[{"status":"public","article_processing_charge":"No","article_type":"letter_note","language":[{"iso":"eng"}],"_id":"17987","year":"2014","intvolume":"        14","month":"02","scopus_import":"1","extern":"1","title":"Tunable charge transport in single-molecule junctions via electrolytic gating","date_published":"2014-02-02T00:00:00Z","date_created":"2024-09-09T11:24:14Z","author":[{"full_name":"Capozzi, Brian","first_name":"Brian","last_name":"Capozzi"},{"full_name":"Chen, Qishui","first_name":"Qishui","last_name":"Chen"},{"first_name":"Pierre","last_name":"Darancet","full_name":"Darancet, Pierre"},{"first_name":"Michele","last_name":"Kotiuga","full_name":"Kotiuga, Michele"},{"full_name":"Buzzeo, Marisa","first_name":"Marisa","last_name":"Buzzeo"},{"full_name":"Neaton, Jeffrey B.","last_name":"Neaton","first_name":"Jeffrey B."},{"first_name":"Colin","last_name":"Nuckolls","full_name":"Nuckolls, Colin"},{"orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha","first_name":"Latha","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"}],"date_updated":"2025-01-02T14:15:49Z","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"volume":14,"OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"external_id":{"pmid":["24490721"]},"oa_version":"None","abstract":[{"lang":"eng","text":"We modulate the conductance of electrochemically inactive molecules in single-molecule junctions using an electrolytic gate to controllably tune the energy level alignment of the system. Molecular junctions that conduct through their highest occupied molecular orbital show a decrease in conductance when applying a positive electrochemical potential, and those that conduct though their lowest unoccupied molecular orbital show the opposite trend. We fit the experimentally measured conductance data as a function of gate voltage with a Lorentzian function and find the fitting parameters to be in quantitative agreement with self-energy corrected density functional theory calculations of transmission probability across single-molecule junctions. This work shows that electrochemical gating can directly modulate the alignment of the conducting orbital relative to the metal Fermi energy, thereby changing the junction transport properties."}],"page":"1400-1404","day":"02","citation":{"ieee":"B. Capozzi <i>et al.</i>, “Tunable charge transport in single-molecule junctions via electrolytic gating,” <i>Nano Letters</i>, vol. 14, no. 3. American Chemical Society, pp. 1400–1404, 2014.","short":"B. Capozzi, Q. Chen, P. Darancet, M. Kotiuga, M. Buzzeo, J.B. Neaton, C. Nuckolls, L. Venkataraman, Nano Letters 14 (2014) 1400–1404.","mla":"Capozzi, Brian, et al. “Tunable Charge Transport in Single-Molecule Junctions via Electrolytic Gating.” <i>Nano Letters</i>, vol. 14, no. 3, American Chemical Society, 2014, pp. 1400–04, doi:<a href=\"https://doi.org/10.1021/nl404459q\">10.1021/nl404459q</a>.","apa":"Capozzi, B., Chen, Q., Darancet, P., Kotiuga, M., Buzzeo, M., Neaton, J. B., … Venkataraman, L. (2014). Tunable charge transport in single-molecule junctions via electrolytic gating. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/nl404459q\">https://doi.org/10.1021/nl404459q</a>","ama":"Capozzi B, Chen Q, Darancet P, et al. Tunable charge transport in single-molecule junctions via electrolytic gating. <i>Nano Letters</i>. 2014;14(3):1400-1404. doi:<a href=\"https://doi.org/10.1021/nl404459q\">10.1021/nl404459q</a>","chicago":"Capozzi, Brian, Qishui Chen, Pierre Darancet, Michele Kotiuga, Marisa Buzzeo, Jeffrey B. Neaton, Colin Nuckolls, and Latha Venkataraman. “Tunable Charge Transport in Single-Molecule Junctions via Electrolytic Gating.” <i>Nano Letters</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/nl404459q\">https://doi.org/10.1021/nl404459q</a>.","ista":"Capozzi B, Chen Q, Darancet P, Kotiuga M, Buzzeo M, Neaton JB, Nuckolls C, Venkataraman L. 2014. Tunable charge transport in single-molecule junctions via electrolytic gating. Nano Letters. 14(3), 1400–1404."},"doi":"10.1021/nl404459q","issue":"3","quality_controlled":"1","publication_status":"published","type":"journal_article","publisher":"American Chemical Society","publication":"Nano Letters"},{"status":"public","article_type":"letter_note","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"17988","year":"2014","intvolume":"        14","title":"Determination of energy level alignment and coupling strength in 4,4′-bipyridine single-molecule junctions","scopus_import":"1","month":"01","extern":"1","date_published":"2014-01-21T00:00:00Z","author":[{"full_name":"Kim, Taekyeong","first_name":"Taekyeong","last_name":"Kim"},{"full_name":"Darancet, Pierre","last_name":"Darancet","first_name":"Pierre"},{"full_name":"Widawsky, Jonathan R.","last_name":"Widawsky","first_name":"Jonathan R."},{"first_name":"Michele","last_name":"Kotiuga","full_name":"Kotiuga, Michele"},{"last_name":"Quek","first_name":"Su Ying","full_name":"Quek, Su Ying"},{"first_name":"Jeffrey B.","last_name":"Neaton","full_name":"Neaton, Jeffrey B."},{"full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","last_name":"Venkataraman","first_name":"Latha"}],"date_created":"2024-09-09T11:24:55Z","date_updated":"2025-01-03T07:44:13Z","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"volume":14,"OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"external_id":{"pmid":["24446585"]},"oa_version":"None","abstract":[{"lang":"eng","text":"We measure conductance and thermopower of single Au–4,4′-bipyridine–Au junctions in distinct low and high conductance binding geometries accessed by modulating the electrode separation. We use these data to determine the electronic energy level alignment and coupling strength for these junctions, which are known to conduct through the lowest unoccupied molecular orbital (LUMO). Contrary to intuition, we find that, in the high-conductance junction, the LUMO resonance energy is further away from the Au Fermi energy than in the low-conductance junction. However, the LUMO of the high-conducting junction is better coupled to the electrode. These results are in good quantitative agreement with self-energy corrected zero-bias density functional theory calculations. Our calculations show further that measurements of conductance and thermopower in amine-terminated oligophenyl–Au junctions, where conduction occurs through the highest occupied molecular orbitals, cannot be used to extract electronic parameters as their transmission functions do not follow a simple Lorentzian form."}],"page":"794-798","citation":{"ieee":"T. Kim <i>et al.</i>, “Determination of energy level alignment and coupling strength in 4,4′-bipyridine single-molecule junctions,” <i>Nano Letters</i>, vol. 14, no. 2. American Chemical Society, pp. 794–798, 2014.","short":"T. Kim, P. Darancet, J.R. Widawsky, M. Kotiuga, S.Y. Quek, J.B. Neaton, L. Venkataraman, Nano Letters 14 (2014) 794–798.","apa":"Kim, T., Darancet, P., Widawsky, J. R., Kotiuga, M., Quek, S. Y., Neaton, J. B., &#38; Venkataraman, L. (2014). Determination of energy level alignment and coupling strength in 4,4′-bipyridine single-molecule junctions. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/nl404143v\">https://doi.org/10.1021/nl404143v</a>","ama":"Kim T, Darancet P, Widawsky JR, et al. Determination of energy level alignment and coupling strength in 4,4′-bipyridine single-molecule junctions. <i>Nano Letters</i>. 2014;14(2):794-798. doi:<a href=\"https://doi.org/10.1021/nl404143v\">10.1021/nl404143v</a>","ista":"Kim T, Darancet P, Widawsky JR, Kotiuga M, Quek SY, Neaton JB, Venkataraman L. 2014. Determination of energy level alignment and coupling strength in 4,4′-bipyridine single-molecule junctions. Nano Letters. 14(2), 794–798.","chicago":"Kim, Taekyeong, Pierre Darancet, Jonathan R. Widawsky, Michele Kotiuga, Su Ying Quek, Jeffrey B. Neaton, and Latha Venkataraman. “Determination of Energy Level Alignment and Coupling Strength in 4,4′-Bipyridine Single-Molecule Junctions.” <i>Nano Letters</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/nl404143v\">https://doi.org/10.1021/nl404143v</a>.","mla":"Kim, Taekyeong, et al. “Determination of Energy Level Alignment and Coupling Strength in 4,4′-Bipyridine Single-Molecule Junctions.” <i>Nano Letters</i>, vol. 14, no. 2, American Chemical Society, 2014, pp. 794–98, doi:<a href=\"https://doi.org/10.1021/nl404143v\">10.1021/nl404143v</a>."},"day":"21","doi":"10.1021/nl404143v","issue":"2","quality_controlled":"1","type":"journal_article","publication_status":"published","publisher":"American Chemical Society","publication":"Nano Letters"},{"doi":"10.1021/ja411143s","issue":"3","citation":{"ieee":"W. Chen, H. Li, J. R. Widawsky, C. Appayee, L. Venkataraman, and R. Breslow, “Aromaticity decreases single-molecule junction sonductance,” <i>Journal of the American Chemical Society</i>, vol. 136, no. 3. American Chemical Society, pp. 918–920, 2014.","short":"W. Chen, H. Li, J.R. Widawsky, C. Appayee, L. Venkataraman, R. Breslow, Journal of the American Chemical Society 136 (2014) 918–920.","mla":"Chen, Wenbo, et al. “Aromaticity Decreases Single-Molecule Junction Sonductance.” <i>Journal of the American Chemical Society</i>, vol. 136, no. 3, American Chemical Society, 2014, pp. 918–20, doi:<a href=\"https://doi.org/10.1021/ja411143s\">10.1021/ja411143s</a>.","ama":"Chen W, Li H, Widawsky JR, Appayee C, Venkataraman L, Breslow R. Aromaticity decreases single-molecule junction sonductance. <i>Journal of the American Chemical Society</i>. 