[{"language":[{"iso":"eng"}],"doi":"10.1006/inco.2001.3085","acknowledgement":"We thank Ramin Hojati, Doron Bustan, and the anonymous reviewers for their comments on this paper.","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","day":"25","oa_version":"Published Version","type":"journal_article","date_updated":"2023-06-05T07:53:27Z","scopus_import":"1","publication_identifier":{"issn":["0890-5401"]},"page":"64 - 81","date_published":"2002-02-25T00:00:00Z","_id":"4474","oa":1,"title":"Fair simulation","publication":"Information and Computation","abstract":[{"lang":"eng","text":"The simulation preorder for labeled transition systems is defined locally, and operationally, as a game that relates states with their immediate successor states. Simulation enjoys many appealing properties. First, simulation has a denotational characterization: system S simulates system I iff every computation tree embedded in the unrolling of I can be embedded also in the unrolling of S. Second, simulation has a logical characterization: S simulates I iff every universal branching-time formula satisfied by S is satisfied also by I. It follows that simulation is a suitable notion of implementation, and it is the coarsest abstraction of a system that preserves universal branching-time properties. Third, based on its local definition, simulation between finite-state systems can be checked in polynomial time. Finally, simulation implies trace containment, which cannot be defined locally and requires polynomial space for verification. Hence simulation is widely used both in manual and in automatic verification. Liveness assumptions about transition systems are typically modeled using fairness constraints. Existing notions of simulation for fair transition systems, however, are not local, and as a result, many appealing properties of the simulation preorder are lost. We propose a new view of fair simulation by extending the local definition of simulation to account for fairness: system View the MathML sourcefairly simulates system View the MathML source iff in the simulation game, there is a strategy that matches with each fair computation of View the MathML source a fair computation of View the MathML source. Our definition enjoys a denotational characterization and has a logical characterization: View the MathML source fairly simulates View the MathML source iff every fair computation tree (whose infinite paths are fair) embedded in the unrolling of View the MathML source can be embedded also in the unrolling of View the MathML source or, equivalently, iff every Fair-∀AFMC formula satisfied by View the MathML source is satisfied also by View the MathML source (∀AFMC is the universal fragment of the alternation-free μ-calculus). The locality of the definition leads us to a polynomial-time algorithm for checking fair simulation for finite-state systems with weak and strong fairness constraints. Finally, fair simulation implies fair trace containment and is therefore useful as an efficiently computable local criterion for proving linear-time abstraction hierarchies of fair systems."}],"publication_status":"published","quality_controlled":"1","extern":"1","author":[{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"},{"full_name":"Rajamani, Sriram","last_name":"Rajamani","first_name":"Sriram"}],"main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S0890540101930858?via%3Dihub"}],"citation":{"ieee":"T. A. Henzinger, O. Kupferman, and S. Rajamani, “Fair simulation,” Information and Computation, vol. 173, no. 1. Elsevier, pp. 64–81, 2002.","ama":"Henzinger TA, Kupferman O, Rajamani S. Fair simulation. Information and Computation. 2002;173(1):64-81. doi:10.1006/inco.2001.3085","short":"T.A. Henzinger, O. Kupferman, S. Rajamani, Information and Computation 173 (2002) 64–81.","chicago":"Henzinger, Thomas A, Orna Kupferman, and Sriram Rajamani. “Fair Simulation.” Information and Computation. Elsevier, 2002. https://doi.org/10.1006/inco.2001.3085.","ista":"Henzinger TA, Kupferman O, Rajamani S. 2002. Fair simulation. Information and Computation. 173(1), 64–81.","apa":"Henzinger, T. A., Kupferman, O., & Rajamani, S. (2002). Fair simulation. Information and Computation. Elsevier. https://doi.org/10.1006/inco.2001.3085","mla":"Henzinger, Thomas A., et al. “Fair Simulation.” Information and Computation, vol. 173, no. 1, Elsevier, 2002, pp. 64–81, doi:10.1006/inco.2001.3085."},"year":"2002","publist_id":"255","intvolume":" 173","status":"public","month":"02","date_created":"2018-12-11T12:09:02Z","volume":173,"issue":"1","publisher":"Elsevier","article_type":"original"},{"status":"public","date_created":"2018-12-11T12:09:03Z","conference":{"location":"Portland, OR, USA","start_date":"2002-01-16","name":"POPL: Principles of Programming Languages","end_date":"2002-01-18"},"month":"01","publist_id":"254","publication_identifier":{"isbn":["9781581134506"]},"scopus_import":"1","publisher":"ACM","page":"58 - 70","date_published":"2002-01-01T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"One approach to model checking software is based on the abstract-check-refine paradigm: build an abstract model, then check the desired property, and if the check fails, refine the model and start over. We introduce the concept of lazy abstraction to integrate and optimize the three phases of the abstract-check-refine loop. Lazy abstraction continuously builds and refines a single abstract model on demand, driven by the model checker, so that different parts of the model may exhibit different degrees of precision, namely just enough to verify the desired property. We present an algorithm for model checking safety properties using lazy abstraction and describe an implementation of the algorithm applied to C programs. We also provide sufficient conditions for the termination of the method."}],"acknowledgement":"We thank Wes Weimer and Jeff Foster for many useful discussions. \r\n","doi":"10.1145/503272.503279","language":[{"iso":"eng"}],"_id":"4476","publication":"Proceedings of the 29th ACM SIGPLAN-SIGACT symposium on Principles of programming languages","title":"Lazy abstraction","day":"01","year":"2002","type":"conference","date_updated":"2023-06-05T07:45:53Z","oa_version":"None","quality_controlled":"1","extern":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","author":[{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Jhala","first_name":"Ranjit","full_name":"Jhala, Ranjit"},{"full_name":"Majumdar, Ritankar","first_name":"Ritankar","last_name":"Majumdar"},{"first_name":"Grégoire","last_name":"Sutre","full_name":"Sutre, Grégoire"}],"article_processing_charge":"No","citation":{"ista":"Henzinger TA, Jhala R, Majumdar R, Sutre G. 2002. Lazy abstraction. Proceedings of the 29th ACM SIGPLAN-SIGACT symposium on Principles of programming languages. POPL: Principles of Programming Languages, 58–70.","chicago":"Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Grégoire Sutre. “Lazy Abstraction.” In Proceedings of the 29th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, 58–70. ACM, 2002. https://doi.org/10.1145/503272.503279.","short":"T.A. Henzinger, R. Jhala, R. Majumdar, G. Sutre, in:, Proceedings of the 29th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, ACM, 2002, pp. 58–70.","ieee":"T. A. Henzinger, R. Jhala, R. Majumdar, and G. Sutre, “Lazy abstraction,” in Proceedings of the 29th ACM SIGPLAN-SIGACT symposium on Principles of programming languages, Portland, OR, USA, 2002, pp. 58–70.","ama":"Henzinger TA, Jhala R, Majumdar R, Sutre G. Lazy abstraction. In: Proceedings of the 29th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages. ACM; 2002:58-70. doi:10.1145/503272.503279","apa":"Henzinger, T. A., Jhala, R., Majumdar, R., & Sutre, G. (2002). Lazy abstraction. In Proceedings of the 29th ACM SIGPLAN-SIGACT symposium on Principles of programming languages (pp. 58–70). Portland, OR, USA: ACM. https://doi.org/10.1145/503272.503279","mla":"Henzinger, Thomas A., et al. “Lazy Abstraction.” Proceedings of the 29th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, ACM, 2002, pp. 58–70, doi:10.1145/503272.503279."