[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","extern":"1","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Eugster, Patrick","first_name":"Patrick","last_name":"Eugster"},{"first_name":"Maurice","last_name":"Herlihy","full_name":"Herlihy, Maurice"},{"full_name":"Matveev, Alexander","first_name":"Alexander","last_name":"Matveev"},{"full_name":"Shavit, Nir","last_name":"Shavit","first_name":"Nir"}],"citation":{"mla":"Alistarh, Dan-Adrian, et al. <i>StackTrack: An Automated Transactional Approach to Concurrent Memory Reclamation</i>. ACM, 2014, doi:<a href=\"https://doi.org/10.1145/2592798.2592808\">10.1145/2592798.2592808</a>.","apa":"Alistarh, D.-A., Eugster, P., Herlihy, M., Matveev, A., &#38; Shavit, N. (2014). StackTrack: An automated transactional approach to concurrent memory reclamation. Presented at the EuroSys: European Conference on Computer Systems, ACM. <a href=\"https://doi.org/10.1145/2592798.2592808\">https://doi.org/10.1145/2592798.2592808</a>","short":"D.-A. Alistarh, P. Eugster, M. Herlihy, A. Matveev, N. Shavit, in:, ACM, 2014.","chicago":"Alistarh, Dan-Adrian, Patrick Eugster, Maurice Herlihy, Alexander Matveev, and Nir Shavit. “StackTrack: An Automated Transactional Approach to Concurrent Memory Reclamation.” ACM, 2014. <a href=\"https://doi.org/10.1145/2592798.2592808\">https://doi.org/10.1145/2592798.2592808</a>.","ista":"Alistarh D-A, Eugster P, Herlihy M, Matveev A, Shavit N. 2014. StackTrack: An automated transactional approach to concurrent memory reclamation. EuroSys: European Conference on Computer Systems.","ieee":"D.-A. Alistarh, P. Eugster, M. Herlihy, A. Matveev, and N. Shavit, “StackTrack: An automated transactional approach to concurrent memory reclamation,” presented at the EuroSys: European Conference on Computer Systems, 2014.","ama":"Alistarh D-A, Eugster P, Herlihy M, Matveev A, Shavit N. StackTrack: An automated transactional approach to concurrent memory reclamation. In: ACM; 2014. doi:<a href=\"https://doi.org/10.1145/2592798.2592808\">10.1145/2592798.2592808</a>"},"day":"01","year":"2014","date_updated":"2023-02-23T13:14:25Z","type":"conference","oa_version":"None","doi":"10.1145/2592798.2592808","language":[{"iso":"eng"}],"_id":"770","title":"StackTrack: An automated transactional approach to concurrent memory reclamation","publication_status":"published","abstract":[{"text":"Dynamic memory reclamation is arguably the biggest open problem in concurrent data structure design: All known solutions induce high overhead, or must be customized to the specific data structure by the programmer, or both. This paper presents StackTrack, the first concurrent memory reclamation scheme that can be applied automatically by a compiler, while maintaining efficiency. StackTrack eliminates most of the expensive bookkeeping required for memory reclamation by leveraging the power of hardware transactional memory (HTM) in a new way: it tracks thread variables dynamically, and in an atomic fashion. This effectively makes all memory references visible without having threads pay the overhead of writing out this information. Our empirical results show that this new approach matches or outperforms prior, non-automated, techniques.","lang":"eng"}],"acknowledgement":"Dan Alistarh - Part  of  this  work  was  performed  while  the  author  was  a  Postdoctoral\r\nAssociate a MIT CSAIL, supported in part by NSF grant CCF-1217921,\r\nDoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle\r\nand Intel corporations.\r\nPatrick Eugester - Supported in part by DARPA grant N11AP20014 and NSF grant CNS-\r\n1117065.\r\nMaurice Herlihy - Supported by NSF grant 1301924.\r\nNir Shavit - Supported in part by NSF grants CCF-1217921 and CCF-1301926, DoE\r\nASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and\r\nIntel corporations.","date_published":"2014-01-01T00:00:00Z","publisher":"ACM","publist_id":"6888","status":"public","date_created":"2018-12-11T11:48:24Z","month":"01","conference":{"name":"EuroSys: European Conference on Computer Systems"}},{"language":[{"iso":"eng"}],"doi":"10.1145/2611462.2611499","_id":"771","title":"Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems","publication_status":"published","abstract":[{"lang":"eng","text":"We consider the following natural problem: n failure-prone servers, communicating synchronously through message passing, must assign themselves one-to-one to n distinct items. Existing literature suggests two possible approaches to this problem. First, model it as an instance of tight renaming in synchronous message-passing systems; for deterministic solutions, a tight bound of ©(logn) communication rounds is known. Second, model the scenario as an instance of randomized load-balancing, for which elegant sub-logarithmic solutions exist. However, careful examination reveals that known load-balancing schemes do not apply to our scenario, because they either do not tolerate faults or do not ensure one-to-one allocation. It is thus natural to ask if sublogarithmic solutions exist for this apparently simple but intriguing problem. In this paper, we combine the two approaches to provide a new randomized solution for tight renaming, which terminates in O (log log n) communication rounds with high probability, against a strong adaptive adversary. Our solution, called Balls-into-Leaves, combines the deterministic approach with a new randomized scheme to obtain perfectly balanced allocations. The algorithm arranges the items as leaves of a tree, and participants repeatedly perform random choices among the leaves. The algorithm exchanges information in each round to split the participants into progressively smaller groups whose random choices do not conflict. We then extend the algorithm to terminate early in O(log log) rounds w.h.p., where is the actual number of failures. These results imply an exponential separation between deterministic and randomized algorithms for the tight renaming problem in message-passing systems."}],"acknowledgement":"Dan Alistarh was partially supported by the SNF Post-\r\ndoctoral Fellows Program, NSF grant CCF-1217921, DoE\r\nASCR grant ER26116/DE-SC0008923, and by grants from\r\nthe Oracle and Intel corporations.\r\nOksana Denysyuk and Lu ́ıs Rodrigues were partially supported by Funda ̧c ̃ao para a Ciˆencia e Tecnologia (FCT) via\r\nthe project PEPITA (PTDC/EEI-SCR/2776/2012) and via\r\nthe INESC-ID multi-annual funding through the PIDDAC\r\nProgram fund grant, under project PEst-OE/EEI/LA0021/\r\n2013.\r\nNir Shavit was supported in part by NSF grants CCF-1217921 and CCF-1301926, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations.","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Denysyuk, Oksana","first_name":"Oksana","last_name":"Denysyuk"},{"last_name":"Rodrígues","first_name":"Luís","full_name":"Rodrígues, Luís"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"}],"article_processing_charge":"No","citation":{"mla":"Alistarh, Dan-Adrian, et al. <i>Balls-into-Leaves: Sub-Logarithmic Renaming in Synchronous Message-Passing Systems</i>. ACM, 2014, pp. 232–41, doi:<a href=\"https://doi.org/10.1145/2611462.2611499\">10.1145/2611462.2611499</a>.","apa":"Alistarh, D.-A., Denysyuk, O., Rodrígues, L., &#38; Shavit, N. (2014). Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems (pp. 232–241). Presented at the PODC: Principles of Distributed Computing, ACM. <a href=\"https://doi.org/10.1145/2611462.2611499\">https://doi.org/10.1145/2611462.2611499</a>","ista":"Alistarh D-A, Denysyuk O, Rodrígues L, Shavit N. 2014. Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems. PODC: Principles of Distributed Computing, 232–241.","chicago":"Alistarh, Dan-Adrian, Oksana Denysyuk, Luís Rodrígues, and Nir Shavit. “Balls-into-Leaves: Sub-Logarithmic Renaming in Synchronous Message-Passing Systems,” 232–41. ACM, 2014. <a href=\"https://doi.org/10.1145/2611462.2611499\">https://doi.org/10.1145/2611462.2611499</a>.","short":"D.-A. Alistarh, O. Denysyuk, L. Rodrígues, N. Shavit, in:, ACM, 2014, pp. 232–241.","ieee":"D.-A. Alistarh, O. Denysyuk, L. Rodrígues, and N. Shavit, “Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems,” presented at the PODC: Principles of Distributed Computing, 2014, pp. 232–241.","ama":"Alistarh D-A, Denysyuk O, Rodrígues L, Shavit N. Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems. In: ACM; 2014:232-241. doi:<a href=\"https://doi.org/10.1145/2611462.2611499\">10.1145/2611462.2611499</a>"},"day":"01","year":"2014","date_updated":"2023-02-23T13:14:49Z","type":"conference","oa_version":"None","publist_id":"6884","status":"public","date_created":"2018-12-11T11:48:25Z","month":"01","conference":{"name":"PODC: Principles of Distributed Computing"},"page":"232 - 241","date_published":"2014-01-01T00:00:00Z","publisher":"ACM"},{"page":"714 - 723","date_published":"2014-01-01T00:00:00Z","external_id":{"arxiv":["1311.3200"]},"publisher":"ACM","publist_id":"6885","status":"public","date_created":"2018-12-11T11:48:25Z","arxiv":1,"conference":{"name":"STOC: Symposium on Theory of Computing"},"month":"01","article_processing_charge":"No","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Keren","last_name":"Censor Hillel","full_name":"Censor Hillel, Keren"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"mla":"Alistarh, Dan-Adrian, et al. <i>Are Lock-Free Concurrent Algorithms Practically Wait-Free?</i> ACM, 2014, pp. 714–23, doi:<a href=\"https://doi.org/10.1145/2591796.2591836\">10.1145/2591796.2591836</a>.","apa":"Alistarh, D.