2014;136(3):918-920. doi:<a href=\"https://doi.org/10.1021/ja411143s\">10.1021/ja411143s</a>","apa":"Chen, W., Li, H., Widawsky, J. R., Appayee, C., Venkataraman, L., &#38; Breslow, R. (2014). Aromaticity decreases single-molecule junction sonductance. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja411143s\">https://doi.org/10.1021/ja411143s</a>","chicago":"Chen, Wenbo, Haixing Li, Jonathan R. Widawsky, Chandrakumar Appayee, Latha Venkataraman, and Ronald Breslow. “Aromaticity Decreases Single-Molecule Junction Sonductance.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/ja411143s\">https://doi.org/10.1021/ja411143s</a>.","ista":"Chen W, Li H, Widawsky JR, Appayee C, Venkataraman L, Breslow R. 2014. Aromaticity decreases single-molecule junction sonductance. Journal of the American Chemical Society. 136(3), 918–920."},"day":"07","page":"918-920","publication":"Journal of the American Chemical Society","publisher":"American Chemical Society","quality_controlled":"1","type":"journal_article","publication_status":"published","title":"Aromaticity decreases single-molecule junction sonductance","extern":"1","month":"01","scopus_import":"1","date_published":"2014-01-07T00:00:00Z","year":"2014","_id":"17989","intvolume":"       136","article_type":"letter_note","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"None","abstract":[{"text":"We have measured the conductance of single-molecule junctions created with three different molecular wires using the scanning tunneling microscope-based break-junction technique. Each wire contains one of three different cyclic five-membered rings: cyclopentadiene, furan, or thiophene. We find that the single-molecule conductance of these three wires correlates negatively with the resonance energy of the five-membered ring; the nonaromatic cyclopentadiene derivative has the highest conductance, while the most aromatic of this series, thiophene, has the lowest. Furthermore, we show for another wire structure that the conductance of furan-based wires is consistently higher than for analogous thiophene systems, indicating that the negative correlation between conductance and aromaticity is robust. The best conductance would be for a quinoid structure that diminishes aromaticity. The energy penalty for partly adopting the quinoid structure is less with compounds having lower initial aromatic stabilization. An additional effect may reflect the lower HOMOs of aromatic compounds.","lang":"eng"}],"OA_type":"closed access","volume":136,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["24397414"]},"pmid":1,"date_updated":"2025-01-03T07:46:41Z","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"author":[{"last_name":"Chen","first_name":"Wenbo","full_name":"Chen, Wenbo"},{"full_name":"Li, Haixing","last_name":"Li","first_name":"Haixing"},{"last_name":"Widawsky","first_name":"Jonathan R.","full_name":"Widawsky, Jonathan R."},{"first_name":"Chandrakumar","last_name":"Appayee","full_name":"Appayee, Chandrakumar"},{"full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089","last_name":"Venkataraman","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"},{"full_name":"Breslow, Ronald","last_name":"Breslow","first_name":"Ronald"}],"date_created":"2024-09-09T11:25:35Z"},{"volume":111,"OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"external_id":{"pmid":["25024198"]},"oa_version":"None","abstract":[{"text":"Molecular junctions formed using the scanning-tunneling-microscope–based break-junction technique (STM-BJ) have provided unique insight into charge transport at the nanoscale. In most prior work, the same metal, typically Au, Pt, or Ag, is used for both tip and substrate. For such noble metal electrodes, the density of electronic states is approximately constant within a narrow energy window relevant to charge transport. Here, we form molecular junctions using the STM-BJ technique, with an Au metal tip and a microfabricated graphite substrate, and measure the conductance of a series of graphite/amine-terminated oligophenyl/Au molecular junctions. The remarkable mechanical strength of graphite and the single-crystal properties of our substrates allow measurements over few thousand junctions without any change in the surface properties. We show that conductance decays exponentially with molecular backbone length with a decay constant that is essentially the same as that for measurements with two Au electrodes. More importantly, despite the inherent symmetry of the oligophenylamines, we observe rectification in these junctions. State-of-art ab initio conductance calculations are in good agreement with experiment, and explain the rectification. We show that the highly energy-dependent graphite density of states contributes variations in transmission that, when coupled with an asymmetric voltage drop across the junction, leads to the observed rectification. Together, our measurements and calculations show how functionality may emerge from hybrid molecular-scale devices purposefully designed with different electrodes beyond the so-called “wide band limit,” opening up the possibility of assembling molecular junctions with dissimilar electrodes using layered 2D materials.","lang":"eng"}],"author":[{"full_name":"Kim, Taekyeong","first_name":"Taekyeong","last_name":"Kim"},{"full_name":"Liu, Zhen-Fei","last_name":"Liu","first_name":"Zhen-Fei"},{"last_name":"Lee","first_name":"Chulho","full_name":"Lee, Chulho"},{"full_name":"Neaton, Jeffrey B.","first_name":"Jeffrey B.","last_name":"Neaton"},{"first_name":"Latha","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha"}],"date_created":"2024-09-09T11:26:38Z","date_updated":"2025-01-03T07:49:30Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"year":"2014","_id":"17990","intvolume":"       111","title":"Charge transport and rectification in molecular junctions formed with carbon-based electrodes","scopus_import":"1","month":"07","extern":"1","date_published":"2014-07-14T00:00:00Z","status":"public","article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","type":"journal_article","publication_status":"published","citation":{"short":"T. Kim, Z.-F. Liu, C. Lee, J.B. Neaton, L. Venkataraman, Proceedings of the National Academy of Sciences 111 (2014) 10928–10932.","ieee":"T. Kim, Z.-F. Liu, C. Lee, J. B. Neaton, and L. Venkataraman, “Charge transport and rectification in molecular junctions formed with carbon-based electrodes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 30. National Academy of Sciences, pp. 10928–10932, 2014.","chicago":"Kim, Taekyeong, Zhen-Fei Liu, Chulho Lee, Jeffrey B. Neaton, and Latha Venkataraman. “Charge Transport and Rectification in Molecular Junctions Formed with Carbon-Based Electrodes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1406926111\">https://doi.org/10.1073/pnas.1406926111</a>.","ista":"Kim T, Liu Z-F, Lee C, Neaton JB, Venkataraman L. 2014. Charge transport and rectification in molecular junctions formed with carbon-based electrodes. Proceedings of the National Academy of Sciences. 111(30), 10928–10932.","ama":"Kim T, Liu Z-F, Lee C, Neaton JB, Venkataraman L. Charge transport and rectification in molecular junctions formed with carbon-based electrodes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(30):10928-10932. doi:<a href=\"https://doi.org/10.1073/pnas.1406926111\">10.1073/pnas.1406926111</a>","apa":"Kim, T., Liu, Z.-F., Lee, C., Neaton, J. B., &#38; Venkataraman, L. (2014). Charge transport and rectification in molecular junctions formed with carbon-based electrodes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1406926111\">https://doi.org/10.1073/pnas.1406926111</a>","mla":"Kim, Taekyeong, et al. “Charge Transport and Rectification in Molecular Junctions Formed with Carbon-Based Electrodes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 30, National Academy of Sciences, 2014, pp. 10928–32, doi:<a href=\"https://doi.org/10.1073/pnas.1406926111\">10.1073/pnas.1406926111</a>."},"day":"14","issue":"30","doi":"10.1073/pnas.1406926111","page":"10928-10932"},{"department":[{"_id":"JiFr"}],"corr_author":"1","date_updated":"2024-10-09T20:55:54Z","editor":[{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"publication_status":"published","type":"book_chapter","date_created":"2018-12-11T11:54:07Z","author":[{"full_name":"Baster, Pawel","last_name":"Baster","first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"quality_controlled":"1","publication":"Auxin and Its Role in Plant Development","abstract":[{"text":"The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants.","lang":"eng"}],"oa_version":"None","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","language":[{"iso":"eng"}],"page":"143 - 170","status":"public","date_published":"2014-04-01T00:00:00Z","doi":"10.1007/978-3-7091-1526-8_8","scopus_import":1,"month":"04","title":"Auxin on the road navigated by cellular PIN polarity","publist_id":"5304","day":"01","_id":"1806","year":"2014","citation":{"short":"P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.), Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170.","ieee":"P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,” in <i>Auxin and Its Role in Plant Development</i>, E. Zažímalová, J. Petrášek, and E. Benková, Eds. Springer, 2014, pp. 143–170.","chicago":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” In <i>Auxin and Its Role in Plant Development</i>, edited by Eva Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8_8\">https://doi.org/10.1007/978-3-7091-1526-8_8</a>.","ista":"Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity. In: Auxin and Its Role in Plant Development. , 143–170.","apa":"Baster, P., &#38; Friml, J. (2014). Auxin on the road navigated by cellular PIN polarity. In E. Zažímalová, J. Petrášek, &#38; E. Benková (Eds.), <i>Auxin and Its Role in Plant Development</i> (pp. 143–170). Springer. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8_8\">https://doi.org/10.1007/978-3-7091-1526-8_8</a>","ama":"Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In: Zažímalová E, Petrášek J, Benková E, eds. <i>Auxin and Its Role in Plant Development</i>. Springer; 2014:143-170. doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8_8\">10.1007/978-3-7091-1526-8_8</a>","mla":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” <i>Auxin and Its Role in Plant Development</i>, edited by Eva Zažímalová et al., Springer, 2014, pp. 143–70, doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8_8\">10.1007/978-3-7091-1526-8_8</a>."}},{"author":[{"full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814","last_name":"Huber","first_name":"Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"last_name":"Meerwald","first_name":"Peter","full_name":"Meerwald, Peter"},{"full_name":"Kwitt, Roland","first_name":"Roland","last_name":"Kwitt"}],"date_created":"2018-12-11T11:54:10Z","date_updated":"2024-10-09T20:55:54Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":24,"oa":1,"abstract":[{"text":"Watermarking techniques for vector graphics dislocate vertices in order to embed imperceptible, yet detectable, statistical features into the input data. The embedding process may result in a change of the topology of the input data, e.g., by introducing self-intersections, which is undesirable or even disastrous for many applications. In this paper we present a watermarking framework for two-dimensional vector graphics that employs conventional watermarking techniques but still provides the guarantee that the topology of the input data is preserved. The geometric part of this framework computes so-called maximum perturbation regions (MPR) of vertices. We propose two efficient algorithms to compute MPRs based on Voronoi diagrams and constrained triangulations. Furthermore, we present two algorithms to conditionally correct the watermarked data in order to increase the watermark embedding capacity and still guarantee topological correctness. While we focus on the watermarking of input formed by straight-line segments, one of our approaches can also be extended to circular arcs. We conclude the paper by demonstrating and analyzing the applicability of our framework in conjunction with two well-known watermarking techniques.","lang":"eng"}],"oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"intvolume":"        24","_id":"1816","pubrep_id":"443","year":"2014","date_published":"2014-03-16T00:00:00Z","title":"Topology-preserving watermarking of vector graphics","month":"03","scopus_import":1,"type":"journal_article","publication_status":"published","quality_controlled":"1","department":[{"_id":"HeEd"}],"corr_author":"1","file":[{"date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2016-443-v1+1_S0218195914500034.pdf","checksum":"be45c133ab4d43351260e21beaa8f4b1","access_level":"open_access","creator":"system","relation":"main_file","date_created":"2018-12-12T10:08:43Z","file_size":991734,"content_type":"application/pdf","file_id":"4704"}],"publisher":"World Scientific Publishing","has_accepted_license":"1","ddc":["000"],"publication":"International Journal of Computational Geometry and Applications","page":"61 - 86","file_date_updated":"2020-07-14T12:45:17Z","citation":{"short":"S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational Geometry and Applications 24 (2014) 61–86.","ieee":"S. Huber, M. Held, P. Meerwald, and R. Kwitt, “Topology-preserving watermarking of vector graphics,” <i>International Journal of Computational Geometry and Applications</i>, vol. 24, no. 1. World Scientific Publishing, pp. 61–86, 2014.","ista":"Huber S, Held M, Meerwald P, Kwitt R. 2014. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 24(1), 61–86.","chicago":"Huber, Stefan, Martin Held, Peter Meerwald, and Roland Kwitt. “Topology-Preserving Watermarking of Vector Graphics.” <i>International Journal of Computational Geometry and Applications</i>. World Scientific Publishing, 2014. <a href=\"https://doi.org/10.1142/S0218195914500034\">https://doi.org/10.1142/S0218195914500034</a>.","apa":"Huber, S., Held, M., Meerwald, P., &#38; Kwitt, R. (2014). Topology-preserving watermarking of vector graphics. <i>International Journal of Computational Geometry and Applications</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0218195914500034\">https://doi.org/10.1142/S0218195914500034</a>","ama":"Huber S, Held M, Meerwald P, Kwitt R. Topology-preserving watermarking of vector graphics. <i>International Journal of Computational Geometry and Applications</i>. 2014;24(1):61-86. doi:<a href=\"https://doi.org/10.1142/S0218195914500034\">10.1142/S0218195914500034</a>","mla":"Huber, Stefan, et al. “Topology-Preserving Watermarking of Vector Graphics.” <i>International Journal of Computational Geometry and Applications</i>, vol. 24, no. 1, World Scientific Publishing, 2014, pp. 61–86, doi:<a href=\"https://doi.org/10.1142/S0218195914500034\">10.1142/S0218195914500034</a>."},"day":"16","publist_id":"5290","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"Work by Martin Held and Stefan Huber was supported by Austrian Science Fund (FWF): L367-N15 and P25816-N15.","issue":"1","doi":"10.1142/S0218195914500034"},{"publication":"New Journal of Physics","publisher":"IOP Publishing","quality_controlled":"1","type":"journal_article","publication_status":"published","doi":"10.1088/1367-2630/16/9/093028","issue":"9","article_number":"093028","main_file_link":[{"url":"https://doi.org/10.1088/1367-2630/16/9/093028","open_access":"1"}],"citation":{"short":"J. Leonard, M. Lee, A. Morales, T.M. Karg, T. Esslinger, T. Donner, New Journal of Physics 16 (2014).","ieee":"J. Leonard, M. Lee, A. Morales, T. M. Karg, T. Esslinger, and T. Donner, “Optical transport and manipulation of an ultracold atomic cloud using focus-tunable lenses,” <i>New Journal of Physics</i>, vol. 16, no. 9. IOP Publishing, 2014.","chicago":"Leonard, Julian, Moonjoo Lee, Andrea Morales, Thomas M Karg, Tilman Esslinger, and Tobias Donner. “Optical Transport and Manipulation of an Ultracold Atomic Cloud Using Focus-Tunable Lenses.” <i>New Journal of Physics</i>. IOP Publishing, 2014. <a href=\"https://doi.org/10.1088/1367-2630/16/9/093028\">https://doi.org/10.1088/1367-2630/16/9/093028</a>.","ista":"Leonard J, Lee M, Morales A, Karg TM, Esslinger T, Donner T. 2014. Optical transport and manipulation of an ultracold atomic cloud using focus-tunable lenses. New Journal of Physics. 16(9), 093028.","apa":"Leonard, J., Lee, M., Morales, A., Karg, T. M., Esslinger, T., &#38; Donner, T. (2014). Optical transport and manipulation of an ultracold atomic cloud using focus-tunable lenses. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/16/9/093028\">https://doi.org/10.1088/1367-2630/16/9/093028</a>","ama":"Leonard J, Lee M, Morales A, Karg TM, Esslinger T, Donner T. Optical transport and manipulation of an ultracold atomic cloud using focus-tunable lenses. <i>New Journal of Physics</i>. 2014;16(9). doi:<a href=\"https://doi.org/10.1088/1367-2630/16/9/093028\">10.1088/1367-2630/16/9/093028</a>","mla":"Leonard, Julian, et al. “Optical Transport and Manipulation of an Ultracold Atomic Cloud Using Focus-Tunable Lenses.” <i>New Journal of Physics</i>, vol. 16, no. 9, 093028, IOP Publishing, 2014, doi:<a href=\"https://doi.org/10.1088/1367-2630/16/9/093028\">10.1088/1367-2630/16/9/093028</a>."},"day":"23","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We present an optical setup with focus-tunable lenses to dynamically control the waist and focus position of a laser beam, in which we transport a trapped ultracold cloud of 87Rb over a distance of \r\n. The scheme allows us to shift the focus position at constant waist, providing uniform trapping conditions over the full transport length. The fraction of atoms that are transported over the entire distance comes near to unity, while the heating of the cloud is in the range of a few microkelvin. We characterize the position stability of the focus and show that residual drift rates in focus position can be compensated for by counteracting with the tunable lenses. Beyond being a compact and robust scheme to transport ultracold atoms, the reported control of laser beams makes dynamic tailoring of trapping potentials possible. As an example, we steer the size of the atomic cloud by changing the waist size of the dipole beam."