[{"date_published":"2015-01-01T00:00:00Z","arxiv":1,"external_id":{"arxiv":["1405.5689"]},"oa":1,"oa_version":"None","date_created":"2018-12-11T11:48:27Z","_id":"778","extern":"1","publist_id":"6880","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2023-02-23T13:17:35Z","alternative_title":["LNCS"],"title":"Inherent limitations of hybrid transactional memory","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kopinsky","first_name":"Justin","full_name":"Kopinsky, Justin"},{"full_name":"Kuznetsov, Petr","last_name":"Kuznetsov","first_name":"Petr"},{"first_name":"Srivatsan","last_name":"Ravi","full_name":"Ravi, Srivatsan"},{"full_name":"Shavit, Nir","first_name":"Nir","last_name":"Shavit"}],"main_file_link":[{"url":"https://arxiv.org/abs/1405.5689","open_access":"1"}],"acknowledgement":"P. Kuznetsov-The author is supported by the Agence Nationale de la Recherche, ANR-14-CE35-0010-01, project DISCMAT. N. Shavit-Support is gratfeully acknowledgedfrom the National Science Foundation under grants CCF-1217921, CCF-1201926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.","day":"01","doi":"10.1007/978-3-662-48653-5_13","citation":{"short":"D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, N. Shavit, in:, Springer, 2015, pp. 185–199.","ama":"Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. Inherent limitations of hybrid transactional memory. In: Vol 9363. Springer; 2015:185-199. doi:<a href=\"https://doi.org/10.1007/978-3-662-48653-5_13\">10.1007/978-3-662-48653-5_13</a>","ista":"Alistarh D-A, Kopinsky J, Kuznetsov P, Ravi S, Shavit N. 2015. Inherent limitations of hybrid transactional memory. DISC: Distributed Computing, LNCS, vol. 9363, 185–199.","ieee":"D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, and N. Shavit, “Inherent limitations of hybrid transactional memory,” presented at the DISC: Distributed Computing, 2015, vol. 9363, pp. 185–199.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Petr Kuznetsov, Srivatsan Ravi, and Nir Shavit. “Inherent Limitations of Hybrid Transactional Memory,” 9363:185–99. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-662-48653-5_13\">https://doi.org/10.1007/978-3-662-48653-5_13</a>.","mla":"Alistarh, Dan-Adrian, et al. <i>Inherent Limitations of Hybrid Transactional Memory</i>. Vol. 9363, Springer, 2015, pp. 185–99, doi:<a href=\"https://doi.org/10.1007/978-3-662-48653-5_13\">10.1007/978-3-662-48653-5_13</a>.","apa":"Alistarh, D.-A., Kopinsky, J., Kuznetsov, P., Ravi, S., &#38; Shavit, N. (2015). Inherent limitations of hybrid transactional memory (Vol. 9363, pp. 185–199). Presented at the DISC: Distributed Computing, Springer. <a href=\"https://doi.org/10.1007/978-3-662-48653-5_13\">https://doi.org/10.1007/978-3-662-48653-5_13</a>"},"abstract":[{"lang":"eng","text":"Several Hybrid Transactional Memory (HyTM) schemes have recently been proposed to complement the fast, but best-effort nature of Hardware Transactional Memory (HTM) with a slow, reliable software backup. However, the costs of providing concurrency between hardware and software transactions in HyTM are still not well understood. In this paper, we propose a general model for HyTM implementations, which captures the ability of hardware transactions to buffer memory accesses. The model allows us to formally quantify and analyze the amount of overhead (instrumentation) caused by the potential presence of software transactions.We prove that (1) it is impossible to build a strictly serializable HyTM implementation that has both uninstrumented reads and writes, even for very weak progress guarantees, and (2) the instrumentation cost incurred by a hardware transaction in any progressive opaque HyTM is linear in the size of the transaction’s data set.We further describe two implementations which exhibit optimal instrumentation costs for two different progress conditions. In sum, this paper proposes the first formal HyTM model and captures for the first time the trade-off between the degree of hardware-software TM concurrency and the amount of instrumentation overhead."}],"publication_status":"published","type":"conference","publisher":"Springer","intvolume":"      9363","quality_controlled":"1","year":"2015","conference":{"name":"DISC: Distributed Computing"},"language":[{"iso":"eng"}],"volume":9363,"article_processing_charge":"No","month":"01","page":"185 - 199"},{"page":"123 - 132","day":"13","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and  IIS-1447786,  the  Department of Energy under grant ER26116/DE-SC0008923, and the Oracle corporation. In particular, we would like to thank Dave Dice, Alex Kogan, and Mark Moir from the Oracle Scalable Synchronization Research Group for very useful feedback on earlier drafts of this paper.","month":"06","title":"ThreadScan: Automatic and scalable memory reclamation","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"full_name":"Matveev, Alexander","last_name":"Matveev","first_name":"Alexander"},{"full_name":"Leiserson, William","first_name":"William","last_name":"Leiserson"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"}],"article_processing_charge":"No","volume":"2015-June","date_updated":"2023-02-23T12:35:42Z","status":"public","language":[{"iso":"eng"}],"conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6876","extern":"1","_id":"779","type":"conference","publisher":"ACM","oa_version":"None","publication_status":"published","date_created":"2018-12-11T11:48:27Z","abstract":[{"text":"The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU, are either prohibitively expensive or require significant programming expertise, to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated. In this paper, we take a new approach to concurrent memory reclamation: instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads. Initial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free.","lang":"eng"}],"citation":{"ista":"Alistarh D-A, Matveev A, Leiserson W, Shavit N. 2015. ThreadScan: Automatic and scalable memory reclamation. SPAA: Symposium on Parallelism in Algorithms and Architectures vol. 2015–June, 123–132.","chicago":"Alistarh, Dan-Adrian, Alexander Matveev, William Leiserson, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation,” 2015–June:123–32. ACM, 2015. <a href=\"https://doi.org/10.1145/2755573.2755600\">https://doi.org/10.1145/2755573.2755600</a>.","ieee":"D.-A. Alistarh, A. Matveev, W. Leiserson, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, 2015, vol. 2015–June, pp. 123–132.","short":"D.-A. Alistarh, A. Matveev, W. Leiserson, N. Shavit, in:, ACM, 2015, pp. 123–132.","ama":"Alistarh D-A, Matveev A, Leiserson W, Shavit N. ThreadScan: Automatic and scalable memory reclamation. In: Vol 2015-June. ACM; 2015:123-132. doi:<a href=\"https://doi.org/10.1145/2755573.2755600\">10.1145/2755573.2755600</a>","apa":"Alistarh, D.-A., Matveev, A., Leiserson, W., &#38; Shavit, N. (2015). ThreadScan: Automatic and scalable memory reclamation (Vol. 2015–June, pp. 123–132). Presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, ACM. <a href=\"https://doi.org/10.1145/2755573.2755600\">https://doi.org/10.1145/2755573.2755600</a>","mla":"Alistarh, Dan-Adrian, et al. <i>ThreadScan: Automatic and Scalable Memory Reclamation</i>. Vol. 2015–June, ACM, 2015, pp. 123–32, doi:<a href=\"https://doi.org/10.1145/2755573.2755600\">10.1145/2755573.2755600</a>."},"related_material":{"record":[{"relation":"later_version","id":"6001","status":"public"}]},"doi":"10.1145/2755573.2755600","date_published":"2015-06-13T00:00:00Z"},{"date_updated":"2026-05-19T13:03:42Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"01","OA_place":"repository","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and the Oracle and Intel corporations.”","title":"Polylogarithmic-time leader election in population protocols","author":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"}],"main_file_link":[{"url":"https://arxiv.org/abs/1502.05745","open_access":"1"}],"external_id":{"arxiv":["1502.05745"]},"oa":1,"publication_identifier":{"isbn":["9783662476659"],"eisbn":["9783662476666"]},"OA_type":"green","arxiv":1,"date_published":"2015-01-01T00:00:00Z","publist_id":"6877","publication":"Proceedings of the 42nd International Colloquium on Automata, Languages and Programming","extern":"1","_id":"780","oa_version":"Preprint","date_created":"2018-12-11T11:48:28Z","volume":9135,"language":[{"iso":"eng"}],"year":"2015","conference":{"start_date":"2015-07-06","location":"Kyoto, Japan","name":"ICALP: International Colloquium on Automota, Languages and Programming","end_date":"2015-07-10"},"page":"479 - 491","month":"01","article_processing_charge":"No","abstract":[{"text":"Population protocols are networks of finite-state agents, interacting randomly, and updating their states using simple rules. Despite their extreme simplicity, these systems have been shown to cooperatively perform complex computational tasks, such as simulating register machines to compute standard arithmetic functions. The election of a unique leader agent