[{"title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","department":[{"_id":"SiHi"}],"article_processing_charge":"No","author":[{"first_name":"Alfredo","full_name":"Llorca, Alfredo","last_name":"Llorca"},{"first_name":"Gabriele","full_name":"Ciceri, Gabriele","last_name":"Ciceri"},{"full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","last_name":"Beattie","first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wong","full_name":"Wong, Fong K.","first_name":"Fong K."},{"first_name":"Giovanni","full_name":"Diana, Giovanni","last_name":"Diana"},{"full_name":"Serafeimidou, Eleni","last_name":"Serafeimidou","first_name":"Eleni"},{"first_name":"Marian","full_name":"Fernández-Otero, Marian","last_name":"Fernández-Otero"},{"last_name":"Streicher","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"last_name":"Arnold","full_name":"Arnold, Sebastian J.","first_name":"Sebastian J."},{"first_name":"Martin","full_name":"Meyer, Martin","last_name":"Meyer"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Miguel","full_name":"Maravall, Miguel","last_name":"Maravall"},{"first_name":"Oscar","full_name":"Marín, Oscar","last_name":"Marín"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, 10.1101/494088.","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/494088.","ieee":"A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/494088"},"date_updated":"2021-01-12T08:20:00Z","status":"public","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416"}],"type":"preprint","_id":"8547","date_created":"2020-09-21T12:01:50Z","ec_funded":1,"date_published":"2018-12-13T00:00:00Z","doi":"10.1101/494088","language":[{"iso":"eng"}],"publication":"bioRxiv","day":"13","publication_status":"submitted","year":"2018","month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/494088"}],"oa":1,"publisher":"Cold Spring Harbor Laboratory","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","oa_version":"Preprint","abstract":[{"text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex.","lang":"eng"}]},{"oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","date_created":"2018-12-11T11:44:33Z","doi":"10.1007/978-3-319-95246-8_9","date_published":"2018-07-20T00:00:00Z","page":"143 - 161","publication":"Principles of Modeling","day":"20","year":"2018","has_accepted_license":"1","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"editor":[{"first_name":"Marten","last_name":"Lohstroh","full_name":"Lohstroh, Marten"},{"first_name":"Patricia","last_name":"Derler","full_name":"Derler, Patricia"},{"first_name":"Marjan","full_name":"Sirjani, Marjan","last_name":"Sirjani"}],"title":"Computing average response time","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Otop","full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"publist_id":"7968","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:10.1007/978-3-319-95246-8_9.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer; 2018:143-161. doi:10.1007/978-3-319-95246-8_9","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161."},"intvolume":" 10760","month":"07","scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms."}],"ec_funded":1,"volume":10760,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"9995c6ce6957333baf616fc4f20be597","file_id":"7053","creator":"dernst","date_updated":"2020-07-14T12:48:14Z","file_size":516307,"date_created":"2019-11-19T08:22:18Z","file_name":"2018_PrinciplesModeling_Chatterjee.pdf"}],"publication_status":"published","status":"public","type":"book_chapter","_id":"86","file_date_updated":"2020-07-14T12:48:14Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2021-01-12T08:20:14Z"},{"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"mla":"Aubret, Antoine, et al. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” Nature Physics, vol. 14, no. 11, Springer Nature, 2018, pp. 1114–18, doi:10.1038/s41567-018-0227-4.","short":"A. Aubret, M. Youssef, S. Sacanna, J.A. Palacci, Nature Physics 14 (2018) 1114–1118.","ieee":"A. Aubret, M. Youssef, S. Sacanna, and J. A. Palacci, “Targeted assembly and synchronization of self-spinning microgears,” Nature Physics, vol. 14, no. 11. Springer Nature, pp. 1114–1118, 2018.","apa":"Aubret, A., Youssef, M., Sacanna, S., & Palacci, J. A. (2018). Targeted assembly and synchronization of self-spinning microgears. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-018-0227-4","ama":"Aubret A, Youssef M, Sacanna S, Palacci JA. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 2018;14(11):1114-1118. doi:10.1038/s41567-018-0227-4","chicago":"Aubret, Antoine, Mena Youssef, Stefano Sacanna, and Jérémie A Palacci. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” Nature Physics. Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0227-4.","ista":"Aubret A, Youssef M, Sacanna S, Palacci JA. 2018. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 14(11), 1114–1118."},"title":"Targeted assembly and synchronization of self-spinning microgears","author":[{"full_name":"Aubret, Antoine","last_name":"Aubret","first_name":"Antoine"},{"last_name":"Youssef","full_name":"Youssef, Mena","first_name":"Mena"},{"first_name":"Stefano","full_name":"Sacanna, Stefano","last_name":"Sacanna"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci"}],"article_processing_charge":"No","external_id":{"arxiv":["1810.01033"]},"quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"01","publication":"Nature Physics","year":"2018","doi":"10.1038/s41567-018-0227-4","date_published":"2018-11-01T00:00:00Z","date_created":"2021-02-02T13:52:49Z","page":"1114-1118","_id":"9062","status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2023-02-23T13:48:02Z","oa_version":"Preprint","abstract":[{"text":"Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization1. At equilibrium, the structure is encoded through specific interactions2,3,4,5,6,7,8, at an unfavourable entropic cost for the system. An alternative approach, widely used by nature, uses energy input to bypass the entropy bottleneck and develop features otherwise impossible at equilibrium9. Dissipative building blocks that inject energy locally were made available by recent advances in colloidal science10,11 but have not been used to control self-assembly. Here we show the targeted formation of self-powered microgears from active particles and their autonomous synchronization into dynamical superstructures. We use a photoactive component that consumes fuel, haematite, to devise phototactic microswimmers that form self-spinning microgears following spatiotemporal light patterns. The gears are coupled via their chemical clouds by diffusiophoresis12 and constitute the elementary bricks of synchronized superstructures, which autonomously regulate their dynamics. The results are quantitatively rationalized on the basis of a stochastic description of diffusio-phoretic oscillators dynamically coupled by chemical gradients. Our findings harness non-equilibrium phoretic phenomena to program interactions and direct self-assembly with fidelity and specificity. It lays the groundwork for the autonomous construction of dynamical architectures and functional micro-machinery.","lang":"eng"}],"month":"11","intvolume":" 14","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.01033"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"publication_status":"published","volume":14,"issue":"11"},{"title":"Diffraction-unlimited optical imaging for synaptic physiology","author":[{"last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod. https://doi.org/10.20388/omp2018.00s1.001","chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod, 2018. https://doi.org/10.20388/omp2018.00s1.001.","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11."},"date_published":"2018-06-30T00:00:00Z","doi":"10.20388/omp2018.00s1.001","date_created":"2021-03-07T23:01:25Z","page":"11","day":"30","publication":"Opera Medica et Physiologica","year":"2018","publisher":"Lobachevsky State University of Nizhny Novgorod","quality_controlled":"1","oa":1,"department":[{"_id":"JoDa"}],"date_updated":"2021-12-03T07:31:05Z","status":"public","type":"journal_article","article_type":"letter_note","_id":"9229","volume":4,"issue":"S1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2500-2295"],"issn":["2500-2287"]},"publication_status":"published","month":"06","intvolume":" 4","scopus_import":"1","alternative_title":["Molecular and cellular neuroscience"],"main_file_link":[{"open_access":"1","url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience"}],"oa_version":"Published Version"},{"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"}],"article_number":"23","author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni"},{"first_name":"Shibashis","full_name":"Guha, Shibashis","last_name":"Guha"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"article_processing_charge":"No","title":"Timed network games with clocks","citation":{"chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.","ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"doi":"10.4230/LIPICS.MFCS.2018.23","date_published":"2018-08-01T00:00:00Z","date_created":"2019-02-14T14:12:09Z","has_accepted_license":"1","year":"2018","day":"01","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2018-08-27","end_date":"2018-08-31","location":"Liverpool, United Kingdom"},"status":"public","_id":"6005","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:15Z","date_updated":"2023-02-23T14:02:58Z","ddc":["000"],"alternative_title":["LIPIcs"],"scopus_import":"1","month":"08","intvolume":" 