}],"volume":16,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-07T12:07:48Z","publication_identifier":{"issn":["1367-2630"]},"author":[{"id":"b75b3f45-7995-11ef-9bfd-9a9cd02c3577","last_name":"Leonard","first_name":"Julian","full_name":"Leonard, Julian"},{"first_name":"Moonjoo","last_name":"Lee","full_name":"Lee, Moonjoo"},{"last_name":"Morales","first_name":"Andrea","full_name":"Morales, Andrea"},{"first_name":"Thomas M","last_name":"Karg","full_name":"Karg, Thomas M"},{"full_name":"Esslinger, Tilman","first_name":"Tilman","last_name":"Esslinger"},{"last_name":"Donner","first_name":"Tobias","full_name":"Donner, Tobias"}],"date_created":"2024-10-07T11:50:00Z","title":"Optical transport and manipulation of an ultracold atomic cloud using focus-tunable lenses","scopus_import":"1","month":"09","extern":"1","date_published":"2014-09-23T00:00:00Z","year":"2014","_id":"18200","intvolume":"        16","article_type":"original","article_processing_charge":"Yes","language":[{"iso":"eng"}],"status":"public"},{"date_updated":"2025-09-29T13:13:35Z","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"date_created":"2018-12-11T11:54:11Z","author":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"abstract":[{"text":"We review recent progress towards a rigorous understanding of the Bogoliubov approximation for bosonic quantum many-body systems. We focus, in particular, on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A list of open problems will be discussed at the end.","lang":"eng"}],"oa_version":"Submitted Version","external_id":{"isi":["000341174600010"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"volume":55,"language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","date_published":"2014-06-26T00:00:00Z","month":"06","scopus_import":"1","title":"Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation","intvolume":"        55","year":"2014","_id":"1821","pubrep_id":"532","department":[{"_id":"RoSe"}],"file":[{"content_type":"application/pdf","file_size":269171,"file_id":"5172","file_name":"IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf","date_updated":"2020-07-14T12:45:17Z","creator":"system","access_level":"open_access","checksum":"ed0efc93c10f1341155f0316af617b82","relation":"main_file","date_created":"2018-12-12T10:15:49Z"}],"corr_author":"1","publication_status":"published","type":"journal_article","quality_controlled":"1","publication":"Journal of Mathematical Physics","ddc":["510","530"],"publisher":"American Institute of Physics","has_accepted_license":"1","file_date_updated":"2020-07-14T12:45:17Z","article_number":"1.4881536","doi":"10.1063/1.4881536","issue":"7","isi":1,"day":"26","publist_id":"5285","citation":{"ieee":"R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation,” <i>Journal of Mathematical Physics</i>, vol. 55, no. 7. American Institute of Physics, 2014.","short":"R. Seiringer, Journal of Mathematical Physics 55 (2014).","mla":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” <i>Journal of Mathematical Physics</i>, vol. 55, no. 7, 1.4881536, American Institute of Physics, 2014, doi:<a href=\"https://doi.org/10.1063/1.4881536\">10.1063/1.4881536</a>.","apa":"Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4881536\">https://doi.org/10.1063/1.4881536</a>","ama":"Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. <i>Journal of Mathematical Physics</i>. 2014;55(7). doi:<a href=\"https://doi.org/10.1063/1.4881536\">10.1063/1.4881536</a>","ista":"Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 55(7), 1.4881536.","chicago":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2014. <a href=\"https://doi.org/10.1063/1.4881536\">https://doi.org/10.1063/1.4881536</a>."}},{"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"        55","isi":1,"publist_id":"5284","day":"01","_id":"1822","year":"2014","citation":{"mla":"Jakšić, Vojkan, et al. “Introduction.” <i>Journal of Mathematical Physics</i>, vol. 55, no. 7, 075101, American Institute of Physics, 2014, doi:<a href=\"https://doi.org/10.1063/1.4884877\">10.1063/1.4884877</a>.","ama":"Jakšić V, Pillet C, Seiringer R. Introduction. <i>Journal of Mathematical Physics</i>. 2014;55(7). doi:<a href=\"https://doi.org/10.1063/1.4884877\">10.1063/1.4884877</a>","apa":"Jakšić, V., Pillet, C., &#38; Seiringer, R. (2014). Introduction. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4884877\">https://doi.org/10.1063/1.4884877</a>","ista":"Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical Physics. 55(7), 075101.","chicago":"Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2014. <a href=\"https://doi.org/10.1063/1.4884877\">https://doi.org/10.1063/1.4884877</a>.","ieee":"V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” <i>Journal of Mathematical Physics</i>, vol. 55, no. 7. American Institute of Physics, 2014.","short":"V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014)."},"article_number":"075101","date_published":"2014-07-01T00:00:00Z","doi":"10.1063/1.4884877","scopus_import":"1","issue":"7","month":"07","title":"Introduction","publication_status":"published","type":"journal_article","date_created":"2018-12-11T11:54:12Z","quality_controlled":"1","author":[{"first_name":"Vojkan","last_name":"Jakšić","full_name":"Jakšić, Vojkan"},{"first_name":"Claude","last_name":"Pillet","full_name":"Pillet, Claude"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"department":[{"_id":"RoSe"}],"date_updated":"2025-09-29T13:12:51Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000341174600001"]},"publisher":"American Institute of Physics","volume":55,"publication":"Journal of Mathematical Physics","oa_version":"None"},{"doi":"10.1007/978-3-319-03194-1_3","month":"01","scopus_import":1,"title":"Movement templates for learning of hitting and batting","date_published":"2014-01-01T00:00:00Z","day":"01","publist_id":"5274","_id":"1829","year":"2014","citation":{"mla":"Muelling, Katharina, et al. “Movement Templates for Learning of Hitting and Batting.” <i>Learning Motor Skills</i>, edited by Jens Kober and Jan Peters, vol. 97, Springer, 2014, pp. 69–82, doi:<a href=\"https://doi.org/10.1007/978-3-319-03194-1_3\">10.1007/978-3-319-03194-1_3</a>.","ama":"Muelling K, Kroemer O, Lampert C, Schölkopf B. Movement templates for learning of hitting and batting. In: Kober J, Peters J, eds. <i>Learning Motor Skills</i>. Vol 97. From Algorithms to Robot Experiments. Springer; 2014:69-82. doi:<a href=\"https://doi.org/10.1007/978-3-319-03194-1_3\">10.1007/978-3-319-03194-1_3</a>","apa":"Muelling, K., Kroemer, O., Lampert, C., &#38; Schölkopf, B. (2014). Movement templates for learning of hitting and batting. In J. Kober &#38; J. Peters (Eds.), <i>Learning Motor Skills</i> (Vol. 97, pp. 69–82). Springer. <a href=\"https://doi.org/10.1007/978-3-319-03194-1_3\">https://doi.org/10.1007/978-3-319-03194-1_3</a>","chicago":"Muelling, Katharina, Oliver Kroemer, Christoph Lampert, and Bernhard Schölkopf. “Movement Templates for Learning of Hitting and Batting.” In <i>Learning Motor Skills</i>, edited by Jens Kober and Jan Peters, 97:69–82. From Algorithms to Robot Experiments. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-03194-1_3\">https://doi.org/10.1007/978-3-319-03194-1_3</a>.","ista":"Muelling K, Kroemer O, Lampert C, Schölkopf B. 2014.Movement templates for learning of hitting and batting. In: Learning Motor Skills. Springer Tracts in Advanced Robotics, vol. 97, 69–82.","ieee":"K. Muelling, O. Kroemer, C. Lampert, and B. Schölkopf, “Movement templates for learning of hitting and batting,” in <i>Learning Motor Skills</i>, vol. 97, J. Kober and J. Peters, Eds. Springer, 2014, pp. 69–82.","short":"K. Muelling, O. Kroemer, C. Lampert, B. Schölkopf, in:, J. Kober, J. Peters (Eds.), Learning Motor Skills, Springer, 2014, pp. 69–82."},"intvolume":"        97","language":[{"iso":"eng"}],"status":"public","page":"69 - 82","oa_version":"None","publication":"Learning Motor Skills","abstract":[{"lang":"eng","text":"Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or baseball batting, depend on predictions where the ball can be intercepted and how it can properly be returned to the opponent. These predictions get more accurate over time, hence the behaviors need to be continuously modified. As a result, movement templates with a learned global shape need to be adapted during the execution so that the racket reaches a target position and velocity that will return the ball over to the other side of the net or court. It requires altering learned movements to hit a varying target with the necessary velocity at a specific instant in time. Such a task cannot be incorporated straightforwardly in most movement representations suitable for learning. For example, the standard formulation of the dynamical system based motor primitives (introduced by Ijspeert et al (2002b)) does not satisfy this property despite their flexibility which has allowed learning tasks ranging from locomotion to kendama. In order to fulfill this requirement, we reformulate the Ijspeert framework to incorporate the possibility of specifying a desired hitting point and a desired hitting velocity while maintaining all advantages of the original formulation.We show that the proposed movement template formulation works well in two scenarios, i.e., for hitting a ball on a string with a table tennis racket at a specified velocity and for returning balls launched by a ball gun successfully over the net using forehand movements."