-A., Censor Hillel, K., &#38; Shavit, N. (2014). Are lock-free concurrent algorithms practically wait-free? (pp. 714–723). Presented at the STOC: Symposium on Theory of Computing, ACM. <a href=\"https://doi.org/10.1145/2591796.2591836\">https://doi.org/10.1145/2591796.2591836</a>","chicago":"Alistarh, Dan-Adrian, Keren Censor Hillel, and Nir Shavit. “Are Lock-Free Concurrent Algorithms Practically Wait-Free?,” 714–23. ACM, 2014. <a href=\"https://doi.org/10.1145/2591796.2591836\">https://doi.org/10.1145/2591796.2591836</a>.","short":"D.-A. Alistarh, K. Censor Hillel, N. Shavit, in:, ACM, 2014, pp. 714–723.","ista":"Alistarh D-A, Censor Hillel K, Shavit N. 2014. Are lock-free concurrent algorithms practically wait-free? STOC: Symposium on Theory of Computing, 714–723.","ieee":"D.-A. Alistarh, K. Censor Hillel, and N. Shavit, “Are lock-free concurrent algorithms practically wait-free?,” presented at the STOC: Symposium on Theory of Computing, 2014, pp. 714–723.","ama":"Alistarh D-A, Censor Hillel K, Shavit N. Are lock-free concurrent algorithms practically wait-free? In: ACM; 2014:714-723. doi:<a href=\"https://doi.org/10.1145/2591796.2591836\">10.1145/2591796.2591836</a>"},"main_file_link":[{"url":"https://arxiv.org/abs/1311.3200","open_access":"1"}],"day":"01","year":"2014","type":"conference","date_updated":"2023-02-23T13:15:13Z","oa_version":"Preprint","doi":"10.1145/2591796.2591836","oa":1,"language":[{"iso":"eng"}],"_id":"772","title":"Are lock-free concurrent algorithms practically wait-free?","publication_status":"published","abstract":[{"text":"Lock-free concurrent algorithms guarantee that some concurrent operation will always make progress in a finite number of steps. Yet programmers prefer to treat concurrent code as if it were wait-free, guaranteeing that all operations always make progress. Unfortunately, designing wait-free algorithms is generally a very complex task, and the resulting algorithms are not always efficient. While obtaining efficient wait-free algorithms has been a long-time goal for the theory community, most non-blocking commercial code is only lock-free. This paper suggests a simple solution to this problem. We show that, for a large class of lock-free algorithms, under scheduling conditions which approximate those found in commercial hardware architectures, lock-free algorithms behave as if they are wait-free. In other words, programmers can keep on designing simple lock-free algorithms instead of complex wait-free ones, and in practice, they will get wait-free progress. Our main contribution is a new way of analyzing a general class of lock-free algorithms under a stochastic scheduler. Our analysis relates the individual performance of processes with the global performance of the system using Markov chain lifting between a complex per-process chain and a simpler system progress chain. We show that lock-free algorithms are not only wait-free with probability 1, but that in fact a general subset of lock-free algorithms can be closely bounded in terms of the average number of steps required until an operation completes. To the best of our knowledge, this is the first attempt to analyze progress conditions, typically stated in relation to a worst case adversary, in a stochastic model capturing their expected asymptotic behavior.","lang":"eng"}],"acknowledgement":"Dan Alistarh - Part of this work was performed while the author was a Postdoctoral Associate at MIT CSAIL, where he was supported by SNF\r\nPostdoctoral Fellows Program, NSF grant CCF-1217921, DoE\r\nASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations.\r\nKeron Censor-Hillel - Shalon Fellow\r\nNir Shavit - This work was supported in part by NSF grants CCF-1217921 and\r\nCCF-1301926, DoE ASCR grant ER26116/DE-SC0008923, and\r\nby grants from the Oracle and Intel corporations."},{"citation":{"apa":"Alistarh, D.-A., Aspnes, J., King, V., &#38; Saia, J. (2014). Communication-efficient randomized consensus. In F. Kuhn (Ed.) (Vol. 8784, pp. 61–75). Presented at the DISC: Distributed Computing, Austin, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-662-45174-8_5\">https://doi.org/10.1007/978-3-662-45174-8_5</a>","mla":"Alistarh, Dan-Adrian, et al. <i>Communication-Efficient Randomized Consensus</i>. Edited by Fabian Kuhn, vol. 8784, Springer, 2014, pp. 61–75, doi:<a href=\"https://doi.org/10.1007/978-3-662-45174-8_5\">10.1007/978-3-662-45174-8_5</a>.","ama":"Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. In: Kuhn F, ed. Vol 8784. Springer; 2014:61-75. doi:<a href=\"https://doi.org/10.1007/978-3-662-45174-8_5\">10.1007/978-3-662-45174-8_5</a>","ieee":"D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” presented at the DISC: Distributed Computing, Austin, USA, 2014, vol. 8784, pp. 61–75.","ista":"Alistarh D-A, Aspnes J, King V, Saia J. 2014. Communication-efficient randomized consensus. DISC: Distributed Computing, LNCS, vol. 8784, 61–75.","short":"D.-A. Alistarh, J. Aspnes, V. King, J. Saia, in:, F. Kuhn (Ed.), Springer, 2014, pp. 61–75.","chicago":"Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” edited by Fabian Kuhn, 8784:61–75. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-662-45174-8_5\">https://doi.org/10.1007/978-3-662-45174-8_5</a>."},"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"},{"last_name":"Aspnes","first_name":"James","full_name":"Aspnes, James"},{"full_name":"King, Valerie","last_name":"King","first_name":"Valerie"},{"full_name":"Saia, Jared","first_name":"Jared","last_name":"Saia"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T13:15:36Z","type":"conference","oa_version":"None","day":"01","year":"2014","title":"Communication-efficient randomized consensus","doi":"10.1007/978-3-662-45174-8_5","language":[{"iso":"eng"}],"_id":"773","publication_status":"published","abstract":[{"lang":"eng","text":"We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n/2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(n log3n) messages in expectation, which is again within logarithmic factors of optimal.We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt + t2log2t) total messages. Our protocol uses messages of size O(log n), and can therefore scale to large networks.\r\n\r\nWe consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary.\r\n\r\nOur approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model."}],"date_published":"2014-01-01T00:00:00Z","page":"61 - 75","volume":8784,"publisher":"Springer","editor":[{"full_name":"Kuhn, Fabian","last_name":"Kuhn","first_name":"Fabian"}],"intvolume":"      8784","alternative_title":["LNCS"],"publist_id":"6881","date_created":"2018-12-11T11:48:25Z","month":"01","conference":{"name":"DISC: Distributed Computing","end_date":"2014-10-15","start_date":"2014-10-12","location":"Austin, USA"},"status":"public"},{"language":[{"iso":"eng"}],"doi":"10.1145/2611462.2611502","_id":"774","title":"Brief announcement: Are lock-free concurrent algorithms practically wait-free?","publication_status":"published","abstract":[{"lang":"eng","text":"Lock-free concurrent algorithms guarantee that some concurrent operation will always make progress in a finite number of steps. Yet programmers would prefer to treat concurrent code as if it were wait-free, guaranteeing that all operations always make progress. Unfortunately, designing wait-free algorithms is in general a complex undertaking, and the resulting algorithms are not always efficient, so most non-blocking commercial code is only lock-free, and the design of efficient wait-free algorithms has been left to the academic community. In [2], we suggest a solution to this problem. We show that, for a large class of lock-free algorithms, under scheduling conditions which approximate those found in commercial hardware architectures, lock-free algorithms behave as if they are wait-free. In other words, programmers can keep on designing simple lock-free algorithms instead of complex wait-free ones, and in practice, they will get wait-free progress. Our main contribution is a new way of analyzing a general class of lock-free algorithms under a stochastic scheduler. Our analysis relates the individual performance of processes with the global performance of the system using Markov chain lifting between a complex per-process chain and a simpler system progress chain. We show that lock-free algorithms are not only wait-free with probability 1, but that in fact a broad subset of lock-free algorithms can be closely bounded in terms of the average number of steps required until an operation completes."}],"acknowledgement":"Dan Alistarh - Part  of  this  work  was  performed  while  the  author  was  a\r\nPostdoctoral Associate at MIT CSAIL, where he was supported  by  SNF  Postdoctoral  Fellows  Program,  NSF  grant\r\nCCF-1217921, DoE ASCR grant ER26116/DE-SC0008923,\r\nand by grants from the Oracle and Intel corporations.\r\nKeren Censor-Hille - Shalon Fellow\r\nNir Shavit - This  work  was  supported  in  part  by  NSF  grants  CCF-1217921 and CCF-1301926, DoE ASCR grant ER26116/DE-\r\nSC0008923, and by grants from the Oracle and Intel corporations.","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"last_name":"Censor Hille","first_name":"Keren","full_name":"Censor Hille, Keren"},{"full_name":"Shavit, Nir","last_name":"Shavit","first_name":"Nir"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"mla":"Alistarh, Dan-Adrian, et al. <i>Brief Announcement: Are Lock-Free Concurrent Algorithms Practically Wait-Free?</i> ACM, 2014, pp. 50–52, doi:<a href=\"https://doi.org/10.1145/2611462.2611502\">10.1145/2611462.2611502</a>.","apa":"Alistarh, D.-A., Censor Hille, K., &#38; Shavit, N. (2014). Brief announcement: Are lock-free concurrent algorithms practically wait-free? (pp. 50–52). Presented at the PODC: Principles of Distributed Computing, ACM. <a href=\"https://doi.org/10.1145/2611462.2611502\">https://doi.org/10.1145/2611462.2611502</a>","short":"D.