is a key requirement in such computational constructions. Yet, the fastest currently known population protocol for electing a leader only has linear convergence time, and it has recently been shown that no population protocol using a constant number of states per node may overcome this linear bound. In this paper, we give the first population protocol for leader election with polylogarithmic convergence time, using polylogarithmic memory states per node. The protocol structure is quite simple: each node has an associated value, and is either a leader (still in contention) or a minion (following some leader). A leader keeps incrementing its value and “defeats” other leaders in one-to-one interactions, and will drop from contention and become a minion if it meets a leader with higher value. Importantly, a leader also drops out if it meets a minion with higher absolute value. While these rules are quite simple, the proof that this algorithm achieves polylogarithmic convergence time is non-trivial. In particular, the argument combines careful use of concentration inequalities with anti-concentration bounds, showing that the leaders’ values become spread apart as the execution progresses, which in turn implies that straggling leaders get quickly eliminated. We complement our analysis with empirical results, showing that our protocol converges extremely fast, even for large network sizes.","lang":"eng"}],"citation":{"mla":"Alistarh, Dan-Adrian, and Rati Gelashvili. “Polylogarithmic-Time Leader Election in Population Protocols.” <i>Proceedings of the 42nd International Colloquium on Automata, Languages and Programming</i>, vol. 9135, Springer Nature, 2015, pp. 479–91, doi:<a href=\"https://doi.org/10.1007/978-3-662-47666-6_38\">10.1007/978-3-662-47666-6_38</a>.","apa":"Alistarh, D.-A., &#38; Gelashvili, R. (2015). Polylogarithmic-time leader election in population protocols. In <i>Proceedings of the 42nd International Colloquium on Automata, Languages and Programming</i> (Vol. 9135, pp. 479–491). Kyoto, Japan: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-47666-6_38\">https://doi.org/10.1007/978-3-662-47666-6_38</a>","ama":"Alistarh D-A, Gelashvili R. Polylogarithmic-time leader election in population protocols. In: <i>Proceedings of the 42nd International Colloquium on Automata, Languages and Programming</i>. Vol 9135. Springer Nature; 2015:479-491. doi:<a href=\"https://doi.org/10.1007/978-3-662-47666-6_38\">10.1007/978-3-662-47666-6_38</a>","short":"D.-A. Alistarh, R. Gelashvili, in:, Proceedings of the 42nd International Colloquium on Automata, Languages and Programming, Springer Nature, 2015, pp. 479–491.","chicago":"Alistarh, Dan-Adrian, and Rati Gelashvili. “Polylogarithmic-Time Leader Election in Population Protocols.” In <i>Proceedings of the 42nd International Colloquium on Automata, Languages and Programming</i>, 9135:479–91. Springer Nature, 2015. <a href=\"https://doi.org/10.1007/978-3-662-47666-6_38\">https://doi.org/10.1007/978-3-662-47666-6_38</a>.","ieee":"D.-A. Alistarh and R. Gelashvili, “Polylogarithmic-time leader election in population protocols,” in <i>Proceedings of the 42nd International Colloquium on Automata, Languages and Programming</i>, Kyoto, Japan, 2015, vol. 9135, pp. 479–491.","ista":"Alistarh D-A, Gelashvili R. 2015. Polylogarithmic-time leader election in population protocols. Proceedings of the 42nd International Colloquium on Automata, Languages and Programming. ICALP: International Colloquium on Automota, Languages and Programming vol. 9135, 479–491."},"doi":"10.1007/978-3-662-47666-6_38","intvolume":"      9135","publisher":"Springer Nature","type":"conference","publication_status":"published"},{"date_published":"2015-07-21T00:00:00Z","doi":"10.1145/2767386.2767429","citation":{"apa":"Alistarh, D.-A., Gelashvili, R., &#38; Vojnović, M. (2015). Fast and exact majority in population protocols (Vol. 2015–July, pp. 47–56). Presented at the PODC: Principles of Distributed Computing, ACM. <a href=\"https://doi.org/10.1145/2767386.2767429\">https://doi.org/10.1145/2767386.2767429</a>","mla":"Alistarh, Dan-Adrian, et al. <i>Fast and Exact Majority in Population Protocols</i>. Vol. 2015–July, ACM, 2015, pp. 47–56, doi:<a href=\"https://doi.org/10.1145/2767386.2767429\">10.1145/2767386.2767429</a>.","ista":"Alistarh D-A, Gelashvili R, Vojnović M. 2015. Fast and exact majority in population protocols. PODC: Principles of Distributed Computing vol. 2015–July, 47–56.","ieee":"D.-A. Alistarh, R. Gelashvili, and M. Vojnović, “Fast and exact majority in population protocols,” presented at the PODC: Principles of Distributed Computing, 2015, vol. 2015–July, pp. 47–56.","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Milan Vojnović. “Fast and Exact Majority in Population Protocols,” 2015–July:47–56. ACM, 2015. <a href=\"https://doi.org/10.1145/2767386.2767429\">https://doi.org/10.1145/2767386.2767429</a>.","short":"D.-A. Alistarh, R. Gelashvili, M. Vojnović, in:, ACM, 2015, pp. 47–56.","ama":"Alistarh D-A, Gelashvili R, Vojnović M. Fast and exact majority in population protocols. In: Vol 2015-July. ACM; 2015:47-56. doi:<a href=\"https://doi.org/10.1145/2767386.2767429\">10.1145/2767386.2767429</a>"},"abstract":[{"text":"Population protocols, roughly defined as systems consisting of large numbers of simple identical agents, interacting at random and updating their state following simple rules, are an important research topic at the intersection of distributed computing and biology. One of the fundamental tasks that a population protocol may solve is majority: each node starts in one of two states; the goal is for all nodes to reach a correct consensus on which of the two states was initially the majority. Despite considerable research effort, known protocols for this problem are either exact but slow (taking linear parallel time to converge), or fast but approximate (with non-zero probability of error). In this paper, we show that this trade-off between preciasion and speed is not inherent. We present a new protocol called Average and Conquer (AVC) that solves majority ex-actly in expected parallel convergence time O(log n/(sε) + log n log s), where n is the number of nodes, εn is the initial node advantage of the majority state, and s = Ω(log n log log n) is the number of states the protocol employs. This shows that the majority problem can be solved exactly in time poly-logarithmic in n, provided that the memory per node is s = Ω(1/ε + lognlog1/ε). On the negative side, we establish a lower bound of Ω(1/ε) on the expected paraallel convergence time for the case of four memory states per node, and a lower bound of Ω(logn) parallel time for protocols using any number of memory states per node.per node, and a lower bound of (log n) parallel time for protocols using any number of memory states per node.","lang":"eng"}],"date_created":"2018-12-11T11:48:28Z","publication_status":"published","oa_version":"None","publisher":"ACM","_id":"781","type":"conference","extern":"1","publist_id":"6873","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"PODC: Principles of Distributed Computing"},"year":"2015","language":[{"iso":"eng"}],"status":"public","date_updated":"2023-02-23T13:18:35Z","volume":"2015-July","article_processing_charge":"No","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"},{"full_name":"Vojnović, Milan","last_name":"Vojnović","first_name":"Milan"}],"title":"Fast and exact majority in population protocols","month":"07","page":"47 - 56","day":"21"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-05-19T13:21:59Z","status":"public","main_file_link":[{"open_access":"1","url":"http://dx.doi.org/10.1145/2767386.2767430"}],"title":"Lock-Free algorithms under stochastic schedulers","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Thomas","last_name":"Sauerwald","full_name":"Sauerwald, Thomas"},{"first_name":"Milan","last_name":"Vojnović","full_name":"Vojnović, Milan"}],"day":"21","OA_place":"publisher","publication_identifier":{"eisbn":["9781450336178"]},"OA_type":"free access","date_published":"2015-07-21T00:00:00Z","oa":1,"_id":"782","date_created":"2018-12-11T11:48:28Z","oa_version":"Accepted Version","publist_id":"6874","extern":"1","publication":"Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing","conference":{"start_date":"2015-07-21","name":"PODC: Principles of Distributed Computing","end_date":"2015-7-23","location":"New York, NY, United States"},"year":"2015","quality_controlled":"1","volume":"2015-July","language":[{"iso":"eng"}],"article_processing_charge":"No","page":"251 - 260","month":"07","doi":"10.1145/2767386.2767430","scopus_import":"1","abstract":[{"text":"In this work, we consider the following random process, mo- Tivated by the analysis of lock-free concurrent algorithms under high memory contention. In each round, a new scheduling step is allocated to one of n threads, according to a distribution p = (p1; p2; : : : ; pn), where thread i is scheduled with probability pi. When some thread first reaches a set