}},{"day":"19","oa_version":"None","date_updated":"2023-06-02T12:01:22Z","type":"conference","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","acknowledgement":"This research was supported in part by the AFOSR grant F49620-00-1-0327, the DARPA grant F33615-00-C-1693, the MARCO grant 98-DT-660, the NSF grant CCR-9988172, the SRC grant 99-TJ-683.003, and the NSF CAREER award CCR-0132780.","language":[{"iso":"eng"}],"doi":"10.1007/3-540-45657-0_34","page":"414 - 427","date_published":"2002-06-19T00:00:00Z","scopus_import":"1","publication_identifier":{"isbn":["9783540439974"]},"alternative_title":["LNCS"],"year":"2002","quality_controlled":"1","extern":"1","author":[{"first_name":"Arindam","last_name":"Chakrabarti","full_name":"Chakrabarti, Arindam"},{"full_name":"De Alfaro, Luca","last_name":"De Alfaro","first_name":"Luca"},{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mang, Freddy","last_name":"Mang","first_name":"Freddy"}],"citation":{"mla":"Chakrabarti, Arindam, et al. “Synchronous and Bidirectional Component Interfaces.” Proceedings of the 14th International Conference on Computer Aided Verification, vol. 2404, Springer, 2002, pp. 414–27, doi:10.1007/3-540-45657-0_34.","apa":"Chakrabarti, A., De Alfaro, L., Henzinger, T. A., & Mang, F. (2002). Synchronous and bidirectional component interfaces. In Proceedings of the 14th International Conference on Computer Aided Verification (Vol. 2404, pp. 414–427). Copenhagen, Denmark: Springer. https://doi.org/10.1007/3-540-45657-0_34","ieee":"A. Chakrabarti, L. De Alfaro, T. A. Henzinger, and F. Mang, “Synchronous and bidirectional component interfaces,” in Proceedings of the 14th International Conference on Computer Aided Verification, Copenhagen, Denmark, 2002, vol. 2404, pp. 414–427.","ama":"Chakrabarti A, De Alfaro L, Henzinger TA, Mang F. Synchronous and bidirectional component interfaces. In: Proceedings of the 14th International Conference on Computer Aided Verification. Vol 2404. Springer; 2002:414-427. doi:10.1007/3-540-45657-0_34","short":"A. Chakrabarti, L. De Alfaro, T.A. Henzinger, F. Mang, in:, Proceedings of the 14th International Conference on Computer Aided Verification, Springer, 2002, pp. 414–427.","chicago":"Chakrabarti, Arindam, Luca De Alfaro, Thomas A Henzinger, and Freddy Mang. “Synchronous and Bidirectional Component Interfaces.” In Proceedings of the 14th International Conference on Computer Aided Verification, 2404:414–27. Springer, 2002. https://doi.org/10.1007/3-540-45657-0_34.","ista":"Chakrabarti A, De Alfaro L, Henzinger TA, Mang F. 2002. Synchronous and bidirectional component interfaces. Proceedings of the 14th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 2404, 414–427."},"abstract":[{"text":"We present interface models that describe both the input assumptions of a component, and its output behavior. By enabling us to check that the input assumptions of a component are met in a design, interface models provide a compatibility check for component-based design. When refining a design into an implementation, interface models require that the output behavior of a component satisfies the design specification only when the input assumptions of the specification are satisfied, yielding greater flexibility in the choice of implementations. Technically, our interface models are games between two players, Input and Output; the duality of the players accounts for the dual roles of inputs and outputs in composition and refinement. We present two interface models in detail, one for a simple synchronous form of interaction between components typical in hardware, and the other for more complex synchronous interactions on bidirectional connections. As an example, we specify the interface of a bidirectional bus, with the input assumption that at any time at most one component has write access to the bus. For these interface models, we present algorithms for compatibility and refinement checking, and we describe efficient symbolic implementations.","lang":"eng"}],"publication_status":"published","_id":"4562","title":"Synchronous and bidirectional component interfaces","publication":"Proceedings of the 14th International Conference on Computer Aided Verification","publisher":"Springer","volume":2404,"status":"public","month":"06","conference":{"location":"Copenhagen, Denmark","start_date":"2002-07-27","name":"CAV: Computer Aided Verification","end_date":"2002-07-31"},"date_created":"2018-12-11T12:09:29Z","publist_id":"146","intvolume":" 2404"},{"acknowledgement":"This research was supported in part by the AFOSR grant F49620-00-1-0327, the DARPA grant F33615-00-C-1693, the MARCO grant 98-DT-660, the NSF grants CCR-9988172, CCR-0085949, CCR-0132780, the SRC grant 99-TJ-683, and the Polish KBN grant 7-T11C-027-20.","doi":"10.1007/3-540-45657-0_35","language":[{"iso":"eng"}],"type":"conference","date_updated":"2023-06-05T07:38:10Z","oa_version":"None","day":"19","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","alternative_title":["LNCS"],"publication_identifier":{"isbn":[" 9783540439974"]},"scopus_import":"1","date_published":"2002-06-19T00:00:00Z","page":"428 - 441","publication_status":"published","abstract":[{"lang":"eng","text":"We present a formal methodology and tool for uncovering errors in the interaction of software modules. Our methodology consists of a suite of languages for defining software interfaces, and algorithms for checking interface compatibility. We focus on interfaces that explain the method-call dependencies between software modules. Such an interface makes assumptions about the environment in the form of call and availability constraints. A call constraint restricts the accessibility of local methods to certain external methods. An availability constraint restricts the accessibility of local methods to certain states of the module. For example, the interface for a file server with local methods open and read may assert that a file cannot be read without having been opened. Checking interface compatibility requires the solution of games, and in the presence of availability constraints, of pushdown games. Based on this methodology, we have implemented a tool that has uncovered incompatibilities in TinyOS, a small operating system for sensor nodes in adhoc networks."}],"publication":"Proceedings of the 14th International Conference on Computer Aided Verification","title":"Interface compatibility checking for software modules","_id":"4563","year":"2002","citation":{"apa":"Chakrabarti, A., De Alfaro, L., Henzinger, T. A., Jurdziński, M., & Mang, F. (2002). Interface compatibility checking for software modules. In Proceedings of the 14th International Conference on Computer Aided Verification (Vol. 2404, pp. 428–441). Copenhagen, Denmark: Springer. https://doi.org/10.1007/3-540-45657-0_35","mla":"Chakrabarti, Arindam, et al. “Interface Compatibility Checking for Software Modules.” Proceedings of the 14th International Conference on Computer Aided Verification, vol. 2404, Springer, 2002, pp. 428–41, doi:10.1007/3-540-45657-0_35.","ista":"Chakrabarti A, De Alfaro L, Henzinger TA, Jurdziński M, Mang F. 2002. Interface compatibility checking for software modules. Proceedings of the 14th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 2404, 428–441.","short":"A. Chakrabarti, L. De Alfaro, T.A. Henzinger, M. Jurdziński, F. Mang, in:, Proceedings of the 14th International Conference on Computer Aided Verification, Springer, 2002, pp. 428–441.","chicago":"Chakrabarti, Arindam, Luca De Alfaro, Thomas A Henzinger, Marcin Jurdziński, and Freddy Mang. “Interface Compatibility Checking for Software Modules.” In Proceedings of the 14th International Conference on Computer Aided Verification, 2404:428–41. Springer, 2002. https://doi.org/10.1007/3-540-45657-0_35.","ieee":"A. Chakrabarti, L. De Alfaro, T. A. Henzinger, M. Jurdziński, and F. Mang, “Interface compatibility checking for software modules,” in Proceedings of the 14th International Conference on Computer Aided Verification, Copenhagen, Denmark, 2002, vol. 2404, pp. 428–441.","ama":"Chakrabarti A, De Alfaro L, Henzinger TA, Jurdziński M, Mang F. Interface compatibility checking for software modules. In: Proceedings of the 14th International Conference on Computer Aided Verification. Vol 2404. Springer; 2002:428-441. doi:10.1007/3-540-45657-0_35"},"quality_controlled":"1","extern":"1","author":[{"full_name":"Chakrabarti, Arindam","first_name":"Arindam","last_name":"Chakrabarti"},{"first_name":"Luca","last_name":"De Alfaro","full_name":"De Alfaro, Luca"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jurdziński","first_name":"Marcin","full_name":"Jurdziński, Marcin"},{"first_name":"Freddy","last_name":"Mang","full_name":"Mang, Freddy"}],"date_created":"2018-12-11T12:09:30Z","month":"06","conference":{"start_date":"2002-07-27","location":"Copenhagen, Denmark","name":"CAV: Computer Aided Verification","end_date":"2002-07-31"},"status":"public","intvolume":" 2404","publist_id":"147","publisher":"Springer","volume":2404},{"article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","date_updated":"2023-06-02T10:29:10Z","type":"conference","oa_version":"None","day":"14","doi":"10.1007/3-540-45873-5_13","language":[{"iso":"eng"}],"acknowledgement":"Partially supported by the FNRS, Belgium, under grant 1.5.096.01.\r\nPartially supported by the DARPA SEC grant F33615-C-98-3614, the AFOSR MURI grant F49620-00-1-0327, the NSF Theory grant CCR-9988172, and the MARCO GSRC grant 98-DT-660.