-A. Alistarh, K. Censor Hille, N. Shavit, in:, ACM, 2014, pp. 50–52.","chicago":"Alistarh, Dan-Adrian, Keren Censor Hille, and Nir Shavit. “Brief Announcement: Are Lock-Free Concurrent Algorithms Practically Wait-Free?,” 50–52. ACM, 2014. <a href=\"https://doi.org/10.1145/2611462.2611502\">https://doi.org/10.1145/2611462.2611502</a>.","ista":"Alistarh D-A, Censor Hille K, Shavit N. 2014. Brief announcement: Are lock-free concurrent algorithms practically wait-free? PODC: Principles of Distributed Computing, 50–52.","ama":"Alistarh D-A, Censor Hille K, Shavit N. Brief announcement: Are lock-free concurrent algorithms practically wait-free? In: ACM; 2014:50-52. doi:<a href=\"https://doi.org/10.1145/2611462.2611502\">10.1145/2611462.2611502</a>","ieee":"D.-A. Alistarh, K. Censor Hille, and N. Shavit, “Brief announcement: Are lock-free concurrent algorithms practically wait-free?,” presented at the PODC: Principles of Distributed Computing, 2014, pp. 50–52."},"day":"01","year":"2014","date_updated":"2023-02-23T13:15:54Z","type":"conference","oa_version":"None","publist_id":"6882","status":"public","date_created":"2018-12-11T11:48:26Z","month":"01","conference":{"name":"PODC: Principles of Distributed Computing"},"page":"50 - 52","date_published":"2014-01-01T00:00:00Z","publisher":"ACM"},{"abstract":[{"text":"Experimental studies have demonstrated that environmental variation can create genotype‐environment interactions (GEIs) in the traits involved in sexual selection. Understanding the genetic architecture of phenotype across environments will require statistical tests that can describe both changes in genetic variance and covariance across environments. This chapter outlines the theoretical framework for the processes of sexual selection in the wild, identifying key parameters in wild systems, and highlighting the potential effects of the environment. It describes the proposed approaches for the estimation of these key parameters in a quantitative genetic framework within naturally occurring pedigreed populations. The chapter provides a worked example for a range of analysis methods. It aims to provide an overview of the analytical methods that can be used to model GEIs for traits involved in sexual selection in naturally occurring pedigreed populations.","lang":"eng"}],"publication_status":"published","_id":"7743","doi":"10.1002/9781118912591.ch6","language":[{"iso":"eng"}],"publication":"Genotype-by-Environment Interactions and Sexual Selection","title":"Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations","year":"2014","day":"29","oa_version":"None","date_updated":"2021-01-12T08:15:13Z","type":"book_chapter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","first_name":"Matthew Richard"},{"first_name":"Anna","last_name":"Qvarnström","full_name":"Qvarnström, Anna"}],"quality_controlled":"1","extern":"1","article_processing_charge":"No","citation":{"ieee":"M. R. Robinson and A. Qvarnström, “Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations,” in <i>Genotype-by-Environment Interactions and Sexual Selection</i>, J. Hunt and D. Hosken, Eds. Chichester, UK: Wiley, 2014, pp. 137–168.","ama":"Robinson MR, Qvarnström A. Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations. In: Hunt J, Hosken D, eds. <i>Genotype-by-Environment Interactions and Sexual Selection</i>. Chichester, UK: Wiley; 2014:137-168. doi:<a href=\"https://doi.org/10.1002/9781118912591.ch6\">10.1002/9781118912591.ch6</a>","short":"M.R. Robinson, A. Qvarnström, in:, J. Hunt, D. Hosken (Eds.), Genotype-by-Environment Interactions and Sexual Selection, Wiley, Chichester, UK, 2014, pp. 137–168.","chicago":"Robinson, Matthew Richard, and Anna Qvarnström. “Influence of the Environment on the Genetic Architecture of Traits Involved in Sexual Selection within Wild Populations.” In <i>Genotype-by-Environment Interactions and Sexual Selection</i>, edited by John Hunt and David Hosken, 137–68. Chichester, UK: Wiley, 2014. <a href=\"https://doi.org/10.1002/9781118912591.ch6\">https://doi.org/10.1002/9781118912591.ch6</a>.","ista":"Robinson MR, Qvarnström A. 2014.Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations. In: Genotype-by-Environment Interactions and Sexual Selection. , 137–168.","mla":"Robinson, Matthew Richard, and Anna Qvarnström. “Influence of the Environment on the Genetic Architecture of Traits Involved in Sexual Selection within Wild Populations.” <i>Genotype-by-Environment Interactions and Sexual Selection</i>, edited by John Hunt and David Hosken, Wiley, 2014, pp. 137–68, doi:<a href=\"https://doi.org/10.1002/9781118912591.ch6\">10.1002/9781118912591.ch6</a>.","apa":"Robinson, M. R., &#38; Qvarnström, A. (2014). Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations. In J. Hunt &#38; D. Hosken (Eds.), <i>Genotype-by-Environment Interactions and Sexual Selection</i> (pp. 137–168). Chichester, UK: Wiley. <a href=\"https://doi.org/10.1002/9781118912591.ch6\">https://doi.org/10.1002/9781118912591.ch6</a>"},"status":"public","month":"08","date_created":"2020-04-30T10:58:39Z","place":"Chichester, UK","publication_identifier":{"isbn":["9780470671795"],"eisbn":["9781118912591"]},"editor":[{"full_name":"Hunt, John","last_name":"Hunt","first_name":"John"},{"first_name":"David","last_name":"Hosken","full_name":"Hosken, David"}],"publisher":"Wiley","page":"137-168","date_published":"2014-08-29T00:00:00Z"},{"publication_identifier":{"issn":["0168-9525"]},"intvolume":"        30","status":"public","month":"04","date_created":"2020-04-30T10:58:58Z","volume":30,"issue":"4","page":"124-132","date_published":"2014-04-01T00:00:00Z","publisher":"Elsevier","article_type":"original","_id":"7744","doi":"10.1016/j.tig.2014.02.003","language":[{"iso":"eng"}],"publication":"Trends in Genetics","title":"Explaining additional genetic variation in complex traits","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","quality_controlled":"1","article_processing_charge":"No","author":[{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"},{"last_name":"Wray","first_name":"Naomi R.","full_name":"Wray, Naomi R."},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."}],"citation":{"mla":"Robinson, Matthew Richard, et al. “Explaining Additional Genetic Variation in Complex Traits.” <i>Trends in Genetics</i>, vol. 30, no. 4, Elsevier, 2014, pp. 124–32, doi:<a href=\"https://doi.org/10.1016/j.tig.2014.02.003\">10.1016/j.tig.2014.02.003</a>.","apa":"Robinson, M. R., Wray, N. R., &#38; Visscher, P. M. (2014). Explaining additional genetic variation in complex traits. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2014.02.003\">https://doi.org/10.1016/j.tig.2014.02.003</a>","ieee":"M. R. Robinson, N. R. Wray, and P. M. Visscher, “Explaining additional genetic variation in complex traits,” <i>Trends in Genetics</i>, vol. 30, no. 4. Elsevier, pp. 124–132, 2014.","ama":"Robinson MR, Wray NR, Visscher PM. Explaining additional genetic variation in complex traits. <i>Trends in Genetics</i>. 2014;30(4):124-132. doi:<a href=\"https://doi.org/10.1016/j.tig.2014.02.003\">10.1016/j.tig.2014.02.003</a>","short":"M.R. Robinson, N.R. Wray, P.M. Visscher, Trends in Genetics 30 (2014) 124–132.","chicago":"Robinson, Matthew Richard, Naomi R. Wray, and Peter M. Visscher. “Explaining Additional Genetic Variation in Complex Traits.” <i>Trends in Genetics</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tig.2014.02.003\">https://doi.org/10.1016/j.tig.2014.02.003</a>.","ista":"Robinson MR, Wray NR, Visscher PM. 2014. Explaining additional genetic variation in complex traits. Trends in Genetics. 30(4), 124–132."},"year":"2014","day":"01","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T08:15:14Z"},{"status":"public","conference":{"name":"ICDCS: International Conference on Distributed Computing Systems"},"arxiv":1,"month":"08","date_created":"2018-12-11T11:48:26Z","publist_id":"6883","publisher":"IEEE","page":"348 - 357","external_id":{"arxiv":["1405.5461"]},"date_published":"2014-08-29T00:00:00Z","abstract":[{"text":"The long-lived renaming problem appears in shared-memory systems where a set of threads need to register and deregister frequently from the computation, while concurrent operations scan the set of currently registered threads. Instances of this problem show up in concurrent implementations of transactional memory, flat combining, thread barriers, and memory reclamation schemes for lock-free data structures. In this paper, we analyze a randomized solution for long-lived renaming. The algorithmic technique we consider, called the Level Array, has previously been used for hashing and one-shot (single-use) renaming. Our main contribution is to prove that, in long-lived executions, where processes may register and deregister polynomially many times, the technique guarantees constant steps on average and O (log log n) steps with high probability for registering, unit cost for deregistering, and O (n) steps for collect queries, where n is an upper bound on the number of processes that may be active at any point in time. We also show that the algorithm has the surprising property that it is self-healing: under reasonable assumptions on the schedule, operations running while the data structure is in a degraded state implicitly help the data structure re-balance itself. This subtle mechanism obviates the need for expensive periodic rebuilding procedures. Our benchmarks validate this approach, showing that, for typical use parameters, the average number of steps a process takes to register is less than two and the worst-case number of steps is bounded by six, even in executions with billions of operations. We contrast this with other randomized implementations, whose worst-case behavior we show to be unreliable, and with deterministic implementations, whose cost is linear in n.","lang":"eng"}],"publication_status":"published","_id":"775","language":[{"iso":"eng"}],"doi":"10.1109/ICDCS.2014.43","oa":1,"title":"The levelarray: A fast, practical long-lived renaming algorithm","year":"2014","day":"29","oa_version":"Preprint","type":"conference","date_updated":"2023-02-23T13:16:18Z","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"full_name":"Kopinsky, Justin","first_name":"Justin","last_name":"Kopinsky"},{"full_name":"Matveev, Alexander","first_name":"Alexander","last_name":"Matveev"},{"first_name":"Nir","last_name":"Shavit","full_name":"Shavit, Nir"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Alistarh D-A, Kopinsky J, Matveev A, Shavit N. The levelarray: A fast, practical long-lived renaming algorithm. In: IEEE; 2014:348-357. doi:<a href=\"https://doi.org/10.1109/ICDCS.2014.43\">10.1109/ICDCS.2014.43</a>","ieee":"D.