threshold of executed steps, it registers a win, completing its current operation, and resets its step count to 1. At the same time, threads whose step count was close to the threshold also get reset because of the win, but to 0 steps, being penalized for almost winning. We are interested in two questions: how often does some thread complete an operation (system latency), and how often does a specific thread complete an operation (individual latency)? We provide asymptotically tight bounds for the system and individual latency of this general concurrency pattern, for arbitrary scheduling distributions p. Surprisingly, a sim- ple characterization exists: in expectation, the system will complete a new operation every Θ(1/p 2) steps, while thread i will complete a new operation every Θ(1/2=p i ) steps. The proof is interesting in its own right, as it requires a careful analysis of how the higher norms of the vector p inuence the thread step counts and latencies in this random process. Our result offers a simple connection between the scheduling distribution and the average performance of concurrent algorithms, which has several applications.","lang":"eng"}],"citation":{"mla":"Alistarh, Dan-Adrian, et al. “Lock-Free Algorithms under Stochastic Schedulers.” <i>Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing</i>, vol. 2015–July, Association for Computing Machinery, 2015, pp. 251–60, doi:<a href=\"https://doi.org/10.1145/2767386.2767430\">10.1145/2767386.2767430</a>.","apa":"Alistarh, D.-A., Sauerwald, T., &#38; Vojnović, M. (2015). Lock-Free algorithms under stochastic schedulers. In <i>Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing</i> (Vol. 2015–July, pp. 251–260). New York, NY, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/2767386.2767430\">https://doi.org/10.1145/2767386.2767430</a>","ista":"Alistarh D-A, Sauerwald T, Vojnović M. 2015. Lock-Free algorithms under stochastic schedulers. Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing vol. 2015–July, 251–260.","chicago":"Alistarh, Dan-Adrian, Thomas Sauerwald, and Milan Vojnović. “Lock-Free Algorithms under Stochastic Schedulers.” In <i>Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing</i>, 2015–July:251–60. Association for Computing Machinery, 2015. <a href=\"https://doi.org/10.1145/2767386.2767430\">https://doi.org/10.1145/2767386.2767430</a>.","ieee":"D.-A. Alistarh, T. Sauerwald, and M. Vojnović, “Lock-Free algorithms under stochastic schedulers,” in <i>Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing</i>, New York, NY, United States, 2015, vol. 2015–July, pp. 251–260.","ama":"Alistarh D-A, Sauerwald T, Vojnović M. Lock-Free algorithms under stochastic schedulers. In: <i>Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing</i>. Vol 2015-July. Association for Computing Machinery; 2015:251-260. doi:<a href=\"https://doi.org/10.1145/2767386.2767430\">10.1145/2767386.2767430</a>","short":"D.-A. Alistarh, T. Sauerwald, M. Vojnović, in:, Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2015, pp. 251–260."},"publisher":"Association for Computing Machinery","type":"conference","publication_status":"published"},{"doi":"10.1145/2767386.2767420","scopus_import":"1","abstract":[{"lang":"eng","text":"The problem of electing a leader from among n contenders is one of the fundamental questions in distributed computing. In its simplest formulation, the task is as follows: given n processors, all participants must eventually return a win or lose indication, such that a single contender may win. Despite a considerable amount of work on leader election, the following question is still open: can we elect a leader in an asynchronous fault-prone system faster than just running a Θ(log n)-time tournament, against a strong adaptive adversary? In this paper, we answer this question in the affirmative, improving on a decades-old upper bound. We introduce two new algorithmic ideas to reduce the time complexity of electing a leader to O(log∗ n), using O(n2) point-to-point messages. A non-trivial application of our algorithm is a new upper bound for the tight renaming problem, assigning n items to the n participants in expected O(log2 n) time and O(n2) messages. We complement our results with lower bound of Ω(n2) messages for solving these two problems, closing the question of their message complexity."}],"citation":{"mla":"Alistarh, Dan-Adrian, et al. “How to Elect a Leader Faster than a Tournament.” <i>Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2015, pp. 365–74, doi:<a href=\"https://doi.org/10.1145/2767386.2767420\">10.1145/2767386.2767420</a>.","apa":"Alistarh, D.-A., Gelashvili, R., &#38; Vladu, A. (2015). How to elect a leader faster than a tournament. In <i>Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing</i> (pp. 365–374). New York, NY, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/2767386.2767420\">https://doi.org/10.1145/2767386.2767420</a>","ama":"Alistarh D-A, Gelashvili R, Vladu A. How to elect a leader faster than a tournament. In: <i>Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2015:365-374. doi:<a href=\"https://doi.org/10.1145/2767386.2767420\">10.1145/2767386.2767420</a>","short":"D.-A. Alistarh, R. Gelashvili, A. Vladu, in:, Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2015, pp. 365–374.","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Adrian Vladu. “How to Elect a Leader Faster than a Tournament.” In <i>Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing</i>, 365–74. Association for Computing Machinery, 2015. <a href=\"https://doi.org/10.1145/2767386.2767420\">https://doi.org/10.1145/2767386.2767420</a>.","ista":"Alistarh D-A, Gelashvili R, Vladu A. 2015. How to elect a leader faster than a tournament. Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 365–374.","ieee":"D.-A. Alistarh, R. Gelashvili, and A. Vladu, “How to elect a leader faster than a tournament,” in <i>Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing</i>, New York, NY, United States, 2015, pp. 365–374."},"publisher":"Association for Computing Machinery","type":"conference","publication_status":"published","conference":{"end_date":"2015-07-23","name":"PODC: Principles of Distributed Computing","location":"New York, NY, United States","start_date":"2015-07-21"},"year":"2015","quality_controlled":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","page":"365 - 374","month":"07","publication_identifier":{"isbn":["9781450336178"]},"OA_type":"free access","arxiv":1,"date_published":"2015-07-21T00:00:00Z","external_id":{"arxiv":["1411.1001"]},"oa":1,"_id":"783","oa_version":"Accepted Version","date_created":"2018-12-11T11:48:28Z","publist_id":"6875","extern":"1","publication":"Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-05-19T13:27:49Z","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/2767386.2767420"}],"author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"},{"first_name":"Adrian","last_name":"Vladu","full_name":"Vladu, Adrian"}],"title":"How to elect a leader faster than a tournament","day":"21","OA_place":"publisher","acknowledgement":"Support is gratefully acknowledged from the National Science Foundation under grants CCF-1217921, CCF-1301926,\r\nand  IIS-1447786,  the  Department  of  Energy  under  grant\r\nER26116/DE-SC0008923,  and the  Oracle  and Intel  corporations.\r\nThe authors would like to thank Prof.  Nir Shavit for ad-\r\nvice and encouragement during this work,  and the anonymous reviewers for their very useful suggestions."},{"publist_id":"6872","extern":"1","_id":"784","publisher":"ACM","type":"conference","oa_version":"None","publication_status":"published","date_created":"2018-12-11T11:48:29Z","abstract":[{"text":"We demonstrate an optical switch design that can scale up to a thousand ports with high per-port bandwidth (25 Gbps+) and low switching latency (40 ns). Our design uses a broadcast and select architecture, based on a passive star coupler and fast tunable transceivers. In addition we employ time division multiplexing to achieve very low switching latency. Our demo shows the feasibility of the switch data plane using a small testbed, comprising two transmitters and a receiver, connected through a star coupler.","lang":"eng"}],"citation":{"apa":"Alistarh, D.-A., Ballani, H., Costa, P., Funnell, A., Benjamin, J., Watts, P., &#38; Thomsen, B. (2015). A high-radix, low-latency optical switch for data centers (pp. 367–368). Presented at the SIGCOMM: Special Interest Group on Data Communication, London, United Kindgdom: ACM. <a href=\"https://doi.org/10.1145/2785956.2790035\">https://doi.org/10.1145/2785956.2790035</a>","mla":"Alistarh, Dan-Adrian, et al. <i>A High-Radix, Low-Latency Optical Switch for Data Centers</i>. ACM, 2015, pp. 367–68, doi:<a href=\"https://doi.org/10.1145/2785956.2790035\">10.1145/2785956.2790035</a>.","short":"D.-A. Alistarh, H. Ballani, P. Costa, A. Funnell, J. Benjamin, P. Watts, B. Thomsen, in:, ACM, 2015, pp. 367–368.","ama":"Alistarh D-A, Ballani H, Costa P, et al. A high-radix, low-latency optical switch for data centers. In: ACM; 2015:367-368. doi:<a href=\"https://doi.org/10.1145/2785956.2790035\">10.1145/2785956.2790035</a>","ieee":"D.