--- _id: '9057' abstract: - lang: eng text: Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on developing artificial systems that can mimic microorganisms, in particular their self-propulsion. We report on the design and characterization of synthetic self-propelled particles that migrate upstream, known as positive rheotaxis. This phenomenon results from a purely physical mechanism involving the interplay between the polarity of the particles and their alignment by a viscous torque. We show quantitative agreement between experimental data and a simple model of an overdamped Brownian pendulum. The model notably predicts the existence of a stagnation point in a diverging flow. We take advantage of this property to demonstrate that our active particles can sense and predictably organize in an imposed flow. Our colloidal system represents an important step toward the realization of biomimetic microsystems with the ability to sense and respond to environmental changes. article_number: e1400214 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Stefano full_name: Sacanna, Stefano last_name: Sacanna - first_name: Anaïs full_name: Abramian, Anaïs last_name: Abramian - first_name: Jérémie full_name: Barral, Jérémie last_name: Barral - first_name: Kasey full_name: Hanson, Kasey last_name: Hanson - first_name: Alexander Y. full_name: Grosberg, Alexander Y. last_name: Grosberg - first_name: David J. full_name: Pine, David J. last_name: Pine - first_name: Paul M. full_name: Chaikin, Paul M. last_name: Chaikin citation: ama: Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. Science Advances. 2015;1(4). doi:10.1126/sciadv.1400214 apa: Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. Science Advances. American Association for the Advancement of Science . https://doi.org/10.1126/sciadv.1400214 chicago: Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” Science Advances. American Association for the Advancement of Science , 2015. https://doi.org/10.1126/sciadv.1400214. ieee: J. A. Palacci et al., “Artificial rheotaxis,” Science Advances, vol. 1, no. 4. American Association for the Advancement of Science , 2015. ista: Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ, Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214. mla: Palacci, Jérémie A., et al. “Artificial Rheotaxis.” Science Advances, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:10.1126/sciadv.1400214. short: J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg, D.J. Pine, P.M. Chaikin, Science Advances 1 (2015). date_created: 2021-02-02T13:15:02Z date_published: 2015-05-01T00:00:00Z date_updated: 2023-02-23T13:47:52Z day: '01' ddc: - '530' doi: 10.1126/sciadv.1400214 extern: '1' external_id: arxiv: - '1505.05111' pmid: - '26601175' file: - access_level: open_access checksum: b97d62433581875c1b85210c5f6ae370 content_type: application/pdf creator: cziletti date_created: 2021-02-02T13:22:19Z date_updated: 2021-02-02T13:22:19Z file_id: '9058' file_name: 2015_ScienceAdvances_Palacci.pdf file_size: 2416780 relation: main_file success: 1 file_date_updated: 2021-02-02T13:22:19Z has_accepted_license: '1' intvolume: ' 1' issue: '4' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: 'American Association for the Advancement of Science ' quality_controlled: '1' scopus_import: '1' status: public title: Artificial rheotaxis tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 1 year: '2015' ... --- _id: '906' abstract: - lang: eng text: The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1. acknowledgement: 'Funding: The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)" and (BFU2012-31329), the European Union and the European Research Council under grant agreement 335980_EinME. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Our author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher until last days. A number of his work remains unfinished. We mourn premature care of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for the sequencing.' author: - first_name: Oksana full_name: Arkhipova, Oksana V last_name: Arkhipova - first_name: Margarita full_name: Meer, Margarita V last_name: Meer - first_name: Galina full_name: Mikoulinskaia, Galina V last_name: Mikoulinskaia - first_name: Marina full_name: Zakharova, Marina V last_name: Zakharova - first_name: Alexander full_name: Galushko, Alexander S last_name: Galushko - first_name: Vasilii full_name: Akimenko, Vasilii K last_name: Akimenko - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888 apa: Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0125888 chicago: Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888. ieee: O. Arkhipova et al., “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015. ista: Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V, Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5). mla: Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888. short: O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015). date_created: 2018-12-11T11:49:08Z date_published: 2015-05-11T00:00:00Z date_updated: 2021-01-12T08:21:48Z day: '11' doi: 10.1371/journal.pone.0125888 extern: 1 intvolume: ' 10' issue: '5' month: '05' publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '6742' quality_controlled: 0 status: public title: Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer 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 volume: 10 year: '2015' ... --- _id: '9141' abstract: - lang: eng text: The breaking of internal tides is believed to provide a large part of the power needed to mix the abyssal ocean and sustain the meridional overturning circulation. Both the fraction of internal tide energy that is dissipated locally and the resulting vertical mixing distribution are crucial for the ocean state, but remain poorly quantified. Here we present a first worldwide estimate of mixing due to internal tides generated at small‐scale abyssal hills. Our estimate is based on linear wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that a large fraction of abyssal‐hill generated internal tide energy is locally dissipated over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs above ridge crests, and, upon rescaling by the local stratification, follows a monotonic exponential decay with height off the bottom, with a nonuniform decay scale. We however show that a substantial part of the dissipation occurs over the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to the interplay of wave amplitude with stratification. We link the three‐dimensional map of dissipation to abyssal hills characteristics, ocean stratification, and tidal forcing, and discuss its potential implementation in time‐evolving parameterizations for global climate models. Current tidal parameterizations only account for waves generated at large‐scale satellite‐resolved bathymetry. Our results suggest that the presence of small‐scale, mostly unresolved abyssal hills could significantly enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean ridges in the Southern