\r\nPartially supported by a “Crédit aux chercheurs” from the Belgian National Fund for Scientific Research.","date_published":"2002-03-14T00:00:00Z","page":"134 - 148","alternative_title":["LNCS"],"publication_identifier":{"isbn":["9783540433217"]},"scopus_import":"1","citation":{"ieee":"F. Cassez, T. A. Henzinger, and J. Raskin, “A comparison of control problems for timed and hybrid systems,” in Proceedings of the 5th International Workshop on Hybrid Systems: Computation and Control, Stanford, CA, USA, 2002, vol. 2289, pp. 134–148.","ama":"Cassez F, Henzinger TA, Raskin J. A comparison of control problems for timed and hybrid systems. In: Proceedings of the 5th International Workshop on Hybrid Systems: Computation and Control. Vol 2289. Springer; 2002:134-148. doi:10.1007/3-540-45873-5_13","ista":"Cassez F, Henzinger TA, Raskin J. 2002. A comparison of control problems for timed and hybrid systems. Proceedings of the 5th International Workshop on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, LNCS, vol. 2289, 134–148.","short":"F. Cassez, T.A. Henzinger, J. Raskin, in:, Proceedings of the 5th International Workshop on Hybrid Systems: Computation and Control, Springer, 2002, pp. 134–148.","chicago":"Cassez, Franck, Thomas A Henzinger, and Jean Raskin. “A Comparison of Control Problems for Timed and Hybrid Systems.” In Proceedings of the 5th International Workshop on Hybrid Systems: Computation and Control, 2289:134–48. Springer, 2002. https://doi.org/10.1007/3-540-45873-5_13.","mla":"Cassez, Franck, et al. “A Comparison of Control Problems for Timed and Hybrid Systems.” Proceedings of the 5th International Workshop on Hybrid Systems: Computation and Control, vol. 2289, Springer, 2002, pp. 134–48, doi:10.1007/3-540-45873-5_13.","apa":"Cassez, F., Henzinger, T. A., & Raskin, J. (2002). A comparison of control problems for timed and hybrid systems. In Proceedings of the 5th International Workshop on Hybrid Systems: Computation and Control (Vol. 2289, pp. 134–148). Stanford, CA, USA: Springer. https://doi.org/10.1007/3-540-45873-5_13"},"quality_controlled":"1","extern":"1","author":[{"first_name":"Franck","last_name":"Cassez","full_name":"Cassez, Franck"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Raskin","first_name":"Jean","full_name":"Raskin, Jean"}],"year":"2002","publication":"Proceedings of the 5th International Workshop on Hybrid Systems: Computation and Control","title":"A comparison of control problems for timed and hybrid systems","_id":"4565","publication_status":"published","abstract":[{"lang":"eng","text":"In the literature, we find several formulations of the control\r\nproblem for timed and hybrid systems. We argue that formulations where\r\na controller can cause an action at any point in dense (rational or real)\r\ntime are problematic, by presenting an example where the controller\r\nmust act faster and faster, yet causes no Zeno effects (say, the control\r\nactions are at times 0, 1/2, 1, 1 1/4, 2, 2 1/8, 3, 3 1/16 ,...). Such a controller is,\r\nof course, not implementable in software. Such controllers are avoided by formulations where the controller can cause actions only at discrete (integer) points in time. While the resulting control problem is well- understood if the time unit, or “sampling rate” of the controller, is fixed a priori, we define a novel, stronger formulation: the discrete-time control problem with unknown sampling rate asks if a sampling controller exists for some sampling rate. We prove that this problem is undecidable even in the special case of timed automata."}],"volume":2289,"publisher":"Springer","intvolume":" 2289","publist_id":"144","date_created":"2018-12-11T12:09:30Z","month":"03","conference":{"name":"HSCC: Hybrid Systems - Computation and Control","end_date":"2002-03-27","location":"Stanford, CA, USA","start_date":"2002-03-25"},"status":"public"},{"date_published":"2002-09-01T00:00:00Z","page":"672 - 713","publication_identifier":{"issn":["0004-5411"]},"scopus_import":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","date_updated":"2023-06-02T10:07:22Z","type":"journal_article","oa_version":"None","day":"01","doi":"10.1145/585265.585270","language":[{"iso":"eng"}],"acknowledgement":"We thank Luca de Alfaro, Kousha Etessami, Salvatore La Torre, P. Madhusudan, Amir Pnueli, Moshe Vardi, Thomas Wilke, and Mihalis Yannakakis for helpful discussions. We also thank Freddy Mang for comments on a draft of this manuscript.","volume":49,"issue":"5","publisher":"ACM","article_type":"original","intvolume":" 49","publist_id":"110","date_created":"2018-12-11T12:09:40Z","month":"09","status":"public","citation":{"mla":"Alur, Rajeev, et al. “Alternating-Time Temporal Logic.” Journal of the ACM, vol. 49, no. 5, ACM, 2002, pp. 672–713, doi:10.1145/585265.585270.","apa":"Alur, R., Henzinger, T. A., & Kupferman, O. (2002). Alternating-time temporal logic. Journal of the ACM. ACM. https://doi.org/10.1145/585265.585270","ista":"Alur R, Henzinger TA, Kupferman O. 2002. Alternating-time temporal logic. Journal of the ACM. 49(5), 672–713.","chicago":"Alur, Rajeev, Thomas A Henzinger, and Orna Kupferman. “Alternating-Time Temporal Logic.” Journal of the ACM. ACM, 2002. https://doi.org/10.1145/585265.585270.","short":"R. Alur, T.A. Henzinger, O. Kupferman, Journal of the ACM 49 (2002) 672–713.","ama":"Alur R, Henzinger TA, Kupferman O. Alternating-time temporal logic. Journal of the ACM. 2002;49(5):672-713. doi:10.1145/585265.585270","ieee":"R. Alur, T. A. Henzinger, and O. Kupferman, “Alternating-time temporal logic,” Journal of the ACM, vol. 49, no. 5. ACM, pp. 672–713, 2002."},"author":[{"last_name":"Alur","first_name":"Rajeev","full_name":"Alur, Rajeev"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"}],"quality_controlled":"1","extern":"1","year":"2002","title":"Alternating-time temporal logic","publication":"Journal of the ACM","_id":"4595","publication_status":"published","abstract":[{"text":"Temporal logic comes in two varieties: linear-time temporal logic assumes implicit universal quantification over all paths that are generated by the execution of a system; branching-time temporal logic allows explicit existential and universal quantification over all paths. We introduce a third, more general variety of temporal logic: alternating-time temporal logic offers selective quantification over those paths that are possible outcomes of games, such as the game in which the system and the environment alternate moves. While linear-time and branching-time logics are natural specification languages for closed systems, alternating-time logics are natural specification languages for open systems. For example, by preceding the temporal operator "eventually" with a selective path quantifier, we can specify that in the game between the system and the environment, the system has a strategy to reach a certain state. The problems of receptiveness, realizability, and controllability can be formulated as model-checking problems for alternating-time formulas. Depending on whether or not we admit arbitrary nesting of selective path quantifiers and temporal operators, we obtain the two alternating-time temporal logics ATL and ATL*.ATL and ATL* are interpreted over concurrent game structures. Every state transition of a concurrent game structure results from a choice of moves, one for each player. The players represent individual components and the environment of an open system. Concurrent game structures can capture various forms of synchronous composition for open systems, and if augmented with fairness constraints, also asynchronous composition. Over structures without fairness constraints, the model-checking complexity of ATL is linear in the size of the game structure and length of the formula, and the symbolic model-checking algorithm for CTL extends with few modifications to ATL. Over structures with weak-fairness constraints, ATL model checking requires the solution of 1-pair Rabin games, and can be done in polynomial time. Over structures with strong-fairness constraints, ATL model checking requires the solution of games with Boolean combinations of Büchi conditions, and can be done in PSPACE. In the case of ATL*, the model-checking problem is closely related to the synthesis problem for linear-time formulas, and requires doubly exponential time.","lang":"eng"}]},{"publication_status":"published","abstract":[{"lang":"eng","text":"We present a theory of timed interfaces, which is capable of specifying both the timing of the inputs a component expects from the environment, and the timing of the outputs it can produce. Two timed interfaces are compatible if there is a way to use them together such that their timing expectations are met. Our theory provides algorithms for checking the compatibility between two interfaces and for deriving the composite interface; the theory can thus be viewed as a type system for real-time interaction. Technically, a timed interface is encoded as a timed game between two players, representing the inputs and outputs of the component. The algorithms for compatibility checking and interface composition are thus derived from algorithms for solving timed games."}],"title":"Timed interfaces","publication":"Proceedings of the 2nd International Conference on Embedded Software","_id":"4631","year":"2002","citation":{"apa":"De Alfaro, L., Henzinger, T. A., & Stoelinga, M. (2002). Timed interfaces. In Proceedings of the 2nd International Conference on Embedded Software (Vol. 2491, pp. 108–122). Grenoble, France: ACM. https://doi.org/10.1007/3-540-45828-X_9","mla":"De Alfaro, Luca, et al. “Timed Interfaces.” Proceedings of the 2nd International Conference on Embedded Software, vol. 2491, ACM, 2002, pp. 108–22, doi:10.1007/3-540-45828-X_9.","ieee":"L. De Alfaro, T. A. Henzinger, and M. Stoelinga, “Timed interfaces,” in Proceedings of the 2nd International Conference on Embedded Software, Grenoble, France, 2002, vol. 2491, pp. 108–122.","ama":"De Alfaro L, Henzinger TA, Stoelinga M. Timed interfaces. In: Proceedings of the 2nd International Conference on Embedded Software. Vol 2491. ACM; 2002:108-122. doi:10.1007/3-540-45828-X_9","ista":"De Alfaro L, Henzinger TA, Stoelinga M. 2002. Timed interfaces. Proceedings of the 2nd International Conference on Embedded Software. EMSOFT: Embedded Software , LNCS, vol. 2491, 108–122.","chicago":"De Alfaro, Luca, Thomas A Henzinger, and Mariëlle Stoelinga. “Timed Interfaces.” In Proceedings of the 2nd International Conference on Embedded Software, 2491:108–22. ACM, 2002. https://doi.org/10.1007/3-540-45828-X_9.","short":"L. De Alfaro, T.A. Henzinger, M. Stoelinga, in:, Proceedings of the 2nd International Conference on Embedded Software, ACM, 2002, pp. 108–122."