--- _id: '6338' abstract: - lang: eng text: Hippocampal activity patterns representing movement trajectories are reactivated in immobility and sleep periods, a process associated with memory recall, consolidation, and decision making. It is thought that only fixed, behaviorally relevant patterns can be reactivated, which are stored across hippocampal synaptic connections. To test whether some generalized rules govern reactivation, we examined trajectory reactivation following non-stereotypical exploration of familiar open-field environments. We found that random trajectories of varying lengths and timescales were reactivated, resembling that of Brownian motion of particles. The animals’ behavioral trajectory did not follow Brownian diffusion demonstrating that the exact behavioral experience is not reactivated. Therefore, hippocampal circuits are able to generate random trajectories of any recently active map by following diffusion dynamics. This ability of hippocampal circuits to generate representations of all behavioral outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent cognitive functions such as learning, generalization, and planning. article_processing_charge: No article_type: original author: - first_name: Federico full_name: Stella, Federico id: 39AF1E74-F248-11E8-B48F-1D18A9856A87 last_name: Stella orcid: 0000-0001-9439-3148 - first_name: Peter full_name: Baracskay, Peter id: 361CC00E-F248-11E8-B48F-1D18A9856A87 last_name: Baracskay - first_name: Joseph full_name: O'Neill, Joseph id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 2019;102:450-461. doi:10.1016/j.neuron.2019.01.052 apa: Stella, F., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.052 chicago: Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.052. ieee: F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation of random trajectories resembling Brownian diffusion,” Neuron, vol. 102. Elsevier, pp. 450–461, 2019. ista: Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461. mla: Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron, vol. 102, Elsevier, 2019, pp. 450–61, doi:10.1016/j.neuron.2019.01.052. short: F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461. date_created: 2019-04-17T08:28:59Z date_published: 2019-04-17T00:00:00Z date_updated: 2026-06-18T19:03:23Z day: '17' ddc: - '570' department: - _id: JoCs doi: 10.1016/j.neuron.2019.01.052 ec_funded: 1 external_id: isi: - '000465169700017' pmid: - '30819547' intvolume: ' 102' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.neuron.2019.01.052 month: '04' oa: 1 oa_version: Published Version page: 450-461 pmid: 1 project: - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex - _id: 2654F984-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 3713-B27 name: Interneuro plasticity during spatial learning publication: Neuron publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/ scopus_import: '1' status: public title: Hippocampal reactivation of random trajectories resembling Brownian diffusion type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 102 year: '2019' ... --- _id: '6348' abstract: - lang: eng text: 'High-speed optical telecommunication is enabled by wavelength-division multiplexing, whereby hundreds of individually stabilized lasers encode information within a single-mode optical fibre. Higher bandwidths require higher total optical power, but the power sent into the fibre is limited by optical nonlinearities within the fibre, and energy consumption by the light sources starts to become a substantial cost factor1. Optical frequency combs have been suggested to remedy this problem by generating numerous discrete, equidistant laser lines within a monolithic device; however, at present their stability and coherence allow them to operate only within small parameter ranges2,3,4. Here we show that a broadband frequency comb realized through the electro-optic effect within a high-quality whispering-gallery-mode resonator can operate at low microwave and optical powers. Unlike the usual third-order Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear effect, which is much more efficient. Our result uses a fixed microwave signal that is mixed with an optical-pump signal to generate a coherent frequency comb with a precisely determined carrier separation. The resonant enhancement enables us to work with microwave powers that are three orders of magnitude lower than those in commercially available devices. We emphasize the practical relevance of our results to high rates of data communication. To circumvent the limitations imposed by nonlinear effects in optical communication fibres, one has to solve two problems: to provide a compact and fully integrated, yet high-quality and coherent, frequency comb generator; and to calculate nonlinear signal propagation in real time5. We report a solution to the first problem.' article_processing_charge: No arxiv: 1 author: - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: Florian full_name: Sedlmeir, Florian last_name: Sedlmeir - first_name: Madhuri full_name: Kumari, Madhuri last_name: Kumari - first_name: Gerd full_name: Leuchs, Gerd last_name: Leuchs - first_name: Harald G.L. full_name: Schwefel, Harald G.L. last_name: Schwefel citation: ama: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic frequency comb. Nature. 2019;568(7752):378-381. doi:10.1038/s41586-019-1110-x apa: Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1110-x chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1110-x. ieee: A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel, “Resonant electro-optic frequency comb,” Nature, vol. 568, no. 7752. Springer Nature, pp. 378–381, 2019. ista: Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant electro-optic frequency comb. Nature. 568(7752), 378–381. mla: Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.” Nature, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:10.1038/s41586-019-1110-x. short: A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature 568 (2019) 378–381. date_created: 2019-04-28T21:59:13Z date_published: 2019-04-18T00:00:00Z date_updated: 2025-07-10T11:53:19Z day: '18' department: - _id: JoFi doi: 10.1038/s41586-019-1110-x external_id: arxiv: - '1808.10608' isi: - '000464950700053' intvolume: ' 568' isi: 1 issue: '7752' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1808.10608 month: '04' oa: 1 oa_version: Preprint page: 378-381 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41586-019-1220-5 scopus_import: '1' status: public title: Resonant electro-optic frequency comb type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 568 year: '2019' ... --- _id: '6352' abstract: - lang: eng text: Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10% O2) and normal (21% O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure. acknowledgement: The studies were supported by the Austrian Federal Ministry of Economy, Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding the Center of Optimized Structural Stud-ies, grant No. 253275 article_processing_charge: Yes (via OA deal) author: - first_name: Andrey Alexandrovich full_name: Temnov, Andrey Alexandrovich last_name: Temnov - first_name: Konstantin Arkadevich full_name: Rogov, Konstantin Arkadevich last_name: Rogov - first_name: Alla Nikolaevna full_name: Sklifas, Alla Nikolaevna last_name: Sklifas - first_name: Elena Valerievna full_name: Klychnikova, Elena Valerievna last_name: Klychnikova - first_name: Markus full_name: Hartl, Markus last_name: Hartl - first_name: Kristina full_name: Djinovic-Carugo, Kristina last_name: Djinovic-Carugo - first_name: Alexej full_name: Charnagalov, Alexej id: 49F06DBA-F248-11E8-B48F-1D18A9856A87 last_name: Charnagalov citation: ama: Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. 2019. doi:10.1007/s11033-019-04765-z apa: Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M., Djinovic-Carugo, K., & Charnagalov, A. (2019). Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. Springer. https://doi.org/10.1007/s11033-019-04765-z chicago: Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo, and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular Biology Reports. Springer, 2019. https://doi.org/10.1007/s11033-019-04765-z. ieee: A. A. Temnov et al., “Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure,” Molecular Biology Reports. Springer, 2019. ista: Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports. mla: Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” Molecular Biology Reports, Springer, 2019, doi:10.1007/s11033-019-04765-z. short: A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019). corr_author: '1' date_created: 2019-04-28T21:59:14Z date_published: 2019-04-12T00:00:00Z date_updated: 2026-04-16T09:49:11Z day: '12' ddc: - '570' department: - _id: LeSa doi: 10.1007/s11033-019-04765-z external_id: isi: - '000470332600049' file: - access_level: open_access checksum: 45bf040bbce1cea274f6013fa18ba21b content_type: application/pdf creator: dernst date_created: 2019-04-30T09:52:36Z date_updated: 2020-07-14T12:47:28Z file_id: '6362' file_name: 2019_MolecularBioReport_Temnov.pdf file_size: 1948014 relation: main_file file_date_updated: 2020-07-14T12:47:28Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Molecular Biology Reports publication_identifier: eissn: - 1573-4978 issn: - 0301-4851 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2019' ... --- _id: '6366' abstract: - lang: eng text: Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl. article_processing_charge: No article_type: original author: - first_name: Julia full_name: Bellstaedt, Julia last_name: Bellstaedt - first_name: Jana full_name: Trenner, Jana last_name: Trenner - first_name: Rebecca full_name: Lippmann, Rebecca last_name: Lippmann - first_name: Yvonne full_name: Poeschl, Yvonne last_name: Poeschl - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Marcel full_name: Quint, Marcel last_name: Quint - first_name: Carolin full_name: Delker, Carolin last_name: Delker citation: ama: Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 2019;180(2):757-766. doi:10.1104/pp.18.01377 apa: Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J., … Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01377 chicago: Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01377. ieee: J. Bellstaedt et al., “A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 757–766, 2019. ista: Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M, Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766. mla: Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 757–66, doi:10.1104/pp.18.01377. short: J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766. date_created: 2019-04-30T15:24:22Z date_published: 2019-06-01T00:00:00Z date_updated: 2026-06-18T19:03:49Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1104/pp.18.01377 external_id: isi: - '000470086100019' pmid: - '31000634' intvolume: ' 180' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: www.doi.org/10.1104/pp.18.01377 month: '06' oa: 1 oa_version: Published Version page: 757-766 pmid: 1 publication: Plant Physiology publication_identifier: eissn: - 1532-2548 issn: - 0032-0889 publication_status: published publisher: ASPB quality_controlled: '1' scopus_import: '1' status: public title: A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 180 year: '2019' ... --- _id: '6412' abstract: - lang: eng text: Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates. article_number: '1931' article_processing_charge: No author: - first_name: Hagar F. full_name: Moussa, Hagar F. last_name: Moussa - first_name: Daniel full_name: Bsteh, Daniel last_name: Bsteh - first_name: Ramesh full_name: Yelagandula, Ramesh last_name: Yelagandula - first_name: Carina full_name: Pribitzer, Carina last_name: Pribitzer - first_name: Karin full_name: Stecher, Karin last_name: Stecher - first_name: Katarina full_name: Bartalska, Katarina id: 4D883232-F248-11E8-B48F-1D18A9856A87 last_name: Bartalska - first_name: Luca full_name: Michetti, Luca last_name: Michetti - first_name: Jingkui full_name: Wang, Jingkui last_name: Wang - first_name: Jorge A. full_name: Zepeda-Martinez, Jorge A. last_name: Zepeda-Martinez - first_name: Ulrich full_name: Elling, Ulrich last_name: Elling - first_name: Jacob I. full_name: Stuckey, Jacob I. last_name: Stuckey - first_name: Lindsey I. full_name: James, Lindsey I. last_name: James - first_name: Stephen V. full_name: Frye, Stephen V. last_name: Frye - first_name: Oliver full_name: Bell, Oliver last_name: Bell citation: ama: Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09628-6 apa: Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09628-6 chicago: Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6. ieee: H. F. Moussa et al., “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019. ista: Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931. mla: Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6. short: H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019). date_created: 2019-05-13T07:58:35Z date_published: 2019-04-29T00:00:00Z date_updated: 2026-04-03T09:38:23Z day: '29' ddc: - '570' department: - _id: SaSi doi: 10.1038/s41467-019-09628-6 external_id: isi: - '000466118700002' file: - access_level: open_access checksum: 6550a328335396c856db4cbdda7d2994 content_type: application/pdf creator: dernst date_created: 2019-05-14T08:45:51Z date_updated: 2020-07-14T12:47:29Z file_id: '6448' file_name: 2019_NatureComm_Moussa.pdf file_size: 1223647 relation: main_file file_date_updated: 2020-07-14T12:47:29Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing 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: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 10 year: '2019' ... --- _id: '6413' abstract: - lang: eng text: Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Baofang full_name: Song, Baofang last_name: Song - first_name: Carlos full_name: Plana, Carlos last_name: Plana - first_name: Jose M full_name: Lopez Alonso, Jose M id: 40770848-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Alonso orcid: 0000-0002-0384-2022 - first_name: Marc full_name: Avila, Marc last_name: Avila citation: ama: Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 2019;117:14-24. doi:10.1016/j.ijmultiphaseflow.2019.04.027 apa: Song, B., Plana, C., Lopez Alonso, J. M., & Avila, M. (2019). Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. Elsevier. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027 chicago: Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow. Elsevier, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027. ieee: B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” International Journal of Multiphase Flow, vol. 117. Elsevier, pp. 14–24, 2019. ista: Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24. mla: Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow, vol. 117, Elsevier, 2019, pp. 14–24, doi:10.1016/j.ijmultiphaseflow.2019.04.027. short: B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24. date_created: 2019-05-13T07:58:35Z date_published: 2019-08-01T00:00:00Z date_updated: 2026-04-16T09:49:27Z day: '01' department: - _id: BjHo doi: 10.1016/j.ijmultiphaseflow.2019.04.027 external_id: arxiv: - '1902.07351' isi: - '000474496000002' intvolume: ' 117' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.07351 month: '08' oa: 1 oa_version: Preprint page: 14-24 publication: International Journal of Multiphase Flow publication_identifier: issn: - 0301-9322 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Phase-field simulation of core-annular pipe flow type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 117 year: '2019' ... --- _id: '6418' abstract: - lang: eng text: Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general. acknowledged_ssus: - _id: ScienComp article_processing_charge: No author: - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Ariana full_name: Macon, Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: William J full_name: Gammerdinger, William J id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87 last_name: Gammerdinger orcid: 0000-0001-9638-1220 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 2019;11(4):1033-1044. doi:10.1093/gbe/evz053 