117","abstract":[{"lang":"eng","text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"earlier_version","id":"963","status":"public"}]},"volume":117,"license":"https://creativecommons.org/licenses/by/4.0/","publication_identifier":{"issn":["1868-8969"]},"publication_status":"published","file":[{"date_created":"2019-02-14T14:22:04Z","file_name":"2018_LIPIcs_Avni.pdf","date_updated":"2020-07-14T12:47:15Z","file_size":542889,"creator":"dernst","file_id":"6007","checksum":"41ab2ae9b63f5eb49fa995250c0ba128","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}]},{"_id":"9668","status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2021-08-09T12:36:47Z","pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Estimating the homogeneous ice nucleation rate from undercooled liquid water is crucial for understanding many important physical phenomena and technological applications, and challenging for both experiments and theory. From a theoretical point of view, difficulties arise due to the long time scales required, as well as the numerous nucleation pathways involved to form ice nuclei with different stacking disorders. We computed the homogeneous ice nucleation rate at a physically relevant undercooling for a single-site water model, taking into account the diffuse nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition rate of particles to the critical nucleus. We disentangled and investigated the relative importance of all the terms, including interfacial free energy, entropic contributions and the kinetic prefactor, that contribute to the overall nucleation rate. Breaking down the problem into pieces not only provides physical insights into ice nucleation, but also sheds light on the long-standing discrepancy between different theoretical predictions, as well as between theoretical and experimental determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings and suggest strategies to systematically improve the existing simulation methods."}],"intvolume":" 20","month":"12","main_file_link":[{"url":"https://arxiv.org/abs/1807.05551","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1463-9084"],"issn":["1463-9076"]},"issue":"45","volume":20,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Cheng, Bingqing, et al. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical Physics, vol. 20, no. 45, Royal Society of Chemistry, 2018, pp. 28732–40, doi:10.1039/c8cp04561e.","ama":"Cheng B, Dellago C, Ceriotti M. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. 2018;20(45):28732-28740. doi:10.1039/c8cp04561e","apa":"Cheng, B., Dellago, C., & Ceriotti, M. (2018). Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. Royal Society of Chemistry. https://doi.org/10.1039/c8cp04561e","ieee":"B. Cheng, C. Dellago, and M. Ceriotti, “Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics,” Physical Chemistry Chemical Physics, vol. 20, no. 45. Royal Society of Chemistry, pp. 28732–28740, 2018.","short":"B. Cheng, C. Dellago, M. Ceriotti, Physical Chemistry Chemical Physics 20 (2018) 28732–28740.","chicago":"Cheng, Bingqing, Christoph Dellago, and Michele Ceriotti. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical Physics. Royal Society of Chemistry, 2018. https://doi.org/10.1039/c8cp04561e.","ista":"Cheng B, Dellago C, Ceriotti M. 2018. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. 20(45), 28732–28740."},"title":"Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics","external_id":{"pmid":["30412211"],"arxiv":["1807.05551"]},"article_processing_charge":"No","author":[{"last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"Christoph","last_name":"Dellago","full_name":"Dellago, Christoph"},{"last_name":"Ceriotti","full_name":"Ceriotti, Michele","first_name":"Michele"}],"oa":1,"publisher":"Royal Society of Chemistry","quality_controlled":"1","publication":"Physical Chemistry Chemical Physics","day":"07","year":"2018","date_created":"2021-07-15T12:51:44Z","doi":"10.1039/c8cp04561e","date_published":"2018-12-07T00:00:00Z","page":"28732-28740"},{"article_processing_charge":"No","external_id":{"arxiv":["1710.02815"]},"author":[{"last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"Michele","full_name":"Ceriotti, Michele","last_name":"Ceriotti"}],"title":"Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids","citation":{"ista":"Cheng B, Ceriotti M. 2018. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. 97(5), 054102.","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.054102.","ama":"Cheng B, Ceriotti M. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. 2018;97(5). doi:10.1103/physrevb.97.054102","apa":"Cheng, B., & Ceriotti, M. (2018). Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.97.054102","short":"B. Cheng, M. Ceriotti, Physical Review B 97 (2018).","ieee":"B. Cheng and M. Ceriotti, “Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids,” Physical Review B, vol. 97, no. 5. American Physical Society, 2018.","mla":"Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical Review B, vol. 97, no. 5, 054102, American Physical Society, 2018, doi:10.1103/physrevb.97.054102."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_number":"054102","date_created":"2021-07-19T09:39:48Z","doi":"10.1103/physrevb.97.054102","date_published":"2018-02-01T00:00:00Z","year":"2018","publication":"Physical Review B","day":"01","oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_updated":"2021-08-09T12:38:26Z","extern":"1","type":"journal_article","article_type":"original","status":"public","_id":"9687","volume":97,"issue":"5","publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1710.02815","open_access":"1"}],"scopus_import":"1","intvolume":" 97","month":"02","abstract":[{"text":"The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures.","lang":"eng"}],"oa_version":"Preprint"},{"citation":{"ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","short":"J. Polechova, PLoS Biology 16 (2018).","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Polechova","orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka"}],"publist_id":"7550","title":"Is the sky the limit? On the expansion threshold of a species’ range","article_number":"e2005372","has_accepted_license":"1","year":"2018","day":"15","publication":"PLoS Biology","doi":"10.1371/journal.pbio.2005372","date_published":"2018-06-15T00:00:00Z","date_created":"2018-12-11T11:45:46Z","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"date_updated":"2023-02-23T14:10:16Z","ddc":["576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:01Z","_id":"315","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["15449173"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-07-14T12:46:01Z","file_size":6968201,"date_created":"2019-01-22T08:30:03Z","file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5870","checksum":"908c52751bba30c55ed36789e5e4c84d"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"research_data","id":"9839","status":"public"}]},"volume":16,"issue":"6","abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"06","intvolume":" 16"},{"language":[{"iso":"eng"}],"publication":"Communications in Mathematical Physics","day":"05","year":"2018","publication_status":"published","publication_identifier":{"issn":["0010-3616","1432-0916"]},"date_created":"2020-09-17T10:41:43Z","volume":366,"date_published":"2018-09-05T00:00:00Z","issue":"3","doi":"10.1007/s00220-018-3248-z","page":"1173-1228","oa_version":"None","abstract":[{"lang":"eng","text":"The restricted planar elliptic three body problem (RPETBP) describes the motion of a massless particle (a comet or an asteroid) under the gravitational field of two massive bodies (the primaries, say the Sun and Jupiter) revolving around their center of mass on elliptic orbits with some positive eccentricity. The aim of this paper is to show the existence of orbits whose angular momentum performs arbitrary excursions in a large region. In particular, there exist diffusive orbits, that is, with a large variation of angular momentum. The leading idea of the proof consists in analyzing parabolic motions of the comet. By a well-known result of McGehee, the union of future (resp. past) parabolic orbits is an analytic manifold P+ (resp. P−). In a properly chosen coordinate system these manifolds are stable (resp. unstable) manifolds of a manifold at infinity P∞, which we call the manifold at parabolic infinity. On P∞ it is possible to define two scattering maps, which contain the map structure of the homoclinic trajectories to it, i.e. orbits parabolic both in the future and the past. Since the inner dynamics inside P∞ is trivial, two different scattering maps are used. The combination of these two scattering maps permits the design of the desired diffusive pseudo-orbits. Using shadowing techniques and these pseudo orbits we show the existence of true trajectories of the RPETBP whose angular momentum varies in any predetermined fashion."}],"intvolume":" 366","month":"09","quality_controlled":"1","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T08:19:08Z","citation":{"chicago":"Delshams, Amadeu, Vadim Kaloshin, Abraham de la Rosa, and Tere M. Seara. “Global Instability in the Restricted Planar Elliptic Three Body Problem.” Communications in Mathematical Physics. Springer Nature, 2018. https://doi.org/10.1007/s00220-018-3248-z.","ista":"Delshams A, Kaloshin V, de la Rosa A, Seara TM. 2018. Global instability in the restricted planar elliptic three body problem. Communications in Mathematical Physics. 