[{"intvolume":"        68","doi":"10.1107/s1744309112034926","_id":"21154","author":[{"full_name":"Chakraborty, Arka","first_name":"Arka","last_name":"Chakraborty"},{"first_name":"Pradeep K","full_name":"Mandal, Pradeep K","orcid":"0000-0001-5996-956X","id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","last_name":"Mandal"},{"full_name":"Gautham, Namasivayam","first_name":"Namasivayam","last_name":"Gautham"}],"status":"public","oa_version":"None","fulldoi":"https://doi.org/10.1107/s1744309112034926","article_processing_charge":"No","language":[{"iso":"eng"}],"day":"01","OA_type":"closed access","publication_status":"published","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2012-10-01T00:00:00Z","abstract":[{"lang":"eng","text":"The crystal structure of the decamer sequence d(CCGGGACCGG)4 has previously been reported at 2.16 Å resolution as a four-way junction. Here, the structure of this sequence is reported at the significantly higher resolution of 1.6 Å, which is the highest resolution reported for a four-way junction. This allowed the unambiguous identification of an extensive hydration network with distinct patterns and solvent-mediated interactions that shed new light on the role of water in the formation and stabilization of junction structures."}],"citation":{"mla":"Chakraborty, Arka, et al. “Structure of d(CCGGGACCGG)4 as a Four-Way Junction at 1.6 Å Resolution: New Insights into Solvent Interactions.” <i>Acta Crystallographica Section F Structural Biology Communications</i>, vol. 68, no. 10, International Union of Crystallography, 2012, pp. 1169–74, doi:<a href=\"https://doi.org/10.1107/s1744309112034926\">10.1107/s1744309112034926</a>.","ista":"Chakraborty A, Mandal PK, Gautham N. 2012. Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6 Å resolution: New insights into solvent interactions. Acta Crystallographica Section F Structural Biology Communications. 68(10), 1169–1174.","short":"A. Chakraborty, P.K. Mandal, N. Gautham, Acta Crystallographica Section F Structural Biology Communications 68 (2012) 1169–1174.","apa":"Chakraborty, A., Mandal, P. K., &#38; Gautham, N. (2012). Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6 Å resolution: New insights into solvent interactions. <i>Acta Crystallographica Section F Structural Biology Communications</i>. International Union of Crystallography. <a href=\"https://doi.org/10.1107/s1744309112034926\">https://doi.org/10.1107/s1744309112034926</a>","ieee":"A. Chakraborty, P. K. Mandal, and N. Gautham, “Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6 Å resolution: New insights into solvent interactions,” <i>Acta Crystallographica Section F Structural Biology Communications</i>, vol. 68, no. 10. International Union of Crystallography, pp. 1169–1174, 2012.","chicago":"Chakraborty, Arka, Pradeep K Mandal, and Namasivayam Gautham. “Structure of d(CCGGGACCGG)4 as a Four-Way Junction at 1.6 Å Resolution: New Insights into Solvent Interactions.” <i>Acta Crystallographica Section F Structural Biology Communications</i>. International Union of Crystallography, 2012. <a href=\"https://doi.org/10.1107/s1744309112034926\">https://doi.org/10.1107/s1744309112034926</a>.","ama":"Chakraborty A, Mandal PK, Gautham N. Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6 Å resolution: New insights into solvent interactions. <i>Acta Crystallographica Section F Structural Biology Communications</i>. 2012;68(10):1169-1174. doi:<a href=\"https://doi.org/10.1107/s1744309112034926\">10.1107/s1744309112034926</a>"},"title":"Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6 Å resolution: New insights into solvent interactions","month":"10","page":"1169-1174","type":"journal_article","publisher":"International Union of Crystallography","publication_identifier":{"issn":["1744-3091"]},"article_type":"original","date_updated":"2026-02-23T08:21:09Z","extern":"1","date_created":"2026-02-06T12:19:40Z","issue":"10","volume":68,"publication":"Acta Crystallographica Section F Structural Biology Communications","has_accepted_license":"1"},{"publist_id":"4908","fulldoi":"https://doi.org/10.1214/11-AOP662","doi":"10.1214/11-AOP662","intvolume":"        40","_id":"2125","author":[{"first_name":"Martin","full_name":"Hairer, Martin M","last_name":"Hairer"},{"full_name":"Jan Maas","first_name":"Jan","last_name":"Maas","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"page":"1675 - 1714","quality_controlled":0,"status":"public","type":"journal_article","publisher":"Institute of Mathematical Statistics","date_updated":"2021-01-12T06:55:27Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1011.0966"}],"day":"01","extern":1,"oa":1,"volume":40,"abstract":[{"text":"We consider a class of stochastic PDEs of Burgers type in spatial dimension 1, driven by space–time white noise. Even though it is well known that these equations are well posed, it turns out that if one performs a spatial discretization of the nonlinearity in the “wrong” way, then the sequence of approximate equations does converge to a limit, but this limit exhibits an additional correction term. This correction term is proportional to the local quadratic cross-variation (in space) of the gradient of the conserved quantity with the solution itself. This can be understood as a consequence of the fact that for any fixed time, the law of the solution is locally equivalent to Wiener measure, where space plays the role of time. In this sense, the correction term is similar to the usual Itô–Stratonovich correction term that arises when one considers different temporal discretizations of stochastic ODEs.","lang":"eng"}],"date_published":"2012-07-01T00:00:00Z","month":"07","citation":{"short":"M. Hairer, J. Maas, Annals of Probability 40 (2012) 1675–1714.","ieee":"M. Hairer and J. Maas, “A spatial version of the Itô-Stratonovich correction,” <i>Annals of Probability</i>, vol. 40, no. 4. Institute of Mathematical Statistics, pp. 1675–1714, 2012.","apa":"Hairer, M., &#38; Maas, J. (2012). A spatial version of the Itô-Stratonovich correction. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/11-AOP662\">https://doi.org/10.1214/11-AOP662</a>","ama":"Hairer M, Maas J. A spatial version of the Itô-Stratonovich correction. <i>Annals of Probability</i>. 2012;40(4):1675-1714. doi:<a href=\"https://doi.org/10.1214/11-AOP662\">10.1214/11-AOP662</a>","chicago":"Hairer, Martin, and Jan Maas. “A Spatial Version of the Itô-Stratonovich Correction.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2012. <a href=\"https://doi.org/10.1214/11-AOP662\">https://doi.org/10.1214/11-AOP662</a>.","mla":"Hairer, Martin, and Jan Maas. “A Spatial Version of the Itô-Stratonovich Correction.” <i>Annals of Probability</i>, vol. 40, no. 4, Institute of Mathematical Statistics, 2012, pp. 1675–714, doi:<a href=\"https://doi.org/10.1214/11-AOP662\">10.1214/11-AOP662</a>.","ista":"Hairer M, Maas J. 2012. A spatial version of the Itô-Stratonovich correction. Annals of Probability. 40(4), 1675–1714."},"title":"A spatial version of the Itô-Stratonovich correction","publication":"Annals of Probability","acknowledgement":"Supported by Rubicon Grant 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). Supported by the EPSRC Grants EP/E002269/1 and EP/D071593/1, a Wolfson Research Merit Award of the Royal Society and a Philip Leverhulme prize of the Lev","year":"2012","date_created":"2018-12-11T11:55:51Z","issue":"4"},{"type":"journal_article","publisher":"Springer","doi":"10.1007/s00205-012-0554-z","intvolume":"       206","_id":"2127","status":"public","quality_controlled":0,"page":"997 - 1038","author":[{"first_name":"Matthias","full_name":"Erbar, Matthias","last_name":"Erbar"},{"first_name":"Jan","full_name":"Jan Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","last_name":"Maas"}],"publist_id":"4906","fulldoi":"https://doi.org/10.1007/s00205-012-0554-z","date_updated":"2021-01-12T06:55:28Z","day":"01","extern":1,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1111.2687","open_access":"1"}],"publication_status":"published","date_created":"2018-12-11T11:55:52Z","issue":"3","year":"2012","publication":"Archive for Rational Mechanics and Analysis","citation":{"ista":"Erbar M, Maas J. 2012. Ricci curvature of finite Markov chains via convexity of the entropy. Archive for Rational Mechanics and Analysis. 206(3), 997–1038.","mla":"Erbar, Matthias, and Jan Maas. “Ricci Curvature of Finite Markov Chains via Convexity of the Entropy.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 206, no. 3, Springer, 2012, pp. 997–1038, doi:<a href=\"https://doi.org/10.1007/s00205-012-0554-z\">10.1007/s00205-012-0554-z</a>.","short":"M. Erbar, J. Maas, Archive for Rational Mechanics and Analysis 206 (2012) 997–1038.","ieee":"M. Erbar and J. Maas, “Ricci curvature of finite Markov chains via convexity of the entropy,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 206, no. 3. Springer, pp. 997–1038, 2012.","apa":"Erbar, M., &#38; Maas, J. (2012). Ricci curvature of finite Markov chains via convexity of the entropy. <i>Archive for Rational Mechanics and Analysis</i>. Springer. <a href=\"https://doi.org/10.1007/s00205-012-0554-z\">https://doi.org/10.1007/s00205-012-0554-z</a>","ama":"Erbar M, Maas J. Ricci curvature of finite Markov chains via convexity of the entropy. <i>Archive for Rational Mechanics and Analysis</i>. 