apa: Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053 chicago: Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz053. ieee: A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019. ista: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044. mla: Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053. short: A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044. date_created: 2019-05-13T07:58:38Z date_published: 2019-04-01T00:00:00Z date_updated: 2025-04-14T07:41:21Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/gbe/evz053 ec_funded: 1 external_id: isi: - '000476569800003' file: - access_level: open_access checksum: 7d0ede297b6741f3dc89cd59017c7642 content_type: application/pdf creator: dernst date_created: 2019-05-14T08:29:38Z date_updated: 2020-07-14T12:47:29Z file_id: '6446' file_name: 2019_GBE_Huylmans.pdf file_size: 1256303 relation: main_file file_date_updated: 2020-07-14T12:47:29Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1033-1044 project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication: Genome biology and evolution publication_identifier: eissn: - 1759-6653 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: record: - id: '6060' relation: popular_science status: public scopus_import: '1' status: public title: Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2019' ... --- OA_place: repository OA_type: green _id: '19818' abstract: - lang: eng text: "We revisit the enduring problem of the 2×2×2 charge density wave (CDW) order in TiSe2, utilizing photon energy-dependent angle-resolved photoemission spectroscopy to probe the full three-dimensional high- and low-temperature electronic structure. Our measurements demonstrate how a mismatch of dimensionality between the 3D conduction bands and the quasi-2D valence bands in this system leads to a hybridization that is strongly \U0001D458\U0001D467 dependent. While such a momentum-selective coupling can provide the energy gain required to form the CDW, we show how additional “passenger” states remain, which couple only weakly to the CDW and thus dominate the low-energy physics in the ordered phase of TiSe2." article_number: '076404' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Matthew D. full_name: Watson, Matthew D. last_name: Watson - first_name: Oliver J. full_name: Clark, Oliver J. last_name: Clark - first_name: Federico full_name: Mazzola, Federico last_name: Mazzola - first_name: Igor full_name: Marković, Igor last_name: Marković - first_name: Veronika full_name: Sunko, Veronika id: 23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3 last_name: Sunko orcid: 0000-0003-2724-3523 - first_name: Timur K. full_name: Kim, Timur K. last_name: Kim - first_name: Kai full_name: Rossnagel, Kai last_name: Rossnagel - first_name: Philip D. C. full_name: King, Philip D. C. last_name: King citation: ama: "Watson MD, Clark OJ, Mazzola F, et al. Orbital- and \U0001D458\U0001D467-selective hybridization of Se 4⁢\U0001D45D and Ti 3⁢\U0001D451 states in the charge density wave phase of TiSe2. Physical Review Letters. 2019;122(7). doi:10.1103/physrevlett.122.076404" apa: "Watson, M. D., Clark, O. J., Mazzola, F., Marković, I., Sunko, V., Kim, T. K., … King, P. D. C. (2019). Orbital- and \U0001D458\U0001D467-selective hybridization of Se 4⁢\U0001D45D and Ti 3⁢\U0001D451 states in the charge density wave phase of TiSe2. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.122.076404" chicago: "Watson, Matthew D., Oliver J. Clark, Federico Mazzola, Igor Marković, Veronika Sunko, Timur K. Kim, Kai Rossnagel, and Philip D. C. King. “Orbital- and \U0001D458\U0001D467-Selective Hybridization of Se 4⁢\U0001D45D and Ti 3⁢\U0001D451 States in the Charge Density Wave Phase of TiSe2.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.122.076404." ieee: "M. D. Watson et al., “Orbital- and \U0001D458\U0001D467-selective hybridization of Se 4⁢\U0001D45D and Ti 3⁢\U0001D451 states in the charge density wave phase of TiSe2,” Physical Review Letters, vol. 122, no. 7. American Physical Society, 2019." ista: "Watson MD, Clark OJ, Mazzola F, Marković I, Sunko V, Kim TK, Rossnagel K, King PDC. 2019. Orbital- and \U0001D458\U0001D467-selective hybridization of Se 4⁢\U0001D45D and Ti 3⁢\U0001D451 states in the charge density wave phase of TiSe2. Physical Review Letters. 122(7), 076404." mla: "Watson, Matthew D., et al. “Orbital- and \U0001D458\U0001D467-Selective Hybridization of Se 4⁢\U0001D45D and Ti 3⁢\U0001D451 States in the Charge Density Wave Phase of TiSe2.” Physical Review Letters, vol. 122, no. 7, 076404, American Physical Society, 2019, doi:10.1103/physrevlett.122.076404." short: M.D. Watson, O.J. Clark, F. Mazzola, I. Marković, V. Sunko, T.K. Kim, K. Rossnagel, P.D.C. King, Physical Review Letters 122 (2019). date_created: 2025-06-10T09:18:44Z date_published: 2019-02-22T00:00:00Z date_updated: 2025-06-10T12:34:24Z day: '22' doi: 10.1103/physrevlett.122.076404 extern: '1' external_id: arxiv: - '1808.07141' pmid: - '30848608' intvolume: ' 122' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1808.07141 month: '02' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: "Orbital- and \U0001D458\U0001D467-selective hybridization of Se 4⁢\U0001D45D and Ti 3⁢\U0001D451 states in the charge density wave phase of TiSe2" type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 122 year: '2019' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19824' abstract: - lang: eng text: Pressure represents a clean tuning parameter for traversing the complex phase diagrams of interacting electron systems, and as such has proved of key importance in the study of quantum materials. Application of controlled uniaxial pressure has recently been shown to more than double the transition temperature of the unconventional superconductor Sr2RuO4, leading to a pronounced peak in Tc versus strain whose origin is still under active debate. Here we develop a simple and compact method to passively apply large uniaxial pressures in restricted sample environments, and utilise this to study the evolution of the electronic structure of Sr2RuO4 using angle-resolved photoemission. We directly visualise how uniaxial stress drives a Lifshitz transition of the γ-band Fermi surface, pointing to the key role of strain-tuning its associated van Hove singularity to the Fermi level in mediating the peak in Tc. Our measurements provide stringent constraints for theoretical models of the strain-tuned electronic structure evolution of Sr2RuO4. More generally, our experimental approach opens the door to future studies of strain-tuned phase transitions not only using photoemission but also other experimental techniques where large pressure cells or piezoelectric-based devices may be difficult to implement. article_number: '46' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Veronika full_name: Sunko, Veronika id: 23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3 last_name: Sunko orcid: 0000-0003-2724-3523 - first_name: Edgar full_name: Abarca Morales, Edgar last_name: Abarca Morales - first_name: Igor full_name: Marković, Igor last_name: Marković - first_name: Mark E. full_name: Barber, Mark E. last_name: Barber - first_name: Dijana full_name: Milosavljević, Dijana last_name: Milosavljević - first_name: Federico full_name: Mazzola, Federico last_name: Mazzola - first_name: Dmitry A. full_name: Sokolov, Dmitry A. last_name: Sokolov - first_name: Naoki full_name: Kikugawa, Naoki last_name: Kikugawa - first_name: Cephise full_name: Cacho, Cephise last_name: Cacho - first_name: Pavel full_name: Dudin, Pavel last_name: Dudin - first_name: Helge full_name: Rosner, Helge last_name: Rosner - first_name: Clifford W. full_name: Hicks, Clifford W. last_name: Hicks - first_name: Philip D. C. full_name: King, Philip D. C. last_name: King - first_name: Andrew P. full_name: Mackenzie, Andrew P. last_name: Mackenzie citation: ama: Sunko V, Abarca Morales E, Marković I, et al. Direct observation of a uniaxial stress-driven Lifshitz transition in Sr2RuO4. npj Quantum Materials. 