366(3), 1173–1228.","mla":"Delshams, Amadeu, et al. “Global Instability in the Restricted Planar Elliptic Three Body Problem.” Communications in Mathematical Physics, vol. 366, no. 3, Springer Nature, 2018, pp. 1173–228, doi:10.1007/s00220-018-3248-z.","apa":"Delshams, A., Kaloshin, V., de la Rosa, A., & Seara, T. M. (2018). Global instability in the restricted planar elliptic three body problem. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-018-3248-z","ama":"Delshams A, Kaloshin V, de la Rosa A, Seara TM. Global instability in the restricted planar elliptic three body problem. Communications in Mathematical Physics. 2018;366(3):1173-1228. doi:10.1007/s00220-018-3248-z","short":"A. Delshams, V. Kaloshin, A. de la Rosa, T.M. Seara, Communications in Mathematical Physics 366 (2018) 1173–1228.","ieee":"A. Delshams, V. Kaloshin, A. de la Rosa, and T. M. Seara, “Global instability in the restricted planar elliptic three body problem,” Communications in Mathematical Physics, vol. 366, no. 3. Springer Nature, pp. 1173–1228, 2018."},"title":"Global instability in the restricted planar elliptic three body problem","article_processing_charge":"No","author":[{"full_name":"Delshams, Amadeu","last_name":"Delshams","first_name":"Amadeu"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"},{"first_name":"Abraham","last_name":"de la Rosa","full_name":"de la Rosa, Abraham"},{"full_name":"Seara, Tere M.","last_name":"Seara","first_name":"Tere M."}],"_id":"8417","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"status":"public","article_type":"original","type":"journal_article"},{"_id":"8422","keyword":["Geometry and Topology","Analysis"],"status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2021-01-12T08:19:11Z","oa_version":"Preprint","abstract":[{"text":"The Birkhoff conjecture says that the boundary of a strictly convex integrable billiard table is necessarily an ellipse. In this article, we consider a stronger notion of integrability, namely integrability close to the boundary, and prove a local version of this conjecture: a small perturbation of an ellipse of small eccentricity which preserves integrability near the boundary, is itself an ellipse. This extends the result in Avila et al. (Ann Math 184:527–558, ADK16), where integrability was assumed on a larger set. In particular, it shows that (local) integrability near the boundary implies global integrability. One of the crucial ideas in the proof consists in analyzing Taylor expansion of the corresponding action-angle coordinates with respect to the eccentricity parameter, deriving and studying higher order conditions for the preservation of integrable rational caustics.","lang":"eng"}],"intvolume":" 28","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/1705.10601","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1016-443X","1420-8970"]},"volume":28,"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Huang, Guan, et al. “Nearly Circular Domains Which Are Integrable Close to the Boundary Are Ellipses.” Geometric and Functional Analysis, vol. 28, no. 2, Springer Nature, 2018, pp. 334–92, doi:10.1007/s00039-018-0440-4.","ama":"Huang G, Kaloshin V, Sorrentino A. Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. 2018;28(2):334-392. doi:10.1007/s00039-018-0440-4","apa":"Huang, G., Kaloshin, V., & Sorrentino, A. (2018). Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. Springer Nature. https://doi.org/10.1007/s00039-018-0440-4","short":"G. Huang, V. Kaloshin, A. Sorrentino, Geometric and Functional Analysis 28 (2018) 334–392.","ieee":"G. Huang, V. Kaloshin, and A. Sorrentino, “Nearly circular domains which are integrable close to the boundary are ellipses,” Geometric and Functional Analysis, vol. 28, no. 2. Springer Nature, pp. 334–392, 2018.","chicago":"Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “Nearly Circular Domains Which Are Integrable Close to the Boundary Are Ellipses.” Geometric and Functional Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00039-018-0440-4.","ista":"Huang G, Kaloshin V, Sorrentino A. 2018. Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. 28(2), 334–392."},"title":"Nearly circular domains which are integrable close to the boundary are ellipses","external_id":{"arxiv":["1705.10601"]},"article_processing_charge":"No","author":[{"first_name":"Guan","full_name":"Huang, Guan","last_name":"Huang"},{"last_name":"Kaloshin","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim"},{"last_name":"Sorrentino","full_name":"Sorrentino, Alfonso","first_name":"Alfonso"}],"oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Geometric and Functional Analysis","day":"18","year":"2018","date_created":"2020-09-17T10:42:30Z","doi":"10.1007/s00039-018-0440-4","date_published":"2018-03-18T00:00:00Z","page":"334-392"}]