[{"date_updated":"2025-09-30T09:50:22Z","isi":1,"date_created":"2018-12-11T11:46:40Z","citation":{"ieee":"N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction and recolonization in two dimensions: Quantifying phylogeography,” <i>Evolution</i>, vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.","chicago":"Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” <i>Evolution</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">https://doi.org/10.1111/j.1558-5646.2010.01019.x</a>.","ama":"Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. <i>Evolution</i>. 2010;64(9):2701-2715. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">10.1111/j.1558-5646.2010.01019.x</a>","short":"N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715.","mla":"Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” <i>Evolution</i>, vol. 64, no. 9, Wiley-Blackwell, 2010, pp. 2701–15, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">10.1111/j.1558-5646.2010.01019.x</a>.","apa":"Barton, N. H., Kelleher, J., &#38; Etheridge, A. (2010). A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">https://doi.org/10.1111/j.1558-5646.2010.01019.x</a>","ista":"Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9), 2701–2715."},"year":"2010","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","type":"journal_article","scopus_import":"1","oa_version":"None","external_id":{"isi":["000281636400017"]},"month":"09","publication":"Evolution","page":"2701 - 2715","status":"public","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"intvolume":"        64","title":"A new model for extinction and recolonization in two dimensions: Quantifying phylogeography","publist_id":"2780","article_processing_charge":"No","acknowledgement":"This work has made use of the resources provided by the Edinburgh Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative. NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1.","author":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"}],"publication_status":"published","date_published":"2010-09-01T00:00:00Z","volume":64,"fulldoi":"https://doi.org/10.1111/j.1558-5646.2010.01019.x","issue":"9","quality_controlled":"1","abstract":[{"text":"Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci.","lang":"eng"}],"day":"01","_id":"474","doi":"10.1111/j.1558-5646.2010.01019.x","publisher":"Wiley-Blackwell"},{"date_created":"2018-12-11T11:46:45Z","file":[{"date_updated":"2020-07-14T12:46:35Z","file_id":"4690","file_name":"IST-2018-948-v1+1_2011_Cerny_Expressiveness_of.pdf","relation":"main_file","date_created":"2018-12-12T10:08:29Z","content_type":"application/pdf","file_size":492344,"access_level":"open_access","checksum":"5845be5aa19791830f7407d8853f2df0","creator":"system"}],"citation":{"short":"R. Alur, P. Cerny, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12.","ama":"Alur R, Cerny P. Expressiveness of streaming string transducers. In: Vol 8. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:1-12. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">10.4230/LIPIcs.FSTTCS.2010.1</a>","mla":"Alur, Rajeev, and Pavol Cerny. <i>Expressiveness of Streaming String Transducers</i>. Vol. 8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">10.4230/LIPIcs.FSTTCS.2010.1</a>.","apa":"Alur, R., &#38; Cerny, P. (2010). Expressiveness of streaming string transducers (Vol. 8, pp. 1–12). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1</a>","ista":"Alur R, Cerny P. 2010. Expressiveness of streaming string transducers. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 8, 1–12.","ieee":"R. Alur and P. Cerny, “Expressiveness of streaming string transducers,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India, 2010, vol. 8, pp. 1–12.","chicago":"Alur, Rajeev, and Pavol Cerny. “Expressiveness of Streaming String Transducers,” 8:1–12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1</a>."},"oa":1,"date_updated":"2025-09-30T09:49:32Z","isi":1,"ddc":["005"],"alternative_title":["LIPIcs"],"oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"scopus_import":"1","pubrep_id":"948","external_id":{"isi":["000310361000001"]},"month":"01","year":"2010","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","type":"conference","publist_id":"7331","article_processing_charge":"No","intvolume":"         8","title":"Expressiveness of streaming string transducers","publication_status":"published","author":[{"last_name":"Alur","full_name":"Alur, Rajeev","first_name":"Rajeev"},{"last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","first_name":"Pavol"}],"date_published":"2010-01-01T00:00:00Z","volume":8,"page":"1 - 12","status":"public","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"488","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:46:35Z","doi":"10.4230/LIPIcs.FSTTCS.2010.1","fulldoi":"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1","has_accepted_license":"1","conference":{"name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","start_date":"2010-12-15","end_date":"2010-12-18","location":"Chennai, India"},"quality_controlled":"1","day":"01","abstract":[{"text":"Streaming string transducers [1] define (partial) functions from input strings to output strings. A streaming string transducer makes a single pass through the input string and uses a finite set of variables that range over strings from the output alphabet. At every step, the transducer processes an input symbol, and updates all the variables in parallel using assignments whose right-hand-sides are concatenations of output symbols and variables with the restriction that a variable can be used at most once in a right-hand-side expression. It has been shown that streaming string transducers operating on strings over infinite data domains are of interest in algorithmic verification of list-processing programs, as they lead to PSPACE decision procedures for checking pre/post conditions and for checking semantic equivalence, for a well-defined class of heap-manipulating programs. In order to understand the theoretical expressiveness of streaming transducers, we focus on streaming transducers processing strings over finite alphabets, given the existence of a robust and well-studied class of &quot;regular&quot; transductions for this case. Such regular transductions can be defined either by two-way deterministic finite-state transducers, or using a logical MSO-based characterization. Our main result is that the expressiveness of streaming string transducers coincides exactly with this class of regular transductions. ","lang":"eng"}]},{"date_created":"2018-12-11T11:46:45Z","arxiv":1,"oa":1,"citation":{"ieee":"J. Cristau, C. David, and F. Horn, “How do we remember the past in randomised strategies?,” in <i>Proceedings of GandALF 2010</i>, Minori, Amalfi Coast, Italy, 2010, vol. 25, pp. 30–39.","chicago":"Cristau, Julien, Claire David, and Florian Horn. “How Do We Remember the Past in Randomised Strategies?” In <i>Proceedings of GandALF 2010</i>, 25:30–39. Open Publishing Association, 2010. <a href=\"https://doi.org/10.4204/EPTCS.25.7\">https://doi.org/10.4204/EPTCS.25.7</a>.","short":"J. Cristau, C. David, F. Horn, in:, Proceedings of GandALF 2010, Open Publishing Association, 2010, pp. 30–39.","ama":"Cristau J, David C, Horn F. How do we remember the past in randomised strategies? In: <i>Proceedings of GandALF 2010</i>. Vol 25. Open Publishing Association; 2010:30-39. doi:<a href=\"https://doi.org/10.4204/EPTCS.25.7\">10.4204/EPTCS.25.7</a>","ista":"Cristau J, David C, Horn F. 2010. How do we remember the past in randomised strategies? Proceedings of GandALF 2010. GandALF: Games, Automata, Logic, and Formal Verification, EPTCS, vol. 25, 30–39.","apa":"Cristau, J., David, C., &#38; Horn, F. (2010). How do we remember the past in randomised strategies? In <i>Proceedings of GandALF 2010</i> (Vol. 25, pp. 30–39). Minori, Amalfi Coast, Italy: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.25.7\">https://doi.org/10.4204/EPTCS.25.7</a>","mla":"Cristau, Julien, et al. “How Do We Remember the Past in Randomised Strategies?” <i>Proceedings of GandALF 2010</i>, vol. 25, Open Publishing Association, 2010, pp. 30–39, doi:<a href=\"https://doi.org/10.4204/EPTCS.25.7\">10.4204/EPTCS.25.7</a>."