2012;206(3):997-1038. doi:<a href=\"https://doi.org/10.1007/s00205-012-0554-z\">10.1007/s00205-012-0554-z</a>","chicago":"Erbar, Matthias, and Jan Maas. “Ricci Curvature of Finite Markov Chains via Convexity of the Entropy.” <i>Archive for Rational Mechanics and Analysis</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s00205-012-0554-z\">https://doi.org/10.1007/s00205-012-0554-z</a>."},"title":"Ricci curvature of finite Markov chains via convexity of the entropy","month":"12","acknowledgement":"Jan Maas is supported by Rubicon subsidy 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO).","volume":206,"abstract":[{"lang":"eng","text":"We study a new notion of Ricci curvature that applies to Markov chains on discrete spaces. This notion relies on geodesic convexity of the entropy and is analogous to the one introduced by Lott, Sturm, and Villani for geodesic measure spaces. In order to apply to the discrete setting, the role of the Wasserstein metric is taken over by a different metric, having the property that continuous time Markov chains are gradient flows of the entropy. Using this notion of Ricci curvature we prove discrete analogues of fundamental results by Bakry–Émery and Otto–Villani. Further, we show that Ricci curvature bounds are preserved under tensorisation. As a special case we obtain the sharp Ricci curvature lower bound for the discrete hypercube."}],"date_published":"2012-12-01T00:00:00Z"},{"publist_id":"4907","fulldoi":"https://doi.org/10.1007/s11512-010-0143-z","doi":"10.1007/s11512-010-0143-z","intvolume":"        50","author":[{"last_name":"Maas","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Jan Maas","first_name":"Jan"},{"last_name":"Van Neerven","full_name":"van Neerven, Jan M","first_name":"Jan"},{"last_name":"Portal","full_name":"Portal, Pierre","first_name":"Pierre"}],"_id":"2128","page":"379 - 395","quality_controlled":0,"status":"public","type":"journal_article","publisher":"Springer","date_updated":"2021-01-12T06:55:28Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1002.4911"}],"day":"01","extern":1,"oa":1,"abstract":[{"text":"We introduce a technique for handling Whitney decompositions in Gaussian harmonic analysis and apply it to the study of Gaussian analogues of the classical tent spaces T 1,q of Coifman–Meyer–Stein.","lang":"eng"}],"volume":50,"date_published":"2012-10-01T00:00:00Z","citation":{"mla":"Maas, Jan, et al. “Whitney Coverings and the Tent Spaces T 1,q (γ) for the Gaussian Measure.” <i>Arkiv För Matematik</i>, vol. 50, no. 2, Springer, 2012, pp. 379–95, doi:<a href=\"https://doi.org/10.1007/s11512-010-0143-z\">10.1007/s11512-010-0143-z</a>.","ista":"Maas J, Van Neerven J, Portal P. 2012. Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure. Arkiv för Matematik. 50(2), 379–395.","ieee":"J. Maas, J. Van Neerven, and P. Portal, “Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure,” <i>Arkiv för Matematik</i>, vol. 50, no. 2. Springer, pp. 379–395, 2012.","short":"J. Maas, J. Van Neerven, P. Portal, Arkiv För Matematik 50 (2012) 379–395.","apa":"Maas, J., Van Neerven, J., &#38; Portal, P. (2012). Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure. <i>Arkiv För Matematik</i>. Springer. <a href=\"https://doi.org/10.1007/s11512-010-0143-z\">https://doi.org/10.1007/s11512-010-0143-z</a>","chicago":"Maas, Jan, Jan Van Neerven, and Pierre Portal. “Whitney Coverings and the Tent Spaces T 1,q (γ) for the Gaussian Measure.” <i>Arkiv För Matematik</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s11512-010-0143-z\">https://doi.org/10.1007/s11512-010-0143-z</a>.","ama":"Maas J, Van Neerven J, Portal P. Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure. <i>Arkiv för Matematik</i>. 2012;50(2):379-395. doi:<a href=\"https://doi.org/10.1007/s11512-010-0143-z\">10.1007/s11512-010-0143-z</a>"},"title":"Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure","publication":"Arkiv för Matematik","month":"10","acknowledgement":"J. Maas was supported by Rubicon subsidy 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). J. van Neerven was supported by VICI subsidy 639.033.604 of the Netherlands Organisation for Scientific Research (NWO).","year":"2012","date_created":"2018-12-11T11:55:52Z","issue":"2"},{"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"pmid":1,"type":"journal_article","publisher":"American Chemical Society","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"page":"19564-19567","date_updated":"2024-10-14T12:21:27Z","article_type":"original","extern":"1","publication":"Journal of the American Chemical Society","volume":134,"date_created":"2023-08-01T09:47:42Z","issue":"48","fulldoi":"https://doi.org/10.1021/ja309633v","oa_version":"Published Version","doi":"10.1021/ja309633v","intvolume":"       134","_id":"13407","quality_controlled":"1","status":"public","author":[{"last_name":"Chovnik","full_name":"Chovnik, Olga","first_name":"Olga"},{"last_name":"Balgley","first_name":"Renata","full_name":"Balgley, Renata"},{"last_name":"Goldman","first_name":"Joel R.","full_name":"Goldman, Joel R."},{"full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"scopus_import":"1","article_processing_charge":"No","external_id":{"pmid":["23181449"]},"publication_status":"published","day":"26","language":[{"iso":"eng"}],"title":"Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets","month":"11","citation":{"mla":"Chovnik, Olga, et al. “Dynamically Self-Assembling Carriers Enable Guiding of Diamagnetic Particles by Weak Magnets.” <i>Journal of the American Chemical Society</i>, vol. 134, no. 48, American Chemical Society, 2012, pp. 19564–67, doi:<a href=\"https://doi.org/10.1021/ja309633v\">10.1021/ja309633v</a>.","ista":"Chovnik O, Balgley R, Goldman JR, Klajn R. 2012. Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. Journal of the American Chemical Society. 134(48), 19564–19567.","short":"O. Chovnik, R. Balgley, J.R. Goldman, R. Klajn, Journal of the American Chemical Society 134 (2012) 19564–19567.","apa":"Chovnik, O., Balgley, R., Goldman, J. R., &#38; Klajn, R. (2012). Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja309633v\">https://doi.org/10.1021/ja309633v</a>","ieee":"O. Chovnik, R. Balgley, J. R. Goldman, and R. Klajn, “Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets,” <i>Journal of the American Chemical Society</i>, vol. 134, no. 48. American Chemical Society, pp. 19564–19567, 2012.","chicago":"Chovnik, Olga, Renata Balgley, Joel R. Goldman, and Rafal Klajn. “Dynamically Self-Assembling Carriers Enable Guiding of Diamagnetic Particles by Weak Magnets.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2012. <a href=\"https://doi.org/10.1021/ja309633v\">https://doi.org/10.1021/ja309633v</a>.","ama":"Chovnik O, Balgley R, Goldman JR, Klajn R. Dynamically self-assembling carriers enable guiding of diamagnetic particles by weak magnets. <i>Journal of the American Chemical Society</i>. 2012;134(48):19564-19567. doi:<a href=\"https://doi.org/10.1021/ja309633v\">10.1021/ja309633v</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We show that diamagnetic particles can be remotely manipulated by a magnet by the reversible adsorption of dual-responsive, light-switchable/superparamagnetic nanoparticles down to their surface. Adsorption occurs upon exposure to UV light, and can be reversed thermally or by ambient light. The dynamic self-assembly of thin films of the dual-responsive nanoparticles induces attractive interactions between diamagnetic particles. We demonstrate that catalytic amounts of the dual-responsive nanoparticles are sufficient to magnetically guide and deliver the diamagnetic particles to desired locations, where they can then be released by disassembling the dynamic layers of superparamagnetic nanoparticles with visible light."}],"date_published":"2012-11-26T00:00:00Z","year":"2012"},{"pmid":1,"publication_identifier":{"eissn":["1613-6829"],"issn":["1613-6810"]},"keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"page":"654-660","publisher":"Wiley","type":"journal_article","date_updated":"2024-10-14T12:21:38Z","article_type":"original","extern":"1","volume":8,"publication":"Small","issue":"5","date_created":"2023-08-01T09:47:55Z","fulldoi":"https://doi.org/10.1002/smll.201101882","status":"public","_id":"13408","author":[{"first_name":"Yonatan","full_name":"Ridelman, Yonatan","last_name":"Ridelman"},{"last_name":"Singh","full_name":"Singh, Gurvinder","first_name":"Gurvinder"},{"first_name":"Ronit","full_name":"Popovitz-Biro, Ronit","last_name":"Popovitz-Biro"},{"first_name":"Sharon G.","full_name":"Wolf, Sharon G.","last_name":"Wolf"},{"last_name":"Das","full_name":"Das, Sanjib","first_name":"Sanjib"},{"full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"quality_controlled":"1","intvolume":"         8","doi":"10.1002/smll.201101882","oa_version":"None","article_processing_charge":"No","scopus_import":"1","external_id":{"pmid":["22392681"]},"publication_status":"published","day":"12","language":[{"iso":"eng"}],"abstract":[{"text":"Well-defined metallic nanobowls can be prepared by extending the concept of a protecting group to colloidal synthesis. Magnetic nanoparticles are employed as “protecting groups” during the galvanic replacement of silver with gold. The replacement reaction is accompanied by spontantous dissociation of the protecting groups, leaving behind metallic nanobowls.","lang":"eng"}],"date_published":"2012-03-12T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","title":"Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles","citation":{"ista":"Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. 