2019;4. doi:10.1038/s41535-019-0185-9 apa: Sunko, V., Abarca Morales, E., Marković, I., Barber, M. E., Milosavljević, D., Mazzola, F., … Mackenzie, A. P. (2019). Direct observation of a uniaxial stress-driven Lifshitz transition in Sr2RuO4. Npj Quantum Materials. Springer Nature. https://doi.org/10.1038/s41535-019-0185-9 chicago: Sunko, Veronika, Edgar Abarca Morales, Igor Marković, Mark E. Barber, Dijana Milosavljević, Federico Mazzola, Dmitry A. Sokolov, et al. “Direct Observation of a Uniaxial Stress-Driven Lifshitz Transition in Sr2RuO4.” Npj Quantum Materials. Springer Nature, 2019. https://doi.org/10.1038/s41535-019-0185-9. ieee: V. Sunko et al., “Direct observation of a uniaxial stress-driven Lifshitz transition in Sr2RuO4,” npj Quantum Materials, vol. 4. Springer Nature, 2019. ista: Sunko V, Abarca Morales E, Marković I, Barber ME, Milosavljević D, Mazzola F, Sokolov DA, Kikugawa N, Cacho C, Dudin P, Rosner H, Hicks CW, King PDC, Mackenzie AP. 2019. Direct observation of a uniaxial stress-driven Lifshitz transition in Sr2RuO4. npj Quantum Materials. 4, 46. mla: Sunko, Veronika, et al. “Direct Observation of a Uniaxial Stress-Driven Lifshitz Transition in Sr2RuO4.” Npj Quantum Materials, vol. 4, 46, Springer Nature, 2019, doi:10.1038/s41535-019-0185-9. short: V. Sunko, E. Abarca Morales, I. Marković, M.E. Barber, D. Milosavljević, F. Mazzola, D.A. Sokolov, N. Kikugawa, C. Cacho, P. Dudin, H. Rosner, C.W. Hicks, P.D.C. King, A.P. Mackenzie, Npj Quantum Materials 4 (2019). date_created: 2025-06-10T09:21:37Z date_published: 2019-08-19T00:00:00Z date_updated: 2025-06-11T14:14:26Z day: '19' ddc: - '530' doi: 10.1038/s41535-019-0185-9 extern: '1' external_id: arxiv: - '1903.09581' has_accepted_license: '1' intvolume: ' 4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41535-019-0185-9 month: '08' oa: 1 oa_version: Published Version publication: npj Quantum Materials publication_identifier: issn: - 2397-4648 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Direct observation of a uniaxial stress-driven Lifshitz transition in Sr2RuO4 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: 4 year: '2019' ... --- OA_place: repository OA_type: green _id: '19825' abstract: - lang: eng text: "We study the electronic structure of delafossite PtCoO2 to elucidate its extremely small resistivity and high mobility. The band exhibits steep dispersion near the Fermi level despite the fact that it is formed mainly by Pt \U0001D451 orbitals that are typically localized. We propose a picture based on two hidden kagome-lattice-like electronic structures: one originating from Pt \U0001D460+\U0001D45D\U0001D465/\U0001D45D\U0001D466 orbitals, and the other from Pt \U0001D4513⁢\U0001D4672−\U0001D45F2+\U0001D451\U0001D465⁢\U0001D466/\U0001D451\U0001D4652−\U0001D4662 orbitals, each placed on the bonds of the triangular lattice. In particular, we find that the underlying Pt \U0001D460+\U0001D45D\U0001D465/\U0001D45D\U0001D466 bands actually determine the steepness of the original dispersion, so that the large Fermi velocity can be attributed to the large width of the Pt \U0001D460+\U0001D45D\U0001D465/\U0001D45D\U0001D466 band. In addition, the kagome-like electronic structure gives rise to “orbital-momentum locking” on the Fermi surface, which reduces the electron scattering by impurities. We conclude that the combination of the large Fermi velocity and the orbital-momentum locking is likely to be the origin of the extremely small resistivity in PtCoO2." article_number: '045002' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Hidetomo full_name: Usui, Hidetomo last_name: Usui - first_name: Masayuki full_name: Ochi, Masayuki last_name: Ochi - first_name: Sota full_name: Kitamura, Sota last_name: Kitamura - first_name: Takashi full_name: Oka, Takashi last_name: Oka - first_name: Daisuke full_name: Ogura, Daisuke last_name: Ogura - first_name: Helge full_name: Rosner, Helge last_name: Rosner - first_name: Maurits W. full_name: Haverkort, Maurits W. last_name: Haverkort - first_name: Veronika full_name: Sunko, Veronika id: 23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3 last_name: Sunko orcid: 0000-0003-2724-3523 - first_name: Philip D. C. full_name: King, Philip D. C. last_name: King - first_name: Andrew P. full_name: Mackenzie, Andrew P. last_name: Mackenzie - first_name: Kazuhiko full_name: Kuroki, Kazuhiko last_name: Kuroki citation: ama: Usui H, Ochi M, Kitamura S, et al. Hidden kagome-lattice picture and origin of high conductivity in delafossite PtCoO2. Physical Review Materials. 2019;3(4). doi:10.1103/physrevmaterials.3.045002 apa: Usui, H., Ochi, M., Kitamura, S., Oka, T., Ogura, D., Rosner, H., … Kuroki, K. (2019). Hidden kagome-lattice picture and origin of high conductivity in delafossite PtCoO2. Physical Review Materials. American Physical Society. https://doi.org/10.1103/physrevmaterials.3.045002 chicago: Usui, Hidetomo, Masayuki Ochi, Sota Kitamura, Takashi Oka, Daisuke Ogura, Helge Rosner, Maurits W. Haverkort, et al. “Hidden Kagome-Lattice Picture and Origin of High Conductivity in Delafossite PtCoO2.” Physical Review Materials. American Physical Society, 2019. https://doi.org/10.1103/physrevmaterials.3.045002. ieee: H. Usui et al., “Hidden kagome-lattice picture and origin of high conductivity in delafossite PtCoO2,” Physical Review Materials, vol. 3, no. 4. American Physical Society, 2019. ista: Usui H, Ochi M, Kitamura S, Oka T, Ogura D, Rosner H, Haverkort MW, Sunko V, King PDC, Mackenzie AP, Kuroki K. 2019. Hidden kagome-lattice picture and origin of high conductivity in delafossite PtCoO2. Physical Review Materials. 3(4), 045002. mla: Usui, Hidetomo, et al. “Hidden Kagome-Lattice Picture and Origin of High Conductivity in Delafossite PtCoO2.” Physical Review Materials, vol. 3, no. 4, 045002, American Physical Society, 2019, doi:10.1103/physrevmaterials.3.045002. short: H. Usui, M. Ochi, S. Kitamura, T. Oka, D. Ogura, H. Rosner, M.W. Haverkort, V. Sunko, P.D.C. King, A.P. Mackenzie, K. Kuroki, Physical Review Materials 3 (2019). date_created: 2025-06-10T09:22:04Z date_published: 2019-04-12T00:00:00Z date_updated: 2025-06-11T06:05:56Z day: '12' doi: 10.1103/physrevmaterials.3.045002 extern: '1' external_id: arxiv: - '1812.07213' intvolume: ' 3' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1812.07213 month: '04' oa: 1 oa_version: Preprint publication: Physical Review Materials publication_identifier: issn: - 2475-9953 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Hidden kagome-lattice picture and origin of high conductivity in delafossite PtCoO2 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2019' ... --- OA_place: repository OA_type: green _id: '19826' abstract: - lang: eng text: We investigate the electronic structure of a two-dimensional electron gas created at the surface of the multivalley semimetal 1⁢T −PtSe2. Using angle-resolved photoemission and first-principles-based surface space-charge calculations, we show how the induced quantum well sub-band states form multiple Fermi surfaces, which exhibit highly anisotropic Rashba-like spin splittings. We further show how the presence of both electronlike and holelike bulk carriers causes the near-surface band bending potential to develop an unusual nonmonotonic form, with spatially segregated electron accumulation and hole accumulation regions, which in turn amplifies the induced spin splitting. Our results thus demonstrate the novel environment that semimetals provide for tailoring electrostatically induced potential profiles and their corresponding quantum sub-band states. article_number: '045438' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: O. J. full_name: Clark, O. J. last_name: Clark - first_name: F. full_name: Mazzola, F. last_name: Mazzola - first_name: J. full_name: Feng, J. last_name: Feng - first_name: Veronika full_name: Sunko, Veronika id: 23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3 last_name: Sunko orcid: 0000-0003-2724-3523 - first_name: I. full_name: Marković, I. last_name: Marković - first_name: L. full_name: Bawden, L. last_name: Bawden - first_name: T. K. full_name: Kim, T. K. last_name: Kim - first_name: P. D. C. full_name: King, P. D. C. last_name: King - first_name: M. S. full_name: Bahramy, M. S. last_name: Bahramy citation: ama: Clark OJ, Mazzola F, Feng J, et al. Dual quantum confinement and anisotropic spin splitting in the multivalley semimetal PtSe2. Physical Review B. 2019;99(4). doi:10.1103/physrevb.99.045438 apa: Clark, O. J., Mazzola, F., Feng, J., Sunko, V., Marković, I., Bawden, L., … Bahramy, M. S. (2019). Dual quantum confinement and anisotropic spin splitting in the multivalley semimetal PtSe2. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.99.045438 chicago: Clark, O. J., F. Mazzola, J. Feng, Veronika Sunko, I. Marković, L. Bawden, T. K. Kim, P. D. C. King, and M. S. Bahramy. “Dual Quantum Confinement and Anisotropic Spin Splitting in the Multivalley Semimetal PtSe2.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.99.045438. ieee: O. J. Clark et al., “Dual quantum confinement and anisotropic spin splitting in the multivalley semimetal PtSe2,” Physical Review B, vol. 99, no. 4. American Physical Society, 2019. ista: Clark OJ, Mazzola F, Feng J, Sunko V, Marković I, Bawden L, Kim TK, King PDC, Bahramy MS. 2019. Dual quantum confinement and anisotropic spin splitting in the multivalley semimetal PtSe2. Physical Review B. 99(4), 045438. mla: Clark, O. J., et al. “Dual Quantum Confinement and Anisotropic Spin Splitting in the Multivalley Semimetal PtSe2.” Physical Review B, vol. 99, no. 4, 045438, American Physical Society, 2019, doi:10.1103/physrevb.99.045438. short: O.J. Clark, F. Mazzola, J. Feng, V. Sunko, I. Marković, L. Bawden, T.K. Kim, P.D.C. King, M.S. Bahramy, Physical Review B 99 (2019). date_created: 2025-06-10T09:22:38Z date_published: 2019-01-25T00:00:00Z date_updated: 2025-06-11T06:08:51Z day: '25' doi: 10.1103/physrevb.99.045438 extern: '1' external_id: arxiv: - '1812.04485' intvolume: ' 99' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1812.04485 month: '01' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Dual quantum confinement and anisotropic spin splitting in the multivalley semimetal PtSe2 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2019' ... --- OA_place: repository OA_type: green _id: '19987' abstract: - lang: eng text: 'These lecture notes are based on Yang’s talk at the MATRIX program Geometric R-Matrices: from Geometry to Probability, at the University of Melbourne, Dec. 18–22, 2017, and Zhao’s talk at Perimeter Institute for Theoretical Physics in January 2018. We give an introductory survey of the results in Yang and Zhao (Quiver varieties and elliptic quantum groups, 2017. arxiv1708.01418). We discuss a sheafified elliptic quantum group associated to any symmetric Kac-Moody Lie algebra. The sheafification is obtained by applying the equivariant elliptic cohomological theory to the moduli space of representations of a preprojective algebra. By construction, the elliptic quantum group naturally acts on the equivariant elliptic cohomology of Nakajima quiver varieties. As an application, we obtain a relation between the sheafified elliptic quantum group and the global affine Grassmannian over an elliptic curve.' acknowledgement: 'Y.Y. would like to thank the organizers of the MATRIX program Geometric R-Matrices: from Geometry to Probability for their kind invitation, and many participants of the program for useful discussions, including Vassily Gorbounov, Andrei Okounkov, Allen Knutson, Hitoshi Konno, Paul Zinn-Justin. Proposition 1 and Sect. 3.3 are new, for which we thank Hitoshi Konno for interesting discussions and communications. These notes were written when both authors were visiting the Perimeter Institute for Theoretical Physics (PI). We are grateful to PI for the hospitality.' alternative_title: - MATRIX Book Series article_processing_charge: No arxiv: 1 author: - first_name: Yaping full_name: Yang, Yaping id: 360D8648-F248-11E8-B48F-1D18A9856A87 last_name: Yang - first_name: Gufang full_name: Zhao, Gufang id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87 last_name: Zhao citation: ama: 'Yang Y, Zhao G. How to Sheafify an Elliptic Quantum Group. In: 2017 MATRIX Annals. Vol 2. MXBS. Cham: Springer International Publishing; 2019:675-691. doi:10.1007/978-3-030-04161-8_54' apa: 'Yang, Y., & Zhao, G. (2019). How to Sheafify an Elliptic Quantum Group. In 2017 MATRIX Annals (Vol. 2, pp. 675–691). Cham: Springer International Publishing. https://doi.org/10.1007/978-3-030-04161-8_54' chicago: 'Yang, Yaping, and Gufang Zhao. “How to Sheafify an Elliptic Quantum Group.” In 2017 MATRIX Annals, 2:675–91. MXBS. Cham: Springer International Publishing, 2019. https://doi.org/10.1007/978-3-030-04161-8_54.' ieee: 'Y. Yang and G. Zhao, “How to Sheafify an Elliptic Quantum Group,” in 2017 MATRIX Annals, vol. 2, Cham: Springer International Publishing, 2019, pp. 675–691.' ista: 'Yang Y, Zhao G. 2019.How to Sheafify an Elliptic Quantum Group. In: 2017 MATRIX Annals. MATRIX Book Series, vol. 2, 675–691.' mla: Yang, Yaping, and Gufang Zhao. “How to Sheafify an Elliptic Quantum Group.” 2017 MATRIX Annals, vol. 2, Springer International Publishing, 2019, pp. 675–91, doi:10.1007/978-3-030-04161-8_54. short: Y. Yang, G. Zhao, in:, 2017 MATRIX Annals, Springer International Publishing, Cham, 2019, pp. 675–691. date_created: 2025-07-10T13:31:38Z date_published: 2019-03-25T00:00:00Z date_updated: 2025-09-23T11:59:52Z day: '25' department: - _id: TaHa doi: 10.1007/978-3-030-04161-8_54 external_id: arxiv: - '1803.06627' intvolume: ' 2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1803.06627 month: '03' oa: 1 oa_version: Preprint page: 675-691 place: Cham publication: 2017 MATRIX Annals publication_identifier: eisbn: - '9783030041618' eissn: - 2523-305X isbn: - '9783030041601' issn: - 2523-3041 publication_status: published publisher: Springer International Publishing quality_controlled: '1' series_title: MXBS status: public title: How to Sheafify an Elliptic Quantum Group type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2019' ... --- OA_place: repository OA_type: green _id: '19988' abstract: - lang: eng text: Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady-state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental knowledge on kinetic laws and parameters, but it should be supported by a correct implementation of thermodynamic constraints. In this chapter, we review the latter aspect, highlighting its computational challenges and physical insights. The simple introduction of Gibbs inequalities avoids the presence of unfeasible loops allowing for correct timescale analysis, but leads to possibly non-convex feasible flux spaces whose exploration needs efficient algorithms. We briefly review the implementation of thermodynamics through variational principles in constraint-based models of metabolic networks. article_processing_charge: No arxiv: 1 author: - first_name: A full_name: De Martino, A last_name: De Martino - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: E full_name: Marinari, E last_name: Marinari citation: ama: 'De Martino A, De Martino D, Marinari E. The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges. In: Chemical Kinetics. World Scientific Publishing; 2019:455-471. doi:10.1142/9781786347015_0018' apa: 'De Martino, A., De Martino, D., & Marinari, E. (2019). The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges. In Chemical Kinetics (pp. 455–471). World Scientific Publishing. https://doi.org/10.1142/9781786347015_0018' chicago: 'De Martino, A, Daniele De Martino, and E Marinari. “The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges.” In Chemical Kinetics, 455–71. World Scientific Publishing, 2019. https://doi.org/10.1142/9781786347015_0018.' ieee: 'A. De Martino, D. De Martino, and E. Marinari, “The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges,” in Chemical Kinetics, World Scientific Publishing, 2019, pp. 455–471.' ista: 'De Martino A, De Martino D, Marinari E. 2019.The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges. In: Chemical Kinetics. , 455–471.' mla: 'De Martino, A., et al. “The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges.” Chemical