-A. Alistarh, J. Kopinsky, A. Matveev, and N. Shavit, “The levelarray: A fast, practical long-lived renaming algorithm,” presented at the ICDCS: International Conference on Distributed Computing Systems, 2014, pp. 348–357.","short":"D.-A. Alistarh, J. Kopinsky, A. Matveev, N. Shavit, in:, IEEE, 2014, pp. 348–357.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Alexander Matveev, and Nir Shavit. “The Levelarray: A Fast, Practical Long-Lived Renaming Algorithm,” 348–57. IEEE, 2014. <a href=\"https://doi.org/10.1109/ICDCS.2014.43\">https://doi.org/10.1109/ICDCS.2014.43</a>.","ista":"Alistarh D-A, Kopinsky J, Matveev A, Shavit N. 2014. The levelarray: A fast, practical long-lived renaming algorithm. ICDCS: International Conference on Distributed Computing Systems, 348–357.","mla":"Alistarh, Dan-Adrian, et al. <i>The Levelarray: A Fast, Practical Long-Lived Renaming Algorithm</i>. IEEE, 2014, pp. 348–57, doi:<a href=\"https://doi.org/10.1109/ICDCS.2014.43\">10.1109/ICDCS.2014.43</a>.","apa":"Alistarh, D.-A., Kopinsky, J., Matveev, A., &#38; Shavit, N. (2014). The levelarray: A fast, practical long-lived renaming algorithm (pp. 348–357). Presented at the ICDCS: International Conference on Distributed Computing Systems, IEEE. <a href=\"https://doi.org/10.1109/ICDCS.2014.43\">https://doi.org/10.1109/ICDCS.2014.43</a>"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1405.5461"}]},{"type":"journal_article","date_updated":"2021-01-12T08:15:24Z","oa_version":"None","day":"05","year":"2014","citation":{"mla":"Lohr, Matthew A., et al. “Vibrational and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” <i>Physical Review E</i>, vol. 90, no. 6, 062305, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.90.062305\">10.1103/physreve.90.062305</a>.","apa":"Lohr, M. A., Still, T., Ganti, R., Gratale, M. D., Davidson, Z. S., Aptowicz, K. B., … Yodh, A. G. (2014). Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.90.062305\">https://doi.org/10.1103/physreve.90.062305</a>","chicago":"Lohr, Matthew A., Tim Still, Raman Ganti, Matthew D. Gratale, Zoey S. Davidson, Kevin B. Aptowicz, Carl Peter Goodrich, Daniel M. Sussman, and A. G. Yodh. “Vibrational and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.90.062305\">https://doi.org/10.1103/physreve.90.062305</a>.","short":"M.A. Lohr, T. Still, R. Ganti, M.D. Gratale, Z.S. Davidson, K.B. Aptowicz, C.P. Goodrich, D.M. Sussman, A.G. Yodh, Physical Review E 90 (2014).","ista":"Lohr MA, Still T, Ganti R, Gratale MD, Davidson ZS, Aptowicz KB, Goodrich CP, Sussman DM, Yodh AG. 2014. Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. Physical Review E. 90(6), 062305.","ieee":"M. A. Lohr <i>et al.</i>, “Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings,” <i>Physical Review E</i>, vol. 90, no. 6. American Physical Society, 2014.","ama":"Lohr MA, Still T, Ganti R, et al. Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. <i>Physical Review E</i>. 2014;90(6). doi:<a href=\"https://doi.org/10.1103/physreve.90.062305\">10.1103/physreve.90.062305</a>"},"extern":"1","author":[{"full_name":"Lohr, Matthew A.","first_name":"Matthew A.","last_name":"Lohr"},{"first_name":"Tim","last_name":"Still","full_name":"Still, Tim"},{"last_name":"Ganti","first_name":"Raman","full_name":"Ganti, Raman"},{"last_name":"Gratale","first_name":"Matthew D.","full_name":"Gratale, Matthew D."},{"full_name":"Davidson, Zoey S.","last_name":"Davidson","first_name":"Zoey S."},{"full_name":"Aptowicz, Kevin B.","last_name":"Aptowicz","first_name":"Kevin B."},{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","last_name":"Goodrich"},{"last_name":"Sussman","first_name":"Daniel M.","full_name":"Sussman, Daniel M."},{"last_name":"Yodh","first_name":"A. G.","full_name":"Yodh, A. G."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_processing_charge":"No","publication_status":"published","abstract":[{"lang":"eng","text":"We investigate the vibrational modes of quasi-two-dimensional disordered colloidal packings of hard colloidal spheres with short-range attractions as a function of packing fraction. Certain properties of the vibrational density of states (vDOS) are shown to correlate with the density and structure of the samples (i.e., in sparsely versus densely packed samples). Specifically, a crossover from dense glassy to sparse gel-like states is suggested by an excess of phonon modes at low frequency and by a variation in the slope of the vDOS with frequency at low frequency. This change in phonon mode distribution is demonstrated to arise largely from localized vibrations that involve individual and/or small clusters of particles with few local bonds. Conventional order parameters and void statistics did not exhibit obvious gel-glass signatures as a function of volume fraction. These mode behaviors and accompanying structural insights offer a potentially new set of indicators for identification of glass-gel transitions and for assignment of gel-like versus glass-like character to a disordered solid material."}],"publication":"Physical Review E","title":"Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings","language":[{"iso":"eng"}],"doi":"10.1103/physreve.90.062305","_id":"7768","article_type":"original","publisher":"American Physical Society","date_published":"2014-12-05T00:00:00Z","volume":90,"issue":"6","date_created":"2020-04-30T11:41:54Z","month":"12","status":"public","article_number":"062305","intvolume":"        90","publication_identifier":{"issn":["1539-3755","1550-2376"]}},{"issue":"2","volume":90,"date_published":"2014-08-27T00:00:00Z","publisher":"American Physical Society","article_type":"original","publication_identifier":{"issn":["1539-3755","1550-2376"]},"intvolume":"        90","status":"public","article_number":"022138","date_created":"2020-04-30T11:42:09Z","month":"08","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_processing_charge":"No","author":[{"first_name":"Carl Peter","last_name":"Goodrich","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"Dagois-Bohy, Simon","first_name":"Simon","last_name":"Dagois-Bohy"},{"full_name":"Tighe, Brian P.","first_name":"Brian P.","last_name":"Tighe"},{"full_name":"van Hecke, Martin","first_name":"Martin","last_name":"van Hecke"},{"first_name":"Andrea J.","last_name":"Liu","full_name":"Liu, Andrea J."},{"full_name":"Nagel, Sidney R.","last_name":"Nagel","first_name":"Sidney R."}],"citation":{"apa":"Goodrich, C. P., Dagois-Bohy, S., Tighe, B. P., van Hecke, M., Liu, A. J., &#38; Nagel, S. R. (2014). Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.90.022138\">https://doi.org/10.1103/physreve.90.022138</a>","mla":"Goodrich, Carl Peter, et al. “Jamming in Finite Systems: Stability, Anisotropy, Fluctuations, and Scaling.” <i>Physical Review E</i>, vol. 90, no. 2, 022138, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.90.022138\">10.1103/physreve.90.022138</a>.","ieee":"C. P. Goodrich, S. Dagois-Bohy, B. P. Tighe, M. van Hecke, A. J. Liu, and S. R. Nagel, “Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling,” <i>Physical Review E</i>, vol. 90, no. 2. American Physical Society, 2014.","ama":"Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. <i>Physical Review E</i>. 2014;90(2). doi:<a href=\"https://doi.org/10.1103/physreve.90.022138\">10.1103/physreve.90.022138</a>","ista":"Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. 2014. Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical Review E. 90(2), 022138.","chicago":"Goodrich, Carl Peter, Simon Dagois-Bohy, Brian P. Tighe, Martin van Hecke, Andrea J. Liu, and Sidney R. Nagel. “Jamming in Finite Systems: Stability, Anisotropy, Fluctuations, and Scaling.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.90.022138\">https://doi.org/10.1103/physreve.90.022138</a>.","short":"C.P. Goodrich, S. Dagois-Bohy, B.P. Tighe, M. van Hecke, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014)."},"day":"27","year":"2014","type":"journal_article","date_updated":"2021-01-12T08:15:24Z","oa_version":"None","language":[{"iso":"eng"}],"doi":"10.1103/physreve.90.022138","_id":"7769","title":"Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling","publication":"Physical Review E","publication_status":"published","abstract":[{"lang":"eng","text":"Athermal packings of soft repulsive spheres exhibit a sharp jamming transition in the thermodynamic limit. Upon further compression, various structural and mechanical properties display clean power-law behavior over many decades in pressure. As with any phase transition, the rounding of such behavior in finite systems close to the transition plays an important role in understanding the nature of the transition itself. The situation for jamming is surprisingly rich: the assumption that jammed packings are isotropic is only strictly true in the large-size limit, and finite-size has a profound effect on the very meaning of jamming. Here, we provide a comprehensive numerical study of finite-size effects in sphere packings above the jamming transition, focusing on stability as well as the scaling of the contact number and the elastic response."