Hemisphere. article_processing_charge: No article_type: original author: - first_name: Adrien full_name: Lefauve, Adrien last_name: Lefauve - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Angélique full_name: Melet, Angélique last_name: Melet citation: ama: 'Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 2015;120(7):4760-4777. doi:10.1002/2014jc010598' apa: 'Lefauve, A., Muller, C. J., & Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. American Geophysical Union. https://doi.org/10.1002/2014jc010598' chicago: 'Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans. American Geophysical Union, 2015. https://doi.org/10.1002/2014jc010598.' ieee: 'A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” Journal of Geophysical Research: Oceans, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.' ista: 'Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.' mla: 'Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” Journal of Geophysical Research: Oceans, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:10.1002/2014jc010598.' short: 'A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777.' date_created: 2021-02-15T14:21:49Z date_published: 2015-06-08T00:00:00Z date_updated: 2022-01-24T13:45:41Z day: '08' doi: 10.1002/2014jc010598 extern: '1' intvolume: ' 120' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/2014JC010598 month: '06' oa: 1 oa_version: Published Version page: 4760-4777 publication: 'Journal of Geophysical Research: Oceans' publication_identifier: issn: - 2169-9275 publication_status: published publisher: American Geophysical Union quality_controlled: '1' status: public title: A three-dimensional map of tidal dissipation over abyssal hills type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 120 year: '2015' ... --- _id: '924' abstract: - lang: eng text: This paper presents a numerical study of a Capillary Pumped Loop evaporator. A two-dimensional unsteady mathematical model of a flat evaporator is developed to simulate heat and mass transfer in unsaturated porous wick with phase change. The liquid-vapor phase change inside the porous wick is described by Langmuir's law. The governing equations are solved by the Finite Element Method. The results are presented then for a sintered nickel wick and methanol as a working fluid. The heat flux required to the transition from the all-liquid wick to the vapor-liquid wick is calculated. The dynamic and thermodynamic behavior of the working fluid in the capillary structure are discussed in this paper. acknowledgement: The work presented in this paper is supported by Alstom Transport, site de Tarbes (Contract number is 11099). article_processing_charge: No author: - first_name: Riadh full_name: Boubaker, Riadh last_name: Boubaker - first_name: Vincent full_name: Platel, Vincent last_name: Platel - first_name: Alexis full_name: Bergès, Alexis last_name: Bergès - first_name: Mathieu full_name: Bancelin, Mathieu last_name: Bancelin - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 2015;76:1-8. doi:10.1016/j.applthermaleng.2014.10.009 apa: Boubaker, R., Platel, V., Bergès, A., Bancelin, M., & Hannezo, E. B. (2015). Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. Elsevier. https://doi.org/10.1016/j.applthermaleng.2014.10.009 chicago: Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering. Elsevier, 2015. https://doi.org/10.1016/j.applthermaleng.2014.10.009. ieee: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop,” Applied Thermal Engineering, vol. 76. Elsevier, pp. 1–8, 2015. ista: Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 76, 1–8. mla: Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” Applied Thermal Engineering, vol. 76, Elsevier, 2015, pp. 1–8, doi:10.1016/j.applthermaleng.2014.10.009. short: R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal Engineering 76 (2015) 1–8. date_created: 2018-12-11T11:49:13Z date_published: 2015-02-05T00:00:00Z date_updated: 2021-01-12T08:21:56Z day: '05' doi: 10.1016/j.applthermaleng.2014.10.009 extern: '1' intvolume: ' 76' language: - iso: eng month: '02' oa_version: None page: 1 - 8 publication: Applied Thermal Engineering publication_status: published publisher: Elsevier publist_id: '6514' status: public title: Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 76 year: '2015' ... --- _id: '928' abstract: - lang: eng text: The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events. article_number: e09206 author: - first_name: Ivonne full_name: Sehring, Ivonne last_name: Sehring - first_name: Pierre full_name: Recho, Pierre last_name: Recho - first_name: Elsa full_name: Denker, Elsa last_name: Denker - first_name: Matthew full_name: Kourakis, Matthew last_name: Kourakis - first_name: Birthe full_name: Mathiesen, Birthe last_name: Mathiesen - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Bo full_name: Dong, Bo last_name: Dong - first_name: Di full_name: Jiang, Di last_name: Jiang citation: ama: Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 2015;4. doi:10.7554/eLife.09206 apa: Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.09206 chicago: Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife. eLife Sciences Publications, 2015. https://doi.org/10.7554/eLife.09206. ieee: I. Sehring et al., “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” eLife, vol. 4. eLife Sciences Publications, 2015. ista: Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B, Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 4, e09206. mla: Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” ELife, vol. 4, e09206, eLife Sciences Publications, 2015, doi:10.7554/eLife.09206. short: I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015). date_created: 2018-12-11T11:49:15Z date_published: 2015-10-21T00:00:00Z date_updated: 2021-01-12T08:21:58Z day: '21' ddc: - '539' - '570' doi: 10.7554/eLife.09206 extern: '1' file: - access_level: open_access checksum: 1e4024b3161adcae4a53a0b3dc8a946e content_type: application/pdf creator: dernst date_created: 2018-12-20T15:50:56Z date_updated: 2020-07-14T12:48:15Z file_id: '5769' file_name: 2015_eLife_Sehring.pdf file_size: 7202224 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '6512' quality_controlled: '1' status: public title: Assembly and positioning of actomyosin rings by contractility and planar cell polarity 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: '2015' ... --- _id: '929' abstract: - lang: eng text: 'An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. ' acknowledgement: We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro, Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto), and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions and discussion. This work was supported by the Taishan Scholar Program of Shandong and the Fundamental Research Funds for the Central Universities in China (3005000-841412019) (to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges support from the Young Researcher Prize of the Bettencourt-Schueller Foundation. article_processing_charge: No author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Bo full_name: Dong, Bo last_name: Dong - first_name: Pierre full_name: Recho, Pierre last_name: Recho - first_name: Jean full_name: Joanny, Jean last_name: Joanny - first_name: Shigeo full_name: Hayashi, Shigeo last_name: Hayashi citation: ama: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 2015;112(28):8620-8625. doi:10.1073/pnas.1504762112 apa: Hannezo, E. B., Dong, B., Recho, P., Joanny, J., & Hayashi, S. (2015). Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1504762112 chicago: Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1504762112. ieee: E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes,” PNAS, vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015. ista: Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 112(28), 8620–8625. mla: Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” PNAS, vol. 112, no. 28, National Academy of Sciences, 2015, pp. 8620–25, doi:10.1073/pnas.1504762112. short: E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625. date_created: 2018-12-11T11:49:15Z date_published: 2015-07-14T00:00:00Z date_updated: 2021-01-12T08:21:59Z day: '14' doi: 10.1073/pnas.1504762112 extern: '1' intvolume: ' 112' issue: '28' language: - iso: eng month: '07' oa_version: None page: 8620 - 8625 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6513' status: public title: Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '933' abstract: - lang: eng text: Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data. author: - first_name: Simón full_name: García, Simón last_name: García - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jens full_name: Elgeti, Jens last_name: Elgeti - first_name: Jean full_name: Joanny, Jean last_name: Joanny - first_name: Pascal full_name: Silberzan, Pascal last_name: Silberzan - first_name: Nir full_name: Gov, Nir last_name: Gov citation: ama: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 2015;112(50):15314-15319. doi:10.1073/pnas.1510973112 apa: García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., & Gov, N. (2015). Physics of active jamming during collective cellular motion in a monolayer. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510973112 chicago: García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan, and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510973112. ieee: S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov, “Physics of active jamming during collective cellular motion in a monolayer,” PNAS, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319, 2015. ista: García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 112(50), 15314–15319. mla: García, Simón, et al. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” PNAS, vol. 112, no. 50, National Academy of Sciences, 2015, pp. 15314–19, doi:10.1073/pnas.1510973112. short: S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319. date_created: 2018-12-11T11:49:16Z date_published: 2015-12-15T00:00:00Z date_updated: 2021-01-12T08:22:01Z day: '15' doi: 10.1073/pnas.1510973112 extern: '1' external_id: pmid: - '26627719' intvolume: ' 112' issue: '50' language: - iso: eng main_file_link: - open_access: '1' url: https://www.pnas.org/content/pnas/112/50/15314.full.pdf month: '12' oa: 1 oa_version: None page: 15314 - 15319 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6511' quality_controlled: '1' status: public title: Physics of active jamming during collective cellular motion in a monolayer type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '9532' abstract: - lang: eng text: Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings. article_processing_charge: No article_type: review author: - first_name: Jessica A. full_name: Rodrigues, Jessica A. last_name: Rodrigues - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115 apa: Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.269902.115 chicago: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115. ieee: J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015. ista: Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531. mla: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115. short: J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531. date_created: 2021-06-08T09:56:24Z date_published: 2015-12-15T00:00:00Z date_updated: 2021-12-14T07:58:15Z day: '15' ddc: - '570' department: - _id: DaZi doi: 10.1101/gad.269902.115 extern: '1' external_id: pmid: - '26680300' file: - access_level: open_access checksum: 086a88cfca4677646da26ed960cb02e9 content_type: application/pdf creator: asandaue date_created: 2021-06-08T09:55:10Z date_updated: 2021-06-08T09:55:10Z file_id: '9533' file_name: 2015_GenesAndDevelopment_Rodrigues.pdf file_size: 1116846 relation: main_file success: 1 file_date_updated: 2021-06-08T09:55:10Z has_accepted_license: '1' intvolume: ' 29' issue: '24' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 2517–2531 pmid: 1 publication: Genes and Development publication_identifier: eissn: - 1549-5477 issn: - 0890-9369 publication_status: published publisher: Cold Spring Harbor Laboratory Press quality_controlled: '1' scopus_import: '1' status: public title: Evolution and function of genomic imprinting in plants tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 29 year: '2015' ... --- _id: '9575' abstract: - lang: eng text: We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Michael full_name: Krivelevich, Michael last_name: Krivelevich - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Benny full_name: Sudakov, Benny last_name: Sudakov citation: ama: Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 2015;49:181-187. doi:10.1016/j.endm.2015.06.027 apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2015.06.027 chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics. Elsevier, 2015. https://doi.org/10.1016/j.endm.2015.06.027. ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” Electronic Notes in Discrete Mathematics, vol. 49. Elsevier, pp. 181–187, 2015. ista: Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187. mla: Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” Electronic Notes in Discrete Mathematics, vol. 49, Elsevier, 2015, pp. 181–87, doi:10.1016/j.endm.2015.06.027. short: M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187. date_created: 2021-06-21T06:40:34Z date_published: 2015-11-01T00:00:00Z date_updated: 2023-02-23T14:01:28Z day: '01' doi: 10.1016/j.endm.2015.06.027 extern: '1' external_id: arxiv: - '1501.04816' intvolume: ' 49' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1501.04816 month: '11' oa: 1 oa_version: Preprint page: 181-187 publication: Electronic Notes in Discrete Mathematics publication_identifier: issn: - 1571-0653 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Cycles and matchings in randomly perturbed digraphs and hypergraphs type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 49 year: '2015' ... --- _id: '9673' abstract: - lang: eng text: Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation. article_processing_charge: No