Kinetics, World Scientific Publishing, 2019, pp. 455–71, doi:10.1142/9781786347015_0018.' short: A. De Martino, D. De Martino, E. Marinari, in:, Chemical Kinetics, World Scientific Publishing, 2019, pp. 455–471. date_created: 2025-07-10T13:34:01Z date_published: 2019-09-01T00:00:00Z date_updated: 2025-09-23T11:53:34Z day: '01' department: - _id: GaTk doi: 10.1142/9781786347015_0018 external_id: arxiv: - '1902.07129' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1902.07129 month: '09' oa: 1 oa_version: Preprint page: 455-471 publication: Chemical Kinetics publication_identifier: eisbn: - '9781786347022' isbn: - '9781786347008' publication_status: published publisher: World Scientific Publishing quality_controlled: '1' status: public title: 'The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges' type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- OA_place: publisher OA_type: hybrid _id: '10190' abstract: - lang: eng text: 'The verification of concurrent programs remains an open challenge, as thread interaction has to be accounted for, which leads to state-space explosion. Stateless model checking battles this problem by exploring traces rather than states of the program. As there are exponentially many traces, dynamic partial-order reduction (DPOR) techniques are used to partition the trace space into equivalence classes, and explore a few representatives from each class. The standard equivalence that underlies most DPOR techniques is the happens-before equivalence, however recent works have spawned a vivid interest towards coarser equivalences. The efficiency of such approaches is a product of two parameters: (i) the size of the partitioning induced by the equivalence, and (ii) the time spent by the exploration algorithm in each class of the partitioning. In this work, we present a new equivalence, called value-happens-before and show that it has two appealing features. First, value-happens-before is always at least as coarse as the happens-before equivalence, and can be even exponentially coarser. Second, the value-happens-before partitioning is efficiently explorable when the number of threads is bounded. We present an algorithm called value-centric DPOR (VCDPOR), which explores the underlying partitioning using polynomial time per class. Finally, we perform an experimental evaluation of VCDPOR on various benchmarks, and compare it against other state-of-the-art approaches. Our results show that value-happens-before typically induces a significant reduction in the size of the underlying partitioning, which leads to a considerable reduction in the running time for exploring the whole partitioning.' acknowledgement: "The authors would also like to thank anonymous referees for their valuable comments and helpful suggestions. This work is supported by the Austrian Science Fund (FWF) NFN grants S11407-N23 (RiSE/SHiNE) and S11402-N23 (RiSE/SHiNE), by the Vienna Science and Technology Fund (WWTF) Project ICT15-003, and by the Austrian Science Fund (FWF) Schrodinger grant J-4220.\r\n" article_number: '124' article_processing_charge: No arxiv: 1 author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Viktor full_name: Toman, Viktor id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87 last_name: Toman orcid: 0000-0001-9036-063X citation: ama: 'Chatterjee K, Pavlogiannis A, Toman V. Value-centric dynamic partial order reduction. In: Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. Vol 3. ACM; 2019. doi:10.1145/3360550' apa: 'Chatterjee, K., Pavlogiannis, A., & Toman, V. (2019). Value-centric dynamic partial order reduction. In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications (Vol. 3). Athens, Greece: ACM. https://doi.org/10.1145/3360550' chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Viktor Toman. “Value-Centric Dynamic Partial Order Reduction.” In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, Vol. 3. ACM, 2019. https://doi.org/10.1145/3360550. ieee: K. Chatterjee, A. Pavlogiannis, and V. Toman, “Value-centric dynamic partial order reduction,” in Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, Athens, Greece, 2019, vol. 3. ista: 'Chatterjee K, Pavlogiannis A, Toman V. 2019. Value-centric dynamic partial order reduction. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 124.' mla: Chatterjee, Krishnendu, et al. “Value-Centric Dynamic Partial Order Reduction.” Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, vol. 3, 124, ACM, 2019, doi:10.1145/3360550. short: K. Chatterjee, A. Pavlogiannis, V. Toman, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, ACM, 2019. conference: end_date: 2019-10-25 location: Athens, Greece name: 'OOPSLA: Object-oriented Programming, Systems, Languages and Applications' start_date: 2019-10-23 corr_author: '1' date_created: 2021-10-27T14:57:06Z date_published: 2019-10-10T00:00:00Z date_updated: 2026-04-08T07:00:31Z day: '10' ddc: - '000' department: - _id: GradSch - _id: KrCh doi: 10.1145/3360550 external_id: arxiv: - '1909.00989' file: - access_level: open_access checksum: 2149979c46964c4d117af06ccb6c0834 content_type: application/pdf creator: cchlebak date_created: 2021-11-12T11:41:56Z date_updated: 2021-11-12T11:41:56Z file_id: '10278' file_name: 2019_ACM_Chatterjee.pdf file_size: 570829 relation: main_file success: 1 file_date_updated: 2021-11-12T11:41:56Z has_accepted_license: '1' intvolume: ' 3' keyword: - safety - risk - reliability and quality - software language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications publication_identifier: eissn: - 2475-1421 publication_status: published publisher: ACM quality_controlled: '1' related_material: record: - id: '10199' relation: dissertation_contains status: public scopus_import: '1' status: public title: Value-centric dynamic partial order reduction tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2019' ... --- _id: '10354' abstract: - lang: eng text: "Background\r\nESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filaments do not consume energy themselves, but work in conjunction with another ATP-consuming complex. Despite rapid progress in describing the cell biology of ESCRT-III, we lack an understanding of the physical mechanisms behind its force production and membrane remodelling.\r\nResults\r\nHere we present a minimal coarse-grained model that captures all the experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of downward and upward cones and tubules. This model suggests that a change in the geometry of membrane bound ESCRT-III filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then show that such repetitive filament geometry transitions can induce the fission of cargo-containing vesicles.\r\nConclusions\r\nOur model provides a general physical mechanism that explains the full range of ESCRT-III-dependent membrane remodelling and scission events observed in cells. This mechanism for filament force production is distinct from the mechanisms described for other cytoskeletal elements discovered so far. The mechanistic principles revealed here suggest new ways of manipulating ESCRT-III-driven processes in cells and could be used to guide the engineering of synthetic membrane-sculpting systems." acknowledgement: We thank Jeremy Carlton, Mike Staddon, Geraint Harker, and the Wellcome Trust Consortium “Archaeal Origins of Eukaryotic Cell Organisation” for fruitful conversations. We thank Peter Wirnsberger and Tine Curk for discussions about the membrane model implementation. article_number: '82' article_processing_charge: No article_type: original author: - first_name: Lena full_name: Harker-Kirschneck, Lena last_name: Harker-Kirschneck - first_name: Buzz full_name: Baum, Buzz last_name: Baum - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Harker-Kirschneck L, Baum B, Šarić A. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 2019;17(1). doi:10.1186/s12915-019-0700-2 apa: Harker-Kirschneck, L., Baum, B., & Šarić, A. (2019). Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. Springer Nature. https://doi.org/10.1186/s12915-019-0700-2 chicago: Harker-Kirschneck, Lena, Buzz Baum, and Anđela Šarić. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology. Springer Nature, 2019. https://doi.org/10.1186/s12915-019-0700-2. ieee: L. Harker-Kirschneck, B. Baum, and A. Šarić, “Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico,” BMC Biology, vol. 17, no. 1. Springer Nature, 2019. ista: Harker-Kirschneck L, Baum B, Šarić A. 2019. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 17(1), 82. mla: Harker-Kirschneck, Lena, et al. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology, vol. 17, no. 1, 82, Springer Nature, 2019, doi:10.1186/s12915-019-0700-2. short: L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019). date_created: 2021-11-26T11:25:03Z date_published: 2019-10-22T00:00:00Z date_updated: 2021-11-26T11:54:29Z day: '22' ddc: - '570' doi: 10.1186/s12915-019-0700-2 extern: '1' external_id: pmid: - '31640700' file: - access_level: open_access checksum: 31d8bae55a376d30925f53f7e1a02396 content_type: application/pdf creator: cchlebak date_created: 2021-11-26T11:37:54Z date_updated: 2021-11-26T11:37:54Z file_id: '10356' file_name: 2019_BMCBio_Harker_Kirschneck.pdf file_size: 1648926 relation: main_file success: 1 file_date_updated: 2021-11-26T11:37:54Z has_accepted_license: '1' intvolume: ' 17' issue: '1' keyword: - cell biology language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/559898 month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: BMC Biology publication_identifier: issn: - 1741-7007 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 17 year: '2019' ... --- _id: '10355' abstract: - lang: eng text: The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments. acknowledgement: We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations. article_processing_charge: No article_type: original author: - first_name: Anne E full_name: Hafner, Anne E last_name: Hafner - first_name: Johannes full_name: Krausser, Johannes last_name: Krausser - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 2019;58:43-52. doi:10.1016/j.sbi.2019.05.018 apa: Hafner, A. E., Krausser, J., & Šarić, A. (2019). Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.05.018 chicago: Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.05.018. ieee: A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for molecular self-organisation in biology,” Current Opinion in Structural Biology, vol. 58. Elsevier, pp. 43–52, 2019. ista: Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52. mla: Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology, vol. 58, Elsevier, 2019, pp. 43–52, doi:10.1016/j.sbi.2019.05.018. short: A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology 58 (2019) 43–52. date_created: 2021-11-26T11:33:21Z date_published: 2019-06-18T00:00:00Z date_updated: 2021-11-26T11:54:25Z day: '18' doi: 10.1016/j.sbi.2019.05.018 extern: '1' external_id: pmid: - '31226513' intvolume: ' 58' keyword: - molecular biology - structural biology language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1906.09349 month: '06' oa: 1 oa_version: Preprint page: 43-52 pmid: 1 publication: Current Opinion in Structural Biology publication_identifier: issn: - 0959-440X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Minimal coarse-grained models for molecular self-organisation in biology type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 58 year: '2019' ... --- _id: '105' abstract: - lang: eng text: 'Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771.' acknowledgement: 'This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.' article_processing_charge: No article_type: original author: - first_name: Ashley full_name: Marsh, Ashley last_name: Marsh - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Paul full_name: Lockhart, Paul last_name: Lockhart - first_name: Richard full_name: Leventer, Richard last_name: Leventer citation: ama: Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 2019;27:161-166. doi:10.1038/s41431-018-0231-2 apa: Marsh, A., Novarino, G., Lockhart, P., & Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-018-0231-2 chicago: Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41431-018-0231-2. ieee: A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” European Journal of Human Genetics, vol. 27. Springer Nature, pp. 161–166, 2019. ista: Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166. mla: Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics, vol. 27, Springer Nature, 2019, pp. 161–66, doi:10.1038/s41431-018-0231-2. short: A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166. date_created: 2018-12-11T11:44:39Z date_published: 2019-01-01T00:00:00Z date_updated: 2026-06-18T08:42:55Z day: '01' ddc: - '570' department: - _id: GaNo doi: 10.1038/s41431-018-0231-2 external_id: isi: - '000454111500019' pmid: - '30089829' intvolume: ' 27' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41431-018-0231-2 month: '01' oa: 1 oa_version: Published Version page: 161-166 pmid: 1 publication: European Journal of Human Genetics publication_status: published publisher: Springer Nature publist_id: '7949' quality_controlled: '1' scopus_import: '1' status: public title: CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2019' ... --- _id: '10619' abstract: - lang: eng text: The quantum anomalous Hall (QAH) effect combines topology and magnetism to produce precisely quantized Hall resistance at zero magnetic field. We report the observation of a QAH effect in twisted bilayer graphene aligned to hexagonal boron nitride. The effect is driven by intrinsic strong interactions, which polarize the electrons into a single spin- and valley-resolved moiré miniband with Chern number C = 1. In contrast to magnetically doped systems, the measured transport energy gap is larger than the Curie temperature for magnetic ordering, and quantization to within 0.1% of the von Klitzing constant persists to temperatures of several kelvin at zero magnetic field. Electrical currents as small as 1 nanoampere controllably switch the magnetic order between states of opposite polarization, forming an electrically rewritable magnetic memory. acknowledgement: The authors acknowledge discussions with A. Macdonald, Y. Saito, and M. Zaletel. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: M. full_name: Serlin, M. last_name: Serlin - first_name: C. L. full_name: Tschirhart, C. L. last_name: Tschirhart - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Y. full_name: Zhang, Y. last_name: Zhang - first_name: J. full_name: Zhu, J. last_name: Zhu - first_name: K. full_name: Watanabe, K. last_name: Watanabe - first_name: T. full_name: Taniguchi, T. last_name: Taniguchi - first_name: L. full_name: Balents, L. last_name: Balents - first_name: A. F. full_name: Young, A. F. last_name: Young citation: ama: Serlin M, Tschirhart CL, Polshyn H, et al. Intrinsic quantized anomalous Hall effect in a moiré heterostructure. Science. 2019;367(6480):900-903. doi:10.1126/science.aay5533 apa: Serlin, M., Tschirhart, C. L., Polshyn, H., Zhang, Y., Zhu, J., Watanabe, K., … Young, A. F. (2019). Intrinsic quantized anomalous Hall effect in a moiré heterostructure. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aay5533 chicago: Serlin, M., C. L. Tschirhart, Hryhoriy Polshyn, Y. Zhang, J. Zhu, K. Watanabe, T. Taniguchi, L. Balents, and A. F. Young. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure.” Science. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/science.aay5533. ieee: M. Serlin et al., “Intrinsic quantized anomalous Hall effect in a moiré heterostructure,” Science, vol. 367, no. 6480. American Association for the Advancement of Science, pp. 900–903, 2019. ista: Serlin M, Tschirhart CL, Polshyn H, Zhang Y, Zhu J, Watanabe K, Taniguchi T, Balents L, Young AF. 2019. Intrinsic quantized anomalous Hall effect in a moiré heterostructure. Science. 