}]},{"abstract":[{"lang":"eng","text":"Packings of frictionless athermal particles that interact only when they overlap experience a jamming transition as a function of packing density. Such packings provide the foundation for the theory of jamming. This theory rests on the observation that, despite the multitude of disordered configurations, the mechanical response to linear order depends only on the distance to the transition. We investigate the validity and utility of such measurements that invoke the harmonic approximation and show that, despite particles coming in and out of contact, there is a well-defined linear regime in the thermodynamic limit."}],"publication_status":"published","publication":"Physical Review E","title":"Contact nonlinearities and linear response in jammed particulate packings","_id":"7770","language":[{"iso":"eng"}],"doi":"10.1103/physreve.90.022201","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T08:15:25Z","year":"2014","day":"04","citation":{"ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Contact nonlinearities and linear response in jammed particulate packings,” <i>Physical Review E</i>, vol. 90, no. 2. American Physical Society, 2014.","ama":"Goodrich CP, Liu AJ, Nagel SR. Contact nonlinearities and linear response in jammed particulate packings. <i>Physical Review E</i>. 2014;90(2). doi:<a href=\"https://doi.org/10.1103/physreve.90.022201\">10.1103/physreve.90.022201</a>","ista":"Goodrich CP, Liu AJ, Nagel SR. 2014. Contact nonlinearities and linear response in jammed particulate packings. Physical Review E. 90(2), 022201.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014).","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Contact Nonlinearities and Linear Response in Jammed Particulate Packings.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.90.022201\">https://doi.org/10.1103/physreve.90.022201</a>.","mla":"Goodrich, Carl Peter, et al. “Contact Nonlinearities and Linear Response in Jammed Particulate Packings.” <i>Physical Review E</i>, vol. 90, no. 2, 022201, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.90.022201\">10.1103/physreve.90.022201</a>.","apa":"Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2014). Contact nonlinearities and linear response in jammed particulate packings. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.90.022201\">https://doi.org/10.1103/physreve.90.022201</a>"},"extern":"1","article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter"},{"full_name":"Liu, Andrea J.","last_name":"Liu","first_name":"Andrea J."},{"last_name":"Nagel","first_name":"Sidney R.","full_name":"Nagel, Sidney R."}],"month":"08","date_created":"2020-04-30T11:42:24Z","status":"public","article_number":"022201","intvolume":"        90","publication_identifier":{"issn":["1539-3755","1550-2376"]},"article_type":"original","publisher":"American Physical Society","date_published":"2014-08-04T00:00:00Z","issue":"2","volume":90},{"article_type":"letter_note","publisher":"American Physical Society","issue":"4","volume":112,"month":"04","date_created":"2020-04-30T11:42:39Z","status":"public","article_number":"049801 ","intvolume":"       112","year":"2014","main_file_link":[{"url":"https://arxiv.org/abs/1306.1285","open_access":"1"}],"citation":{"ista":"Goodrich CP, Liu AJ, Nagel SR. 2014. Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic”. Physical Review Letters. 112(4), 049801.","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Comment on ‘Repulsive Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’” <i>Physical Review Letters</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physrevlett.112.049801\">https://doi.org/10.1103/physrevlett.112.049801</a>.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 112 (2014).","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Comment on ‘Repulsive contact interactions make jammed particulate systems inherently nonharmonic,’” <i>Physical Review Letters</i>, vol. 112, no. 4. American Physical Society, 2014.","ama":"Goodrich CP, Liu AJ, Nagel SR. Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic.” <i>Physical Review Letters</i>. 2014;112(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.112.049801\">10.1103/physrevlett.112.049801</a>","apa":"Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2014). Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic.” <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.112.049801\">https://doi.org/10.1103/physrevlett.112.049801</a>","mla":"Goodrich, Carl Peter, et al. “Comment on ‘Repulsive Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’” <i>Physical Review Letters</i>, vol. 112, no. 4, 049801, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physrevlett.112.049801\">10.1103/physrevlett.112.049801</a>."},"author":[{"last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"full_name":"Nagel, Sidney R.","first_name":"Sidney R.","last_name":"Nagel"}],"extern":"1","abstract":[{"text":"In their Letter, Schreck, Bertrand, O'Hern and Shattuck [Phys. Rev. Lett. 107, 078301 (2011)] study nonlinearities in jammed particulate systems that arise when contacts are altered. They conclude that there is \"no harmonic regime in the large system limit for all compressions\" and \"at jamming onset for any system size.\" Their argument rests on the claim that for finite-range repulsive potentials, of the form used in studies of jamming, the breaking or forming of a single contact is sufficient to destroy the linear regime. We dispute these conclusions and argue that linear response is both justified and essential for understanding the nature of the jammed solid. ","lang":"eng"}],"publication_status":"published","publication":"Physical Review Letters","title":"Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic”","_id":"7771","oa":1,"external_id":{"arxiv":["1306.1285"]},"date_published":"2014-04-20T00:00:00Z","arxiv":1,"publication_identifier":{"issn":["0031-9007","1079-7114"]},"oa_version":"Preprint","type":"journal_article","date_updated":"2021-01-12T08:15:26Z","day":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","doi":"10.1103/physrevlett.112.049801","language":[{"iso":"eng"}]},{"publication_status":"published","abstract":[{"lang":"eng","text":"Particle tracking and displacement covariance matrix techniques are employed to investigate the phonon dispersion relations of two-dimensional colloidal glasses composed of soft, thermoresponsive microgel particles whose temperature-sensitive size permits in situ variation of particle packing fraction. Bulk, B, and shear, G, moduli of the colloidal glasses are extracted from the dispersion relations as a function of packing fraction, and variation of the ratio G/B with packing fraction is found to agree quantitatively with predictions for jammed packings of frictional soft particles. In addition, G and B individually agree with numerical predictions for frictional particles. This remarkable level of agreement enabled us to extract an energy scale for the interparticle interaction from the individual elastic constants and to derive an approximate estimate for the interparticle friction coefficient."}],"doi":"10.1103/physreve.89.012301","language":[{"iso":"eng"}],"_id":"7772","publication":"Physical Review E","title":"Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions","day":"03","year":"2014","type":"journal_article","date_updated":"2021-01-12T08:15:26Z","oa_version":"None","author":[{"first_name":"Tim","last_name":"Still","full_name":"Still, Tim"},{"full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","first_name":"Carl Peter"},{"last_name":"Chen","first_name":"Ke","full_name":"Chen, Ke"},{"last_name":"Yunker","first_name":"Peter J.","full_name":"Yunker, Peter J."},{"full_name":"Schoenholz, Samuel","first_name":"Samuel","last_name":"Schoenholz"},{"first_name":"Andrea J.","last_name":"Liu","full_name":"Liu, Andrea J."},{"full_name":"Yodh, A. G.","last_name":"Yodh","first_name":"A. G."}],"extern":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","citation":{"ama":"Still T, Goodrich CP, Chen K, et al. Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions. <i>Physical Review E</i>. 2014;89(1). doi:<a href=\"https://doi.org/10.1103/physreve.89.012301\">10.1103/physreve.89.012301</a>","ieee":"T. Still <i>et al.</i>, “Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions,” <i>Physical Review E</i>, vol. 89, no. 1. American Physical Society, 2014.","chicago":"Still, Tim, Carl Peter Goodrich, Ke Chen, Peter J. Yunker, Samuel Schoenholz, Andrea J. Liu, and A. G. Yodh. “Phonon Dispersion and Elastic Moduli of Two-Dimensional Disordered Colloidal Packings of Soft Particles with Frictional Interactions.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.89.012301\">https://doi.org/10.1103/physreve.89.012301</a>.","short":"T. Still, C.P. Goodrich, K. Chen, P.J. Yunker, S. Schoenholz, A.J. Liu, A.G. Yodh, Physical Review E 89 (2014).","ista":"Still T, Goodrich CP, Chen K, Yunker PJ, Schoenholz S, Liu AJ, Yodh AG. 2014. Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions. Physical Review E. 89(1), 012301.","apa":"Still, T., Goodrich, C. P., Chen, K., Yunker, P. J., Schoenholz, S., Liu, A. J., &#38; Yodh, A. G. (2014). Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.89.012301\">https://doi.org/10.1103/physreve.89.012301</a>","mla":"Still, Tim, et al. “Phonon Dispersion and Elastic Moduli of Two-Dimensional Disordered Colloidal Packings of Soft Particles with Frictional Interactions.” <i>Physical Review E</i>, vol. 89, no. 1, 012301, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.89.012301\">10.1103/physreve.89.012301</a>."},"article_number":"012301","status":"public","date_created":"2020-04-30T11:43:02Z","month":"01","publication_identifier":{"issn":["1539-3755","1550-2376"]},"intvolume":"        89","article_type":"original","publisher":"American Physical Society","issue":"1","volume":89,"date_published":"2014-01-03T00:00:00Z"},{"_id":"7773","doi":"10.1038/nphys3006","language":[{"iso":"eng"}],"publication":"Nature Physics","title":"Solids between the mechanical extremes of order and disorder","abstract":[{"text":"For more than a century, physicists have described real solids in terms of perturbations about perfect crystalline order1. Such an approach takes us only so far: a glass, another ubiquitous form of rigid matter, cannot be described in any meaningful sense as a defected crystal2. Is there an opposite extreme to a crystal—a solid with complete disorder—that forms an alternative starting point for understanding real materials? Here, we argue that the solid comprising particles with finite-ranged interactions at the jamming transition3,4,5 constitutes such a limit. It has been shown that the physics associated with this transition can be extended to interactions that are long ranged6. We demonstrate that jamming physics is not restricted to amorphous systems, but dominates the behaviour of solids with surprisingly high order. Just as the free-electron and tight-binding models represent two idealized cases from which to understand electronic structure1, we identify two extreme limits of mechanical behaviour. Thus, the physics of jamming can be set side by side with the physics of crystals to provide an organizing structure for understanding the mechanical properties of solids over the entire spectrum of disorder.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"last_name":"Nagel","first_name":"Sidney R.","full_name":"Nagel, Sidney R."}],"quality_controlled":"1","article_processing_charge":"No","citation":{"ista":"Goodrich CP, Liu AJ, Nagel SR. 2014. Solids between the mechanical extremes of order and disorder. Nature Physics. 10(8), 578–581.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Nature Physics 10 (2014) 578–581.","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Solids between the Mechanical Extremes of Order and Disorder.” <i>Nature Physics</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1038/nphys3006\">https://doi.org/10.1038/nphys3006</a>.","ama":"Goodrich CP, Liu AJ, Nagel SR. Solids between the mechanical extremes of order and disorder. <i>Nature Physics</i>. 2014;10(8):578-581. doi:<a href=\"https://doi.org/10.1038/nphys3006\">10.1038/nphys3006</a>","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Solids between the mechanical extremes of order and disorder,” <i>Nature Physics</i>, vol. 10, no. 8. Springer Nature, pp. 578–581, 2014.","apa":"Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2014). Solids between the mechanical extremes of order and disorder. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nphys3006\">https://doi.org/10.1038/nphys3006</a>","mla":"Goodrich, Carl Peter, et al. “Solids between the Mechanical Extremes of Order and Disorder.” <i>Nature Physics</i>, vol. 10, no. 8, Springer Nature, 2014, pp. 578–81, doi:<a href=\"https://doi.org/10.1038/nphys3006\">10.1038/nphys3006</a>."},"year":"2014","day":"06","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T08:15:26Z","publication_identifier":{"issn":["1745-2473","1745-2481"]},"intvolume":"        10","status":"public","month":"07","date_created":"2020-04-30T11:43:29Z","volume":10,"page":"578-581","issue":"8","date_published":"2014-07-06T00:00:00Z","publisher":"Springer Nature","article_type":"original"},{"doi":"10.1073/pnas.1321869111","language":[{"iso":"eng"}],"day":"15","date_updated":"2021-01-12T08:16:34Z","type":"journal_article","oa_version":"Published Version","article_processing_charge":"No","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"page":"E2895-E2904","date_published":"2014-07-15T00:00:00Z","external_id":{"pmid":["24982196"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Most excitatory inputs in the mammalian brain are made on dendritic spines, rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical isolation can underlie input-specific synaptic plasticity, providing a raison d'etre for spines. However, recent results indicate that the spine can experience a membrane potential different from that in the parent dendrite, as though the spine neck electrically isolated the spine. Here we use two-photon calcium imaging of mouse neocortical pyramidal neurons to analyze the correlation between the morphologies of spines activated under minimal synaptic stimulation and the excitatory postsynaptic potentials they generate. We find that excitatory postsynaptic potential amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike timing-dependent plasticity protocol, in which two-photon glutamate uncaging over a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine neck and concomitant increases in the amplitude of the evoked spine potentials. Using numerical simulations, we explore the parameter regimes for the spine neck resistance and synaptic conductance changes necessary to explain our observations. Our data, directly correlating synaptic and morphological plasticity, imply that long-necked spines have small or negligible somatic voltage contributions, but that, upon synaptic stimulation paired with postsynaptic activity, they can shorten their necks and increase synaptic efficacy, thus changing the input/output gain of pyramidal neurons. "}],"oa":1,"_id":"8021","publication":"Proceedings of the National Academy of Sciences","title":"Activity-dependent dendritic spine neck changes are correlated with synaptic strength","pmid":1,"year":"2014","quality_controlled":"1","author":[{"last_name":"Araya","first_name":"R.","full_name":"Araya, R."},{"first_name":"Tim P","last_name":"Vogels","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"first_name":"R.","last_name":"Yuste","full_name":"Yuste, R."}],"extern":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104910/","open_access":"1"}],"citation":{"apa":"Araya, R., Vogels, T. P., &#38; Yuste, R. (2014). Activity-dependent dendritic spine neck changes are correlated with synaptic strength. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1321869111\">https://doi.org/10.1073/pnas.1321869111</a>","mla":"Araya, R., et al. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated with Synaptic Strength.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 28, Proceedings of the National Academy of Sciences, 2014, pp. E2895–904, doi:<a href=\"https://doi.org/10.1073/pnas.1321869111\">10.1073/pnas.1321869111</a>.","ieee":"R. Araya, T. P. Vogels, and R. Yuste, “Activity-dependent dendritic spine neck changes are correlated with synaptic strength,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 28. Proceedings of the National Academy of Sciences, pp. E2895–E2904, 2014.","ama":"Araya R, Vogels TP, Yuste R. Activity-dependent dendritic spine neck changes are correlated with synaptic strength. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(28):E2895-E2904. doi:<a href=\"https://doi.org/10.1073/pnas.1321869111\">10.1073/pnas.1321869111</a>","ista":"Araya R, Vogels TP, Yuste R. 2014. Activity-dependent dendritic spine neck changes are correlated with synaptic strength. Proceedings of the National Academy of Sciences. 111(28), E2895–E2904.","short":"R. Araya, T.P. Vogels, R. Yuste, Proceedings of the National Academy of Sciences 111 (2014) E2895–E2904.","chicago":"Araya, R., Tim P Vogels, and R. Yuste. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated with Synaptic Strength.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1321869111\">https://doi.org/10.1073/pnas.1321869111</a>."},"status":"public","date_created":"2020-06-25T13:06:24Z","month":"07","intvolume":"       111","publisher":"Proceedings of the National Academy of Sciences","article_type":"original","volume":111,"issue":"28"},{"volume":82,"issue":"6","publisher":"Elsevier","article_type":"original","intvolume":"        82","status":"public","date_created":"2020-06-25T13:07:37Z","month":"06","extern":"1","author":[{"last_name":"Hennequin","first_name":"Guillaume","full_name":"Hennequin, Guillaume"},{"last_name":"Vogels","first_name":"Tim P","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"last_name":"Gerstner","first_name":"Wulfram","full_name":"Gerstner, Wulfram"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364799/"}],"citation":{"ama":"Hennequin G, Vogels TP, Gerstner W. Optimal control of transient dynamics in balanced networks supports generation of complex movements. <i>Neuron</i>. 2014;82(6):1394-1406. doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.04.045\">10.1016/j.neuron.2014.04.045</a>","ieee":"G. Hennequin, T. P. Vogels, and W. Gerstner, “Optimal control of transient dynamics in balanced networks supports generation of complex movements,” <i>Neuron</i>, vol. 82, no. 6. Elsevier, pp. 1394–1406, 2014.","chicago":"Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2014.04.045\">https://doi.org/10.1016/j.neuron.2014.04.045</a>.","short":"G. Hennequin, T.P. Vogels, W. Gerstner, Neuron 82 (2014) 1394–1406.","ista":"Hennequin G, Vogels TP, Gerstner W. 2014. Optimal control of transient dynamics in balanced networks supports generation of complex movements. Neuron. 