},"date_updated":"2026-06-18T18:51:53Z","ddc":["000"],"main_file_link":[{"url":"https://arxiv.org/abs/1006.1404","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","alternative_title":["EPTCS"],"external_id":{"arxiv":["1006.1404"]},"month":"06","year":"2010","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","type":"conference","title":"How do we remember the past in randomised strategies?","intvolume":"        25","article_processing_charge":"No","publist_id":"7332","publication_status":"published","author":[{"full_name":"Cristau, Julien","last_name":"Cristau","first_name":"Julien"},{"first_name":"Claire","last_name":"David","full_name":"David, Claire"},{"first_name":"Florian","last_name":"Horn","full_name":"Horn, Florian","id":"37327ACE-F248-11E8-B48F-1D18A9856A87"}],"volume":25,"date_published":"2010-06-09T00:00:00Z","publication":"Proceedings of GandALF 2010","status":"public","page":"30 - 39","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"_id":"489","doi":"10.4204/EPTCS.25.7","publisher":"Open Publishing Association","conference":{"location":"Minori, Amalfi Coast, Italy","name":"GandALF: Games, Automata, Logic, and Formal Verification","start_date":"2010-06-17","end_date":"2010-06-18"},"fulldoi":"https://doi.org/10.4204/EPTCS.25.7","quality_controlled":"1","abstract":[{"text":"Graph games of infinite length are a natural model for open reactive processes: one player represents the controller, trying to ensure a given specification, and the other represents a hostile environment. The evolution of the system depends on the decisions of both players, supplemented by chance. In this work, we focus on the notion of randomised strategy. More specifically, we show that three natural definitions may lead to very different results: in the most general cases, an almost-surely winning situation may become almost-surely losing if the player is only allowed to use a weaker notion of strategy. In more reasonable settings, translations exist, but they require infinite memory, even in simple cases. Finally, some traditional problems becomes undecidable for the strongest type of strategies.","lang":"eng"}],"day":"09"},{"isi":1,"date_updated":"2025-09-30T09:48:58Z","citation":{"ieee":"J. Hoenicke, K. Leino, A. Podelski, M. Schäf, and T. Wies, “Doomed program points,” <i>Formal Methods in System Design</i>, vol. 37, no. 2–3. Springer, pp. 171–199, 2010.","chicago":"Hoenicke, Jochen, Kari Leino, Andreas Podelski, Martin Schäf, and Thomas Wies. “Doomed Program Points.” <i>Formal Methods in System Design</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s10703-010-0102-0\">https://doi.org/10.1007/s10703-010-0102-0</a>.","ama":"Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. Doomed program points. <i>Formal Methods in System Design</i>. 2010;37(2-3):171-199. doi:<a href=\"https://doi.org/10.1007/s10703-010-0102-0\">10.1007/s10703-010-0102-0</a>","short":"J. Hoenicke, K. Leino, A. Podelski, M. Schäf, T. Wies, Formal Methods in System Design 37 (2010) 171–199.","apa":"Hoenicke, J., Leino, K., Podelski, A., Schäf, M., &#38; Wies, T. (2010). Doomed program points. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-010-0102-0\">https://doi.org/10.1007/s10703-010-0102-0</a>","mla":"Hoenicke, Jochen, et al. “Doomed Program Points.” <i>Formal Methods in System Design</i>, vol. 37, no. 2–3, Springer, 2010, pp. 171–99, doi:<a href=\"https://doi.org/10.1007/s10703-010-0102-0\">10.1007/s10703-010-0102-0</a>.","ista":"Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. 2010. Doomed program points. Formal Methods in System Design. 37(2–3), 171–199."},"date_created":"2018-12-11T11:47:01Z","corr_author":"1","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2010","month":"12","external_id":{"isi":["000286631700004"]},"oa_version":"None","scopus_import":"1","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"status":"public","page":"171 - 199","publication":"Formal Methods in System Design","volume":37,"date_published":"2010-12-01T00:00:00Z","publication_status":"published","author":[{"full_name":"Hoenicke, Jochen","last_name":"Hoenicke","first_name":"Jochen"},{"first_name":"Kari","full_name":"Leino, Kari","last_name":"Leino"},{"full_name":"Podelski, Andreas","last_name":"Podelski","first_name":"Andreas"},{"first_name":"Martin","last_name":"Schäf","full_name":"Schäf, Martin"},{"last_name":"Wies","full_name":"Wies, Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"}],"publist_id":"7284","article_processing_charge":"No","title":"Doomed program points","intvolume":"        37","day":"01","abstract":[{"text":"Any programming error that can be revealed before compiling a program saves precious time for the programmer. While integrated development environments already do a good job by detecting, e.g., data-flow abnormalities, current static analysis tools suffer from false positives (&quot;noise&quot;) or require strong user interaction. We propose to avoid this deficiency by defining a new class of errors. A program fragment is doomed if its execution will inevitably fail, regardless of which state it is started in. We use a formal verification method to identify such errors fully automatically and, most significantly, without producing noise. We report on experiments with a prototype tool.","lang":"eng"}],"quality_controlled":"1","fulldoi":"https://doi.org/10.1007/s10703-010-0102-0","issue":"2-3","publisher":"Springer","doi":"10.1007/s10703-010-0102-0","_id":"533"},{"citation":{"apa":"Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., &#38; Singh, R. (2010). <i>Quantitative synthesis for concurrent programs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>.","ista":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative synthesis for concurrent programs, IST Austria, 17p.","ama":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>","short":"K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative Synthesis for Concurrent Programs, IST Austria, 2010.","chicago":"Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>.","ieee":"K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, <i>Quantitative synthesis for concurrent programs</i>. IST Austria, 2010."},"oa":1,"file":[{"relation":"main_file","file_id":"5515","date_updated":"2020-07-14T12:46:42Z","file_name":"IST-2010-0004_IST-2010-0004.pdf","checksum":"da38782d2388a6fa32109d10bb9bad67","creator":"system","date_created":"2018-12-12T11:53:53Z","file_size":429101,"content_type":"application/pdf","access_level":"open_access"}],"date_created":"2018-12-12T11:39:03Z","ddc":["000","005"],"date_updated":"2025-04-15T08:12:00Z","month":"10","alternative_title":["IST Austria Technical Report"],"oa_version":"Published Version","pubrep_id":"24","type":"technical_report","publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2010","date_published":"2010-10-07T00:00:00Z","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","full_name":"Cerny, Pavol","first_name":"Pavol"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","first_name":"Arjun"},{"full_name":"Singh, Rohit","last_name":"Singh","first_name":"Rohit"}],"publication_status":"published","title":"Quantitative synthesis for concurrent programs","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"3366","relation":"later_version"}]},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"status":"public","page":"17","publisher":"IST Austria","file_date_updated":"2020-07-14T12:46:42Z","doi":"10.15479/AT:IST-2010-0004","_id":"5388","day":"07","abstract":[{"lang":"eng","text":"We present an algorithmic method for the synthesis of concurrent programs that are optimal with respect to quantitative performance measures. The input consists of a sequential sketch, that is, a program that does not contain synchronization constructs, and of a parametric performance model that assigns costs to actions such as locking, context switching, and idling. The quantitative synthesis problem is to automatically introduce synchronization constructs into the sequential sketch so that both correctness is guaranteed and worst-case (or average-case) performance is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe show that for worst-case performance, the problem can be modeled\r\nas a 2-player graph game with quantitative (limit-average) objectives, and\r\nfor average-case performance, as a 2 1/2 -player graph game (with probabilistic transitions). In both cases, the optimal correct program is derived from an optimal strategy in the corresponding quantitative game. We prove that the respective game problems are computationally expensive (NP-complete), and present several techniques that overcome the theoretical difficulty in cases of concurrent programs of practical interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic syn- thesis of programs that access a concurrent list. For certain parameter val- ues, our method automatically synthesizes various classical synchronization schemes for implementing a concurrent list, such as fine-grained locking or a lazy algorithm. For other parameter values, a new, hybrid synchronization style is synthesized, which uses both the lazy approach and coarse-grained locks (instead of standard fine-grained locks). The trade-off occurs because while fine-grained locking tends to decrease the cost that is due to waiting for locks, it increases cache size requirements."