}],"volume":97,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","alternative_title":["Springer Tracts in Advanced Robotics"],"date_updated":"2021-01-12T06:53:28Z","department":[{"_id":"ChLa"}],"date_created":"2018-12-11T11:54:14Z","series_title":"From Algorithms to Robot Experiments","quality_controlled":"1","author":[{"full_name":"Muelling, Katharina","first_name":"Katharina","last_name":"Muelling"},{"full_name":"Kroemer, Oliver","last_name":"Kroemer","first_name":"Oliver"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"}],"publication_status":"published","editor":[{"full_name":"Kober, Jens","last_name":"Kober","first_name":"Jens"},{"first_name":"Jan","last_name":"Peters","full_name":"Peters, Jan"}],"type":"book_chapter"},{"page":"144-163","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","intvolume":"        50","day":"01","year":"2014","_id":"18353","citation":{"chicago":"Raviv, Dan, Alex M. Bronstein, Michael M. Bronstein, Dan Waisman, Nir Sochen, and Ron Kimmel. “Equi-Affine Invariant Geometry for Shape Analysis.” <i>Journal of Mathematical Imaging and Vision</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1007/s10851-013-0467-y\">https://doi.org/10.1007/s10851-013-0467-y</a>.","ista":"Raviv D, Bronstein AM, Bronstein MM, Waisman D, Sochen N, Kimmel R. 2014. Equi-affine invariant geometry for shape analysis. Journal of Mathematical Imaging and Vision. 50, 144–163.","ama":"Raviv D, Bronstein AM, Bronstein MM, Waisman D, Sochen N, Kimmel R. Equi-affine invariant geometry for shape analysis. <i>Journal of Mathematical Imaging and Vision</i>. 2014;50:144-163. doi:<a href=\"https://doi.org/10.1007/s10851-013-0467-y\">10.1007/s10851-013-0467-y</a>","apa":"Raviv, D., Bronstein, A. M., Bronstein, M. M., Waisman, D., Sochen, N., &#38; Kimmel, R. (2014). Equi-affine invariant geometry for shape analysis. <i>Journal of Mathematical Imaging and Vision</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10851-013-0467-y\">https://doi.org/10.1007/s10851-013-0467-y</a>","mla":"Raviv, Dan, et al. “Equi-Affine Invariant Geometry for Shape Analysis.” <i>Journal of Mathematical Imaging and Vision</i>, vol. 50, Springer Nature, 2014, pp. 144–63, doi:<a href=\"https://doi.org/10.1007/s10851-013-0467-y\">10.1007/s10851-013-0467-y</a>.","short":"D. Raviv, A.M. Bronstein, M.M. Bronstein, D. Waisman, N. Sochen, R. Kimmel, Journal of Mathematical Imaging and Vision 50 (2014) 144–163.","ieee":"D. Raviv, A. M. Bronstein, M. M. Bronstein, D. Waisman, N. Sochen, and R. Kimmel, “Equi-affine invariant geometry for shape analysis,” <i>Journal of Mathematical Imaging and Vision</i>, vol. 50. Springer Nature, pp. 144–163, 2014."},"date_published":"2014-09-01T00:00:00Z","doi":"10.1007/s10851-013-0467-y","extern":"1","scopus_import":"1","month":"09","title":"Equi-affine invariant geometry for shape analysis","publication_status":"published","type":"journal_article","date_created":"2024-10-15T11:20:54Z","author":[{"full_name":"Raviv, Dan","last_name":"Raviv","first_name":"Dan"},{"first_name":"Alexander","last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander"},{"full_name":"Bronstein, Michael M.","first_name":"Michael M.","last_name":"Bronstein"},{"first_name":"Dan","last_name":"Waisman","full_name":"Waisman, Dan"},{"last_name":"Sochen","first_name":"Nir","full_name":"Sochen, Nir"},{"full_name":"Kimmel, Ron","first_name":"Ron","last_name":"Kimmel"}],"quality_controlled":"1","publication_identifier":{"issn":["0924-9907"],"eissn":["1573-7683"]},"date_updated":"2024-11-12T08:51:43Z","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":50,"publication":"Journal of Mathematical Imaging and Vision","abstract":[{"lang":"eng","text":"Traditional models of bendable surfaces are based on the exact or approximate invariance to deformations that do not tear or stretch the shape, leaving intact an intrinsic geometry associated with it. These geometries are typically defined using either the shortest path length (geodesic distance), or properties of heat diffusion (diffusion distance) on the surface. Both measures are implicitly derived from the metric induced by the ambient Euclidean space. In this paper, we depart from this restrictive assumption by observing that a different choice of the metric results in a richer set of geometric invariants. We apply equi-affine geometry for analyzing arbitrary shapes with positive Gaussian curvature. The potential of the proposed framework is explored in a range of applications such as shape matching and retrieval, symmetry detection, and computation of Voroni tessellation. We show that in some shape analysis tasks, equi-affine-invariant intrinsic geometries often outperform their Euclidean-based counterparts. We further explore the potential of this metric in facial anthropometry of newborns. We show that intrinsic properties of this homogeneous group are better captured using the equi-affine metric."}],"oa_version":"None"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","conference":{"start_date":"2014-05-12","name":"4th Joint Workshop on Hands-Free Speech Communication and Microphone Arrays","end_date":"2014-05-14","location":"Villers-les-Nancy, France"},"title":"Supervised non-euclidean sparse NMF via bilevel optimization with applications to speech enhancement","extern":"1","month":"06","scopus_import":"1","doi":"10.1109/hscma.2014.6843241","date_published":"2014-06-26T00:00:00Z","article_number":"6843241","_id":"18384","citation":{"short":"P. Sprechmann, A.M. Bronstein, G. Sapiro, in:, 2014 4th Joint Workshop on Hands-Free Speech Communication and Microphone Arrays (HSCMA), IEEE, 2014.","ieee":"P. Sprechmann, A. M. Bronstein, and G. Sapiro, “Supervised non-euclidean sparse NMF via bilevel optimization with applications to speech enhancement,” in <i>2014 4th Joint Workshop on Hands-free Speech Communication and Microphone Arrays (HSCMA)</i>, Villers-les-Nancy, France, 2014.","mla":"Sprechmann, Pablo, et al. “Supervised Non-Euclidean Sparse NMF via Bilevel Optimization with Applications to Speech Enhancement.” <i>2014 4th Joint Workshop on Hands-Free Speech Communication and Microphone Arrays (HSCMA)</i>, 6843241, IEEE, 2014, doi:<a href=\"https://doi.org/10.1109/hscma.2014.6843241\">10.1109/hscma.2014.6843241</a>.","ista":"Sprechmann P, Bronstein AM, Sapiro G. 2014. Supervised non-euclidean sparse NMF via bilevel optimization with applications to speech enhancement. 2014 4th Joint Workshop on Hands-free Speech Communication and Microphone Arrays (HSCMA). 4th Joint Workshop on Hands-Free Speech Communication and Microphone Arrays, 6843241.","chicago":"Sprechmann, Pablo, Alex M. Bronstein, and Guillermo Sapiro. “Supervised Non-Euclidean Sparse NMF via Bilevel Optimization with Applications to Speech Enhancement.” In <i>2014 4th Joint Workshop on Hands-Free Speech Communication and Microphone Arrays (HSCMA)</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/hscma.2014.6843241\">https://doi.org/10.1109/hscma.2014.6843241</a>.","ama":"Sprechmann P, Bronstein AM, Sapiro G. Supervised non-euclidean sparse NMF via bilevel optimization with applications to speech enhancement. In: <i>2014 4th Joint Workshop on Hands-Free Speech Communication and Microphone Arrays (HSCMA)</i>. IEEE; 2014. doi:<a href=\"https://doi.org/10.1109/hscma.2014.6843241\">10.1109/hscma.2014.6843241</a>","apa":"Sprechmann, P., Bronstein, A. M., &#38; Sapiro, G. (2014). Supervised non-euclidean sparse NMF via bilevel optimization with applications to speech enhancement. In <i>2014 4th Joint Workshop on Hands-free Speech Communication and Microphone Arrays (HSCMA)</i>. Villers-les-Nancy, France: IEEE. <a href=\"https://doi.org/10.1109/hscma.2014.6843241\">https://doi.org/10.1109/hscma.2014.6843241</a>"},"year":"2014","day":"26","date_updated":"2024-12-04T13:47:13Z","publication_identifier":{"eisbn":["9781479931095"]},"author":[{"first_name":"Pablo","last_name":"Sprechmann","full_name":"Sprechmann, Pablo"},{"full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730","last_name":"Bronstein","first_name":"Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6"},{"full_name":"Sapiro, Guillermo","first_name":"Guillermo","last_name":"Sapiro"}],"quality_controlled":"1","date_created":"2024-10-15T11:20:54Z","type":"conference","publication_status":"published","oa_version":"None","abstract":[{"text":"Traditionally, NMF algorithms consist of two separate stages: a training stage, in which a generative model is learned; and a testing stage in which the pre-learned model is used in a high level task such as enhancement, separation, or classification. As an alternative, we propose a task-supervised NMF method for the adaptation of the basis spectra learned in the first stage to enhance the performance on the specific task used in the second stage. We cast this problem as a bilevel optimization program that can be efficiently solved via stochastic gradient descent. The proposed approach is general enough to handle sparsity priors of the activations, and allow non-Euclidean data terms such as β-divergences. The framework is evaluated on single-channel speech enhancement tasks.","lang":"eng"}],"publication":"2014 4th Joint Workshop on Hands-free Speech Communication and Microphone Arrays (HSCMA)","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE"},{"page":"171-180","citation":{"ista":"Litman R, Bronstein AM. 2014. Learning spectral descriptors for deformable shape correspondence. IEEE Transactions on Pattern Analysis and Machine Intelligence. 36(1), 171–180.","chicago":"Litman, R., and Alex M. Bronstein. “Learning Spectral Descriptors for Deformable Shape Correspondence.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/tpami.2013.148\">https://doi.org/10.1109/tpami.2013.148</a>.","ama":"Litman R, Bronstein AM. Learning spectral descriptors for deformable shape correspondence. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2014;36(1):171-180. doi:<a href=\"https://doi.org/10.1109/tpami.2013.148\">10.1109/tpami.2013.148</a>","apa":"Litman, R., &#38; Bronstein, A. M. (2014). Learning spectral descriptors for deformable shape correspondence. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/tpami.2013.148\">https://doi.org/10.1109/tpami.2013.148</a>","mla":"Litman, R., and Alex M. Bronstein. “Learning Spectral Descriptors for Deformable Shape Correspondence.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 1, IEEE, 2014, pp. 171–80, doi:<a href=\"https://doi.org/10.1109/tpami.2013.148\">10.1109/tpami.2013.148</a>.","short":"R. Litman, A.M. Bronstein, IEEE Transactions on Pattern Analysis and Machine Intelligence 36 (2014) 171–180.","ieee":"R. Litman and A. M. Bronstein, “Learning spectral descriptors for deformable shape correspondence,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 1. IEEE, pp. 171–180, 2014."},"day":"01","doi":"10.1109/tpami.2013.148","issue":"1","type":"journal_article","publication_status":"published","quality_controlled":"1","publisher":"IEEE","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"        36","_id":"18413","year":"2014","date_published":"2014-01-01T00:00:00Z","title":"Learning spectral descriptors for deformable shape correspondence","extern":"1","scopus_import":"1","month":"01","author":[{"full_name":"Litman, R.","first_name":"R.","last_name":"Litman"},{"id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander","last_name":"Bronstein","orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander"}],"date_created":"2024-10-15T11:20:55Z","publication_identifier":{"eissn":["1939-3539"],"issn":["0162-8828"]},"date_updated":"2024-12-12T12:42:56Z","external_id":{"pmid":["24231874"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pmid":1,"volume":36,"abstract":[{"lang":"eng","text":"Informative and discriminative feature descriptors play a fundamental role in deformable shape analysis. For example, they have been successfully employed in correspondence, registration, and retrieval tasks. In recent years, significant attention has been devoted to descriptors obtained from the spectral decomposition of the Laplace-Beltrami operator associated with the shape. Notable examples in this family are the heat kernel signature (HKS) and the recently introduced wave kernel signature (WKS). The Laplacian-based descriptors achieve state-of-the-art performance in numerous shape analysis tasks; they are computationally efficient, isometry-invariant by construction, and can gracefully cope with a variety of transformations. In this paper, we formulate a generic family of parametric spectral descriptors. We argue that to be optimized for a specific task, the descriptor should take into account the statistics of the corpus of shapes to which it is applied (the \"signal\") and those of the class of transformations to which it is made insensitive (the \"noise\"). While such statistics are hard to model axiomatically, they can be learned from examples. Following the spirit of the Wiener filter in signal processing, we show a learning scheme for the construction of optimized spectral descriptors and relate it to Mahalanobis metric learning. The superiority of the proposed approach in generating correspondences is demonstrated on synthetic and scanned human figures. We also show that the learned descriptors are robust enough to be learned on synthetic data and transferred successfully to scanned shapes."}],"oa_version":"None"},{"language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","date_published":"2014-04-01T00:00:00Z","title":"Multimodal similarity-preserving hashing","extern":"1","scopus_import":"1","month":"04","intvolume":"        36","year":"2014","_id":"18414","publication_identifier":{"eissn":["1939-3539"],"issn":["0162-8828"]},"date_updated":"2024-12-12T13:04:27Z","author":[{"last_name":"Masci","first_name":"Jonathan","full_name":"Masci, Jonathan"},{"first_name":"Michael M.","last_name":"Bronstein","full_name":"Bronstein, Michael M."},{"full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein","first_name":"Alexander"},{"full_name":"Schmidhuber, Jurgen","last_name":"Schmidhuber","first_name":"Jurgen"}],"date_created":"2024-10-15T11:20:55Z","abstract":[{"lang":"eng","text":"We introduce an efficient computational framework for hashing data belonging to multiple modalities into a single representation space where they become mutually comparable. The proposed approach is based on a novel coupled siamese neural network architecture and allows unified treatment of intra- and inter-modality similarity learning. Unlike existing cross-modality similarity learning approaches, our hashing functions are not limited to binarized linear projections and can assume arbitrarily complex forms. We show experimentally that our method significantly outperforms state-of-the-art hashing approaches on multimedia retrieval tasks."}],"oa_version":"Preprint","arxiv":1,"external_id":{"pmid":["26353203"],"arxiv":["1207.1522"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pmid":1,"volume":36,"oa":1,"page":"824-830","doi":"10.1109/tpami.2013.225","issue":"4","citation":{"ieee":"J. Masci, M. M. Bronstein, A. M. Bronstein, and J. Schmidhuber, “Multimodal similarity-preserving hashing,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 4. IEEE, pp. 824–830, 2014.","short":"J. Masci, M.M. Bronstein, A.M. Bronstein, J. Schmidhuber, IEEE Transactions on Pattern Analysis and Machine Intelligence 36 (2014) 824–830.","ama":"Masci J, Bronstein MM, Bronstein AM, Schmidhuber J. Multimodal similarity-preserving hashing. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2014;36(4):824-830. doi:<a href=\"https://doi.org/10.1109/tpami.2013.225\">10.1109/tpami.2013.225</a>","apa":"Masci, J., Bronstein, M. M., Bronstein, A. M., &#38; Schmidhuber, J. (2014). Multimodal similarity-preserving hashing. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/tpami.2013.225\">https://doi.org/10.1109/tpami.2013.225</a>","ista":"Masci J, Bronstein MM, Bronstein AM, Schmidhuber J. 2014. Multimodal similarity-preserving hashing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 36(4), 824–830.","chicago":"Masci, Jonathan, Michael M. Bronstein, Alex M. Bronstein, and Jurgen Schmidhuber. “Multimodal Similarity-Preserving Hashing.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/tpami.2013.225\">https://doi.org/10.1109/tpami.2013.225</a>.","mla":"Masci, Jonathan, et al. “Multimodal Similarity-Preserving Hashing.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 4, IEEE, 2014, pp. 824–30, doi:<a href=\"https://doi.org/10.1109/tpami.2013.225\">10.1109/tpami.2013.225</a>."},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1207.1522","open_access":"1"}],"day":"01","type":"journal_article","publication_status":"published","quality_controlled":"1","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","publisher":"IEEE"},{"publist_id":"5260","day":"14","isi":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.7004"}],"citation":{"short":"J. Cibulka, P. Gao, M. Krcál, T. Valla, P. Valtr, Discrete &#38; Computational Geometry 53 (2014) 64–79.","ieee":"J. Cibulka, P. Gao, M. Krcál, T. Valla, and P. Valtr, “On the geometric ramsey number of outerplanar graphs,” <i>Discrete &#38; Computational Geometry</i>, vol. 53, no. 1. Springer, pp. 64–79, 2014.","mla":"Cibulka, Josef, et al. “On the Geometric Ramsey Number of Outerplanar Graphs.” <i>Discrete &#38; Computational Geometry</i>, vol. 53, no. 1, Springer, 2014, pp. 64–79, doi:<a href=\"https://doi.org/10.1007/s00454-014-9646-x\">10.1007/s00454-014-9646-x</a>.","ista":"Cibulka J, Gao P, Krcál M, Valla T, Valtr P. 2014. On the geometric ramsey number of outerplanar graphs. Discrete &#38; Computational Geometry. 53(1), 64–79.","chicago":"Cibulka, Josef, Pu Gao, Marek Krcál, Tomáš Valla, and Pavel Valtr. “On the Geometric Ramsey Number of Outerplanar Graphs.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00454-014-9646-x\">https://doi.org/10.1007/s00454-014-9646-x</a>.","ama":"Cibulka J, Gao P, Krcál M, Valla T, Valtr P. On the geometric ramsey number of outerplanar graphs. <i>Discrete &#38; Computational Geometry</i>. 2014;53(1):64-79. doi:<a href=\"https://doi.org/10.1007/s00454-014-9646-x\">10.1007/s00454-014-9646-x</a>","apa":"Cibulka, J., Gao, P., Krcál, M., Valla, T., &#38; Valtr, P. (2014). On the geometric ramsey number of outerplanar graphs. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-014-9646-x\">https://doi.org/10.1007/s00454-014-9646-x</a>"},"issue":"1","doi":"10.1007/s00454-014-9646-x","acknowledgement":"Marek Krčál was supported by the ERC Advanced Grant No. 267165.","page":"64 - 79","publisher":"Springer","publication":"Discrete & Computational Geometry","publication_status":"published","type":"journal_article","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"intvolume":"        53","_id":"1842","year":"2014","date_published":"2014-11-14T00:00:00Z","month":"11","scopus_import":"1","title":"On the geometric ramsey number of outerplanar graphs","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"isi":["000346774600005"],"arxiv":["1310.7004"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":53,"oa":1,"abstract":[{"lang":"eng","text":"We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2 outerplanar triangulations in both convex and general cases. We also prove that the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by O(n3) and O(n10), in the convex and general case, respectively. We then apply similar methods to prove an (Formula presented.) upper bound on the Ramsey number of a path with n ordered vertices."