2012. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 8(5), 654–660.","mla":"Ridelman, Yonatan, et al. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” <i>Small</i>, vol. 8, no. 5, Wiley, 2012, pp. 654–60, doi:<a href=\"https://doi.org/10.1002/smll.201101882\">10.1002/smll.201101882</a>.","chicago":"Ridelman, Yonatan, Gurvinder Singh, Ronit Popovitz-Biro, Sharon G. Wolf, Sanjib Das, and Rafal Klajn. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” <i>Small</i>. Wiley, 2012. <a href=\"https://doi.org/10.1002/smll.201101882\">https://doi.org/10.1002/smll.201101882</a>.","ama":"Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. <i>Small</i>. 2012;8(5):654-660. doi:<a href=\"https://doi.org/10.1002/smll.201101882\">10.1002/smll.201101882</a>","short":"Y. Ridelman, G. Singh, R. Popovitz-Biro, S.G. Wolf, S. Das, R. Klajn, Small 8 (2012) 654–660.","ieee":"Y. Ridelman, G. Singh, R. Popovitz-Biro, S. G. Wolf, S. Das, and R. Klajn, “Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles,” <i>Small</i>, vol. 8, no. 5. Wiley, pp. 654–660, 2012.","apa":"Ridelman, Y., Singh, G., Popovitz-Biro, R., Wolf, S. G., Das, S., &#38; Klajn, R. (2012). Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. <i>Small</i>. Wiley. <a href=\"https://doi.org/10.1002/smll.201101882\">https://doi.org/10.1002/smll.201101882</a>"},"year":"2012"},{"date_created":"2018-12-11T11:51:42Z","ec_funded":1,"publication":"Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering","acknowledgement":"This  research  was  supported  by  the  Canadian  NSERC grant   RGPIN   341819-07,    the   ERC   Advanced   Grant QUAREM, and the Austrian Science Fund NFN RiSE.","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1109.6926","open_access":"1"}],"date_updated":"2025-06-11T08:07:37Z","type":"conference","publisher":"ACM","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Software model checking, as an undecidable problem, has three possible outcomes: (1) the program satisfies the specification, (2) the program does not satisfy the specification, and (3) the model checker fails. The third outcome usually manifests itself in a space-out, time-out, or one component of the verification tool giving up; in all of these failing cases, significant computation is performed by the verification tool before the failure, but no result is reported. We propose to reformulate the model-checking problem as follows, in order to have the verification tool report a summary of the performed work even in case of failure: given a program and a specification, the model checker returns a condition Ψ - usually a state predicate - such that the program satisfies the specification under the condition Ψ - that is, as long as the program does not leave the states in which Ψ is satisfied. In our experiments, we investigated as one major application of conditional model checking the sequential combination of model checkers with information passing. We give the condition that one model checker produces, as input to a second conditional model checker, such that the verification problem for the second is restricted to the part of the state space that is not covered by the condition, i.e., the second model checker works on the problems that the first model checker could not solve. Our experiments demonstrate that repeated application of conditional model checkers, passing information from one model checker to the next, can significantly improve the verification results and performance, i.e., we can now verify programs that we could not verify before."}],"date_published":"2012-11-01T00:00:00Z","citation":{"ama":"Beyer D, Henzinger TA, Keremoglu M, Wendler P. Conditional model checking: A technique to pass information between verifiers. In: <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>. ACM; 2012. doi:<a href=\"https://doi.org/10.1145/2393596.2393664\">10.1145/2393596.2393664</a>","chicago":"Beyer, Dirk, Thomas A Henzinger, Mehmet Keremoglu, and Philipp Wendler. “Conditional Model Checking: A Technique to Pass Information between Verifiers.” In <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>. ACM, 2012. <a href=\"https://doi.org/10.1145/2393596.2393664\">https://doi.org/10.1145/2393596.2393664</a>.","ieee":"D. Beyer, T. A. Henzinger, M. Keremoglu, and P. Wendler, “Conditional model checking: A technique to pass information between verifiers,” in <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>, Cary, NC, USA, 2012.","short":"D. Beyer, T.A. Henzinger, M. Keremoglu, P. Wendler, in:, Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering, ACM, 2012.","apa":"Beyer, D., Henzinger, T. A., Keremoglu, M., &#38; Wendler, P. (2012). Conditional model checking: A technique to pass information between verifiers. In <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>. Cary, NC, USA: ACM. <a href=\"https://doi.org/10.1145/2393596.2393664\">https://doi.org/10.1145/2393596.2393664</a>","mla":"Beyer, Dirk, et al. “Conditional Model Checking: A Technique to Pass Information between Verifiers.” <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>, 57, ACM, 2012, doi:<a href=\"https://doi.org/10.1145/2393596.2393664\">10.1145/2393596.2393664</a>.","ista":"Beyer D, Henzinger TA, Keremoglu M, Wendler P. 2012. Conditional model checking: A technique to pass information between verifiers. Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering. FSE: Foundations of Software Engineering, 57."},"title":"Conditional model checking: A technique to pass information between verifiers","month":"11","day":"01","language":[{"iso":"eng"}],"project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","department":[{"_id":"ToHe"}],"conference":{"end_date":"2012-11-16","location":"Cary, NC, USA","start_date":"2012-11-11","name":"FSE: Foundations of Software Engineering"},"external_id":{"arxiv":["1109.6926"]},"article_number":"57","article_processing_charge":"No","arxiv":1,"scopus_import":"1","doi":"10.1145/2393596.2393664","_id":"1384","status":"public","quality_controlled":"1","author":[{"full_name":"Beyer, Dirk","first_name":"Dirk","last_name":"Beyer"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"last_name":"Keremoglu","full_name":"Keremoglu, Mehmet","first_name":"Mehmet"},{"first_name":"Philipp","full_name":"Wendler, Philipp","last_name":"Wendler"}],"oa_version":"Preprint","publist_id":"5826","fulldoi":"https://doi.org/10.1145/2393596.2393664"},{"date_updated":"2021-01-12T06:50:58Z","fulldoi":"https://doi.org/10.2140/gt.2012.16.1609","publist_id":"5726","publisher":"University of Warwick","type":"journal_article","_id":"1471","quality_controlled":0,"author":[{"last_name":"Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Tamas Hausel","first_name":"Tamas"},{"last_name":"Pauly","first_name":"Christian","full_name":"Pauly, Christian"}],"status":"public","page":"1609 - 1638","intvolume":"        16","doi":"10.2140/gt.2012.16.1609","title":"Prym varieties of spectral covers","citation":{"ista":"Hausel T, Pauly C. 2012. Prym varieties of spectral covers. Geometry and Topology. 16(3), 1609–1638.","mla":"Hausel, Tamás, and Christian Pauly. “Prym Varieties of Spectral Covers.” <i>Geometry and Topology</i>, vol. 16, no. 3, University of Warwick, 2012, pp. 1609–38, doi:<a href=\"https://doi.org/10.2140/gt.2012.16.1609\">10.2140/gt.2012.16.1609</a>.","ama":"Hausel T, Pauly C. Prym varieties of spectral covers. <i>Geometry and Topology</i>. 2012;16(3):1609-1638. doi:<a href=\"https://doi.org/10.2140/gt.2012.16.1609\">10.2140/gt.2012.16.1609</a>","chicago":"Hausel, Tamás, and Christian Pauly. “Prym Varieties of Spectral Covers.” <i>Geometry and Topology</i>. University of Warwick, 2012. <a href=\"https://doi.org/10.2140/gt.2012.16.1609\">https://doi.org/10.2140/gt.2012.16.1609</a>.","apa":"Hausel, T., &#38; Pauly, C. (2012). Prym varieties of spectral covers. <i>Geometry and Topology</i>. University of Warwick. <a href=\"https://doi.org/10.2140/gt.2012.16.1609\">https://doi.org/10.2140/gt.2012.16.1609</a>","ieee":"T. Hausel and C. Pauly, “Prym varieties of spectral covers,” <i>Geometry and Topology</i>, vol. 16, no. 3. University of Warwick, pp. 1609–1638, 2012.","short":"T. Hausel, C. Pauly, Geometry and Topology 16 (2012) 1609–1638."