}],"has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT:IST-2010-0004"},{"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"4393"},{"status":"public","id":"3249","relation":"later_version"}]},"page":"24","status":"public","department":[{"_id":"ToHe"}],"date_published":"2010-06-04T00:00:00Z","title":"Simulation distances","publication_status":"published","author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","last_name":"Cerny","first_name":"Pavol"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Arjun","last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun"}],"day":"04","abstract":[{"text":"Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of “fit” or “desirability.” We extend the simulation preorder to the quantitative setting, by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the im- plementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes.","lang":"eng"}],"has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT:IST-2010-0003","publisher":"IST Austria","doi":"10.15479/AT:IST-2010-0003","file_date_updated":"2020-07-14T12:46:42Z","_id":"5389","ddc":["005"],"date_updated":"2026-06-18T18:41:23Z","citation":{"short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria, 2010.","ama":"Cerny P, Henzinger TA, Radhakrishna A. <i>Simulation Distances</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria, 24p.","mla":"Cerny, Pavol, et al. <i>Simulation Distances</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>.","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2010). <i>Simulation distances</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, <i>Simulation distances</i>. IST Austria, 2010.","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. <i>Simulation Distances</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>."},"oa":1,"date_created":"2018-12-12T11:39:03Z","file":[{"date_updated":"2020-07-14T12:46:42Z","file_id":"5547","file_name":"IST-2010-0003_IST-2010-0003.pdf","relation":"main_file","date_created":"2018-12-12T11:54:25Z","access_level":"open_access","file_size":367246,"content_type":"application/pdf","checksum":"284ded99764e32a583a8ea83fcea254b","creator":"system"}],"publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"technical_report","year":"2010","month":"06","alternative_title":["IST Austria Technical Report"],"oa_version":"Published Version","pubrep_id":"25"},{"oa_version":"Published Version","alternative_title":["IST Austria Technical Report"],"pubrep_id":"26","_id":"5390","month":"06","publisher":"IST Austria","file_date_updated":"2020-07-14T12:46:43Z","doi":"10.15479/AT:IST-2010-0002","fulldoi":"https://doi.org/10.15479/AT:IST-2010-0002","has_accepted_license":"1","year":"2010","day":"04","type":"technical_report","abstract":[{"text":"The class of ω regular languages provide a robust specification language in verification. Every ω-regular condition can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. In this work we consider the finitary parity and Streett (fairness) conditions. We present the topological, automata-theoretic and logical characterization of finitary languages defined by finitary parity and Streett conditions. We (a) show that the finitary parity and Streett languages are Σ2-complete; (b) present a complete characterization of the expressive power of various classes of automata with finitary and infinitary conditions (in particular we show that non-deterministic finitary parity and Streett automata cannot be determinized to deterministic finitary parity or Streett automata); and (c) show that the languages defined by non-deterministic finitary parity automata exactly characterize the star-free fragment of ωB-regular languages.","lang":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fijalkow","full_name":"Fijalkow, Nathanaël","first_name":"Nathanaël"}],"title":"Topological, automata-theoretic and logical characterization of finitary languages","date_created":"2018-12-12T11:39:03Z","file":[{"date_created":"2018-12-12T11:54:10Z","content_type":"application/pdf","file_size":395662,"access_level":"open_access","checksum":"283d3604d76dd4d5161585d4c8625fbe","creator":"system","file_id":"5532","date_updated":"2020-07-14T12:46:43Z","file_name":"IST-2010-0002_IST-2010-0002.pdf","relation":"main_file"}],"citation":{"mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>.","apa":"Chatterjee, K., &#38; Fijalkow, N. (2010). <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>","ista":"Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical characterization of finitary languages, IST Austria, 21p.","ama":"Chatterjee K, Fijalkow N. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>","short":"K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization of Finitary Languages, IST Austria, 2010.","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>.","ieee":"K. Chatterjee and N. Fijalkow, <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria, 2010."},"date_published":"2010-06-04T00:00:00Z","oa":1,"department":[{"_id":"KrCh"}],"date_updated":"2020-07-14T23:04:41Z","page":"21","status":"public","language":[{"iso":"eng"}],"ddc":["000"]},{"department":[{"_id":"ToHe"}],"page":"27","status":"public","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"4390"}]},"author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"first_name":"Arjun","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna"},{"first_name":"Damien","last_name":"Zufferey","full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Swarat","last_name":"Chaudhuri","full_name":"Chaudhuri, Swarat"},{"full_name":"Alur, Rajeev","last_name":"Alur","first_name":"Rajeev"}],"publication_status":"published","title":"Model checking of linearizability of concurrent list implementations","date_published":"2010-04-19T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT:IST-2010-0001","has_accepted_license":"1","day":"19","abstract":[{"text":"Concurrent data structures with fine-grained synchronization are notoriously difficult to implement correctly. The difficulty of reasoning about these implementations does not stem from the number of variables or the program size, but rather from the large number of possible interleavings. These implementations are therefore prime candidates for model checking. We introduce an algorithm for verifying linearizability of singly-linked heap-based concurrent data structures. We consider a model consisting of an unbounded heap where each node consists an element from an unbounded data domain, with a restricted set of operations for testing and updating pointers and data elements. Our main result is that linearizability is decidable for programs that invoke a fixed number of methods, possibly in parallel. This decidable fragment covers many of the common implementation techniques — fine-grained locking, lazy synchronization, and lock-free synchronization. We also show how the technique can be used to verify optimistic implementations with the help of programmer annotations. We developed a verification tool CoLT and evaluated it on a representative sample of Java implementations of the concurrent set data structure. The tool verified linearizability of a number of implementations, found a known error in a lock-free imple- mentation and proved that the corrected version is linearizable.","lang":"eng"}],"_id":"5391","publisher":"IST Austria","doi":"10.15479/AT:IST-2010-0001","file_date_updated":"2020-07-14T12:46:43Z","date_updated":"2024-10-21T06:03:05Z","ddc":["004"],"file":[{"file_name":"IST-2010-0001_IST-2010-0001.pdf","date_updated":"2020-07-14T12:46:43Z","file_id":"5505","relation":"main_file","access_level":"open_access","file_size":372286,"content_type":"application/pdf","date_created":"2018-12-12T11:53:44Z","creator":"system","checksum":"986645caad7dd85a6a091488f6c646dc"}],"date_created":"2018-12-12T11:39:04Z","citation":{"chicago":"Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and Rajeev Alur. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>.","ieee":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria, 2010.","ista":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking of linearizability of concurrent list implementations, IST Austria, 27p.","apa":"Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., &#38; Alur, R. (2010). <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>","mla":"Cerny, Pavol, et al. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>.","ama":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>","short":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking of Linearizability of Concurrent List Implementations, IST Austria, 2010."},"oa":1,"year":"2010","type":"technical_report","publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["IST Austria Technical Report"],"oa_version":"Published Version","pubrep_id":"27","month":"04"},{"publication_status":"published","author":[{"last_name":"Juhás","full_name":"Juhás, Gabriel","first_name":"Gabriel"},{"last_name":"Kazlov","full_name":"Kazlov, Igor","id":"4A997E50-F248-11E8-B48F-1D18A9856A87","first_name":"Igor"},{"first_name":"Ana","full_name":"Juhásová, Ana","last_name":"Juhásová"}],"date_created":"2019-02-08T09:33:41Z","title":"Instance Deadlock: A Mystery behind Frozen Programs","article_processing_charge":"No","date_published":"2010-01-01T00:00:00Z","citation":{"short":"G. Juhás, I. Kazlov, A. Juhásová, in:, Applications and Theory of Petri Nets, Springer Berlin Heidelberg, Berlin, Heidelberg, 2010, pp. 1–17.","ama":"Juhás G, Kazlov I, Juhásová A. Instance Deadlock: A Mystery behind Frozen Programs. In: <i>Applications and Theory of Petri Nets</i>. Berlin, Heidelberg: Springer Berlin Heidelberg; 2010:1-17. doi:<a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">10.1007/978-3-642-13675-7_1</a>","ista":"Juhás G, Kazlov I, Juhásová A. 2010.Instance Deadlock: A Mystery behind Frozen Programs. In: Applications and Theory of Petri Nets. , 1–17.","mla":"Juhás, Gabriel, et al. “Instance Deadlock: A Mystery behind Frozen Programs.” <i>Applications and Theory of Petri Nets</i>, Springer Berlin Heidelberg, 2010, pp. 1–17, doi:<a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">10.1007/978-3-642-13675-7_1</a>.","apa":"Juhás, G., Kazlov, I., &#38; Juhásová, A. (2010). Instance Deadlock: A Mystery behind Frozen Programs. In <i>Applications and Theory of Petri Nets</i> (pp. 1–17). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">https://doi.org/10.1007/978-3-642-13675-7_1</a>","ieee":"G. Juhás, I. Kazlov, and A. Juhásová, “Instance Deadlock: A Mystery behind Frozen Programs,” in <i>Applications and Theory of Petri Nets</i>, Berlin, Heidelberg: Springer Berlin Heidelberg, 2010, pp. 1–17.","chicago":"Juhás, Gabriel, Igor Kazlov, and Ana Juhásová. “Instance Deadlock: A Mystery behind Frozen Programs.” In <i>Applications and Theory of Petri Nets</i>, 1–17. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. <a href=\"https://doi.org/10.1007/978-3-642-13675-7_1\">https://doi.org/10.1007/978-3-642-13675-7_1</a>."},"publication":"Applications and Theory of Petri Nets","date_updated":"2022-04-01T13:45:24Z","status":"public","page":"1-17","language":[{"iso":"eng"}],"_id":"5940","oa_version":"None","doi":"10.1007/978-3-642-13675-7_1","publisher":"Springer Berlin Heidelberg","fulldoi":"https://doi.org/10.1007/978-3-642-13675-7_1","extern":"1","year":"2010","type":"book_chapter","place":"Berlin, Heidelberg","user_id":"4A997E50-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["9783642136740","9783642136757"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","type":"journal_article","abstract":[{"lang":"eng","text":"It is not well understood how the human Mediator complex, transcription factor IIH and RNA polymerase II (Pol II) work together with activators to initiate transcription. Activator binding alters Mediator structure, yet the functional consequences of such structural shifts remain unknown. The p53 C terminus and its activation domain interact with different Mediator subunits, and we find that each interaction differentially affects Mediator structure; strikingly, distinct p53-Mediator structures differentially affect Pol II activity. Only the p53 activation domain induces the formation of a large pocket domain at the Mediator-Pol II interaction site, and this correlates with activation of stalled Pol II to a productively elongating state. Moreover, we define a Mediator requirement for TFIIH-dependent Pol II C-terminal domain phosphorylation and identify substantial differences in Pol II C-terminal domain processing that correspond to distinct p53-Mediator structural states. Our results define a fundamental mechanism by which p53 activates transcription and suggest that Mediator structural shifts trigger activation of stalled Pol II complexes."}],"year":"2010","issue":"6","fulldoi":"https://doi.org/10.1038/nsmb.1816","extern":"1","publisher":"Nature Publishing Group","doi":"10.1038/nsmb.1816","month":"06","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2932482/"}],"oa_version":"None","_id":"598","language":[{"iso":"eng"}],"status":"public","page":"753 - 760","date_updated":"2021-01-12T08:05:28Z","publication":"Nature Structural and Molecular Biology","citation":{"ama":"Meyer K, Lin S, Bernecky C, Gao Y, Taatjes D. P53 activates transcription by directing structural shifts in Mediator. <i>Nature Structural and Molecular Biology</i>. 2010;17(6):753-760. doi:<a href=\"https://doi.org/10.1038/nsmb.1816\">10.1038/nsmb.1816</a>","short":"K. Meyer, S. Lin, C. Bernecky, Y. Gao, D. Taatjes, Nature Structural and Molecular Biology 17 (2010) 753–760.","ista":"Meyer K, Lin S, Bernecky C, Gao Y, Taatjes D. 2010. P53 activates transcription by directing structural shifts in Mediator. Nature Structural and Molecular Biology. 17(6), 753–760.","mla":"Meyer, Krista, et al. “P53 Activates Transcription by Directing Structural Shifts in Mediator.” <i>Nature Structural and Molecular Biology</i>, vol. 17, no. 6, Nature Publishing Group, 2010, pp. 753–60, doi:<a href=\"https://doi.org/10.1038/nsmb.1816\">10.1038/nsmb.1816</a>.","apa":"Meyer, K., Lin, S., Bernecky, C., Gao, Y., &#38; Taatjes, D. (2010). P53 activates transcription by directing structural shifts in Mediator. <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nsmb.1816\">https://doi.org/10.1038/nsmb.1816</a>","ieee":"K. Meyer, S. Lin, C. Bernecky, Y. Gao, and D. Taatjes, “P53 activates transcription by directing structural shifts in Mediator,” <i>Nature Structural and Molecular Biology</i>, vol. 17, no. 6. Nature Publishing Group, pp. 753–760, 2010.","chicago":"Meyer, Krista, Shih Lin, Carrie Bernecky, Yuefeng Gao, and Dylan Taatjes. “P53 Activates Transcription by Directing Structural Shifts in Mediator.” <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nsmb.1816\">https://doi.org/10.1038/nsmb.1816</a>."},"volume":17,"oa":1,"date_published":"2010-06-01T00:00:00Z","article_processing_charge":"No","publist_id":"7210","date_created":"2018-12-11T11:47:24Z","title":"P53 activates transcription by directing structural shifts in Mediator","intvolume":"        17","author":[{"first_name":"Krista","last_name":"Meyer","full_name":"Meyer, Krista"},{"full_name":"Lin, Shih","last_name":"Lin","first_name":"Shih"},{"first_name":"Carrie A","last_name":"Bernecky","full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036"},{"last_name":"Gao","full_name":"Gao, Yuefeng","first_name":"Yuefeng"},{"first_name":"Dylan","full_name":"Taatjes, Dylan","last_name":"Taatjes"}],"publication_status":"published"},{"date_created":"2019-03-20T15:20:30Z","file":[{"checksum":"a01e6bbe15f044c0c79a26d7d881953e","creator":"kschuh","date_created":"2019-03-20T15:22:48Z","file_size":578059,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6143","date_updated":"2020-07-14T12:47:20Z","file_name":"2010_PLOS_Weber.PDF"}],"citation":{"ama":"Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M. Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. <i>PLoS ONE</i>. 2010;5(11). doi:<a href=\"https://doi.org/10.1371/journal.pone.0013922\">10.1371/journal.pone.0013922</a>","short":"K.P. Weber, S. De, I. Kozarewa, D.J. Turner, M.M. Babu, M. de Bono, PLoS ONE 5 (2010).","mla":"Weber, Katherine P., et al. “Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. Elegans.” <i>PLoS ONE</i>, vol. 5, no. 11, e13922, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pone.0013922\">10.1371/journal.pone.0013922</a>.","apa":"Weber, K. P., De, S., Kozarewa, I., Turner, D. J., Babu, M. M., &#38; de Bono, M. (2010). Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0013922\">https://doi.org/10.1371/journal.pone.0013922</a>","ista":"Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M. 2010. Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. PLoS ONE. 5(11), e13922.","ieee":"K. P. Weber, S. De, I. Kozarewa, D. J. Turner, M. M. Babu, and M. de Bono, “Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans,” <i>PLoS ONE</i>, vol. 5, no. 11. Public Library of Science, 2010.","chicago":"Weber, Katherine P., Subhajyoti De, Iwanka Kozarewa, Daniel J. Turner, M. Madan Babu, and Mario de Bono. “Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. Elegans.” <i>PLoS ONE</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pone.0013922\">https://doi.org/10.1371/journal.pone.0013922</a>."},"oa":1,"date_updated":"2021-01-12T08:06:20Z","ddc":["570"],"oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"month":"11","external_id":{"pmid":["21085631"]},"extern":"1","year":"2010","type":"journal_article","publication_identifier":{"issn":["1932-6203"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Weber, Katherine P.","last_name":"Weber","first_name":"Katherine P."},{"last_name":"De","full_name":"De, Subhajyoti","first_name":"Subhajyoti"},{"first_name":"Iwanka","full_name":"Kozarewa, Iwanka","last_name":"Kozarewa"},{"full_name":"Turner, Daniel J.","last_name":"Turner","first_name":"Daniel J."},{"first_name":"M. Madan","full_name":"Babu, M. Madan","last_name":"Babu"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","first_name":"Mario"}],"publication_status":"published","title":"Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans","intvolume":"         5","volume":5,"date_published":"2010-11-11T00:00:00Z","pmid":1,"status":"public","publication":"PLoS ONE","article_number":"e13922","language":[{"iso":"eng"}],"_id":"6142","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0013922","file_date_updated":"2020-07-14T12:47:20Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.1371/journal.pone.0013922","issue":"11","day":"11","abstract":[{"lang":"eng","text":"Defining the mutational landscape when individuals of a species grow separately and diverge over many generations can provide insights into trait evolution. A specific example of this involves studying changes associated with domestication where different lines of the same wild stock have been cultivated independently in different standard environments. Whole genome sequence comparison of such lines permits estimation of mutation rates, inference of genes' ancestral states and ancestry of existing strains, and correction of sequencing errors in genome databases. Here we study domestication of the C. elegans Bristol strain as a model, and report the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately from shortly after the Bristol strain was isolated until methods to freeze C. elegans were developed. We find that during this time the two strains have accumulated 1208 genetic differences. We describe phenotypic variation between N2 and LSJ1 in the rate at which embryos develop, the rate of production of eggs, the maturity of eggs at laying, and feeding behavior, all the result of post-isolation changes. We infer the ancestral alleles in the original Bristol isolate and highlight 2038 likely sequencing errors in the original N2 reference genome sequence. Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication."}],"quality_controlled":"1"},{"type":"book_chapter","abstract":[{"text":"Sinclair Ross’s novel As for Me and My House has long since been canonized as Canadian prairie fiction. Accordingly, it has been the subject of many critical studies and academic papers. Most commentators have concentrated on such literary issues as the representation of the western landscape or the reliability of the female narrator. But so far little consideration has been given to the social and cultural implications of the novel. Few attempts have been made to analyze the text from a cultural perspective including such social markers as class, gender and ethnicity. That is all the more surprising because Sinclair Ross has often been credited for being a realistic author and As for Me and My House has often been interpreted as a regional novel characteristic of a particular time and place.","lang":"eng"}],"day":"01","quality_controlled":0,"extern":1,"year":"2010","month":"01","publisher":"Facultas.WUV","_id":"619","publication":"Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l'Ouest canadien","date_updated":"2021-01-12T08:06:40Z","page":"173 - 179","status":"public","date_published":"2010-01-01T00:00:00Z","citation":{"short":"W. Zacharasiewicz, F. Kirsch, in:, Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien, Facultas.WUV, 2010, pp. 173–179.","ama":"Zacharasiewicz W, Kirsch F. “This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House. In: <i>Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien</i>. Facultas.WUV; 2010:173-179.","ista":"Zacharasiewicz W, Kirsch F. 2010.“This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House. In: Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien. , 173–179.","mla":"Zacharasiewicz, Waldemar, and Fritz Kirsch. “‘This Is a Fundamentalist Town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House.” <i>Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien</i>, Facultas.WUV, 2010, pp. 173–79.","apa":"Zacharasiewicz, W., &#38; Kirsch, F. (2010). “This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House. In <i>Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien</i> (pp. 173–179). Facultas.WUV.","ieee":"W. Zacharasiewicz and F. Kirsch, “‘This is a fundamentalist town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House,” in <i>Social and cultural interaction and literary landscapes in the Canadian West : impressions of an exploratory field trip and academic interaction in the Canadian West : Rapports interculturels et paysages littéraires dans l’Ouest canadien</i>, Facultas.WUV, 2010, pp. 173–179.","chicago":"Zacharasiewicz, Waldemar, and Fritz Kirsch. “‘This Is a Fundamentalist Town’: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House.” In <i>Social and Cultural Interaction and Literary Landscapes in the Canadian West : Impressions of an Exploratory Field Trip and Academic Interaction in the Canadian West : Rapports Interculturels et Paysages Littéraires Dans l’Ouest Canadien</i>, 173–79. Facultas.WUV, 2010."},"publication_status":"published","author":[{"first_name":"Waldemar","last_name":"Zacharasiewicz","full_name":"Zacharasiewicz, Waldemar"},{"last_name":"Kirsch","full_name":"Kirsch, Fritz Peter","first_name":"Fritz"}],"title":"“This is a fundamentalist town”: The Prairie Town as a Site of Social and Cultural Conflict in Sinclair Ross’s As for Me and My House","date_created":"2018-12-11T11:47:32Z","publist_id":"7185"},{"publication":"Nature Medicine","date_updated":"2021-01-12T08:06:43Z","status":"public","page":"1439-1443","language":[{"iso":"eng"}],"author":[{"first_name":"L","last_name":"Zhou","full_name":"Zhou, L"},{"last_name":"Li","full_name":"Li, F","first_name":"F"},{"first_name":"Haibing","full_name":"Xu, Haibing","id":"310349D0-F248-11E8-B48F-1D18A9856A87","last_name":"Xu"},{"first_name":"CX","last_name":"Luo","full_name":"Luo, CX"},{"first_name":"HY","full_name":"Wu, HY","last_name":"Wu"},{"last_name":"Zhu","full_name":"Zhu, MM","first_name":"MM"},{"full_name":"Lu, W","last_name":"Lu","first_name":"W"},{"last_name":"Ji","full_name":"Ji, X","first_name":"X"},{"first_name":"QG","full_name":"Zhou, QG","last_name":"Zhou"},{"full_name":"Zhu, DY","last_name":"Zhu","first_name":"DY"}],"publication_status":"published","date_created":"2019-04-04T14:55:32Z","title":"Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95","intvolume":"        16","date_published":"2010-11-21T00:00:00Z","pmid":1,"volume":16,"citation":{"short":"L. Zhou, F. Li, H. Xu, C. Luo, H. Wu, M. Zhu, W. Lu, X. Ji, Q. Zhou, D. Zhu, Nature Medicine 16 (2010) 1439–1443.","ama":"Zhou L, Li F, Xu H, et al. Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. <i>Nature Medicine</i>. 2010;16(12):1439-1443. doi:<a href=\"https://doi.org/10.1038/nm.2245\">10.1038/nm.2245</a>","apa":"Zhou, L., Li, F., Xu, H., Luo, C., Wu, H., Zhu, M., … Zhu, D. (2010). Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. <i>Nature Medicine</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nm.2245\">https://doi.org/10.1038/nm.2245</a>","mla":"Zhou, L., et al. “Treatment of Cerebral Ischemia by Disrupting Ischemia-Induced Interaction of NNOS with PSD-95.” <i>Nature Medicine</i>, vol. 16, no. 12, Nature Publishing Group, 2010, pp. 1439–43, doi:<a href=\"https://doi.org/10.1038/nm.2245\">10.1038/nm.2245</a>.","ista":"Zhou L, Li F, Xu H, Luo C, Wu H, Zhu M, Lu W, Ji X, Zhou Q, Zhu D. 2010. Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95. Nature Medicine. 16(12), 1439–1443.","ieee":"L. Zhou <i>et al.</i>, “Treatment of cerebral ischemia by disrupting ischemia-induced interaction of nNOS with PSD-95,” <i>Nature Medicine</i>, vol. 16, no. 12. Nature Publishing Group, pp. 1439–1443, 2010.","chicago":"Zhou, L, F Li, Haibing Xu, CX Luo, HY Wu, MM Zhu, W Lu, X Ji, QG Zhou, and DY Zhu. “Treatment of Cerebral Ischemia by Disrupting Ischemia-Induced Interaction of NNOS with PSD-95.” <i>Nature Medicine</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nm.2245\">https://doi.org/10.1038/nm.2245</a>."},"extern":"1","fulldoi":"https://doi.org/10.1038/nm.2245","issue":"12","year":"2010","type":"journal_article","abstract":[{"lang":"eng","text":"Stroke is a major public health problem leading to high rates of death and disability in adults. Excessive stimulation of N-methyl-D-aspartate receptors (NMDARs) and the resulting neuronal nitric oxide synthase (nNOS) activation are crucial for neuronal injury after stroke insult. However, directly inhibiting NMDARs or nNOS can cause severe side effects because they have key physiological functions in the CNS. Here we show that cerebral ischemia induces the interaction of nNOS with postsynaptic density protein-95 (PSD-95). Disrupting nNOS-PSD-95 interaction via overexpressing the N-terminal amino acid residues 1-133 of nNOS (nNOS-N(1-133)) prevented glutamate-induced excitotoxicity and cerebral ischemic damage. Given the mechanism of nNOS-PSD-95 interaction, we developed a series of compounds and discovered a small-molecular inhibitor of the nNOS-PSD-95 interaction, ZL006. This drug blocked the ischemia-induced nNOS-PSD-95 association selectively, had potent neuroprotective activity in vitro and ameliorated focal cerebral ischemic damage in mice and rats subjected to middle cerebral artery occlusion (MCAO) and reperfusion. Moreover, it readily crossed the blood-brain barrier, did not inhibit NMDAR function, catalytic activity of nNOS or spatial memory, and had no effect on aggressive behaviors. Thus, this new drug may serve as a treatment for stroke, perhaps without major side effects. "}],"day":"21","quality_controlled":"1","publication_identifier":{"issn":["1078-8956","1546-170x"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6198","oa_version":"None","month":"11","doi":"10.1038/nm.2245","external_id":{"pmid":["21102461"]},"publisher":"Nature Publishing Group"},{"publisher":"Wiley-Blackwell","doi":"10.1111/j.1558-5646.2009.00853.x","month":"03","_id":"2071","quality_controlled":0,"day":"01","abstract":[{"text":"The X or Z chromosome has several characteristics that distinguish it from