-A. Alistarh <i>et al.</i>, “A high-radix, low-latency optical switch for data centers,” presented at the SIGCOMM: Special Interest Group on Data Communication, London, United Kindgdom, 2015, pp. 367–368.","ista":"Alistarh D-A, Ballani H, Costa P, Funnell A, Benjamin J, Watts P, Thomsen B. 2015. A high-radix, low-latency optical switch for data centers. SIGCOMM: Special Interest Group on Data Communication, 367–368.","chicago":"Alistarh, Dan-Adrian, Hitesh Ballani, Paolo Costa, Adam Funnell, Joshua Benjamin, Philip Watts, and Benn Thomsen. “A High-Radix, Low-Latency Optical Switch for Data Centers,” 367–68. ACM, 2015. <a href=\"https://doi.org/10.1145/2785956.2790035\">https://doi.org/10.1145/2785956.2790035</a>."},"publication_identifier":{"isbn":["978-1-4503-3542-3"]},"doi":"10.1145/2785956.2790035","date_published":"2015-01-01T00:00:00Z","day":"01","page":"367 - 368","month":"01","title":"A high-radix, low-latency optical switch for data centers","author":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hitesh","last_name":"Ballani","full_name":"Ballani, Hitesh"},{"full_name":"Costa, Paolo","last_name":"Costa","first_name":"Paolo"},{"first_name":"Adam","last_name":"Funnell","full_name":"Funnell, Adam"},{"full_name":"Benjamin, Joshua","first_name":"Joshua","last_name":"Benjamin"},{"last_name":"Watts","first_name":"Philip","full_name":"Watts, Philip"},{"first_name":"Benn","last_name":"Thomsen","full_name":"Thomsen, Benn"}],"date_updated":"2023-02-23T13:18:57Z","language":[{"iso":"eng"}],"status":"public","year":"2015","conference":{"start_date":"2015-08-17","location":"London, United Kindgdom","name":"SIGCOMM: Special Interest Group on Data Communication","end_date":"2015-08-21"},"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"volume":25,"language":[{"iso":"eng"}],"year":"2015","quality_controlled":"1","issue":"12","page":"1423 - 1430","month":"12","isi":1,"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol-phospholipase C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis."}],"citation":{"mla":"Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” <i>Glycobiology</i>, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30, doi:<a href=\"https://doi.org/10.1093/glycob/cwv059\">10.1093/glycob/cwv059</a>.","apa":"Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., &#38; Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. <i>Glycobiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/glycob/cwv059\">https://doi.org/10.1093/glycob/cwv059</a>","ama":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. <i>Glycobiology</i>. 2015;25(12):1423-1430. doi:<a href=\"https://doi.org/10.1093/glycob/cwv059\">10.1093/glycob/cwv059</a>","short":"J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier, Glycobiology 25 (2015) 1423–1430.","ista":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. 25(12), 1423–1430.","chicago":"Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” <i>Glycobiology</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/glycob/cwv059\">https://doi.org/10.1093/glycob/cwv059</a>.","ieee":"J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier, “Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” <i>Glycobiology</i>, vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015."},"doi":"10.1093/glycob/cwv059","scopus_import":"1","intvolume":"        25","publisher":"Oxford University Press","type":"journal_article","publication_status":"published","date_updated":"2025-09-23T08:14:24Z","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"CaHe"}],"day":"01","author":[{"first_name":"Jakob","last_name":"Engel","full_name":"Engel, Jakob"},{"id":"309D50DA-F248-11E8-B48F-1D18A9856A87","last_name":"Schmalhorst","first_name":"Philipp S","orcid":"0000-0002-5795-0133","full_name":"Schmalhorst, Philipp S"},{"full_name":"Kruger, Anke","first_name":"Anke","last_name":"Kruger"},{"first_name":"Christina","last_name":"Muller","full_name":"Muller, Christina"},{"full_name":"Buettner, Falk","first_name":"Falk","last_name":"Buettner"},{"first_name":"Françoise","last_name":"Routier","full_name":"Routier, Françoise"}],"title":"Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis","external_id":{"pmid":["26306635"],"isi":["000368443700010"]},"date_published":"2015-12-01T00:00:00Z","publist_id":"6851","publication":"Glycobiology","pmid":1,"_id":"802","oa_version":"None","date_created":"2018-12-11T11:48:35Z"},{"intvolume":"       517","publication_status":"published","type":"journal_article","publisher":"Springer Nature","citation":{"ieee":"F. K. Schur <i>et al.</i>, “Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution,” <i>Nature</i>, vol. 517, no. 7535. Springer Nature, pp. 505–508, 2015.","ista":"Schur FK, Hagen W, Rumlová M, Ruml T, Müller B, Kraüsslich H, Briggs J. 2015. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. Nature. 517(7535), 505–508.","chicago":"Schur, Florian KM, Wim Hagen, Michaela Rumlová, Tomáš Ruml, B Müller, Hans Kraüsslich, and John Briggs. “Structure of the Immature HIV-1 Capsid in Intact Virus Particles at 8.8 Å Resolution.” <i>Nature</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nature13838\">https://doi.org/10.1038/nature13838</a>.","ama":"Schur FK, Hagen W, Rumlová M, et al. Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. <i>Nature</i>. 2015;517(7535):505-508. doi:<a href=\"https://doi.org/10.1038/nature13838\">10.1038/nature13838</a>","short":"F.K. Schur, W. Hagen, M. Rumlová, T. Ruml, B. Müller, H. Kraüsslich, J. Briggs, Nature 517 (2015) 505–508.","mla":"Schur, Florian KM, et al. “Structure of the Immature HIV-1 Capsid in Intact Virus Particles at 8.8 Å Resolution.” <i>Nature</i>, vol. 517, no. 7535, Springer Nature, 2015, pp. 505–08, doi:<a href=\"https://doi.org/10.1038/nature13838\">10.1038/nature13838</a>.","apa":"Schur, F. K., Hagen, W., Rumlová, M., Ruml, T., Müller, B., Kraüsslich, H., &#38; Briggs, J. (2015). Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature13838\">https://doi.org/10.1038/nature13838</a>"},"abstract":[{"lang":"eng","text":"Human immunodeficiency virus type 1 (HIV-1) assembly proceeds in two stages. First, the 55 kilodalton viral Gag polyprotein assembles into a hexameric protein lattice at the plasma membrane of the infected cell, inducing budding and release of an immature particle. Second, Gag is cleaved by the viral protease, leading to internal rearrangement of the virus into the mature, infectious form. Immature and mature HIV-1 particles are heterogeneous in size and morphology, preventing high-resolution analysis of their protein arrangement in situ by conventional structural biology methods. Here we apply cryo-electron tomography and sub-tomogram averaging methods to resolve the structure of the capsid lattice within intact immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning of all α-helices. The resulting model reveals tertiary and quaternary structural interactions that mediate HIV-1 assembly. Strikingly, these interactions differ from those predicted by the current model based on in vitro-assembled arrays of Gag-derived proteins from Mason-Pfizer monkey virus. To validate this difference, we solve the structure of the capsid lattice within intact immature Mason-Pfizer monkey virus particles. Comparison with the immature HIV-1 structure reveals that retroviral capsid proteins, while having conserved tertiary structures, adopt different quaternary arrangements during virus assembly. The approach demonstrated here should be applicable to determine structures of other proteins at subnanometre resolution within heterogeneous environments."}],"scopus_import":"1","doi":"10.1038/nature13838","month":"01","issue":"7535","page":"505 - 508","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":517,"quality_controlled":"1","year":"2015","extern":"1","publication":"Nature","publist_id":"6836","date_created":"2018-12-11T11:48:39Z","oa_version":"None","_id":"814","pmid":1,"external_id":{"pmid":["25363765"]},"date_published":"2015-01-22T00:00:00Z","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"OA_type":"closed access","acknowledgement":"This study was supported by Deutsche Forschungsgemeinschaft grants BR 3635/2-1 to J.A.G.B., KR 906/7-1 to H.