},"extern":"1","author":[{"last_name":"De Alfaro","first_name":"Luca","full_name":"De Alfaro, Luca"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Stoelinga, Mariëlle","first_name":"Mariëlle","last_name":"Stoelinga"}],"quality_controlled":"1","date_created":"2018-12-11T12:09:51Z","conference":{"name":"EMSOFT: Embedded Software ","end_date":"2002-10-09","location":"Grenoble, France","start_date":"2002-10-07"},"month":"10","status":"public","intvolume":" 2491","publist_id":"76","publisher":"ACM","volume":2491,"acknowledgement":"This research was supported in part by the NSF CAREER award CCR-0132780, the NSF grant CCR-9988172 the AFOSR MURI grant F49620-00-1-0327, the DARPA PCES grant F33615-00-C-1693, the MARCO GSRC grant 98-DT-660, and the ONR grant N00014-02-1-0671.","doi":"10.1007/3-540-45828-X_9","language":[{"iso":"eng"}],"type":"conference","date_updated":"2023-06-02T10:00:32Z","oa_version":"None","day":"24","article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","alternative_title":["LNCS"],"publication_identifier":{"isbn":["9783540443070"]},"date_published":"2002-10-24T00:00:00Z","page":"108 - 122"},{"publication_status":"published","title":"Footprints of primordial introns on the eukaryotic genome: still no clear traces ","publication":"Trends in Genetics","pmid":1,"_id":"841","year":"2001","citation":{"mla":"Wolf, Yuri, et al. “Footprints of Primordial Introns on the Eukaryotic Genome: Still No Clear Traces .” Trends in Genetics, vol. 17, no. 9, Elsevier, 2001, pp. 499–501, doi:10.1016/S0168-9525(01)02376-9.","apa":"Wolf, Y., Kondrashov, F., & Koonin, E. (2001). Footprints of primordial introns on the eukaryotic genome: still no clear traces . Trends in Genetics. Elsevier. https://doi.org/10.1016/S0168-9525(01)02376-9","chicago":"Wolf, Yuri, Fyodor Kondrashov, and Eugene Koonin. “Footprints of Primordial Introns on the Eukaryotic Genome: Still No Clear Traces .” Trends in Genetics. Elsevier, 2001. https://doi.org/10.1016/S0168-9525(01)02376-9.","short":"Y. Wolf, F. Kondrashov, E. Koonin, Trends in Genetics 17 (2001) 499–501.","ista":"Wolf Y, Kondrashov F, Koonin E. 2001. Footprints of primordial introns on the eukaryotic genome: still no clear traces . Trends in Genetics. 17(9), 499–501.","ama":"Wolf Y, Kondrashov F, Koonin E. Footprints of primordial introns on the eukaryotic genome: still no clear traces . Trends in Genetics. 2001;17(9):499-501. doi:10.1016/S0168-9525(01)02376-9","ieee":"Y. Wolf, F. Kondrashov, and E. Koonin, “Footprints of primordial introns on the eukaryotic genome: still no clear traces ,” Trends in Genetics, vol. 17, no. 9. Elsevier, pp. 499–501, 2001."},"extern":"1","author":[{"full_name":"Wolf, Yuri","last_name":"Wolf","first_name":"Yuri"},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"first_name":"Eugene","last_name":"Koonin","full_name":"Koonin, Eugene"}],"quality_controlled":"1","date_created":"2018-12-11T11:48:47Z","month":"09","status":"public","intvolume":" 17","publist_id":"6805","article_type":"original","publisher":"Elsevier","volume":17,"issue":"9","language":[{"iso":"eng"}],"doi":"10.1016/S0168-9525(01)02376-9","type":"journal_article","date_updated":"2023-06-02T09:38:37Z","oa_version":"None","day":"01","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","publication_identifier":{"issn":["0168-9479"]},"scopus_import":"1","date_published":"2001-09-01T00:00:00Z","external_id":{"pmid":["11721681"]},"page":"499 - 501"},{"date_created":"2018-12-11T11:48:50Z","month":"01","status":"public","intvolume":" 17","publist_id":"6796","article_type":"original","publisher":"Wiley-Blackwell","issue":"2","volume":17,"publication_status":"published","abstract":[{"text":"The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called "hotspots," in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG-PUBL program, (FTP: sunsite.unc.edu/pub/academic/ biology/dna-mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis.","lang":"eng"}],"publication":"Human Mutation","title":"Use of mutation spectra analysis software","pmid":1,"_id":"851","year":"2001","citation":{"mla":"Rogozin, Igor, et al. “Use of Mutation Spectra Analysis Software.” Human Mutation, vol. 17, no. 2, Wiley-Blackwell, 2001, pp. 83–102, doi:10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E.","apa":"Rogozin, I., Kondrashov, F., & Glazko, G. (2001). Use of mutation spectra analysis software. Human Mutation. Wiley-Blackwell. https://doi.org/10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E","short":"I. Rogozin, F. Kondrashov, G. Glazko, Human Mutation 17 (2001) 83–102.","chicago":"Rogozin, Igor, Fyodor Kondrashov, and Galina Glazko. “Use of Mutation Spectra Analysis Software.” Human Mutation. Wiley-Blackwell, 2001. https://doi.org/10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E.","ista":"Rogozin I, Kondrashov F, Glazko G. 2001. Use of mutation spectra analysis software. Human Mutation. 17(2), 83–102.","ama":"Rogozin I, Kondrashov F, Glazko G. Use of mutation spectra analysis software. Human Mutation. 2001;17(2):83-102. doi:10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E","ieee":"I. Rogozin, F. Kondrashov, and G. Glazko, “Use of mutation spectra analysis software,” Human Mutation, vol. 17, no. 2. Wiley-Blackwell, pp. 83–102, 2001."},"extern":"1","author":[{"first_name":"Igor","last_name":"Rogozin","full_name":"Rogozin, Igor"},{"first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Galina","last_name":"Glazko","full_name":"Glazko, Galina"}],"quality_controlled":"1","publication_identifier":{"issn":["1059-7794"]},"scopus_import":"1","date_published":"2001-01-01T00:00:00Z","external_id":{"pmid":["11180592"]},"page":"83 - 102","acknowledgement":"Russian Fund of Fundamental Research. Grant Number: 99-04-49535. NIH. Grant Number: GM 20293. NASA. Grant Number: NCC2-1057","doi":"10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E","language":[{"iso":"eng"}],"type":"journal_article","date_updated":"2023-06-02T09:22:17Z","oa_version":"None","day":"01","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No"},{"issue":"5","volume":7,"page":"28-36","date_published":"2001-04-24T00:00:00Z","keyword":["General Mathematics"],"publisher":"American Mathematical Society","article_type":"original","publication_identifier":{"issn":["1079-6762"]},"intvolume":" 7","status":"public","date_created":"2020-09-18T10:49:43Z","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","extern":"1","author":[{"first_name":"Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"last_name":"Hunt","first_name":"Brian R.","full_name":"Hunt, Brian R."}],"article_processing_charge":"No","citation":{"chicago":"Kaloshin, Vadim, and Brian R. Hunt. “A Stretched Exponential Bound on the Rate of Growth of the Number of Periodic Points for Prevalent Diffeomorphisms II.” Electronic Research Announcements of the American Mathematical Society. American Mathematical Society, 2001. https://doi.org/10.1090/s1079-6762-01-00091-9.","short":"V. Kaloshin, B.R. Hunt, Electronic Research Announcements of the American Mathematical Society 7 (2001) 28–36.","ista":"Kaloshin V, Hunt BR. 2001. A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II. Electronic Research Announcements of the American Mathematical Society. 7(5), 28–36.","ama":"Kaloshin V, Hunt BR. A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II. Electronic Research Announcements of the American Mathematical Society. 2001;7(5):28-36. doi:10.1090/s1079-6762-01-00091-9","ieee":"V. Kaloshin and B. R. Hunt, “A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II,” Electronic Research Announcements of the American Mathematical Society, vol. 7, no. 5. American Mathematical Society, pp. 28–36, 2001.","apa":"Kaloshin, V., & Hunt, B. R. (2001). A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II. Electronic Research Announcements of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/s1079-6762-01-00091-9","mla":"Kaloshin, Vadim, and Brian R. Hunt. “A Stretched Exponential Bound on the Rate of Growth of the Number of Periodic Points for Prevalent Diffeomorphisms II.” Electronic Research Announcements of the American Mathematical Society, vol. 7, no. 5, American Mathematical Society, 2001, pp. 28–36, doi:10.1090/s1079-6762-01-00091-9."