article_type: original author: - first_name: H.S. full_name: Leung, H.S. last_name: Leung - first_name: P.S.S. full_name: Leung, P.S.S. last_name: Leung - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: A.H.W. full_name: Ngan, A.H.W. last_name: Ngan citation: ama: Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 2015;67:1-25. doi:10.1016/j.ijplas.2014.09.009 apa: Leung, H. S., Leung, P. S. S., Cheng, B., & Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. Elsevier. https://doi.org/10.1016/j.ijplas.2014.09.009 chicago: Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity. Elsevier, 2015. https://doi.org/10.1016/j.ijplas.2014.09.009. ieee: H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions,” International Journal of Plasticity, vol. 67. Elsevier, pp. 1–25, 2015. ista: Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 67, 1–25. mla: Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” International Journal of Plasticity, vol. 67, Elsevier, 2015, pp. 1–25, doi:10.1016/j.ijplas.2014.09.009. short: H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25. date_created: 2021-07-15T14:09:32Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-02-23T14:04:28Z day: '01' doi: 10.1016/j.ijplas.2014.09.009 extern: '1' intvolume: ' 67' language: - iso: eng month: '04' oa_version: None page: 1-25 publication: International Journal of Plasticity publication_identifier: issn: - 0749-6419 publication_status: published publisher: Elsevier scopus_import: '1' status: public title: A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 67 year: '2015' ... --- _id: '9684' abstract: - lang: eng text: The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept. article_number: '035001' article_processing_charge: No article_type: original author: - first_name: P S S full_name: Leung, P S S last_name: Leung - first_name: H S full_name: Leung, H S last_name: Leung - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: A H W full_name: Ngan, A H W last_name: Ngan citation: ama: Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 2015;23(3). doi:10.1088/0965-0393/23/3/035001 apa: Leung, P. S. S., Leung, H. S., Cheng, B., & Ngan, A. H. W. (2015). Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. IOP Publishing. https://doi.org/10.1088/0965-0393/23/3/035001 chicago: Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering. IOP Publishing, 2015. https://doi.org/10.1088/0965-0393/23/3/035001. ieee: P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence of yield strength simulated by a dislocation-density function dynamics approach,” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3. IOP Publishing, 2015. ista: Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 23(3), 035001. mla: Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” Modelling and Simulation in Materials Science and Engineering, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:10.1088/0965-0393/23/3/035001. short: P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation in Materials Science and Engineering 23 (2015). date_created: 2021-07-19T09:11:12Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-02-23T14:04:54Z day: '01' doi: 10.1088/0965-0393/23/3/035001 extern: '1' intvolume: ' 23' issue: '3' language: - iso: eng month: '04' oa_version: None publication: Modelling and Simulation in Materials Science and Engineering publication_identifier: eissn: - 1361-651X issn: - 0965-0393 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Size dependence of yield strength simulated by a dislocation-density function dynamics approach type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 23 year: '2015' ... --- _id: '9688' abstract: - lang: eng text: The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification. article_number: '180102' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Gareth A. full_name: Tribello, Gareth A. last_name: Tribello - first_name: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: ama: Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 2015;92(18). doi:10.1103/physrevb.92.180102 apa: Cheng, B., Tribello, G. A., & Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/physrevb.92.180102 chicago: Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2015. https://doi.org/10.1103/physrevb.92.180102. ieee: B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18. American Physical Society, 2015. ista: Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 92(18), 180102. mla: Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” Physical Review B - Condensed Matter and Materials Physics, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:10.1103/physrevb.92.180102. short: B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015). date_created: 2021-07-19T10:07:22Z date_published: 2015-11-01T00:00:00Z date_updated: 2021-08-09T12:38:49Z day: '01' doi: 10.1103/physrevb.92.180102 extern: '1' external_id: arxiv: - '1511.08668' intvolume: ' 92' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.08668 month: '11' oa: 1 oa_version: Preprint publication: Physical Review B - Condensed Matter and Materials Physics publication_identifier: eissn: - 1550-235X issn: - 1098-0121 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Solid-liquid interfacial free energy out of equilibrium type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 92 year: '2015' ... --- _id: '11837' abstract: - lang: eng text: "Online social networks allow the collection of large amounts of data about the influence between users connected by a friendship-like relationship. When distributing items among agents forming a social network, this information allows us to exploit network externalities that each agent receives from his neighbors that get the same item. In this paper we consider Friends-of-Friends (2-hop) network externalities, i.e., externalities that not only depend on the neighbors that get the same item but also on neighbors of neighbors. For these externalities we study a setting where multiple different items are assigned to unit-demand agents. Specifically, we study the problem of welfare maximization under different types of externality functions. Let n be the number of agents and m be the number of items. Our contributions are the following: (1) We show that welfare maximization is APX-hard; we show that even for step functions with 2-hop (and also with 1-hop) externalities it is NP-hard to approximate social welfare better than (1-1/e). (2) On the positive side we present (i) an O(sqrt n)-approximation algorithm for general concave externality functions,\r\n(ii) an O(\\log m)-approximation algorithm for linear externality functions, and (iii) an (1-1/e)\\frac{1}{6}-approximation algorithm for 2-hop step function externalities. We also improve the result from [6] for 1-hop step function externalities by giving a (1-1/e)/2-approximation algorithm." alternative_title: - LIPIcs article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Wolfgang full_name: Dvorák, Wolfgang last_name: Dvorák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: ' Martin' full_name: Starnberger, Martin last_name: Starnberger citation: ama: 'Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. Welfare maximization with friends-of-friends network externalities. In: 32nd International Symposium on Theoretical Aspects of Computer Science. Vol 30. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:90-102. doi:10.4230/LIPICS.STACS.2015.90' apa: 'Bhattacharya, S., Dvorák, W., Henzinger, M. H., & Starnberger, Martin. (2015). Welfare maximization with friends-of-friends network externalities. In 32nd International Symposium on Theoretical Aspects of Computer Science (Vol. 30, pp. 90–102). Garching, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.STACS.2015.90' chicago: Bhattacharya, Sayan, Wolfgang Dvorák, Monika H Henzinger, and Martin Starnberger. “Welfare Maximization with Friends-of-Friends Network Externalities.” In 32nd International Symposium on Theoretical Aspects of Computer Science, 30:90–102. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPICS.STACS.2015.90. ieee: S. Bhattacharya, W. Dvorák, M. H. Henzinger, and Martin Starnberger, “Welfare maximization with friends-of-friends network externalities,” in 32nd International Symposium on Theoretical Aspects of Computer Science, Garching, Germany, 2015, vol. 30, pp. 90–102. ista: 'Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. 2015. Welfare maximization with friends-of-friends network externalities. 32nd International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 30, 90–102.' mla: Bhattacharya, Sayan, et al. “Welfare Maximization with Friends-of-Friends Network Externalities.” 32nd International Symposium on Theoretical Aspects of Computer Science, vol. 30, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPICS.STACS.2015.90. short: S. Bhattacharya, W. Dvorák, M.H. Henzinger, Martin Starnberger, in:, 32nd International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102. conference: end_date: 2015-03-07 location: Garching, Germany name: 'STACS: Symposium on Theoretical Aspects of Computer Science' start_date: 2015-03-04 date_created: 2022-08-12T11:39:40Z date_published: 2015-02-26T00:00:00Z date_updated: 2023-02-21T16:32:37Z day: '26' doi: 10.4230/LIPICS.STACS.2015.90 extern: '1' intvolume: ' 30' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPICS.STACS.2015.90 month: '02' oa: 1 oa_version: Published Version page: 90-102 publication: 32nd International Symposium on Theoretical Aspects of Computer Science publication_identifier: isbn: - 978-3-939897-78-1 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '11903' relation: later_version status: public scopus_import: '1' status: public title: Welfare maximization with friends-of-friends network externalities type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2015' ... --- _id: '11845' abstract: - lang: eng text: "Phylogenetic diversity (PD) is a measure of biodiversity based on the evolutionary history of species. Here, we discuss several optimization problems related to the use of PD, and the more general measure split diversity (SD), in conservation prioritization.\r\nDepending on the conservation goal and the information available about species, one can construct optimization routines that incorporate various conservation constraints. We demonstrate how this information can be used to select sets of species for conservation action. Specifically, we discuss the use of species' geographic distributions, the choice of candidates under economic pressure, and the use of predator–prey interactions between the species in a community to define viability constraints.\r\nDespite such optimization problems falling into the area of NP hard problems, it is possible to solve them in a reasonable amount of time using integer programming. We apply integer linear programming to a variety of models for conservation prioritization that incorporate the SD measure.\r\nWe exemplarily show the results for two data sets: the Cape region of South Africa and a Caribbean coral reef community. Finally, we provide user-friendly software at http://www.cibiv.at/software/pda." article_processing_charge: No article_type: original author: - first_name: Olga full_name: Chernomor, Olga last_name: Chernomor - first_name: Bui Quang full_name: Minh, Bui Quang last_name: Minh - first_name: Félix full_name: Forest, Félix last_name: Forest - first_name: Steffen full_name: Klaere, Steffen last_name: Klaere - first_name: Travis full_name: Ingram, Travis last_name: Ingram - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Arndt full_name: von Haeseler, Arndt last_name: von Haeseler citation: ama: Chernomor O, Minh BQ, Forest F, et al. Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. 2015;6(1):83-91. doi:10.1111/2041-210x.12299 apa: Chernomor, O., Minh, B. Q., Forest, F., Klaere, S., Ingram, T., Henzinger, M. H., & von Haeseler, A. (2015). Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. Wiley. https://doi.org/10.1111/2041-210x.12299 chicago: Chernomor, Olga, Bui Quang Minh, Félix Forest, Steffen Klaere, Travis Ingram, Monika H Henzinger, and Arndt von Haeseler. “Split Diversity in Constrained Conservation Prioritization Using Integer Linear Programming.” Methods in Ecology and Evolution. Wiley, 2015. https://doi.org/10.1111/2041-210x.12299. ieee: O. Chernomor et al., “Split diversity in constrained conservation prioritization using integer linear programming,” Methods in Ecology and Evolution, vol. 6, no. 1. Wiley, pp. 83–91, 2015. ista: Chernomor O, Minh BQ, Forest F, Klaere S, Ingram T, Henzinger MH, von Haeseler A. 2015. Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. 6(1), 83–91. mla: Chernomor, Olga, et al. “Split Diversity in Constrained Conservation Prioritization Using Integer Linear Programming.” Methods in Ecology and Evolution, vol. 6, no. 1, Wiley, 2015, pp. 83–91, doi:10.1111/2041-210x.12299. short: O. Chernomor, B.Q. Minh, F. Forest, S. Klaere, T. Ingram, M.H. Henzinger, A. von Haeseler, Methods in Ecology and Evolution 6 (2015) 83–91. date_created: 2022-08-16T06:43:49Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-17T09:30:08Z day: '01' ddc: - '570' doi: 10.1111/2041-210x.12299 extern: '1' external_id: pmid: - '25893087' file: - access_level: open_access checksum: 880e78f09f0ac99cb351c48dc97623b6 content_type: application/pdf creator: asandaue date_created: 2022-08-16T06:52:53Z date_updated: 2022-08-16T06:52:53Z file_id: '11846' file_name: 2015_MethodsInEcologyAndEvolutionChernomor.pdf file_size: 411415 relation: main_file success: 1 file_date_updated: 2022-08-16T06:52:53Z has_accepted_license: '1' intvolume: ' 6' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 83-91 pmid: 1 publication: Methods in Ecology and Evolution publication_identifier: eissn: - 2041-210X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Split diversity in constrained conservation prioritization using integer linear programming 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: 6 year: '2015' ... --- _id: '11868' abstract: - lang: eng