},"publication":"Geometry and Topology","month":"08","volume":16,"abstract":[{"text":"Given a possibly reducible and non-reduced spectral cover π: X → C over a smooth projective complex curve C we determine the group of connected components of the Prym variety Prym(X/C). As an immediate application we show that the finite group of n-torsion points of the Jacobian of C acts trivially on the cohomology of the twisted SL n-Higgs moduli space up to the degree which is predicted by topological mirror symmetry. In particular this yields a new proof of a result of Harder-Narasimhan, showing that this finite group acts trivially on the cohomology of the twisted SL n stable bundle moduli space.","lang":"eng"}],"date_published":"2012-08-01T00:00:00Z","issue":"3","date_created":"2018-12-11T11:52:13Z","year":"2012","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1012.4748"}],"publication_status":"published","oa":1,"extern":1,"day":"01"},{"fulldoi":"https://doi.org/10.4007/annals.2012.175.3.7","publist_id":"5727","_id":"1472","page":"1329 - 1407","quality_controlled":0,"author":[{"full_name":"De Cataldo, Mark A","first_name":"Mark","last_name":"De Cataldo"},{"last_name":"Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Tamas Hausel","first_name":"Tamas"},{"first_name":"Luca","full_name":"Migliorini, Luca","last_name":"Migliorini"}],"status":"public","intvolume":"       175","doi":"10.4007/annals.2012.175.3.7","publisher":"Princeton University Press","type":"journal_article","date_updated":"2021-01-12T06:50:59Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1004.1420"}],"extern":1,"oa":1,"day":"01","date_published":"2012-05-01T00:00:00Z","abstract":[{"text":"For G = GL 2, PGL 2, SL 2 we prove that the perverse filtration associated with the Hitchin map on the rational cohomology of the moduli space of twisted G-Higgs bundles on a compact Riemann surface C agrees with the weight filtration on the rational cohomology of the twisted G character variety of C when the cohomologies are identified via non-Abelian Hodge theory. The proof is accomplished by means of a study of the topology of the Hitchin map over the locus of integral spectral curves.","lang":"eng"}],"volume":175,"acknowledgement":"Mark Andrea A. de Cataldo was partially supported by N.S.A. and N.S.F. Tamás Hausel was supported by a Royal Society University Research Fellowship. Luca Migliorini was partially supported by PRIN 2007 project \"Spazi di moduli e teoria di Lie\"","citation":{"mla":"De Cataldo, Mark, et al. “Topology of Hitchin Systems and Hodge Theory of Character Varieties: The Case A 1.” <i>Annals of Mathematics</i>, vol. 175, no. 3, Princeton University Press, 2012, pp. 1329–407, doi:<a href=\"https://doi.org/10.4007/annals.2012.175.3.7\">10.4007/annals.2012.175.3.7</a>.","ista":"De Cataldo M, Hausel T, Migliorini L. 2012. Topology of hitchin systems and Hodge theory of character varieties: The case A 1. Annals of Mathematics. 175(3), 1329–1407.","chicago":"De Cataldo, Mark, Tamás Hausel, and Luca Migliorini. “Topology of Hitchin Systems and Hodge Theory of Character Varieties: The Case A 1.” <i>Annals of Mathematics</i>. Princeton University Press, 2012. <a href=\"https://doi.org/10.4007/annals.2012.175.3.7\">https://doi.org/10.4007/annals.2012.175.3.7</a>.","ama":"De Cataldo M, Hausel T, Migliorini L. Topology of hitchin systems and Hodge theory of character varieties: The case A 1. <i>Annals of Mathematics</i>. 2012;175(3):1329-1407. doi:<a href=\"https://doi.org/10.4007/annals.2012.175.3.7\">10.4007/annals.2012.175.3.7</a>","ieee":"M. De Cataldo, T. Hausel, and L. Migliorini, “Topology of hitchin systems and Hodge theory of character varieties: The case A 1,” <i>Annals of Mathematics</i>, vol. 175, no. 3. Princeton University Press, pp. 1329–1407, 2012.","short":"M. De Cataldo, T. Hausel, L. Migliorini, Annals of Mathematics 175 (2012) 1329–1407.","apa":"De Cataldo, M., Hausel, T., &#38; Migliorini, L. (2012). Topology of hitchin systems and Hodge theory of character varieties: The case A 1. <i>Annals of Mathematics</i>. Princeton University Press. <a href=\"https://doi.org/10.4007/annals.2012.175.3.7\">https://doi.org/10.4007/annals.2012.175.3.7</a>"},"publication":"Annals of Mathematics","month":"05","title":"Topology of hitchin systems and Hodge theory of character varieties: The case A 1","year":"2012","issue":"3","date_created":"2018-12-11T11:52:13Z"},{"date_published":"2012-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"Supermassive black holes (SMBHs) are common in local galactic nuclei, and SMBHs as massive as several billion solar masses already exist at redshift z = 6. These earliest SMBHs may grow by the combination of radiation-pressure-limited accretion and mergers of stellar-mass seed BHs, left behind by the first generation of metal-free stars, or may be formed by more rapid direct collapse of gas in rare special environments where dense gas can accumulate without first fragmenting into stars. This chapter offers a review of these two competing scenarios, as well as some more exotic alternative ideas. It also briefly discusses how the different models may be distinguished in the future by observations with JWST, LISA and other instruments."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Haiman Z. The Formation of the First Massive Black Holes. In: Wiklind T, Mobasher B, Brumm V, eds. <i>The First Galaxies</i>. Berlin, Heidelberg: Springer Berlin Heidelberg; 2012:293-341. doi:<a href=\"https://doi.org/10.1007/978-3-642-32362-1_6\">10.1007/978-3-642-32362-1_6</a>","chicago":"Haiman, Zoltán. “The Formation of the First Massive Black Holes.” In <i>The First Galaxies</i>, edited by Tommy Wiklind, Bahram Mobasher, and Volker Brumm, 293–341. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. <a href=\"https://doi.org/10.1007/978-3-642-32362-1_6\">https://doi.org/10.1007/978-3-642-32362-1_6</a>.","apa":"Haiman, Z. (2012). The Formation of the First Massive Black Holes. In T. Wiklind, B. Mobasher, &#38; V. Brumm (Eds.), <i>The First Galaxies</i> (pp. 293–341). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-642-32362-1_6\">https://doi.org/10.1007/978-3-642-32362-1_6</a>","short":"Z. Haiman, in:, T. Wiklind, B. Mobasher, V. Brumm (Eds.), The First Galaxies, Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, pp. 293–341.","ieee":"Z. Haiman, “The Formation of the First Massive Black Holes,” in <i>The First Galaxies</i>, T. Wiklind, B. Mobasher, and V. Brumm, Eds. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012, pp. 293–341.","ista":"Haiman Z. 2012.The Formation of the First Massive Black Holes. In: The First Galaxies. Astrophysics and Space Science Library, , 293–341.","mla":"Haiman, Zoltán. “The Formation of the First Massive Black Holes.” <i>The First Galaxies</i>, edited by Tommy Wiklind et al., Springer Berlin Heidelberg, 2012, pp. 293–341, doi:<a href=\"https://doi.org/10.1007/978-3-642-32362-1_6\">10.1007/978-3-642-32362-1_6</a>."},"title":"The Formation of the First Massive Black Holes","month":"01","year":"2012","publication_status":"published","day":"01","language":[{"iso":"eng"}],"editor":[{"last_name":"Wiklind","full_name":"Wiklind, Tommy","first_name":"Tommy"},{"last_name":"Mobasher","full_name":"Mobasher, Bahram","first_name":"Bahram"},{"full_name":"Brumm, Volker","first_name":"Volker","last_name":"Brumm"}],"OA_type":"green","arxiv":1,"article_processing_charge":"No","OA_place":"repository","scopus_import":"1","external_id":{"arxiv":["1203.6075"]},"fulldoi":"https://doi.org/10.1007/978-3-642-32362-1_6","_id":"18737","quality_controlled":"1","status":"public","author":[{"last_name":"Haiman","orcid":"0000-0003-3633-5403","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","full_name":"Haiman, Zoltán","first_name":"Zoltán"}],"doi":"10.1007/978-3-642-32362-1_6","oa_version":"Preprint","alternative_title":["Astrophysics and Space Science Library"],"publication":"The First Galaxies","date_created":"2025-01-03T12:30:53Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1203.6075"}],"extern":"1","oa":1,"place":"Berlin, Heidelberg","date_updated":"2025-01-07T13:01:05Z","publication_identifier":{"isbn":["9783642323614"],"eisbn":["9783642323621"],"issn":["0067-0057"],"eissn":["2214-7985"]},"page":"293-341","publisher":"Springer Berlin Heidelberg","type":"book_chapter"},{"publication_status":"published","extern":1,"day":"01","acknowledgement":"This work was funded by the Medical Research Council.","title":"Structure of Escherichia coli OmpF porin from lipidic mesophase","publication":"Journal of Structural Biology","month":"06","citation":{"ista":"Efremov R, Sazanov LA. 2012. Structure of Escherichia coli OmpF porin from lipidic mesophase. Journal of Structural Biology. 178(3), 311–318.","mla":"Efremov, Rouslan, and Leonid A. Sazanov. “Structure of Escherichia Coli OmpF Porin from Lipidic Mesophase.” <i>Journal of Structural Biology</i>, vol. 178, no. 3, Academic Press, 2012, pp. 311–18, doi:<a href=\"https://doi.org/10.1016/j.jsb.2012.03.005\">10.1016/j.jsb.2012.03.005</a>.","ama":"Efremov R, Sazanov LA. Structure of Escherichia coli OmpF porin from lipidic mesophase. <i>Journal of Structural Biology</i>. 