: https://doi.org/10.5802/jep.320 has_accepted_license: '1' intvolume: ' 12' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1677-1691 project: - _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3 grant_number: P36278 name: Rational curves via function field analytic number theory publication: Journal de l'Ecole Polytechnique - Mathematiques publication_identifier: eissn: - 2270-518X issn: - 2429-7100 publication_status: published publisher: Ecole Polytechnique quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Solubility of a resultant equation and applications 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: 12 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20249' abstract: - lang: eng text: We develop a heuristic for the density of integer points on affine cubic surfaces. Our heuristic applies to smooth surfaces defined by cubic polynomials that are log K3, but it can also be adjusted to handle singular cubic surfaces. We compare our heuristic to Heath-Brown’s prediction for sums of three cubes, as well as to asymptotic formulae in the literature around Zagier’s work on the Markoff cubic surface, and work of Baragar and Umeda on further surfaces of Markoff-type. We also test our heuristic against numerical data for several families of cubic surfaces. acknowledgement: "The authors owe a debt of thanks to Yonatan Harpaz for asking about circle method heuristics for log K3 surfaces. His contribution to the resulting discussion is gratefully acknowledged. Thanks are also due to Andrew Sutherland for help with numerical data for the equation x^3 + y^3 + z^3 = 1, together with Alex Gamburd, Amit Ghosh, Peter Sarnak and Matteo Verzobio for their interest in this paper. Special thanks are due to Victor Wang for helpful conversations about the circle method heuristics and to the anonymous referee for several useful comments. While working on this paper, the authors were supported by a FWF grant (DOI 10.55776/P32428), and the first author was supported by a further FWF grant (DOI 10.55776/P36278) and a grant from the School of Mathematics at the Institute for Advanced Study in Princeton.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria)." article_number: '81' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Florian Alexander full_name: Wilsch, Florian Alexander id: 560601DA-8D36-11E9-A136-7AC1E5697425 last_name: Wilsch orcid: 0000-0001-7302-8256 citation: ama: 'Browning TD, Wilsch FA. Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. 2025;31(4). doi:10.1007/s00029-025-01074-1' apa: 'Browning, T. D., & Wilsch, F. A. (2025). Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. Springer Nature. https://doi.org/10.1007/s00029-025-01074-1' chicago: 'Browning, Timothy D, and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” Selecta Mathematica New Series. Springer Nature, 2025. https://doi.org/10.1007/s00029-025-01074-1.' ieee: 'T. D. Browning and F. A. Wilsch, “Integral points on cubic surfaces: heuristics and numerics,” Selecta Mathematica New Series, vol. 31, no. 4. Springer Nature, 2025.' ista: 'Browning TD, Wilsch FA. 2025. Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. 31(4), 81.' mla: 'Browning, Timothy D., and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” Selecta Mathematica New Series, vol. 31, no. 4, 81, Springer Nature, 2025, doi:10.1007/s00029-025-01074-1.' short: T.D. Browning, F.A. Wilsch, Selecta Mathematica New Series 31 (2025). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The data used in Sections 6 and 9 is hosted on the Göttingen Research Online Data repository [https://doi.org/10.25625/4FLFH8]. The code used to determine the data in Sections 6.2, 9.1 and 9.2 is found on the second author’s github page. date_created: 2025-08-31T22:01:31Z date_published: 2025-09-01T00:00:00Z date_updated: 2026-08-12T12:15:32Z day: '01' ddc: - '500' department: - _id: TiBr doi: 10.1007/s00029-025-01074-1 external_id: arxiv: - '2407.16315' isi: - '001552779800001' file: - access_level: open_access checksum: 89352f1f7e8d2b367ae5f4e9bf9eb1f5 content_type: application/pdf creator: dernst date_created: 2025-09-03T06:44:44Z date_updated: 2025-09-03T06:44:44Z file_id: '20281' file_name: 2025_SelectaMathematica_Browning.pdf file_size: 2484757 relation: main_file success: 1 file_date_updated: 2025-09-03T06:44:44Z fulldoi: https://doi.org/10.1007/s00029-025-01074-1 has_accepted_license: '1' intvolume: ' 31' isi: 1 issue: '4' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 26AEDAB2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P32428 name: New frontiers of the Manin conjecture - _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3 grant_number: P36278 name: Rational curves via function field analytic number theory publication: Selecta Mathematica New Series publication_identifier: eissn: - 1420-9020 issn: - 1022-1824 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: software url: https://github.com/fwilsch/cubicpts record: - id: '22234' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: 'Integral points on cubic surfaces: heuristics and numerics' 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: 31 year: '2025' ...