the autosomes, namely hemizygosity in the heterogametic sex, and a potentially different effective population size, both of which may influence the rate and nature of evolution. In particular, there may be an accelerated rate of adaptive change for X-linked compared to autosomal coding sequences, often referred to as the Faster-X effect. Empirical studies have indicated that the strength of Faster-X evolution varies among different species, and theoretical treatments have shown that demography and mating system can substantially affect the degree of Faster-X evolution. Here we integrate genomic data on Faster-X evolution from a variety of animals with the demographic factors, mating system, and sex chromosome regulatory characteristics that may influence it. Our results suggest that differences in effective population size and mechanisms of dosage compensation may influence the perceived extent of Faster-X evolution, and help to explain several clade-specific patterns that we observe.","lang":"eng"}],"type":"journal_article","year":"2010","fulldoi":"https://doi.org/10.1111/j.1558-5646.2009.00853.x","extern":1,"issue":"3","citation":{"ieee":"J. Mank, B. Vicoso, S. Berlin, and B. Charlesworth, “Effective population size and the Faster-X effect: Empirical results and their interpretation,” <i>Evolution</i>, vol. 64, no. 3. Wiley-Blackwell, pp. 663–674, 2010.","chicago":"Mank, Judith, Beatriz Vicoso, Sofia Berlin, and Brian Charlesworth. “Effective Population Size and the Faster-X Effect: Empirical Results and Their Interpretation.” <i>Evolution</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00853.x\">https://doi.org/10.1111/j.1558-5646.2009.00853.x</a>.","ama":"Mank J, Vicoso B, Berlin S, Charlesworth B. Effective population size and the Faster-X effect: Empirical results and their interpretation. <i>Evolution</i>. 2010;64(3):663-674. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00853.x\">10.1111/j.1558-5646.2009.00853.x</a>","short":"J. Mank, B. Vicoso, S. Berlin, B. Charlesworth, Evolution 64 (2010) 663–674.","mla":"Mank, Judith, et al. “Effective Population Size and the Faster-X Effect: Empirical Results and Their Interpretation.” <i>Evolution</i>, vol. 64, no. 3, Wiley-Blackwell, 2010, pp. 663–74, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00853.x\">10.1111/j.1558-5646.2009.00853.x</a>.","apa":"Mank, J., Vicoso, B., Berlin, S., &#38; Charlesworth, B. (2010). Effective population size and the Faster-X effect: Empirical results and their interpretation. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00853.x\">https://doi.org/10.1111/j.1558-5646.2009.00853.x</a>","ista":"Mank J, Vicoso B, Berlin S, Charlesworth B. 2010. Effective population size and the Faster-X effect: Empirical results and their interpretation. Evolution. 64(3), 663–674."},"date_published":"2010-03-01T00:00:00Z","volume":64,"acknowledgement":"We gratefully acknowledge funding from the Royal Society (to JEM)","publist_id":"4967","intvolume":"        64","title":"Effective population size and the Faster-X effect: Empirical results and their interpretation","date_created":"2018-12-11T11:55:32Z","author":[{"full_name":"Mank, Judith E","last_name":"Mank","first_name":"Judith"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Beatriz Vicoso","first_name":"Beatriz"},{"first_name":"Sofia","last_name":"Berlin","full_name":"Berlin, Sofia"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"}],"publication_status":"published","page":"663 - 674","status":"public","date_updated":"2021-01-12T06:55:07Z","publication":"Evolution"},{"volume":499,"date_published":"2010-01-01T00:00:00Z","citation":{"apa":"Bickel, B. (2010). <i>Measurement-based modeling and fabrication of deformable materials for human faces</i>. <i>Unknown</i>. Unknown. <a href=\"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908\">https://doi.org/dx.doi.org/10.3929/ethz-a-006354908</a>","mla":"Bickel, Bernd. “Measurement-Based Modeling and Fabrication of Deformable Materials for Human Faces.” <i>Unknown</i>, vol. 499, no. 7458, Unknown, 2010, doi:<a href=\"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908\">dx.doi.org/10.3929/ethz-a-006354908</a>.","ista":"Bickel B. 2010. Measurement-based modeling and fabrication of deformable materials for human faces. Unknown.","short":"B. Bickel, Measurement-Based Modeling and Fabrication of Deformable Materials for Human Faces, Unknown, 2010.","ama":"Bickel B. Measurement-based modeling and fabrication of deformable materials for human faces. <i>Unknown</i>. 2010;499(7458). doi:<a href=\"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908\">dx.doi.org/10.3929/ethz-a-006354908</a>","chicago":"Bickel, Bernd. “Measurement-Based Modeling and Fabrication of Deformable Materials for Human Faces.” <i>Unknown</i>. Unknown, 2010. <a href=\"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908\">https://doi.org/dx.doi.org/10.3929/ethz-a-006354908</a>.","ieee":"B. Bickel, “Measurement-based modeling and fabrication of deformable materials for human faces,” Unknown, 2010."},"publication_status":"published","author":[{"orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bernd Bickel","first_name":"Bernd"}],"date_created":"2018-12-11T11:55:34Z","title":"Measurement-based modeling and fabrication of deformable materials for human faces","intvolume":"       499","publist_id":"4963","publication":"Unknown","status":"public","date_updated":"2021-01-12T06:55:09Z","month":"01","doi":"dx.doi.org/10.3929/ethz-a-006354908","publisher":"Unknown","_id":"2075","abstract":[{"lang":"eng","text":"This thesis investigates the combination of data-driven and physically based techniques for acquiring, modeling, and animating deformable materials, with a special focus on human faces. Furthermore, based on these techniques, we introduce a data-driven process for designing and fabricating materials with desired deformation behavior. \nRealistic simulation behavior, surface details, and appearance are still demanding tasks. Neither pure data-driven, pure procedural, nor pure physical methods are best suited for accurate synthesis of facial motion and details (both for appearance and geometry), due to the difficulties in model design, parameter estimation, and desired controllability for animators. Capturing of a small but representative amount of real data, and then synthesizing diverse on-demand examples with physically-based models and real data as input benefits from both sides: Highly realistic model behavior due to real-world data and controllability due to physically-based models.\nTo model the face and its behavior, hybrid physically-based and data-driven approaches are elaborated. We investigate surface-based representations as well as a solid representation based on FEM. To achieve realistic behavior, we propose to build light-weighted data capture devices to acquire real-world data to estimate model parameters and to employ concepts from data-driven modeling techniques and machine learning. The resulting models support simple acquisition systems, offer techniques to process and extract model parameters from real-world data, provide a compact representation of the facial geometry and its motion, and allow intuitive editing. We demonstrate applications such as capture of facial geometry and motion and real-time animation and transfer of facial details, and show that our soft tissue model can react to external forces and produce realistic deformations beyond facial expressions.\nBased on this model, we furthermore introduce a data-driven process for designing and fabricating materials with desired deformation behavior. The process starts with measuring deformation properties of base materials. Each material is represented as a non-linear stress-strain relationship in a finite-element model. For material design and fabrication, we introduce an optimization process that finds the best combination of base materials that meets a user’s criteria specified by example deformations. Our algorithm employs a number of strategies to prune poor solutions from the combinatorial search space. We finally demonstrate the complete process by designing and fabricating objects with complex heterogeneous materials using modern multi-material 3D printers.\n"}],"type":"dissertation","day":"01","quality_controlled":0,"issue":"7458","fulldoi":"https://doi.org/dx.doi.org/10.3929/ethz-a-006354908","extern":1,"year":"2010"},{"arxiv":1,"date_created":"2021-10-12T08:34:23Z","oa":1,"citation":{"ieee":"A. Šarić and A. Cacciuto, “Particle self-assembly on soft elastic shells,” <i>Soft Matter</i>, vol. 7, no. 5. Royal Society of Chemistry (RSC), pp. 1874–1878, 2010.","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Particle Self-Assembly on Soft Elastic Shells.” <i>Soft Matter</i>. Royal Society of Chemistry (RSC), 2010. <a href=\"https://doi.org/10.1039/c0sm01143f\">https://doi.org/10.1039/c0sm01143f</a>.","ama":"Šarić A, Cacciuto A. Particle self-assembly on soft elastic shells. <i>Soft Matter</i>. 