82(6), 1394–1406.","mla":"Hennequin, Guillaume, et al. “Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.” <i>Neuron</i>, vol. 82, no. 6, Elsevier, 2014, pp. 1394–406, doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.04.045\">10.1016/j.neuron.2014.04.045</a>.","apa":"Hennequin, G., Vogels, T. P., &#38; Gerstner, W. (2014). Optimal control of transient dynamics in balanced networks supports generation of complex movements. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2014.04.045\">https://doi.org/10.1016/j.neuron.2014.04.045</a>"},"year":"2014","oa":1,"_id":"8022","publication":"Neuron","title":"Optimal control of transient dynamics in balanced networks supports generation of complex movements","pmid":1,"publication_status":"published","abstract":[{"text":"Populations of neurons in motor cortex engage in complex transient dynamics of large amplitude during the execution of limb movements. Traditional network models with stochastically assigned synapses cannot reproduce this behavior. Here we introduce a class of cortical architectures with strong and random excitatory recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from a control theory perspective. Such networks transiently amplify specific activity states and can be used to reliably execute multidimensional movement patterns. Similar to the experimental observations, these transients must be preceded by a steady-state initialization phase from which the network relaxes back into the background state by way of complex internal dynamics. In our networks, excitation and inhibition are as tightly balanced as recently reported in experiments across several brain areas, suggesting inhibitory control of complex excitatory recurrence as a generic organizational principle in cortex.","lang":"eng"}],"page":"1394-1406","date_published":"2014-06-18T00:00:00Z","external_id":{"pmid":["24945778"]},"publication_identifier":{"issn":["0896-6273"]},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","article_processing_charge":"No","day":"18","type":"journal_article","date_updated":"2021-01-12T08:16:35Z","oa_version":"Submitted Version","language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2014.04.045"},{"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by/3.0/","language":[{"iso":"eng"}],"doi":"10.1152/jn.00629.2013","article_processing_charge":"No","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","day":"15","oa_version":"Published Version","date_updated":"2021-01-12T08:16:35Z","type":"journal_article","publication_identifier":{"eissn":["1522-1598"],"issn":["0022-3077"]},"page":"1801-1814","external_id":{"pmid":["24944218"]},"file":[{"file_size":1632295,"content_type":"application/pdf","creator":"cziletti","relation":"main_file","date_created":"2020-07-16T10:12:13Z","file_name":"2014_JNeurophysiol_Tomm.pdf","checksum":"7c06a086da6f924342650de6dc555c3f","access_level":"open_access","success":1,"date_updated":"2020-07-16T10:12:13Z","file_id":"8122"}],"date_published":"2014-10-15T00:00:00Z","_id":"8023","ddc":["570"],"oa":1,"pmid":1,"title":"Connection-type-specific biases make uniform random network models consistent with cortical recordings","publication":"Journal of Neurophysiology","abstract":[{"lang":"eng","text":"Uniform random sparse network architectures are ubiquitous in computational neuroscience, but the implicit hypothesis that they are a good representation of real neuronal networks has been met with skepticism. Here we used two experimental data sets, a study of triplet connectivity statistics and a data set measuring neuronal responses to channelrhodopsin stimuli, to evaluate the fidelity of thousands of model networks. Network architectures comprised three neuron types (excitatory, fast spiking, and nonfast spiking inhibitory) and were created from a set of rules that govern the statistics of the resulting connection types. In a high-dimensional parameter scan, we varied the degree distributions (i.e., how many cells each neuron connects with) and the synaptic weight correlations of synapses from or onto the same neuron. These variations converted initially uniform random and homogeneously connected networks, in which every neuron sent and received equal numbers of synapses with equal synaptic strength distributions, to highly heterogeneous networks in which the number of synapses per neuron, as well as average synaptic strength of synapses from or to a neuron were variable. By evaluating the impact of each variable on the network structure and dynamics, and their similarity to the experimental data, we could falsify the uniform random sparse connectivity hypothesis for 7 of 36 connectivity parameters, but we also confirmed the hypothesis in 8 cases. Twenty-one parameters had no substantial impact on the results of the test protocols we used."}],"publication_status":"published","extern":"1","author":[{"last_name":"Tomm","first_name":"Christian","full_name":"Tomm, Christian"},{"full_name":"Avermann, Michael","last_name":"Avermann","first_name":"Michael"},{"last_name":"Petersen","first_name":"Carl","full_name":"Petersen, Carl"},{"last_name":"Gerstner","first_name":"Wulfram","full_name":"Gerstner, Wulfram"},{"first_name":"Tim P","last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"quality_controlled":"1","citation":{"ama":"Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. Connection-type-specific biases make uniform random network models consistent with cortical recordings. <i>Journal of Neurophysiology</i>. 2014;112(8):1801-1814. doi:<a href=\"https://doi.org/10.1152/jn.00629.2013\">10.1152/jn.00629.2013</a>","ieee":"C. Tomm, M. Avermann, C. Petersen, W. Gerstner, and T. P. Vogels, “Connection-type-specific biases make uniform random network models consistent with cortical recordings,” <i>Journal of Neurophysiology</i>, vol. 112, no. 8. American Physiological Society, pp. 1801–1814, 2014.","ista":"Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. 2014. Connection-type-specific biases make uniform random network models consistent with cortical recordings. Journal of Neurophysiology. 112(8), 1801–1814.","short":"C. Tomm, M. Avermann, C. Petersen, W. Gerstner, T.P. Vogels, Journal of Neurophysiology 112 (2014) 1801–1814.","chicago":"Tomm, Christian, Michael Avermann, Carl Petersen, Wulfram Gerstner, and Tim P Vogels. “Connection-Type-Specific Biases Make Uniform Random Network Models Consistent with Cortical Recordings.” <i>Journal of Neurophysiology</i>. American Physiological Society, 2014. <a href=\"https://doi.org/10.1152/jn.00629.2013\">https://doi.org/10.1152/jn.00629.2013</a>.","apa":"Tomm, C., Avermann, M., Petersen, C., Gerstner, W., &#38; Vogels, T. P. (2014). Connection-type-specific biases make uniform random network models consistent with cortical recordings. <i>Journal of Neurophysiology</i>. American Physiological Society. <a href=\"https://doi.org/10.1152/jn.00629.2013\">https://doi.org/10.1152/jn.00629.2013</a>","mla":"Tomm, Christian, et al. “Connection-Type-Specific Biases Make Uniform Random Network Models Consistent with Cortical Recordings.” <i>Journal of Neurophysiology</i>, vol. 112, no. 8, American Physiological Society, 2014, pp. 1801–14, doi:<a href=\"https://doi.org/10.1152/jn.00629.2013\">10.1152/jn.00629.2013</a>."},"year":"2014","tmp":{"short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"intvolume":"       112","status":"public","month":"10","date_created":"2020-06-25T13:08:30Z","issue":"8","volume":112,"article_type":"original","publisher":"American Physiological Society","file_date_updated":"2020-07-16T10:12:13Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer"}],"quality_controlled":"1","citation":{"mla":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” <i>Proceeding of the International Congress of Mathematicans</i>, vol. 3, International Congress of Mathematicians, 2014, pp. 1175–94.","apa":"Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum systems. In <i>Proceeding of the International Congress of Mathematicans</i> (Vol. 3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.","chicago":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” In <i>Proceeding of the International Congress of Mathematicans</i>, 3:1175–94. International Congress of Mathematicians, 2014.","short":"R. Seiringer, in:, Proceeding of the International Congress of Mathematicans, International Congress of Mathematicians, 2014, pp. 1175–1194.","ista":"Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum systems. Proceeding of the International Congress of Mathematicans. ICM: International Congress of Mathematicans vol. 3, 1175–1194.","ieee":"R. Seiringer, “Structure of the excitation spectrum for many-body quantum systems,” in <i>Proceeding of the International Congress of Mathematicans</i>, Seoul, South Korea, 2014, vol. 3, pp. 1175–1194.","ama":"Seiringer R. Structure of the excitation spectrum for many-body quantum systems. In: <i>Proceeding of the International Congress of Mathematicans</i>. Vol 3. International Congress of Mathematicians; 2014:1175-1194."