}],"arxiv":1,"oa_version":"Submitted Version","date_created":"2018-12-11T11:54:18Z","author":[{"last_name":"Cibulka","first_name":"Josef","full_name":"Cibulka, Josef"},{"first_name":"Pu","last_name":"Gao","full_name":"Gao, Pu"},{"first_name":"Marek","last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek"},{"full_name":"Valla, Tomáš","first_name":"Tomáš","last_name":"Valla"},{"full_name":"Valtr, Pavel","first_name":"Pavel","last_name":"Valtr"}],"date_updated":"2025-09-29T13:11:56Z"},{"author":[{"first_name":"Roee","last_name":"Litman","full_name":"Litman, Roee"},{"full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein","first_name":"Alexander"},{"full_name":"Bronstein, Michael","last_name":"Bronstein","first_name":"Michael"},{"last_name":"Castellani","first_name":"Umberto","full_name":"Castellani, Umberto"}],"quality_controlled":"1","date_created":"2024-10-15T11:20:55Z","type":"journal_article","publication_status":"published","date_updated":"2024-12-19T10:20:12Z","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"volume":33,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","oa_version":"None","abstract":[{"text":"We present a method for supervised learning of shape descriptors for shape retrieval applications. Many content-based shape retrieval approaches follow the bag-of-features (BoF) paradigm commonly used in text and image retrieval by first computing local shape descriptors, and then representing them in a ‘geometric dictionary’ using vector quantization. A major drawback of such approaches is that the dictionary is constructed in an unsupervised manner using clustering, unaware of the last stage of the process (pooling of the local descriptors into a BoF, and comparison of the latter using some metric). In this paper, we replace the clustering with dictionary learning, where every atom acts as a feature, followed by sparse coding and pooling to get the final BoF descriptor. Both the dictionary and the sparse codes can be learned in the supervised regime via bi-level optimization using a task-specific objective that promotes invariance desired in the specific application. We show significant performance improvement on several standard shape retrieval benchmarks.","lang":"eng"}],"publication":"Computer Graphics Forum","status":"public","page":"127-136","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"18423","citation":{"short":"R. Litman, A.M. Bronstein, M. Bronstein, U. Castellani, Computer Graphics Forum 33 (2014) 127–136.","ieee":"R. Litman, A. M. Bronstein, M. Bronstein, and U. Castellani, “Supervised learning of bag‐of‐features shape descriptors using sparse coding,” <i>Computer Graphics Forum</i>, vol. 33, no. 5. Wiley, pp. 127–136, 2014.","mla":"Litman, Roee, et al. “Supervised Learning of Bag‐of‐features Shape Descriptors Using Sparse Coding.” <i>Computer Graphics Forum</i>, vol. 33, no. 5, Wiley, 2014, pp. 127–36, doi:<a href=\"https://doi.org/10.1111/cgf.12438\">10.1111/cgf.12438</a>.","ista":"Litman R, Bronstein AM, Bronstein M, Castellani U. 2014. Supervised learning of bag‐of‐features shape descriptors using sparse coding. Computer Graphics Forum. 33(5), 127–136.","chicago":"Litman, Roee, Alex M. Bronstein, Michael Bronstein, and Umberto Castellani. “Supervised Learning of Bag‐of‐features Shape Descriptors Using Sparse Coding.” <i>Computer Graphics Forum</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/cgf.12438\">https://doi.org/10.1111/cgf.12438</a>.","ama":"Litman R, Bronstein AM, Bronstein M, Castellani U. Supervised learning of bag‐of‐features shape descriptors using sparse coding. <i>Computer Graphics Forum</i>. 2014;33(5):127-136. doi:<a href=\"https://doi.org/10.1111/cgf.12438\">10.1111/cgf.12438</a>","apa":"Litman, R., Bronstein, A. M., Bronstein, M., &#38; Castellani, U. (2014). Supervised learning of bag‐of‐features shape descriptors using sparse coding. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.12438\">https://doi.org/10.1111/cgf.12438</a>"},"year":"2014","day":"01","intvolume":"        33","title":"Supervised learning of bag‐of‐features shape descriptors using sparse coding","month":"08","issue":"5","scopus_import":"1","doi":"10.1111/cgf.12438","extern":"1","date_published":"2014-08-01T00:00:00Z"},{"external_id":{"isi":["000350050700012"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":32,"oa":1,"abstract":[{"text":"Local protein interactions (&quot;molecular context&quot; effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.","lang":"eng"}],"oa_version":"Published Version","author":[{"full_name":"Risso, Valeria","first_name":"Valeria","last_name":"Risso"},{"full_name":"Manssour Triedo, Fadia","last_name":"Manssour Triedo","first_name":"Fadia"},{"full_name":"Delgado Delgado, Asuncion","first_name":"Asuncion","last_name":"Delgado Delgado"},{"first_name":"Rocio","last_name":"Arco","full_name":"Arco, Rocio"},{"last_name":"Barroso Deljesús","first_name":"Alicia","full_name":"Barroso Deljesús, Alicia"},{"orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","last_name":"Inglés Prieto"},{"first_name":"Raquel","last_name":"Godoy Ruiz","full_name":"Godoy Ruiz, Raquel"},{"last_name":"Gavira","first_name":"Josè","full_name":"Gavira, Josè"},{"last_name":"Gaucher","first_name":"Eric","full_name":"Gaucher, Eric"},{"last_name":"Ibarra Molero","first_name":"Beatriz","full_name":"Ibarra Molero, Beatriz"},{"last_name":"Sánchez Ruiz","first_name":"Jose","full_name":"Sánchez Ruiz, Jose"}],"date_created":"2018-12-11T11:54:19Z","date_updated":"2025-09-29T13:11:19Z","intvolume":"        32","year":"2014","_id":"1844","pubrep_id":"430","date_published":"2014-11-12T00:00:00Z","title":"Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history","scopus_import":"1","month":"11","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Oxford University Press","has_accepted_license":"1","publication":"Molecular Biology and Evolution","ddc":["571"],"type":"journal_article","publication_status":"published","quality_controlled":"1","department":[{"_id":"HaJa"}],"file":[{"relation":"main_file","date_created":"2018-12-12T10:16:56Z","date_updated":"2020-07-14T12:45:19Z","file_name":"IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf","creator":"system","checksum":"06215318e66be8f3e0c33abb07e9d3da","access_level":"open_access","file_id":"5247","content_type":"application/pdf","file_size":1545246}],"citation":{"ieee":"V. Risso <i>et al.</i>, “Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history,” <i>Molecular Biology and Evolution</i>, vol. 32, no. 2. Oxford University Press, pp. 440–455, 2014.","short":"V. Risso, F. Manssour Triedo, A. Delgado Delgado, R. Arco, A. Barroso Deljesús, Á. Inglés Prieto, R. Godoy Ruiz, J. Gavira, E. Gaucher, B. Ibarra Molero, J. Sánchez Ruiz, Molecular Biology and Evolution 32 (2014) 440–455.","mla":"Risso, Valeria, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” <i>Molecular Biology and Evolution</i>, vol. 32, no. 2, Oxford University Press, 2014, pp. 440–55, doi:<a href=\"https://doi.org/10.1093/molbev/msu312\">10.1093/molbev/msu312</a>.","apa":"Risso, V., Manssour Triedo, F., Delgado Delgado, A., Arco, R., Barroso Deljesús, A., Inglés Prieto, Á., … Sánchez Ruiz, J. (2014). Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msu312\">https://doi.org/10.1093/molbev/msu312</a>","ama":"Risso V, Manssour Triedo F, Delgado Delgado A, et al. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. <i>Molecular Biology and Evolution</i>. 2014;32(2):440-455. doi:<a href=\"https://doi.org/10.1093/molbev/msu312\">10.1093/molbev/msu312</a>","ista":"Risso V, Manssour Triedo F, Delgado Delgado A, Arco R, Barroso Deljesús A, Inglés Prieto Á, Godoy Ruiz R, Gavira J, Gaucher E, Ibarra Molero B, Sánchez Ruiz J. 2014. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 32(2), 440–455.","chicago":"Risso, Valeria, Fadia Manssour Triedo, Asuncion Delgado Delgado, Rocio Arco, Alicia Barroso Deljesús, Álvaro Inglés Prieto, Raquel Godoy Ruiz, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/molbev/msu312\">https://doi.org/10.1093/molbev/msu312</a>."},"day":"12","publist_id":"5257","isi":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"doi":"10.1093/molbev/msu312","issue":"2","page":"440 - 455","file_date_updated":"2020-07-14T12:45:19Z"},{"department":[{"_id":"JiFr"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","publication":"Current Biology","publisher":"Cell Press","page":"2335 - 2342","doi":"10.1016/j.cub.2014.08.036","issue":"19","acknowledgement":"This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). ","day":"06","isi":1,"publist_id":"5248","citation":{"ieee":"M. Sassi <i>et al.</i>, “An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis,” <i>Current Biology</i>, vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014.","short":"M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B. Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas, Current Biology 24 (2014) 2335–2342.","mla":"Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” <i>Current Biology</i>, vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:<a href=\"https://doi.org/10.1016/j.cub.2014.08.036\">10.1016/j.cub.2014.08.036</a>.","apa":"Sassi, M., Ali, O., Boudon, F., Cloarec, G., Abad, U., Cellier, C., … Traas, J. (2014). An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2014.08.036\">https://doi.org/10.1016/j.cub.2014.08.036</a>","ama":"Sassi M, Ali O, Boudon F, et al. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. <i>Current Biology</i>. 2014;24(19):2335-2342. doi:<a href=\"https://doi.org/10.1016/j.cub.2014.08.036\">10.1016/j.cub.2014.08.036</a>","chicago":"Sassi, Massimiliano, Olivier Ali, Frédéric Boudon, Gladys Cloarec, Ursula Abad, Coralie Cellier, Xu Chen, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” <i>Current Biology</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cub.2014.08.036\">https://doi.org/10.1016/j.cub.2014.08.036</a>.","ista":"Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B, Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. 2014. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 24(19), 2335–2342."},"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01074821","open_access":"1"}],"date_updated":"2025-09-29T13:10:45Z","date_created":"2018-12-11T11:54:22Z","author":[{"first_name":"Massimiliano","last_name":"Sassi","full_name":"Sassi, Massimiliano"},{"full_name":"Ali, Olivier","last_name":"Ali","first_name":"Olivier"},{"first_name":"Frédéric","last_name":"Boudon","full_name":"Boudon, Frédéric"},{"full_name":"Cloarec, Gladys","last_name":"Cloarec","first_name":"Gladys"},{"full_name":"Abad, Ursula","last_name":"Abad","first_name":"Ursula"},{"full_name":"Cellier, Coralie","last_name":"Cellier","first_name":"Coralie"},{"full_name":"Chen, Xu","last_name":"Chen","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin","last_name":"Gilles","full_name":"Gilles, Benjamin"},{"first_name":"Pascale","last_name":"Milani","full_name":"Milani, Pascale"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml"},{"full_name":"Vernoux, Teva","first_name":"Teva","last_name":"Vernoux"},{"full_name":"Godin, Christophe","last_name":"Godin","first_name":"Christophe"},{"first_name":"Olivier","last_name":"Hamant","full_name":"Hamant, Olivier"},{"full_name":"Traas, Jan","first_name":"Jan","last_name":"Traas"}],"oa_version":"Submitted Version","abstract":[{"text":"To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the individual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferentiated cells where complex changes in growth rates and directions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dynamics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, including AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner.","lang":"eng"}],"oa":1,"volume":24,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000342747600031"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","month":"10","title":"An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis","date_published":"2014-10-06T00:00:00Z","_id":"1852","year":"2014","intvolume":"        24"},{"language":[{"iso":"eng"}],"status":"public","conference":{"start_date":"2014-10-06","location":"Cambridge, USA","end_date":"2014-10-08","name":"IOT: Internet of Things"},"page":"85 - 90","title":"Game theoretic secure localization in wireless sensor networks","scopus_import":"1","doi":"10.1109/IOT.2014.7030120","month":"02","date_published":"2014-02-03T00:00:00Z","_id":"1853","citation":{"short":"S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90.","ieee":"S. Jha, S. Tripakis, S. Seshia, and K. Chatterjee, “Game theoretic secure localization in wireless sensor networks,” presented at the IOT: Internet of Things, Cambridge, USA, 2014, pp. 85–90.","mla":"Jha, Susmit, et al. <i>Game Theoretic Secure Localization in Wireless Sensor Networks</i>. IEEE, 2014, pp. 85–90, doi:<a href=\"https://doi.org/10.1109/IOT.2014.7030120\">10.1109/IOT.2014.7030120</a>.","chicago":"Jha, Susmit, Stavros Tripakis, Sanjit Seshia, and Krishnendu Chatterjee. “Game Theoretic Secure Localization in Wireless Sensor Networks,” 85–90. IEEE, 2014. <a href=\"https://doi.org/10.1109/IOT.2014.7030120\">https://doi.org/10.1109/IOT.2014.7030120</a>.","ista":"Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization in wireless sensor networks. IOT: Internet of Things, 85–90.","apa":"Jha, S., Tripakis, S., Seshia, S., &#38; Chatterjee, K. (2014). Game theoretic secure localization in wireless sensor networks (pp. 85–90). Presented at the IOT: Internet of Things, Cambridge, USA: IEEE. <a href=\"https://doi.org/10.1109/IOT.2014.7030120\">https://doi.org/10.1109/IOT.2014.7030120</a>","ama":"Jha S, Tripakis S, Seshia S, Chatterjee K. Game theoretic secure localization in wireless sensor networks. In: IEEE; 2014:85-90. doi:<a href=\"https://doi.org/10.1109/IOT.2014.7030120\">10.1109/IOT.2014.7030120</a>"},"year":"2014","day":"03","publist_id":"5247","date_updated":"2024-10-21T06:02:48Z","department":[{"_id":"KrCh"}],"quality_controlled":"1","author":[{"first_name":"Susmit","last_name":"Jha","full_name":"Jha, Susmit"},{"first_name":"Stavros","last_name":"Tripakis","full_name":"Tripakis, Stavros"},{"last_name":"Seshia","first_name":"Sanjit","full_name":"Seshia, Sanjit"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"}],"date_created":"2018-12-11T11:54:22Z","type":"conference","publication_status":"published","oa_version":"None","abstract":[{"lang":"eng","text":"Wireless sensor networks (WSNs) composed of low-power, low-cost sensor nodes are expected to form the backbone of future intelligent networks for a broad range of civil, industrial and military applications. These sensor nodes are often deployed through random spreading, and function in dynamic environments. Many applications of WSNs such as pollution tracking, forest fire detection, and military surveillance require knowledge of the location of constituent nodes. But the use of technologies such as GPS on all nodes is prohibitive due to power and cost constraints. So, the sensor nodes need to autonomously determine their locations. Most localization techniques use anchor nodes with known locations to determine the position of remaining nodes. Localization techniques have two conflicting requirements. On one hand, an ideal localization technique should be computationally simple and on the other hand, it must be resistant to attacks that compromise anchor nodes. In this paper, we propose a computationally light-weight game theoretic secure localization technique and demonstrate its effectiveness in comparison to existing techniques."}],"publisher":"IEEE","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"has_accepted_license":"1","publisher":"Wiley","ddc":["000"],"publication":"Computer Graphics Forum","quality_controlled":"1","publication_status":"published","type":"journal_article","file":[{"file_id":"5182","content_type":"application/pdf","file_size":24817484,"relation":"main_file","date_created":"2018-12-12T10:15:58Z","file_name":"IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf","date_updated":"2020-07-14T12:45:19Z","access_level":"open_access","checksum":"91946bfc509c77f5fd3151a3ff2b2c8f","creator":"system"}],"department":[{"_id":"ChWo"}],"isi":1,"publist_id":"5246","day":"05","citation":{"chicago":"Guerrero, Paul, Thomas Auzinger, Michael Wimmer, and Stefan Jeschke. “Partial Shape Matching Using Transformation Parameter Similarity.” <i>Computer Graphics Forum</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/cgf.12509\">https://doi.org/10.1111/cgf.12509</a>.","ista":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252.","ama":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. Partial shape matching using transformation parameter similarity. <i>Computer Graphics Forum</i>. 2014;34(1):239-252. doi:<a href=\"https://doi.org/10.1111/cgf.12509\">10.1111/cgf.12509</a>","apa":"Guerrero, P., Auzinger, T., Wimmer, M., &#38; Jeschke, S. (2014). Partial shape matching using transformation parameter similarity. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.12509\">https://doi.org/10.1111/cgf.12509</a>","mla":"Guerrero, Paul, et al. “Partial Shape Matching Using Transformation Parameter Similarity.” <i>Computer Graphics Forum</i>, vol. 34, no. 1, Wiley, 2014, pp. 239–52, doi:<a href=\"https://doi.org/10.1111/cgf.12509\">10.1111/cgf.12509</a>.","short":"P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 34 (2014) 239–252.","ieee":"P. Guerrero, T. Auzinger, M. Wimmer, and S. Jeschke, “Partial shape matching using transformation parameter similarity,” <i>Computer Graphics Forum</i>, vol. 34, no. 1. Wiley, pp. 239–252, 2014."},"doi":"10.1111/cgf.12509","issue":"1","page":"239 - 252","file_date_updated":"2020-07-14T12:45:19Z","volume":34,"oa":1,"external_id":{"isi":["000350145600019"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching. In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching."}],"date_created":"2018-12-11T11:54:22Z","author":[{"last_name":"Guerrero","first_name":"Paul","full_name":"Guerrero, Paul"},{"orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Auzinger"},{"full_name":"Wimmer, Michael","last_name":"Wimmer","first_name":"Michael"},{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke","first_name":"Stefan","full_name":"Jeschke, Stefan"}],"date_updated":"2025-09-23T09:47:49Z","year":"2014","_id":"1854","pubrep_id":"574","intvolume":"        34","scopus_import":"1","month":"11","title":"Partial shape matching using transformation parameter similarity","date_published":"2014-11-05T00:00:00Z","status":"public","article_processing_charge":"No","language":[{"iso":"eng"}]}]