text: "Consider the following Online Boolean Matrix-Vector Multiplication problem: We are given an n x n matrix M and will receive n column-vectors of size n, denoted by v1, ..., vn, one by one. After seeing each vector vi, we have to output the product Mvi before we can see the next vector. A naive algorithm can solve this problem using O(n3) time in total, and its running time can be slightly improved to O(n3/log2 n) [Williams SODA'07]. We show that a conjecture that there is no truly subcubic (O(n3-ε)) time algorithm for this problem can be used to exhibit the underlying polynomial time hardness shared by many dynamic problems. For a number of problems, such as subgraph connectivity, Pagh's problem, d-failure connectivity, decremental single-source shortest paths, and decremental transitive closure, this conjecture implies tight hardness results. Thus, proving or disproving this conjecture will be very interesting as it will either imply several tight unconditional lower bounds or break through a common barrier that blocks progress with these problems. This conjecture might also be considered as strong evidence against any further improvement for these problems since refuting it will imply a major breakthrough for combinatorial Boolean matrix multiplication and other long-standing problems if the term \"combinatorial algorithms\" is interpreted as \"Strassen-like algorithms\" [Ballard et al. SPAA'11].\r\n\r\nThe conjecture also leads to hardness results for problems that were previously based on diverse problems and conjectures -- such as 3SUM, combinatorial Boolean matrix multiplication, triangle detection, and multiphase -- thus providing a uniform way to prove polynomial hardness results for dynamic algorithms; some of the new proofs are also simpler or even become trivial. The conjecture also leads to stronger and new, non-trivial, hardness results, e.g., for the fully-dynamic densest subgraph and diameter problems." article_number: 21-30 article_processing_charge: No arxiv: 1 author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai - first_name: Thatchaphol full_name: Saranurak, Thatchaphol last_name: Saranurak citation: ama: 'Henzinger MH, Krinninger S, Nanongkai D, Saranurak T. Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. In: 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2015. doi:10.1145/2746539.2746609' apa: 'Henzinger, M. H., Krinninger, S., Nanongkai, D., & Saranurak, T. (2015). Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. In 47th Annual ACM Symposium on Theory of Computing. Portland, OR, United States: Association for Computing Machinery. https://doi.org/10.1145/2746539.2746609' chicago: Henzinger, Monika H, Sebastian Krinninger, Danupon Nanongkai, and Thatchaphol Saranurak. “Unifying and Strengthening Hardness for Dynamic Problems via the Online Matrix-Vector Multiplication Conjecture.” In 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery, 2015. https://doi.org/10.1145/2746539.2746609. ieee: M. H. Henzinger, S. Krinninger, D. Nanongkai, and T. Saranurak, “Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture,” in 47th Annual ACM Symposium on Theory of Computing, Portland, OR, United States, 2015. ista: 'Henzinger MH, Krinninger S, Nanongkai D, Saranurak T. 2015. Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. 47th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 21–30.' mla: Henzinger, Monika H., et al. “Unifying and Strengthening Hardness for Dynamic Problems via the Online Matrix-Vector Multiplication Conjecture.” 47th Annual ACM Symposium on Theory of Computing, 21–30, Association for Computing Machinery, 2015, doi:10.1145/2746539.2746609. short: M.H. Henzinger, S. Krinninger, D. Nanongkai, T. Saranurak, in:, 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015. conference: end_date: 2015-06-17 location: Portland, OR, United States name: 'STOC: Symposium on Theory of Computing' start_date: 2015-06-14 date_created: 2022-08-16T09:31:21Z date_published: 2015-06-14T00:00:00Z date_updated: 2023-02-17T11:09:54Z day: '14' doi: 10.1145/2746539.2746609 extern: '1' external_id: arxiv: - '1511.06773' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.06773 month: '06' oa: 1 oa_version: Preprint publication: 47th Annual ACM Symposium on Theory of Computing publication_identifier: isbn: - 978-145033536-2 issn: - '0737.8017' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '11869' abstract: - lang: eng text: "While in many graph mining applications it is crucial to handle a stream of updates efficiently in terms of both time and space, not much was known about achieving such type of algorithm. In this paper we study this issue for a problem which lies at the core of many graph mining applications called densest subgraph problem. We develop an algorithm that achieves time- and space-efficiency for this problem simultaneously. It is one of the first of its kind for graph problems to the best of our knowledge.\r\n\r\nGiven an input graph, the densest subgraph is the subgraph that maximizes the ratio between the number of edges and the number of nodes. For any ε>0, our algorithm can, with high probability, maintain a (4+ε)-approximate solution under edge insertions and deletions using ~O(n) space and ~O(1) amortized time per update; here, $n$ is the number of nodes in the graph and ~O hides the O(polylog_{1+ε} n) term. The approximation ratio can be improved to (2+ε) with more time. It can be extended to a (2+ε)-approximation sublinear-time algorithm and a distributed-streaming algorithm. Our algorithm is the first streaming algorithm that can maintain the densest subgraph in one pass. Prior to this, no algorithm could do so even in the special case of an incremental stream and even when there is no time restriction. The previously best algorithm in this setting required O(log n) passes [BahmaniKV12]. The space required by our algorithm is tight up to a polylogarithmic factor." article_processing_charge: No arxiv: 1 author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai - first_name: Charalampos full_name: Tsourakakis, Charalampos last_name: Tsourakakis citation: ama: 'Bhattacharya S, Henzinger MH, Nanongkai D, Tsourakakis C. Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. In: 47th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2015:173-182. doi:10.1145/2746539.2746592' apa: 'Bhattacharya, S., Henzinger, M. H., Nanongkai, D., & Tsourakakis, C. (2015). Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. In 47th Annual ACM Symposium on Theory of Computing (pp. 173–182). Portland, OR, United States: Association for Computing Machinery. https://doi.org/10.1145/2746539.2746592' chicago: Bhattacharya, Sayan, Monika H Henzinger, Danupon Nanongkai, and Charalampos Tsourakakis. “Space- and Time-Efficient Algorithm for Maintaining Dense Subgraphs on One-Pass Dynamic Streams.” In 47th Annual ACM Symposium on Theory of Computing, 173–82. Association for Computing Machinery, 2015. https://doi.org/10.1145/2746539.2746592. ieee: S. Bhattacharya, M. H. Henzinger, D. Nanongkai, and C. Tsourakakis, “Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams,” in 47th Annual ACM Symposium on Theory of Computing, Portland, OR, United States, 2015, pp. 173–182. ista: 'Bhattacharya S, Henzinger MH, Nanongkai D, Tsourakakis C. 2015. Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. 47th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 173–182.' mla: Bhattacharya, Sayan, et al. “Space- and Time-Efficient Algorithm for Maintaining Dense Subgraphs on One-Pass Dynamic Streams.” 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015, pp. 173–82, doi:10.1145/2746539.2746592. short: S. Bhattacharya, M.H. Henzinger, D. Nanongkai, C. Tsourakakis, in:, 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015, pp. 173–182. conference: end_date: 2015-06-17 location: Portland, OR, United States name: 'STOC: Symposium on Theory of Computing' start_date: 2015-06-14 date_created: 2022-08-16T09:36:48Z date_published: 2015-06-01T00:00:00Z date_updated: 2023-02-17T11:17:03Z day: '01' doi: 10.1145/2746539.2746592 extern: '1' external_id: arxiv: - '1504.02268' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.02268 month: '06' oa: 1 oa_version: Preprint page: 173 - 182 publication: 47th Annual ACM Symposium on Theory of Computing publication_identifier: isbn: - 978-145033536-2 issn: - 0737-8017 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '11901' abstract: - lang: eng text: We consider auctions of indivisible items to unit-demand bidders with budgets. This setting was suggested as an expressive model for single sponsored search auctions. Prior work presented mechanisms that compute bidder-optimal outcomes and are truthful for a restricted set of inputs, i.e., inputs in so-called general position. This condition is easily violated. We provide the first mechanism that is truthful in expectation for all inputs and achieves for each bidder no worse utility than the bidder-optimal outcome. Additionally we give a complete characterization for which inputs mechanisms that compute bidder-optimal outcomes are truthful. article_processing_charge: No article_type: original author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer citation: ama: Henzinger MH, Loitzenbauer V. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 2015;573:1-15. doi:10.1016/j.tcs.2015.01.033 apa: Henzinger, M. H., & Loitzenbauer, V. (2015). Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.01.033 chicago: Henzinger, Monika H, and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.01.033. ieee: M. H. Henzinger and V. Loitzenbauer, “Truthful unit-demand auctions with budgets revisited,” Theoretical Computer Science, vol. 573. Elsevier, pp. 1–15, 2015. ista: Henzinger MH, Loitzenbauer V. 2015. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 573, 1–15. mla: Henzinger, Monika H., and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” Theoretical Computer Science, vol. 573, Elsevier, 2015, pp. 1–15, doi:10.1016/j.tcs.2015.01.033. short: M.H. Henzinger, V. Loitzenbauer, Theoretical Computer Science 573 (2015) 1–15. date_created: 2022-08-17T09:06:53Z date_published: 2015-03-30T00:00:00Z date_updated: 2023-02-17T14:50:04Z day: '30' doi: 10.1016/j.tcs.2015.01.033 extern: '1' intvolume: ' 573' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.tcs.2015.01.033 month: '03' oa: 1 oa_version: None page: 1-15 publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Truthful unit-demand auctions with budgets revisited type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 573 year: '2015' ... --- _id: '11962' abstract: - lang: eng text: One of the rare alternative reagents for the reduction of carbon–carbon double bonds is diimide (HNNH), which can be generated in situ from hydrazine hydrate (N2H4⋅H2O) and O2. Although this selective method is extremely clean and powerful, it is rarely used, as the rate-determining oxidation of hydrazine in the absence of a catalyst is relatively slow using conventional batch protocols. A continuous high-temperature/high-pressure methodology dramatically enhances the initial oxidation step, at the same time allowing for a safe and scalable processing of the hazardous reaction mixture. Simple alkenes can be selectively reduced within 10–20 min at 100–120 °C and 20 bar O2 pressure. The development of a multi-injection reactor platform for the periodic addition of N2H4⋅H2O enables the reduction of less reactive olefins even at lower reaction temperatures. This concept was utilized for the highly selective reduction of artemisinic acid to dihydroartemisinic acid, the precursor molecule for the semisynthesis of the antimalarial drug artemisinin. The industrially relevant reduction was achieved by using four consecutive liquid feeds (of N2H4⋅H2O) and residence time units resulting in a highly selective reduction within approximately 40 min at 60 °C and 20 bar O2 pressure, providing dihydroartemisinic acid in ≥93 % yield and ≥95 % selectivity. article_processing_charge: No article_type: original author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Toma full_name: Glasnov, Toma last_name: Glasnov - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe citation: ama: Pieber B, Glasnov T, Kappe CO. Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. 2015;21(11):4368-4376. doi:10.1002/chem.201406439 apa: Pieber, B., Glasnov, T., & Kappe, C. O. (2015). Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. Wiley. https://doi.org/10.1002/chem.201406439 chicago: Pieber, Bartholomäus, Toma Glasnov, and C. Oliver Kappe. “Continuous Flow Reduction of Artemisinic Acid Utilizing Multi-Injection Strategies-Closing the Gap towards a Fully Continuous Synthesis of Antimalarial Drugs.” Chemistry - A European Journal. Wiley, 2015. https://doi.org/10.1002/chem.201406439. ieee: B. Pieber, T. Glasnov, and C. O. Kappe, “Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs,” Chemistry - A European Journal, vol. 21, no. 11. Wiley, pp. 4368–4376, 2015. ista: Pieber B, Glasnov T, Kappe CO. 2015. Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. 