2012;178(3):311-318. doi:<a href=\"https://doi.org/10.1016/j.jsb.2012.03.005\">10.1016/j.jsb.2012.03.005</a>","chicago":"Efremov, Rouslan, and Leonid A Sazanov. “Structure of Escherichia Coli OmpF Porin from Lipidic Mesophase.” <i>Journal of Structural Biology</i>. Academic Press, 2012. <a href=\"https://doi.org/10.1016/j.jsb.2012.03.005\">https://doi.org/10.1016/j.jsb.2012.03.005</a>.","short":"R. Efremov, L.A. Sazanov, Journal of Structural Biology 178 (2012) 311–318.","ieee":"R. Efremov and L. A. Sazanov, “Structure of Escherichia coli OmpF porin from lipidic mesophase,” <i>Journal of Structural Biology</i>, vol. 178, no. 3. Academic Press, pp. 311–318, 2012.","apa":"Efremov, R., &#38; Sazanov, L. A. (2012). Structure of Escherichia coli OmpF porin from lipidic mesophase. <i>Journal of Structural Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jsb.2012.03.005\">https://doi.org/10.1016/j.jsb.2012.03.005</a>"},"date_published":"2012-06-01T00:00:00Z","abstract":[{"text":"Outer membrane protein F, a major component of the Escherichia coli outer membrane, was crystallized for the first time in lipidic mesophase of monoolein in novel space groups, P1 and H32. Due to ease of its purification and crystallization OmpF can be used as a benchmark protein for establishing membrane protein crystallization in meso, as a &quot;membrane lyzozyme&quot; The packing of porin trimers in the crystals of space group H32 is similar to natural outer membranes, providing the first high-resolution insight into the close to native packing of OmpF. Surprisingly, interaction between trimers is mediated exclusively by lipids, without direct protein-protein contacts. Multiple ordered lipids are observed and many of them occupy identical positions independently of the space group, identifying preferential interaction sites of lipid acyl chains. Presence of ordered aliphatic chains close to a positively charged area on the porin surface suggests a position for a lipopolysaccharide binding site on the surface of the major E. coli porins.","lang":"eng"}],"volume":178,"issue":"3","date_created":"2018-12-11T11:54:59Z","year":"2012","publist_id":"5109","fulldoi":"https://doi.org/10.1016/j.jsb.2012.03.005","publisher":"Academic Press","type":"journal_article","_id":"1972","author":[{"last_name":"Efremov","first_name":"Rouslan","full_name":"Efremov, Rouslan G"},{"first_name":"Leonid A","full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"}],"page":"311 - 318","quality_controlled":0,"status":"public","doi":"10.1016/j.jsb.2012.03.005","intvolume":"       178","date_updated":"2021-01-12T06:54:26Z"},{"_id":"1976","author":[{"last_name":"Efremov","first_name":"Rouslan","full_name":"Efremov, Rouslan G"},{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Leonid Sazanov"}],"page":"1785 - 1795","quality_controlled":0,"status":"public","doi":"10.1016/j.bbabio.2012.02.015","intvolume":"      1817","publisher":"Elsevier","type":"review","fulldoi":"https://doi.org/10.1016/j.bbabio.2012.02.015","publist_id":"5108","date_updated":"2019-04-26T07:22:06Z","extern":1,"day":"01","publication_status":"published","year":"2012","issue":"10","date_created":"2018-12-11T11:55:00Z","abstract":[{"lang":"eng","text":"Complex I is a key enzyme of the respiratory chain in many organisms. This multi-protein complex with an intricate evolutionary history originated from the unification of prebuilt modules of hydrogenases and transporters. Using recently determined crystallographic structures of complex I we reanalyzed evolutionarily related complexes that couple oxidoreduction to trans-membrane ion translocation. Our analysis points to the previously unnoticed structural homology of the electron input module of formate dehydrogenlyases and subunit NuoG of complex I. We also show that all related to complex I hydrogenases likely operate via a conformation driven mechanism with structural changes generated in the conserved coupling site located at the interface of subunits NuoB/D/H. The coupling apparently originated once in evolutionary history, together with subunit NuoH joining hydrogenase and transport modules. Analysis of quinone oxidoreduction properties and the structure of complex I allows us to suggest a fully reversible coupling mechanism. Our model predicts that: 1) proton access to the ketone groups of the bound quinone is rigorously controlled by the protein, 2) the negative electric charge of the anionic ubiquinol head group is a major driving force for conformational changes."}],"volume":1817,"date_published":"2012-10-01T00:00:00Z","acknowledgement":"The work in authors' laboratory was funded by the Medical Research Council.","citation":{"chicago":"Efremov, Rouslan, and Leonid A Sazanov. “The Coupling Mechanism of Respiratory Complex i - A Structural and Evolutionary Perspective.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.bbabio.2012.02.015\">https://doi.org/10.1016/j.bbabio.2012.02.015</a>.","ama":"Efremov R, Sazanov LA. The coupling mechanism of respiratory complex i - A structural and evolutionary perspective. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. 2012;1817(10):1785-1795. doi:<a href=\"https://doi.org/10.1016/j.bbabio.2012.02.015\">10.1016/j.bbabio.2012.02.015</a>","ieee":"R. Efremov and L. A. Sazanov, “The coupling mechanism of respiratory complex i - A structural and evolutionary perspective,” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1817, no. 10. Elsevier, pp. 1785–1795, 2012.","short":"R. Efremov, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1817 (2012) 1785–1795.","apa":"Efremov, R., &#38; Sazanov, L. A. (2012). The coupling mechanism of respiratory complex i - A structural and evolutionary perspective. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbabio.2012.02.015\">https://doi.org/10.1016/j.bbabio.2012.02.015</a>","mla":"Efremov, Rouslan, and Leonid A. Sazanov. “The Coupling Mechanism of Respiratory Complex i - A Structural and Evolutionary Perspective.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1817, no. 10, Elsevier, 2012, pp. 1785–95, doi:<a href=\"https://doi.org/10.1016/j.bbabio.2012.02.015\">10.1016/j.bbabio.2012.02.015</a>.","ista":"Efremov R, Sazanov LA. 2012. The coupling mechanism of respiratory complex i - A structural and evolutionary perspective. Biochimica et Biophysica Acta - Bioenergetics. 1817(10), 1785–1795."},"title":"The coupling mechanism of respiratory complex i - A structural and evolutionary perspective","month":"10","publication":"Biochimica et Biophysica Acta - Bioenergetics"},{"extern":"1","oa":1,"pubrep_id":"946","date_created":"2018-12-11T11:46:46Z","volume":12,"publication":"BMC Plant Biology","has_accepted_license":"1","type":"journal_article","publisher":"BioMed Central","isi":1,"file":[{"date_updated":"2020-07-14T12:46:35Z","file_name":"IST-2018-946-v1+1_2012_Symonova_GiA_Roots.pdf","file_id":"4953","date_created":"2018-12-12T10:12:35Z","file_size":1691436,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"system","checksum":"0c629e36acd5f2878ff7dd088d67d494"}],"license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2025-09-30T08:36:34Z","day":"26","language":[{"iso":"eng"}],"publication_status":"published","file_date_updated":"2020-07-14T12:46:35Z","year":"2012","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Background: Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks.Results: We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user.Conclusions: We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.","lang":"eng"}],"date_published":"2012-07-26T00:00:00Z","month":"07","title":"GiA Roots: Software for the high throughput analysis of plant root system architecture","citation":{"short":"T. Galkovskyi, Y. Mileyko, A. Bucksch, B. Moore, O. Symonova, C. Price, C. Topp, A. Iyer Pascuzzi, P. Zurek, S. Fang, J. Harer, P. Benfey, J. Weitz, BMC Plant Biology 12 (2012).","apa":"Galkovskyi, T., Mileyko, Y., Bucksch, A., Moore, B., Symonova, O., Price, C., … Weitz, J. (2012). GiA Roots: Software for the high throughput analysis of plant root system architecture. <i>BMC Plant Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2229-12-116\">https://doi.org/10.1186/1471-2229-12-116</a>","ieee":"T. Galkovskyi <i>et al.</i>, “GiA Roots: Software for the high throughput analysis of plant root system architecture,” <i>BMC Plant Biology</i>, vol. 12. BioMed Central, 2012.","chicago":"Galkovskyi, Taras, Yuriy Mileyko, Alexander Bucksch, Brad Moore, Olga Symonova, Charles Price, Chrostopher Topp, et al. “GiA Roots: Software for the High Throughput Analysis of Plant Root System Architecture.” <i>BMC Plant Biology</i>. BioMed Central, 2012. <a href=\"https://doi.org/10.1186/1471-2229-12-116\">https://doi.org/10.1186/1471-2229-12-116</a>.","ama":"Galkovskyi T, Mileyko Y, Bucksch A, et al. GiA Roots: Software for the high throughput analysis of plant root system architecture. <i>BMC Plant Biology</i>. 2012;12. doi:<a href=\"https://doi.org/10.1186/1471-2229-12-116\">10.1186/1471-2229-12-116</a>","mla":"Galkovskyi, Taras, et al. “GiA Roots: Software for the High Throughput Analysis of Plant Root System Architecture.” <i>BMC Plant Biology</i>, vol. 12, 116, BioMed Central, 2012, doi:<a href=\"https://doi.org/10.1186/1471-2229-12-116\">10.1186/1471-2229-12-116</a>.","ista":"Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price C, Topp C, Iyer Pascuzzi A, Zurek P, Fang S, Harer J, Benfey P, Weitz J. 2012. GiA Roots: Software for the high throughput analysis of plant root system architecture. BMC Plant Biology. 