367(6480), 900–903. mla: Serlin, M., et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure.” Science, vol. 367, no. 6480, American Association for the Advancement of Science, 2019, pp. 900–03, doi:10.1126/science.aay5533. short: M. Serlin, C.L. Tschirhart, H. Polshyn, Y. Zhang, J. Zhu, K. Watanabe, T. Taniguchi, L. Balents, A.F. Young, Science 367 (2019) 900–903. date_created: 2022-01-13T14:21:32Z date_published: 2019-12-19T00:00:00Z date_updated: 2023-02-21T16:00:09Z day: '19' doi: 10.1126/science.aay5533 extern: '1' external_id: arxiv: - '1907.00261' pmid: - '31857492' intvolume: ' 367' issue: '6480' keyword: - multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.00261 month: '12' oa: 1 oa_version: Preprint page: 900-903 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: record: - id: '10697' relation: other status: public - id: '10698' relation: other status: public - id: '10699' relation: other status: public scopus_import: '1' status: public title: Intrinsic quantized anomalous Hall effect in a moiré heterostructure type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 367 year: '2019' ... --- _id: '10621' abstract: - lang: eng text: Twisted bilayer graphene has recently emerged as a platform for hosting correlated phenomena. For twist angles near θ ≈ 1.1°, the low-energy electronic structure of twisted bilayer graphene features isolated bands with a flat dispersion1,2. Recent experiments have observed a variety of low-temperature phases that appear to be driven by electron interactions, including insulating states, superconductivity and magnetism3,4,5,6. Here we report electrical transport measurements up to room temperature for twist angles varying between 0.75° and 2°. We find that the resistivity, ρ, scales linearly with temperature, T, over a wide range of T before falling again owing to interband activation. The T-linear response is much larger than observed in monolayer graphene for all measured devices, and in particular increases by more than three orders of magnitude in the range where the flat band exists. Our results point to the dominant role of electron–phonon scattering in twisted bilayer graphene, with possible implications for the origin of the observed superconductivity. acknowledgement: The authors thank S. Das Sarma and F. Wu for sharing their unpublished theoretical results, and acknowledge further discussions with L. Balents and T. Senthil. Work at both Columbia and UCSB was funded by the Army Research Office under award W911NF-17-1-0323. Sample device design and fabrication was partially supported by DoE Pro-QM EFRC (DE-SC0019443). A.F.Y. and C.R.D. separately acknowledge the support of the David and Lucile Packard Foundation. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan and the CREST (JPMJCR15F3), JST. A portion of this work was carried out at the KITP, Santa Barbara, supported by the National Science Foundation under grant number NSF PHY-1748958. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Matthew full_name: Yankowitz, Matthew last_name: Yankowitz - first_name: Shaowen full_name: Chen, Shaowen last_name: Chen - first_name: Yuxuan full_name: Zhang, Yuxuan last_name: Zhang - first_name: K. full_name: Watanabe, K. last_name: Watanabe - first_name: T. full_name: Taniguchi, T. last_name: Taniguchi - first_name: Cory R. full_name: Dean, Cory R. last_name: Dean - first_name: Andrea F. full_name: Young, Andrea F. last_name: Young citation: ama: Polshyn H, Yankowitz M, Chen S, et al. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 2019;15(10):1011-1016. doi:10.1038/s41567-019-0596-3 apa: Polshyn, H., Yankowitz, M., Chen, S., Zhang, Y., Watanabe, K., Taniguchi, T., … Young, A. F. (2019). Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-019-0596-3 chicago: Polshyn, Hryhoriy, Matthew Yankowitz, Shaowen Chen, Yuxuan Zhang, K. Watanabe, T. Taniguchi, Cory R. Dean, and Andrea F. Young. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” Nature Physics. Springer Nature, 2019. https://doi.org/10.1038/s41567-019-0596-3. ieee: H. Polshyn et al., “Large linear-in-temperature resistivity in twisted bilayer graphene,” Nature Physics, vol. 15, no. 10. Springer Nature, pp. 1011–1016, 2019. ista: Polshyn H, Yankowitz M, Chen S, Zhang Y, Watanabe K, Taniguchi T, Dean CR, Young AF. 2019. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 15(10), 1011–1016. mla: Polshyn, Hryhoriy, et al. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” Nature Physics, vol. 15, no. 10, Springer Nature, 2019, pp. 1011–16, doi:10.1038/s41567-019-0596-3. short: H. Polshyn, M. Yankowitz, S. Chen, Y. Zhang, K. Watanabe, T. Taniguchi, C.R. Dean, A.F. Young, Nature Physics 15 (2019) 1011–1016. date_created: 2022-01-13T15:00:58Z date_published: 2019-08-05T00:00:00Z date_updated: 2022-01-20T09:33:38Z day: '05' doi: 10.1038/s41567-019-0596-3 extern: '1' external_id: arxiv: - '1902.00763' intvolume: ' 15' issue: '10' keyword: - general physics and astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.00763 month: '08' oa: 1 oa_version: Preprint page: 1011-1016 publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Large linear-in-temperature resistivity in twisted bilayer graphene type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 15 year: '2019' ... --- _id: '10622' abstract: - lang: eng text: We demonstrate a method for manipulating small ensembles of vortices in multiply connected superconducting structures. A micron-size magnetic particle attached to the tip of a silicon cantilever is used to locally apply magnetic flux through the superconducting structure. By scanning the tip over the surface of the device and by utilizing the dynamical coupling between the vortices and the cantilever, a high-resolution spatial map of the different vortex configurations is obtained. Moving the tip to a particular location in the map stabilizes a distinct multivortex configuration. Thus, the scanning of the tip over a particular trajectory in space permits nontrivial operations to be performed, such as braiding of individual vortices within a larger vortex ensemble—a key capability required by many proposals for topological quantum computing. acknowledgement: We are grateful to Nadya Mason, Taylor Hughes, and Alexey Bezryadin for useful discussions. This work was supported by the DOE Basic Energy Sciences under DE-SC0012649 and the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Tyler full_name: Naibert, Tyler last_name: Naibert - first_name: Raffi full_name: Budakian, Raffi last_name: Budakian citation: ama: Polshyn H, Naibert T, Budakian R. Manipulating multivortex states in superconducting structures. Nano Letters. 2019;19(8):5476-5482. doi:10.1021/acs.nanolett.9b01983 apa: Polshyn, H., Naibert, T., & Budakian, R. (2019). Manipulating multivortex states in superconducting structures. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b01983 chicago: Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “Manipulating Multivortex States in Superconducting Structures.” Nano Letters. American Chemical Society, 2019. https://doi.org/10.1021/acs.nanolett.9b01983. ieee: H. Polshyn, T. Naibert, and R. Budakian, “Manipulating multivortex states in superconducting structures,” Nano Letters, vol. 19, no. 8. American Chemical Society, pp. 5476–5482, 2019. ista: Polshyn H, Naibert T, Budakian R. 2019. Manipulating multivortex states in superconducting structures. Nano Letters. 19(8), 5476–5482. mla: Polshyn, Hryhoriy, et al. “Manipulating Multivortex States in Superconducting Structures.” Nano Letters, vol. 19, no. 8, American Chemical Society, 2019, pp. 5476–82, doi:10.1021/acs.nanolett.9b01983. short: H. Polshyn, T. Naibert, R. Budakian, Nano Letters 19 (2019) 5476–5482. date_created: 2022-01-13T15:11:14Z date_published: 2019-06-27T00:00:00Z date_updated: 2022-01-13T15:41:24Z day: '27' doi: 10.1021/acs.nanolett.9b01983 extern: '1' external_id: arxiv: - '1905.06303' pmid: - '31246034' intvolume: ' 19' issue: '8' keyword: - mechanical engineering - condensed matter physics - general materials science - general chemistry - bioengineering language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.06303 month: '06' oa: 1 oa_version: Preprint page: 5476-5482 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Manipulating multivortex states in superconducting structures type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 19 year: '2019' ...