-G.K. and by Grant Agency of the Czech Republic 14-15326S to M.R. The Briggs laboratory acknowledges financial support from the European Molecular Biology Laboratory and from the Chica und Heinz Schaller Stiftung. We thank B. Glass, M. Anders and S. Mattei for preparation of samples, and R. Hadravova, K. H. Bui, F. Thommen, M. Schorb, S. Dodonova, S. Glatt, P. Ulbrich and T. Bharat for technical support and/or discussion. This study was technically supported by the European Molecular Biology Laboratory IT services unit.","article_type":"letter_note","day":"22","title":"Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian","orcid":"0000-0003-4790-8078","first_name":"Florian","last_name":"Schur"},{"first_name":"Wim","last_name":"Hagen","full_name":"Hagen, Wim"},{"full_name":"Rumlová, Michaela","last_name":"Rumlová","first_name":"Michaela"},{"last_name":"Ruml","first_name":"Tomáš","full_name":"Ruml, Tomáš"},{"first_name":"B","last_name":"Müller","full_name":"Müller, B"},{"first_name":"Hans","last_name":"Kraüsslich","full_name":"Kraüsslich, Hans"},{"full_name":"Briggs, John","first_name":"John","last_name":"Briggs"}],"status":"public","date_updated":"2026-05-19T08:19:41Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"day":"22","article_type":"original","OA_place":"publisher","title":"The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1128/jvi.01502-15"}],"author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian","orcid":"0000-0003-4790-8078","first_name":"Florian","last_name":"Schur"},{"full_name":"Dick, Robert","last_name":"Dick","first_name":"Robert"},{"first_name":"Wim","last_name":"Hagen","full_name":"Hagen, Wim"},{"full_name":"Vogt, Volker","first_name":"Volker","last_name":"Vogt"},{"first_name":"John","last_name":"Briggs","full_name":"Briggs, John"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-05-18T12:47:51Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publist_id":"6837","extern":"1","publication":"Journal of Virology","pmid":1,"_id":"815","oa_version":"Published Version","date_created":"2018-12-11T11:48:39Z","external_id":{"pmid":["26223638"]},"oa":1,"OA_type":"gold","publication_identifier":{"eissn":["1098-5514"],"issn":["0022-538X"]},"date_published":"2015-09-22T00:00:00Z","DOAJ_listed":"1","issue":"20","page":"10294 - 10302","month":"09","article_processing_charge":"No","volume":89,"language":[{"iso":"eng"}],"year":"2015","quality_controlled":"1","intvolume":"        89","type":"journal_article","publisher":"ASM","publication_status":"published","abstract":[{"text":"The polyprotein Gag is the primary structural component of retroviruses. Gag consists of independently folded domains connected by flexible linkers. Interactions between the conserved capsid (CA) domains of Gag mediate formation of hexameric protein lattices that drive assembly of immature virus particles. Proteolytic cleavage of Gag by the viral protease (PR) is required for maturation of retroviruses from an immature form into an infectious form. Within the assembled Gag lattices of HIV-1 and Mason- Pfizer monkey virus (M-PMV), the C-terminal domain of CA adopts similar quaternary arrangements, while the N-terminal domain of CA is packed in very different manners. Here, we have used cryo-electron tomography and subtomogram averaging to study in vitro-assembled, immature virus-like Rous sarcoma virus (RSV) Gag particles and have determined the structure of CA and the surrounding regions to a resolution of ~8 Å. We found that the C-terminal domain of RSV CA is arranged similarly to HIV-1 and M-PMV, whereas the N-terminal domain of CA adopts a novel arrangement in which the upstream p10 domain folds back into the CA lattice. In this position the cleavage site between CA and p10 appears to be inaccessible to PR. Below CA, an extended density is consistent with the presence of a six-helix bundle formed by the spacer-peptide region. We have also assessed the affect of lattice assembly on proteolytic processing by exogenous PR. The cleavage between p10 and CA is indeed inhibited in the assembled lattice, a finding consistent with structural regulation of proteolytic maturation.\r\n","lang":"eng"}],"citation":{"apa":"Schur, F. K., Dick, R., Hagen, W., Vogt, V., &#38; Briggs, J. (2015). The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. <i>Journal of Virology</i>. ASM. <a href=\"https://doi.org/10.1128/JVI.01502-15\">https://doi.org/10.1128/JVI.01502-15</a>","mla":"Schur, Florian KM, et al. “The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.” <i>Journal of Virology</i>, vol. 89, no. 20, ASM, 2015, pp. 10294–302, doi:<a href=\"https://doi.org/10.1128/JVI.01502-15\">10.1128/JVI.01502-15</a>.","ama":"Schur FK, Dick R, Hagen W, Vogt V, Briggs J. The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. <i>Journal of Virology</i>. 2015;89(20):10294-10302. doi:<a href=\"https://doi.org/10.1128/JVI.01502-15\">10.1128/JVI.01502-15</a>","short":"F.K. Schur, R. Dick, W. Hagen, V. Vogt, J. Briggs, Journal of Virology 89 (2015) 10294–10302.","ista":"Schur FK, Dick R, Hagen W, Vogt V, Briggs J. 2015. The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly. Journal of Virology. 89(20), 10294–10302.","chicago":"Schur, Florian KM, Robert Dick, Wim Hagen, Volker Vogt, and John Briggs. “The Structure of Immature Virus like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the P10 Domain in Assembly.” <i>Journal of Virology</i>. ASM, 2015. <a href=\"https://doi.org/10.1128/JVI.01502-15\">https://doi.org/10.1128/JVI.01502-15</a>.","ieee":"F. K. Schur, R. Dick, W. Hagen, V. Vogt, and J. Briggs, “The structure of immature virus like Rous sarcoma virus gag particles reveals a structural role for the p10 domain in assembly,” <i>Journal of Virology</i>, vol. 89, no. 20. ASM, pp. 10294–10302, 2015."},"doi":"10.1128/JVI.01502-15","scopus_import":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","status":"public","language":[{"iso":"eng"}],"date_updated":"2026-04-08T07:25:54Z","article_processing_charge":"No","author":[{"full_name":"Avvakumov, Sergey","orcid":"0000-0002-7840-5062","first_name":"Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac","last_name":"Mabillard","full_name":"Mabillard, Isaac"},{"full_name":"Skopenkov, A.","first_name":"A.","last_name":"Skopenkov"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"title":"Eliminating higher-multiplicity intersections, III. Codimension 2","month":"11","acknowledgement":"We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful discussions.","department":[{"_id":"UlWa"}],"day":"15","date_published":"2015-11-15T00:00:00Z","arxiv":1,"doi":"10.48550/arXiv.1511.03501","related_material":{"record":[{"relation":"later_version","id":"9308","status":"public"},{"status":"public","id":"10220","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"8156"}]},"oa":1,"external_id":{"arxiv":["1511.03501"]},"citation":{"mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” <i>ArXiv</i>, 1511.03501, doi:<a href=\"https://doi.org/10.48550/arXiv.1511.03501\">10.48550/arXiv.1511.03501</a>.","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A., &#38; Wagner, U. (n.d.). Eliminating higher-multiplicity intersections, III. Codimension 2. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1511.03501\">https://doi.org/10.48550/arXiv.1511.03501</a>","chicago":"Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1511.03501\">https://doi.org/10.48550/arXiv.1511.03501</a>.","ista":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv, 1511.03501.","ieee":"S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections, III. Codimension 2,” <i>arXiv</i>. .","ama":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1511.03501\">10.48550/arXiv.1511.03501</a>","short":"S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.)."},"abstract":[{"text":"We study conditions under which a finite simplicial complex $K$ can be mapped to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint simplices of $K$ do not have a common point. We show that if $r$ is not a prime power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex in $\\mathbb R^d$. This improves on previous constructions of counterexamples (for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P. Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors. The counterexamples are obtained by proving the following algebraic criterion in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero. This result can be restated in terms of cohomological obstructions or equivariant maps, and extends an analogous codimension 3 criterion by the second and fourth authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample.","lang":"eng"}],"date_created":"2020-07-30T10:45:19Z","article_number":"1511.03501","oa_version":"Preprint","publication_status":"draft","_id":"8183","type":"preprint","corr_author":"1","publication":"arXiv"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","year":"2015","language":[{"iso":"eng"}],"status":"public","date_updated":"2021-01-12T08:17:42Z","volume":135,"article_processing_charge":"No","author":[{"last_name":"Einhorn","first_name":"Lukas","full_name":"Einhorn, Lukas"},{"last_name":"Fazekas","first_name":"Judit","full_name":"Fazekas, Judit","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Muhr","first_name":"Martina","full_name":"Muhr, Martina"},{"last_name":"Schoos","first_name":"Alexandra","full_name":"Schoos, Alexandra"},{"last_name":"Oida","first_name":"Kumiko","full_name":"Oida, Kumiko"},{"full_name":"Singer, Josef","last_name":"Singer","first_name":"Josef"},{"last_name":"Panakova","first_name":"Lucia","full_name":"Panakova, Lucia"},{"full_name":"Manzano-Szalai, Krisztina","first_name":"Krisztina","last_name":"Manzano-Szalai"},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"}],"title":"Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients","month":"02","article_type":"original","issue":"2","day":"01","date_published":"2015-02-01T00:00:00Z","doi":"10.1016/j.jaci.2014.12.1263","publication_identifier":{"issn":["0091-6749"]},"citation":{"apa":"Einhorn, L., Singer, J., Muhr, M., Schoos, A., Oida, K., Singer, J., … Jensen-Jarolim, E. (2015). Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. <i>Journal of Allergy and Clinical Immunology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jaci.2014.12.1263\">https://doi.org/10.1016/j.jaci.2014.12.1263</a>","mla":"Einhorn, Lukas, et al. “Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved Allergy Diagnosis in Veterinary Patients.” <i>Journal of Allergy and Clinical Immunology</i>, vol. 135, no. 2, AB101, Elsevier, 2015, doi:<a href=\"https://doi.org/10.1016/j.jaci.2014.12.1263\">10.1016/j.jaci.2014.12.1263</a>.","ama":"Einhorn L, Singer J, Muhr M, et al. Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. <i>Journal of Allergy and Clinical Immunology</i>. 2015;135(2). doi:<a href=\"https://doi.org/10.1016/j.jaci.2014.12.1263\">10.1016/j.jaci.2014.12.1263</a>","short":"L. Einhorn, J. Singer, M. Muhr, A. Schoos, K. Oida, J. Singer, L. Panakova, K. Manzano-Szalai, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 135 (2015).","ieee":"L. Einhorn <i>et al.</i>, “Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients,” <i>Journal of Allergy and Clinical Immunology</i>, vol. 135, no. 2. Elsevier, 2015.","ista":"Einhorn L, Singer J, Muhr M, Schoos A, Oida K, Singer J, Panakova L, Manzano-Szalai K, Jensen-Jarolim E. 2015. Generation of recombinant FcεRIα of dog, cat and horse for component-resolved allergy diagnosis in veterinary patients. Journal of Allergy and Clinical Immunology. 135(2), AB101.","chicago":"Einhorn, Lukas, Judit Singer, Martina Muhr, Alexandra Schoos, Kumiko Oida, Josef Singer, Lucia Panakova, Krisztina Manzano-Szalai, and Erika Jensen-Jarolim. “Generation of Recombinant FcεRIα of Dog, Cat and Horse for Component-Resolved Allergy Diagnosis in Veterinary Patients.” <i>Journal of Allergy and Clinical Immunology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jaci.2014.12.1263\">https://doi.org/10.1016/j.jaci.2014.12.1263</a>."},"date_created":"2020-08-10T11:54:09Z","article_number":"AB101","oa_version":"None","publication_status":"published","publisher":"Elsevier","_id":"8242","type":"journal_article","publication":"Journal of Allergy and Clinical Immunology","extern":"1","intvolume":"       135"},{"date_published":"2015-04-20T00:00:00Z","DOAJ_listed":"1","publication_identifier":{"eissn":["2331-8325"]},"OA_type":"gold","external_id":{"pmid":["27331080"]},"oa":1,"oa_version":"Published Version","date_created":"2018-12-11T11:48:44Z","pmid":1,"_id":"832","extern":"1","publication":"Bio-protocol","publist_id":"6816","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-05-19T09:39:29Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.21769/BioProtoc.1446"}],"author":[{"first_name":"Peter","last_name":"Marhavy","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"title":"Real time analysis of lateral root organogenesis in arabidopsis","article_type":"original","OA_place":"publisher","acknowledgement":"European Research Council with a Starting Independent Research grant: ERC-2007-Stg-207362-HCPO, Czech Science Foundation: GA13-39982S\r\nWe thank Matyas Fendrych for critical reading and comments. The protocol was developed based on previously published work of De Rybel et al. (2010) and Laskowski et al. (2008). ","day":"20","doi":"10.21769/BioProtoc.1446","citation":{"ieee":"P. Marhavý and E. Benková, “Real time analysis of lateral root organogenesis in arabidopsis,” <i>Bio-protocol</i>, vol. 5, no. 8. Bio-protocol LLC, 2015.","ista":"Marhavý P, Benková E. 2015. Real time analysis of lateral root organogenesis in arabidopsis. Bio-protocol. 5(8).","chicago":"Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis in Arabidopsis.” <i>Bio-Protocol</i>. Bio-protocol LLC, 2015. <a href=\"https://doi.org/10.21769/BioProtoc.1446\">https://doi.org/10.21769/BioProtoc.1446</a>.","ama":"Marhavý P, Benková E. Real time analysis of lateral root organogenesis in arabidopsis. <i>Bio-protocol</i>. 2015;5(8). doi:<a href=\"https://doi.org/10.21769/BioProtoc.1446\">10.21769/BioProtoc.1446</a>","short":"P. Marhavý, E. Benková, Bio-Protocol 5 (2015).","mla":"Marhavý, Peter, and Eva Benková. “Real Time Analysis of Lateral Root Organogenesis in Arabidopsis.” <i>Bio-Protocol</i>, vol. 5, no. 8, Bio-protocol LLC, 2015, doi:<a href=\"https://doi.org/10.21769/BioProtoc.1446\">10.21769/BioProtoc.1446</a>.","apa":"Marhavý, P., &#38; Benková, E. (2015). Real time analysis of lateral root organogenesis in arabidopsis. <i>Bio-Protocol</i>. Bio-protocol LLC. <a href=\"https://doi.org/10.21769/BioProtoc.1446\">https://doi.org/10.21769/BioProtoc.1446</a>"},"abstract":[{"lang":"eng","text":"Plants maintain capacity to form new organs such as leaves, flowers, lateral shoots and roots throughout their postembryonic lifetime. Lateral roots (LRs) originate from a few pericycle cells that acquire attributes of founder cells (FCs), undergo series of anticlinal divisions, and give rise to a few short initial cells. After initiation, coordinated cell division and differentiation occur, giving rise to lateral root primordia (LRP). Primordia continue to grow, emerge through the cortex and epidermal layers of the primary root, and finally a new apical meristem is established taking over the responsibility for growth of mature lateral roots [for detailed description of the individual stages of lateral root organogenesis see Malamy and Benfey (1997)]. To examine this highly dynamic developmental process and to investigate a role of various hormonal, genetic and environmental factors in the regulation of lateral root organogenesis, the real time imaging based analyses represent extremely powerful tools (Laskowski et al., 2008; De Smet et al., 2012; Marhavy et al., 2013 and 2014). Herein, we describe a protocol for real time lateral root primordia (LRP) analysis, which enables the monitoring of an onset of the specific gene expression and subcellular protein localization during primordia organogenesis, as well as the evaluation of the impact of genetic and environmental perturbations on LRP organogenesis."}],"publication_status":"published","publisher":"Bio-protocol LLC","type":"journal_article","intvolume":"         5","quality_controlled":"1","year":"2015","language":[{"iso":"eng"}],"volume":5,"article_processing_charge":"No","month":"04","issue":"8"},{"day":"05","article_type":"original","OA_place":"publisher","title":"Observing the overall rocking motion of a protein in a crystal","author":[{"first_name":"Peixiang","last_name":"Ma","full_name":"Ma, Peixiang"},{"full_name":"Xue, Yi","last_name":"Xue","first_name":"Yi"},{"last_name":"Coquelle","first_name":"Nicolas","full_name":"Coquelle, Nicolas"},{"full_name":"Haller, Jens D.","first_name":"Jens D.","last_name":"Haller"},{"first_name":"Tairan","last_name":"Yuwen","full_name":"Yuwen, Tairan"},{"last_name":"Ayala","first_name":"Isabel","full_name":"Ayala, Isabel"},{"full_name":"Mikhailovskii, Oleg","last_name":"Mikhailovskii","first_name":"Oleg"},{"last_name":"Willbold","first_name":"Dieter","full_name":"Willbold, Dieter"},{"first_name":"Jacques-Philippe","last_name":"Colletier","full_name":"Colletier, Jacques-Philippe"},{"full_name":"Skrynnikov, Nikolai R.","first_name":"Nikolai R.","last_name":"Skrynnikov"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"main_file_link":[{"url":"https://doi.org/10.1038/ncomms9361","open_access":"1"}],"date_updated":"2025-01-22T14:39:22Z","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","publication":"Nature Communications","_id":"8456","oa_version":"Published Version","article_number":"8361","date_created":"2020-09-18T10:07:36Z","oa":1,"OA_type":"gold","publication_identifier":{"issn":["2041-1723"]},"date_published":"2015-10-05T00:00:00Z","month":"10","article_processing_charge":"Yes","volume":6,"language":[{"iso":"eng"}],"year":"2015","quality_controlled":"1","intvolume":"         6","publisher":"Springer Nature","type":"journal_article","publication_status":"published","abstract":[{"lang":"eng","text":"The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments."}],"citation":{"apa":"Ma, P., Xue, Y., Coquelle, N., Haller, J. D., Yuwen, T., Ayala, I., … Schanda, P. (2015). Observing the overall rocking motion of a protein in a crystal. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ncomms9361\">https://doi.org/10.1038/ncomms9361</a>","mla":"Ma, Peixiang, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” <i>Nature Communications</i>, vol. 6, 8361, Springer Nature, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms9361\">10.1038/ncomms9361</a>.","ieee":"P. Ma <i>et al.