12, 116."},"intvolume":"        12","doi":"10.1186/1471-2229-12-116","status":"public","_id":"492","quality_controlled":"1","author":[{"last_name":"Galkovskyi","first_name":"Taras","full_name":"Galkovskyi, Taras"},{"full_name":"Mileyko, Yuriy","first_name":"Yuriy","last_name":"Mileyko"},{"last_name":"Bucksch","first_name":"Alexander","full_name":"Bucksch, Alexander"},{"first_name":"Brad","full_name":"Moore, Brad","last_name":"Moore"},{"last_name":"Symonova","orcid":"0000-0003-2012-9947","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","full_name":"Symonova, Olga","first_name":"Olga"},{"first_name":"Charles","full_name":"Price, Charles","last_name":"Price"},{"full_name":"Topp, Chrostopher","first_name":"Chrostopher","last_name":"Topp"},{"full_name":"Iyer Pascuzzi, Anjali","first_name":"Anjali","last_name":"Iyer Pascuzzi"},{"last_name":"Zurek","full_name":"Zurek, Paul","first_name":"Paul"},{"last_name":"Fang","full_name":"Fang, Suqin","first_name":"Suqin"},{"first_name":"John","full_name":"Harer, John","last_name":"Harer"},{"full_name":"Benfey, Philip","first_name":"Philip","last_name":"Benfey"},{"last_name":"Weitz","first_name":"Joshua","full_name":"Weitz, Joshua"}],"oa_version":"Published Version","ddc":["005","514","516"],"publist_id":"7328","fulldoi":"https://doi.org/10.1186/1471-2229-12-116","external_id":{"isi":["000309114300001"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"116","article_processing_charge":"No","scopus_import":"1"},{"date_updated":"2025-09-30T08:35:59Z","file":[{"file_size":2693701,"content_type":"application/pdf","access_level":"open_access","creator":"system","relation":"main_file","checksum":"195238221c4b0b0f4035f6f6c16ea17c","date_updated":"2020-07-14T12:46:35Z","file_name":"IST-2018-945-v1+1_2012_Schloegl_Review_of.pdf","file_id":"5356","date_created":"2018-12-12T10:18:34Z"}],"isi":1,"type":"journal_article","publisher":"Frontiers Research Foundation","publication":"Frontiers in Neuroscience","acknowledgement":"The studies were in part or completely supported by the Bundesministerium für Bildung und Forschung (BMBF), Fkz 01IB001A, 01GQ0850, by the German Science Foundation (DFG, contract MU 987/3-2), by the European ICT Programme Projects FP7-224631 and 216886, the World Class University Program through the National Research Foundation of Korea funded by the Ministry of Education, Science, and Technology (Grant R31-10008), the US Army Research Office [W911NF-08-1-0216 (Gerwin Schalk) and W911NF-07-1-0415 (Gerwin Schalk)] and the NIH [EB006356 (Gerwin Schalk) and EB000856 (Gerwin Schalk), the WIN-Kolleg of the Heidelberg Academy of Sciences and Humanities, German Federal Ministry of Education and Research grants 01GQ0420, 01GQ0761, 01GQ0762, and 01GQ0830, German Research Foundation grants 550/B5 and C6, and by a scholarship from the German National Academic Foundation. This paper only reflects the authors’ views and funding agencies are not liable for any use that may be made of the information contained herein.\r\n","has_accepted_license":"1","volume":6,"date_created":"2018-12-11T11:46:46Z","pubrep_id":"945","oa":1,"scopus_import":"1","article_processing_charge":"No","external_id":{"isi":["000209165300066"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"55","fulldoi":"https://doi.org/10.3389/fnins.2012.00055","publist_id":"7327","ddc":["004"],"oa_version":"Published Version","intvolume":"         6","doi":"10.3389/fnins.2012.00055","_id":"493","quality_controlled":"1","status":"public","author":[{"full_name":"Tangermann, Michael","first_name":"Michael","last_name":"Tangermann"},{"last_name":"Müller","first_name":"Klaus","full_name":"Müller, Klaus"},{"full_name":"Aertsen, Ad","first_name":"Ad","last_name":"Aertsen"},{"last_name":"Birbaumer","first_name":"Niels","full_name":"Birbaumer, Niels"},{"full_name":"Braun, Christoph","first_name":"Christoph","last_name":"Braun"},{"first_name":"Clemens","full_name":"Brunner, Clemens","last_name":"Brunner"},{"first_name":"Robert","full_name":"Leeb, Robert","last_name":"Leeb"},{"last_name":"Mehring","full_name":"Mehring, Carsten","first_name":"Carsten"},{"first_name":"Kai","full_name":"Miller, Kai","last_name":"Miller"},{"last_name":"Müller Putz","first_name":"Gernot","full_name":"Müller Putz, Gernot"},{"first_name":"Guido","full_name":"Nolte, Guido","last_name":"Nolte"},{"first_name":"Gert","full_name":"Pfurtscheller, Gert","last_name":"Pfurtscheller"},{"last_name":"Preissl","full_name":"Preissl, Hubert","first_name":"Hubert"},{"last_name":"Schalk","first_name":"Gerwin","full_name":"Schalk, Gerwin"},{"last_name":"Schlögl","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","first_name":"Alois"},{"last_name":"Vidaurre","first_name":"Carmen","full_name":"Vidaurre, Carmen"},{"full_name":"Waldert, Stephan","first_name":"Stephan","last_name":"Waldert"},{"last_name":"Blankertz","full_name":"Blankertz, Benjamin","first_name":"Benjamin"}],"title":"Review of the BCI competition IV","citation":{"mla":"Tangermann, Michael, et al. “Review of the BCI Competition IV.” <i>Frontiers in Neuroscience</i>, vol. 6, 55, Frontiers Research Foundation, 2012, doi:<a href=\"https://doi.org/10.3389/fnins.2012.00055\">10.3389/fnins.2012.00055</a>.","ista":"Tangermann M, Müller K, Aertsen A, Birbaumer N, Braun C, Brunner C, Leeb R, Mehring C, Miller K, Müller Putz G, Nolte G, Pfurtscheller G, Preissl H, Schalk G, Schlögl A, Vidaurre C, Waldert S, Blankertz B. 2012. Review of the BCI competition IV. Frontiers in Neuroscience. 6, 55.","short":"M. Tangermann, K. Müller, A. Aertsen, N. Birbaumer, C. Braun, C. Brunner, R. Leeb, C. Mehring, K. Miller, G. Müller Putz, G. Nolte, G. Pfurtscheller, H. Preissl, G. Schalk, A. Schlögl, C. Vidaurre, S. Waldert, B. Blankertz, Frontiers in Neuroscience 6 (2012).","ieee":"M. Tangermann <i>et al.</i>, “Review of the BCI competition IV,” <i>Frontiers in Neuroscience</i>, vol. 6. Frontiers Research Foundation, 2012.","apa":"Tangermann, M., Müller, K., Aertsen, A., Birbaumer, N., Braun, C., Brunner, C., … Blankertz, B. (2012). Review of the BCI competition IV. <i>Frontiers in Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fnins.2012.00055\">https://doi.org/10.3389/fnins.2012.00055</a>","chicago":"Tangermann, Michael, Klaus Müller, Ad Aertsen, Niels Birbaumer, Christoph Braun, Clemens Brunner, Robert Leeb, et al. “Review of the BCI Competition IV.” <i>Frontiers in Neuroscience</i>. Frontiers Research Foundation, 2012. <a href=\"https://doi.org/10.3389/fnins.2012.00055\">https://doi.org/10.3389/fnins.2012.00055</a>.","ama":"Tangermann M, Müller K, Aertsen A, et al. Review of the BCI competition IV. <i>Frontiers in Neuroscience</i>. 2012;6. doi:<a href=\"https://doi.org/10.3389/fnins.2012.00055\">10.3389/fnins.2012.00055</a>"},"month":"07","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2012-07-13T00:00:00Z","abstract":[{"text":"The BCI competition IV stands in the tradition of prior BCI competitions that aim to provide high quality neuroscientific data for open access to the scientific community. As experienced already in prior competitions not only scientists from the narrow field of BCI compete, but scholars with a broad variety of backgrounds and nationalities. They include high specialists as well as students.The goals of all BCI competitions have always been to challenge with respect to novel paradigms and complex data. We report on the following challenges: (1) asynchronous data, (2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer, (5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after past competitions, our hope is that winning entries may enhance the analysis methods of future BCIs.","lang":"eng"}],"year":"2012","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:46:35Z","publication_status":"published","day":"13","language":[{"iso":"eng"}]},{"page":"238 - 246","type":"conference","publisher":"Open Publishing Association","date_updated":"2024-10-09T20:55:00Z","file":[{"date_created":"2018-12-12T10:15:31Z","date_updated":"2020-07-14T12:46:35Z","file_name":"IST-2018-944-v1+1_2012_Rubin_A_Myhill.pdf","file_id":"5152","relation":"main_file","creator":"system","checksum":"56277f95edc9d531fa3bdc5f9579fda8","content_type":"application/pdf","file_size":97736,"access_level":"open_access"}],"pubrep_id":"944","oa":1,"ec_funded":1,"volume":96,"alternative_title":["EPTCS"],"publication":"Proceedings GandALF 2012","has_accepted_license":"1","date_created":"2018-12-11T11:46:47Z","ddc":["004"],"publist_id":"7325","fulldoi":"https://doi.org/10.4204/EPTCS.96.18","intvolume":"        96","doi":"10.4204/EPTCS.96.18","author":[{"full_name":"Kruckman, Alex","first_name":"Alex","last_name":"Kruckman"},{"first_name":"Sasha","full_name":"Rubin, Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","last_name":"Rubin"},{"full_name":"Sheridan, John","first_name":"John","last_name":"Sheridan"},{"first_name":"Ben","full_name":"Zax, Ben","last_name":"Zax"}],"_id":"495","status":"public","quality_controlled":"1","corr_author":"1","oa_version":"Published Version","scopus_import":1,"conference":{"name":"GandALF: Games, Automata, Logics and Formal Verification","start_date":"2012-09-06","end_date":"2012-09-08","location":"Napoli, Italy"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","file_date_updated":"2020-07-14T12:46:35Z","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"day":"07","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2012-10-07T00:00:00Z","abstract":[{"text":"An automaton with advice is a finite state automaton which has access to an additional fixed infinite string called an advice tape. We refine the Myhill-Nerode theorem to characterize the languages of finite strings that are accepted by automata with advice. We do the same for tree automata with advice.","lang":"eng"}],"title":"A Myhill Nerode theorem for automata with advice","citation":{"short":"A. Kruckman, S. Rubin, J. Sheridan, B. Zax, in:, Proceedings GandALF 2012, Open Publishing Association, 2012, pp. 238–246.","ieee":"A. Kruckman, S. Rubin, J. Sheridan, and B. Zax, “A Myhill Nerode theorem for automata with advice,” in <i>Proceedings GandALF 2012</i>, Napoli, Italy, 2012, vol. 96, pp. 238–246.","apa":"Kruckman, A., Rubin, S., Sheridan, J., &#38; Zax, B. (2012). A Myhill Nerode theorem for automata with advice. In <i>Proceedings GandALF 2012</i> (Vol. 96, pp. 238–246). Napoli, Italy: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.96.18\">https://doi.org/10.4204/EPTCS.96.18</a>","ama":"Kruckman A, Rubin S, Sheridan J, Zax B. A Myhill Nerode theorem for automata with advice. In: <i>Proceedings GandALF 2012</i>. Vol 96. Open Publishing Association; 2012:238-246. doi:<a href=\"https://doi.org/10.4204/EPTCS.96.18\">10.4204/EPTCS.96.18</a>","chicago":"Kruckman, Alex, Sasha Rubin, John Sheridan, and Ben Zax. “A Myhill Nerode Theorem for Automata with Advice.” In <i>Proceedings GandALF 2012</i>, 96:238–46. Open Publishing Association, 2012. <a href=\"https://doi.org/10.4204/EPTCS.96.18\">https://doi.org/10.4204/EPTCS.96.18</a>.","mla":"Kruckman, Alex, et al. “A Myhill Nerode Theorem for Automata with Advice.” <i>Proceedings GandALF 2012</i>, vol. 96, Open Publishing Association, 2012, pp. 238–46, doi:<a href=\"https://doi.org/10.4204/EPTCS.96.18\">10.4204/EPTCS.96.18</a>.","ista":"Kruckman A, Rubin S, Sheridan J, Zax B. 2012. A Myhill Nerode theorem for automata with advice. Proceedings GandALF 2012. GandALF: Games, Automata, Logics and Formal Verification, EPTCS, vol. 96, 238–246."},"month":"10","year":"2012"},{"isi":1,"type":"conference","publisher":"IEEE","date_updated":"2025-09-30T08:34:47Z","main_file_link":[{"url":"https://arise.or.at/pubpdf/Interpretations_in_Trees_with_Countably_Many_Branches.pdf","open_access":"1"}],"oa":1,"ec_funded":1,"alternative_title":["LICS"],"date_created":"2018-12-11T11:46:47Z","publist_id":"7324","fulldoi":"https://doi.org/10.1109/LICS.2012.65","doi":"10.1109/LICS.2012.65","status":"public","_id":"496","author":[{"full_name":"Rabinovich, Alexander","first_name":"Alexander","last_name":"Rabinovich"},{"first_name":"Sasha","full_name":"Rubin, Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","last_name":"Rubin"}],"quality_controlled":"1","oa_version":"Preprint","article_processing_charge":"No","scopus_import":"1","conference":{"location":"Dubrovnik, Croatia","end_date":"2012-06-28","name":"LICS: Logic in Computer Science","start_date":"2012-06-25"},"external_id":{"isi":["000309059900061"]},"article_number":"6280474","publication_status":"published","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"day":"01","project":[{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"We study the expressive power of logical interpretations on the class of scattered trees, namely those with countably many infinite branches. Scattered trees can be thought of as the tree analogue of scattered linear orders. Every scattered tree has an ordinal rank that reflects the structure of its infinite branches. We prove, roughly, that trees and orders of large rank cannot be interpreted in scattered trees of small rank. We consider a quite general notion of interpretation: each element of the interpreted structure is represented by a set of tuples of subsets of the interpreting tree. Our trees are countable, not necessarily finitely branching, and may have finitely many unary predicates as labellings. We also show how to replace injective set-interpretations in (not necessarily scattered) trees by 'finitary' set-interpretations."}],"date_published":"2012-01-01T00:00:00Z","month":"01","citation":{"short":"A. Rabinovich, S. Rubin, in:, IEEE, 2012.","apa":"Rabinovich, A., &#38; Rubin, S. (2012). Interpretations in trees with countably many branches. Presented at the LICS: Logic in Computer Science, Dubrovnik, Croatia: IEEE. <a href=\"https://doi.org/10.1109/LICS.2012.65\">https://doi.org/10.1109/LICS.2012.65</a>","ieee":"A. Rabinovich and S. Rubin, “Interpretations in trees with countably many branches,” presented at the LICS: Logic in Computer Science, Dubrovnik, Croatia, 2012.","ama":"Rabinovich A, Rubin S. Interpretations in trees with countably many branches. In: IEEE; 2012. doi:<a href=\"https://doi.org/10.1109/LICS.2012.65\">10.1109/LICS.2012.65</a>","chicago":"Rabinovich, Alexander, and Sasha Rubin. “Interpretations in Trees with Countably Many Branches.” IEEE, 2012. <a href=\"https://doi.org/10.1109/LICS.2012.65\">https://doi.org/10.1109/LICS.2012.65</a>.","mla":"Rabinovich, Alexander, and Sasha Rubin. <i>Interpretations in Trees with Countably Many Branches</i>. 6280474, IEEE, 2012, doi:<a href=\"https://doi.org/10.1109/LICS.2012.65\">10.1109/LICS.2012.65</a>.","ista":"Rabinovich A, Rubin S. 2012. Interpretations in trees with countably many branches. LICS: Logic in Computer Science, LICS, , 6280474."},"title":"Interpretations in trees with countably many branches","year":"2012"},{"oa":1,"pubrep_id":"943","date_created":"2018-12-11T11:46:48Z","ec_funded":1,"alternative_title":["LIPIcs"],"volume":16,"has_accepted_license":"1","page":"167 - 182","related_material":{"record":[{"id":"5378","status":"public","relation":"earlier_version"}]},"type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file":[{"date_created":"2018-12-12T10:08:50Z","date_updated":"2020-07-14T12:46:35Z","file_name":"IST-2018-943-v1+1_2012_Chatterjee_Faster_Algorithms.pdf","file_id":"4712","relation":"main_file","creator":"system","checksum":"f1b0dd99240800db2d7dbf9b5131fe5e","file_size":471236,"content_type":"application/pdf","access_level":"open_access"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_updated":"2025-01-14T12:24:50Z","language":[{"iso":"eng"}],"day":"01","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","file_date_updated":"2020-07-14T12:46:35Z","department":[{"_id":"KrCh"}],"year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm. © Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath."}],"date_published":"2012-09-01T00:00:00Z","title":"Faster algorithms for alternating refinement relations","month":"09","citation":{"ama":"Chatterjee K, Chaubal S, Kamath P. Faster algorithms for alternating refinement relations. In: Vol 16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2012:167-182. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2012.167\">10.4230/LIPIcs.CSL.2012.167</a>","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. “Faster Algorithms for Alternating Refinement Relations,” 16:167–82. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2012.167\">https://doi.org/10.4230/LIPIcs.CSL.2012.167</a>.","short":"K. Chatterjee, S. Chaubal, P. Kamath, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 167–182.","ieee":"K. Chatterjee, S. Chaubal, and P. Kamath, “Faster algorithms for alternating refinement relations,” presented at the EACSL: European Association for Computer Science Logic, Fontainebleau, France, 2012, vol. 16, pp. 167–182.","apa":"Chatterjee, K., Chaubal, S., &#38; Kamath, P. (2012). Faster algorithms for alternating refinement relations (Vol. 16, pp. 167–182). Presented at the EACSL: European Association for Computer Science Logic, Fontainebleau, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2012.167\">https://doi.org/10.4230/LIPIcs.CSL.2012.167</a>","mla":"Chatterjee, Krishnendu, et al. <i>Faster Algorithms for Alternating Refinement Relations</i>. Vol. 16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 167–82, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2012.167\">10.4230/LIPIcs.CSL.2012.167</a>.","ista":"Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations. EACSL: European Association for Computer Science Logic, LIPIcs, vol. 16, 167–182."},"doi":"10.4230/LIPIcs.CSL.2012.167","intvolume":"        16","quality_controlled":"1","_id":"497","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Chaubal","first_name":"Siddhesh","full_name":"Chaubal, Siddhesh"},{"full_name":"Kamath, Pritish","first_name":"Pritish","last_name":"Kamath"}],"status":"public","oa_version":"Published Version","ddc":["004"],"fulldoi":"https://doi.org/10.4230/LIPIcs.CSL.2012.167","publist_id":"7323","conference":{"location":"Fontainebleau, France","end_date":"2012-09-06","start_date":"2012-09-03","name":"EACSL: European Association for Computer Science Logic"},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"scopus_import":1},{"year":"2012","citation":{"mla":"Pickup, Melinda, et al. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” <i>Evolutionary Applications</i>, vol. 5, no. 8, Wiley-Blackwell, 2012, pp. 913–24, doi:<a href=\"https://doi.org/10.1111/j.1752-4571.2012.00284.x\">10.1111/j.1752-4571.2012.00284.x</a>.","ista":"Pickup M, Field D, Rowell D, Young A. 2012. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. 5(8), 913–924.","apa":"Pickup, M., Field, D., Rowell, D., &#38; Young, A. (2012). Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. <i>Evolutionary Applications</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1752-4571.2012.00284.x\">https://doi.org/10.1111/j.1752-4571.2012.00284.x</a>","ieee":"M. Pickup, D. Field, D. Rowell, and A. Young, “Predicting local adaptation in fragmented plant populations: Implications for restoration genetics,” <i>Evolutionary Applications</i>, vol. 5, no. 8. Wiley-Blackwell, pp. 913–924, 2012.","short":"M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012) 913–924.","chicago":"Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” <i>Evolutionary Applications</i>. Wiley-Blackwell, 2012. <a href=\"https://doi.org/10.1111/j.1752-4571.2012.00284.x\">https://doi.org/10.1111/j.1752-4571.2012.00284.x</a>.","ama":"Pickup M, Field D, Rowell D, Young A. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. <i>Evolutionary Applications</i>. 2012;5(8):913-924. doi:<a href=\"https://doi.org/10.1111/j.1752-4571.2012.00284.x\">10.1111/j.1752-4571.2012.00284.x</a>"},"month":"12","title":"Predicting local adaptation in fragmented plant populations: Implications for restoration genetics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration.","lang":"eng"}],"date_published":"2012-12-01T00:00:00Z","language":[{"iso":"eng"}],"day":"01","file_date_updated":"2020-07-14T12:46:35Z","department":[{"_id":"NiBa"}],"publication_status":"published","external_id":{"isi":["000312808900013"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"article_processing_charge":"No","corr_author":"1","oa_version":"Published Version","doi":"10.1111/j.1752-4571.2012.00284.x","intvolume":"         5","author":[{"full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"first_name":"David","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","last_name":"Field"},{"first_name":"David","full_name":"Rowell, David","last_name":"Rowell"},{"full_name":"Young, Andrew","first_name":"Andrew","last_name":"Young"}],"_id":"498","status":"public","quality_controlled":"1","publist_id":"7322","fulldoi":"https://doi.org/10.1111/j.1752-4571.2012.00284.x","ddc":["576"],"date_created":"2018-12-11T11:46:48Z","issue":"8","publication":"Evolutionary Applications","acknowledgement":"We thank Graham Pickup, David Steer, Linda Broadhurst, Lan Li and Carole Elliott for technical assistance. The New\r\nSouth Wales Department of Environment and Climate Change, ACT Parks, Conservation and Lands and the\r\nDepartment of Sustainability and Environment in Victoria provided permits for seed and soil collection. We thank\r\nSpencer C. H. Barrett for comments that improved the quality of the manuscript.\r\n","has_accepted_license":"1","volume":5,"oa":1,"pubrep_id":"942","file":[{"file_size":396136,"content_type":"application/pdf","access_level":"open_access","creator":"system","relation":"main_file","checksum":"233007138606aca5a2f75f7ae1742f43","date_updated":"2020-07-14T12:46:35Z","file_id":"4821","file_name":"IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf","date_created":"2018-12-12T10:10:33Z"}],"date_updated":"2025-09-30T08:33:55Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","type":"journal_article","publisher":"Wiley-Blackwell","page":"913 - 924","isi":1},{"oa":1,"pubrep_id":"10","date_created":"2018-12-12T11:38:59Z","alternative_title":["IST Austria Technical Report"],"has_accepted_license":"1","related_material":{"record":[{"relation":"later_version","status":"public","id":"2956"}]},"page":"33","type":"technical_report","publisher":"IST Austria","publication_identifier":{"issn":["2664-1690"]},"file":[{"access_level":"open_access","content_type":"application/pdf","file_size":592098,"checksum":"a03c08c1589dbb0c96183a8bcf3ab240","relation":"main_file","creator":"system","file_name":"IST-2012-002_IST-2012-0002.pdf","file_id":"5522","date_updated":"2020-07-14T12:46:38Z","date_created":"2018-12-12T11:54:00Z"}],"date_updated":"2025-09-30T08:08:12Z","language":[{"iso":"eng"}],"day":"02","publication_status":"published","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:38Z","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work we consider solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and ω-regular objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean-payoff objectives. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two- player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP- hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two- player pushdown games. Finally we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded."}],"date_published":"2012-07-02T00:00:00Z","title":"Mean-payoff pushdown games","month":"07","citation":{"ama":"Chatterjee K, Velner Y. <i>Mean-Payoff Pushdown Games</i>. IST Austria; 2012. doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0002\">10.15479/AT:IST-2012-0002</a>","chicago":"Chatterjee, Krishnendu, and Yaron Velner. <i>Mean-Payoff Pushdown Games</i>. IST Austria, 2012. <a href=\"https://doi.org/10.15479/AT:IST-2012-0002\">https://doi.org/10.15479/AT:IST-2012-0002</a>.","ieee":"K. Chatterjee and Y. Velner, <i>Mean-payoff pushdown games</i>. IST Austria, 2012.","apa":"Chatterjee, K., &#38; Velner, Y. (2012). <i>Mean-payoff pushdown games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2012-0002\">https://doi.org/10.15479/AT:IST-2012-0002</a>","short":"K. Chatterjee, Y. Velner, Mean-Payoff Pushdown Games, IST Austria, 2012.","mla":"Chatterjee, Krishnendu, and Yaron Velner. <i>Mean-Payoff Pushdown Games</i>. IST Austria, 2012, doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0002\">10.15479/AT:IST-2012-0002</a>.","ista":"Chatterjee K, Velner Y. 2012. Mean-payoff pushdown games, IST Austria, 33p."},"doi":"10.15479/AT:IST-2012-0002","_id":"5377","status":"public","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"}],"corr_author":"1","oa_version":"Published Version","ddc":["000","005"],"fulldoi":"https://doi.org/10.15479/AT:IST-2012-0002","article_processing_charge":"No"},{"month":"07","citation":{"ista":"Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations, IST Austria, 21p.","mla":"Chatterjee, Krishnendu, et al. <i>Faster Algorithms for Alternating Refinement Relations</i>. IST Austria, 2012, doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">10.15479/AT:IST-2012-0001</a>.","short":"K. Chatterjee, S. Chaubal, P. Kamath, Faster Algorithms for Alternating Refinement Relations, IST Austria, 2012.","apa":"Chatterjee, K., Chaubal, S., &#38; Kamath, P. (2012). <i>Faster algorithms for alternating refinement relations</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">https://doi.org/10.15479/AT:IST-2012-0001</a>","ieee":"K. Chatterjee, S. Chaubal, and P. Kamath, <i>Faster algorithms for alternating refinement relations</i>. IST Austria, 2012.","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. <i>Faster Algorithms for Alternating Refinement Relations</i>. IST Austria, 2012. <a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">https://doi.org/10.15479/AT:IST-2012-0001</a>.","ama":"Chatterjee K, Chaubal S, Kamath P. <i>Faster Algorithms for Alternating Refinement Relations</i>. IST Austria; 2012. doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">10.15479/AT:IST-2012-0001</a>"},"title":"Faster algorithms for alternating refinement relations","date_published":"2012-07-04T00:00:00Z","abstract":[{"text":"One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:39Z","publication_status":"published","language":[{"iso":"eng"}],"day":"04","article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT:IST-2012-0001","ddc":["000","005"],"oa_version":"Published Version","corr_author":"1","_id":"5378","status":"public","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Siddhesh","full_name":"Chaubal, Siddhesh","last_name":"Chaubal"},{"last_name":"Kamath","full_name":"Kamath, Pritish","first_name":"Pritish"}],"doi":"10.15479/AT:IST-2012-0001","has_accepted_license":"1","alternative_title":["IST Austria Technical Report"],"date_created":"2018-12-12T11:38:59Z","pubrep_id":"14","oa":1,"date_updated":"2025-04-15T08:12:24Z","file":[{"access_level":"open_access","file_size":394256,"content_type":"application/pdf","checksum":"ec8d1857cc7095d3de5107a0162ced37","relation":"main_file","creator":"system","file_name":"IST-2012-0001_IST-2012-0001.pdf","file_id":"5489","date_updated":"2020-07-14T12:46:39Z","date_created":"2018-12-12T11:53:28Z"}],"publication_identifier":{"issn":["2664-1690"]},"publisher":"IST Austria","type":"technical_report","page":"21","related_material":{"record":[{"relation":"later_version","status":"public","id":"497"}]}}]