},"main_file_link":[{"url":"http://www.icm2014.org/en/vod/proceedings.html","open_access":"1"}],"day":"01","year":"2014","type":"conference","date_updated":"2023-10-17T11:12:33Z","oa_version":"Published Version","language":[{"iso":"eng"}],"oa":1,"_id":"8044","department":[{"_id":"RoSe"}],"title":"Structure of the excitation spectrum for many-body quantum systems","publication":"Proceeding of the International Congress of Mathematicans","publication_status":"published","abstract":[{"text":"Many questions concerning models in quantum mechanics require a detailed analysis of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable Hilbert space. Of particular relevance for an understanding of the low-temperature properties of a system is the structure of the excitation spectrum, which is the part of the spectrum close to the spectral bottom. We present recent progress on this question for bosonic many-body quantum systems with weak two-body interactions. Such system are currently of great interest, due to their experimental realization in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations, which predicts that the low-energy spectrum is made up of sums of elementary excitations, with linear dispersion law at low momentum. The latter property is crucial for the superfluid behavior the system.","lang":"eng"}],"volume":3,"page":"1175-1194","date_published":"2014-08-01T00:00:00Z","publisher":"International Congress of Mathematicians","publication_identifier":{"isbn":["9788961058063"]},"scopus_import":"1","intvolume":"         3","status":"public","date_created":"2020-06-29T07:59:35Z","conference":{"location":"Seoul, South Korea","start_date":"2014-08-13","name":"ICM: International Congress of Mathematicans","end_date":"2014-08-21"},"month":"08"},{"_id":"809","doi":"10.1073/pnas.1401455111","publication":"PNAS","title":"Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly","abstract":[{"text":"The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles to form mature infectious virions. Obtaining a structural model of the assembled lattice of Gag within immature virus particles is necessary to understand the interactions that mediate assembly of HIV-1 particles in the infected cell, and to describe the substrate that is subsequently cleaved by the viral protease. An 8-Å resolution structure of an immature virus-like tubular array assembled from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus (M-PMV) has previously been reported, and a model for the arrangement of the HIV-1 capsid (CA) domains has been generated based on homology to this structure. Here we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like arrangement of the C-terminal CA domains and have solved their structure by using hybrid cryo-EM and tomography analysis. The structure reveals the arrangement of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and provides, to our knowledge, the first high-resolution view of the region immediately downstream of CA, which is essential for assembly, and is significantly different from the respective region in M-PMV. Our results reveal a hollow column of density for this region in HIV-1 that is compatible with the presence of a six-helix bundle at this position.","lang":"eng"}],"publication_status":"published","acknowledgement":"The authors thank Leonardo Trabuco for help with running MDFF, Maria Anders for preparing amprenavir-inhibited virus, Marie-Christine Vaney for help with X-ray data processing and structure refinement, Ahmed Haouz and Patrick Weber (robotized crystallization facility Proteopole, Institut Pasteur) for help in crystal screening, and the European Molecular Biology Laboratory (EMBL) Information Technology Services Unit and Frank Thommen for technical support. This study was supported by Deutsche Forschungsgemeinschaft Grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1 (to H.-G.K.) and a Federation of European Biochemical Societies long-term fellowship (to T.A.M.B.). The laboratory of J.A.G.B. acknowledges financial support from EMBL and the Chica und Heinz Schaller Stiftung. ","author":[{"first_name":"Tanmay","last_name":"Bharata","full_name":"Bharata, Tanmay A"},{"last_name":"Menendez","first_name":"Luis","full_name":"Menendez, Luis R"},{"full_name":"Hagena, Wim J","first_name":"Wim","last_name":"Hagena"},{"first_name":"Vanda","last_name":"Luxd","full_name":"Luxd, Vanda"},{"last_name":"Igonete","first_name":"Sebastien","full_name":"Igonete, Sebastien"},{"first_name":"Martin","last_name":"Schorba","full_name":"Schorba, Martin"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Florian Schur","orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian"},{"full_name":"Kraüsslich, Hans Georg","first_name":"Hans","last_name":"Kraüsslich"},{"full_name":"Briggsa, John A","first_name":"John","last_name":"Briggsa"}],"quality_controlled":0,"extern":1,"citation":{"apa":"Bharata, T., Menendez, L., Hagena, W., Luxd, V., Igonete, S., Schorba, M., … Briggsa, J. (2014). Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1401455111\">https://doi.org/10.1073/pnas.1401455111</a>","mla":"Bharata, Tanmay, et al. “Cryo Electron Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature Virus Assembly.” <i>PNAS</i>, vol. 111, no. 22, National Academy of Sciences, 2014, pp. 8233–38, doi:<a href=\"https://doi.org/10.1073/pnas.1401455111\">10.1073/pnas.1401455111</a>.","ista":"Bharata T, Menendez L, Hagena W, Luxd V, Igonete S, Schorba M, Schur FK, Kraüsslich H, Briggsa J. 2014. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. PNAS. 111(22), 8233–8238.","short":"T. Bharata, L. Menendez, W. Hagena, V. Luxd, S. Igonete, M. Schorba, F.K. Schur, H. Kraüsslich, J. Briggsa, PNAS 111 (2014) 8233–8238.","chicago":"Bharata, Tanmay, Luis Menendez, Wim Hagena, Vanda Luxd, Sebastien Igonete, Martin Schorba, Florian KM Schur, Hans Kraüsslich, and John Briggsa. “Cryo Electron Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature Virus Assembly.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1401455111\">https://doi.org/10.1073/pnas.1401455111</a>.","ieee":"T. Bharata <i>et al.</i>, “Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly,” <i>PNAS</i>, vol. 111, no. 22. National Academy of Sciences, pp. 8233–8238, 2014.","ama":"Bharata T, Menendez L, Hagena W, et al. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. <i>PNAS</i>. 2014;111(22):8233-8238. doi:<a href=\"https://doi.org/10.1073/pnas.1401455111\">10.1073/pnas.1401455111</a>"},"year":"2014","day":"03","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","date_updated":"2021-01-12T08:16:50Z","publist_id":"6838","intvolume":"       111","status":"public","month":"06","date_created":"2018-12-11T11:48:37Z","issue":"22","volume":111,"page":"8233 - 8238","date_published":"2014-06-03T00:00:00Z","publisher":"National Academy of Sciences"},{"conference":{"location":"Seoul, Korea","start_date":"2014-08-13","end_date":"2014-08-21","name":"ICM: International Congress of Mathematicians"},"month":"08","date_created":"2018-12-11T11:52:25Z","status":"public","intvolume":"         3","publist_id":"5670","publisher":"International Congress of Mathematicians","volume":3,"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"abstract":[{"text":"The Wigner-Dyson-Gaudin-Mehta conjecture asserts that the local eigenvalue statistics of large real and complex Hermitian matrices with independent, identically distributed entries are universal in a sense that they depend only on the symmetry class of the matrix and otherwise are independent of the details of the distribution. We present the recent solution to this half-century old conjecture. We explain how stochastic tools, such as the Dyson Brownian motion, and PDE ideas, such as De Giorgi-Nash-Moser regularity theory, were combined in the solution. We also show related results for log-gases that represent a universal model for strongly correlated systems. Finally, in the spirit of Wigner’s original vision, we discuss the extensions of these universality results to more realistic physical systems such as random band matrices.","lang":"eng"}],"publication_status":"published","publication":"Proceedings of the International Congress of Mathematicians","title":"Random matrices, log-gases and Hölder regularity","_id":"1507","oa":1,"year":"2014","citation":{"mla":"Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” <i>Proceedings of the International Congress of Mathematicians</i>, vol. 3, International Congress of Mathematicians, 2014, pp. 214–36.","apa":"Erdös, L. (2014). Random matrices, log-gases and Hölder regularity. In <i>Proceedings of the International Congress of Mathematicians</i> (Vol. 3, pp. 214–236). Seoul, Korea: International Congress of Mathematicians.","ama":"Erdös L. Random matrices, log-gases and Hölder regularity. In: <i>Proceedings of the International Congress of Mathematicians</i>. Vol 3. International Congress of Mathematicians; 2014:214-236.","ieee":"L. Erdös, “Random matrices, log-gases and Hölder regularity,” in <i>Proceedings of the International Congress of Mathematicians</i>, Seoul, Korea, 2014, vol. 3, pp. 214–236.","ista":"Erdös L. 2014. Random matrices, log-gases and Hölder regularity. Proceedings of the International Congress of Mathematicians. ICM: International Congress of Mathematicians vol. 3, 214–236.","chicago":"Erdös, László. “Random Matrices, Log-Gases and Hölder Regularity.” In <i>Proceedings of the International Congress of Mathematicians</i>, 3:214–36. International Congress of Mathematicians, 2014.","short":"L. Erdös, in:, Proceedings of the International Congress of Mathematicians, International Congress of Mathematicians, 2014, pp. 214–236."},"main_file_link":[{"url":"http://arxiv.org/abs/1407.5752","open_access":"1"}],"author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László"}],"quality_controlled":"1","scopus_import":"1","date_published":"2014-08-01T00:00:00Z","page":"214 - 236","acknowledgement":"The author is partially supported by SFB-TR 12 Grant of the German Research Council.","ec_funded":1,"department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"oa_version":"Submitted Version","date_updated":"2023-10-17T11:12:55Z","type":"conference","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No"}]