</i>, “Observing the overall rocking motion of a protein in a crystal,” <i>Nature Communications</i>, vol. 6. Springer Nature, 2015.","ista":"Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier J-P, Skrynnikov NR, Schanda P. 2015. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 6, 8361.","chicago":"Ma, Peixiang, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel Ayala, Oleg Mikhailovskii, et al. “Observing the Overall Rocking Motion of a Protein in a Crystal.” <i>Nature Communications</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/ncomms9361\">https://doi.org/10.1038/ncomms9361</a>.","ama":"Ma P, Xue Y, Coquelle N, et al. Observing the overall rocking motion of a protein in a crystal. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms9361\">10.1038/ncomms9361</a>","short":"P. Ma, Y. Xue, N. Coquelle, J.D. Haller, T. Yuwen, I. Ayala, O. Mikhailovskii, D. Willbold, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications 6 (2015)."},"doi":"10.1038/ncomms9361","scopus_import":"1"},{"language":[{"iso":"eng"}],"status":"public","volume":4,"date_updated":"2021-01-12T08:19:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","year":"2015","article_type":"original","month":"09","issue":"3","day":"10","page":"699-708","article_processing_charge":"No","author":[{"first_name":"Peixiang","last_name":"Ma","full_name":"Ma, Peixiang"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"}],"title":"Conformational exchange processes in biological systems: Detection by solid-state NMR","citation":{"ieee":"P. Ma and P. Schanda, “Conformational exchange processes in biological systems: Detection by solid-state NMR,” <i>eMagRes</i>, vol. 4, no. 3. Wiley, pp. 699–708, 2015.","ista":"Ma P, Schanda P. 2015. Conformational exchange processes in biological systems: Detection by solid-state NMR. eMagRes. 4(3), 699–708.","chicago":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” <i>EMagRes</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/9780470034590.emrstm1418\">https://doi.org/10.1002/9780470034590.emrstm1418</a>.","short":"P. Ma, P. Schanda, EMagRes 4 (2015) 699–708.","ama":"Ma P, Schanda P. Conformational exchange processes in biological systems: Detection by solid-state NMR. <i>eMagRes</i>. 2015;4(3):699-708. doi:<a href=\"https://doi.org/10.1002/9780470034590.emrstm1418\">10.1002/9780470034590.emrstm1418</a>","apa":"Ma, P., &#38; Schanda, P. (2015). Conformational exchange processes in biological systems: Detection by solid-state NMR. <i>EMagRes</i>. Wiley. <a href=\"https://doi.org/10.1002/9780470034590.emrstm1418\">https://doi.org/10.1002/9780470034590.emrstm1418</a>","mla":"Ma, Peixiang, and Paul Schanda. “Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR.” <i>EMagRes</i>, vol. 4, no. 3, Wiley, 2015, pp. 699–708, doi:<a href=\"https://doi.org/10.1002/9780470034590.emrstm1418\">10.1002/9780470034590.emrstm1418</a>."},"abstract":[{"text":"We review recent advances in methodologies to study microseconds‐to‐milliseconds exchange processes in biological molecules using magic‐angle spinning solid‐state nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS ssNMR, as compared to solution‐state NMR, are elucidated using numerical simulations and experimental data. These simulations reveal the potential of MAS NMR to provide detailed insight into short‐lived conformations of biological molecules. Recent studies of conformational exchange dynamics in microcrystalline ubiquitin are discussed.","lang":"eng"}],"date_published":"2015-09-10T00:00:00Z","publication_identifier":{"isbn":["9780470034590","9780470058213"]},"doi":"10.1002/9780470034590.emrstm1418","publication":"eMagRes","extern":"1","intvolume":"         4","publication_status":"published","oa_version":"None","date_created":"2020-09-18T10:07:45Z","publisher":"Wiley","_id":"8457","type":"journal_article"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","year":"2015","language":[{"iso":"eng"}],"status":"public","volume":32,"date_updated":"2025-09-22T14:32:37Z","article_processing_charge":"No","isi":1,"title":"A model of substitution trajectories in sequence space and long-term protein evolution","author":[{"full_name":"Usmanova, Dinara","last_name":"Usmanova","first_name":"Dinara"},{"full_name":"Ferretti, Luca","last_name":"Ferretti","first_name":"Luca"},{"last_name":"Povolotskaya","first_name":"Inna","full_name":"Povolotskaya, Inna"},{"full_name":"Vlasov, Peter","last_name":"Vlasov","first_name":"Peter"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"}],"month":"02","page":"542 - 554","issue":"2","day":"01","date_published":"2015-02-01T00:00:00Z","doi":"10.1093/molbev/msu318","citation":{"apa":"Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., &#38; Kondrashov, F. (2015). A model of substitution trajectories in sequence space and long-term protein evolution. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msu318\">https://doi.org/10.1093/molbev/msu318</a>","mla":"Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” <i>Molecular Biology and Evolution</i>, vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:<a href=\"https://doi.org/10.1093/molbev/msu318\">10.1093/molbev/msu318</a>.","ista":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model of substitution trajectories in sequence space and long-term protein evolution. Molecular Biology and Evolution. 32(2), 542–554.","ieee":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A model of substitution trajectories in sequence space and long-term protein evolution,” <i>Molecular Biology and Evolution</i>, vol. 32, no. 2. Oxford University Press, pp. 542–554, 2015.","chicago":"Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/molbev/msu318\">https://doi.org/10.1093/molbev/msu318</a>.","ama":"Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of substitution trajectories in sequence space and long-term protein evolution. <i>Molecular Biology and Evolution</i>. 2015;32(2):542-554. doi:<a href=\"https://doi.org/10.1093/molbev/msu318\">10.1093/molbev/msu318</a>","short":"D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular Biology and Evolution 32 (2015) 542–554."},"external_id":{"isi":["000350050700020"]},"abstract":[{"text":"The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.","lang":"eng"}],"publication_status":"published","oa_version":"None","date_created":"2018-12-11T11:48:49Z","type":"journal_article","_id":"848","publisher":"Oxford University Press","extern":"1","publication":"Molecular Biology and Evolution","publist_id":"6804","intvolume":"        32"},{"oa_version":"None","publication_status":"published","date_created":"2020-09-18T10:46:14Z","_id":"8495","type":"journal_article","publisher":"American Mathematical Society","publication":"Proceedings of the American Mathematical Society","extern":"1","intvolume":"       144","date_published":"2015-12-21T00:00:00Z","publication_identifier":{"issn":["0002-9939","1088-6826"]},"doi":"10.1090/proc/12796","citation":{"ama":"Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems close to integrable. <i>Proceedings of the American Mathematical Society</i>. 2015;144(4):1553-1560. doi:<a href=\"https://doi.org/10.1090/proc/12796\">10.1090/proc/12796</a>","short":"A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society 144 (2015) 1553–1560.","ieee":"A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian systems close to integrable,” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015.","chicago":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2015. <a href=\"https://doi.org/10.1090/proc/12796\">https://doi.org/10.1090/proc/12796</a>.","ista":"Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 144(4), 1553–1560.","mla":"Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:<a href=\"https://doi.org/10.1090/proc/12796\">10.1090/proc/12796</a>.","apa":"Bounemoura, A., &#38; Kaloshin, V. (2015). A note on micro-instability for Hamiltonian systems close to integrable. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/12796\">https://doi.org/10.1090/proc/12796</a>"},"abstract":[{"text":"In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \\sqrt {\\varepsilon }$, after a time of order $ \\sqrt {\\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting.","lang":"eng"}],"article_processing_charge":"No","title":"A note on micro-instability for Hamiltonian systems close to integrable","author":[{"first_name":"Abed","last_name":"Bounemoura","full_name":"Bounemoura, Abed"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","first_name":"Vadim","last_name":"Kaloshin"}],"article_type":"letter_note","month":"12","page":"1553-1560","day":"21","issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","year":"2015","status":"public","language":[{"iso":"eng"}],"volume":144,"date_updated":"2021-01-12T08:19:40Z"},{"title":"Arnold diffusion for smooth convex systems of two and a half degrees of freedom","author":[{"last_name":"Kaloshin","first_name":"Vadim","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"last_name":"Zhang","first_name":"K","full_name":"Zhang, K"}],"article_processing_charge":"No","day":"30","issue":"8","page":"2699-2720","month":"06","article_type":"original","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"],"date_updated":"2021-01-12T08:19:41Z","volume":28,"status":"public","language":[{"iso":"eng"}],"_id":"8498","publisher":"IOP Publishing","type":"journal_article","date_created":"2020-09-18T10:46:43Z","publication_status":"published","oa_version":"None","intvolume":"        28","extern":"1","publication":"Nonlinearity","doi":"10.1088/0951-7715/28/8/2699","publication_identifier":{"issn":["0951-7715","1361-6544"]},"date_published":"2015-06-30T00:00:00Z","abstract":[{"text":"In the present note we announce a proof of a strong form of Arnold diffusion for smooth convex Hamiltonian systems. Let ${\\mathbb T}^2$  be a 2-dimensional torus and B2 be the unit ball around the origin in ${\\mathbb R}^2$ . Fix ρ > 0. Our main result says that for a 'generic' time-periodic perturbation of an integrable system of two degrees of freedom $H_0(p)+\\varepsilon H_1(\\theta,p,t),\\quad \\ \\theta\\in {\\mathbb T}^2,\\ p\\in B^2,\\ t\\in {\\mathbb T}={\\mathbb R}/{\\mathbb Z}$ , with a strictly convex H0, there exists a ρ-dense orbit (θε, pε, t)(t) in ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ , namely, a ρ-neighborhood of the orbit contains ${\\mathbb T}^2 \\times B^2 \\times {\\mathbb T}$ .\r\n\r\nOur proof is a combination of geometric and variational methods. The fundamental elements of the construction are the usage of crumpled normally hyperbolic invariant cylinders from [9], flower and simple normally hyperbolic invariant manifolds from [36] as well as their kissing property at a strong double resonance. This allows us to build a 'connected' net of three-dimensional normally hyperbolic invariant manifolds. To construct diffusing orbits along this net we employ a version of the Mather variational method [41] equipped with weak KAM theory [28], proposed by Bernard in [7].","lang":"eng"}],"citation":{"mla":"Kaloshin, Vadim, and K. Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” <i>Nonlinearity</i>, vol. 28, no. 8, IOP Publishing, 2015, pp. 2699–720, doi:<a href=\"https://doi.org/10.1088/0951-7715/28/8/2699\">10.1088/0951-7715/28/8/2699</a>.","apa":"Kaloshin, V., &#38; Zhang, K. (2015). Arnold diffusion for smooth convex systems of two and a half degrees of freedom. <i>Nonlinearity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/0951-7715/28/8/2699\">https://doi.org/10.1088/0951-7715/28/8/2699</a>","ama":"Kaloshin V, Zhang K. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. <i>Nonlinearity</i>. 2015;28(8):2699-2720. doi:<a href=\"https://doi.org/10.1088/0951-7715/28/8/2699\">10.1088/0951-7715/28/8/2699</a>","short":"V. Kaloshin, K. Zhang, Nonlinearity 28 (2015) 2699–2720.","ista":"Kaloshin V, Zhang K. 2015. Arnold diffusion for smooth convex systems of two and a half degrees of freedom. Nonlinearity. 28(8), 2699–2720.","chicago":"Kaloshin, Vadim, and K Zhang. “Arnold Diffusion for Smooth Convex Systems of Two and a Half Degrees of Freedom.” <i>Nonlinearity</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/0951-7715/28/8/2699\">https://doi.org/10.1088/0951-7715/28/8/2699</a>.","ieee":"V. Kaloshin and K. Zhang, “Arnold diffusion for smooth convex systems of two and a half degrees of freedom,” <i>Nonlinearity</i>, vol. 28, no. 8. IOP Publishing, pp. 2699–2720, 2015."}},{"date_published":"2015-02-05T00:00:00Z","doi":"10.4171/jems/499","publication_identifier":{"issn":["1435-9855"]},"citation":{"apa":"Guardia, M., &#38; Kaloshin, V. (2015). Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. <i>Journal of the European Mathematical Society</i>. European Mathematical Society Publishing House. <a href=\"https://doi.org/10.4171/jems/499\">https://doi.org/10.4171/jems/499</a>","mla":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” <i>Journal of the European Mathematical Society</i>, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 71–149, doi:<a href=\"https://doi.org/10.4171/jems/499\">10.4171/jems/499</a>.","chicago":"Guardia, Marcel, and Vadim Kaloshin. “Growth of Sobolev Norms in the Cubic Defocusing Nonlinear Schrödinger Equation.” <i>Journal of the European Mathematical Society</i>. European Mathematical Society Publishing House, 2015. <a href=\"https://doi.org/10.4171/jems/499\">https://doi.org/10.4171/jems/499</a>.","ista":"Guardia M, Kaloshin V. 2015. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. Journal of the European Mathematical Society. 17(1), 71–149.","ieee":"M. Guardia and V. Kaloshin, “Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation,” <i>Journal of the European Mathematical Society</i>, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 71–149, 2015.","ama":"Guardia M, Kaloshin V. Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation. <i>Journal of the European Mathematical Society</i>. 2015;17(1):71-149. doi:<a href=\"https://doi.org/10.4171/jems/499\">10.4171/jems/499</a>","short":"M. Guardia, V. Kaloshin, Journal of the European Mathematical Society 17 (2015) 71–149."},"abstract":[{"lang":"eng","text":"We consider the cubic defocusing nonlinear Schrödinger equation in the two dimensional torus. Fix s>1. Recently Colliander, Keel, Staffilani, Tao and Takaoka proved the existence of solutions with s-Sobolev norm growing in time.\r\n\r\nWe establish the existence of solutions with polynomial time estimates. More exactly, there is c>0 such that for any K≫1 we find a solution u and a time T such that ∥u(T)∥Hs≥K∥u(0)∥Hs. Moreover, the time T satisfies the polynomial bound 0<T<Kc."}],"date_created":"2020-09-18T10:46:50Z","oa_version":"None","publication_status":"published","_id":"8499","type":"journal_article","publisher":"European Mathematical Society Publishing House","publication":"Journal of the European Mathematical Society","extern":"1","intvolume":"        17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","year":"2015","status":"public","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:19:41Z","volume":17,"article_processing_charge":"No","title":"Growth of Sobolev norms in the cubic defocusing nonlinear Schrödinger equation","author":[{"first_name":"Marcel","last_name":"Guardia","full_name":"Guardia, Marcel"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","first_name":"Vadim","last_name":"Kaloshin"}],"month":"02","article_type":"original","day":"05","page":"71-149","issue":"1"},{"date_updated":"2026-05-19T13:15:29Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"28","acknowledgement":"We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.\r\n","OA_place":"publisher","article_type":"original","title":"Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1511328112","open_access":"1"}],"author":[{"first_name":"Colin","last_name":"Kretz","full_name":"Kretz, Colin"},{"full_name":"Dai, Manhong","first_name":"Manhong","last_name":"Dai"},{"full_name":"Soylemez, Onuralp","first_name":"Onuralp","last_name":"Soylemez"},{"full_name":"Yee, Andrew","first_name":"Andrew","last_name":"Yee"},{"last_name":"Desch","first_name":"Karl","full_name":"Desch, Karl"},{"last_name":"Siemieniak","first_name":"David","full_name":"Siemieniak, David"},{"first_name":"Kärt","last_name":"Tomberg","full_name":"Tomberg, Kärt"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"last_name":"Meng","first_name":"Fan","full_name":"Meng, Fan"},{"full_name":"Ginsburg, David","first_name":"David","last_name":"Ginsburg"}],"oa":1,"external_id":{"pmid":[" 26170332"]},"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"OA_type":"free access","date_published":"2015-07-28T00:00:00Z","publist_id":"6783","extern":"1","publication":"PNAS","_id":"866","pmid":1,"date_created":"2018-12-11T11:48:55Z","oa_version":"Accepted Version","volume":112,"language":[{"iso":"eng"}],"year":"2015","quality_controlled":"1","issue":"30","page":"9328 - 9333","month":"07","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF."}],"citation":{"ieee":"C. Kretz <i>et al.</i>, “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” <i>PNAS</i>, vol. 112, no. 30. National Academy of Sciences, pp. 9328–9333, 2015.","chicago":"Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1511328112\">https://doi.org/10.1073/pnas.1511328112</a>.","ista":"Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.","ama":"Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. <i>PNAS</i>. 2015;112(30):9328-9333. doi:<a href=\"https://doi.org/10.1073/pnas.1511328112\">10.1073/pnas.1511328112</a>","short":"C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.","mla":"Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” <i>PNAS</i>, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:<a href=\"https://doi.org/10.1073/pnas.1511328112\">10.1073/pnas.1511328112</a>.","apa":"Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1511328112\">https://doi.org/10.1073/pnas.1511328112</a>"},"doi":"10.1073/pnas.1511328112","scopus_import":"1","intvolume":"       112","publisher":"National Academy of Sciences","type":"journal_article","publication_status":"published"}]