2010;7(5):1874-1878. doi:<a href=\"https://doi.org/10.1039/c0sm01143f\">10.1039/c0sm01143f</a>","short":"A. Šarić, A. Cacciuto, Soft Matter 7 (2010) 1874–1878.","ista":"Šarić A, Cacciuto A. 2010. Particle self-assembly on soft elastic shells. Soft Matter. 7(5), 1874–1878.","mla":"Šarić, Anđela, and Angelo Cacciuto. “Particle Self-Assembly on Soft Elastic Shells.” <i>Soft Matter</i>, vol. 7, no. 5, Royal Society of Chemistry (RSC), 2010, pp. 1874–78, doi:<a href=\"https://doi.org/10.1039/c0sm01143f\">10.1039/c0sm01143f</a>.","apa":"Šarić, A., &#38; Cacciuto, A. (2010). Particle self-assembly on soft elastic shells. <i>Soft Matter</i>. Royal Society of Chemistry (RSC). <a href=\"https://doi.org/10.1039/c0sm01143f\">https://doi.org/10.1039/c0sm01143f</a>"},"article_type":"original","date_updated":"2021-10-12T09:49:27Z","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1010.2453"}],"month":"12","external_id":{"arxiv":["1010.2453"]},"extern":"1","year":"2010","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["1744-683X","1744-6848"]},"author":[{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"first_name":"Angelo","full_name":"Cacciuto, Angelo","last_name":"Cacciuto"}],"publication_status":"published","intvolume":"         7","title":"Particle self-assembly on soft elastic shells","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426. We thank Josep C. Pàmies for helpful discussions.","article_processing_charge":"No","date_published":"2010-12-23T00:00:00Z","volume":7,"publication":"Soft Matter","status":"public","page":"1874-1878","language":[{"iso":"eng"}],"_id":"10127","keyword":["condensed matter physics","general chemistry"],"doi":"10.1039/c0sm01143f","publisher":"Royal Society of Chemistry (RSC)","fulldoi":"https://doi.org/10.1039/c0sm01143f","issue":"5","abstract":[{"text":"We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells. The morphology of the patterns can be controlled by the mechanical properties of the surface, and can be fine-tuned by varying the binding energy of the particles. We also repeat our calculations for a fully flexible chain and find that the chain conformations follow patterns similar to those formed by the nanoparticles under analogous conditions. We propose a simple way of understanding and sorting the different structures and relate it to the underlying shape transition of the shell. Finally, we discuss the implications of our results.","lang":"eng"}],"day":"23","quality_controlled":"1"},{"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"_id":"10128","doi":"10.1039/b923041f","publisher":"Royal Society of Chemistry ","issue":"18","fulldoi":"https://doi.org/10.1039/b923041f","quality_controlled":"1","abstract":[{"lang":"eng","text":"An extensive computational study of the conformational preferences of three capped dipeptides: Ac-Xxx-Phe-NH2, Xxx = Gly, Ala, Val is reported. On the basis of local second-order Møller–Plesset perturbation theory (LMP2) and DFT computations we were able to identify the experimentally observed conformers as γL–γL(g−) and β-turn I(g+) in Ac-Gly-Phe-NH2, and Ac-Ala-Phe-NH2, and as the closely related γL(g+)–γL(g−) and β-turn I(a,g+) in Ac-Val-Phe-NH2. In contrast to the experimental observation that peptides with bulky side chain have a propensity for β-turns, we show that in Ac-Val-Phe-NH2 the minimum energy structure corresponds to the experimentally non detected β-strand."}],"day":"16","title":"Quantum mechanical study of secondary structure formation in protected dipeptides","intvolume":"        12","acknowledgement":"This work has been supported by the MZOŠ projects 098-0352851-2921 and 119-1191342-2959.","article_processing_charge":"No","author":[{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Hrenar, T.","last_name":"Hrenar","first_name":"T."},{"last_name":"Mališ","full_name":"Mališ, M.","first_name":"M."},{"full_name":"Došlić, N.","last_name":"Došlić","first_name":"N."}],"publication_status":"published","pmid":1,"date_published":"2010-03-16T00:00:00Z","volume":12,"publication":"Physical Chemistry Chemical Physics","page":"4678-4685","status":"public","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://europepmc.org/article/med/20428547"}],"oa_version":"None","external_id":{"pmid":["20428547"]},"month":"03","year":"2010","extern":"1","publication_identifier":{"issn":["1463-9076","1463-9084"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","date_created":"2021-10-12T08:44:34Z","citation":{"chicago":"Šarić, Anđela, T. Hrenar, M. Mališ, and N. Došlić. “Quantum Mechanical Study of Secondary Structure Formation in Protected Dipeptides.” <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry , 2010. <a href=\"https://doi.org/10.1039/b923041f\">https://doi.org/10.1039/b923041f</a>.","ieee":"A. Šarić, T. Hrenar, M. Mališ, and N. Došlić, “Quantum mechanical study of secondary structure formation in protected dipeptides,” <i>Physical Chemistry Chemical Physics</i>, vol. 12, no. 18. Royal Society of Chemistry , pp. 4678–4685, 2010.","ista":"Šarić A, Hrenar T, Mališ M, Došlić N. 2010. Quantum mechanical study of secondary structure formation in protected dipeptides. Physical Chemistry Chemical Physics. 12(18), 4678–4685.","apa":"Šarić, A., Hrenar, T., Mališ, M., &#38; Došlić, N. (2010). Quantum mechanical study of secondary structure formation in protected dipeptides. <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/b923041f\">https://doi.org/10.1039/b923041f</a>","mla":"Šarić, Anđela, et al. “Quantum Mechanical Study of Secondary Structure Formation in Protected Dipeptides.” <i>Physical Chemistry Chemical Physics</i>, vol. 12, no. 18, Royal Society of Chemistry , 2010, pp. 4678–85, doi:<a href=\"https://doi.org/10.1039/b923041f\">10.1039/b923041f</a>.","short":"A. Šarić, T. Hrenar, M. Mališ, N. Došlić, Physical Chemistry Chemical Physics 12 (2010) 4678–4685.","ama":"Šarić A, Hrenar T, Mališ M, Došlić N. Quantum mechanical study of secondary structure formation in protected dipeptides. <i>Physical Chemistry Chemical Physics</i>. 2010;12(18):4678-4685. doi:<a href=\"https://doi.org/10.1039/b923041f\">10.1039/b923041f</a>"},"date_updated":"2021-10-12T09:49:22Z","article_type":"original"},{"publication_status":"published","author":[{"orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"first_name":"Behnaz","full_name":"Bozorgui, Behnaz","last_name":"Bozorgui"},{"first_name":"Angelo","full_name":"Cacciuto, Angelo","last_name":"Cacciuto"}],"article_processing_charge":"No","acknowledgement":"This work was supported by the National Science Foundation under CAREER Grant No. DMR-0846426 and partly by Columbia University.","title":"Packing of soft asymmetric dumbbells","intvolume":"       115","volume":115,"pmid":1,"date_published":"2010-10-15T00:00:00Z","page":"7182-7189","status":"public","publication":"The Journal of Physical Chemistry B","language":[{"iso":"eng"}],"_id":"10390","keyword":["materials chemistry"],"publisher":"American Chemical Society","doi":"10.1021/jp107545w","issue":"22","fulldoi":"https://doi.org/10.1021/jp107545w","day":"15","abstract":[{"lang":"eng","text":"We use numerical simulations to study the phase behavior of a system of purely repulsive soft dumbbells as a function of size ratio of the two components and their relative degree of deformability. We find a plethora of different phases, which includes most of the mesophases observed in self-assembly of block copolymers but also crystalline structures formed by asymmetric, hard binary mixtures. Our results detail the phenomenological behavior of these systems when softness is introduced in terms of two different classes of interparticle interactions: (a) the elastic Hertz potential, which has a finite energy cost for complete overlap of any two components, and (b) a generic power-law repulsion with tunable exponent. We discuss how simple geometric arguments can be used to account for the large structural variety observed in these systems and detail the similarities and differences in the phase behavior for the two classes of potentials under consideration."}],"quality_controlled":"1","arxiv":1,"date_created":"2021-11-29T15:13:17Z","citation":{"apa":"Šarić, A., Bozorgui, B., &#38; Cacciuto, A. (2010). Packing of soft asymmetric dumbbells. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jp107545w\">https://doi.org/10.1021/jp107545w</a>","mla":"Šarić, Anđela, et al. “Packing of Soft Asymmetric Dumbbells.” <i>The Journal of Physical Chemistry B</i>, vol. 115, no. 22, American Chemical Society, 2010, pp. 7182–89, doi:<a href=\"https://doi.org/10.1021/jp107545w\">10.1021/jp107545w</a>.","ista":"Šarić A, Bozorgui B, Cacciuto A. 2010. Packing of soft asymmetric dumbbells. The Journal of Physical Chemistry B. 115(22), 7182–7189.","ama":"Šarić A, Bozorgui B, Cacciuto A. Packing of soft asymmetric dumbbells. <i>The Journal of Physical Chemistry B</i>. 2010;115(22):7182-7189. doi:<a href=\"https://doi.org/10.1021/jp107545w\">10.1021/jp107545w</a>","short":"A. Šarić, B. Bozorgui, A. Cacciuto, The Journal of Physical Chemistry B 115 (2010) 7182–7189.","chicago":"Šarić, Anđela, Behnaz Bozorgui, and Angelo Cacciuto. “Packing of Soft Asymmetric Dumbbells.