},"day":"24","year":"2001","type":"journal_article","date_updated":"2021-01-12T08:19:51Z","oa_version":"None","doi":"10.1090/s1079-6762-01-00091-9","language":[{"iso":"eng"}],"_id":"8521","title":"A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II","publication":"Electronic Research Announcements of the American Mathematical Society","publication_status":"published","abstract":[{"text":"We continue the previous article's discussion of bounds, for prevalent diffeomorphisms of smooth compact manifolds, on the growth of the number of periodic points and the decay of their hyperbolicity as a function of their period $n$. In that article we reduced the main results to a problem, for certain families of diffeomorphisms, of bounding the measure of parameter values for which the diffeomorphism has (for a given period $n$) an almost periodic point that is almost nonhyperbolic. We also formulated our results for $1$-dimensional endomorphisms on a compact interval. In this article we describe some of the main techniques involved and outline the rest of the proof. To simplify notation, we concentrate primarily on the $1$-dimensional case.","lang":"eng"}]},{"intvolume":" 7","publication_identifier":{"issn":["1079-6762"]},"month":"04","date_created":"2020-09-18T10:49:56Z","status":"public","keyword":["General Mathematics"],"date_published":"2001-04-18T00:00:00Z","page":"17-27","issue":"4","volume":7,"publisher":"American Mathematical Society","article_type":"original","title":"A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I","publication":"Electronic Research Announcements of the American Mathematical Society","_id":"8522","language":[{"iso":"eng"}],"doi":"10.1090/s1079-6762-01-00090-7","abstract":[{"lang":"eng","text":"For diffeomorphisms of smooth compact manifolds, we consider the problem of how fast the number of periodic points with period $n$grows as a function of $n$. In many familiar cases (e.g., Anosov systems) the growth is exponential, but arbitrarily fast growth is possible; in fact, the first author has shown that arbitrarily fast growth is topologically (Baire) generic for $C^2$ or smoother diffeomorphisms. In the present work we show that, by contrast, for a measure-theoretic notion of genericity we call ``prevalence'', the growth is not much faster than exponential. Specifically, we show that for each $\\delta > 0$, there is a prevalent set of ( $C^{1+\\rho}$ or smoother) diffeomorphisms for which the number of period $n$ points is bounded above by $\\operatorname{exp}(C n^{1+\\delta})$ for some $C$ independent of $n$. We also obtain a related bound on the decay of the hyperbolicity of the periodic points as a function of $n$. The contrast between topologically generic and measure-theoretically generic behavior for the growth of the number of periodic points and the decay of their hyperbolicity shows this to be a subtle and complex phenomenon, reminiscent of KAM theory."}],"publication_status":"published","citation":{"mla":"Kaloshin, Vadim, and Brian R. Hunt. “A Stretched Exponential Bound on the Rate of Growth of the Number of Periodic Points for Prevalent Diffeomorphisms I.” Electronic Research Announcements of the American Mathematical Society, vol. 7, no. 4, American Mathematical Society, 2001, pp. 17–27, doi:10.1090/s1079-6762-01-00090-7.","apa":"Kaloshin, V., & Hunt, B. R. (2001). A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I. Electronic Research Announcements of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/s1079-6762-01-00090-7","chicago":"Kaloshin, Vadim, and Brian R. Hunt. “A Stretched Exponential Bound on the Rate of Growth of the Number of Periodic Points for Prevalent Diffeomorphisms I.” Electronic Research Announcements of the American Mathematical Society. American Mathematical Society, 2001. https://doi.org/10.1090/s1079-6762-01-00090-7.","short":"V. Kaloshin, B.R. Hunt, Electronic Research Announcements of the American Mathematical Society 7 (2001) 17–27.","ista":"Kaloshin V, Hunt BR. 2001. A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I. Electronic Research Announcements of the American Mathematical Society. 7(4), 17–27.","ama":"Kaloshin V, Hunt BR. A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I. Electronic Research Announcements of the American Mathematical Society. 2001;7(4):17-27. doi:10.1090/s1079-6762-01-00090-7","ieee":"V. Kaloshin and B. R. Hunt, “A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I,” Electronic Research Announcements of the American Mathematical Society, vol. 7, no. 4. American Mathematical Society, pp. 17–27, 2001."},"quality_controlled":"1","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","first_name":"Vadim"},{"full_name":"Hunt, Brian R.","first_name":"Brian R.","last_name":"Hunt"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","oa_version":"None","date_updated":"2021-01-12T08:19:51Z","type":"journal_article","year":"2001","day":"18"},{"publication_identifier":{"issn":["1016-443X","1420-8970"]},"intvolume":" 11","status":"public","month":"12","date_created":"2020-09-18T10:50:11Z","issue":"5","page":"953-970","volume":11,"date_published":"2001-12-01T00:00:00Z","article_type":"original","publisher":"Springer Nature","_id":"8524","language":[{"iso":"eng"}],"doi":"10.1007/s00039-001-8222-8","title":"Diophantine properties of elements of SO(3)","publication":"Geometric And Functional Analysis","abstract":[{"text":"A number α∈R is diophantine if it is not well approximable by rationals, i.e. for some C,ε>0 and any relatively prime p,q∈Z we have |αq−p|>Cq−1−ε. It is well-known and is easy to prove that almost every α in R is diophantine. In this paper we address a noncommutative version of the diophantine properties. Consider a pair A,B∈SO(3) and for each n∈Z+ take all possible words in A, A -1, B, and B - 1 of length n, i.e. for a multiindex I=(i1,i1,…,im,jm) define |I|=∑mk=1(|ik|+|jk|)=n and \\( W_n(A,B ) = \\{W_{\\cal I}(A,B) = A^{i_1} B^{j_1} \\dots A^{i_m} B^{j_m}\\}_{|{\\cal I|}=n \\).¶Gamburd—Jakobson—Sarnak [GJS] raised the problem: prove that for Haar almost every pair A,B∈SO(3) the closest distance of words of length n to the identity, i.e. sA,B(n)=min|I|=n∥WI(A,B)−E∥, is bounded from below by an exponential function in n. This is the analog of the diophantine property for elements of SO(3). In this paper we prove that s A,B (n) is bounded from below by an exponential function in n 2. We also exhibit obstructions to a “simple” proof of the exponential estimate in n.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","extern":"1","author":[{"last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"full_name":"Rodnianski, I.","first_name":"I.","last_name":"Rodnianski"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","citation":{"mla":"Kaloshin, Vadim, and I. Rodnianski. “Diophantine Properties of Elements of SO(3).” Geometric And Functional Analysis, vol. 11, no. 5, Springer Nature, 2001, pp. 953–70, doi:10.1007/s00039-001-8222-8.","apa":"Kaloshin, V., & Rodnianski, I. (2001). Diophantine properties of elements of SO(3). Geometric And Functional Analysis. Springer Nature. https://doi.org/10.1007/s00039-001-8222-8","ama":"Kaloshin V, Rodnianski I. Diophantine properties of elements of SO(3). Geometric And Functional Analysis. 2001;11(5):953-970. doi:10.1007/s00039-001-8222-8","ieee":"V. Kaloshin and I. Rodnianski, “Diophantine properties of elements of SO(3),” Geometric And Functional Analysis, vol. 11, no. 5. Springer Nature, pp. 953–970, 2001.","chicago":"Kaloshin, Vadim, and I. Rodnianski. “Diophantine Properties of Elements of SO(3).” Geometric And Functional Analysis. Springer Nature, 2001. https://doi.org/10.1007/s00039-001-8222-8.","short":"V. Kaloshin, I. Rodnianski, Geometric And Functional Analysis 11 (2001) 953–970.","ista":"Kaloshin V, Rodnianski I. 2001. Diophantine properties of elements of SO(3). Geometric And Functional Analysis. 11(5), 953–970."},"year":"2001","day":"01","oa_version":"None","date_updated":"2021-01-12T08:19:52Z","type":"journal_article"},{"page":"890 - 900","date_published":"2001-10-01T00:00:00Z","external_id":{"pmid":["11673233"]},"publication_identifier":{"issn":["1367-4803"]},"scopus_import":"1","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","day":"01","date_updated":"2023-06-02T09:08:25Z","type":"journal_article","oa_version":"None","doi":"10.1093/bioinformatics/17.10.890","language":[{"iso":"eng"}],"acknowledgement":"This work has been partially supported by EU 'TRADAT' project and by CNR Genetic Engineering (Italy), the RFBR grant for support of scientific schools (00-15-97968) and SD RAS grant for young scientists (AVK). The authors wish to thank J.Lyons-Weiler for helpful comments and A. Sorokin for help with the ATG_EVALUATOR program.","issue":"10","volume":17,"publisher":"Oxford University Press","article_type":"original","publist_id":"6795","intvolume":" 17","status":"public","date_created":"2018-12-11T11:48:52Z","month":"10","quality_controlled":"1","extern":"1","author":[{"full_name":"Rogozin, Igor","last_name":"Rogozin","first_name":"Igor"},{"first_name":"Alex","last_name":"Kochetov","full_name":"Kochetov, Alex"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"},{"last_name":"Koonin","first_name":"Eugene","full_name":"Koonin, Eugene"},{"last_name":"Milanesi","first_name":"Luciano","full_name":"Milanesi, Luciano"}],"citation":{"ama":"Rogozin I, Kochetov A, Kondrashov F, Koonin E, Milanesi L. Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon. Bioinformatics. 2001;17(10):890-900. doi:10.1093/bioinformatics/17.10.890","ieee":"I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, and L. Milanesi, “Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon,” Bioinformatics, vol. 17, no. 10. Oxford University Press, pp. 890–900, 2001.","ista":"Rogozin I, Kochetov A, Kondrashov F, Koonin E, Milanesi L. 2001. Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon. Bioinformatics. 17(10), 890–900.","chicago":"Rogozin, Igor, Alex Kochetov, Fyodor Kondrashov, Eugene Koonin, and Luciano Milanesi. “Presence of ATG Triplets in 5′ Untranslated Regions of Eukaryotic CDNAs Correlates with a ’weak’context of the Start Codon.” Bioinformatics. Oxford University Press, 2001. https://doi.org/10.1093/bioinformatics/17.10.890.","short":"I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, L. Milanesi, Bioinformatics 17 (2001) 890–900.","apa":"Rogozin, I., Kochetov, A., Kondrashov, F., Koonin, E., & Milanesi, L. (2001). Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context of the start codon. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/17.10.890","mla":"Rogozin, Igor, et al. “Presence of ATG Triplets in 5′ Untranslated Regions of Eukaryotic CDNAs Correlates with a ’weak’context of the Start Codon.” Bioinformatics, vol. 17, no. 10, Oxford University Press, 2001, pp. 890–900, doi:10.1093/bioinformatics/17.10.890."},"year":"2001","_id":"855","title":"Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a 'weak'context of the start codon","publication":"Bioinformatics","pmid":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Motivation: The context of the start codon (typically, AUG) and the features of the 5′ Untranslated Regions (5′ UTRs) are important for understanding translation regulation in eukaryotic mRNAs and for accurate prediction of the coding region in genomic and cDNA sequences. The presence of AUG triplets in 5′ UTRs (upstream AUGs) might effect the initiation rate and, in the context of gene prediction, could reduce the accuracy of the identification of the authentic start. To reveal potential connections between the presence of upstream AUGs and other features of 5′ UTRs, such as their length and the start codon context, we undertook a systematic analysis of the available eukaryotic 5′ UTR sequences. Results: We show that a large fraction of 5′ UTRs in the available cDNA sequences, 15-53% depending on the organism, contain upstream ATGs. A negative correlation was observed between the information content of the translation start signal and the length of the 5′ UTR. Similarly, a negative correlation exists between the 'strength' of the start context and the number of upstream ATGs. Typically, cDNAs containing long 5′ UTRs with multiple upstream ATGs have a 'weak' start context, and in contrast, cDNAs containing short 5′ UTRs without ATGs have 'strong' starts. These counter-intuitive results may be interpreted in terms of upstream AUGs having an important role in the regulation of translation efficiency by ensuring low basal translation level via double negative control and creating the potential for additional regulatory mechanisms. One of such mechanisms, supported by experimental studies of some mRNAs, includes removal of the AUG-containing portion of the 5′ UTR by alternative splicing."}]},{"page":"2661 - 2669","external_id":{"pmid":["11726553"]},"date_published":"2001-11-01T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["0964-6906"]},"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","day":"01","oa_version":"Published Version","type":"journal_article","date_updated":"2023-06-02T08:39:47Z","doi":"10.1093/hmg/10.23.2661","language":[{"iso":"eng"}],"issue":"23","volume":10,"publisher":"Oxford University Press","article_type":"original","publist_id":"6777","intvolume":" 10","status":"public","month":"11","date_created":"2018-12-11T11:48:55Z","quality_controlled":"1","author":[{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"first_name":"Eugene","last_name":"Koonin","full_name":"Koonin, Eugene"}],"extern":"1","citation":{"ieee":"F. Kondrashov and E. Koonin, “Origin of alternative splicing by tandem exon duplication,” Human Molecular Genetics, vol. 10, no. 23. Oxford University Press, pp. 2661–2669, 2001.","ama":"Kondrashov F, Koonin E. Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics. 2001;10(23):2661-2669. doi:10.1093/hmg/10.23.2661","ista":"Kondrashov F, Koonin E. 2001. Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics. 10(23), 2661–2669.","short":"F. Kondrashov, E. Koonin, Human Molecular Genetics 10 (2001) 2661–2669.","chicago":"Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing by Tandem Exon Duplication.” Human Molecular Genetics. Oxford University Press, 2001. https://doi.org/10.1093/hmg/10.23.2661.","apa":"Kondrashov, F., & Koonin, E. (2001). Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/10.23.2661","mla":"Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing by Tandem Exon Duplication.” Human Molecular Genetics, vol. 10, no. 23, Oxford University Press, 2001, pp. 2661–69, doi:10.1093/hmg/10.23.2661."},"year":"2001","_id":"867","pmid":1,"title":"Origin of alternative splicing by tandem exon duplication","publication":"Human Molecular Genetics","abstract":[{"text":"Genes with new functions often evolve by gene duplication. Alternative splicing is another means of evolutionary innovation in eukaryotes, which allows a single gene to encode functionally diverse proteins. We investigate a connection between these two evolutionary phenomena. For ∼10% of the described cases of substitution alternative splicing, such that either one or another amino acid sequence is included into the protein, evidence of origin by tandem exon duplication was found. This is a conservative estimate because alternative exons are typically short and, on many occasions, duplicates may have diverged beyond recognition. Dating exon duplications through a combination of the available experimental data on alternative splicing in orthologous genes from different species and computational analysis indicates that most of the duplications antedate at least the radiation of mammalian orders or even the radiation of vertebrate classes. At present, tandem exon duplication is the only mechanism of evolution of substitution alternative splicing that can be specifically demonstrated. Along with gene duplication, this could be a major route for generating functional diversity during evolution of multicellular eukaryotes.","lang":"eng"}],"publication_status":"published"},{"article_type":"original","publisher":"National Academy of Sciences","issue":"21","volume":98,"date_created":"2018-12-11T11:48:58Z","month":"10","status":"public","intvolume":" 98","publist_id":"6774","year":"2001","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59772/"}],"citation":{"ama":"Kondrashov F, Kondrashov A. Multidimensional epistasis and the disadvantage of sex. PNAS. 2001;98(21):12089-12092. doi:10.1073/pnas.211214298","ieee":"F. Kondrashov and A. Kondrashov, “Multidimensional epistasis and the disadvantage of sex,” PNAS, vol. 98, no. 21. National Academy of Sciences, pp. 12089–12092, 2001.","short":"F. Kondrashov, A. Kondrashov, PNAS 98 (2001) 12089–12092.","chicago":"Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis and the Disadvantage of Sex.” PNAS. National Academy of Sciences, 2001. https://doi.org/10.1073/pnas.211214298.","ista":"Kondrashov F, Kondrashov A. 2001. Multidimensional epistasis and the disadvantage of sex. PNAS. 98(21), 12089–12092.","apa":"Kondrashov, F., & Kondrashov, A. (2001). Multidimensional epistasis and the disadvantage of sex. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.211214298","mla":"Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis and the Disadvantage of Sex.” PNAS, vol. 98, no. 21, National Academy of Sciences, 2001, pp. 12089–92, doi:10.1073/pnas.211214298."},"extern":"1","author":[{"last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"first_name":"Alexey","last_name":"Kondrashov","full_name":"Kondrashov, Alexey"}],"quality_controlled":"1","publication_status":"published","abstract":[{"text":"Sex is thought to facilitate accumulation of initially rare beneficial mutations by allowing simultaneous allele replacements at many loci. However, this advantage of sex depends on a restrictive assumption that the fitness of a genotype is determined by fitness potential, a single intermediate variable to which all loci contribute additively, so that new alleles can accumulate in any order. Individual-based simulations of sexual and asexual populations reveal that under generic selection, sex often retards adaptive evolution. When new alleles are beneficial only if they accumulate in a prescribed order, a sexual population may evolve two or more times slower than an asexual population because only asexual reproduction allows some overlap of successive allele replacements. Many other fitness surfaces lead to an even greater disadvantage of sex. Thus, either sex exists in spite of its impact on the rate of adaptive allele replacements, or natural fitness surfaces have rather specific properties, at least at the scale of intrapopulation genetic variability.","lang":"eng"}],"publication":"PNAS","title":"Multidimensional epistasis and the disadvantage of sex","pmid":1,"oa":1,"_id":"874","date_published":"2001-10-09T00:00:00Z","external_id":{"pmid":["11593020"]},"page":"12089 - 12092","publication_identifier":{"issn":["0027-8424"]},"scopus_import":"1","date_updated":"2023-06-02T08:18:22Z","type":"journal_article","oa_version":"Published Version","day":"09","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","doi":"10.1073/pnas.211214298","language":[{"iso":"eng"}]},{"publist_id":"6758","intvolume":" 2","status":"public","article_number":"research0053.1","date_created":"2018-12-11T11:49:02Z","month":"01","issue":"12","volume":2,"publisher":"BioMed Central","article_type":"original","oa":1,"_id":"888","publication":"Genome Biology","title":"Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins ","pmid":1,"publication_status":"published","abstract":[{"lang":"eng","text":"BACKGROUND: Detection of changes in a protein's evolutionary rate may reveal cases of change in that protein's function. We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins. The test was performed on clusters of orthologous protein sequences from complete bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat). RESULTS: Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life. However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation that is consistent with an acceleration of the rate of amino-acid substitution, which may be due to functional diversification. Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery of the cells and mediate their interaction with the environment. CONCLUSIONS: Relative rates of protein evolution are remarkably constant for the three species groups analyzed here. Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs. Functional diversification between orthologs is thought to be a relatively rare event. However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins."}],"quality_controlled":"1","extern":"1","author":[{"first_name":"Ingo","last_name":"Jordan","full_name":"Jordan, Ingo"},{"last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"first_name":"Igor","last_name":"Rogozin","full_name":"Rogozin, Igor"},{"last_name":"Tatusov","first_name":"Roman","full_name":"Tatusov, Roman"},{"full_name":"Wolf, Yuri","last_name":"Wolf","first_name":"Yuri"},{"full_name":"Koonin, Eugene","last_name":"Koonin","first_name":"Eugene"}],"citation":{"mla":"Jordan, Ingo, et al. “Constant Relative Rate of Protein Evolution and Detection of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins .” Genome Biology, vol. 2, no. 12, research0053.1, BioMed Central, 2001, doi:10.1186/gb-2001-2-12-research0053.","apa":"Jordan, I., Kondrashov, F., Rogozin, I., Tatusov, R., Wolf, Y., & Koonin, E. (2001). Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins . Genome Biology. BioMed Central. https://doi.org/10.1186/gb-2001-2-12-research0053","ama":"Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins . Genome Biology. 2001;2(12). doi:10.1186/gb-2001-2-12-research0053","ieee":"I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, and E. Koonin, “Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins ,” Genome Biology, vol. 2, no. 12. BioMed Central, 2001.","short":"I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, E. Koonin, Genome Biology 2 (2001).","chicago":"Jordan, Ingo, Fyodor Kondrashov, Igor Rogozin, Roman Tatusov, Yuri Wolf, and Eugene Koonin. “Constant Relative Rate of Protein Evolution and Detection of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins .” Genome Biology. BioMed Central, 2001. https://doi.org/10.1186/gb-2001-2-12-research0053.","ista":"Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. 2001. Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins . Genome Biology. 2(12), research0053.1."},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC64838/"}],"year":"2001","publication_identifier":{"issn":["1465-6906"]},"scopus_import":"1","date_published":"2001-01-01T00:00:00Z","external_id":{"pmid":["11790256"]},"doi":"10.1186/gb-2001-2-12-research0053","language":[{"iso":"eng"}],"acknowledgement":"We thank Alexey Kondrashov for many helpful discussions and constructive criticisms, Charles DeLisi, David Landsman, Detlef Leipe, Wojciech Makalowski and Itai Yanai for critical reading of the manuscript and constructive comments and L. Aravind for advice on protein function prediction. The release of the unpublished P. furiosus genome sequence by the Utah Genome Center at the University of Utah is acknowledged and appreciated.","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","day":"01","type":"journal_article","date_updated":"2023-05-31T12:15:37Z","oa_version":"Published Version"},{"main_file_link":[{"url":"http://arxiv.org/abs/math/0106140","open_access":"1"}],"citation":{"ama":"Hausel T, Thaddeus M. Examples of mirror partners arising from integrable systems. Comptes Rendus de l’Academie des Sciences - Series I: Mathematics. 2001;333(4):313-318. doi:10.1016/S0764-4442(01)02057-2","ieee":"T. Hausel and M. Thaddeus, “Examples of mirror partners arising from integrable systems,” Comptes Rendus de l’Academie des Sciences - Series I: Mathematics, vol. 333, no. 4. Elsevier, pp. 313–318, 2001.","short":"T. Hausel, M. Thaddeus, Comptes Rendus de l’Academie Des Sciences - Series I: Mathematics 333 (2001) 313–318.","chicago":"Hausel, Tamás, and Michael Thaddeus. “Examples of Mirror Partners Arising from Integrable Systems.” Comptes Rendus de l’Academie Des Sciences - Series I: Mathematics. Elsevier, 2001. https://doi.org/10.1016/S0764-4442(01)02057-2.","ista":"Hausel T, Thaddeus M. 2001. Examples of mirror partners arising from integrable systems. Comptes Rendus de l’Academie des Sciences - Series I: Mathematics. 333(4), 313–318.","apa":"Hausel, T., & Thaddeus, M. (2001). Examples of mirror partners arising from integrable systems. Comptes Rendus de l’Academie Des Sciences - Series I: Mathematics. Elsevier. https://doi.org/10.1016/S0764-4442(01)02057-2","mla":"Hausel, Tamás, and Michael Thaddeus. “Examples of Mirror Partners Arising from Integrable Systems.” Comptes Rendus de l’Academie Des Sciences - Series I: Mathematics, vol. 333, no. 4, Elsevier, 2001, pp. 313–18, doi:10.1016/S0764-4442(01)02057-2."},"author":[{"last_name":"Hausel","first_name":"Tamas","full_name":"Hausel, Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Thaddeus","full_name":"Thaddeus, Michael"}],"quality_controlled":"1","extern":"1","year":"2001","publication":"Comptes Rendus de l'Academie des Sciences - Series I: Mathematics","title":"Examples of mirror partners arising from integrable systems","_id":"1452","oa":1,"abstract":[{"lang":"eng","text":"In this Note we present pairs of hyperkähler orbifolds which satisfy two different versions of mirror symmetry. On the one hand, we show that their Hodge numbers (or more precisely, stringy E-polynomials) are equal. On the other hand, we show that they satisfy the prescription of Strominger, Yau, and Zaslow (which in the present case goes back to Bershadsky, Johansen, Sadov and Vafa): that a Calabi-Yau and its mirror should fiber over the same real manifold, with special Lagrangian fibers which are tori dual to each other. Our examples arise as moduli spaces of local systems on a curve with structure group SL(n); the mirror is the corresponding space with structure group PGL(n). The special Lagrangian tori come from an algebraically completely integrable Hamiltonian system: the Hitchin system."}],"publication_status":"published","issue":"4","volume":333,"article_type":"original","publisher":"Elsevier","intvolume":" 333","publist_id":"5742","month":"08","date_created":"2018-12-11T11:52:06Z","status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","oa_version":"Preprint","type":"journal_article","date_updated":"2023-05-31T09:57:48Z","day":"15","doi":"10.1016/S0764-4442(01)02057-2","language":[{"iso":"eng"}],"acknowledgement":"The authors are grateful for Nigel Hitchin for suggesting the similarity between [4] and [12] in 1996 and for Pierre Deligne for numerous useful comments","external_id":{"arxiv":["math/0106140"]},"date_published":"2001-08-15T00:00:00Z","page":"313 - 318","scopus_import":"1","publication_identifier":{"issn":["0764-4442"]},"arxiv":1},{"arxiv":1,"publication_identifier":{"issn":["0370-2693"]},"scopus_import":"1","page":"189 - 199","date_published":"2001-08-09T00:00:00Z","external_id":{"arxiv":["hep-th/0105118"]},"acknowledgement":"We would like to acknowledge the financial support provided by the Miller Institute of Basic Research in Science, the Japan Society for the Promotion of Science, grant No. P99736 and the partial support by OTKA grant No. T032478.","doi":"10.1016/S0370-2693(01)00821-8","language":[{"iso":"eng"}],"day":"09","date_updated":"2023-05-31T11:51:37Z","type":"journal_article","oa_version":"Preprint","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","article_processing_charge":"No","status":"public","date_created":"2018-12-11T11:52:07Z","month":"08","publist_id":"5743","intvolume":" 514","publisher":"Elsevier","article_type":"original","volume":514,"issue":"1-2","publication_status":"published","abstract":[{"text":"In this Letter we exhibit a one-parameter family of new Taub-NUT instantons parameterized by a half-line. The endpoint of the half-line will be the reducible Yang-Mills instanton corresponding to the Eguchi-Hanson-Gibbons L2 harmonic 2-form, while at an inner point we recover the Pope-Yuille instanton constructed as a projection of the Levi-Civitá connection onto the positive su(2)+ ⊂ so(4) subalgebra. Our method imitates the Jackiw-Nohl-Rebbi construction originally designed for flat R4. That is we find a one-parameter family of harmonic functions on the Taub-NUT space with a point singularity, rescale the metric and project the obtained Levi-Civitá connection onto the other negative su(2)- ⊂ so(4) part. Our solutions will possess the full U(2) symmetry, and thus provide more solutions to the recently proposed U(2) symmetric ansatz of Kim and Yoon.","lang":"eng"}],"oa":1,"_id":"1453","publication":"Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics","title":"Geometric construction of new Yang-Mills instantons over Taub-NUT space","year":"2001","extern":"1","author":[{"last_name":"Etesi","first_name":"Gábor","full_name":"Etesi, Gábor"},{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Hausel, Tamas","last_name":"Hausel","first_name":"Tamas"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/hep-th/0105118"}],"citation":{"ista":"Etesi G, Hausel T. 2001. Geometric construction of new Yang-Mills instantons over Taub-NUT space. Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics. 514(1–2), 189–199.","chicago":"Etesi, Gábor, and Tamás Hausel. “Geometric Construction of New Yang-Mills Instantons over Taub-NUT Space.” Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics. Elsevier, 2001. https://doi.org/10.1016/S0370-2693(01)00821-8.","short":"G. Etesi, T. Hausel, Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics 514 (2001) 189–199.","ieee":"G. Etesi and T. Hausel, “Geometric construction of new Yang-Mills instantons over Taub-NUT space,” Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics, vol. 514, no. 1–2. Elsevier, pp. 189–199, 2001.","ama":"Etesi G, Hausel T. Geometric construction of new Yang-Mills instantons over Taub-NUT space. Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics. 2001;514(1-2):189-199. doi:10.1016/S0370-2693(01)00821-8","mla":"Etesi, Gábor, and Tamás Hausel. “Geometric Construction of New Yang-Mills Instantons over Taub-NUT Space.” Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics, vol. 514, no. 1–2, Elsevier, 2001, pp. 189–99, doi:10.1016/S0370-2693(01)00821-8.","apa":"Etesi, G., & Hausel, T. (2001). Geometric construction of new Yang-Mills instantons over Taub-NUT space. Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics. Elsevier. https://doi.org/10.1016/S0370-2693(01)00821-8"}},{"article_processing_charge":"No","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","oa_version":"Preprint","type":"journal_article","date_updated":"2023-05-31T12:08:45Z","day":"01","doi":"10.1016/S0393-0440(00)00040-1","language":[{"iso":"eng"}],"acknowledgement":"The work in this paper was done when Tamás Hausel visited the Yukawa Institute of Kyoto University in February 2000. We are grateful for Prof. G.W. Gibbons for insightful discussions and Prof. H. Kodama and the Yukawa Institute for the invitation and hospitality.","external_id":{"arxiv":["hep-th/0003239"]},"date_published":"2001-01-01T00:00:00Z","page":"126 - 136","scopus_import":"1","publication_identifier":{"issn":["0393-0440"]},"arxiv":1,"main_file_link":[{"url":"http://arxiv.org/abs/hep-th/0003239","open_access":"1"}],"citation":{"mla":"Etesi, Gábor, and Tamás Hausel. “Geometric Interpretation of Schwarzschild Instantons.” Journal of Geometry and Physics, vol. 37, no. 1–2, Elsevier, 2001, pp. 126–36, doi:10.1016/S0393-0440(00)00040-1.","apa":"Etesi, G., & Hausel, T. (2001). Geometric interpretation of Schwarzschild instantons. Journal of Geometry and Physics. Elsevier. https://doi.org/10.1016/S0393-0440(00)00040-1","ieee":"G. Etesi and T. Hausel, “Geometric interpretation of Schwarzschild instantons,” Journal of Geometry and Physics, vol. 37, no. 1–2. Elsevier, pp. 126–136, 2001.","ama":"Etesi G, Hausel T. Geometric interpretation of Schwarzschild instantons. Journal of Geometry and Physics. 2001;37(1-2):126-136. doi:10.1016/S0393-0440(00)00040-1","short":"G. Etesi, T. Hausel, Journal of Geometry and Physics 37 (2001) 126–136.","chicago":"Etesi, Gábor, and Tamás Hausel. “Geometric Interpretation of Schwarzschild Instantons.” Journal of Geometry and Physics. Elsevier, 2001. https://doi.org/10.1016/S0393-0440(00)00040-1.","ista":"Etesi G, Hausel T. 2001. Geometric interpretation of Schwarzschild instantons. Journal of Geometry and Physics. 37(1–2), 126–136."},"author":[{"full_name":"Etesi, Gábor","last_name":"Etesi","first_name":"Gábor"},{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Hausel, Tamas","last_name":"Hausel","first_name":"Tamas"}],"quality_controlled":"1","extern":"1","year":"2001","title":"Geometric interpretation of Schwarzschild instantons","publication":"Journal of Geometry and Physics","_id":"1454","oa":1,"abstract":[{"lang":"eng","text":"We address the problem of finding Abelian instantons of finite energy on the Euclidean Schwarzschild manifold. This amounts to construct self-dual L2 harmonic 2-forms on the space. Gibbons found a non-topological L2 harmonic form in the Taub-NUT metric, leading to Abelian instantons with continuous energy. We imitate his construction in the case of the Euclidean Schwarzschild manifold and find a non-topological self-dual L2 harmonic 2-form on it. We show how this gives rise to Abelian instantons and identify them with SU(2)-instantons of Pontryagin number 2n2 found by Charap and Duff in 1977. Using results of Dodziuk and Hitchin we also calculate the full L2 harmonic space for the Euclidean Schwarzschild manifold."}],"publication_status":"published","volume":37,"issue":"1-2","article_type":"original","publisher":"Elsevier","intvolume":" 37","publist_id":"5744","month":"01","date_created":"2018-12-11T11:52:07Z","status":"public"},{"department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}],"doi":"10.1126/science.1059745","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"None","type":"journal_article","date_updated":"2021-12-14T08:40:32Z","day":"15","scopus_import":"1","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"external_id":{"pmid":["11349138"]},"keyword":["Multidisciplinary"],"date_published":"2001-06-15T00:00:00Z","page":"2077-2080","pmid":1,"title":"Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation","publication":"Science","_id":"9444","abstract":[{"text":"Epigenetic silenced alleles of the Arabidopsis SUPERMANlocus (the clark kent alleles) are associated with dense hypermethylation at noncanonical cytosines (CpXpG and asymmetric sites, where X = A, T, C, or G). A genetic screen for suppressors of a hypermethylated clark kent mutant identified nine loss-of-function alleles of CHROMOMETHYLASE3(CMT3), a novel cytosine methyltransferase homolog. These cmt3 mutants display a wild-type morphology but exhibit decreased CpXpG methylation of the SUP gene and of other sequences throughout the genome. They also show reactivated expression of endogenous retrotransposon sequences. These results show that a non-CpG DNA methyltransferase is responsible for maintaining epigenetic gene silencing.","lang":"eng"}],"publication_status":"published","citation":{"ieee":"A. M. Lindroth et al., “Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation,” Science, vol. 292, no. 5524. American Association for the Advancement of Science, pp. 2077–2080, 2001.","ama":"Lindroth AM, Cao X, Jackson JP, et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 2001;292(5524):2077-2080. doi:10.1126/science.1059745","chicago":"Lindroth, A. M., Xiaofeng Cao, James P. Jackson, Daniel Zilberman, Claire M. McCallum, Steven Henikoff, and Steven E. Jacobsen. “Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation.” Science. American Association for the Advancement of Science, 2001. https://doi.org/10.1126/science.1059745.","short":"A.M. Lindroth, X. Cao, J.P. Jackson, D. Zilberman, C.M. McCallum, S. Henikoff, S.E. Jacobsen, Science 292 (2001) 2077–2080.","ista":"Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE. 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 292(5524), 2077–2080.","apa":"Lindroth, A. M., Cao, X., Jackson, J. P., Zilberman, D., McCallum, C. M., Henikoff, S., & Jacobsen, S. E. (2001). Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1059745","mla":"Lindroth, A. M., et al. “Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation.” Science, vol. 292, no. 5524, American Association for the Advancement of Science, 2001, pp. 2077–80, doi:10.1126/science.1059745."},"extern":"1","author":[{"last_name":"Lindroth","first_name":"A. M.","full_name":"Lindroth, A. M."},{"first_name":"Xiaofeng","last_name":"Cao","full_name":"Cao, Xiaofeng"},{"full_name":"Jackson, James P.","last_name":"Jackson","first_name":"James P."},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"},{"full_name":"McCallum, Claire M.","last_name":"McCallum","first_name":"Claire M."},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"},{"first_name":"Steven E.","last_name":"Jacobsen","full_name":"Jacobsen, Steven E."}],"quality_controlled":"1","year":"2001","intvolume":" 292","month":"06","date_created":"2021-06-02T13:35:16Z","status":"public","issue":"5524","volume":292,"article_type":"original","publisher":"American Association for the Advancement of Science"}]