21(11), 4368–4376. mla: Pieber, Bartholomäus, et al. “Continuous Flow Reduction of Artemisinic Acid Utilizing Multi-Injection Strategies-Closing the Gap towards a Fully Continuous Synthesis of Antimalarial Drugs.” Chemistry - A European Journal, vol. 21, no. 11, Wiley, 2015, pp. 4368–76, doi:10.1002/chem.201406439. short: B. Pieber, T. Glasnov, C.O. Kappe, Chemistry - A European Journal 21 (2015) 4368–4376. date_created: 2022-08-24T11:11:10Z date_published: 2015-03-09T00:00:00Z date_updated: 2023-02-21T10:09:30Z day: '09' doi: 10.1002/chem.201406439 extern: '1' external_id: pmid: - '25655090' intvolume: ' 21' issue: '11' language: - iso: eng month: '03' oa_version: None page: 4368-4376 pmid: 1 publication: Chemistry - A European Journal publication_identifier: eissn: - 1521-3765 issn: - 0947-6539 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2015' ... --- _id: '11977' abstract: - lang: eng text: The development of a continuous flow multistep strategy for the synthesis of linear peptoids and their subsequent macrocyclization via Click chemistry is described. The central transformation of this process is an Ugi four-component reaction generating the peptidomimetic core structure. In order to avoid exposure to the often toxic and malodorous isocyanide building blocks, the continuous approach was telescoped by the dehydration of the corresponding formamide. In a concurrent operation, the highly energetic azide moiety required for the subsequent intramolecular copper-catalyzed azide–alkyne cycloaddition (Click reaction) was installed by nucleophilic substitution from a bromide precursor. All steps yielding to the linear core structures can be conveniently coupled without the need for purification steps resulting in a single process generating the desired peptidomimetics in good to excellent yields within a 25 min reaction time. The following macrocyclization was realized in a coil reactor made of copper without any additional additive. A careful process intensification study demonstrated that this transformation occurs quantitatively within 25 min at 140 °C. Depending on the resulting ring strain, either a dimeric or a monomeric form of the cyclic product was obtained. article_processing_charge: No article_type: original author: - first_name: Carlos Eduardo M. full_name: Salvador, Carlos Eduardo M. last_name: Salvador - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Philipp M. full_name: Neu, Philipp M. last_name: Neu - first_name: Ana full_name: Torvisco, Ana last_name: Torvisco - first_name: Carlos full_name: Kleber Z. Andrade, Carlos last_name: Kleber Z. Andrade - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe citation: ama: Salvador CEM, Pieber B, Neu PM, Torvisco A, Kleber Z. Andrade C, Kappe CO. A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. 2015;80(9):4590-4602. doi:10.1021/acs.joc.5b00445 apa: Salvador, C. E. M., Pieber, B., Neu, P. M., Torvisco, A., Kleber Z. Andrade, C., & Kappe, C. O. (2015). A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. American Chemical Society. https://doi.org/10.1021/acs.joc.5b00445 chicago: Salvador, Carlos Eduardo M., Bartholomäus Pieber, Philipp M. Neu, Ana Torvisco, Carlos Kleber Z. Andrade, and C. Oliver Kappe. “A Sequential Ugi Multicomponent/Cu-Catalyzed Azide–Alkyne Cycloaddition Approach for the Continuous Flow Generation of Cyclic Peptoids.” The Journal of Organic Chemistry. American Chemical Society, 2015. https://doi.org/10.1021/acs.joc.5b00445. ieee: C. E. M. Salvador, B. Pieber, P. M. Neu, A. Torvisco, C. Kleber Z. Andrade, and C. O. Kappe, “A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids,” The Journal of Organic Chemistry, vol. 80, no. 9. American Chemical Society, pp. 4590–4602, 2015. ista: Salvador CEM, Pieber B, Neu PM, Torvisco A, Kleber Z. Andrade C, Kappe CO. 2015. A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. 80(9), 4590–4602. mla: Salvador, Carlos Eduardo M., et al. “A Sequential Ugi Multicomponent/Cu-Catalyzed Azide–Alkyne Cycloaddition Approach for the Continuous Flow Generation of Cyclic Peptoids.” The Journal of Organic Chemistry, vol. 80, no. 9, American Chemical Society, 2015, pp. 4590–602, doi:10.1021/acs.joc.5b00445. short: C.E.M. Salvador, B. Pieber, P.M. Neu, A. Torvisco, C. Kleber Z. Andrade, C.O. Kappe, The Journal of Organic Chemistry 80 (2015) 4590–4602. date_created: 2022-08-25T10:52:24Z date_published: 2015-05-01T00:00:00Z date_updated: 2023-02-21T10:10:04Z day: '01' doi: 10.1021/acs.joc.5b00445 extern: '1' external_id: pmid: - '25842982' intvolume: ' 80' issue: '9' language: - iso: eng month: '05' oa_version: None page: 4590-4602 pmid: 1 publication: The Journal of Organic Chemistry publication_identifier: eissn: - 1520-6904 issn: - 0022-3263 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 80 year: '2015' ... --- _id: '11989' abstract: - lang: eng text: In recent years, the high demand for sustainable processes resulted in the development of highly attractive oxidation protocols utilizing molecular oxygen or even air instead of more uneconomic and often toxic reagents. The application of these sustainable, gaseous oxidants in conventional batch reactors is often associated with severe safety risks and process challenges especially on larger scales. Continuous flow technology offers the possibility to minimize these safety hazards and concurrently allows working in high-temperature/high-pressure regimes to access highly efficient oxidation protocols. This review article critically discusses recent literature examples of flow methodologies for selective aerobic oxidations of organic compounds. Several technologies and reactor designs for biphasic gas/liquid as well as supercritical reaction media are presented in detail. © Springer International Publishing Switzerland 2015. alternative_title: - Topics in Organometallic Chemistry article_processing_charge: No author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe citation: ama: 'Pieber B, Kappe CO. Aerobic oxidations in continuous flow. In: Noël T, ed. Organometallic Flow Chemistry. Vol 57. 1st ed. TOPORGAN. Cham: Springer Nature; 2015:97–136. doi:10.1007/3418_2015_133' apa: 'Pieber, B., & Kappe, C. O. (2015). Aerobic oxidations in continuous flow. In T. Noël (Ed.), Organometallic Flow Chemistry (1st ed., Vol. 57, pp. 97–136). Cham: Springer Nature. https://doi.org/10.1007/3418_2015_133' chicago: 'Pieber, Bartholomäus, and C. Oliver Kappe. “Aerobic Oxidations in Continuous Flow.” In Organometallic Flow Chemistry, edited by Timothy Noël, 1st ed., 57:97–136. TOPORGAN. Cham: Springer Nature, 2015. https://doi.org/10.1007/3418_2015_133.' ieee: 'B. Pieber and C. O. Kappe, “Aerobic oxidations in continuous flow,” in Organometallic Flow Chemistry, 1st ed., vol. 57, T. Noël, Ed. Cham: Springer Nature, 2015, pp. 97–136.' ista: 'Pieber B, Kappe CO. 2015.Aerobic oxidations in continuous flow. In: Organometallic Flow Chemistry. Topics in Organometallic Chemistry, vol. 57, 97–136.' mla: Pieber, Bartholomäus, and C. Oliver Kappe. “Aerobic Oxidations in Continuous Flow.” Organometallic Flow Chemistry, edited by Timothy Noël, 1st ed., vol. 57, Springer Nature, 2015, pp. 97–136, doi:10.1007/3418_2015_133. short: B. Pieber, C.O. Kappe, in:, T. Noël (Ed.), Organometallic Flow Chemistry, 1st ed., Springer Nature, Cham, 2015, pp. 97–136. date_created: 2022-08-25T11:58:38Z date_published: 2015-06-10T00:00:00Z date_updated: 2023-02-21T10:10:35Z day: '10' doi: 10.1007/3418_2015_133 edition: '1' editor: - first_name: Timothy full_name: Noël, Timothy last_name: Noël extern: '1' intvolume: ' 57' language: - iso: eng month: '06' oa_version: None page: 97–136 place: Cham publication: Organometallic Flow Chemistry publication_identifier: eisbn: - '9783319332437' eissn: - 1616-8534 isbn: - '9783319332413' issn: - 1436-6002 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: TOPORGAN status: public title: Aerobic oxidations in continuous flow type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2015' ...