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2010. <a href=\"https://doi.org/10.1021/jp107545w\">https://doi.org/10.1021/jp107545w</a>.","ieee":"A. Šarić, B. Bozorgui, and A. Cacciuto, “Packing of soft asymmetric dumbbells,” <i>The Journal of Physical Chemistry B</i>, vol. 115, no. 22. American Chemical Society, pp. 7182–7189, 2010."},"oa":1,"article_type":"original","date_updated":"2021-11-29T16:20:29Z","oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1010.2458","open_access":"1"}],"month":"10","external_id":{"pmid":["20949934"],"arxiv":["1010.2458"]},"extern":"1","year":"2010","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["1520-6106"],"eissn":["1520-5207"]}},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"type":"journal_article","year":"2010","extern":"1","external_id":{"arxiv":["1005.2429"],"pmid":["20867183"]},"month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1005.2429"}],"scopus_import":"1","oa_version":"Preprint","date_updated":"2021-11-30T08:11:19Z","article_type":"original","oa":1,"citation":{"ieee":"A. Šarić, J. C. Pàmies, and A. Cacciuto, “Effective elasticity of a flexible filament bound to a deformable cylindrical surface,” <i>Physical Review Letters</i>, vol. 104, no. 22. American Physical Society, 2010.","chicago":"Šarić, Anđela, Josep C. Pàmies, and Angelo Cacciuto. “Effective Elasticity of a Flexible Filament Bound to a Deformable Cylindrical Surface.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/physrevlett.104.226101\">https://doi.org/10.1103/physrevlett.104.226101</a>.","ama":"Šarić A, Pàmies JC, Cacciuto A. Effective elasticity of a flexible filament bound to a deformable cylindrical surface. <i>Physical Review Letters</i>. 2010;104(22). doi:<a href=\"https://doi.org/10.1103/physrevlett.104.226101\">10.1103/physrevlett.104.226101</a>","short":"A. Šarić, J.C. Pàmies, A. Cacciuto, Physical Review Letters 104 (2010).","apa":"Šarić, A., Pàmies, J. C., &#38; Cacciuto, A. (2010). Effective elasticity of a flexible filament bound to a deformable cylindrical surface. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.104.226101\">https://doi.org/10.1103/physrevlett.104.226101</a>","mla":"Šarić, Anđela, et al. “Effective Elasticity of a Flexible Filament Bound to a Deformable Cylindrical Surface.” <i>Physical Review Letters</i>, vol. 104, no. 22, 226101, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/physrevlett.104.226101\">10.1103/physrevlett.104.226101</a>.","ista":"Šarić A, Pàmies JC, Cacciuto A. 2010. Effective elasticity of a flexible filament bound to a deformable cylindrical surface. Physical Review Letters. 104(22), 226101."},"date_created":"2021-11-29T15:14:33Z","arxiv":1,"quality_controlled":"1","abstract":[{"text":"We use numerical simulations to show how a fully flexible filament binding to a deformable cylindrical surface may acquire a macroscopic persistence length and a helical conformation. This is a result of the nontrivial elastic response to deformations of elastic sheets. We find that the filament’s helical pitch is completely determined by the mechanical properties of the surface, and can be easily tuned by varying the surface stretching rigidity. We propose simple scaling arguments to understand the physical mechanism behind this phenomenon and present a phase diagram indicating under what conditions one should expect a fully flexible chain to behave as a helical semiflexible filament. Finally, we discuss the implications of our results.","lang":"eng"}],"day":"03","fulldoi":"https://doi.org/10.1103/physrevlett.104.226101","issue":"22","doi":"10.1103/physrevlett.104.226101","publisher":"American Physical Society","keyword":["general physics and astronomy"],"_id":"10391","language":[{"iso":"eng"}],"publication":"Physical Review Letters","article_number":"226101","status":"public","date_published":"2010-06-03T00:00:00Z","pmid":1,"volume":104,"intvolume":"       104","title":"Effective elasticity of a flexible filament bound to a deformable cylindrical surface","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426.","article_processing_charge":"No","author":[{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela"},{"last_name":"Pàmies","full_name":"Pàmies, Josep C.","first_name":"Josep C."},{"full_name":"Cacciuto, Angelo","last_name":"Cacciuto","first_name":"Angelo"}],"publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","type":"conference","abstract":[{"text":"Recent years have seen tremendous progress in the field of cold and ultracold molecules. A central goal in the field is currently the realization of stable rovibronic ground-state molecular samples in the regime of quantum degeneracy, e.g. in the form of molecular Bose-Einstein condensates, molecular degenerate Fermi gases, or, when an optical lattice is present, molecular Mott-insulator phases. However, molecular samples are not readily cooled to the extremely low temperatures at which quantum degeneracy occurs. In particular, laser cooling, the \\'workhorse\\' for the field of atomic quantum gases, is generally not applicable to molecular samples. Here we take an important step beyond previous work1 and provide details on the realization of an ultracold quantum gas of ground-state dimer molecules trapped in an optical lattice as recently reported in Ref. 2. We demonstrate full control over all internal and external quantum degrees of freedom for the ground-state molecules by deterministically preparing the molecules in a single quantum state, i.e. in a specific hyperfine sublevel of the rovibronic ground state, while the molecules are trapped in the motional ground state of the individual lattice wells. We circumvent the problem of cooling by associating weakly-bound molecules out of a zero-temperature atomic Mott-insulator state and by transferring these to the absolute ground state in a four-photon STIRAP process. Our preparation procedure directly leads to a long-lived, lattice-trapped molecular many-body state, which we expect to form the platform for many of the envisioned future experiments with molecular quantum gases, e.g. on precision molecular spectroscopy, quantum information science, and dipolar quantum systems.","lang":"eng"}],"year":"2010","fulldoi":"https://doi.org/10.1142/9789814282345_0024","extern":"1","conference":{"name":"ICOLS: International Conference on Laser Spectroscopy"},"publisher":"World Scientific Publishing","doi":"10.1142/9789814282345_0024","month":"01","oa_version":"None","_id":"1042","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:47:52Z","status":"public","page":"256 - 269","citation":{"ista":"Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Nägerl H. 2010. Production of a quantum gas of rovibronic ground-state molecules in an optical lattice. ICOLS: International Conference on Laser Spectroscopy, 256–269.","mla":"Danzl, Johann G., et al. <i>Production of a Quantum Gas of Rovibronic Ground-State Molecules in an Optical Lattice</i>. World Scientific Publishing, 2010, pp. 256–69, doi:<a href=\"https://doi.org/10.1142/9789814282345_0024\">10.1142/9789814282345_0024</a>.","apa":"Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Hart, R., &#38; Nägerl, H. (2010). Production of a quantum gas of rovibronic ground-state molecules in an optical lattice (pp. 256–269). Presented at the ICOLS: International Conference on Laser Spectroscopy, World Scientific Publishing. <a href=\"https://doi.org/10.1142/9789814282345_0024\">https://doi.org/10.1142/9789814282345_0024</a>","ama":"Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Nägerl H. Production of a quantum gas of rovibronic ground-state molecules in an optical lattice. In: World Scientific Publishing; 2010:256-269. doi:<a href=\"https://doi.org/10.1142/9789814282345_0024\">10.1142/9789814282345_0024</a>","short":"J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, H. Nägerl, in:, World Scientific Publishing, 2010, pp. 256–269.","chicago":"Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell Hart, and Hanns Nägerl. “Production of a Quantum Gas of Rovibronic Ground-State Molecules in an Optical Lattice,” 256–69. World Scientific Publishing, 2010. <a href=\"https://doi.org/10.1142/9789814282345_0024\">https://doi.org/10.1142/9789814282345_0024</a>.","ieee":"J. G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, and H. Nägerl, “Production of a quantum gas of rovibronic ground-state molecules in an optical lattice,” presented at the ICOLS: International Conference on Laser Spectroscopy, 2010, pp. 256–269."},"date_published":"2010-01-01T00:00:00Z","article_processing_charge":"No","publist_id":"6346","title":"Production of a quantum gas of rovibronic ground-state molecules in an optical lattice","date_created":"2018-12-11T11:49:50Z","publication_status":"published","author":[{"first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mark","full_name":"Mark, Manfred","first_name":"Manfred"},{"first_name":"Elmar","full_name":"Haller, Elmar","last_name":"Haller"},{"last_name":"Gustavsson","full_name":"Gustavsson, Mattias","first_name":"Mattias"},{"first_name":"Russell","last_name":"Hart","full_name":"Hart, Russell"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"}]}]